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' => 'HOM05D001484', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p31500' => 'bna', 'A05p00020' => 'bna', 'A07p08820' => 'bna', 'Aa31LG4G3300' => 'aar', 'Aa31LG8G10030' => 'aar', 'Actinidia00731' => 'ach', 'Actinidia11473' => 'ach', 'Actinidia23469' => 'ach', 'Actinidia24318' => 'ach', 'Actinidia40196' => 'ach', 'Actinidia40197' => 'ach', 'Actinidia40198' => 'ach', 'Ah.08g212990' => 'amhyb', 'Ah.15g091720' => 'amhyb', 'AL3G38260' => 'aly', 'AL4G47710' => 'aly', 'Aqoxy2G00671' => 'aox', 'Aqoxy2G03236' => 'aox', 'arahy.Tifrunner.gnm1.ann1.05IDCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KR684' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATY3SJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK6QJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6APGL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IDT7Z9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM073U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ0R87' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LE7RV4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT4QRX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V5ENPK' => 'arhy', 'AT2G48110' => 'ath', 'AT3G23590' => 'ath', 'ATR0626G186' => 'atr', 'ATR1127G141' => 'atr', 'Atru.chr4.2583' => 'acertr', 'Atru.chr5.1358' => 'acertr', 'Atru.chr5.1359' => 'acertr', 'Atru.chr8.46' => 'acertr', 'AUR62002640' => 'cqu', 'AUR62030055' => 'cqu', 'AUR62033713' => 'cqu', 'AUR62033714' => 'cqu', 'AUR62036795' => 'cqu', 'AUR62039891' => 'cqu', 'BcaB02g08737' => 'bca', 'BcaB04g20441' => 'bca', 'BcaB06g26509' => 'bca', 'BcaB06g26510' => 'bca', 'BcaB06g26511' => 'bca', 'BcaB06g26512' => 'bca', 'BcaB06g26513' => 'bca', 'BcaC02g12564' => 'bca', 'BcaC02g12565' => 'bca', 'BcaC02g12794' => 'bca', 'BcaC02g12795' => 'bca', 'BcaC02g12796' => 'bca', 'BcaC06g35541' => 'bca', 'BNapus_Darmor_BZH_scaffold_188p00080' => 'bna', 'BNapus_Darmor_BZH_scaffold_188p00090' => 'bna', 'BolC1t03972H' => 'bol', 'BolC1t03973H' => 'bol', 'BolC4t21680H' => 'bol', 'BolC7t41863H' => 'bol', 'BolSC55t61227H' => 'bol', 'BolSC55t61228H' => 'bol', 'BraA01t03278Z' => 'bra', 'BraA05t18998Z' => 'bra', 'BraA07t28673Z' => 'bra', 'C01p40150' => 'bna', 'C05p12370' => 'bna', 'C07p13680' => 'bna', 'CAN.G1006.16' => 'can', 'CAN.G1006.17' => 'can', 'CAN.G1170.2' => 'can', 'CAN.G962.7' => 'can', 'CANSAT25G2179' => 'cansat', 'CANSAT78G1573' => 'cansat', 'CARHR099510' => 'chi', 'CARHR143510' => 'chi', 'Carub.0003s2380' => 'cru', 'Carub.0004s3082' => 'cru', 'Ca_00614_v3' => 'car', 'Ca_07801_v3' => 'car', 'Ca_08567_v3' => 'car', 'Ca_09571_v3' => 'car', 'CBR_g19290' => 'cbr', 'Cc01_g19770' => 'ccan', 'Cc03_g03030' => 'ccan', 'CDE07G0968' => 'cde', 'CDE09G1441' => 'cde', 'Cfa006103' => 'cfa', 'Cfa015573' => 'cfa', 'Cfa016988' => 'cfa', 'Ciclev10006738m.g' => 'ccl', 'Ciclev10010920m.g' => 'ccl', 'Ciclev10018517m.g' => 'ccl', 'CiPaw.01G159200' => 'cil', 'CiPaw.02G091000' => 'cil', 'CiPaw.02G091100' => 'cil', 'CiPaw.08G103100' => 'cil', 'CiPaw.09G224900' => 'cil', 'ClCG06G005740' => 'cla', 'ClCG07G000090' => 'cla', 'ClCG07G000100' => 'cla', 'COL.COLO4_09143' => 'col', 'COL.COLO4_25124' => 'col', 'Cpa.g.sc16.34' => 'cpa', 'Cpa.g.sc3504.1' => 'cpa', 'Cpa.g.sc60.37' => 'cpa', 'CsaV3_6G018520' => 'csa', 'CsaV3_6G036860' => 'csa', 'CSS0001072' => 'camsi', 'CSS0020208' => 'camsi', 'CSS0021253' => 'camsi', 'CSS0022190' => 'camsi', 'CSS0036150' => 'camsi', 'CSS0040442' => 'camsi', 'CSS0042300' => 'camsi', 'CSS0045298' => 'camsi', 'DCAR_012449' => 'dca', 'DCAR_018405' => 'dca', 'DCAR_024573' => 'dca', 'DCAR_030591' => 'dca', 'Dinv16926' => 'din', 'Dinv32963' => 'din', 'Dinv38382' => 'din', 'Dinv38383' => 'din', 'Duzib133G0974' => 'dzi', 'Duzib138G1867' => 'dzi', 'Duzib211G0420' => 'dzi', 'Duzib212G0930' => 'dzi', 'ECA234G1645' => 'eca', 'ECA247G3467' => 'eca', 'ECA248G1703' => 'eca', 'EL10Ac3g06327' => 'bvu', 'EL10Ac7g17204' => 'bvu', 'Eucgr.A00855' => 'egr', 'Eucgr.A00858' => 'egr', 'Eucgr.H01520' => 'egr', 'Eucgr.H03604' => 'egr', 'Eucgr.L03465' => 'egr', 'Eucgr.L03466' => 'egr', 'FAN01G0988' => 'fan', 'FAN02G3892' => 'fan', 'FAN05G3381' => 'fan', 'FAN07G0967' => 'fan', 'FAN07G1493' => 'fan', 'FAN08G3125' => 'fan', 'FAN09G0402' => 'fan', 'FAN12G2594' => 'fan', 'FAN12G3879' => 'fan', 'FAN14G1546' => 'fan', 'FAN15G3626' => 'fan', 'FAN17G0588' => 'fan', 'FAN17G0609' => 'fan', 'FAN18G2817' => 'fan', 'FAN19G1305' => 'fan', 'FAN20G1787' => 'fan', 'FAN22G0073' => 'fan', 'FAN22G0352' => 'fan', 'FAN22G0368' => 'fan', 'FAN22G2273' => 'fan', 'FAN24G1998' => 'fan', 'FAN27G1317' => 'fan', 'FvH4_2g23980' => 'fve', 'FvH4_4g14380' => 'fve', 'FvH4_4g14390' => 'fve', 'FvH4_6g09250' => 'fve', 'Glyma.03G151100' => 'gma', 'Glyma.04G122550' => 'gma', 'Glyma.05G001600' => 'gma', 'Glyma.09G270766' => 'gma', 'Glyma.09G270832' => 'gma', 'Glyma.13G209800' => 'gma', 'Glyma.15G102800' => 'gma', 'Glyma.18G218900' => 'gma', 'Glyma.19G001500' => 'gma', 'Glyma.19G153600' => 'gma', 'Gohir.A02G028600' => 'ghi', 'Gohir.A08G045000' => 'ghi', 'Gohir.A11G120500' => 'ghi', 'Gohir.A12G006200' => 'ghi', 'Gohir.A12G006250' => 'ghi', 'Gohir.D02G036300' => 'ghi', 'Gohir.D08G054700' => 'ghi', 'Gohir.D11G125600' => 'ghi', 'Gohir.D12G005700' => 'ghi', 'Gorai.004G055200' => 'gra', 'Gorai.005G040400' => 'gra', 'Gorai.007G134500' => 'gra', 'Gorai.008G005500' => 'gra', 'GSVIVG01011094001' => 'vvi', 'GSVIVG01017879001' => 'vvi', 'GSVIVG01025988001' => 'vvi', 'GSVIVG01029847001' => 'vvi', 'HanXRQChr10g0282901' => 'han', 'HanXRQChr10g0310371' => 'han', 'HanXRQChr10g0315041' => 'han', 'HanXRQChr11g0327651' => 'han', 'HanXRQChr12g0359391' => 'han', 'Haze_00972' => 'cav', 'Haze_00973' => 'cav', 'Haze_00974' => 'cav', 'Haze_04747' => 'cav', 'Haze_04749' => 'cav', 'Haze_04750' => 'cav', 'Haze_21217' => 'cav', 'Hma1.2p1_1037F.1_g250680' => 'hma', 'Hma1.2p1_1644F.1_g295320' => 'hma', 'HPP92_011322' => 'vpl', 'HPP92_011323' => 'vpl', 'HPP92_011324' => 'vpl', 'HPP92_011325' => 'vpl', 'HPP92_011326' => 'vpl', 'Hund12205' => 'sun', 'Hund17957' => 'sun', 'Lalb_Chr06g0176771' => 'lal', 'Lalb_Chr18g0056021' => 'lal', 'Lalb_Chr18g0056031' => 'lal', 'Lalb_Chr18g0056041' => 'lal', 'Lalb_Chr20g0107751' => 'lal', 'Lalb_Chr20g0118371' => 'lal', 'Lj1g0010239' => 'lja', 'Lj1g0017101' => 'lja', 'Lj2A1178G40' => 'lonja', 'Lj2A54G84' => 'lonja', 'Lj2g0015248' => 'lja', 'Lj3A761T51' => 'lonja', 'Lj6g0018116' => 'lja', 'Lsat_1_v5_gn_4_136040' => 'lsa', 'Lsat_1_v5_gn_5_187461' => 'lsa', 'Lsat_1_v5_gn_5_77001' => 'lsa', 'Lsat_1_v5_gn_9_4461' => 'lsa', 'Manes.01G210100' => 'mes', 'Manes.03G185600' => 'mes', 'Manes.05G073300' => 'mes', 'Manes.09G120300' => 'mes', 'Manes.15G022100' => 'mes', 'Mapoly0096s0053' => 'mpo', 'MBI03_g14058_MAGBIO' => 'mbi', 'MBI03_g33876_MAGBIO' => 'mbi', 'MBI03_g36854_MAGBIO' => 'mbi', 'MBI17_g11997_MAGBIO' => 'mbi', 'MD03G1269000' => 'mdo', 'MD04G1179600' => 'mdo', 'MD11G1289800' => 'mdo', 'MD12G1194700' => 'mdo', 'MD13G1182100' => 'mdo', 'MD13G1182200' => 'mdo', 'MD16G1182600' => 'mdo', 'Medtr2g021400' => 'mtr', 'Medtr2g021470' => 'mtr', 'Medtr2g105810' => 'mtr', 'Medtr3g033580' => 'mtr', 'Medtr6g007970' => 'mtr', 'Medtr7g056330' => 'mtr', 'Medtr7g074290' => 'mtr', 'Medtr7g074380' => 'mtr', 'Medtr7g094550' => 'mtr', 'Medtr8g069995' => 'mtr', 'MELO3C014345.2' => 'cme', 'MELO3C021395.2' => 'cme', 'Migut.D00262' => 'egut', 'Migut.G00257' => 'egut', 'MSTRG.21575' => 'ama', 'MSTRG.3985' => 'ama', 'Nitab4.5_0000295g0140' => 'nta', 'Nitab4.5_0000732g0140' => 'nta', 'Nitab4.5_0003162g0020' => 'nta', 'Nitab4.5_0006180g0090' => 'nta', 'Nitab4.5_0006390g0010' => 'nta', 'Nitab4.5_0007392g0040' => 'nta', 'Nn1g02140' => 'nnu', 'Nn4g26168' => 'nnu', 'Nn5g26754' => 'nnu', 'Oeu001433.1' => 'oeu', 'Oeu010299.2' => 'oeu', 'Oeu011171.1' => 'oeu', 'Oeu037675.1' => 'oeu', 'Oeu038359.1' => 'oeu', 'Oeu063834.1' => 'oeu', 'Oeu063835.1' => 'oeu', 'Os05g0312000' => 'osa', 'Os07g0211101' => 'osa', 'Os07g0211200' => 'osa', 'Os07g0681500' => 'osa', 'Peaxi162Scf00095g01015' => 'pax', 'Peaxi162Scf00104g00329' => 'pax', 'Peaxi162Scf00161g00137' => 'pax', 'PGR004G1665' => 'pgr', 'PGR031G2937' => 'pgr', 'PGR119G2145' => 'pgr', 'PGSC0003DMG400004351' => 'stu', 'PGSC0003DMG400014625' => 'stu', 'PGSC0003DMG401000943' => 'stu', 'Phvul.001G148600' => 'pvu', 'Phvul.004G001700' => 'pvu', 'Phvul.006G154900' => 'pvu', 'Phvul.008G078200' => 'pvu', 'Phvul.011G136500' => 'pvu', 'Potri.002G215600' => 'ptr', 'Potri.008G201600' => 'ptr', 'Potri.014G138400' => 'ptr', 'Potri.016G142500' => 'ptr', 'Pp3c16_10580' => 'ppa', 'Pp3c5_25280' => 'ppa', 'Prupe.1G150000' => 'ppe', 'Prupe.1G150100' => 'ppe', 'Prupe.6G299600' => 'ppe', 'Prupe.8G245000' => 'ppe', 'Psat0s4927g0040' => 'psa', 'Psat1g052080' => 'psa', 'Psat1g183800' => 'psa', 'Psat3g113840' => 'psa', 'Psat3g126120' => 'psa', 'Psat3g126160' => 'psa', 'Psat3g158760' => 'psa', 'Psat3g158840' => 'psa', 'PSO170G2858' => 'pso', 'PSO339G0606' => 'pso', 'PSO384G4709' => 'pso', 'PSO407G0334' => 'pso', 'QL04p040276' => 'qlo', 'QL06p005458' => 'qlo', 'QL06p005472' => 'qlo', 'QL07p030546' => 'qlo', 'QL07p031519' => 'qlo', 'QL09p050949' => 'qlo', 'QL09p050966' => 'qlo', 'QL09p051067' => 'qlo', 'QL12p022706' => 'qlo', 'RcHm_v2.0_Chr2g0119601' => 'rch', 'RcHm_v2.0_Chr3g0459591' => 'rch', 'RcHm_v2.0_Chr4g0418521' => 'rch', 'RcHm_v2.0_Chr4g0418531' => 'rch', 'RcHm_v2.0_Chr4g0418541' => 'rch', 'RcHm_v2.0_Chr6g0291641' => 'rch', 'Rhsim01G0086300' => 'rsi', 'Rhsim01G0276300' => 'rsi', 'Rhsim01G0276500' => 'rsi', 'Rhsim04G0207700' => 'rsi', 'Rhsim05G0234500' => 'rsi', 'Rhsim13G0022400' => 'rsi', 'Sabra02G0167900' => 'sbr', 'Sabra04G0158500' => 'sbr', 'Sabra08G0159800' => 'sbr', 'Sabra10G0011500' => 'sbr', 'Sabra14G0104400' => 'sbr', 'SalBow2G2440' => 'sbo', 'SalBow4G2265' => 'sbo', 'Sc02g0000060' => 'sci', 'Sc05g0005020' => 'sci', 'Sc13g0003890' => 'sci', 'Sed0014865' => 'sed', 'Sed0017224' => 'sed', 'Sed0026391' => 'sed', 'SEGI_00063' => 'sgi', 'SEGI_10967' => 'sgi', 'SEGI_17510' => 'sgi', 'SEGI_24396' => 'sgi', 'SEGI_39719' => 'sgi', 'SEGI_41392' => 'sgi', 'SGA_v2.0_scaffold11G05794' => 'sas', 'SGA_v2.0_scaffold142G35607' => 'sas', 'SGA_v2.0_scaffold1G00447' => 'sas', 'SHI15388' => 'shi', 'SHI15394' => 'shi', 'SHI15396' => 'shi', 'SHI15399' => 'shi', 'SMO343G0151' => 'smo', 'SMO367G1118' => 'smo', 'Solyc01g080200.3' => 'sly', 'Solyc06g008960.3' => 'sly', 'Solyc09g064780.3' => 'sly', 'Sopen01g031980' => 'spe', 'Sopen06g003710' => 'spe', 'Sopen09g026460' => 'spe', 'Sp3g21240' => 'spa', 'Sp4g30030' => 'spa', 'TAR365G0022' => 'tar', 'TAR365G1023' => 'tar', 'TAR365G1253' => 'tar', 'TAR623G0078' => 'tar', 'TAR623G1721' => 'tar', 'TAR633G0959' => 'tar', 'THA.LOC104802225' => 'tha', 'THA.LOC104804769' => 'tha', 'THA.LOC104808660' => 'tha', 'THA.LOC104812792' => 'tha', 'Thecc.01G284000' => 'tca', 'Thecc.04G220600' => 'tca', 'Thecc.05G268900' => 'tca', 'Thecc.08G171100' => 'tca', 'Thhalv10001284m.g' => 'esa', 'Thhalv10019912m.g' => 'esa', 'TPR.G14189' => 'tpr', 'TPR.G18110' => 'tpr', 'TPR.G18130' => 'tpr', 'TPR.G18131' => 'tpr', 'TPR.G18140' => 'tpr', 'TPR.G24282' => 'tpr', 'TPR.G25221' => 'tpr', 'TPR.G29267' => 'tpr', 'TPR.G35315' => 'tpr', 'TPR.G36173' => 'tpr', 'TWI09G0794' => 'twi', 'TWI59G1348' => 'twi', 'TWI74G0430' => 'twi', 'unitig_26.g8940' => 'ugi', 'unitig_749.g13744' => 'ugi', 'unitig_749.g13745' => 'ugi', 'vmacro08269' => 'vma', 'vmacro14937' => 'vma', 'vmacro20401' => 'vma', 'VMungo0464G1349' => 'vmu', 'VMungo0540G0289' => 'vmu', 'VMungo1215G1590' => 'vmu', 'VMungo1309G0221' => 'vmu', 'VMungo1309G2815' => 'vmu', 'VMungo1383G0239' => 'vmu', 'VMungo1383G2910' => 'vmu', 'Zm00001eb095270' => 'zma', 'Zm00001eb095280' => 'zma', 'Zm00001eb111630' => 'zma', 'Zm00001eb237080' => 'zma', 'Zm00001eb273740' => 'zma', 'Zm00001eb285040' => 'zma', 'Zm00001eb330790' => 'zma', 'Zm00001eb337380' => 'zma' ), 'gf_id' => 'HOM05D001484', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001484' ), 'data_identifier' => 'HOM05D001484', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001484', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p31500' => 'bna', 'A05p00020' => 'bna', 'A07p08820' => 'bna', 'Aa31LG4G3300' => 'aar', 'Aa31LG8G10030' => 'aar', 'Actinidia00731' => 'ach', 'Actinidia11473' => 'ach', 'Actinidia23469' => 'ach', 'Actinidia24318' => 'ach', 'Actinidia40196' => 'ach', 'Actinidia40197' => 'ach', 'Actinidia40198' => 'ach', 'Ah.08g212990' => 'amhyb', 'Ah.15g091720' => 'amhyb', 'AL3G38260' => 'aly', 'AL4G47710' => 'aly', 'Aqoxy2G00671' => 'aox', 'Aqoxy2G03236' => 'aox', 'arahy.Tifrunner.gnm1.ann1.05IDCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KR684' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATY3SJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK6QJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6APGL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IDT7Z9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM073U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ0R87' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LE7RV4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT4QRX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V5ENPK' => 'arhy', 'AT2G48110' => 'ath', 'AT3G23590' => 'ath', 'ATR0626G186' => 'atr', 'ATR1127G141' => 'atr', 'Atru.chr4.2583' => 'acertr', 'Atru.chr5.1358' => 'acertr', 'Atru.chr5.1359' => 'acertr', 'Atru.chr8.46' => 'acertr', 'AUR62002640' => 'cqu', 'AUR62030055' => 'cqu', 'AUR62033713' => 'cqu', 'AUR62033714' => 'cqu', 'AUR62036795' => 'cqu', 'AUR62039891' => 'cqu', 'BcaB02g08737' => 'bca', 'BcaB04g20441' => 'bca', 'BcaB06g26509' => 'bca', 'BcaB06g26510' => 'bca', 'BcaB06g26511' => 'bca', 'BcaB06g26512' => 'bca', 'BcaB06g26513' => 'bca', 'BcaC02g12564' => 'bca', 'BcaC02g12565' => 'bca', 'BcaC02g12794' => 'bca', 'BcaC02g12795' => 'bca', 'BcaC02g12796' => 'bca', 'BcaC06g35541' => 'bca', 'BNapus_Darmor_BZH_scaffold_188p00080' => 'bna', 'BNapus_Darmor_BZH_scaffold_188p00090' => 'bna', 'BolC1t03972H' => 'bol', 'BolC1t03973H' => 'bol', 'BolC4t21680H' => 'bol', 'BolC7t41863H' => 'bol', 'BolSC55t61227H' => 'bol', 'BolSC55t61228H' => 'bol', 'BraA01t03278Z' => 'bra', 'BraA05t18998Z' => 'bra', 'BraA07t28673Z' => 'bra', 'C01p40150' => 'bna', 'C05p12370' => 'bna', 'C07p13680' => 'bna', 'CAN.G1006.16' => 'can', 'CAN.G1006.17' => 'can', 'CAN.G1170.2' => 'can', 'CAN.G962.7' => 'can', 'CANSAT25G2179' => 'cansat', 'CANSAT78G1573' => 'cansat', 'CARHR099510' => 'chi', 'CARHR143510' => 'chi', 'Carub.0003s2380' => 'cru', 'Carub.0004s3082' => 'cru', 'Ca_00614_v3' => 'car', 'Ca_07801_v3' => 'car', 'Ca_08567_v3' => 'car', 'Ca_09571_v3' => 'car', 'CBR_g19290' => 'cbr', 'Cc01_g19770' => 'ccan', 'Cc03_g03030' => 'ccan', 'CDE07G0968' => 'cde', 'CDE09G1441' => 'cde', 'Cfa006103' => 'cfa', 'Cfa015573' => 'cfa', 'Cfa016988' => 'cfa', 'Ciclev10006738m.g' => 'ccl', 'Ciclev10010920m.g' => 'ccl', 'Ciclev10018517m.g' => 'ccl', 'CiPaw.01G159200' => 'cil', 'CiPaw.02G091000' => 'cil', 'CiPaw.02G091100' => 'cil', 'CiPaw.08G103100' => 'cil', 'CiPaw.09G224900' => 'cil', 'ClCG06G005740' => 'cla', 'ClCG07G000090' => 'cla', 'ClCG07G000100' => 'cla', 'COL.COLO4_09143' => 'col', 'COL.COLO4_25124' => 'col', 'Cpa.g.sc16.34' => 'cpa', 'Cpa.g.sc3504.1' => 'cpa', 'Cpa.g.sc60.37' => 'cpa', 'CsaV3_6G018520' => 'csa', 'CsaV3_6G036860' => 'csa', 'CSS0001072' => 'camsi', 'CSS0020208' => 'camsi', 'CSS0021253' => 'camsi', 'CSS0022190' => 'camsi', 'CSS0036150' => 'camsi', 'CSS0040442' => 'camsi', 'CSS0042300' => 'camsi', 'CSS0045298' => 'camsi', 'DCAR_012449' => 'dca', 'DCAR_018405' => 'dca', 'DCAR_024573' => 'dca', 'DCAR_030591' => 'dca', 'Dinv16926' => 'din', 'Dinv32963' => 'din', 'Dinv38382' => 'din', 'Dinv38383' => 'din', 'Duzib133G0974' => 'dzi', 'Duzib138G1867' => 'dzi', 'Duzib211G0420' => 'dzi', 'Duzib212G0930' => 'dzi', 'ECA234G1645' => 'eca', 'ECA247G3467' => 'eca', 'ECA248G1703' => 'eca', 'EL10Ac3g06327' => 'bvu', 'EL10Ac7g17204' => 'bvu', 'Eucgr.A00855' => 'egr', 'Eucgr.A00858' => 'egr', 'Eucgr.H01520' => 'egr', 'Eucgr.H03604' => 'egr', 'Eucgr.L03465' => 'egr', 'Eucgr.L03466' => 'egr', 'FAN01G0988' => 'fan', 'FAN02G3892' => 'fan', 'FAN05G3381' => 'fan', 'FAN07G0967' => 'fan', 'FAN07G1493' => 'fan', 'FAN08G3125' => 'fan', 'FAN09G0402' => 'fan', 'FAN12G2594' => 'fan', 'FAN12G3879' => 'fan', 'FAN14G1546' => 'fan', 'FAN15G3626' => 'fan', 'FAN17G0588' => 'fan', 'FAN17G0609' => 'fan', 'FAN18G2817' => 'fan', 'FAN19G1305' => 'fan', 'FAN20G1787' => 'fan', 'FAN22G0073' => 'fan', 'FAN22G0352' => 'fan', 'FAN22G0368' => 'fan', 'FAN22G2273' => 'fan', 'FAN24G1998' => 'fan', 'FAN27G1317' => 'fan', 'FvH4_2g23980' => 'fve', 'FvH4_4g14380' => 'fve', 'FvH4_4g14390' => 'fve', 'FvH4_6g09250' => 'fve', 'Glyma.03G151100' => 'gma', 'Glyma.04G122550' => 'gma', 'Glyma.05G001600' => 'gma', 'Glyma.09G270766' => 'gma', 'Glyma.09G270832' => 'gma', 'Glyma.13G209800' => 'gma', 'Glyma.15G102800' => 'gma', 'Glyma.18G218900' => 'gma', 'Glyma.19G001500' => 'gma', 'Glyma.19G153600' => 'gma', 'Gohir.A02G028600' => 'ghi', 'Gohir.A08G045000' => 'ghi', 'Gohir.A11G120500' => 'ghi', 'Gohir.A12G006200' => 'ghi', 'Gohir.A12G006250' => 'ghi', 'Gohir.D02G036300' => 'ghi', 'Gohir.D08G054700' => 'ghi', 'Gohir.D11G125600' => 'ghi', 'Gohir.D12G005700' => 'ghi', 'Gorai.004G055200' => 'gra', 'Gorai.005G040400' => 'gra', 'Gorai.007G134500' => 'gra', 'Gorai.008G005500' => 'gra', 'GSVIVG01011094001' => 'vvi', 'GSVIVG01017879001' => 'vvi', 'GSVIVG01025988001' => 'vvi', 'GSVIVG01029847001' => 'vvi', 'HanXRQChr10g0282901' => 'han', 'HanXRQChr10g0310371' => 'han', 'HanXRQChr10g0315041' => 'han', 'HanXRQChr11g0327651' => 'han', 'HanXRQChr12g0359391' => 'han', 'Haze_00972' => 'cav', 'Haze_00973' => 'cav', 'Haze_00974' => 'cav', 'Haze_04747' => 'cav', 'Haze_04749' => 'cav', 'Haze_04750' => 'cav', 'Haze_21217' => 'cav', 'Hma1.2p1_1037F.1_g250680' => 'hma', 'Hma1.2p1_1644F.1_g295320' => 'hma', 'HPP92_011322' => 'vpl', 'HPP92_011323' => 'vpl', 'HPP92_011324' => 'vpl', 'HPP92_011325' => 'vpl', 'HPP92_011326' => 'vpl', 'Hund12205' => 'sun', 'Hund17957' => 'sun', 'Lalb_Chr06g0176771' => 'lal', 'Lalb_Chr18g0056021' => 'lal', 'Lalb_Chr18g0056031' => 'lal', 'Lalb_Chr18g0056041' => 'lal', 'Lalb_Chr20g0107751' => 'lal', 'Lalb_Chr20g0118371' => 'lal', 'Lj1g0010239' => 'lja', 'Lj1g0017101' => 'lja', 'Lj2A1178G40' => 'lonja', 'Lj2A54G84' => 'lonja', 'Lj2g0015248' => 'lja', 'Lj3A761T51' => 'lonja', 'Lj6g0018116' => 'lja', 'Lsat_1_v5_gn_4_136040' => 'lsa', 'Lsat_1_v5_gn_5_187461' => 'lsa', 'Lsat_1_v5_gn_5_77001' => 'lsa', 'Lsat_1_v5_gn_9_4461' => 'lsa', 'Manes.01G210100' => 'mes', 'Manes.03G185600' => 'mes', 'Manes.05G073300' => 'mes', 'Manes.09G120300' => 'mes', 'Manes.15G022100' => 'mes', 'Mapoly0096s0053' => 'mpo', 'MBI03_g14058_MAGBIO' => 'mbi', 'MBI03_g33876_MAGBIO' => 'mbi', 'MBI03_g36854_MAGBIO' => 'mbi', 'MBI17_g11997_MAGBIO' => 'mbi', 'MD03G1269000' => 'mdo', 'MD04G1179600' => 'mdo', 'MD11G1289800' => 'mdo', 'MD12G1194700' => 'mdo', 'MD13G1182100' => 'mdo', 'MD13G1182200' => 'mdo', 'MD16G1182600' => 'mdo', 'Medtr2g021400' => 'mtr', 'Medtr2g021470' => 'mtr', 'Medtr2g105810' => 'mtr', 'Medtr3g033580' => 'mtr', 'Medtr6g007970' => 'mtr', 'Medtr7g056330' => 'mtr', 'Medtr7g074290' => 'mtr', 'Medtr7g074380' => 'mtr', 'Medtr7g094550' => 'mtr', 'Medtr8g069995' => 'mtr', 'MELO3C014345.2' => 'cme', 'MELO3C021395.2' => 'cme', 'Migut.D00262' => 'egut', 'Migut.G00257' => 'egut', 'MSTRG.21575' => 'ama', 'MSTRG.3985' => 'ama', 'Nitab4.5_0000295g0140' => 'nta', 'Nitab4.5_0000732g0140' => 'nta', 'Nitab4.5_0003162g0020' => 'nta', 'Nitab4.5_0006180g0090' => 'nta', 'Nitab4.5_0006390g0010' => 'nta', 'Nitab4.5_0007392g0040' => 'nta', 'Nn1g02140' => 'nnu', 'Nn4g26168' => 'nnu', 'Nn5g26754' => 'nnu', 'Oeu001433.1' => 'oeu', 'Oeu010299.2' => 'oeu', 'Oeu011171.1' => 'oeu', 'Oeu037675.1' => 'oeu', 'Oeu038359.1' => 'oeu', 'Oeu063834.1' => 'oeu', 'Oeu063835.1' => 'oeu', 'Os05g0312000' => 'osa', 'Os07g0211101' => 'osa', 'Os07g0211200' => 'osa', 'Os07g0681500' => 'osa', 'Peaxi162Scf00095g01015' => 'pax', 'Peaxi162Scf00104g00329' => 'pax', 'Peaxi162Scf00161g00137' => 'pax', 'PGR004G1665' => 'pgr', 'PGR031G2937' => 'pgr', 'PGR119G2145' => 'pgr', 'PGSC0003DMG400004351' => 'stu', 'PGSC0003DMG400014625' => 'stu', 'PGSC0003DMG401000943' => 'stu', 'Phvul.001G148600' => 'pvu', 'Phvul.004G001700' => 'pvu', 'Phvul.006G154900' => 'pvu', 'Phvul.008G078200' => 'pvu', 'Phvul.011G136500' => 'pvu', 'Potri.002G215600' => 'ptr', 'Potri.008G201600' => 'ptr', 'Potri.014G138400' => 'ptr', 'Potri.016G142500' => 'ptr', 'Pp3c16_10580' => 'ppa', 'Pp3c5_25280' => 'ppa', 'Prupe.1G150000' => 'ppe', 'Prupe.1G150100' => 'ppe', 'Prupe.6G299600' => 'ppe', 'Prupe.8G245000' => 'ppe', 'Psat0s4927g0040' => 'psa', 'Psat1g052080' => 'psa', 'Psat1g183800' => 'psa', 'Psat3g113840' => 'psa', 'Psat3g126120' => 'psa', 'Psat3g126160' => 'psa', 'Psat3g158760' => 'psa', 'Psat3g158840' => 'psa', 'PSO170G2858' => 'pso', 'PSO339G0606' => 'pso', 'PSO384G4709' => 'pso', 'PSO407G0334' => 'pso', 'QL04p040276' => 'qlo', 'QL06p005458' => 'qlo', 'QL06p005472' => 'qlo', 'QL07p030546' => 'qlo', 'QL07p031519' => 'qlo', 'QL09p050949' => 'qlo', 'QL09p050966' => 'qlo', 'QL09p051067' => 'qlo', 'QL12p022706' => 'qlo', 'RcHm_v2.0_Chr2g0119601' => 'rch', 'RcHm_v2.0_Chr3g0459591' => 'rch', 'RcHm_v2.0_Chr4g0418521' => 'rch', 'RcHm_v2.0_Chr4g0418531' => 'rch', 'RcHm_v2.0_Chr4g0418541' => 'rch', 'RcHm_v2.0_Chr6g0291641' => 'rch', 'Rhsim01G0086300' => 'rsi', 'Rhsim01G0276300' => 'rsi', 'Rhsim01G0276500' => 'rsi', 'Rhsim04G0207700' => 'rsi', 'Rhsim05G0234500' => 'rsi', 'Rhsim13G0022400' => 'rsi', 'Sabra02G0167900' => 'sbr', 'Sabra04G0158500' => 'sbr', 'Sabra08G0159800' => 'sbr', 'Sabra10G0011500' => 'sbr', 'Sabra14G0104400' => 'sbr', 'SalBow2G2440' => 'sbo', 'SalBow4G2265' => 'sbo', 'Sc02g0000060' => 'sci', 'Sc05g0005020' => 'sci', 'Sc13g0003890' => 'sci', 'Sed0014865' => 'sed', 'Sed0017224' => 'sed', 'Sed0026391' => 'sed', 'SEGI_00063' => 'sgi', 'SEGI_10967' => 'sgi', 'SEGI_17510' => 'sgi', 'SEGI_24396' => 'sgi', 'SEGI_39719' => 'sgi', 'SEGI_41392' => 'sgi', 'SGA_v2.0_scaffold11G05794' => 'sas', 'SGA_v2.0_scaffold142G35607' => 'sas', 'SGA_v2.0_scaffold1G00447' => 'sas', 'SHI15388' => 'shi', 'SHI15394' => 'shi', 'SHI15396' => 'shi', 'SHI15399' => 'shi', 'SMO343G0151' => 'smo', 'SMO367G1118' => 'smo', 'Solyc01g080200.3' => 'sly', 'Solyc06g008960.3' => 'sly', 'Solyc09g064780.3' => 'sly', 'Sopen01g031980' => 'spe', 'Sopen06g003710' => 'spe', 'Sopen09g026460' => 'spe', 'Sp3g21240' => 'spa', 'Sp4g30030' => 'spa', 'TAR365G0022' => 'tar', 'TAR365G1023' => 'tar', 'TAR365G1253' => 'tar', 'TAR623G0078' => 'tar', 'TAR623G1721' => 'tar', 'TAR633G0959' => 'tar', 'THA.LOC104802225' => 'tha', 'THA.LOC104804769' => 'tha', 'THA.LOC104808660' => 'tha', 'THA.LOC104812792' => 'tha', 'Thecc.01G284000' => 'tca', 'Thecc.04G220600' => 'tca', 'Thecc.05G268900' => 'tca', 'Thecc.08G171100' => 'tca', 'Thhalv10001284m.g' => 'esa', 'Thhalv10019912m.g' => 'esa', 'TPR.G14189' => 'tpr', 'TPR.G18110' => 'tpr', 'TPR.G18130' => 'tpr', 'TPR.G18131' => 'tpr', 'TPR.G18140' => 'tpr', 'TPR.G24282' => 'tpr', 'TPR.G25221' => 'tpr', 'TPR.G29267' => 'tpr', 'TPR.G35315' => 'tpr', 'TPR.G36173' => 'tpr', 'TWI09G0794' => 'twi', 'TWI59G1348' => 'twi', 'TWI74G0430' => 'twi', 'unitig_26.g8940' => 'ugi', 'unitig_749.g13744' => 'ugi', 'unitig_749.g13745' => 'ugi', 'vmacro08269' => 'vma', 'vmacro14937' => 'vma', 'vmacro20401' => 'vma', 'VMungo0464G1349' => 'vmu', 'VMungo0540G0289' => 'vmu', 'VMungo1215G1590' => 'vmu', 'VMungo1309G0221' => 'vmu', 'VMungo1309G2815' => 'vmu', 'VMungo1383G0239' => 'vmu', 'VMungo1383G2910' => 'vmu', 'Zm00001eb095270' => 'zma', 'Zm00001eb095280' => 'zma', 'Zm00001eb111630' => 'zma', 'Zm00001eb237080' => 'zma', 'Zm00001eb273740' => 'zma', 'Zm00001eb285040' => 'zma', 'Zm00001eb330790' => 'zma', 'Zm00001eb337380' => 'zma' ) $gf_id = 'HOM05D001484' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001484' ) $data_identifier = 'HOM05D001484' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 2, 'aly' => (int) 2, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 22, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 7, 'hma' => (int) 2, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 7, 'mtr' => (int) 10, 'cme' => (int) 2, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 4, 'ppa' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 4, 'qlo' => (int) 9, 'rch' => (int) 6, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 10, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 7, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb337380' $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' => 'HOM05D001484', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p31500' => 'bna', 'A05p00020' => 'bna', 'A07p08820' => 'bna', 'Aa31LG4G3300' => 'aar', 'Aa31LG8G10030' => 'aar', 'Actinidia00731' => 'ach', 'Actinidia11473' => 'ach', 'Actinidia23469' => 'ach', 'Actinidia24318' => 'ach', 'Actinidia40196' => 'ach', 'Actinidia40197' => 'ach', 'Actinidia40198' => 'ach', 'Ah.08g212990' => 'amhyb', 'Ah.15g091720' => 'amhyb', 'AL3G38260' => 'aly', 'AL4G47710' => 'aly', 'Aqoxy2G00671' => 'aox', 'Aqoxy2G03236' => 'aox', 'arahy.Tifrunner.gnm1.ann1.05IDCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KR684' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATY3SJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK6QJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6APGL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IDT7Z9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM073U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ0R87' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LE7RV4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT4QRX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V5ENPK' => 'arhy', 'AT2G48110' => 'ath', 'AT3G23590' => 'ath', 'ATR0626G186' => 'atr', 'ATR1127G141' => 'atr', 'Atru.chr4.2583' => 'acertr', 'Atru.chr5.1358' => 'acertr', 'Atru.chr5.1359' => 'acertr', 'Atru.chr8.46' => 'acertr', 'AUR62002640' => 'cqu', 'AUR62030055' => 'cqu', 'AUR62033713' => 'cqu', 'AUR62033714' => 'cqu', 'AUR62036795' => 'cqu', 'AUR62039891' => 'cqu', 'BcaB02g08737' => 'bca', 'BcaB04g20441' => 'bca', 'BcaB06g26509' => 'bca', 'BcaB06g26510' => 'bca', 'BcaB06g26511' => 'bca', 'BcaB06g26512' => 'bca', 'BcaB06g26513' => 'bca', 'BcaC02g12564' => 'bca', 'BcaC02g12565' => 'bca', 'BcaC02g12794' => 'bca', 'BcaC02g12795' => 'bca', 'BcaC02g12796' => 'bca', 'BcaC06g35541' => 'bca', 'BNapus_Darmor_BZH_scaffold_188p00080' => 'bna', 'BNapus_Darmor_BZH_scaffold_188p00090' => 'bna', 'BolC1t03972H' => 'bol', 'BolC1t03973H' => 'bol', 'BolC4t21680H' => 'bol', 'BolC7t41863H' => 'bol', 'BolSC55t61227H' => 'bol', 'BolSC55t61228H' => 'bol', 'BraA01t03278Z' => 'bra', 'BraA05t18998Z' => 'bra', 'BraA07t28673Z' => 'bra', 'C01p40150' => 'bna', 'C05p12370' => 'bna', 'C07p13680' => 'bna', 'CAN.G1006.16' => 'can', 'CAN.G1006.17' => 'can', 'CAN.G1170.2' => 'can', 'CAN.G962.7' => 'can', 'CANSAT25G2179' => 'cansat', 'CANSAT78G1573' => 'cansat', 'CARHR099510' => 'chi', 'CARHR143510' => 'chi', 'Carub.0003s2380' => 'cru', 'Carub.0004s3082' => 'cru', 'Ca_00614_v3' => 'car', 'Ca_07801_v3' => 'car', 'Ca_08567_v3' => 'car', 'Ca_09571_v3' => 'car', 'CBR_g19290' => 'cbr', 'Cc01_g19770' => 'ccan', 'Cc03_g03030' => 'ccan', 'CDE07G0968' => 'cde', 'CDE09G1441' => 'cde', 'Cfa006103' => 'cfa', 'Cfa015573' => 'cfa', 'Cfa016988' => 'cfa', 'Ciclev10006738m.g' => 'ccl', 'Ciclev10010920m.g' => 'ccl', 'Ciclev10018517m.g' => 'ccl', 'CiPaw.01G159200' => 'cil', 'CiPaw.02G091000' => 'cil', 'CiPaw.02G091100' => 'cil', 'CiPaw.08G103100' => 'cil', 'CiPaw.09G224900' => 'cil', 'ClCG06G005740' => 'cla', 'ClCG07G000090' => 'cla', 'ClCG07G000100' => 'cla', 'COL.COLO4_09143' => 'col', 'COL.COLO4_25124' => 'col', 'Cpa.g.sc16.34' => 'cpa', 'Cpa.g.sc3504.1' => 'cpa', 'Cpa.g.sc60.37' => 'cpa', 'CsaV3_6G018520' => 'csa', 'CsaV3_6G036860' => 'csa', 'CSS0001072' => 'camsi', 'CSS0020208' => 'camsi', 'CSS0021253' => 'camsi', 'CSS0022190' => 'camsi', 'CSS0036150' => 'camsi', 'CSS0040442' => 'camsi', 'CSS0042300' => 'camsi', 'CSS0045298' => 'camsi', 'DCAR_012449' => 'dca', 'DCAR_018405' => 'dca', 'DCAR_024573' => 'dca', 'DCAR_030591' => 'dca', 'Dinv16926' => 'din', 'Dinv32963' => 'din', 'Dinv38382' => 'din', 'Dinv38383' => 'din', 'Duzib133G0974' => 'dzi', 'Duzib138G1867' => 'dzi', 'Duzib211G0420' => 'dzi', 'Duzib212G0930' => 'dzi', 'ECA234G1645' => 'eca', 'ECA247G3467' => 'eca', 'ECA248G1703' => 'eca', 'EL10Ac3g06327' => 'bvu', 'EL10Ac7g17204' => 'bvu', 'Eucgr.A00855' => 'egr', 'Eucgr.A00858' => 'egr', 'Eucgr.H01520' => 'egr', 'Eucgr.H03604' => 'egr', 'Eucgr.L03465' => 'egr', 'Eucgr.L03466' => 'egr', 'FAN01G0988' => 'fan', 'FAN02G3892' => 'fan', 'FAN05G3381' => 'fan', 'FAN07G0967' => 'fan', 'FAN07G1493' => 'fan', 'FAN08G3125' => 'fan', 'FAN09G0402' => 'fan', 'FAN12G2594' => 'fan', 'FAN12G3879' => 'fan', 'FAN14G1546' => 'fan', 'FAN15G3626' => 'fan', 'FAN17G0588' => 'fan', 'FAN17G0609' => 'fan', 'FAN18G2817' => 'fan', 'FAN19G1305' => 'fan', 'FAN20G1787' => 'fan', 'FAN22G0073' => 'fan', 'FAN22G0352' => 'fan', 'FAN22G0368' => 'fan', 'FAN22G2273' => 'fan', 'FAN24G1998' => 'fan', 'FAN27G1317' => 'fan', 'FvH4_2g23980' => 'fve', 'FvH4_4g14380' => 'fve', 'FvH4_4g14390' => 'fve', 'FvH4_6g09250' => 'fve', 'Glyma.03G151100' => 'gma', 'Glyma.04G122550' => 'gma', 'Glyma.05G001600' => 'gma', 'Glyma.09G270766' => 'gma', 'Glyma.09G270832' => 'gma', 'Glyma.13G209800' => 'gma', 'Glyma.15G102800' => 'gma', 'Glyma.18G218900' => 'gma', 'Glyma.19G001500' => 'gma', 'Glyma.19G153600' => 'gma', 'Gohir.A02G028600' => 'ghi', 'Gohir.A08G045000' => 'ghi', 'Gohir.A11G120500' => 'ghi', 'Gohir.A12G006200' => 'ghi', 'Gohir.A12G006250' => 'ghi', 'Gohir.D02G036300' => 'ghi', 'Gohir.D08G054700' => 'ghi', 'Gohir.D11G125600' => 'ghi', 'Gohir.D12G005700' => 'ghi', 'Gorai.004G055200' => 'gra', 'Gorai.005G040400' => 'gra', 'Gorai.007G134500' => 'gra', 'Gorai.008G005500' => 'gra', 'GSVIVG01011094001' => 'vvi', 'GSVIVG01017879001' => 'vvi', 'GSVIVG01025988001' => 'vvi', 'GSVIVG01029847001' => 'vvi', 'HanXRQChr10g0282901' => 'han', 'HanXRQChr10g0310371' => 'han', 'HanXRQChr10g0315041' => 'han', 'HanXRQChr11g0327651' => 'han', 'HanXRQChr12g0359391' => 'han', 'Haze_00972' => 'cav', 'Haze_00973' => 'cav', 'Haze_00974' => 'cav', 'Haze_04747' => 'cav', 'Haze_04749' => 'cav', 'Haze_04750' => 'cav', 'Haze_21217' => 'cav', 'Hma1.2p1_1037F.1_g250680' => 'hma', 'Hma1.2p1_1644F.1_g295320' => 'hma', 'HPP92_011322' => 'vpl', 'HPP92_011323' => 'vpl', 'HPP92_011324' => 'vpl', 'HPP92_011325' => 'vpl', 'HPP92_011326' => 'vpl', 'Hund12205' => 'sun', 'Hund17957' => 'sun', 'Lalb_Chr06g0176771' => 'lal', 'Lalb_Chr18g0056021' => 'lal', 'Lalb_Chr18g0056031' => 'lal', 'Lalb_Chr18g0056041' => 'lal', 'Lalb_Chr20g0107751' => 'lal', 'Lalb_Chr20g0118371' => 'lal', 'Lj1g0010239' => 'lja', 'Lj1g0017101' => 'lja', 'Lj2A1178G40' => 'lonja', 'Lj2A54G84' => 'lonja', 'Lj2g0015248' => 'lja', 'Lj3A761T51' => 'lonja', 'Lj6g0018116' => 'lja', 'Lsat_1_v5_gn_4_136040' => 'lsa', 'Lsat_1_v5_gn_5_187461' => 'lsa', 'Lsat_1_v5_gn_5_77001' => 'lsa', 'Lsat_1_v5_gn_9_4461' => 'lsa', 'Manes.01G210100' => 'mes', 'Manes.03G185600' => 'mes', 'Manes.05G073300' => 'mes', 'Manes.09G120300' => 'mes', 'Manes.15G022100' => 'mes', 'Mapoly0096s0053' => 'mpo', 'MBI03_g14058_MAGBIO' => 'mbi', 'MBI03_g33876_MAGBIO' => 'mbi', 'MBI03_g36854_MAGBIO' => 'mbi', 'MBI17_g11997_MAGBIO' => 'mbi', 'MD03G1269000' => 'mdo', 'MD04G1179600' => 'mdo', 'MD11G1289800' => 'mdo', 'MD12G1194700' => 'mdo', 'MD13G1182100' => 'mdo', 'MD13G1182200' => 'mdo', 'MD16G1182600' => 'mdo', 'Medtr2g021400' => 'mtr', 'Medtr2g021470' => 'mtr', 'Medtr2g105810' => 'mtr', 'Medtr3g033580' => 'mtr', 'Medtr6g007970' => 'mtr', 'Medtr7g056330' => 'mtr', 'Medtr7g074290' => 'mtr', 'Medtr7g074380' => 'mtr', 'Medtr7g094550' => 'mtr', 'Medtr8g069995' => 'mtr', 'MELO3C014345.2' => 'cme', 'MELO3C021395.2' => 'cme', 'Migut.D00262' => 'egut', 'Migut.G00257' => 'egut', 'MSTRG.21575' => 'ama', 'MSTRG.3985' => 'ama', 'Nitab4.5_0000295g0140' => 'nta', 'Nitab4.5_0000732g0140' => 'nta', 'Nitab4.5_0003162g0020' => 'nta', 'Nitab4.5_0006180g0090' => 'nta', 'Nitab4.5_0006390g0010' => 'nta', 'Nitab4.5_0007392g0040' => 'nta', 'Nn1g02140' => 'nnu', 'Nn4g26168' => 'nnu', 'Nn5g26754' => 'nnu', 'Oeu001433.1' => 'oeu', 'Oeu010299.2' => 'oeu', 'Oeu011171.1' => 'oeu', 'Oeu037675.1' => 'oeu', 'Oeu038359.1' => 'oeu', 'Oeu063834.1' => 'oeu', 'Oeu063835.1' => 'oeu', 'Os05g0312000' => 'osa', 'Os07g0211101' => 'osa', 'Os07g0211200' => 'osa', 'Os07g0681500' => 'osa', 'Peaxi162Scf00095g01015' => 'pax', 'Peaxi162Scf00104g00329' => 'pax', 'Peaxi162Scf00161g00137' => 'pax', 'PGR004G1665' => 'pgr', 'PGR031G2937' => 'pgr', 'PGR119G2145' => 'pgr', 'PGSC0003DMG400004351' => 'stu', 'PGSC0003DMG400014625' => 'stu', 'PGSC0003DMG401000943' => 'stu', 'Phvul.001G148600' => 'pvu', 'Phvul.004G001700' => 'pvu', 'Phvul.006G154900' => 'pvu', 'Phvul.008G078200' => 'pvu', 'Phvul.011G136500' => 'pvu', 'Potri.002G215600' => 'ptr', 'Potri.008G201600' => 'ptr', 'Potri.014G138400' => 'ptr', 'Potri.016G142500' => 'ptr', 'Pp3c16_10580' => 'ppa', 'Pp3c5_25280' => 'ppa', 'Prupe.1G150000' => 'ppe', 'Prupe.1G150100' => 'ppe', 'Prupe.6G299600' => 'ppe', 'Prupe.8G245000' => 'ppe', 'Psat0s4927g0040' => 'psa', 'Psat1g052080' => 'psa', 'Psat1g183800' => 'psa', 'Psat3g113840' => 'psa', 'Psat3g126120' => 'psa', 'Psat3g126160' => 'psa', 'Psat3g158760' => 'psa', 'Psat3g158840' => 'psa', 'PSO170G2858' => 'pso', 'PSO339G0606' => 'pso', 'PSO384G4709' => 'pso', 'PSO407G0334' => 'pso', 'QL04p040276' => 'qlo', 'QL06p005458' => 'qlo', 'QL06p005472' => 'qlo', 'QL07p030546' => 'qlo', 'QL07p031519' => 'qlo', 'QL09p050949' => 'qlo', 'QL09p050966' => 'qlo', 'QL09p051067' => 'qlo', 'QL12p022706' => 'qlo', 'RcHm_v2.0_Chr2g0119601' => 'rch', 'RcHm_v2.0_Chr3g0459591' => 'rch', 'RcHm_v2.0_Chr4g0418521' => 'rch', 'RcHm_v2.0_Chr4g0418531' => 'rch', 'RcHm_v2.0_Chr4g0418541' => 'rch', 'RcHm_v2.0_Chr6g0291641' => 'rch', 'Rhsim01G0086300' => 'rsi', 'Rhsim01G0276300' => 'rsi', 'Rhsim01G0276500' => 'rsi', 'Rhsim04G0207700' => 'rsi', 'Rhsim05G0234500' => 'rsi', 'Rhsim13G0022400' => 'rsi', 'Sabra02G0167900' => 'sbr', 'Sabra04G0158500' => 'sbr', 'Sabra08G0159800' => 'sbr', 'Sabra10G0011500' => 'sbr', 'Sabra14G0104400' => 'sbr', 'SalBow2G2440' => 'sbo', 'SalBow4G2265' => 'sbo', 'Sc02g0000060' => 'sci', 'Sc05g0005020' => 'sci', 'Sc13g0003890' => 'sci', 'Sed0014865' => 'sed', 'Sed0017224' => 'sed', 'Sed0026391' => 'sed', 'SEGI_00063' => 'sgi', 'SEGI_10967' => 'sgi', 'SEGI_17510' => 'sgi', 'SEGI_24396' => 'sgi', 'SEGI_39719' => 'sgi', 'SEGI_41392' => 'sgi', 'SGA_v2.0_scaffold11G05794' => 'sas', 'SGA_v2.0_scaffold142G35607' => 'sas', 'SGA_v2.0_scaffold1G00447' => 'sas', 'SHI15388' => 'shi', 'SHI15394' => 'shi', 'SHI15396' => 'shi', 'SHI15399' => 'shi', 'SMO343G0151' => 'smo', 'SMO367G1118' => 'smo', 'Solyc01g080200.3' => 'sly', 'Solyc06g008960.3' => 'sly', 'Solyc09g064780.3' => 'sly', 'Sopen01g031980' => 'spe', 'Sopen06g003710' => 'spe', 'Sopen09g026460' => 'spe', 'Sp3g21240' => 'spa', 'Sp4g30030' => 'spa', 'TAR365G0022' => 'tar', 'TAR365G1023' => 'tar', 'TAR365G1253' => 'tar', 'TAR623G0078' => 'tar', 'TAR623G1721' => 'tar', 'TAR633G0959' => 'tar', 'THA.LOC104802225' => 'tha', 'THA.LOC104804769' => 'tha', 'THA.LOC104808660' => 'tha', 'THA.LOC104812792' => 'tha', 'Thecc.01G284000' => 'tca', 'Thecc.04G220600' => 'tca', 'Thecc.05G268900' => 'tca', 'Thecc.08G171100' => 'tca', 'Thhalv10001284m.g' => 'esa', 'Thhalv10019912m.g' => 'esa', 'TPR.G14189' => 'tpr', 'TPR.G18110' => 'tpr', 'TPR.G18130' => 'tpr', 'TPR.G18131' => 'tpr', 'TPR.G18140' => 'tpr', 'TPR.G24282' => 'tpr', 'TPR.G25221' => 'tpr', 'TPR.G29267' => 'tpr', 'TPR.G35315' => 'tpr', 'TPR.G36173' => 'tpr', 'TWI09G0794' => 'twi', 'TWI59G1348' => 'twi', 'TWI74G0430' => 'twi', 'unitig_26.g8940' => 'ugi', 'unitig_749.g13744' => 'ugi', 'unitig_749.g13745' => 'ugi', 'vmacro08269' => 'vma', 'vmacro14937' => 'vma', 'vmacro20401' => 'vma', 'VMungo0464G1349' => 'vmu', 'VMungo0540G0289' => 'vmu', 'VMungo1215G1590' => 'vmu', 'VMungo1309G0221' => 'vmu', 'VMungo1309G2815' => 'vmu', 'VMungo1383G0239' => 'vmu', 'VMungo1383G2910' => 'vmu', 'Zm00001eb095270' => 'zma', 'Zm00001eb095280' => 'zma', 'Zm00001eb111630' => 'zma', 'Zm00001eb237080' => 'zma', 'Zm00001eb273740' => 'zma', 'Zm00001eb285040' => 'zma', 'Zm00001eb330790' => 'zma', 'Zm00001eb337380' => 'zma' ), 'gf_id' => 'HOM05D001484', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001484' ), 'data_identifier' => 'HOM05D001484', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001484', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p31500' => 'bna', 'A05p00020' => 'bna', 'A07p08820' => 'bna', 'Aa31LG4G3300' => 'aar', 'Aa31LG8G10030' => 'aar', 'Actinidia00731' => 'ach', 'Actinidia11473' => 'ach', 'Actinidia23469' => 'ach', 'Actinidia24318' => 'ach', 'Actinidia40196' => 'ach', 'Actinidia40197' => 'ach', 'Actinidia40198' => 'ach', 'Ah.08g212990' => 'amhyb', 'Ah.15g091720' => 'amhyb', 'AL3G38260' => 'aly', 'AL4G47710' => 'aly', 'Aqoxy2G00671' => 'aox', 'Aqoxy2G03236' => 'aox', 'arahy.Tifrunner.gnm1.ann1.05IDCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KR684' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATY3SJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK6QJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6APGL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IDT7Z9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM073U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ0R87' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LE7RV4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT4QRX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V5ENPK' => 'arhy', 'AT2G48110' => 'ath', 'AT3G23590' => 'ath', 'ATR0626G186' => 'atr', 'ATR1127G141' => 'atr', 'Atru.chr4.2583' => 'acertr', 'Atru.chr5.1358' => 'acertr', 'Atru.chr5.1359' => 'acertr', 'Atru.chr8.46' => 'acertr', 'AUR62002640' => 'cqu', 'AUR62030055' => 'cqu', 'AUR62033713' => 'cqu', 'AUR62033714' => 'cqu', 'AUR62036795' => 'cqu', 'AUR62039891' => 'cqu', 'BcaB02g08737' => 'bca', 'BcaB04g20441' => 'bca', 'BcaB06g26509' => 'bca', 'BcaB06g26510' => 'bca', 'BcaB06g26511' => 'bca', 'BcaB06g26512' => 'bca', 'BcaB06g26513' => 'bca', 'BcaC02g12564' => 'bca', 'BcaC02g12565' => 'bca', 'BcaC02g12794' => 'bca', 'BcaC02g12795' => 'bca', 'BcaC02g12796' => 'bca', 'BcaC06g35541' => 'bca', 'BNapus_Darmor_BZH_scaffold_188p00080' => 'bna', 'BNapus_Darmor_BZH_scaffold_188p00090' => 'bna', 'BolC1t03972H' => 'bol', 'BolC1t03973H' => 'bol', 'BolC4t21680H' => 'bol', 'BolC7t41863H' => 'bol', 'BolSC55t61227H' => 'bol', 'BolSC55t61228H' => 'bol', 'BraA01t03278Z' => 'bra', 'BraA05t18998Z' => 'bra', 'BraA07t28673Z' => 'bra', 'C01p40150' => 'bna', 'C05p12370' => 'bna', 'C07p13680' => 'bna', 'CAN.G1006.16' => 'can', 'CAN.G1006.17' => 'can', 'CAN.G1170.2' => 'can', 'CAN.G962.7' => 'can', 'CANSAT25G2179' => 'cansat', 'CANSAT78G1573' => 'cansat', 'CARHR099510' => 'chi', 'CARHR143510' => 'chi', 'Carub.0003s2380' => 'cru', 'Carub.0004s3082' => 'cru', 'Ca_00614_v3' => 'car', 'Ca_07801_v3' => 'car', 'Ca_08567_v3' => 'car', 'Ca_09571_v3' => 'car', 'CBR_g19290' => 'cbr', 'Cc01_g19770' => 'ccan', 'Cc03_g03030' => 'ccan', 'CDE07G0968' => 'cde', 'CDE09G1441' => 'cde', 'Cfa006103' => 'cfa', 'Cfa015573' => 'cfa', 'Cfa016988' => 'cfa', 'Ciclev10006738m.g' => 'ccl', 'Ciclev10010920m.g' => 'ccl', 'Ciclev10018517m.g' => 'ccl', 'CiPaw.01G159200' => 'cil', 'CiPaw.02G091000' => 'cil', 'CiPaw.02G091100' => 'cil', 'CiPaw.08G103100' => 'cil', 'CiPaw.09G224900' => 'cil', 'ClCG06G005740' => 'cla', 'ClCG07G000090' => 'cla', 'ClCG07G000100' => 'cla', 'COL.COLO4_09143' => 'col', 'COL.COLO4_25124' => 'col', 'Cpa.g.sc16.34' => 'cpa', 'Cpa.g.sc3504.1' => 'cpa', 'Cpa.g.sc60.37' => 'cpa', 'CsaV3_6G018520' => 'csa', 'CsaV3_6G036860' => 'csa', 'CSS0001072' => 'camsi', 'CSS0020208' => 'camsi', 'CSS0021253' => 'camsi', 'CSS0022190' => 'camsi', 'CSS0036150' => 'camsi', 'CSS0040442' => 'camsi', 'CSS0042300' => 'camsi', 'CSS0045298' => 'camsi', 'DCAR_012449' => 'dca', 'DCAR_018405' => 'dca', 'DCAR_024573' => 'dca', 'DCAR_030591' => 'dca', 'Dinv16926' => 'din', 'Dinv32963' => 'din', 'Dinv38382' => 'din', 'Dinv38383' => 'din', 'Duzib133G0974' => 'dzi', 'Duzib138G1867' => 'dzi', 'Duzib211G0420' => 'dzi', 'Duzib212G0930' => 'dzi', 'ECA234G1645' => 'eca', 'ECA247G3467' => 'eca', 'ECA248G1703' => 'eca', 'EL10Ac3g06327' => 'bvu', 'EL10Ac7g17204' => 'bvu', 'Eucgr.A00855' => 'egr', 'Eucgr.A00858' => 'egr', 'Eucgr.H01520' => 'egr', 'Eucgr.H03604' => 'egr', 'Eucgr.L03465' => 'egr', 'Eucgr.L03466' => 'egr', 'FAN01G0988' => 'fan', 'FAN02G3892' => 'fan', 'FAN05G3381' => 'fan', 'FAN07G0967' => 'fan', 'FAN07G1493' => 'fan', 'FAN08G3125' => 'fan', 'FAN09G0402' => 'fan', 'FAN12G2594' => 'fan', 'FAN12G3879' => 'fan', 'FAN14G1546' => 'fan', 'FAN15G3626' => 'fan', 'FAN17G0588' => 'fan', 'FAN17G0609' => 'fan', 'FAN18G2817' => 'fan', 'FAN19G1305' => 'fan', 'FAN20G1787' => 'fan', 'FAN22G0073' => 'fan', 'FAN22G0352' => 'fan', 'FAN22G0368' => 'fan', 'FAN22G2273' => 'fan', 'FAN24G1998' => 'fan', 'FAN27G1317' => 'fan', 'FvH4_2g23980' => 'fve', 'FvH4_4g14380' => 'fve', 'FvH4_4g14390' => 'fve', 'FvH4_6g09250' => 'fve', 'Glyma.03G151100' => 'gma', 'Glyma.04G122550' => 'gma', 'Glyma.05G001600' => 'gma', 'Glyma.09G270766' => 'gma', 'Glyma.09G270832' => 'gma', 'Glyma.13G209800' => 'gma', 'Glyma.15G102800' => 'gma', 'Glyma.18G218900' => 'gma', 'Glyma.19G001500' => 'gma', 'Glyma.19G153600' => 'gma', 'Gohir.A02G028600' => 'ghi', 'Gohir.A08G045000' => 'ghi', 'Gohir.A11G120500' => 'ghi', 'Gohir.A12G006200' => 'ghi', 'Gohir.A12G006250' => 'ghi', 'Gohir.D02G036300' => 'ghi', 'Gohir.D08G054700' => 'ghi', 'Gohir.D11G125600' => 'ghi', 'Gohir.D12G005700' => 'ghi', 'Gorai.004G055200' => 'gra', 'Gorai.005G040400' => 'gra', 'Gorai.007G134500' => 'gra', 'Gorai.008G005500' => 'gra', 'GSVIVG01011094001' => 'vvi', 'GSVIVG01017879001' => 'vvi', 'GSVIVG01025988001' => 'vvi', 'GSVIVG01029847001' => 'vvi', 'HanXRQChr10g0282901' => 'han', 'HanXRQChr10g0310371' => 'han', 'HanXRQChr10g0315041' => 'han', 'HanXRQChr11g0327651' => 'han', 'HanXRQChr12g0359391' => 'han', 'Haze_00972' => 'cav', 'Haze_00973' => 'cav', 'Haze_00974' => 'cav', 'Haze_04747' => 'cav', 'Haze_04749' => 'cav', 'Haze_04750' => 'cav', 'Haze_21217' => 'cav', 'Hma1.2p1_1037F.1_g250680' => 'hma', 'Hma1.2p1_1644F.1_g295320' => 'hma', 'HPP92_011322' => 'vpl', 'HPP92_011323' => 'vpl', 'HPP92_011324' => 'vpl', 'HPP92_011325' => 'vpl', 'HPP92_011326' => 'vpl', 'Hund12205' => 'sun', 'Hund17957' => 'sun', 'Lalb_Chr06g0176771' => 'lal', 'Lalb_Chr18g0056021' => 'lal', 'Lalb_Chr18g0056031' => 'lal', 'Lalb_Chr18g0056041' => 'lal', 'Lalb_Chr20g0107751' => 'lal', 'Lalb_Chr20g0118371' => 'lal', 'Lj1g0010239' => 'lja', 'Lj1g0017101' => 'lja', 'Lj2A1178G40' => 'lonja', 'Lj2A54G84' => 'lonja', 'Lj2g0015248' => 'lja', 'Lj3A761T51' => 'lonja', 'Lj6g0018116' => 'lja', 'Lsat_1_v5_gn_4_136040' => 'lsa', 'Lsat_1_v5_gn_5_187461' => 'lsa', 'Lsat_1_v5_gn_5_77001' => 'lsa', 'Lsat_1_v5_gn_9_4461' => 'lsa', 'Manes.01G210100' => 'mes', 'Manes.03G185600' => 'mes', 'Manes.05G073300' => 'mes', 'Manes.09G120300' => 'mes', 'Manes.15G022100' => 'mes', 'Mapoly0096s0053' => 'mpo', 'MBI03_g14058_MAGBIO' => 'mbi', 'MBI03_g33876_MAGBIO' => 'mbi', 'MBI03_g36854_MAGBIO' => 'mbi', 'MBI17_g11997_MAGBIO' => 'mbi', 'MD03G1269000' => 'mdo', 'MD04G1179600' => 'mdo', 'MD11G1289800' => 'mdo', 'MD12G1194700' => 'mdo', 'MD13G1182100' => 'mdo', 'MD13G1182200' => 'mdo', 'MD16G1182600' => 'mdo', 'Medtr2g021400' => 'mtr', 'Medtr2g021470' => 'mtr', 'Medtr2g105810' => 'mtr', 'Medtr3g033580' => 'mtr', 'Medtr6g007970' => 'mtr', 'Medtr7g056330' => 'mtr', 'Medtr7g074290' => 'mtr', 'Medtr7g074380' => 'mtr', 'Medtr7g094550' => 'mtr', 'Medtr8g069995' => 'mtr', 'MELO3C014345.2' => 'cme', 'MELO3C021395.2' => 'cme', 'Migut.D00262' => 'egut', 'Migut.G00257' => 'egut', 'MSTRG.21575' => 'ama', 'MSTRG.3985' => 'ama', 'Nitab4.5_0000295g0140' => 'nta', 'Nitab4.5_0000732g0140' => 'nta', 'Nitab4.5_0003162g0020' => 'nta', 'Nitab4.5_0006180g0090' => 'nta', 'Nitab4.5_0006390g0010' => 'nta', 'Nitab4.5_0007392g0040' => 'nta', 'Nn1g02140' => 'nnu', 'Nn4g26168' => 'nnu', 'Nn5g26754' => 'nnu', 'Oeu001433.1' => 'oeu', 'Oeu010299.2' => 'oeu', 'Oeu011171.1' => 'oeu', 'Oeu037675.1' => 'oeu', 'Oeu038359.1' => 'oeu', 'Oeu063834.1' => 'oeu', 'Oeu063835.1' => 'oeu', 'Os05g0312000' => 'osa', 'Os07g0211101' => 'osa', 'Os07g0211200' => 'osa', 'Os07g0681500' => 'osa', 'Peaxi162Scf00095g01015' => 'pax', 'Peaxi162Scf00104g00329' => 'pax', 'Peaxi162Scf00161g00137' => 'pax', 'PGR004G1665' => 'pgr', 'PGR031G2937' => 'pgr', 'PGR119G2145' => 'pgr', 'PGSC0003DMG400004351' => 'stu', 'PGSC0003DMG400014625' => 'stu', 'PGSC0003DMG401000943' => 'stu', 'Phvul.001G148600' => 'pvu', 'Phvul.004G001700' => 'pvu', 'Phvul.006G154900' => 'pvu', 'Phvul.008G078200' => 'pvu', 'Phvul.011G136500' => 'pvu', 'Potri.002G215600' => 'ptr', 'Potri.008G201600' => 'ptr', 'Potri.014G138400' => 'ptr', 'Potri.016G142500' => 'ptr', 'Pp3c16_10580' => 'ppa', 'Pp3c5_25280' => 'ppa', 'Prupe.1G150000' => 'ppe', 'Prupe.1G150100' => 'ppe', 'Prupe.6G299600' => 'ppe', 'Prupe.8G245000' => 'ppe', 'Psat0s4927g0040' => 'psa', 'Psat1g052080' => 'psa', 'Psat1g183800' => 'psa', 'Psat3g113840' => 'psa', 'Psat3g126120' => 'psa', 'Psat3g126160' => 'psa', 'Psat3g158760' => 'psa', 'Psat3g158840' => 'psa', 'PSO170G2858' => 'pso', 'PSO339G0606' => 'pso', 'PSO384G4709' => 'pso', 'PSO407G0334' => 'pso', 'QL04p040276' => 'qlo', 'QL06p005458' => 'qlo', 'QL06p005472' => 'qlo', 'QL07p030546' => 'qlo', 'QL07p031519' => 'qlo', 'QL09p050949' => 'qlo', 'QL09p050966' => 'qlo', 'QL09p051067' => 'qlo', 'QL12p022706' => 'qlo', 'RcHm_v2.0_Chr2g0119601' => 'rch', 'RcHm_v2.0_Chr3g0459591' => 'rch', 'RcHm_v2.0_Chr4g0418521' => 'rch', 'RcHm_v2.0_Chr4g0418531' => 'rch', 'RcHm_v2.0_Chr4g0418541' => 'rch', 'RcHm_v2.0_Chr6g0291641' => 'rch', 'Rhsim01G0086300' => 'rsi', 'Rhsim01G0276300' => 'rsi', 'Rhsim01G0276500' => 'rsi', 'Rhsim04G0207700' => 'rsi', 'Rhsim05G0234500' => 'rsi', 'Rhsim13G0022400' => 'rsi', 'Sabra02G0167900' => 'sbr', 'Sabra04G0158500' => 'sbr', 'Sabra08G0159800' => 'sbr', 'Sabra10G0011500' => 'sbr', 'Sabra14G0104400' => 'sbr', 'SalBow2G2440' => 'sbo', 'SalBow4G2265' => 'sbo', 'Sc02g0000060' => 'sci', 'Sc05g0005020' => 'sci', 'Sc13g0003890' => 'sci', 'Sed0014865' => 'sed', 'Sed0017224' => 'sed', 'Sed0026391' => 'sed', 'SEGI_00063' => 'sgi', 'SEGI_10967' => 'sgi', 'SEGI_17510' => 'sgi', 'SEGI_24396' => 'sgi', 'SEGI_39719' => 'sgi', 'SEGI_41392' => 'sgi', 'SGA_v2.0_scaffold11G05794' => 'sas', 'SGA_v2.0_scaffold142G35607' => 'sas', 'SGA_v2.0_scaffold1G00447' => 'sas', 'SHI15388' => 'shi', 'SHI15394' => 'shi', 'SHI15396' => 'shi', 'SHI15399' => 'shi', 'SMO343G0151' => 'smo', 'SMO367G1118' => 'smo', 'Solyc01g080200.3' => 'sly', 'Solyc06g008960.3' => 'sly', 'Solyc09g064780.3' => 'sly', 'Sopen01g031980' => 'spe', 'Sopen06g003710' => 'spe', 'Sopen09g026460' => 'spe', 'Sp3g21240' => 'spa', 'Sp4g30030' => 'spa', 'TAR365G0022' => 'tar', 'TAR365G1023' => 'tar', 'TAR365G1253' => 'tar', 'TAR623G0078' => 'tar', 'TAR623G1721' => 'tar', 'TAR633G0959' => 'tar', 'THA.LOC104802225' => 'tha', 'THA.LOC104804769' => 'tha', 'THA.LOC104808660' => 'tha', 'THA.LOC104812792' => 'tha', 'Thecc.01G284000' => 'tca', 'Thecc.04G220600' => 'tca', 'Thecc.05G268900' => 'tca', 'Thecc.08G171100' => 'tca', 'Thhalv10001284m.g' => 'esa', 'Thhalv10019912m.g' => 'esa', 'TPR.G14189' => 'tpr', 'TPR.G18110' => 'tpr', 'TPR.G18130' => 'tpr', 'TPR.G18131' => 'tpr', 'TPR.G18140' => 'tpr', 'TPR.G24282' => 'tpr', 'TPR.G25221' => 'tpr', 'TPR.G29267' => 'tpr', 'TPR.G35315' => 'tpr', 'TPR.G36173' => 'tpr', 'TWI09G0794' => 'twi', 'TWI59G1348' => 'twi', 'TWI74G0430' => 'twi', 'unitig_26.g8940' => 'ugi', 'unitig_749.g13744' => 'ugi', 'unitig_749.g13745' => 'ugi', 'vmacro08269' => 'vma', 'vmacro14937' => 'vma', 'vmacro20401' => 'vma', 'VMungo0464G1349' => 'vmu', 'VMungo0540G0289' => 'vmu', 'VMungo1215G1590' => 'vmu', 'VMungo1309G0221' => 'vmu', 'VMungo1309G2815' => 'vmu', 'VMungo1383G0239' => 'vmu', 'VMungo1383G2910' => 'vmu', 'Zm00001eb095270' => 'zma', 'Zm00001eb095280' => 'zma', 'Zm00001eb111630' => 'zma', 'Zm00001eb237080' => 'zma', 'Zm00001eb273740' => 'zma', 'Zm00001eb285040' => 'zma', 'Zm00001eb330790' => 'zma', 'Zm00001eb337380' => 'zma' ) $gf_id = 'HOM05D001484' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001484' ) $data_identifier = 'HOM05D001484' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 2, 'aly' => (int) 2, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 22, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 7, 'hma' => (int) 2, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 7, 'mtr' => (int) 10, 'cme' => (int) 2, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 4, 'ppa' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 4, 'qlo' => (int) 9, 'rch' => (int) 6, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 10, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 7, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb337380' $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' => 'HOM05D001484', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p31500' => 'bna', 'A05p00020' => 'bna', 'A07p08820' => 'bna', 'Aa31LG4G3300' => 'aar', 'Aa31LG8G10030' => 'aar', 'Actinidia00731' => 'ach', 'Actinidia11473' => 'ach', 'Actinidia23469' => 'ach', 'Actinidia24318' => 'ach', 'Actinidia40196' => 'ach', 'Actinidia40197' => 'ach', 'Actinidia40198' => 'ach', 'Ah.08g212990' => 'amhyb', 'Ah.15g091720' => 'amhyb', 'AL3G38260' => 'aly', 'AL4G47710' => 'aly', 'Aqoxy2G00671' => 'aox', 'Aqoxy2G03236' => 'aox', 'arahy.Tifrunner.gnm1.ann1.05IDCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KR684' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATY3SJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK6QJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6APGL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IDT7Z9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM073U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ0R87' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LE7RV4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT4QRX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V5ENPK' => 'arhy', 'AT2G48110' => 'ath', 'AT3G23590' => 'ath', 'ATR0626G186' => 'atr', 'ATR1127G141' => 'atr', 'Atru.chr4.2583' => 'acertr', 'Atru.chr5.1358' => 'acertr', 'Atru.chr5.1359' => 'acertr', 'Atru.chr8.46' => 'acertr', 'AUR62002640' => 'cqu', 'AUR62030055' => 'cqu', 'AUR62033713' => 'cqu', 'AUR62033714' => 'cqu', 'AUR62036795' => 'cqu', 'AUR62039891' => 'cqu', 'BcaB02g08737' => 'bca', 'BcaB04g20441' => 'bca', 'BcaB06g26509' => 'bca', 'BcaB06g26510' => 'bca', 'BcaB06g26511' => 'bca', 'BcaB06g26512' => 'bca', 'BcaB06g26513' => 'bca', 'BcaC02g12564' => 'bca', 'BcaC02g12565' => 'bca', 'BcaC02g12794' => 'bca', 'BcaC02g12795' => 'bca', 'BcaC02g12796' => 'bca', 'BcaC06g35541' => 'bca', 'BNapus_Darmor_BZH_scaffold_188p00080' => 'bna', 'BNapus_Darmor_BZH_scaffold_188p00090' => 'bna', 'BolC1t03972H' => 'bol', 'BolC1t03973H' => 'bol', 'BolC4t21680H' => 'bol', 'BolC7t41863H' => 'bol', 'BolSC55t61227H' => 'bol', 'BolSC55t61228H' => 'bol', 'BraA01t03278Z' => 'bra', 'BraA05t18998Z' => 'bra', 'BraA07t28673Z' => 'bra', 'C01p40150' => 'bna', 'C05p12370' => 'bna', 'C07p13680' => 'bna', 'CAN.G1006.16' => 'can', 'CAN.G1006.17' => 'can', 'CAN.G1170.2' => 'can', 'CAN.G962.7' => 'can', 'CANSAT25G2179' => 'cansat', 'CANSAT78G1573' => 'cansat', 'CARHR099510' => 'chi', 'CARHR143510' => 'chi', 'Carub.0003s2380' => 'cru', 'Carub.0004s3082' => 'cru', 'Ca_00614_v3' => 'car', 'Ca_07801_v3' => 'car', 'Ca_08567_v3' => 'car', 'Ca_09571_v3' => 'car', 'CBR_g19290' => 'cbr', 'Cc01_g19770' => 'ccan', 'Cc03_g03030' => 'ccan', 'CDE07G0968' => 'cde', 'CDE09G1441' => 'cde', 'Cfa006103' => 'cfa', 'Cfa015573' => 'cfa', 'Cfa016988' => 'cfa', 'Ciclev10006738m.g' => 'ccl', 'Ciclev10010920m.g' => 'ccl', 'Ciclev10018517m.g' => 'ccl', 'CiPaw.01G159200' => 'cil', 'CiPaw.02G091000' => 'cil', 'CiPaw.02G091100' => 'cil', 'CiPaw.08G103100' => 'cil', 'CiPaw.09G224900' => 'cil', 'ClCG06G005740' => 'cla', 'ClCG07G000090' => 'cla', 'ClCG07G000100' => 'cla', 'COL.COLO4_09143' => 'col', 'COL.COLO4_25124' => 'col', 'Cpa.g.sc16.34' => 'cpa', 'Cpa.g.sc3504.1' => 'cpa', 'Cpa.g.sc60.37' => 'cpa', 'CsaV3_6G018520' => 'csa', 'CsaV3_6G036860' => 'csa', 'CSS0001072' => 'camsi', 'CSS0020208' => 'camsi', 'CSS0021253' => 'camsi', 'CSS0022190' => 'camsi', 'CSS0036150' => 'camsi', 'CSS0040442' => 'camsi', 'CSS0042300' => 'camsi', 'CSS0045298' => 'camsi', 'DCAR_012449' => 'dca', 'DCAR_018405' => 'dca', 'DCAR_024573' => 'dca', 'DCAR_030591' => 'dca', 'Dinv16926' => 'din', 'Dinv32963' => 'din', 'Dinv38382' => 'din', 'Dinv38383' => 'din', 'Duzib133G0974' => 'dzi', 'Duzib138G1867' => 'dzi', 'Duzib211G0420' => 'dzi', 'Duzib212G0930' => 'dzi', 'ECA234G1645' => 'eca', 'ECA247G3467' => 'eca', 'ECA248G1703' => 'eca', 'EL10Ac3g06327' => 'bvu', 'EL10Ac7g17204' => 'bvu', 'Eucgr.A00855' => 'egr', 'Eucgr.A00858' => 'egr', 'Eucgr.H01520' => 'egr', 'Eucgr.H03604' => 'egr', 'Eucgr.L03465' => 'egr', 'Eucgr.L03466' => 'egr', 'FAN01G0988' => 'fan', 'FAN02G3892' => 'fan', 'FAN05G3381' => 'fan', 'FAN07G0967' => 'fan', 'FAN07G1493' => 'fan', 'FAN08G3125' => 'fan', 'FAN09G0402' => 'fan', 'FAN12G2594' => 'fan', 'FAN12G3879' => 'fan', 'FAN14G1546' => 'fan', 'FAN15G3626' => 'fan', 'FAN17G0588' => 'fan', 'FAN17G0609' => 'fan', 'FAN18G2817' => 'fan', 'FAN19G1305' => 'fan', 'FAN20G1787' => 'fan', 'FAN22G0073' => 'fan', 'FAN22G0352' => 'fan', 'FAN22G0368' => 'fan', 'FAN22G2273' => 'fan', 'FAN24G1998' => 'fan', 'FAN27G1317' => 'fan', 'FvH4_2g23980' => 'fve', 'FvH4_4g14380' => 'fve', 'FvH4_4g14390' => 'fve', 'FvH4_6g09250' => 'fve', 'Glyma.03G151100' => 'gma', 'Glyma.04G122550' => 'gma', 'Glyma.05G001600' => 'gma', 'Glyma.09G270766' => 'gma', 'Glyma.09G270832' => 'gma', 'Glyma.13G209800' => 'gma', 'Glyma.15G102800' => 'gma', 'Glyma.18G218900' => 'gma', 'Glyma.19G001500' => 'gma', 'Glyma.19G153600' => 'gma', 'Gohir.A02G028600' => 'ghi', 'Gohir.A08G045000' => 'ghi', 'Gohir.A11G120500' => 'ghi', 'Gohir.A12G006200' => 'ghi', 'Gohir.A12G006250' => 'ghi', 'Gohir.D02G036300' => 'ghi', 'Gohir.D08G054700' => 'ghi', 'Gohir.D11G125600' => 'ghi', 'Gohir.D12G005700' => 'ghi', 'Gorai.004G055200' => 'gra', 'Gorai.005G040400' => 'gra', 'Gorai.007G134500' => 'gra', 'Gorai.008G005500' => 'gra', 'GSVIVG01011094001' => 'vvi', 'GSVIVG01017879001' => 'vvi', 'GSVIVG01025988001' => 'vvi', 'GSVIVG01029847001' => 'vvi', 'HanXRQChr10g0282901' => 'han', 'HanXRQChr10g0310371' => 'han', 'HanXRQChr10g0315041' => 'han', 'HanXRQChr11g0327651' => 'han', 'HanXRQChr12g0359391' => 'han', 'Haze_00972' => 'cav', 'Haze_00973' => 'cav', 'Haze_00974' => 'cav', 'Haze_04747' => 'cav', 'Haze_04749' => 'cav', 'Haze_04750' => 'cav', 'Haze_21217' => 'cav', 'Hma1.2p1_1037F.1_g250680' => 'hma', 'Hma1.2p1_1644F.1_g295320' => 'hma', 'HPP92_011322' => 'vpl', 'HPP92_011323' => 'vpl', 'HPP92_011324' => 'vpl', 'HPP92_011325' => 'vpl', 'HPP92_011326' => 'vpl', 'Hund12205' => 'sun', 'Hund17957' => 'sun', 'Lalb_Chr06g0176771' => 'lal', 'Lalb_Chr18g0056021' => 'lal', 'Lalb_Chr18g0056031' => 'lal', 'Lalb_Chr18g0056041' => 'lal', 'Lalb_Chr20g0107751' => 'lal', 'Lalb_Chr20g0118371' => 'lal', 'Lj1g0010239' => 'lja', 'Lj1g0017101' => 'lja', 'Lj2A1178G40' => 'lonja', 'Lj2A54G84' => 'lonja', 'Lj2g0015248' => 'lja', 'Lj3A761T51' => 'lonja', 'Lj6g0018116' => 'lja', 'Lsat_1_v5_gn_4_136040' => 'lsa', 'Lsat_1_v5_gn_5_187461' => 'lsa', 'Lsat_1_v5_gn_5_77001' => 'lsa', 'Lsat_1_v5_gn_9_4461' => 'lsa', 'Manes.01G210100' => 'mes', 'Manes.03G185600' => 'mes', 'Manes.05G073300' => 'mes', 'Manes.09G120300' => 'mes', 'Manes.15G022100' => 'mes', 'Mapoly0096s0053' => 'mpo', 'MBI03_g14058_MAGBIO' => 'mbi', 'MBI03_g33876_MAGBIO' => 'mbi', 'MBI03_g36854_MAGBIO' => 'mbi', 'MBI17_g11997_MAGBIO' => 'mbi', 'MD03G1269000' => 'mdo', 'MD04G1179600' => 'mdo', 'MD11G1289800' => 'mdo', 'MD12G1194700' => 'mdo', 'MD13G1182100' => 'mdo', 'MD13G1182200' => 'mdo', 'MD16G1182600' => 'mdo', 'Medtr2g021400' => 'mtr', 'Medtr2g021470' => 'mtr', 'Medtr2g105810' => 'mtr', 'Medtr3g033580' => 'mtr', 'Medtr6g007970' => 'mtr', 'Medtr7g056330' => 'mtr', 'Medtr7g074290' => 'mtr', 'Medtr7g074380' => 'mtr', 'Medtr7g094550' => 'mtr', 'Medtr8g069995' => 'mtr', 'MELO3C014345.2' => 'cme', 'MELO3C021395.2' => 'cme', 'Migut.D00262' => 'egut', 'Migut.G00257' => 'egut', 'MSTRG.21575' => 'ama', 'MSTRG.3985' => 'ama', 'Nitab4.5_0000295g0140' => 'nta', 'Nitab4.5_0000732g0140' => 'nta', 'Nitab4.5_0003162g0020' => 'nta', 'Nitab4.5_0006180g0090' => 'nta', 'Nitab4.5_0006390g0010' => 'nta', 'Nitab4.5_0007392g0040' => 'nta', 'Nn1g02140' => 'nnu', 'Nn4g26168' => 'nnu', 'Nn5g26754' => 'nnu', 'Oeu001433.1' => 'oeu', 'Oeu010299.2' => 'oeu', 'Oeu011171.1' => 'oeu', 'Oeu037675.1' => 'oeu', 'Oeu038359.1' => 'oeu', 'Oeu063834.1' => 'oeu', 'Oeu063835.1' => 'oeu', 'Os05g0312000' => 'osa', 'Os07g0211101' => 'osa', 'Os07g0211200' => 'osa', 'Os07g0681500' => 'osa', 'Peaxi162Scf00095g01015' => 'pax', 'Peaxi162Scf00104g00329' => 'pax', 'Peaxi162Scf00161g00137' => 'pax', 'PGR004G1665' => 'pgr', 'PGR031G2937' => 'pgr', 'PGR119G2145' => 'pgr', 'PGSC0003DMG400004351' => 'stu', 'PGSC0003DMG400014625' => 'stu', 'PGSC0003DMG401000943' => 'stu', 'Phvul.001G148600' => 'pvu', 'Phvul.004G001700' => 'pvu', 'Phvul.006G154900' => 'pvu', 'Phvul.008G078200' => 'pvu', 'Phvul.011G136500' => 'pvu', 'Potri.002G215600' => 'ptr', 'Potri.008G201600' => 'ptr', 'Potri.014G138400' => 'ptr', 'Potri.016G142500' => 'ptr', 'Pp3c16_10580' => 'ppa', 'Pp3c5_25280' => 'ppa', 'Prupe.1G150000' => 'ppe', 'Prupe.1G150100' => 'ppe', 'Prupe.6G299600' => 'ppe', 'Prupe.8G245000' => 'ppe', 'Psat0s4927g0040' => 'psa', 'Psat1g052080' => 'psa', 'Psat1g183800' => 'psa', 'Psat3g113840' => 'psa', 'Psat3g126120' => 'psa', 'Psat3g126160' => 'psa', 'Psat3g158760' => 'psa', 'Psat3g158840' => 'psa', 'PSO170G2858' => 'pso', 'PSO339G0606' => 'pso', 'PSO384G4709' => 'pso', 'PSO407G0334' => 'pso', 'QL04p040276' => 'qlo', 'QL06p005458' => 'qlo', 'QL06p005472' => 'qlo', 'QL07p030546' => 'qlo', 'QL07p031519' => 'qlo', 'QL09p050949' => 'qlo', 'QL09p050966' => 'qlo', 'QL09p051067' => 'qlo', 'QL12p022706' => 'qlo', 'RcHm_v2.0_Chr2g0119601' => 'rch', 'RcHm_v2.0_Chr3g0459591' => 'rch', 'RcHm_v2.0_Chr4g0418521' => 'rch', 'RcHm_v2.0_Chr4g0418531' => 'rch', 'RcHm_v2.0_Chr4g0418541' => 'rch', 'RcHm_v2.0_Chr6g0291641' => 'rch', 'Rhsim01G0086300' => 'rsi', 'Rhsim01G0276300' => 'rsi', 'Rhsim01G0276500' => 'rsi', 'Rhsim04G0207700' => 'rsi', 'Rhsim05G0234500' => 'rsi', 'Rhsim13G0022400' => 'rsi', 'Sabra02G0167900' => 'sbr', 'Sabra04G0158500' => 'sbr', 'Sabra08G0159800' => 'sbr', 'Sabra10G0011500' => 'sbr', 'Sabra14G0104400' => 'sbr', 'SalBow2G2440' => 'sbo', 'SalBow4G2265' => 'sbo', 'Sc02g0000060' => 'sci', 'Sc05g0005020' => 'sci', 'Sc13g0003890' => 'sci', 'Sed0014865' => 'sed', 'Sed0017224' => 'sed', 'Sed0026391' => 'sed', 'SEGI_00063' => 'sgi', 'SEGI_10967' => 'sgi', 'SEGI_17510' => 'sgi', 'SEGI_24396' => 'sgi', 'SEGI_39719' => 'sgi', 'SEGI_41392' => 'sgi', 'SGA_v2.0_scaffold11G05794' => 'sas', 'SGA_v2.0_scaffold142G35607' => 'sas', 'SGA_v2.0_scaffold1G00447' => 'sas', 'SHI15388' => 'shi', 'SHI15394' => 'shi', 'SHI15396' => 'shi', 'SHI15399' => 'shi', 'SMO343G0151' => 'smo', 'SMO367G1118' => 'smo', 'Solyc01g080200.3' => 'sly', 'Solyc06g008960.3' => 'sly', 'Solyc09g064780.3' => 'sly', 'Sopen01g031980' => 'spe', 'Sopen06g003710' => 'spe', 'Sopen09g026460' => 'spe', 'Sp3g21240' => 'spa', 'Sp4g30030' => 'spa', 'TAR365G0022' => 'tar', 'TAR365G1023' => 'tar', 'TAR365G1253' => 'tar', 'TAR623G0078' => 'tar', 'TAR623G1721' => 'tar', 'TAR633G0959' => 'tar', 'THA.LOC104802225' => 'tha', 'THA.LOC104804769' => 'tha', 'THA.LOC104808660' => 'tha', 'THA.LOC104812792' => 'tha', 'Thecc.01G284000' => 'tca', 'Thecc.04G220600' => 'tca', 'Thecc.05G268900' => 'tca', 'Thecc.08G171100' => 'tca', 'Thhalv10001284m.g' => 'esa', 'Thhalv10019912m.g' => 'esa', 'TPR.G14189' => 'tpr', 'TPR.G18110' => 'tpr', 'TPR.G18130' => 'tpr', 'TPR.G18131' => 'tpr', 'TPR.G18140' => 'tpr', 'TPR.G24282' => 'tpr', 'TPR.G25221' => 'tpr', 'TPR.G29267' => 'tpr', 'TPR.G35315' => 'tpr', 'TPR.G36173' => 'tpr', 'TWI09G0794' => 'twi', 'TWI59G1348' => 'twi', 'TWI74G0430' => 'twi', 'unitig_26.g8940' => 'ugi', 'unitig_749.g13744' => 'ugi', 'unitig_749.g13745' => 'ugi', 'vmacro08269' => 'vma', 'vmacro14937' => 'vma', 'vmacro20401' => 'vma', 'VMungo0464G1349' => 'vmu', 'VMungo0540G0289' => 'vmu', 'VMungo1215G1590' => 'vmu', 'VMungo1309G0221' => 'vmu', 'VMungo1309G2815' => 'vmu', 'VMungo1383G0239' => 'vmu', 'VMungo1383G2910' => 'vmu', 'Zm00001eb095270' => 'zma', 'Zm00001eb095280' => 'zma', 'Zm00001eb111630' => 'zma', 'Zm00001eb237080' => 'zma', 'Zm00001eb273740' => 'zma', 'Zm00001eb285040' => 'zma', 'Zm00001eb330790' => 'zma', 'Zm00001eb337380' => 'zma' ), 'gf_id' => 'HOM05D001484', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001484' ), 'data_identifier' => 'HOM05D001484', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001484', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p31500' => 'bna', 'A05p00020' => 'bna', 'A07p08820' => 'bna', 'Aa31LG4G3300' => 'aar', 'Aa31LG8G10030' => 'aar', 'Actinidia00731' => 'ach', 'Actinidia11473' => 'ach', 'Actinidia23469' => 'ach', 'Actinidia24318' => 'ach', 'Actinidia40196' => 'ach', 'Actinidia40197' => 'ach', 'Actinidia40198' => 'ach', 'Ah.08g212990' => 'amhyb', 'Ah.15g091720' => 'amhyb', 'AL3G38260' => 'aly', 'AL4G47710' => 'aly', 'Aqoxy2G00671' => 'aox', 'Aqoxy2G03236' => 'aox', 'arahy.Tifrunner.gnm1.ann1.05IDCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KR684' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATY3SJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK6QJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6APGL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IDT7Z9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM073U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ0R87' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LE7RV4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT4QRX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V5ENPK' => 'arhy', 'AT2G48110' => 'ath', 'AT3G23590' => 'ath', 'ATR0626G186' => 'atr', 'ATR1127G141' => 'atr', 'Atru.chr4.2583' => 'acertr', 'Atru.chr5.1358' => 'acertr', 'Atru.chr5.1359' => 'acertr', 'Atru.chr8.46' => 'acertr', 'AUR62002640' => 'cqu', 'AUR62030055' => 'cqu', 'AUR62033713' => 'cqu', 'AUR62033714' => 'cqu', 'AUR62036795' => 'cqu', 'AUR62039891' => 'cqu', 'BcaB02g08737' => 'bca', 'BcaB04g20441' => 'bca', 'BcaB06g26509' => 'bca', 'BcaB06g26510' => 'bca', 'BcaB06g26511' => 'bca', 'BcaB06g26512' => 'bca', 'BcaB06g26513' => 'bca', 'BcaC02g12564' => 'bca', 'BcaC02g12565' => 'bca', 'BcaC02g12794' => 'bca', 'BcaC02g12795' => 'bca', 'BcaC02g12796' => 'bca', 'BcaC06g35541' => 'bca', 'BNapus_Darmor_BZH_scaffold_188p00080' => 'bna', 'BNapus_Darmor_BZH_scaffold_188p00090' => 'bna', 'BolC1t03972H' => 'bol', 'BolC1t03973H' => 'bol', 'BolC4t21680H' => 'bol', 'BolC7t41863H' => 'bol', 'BolSC55t61227H' => 'bol', 'BolSC55t61228H' => 'bol', 'BraA01t03278Z' => 'bra', 'BraA05t18998Z' => 'bra', 'BraA07t28673Z' => 'bra', 'C01p40150' => 'bna', 'C05p12370' => 'bna', 'C07p13680' => 'bna', 'CAN.G1006.16' => 'can', 'CAN.G1006.17' => 'can', 'CAN.G1170.2' => 'can', 'CAN.G962.7' => 'can', 'CANSAT25G2179' => 'cansat', 'CANSAT78G1573' => 'cansat', 'CARHR099510' => 'chi', 'CARHR143510' => 'chi', 'Carub.0003s2380' => 'cru', 'Carub.0004s3082' => 'cru', 'Ca_00614_v3' => 'car', 'Ca_07801_v3' => 'car', 'Ca_08567_v3' => 'car', 'Ca_09571_v3' => 'car', 'CBR_g19290' => 'cbr', 'Cc01_g19770' => 'ccan', 'Cc03_g03030' => 'ccan', 'CDE07G0968' => 'cde', 'CDE09G1441' => 'cde', 'Cfa006103' => 'cfa', 'Cfa015573' => 'cfa', 'Cfa016988' => 'cfa', 'Ciclev10006738m.g' => 'ccl', 'Ciclev10010920m.g' => 'ccl', 'Ciclev10018517m.g' => 'ccl', 'CiPaw.01G159200' => 'cil', 'CiPaw.02G091000' => 'cil', 'CiPaw.02G091100' => 'cil', 'CiPaw.08G103100' => 'cil', 'CiPaw.09G224900' => 'cil', 'ClCG06G005740' => 'cla', 'ClCG07G000090' => 'cla', 'ClCG07G000100' => 'cla', 'COL.COLO4_09143' => 'col', 'COL.COLO4_25124' => 'col', 'Cpa.g.sc16.34' => 'cpa', 'Cpa.g.sc3504.1' => 'cpa', 'Cpa.g.sc60.37' => 'cpa', 'CsaV3_6G018520' => 'csa', 'CsaV3_6G036860' => 'csa', 'CSS0001072' => 'camsi', 'CSS0020208' => 'camsi', 'CSS0021253' => 'camsi', 'CSS0022190' => 'camsi', 'CSS0036150' => 'camsi', 'CSS0040442' => 'camsi', 'CSS0042300' => 'camsi', 'CSS0045298' => 'camsi', 'DCAR_012449' => 'dca', 'DCAR_018405' => 'dca', 'DCAR_024573' => 'dca', 'DCAR_030591' => 'dca', 'Dinv16926' => 'din', 'Dinv32963' => 'din', 'Dinv38382' => 'din', 'Dinv38383' => 'din', 'Duzib133G0974' => 'dzi', 'Duzib138G1867' => 'dzi', 'Duzib211G0420' => 'dzi', 'Duzib212G0930' => 'dzi', 'ECA234G1645' => 'eca', 'ECA247G3467' => 'eca', 'ECA248G1703' => 'eca', 'EL10Ac3g06327' => 'bvu', 'EL10Ac7g17204' => 'bvu', 'Eucgr.A00855' => 'egr', 'Eucgr.A00858' => 'egr', 'Eucgr.H01520' => 'egr', 'Eucgr.H03604' => 'egr', 'Eucgr.L03465' => 'egr', 'Eucgr.L03466' => 'egr', 'FAN01G0988' => 'fan', 'FAN02G3892' => 'fan', 'FAN05G3381' => 'fan', 'FAN07G0967' => 'fan', 'FAN07G1493' => 'fan', 'FAN08G3125' => 'fan', 'FAN09G0402' => 'fan', 'FAN12G2594' => 'fan', 'FAN12G3879' => 'fan', 'FAN14G1546' => 'fan', 'FAN15G3626' => 'fan', 'FAN17G0588' => 'fan', 'FAN17G0609' => 'fan', 'FAN18G2817' => 'fan', 'FAN19G1305' => 'fan', 'FAN20G1787' => 'fan', 'FAN22G0073' => 'fan', 'FAN22G0352' => 'fan', 'FAN22G0368' => 'fan', 'FAN22G2273' => 'fan', 'FAN24G1998' => 'fan', 'FAN27G1317' => 'fan', 'FvH4_2g23980' => 'fve', 'FvH4_4g14380' => 'fve', 'FvH4_4g14390' => 'fve', 'FvH4_6g09250' => 'fve', 'Glyma.03G151100' => 'gma', 'Glyma.04G122550' => 'gma', 'Glyma.05G001600' => 'gma', 'Glyma.09G270766' => 'gma', 'Glyma.09G270832' => 'gma', 'Glyma.13G209800' => 'gma', 'Glyma.15G102800' => 'gma', 'Glyma.18G218900' => 'gma', 'Glyma.19G001500' => 'gma', 'Glyma.19G153600' => 'gma', 'Gohir.A02G028600' => 'ghi', 'Gohir.A08G045000' => 'ghi', 'Gohir.A11G120500' => 'ghi', 'Gohir.A12G006200' => 'ghi', 'Gohir.A12G006250' => 'ghi', 'Gohir.D02G036300' => 'ghi', 'Gohir.D08G054700' => 'ghi', 'Gohir.D11G125600' => 'ghi', 'Gohir.D12G005700' => 'ghi', 'Gorai.004G055200' => 'gra', 'Gorai.005G040400' => 'gra', 'Gorai.007G134500' => 'gra', 'Gorai.008G005500' => 'gra', 'GSVIVG01011094001' => 'vvi', 'GSVIVG01017879001' => 'vvi', 'GSVIVG01025988001' => 'vvi', 'GSVIVG01029847001' => 'vvi', 'HanXRQChr10g0282901' => 'han', 'HanXRQChr10g0310371' => 'han', 'HanXRQChr10g0315041' => 'han', 'HanXRQChr11g0327651' => 'han', 'HanXRQChr12g0359391' => 'han', 'Haze_00972' => 'cav', 'Haze_00973' => 'cav', 'Haze_00974' => 'cav', 'Haze_04747' => 'cav', 'Haze_04749' => 'cav', 'Haze_04750' => 'cav', 'Haze_21217' => 'cav', 'Hma1.2p1_1037F.1_g250680' => 'hma', 'Hma1.2p1_1644F.1_g295320' => 'hma', 'HPP92_011322' => 'vpl', 'HPP92_011323' => 'vpl', 'HPP92_011324' => 'vpl', 'HPP92_011325' => 'vpl', 'HPP92_011326' => 'vpl', 'Hund12205' => 'sun', 'Hund17957' => 'sun', 'Lalb_Chr06g0176771' => 'lal', 'Lalb_Chr18g0056021' => 'lal', 'Lalb_Chr18g0056031' => 'lal', 'Lalb_Chr18g0056041' => 'lal', 'Lalb_Chr20g0107751' => 'lal', 'Lalb_Chr20g0118371' => 'lal', 'Lj1g0010239' => 'lja', 'Lj1g0017101' => 'lja', 'Lj2A1178G40' => 'lonja', 'Lj2A54G84' => 'lonja', 'Lj2g0015248' => 'lja', 'Lj3A761T51' => 'lonja', 'Lj6g0018116' => 'lja', 'Lsat_1_v5_gn_4_136040' => 'lsa', 'Lsat_1_v5_gn_5_187461' => 'lsa', 'Lsat_1_v5_gn_5_77001' => 'lsa', 'Lsat_1_v5_gn_9_4461' => 'lsa', 'Manes.01G210100' => 'mes', 'Manes.03G185600' => 'mes', 'Manes.05G073300' => 'mes', 'Manes.09G120300' => 'mes', 'Manes.15G022100' => 'mes', 'Mapoly0096s0053' => 'mpo', 'MBI03_g14058_MAGBIO' => 'mbi', 'MBI03_g33876_MAGBIO' => 'mbi', 'MBI03_g36854_MAGBIO' => 'mbi', 'MBI17_g11997_MAGBIO' => 'mbi', 'MD03G1269000' => 'mdo', 'MD04G1179600' => 'mdo', 'MD11G1289800' => 'mdo', 'MD12G1194700' => 'mdo', 'MD13G1182100' => 'mdo', 'MD13G1182200' => 'mdo', 'MD16G1182600' => 'mdo', 'Medtr2g021400' => 'mtr', 'Medtr2g021470' => 'mtr', 'Medtr2g105810' => 'mtr', 'Medtr3g033580' => 'mtr', 'Medtr6g007970' => 'mtr', 'Medtr7g056330' => 'mtr', 'Medtr7g074290' => 'mtr', 'Medtr7g074380' => 'mtr', 'Medtr7g094550' => 'mtr', 'Medtr8g069995' => 'mtr', 'MELO3C014345.2' => 'cme', 'MELO3C021395.2' => 'cme', 'Migut.D00262' => 'egut', 'Migut.G00257' => 'egut', 'MSTRG.21575' => 'ama', 'MSTRG.3985' => 'ama', 'Nitab4.5_0000295g0140' => 'nta', 'Nitab4.5_0000732g0140' => 'nta', 'Nitab4.5_0003162g0020' => 'nta', 'Nitab4.5_0006180g0090' => 'nta', 'Nitab4.5_0006390g0010' => 'nta', 'Nitab4.5_0007392g0040' => 'nta', 'Nn1g02140' => 'nnu', 'Nn4g26168' => 'nnu', 'Nn5g26754' => 'nnu', 'Oeu001433.1' => 'oeu', 'Oeu010299.2' => 'oeu', 'Oeu011171.1' => 'oeu', 'Oeu037675.1' => 'oeu', 'Oeu038359.1' => 'oeu', 'Oeu063834.1' => 'oeu', 'Oeu063835.1' => 'oeu', 'Os05g0312000' => 'osa', 'Os07g0211101' => 'osa', 'Os07g0211200' => 'osa', 'Os07g0681500' => 'osa', 'Peaxi162Scf00095g01015' => 'pax', 'Peaxi162Scf00104g00329' => 'pax', 'Peaxi162Scf00161g00137' => 'pax', 'PGR004G1665' => 'pgr', 'PGR031G2937' => 'pgr', 'PGR119G2145' => 'pgr', 'PGSC0003DMG400004351' => 'stu', 'PGSC0003DMG400014625' => 'stu', 'PGSC0003DMG401000943' => 'stu', 'Phvul.001G148600' => 'pvu', 'Phvul.004G001700' => 'pvu', 'Phvul.006G154900' => 'pvu', 'Phvul.008G078200' => 'pvu', 'Phvul.011G136500' => 'pvu', 'Potri.002G215600' => 'ptr', 'Potri.008G201600' => 'ptr', 'Potri.014G138400' => 'ptr', 'Potri.016G142500' => 'ptr', 'Pp3c16_10580' => 'ppa', 'Pp3c5_25280' => 'ppa', 'Prupe.1G150000' => 'ppe', 'Prupe.1G150100' => 'ppe', 'Prupe.6G299600' => 'ppe', 'Prupe.8G245000' => 'ppe', 'Psat0s4927g0040' => 'psa', 'Psat1g052080' => 'psa', 'Psat1g183800' => 'psa', 'Psat3g113840' => 'psa', 'Psat3g126120' => 'psa', 'Psat3g126160' => 'psa', 'Psat3g158760' => 'psa', 'Psat3g158840' => 'psa', 'PSO170G2858' => 'pso', 'PSO339G0606' => 'pso', 'PSO384G4709' => 'pso', 'PSO407G0334' => 'pso', 'QL04p040276' => 'qlo', 'QL06p005458' => 'qlo', 'QL06p005472' => 'qlo', 'QL07p030546' => 'qlo', 'QL07p031519' => 'qlo', 'QL09p050949' => 'qlo', 'QL09p050966' => 'qlo', 'QL09p051067' => 'qlo', 'QL12p022706' => 'qlo', 'RcHm_v2.0_Chr2g0119601' => 'rch', 'RcHm_v2.0_Chr3g0459591' => 'rch', 'RcHm_v2.0_Chr4g0418521' => 'rch', 'RcHm_v2.0_Chr4g0418531' => 'rch', 'RcHm_v2.0_Chr4g0418541' => 'rch', 'RcHm_v2.0_Chr6g0291641' => 'rch', 'Rhsim01G0086300' => 'rsi', 'Rhsim01G0276300' => 'rsi', 'Rhsim01G0276500' => 'rsi', 'Rhsim04G0207700' => 'rsi', 'Rhsim05G0234500' => 'rsi', 'Rhsim13G0022400' => 'rsi', 'Sabra02G0167900' => 'sbr', 'Sabra04G0158500' => 'sbr', 'Sabra08G0159800' => 'sbr', 'Sabra10G0011500' => 'sbr', 'Sabra14G0104400' => 'sbr', 'SalBow2G2440' => 'sbo', 'SalBow4G2265' => 'sbo', 'Sc02g0000060' => 'sci', 'Sc05g0005020' => 'sci', 'Sc13g0003890' => 'sci', 'Sed0014865' => 'sed', 'Sed0017224' => 'sed', 'Sed0026391' => 'sed', 'SEGI_00063' => 'sgi', 'SEGI_10967' => 'sgi', 'SEGI_17510' => 'sgi', 'SEGI_24396' => 'sgi', 'SEGI_39719' => 'sgi', 'SEGI_41392' => 'sgi', 'SGA_v2.0_scaffold11G05794' => 'sas', 'SGA_v2.0_scaffold142G35607' => 'sas', 'SGA_v2.0_scaffold1G00447' => 'sas', 'SHI15388' => 'shi', 'SHI15394' => 'shi', 'SHI15396' => 'shi', 'SHI15399' => 'shi', 'SMO343G0151' => 'smo', 'SMO367G1118' => 'smo', 'Solyc01g080200.3' => 'sly', 'Solyc06g008960.3' => 'sly', 'Solyc09g064780.3' => 'sly', 'Sopen01g031980' => 'spe', 'Sopen06g003710' => 'spe', 'Sopen09g026460' => 'spe', 'Sp3g21240' => 'spa', 'Sp4g30030' => 'spa', 'TAR365G0022' => 'tar', 'TAR365G1023' => 'tar', 'TAR365G1253' => 'tar', 'TAR623G0078' => 'tar', 'TAR623G1721' => 'tar', 'TAR633G0959' => 'tar', 'THA.LOC104802225' => 'tha', 'THA.LOC104804769' => 'tha', 'THA.LOC104808660' => 'tha', 'THA.LOC104812792' => 'tha', 'Thecc.01G284000' => 'tca', 'Thecc.04G220600' => 'tca', 'Thecc.05G268900' => 'tca', 'Thecc.08G171100' => 'tca', 'Thhalv10001284m.g' => 'esa', 'Thhalv10019912m.g' => 'esa', 'TPR.G14189' => 'tpr', 'TPR.G18110' => 'tpr', 'TPR.G18130' => 'tpr', 'TPR.G18131' => 'tpr', 'TPR.G18140' => 'tpr', 'TPR.G24282' => 'tpr', 'TPR.G25221' => 'tpr', 'TPR.G29267' => 'tpr', 'TPR.G35315' => 'tpr', 'TPR.G36173' => 'tpr', 'TWI09G0794' => 'twi', 'TWI59G1348' => 'twi', 'TWI74G0430' => 'twi', 'unitig_26.g8940' => 'ugi', 'unitig_749.g13744' => 'ugi', 'unitig_749.g13745' => 'ugi', 'vmacro08269' => 'vma', 'vmacro14937' => 'vma', 'vmacro20401' => 'vma', 'VMungo0464G1349' => 'vmu', 'VMungo0540G0289' => 'vmu', 'VMungo1215G1590' => 'vmu', 'VMungo1309G0221' => 'vmu', 'VMungo1309G2815' => 'vmu', 'VMungo1383G0239' => 'vmu', 'VMungo1383G2910' => 'vmu', 'Zm00001eb095270' => 'zma', 'Zm00001eb095280' => 'zma', 'Zm00001eb111630' => 'zma', 'Zm00001eb237080' => 'zma', 'Zm00001eb273740' => 'zma', 'Zm00001eb285040' => 'zma', 'Zm00001eb330790' => 'zma', 'Zm00001eb337380' => 'zma' ) $gf_id = 'HOM05D001484' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001484' ) $data_identifier = 'HOM05D001484' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 2, 'aly' => (int) 2, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 22, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 7, 'hma' => (int) 2, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 7, 'mtr' => (int) 10, 'cme' => (int) 2, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 4, 'ppa' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 4, 'qlo' => (int) 9, 'rch' => (int) 6, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 10, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 7, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb337380' $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' => 'HOM05D001484', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p31500' => 'bna', 'A05p00020' => 'bna', 'A07p08820' => 'bna', 'Aa31LG4G3300' => 'aar', 'Aa31LG8G10030' => 'aar', 'Actinidia00731' => 'ach', 'Actinidia11473' => 'ach', 'Actinidia23469' => 'ach', 'Actinidia24318' => 'ach', 'Actinidia40196' => 'ach', 'Actinidia40197' => 'ach', 'Actinidia40198' => 'ach', 'Ah.08g212990' => 'amhyb', 'Ah.15g091720' => 'amhyb', 'AL3G38260' => 'aly', 'AL4G47710' => 'aly', 'Aqoxy2G00671' => 'aox', 'Aqoxy2G03236' => 'aox', 'arahy.Tifrunner.gnm1.ann1.05IDCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KR684' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATY3SJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK6QJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6APGL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IDT7Z9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM073U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ0R87' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LE7RV4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT4QRX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V5ENPK' => 'arhy', 'AT2G48110' => 'ath', 'AT3G23590' => 'ath', 'ATR0626G186' => 'atr', 'ATR1127G141' => 'atr', 'Atru.chr4.2583' => 'acertr', 'Atru.chr5.1358' => 'acertr', 'Atru.chr5.1359' => 'acertr', 'Atru.chr8.46' => 'acertr', 'AUR62002640' => 'cqu', 'AUR62030055' => 'cqu', 'AUR62033713' => 'cqu', 'AUR62033714' => 'cqu', 'AUR62036795' => 'cqu', 'AUR62039891' => 'cqu', 'BcaB02g08737' => 'bca', 'BcaB04g20441' => 'bca', 'BcaB06g26509' => 'bca', 'BcaB06g26510' => 'bca', 'BcaB06g26511' => 'bca', 'BcaB06g26512' => 'bca', 'BcaB06g26513' => 'bca', 'BcaC02g12564' => 'bca', 'BcaC02g12565' => 'bca', 'BcaC02g12794' => 'bca', 'BcaC02g12795' => 'bca', 'BcaC02g12796' => 'bca', 'BcaC06g35541' => 'bca', 'BNapus_Darmor_BZH_scaffold_188p00080' => 'bna', 'BNapus_Darmor_BZH_scaffold_188p00090' => 'bna', 'BolC1t03972H' => 'bol', 'BolC1t03973H' => 'bol', 'BolC4t21680H' => 'bol', 'BolC7t41863H' => 'bol', 'BolSC55t61227H' => 'bol', 'BolSC55t61228H' => 'bol', 'BraA01t03278Z' => 'bra', 'BraA05t18998Z' => 'bra', 'BraA07t28673Z' => 'bra', 'C01p40150' => 'bna', 'C05p12370' => 'bna', 'C07p13680' => 'bna', 'CAN.G1006.16' => 'can', 'CAN.G1006.17' => 'can', 'CAN.G1170.2' => 'can', 'CAN.G962.7' => 'can', 'CANSAT25G2179' => 'cansat', 'CANSAT78G1573' => 'cansat', 'CARHR099510' => 'chi', 'CARHR143510' => 'chi', 'Carub.0003s2380' => 'cru', 'Carub.0004s3082' => 'cru', 'Ca_00614_v3' => 'car', 'Ca_07801_v3' => 'car', 'Ca_08567_v3' => 'car', 'Ca_09571_v3' => 'car', 'CBR_g19290' => 'cbr', 'Cc01_g19770' => 'ccan', 'Cc03_g03030' => 'ccan', 'CDE07G0968' => 'cde', 'CDE09G1441' => 'cde', 'Cfa006103' => 'cfa', 'Cfa015573' => 'cfa', 'Cfa016988' => 'cfa', 'Ciclev10006738m.g' => 'ccl', 'Ciclev10010920m.g' => 'ccl', 'Ciclev10018517m.g' => 'ccl', 'CiPaw.01G159200' => 'cil', 'CiPaw.02G091000' => 'cil', 'CiPaw.02G091100' => 'cil', 'CiPaw.08G103100' => 'cil', 'CiPaw.09G224900' => 'cil', 'ClCG06G005740' => 'cla', 'ClCG07G000090' => 'cla', 'ClCG07G000100' => 'cla', 'COL.COLO4_09143' => 'col', 'COL.COLO4_25124' => 'col', 'Cpa.g.sc16.34' => 'cpa', 'Cpa.g.sc3504.1' => 'cpa', 'Cpa.g.sc60.37' => 'cpa', 'CsaV3_6G018520' => 'csa', 'CsaV3_6G036860' => 'csa', 'CSS0001072' => 'camsi', 'CSS0020208' => 'camsi', 'CSS0021253' => 'camsi', 'CSS0022190' => 'camsi', 'CSS0036150' => 'camsi', 'CSS0040442' => 'camsi', 'CSS0042300' => 'camsi', 'CSS0045298' => 'camsi', 'DCAR_012449' => 'dca', 'DCAR_018405' => 'dca', 'DCAR_024573' => 'dca', 'DCAR_030591' => 'dca', 'Dinv16926' => 'din', 'Dinv32963' => 'din', 'Dinv38382' => 'din', 'Dinv38383' => 'din', 'Duzib133G0974' => 'dzi', 'Duzib138G1867' => 'dzi', 'Duzib211G0420' => 'dzi', 'Duzib212G0930' => 'dzi', 'ECA234G1645' => 'eca', 'ECA247G3467' => 'eca', 'ECA248G1703' => 'eca', 'EL10Ac3g06327' => 'bvu', 'EL10Ac7g17204' => 'bvu', 'Eucgr.A00855' => 'egr', 'Eucgr.A00858' => 'egr', 'Eucgr.H01520' => 'egr', 'Eucgr.H03604' => 'egr', 'Eucgr.L03465' => 'egr', 'Eucgr.L03466' => 'egr', 'FAN01G0988' => 'fan', 'FAN02G3892' => 'fan', 'FAN05G3381' => 'fan', 'FAN07G0967' => 'fan', 'FAN07G1493' => 'fan', 'FAN08G3125' => 'fan', 'FAN09G0402' => 'fan', 'FAN12G2594' => 'fan', 'FAN12G3879' => 'fan', 'FAN14G1546' => 'fan', 'FAN15G3626' => 'fan', 'FAN17G0588' => 'fan', 'FAN17G0609' => 'fan', 'FAN18G2817' => 'fan', 'FAN19G1305' => 'fan', 'FAN20G1787' => 'fan', 'FAN22G0073' => 'fan', 'FAN22G0352' => 'fan', 'FAN22G0368' => 'fan', 'FAN22G2273' => 'fan', 'FAN24G1998' => 'fan', 'FAN27G1317' => 'fan', 'FvH4_2g23980' => 'fve', 'FvH4_4g14380' => 'fve', 'FvH4_4g14390' => 'fve', 'FvH4_6g09250' => 'fve', 'Glyma.03G151100' => 'gma', 'Glyma.04G122550' => 'gma', 'Glyma.05G001600' => 'gma', 'Glyma.09G270766' => 'gma', 'Glyma.09G270832' => 'gma', 'Glyma.13G209800' => 'gma', 'Glyma.15G102800' => 'gma', 'Glyma.18G218900' => 'gma', 'Glyma.19G001500' => 'gma', 'Glyma.19G153600' => 'gma', 'Gohir.A02G028600' => 'ghi', 'Gohir.A08G045000' => 'ghi', 'Gohir.A11G120500' => 'ghi', 'Gohir.A12G006200' => 'ghi', 'Gohir.A12G006250' => 'ghi', 'Gohir.D02G036300' => 'ghi', 'Gohir.D08G054700' => 'ghi', 'Gohir.D11G125600' => 'ghi', 'Gohir.D12G005700' => 'ghi', 'Gorai.004G055200' => 'gra', 'Gorai.005G040400' => 'gra', 'Gorai.007G134500' => 'gra', 'Gorai.008G005500' => 'gra', 'GSVIVG01011094001' => 'vvi', 'GSVIVG01017879001' => 'vvi', 'GSVIVG01025988001' => 'vvi', 'GSVIVG01029847001' => 'vvi', 'HanXRQChr10g0282901' => 'han', 'HanXRQChr10g0310371' => 'han', 'HanXRQChr10g0315041' => 'han', 'HanXRQChr11g0327651' => 'han', 'HanXRQChr12g0359391' => 'han', 'Haze_00972' => 'cav', 'Haze_00973' => 'cav', 'Haze_00974' => 'cav', 'Haze_04747' => 'cav', 'Haze_04749' => 'cav', 'Haze_04750' => 'cav', 'Haze_21217' => 'cav', 'Hma1.2p1_1037F.1_g250680' => 'hma', 'Hma1.2p1_1644F.1_g295320' => 'hma', 'HPP92_011322' => 'vpl', 'HPP92_011323' => 'vpl', 'HPP92_011324' => 'vpl', 'HPP92_011325' => 'vpl', 'HPP92_011326' => 'vpl', 'Hund12205' => 'sun', 'Hund17957' => 'sun', 'Lalb_Chr06g0176771' => 'lal', 'Lalb_Chr18g0056021' => 'lal', 'Lalb_Chr18g0056031' => 'lal', 'Lalb_Chr18g0056041' => 'lal', 'Lalb_Chr20g0107751' => 'lal', 'Lalb_Chr20g0118371' => 'lal', 'Lj1g0010239' => 'lja', 'Lj1g0017101' => 'lja', 'Lj2A1178G40' => 'lonja', 'Lj2A54G84' => 'lonja', 'Lj2g0015248' => 'lja', 'Lj3A761T51' => 'lonja', 'Lj6g0018116' => 'lja', 'Lsat_1_v5_gn_4_136040' => 'lsa', 'Lsat_1_v5_gn_5_187461' => 'lsa', 'Lsat_1_v5_gn_5_77001' => 'lsa', 'Lsat_1_v5_gn_9_4461' => 'lsa', 'Manes.01G210100' => 'mes', 'Manes.03G185600' => 'mes', 'Manes.05G073300' => 'mes', 'Manes.09G120300' => 'mes', 'Manes.15G022100' => 'mes', 'Mapoly0096s0053' => 'mpo', 'MBI03_g14058_MAGBIO' => 'mbi', 'MBI03_g33876_MAGBIO' => 'mbi', 'MBI03_g36854_MAGBIO' => 'mbi', 'MBI17_g11997_MAGBIO' => 'mbi', 'MD03G1269000' => 'mdo', 'MD04G1179600' => 'mdo', 'MD11G1289800' => 'mdo', 'MD12G1194700' => 'mdo', 'MD13G1182100' => 'mdo', 'MD13G1182200' => 'mdo', 'MD16G1182600' => 'mdo', 'Medtr2g021400' => 'mtr', 'Medtr2g021470' => 'mtr', 'Medtr2g105810' => 'mtr', 'Medtr3g033580' => 'mtr', 'Medtr6g007970' => 'mtr', 'Medtr7g056330' => 'mtr', 'Medtr7g074290' => 'mtr', 'Medtr7g074380' => 'mtr', 'Medtr7g094550' => 'mtr', 'Medtr8g069995' => 'mtr', 'MELO3C014345.2' => 'cme', 'MELO3C021395.2' => 'cme', 'Migut.D00262' => 'egut', 'Migut.G00257' => 'egut', 'MSTRG.21575' => 'ama', 'MSTRG.3985' => 'ama', 'Nitab4.5_0000295g0140' => 'nta', 'Nitab4.5_0000732g0140' => 'nta', 'Nitab4.5_0003162g0020' => 'nta', 'Nitab4.5_0006180g0090' => 'nta', 'Nitab4.5_0006390g0010' => 'nta', 'Nitab4.5_0007392g0040' => 'nta', 'Nn1g02140' => 'nnu', 'Nn4g26168' => 'nnu', 'Nn5g26754' => 'nnu', 'Oeu001433.1' => 'oeu', 'Oeu010299.2' => 'oeu', 'Oeu011171.1' => 'oeu', 'Oeu037675.1' => 'oeu', 'Oeu038359.1' => 'oeu', 'Oeu063834.1' => 'oeu', 'Oeu063835.1' => 'oeu', 'Os05g0312000' => 'osa', 'Os07g0211101' => 'osa', 'Os07g0211200' => 'osa', 'Os07g0681500' => 'osa', 'Peaxi162Scf00095g01015' => 'pax', 'Peaxi162Scf00104g00329' => 'pax', 'Peaxi162Scf00161g00137' => 'pax', 'PGR004G1665' => 'pgr', 'PGR031G2937' => 'pgr', 'PGR119G2145' => 'pgr', 'PGSC0003DMG400004351' => 'stu', 'PGSC0003DMG400014625' => 'stu', 'PGSC0003DMG401000943' => 'stu', 'Phvul.001G148600' => 'pvu', 'Phvul.004G001700' => 'pvu', 'Phvul.006G154900' => 'pvu', 'Phvul.008G078200' => 'pvu', 'Phvul.011G136500' => 'pvu', 'Potri.002G215600' => 'ptr', 'Potri.008G201600' => 'ptr', 'Potri.014G138400' => 'ptr', 'Potri.016G142500' => 'ptr', 'Pp3c16_10580' => 'ppa', 'Pp3c5_25280' => 'ppa', 'Prupe.1G150000' => 'ppe', 'Prupe.1G150100' => 'ppe', 'Prupe.6G299600' => 'ppe', 'Prupe.8G245000' => 'ppe', 'Psat0s4927g0040' => 'psa', 'Psat1g052080' => 'psa', 'Psat1g183800' => 'psa', 'Psat3g113840' => 'psa', 'Psat3g126120' => 'psa', 'Psat3g126160' => 'psa', 'Psat3g158760' => 'psa', 'Psat3g158840' => 'psa', 'PSO170G2858' => 'pso', 'PSO339G0606' => 'pso', 'PSO384G4709' => 'pso', 'PSO407G0334' => 'pso', 'QL04p040276' => 'qlo', 'QL06p005458' => 'qlo', 'QL06p005472' => 'qlo', 'QL07p030546' => 'qlo', 'QL07p031519' => 'qlo', 'QL09p050949' => 'qlo', 'QL09p050966' => 'qlo', 'QL09p051067' => 'qlo', 'QL12p022706' => 'qlo', 'RcHm_v2.0_Chr2g0119601' => 'rch', 'RcHm_v2.0_Chr3g0459591' => 'rch', 'RcHm_v2.0_Chr4g0418521' => 'rch', 'RcHm_v2.0_Chr4g0418531' => 'rch', 'RcHm_v2.0_Chr4g0418541' => 'rch', 'RcHm_v2.0_Chr6g0291641' => 'rch', 'Rhsim01G0086300' => 'rsi', 'Rhsim01G0276300' => 'rsi', 'Rhsim01G0276500' => 'rsi', 'Rhsim04G0207700' => 'rsi', 'Rhsim05G0234500' => 'rsi', 'Rhsim13G0022400' => 'rsi', 'Sabra02G0167900' => 'sbr', 'Sabra04G0158500' => 'sbr', 'Sabra08G0159800' => 'sbr', 'Sabra10G0011500' => 'sbr', 'Sabra14G0104400' => 'sbr', 'SalBow2G2440' => 'sbo', 'SalBow4G2265' => 'sbo', 'Sc02g0000060' => 'sci', 'Sc05g0005020' => 'sci', 'Sc13g0003890' => 'sci', 'Sed0014865' => 'sed', 'Sed0017224' => 'sed', 'Sed0026391' => 'sed', 'SEGI_00063' => 'sgi', 'SEGI_10967' => 'sgi', 'SEGI_17510' => 'sgi', 'SEGI_24396' => 'sgi', 'SEGI_39719' => 'sgi', 'SEGI_41392' => 'sgi', 'SGA_v2.0_scaffold11G05794' => 'sas', 'SGA_v2.0_scaffold142G35607' => 'sas', 'SGA_v2.0_scaffold1G00447' => 'sas', 'SHI15388' => 'shi', 'SHI15394' => 'shi', 'SHI15396' => 'shi', 'SHI15399' => 'shi', 'SMO343G0151' => 'smo', 'SMO367G1118' => 'smo', 'Solyc01g080200.3' => 'sly', 'Solyc06g008960.3' => 'sly', 'Solyc09g064780.3' => 'sly', 'Sopen01g031980' => 'spe', 'Sopen06g003710' => 'spe', 'Sopen09g026460' => 'spe', 'Sp3g21240' => 'spa', 'Sp4g30030' => 'spa', 'TAR365G0022' => 'tar', 'TAR365G1023' => 'tar', 'TAR365G1253' => 'tar', 'TAR623G0078' => 'tar', 'TAR623G1721' => 'tar', 'TAR633G0959' => 'tar', 'THA.LOC104802225' => 'tha', 'THA.LOC104804769' => 'tha', 'THA.LOC104808660' => 'tha', 'THA.LOC104812792' => 'tha', 'Thecc.01G284000' => 'tca', 'Thecc.04G220600' => 'tca', 'Thecc.05G268900' => 'tca', 'Thecc.08G171100' => 'tca', 'Thhalv10001284m.g' => 'esa', 'Thhalv10019912m.g' => 'esa', 'TPR.G14189' => 'tpr', 'TPR.G18110' => 'tpr', 'TPR.G18130' => 'tpr', 'TPR.G18131' => 'tpr', 'TPR.G18140' => 'tpr', 'TPR.G24282' => 'tpr', 'TPR.G25221' => 'tpr', 'TPR.G29267' => 'tpr', 'TPR.G35315' => 'tpr', 'TPR.G36173' => 'tpr', 'TWI09G0794' => 'twi', 'TWI59G1348' => 'twi', 'TWI74G0430' => 'twi', 'unitig_26.g8940' => 'ugi', 'unitig_749.g13744' => 'ugi', 'unitig_749.g13745' => 'ugi', 'vmacro08269' => 'vma', 'vmacro14937' => 'vma', 'vmacro20401' => 'vma', 'VMungo0464G1349' => 'vmu', 'VMungo0540G0289' => 'vmu', 'VMungo1215G1590' => 'vmu', 'VMungo1309G0221' => 'vmu', 'VMungo1309G2815' => 'vmu', 'VMungo1383G0239' => 'vmu', 'VMungo1383G2910' => 'vmu', 'Zm00001eb095270' => 'zma', 'Zm00001eb095280' => 'zma', 'Zm00001eb111630' => 'zma', 'Zm00001eb237080' => 'zma', 'Zm00001eb273740' => 'zma', 'Zm00001eb285040' => 'zma', 'Zm00001eb330790' => 'zma', 'Zm00001eb337380' => 'zma' ), 'gf_id' => 'HOM05D001484', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001484' ), 'data_identifier' => 'HOM05D001484', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001484', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p31500' => 'bna', 'A05p00020' => 'bna', 'A07p08820' => 'bna', 'Aa31LG4G3300' => 'aar', 'Aa31LG8G10030' => 'aar', 'Actinidia00731' => 'ach', 'Actinidia11473' => 'ach', 'Actinidia23469' => 'ach', 'Actinidia24318' => 'ach', 'Actinidia40196' => 'ach', 'Actinidia40197' => 'ach', 'Actinidia40198' => 'ach', 'Ah.08g212990' => 'amhyb', 'Ah.15g091720' => 'amhyb', 'AL3G38260' => 'aly', 'AL4G47710' => 'aly', 'Aqoxy2G00671' => 'aox', 'Aqoxy2G03236' => 'aox', 'arahy.Tifrunner.gnm1.ann1.05IDCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KR684' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATY3SJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK6QJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6APGL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IDT7Z9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM073U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ0R87' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LE7RV4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT4QRX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V5ENPK' => 'arhy', 'AT2G48110' => 'ath', 'AT3G23590' => 'ath', 'ATR0626G186' => 'atr', 'ATR1127G141' => 'atr', 'Atru.chr4.2583' => 'acertr', 'Atru.chr5.1358' => 'acertr', 'Atru.chr5.1359' => 'acertr', 'Atru.chr8.46' => 'acertr', 'AUR62002640' => 'cqu', 'AUR62030055' => 'cqu', 'AUR62033713' => 'cqu', 'AUR62033714' => 'cqu', 'AUR62036795' => 'cqu', 'AUR62039891' => 'cqu', 'BcaB02g08737' => 'bca', 'BcaB04g20441' => 'bca', 'BcaB06g26509' => 'bca', 'BcaB06g26510' => 'bca', 'BcaB06g26511' => 'bca', 'BcaB06g26512' => 'bca', 'BcaB06g26513' => 'bca', 'BcaC02g12564' => 'bca', 'BcaC02g12565' => 'bca', 'BcaC02g12794' => 'bca', 'BcaC02g12795' => 'bca', 'BcaC02g12796' => 'bca', 'BcaC06g35541' => 'bca', 'BNapus_Darmor_BZH_scaffold_188p00080' => 'bna', 'BNapus_Darmor_BZH_scaffold_188p00090' => 'bna', 'BolC1t03972H' => 'bol', 'BolC1t03973H' => 'bol', 'BolC4t21680H' => 'bol', 'BolC7t41863H' => 'bol', 'BolSC55t61227H' => 'bol', 'BolSC55t61228H' => 'bol', 'BraA01t03278Z' => 'bra', 'BraA05t18998Z' => 'bra', 'BraA07t28673Z' => 'bra', 'C01p40150' => 'bna', 'C05p12370' => 'bna', 'C07p13680' => 'bna', 'CAN.G1006.16' => 'can', 'CAN.G1006.17' => 'can', 'CAN.G1170.2' => 'can', 'CAN.G962.7' => 'can', 'CANSAT25G2179' => 'cansat', 'CANSAT78G1573' => 'cansat', 'CARHR099510' => 'chi', 'CARHR143510' => 'chi', 'Carub.0003s2380' => 'cru', 'Carub.0004s3082' => 'cru', 'Ca_00614_v3' => 'car', 'Ca_07801_v3' => 'car', 'Ca_08567_v3' => 'car', 'Ca_09571_v3' => 'car', 'CBR_g19290' => 'cbr', 'Cc01_g19770' => 'ccan', 'Cc03_g03030' => 'ccan', 'CDE07G0968' => 'cde', 'CDE09G1441' => 'cde', 'Cfa006103' => 'cfa', 'Cfa015573' => 'cfa', 'Cfa016988' => 'cfa', 'Ciclev10006738m.g' => 'ccl', 'Ciclev10010920m.g' => 'ccl', 'Ciclev10018517m.g' => 'ccl', 'CiPaw.01G159200' => 'cil', 'CiPaw.02G091000' => 'cil', 'CiPaw.02G091100' => 'cil', 'CiPaw.08G103100' => 'cil', 'CiPaw.09G224900' => 'cil', 'ClCG06G005740' => 'cla', 'ClCG07G000090' => 'cla', 'ClCG07G000100' => 'cla', 'COL.COLO4_09143' => 'col', 'COL.COLO4_25124' => 'col', 'Cpa.g.sc16.34' => 'cpa', 'Cpa.g.sc3504.1' => 'cpa', 'Cpa.g.sc60.37' => 'cpa', 'CsaV3_6G018520' => 'csa', 'CsaV3_6G036860' => 'csa', 'CSS0001072' => 'camsi', 'CSS0020208' => 'camsi', 'CSS0021253' => 'camsi', 'CSS0022190' => 'camsi', 'CSS0036150' => 'camsi', 'CSS0040442' => 'camsi', 'CSS0042300' => 'camsi', 'CSS0045298' => 'camsi', 'DCAR_012449' => 'dca', 'DCAR_018405' => 'dca', 'DCAR_024573' => 'dca', 'DCAR_030591' => 'dca', 'Dinv16926' => 'din', 'Dinv32963' => 'din', 'Dinv38382' => 'din', 'Dinv38383' => 'din', 'Duzib133G0974' => 'dzi', 'Duzib138G1867' => 'dzi', 'Duzib211G0420' => 'dzi', 'Duzib212G0930' => 'dzi', 'ECA234G1645' => 'eca', 'ECA247G3467' => 'eca', 'ECA248G1703' => 'eca', 'EL10Ac3g06327' => 'bvu', 'EL10Ac7g17204' => 'bvu', 'Eucgr.A00855' => 'egr', 'Eucgr.A00858' => 'egr', 'Eucgr.H01520' => 'egr', 'Eucgr.H03604' => 'egr', 'Eucgr.L03465' => 'egr', 'Eucgr.L03466' => 'egr', 'FAN01G0988' => 'fan', 'FAN02G3892' => 'fan', 'FAN05G3381' => 'fan', 'FAN07G0967' => 'fan', 'FAN07G1493' => 'fan', 'FAN08G3125' => 'fan', 'FAN09G0402' => 'fan', 'FAN12G2594' => 'fan', 'FAN12G3879' => 'fan', 'FAN14G1546' => 'fan', 'FAN15G3626' => 'fan', 'FAN17G0588' => 'fan', 'FAN17G0609' => 'fan', 'FAN18G2817' => 'fan', 'FAN19G1305' => 'fan', 'FAN20G1787' => 'fan', 'FAN22G0073' => 'fan', 'FAN22G0352' => 'fan', 'FAN22G0368' => 'fan', 'FAN22G2273' => 'fan', 'FAN24G1998' => 'fan', 'FAN27G1317' => 'fan', 'FvH4_2g23980' => 'fve', 'FvH4_4g14380' => 'fve', 'FvH4_4g14390' => 'fve', 'FvH4_6g09250' => 'fve', 'Glyma.03G151100' => 'gma', 'Glyma.04G122550' => 'gma', 'Glyma.05G001600' => 'gma', 'Glyma.09G270766' => 'gma', 'Glyma.09G270832' => 'gma', 'Glyma.13G209800' => 'gma', 'Glyma.15G102800' => 'gma', 'Glyma.18G218900' => 'gma', 'Glyma.19G001500' => 'gma', 'Glyma.19G153600' => 'gma', 'Gohir.A02G028600' => 'ghi', 'Gohir.A08G045000' => 'ghi', 'Gohir.A11G120500' => 'ghi', 'Gohir.A12G006200' => 'ghi', 'Gohir.A12G006250' => 'ghi', 'Gohir.D02G036300' => 'ghi', 'Gohir.D08G054700' => 'ghi', 'Gohir.D11G125600' => 'ghi', 'Gohir.D12G005700' => 'ghi', 'Gorai.004G055200' => 'gra', 'Gorai.005G040400' => 'gra', 'Gorai.007G134500' => 'gra', 'Gorai.008G005500' => 'gra', 'GSVIVG01011094001' => 'vvi', 'GSVIVG01017879001' => 'vvi', 'GSVIVG01025988001' => 'vvi', 'GSVIVG01029847001' => 'vvi', 'HanXRQChr10g0282901' => 'han', 'HanXRQChr10g0310371' => 'han', 'HanXRQChr10g0315041' => 'han', 'HanXRQChr11g0327651' => 'han', 'HanXRQChr12g0359391' => 'han', 'Haze_00972' => 'cav', 'Haze_00973' => 'cav', 'Haze_00974' => 'cav', 'Haze_04747' => 'cav', 'Haze_04749' => 'cav', 'Haze_04750' => 'cav', 'Haze_21217' => 'cav', 'Hma1.2p1_1037F.1_g250680' => 'hma', 'Hma1.2p1_1644F.1_g295320' => 'hma', 'HPP92_011322' => 'vpl', 'HPP92_011323' => 'vpl', 'HPP92_011324' => 'vpl', 'HPP92_011325' => 'vpl', 'HPP92_011326' => 'vpl', 'Hund12205' => 'sun', 'Hund17957' => 'sun', 'Lalb_Chr06g0176771' => 'lal', 'Lalb_Chr18g0056021' => 'lal', 'Lalb_Chr18g0056031' => 'lal', 'Lalb_Chr18g0056041' => 'lal', 'Lalb_Chr20g0107751' => 'lal', 'Lalb_Chr20g0118371' => 'lal', 'Lj1g0010239' => 'lja', 'Lj1g0017101' => 'lja', 'Lj2A1178G40' => 'lonja', 'Lj2A54G84' => 'lonja', 'Lj2g0015248' => 'lja', 'Lj3A761T51' => 'lonja', 'Lj6g0018116' => 'lja', 'Lsat_1_v5_gn_4_136040' => 'lsa', 'Lsat_1_v5_gn_5_187461' => 'lsa', 'Lsat_1_v5_gn_5_77001' => 'lsa', 'Lsat_1_v5_gn_9_4461' => 'lsa', 'Manes.01G210100' => 'mes', 'Manes.03G185600' => 'mes', 'Manes.05G073300' => 'mes', 'Manes.09G120300' => 'mes', 'Manes.15G022100' => 'mes', 'Mapoly0096s0053' => 'mpo', 'MBI03_g14058_MAGBIO' => 'mbi', 'MBI03_g33876_MAGBIO' => 'mbi', 'MBI03_g36854_MAGBIO' => 'mbi', 'MBI17_g11997_MAGBIO' => 'mbi', 'MD03G1269000' => 'mdo', 'MD04G1179600' => 'mdo', 'MD11G1289800' => 'mdo', 'MD12G1194700' => 'mdo', 'MD13G1182100' => 'mdo', 'MD13G1182200' => 'mdo', 'MD16G1182600' => 'mdo', 'Medtr2g021400' => 'mtr', 'Medtr2g021470' => 'mtr', 'Medtr2g105810' => 'mtr', 'Medtr3g033580' => 'mtr', 'Medtr6g007970' => 'mtr', 'Medtr7g056330' => 'mtr', 'Medtr7g074290' => 'mtr', 'Medtr7g074380' => 'mtr', 'Medtr7g094550' => 'mtr', 'Medtr8g069995' => 'mtr', 'MELO3C014345.2' => 'cme', 'MELO3C021395.2' => 'cme', 'Migut.D00262' => 'egut', 'Migut.G00257' => 'egut', 'MSTRG.21575' => 'ama', 'MSTRG.3985' => 'ama', 'Nitab4.5_0000295g0140' => 'nta', 'Nitab4.5_0000732g0140' => 'nta', 'Nitab4.5_0003162g0020' => 'nta', 'Nitab4.5_0006180g0090' => 'nta', 'Nitab4.5_0006390g0010' => 'nta', 'Nitab4.5_0007392g0040' => 'nta', 'Nn1g02140' => 'nnu', 'Nn4g26168' => 'nnu', 'Nn5g26754' => 'nnu', 'Oeu001433.1' => 'oeu', 'Oeu010299.2' => 'oeu', 'Oeu011171.1' => 'oeu', 'Oeu037675.1' => 'oeu', 'Oeu038359.1' => 'oeu', 'Oeu063834.1' => 'oeu', 'Oeu063835.1' => 'oeu', 'Os05g0312000' => 'osa', 'Os07g0211101' => 'osa', 'Os07g0211200' => 'osa', 'Os07g0681500' => 'osa', 'Peaxi162Scf00095g01015' => 'pax', 'Peaxi162Scf00104g00329' => 'pax', 'Peaxi162Scf00161g00137' => 'pax', 'PGR004G1665' => 'pgr', 'PGR031G2937' => 'pgr', 'PGR119G2145' => 'pgr', 'PGSC0003DMG400004351' => 'stu', 'PGSC0003DMG400014625' => 'stu', 'PGSC0003DMG401000943' => 'stu', 'Phvul.001G148600' => 'pvu', 'Phvul.004G001700' => 'pvu', 'Phvul.006G154900' => 'pvu', 'Phvul.008G078200' => 'pvu', 'Phvul.011G136500' => 'pvu', 'Potri.002G215600' => 'ptr', 'Potri.008G201600' => 'ptr', 'Potri.014G138400' => 'ptr', 'Potri.016G142500' => 'ptr', 'Pp3c16_10580' => 'ppa', 'Pp3c5_25280' => 'ppa', 'Prupe.1G150000' => 'ppe', 'Prupe.1G150100' => 'ppe', 'Prupe.6G299600' => 'ppe', 'Prupe.8G245000' => 'ppe', 'Psat0s4927g0040' => 'psa', 'Psat1g052080' => 'psa', 'Psat1g183800' => 'psa', 'Psat3g113840' => 'psa', 'Psat3g126120' => 'psa', 'Psat3g126160' => 'psa', 'Psat3g158760' => 'psa', 'Psat3g158840' => 'psa', 'PSO170G2858' => 'pso', 'PSO339G0606' => 'pso', 'PSO384G4709' => 'pso', 'PSO407G0334' => 'pso', 'QL04p040276' => 'qlo', 'QL06p005458' => 'qlo', 'QL06p005472' => 'qlo', 'QL07p030546' => 'qlo', 'QL07p031519' => 'qlo', 'QL09p050949' => 'qlo', 'QL09p050966' => 'qlo', 'QL09p051067' => 'qlo', 'QL12p022706' => 'qlo', 'RcHm_v2.0_Chr2g0119601' => 'rch', 'RcHm_v2.0_Chr3g0459591' => 'rch', 'RcHm_v2.0_Chr4g0418521' => 'rch', 'RcHm_v2.0_Chr4g0418531' => 'rch', 'RcHm_v2.0_Chr4g0418541' => 'rch', 'RcHm_v2.0_Chr6g0291641' => 'rch', 'Rhsim01G0086300' => 'rsi', 'Rhsim01G0276300' => 'rsi', 'Rhsim01G0276500' => 'rsi', 'Rhsim04G0207700' => 'rsi', 'Rhsim05G0234500' => 'rsi', 'Rhsim13G0022400' => 'rsi', 'Sabra02G0167900' => 'sbr', 'Sabra04G0158500' => 'sbr', 'Sabra08G0159800' => 'sbr', 'Sabra10G0011500' => 'sbr', 'Sabra14G0104400' => 'sbr', 'SalBow2G2440' => 'sbo', 'SalBow4G2265' => 'sbo', 'Sc02g0000060' => 'sci', 'Sc05g0005020' => 'sci', 'Sc13g0003890' => 'sci', 'Sed0014865' => 'sed', 'Sed0017224' => 'sed', 'Sed0026391' => 'sed', 'SEGI_00063' => 'sgi', 'SEGI_10967' => 'sgi', 'SEGI_17510' => 'sgi', 'SEGI_24396' => 'sgi', 'SEGI_39719' => 'sgi', 'SEGI_41392' => 'sgi', 'SGA_v2.0_scaffold11G05794' => 'sas', 'SGA_v2.0_scaffold142G35607' => 'sas', 'SGA_v2.0_scaffold1G00447' => 'sas', 'SHI15388' => 'shi', 'SHI15394' => 'shi', 'SHI15396' => 'shi', 'SHI15399' => 'shi', 'SMO343G0151' => 'smo', 'SMO367G1118' => 'smo', 'Solyc01g080200.3' => 'sly', 'Solyc06g008960.3' => 'sly', 'Solyc09g064780.3' => 'sly', 'Sopen01g031980' => 'spe', 'Sopen06g003710' => 'spe', 'Sopen09g026460' => 'spe', 'Sp3g21240' => 'spa', 'Sp4g30030' => 'spa', 'TAR365G0022' => 'tar', 'TAR365G1023' => 'tar', 'TAR365G1253' => 'tar', 'TAR623G0078' => 'tar', 'TAR623G1721' => 'tar', 'TAR633G0959' => 'tar', 'THA.LOC104802225' => 'tha', 'THA.LOC104804769' => 'tha', 'THA.LOC104808660' => 'tha', 'THA.LOC104812792' => 'tha', 'Thecc.01G284000' => 'tca', 'Thecc.04G220600' => 'tca', 'Thecc.05G268900' => 'tca', 'Thecc.08G171100' => 'tca', 'Thhalv10001284m.g' => 'esa', 'Thhalv10019912m.g' => 'esa', 'TPR.G14189' => 'tpr', 'TPR.G18110' => 'tpr', 'TPR.G18130' => 'tpr', 'TPR.G18131' => 'tpr', 'TPR.G18140' => 'tpr', 'TPR.G24282' => 'tpr', 'TPR.G25221' => 'tpr', 'TPR.G29267' => 'tpr', 'TPR.G35315' => 'tpr', 'TPR.G36173' => 'tpr', 'TWI09G0794' => 'twi', 'TWI59G1348' => 'twi', 'TWI74G0430' => 'twi', 'unitig_26.g8940' => 'ugi', 'unitig_749.g13744' => 'ugi', 'unitig_749.g13745' => 'ugi', 'vmacro08269' => 'vma', 'vmacro14937' => 'vma', 'vmacro20401' => 'vma', 'VMungo0464G1349' => 'vmu', 'VMungo0540G0289' => 'vmu', 'VMungo1215G1590' => 'vmu', 'VMungo1309G0221' => 'vmu', 'VMungo1309G2815' => 'vmu', 'VMungo1383G0239' => 'vmu', 'VMungo1383G2910' => 'vmu', 'Zm00001eb095270' => 'zma', 'Zm00001eb095280' => 'zma', 'Zm00001eb111630' => 'zma', 'Zm00001eb237080' => 'zma', 'Zm00001eb273740' => 'zma', 'Zm00001eb285040' => 'zma', 'Zm00001eb330790' => 'zma', 'Zm00001eb337380' => 'zma' ) $gf_id = 'HOM05D001484' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001484' ) $data_identifier = 'HOM05D001484' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 2, 'aly' => (int) 2, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 22, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 7, 'hma' => (int) 2, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 7, 'mtr' => (int) 10, 'cme' => (int) 2, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 4, 'ppa' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 4, 'qlo' => (int) 9, 'rch' => (int) 6, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 10, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 7, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb337380' $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' => 'HOM05D001484', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p31500' => 'bna', 'A05p00020' => 'bna', 'A07p08820' => 'bna', 'Aa31LG4G3300' => 'aar', 'Aa31LG8G10030' => 'aar', 'Actinidia00731' => 'ach', 'Actinidia11473' => 'ach', 'Actinidia23469' => 'ach', 'Actinidia24318' => 'ach', 'Actinidia40196' => 'ach', 'Actinidia40197' => 'ach', 'Actinidia40198' => 'ach', 'Ah.08g212990' => 'amhyb', 'Ah.15g091720' => 'amhyb', 'AL3G38260' => 'aly', 'AL4G47710' => 'aly', 'Aqoxy2G00671' => 'aox', 'Aqoxy2G03236' => 'aox', 'arahy.Tifrunner.gnm1.ann1.05IDCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KR684' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATY3SJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK6QJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6APGL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IDT7Z9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM073U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ0R87' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LE7RV4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT4QRX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V5ENPK' => 'arhy', 'AT2G48110' => 'ath', 'AT3G23590' => 'ath', 'ATR0626G186' => 'atr', 'ATR1127G141' => 'atr', 'Atru.chr4.2583' => 'acertr', 'Atru.chr5.1358' => 'acertr', 'Atru.chr5.1359' => 'acertr', 'Atru.chr8.46' => 'acertr', 'AUR62002640' => 'cqu', 'AUR62030055' => 'cqu', 'AUR62033713' => 'cqu', 'AUR62033714' => 'cqu', 'AUR62036795' => 'cqu', 'AUR62039891' => 'cqu', 'BcaB02g08737' => 'bca', 'BcaB04g20441' => 'bca', 'BcaB06g26509' => 'bca', 'BcaB06g26510' => 'bca', 'BcaB06g26511' => 'bca', 'BcaB06g26512' => 'bca', 'BcaB06g26513' => 'bca', 'BcaC02g12564' => 'bca', 'BcaC02g12565' => 'bca', 'BcaC02g12794' => 'bca', 'BcaC02g12795' => 'bca', 'BcaC02g12796' => 'bca', 'BcaC06g35541' => 'bca', 'BNapus_Darmor_BZH_scaffold_188p00080' => 'bna', 'BNapus_Darmor_BZH_scaffold_188p00090' => 'bna', 'BolC1t03972H' => 'bol', 'BolC1t03973H' => 'bol', 'BolC4t21680H' => 'bol', 'BolC7t41863H' => 'bol', 'BolSC55t61227H' => 'bol', 'BolSC55t61228H' => 'bol', 'BraA01t03278Z' => 'bra', 'BraA05t18998Z' => 'bra', 'BraA07t28673Z' => 'bra', 'C01p40150' => 'bna', 'C05p12370' => 'bna', 'C07p13680' => 'bna', 'CAN.G1006.16' => 'can', 'CAN.G1006.17' => 'can', 'CAN.G1170.2' => 'can', 'CAN.G962.7' => 'can', 'CANSAT25G2179' => 'cansat', 'CANSAT78G1573' => 'cansat', 'CARHR099510' => 'chi', 'CARHR143510' => 'chi', 'Carub.0003s2380' => 'cru', 'Carub.0004s3082' => 'cru', 'Ca_00614_v3' => 'car', 'Ca_07801_v3' => 'car', 'Ca_08567_v3' => 'car', 'Ca_09571_v3' => 'car', 'CBR_g19290' => 'cbr', 'Cc01_g19770' => 'ccan', 'Cc03_g03030' => 'ccan', 'CDE07G0968' => 'cde', 'CDE09G1441' => 'cde', 'Cfa006103' => 'cfa', 'Cfa015573' => 'cfa', 'Cfa016988' => 'cfa', 'Ciclev10006738m.g' => 'ccl', 'Ciclev10010920m.g' => 'ccl', 'Ciclev10018517m.g' => 'ccl', 'CiPaw.01G159200' => 'cil', 'CiPaw.02G091000' => 'cil', 'CiPaw.02G091100' => 'cil', 'CiPaw.08G103100' => 'cil', 'CiPaw.09G224900' => 'cil', 'ClCG06G005740' => 'cla', 'ClCG07G000090' => 'cla', 'ClCG07G000100' => 'cla', 'COL.COLO4_09143' => 'col', 'COL.COLO4_25124' => 'col', 'Cpa.g.sc16.34' => 'cpa', 'Cpa.g.sc3504.1' => 'cpa', 'Cpa.g.sc60.37' => 'cpa', 'CsaV3_6G018520' => 'csa', 'CsaV3_6G036860' => 'csa', 'CSS0001072' => 'camsi', 'CSS0020208' => 'camsi', 'CSS0021253' => 'camsi', 'CSS0022190' => 'camsi', 'CSS0036150' => 'camsi', 'CSS0040442' => 'camsi', 'CSS0042300' => 'camsi', 'CSS0045298' => 'camsi', 'DCAR_012449' => 'dca', 'DCAR_018405' => 'dca', 'DCAR_024573' => 'dca', 'DCAR_030591' => 'dca', 'Dinv16926' => 'din', 'Dinv32963' => 'din', 'Dinv38382' => 'din', 'Dinv38383' => 'din', 'Duzib133G0974' => 'dzi', 'Duzib138G1867' => 'dzi', 'Duzib211G0420' => 'dzi', 'Duzib212G0930' => 'dzi', 'ECA234G1645' => 'eca', 'ECA247G3467' => 'eca', 'ECA248G1703' => 'eca', 'EL10Ac3g06327' => 'bvu', 'EL10Ac7g17204' => 'bvu', 'Eucgr.A00855' => 'egr', 'Eucgr.A00858' => 'egr', 'Eucgr.H01520' => 'egr', 'Eucgr.H03604' => 'egr', 'Eucgr.L03465' => 'egr', 'Eucgr.L03466' => 'egr', 'FAN01G0988' => 'fan', 'FAN02G3892' => 'fan', 'FAN05G3381' => 'fan', 'FAN07G0967' => 'fan', 'FAN07G1493' => 'fan', 'FAN08G3125' => 'fan', 'FAN09G0402' => 'fan', 'FAN12G2594' => 'fan', 'FAN12G3879' => 'fan', 'FAN14G1546' => 'fan', 'FAN15G3626' => 'fan', 'FAN17G0588' => 'fan', 'FAN17G0609' => 'fan', 'FAN18G2817' => 'fan', 'FAN19G1305' => 'fan', 'FAN20G1787' => 'fan', 'FAN22G0073' => 'fan', 'FAN22G0352' => 'fan', 'FAN22G0368' => 'fan', 'FAN22G2273' => 'fan', 'FAN24G1998' => 'fan', 'FAN27G1317' => 'fan', 'FvH4_2g23980' => 'fve', 'FvH4_4g14380' => 'fve', 'FvH4_4g14390' => 'fve', 'FvH4_6g09250' => 'fve', 'Glyma.03G151100' => 'gma', 'Glyma.04G122550' => 'gma', 'Glyma.05G001600' => 'gma', 'Glyma.09G270766' => 'gma', 'Glyma.09G270832' => 'gma', 'Glyma.13G209800' => 'gma', 'Glyma.15G102800' => 'gma', 'Glyma.18G218900' => 'gma', 'Glyma.19G001500' => 'gma', 'Glyma.19G153600' => 'gma', 'Gohir.A02G028600' => 'ghi', 'Gohir.A08G045000' => 'ghi', 'Gohir.A11G120500' => 'ghi', 'Gohir.A12G006200' => 'ghi', 'Gohir.A12G006250' => 'ghi', 'Gohir.D02G036300' => 'ghi', 'Gohir.D08G054700' => 'ghi', 'Gohir.D11G125600' => 'ghi', 'Gohir.D12G005700' => 'ghi', 'Gorai.004G055200' => 'gra', 'Gorai.005G040400' => 'gra', 'Gorai.007G134500' => 'gra', 'Gorai.008G005500' => 'gra', 'GSVIVG01011094001' => 'vvi', 'GSVIVG01017879001' => 'vvi', 'GSVIVG01025988001' => 'vvi', 'GSVIVG01029847001' => 'vvi', 'HanXRQChr10g0282901' => 'han', 'HanXRQChr10g0310371' => 'han', 'HanXRQChr10g0315041' => 'han', 'HanXRQChr11g0327651' => 'han', 'HanXRQChr12g0359391' => 'han', 'Haze_00972' => 'cav', 'Haze_00973' => 'cav', 'Haze_00974' => 'cav', 'Haze_04747' => 'cav', 'Haze_04749' => 'cav', 'Haze_04750' => 'cav', 'Haze_21217' => 'cav', 'Hma1.2p1_1037F.1_g250680' => 'hma', 'Hma1.2p1_1644F.1_g295320' => 'hma', 'HPP92_011322' => 'vpl', 'HPP92_011323' => 'vpl', 'HPP92_011324' => 'vpl', 'HPP92_011325' => 'vpl', 'HPP92_011326' => 'vpl', 'Hund12205' => 'sun', 'Hund17957' => 'sun', 'Lalb_Chr06g0176771' => 'lal', 'Lalb_Chr18g0056021' => 'lal', 'Lalb_Chr18g0056031' => 'lal', 'Lalb_Chr18g0056041' => 'lal', 'Lalb_Chr20g0107751' => 'lal', 'Lalb_Chr20g0118371' => 'lal', 'Lj1g0010239' => 'lja', 'Lj1g0017101' => 'lja', 'Lj2A1178G40' => 'lonja', 'Lj2A54G84' => 'lonja', 'Lj2g0015248' => 'lja', 'Lj3A761T51' => 'lonja', 'Lj6g0018116' => 'lja', 'Lsat_1_v5_gn_4_136040' => 'lsa', 'Lsat_1_v5_gn_5_187461' => 'lsa', 'Lsat_1_v5_gn_5_77001' => 'lsa', 'Lsat_1_v5_gn_9_4461' => 'lsa', 'Manes.01G210100' => 'mes', 'Manes.03G185600' => 'mes', 'Manes.05G073300' => 'mes', 'Manes.09G120300' => 'mes', 'Manes.15G022100' => 'mes', 'Mapoly0096s0053' => 'mpo', 'MBI03_g14058_MAGBIO' => 'mbi', 'MBI03_g33876_MAGBIO' => 'mbi', 'MBI03_g36854_MAGBIO' => 'mbi', 'MBI17_g11997_MAGBIO' => 'mbi', 'MD03G1269000' => 'mdo', 'MD04G1179600' => 'mdo', 'MD11G1289800' => 'mdo', 'MD12G1194700' => 'mdo', 'MD13G1182100' => 'mdo', 'MD13G1182200' => 'mdo', 'MD16G1182600' => 'mdo', 'Medtr2g021400' => 'mtr', 'Medtr2g021470' => 'mtr', 'Medtr2g105810' => 'mtr', 'Medtr3g033580' => 'mtr', 'Medtr6g007970' => 'mtr', 'Medtr7g056330' => 'mtr', 'Medtr7g074290' => 'mtr', 'Medtr7g074380' => 'mtr', 'Medtr7g094550' => 'mtr', 'Medtr8g069995' => 'mtr', 'MELO3C014345.2' => 'cme', 'MELO3C021395.2' => 'cme', 'Migut.D00262' => 'egut', 'Migut.G00257' => 'egut', 'MSTRG.21575' => 'ama', 'MSTRG.3985' => 'ama', 'Nitab4.5_0000295g0140' => 'nta', 'Nitab4.5_0000732g0140' => 'nta', 'Nitab4.5_0003162g0020' => 'nta', 'Nitab4.5_0006180g0090' => 'nta', 'Nitab4.5_0006390g0010' => 'nta', 'Nitab4.5_0007392g0040' => 'nta', 'Nn1g02140' => 'nnu', 'Nn4g26168' => 'nnu', 'Nn5g26754' => 'nnu', 'Oeu001433.1' => 'oeu', 'Oeu010299.2' => 'oeu', 'Oeu011171.1' => 'oeu', 'Oeu037675.1' => 'oeu', 'Oeu038359.1' => 'oeu', 'Oeu063834.1' => 'oeu', 'Oeu063835.1' => 'oeu', 'Os05g0312000' => 'osa', 'Os07g0211101' => 'osa', 'Os07g0211200' => 'osa', 'Os07g0681500' => 'osa', 'Peaxi162Scf00095g01015' => 'pax', 'Peaxi162Scf00104g00329' => 'pax', 'Peaxi162Scf00161g00137' => 'pax', 'PGR004G1665' => 'pgr', 'PGR031G2937' => 'pgr', 'PGR119G2145' => 'pgr', 'PGSC0003DMG400004351' => 'stu', 'PGSC0003DMG400014625' => 'stu', 'PGSC0003DMG401000943' => 'stu', 'Phvul.001G148600' => 'pvu', 'Phvul.004G001700' => 'pvu', 'Phvul.006G154900' => 'pvu', 'Phvul.008G078200' => 'pvu', 'Phvul.011G136500' => 'pvu', 'Potri.002G215600' => 'ptr', 'Potri.008G201600' => 'ptr', 'Potri.014G138400' => 'ptr', 'Potri.016G142500' => 'ptr', 'Pp3c16_10580' => 'ppa', 'Pp3c5_25280' => 'ppa', 'Prupe.1G150000' => 'ppe', 'Prupe.1G150100' => 'ppe', 'Prupe.6G299600' => 'ppe', 'Prupe.8G245000' => 'ppe', 'Psat0s4927g0040' => 'psa', 'Psat1g052080' => 'psa', 'Psat1g183800' => 'psa', 'Psat3g113840' => 'psa', 'Psat3g126120' => 'psa', 'Psat3g126160' => 'psa', 'Psat3g158760' => 'psa', 'Psat3g158840' => 'psa', 'PSO170G2858' => 'pso', 'PSO339G0606' => 'pso', 'PSO384G4709' => 'pso', 'PSO407G0334' => 'pso', 'QL04p040276' => 'qlo', 'QL06p005458' => 'qlo', 'QL06p005472' => 'qlo', 'QL07p030546' => 'qlo', 'QL07p031519' => 'qlo', 'QL09p050949' => 'qlo', 'QL09p050966' => 'qlo', 'QL09p051067' => 'qlo', 'QL12p022706' => 'qlo', 'RcHm_v2.0_Chr2g0119601' => 'rch', 'RcHm_v2.0_Chr3g0459591' => 'rch', 'RcHm_v2.0_Chr4g0418521' => 'rch', 'RcHm_v2.0_Chr4g0418531' => 'rch', 'RcHm_v2.0_Chr4g0418541' => 'rch', 'RcHm_v2.0_Chr6g0291641' => 'rch', 'Rhsim01G0086300' => 'rsi', 'Rhsim01G0276300' => 'rsi', 'Rhsim01G0276500' => 'rsi', 'Rhsim04G0207700' => 'rsi', 'Rhsim05G0234500' => 'rsi', 'Rhsim13G0022400' => 'rsi', 'Sabra02G0167900' => 'sbr', 'Sabra04G0158500' => 'sbr', 'Sabra08G0159800' => 'sbr', 'Sabra10G0011500' => 'sbr', 'Sabra14G0104400' => 'sbr', 'SalBow2G2440' => 'sbo', 'SalBow4G2265' => 'sbo', 'Sc02g0000060' => 'sci', 'Sc05g0005020' => 'sci', 'Sc13g0003890' => 'sci', 'Sed0014865' => 'sed', 'Sed0017224' => 'sed', 'Sed0026391' => 'sed', 'SEGI_00063' => 'sgi', 'SEGI_10967' => 'sgi', 'SEGI_17510' => 'sgi', 'SEGI_24396' => 'sgi', 'SEGI_39719' => 'sgi', 'SEGI_41392' => 'sgi', 'SGA_v2.0_scaffold11G05794' => 'sas', 'SGA_v2.0_scaffold142G35607' => 'sas', 'SGA_v2.0_scaffold1G00447' => 'sas', 'SHI15388' => 'shi', 'SHI15394' => 'shi', 'SHI15396' => 'shi', 'SHI15399' => 'shi', 'SMO343G0151' => 'smo', 'SMO367G1118' => 'smo', 'Solyc01g080200.3' => 'sly', 'Solyc06g008960.3' => 'sly', 'Solyc09g064780.3' => 'sly', 'Sopen01g031980' => 'spe', 'Sopen06g003710' => 'spe', 'Sopen09g026460' => 'spe', 'Sp3g21240' => 'spa', 'Sp4g30030' => 'spa', 'TAR365G0022' => 'tar', 'TAR365G1023' => 'tar', 'TAR365G1253' => 'tar', 'TAR623G0078' => 'tar', 'TAR623G1721' => 'tar', 'TAR633G0959' => 'tar', 'THA.LOC104802225' => 'tha', 'THA.LOC104804769' => 'tha', 'THA.LOC104808660' => 'tha', 'THA.LOC104812792' => 'tha', 'Thecc.01G284000' => 'tca', 'Thecc.04G220600' => 'tca', 'Thecc.05G268900' => 'tca', 'Thecc.08G171100' => 'tca', 'Thhalv10001284m.g' => 'esa', 'Thhalv10019912m.g' => 'esa', 'TPR.G14189' => 'tpr', 'TPR.G18110' => 'tpr', 'TPR.G18130' => 'tpr', 'TPR.G18131' => 'tpr', 'TPR.G18140' => 'tpr', 'TPR.G24282' => 'tpr', 'TPR.G25221' => 'tpr', 'TPR.G29267' => 'tpr', 'TPR.G35315' => 'tpr', 'TPR.G36173' => 'tpr', 'TWI09G0794' => 'twi', 'TWI59G1348' => 'twi', 'TWI74G0430' => 'twi', 'unitig_26.g8940' => 'ugi', 'unitig_749.g13744' => 'ugi', 'unitig_749.g13745' => 'ugi', 'vmacro08269' => 'vma', 'vmacro14937' => 'vma', 'vmacro20401' => 'vma', 'VMungo0464G1349' => 'vmu', 'VMungo0540G0289' => 'vmu', 'VMungo1215G1590' => 'vmu', 'VMungo1309G0221' => 'vmu', 'VMungo1309G2815' => 'vmu', 'VMungo1383G0239' => 'vmu', 'VMungo1383G2910' => 'vmu', 'Zm00001eb095270' => 'zma', 'Zm00001eb095280' => 'zma', 'Zm00001eb111630' => 'zma', 'Zm00001eb237080' => 'zma', 'Zm00001eb273740' => 'zma', 'Zm00001eb285040' => 'zma', 'Zm00001eb330790' => 'zma', 'Zm00001eb337380' => 'zma' ), 'gf_id' => 'HOM05D001484', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001484' ), 'data_identifier' => 'HOM05D001484', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001484', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p31500' => 'bna', 'A05p00020' => 'bna', 'A07p08820' => 'bna', 'Aa31LG4G3300' => 'aar', 'Aa31LG8G10030' => 'aar', 'Actinidia00731' => 'ach', 'Actinidia11473' => 'ach', 'Actinidia23469' => 'ach', 'Actinidia24318' => 'ach', 'Actinidia40196' => 'ach', 'Actinidia40197' => 'ach', 'Actinidia40198' => 'ach', 'Ah.08g212990' => 'amhyb', 'Ah.15g091720' => 'amhyb', 'AL3G38260' => 'aly', 'AL4G47710' => 'aly', 'Aqoxy2G00671' => 'aox', 'Aqoxy2G03236' => 'aox', 'arahy.Tifrunner.gnm1.ann1.05IDCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KR684' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATY3SJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK6QJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6APGL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IDT7Z9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM073U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ0R87' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LE7RV4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT4QRX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V5ENPK' => 'arhy', 'AT2G48110' => 'ath', 'AT3G23590' => 'ath', 'ATR0626G186' => 'atr', 'ATR1127G141' => 'atr', 'Atru.chr4.2583' => 'acertr', 'Atru.chr5.1358' => 'acertr', 'Atru.chr5.1359' => 'acertr', 'Atru.chr8.46' => 'acertr', 'AUR62002640' => 'cqu', 'AUR62030055' => 'cqu', 'AUR62033713' => 'cqu', 'AUR62033714' => 'cqu', 'AUR62036795' => 'cqu', 'AUR62039891' => 'cqu', 'BcaB02g08737' => 'bca', 'BcaB04g20441' => 'bca', 'BcaB06g26509' => 'bca', 'BcaB06g26510' => 'bca', 'BcaB06g26511' => 'bca', 'BcaB06g26512' => 'bca', 'BcaB06g26513' => 'bca', 'BcaC02g12564' => 'bca', 'BcaC02g12565' => 'bca', 'BcaC02g12794' => 'bca', 'BcaC02g12795' => 'bca', 'BcaC02g12796' => 'bca', 'BcaC06g35541' => 'bca', 'BNapus_Darmor_BZH_scaffold_188p00080' => 'bna', 'BNapus_Darmor_BZH_scaffold_188p00090' => 'bna', 'BolC1t03972H' => 'bol', 'BolC1t03973H' => 'bol', 'BolC4t21680H' => 'bol', 'BolC7t41863H' => 'bol', 'BolSC55t61227H' => 'bol', 'BolSC55t61228H' => 'bol', 'BraA01t03278Z' => 'bra', 'BraA05t18998Z' => 'bra', 'BraA07t28673Z' => 'bra', 'C01p40150' => 'bna', 'C05p12370' => 'bna', 'C07p13680' => 'bna', 'CAN.G1006.16' => 'can', 'CAN.G1006.17' => 'can', 'CAN.G1170.2' => 'can', 'CAN.G962.7' => 'can', 'CANSAT25G2179' => 'cansat', 'CANSAT78G1573' => 'cansat', 'CARHR099510' => 'chi', 'CARHR143510' => 'chi', 'Carub.0003s2380' => 'cru', 'Carub.0004s3082' => 'cru', 'Ca_00614_v3' => 'car', 'Ca_07801_v3' => 'car', 'Ca_08567_v3' => 'car', 'Ca_09571_v3' => 'car', 'CBR_g19290' => 'cbr', 'Cc01_g19770' => 'ccan', 'Cc03_g03030' => 'ccan', 'CDE07G0968' => 'cde', 'CDE09G1441' => 'cde', 'Cfa006103' => 'cfa', 'Cfa015573' => 'cfa', 'Cfa016988' => 'cfa', 'Ciclev10006738m.g' => 'ccl', 'Ciclev10010920m.g' => 'ccl', 'Ciclev10018517m.g' => 'ccl', 'CiPaw.01G159200' => 'cil', 'CiPaw.02G091000' => 'cil', 'CiPaw.02G091100' => 'cil', 'CiPaw.08G103100' => 'cil', 'CiPaw.09G224900' => 'cil', 'ClCG06G005740' => 'cla', 'ClCG07G000090' => 'cla', 'ClCG07G000100' => 'cla', 'COL.COLO4_09143' => 'col', 'COL.COLO4_25124' => 'col', 'Cpa.g.sc16.34' => 'cpa', 'Cpa.g.sc3504.1' => 'cpa', 'Cpa.g.sc60.37' => 'cpa', 'CsaV3_6G018520' => 'csa', 'CsaV3_6G036860' => 'csa', 'CSS0001072' => 'camsi', 'CSS0020208' => 'camsi', 'CSS0021253' => 'camsi', 'CSS0022190' => 'camsi', 'CSS0036150' => 'camsi', 'CSS0040442' => 'camsi', 'CSS0042300' => 'camsi', 'CSS0045298' => 'camsi', 'DCAR_012449' => 'dca', 'DCAR_018405' => 'dca', 'DCAR_024573' => 'dca', 'DCAR_030591' => 'dca', 'Dinv16926' => 'din', 'Dinv32963' => 'din', 'Dinv38382' => 'din', 'Dinv38383' => 'din', 'Duzib133G0974' => 'dzi', 'Duzib138G1867' => 'dzi', 'Duzib211G0420' => 'dzi', 'Duzib212G0930' => 'dzi', 'ECA234G1645' => 'eca', 'ECA247G3467' => 'eca', 'ECA248G1703' => 'eca', 'EL10Ac3g06327' => 'bvu', 'EL10Ac7g17204' => 'bvu', 'Eucgr.A00855' => 'egr', 'Eucgr.A00858' => 'egr', 'Eucgr.H01520' => 'egr', 'Eucgr.H03604' => 'egr', 'Eucgr.L03465' => 'egr', 'Eucgr.L03466' => 'egr', 'FAN01G0988' => 'fan', 'FAN02G3892' => 'fan', 'FAN05G3381' => 'fan', 'FAN07G0967' => 'fan', 'FAN07G1493' => 'fan', 'FAN08G3125' => 'fan', 'FAN09G0402' => 'fan', 'FAN12G2594' => 'fan', 'FAN12G3879' => 'fan', 'FAN14G1546' => 'fan', 'FAN15G3626' => 'fan', 'FAN17G0588' => 'fan', 'FAN17G0609' => 'fan', 'FAN18G2817' => 'fan', 'FAN19G1305' => 'fan', 'FAN20G1787' => 'fan', 'FAN22G0073' => 'fan', 'FAN22G0352' => 'fan', 'FAN22G0368' => 'fan', 'FAN22G2273' => 'fan', 'FAN24G1998' => 'fan', 'FAN27G1317' => 'fan', 'FvH4_2g23980' => 'fve', 'FvH4_4g14380' => 'fve', 'FvH4_4g14390' => 'fve', 'FvH4_6g09250' => 'fve', 'Glyma.03G151100' => 'gma', 'Glyma.04G122550' => 'gma', 'Glyma.05G001600' => 'gma', 'Glyma.09G270766' => 'gma', 'Glyma.09G270832' => 'gma', 'Glyma.13G209800' => 'gma', 'Glyma.15G102800' => 'gma', 'Glyma.18G218900' => 'gma', 'Glyma.19G001500' => 'gma', 'Glyma.19G153600' => 'gma', 'Gohir.A02G028600' => 'ghi', 'Gohir.A08G045000' => 'ghi', 'Gohir.A11G120500' => 'ghi', 'Gohir.A12G006200' => 'ghi', 'Gohir.A12G006250' => 'ghi', 'Gohir.D02G036300' => 'ghi', 'Gohir.D08G054700' => 'ghi', 'Gohir.D11G125600' => 'ghi', 'Gohir.D12G005700' => 'ghi', 'Gorai.004G055200' => 'gra', 'Gorai.005G040400' => 'gra', 'Gorai.007G134500' => 'gra', 'Gorai.008G005500' => 'gra', 'GSVIVG01011094001' => 'vvi', 'GSVIVG01017879001' => 'vvi', 'GSVIVG01025988001' => 'vvi', 'GSVIVG01029847001' => 'vvi', 'HanXRQChr10g0282901' => 'han', 'HanXRQChr10g0310371' => 'han', 'HanXRQChr10g0315041' => 'han', 'HanXRQChr11g0327651' => 'han', 'HanXRQChr12g0359391' => 'han', 'Haze_00972' => 'cav', 'Haze_00973' => 'cav', 'Haze_00974' => 'cav', 'Haze_04747' => 'cav', 'Haze_04749' => 'cav', 'Haze_04750' => 'cav', 'Haze_21217' => 'cav', 'Hma1.2p1_1037F.1_g250680' => 'hma', 'Hma1.2p1_1644F.1_g295320' => 'hma', 'HPP92_011322' => 'vpl', 'HPP92_011323' => 'vpl', 'HPP92_011324' => 'vpl', 'HPP92_011325' => 'vpl', 'HPP92_011326' => 'vpl', 'Hund12205' => 'sun', 'Hund17957' => 'sun', 'Lalb_Chr06g0176771' => 'lal', 'Lalb_Chr18g0056021' => 'lal', 'Lalb_Chr18g0056031' => 'lal', 'Lalb_Chr18g0056041' => 'lal', 'Lalb_Chr20g0107751' => 'lal', 'Lalb_Chr20g0118371' => 'lal', 'Lj1g0010239' => 'lja', 'Lj1g0017101' => 'lja', 'Lj2A1178G40' => 'lonja', 'Lj2A54G84' => 'lonja', 'Lj2g0015248' => 'lja', 'Lj3A761T51' => 'lonja', 'Lj6g0018116' => 'lja', 'Lsat_1_v5_gn_4_136040' => 'lsa', 'Lsat_1_v5_gn_5_187461' => 'lsa', 'Lsat_1_v5_gn_5_77001' => 'lsa', 'Lsat_1_v5_gn_9_4461' => 'lsa', 'Manes.01G210100' => 'mes', 'Manes.03G185600' => 'mes', 'Manes.05G073300' => 'mes', 'Manes.09G120300' => 'mes', 'Manes.15G022100' => 'mes', 'Mapoly0096s0053' => 'mpo', 'MBI03_g14058_MAGBIO' => 'mbi', 'MBI03_g33876_MAGBIO' => 'mbi', 'MBI03_g36854_MAGBIO' => 'mbi', 'MBI17_g11997_MAGBIO' => 'mbi', 'MD03G1269000' => 'mdo', 'MD04G1179600' => 'mdo', 'MD11G1289800' => 'mdo', 'MD12G1194700' => 'mdo', 'MD13G1182100' => 'mdo', 'MD13G1182200' => 'mdo', 'MD16G1182600' => 'mdo', 'Medtr2g021400' => 'mtr', 'Medtr2g021470' => 'mtr', 'Medtr2g105810' => 'mtr', 'Medtr3g033580' => 'mtr', 'Medtr6g007970' => 'mtr', 'Medtr7g056330' => 'mtr', 'Medtr7g074290' => 'mtr', 'Medtr7g074380' => 'mtr', 'Medtr7g094550' => 'mtr', 'Medtr8g069995' => 'mtr', 'MELO3C014345.2' => 'cme', 'MELO3C021395.2' => 'cme', 'Migut.D00262' => 'egut', 'Migut.G00257' => 'egut', 'MSTRG.21575' => 'ama', 'MSTRG.3985' => 'ama', 'Nitab4.5_0000295g0140' => 'nta', 'Nitab4.5_0000732g0140' => 'nta', 'Nitab4.5_0003162g0020' => 'nta', 'Nitab4.5_0006180g0090' => 'nta', 'Nitab4.5_0006390g0010' => 'nta', 'Nitab4.5_0007392g0040' => 'nta', 'Nn1g02140' => 'nnu', 'Nn4g26168' => 'nnu', 'Nn5g26754' => 'nnu', 'Oeu001433.1' => 'oeu', 'Oeu010299.2' => 'oeu', 'Oeu011171.1' => 'oeu', 'Oeu037675.1' => 'oeu', 'Oeu038359.1' => 'oeu', 'Oeu063834.1' => 'oeu', 'Oeu063835.1' => 'oeu', 'Os05g0312000' => 'osa', 'Os07g0211101' => 'osa', 'Os07g0211200' => 'osa', 'Os07g0681500' => 'osa', 'Peaxi162Scf00095g01015' => 'pax', 'Peaxi162Scf00104g00329' => 'pax', 'Peaxi162Scf00161g00137' => 'pax', 'PGR004G1665' => 'pgr', 'PGR031G2937' => 'pgr', 'PGR119G2145' => 'pgr', 'PGSC0003DMG400004351' => 'stu', 'PGSC0003DMG400014625' => 'stu', 'PGSC0003DMG401000943' => 'stu', 'Phvul.001G148600' => 'pvu', 'Phvul.004G001700' => 'pvu', 'Phvul.006G154900' => 'pvu', 'Phvul.008G078200' => 'pvu', 'Phvul.011G136500' => 'pvu', 'Potri.002G215600' => 'ptr', 'Potri.008G201600' => 'ptr', 'Potri.014G138400' => 'ptr', 'Potri.016G142500' => 'ptr', 'Pp3c16_10580' => 'ppa', 'Pp3c5_25280' => 'ppa', 'Prupe.1G150000' => 'ppe', 'Prupe.1G150100' => 'ppe', 'Prupe.6G299600' => 'ppe', 'Prupe.8G245000' => 'ppe', 'Psat0s4927g0040' => 'psa', 'Psat1g052080' => 'psa', 'Psat1g183800' => 'psa', 'Psat3g113840' => 'psa', 'Psat3g126120' => 'psa', 'Psat3g126160' => 'psa', 'Psat3g158760' => 'psa', 'Psat3g158840' => 'psa', 'PSO170G2858' => 'pso', 'PSO339G0606' => 'pso', 'PSO384G4709' => 'pso', 'PSO407G0334' => 'pso', 'QL04p040276' => 'qlo', 'QL06p005458' => 'qlo', 'QL06p005472' => 'qlo', 'QL07p030546' => 'qlo', 'QL07p031519' => 'qlo', 'QL09p050949' => 'qlo', 'QL09p050966' => 'qlo', 'QL09p051067' => 'qlo', 'QL12p022706' => 'qlo', 'RcHm_v2.0_Chr2g0119601' => 'rch', 'RcHm_v2.0_Chr3g0459591' => 'rch', 'RcHm_v2.0_Chr4g0418521' => 'rch', 'RcHm_v2.0_Chr4g0418531' => 'rch', 'RcHm_v2.0_Chr4g0418541' => 'rch', 'RcHm_v2.0_Chr6g0291641' => 'rch', 'Rhsim01G0086300' => 'rsi', 'Rhsim01G0276300' => 'rsi', 'Rhsim01G0276500' => 'rsi', 'Rhsim04G0207700' => 'rsi', 'Rhsim05G0234500' => 'rsi', 'Rhsim13G0022400' => 'rsi', 'Sabra02G0167900' => 'sbr', 'Sabra04G0158500' => 'sbr', 'Sabra08G0159800' => 'sbr', 'Sabra10G0011500' => 'sbr', 'Sabra14G0104400' => 'sbr', 'SalBow2G2440' => 'sbo', 'SalBow4G2265' => 'sbo', 'Sc02g0000060' => 'sci', 'Sc05g0005020' => 'sci', 'Sc13g0003890' => 'sci', 'Sed0014865' => 'sed', 'Sed0017224' => 'sed', 'Sed0026391' => 'sed', 'SEGI_00063' => 'sgi', 'SEGI_10967' => 'sgi', 'SEGI_17510' => 'sgi', 'SEGI_24396' => 'sgi', 'SEGI_39719' => 'sgi', 'SEGI_41392' => 'sgi', 'SGA_v2.0_scaffold11G05794' => 'sas', 'SGA_v2.0_scaffold142G35607' => 'sas', 'SGA_v2.0_scaffold1G00447' => 'sas', 'SHI15388' => 'shi', 'SHI15394' => 'shi', 'SHI15396' => 'shi', 'SHI15399' => 'shi', 'SMO343G0151' => 'smo', 'SMO367G1118' => 'smo', 'Solyc01g080200.3' => 'sly', 'Solyc06g008960.3' => 'sly', 'Solyc09g064780.3' => 'sly', 'Sopen01g031980' => 'spe', 'Sopen06g003710' => 'spe', 'Sopen09g026460' => 'spe', 'Sp3g21240' => 'spa', 'Sp4g30030' => 'spa', 'TAR365G0022' => 'tar', 'TAR365G1023' => 'tar', 'TAR365G1253' => 'tar', 'TAR623G0078' => 'tar', 'TAR623G1721' => 'tar', 'TAR633G0959' => 'tar', 'THA.LOC104802225' => 'tha', 'THA.LOC104804769' => 'tha', 'THA.LOC104808660' => 'tha', 'THA.LOC104812792' => 'tha', 'Thecc.01G284000' => 'tca', 'Thecc.04G220600' => 'tca', 'Thecc.05G268900' => 'tca', 'Thecc.08G171100' => 'tca', 'Thhalv10001284m.g' => 'esa', 'Thhalv10019912m.g' => 'esa', 'TPR.G14189' => 'tpr', 'TPR.G18110' => 'tpr', 'TPR.G18130' => 'tpr', 'TPR.G18131' => 'tpr', 'TPR.G18140' => 'tpr', 'TPR.G24282' => 'tpr', 'TPR.G25221' => 'tpr', 'TPR.G29267' => 'tpr', 'TPR.G35315' => 'tpr', 'TPR.G36173' => 'tpr', 'TWI09G0794' => 'twi', 'TWI59G1348' => 'twi', 'TWI74G0430' => 'twi', 'unitig_26.g8940' => 'ugi', 'unitig_749.g13744' => 'ugi', 'unitig_749.g13745' => 'ugi', 'vmacro08269' => 'vma', 'vmacro14937' => 'vma', 'vmacro20401' => 'vma', 'VMungo0464G1349' => 'vmu', 'VMungo0540G0289' => 'vmu', 'VMungo1215G1590' => 'vmu', 'VMungo1309G0221' => 'vmu', 'VMungo1309G2815' => 'vmu', 'VMungo1383G0239' => 'vmu', 'VMungo1383G2910' => 'vmu', 'Zm00001eb095270' => 'zma', 'Zm00001eb095280' => 'zma', 'Zm00001eb111630' => 'zma', 'Zm00001eb237080' => 'zma', 'Zm00001eb273740' => 'zma', 'Zm00001eb285040' => 'zma', 'Zm00001eb330790' => 'zma', 'Zm00001eb337380' => 'zma' ) $gf_id = 'HOM05D001484' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001484' ) $data_identifier = 'HOM05D001484' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 2, 'aly' => (int) 2, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 22, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 7, 'hma' => (int) 2, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 7, 'mtr' => (int) 10, 'cme' => (int) 2, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 4, 'ppa' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 4, 'qlo' => (int) 9, 'rch' => (int) 6, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 10, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 7, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb337380' $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' => 'HOM05D001484', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p31500' => 'bna', 'A05p00020' => 'bna', 'A07p08820' => 'bna', 'Aa31LG4G3300' => 'aar', 'Aa31LG8G10030' => 'aar', 'Actinidia00731' => 'ach', 'Actinidia11473' => 'ach', 'Actinidia23469' => 'ach', 'Actinidia24318' => 'ach', 'Actinidia40196' => 'ach', 'Actinidia40197' => 'ach', 'Actinidia40198' => 'ach', 'Ah.08g212990' => 'amhyb', 'Ah.15g091720' => 'amhyb', 'AL3G38260' => 'aly', 'AL4G47710' => 'aly', 'Aqoxy2G00671' => 'aox', 'Aqoxy2G03236' => 'aox', 'arahy.Tifrunner.gnm1.ann1.05IDCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KR684' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATY3SJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK6QJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6APGL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IDT7Z9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM073U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ0R87' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LE7RV4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT4QRX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V5ENPK' => 'arhy', 'AT2G48110' => 'ath', 'AT3G23590' => 'ath', 'ATR0626G186' => 'atr', 'ATR1127G141' => 'atr', 'Atru.chr4.2583' => 'acertr', 'Atru.chr5.1358' => 'acertr', 'Atru.chr5.1359' => 'acertr', 'Atru.chr8.46' => 'acertr', 'AUR62002640' => 'cqu', 'AUR62030055' => 'cqu', 'AUR62033713' => 'cqu', 'AUR62033714' => 'cqu', 'AUR62036795' => 'cqu', 'AUR62039891' => 'cqu', 'BcaB02g08737' => 'bca', 'BcaB04g20441' => 'bca', 'BcaB06g26509' => 'bca', 'BcaB06g26510' => 'bca', 'BcaB06g26511' => 'bca', 'BcaB06g26512' => 'bca', 'BcaB06g26513' => 'bca', 'BcaC02g12564' => 'bca', 'BcaC02g12565' => 'bca', 'BcaC02g12794' => 'bca', 'BcaC02g12795' => 'bca', 'BcaC02g12796' => 'bca', 'BcaC06g35541' => 'bca', 'BNapus_Darmor_BZH_scaffold_188p00080' => 'bna', 'BNapus_Darmor_BZH_scaffold_188p00090' => 'bna', 'BolC1t03972H' => 'bol', 'BolC1t03973H' => 'bol', 'BolC4t21680H' => 'bol', 'BolC7t41863H' => 'bol', 'BolSC55t61227H' => 'bol', 'BolSC55t61228H' => 'bol', 'BraA01t03278Z' => 'bra', 'BraA05t18998Z' => 'bra', 'BraA07t28673Z' => 'bra', 'C01p40150' => 'bna', 'C05p12370' => 'bna', 'C07p13680' => 'bna', 'CAN.G1006.16' => 'can', 'CAN.G1006.17' => 'can', 'CAN.G1170.2' => 'can', 'CAN.G962.7' => 'can', 'CANSAT25G2179' => 'cansat', 'CANSAT78G1573' => 'cansat', 'CARHR099510' => 'chi', 'CARHR143510' => 'chi', 'Carub.0003s2380' => 'cru', 'Carub.0004s3082' => 'cru', 'Ca_00614_v3' => 'car', 'Ca_07801_v3' => 'car', 'Ca_08567_v3' => 'car', 'Ca_09571_v3' => 'car', 'CBR_g19290' => 'cbr', 'Cc01_g19770' => 'ccan', 'Cc03_g03030' => 'ccan', 'CDE07G0968' => 'cde', 'CDE09G1441' => 'cde', 'Cfa006103' => 'cfa', 'Cfa015573' => 'cfa', 'Cfa016988' => 'cfa', 'Ciclev10006738m.g' => 'ccl', 'Ciclev10010920m.g' => 'ccl', 'Ciclev10018517m.g' => 'ccl', 'CiPaw.01G159200' => 'cil', 'CiPaw.02G091000' => 'cil', 'CiPaw.02G091100' => 'cil', 'CiPaw.08G103100' => 'cil', 'CiPaw.09G224900' => 'cil', 'ClCG06G005740' => 'cla', 'ClCG07G000090' => 'cla', 'ClCG07G000100' => 'cla', 'COL.COLO4_09143' => 'col', 'COL.COLO4_25124' => 'col', 'Cpa.g.sc16.34' => 'cpa', 'Cpa.g.sc3504.1' => 'cpa', 'Cpa.g.sc60.37' => 'cpa', 'CsaV3_6G018520' => 'csa', 'CsaV3_6G036860' => 'csa', 'CSS0001072' => 'camsi', 'CSS0020208' => 'camsi', 'CSS0021253' => 'camsi', 'CSS0022190' => 'camsi', 'CSS0036150' => 'camsi', 'CSS0040442' => 'camsi', 'CSS0042300' => 'camsi', 'CSS0045298' => 'camsi', 'DCAR_012449' => 'dca', 'DCAR_018405' => 'dca', 'DCAR_024573' => 'dca', 'DCAR_030591' => 'dca', 'Dinv16926' => 'din', 'Dinv32963' => 'din', 'Dinv38382' => 'din', 'Dinv38383' => 'din', 'Duzib133G0974' => 'dzi', 'Duzib138G1867' => 'dzi', 'Duzib211G0420' => 'dzi', 'Duzib212G0930' => 'dzi', 'ECA234G1645' => 'eca', 'ECA247G3467' => 'eca', 'ECA248G1703' => 'eca', 'EL10Ac3g06327' => 'bvu', 'EL10Ac7g17204' => 'bvu', 'Eucgr.A00855' => 'egr', 'Eucgr.A00858' => 'egr', 'Eucgr.H01520' => 'egr', 'Eucgr.H03604' => 'egr', 'Eucgr.L03465' => 'egr', 'Eucgr.L03466' => 'egr', 'FAN01G0988' => 'fan', 'FAN02G3892' => 'fan', 'FAN05G3381' => 'fan', 'FAN07G0967' => 'fan', 'FAN07G1493' => 'fan', 'FAN08G3125' => 'fan', 'FAN09G0402' => 'fan', 'FAN12G2594' => 'fan', 'FAN12G3879' => 'fan', 'FAN14G1546' => 'fan', 'FAN15G3626' => 'fan', 'FAN17G0588' => 'fan', 'FAN17G0609' => 'fan', 'FAN18G2817' => 'fan', 'FAN19G1305' => 'fan', 'FAN20G1787' => 'fan', 'FAN22G0073' => 'fan', 'FAN22G0352' => 'fan', 'FAN22G0368' => 'fan', 'FAN22G2273' => 'fan', 'FAN24G1998' => 'fan', 'FAN27G1317' => 'fan', 'FvH4_2g23980' => 'fve', 'FvH4_4g14380' => 'fve', 'FvH4_4g14390' => 'fve', 'FvH4_6g09250' => 'fve', 'Glyma.03G151100' => 'gma', 'Glyma.04G122550' => 'gma', 'Glyma.05G001600' => 'gma', 'Glyma.09G270766' => 'gma', 'Glyma.09G270832' => 'gma', 'Glyma.13G209800' => 'gma', 'Glyma.15G102800' => 'gma', 'Glyma.18G218900' => 'gma', 'Glyma.19G001500' => 'gma', 'Glyma.19G153600' => 'gma', 'Gohir.A02G028600' => 'ghi', 'Gohir.A08G045000' => 'ghi', 'Gohir.A11G120500' => 'ghi', 'Gohir.A12G006200' => 'ghi', 'Gohir.A12G006250' => 'ghi', 'Gohir.D02G036300' => 'ghi', 'Gohir.D08G054700' => 'ghi', 'Gohir.D11G125600' => 'ghi', 'Gohir.D12G005700' => 'ghi', 'Gorai.004G055200' => 'gra', 'Gorai.005G040400' => 'gra', 'Gorai.007G134500' => 'gra', 'Gorai.008G005500' => 'gra', 'GSVIVG01011094001' => 'vvi', 'GSVIVG01017879001' => 'vvi', 'GSVIVG01025988001' => 'vvi', 'GSVIVG01029847001' => 'vvi', 'HanXRQChr10g0282901' => 'han', 'HanXRQChr10g0310371' => 'han', 'HanXRQChr10g0315041' => 'han', 'HanXRQChr11g0327651' => 'han', 'HanXRQChr12g0359391' => 'han', 'Haze_00972' => 'cav', 'Haze_00973' => 'cav', 'Haze_00974' => 'cav', 'Haze_04747' => 'cav', 'Haze_04749' => 'cav', 'Haze_04750' => 'cav', 'Haze_21217' => 'cav', 'Hma1.2p1_1037F.1_g250680' => 'hma', 'Hma1.2p1_1644F.1_g295320' => 'hma', 'HPP92_011322' => 'vpl', 'HPP92_011323' => 'vpl', 'HPP92_011324' => 'vpl', 'HPP92_011325' => 'vpl', 'HPP92_011326' => 'vpl', 'Hund12205' => 'sun', 'Hund17957' => 'sun', 'Lalb_Chr06g0176771' => 'lal', 'Lalb_Chr18g0056021' => 'lal', 'Lalb_Chr18g0056031' => 'lal', 'Lalb_Chr18g0056041' => 'lal', 'Lalb_Chr20g0107751' => 'lal', 'Lalb_Chr20g0118371' => 'lal', 'Lj1g0010239' => 'lja', 'Lj1g0017101' => 'lja', 'Lj2A1178G40' => 'lonja', 'Lj2A54G84' => 'lonja', 'Lj2g0015248' => 'lja', 'Lj3A761T51' => 'lonja', 'Lj6g0018116' => 'lja', 'Lsat_1_v5_gn_4_136040' => 'lsa', 'Lsat_1_v5_gn_5_187461' => 'lsa', 'Lsat_1_v5_gn_5_77001' => 'lsa', 'Lsat_1_v5_gn_9_4461' => 'lsa', 'Manes.01G210100' => 'mes', 'Manes.03G185600' => 'mes', 'Manes.05G073300' => 'mes', 'Manes.09G120300' => 'mes', 'Manes.15G022100' => 'mes', 'Mapoly0096s0053' => 'mpo', 'MBI03_g14058_MAGBIO' => 'mbi', 'MBI03_g33876_MAGBIO' => 'mbi', 'MBI03_g36854_MAGBIO' => 'mbi', 'MBI17_g11997_MAGBIO' => 'mbi', 'MD03G1269000' => 'mdo', 'MD04G1179600' => 'mdo', 'MD11G1289800' => 'mdo', 'MD12G1194700' => 'mdo', 'MD13G1182100' => 'mdo', 'MD13G1182200' => 'mdo', 'MD16G1182600' => 'mdo', 'Medtr2g021400' => 'mtr', 'Medtr2g021470' => 'mtr', 'Medtr2g105810' => 'mtr', 'Medtr3g033580' => 'mtr', 'Medtr6g007970' => 'mtr', 'Medtr7g056330' => 'mtr', 'Medtr7g074290' => 'mtr', 'Medtr7g074380' => 'mtr', 'Medtr7g094550' => 'mtr', 'Medtr8g069995' => 'mtr', 'MELO3C014345.2' => 'cme', 'MELO3C021395.2' => 'cme', 'Migut.D00262' => 'egut', 'Migut.G00257' => 'egut', 'MSTRG.21575' => 'ama', 'MSTRG.3985' => 'ama', 'Nitab4.5_0000295g0140' => 'nta', 'Nitab4.5_0000732g0140' => 'nta', 'Nitab4.5_0003162g0020' => 'nta', 'Nitab4.5_0006180g0090' => 'nta', 'Nitab4.5_0006390g0010' => 'nta', 'Nitab4.5_0007392g0040' => 'nta', 'Nn1g02140' => 'nnu', 'Nn4g26168' => 'nnu', 'Nn5g26754' => 'nnu', 'Oeu001433.1' => 'oeu', 'Oeu010299.2' => 'oeu', 'Oeu011171.1' => 'oeu', 'Oeu037675.1' => 'oeu', 'Oeu038359.1' => 'oeu', 'Oeu063834.1' => 'oeu', 'Oeu063835.1' => 'oeu', 'Os05g0312000' => 'osa', 'Os07g0211101' => 'osa', 'Os07g0211200' => 'osa', 'Os07g0681500' => 'osa', 'Peaxi162Scf00095g01015' => 'pax', 'Peaxi162Scf00104g00329' => 'pax', 'Peaxi162Scf00161g00137' => 'pax', 'PGR004G1665' => 'pgr', 'PGR031G2937' => 'pgr', 'PGR119G2145' => 'pgr', 'PGSC0003DMG400004351' => 'stu', 'PGSC0003DMG400014625' => 'stu', 'PGSC0003DMG401000943' => 'stu', 'Phvul.001G148600' => 'pvu', 'Phvul.004G001700' => 'pvu', 'Phvul.006G154900' => 'pvu', 'Phvul.008G078200' => 'pvu', 'Phvul.011G136500' => 'pvu', 'Potri.002G215600' => 'ptr', 'Potri.008G201600' => 'ptr', 'Potri.014G138400' => 'ptr', 'Potri.016G142500' => 'ptr', 'Pp3c16_10580' => 'ppa', 'Pp3c5_25280' => 'ppa', 'Prupe.1G150000' => 'ppe', 'Prupe.1G150100' => 'ppe', 'Prupe.6G299600' => 'ppe', 'Prupe.8G245000' => 'ppe', 'Psat0s4927g0040' => 'psa', 'Psat1g052080' => 'psa', 'Psat1g183800' => 'psa', 'Psat3g113840' => 'psa', 'Psat3g126120' => 'psa', 'Psat3g126160' => 'psa', 'Psat3g158760' => 'psa', 'Psat3g158840' => 'psa', 'PSO170G2858' => 'pso', 'PSO339G0606' => 'pso', 'PSO384G4709' => 'pso', 'PSO407G0334' => 'pso', 'QL04p040276' => 'qlo', 'QL06p005458' => 'qlo', 'QL06p005472' => 'qlo', 'QL07p030546' => 'qlo', 'QL07p031519' => 'qlo', 'QL09p050949' => 'qlo', 'QL09p050966' => 'qlo', 'QL09p051067' => 'qlo', 'QL12p022706' => 'qlo', 'RcHm_v2.0_Chr2g0119601' => 'rch', 'RcHm_v2.0_Chr3g0459591' => 'rch', 'RcHm_v2.0_Chr4g0418521' => 'rch', 'RcHm_v2.0_Chr4g0418531' => 'rch', 'RcHm_v2.0_Chr4g0418541' => 'rch', 'RcHm_v2.0_Chr6g0291641' => 'rch', 'Rhsim01G0086300' => 'rsi', 'Rhsim01G0276300' => 'rsi', 'Rhsim01G0276500' => 'rsi', 'Rhsim04G0207700' => 'rsi', 'Rhsim05G0234500' => 'rsi', 'Rhsim13G0022400' => 'rsi', 'Sabra02G0167900' => 'sbr', 'Sabra04G0158500' => 'sbr', 'Sabra08G0159800' => 'sbr', 'Sabra10G0011500' => 'sbr', 'Sabra14G0104400' => 'sbr', 'SalBow2G2440' => 'sbo', 'SalBow4G2265' => 'sbo', 'Sc02g0000060' => 'sci', 'Sc05g0005020' => 'sci', 'Sc13g0003890' => 'sci', 'Sed0014865' => 'sed', 'Sed0017224' => 'sed', 'Sed0026391' => 'sed', 'SEGI_00063' => 'sgi', 'SEGI_10967' => 'sgi', 'SEGI_17510' => 'sgi', 'SEGI_24396' => 'sgi', 'SEGI_39719' => 'sgi', 'SEGI_41392' => 'sgi', 'SGA_v2.0_scaffold11G05794' => 'sas', 'SGA_v2.0_scaffold142G35607' => 'sas', 'SGA_v2.0_scaffold1G00447' => 'sas', 'SHI15388' => 'shi', 'SHI15394' => 'shi', 'SHI15396' => 'shi', 'SHI15399' => 'shi', 'SMO343G0151' => 'smo', 'SMO367G1118' => 'smo', 'Solyc01g080200.3' => 'sly', 'Solyc06g008960.3' => 'sly', 'Solyc09g064780.3' => 'sly', 'Sopen01g031980' => 'spe', 'Sopen06g003710' => 'spe', 'Sopen09g026460' => 'spe', 'Sp3g21240' => 'spa', 'Sp4g30030' => 'spa', 'TAR365G0022' => 'tar', 'TAR365G1023' => 'tar', 'TAR365G1253' => 'tar', 'TAR623G0078' => 'tar', 'TAR623G1721' => 'tar', 'TAR633G0959' => 'tar', 'THA.LOC104802225' => 'tha', 'THA.LOC104804769' => 'tha', 'THA.LOC104808660' => 'tha', 'THA.LOC104812792' => 'tha', 'Thecc.01G284000' => 'tca', 'Thecc.04G220600' => 'tca', 'Thecc.05G268900' => 'tca', 'Thecc.08G171100' => 'tca', 'Thhalv10001284m.g' => 'esa', 'Thhalv10019912m.g' => 'esa', 'TPR.G14189' => 'tpr', 'TPR.G18110' => 'tpr', 'TPR.G18130' => 'tpr', 'TPR.G18131' => 'tpr', 'TPR.G18140' => 'tpr', 'TPR.G24282' => 'tpr', 'TPR.G25221' => 'tpr', 'TPR.G29267' => 'tpr', 'TPR.G35315' => 'tpr', 'TPR.G36173' => 'tpr', 'TWI09G0794' => 'twi', 'TWI59G1348' => 'twi', 'TWI74G0430' => 'twi', 'unitig_26.g8940' => 'ugi', 'unitig_749.g13744' => 'ugi', 'unitig_749.g13745' => 'ugi', 'vmacro08269' => 'vma', 'vmacro14937' => 'vma', 'vmacro20401' => 'vma', 'VMungo0464G1349' => 'vmu', 'VMungo0540G0289' => 'vmu', 'VMungo1215G1590' => 'vmu', 'VMungo1309G0221' => 'vmu', 'VMungo1309G2815' => 'vmu', 'VMungo1383G0239' => 'vmu', 'VMungo1383G2910' => 'vmu', 'Zm00001eb095270' => 'zma', 'Zm00001eb095280' => 'zma', 'Zm00001eb111630' => 'zma', 'Zm00001eb237080' => 'zma', 'Zm00001eb273740' => 'zma', 'Zm00001eb285040' => 'zma', 'Zm00001eb330790' => 'zma', 'Zm00001eb337380' => 'zma' ), 'gf_id' => 'HOM05D001484', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001484' ), 'data_identifier' => 'HOM05D001484', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001484', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p31500' => 'bna', 'A05p00020' => 'bna', 'A07p08820' => 'bna', 'Aa31LG4G3300' => 'aar', 'Aa31LG8G10030' => 'aar', 'Actinidia00731' => 'ach', 'Actinidia11473' => 'ach', 'Actinidia23469' => 'ach', 'Actinidia24318' => 'ach', 'Actinidia40196' => 'ach', 'Actinidia40197' => 'ach', 'Actinidia40198' => 'ach', 'Ah.08g212990' => 'amhyb', 'Ah.15g091720' => 'amhyb', 'AL3G38260' => 'aly', 'AL4G47710' => 'aly', 'Aqoxy2G00671' => 'aox', 'Aqoxy2G03236' => 'aox', 'arahy.Tifrunner.gnm1.ann1.05IDCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KR684' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATY3SJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK6QJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6APGL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IDT7Z9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM073U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ0R87' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LE7RV4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT4QRX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V5ENPK' => 'arhy', 'AT2G48110' => 'ath', 'AT3G23590' => 'ath', 'ATR0626G186' => 'atr', 'ATR1127G141' => 'atr', 'Atru.chr4.2583' => 'acertr', 'Atru.chr5.1358' => 'acertr', 'Atru.chr5.1359' => 'acertr', 'Atru.chr8.46' => 'acertr', 'AUR62002640' => 'cqu', 'AUR62030055' => 'cqu', 'AUR62033713' => 'cqu', 'AUR62033714' => 'cqu', 'AUR62036795' => 'cqu', 'AUR62039891' => 'cqu', 'BcaB02g08737' => 'bca', 'BcaB04g20441' => 'bca', 'BcaB06g26509' => 'bca', 'BcaB06g26510' => 'bca', 'BcaB06g26511' => 'bca', 'BcaB06g26512' => 'bca', 'BcaB06g26513' => 'bca', 'BcaC02g12564' => 'bca', 'BcaC02g12565' => 'bca', 'BcaC02g12794' => 'bca', 'BcaC02g12795' => 'bca', 'BcaC02g12796' => 'bca', 'BcaC06g35541' => 'bca', 'BNapus_Darmor_BZH_scaffold_188p00080' => 'bna', 'BNapus_Darmor_BZH_scaffold_188p00090' => 'bna', 'BolC1t03972H' => 'bol', 'BolC1t03973H' => 'bol', 'BolC4t21680H' => 'bol', 'BolC7t41863H' => 'bol', 'BolSC55t61227H' => 'bol', 'BolSC55t61228H' => 'bol', 'BraA01t03278Z' => 'bra', 'BraA05t18998Z' => 'bra', 'BraA07t28673Z' => 'bra', 'C01p40150' => 'bna', 'C05p12370' => 'bna', 'C07p13680' => 'bna', 'CAN.G1006.16' => 'can', 'CAN.G1006.17' => 'can', 'CAN.G1170.2' => 'can', 'CAN.G962.7' => 'can', 'CANSAT25G2179' => 'cansat', 'CANSAT78G1573' => 'cansat', 'CARHR099510' => 'chi', 'CARHR143510' => 'chi', 'Carub.0003s2380' => 'cru', 'Carub.0004s3082' => 'cru', 'Ca_00614_v3' => 'car', 'Ca_07801_v3' => 'car', 'Ca_08567_v3' => 'car', 'Ca_09571_v3' => 'car', 'CBR_g19290' => 'cbr', 'Cc01_g19770' => 'ccan', 'Cc03_g03030' => 'ccan', 'CDE07G0968' => 'cde', 'CDE09G1441' => 'cde', 'Cfa006103' => 'cfa', 'Cfa015573' => 'cfa', 'Cfa016988' => 'cfa', 'Ciclev10006738m.g' => 'ccl', 'Ciclev10010920m.g' => 'ccl', 'Ciclev10018517m.g' => 'ccl', 'CiPaw.01G159200' => 'cil', 'CiPaw.02G091000' => 'cil', 'CiPaw.02G091100' => 'cil', 'CiPaw.08G103100' => 'cil', 'CiPaw.09G224900' => 'cil', 'ClCG06G005740' => 'cla', 'ClCG07G000090' => 'cla', 'ClCG07G000100' => 'cla', 'COL.COLO4_09143' => 'col', 'COL.COLO4_25124' => 'col', 'Cpa.g.sc16.34' => 'cpa', 'Cpa.g.sc3504.1' => 'cpa', 'Cpa.g.sc60.37' => 'cpa', 'CsaV3_6G018520' => 'csa', 'CsaV3_6G036860' => 'csa', 'CSS0001072' => 'camsi', 'CSS0020208' => 'camsi', 'CSS0021253' => 'camsi', 'CSS0022190' => 'camsi', 'CSS0036150' => 'camsi', 'CSS0040442' => 'camsi', 'CSS0042300' => 'camsi', 'CSS0045298' => 'camsi', 'DCAR_012449' => 'dca', 'DCAR_018405' => 'dca', 'DCAR_024573' => 'dca', 'DCAR_030591' => 'dca', 'Dinv16926' => 'din', 'Dinv32963' => 'din', 'Dinv38382' => 'din', 'Dinv38383' => 'din', 'Duzib133G0974' => 'dzi', 'Duzib138G1867' => 'dzi', 'Duzib211G0420' => 'dzi', 'Duzib212G0930' => 'dzi', 'ECA234G1645' => 'eca', 'ECA247G3467' => 'eca', 'ECA248G1703' => 'eca', 'EL10Ac3g06327' => 'bvu', 'EL10Ac7g17204' => 'bvu', 'Eucgr.A00855' => 'egr', 'Eucgr.A00858' => 'egr', 'Eucgr.H01520' => 'egr', 'Eucgr.H03604' => 'egr', 'Eucgr.L03465' => 'egr', 'Eucgr.L03466' => 'egr', 'FAN01G0988' => 'fan', 'FAN02G3892' => 'fan', 'FAN05G3381' => 'fan', 'FAN07G0967' => 'fan', 'FAN07G1493' => 'fan', 'FAN08G3125' => 'fan', 'FAN09G0402' => 'fan', 'FAN12G2594' => 'fan', 'FAN12G3879' => 'fan', 'FAN14G1546' => 'fan', 'FAN15G3626' => 'fan', 'FAN17G0588' => 'fan', 'FAN17G0609' => 'fan', 'FAN18G2817' => 'fan', 'FAN19G1305' => 'fan', 'FAN20G1787' => 'fan', 'FAN22G0073' => 'fan', 'FAN22G0352' => 'fan', 'FAN22G0368' => 'fan', 'FAN22G2273' => 'fan', 'FAN24G1998' => 'fan', 'FAN27G1317' => 'fan', 'FvH4_2g23980' => 'fve', 'FvH4_4g14380' => 'fve', 'FvH4_4g14390' => 'fve', 'FvH4_6g09250' => 'fve', 'Glyma.03G151100' => 'gma', 'Glyma.04G122550' => 'gma', 'Glyma.05G001600' => 'gma', 'Glyma.09G270766' => 'gma', 'Glyma.09G270832' => 'gma', 'Glyma.13G209800' => 'gma', 'Glyma.15G102800' => 'gma', 'Glyma.18G218900' => 'gma', 'Glyma.19G001500' => 'gma', 'Glyma.19G153600' => 'gma', 'Gohir.A02G028600' => 'ghi', 'Gohir.A08G045000' => 'ghi', 'Gohir.A11G120500' => 'ghi', 'Gohir.A12G006200' => 'ghi', 'Gohir.A12G006250' => 'ghi', 'Gohir.D02G036300' => 'ghi', 'Gohir.D08G054700' => 'ghi', 'Gohir.D11G125600' => 'ghi', 'Gohir.D12G005700' => 'ghi', 'Gorai.004G055200' => 'gra', 'Gorai.005G040400' => 'gra', 'Gorai.007G134500' => 'gra', 'Gorai.008G005500' => 'gra', 'GSVIVG01011094001' => 'vvi', 'GSVIVG01017879001' => 'vvi', 'GSVIVG01025988001' => 'vvi', 'GSVIVG01029847001' => 'vvi', 'HanXRQChr10g0282901' => 'han', 'HanXRQChr10g0310371' => 'han', 'HanXRQChr10g0315041' => 'han', 'HanXRQChr11g0327651' => 'han', 'HanXRQChr12g0359391' => 'han', 'Haze_00972' => 'cav', 'Haze_00973' => 'cav', 'Haze_00974' => 'cav', 'Haze_04747' => 'cav', 'Haze_04749' => 'cav', 'Haze_04750' => 'cav', 'Haze_21217' => 'cav', 'Hma1.2p1_1037F.1_g250680' => 'hma', 'Hma1.2p1_1644F.1_g295320' => 'hma', 'HPP92_011322' => 'vpl', 'HPP92_011323' => 'vpl', 'HPP92_011324' => 'vpl', 'HPP92_011325' => 'vpl', 'HPP92_011326' => 'vpl', 'Hund12205' => 'sun', 'Hund17957' => 'sun', 'Lalb_Chr06g0176771' => 'lal', 'Lalb_Chr18g0056021' => 'lal', 'Lalb_Chr18g0056031' => 'lal', 'Lalb_Chr18g0056041' => 'lal', 'Lalb_Chr20g0107751' => 'lal', 'Lalb_Chr20g0118371' => 'lal', 'Lj1g0010239' => 'lja', 'Lj1g0017101' => 'lja', 'Lj2A1178G40' => 'lonja', 'Lj2A54G84' => 'lonja', 'Lj2g0015248' => 'lja', 'Lj3A761T51' => 'lonja', 'Lj6g0018116' => 'lja', 'Lsat_1_v5_gn_4_136040' => 'lsa', 'Lsat_1_v5_gn_5_187461' => 'lsa', 'Lsat_1_v5_gn_5_77001' => 'lsa', 'Lsat_1_v5_gn_9_4461' => 'lsa', 'Manes.01G210100' => 'mes', 'Manes.03G185600' => 'mes', 'Manes.05G073300' => 'mes', 'Manes.09G120300' => 'mes', 'Manes.15G022100' => 'mes', 'Mapoly0096s0053' => 'mpo', 'MBI03_g14058_MAGBIO' => 'mbi', 'MBI03_g33876_MAGBIO' => 'mbi', 'MBI03_g36854_MAGBIO' => 'mbi', 'MBI17_g11997_MAGBIO' => 'mbi', 'MD03G1269000' => 'mdo', 'MD04G1179600' => 'mdo', 'MD11G1289800' => 'mdo', 'MD12G1194700' => 'mdo', 'MD13G1182100' => 'mdo', 'MD13G1182200' => 'mdo', 'MD16G1182600' => 'mdo', 'Medtr2g021400' => 'mtr', 'Medtr2g021470' => 'mtr', 'Medtr2g105810' => 'mtr', 'Medtr3g033580' => 'mtr', 'Medtr6g007970' => 'mtr', 'Medtr7g056330' => 'mtr', 'Medtr7g074290' => 'mtr', 'Medtr7g074380' => 'mtr', 'Medtr7g094550' => 'mtr', 'Medtr8g069995' => 'mtr', 'MELO3C014345.2' => 'cme', 'MELO3C021395.2' => 'cme', 'Migut.D00262' => 'egut', 'Migut.G00257' => 'egut', 'MSTRG.21575' => 'ama', 'MSTRG.3985' => 'ama', 'Nitab4.5_0000295g0140' => 'nta', 'Nitab4.5_0000732g0140' => 'nta', 'Nitab4.5_0003162g0020' => 'nta', 'Nitab4.5_0006180g0090' => 'nta', 'Nitab4.5_0006390g0010' => 'nta', 'Nitab4.5_0007392g0040' => 'nta', 'Nn1g02140' => 'nnu', 'Nn4g26168' => 'nnu', 'Nn5g26754' => 'nnu', 'Oeu001433.1' => 'oeu', 'Oeu010299.2' => 'oeu', 'Oeu011171.1' => 'oeu', 'Oeu037675.1' => 'oeu', 'Oeu038359.1' => 'oeu', 'Oeu063834.1' => 'oeu', 'Oeu063835.1' => 'oeu', 'Os05g0312000' => 'osa', 'Os07g0211101' => 'osa', 'Os07g0211200' => 'osa', 'Os07g0681500' => 'osa', 'Peaxi162Scf00095g01015' => 'pax', 'Peaxi162Scf00104g00329' => 'pax', 'Peaxi162Scf00161g00137' => 'pax', 'PGR004G1665' => 'pgr', 'PGR031G2937' => 'pgr', 'PGR119G2145' => 'pgr', 'PGSC0003DMG400004351' => 'stu', 'PGSC0003DMG400014625' => 'stu', 'PGSC0003DMG401000943' => 'stu', 'Phvul.001G148600' => 'pvu', 'Phvul.004G001700' => 'pvu', 'Phvul.006G154900' => 'pvu', 'Phvul.008G078200' => 'pvu', 'Phvul.011G136500' => 'pvu', 'Potri.002G215600' => 'ptr', 'Potri.008G201600' => 'ptr', 'Potri.014G138400' => 'ptr', 'Potri.016G142500' => 'ptr', 'Pp3c16_10580' => 'ppa', 'Pp3c5_25280' => 'ppa', 'Prupe.1G150000' => 'ppe', 'Prupe.1G150100' => 'ppe', 'Prupe.6G299600' => 'ppe', 'Prupe.8G245000' => 'ppe', 'Psat0s4927g0040' => 'psa', 'Psat1g052080' => 'psa', 'Psat1g183800' => 'psa', 'Psat3g113840' => 'psa', 'Psat3g126120' => 'psa', 'Psat3g126160' => 'psa', 'Psat3g158760' => 'psa', 'Psat3g158840' => 'psa', 'PSO170G2858' => 'pso', 'PSO339G0606' => 'pso', 'PSO384G4709' => 'pso', 'PSO407G0334' => 'pso', 'QL04p040276' => 'qlo', 'QL06p005458' => 'qlo', 'QL06p005472' => 'qlo', 'QL07p030546' => 'qlo', 'QL07p031519' => 'qlo', 'QL09p050949' => 'qlo', 'QL09p050966' => 'qlo', 'QL09p051067' => 'qlo', 'QL12p022706' => 'qlo', 'RcHm_v2.0_Chr2g0119601' => 'rch', 'RcHm_v2.0_Chr3g0459591' => 'rch', 'RcHm_v2.0_Chr4g0418521' => 'rch', 'RcHm_v2.0_Chr4g0418531' => 'rch', 'RcHm_v2.0_Chr4g0418541' => 'rch', 'RcHm_v2.0_Chr6g0291641' => 'rch', 'Rhsim01G0086300' => 'rsi', 'Rhsim01G0276300' => 'rsi', 'Rhsim01G0276500' => 'rsi', 'Rhsim04G0207700' => 'rsi', 'Rhsim05G0234500' => 'rsi', 'Rhsim13G0022400' => 'rsi', 'Sabra02G0167900' => 'sbr', 'Sabra04G0158500' => 'sbr', 'Sabra08G0159800' => 'sbr', 'Sabra10G0011500' => 'sbr', 'Sabra14G0104400' => 'sbr', 'SalBow2G2440' => 'sbo', 'SalBow4G2265' => 'sbo', 'Sc02g0000060' => 'sci', 'Sc05g0005020' => 'sci', 'Sc13g0003890' => 'sci', 'Sed0014865' => 'sed', 'Sed0017224' => 'sed', 'Sed0026391' => 'sed', 'SEGI_00063' => 'sgi', 'SEGI_10967' => 'sgi', 'SEGI_17510' => 'sgi', 'SEGI_24396' => 'sgi', 'SEGI_39719' => 'sgi', 'SEGI_41392' => 'sgi', 'SGA_v2.0_scaffold11G05794' => 'sas', 'SGA_v2.0_scaffold142G35607' => 'sas', 'SGA_v2.0_scaffold1G00447' => 'sas', 'SHI15388' => 'shi', 'SHI15394' => 'shi', 'SHI15396' => 'shi', 'SHI15399' => 'shi', 'SMO343G0151' => 'smo', 'SMO367G1118' => 'smo', 'Solyc01g080200.3' => 'sly', 'Solyc06g008960.3' => 'sly', 'Solyc09g064780.3' => 'sly', 'Sopen01g031980' => 'spe', 'Sopen06g003710' => 'spe', 'Sopen09g026460' => 'spe', 'Sp3g21240' => 'spa', 'Sp4g30030' => 'spa', 'TAR365G0022' => 'tar', 'TAR365G1023' => 'tar', 'TAR365G1253' => 'tar', 'TAR623G0078' => 'tar', 'TAR623G1721' => 'tar', 'TAR633G0959' => 'tar', 'THA.LOC104802225' => 'tha', 'THA.LOC104804769' => 'tha', 'THA.LOC104808660' => 'tha', 'THA.LOC104812792' => 'tha', 'Thecc.01G284000' => 'tca', 'Thecc.04G220600' => 'tca', 'Thecc.05G268900' => 'tca', 'Thecc.08G171100' => 'tca', 'Thhalv10001284m.g' => 'esa', 'Thhalv10019912m.g' => 'esa', 'TPR.G14189' => 'tpr', 'TPR.G18110' => 'tpr', 'TPR.G18130' => 'tpr', 'TPR.G18131' => 'tpr', 'TPR.G18140' => 'tpr', 'TPR.G24282' => 'tpr', 'TPR.G25221' => 'tpr', 'TPR.G29267' => 'tpr', 'TPR.G35315' => 'tpr', 'TPR.G36173' => 'tpr', 'TWI09G0794' => 'twi', 'TWI59G1348' => 'twi', 'TWI74G0430' => 'twi', 'unitig_26.g8940' => 'ugi', 'unitig_749.g13744' => 'ugi', 'unitig_749.g13745' => 'ugi', 'vmacro08269' => 'vma', 'vmacro14937' => 'vma', 'vmacro20401' => 'vma', 'VMungo0464G1349' => 'vmu', 'VMungo0540G0289' => 'vmu', 'VMungo1215G1590' => 'vmu', 'VMungo1309G0221' => 'vmu', 'VMungo1309G2815' => 'vmu', 'VMungo1383G0239' => 'vmu', 'VMungo1383G2910' => 'vmu', 'Zm00001eb095270' => 'zma', 'Zm00001eb095280' => 'zma', 'Zm00001eb111630' => 'zma', 'Zm00001eb237080' => 'zma', 'Zm00001eb273740' => 'zma', 'Zm00001eb285040' => 'zma', 'Zm00001eb330790' => 'zma', 'Zm00001eb337380' => 'zma' ) $gf_id = 'HOM05D001484' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001484' ) $data_identifier = 'HOM05D001484' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 2, 'aly' => (int) 2, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 22, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 7, 'hma' => (int) 2, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 7, 'mtr' => (int) 10, 'cme' => (int) 2, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 4, 'ppa' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 4, 'qlo' => (int) 9, 'rch' => (int) 6, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 10, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 7, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb337380' $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' => 'HOM05D001484', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p31500' => 'bna', 'A05p00020' => 'bna', 'A07p08820' => 'bna', 'Aa31LG4G3300' => 'aar', 'Aa31LG8G10030' => 'aar', 'Actinidia00731' => 'ach', 'Actinidia11473' => 'ach', 'Actinidia23469' => 'ach', 'Actinidia24318' => 'ach', 'Actinidia40196' => 'ach', 'Actinidia40197' => 'ach', 'Actinidia40198' => 'ach', 'Ah.08g212990' => 'amhyb', 'Ah.15g091720' => 'amhyb', 'AL3G38260' => 'aly', 'AL4G47710' => 'aly', 'Aqoxy2G00671' => 'aox', 'Aqoxy2G03236' => 'aox', 'arahy.Tifrunner.gnm1.ann1.05IDCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KR684' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATY3SJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK6QJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6APGL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IDT7Z9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM073U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ0R87' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LE7RV4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT4QRX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V5ENPK' => 'arhy', 'AT2G48110' => 'ath', 'AT3G23590' => 'ath', 'ATR0626G186' => 'atr', 'ATR1127G141' => 'atr', 'Atru.chr4.2583' => 'acertr', 'Atru.chr5.1358' => 'acertr', 'Atru.chr5.1359' => 'acertr', 'Atru.chr8.46' => 'acertr', 'AUR62002640' => 'cqu', 'AUR62030055' => 'cqu', 'AUR62033713' => 'cqu', 'AUR62033714' => 'cqu', 'AUR62036795' => 'cqu', 'AUR62039891' => 'cqu', 'BcaB02g08737' => 'bca', 'BcaB04g20441' => 'bca', 'BcaB06g26509' => 'bca', 'BcaB06g26510' => 'bca', 'BcaB06g26511' => 'bca', 'BcaB06g26512' => 'bca', 'BcaB06g26513' => 'bca', 'BcaC02g12564' => 'bca', 'BcaC02g12565' => 'bca', 'BcaC02g12794' => 'bca', 'BcaC02g12795' => 'bca', 'BcaC02g12796' => 'bca', 'BcaC06g35541' => 'bca', 'BNapus_Darmor_BZH_scaffold_188p00080' => 'bna', 'BNapus_Darmor_BZH_scaffold_188p00090' => 'bna', 'BolC1t03972H' => 'bol', 'BolC1t03973H' => 'bol', 'BolC4t21680H' => 'bol', 'BolC7t41863H' => 'bol', 'BolSC55t61227H' => 'bol', 'BolSC55t61228H' => 'bol', 'BraA01t03278Z' => 'bra', 'BraA05t18998Z' => 'bra', 'BraA07t28673Z' => 'bra', 'C01p40150' => 'bna', 'C05p12370' => 'bna', 'C07p13680' => 'bna', 'CAN.G1006.16' => 'can', 'CAN.G1006.17' => 'can', 'CAN.G1170.2' => 'can', 'CAN.G962.7' => 'can', 'CANSAT25G2179' => 'cansat', 'CANSAT78G1573' => 'cansat', 'CARHR099510' => 'chi', 'CARHR143510' => 'chi', 'Carub.0003s2380' => 'cru', 'Carub.0004s3082' => 'cru', 'Ca_00614_v3' => 'car', 'Ca_07801_v3' => 'car', 'Ca_08567_v3' => 'car', 'Ca_09571_v3' => 'car', 'CBR_g19290' => 'cbr', 'Cc01_g19770' => 'ccan', 'Cc03_g03030' => 'ccan', 'CDE07G0968' => 'cde', 'CDE09G1441' => 'cde', 'Cfa006103' => 'cfa', 'Cfa015573' => 'cfa', 'Cfa016988' => 'cfa', 'Ciclev10006738m.g' => 'ccl', 'Ciclev10010920m.g' => 'ccl', 'Ciclev10018517m.g' => 'ccl', 'CiPaw.01G159200' => 'cil', 'CiPaw.02G091000' => 'cil', 'CiPaw.02G091100' => 'cil', 'CiPaw.08G103100' => 'cil', 'CiPaw.09G224900' => 'cil', 'ClCG06G005740' => 'cla', 'ClCG07G000090' => 'cla', 'ClCG07G000100' => 'cla', 'COL.COLO4_09143' => 'col', 'COL.COLO4_25124' => 'col', 'Cpa.g.sc16.34' => 'cpa', 'Cpa.g.sc3504.1' => 'cpa', 'Cpa.g.sc60.37' => 'cpa', 'CsaV3_6G018520' => 'csa', 'CsaV3_6G036860' => 'csa', 'CSS0001072' => 'camsi', 'CSS0020208' => 'camsi', 'CSS0021253' => 'camsi', 'CSS0022190' => 'camsi', 'CSS0036150' => 'camsi', 'CSS0040442' => 'camsi', 'CSS0042300' => 'camsi', 'CSS0045298' => 'camsi', 'DCAR_012449' => 'dca', 'DCAR_018405' => 'dca', 'DCAR_024573' => 'dca', 'DCAR_030591' => 'dca', 'Dinv16926' => 'din', 'Dinv32963' => 'din', 'Dinv38382' => 'din', 'Dinv38383' => 'din', 'Duzib133G0974' => 'dzi', 'Duzib138G1867' => 'dzi', 'Duzib211G0420' => 'dzi', 'Duzib212G0930' => 'dzi', 'ECA234G1645' => 'eca', 'ECA247G3467' => 'eca', 'ECA248G1703' => 'eca', 'EL10Ac3g06327' => 'bvu', 'EL10Ac7g17204' => 'bvu', 'Eucgr.A00855' => 'egr', 'Eucgr.A00858' => 'egr', 'Eucgr.H01520' => 'egr', 'Eucgr.H03604' => 'egr', 'Eucgr.L03465' => 'egr', 'Eucgr.L03466' => 'egr', 'FAN01G0988' => 'fan', 'FAN02G3892' => 'fan', 'FAN05G3381' => 'fan', 'FAN07G0967' => 'fan', 'FAN07G1493' => 'fan', 'FAN08G3125' => 'fan', 'FAN09G0402' => 'fan', 'FAN12G2594' => 'fan', 'FAN12G3879' => 'fan', 'FAN14G1546' => 'fan', 'FAN15G3626' => 'fan', 'FAN17G0588' => 'fan', 'FAN17G0609' => 'fan', 'FAN18G2817' => 'fan', 'FAN19G1305' => 'fan', 'FAN20G1787' => 'fan', 'FAN22G0073' => 'fan', 'FAN22G0352' => 'fan', 'FAN22G0368' => 'fan', 'FAN22G2273' => 'fan', 'FAN24G1998' => 'fan', 'FAN27G1317' => 'fan', 'FvH4_2g23980' => 'fve', 'FvH4_4g14380' => 'fve', 'FvH4_4g14390' => 'fve', 'FvH4_6g09250' => 'fve', 'Glyma.03G151100' => 'gma', 'Glyma.04G122550' => 'gma', 'Glyma.05G001600' => 'gma', 'Glyma.09G270766' => 'gma', 'Glyma.09G270832' => 'gma', 'Glyma.13G209800' => 'gma', 'Glyma.15G102800' => 'gma', 'Glyma.18G218900' => 'gma', 'Glyma.19G001500' => 'gma', 'Glyma.19G153600' => 'gma', 'Gohir.A02G028600' => 'ghi', 'Gohir.A08G045000' => 'ghi', 'Gohir.A11G120500' => 'ghi', 'Gohir.A12G006200' => 'ghi', 'Gohir.A12G006250' => 'ghi', 'Gohir.D02G036300' => 'ghi', 'Gohir.D08G054700' => 'ghi', 'Gohir.D11G125600' => 'ghi', 'Gohir.D12G005700' => 'ghi', 'Gorai.004G055200' => 'gra', 'Gorai.005G040400' => 'gra', 'Gorai.007G134500' => 'gra', 'Gorai.008G005500' => 'gra', 'GSVIVG01011094001' => 'vvi', 'GSVIVG01017879001' => 'vvi', 'GSVIVG01025988001' => 'vvi', 'GSVIVG01029847001' => 'vvi', 'HanXRQChr10g0282901' => 'han', 'HanXRQChr10g0310371' => 'han', 'HanXRQChr10g0315041' => 'han', 'HanXRQChr11g0327651' => 'han', 'HanXRQChr12g0359391' => 'han', 'Haze_00972' => 'cav', 'Haze_00973' => 'cav', 'Haze_00974' => 'cav', 'Haze_04747' => 'cav', 'Haze_04749' => 'cav', 'Haze_04750' => 'cav', 'Haze_21217' => 'cav', 'Hma1.2p1_1037F.1_g250680' => 'hma', 'Hma1.2p1_1644F.1_g295320' => 'hma', 'HPP92_011322' => 'vpl', 'HPP92_011323' => 'vpl', 'HPP92_011324' => 'vpl', 'HPP92_011325' => 'vpl', 'HPP92_011326' => 'vpl', 'Hund12205' => 'sun', 'Hund17957' => 'sun', 'Lalb_Chr06g0176771' => 'lal', 'Lalb_Chr18g0056021' => 'lal', 'Lalb_Chr18g0056031' => 'lal', 'Lalb_Chr18g0056041' => 'lal', 'Lalb_Chr20g0107751' => 'lal', 'Lalb_Chr20g0118371' => 'lal', 'Lj1g0010239' => 'lja', 'Lj1g0017101' => 'lja', 'Lj2A1178G40' => 'lonja', 'Lj2A54G84' => 'lonja', 'Lj2g0015248' => 'lja', 'Lj3A761T51' => 'lonja', 'Lj6g0018116' => 'lja', 'Lsat_1_v5_gn_4_136040' => 'lsa', 'Lsat_1_v5_gn_5_187461' => 'lsa', 'Lsat_1_v5_gn_5_77001' => 'lsa', 'Lsat_1_v5_gn_9_4461' => 'lsa', 'Manes.01G210100' => 'mes', 'Manes.03G185600' => 'mes', 'Manes.05G073300' => 'mes', 'Manes.09G120300' => 'mes', 'Manes.15G022100' => 'mes', 'Mapoly0096s0053' => 'mpo', 'MBI03_g14058_MAGBIO' => 'mbi', 'MBI03_g33876_MAGBIO' => 'mbi', 'MBI03_g36854_MAGBIO' => 'mbi', 'MBI17_g11997_MAGBIO' => 'mbi', 'MD03G1269000' => 'mdo', 'MD04G1179600' => 'mdo', 'MD11G1289800' => 'mdo', 'MD12G1194700' => 'mdo', 'MD13G1182100' => 'mdo', 'MD13G1182200' => 'mdo', 'MD16G1182600' => 'mdo', 'Medtr2g021400' => 'mtr', 'Medtr2g021470' => 'mtr', 'Medtr2g105810' => 'mtr', 'Medtr3g033580' => 'mtr', 'Medtr6g007970' => 'mtr', 'Medtr7g056330' => 'mtr', 'Medtr7g074290' => 'mtr', 'Medtr7g074380' => 'mtr', 'Medtr7g094550' => 'mtr', 'Medtr8g069995' => 'mtr', 'MELO3C014345.2' => 'cme', 'MELO3C021395.2' => 'cme', 'Migut.D00262' => 'egut', 'Migut.G00257' => 'egut', 'MSTRG.21575' => 'ama', 'MSTRG.3985' => 'ama', 'Nitab4.5_0000295g0140' => 'nta', 'Nitab4.5_0000732g0140' => 'nta', 'Nitab4.5_0003162g0020' => 'nta', 'Nitab4.5_0006180g0090' => 'nta', 'Nitab4.5_0006390g0010' => 'nta', 'Nitab4.5_0007392g0040' => 'nta', 'Nn1g02140' => 'nnu', 'Nn4g26168' => 'nnu', 'Nn5g26754' => 'nnu', 'Oeu001433.1' => 'oeu', 'Oeu010299.2' => 'oeu', 'Oeu011171.1' => 'oeu', 'Oeu037675.1' => 'oeu', 'Oeu038359.1' => 'oeu', 'Oeu063834.1' => 'oeu', 'Oeu063835.1' => 'oeu', 'Os05g0312000' => 'osa', 'Os07g0211101' => 'osa', 'Os07g0211200' => 'osa', 'Os07g0681500' => 'osa', 'Peaxi162Scf00095g01015' => 'pax', 'Peaxi162Scf00104g00329' => 'pax', 'Peaxi162Scf00161g00137' => 'pax', 'PGR004G1665' => 'pgr', 'PGR031G2937' => 'pgr', 'PGR119G2145' => 'pgr', 'PGSC0003DMG400004351' => 'stu', 'PGSC0003DMG400014625' => 'stu', 'PGSC0003DMG401000943' => 'stu', 'Phvul.001G148600' => 'pvu', 'Phvul.004G001700' => 'pvu', 'Phvul.006G154900' => 'pvu', 'Phvul.008G078200' => 'pvu', 'Phvul.011G136500' => 'pvu', 'Potri.002G215600' => 'ptr', 'Potri.008G201600' => 'ptr', 'Potri.014G138400' => 'ptr', 'Potri.016G142500' => 'ptr', 'Pp3c16_10580' => 'ppa', 'Pp3c5_25280' => 'ppa', 'Prupe.1G150000' => 'ppe', 'Prupe.1G150100' => 'ppe', 'Prupe.6G299600' => 'ppe', 'Prupe.8G245000' => 'ppe', 'Psat0s4927g0040' => 'psa', 'Psat1g052080' => 'psa', 'Psat1g183800' => 'psa', 'Psat3g113840' => 'psa', 'Psat3g126120' => 'psa', 'Psat3g126160' => 'psa', 'Psat3g158760' => 'psa', 'Psat3g158840' => 'psa', 'PSO170G2858' => 'pso', 'PSO339G0606' => 'pso', 'PSO384G4709' => 'pso', 'PSO407G0334' => 'pso', 'QL04p040276' => 'qlo', 'QL06p005458' => 'qlo', 'QL06p005472' => 'qlo', 'QL07p030546' => 'qlo', 'QL07p031519' => 'qlo', 'QL09p050949' => 'qlo', 'QL09p050966' => 'qlo', 'QL09p051067' => 'qlo', 'QL12p022706' => 'qlo', 'RcHm_v2.0_Chr2g0119601' => 'rch', 'RcHm_v2.0_Chr3g0459591' => 'rch', 'RcHm_v2.0_Chr4g0418521' => 'rch', 'RcHm_v2.0_Chr4g0418531' => 'rch', 'RcHm_v2.0_Chr4g0418541' => 'rch', 'RcHm_v2.0_Chr6g0291641' => 'rch', 'Rhsim01G0086300' => 'rsi', 'Rhsim01G0276300' => 'rsi', 'Rhsim01G0276500' => 'rsi', 'Rhsim04G0207700' => 'rsi', 'Rhsim05G0234500' => 'rsi', 'Rhsim13G0022400' => 'rsi', 'Sabra02G0167900' => 'sbr', 'Sabra04G0158500' => 'sbr', 'Sabra08G0159800' => 'sbr', 'Sabra10G0011500' => 'sbr', 'Sabra14G0104400' => 'sbr', 'SalBow2G2440' => 'sbo', 'SalBow4G2265' => 'sbo', 'Sc02g0000060' => 'sci', 'Sc05g0005020' => 'sci', 'Sc13g0003890' => 'sci', 'Sed0014865' => 'sed', 'Sed0017224' => 'sed', 'Sed0026391' => 'sed', 'SEGI_00063' => 'sgi', 'SEGI_10967' => 'sgi', 'SEGI_17510' => 'sgi', 'SEGI_24396' => 'sgi', 'SEGI_39719' => 'sgi', 'SEGI_41392' => 'sgi', 'SGA_v2.0_scaffold11G05794' => 'sas', 'SGA_v2.0_scaffold142G35607' => 'sas', 'SGA_v2.0_scaffold1G00447' => 'sas', 'SHI15388' => 'shi', 'SHI15394' => 'shi', 'SHI15396' => 'shi', 'SHI15399' => 'shi', 'SMO343G0151' => 'smo', 'SMO367G1118' => 'smo', 'Solyc01g080200.3' => 'sly', 'Solyc06g008960.3' => 'sly', 'Solyc09g064780.3' => 'sly', 'Sopen01g031980' => 'spe', 'Sopen06g003710' => 'spe', 'Sopen09g026460' => 'spe', 'Sp3g21240' => 'spa', 'Sp4g30030' => 'spa', 'TAR365G0022' => 'tar', 'TAR365G1023' => 'tar', 'TAR365G1253' => 'tar', 'TAR623G0078' => 'tar', 'TAR623G1721' => 'tar', 'TAR633G0959' => 'tar', 'THA.LOC104802225' => 'tha', 'THA.LOC104804769' => 'tha', 'THA.LOC104808660' => 'tha', 'THA.LOC104812792' => 'tha', 'Thecc.01G284000' => 'tca', 'Thecc.04G220600' => 'tca', 'Thecc.05G268900' => 'tca', 'Thecc.08G171100' => 'tca', 'Thhalv10001284m.g' => 'esa', 'Thhalv10019912m.g' => 'esa', 'TPR.G14189' => 'tpr', 'TPR.G18110' => 'tpr', 'TPR.G18130' => 'tpr', 'TPR.G18131' => 'tpr', 'TPR.G18140' => 'tpr', 'TPR.G24282' => 'tpr', 'TPR.G25221' => 'tpr', 'TPR.G29267' => 'tpr', 'TPR.G35315' => 'tpr', 'TPR.G36173' => 'tpr', 'TWI09G0794' => 'twi', 'TWI59G1348' => 'twi', 'TWI74G0430' => 'twi', 'unitig_26.g8940' => 'ugi', 'unitig_749.g13744' => 'ugi', 'unitig_749.g13745' => 'ugi', 'vmacro08269' => 'vma', 'vmacro14937' => 'vma', 'vmacro20401' => 'vma', 'VMungo0464G1349' => 'vmu', 'VMungo0540G0289' => 'vmu', 'VMungo1215G1590' => 'vmu', 'VMungo1309G0221' => 'vmu', 'VMungo1309G2815' => 'vmu', 'VMungo1383G0239' => 'vmu', 'VMungo1383G2910' => 'vmu', 'Zm00001eb095270' => 'zma', 'Zm00001eb095280' => 'zma', 'Zm00001eb111630' => 'zma', 'Zm00001eb237080' => 'zma', 'Zm00001eb273740' => 'zma', 'Zm00001eb285040' => 'zma', 'Zm00001eb330790' => 'zma', 'Zm00001eb337380' => 'zma' ), 'gf_id' => 'HOM05D001484', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001484' ), 'data_identifier' => 'HOM05D001484', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001484', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p31500' => 'bna', 'A05p00020' => 'bna', 'A07p08820' => 'bna', 'Aa31LG4G3300' => 'aar', 'Aa31LG8G10030' => 'aar', 'Actinidia00731' => 'ach', 'Actinidia11473' => 'ach', 'Actinidia23469' => 'ach', 'Actinidia24318' => 'ach', 'Actinidia40196' => 'ach', 'Actinidia40197' => 'ach', 'Actinidia40198' => 'ach', 'Ah.08g212990' => 'amhyb', 'Ah.15g091720' => 'amhyb', 'AL3G38260' => 'aly', 'AL4G47710' => 'aly', 'Aqoxy2G00671' => 'aox', 'Aqoxy2G03236' => 'aox', 'arahy.Tifrunner.gnm1.ann1.05IDCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KR684' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATY3SJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK6QJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6APGL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IDT7Z9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM073U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ0R87' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LE7RV4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT4QRX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V5ENPK' => 'arhy', 'AT2G48110' => 'ath', 'AT3G23590' => 'ath', 'ATR0626G186' => 'atr', 'ATR1127G141' => 'atr', 'Atru.chr4.2583' => 'acertr', 'Atru.chr5.1358' => 'acertr', 'Atru.chr5.1359' => 'acertr', 'Atru.chr8.46' => 'acertr', 'AUR62002640' => 'cqu', 'AUR62030055' => 'cqu', 'AUR62033713' => 'cqu', 'AUR62033714' => 'cqu', 'AUR62036795' => 'cqu', 'AUR62039891' => 'cqu', 'BcaB02g08737' => 'bca', 'BcaB04g20441' => 'bca', 'BcaB06g26509' => 'bca', 'BcaB06g26510' => 'bca', 'BcaB06g26511' => 'bca', 'BcaB06g26512' => 'bca', 'BcaB06g26513' => 'bca', 'BcaC02g12564' => 'bca', 'BcaC02g12565' => 'bca', 'BcaC02g12794' => 'bca', 'BcaC02g12795' => 'bca', 'BcaC02g12796' => 'bca', 'BcaC06g35541' => 'bca', 'BNapus_Darmor_BZH_scaffold_188p00080' => 'bna', 'BNapus_Darmor_BZH_scaffold_188p00090' => 'bna', 'BolC1t03972H' => 'bol', 'BolC1t03973H' => 'bol', 'BolC4t21680H' => 'bol', 'BolC7t41863H' => 'bol', 'BolSC55t61227H' => 'bol', 'BolSC55t61228H' => 'bol', 'BraA01t03278Z' => 'bra', 'BraA05t18998Z' => 'bra', 'BraA07t28673Z' => 'bra', 'C01p40150' => 'bna', 'C05p12370' => 'bna', 'C07p13680' => 'bna', 'CAN.G1006.16' => 'can', 'CAN.G1006.17' => 'can', 'CAN.G1170.2' => 'can', 'CAN.G962.7' => 'can', 'CANSAT25G2179' => 'cansat', 'CANSAT78G1573' => 'cansat', 'CARHR099510' => 'chi', 'CARHR143510' => 'chi', 'Carub.0003s2380' => 'cru', 'Carub.0004s3082' => 'cru', 'Ca_00614_v3' => 'car', 'Ca_07801_v3' => 'car', 'Ca_08567_v3' => 'car', 'Ca_09571_v3' => 'car', 'CBR_g19290' => 'cbr', 'Cc01_g19770' => 'ccan', 'Cc03_g03030' => 'ccan', 'CDE07G0968' => 'cde', 'CDE09G1441' => 'cde', 'Cfa006103' => 'cfa', 'Cfa015573' => 'cfa', 'Cfa016988' => 'cfa', 'Ciclev10006738m.g' => 'ccl', 'Ciclev10010920m.g' => 'ccl', 'Ciclev10018517m.g' => 'ccl', 'CiPaw.01G159200' => 'cil', 'CiPaw.02G091000' => 'cil', 'CiPaw.02G091100' => 'cil', 'CiPaw.08G103100' => 'cil', 'CiPaw.09G224900' => 'cil', 'ClCG06G005740' => 'cla', 'ClCG07G000090' => 'cla', 'ClCG07G000100' => 'cla', 'COL.COLO4_09143' => 'col', 'COL.COLO4_25124' => 'col', 'Cpa.g.sc16.34' => 'cpa', 'Cpa.g.sc3504.1' => 'cpa', 'Cpa.g.sc60.37' => 'cpa', 'CsaV3_6G018520' => 'csa', 'CsaV3_6G036860' => 'csa', 'CSS0001072' => 'camsi', 'CSS0020208' => 'camsi', 'CSS0021253' => 'camsi', 'CSS0022190' => 'camsi', 'CSS0036150' => 'camsi', 'CSS0040442' => 'camsi', 'CSS0042300' => 'camsi', 'CSS0045298' => 'camsi', 'DCAR_012449' => 'dca', 'DCAR_018405' => 'dca', 'DCAR_024573' => 'dca', 'DCAR_030591' => 'dca', 'Dinv16926' => 'din', 'Dinv32963' => 'din', 'Dinv38382' => 'din', 'Dinv38383' => 'din', 'Duzib133G0974' => 'dzi', 'Duzib138G1867' => 'dzi', 'Duzib211G0420' => 'dzi', 'Duzib212G0930' => 'dzi', 'ECA234G1645' => 'eca', 'ECA247G3467' => 'eca', 'ECA248G1703' => 'eca', 'EL10Ac3g06327' => 'bvu', 'EL10Ac7g17204' => 'bvu', 'Eucgr.A00855' => 'egr', 'Eucgr.A00858' => 'egr', 'Eucgr.H01520' => 'egr', 'Eucgr.H03604' => 'egr', 'Eucgr.L03465' => 'egr', 'Eucgr.L03466' => 'egr', 'FAN01G0988' => 'fan', 'FAN02G3892' => 'fan', 'FAN05G3381' => 'fan', 'FAN07G0967' => 'fan', 'FAN07G1493' => 'fan', 'FAN08G3125' => 'fan', 'FAN09G0402' => 'fan', 'FAN12G2594' => 'fan', 'FAN12G3879' => 'fan', 'FAN14G1546' => 'fan', 'FAN15G3626' => 'fan', 'FAN17G0588' => 'fan', 'FAN17G0609' => 'fan', 'FAN18G2817' => 'fan', 'FAN19G1305' => 'fan', 'FAN20G1787' => 'fan', 'FAN22G0073' => 'fan', 'FAN22G0352' => 'fan', 'FAN22G0368' => 'fan', 'FAN22G2273' => 'fan', 'FAN24G1998' => 'fan', 'FAN27G1317' => 'fan', 'FvH4_2g23980' => 'fve', 'FvH4_4g14380' => 'fve', 'FvH4_4g14390' => 'fve', 'FvH4_6g09250' => 'fve', 'Glyma.03G151100' => 'gma', 'Glyma.04G122550' => 'gma', 'Glyma.05G001600' => 'gma', 'Glyma.09G270766' => 'gma', 'Glyma.09G270832' => 'gma', 'Glyma.13G209800' => 'gma', 'Glyma.15G102800' => 'gma', 'Glyma.18G218900' => 'gma', 'Glyma.19G001500' => 'gma', 'Glyma.19G153600' => 'gma', 'Gohir.A02G028600' => 'ghi', 'Gohir.A08G045000' => 'ghi', 'Gohir.A11G120500' => 'ghi', 'Gohir.A12G006200' => 'ghi', 'Gohir.A12G006250' => 'ghi', 'Gohir.D02G036300' => 'ghi', 'Gohir.D08G054700' => 'ghi', 'Gohir.D11G125600' => 'ghi', 'Gohir.D12G005700' => 'ghi', 'Gorai.004G055200' => 'gra', 'Gorai.005G040400' => 'gra', 'Gorai.007G134500' => 'gra', 'Gorai.008G005500' => 'gra', 'GSVIVG01011094001' => 'vvi', 'GSVIVG01017879001' => 'vvi', 'GSVIVG01025988001' => 'vvi', 'GSVIVG01029847001' => 'vvi', 'HanXRQChr10g0282901' => 'han', 'HanXRQChr10g0310371' => 'han', 'HanXRQChr10g0315041' => 'han', 'HanXRQChr11g0327651' => 'han', 'HanXRQChr12g0359391' => 'han', 'Haze_00972' => 'cav', 'Haze_00973' => 'cav', 'Haze_00974' => 'cav', 'Haze_04747' => 'cav', 'Haze_04749' => 'cav', 'Haze_04750' => 'cav', 'Haze_21217' => 'cav', 'Hma1.2p1_1037F.1_g250680' => 'hma', 'Hma1.2p1_1644F.1_g295320' => 'hma', 'HPP92_011322' => 'vpl', 'HPP92_011323' => 'vpl', 'HPP92_011324' => 'vpl', 'HPP92_011325' => 'vpl', 'HPP92_011326' => 'vpl', 'Hund12205' => 'sun', 'Hund17957' => 'sun', 'Lalb_Chr06g0176771' => 'lal', 'Lalb_Chr18g0056021' => 'lal', 'Lalb_Chr18g0056031' => 'lal', 'Lalb_Chr18g0056041' => 'lal', 'Lalb_Chr20g0107751' => 'lal', 'Lalb_Chr20g0118371' => 'lal', 'Lj1g0010239' => 'lja', 'Lj1g0017101' => 'lja', 'Lj2A1178G40' => 'lonja', 'Lj2A54G84' => 'lonja', 'Lj2g0015248' => 'lja', 'Lj3A761T51' => 'lonja', 'Lj6g0018116' => 'lja', 'Lsat_1_v5_gn_4_136040' => 'lsa', 'Lsat_1_v5_gn_5_187461' => 'lsa', 'Lsat_1_v5_gn_5_77001' => 'lsa', 'Lsat_1_v5_gn_9_4461' => 'lsa', 'Manes.01G210100' => 'mes', 'Manes.03G185600' => 'mes', 'Manes.05G073300' => 'mes', 'Manes.09G120300' => 'mes', 'Manes.15G022100' => 'mes', 'Mapoly0096s0053' => 'mpo', 'MBI03_g14058_MAGBIO' => 'mbi', 'MBI03_g33876_MAGBIO' => 'mbi', 'MBI03_g36854_MAGBIO' => 'mbi', 'MBI17_g11997_MAGBIO' => 'mbi', 'MD03G1269000' => 'mdo', 'MD04G1179600' => 'mdo', 'MD11G1289800' => 'mdo', 'MD12G1194700' => 'mdo', 'MD13G1182100' => 'mdo', 'MD13G1182200' => 'mdo', 'MD16G1182600' => 'mdo', 'Medtr2g021400' => 'mtr', 'Medtr2g021470' => 'mtr', 'Medtr2g105810' => 'mtr', 'Medtr3g033580' => 'mtr', 'Medtr6g007970' => 'mtr', 'Medtr7g056330' => 'mtr', 'Medtr7g074290' => 'mtr', 'Medtr7g074380' => 'mtr', 'Medtr7g094550' => 'mtr', 'Medtr8g069995' => 'mtr', 'MELO3C014345.2' => 'cme', 'MELO3C021395.2' => 'cme', 'Migut.D00262' => 'egut', 'Migut.G00257' => 'egut', 'MSTRG.21575' => 'ama', 'MSTRG.3985' => 'ama', 'Nitab4.5_0000295g0140' => 'nta', 'Nitab4.5_0000732g0140' => 'nta', 'Nitab4.5_0003162g0020' => 'nta', 'Nitab4.5_0006180g0090' => 'nta', 'Nitab4.5_0006390g0010' => 'nta', 'Nitab4.5_0007392g0040' => 'nta', 'Nn1g02140' => 'nnu', 'Nn4g26168' => 'nnu', 'Nn5g26754' => 'nnu', 'Oeu001433.1' => 'oeu', 'Oeu010299.2' => 'oeu', 'Oeu011171.1' => 'oeu', 'Oeu037675.1' => 'oeu', 'Oeu038359.1' => 'oeu', 'Oeu063834.1' => 'oeu', 'Oeu063835.1' => 'oeu', 'Os05g0312000' => 'osa', 'Os07g0211101' => 'osa', 'Os07g0211200' => 'osa', 'Os07g0681500' => 'osa', 'Peaxi162Scf00095g01015' => 'pax', 'Peaxi162Scf00104g00329' => 'pax', 'Peaxi162Scf00161g00137' => 'pax', 'PGR004G1665' => 'pgr', 'PGR031G2937' => 'pgr', 'PGR119G2145' => 'pgr', 'PGSC0003DMG400004351' => 'stu', 'PGSC0003DMG400014625' => 'stu', 'PGSC0003DMG401000943' => 'stu', 'Phvul.001G148600' => 'pvu', 'Phvul.004G001700' => 'pvu', 'Phvul.006G154900' => 'pvu', 'Phvul.008G078200' => 'pvu', 'Phvul.011G136500' => 'pvu', 'Potri.002G215600' => 'ptr', 'Potri.008G201600' => 'ptr', 'Potri.014G138400' => 'ptr', 'Potri.016G142500' => 'ptr', 'Pp3c16_10580' => 'ppa', 'Pp3c5_25280' => 'ppa', 'Prupe.1G150000' => 'ppe', 'Prupe.1G150100' => 'ppe', 'Prupe.6G299600' => 'ppe', 'Prupe.8G245000' => 'ppe', 'Psat0s4927g0040' => 'psa', 'Psat1g052080' => 'psa', 'Psat1g183800' => 'psa', 'Psat3g113840' => 'psa', 'Psat3g126120' => 'psa', 'Psat3g126160' => 'psa', 'Psat3g158760' => 'psa', 'Psat3g158840' => 'psa', 'PSO170G2858' => 'pso', 'PSO339G0606' => 'pso', 'PSO384G4709' => 'pso', 'PSO407G0334' => 'pso', 'QL04p040276' => 'qlo', 'QL06p005458' => 'qlo', 'QL06p005472' => 'qlo', 'QL07p030546' => 'qlo', 'QL07p031519' => 'qlo', 'QL09p050949' => 'qlo', 'QL09p050966' => 'qlo', 'QL09p051067' => 'qlo', 'QL12p022706' => 'qlo', 'RcHm_v2.0_Chr2g0119601' => 'rch', 'RcHm_v2.0_Chr3g0459591' => 'rch', 'RcHm_v2.0_Chr4g0418521' => 'rch', 'RcHm_v2.0_Chr4g0418531' => 'rch', 'RcHm_v2.0_Chr4g0418541' => 'rch', 'RcHm_v2.0_Chr6g0291641' => 'rch', 'Rhsim01G0086300' => 'rsi', 'Rhsim01G0276300' => 'rsi', 'Rhsim01G0276500' => 'rsi', 'Rhsim04G0207700' => 'rsi', 'Rhsim05G0234500' => 'rsi', 'Rhsim13G0022400' => 'rsi', 'Sabra02G0167900' => 'sbr', 'Sabra04G0158500' => 'sbr', 'Sabra08G0159800' => 'sbr', 'Sabra10G0011500' => 'sbr', 'Sabra14G0104400' => 'sbr', 'SalBow2G2440' => 'sbo', 'SalBow4G2265' => 'sbo', 'Sc02g0000060' => 'sci', 'Sc05g0005020' => 'sci', 'Sc13g0003890' => 'sci', 'Sed0014865' => 'sed', 'Sed0017224' => 'sed', 'Sed0026391' => 'sed', 'SEGI_00063' => 'sgi', 'SEGI_10967' => 'sgi', 'SEGI_17510' => 'sgi', 'SEGI_24396' => 'sgi', 'SEGI_39719' => 'sgi', 'SEGI_41392' => 'sgi', 'SGA_v2.0_scaffold11G05794' => 'sas', 'SGA_v2.0_scaffold142G35607' => 'sas', 'SGA_v2.0_scaffold1G00447' => 'sas', 'SHI15388' => 'shi', 'SHI15394' => 'shi', 'SHI15396' => 'shi', 'SHI15399' => 'shi', 'SMO343G0151' => 'smo', 'SMO367G1118' => 'smo', 'Solyc01g080200.3' => 'sly', 'Solyc06g008960.3' => 'sly', 'Solyc09g064780.3' => 'sly', 'Sopen01g031980' => 'spe', 'Sopen06g003710' => 'spe', 'Sopen09g026460' => 'spe', 'Sp3g21240' => 'spa', 'Sp4g30030' => 'spa', 'TAR365G0022' => 'tar', 'TAR365G1023' => 'tar', 'TAR365G1253' => 'tar', 'TAR623G0078' => 'tar', 'TAR623G1721' => 'tar', 'TAR633G0959' => 'tar', 'THA.LOC104802225' => 'tha', 'THA.LOC104804769' => 'tha', 'THA.LOC104808660' => 'tha', 'THA.LOC104812792' => 'tha', 'Thecc.01G284000' => 'tca', 'Thecc.04G220600' => 'tca', 'Thecc.05G268900' => 'tca', 'Thecc.08G171100' => 'tca', 'Thhalv10001284m.g' => 'esa', 'Thhalv10019912m.g' => 'esa', 'TPR.G14189' => 'tpr', 'TPR.G18110' => 'tpr', 'TPR.G18130' => 'tpr', 'TPR.G18131' => 'tpr', 'TPR.G18140' => 'tpr', 'TPR.G24282' => 'tpr', 'TPR.G25221' => 'tpr', 'TPR.G29267' => 'tpr', 'TPR.G35315' => 'tpr', 'TPR.G36173' => 'tpr', 'TWI09G0794' => 'twi', 'TWI59G1348' => 'twi', 'TWI74G0430' => 'twi', 'unitig_26.g8940' => 'ugi', 'unitig_749.g13744' => 'ugi', 'unitig_749.g13745' => 'ugi', 'vmacro08269' => 'vma', 'vmacro14937' => 'vma', 'vmacro20401' => 'vma', 'VMungo0464G1349' => 'vmu', 'VMungo0540G0289' => 'vmu', 'VMungo1215G1590' => 'vmu', 'VMungo1309G0221' => 'vmu', 'VMungo1309G2815' => 'vmu', 'VMungo1383G0239' => 'vmu', 'VMungo1383G2910' => 'vmu', 'Zm00001eb095270' => 'zma', 'Zm00001eb095280' => 'zma', 'Zm00001eb111630' => 'zma', 'Zm00001eb237080' => 'zma', 'Zm00001eb273740' => 'zma', 'Zm00001eb285040' => 'zma', 'Zm00001eb330790' => 'zma', 'Zm00001eb337380' => 'zma' ) $gf_id = 'HOM05D001484' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001484' ) $data_identifier = 'HOM05D001484' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 2, 'aly' => (int) 2, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 22, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 7, 'hma' => (int) 2, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 7, 'mtr' => (int) 10, 'cme' => (int) 2, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 4, 'ppa' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 4, 'qlo' => (int) 9, 'rch' => (int) 6, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 10, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 7, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb337380' $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' => 'HOM05D001484', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p31500' => 'bna', 'A05p00020' => 'bna', 'A07p08820' => 'bna', 'Aa31LG4G3300' => 'aar', 'Aa31LG8G10030' => 'aar', 'Actinidia00731' => 'ach', 'Actinidia11473' => 'ach', 'Actinidia23469' => 'ach', 'Actinidia24318' => 'ach', 'Actinidia40196' => 'ach', 'Actinidia40197' => 'ach', 'Actinidia40198' => 'ach', 'Ah.08g212990' => 'amhyb', 'Ah.15g091720' => 'amhyb', 'AL3G38260' => 'aly', 'AL4G47710' => 'aly', 'Aqoxy2G00671' => 'aox', 'Aqoxy2G03236' => 'aox', 'arahy.Tifrunner.gnm1.ann1.05IDCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KR684' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATY3SJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK6QJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6APGL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IDT7Z9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM073U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ0R87' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LE7RV4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT4QRX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V5ENPK' => 'arhy', 'AT2G48110' => 'ath', 'AT3G23590' => 'ath', 'ATR0626G186' => 'atr', 'ATR1127G141' => 'atr', 'Atru.chr4.2583' => 'acertr', 'Atru.chr5.1358' => 'acertr', 'Atru.chr5.1359' => 'acertr', 'Atru.chr8.46' => 'acertr', 'AUR62002640' => 'cqu', 'AUR62030055' => 'cqu', 'AUR62033713' => 'cqu', 'AUR62033714' => 'cqu', 'AUR62036795' => 'cqu', 'AUR62039891' => 'cqu', 'BcaB02g08737' => 'bca', 'BcaB04g20441' => 'bca', 'BcaB06g26509' => 'bca', 'BcaB06g26510' => 'bca', 'BcaB06g26511' => 'bca', 'BcaB06g26512' => 'bca', 'BcaB06g26513' => 'bca', 'BcaC02g12564' => 'bca', 'BcaC02g12565' => 'bca', 'BcaC02g12794' => 'bca', 'BcaC02g12795' => 'bca', 'BcaC02g12796' => 'bca', 'BcaC06g35541' => 'bca', 'BNapus_Darmor_BZH_scaffold_188p00080' => 'bna', 'BNapus_Darmor_BZH_scaffold_188p00090' => 'bna', 'BolC1t03972H' => 'bol', 'BolC1t03973H' => 'bol', 'BolC4t21680H' => 'bol', 'BolC7t41863H' => 'bol', 'BolSC55t61227H' => 'bol', 'BolSC55t61228H' => 'bol', 'BraA01t03278Z' => 'bra', 'BraA05t18998Z' => 'bra', 'BraA07t28673Z' => 'bra', 'C01p40150' => 'bna', 'C05p12370' => 'bna', 'C07p13680' => 'bna', 'CAN.G1006.16' => 'can', 'CAN.G1006.17' => 'can', 'CAN.G1170.2' => 'can', 'CAN.G962.7' => 'can', 'CANSAT25G2179' => 'cansat', 'CANSAT78G1573' => 'cansat', 'CARHR099510' => 'chi', 'CARHR143510' => 'chi', 'Carub.0003s2380' => 'cru', 'Carub.0004s3082' => 'cru', 'Ca_00614_v3' => 'car', 'Ca_07801_v3' => 'car', 'Ca_08567_v3' => 'car', 'Ca_09571_v3' => 'car', 'CBR_g19290' => 'cbr', 'Cc01_g19770' => 'ccan', 'Cc03_g03030' => 'ccan', 'CDE07G0968' => 'cde', 'CDE09G1441' => 'cde', 'Cfa006103' => 'cfa', 'Cfa015573' => 'cfa', 'Cfa016988' => 'cfa', 'Ciclev10006738m.g' => 'ccl', 'Ciclev10010920m.g' => 'ccl', 'Ciclev10018517m.g' => 'ccl', 'CiPaw.01G159200' => 'cil', 'CiPaw.02G091000' => 'cil', 'CiPaw.02G091100' => 'cil', 'CiPaw.08G103100' => 'cil', 'CiPaw.09G224900' => 'cil', 'ClCG06G005740' => 'cla', 'ClCG07G000090' => 'cla', 'ClCG07G000100' => 'cla', 'COL.COLO4_09143' => 'col', 'COL.COLO4_25124' => 'col', 'Cpa.g.sc16.34' => 'cpa', 'Cpa.g.sc3504.1' => 'cpa', 'Cpa.g.sc60.37' => 'cpa', 'CsaV3_6G018520' => 'csa', 'CsaV3_6G036860' => 'csa', 'CSS0001072' => 'camsi', 'CSS0020208' => 'camsi', 'CSS0021253' => 'camsi', 'CSS0022190' => 'camsi', 'CSS0036150' => 'camsi', 'CSS0040442' => 'camsi', 'CSS0042300' => 'camsi', 'CSS0045298' => 'camsi', 'DCAR_012449' => 'dca', 'DCAR_018405' => 'dca', 'DCAR_024573' => 'dca', 'DCAR_030591' => 'dca', 'Dinv16926' => 'din', 'Dinv32963' => 'din', 'Dinv38382' => 'din', 'Dinv38383' => 'din', 'Duzib133G0974' => 'dzi', 'Duzib138G1867' => 'dzi', 'Duzib211G0420' => 'dzi', 'Duzib212G0930' => 'dzi', 'ECA234G1645' => 'eca', 'ECA247G3467' => 'eca', 'ECA248G1703' => 'eca', 'EL10Ac3g06327' => 'bvu', 'EL10Ac7g17204' => 'bvu', 'Eucgr.A00855' => 'egr', 'Eucgr.A00858' => 'egr', 'Eucgr.H01520' => 'egr', 'Eucgr.H03604' => 'egr', 'Eucgr.L03465' => 'egr', 'Eucgr.L03466' => 'egr', 'FAN01G0988' => 'fan', 'FAN02G3892' => 'fan', 'FAN05G3381' => 'fan', 'FAN07G0967' => 'fan', 'FAN07G1493' => 'fan', 'FAN08G3125' => 'fan', 'FAN09G0402' => 'fan', 'FAN12G2594' => 'fan', 'FAN12G3879' => 'fan', 'FAN14G1546' => 'fan', 'FAN15G3626' => 'fan', 'FAN17G0588' => 'fan', 'FAN17G0609' => 'fan', 'FAN18G2817' => 'fan', 'FAN19G1305' => 'fan', 'FAN20G1787' => 'fan', 'FAN22G0073' => 'fan', 'FAN22G0352' => 'fan', 'FAN22G0368' => 'fan', 'FAN22G2273' => 'fan', 'FAN24G1998' => 'fan', 'FAN27G1317' => 'fan', 'FvH4_2g23980' => 'fve', 'FvH4_4g14380' => 'fve', 'FvH4_4g14390' => 'fve', 'FvH4_6g09250' => 'fve', 'Glyma.03G151100' => 'gma', 'Glyma.04G122550' => 'gma', 'Glyma.05G001600' => 'gma', 'Glyma.09G270766' => 'gma', 'Glyma.09G270832' => 'gma', 'Glyma.13G209800' => 'gma', 'Glyma.15G102800' => 'gma', 'Glyma.18G218900' => 'gma', 'Glyma.19G001500' => 'gma', 'Glyma.19G153600' => 'gma', 'Gohir.A02G028600' => 'ghi', 'Gohir.A08G045000' => 'ghi', 'Gohir.A11G120500' => 'ghi', 'Gohir.A12G006200' => 'ghi', 'Gohir.A12G006250' => 'ghi', 'Gohir.D02G036300' => 'ghi', 'Gohir.D08G054700' => 'ghi', 'Gohir.D11G125600' => 'ghi', 'Gohir.D12G005700' => 'ghi', 'Gorai.004G055200' => 'gra', 'Gorai.005G040400' => 'gra', 'Gorai.007G134500' => 'gra', 'Gorai.008G005500' => 'gra', 'GSVIVG01011094001' => 'vvi', 'GSVIVG01017879001' => 'vvi', 'GSVIVG01025988001' => 'vvi', 'GSVIVG01029847001' => 'vvi', 'HanXRQChr10g0282901' => 'han', 'HanXRQChr10g0310371' => 'han', 'HanXRQChr10g0315041' => 'han', 'HanXRQChr11g0327651' => 'han', 'HanXRQChr12g0359391' => 'han', 'Haze_00972' => 'cav', 'Haze_00973' => 'cav', 'Haze_00974' => 'cav', 'Haze_04747' => 'cav', 'Haze_04749' => 'cav', 'Haze_04750' => 'cav', 'Haze_21217' => 'cav', 'Hma1.2p1_1037F.1_g250680' => 'hma', 'Hma1.2p1_1644F.1_g295320' => 'hma', 'HPP92_011322' => 'vpl', 'HPP92_011323' => 'vpl', 'HPP92_011324' => 'vpl', 'HPP92_011325' => 'vpl', 'HPP92_011326' => 'vpl', 'Hund12205' => 'sun', 'Hund17957' => 'sun', 'Lalb_Chr06g0176771' => 'lal', 'Lalb_Chr18g0056021' => 'lal', 'Lalb_Chr18g0056031' => 'lal', 'Lalb_Chr18g0056041' => 'lal', 'Lalb_Chr20g0107751' => 'lal', 'Lalb_Chr20g0118371' => 'lal', 'Lj1g0010239' => 'lja', 'Lj1g0017101' => 'lja', 'Lj2A1178G40' => 'lonja', 'Lj2A54G84' => 'lonja', 'Lj2g0015248' => 'lja', 'Lj3A761T51' => 'lonja', 'Lj6g0018116' => 'lja', 'Lsat_1_v5_gn_4_136040' => 'lsa', 'Lsat_1_v5_gn_5_187461' => 'lsa', 'Lsat_1_v5_gn_5_77001' => 'lsa', 'Lsat_1_v5_gn_9_4461' => 'lsa', 'Manes.01G210100' => 'mes', 'Manes.03G185600' => 'mes', 'Manes.05G073300' => 'mes', 'Manes.09G120300' => 'mes', 'Manes.15G022100' => 'mes', 'Mapoly0096s0053' => 'mpo', 'MBI03_g14058_MAGBIO' => 'mbi', 'MBI03_g33876_MAGBIO' => 'mbi', 'MBI03_g36854_MAGBIO' => 'mbi', 'MBI17_g11997_MAGBIO' => 'mbi', 'MD03G1269000' => 'mdo', 'MD04G1179600' => 'mdo', 'MD11G1289800' => 'mdo', 'MD12G1194700' => 'mdo', 'MD13G1182100' => 'mdo', 'MD13G1182200' => 'mdo', 'MD16G1182600' => 'mdo', 'Medtr2g021400' => 'mtr', 'Medtr2g021470' => 'mtr', 'Medtr2g105810' => 'mtr', 'Medtr3g033580' => 'mtr', 'Medtr6g007970' => 'mtr', 'Medtr7g056330' => 'mtr', 'Medtr7g074290' => 'mtr', 'Medtr7g074380' => 'mtr', 'Medtr7g094550' => 'mtr', 'Medtr8g069995' => 'mtr', 'MELO3C014345.2' => 'cme', 'MELO3C021395.2' => 'cme', 'Migut.D00262' => 'egut', 'Migut.G00257' => 'egut', 'MSTRG.21575' => 'ama', 'MSTRG.3985' => 'ama', 'Nitab4.5_0000295g0140' => 'nta', 'Nitab4.5_0000732g0140' => 'nta', 'Nitab4.5_0003162g0020' => 'nta', 'Nitab4.5_0006180g0090' => 'nta', 'Nitab4.5_0006390g0010' => 'nta', 'Nitab4.5_0007392g0040' => 'nta', 'Nn1g02140' => 'nnu', 'Nn4g26168' => 'nnu', 'Nn5g26754' => 'nnu', 'Oeu001433.1' => 'oeu', 'Oeu010299.2' => 'oeu', 'Oeu011171.1' => 'oeu', 'Oeu037675.1' => 'oeu', 'Oeu038359.1' => 'oeu', 'Oeu063834.1' => 'oeu', 'Oeu063835.1' => 'oeu', 'Os05g0312000' => 'osa', 'Os07g0211101' => 'osa', 'Os07g0211200' => 'osa', 'Os07g0681500' => 'osa', 'Peaxi162Scf00095g01015' => 'pax', 'Peaxi162Scf00104g00329' => 'pax', 'Peaxi162Scf00161g00137' => 'pax', 'PGR004G1665' => 'pgr', 'PGR031G2937' => 'pgr', 'PGR119G2145' => 'pgr', 'PGSC0003DMG400004351' => 'stu', 'PGSC0003DMG400014625' => 'stu', 'PGSC0003DMG401000943' => 'stu', 'Phvul.001G148600' => 'pvu', 'Phvul.004G001700' => 'pvu', 'Phvul.006G154900' => 'pvu', 'Phvul.008G078200' => 'pvu', 'Phvul.011G136500' => 'pvu', 'Potri.002G215600' => 'ptr', 'Potri.008G201600' => 'ptr', 'Potri.014G138400' => 'ptr', 'Potri.016G142500' => 'ptr', 'Pp3c16_10580' => 'ppa', 'Pp3c5_25280' => 'ppa', 'Prupe.1G150000' => 'ppe', 'Prupe.1G150100' => 'ppe', 'Prupe.6G299600' => 'ppe', 'Prupe.8G245000' => 'ppe', 'Psat0s4927g0040' => 'psa', 'Psat1g052080' => 'psa', 'Psat1g183800' => 'psa', 'Psat3g113840' => 'psa', 'Psat3g126120' => 'psa', 'Psat3g126160' => 'psa', 'Psat3g158760' => 'psa', 'Psat3g158840' => 'psa', 'PSO170G2858' => 'pso', 'PSO339G0606' => 'pso', 'PSO384G4709' => 'pso', 'PSO407G0334' => 'pso', 'QL04p040276' => 'qlo', 'QL06p005458' => 'qlo', 'QL06p005472' => 'qlo', 'QL07p030546' => 'qlo', 'QL07p031519' => 'qlo', 'QL09p050949' => 'qlo', 'QL09p050966' => 'qlo', 'QL09p051067' => 'qlo', 'QL12p022706' => 'qlo', 'RcHm_v2.0_Chr2g0119601' => 'rch', 'RcHm_v2.0_Chr3g0459591' => 'rch', 'RcHm_v2.0_Chr4g0418521' => 'rch', 'RcHm_v2.0_Chr4g0418531' => 'rch', 'RcHm_v2.0_Chr4g0418541' => 'rch', 'RcHm_v2.0_Chr6g0291641' => 'rch', 'Rhsim01G0086300' => 'rsi', 'Rhsim01G0276300' => 'rsi', 'Rhsim01G0276500' => 'rsi', 'Rhsim04G0207700' => 'rsi', 'Rhsim05G0234500' => 'rsi', 'Rhsim13G0022400' => 'rsi', 'Sabra02G0167900' => 'sbr', 'Sabra04G0158500' => 'sbr', 'Sabra08G0159800' => 'sbr', 'Sabra10G0011500' => 'sbr', 'Sabra14G0104400' => 'sbr', 'SalBow2G2440' => 'sbo', 'SalBow4G2265' => 'sbo', 'Sc02g0000060' => 'sci', 'Sc05g0005020' => 'sci', 'Sc13g0003890' => 'sci', 'Sed0014865' => 'sed', 'Sed0017224' => 'sed', 'Sed0026391' => 'sed', 'SEGI_00063' => 'sgi', 'SEGI_10967' => 'sgi', 'SEGI_17510' => 'sgi', 'SEGI_24396' => 'sgi', 'SEGI_39719' => 'sgi', 'SEGI_41392' => 'sgi', 'SGA_v2.0_scaffold11G05794' => 'sas', 'SGA_v2.0_scaffold142G35607' => 'sas', 'SGA_v2.0_scaffold1G00447' => 'sas', 'SHI15388' => 'shi', 'SHI15394' => 'shi', 'SHI15396' => 'shi', 'SHI15399' => 'shi', 'SMO343G0151' => 'smo', 'SMO367G1118' => 'smo', 'Solyc01g080200.3' => 'sly', 'Solyc06g008960.3' => 'sly', 'Solyc09g064780.3' => 'sly', 'Sopen01g031980' => 'spe', 'Sopen06g003710' => 'spe', 'Sopen09g026460' => 'spe', 'Sp3g21240' => 'spa', 'Sp4g30030' => 'spa', 'TAR365G0022' => 'tar', 'TAR365G1023' => 'tar', 'TAR365G1253' => 'tar', 'TAR623G0078' => 'tar', 'TAR623G1721' => 'tar', 'TAR633G0959' => 'tar', 'THA.LOC104802225' => 'tha', 'THA.LOC104804769' => 'tha', 'THA.LOC104808660' => 'tha', 'THA.LOC104812792' => 'tha', 'Thecc.01G284000' => 'tca', 'Thecc.04G220600' => 'tca', 'Thecc.05G268900' => 'tca', 'Thecc.08G171100' => 'tca', 'Thhalv10001284m.g' => 'esa', 'Thhalv10019912m.g' => 'esa', 'TPR.G14189' => 'tpr', 'TPR.G18110' => 'tpr', 'TPR.G18130' => 'tpr', 'TPR.G18131' => 'tpr', 'TPR.G18140' => 'tpr', 'TPR.G24282' => 'tpr', 'TPR.G25221' => 'tpr', 'TPR.G29267' => 'tpr', 'TPR.G35315' => 'tpr', 'TPR.G36173' => 'tpr', 'TWI09G0794' => 'twi', 'TWI59G1348' => 'twi', 'TWI74G0430' => 'twi', 'unitig_26.g8940' => 'ugi', 'unitig_749.g13744' => 'ugi', 'unitig_749.g13745' => 'ugi', 'vmacro08269' => 'vma', 'vmacro14937' => 'vma', 'vmacro20401' => 'vma', 'VMungo0464G1349' => 'vmu', 'VMungo0540G0289' => 'vmu', 'VMungo1215G1590' => 'vmu', 'VMungo1309G0221' => 'vmu', 'VMungo1309G2815' => 'vmu', 'VMungo1383G0239' => 'vmu', 'VMungo1383G2910' => 'vmu', 'Zm00001eb095270' => 'zma', 'Zm00001eb095280' => 'zma', 'Zm00001eb111630' => 'zma', 'Zm00001eb237080' => 'zma', 'Zm00001eb273740' => 'zma', 'Zm00001eb285040' => 'zma', 'Zm00001eb330790' => 'zma', 'Zm00001eb337380' => 'zma' ), 'gf_id' => 'HOM05D001484', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001484' ), 'data_identifier' => 'HOM05D001484', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001484', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p31500' => 'bna', 'A05p00020' => 'bna', 'A07p08820' => 'bna', 'Aa31LG4G3300' => 'aar', 'Aa31LG8G10030' => 'aar', 'Actinidia00731' => 'ach', 'Actinidia11473' => 'ach', 'Actinidia23469' => 'ach', 'Actinidia24318' => 'ach', 'Actinidia40196' => 'ach', 'Actinidia40197' => 'ach', 'Actinidia40198' => 'ach', 'Ah.08g212990' => 'amhyb', 'Ah.15g091720' => 'amhyb', 'AL3G38260' => 'aly', 'AL4G47710' => 'aly', 'Aqoxy2G00671' => 'aox', 'Aqoxy2G03236' => 'aox', 'arahy.Tifrunner.gnm1.ann1.05IDCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KR684' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATY3SJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK6QJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6APGL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IDT7Z9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM073U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ0R87' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LE7RV4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT4QRX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V5ENPK' => 'arhy', 'AT2G48110' => 'ath', 'AT3G23590' => 'ath', 'ATR0626G186' => 'atr', 'ATR1127G141' => 'atr', 'Atru.chr4.2583' => 'acertr', 'Atru.chr5.1358' => 'acertr', 'Atru.chr5.1359' => 'acertr', 'Atru.chr8.46' => 'acertr', 'AUR62002640' => 'cqu', 'AUR62030055' => 'cqu', 'AUR62033713' => 'cqu', 'AUR62033714' => 'cqu', 'AUR62036795' => 'cqu', 'AUR62039891' => 'cqu', 'BcaB02g08737' => 'bca', 'BcaB04g20441' => 'bca', 'BcaB06g26509' => 'bca', 'BcaB06g26510' => 'bca', 'BcaB06g26511' => 'bca', 'BcaB06g26512' => 'bca', 'BcaB06g26513' => 'bca', 'BcaC02g12564' => 'bca', 'BcaC02g12565' => 'bca', 'BcaC02g12794' => 'bca', 'BcaC02g12795' => 'bca', 'BcaC02g12796' => 'bca', 'BcaC06g35541' => 'bca', 'BNapus_Darmor_BZH_scaffold_188p00080' => 'bna', 'BNapus_Darmor_BZH_scaffold_188p00090' => 'bna', 'BolC1t03972H' => 'bol', 'BolC1t03973H' => 'bol', 'BolC4t21680H' => 'bol', 'BolC7t41863H' => 'bol', 'BolSC55t61227H' => 'bol', 'BolSC55t61228H' => 'bol', 'BraA01t03278Z' => 'bra', 'BraA05t18998Z' => 'bra', 'BraA07t28673Z' => 'bra', 'C01p40150' => 'bna', 'C05p12370' => 'bna', 'C07p13680' => 'bna', 'CAN.G1006.16' => 'can', 'CAN.G1006.17' => 'can', 'CAN.G1170.2' => 'can', 'CAN.G962.7' => 'can', 'CANSAT25G2179' => 'cansat', 'CANSAT78G1573' => 'cansat', 'CARHR099510' => 'chi', 'CARHR143510' => 'chi', 'Carub.0003s2380' => 'cru', 'Carub.0004s3082' => 'cru', 'Ca_00614_v3' => 'car', 'Ca_07801_v3' => 'car', 'Ca_08567_v3' => 'car', 'Ca_09571_v3' => 'car', 'CBR_g19290' => 'cbr', 'Cc01_g19770' => 'ccan', 'Cc03_g03030' => 'ccan', 'CDE07G0968' => 'cde', 'CDE09G1441' => 'cde', 'Cfa006103' => 'cfa', 'Cfa015573' => 'cfa', 'Cfa016988' => 'cfa', 'Ciclev10006738m.g' => 'ccl', 'Ciclev10010920m.g' => 'ccl', 'Ciclev10018517m.g' => 'ccl', 'CiPaw.01G159200' => 'cil', 'CiPaw.02G091000' => 'cil', 'CiPaw.02G091100' => 'cil', 'CiPaw.08G103100' => 'cil', 'CiPaw.09G224900' => 'cil', 'ClCG06G005740' => 'cla', 'ClCG07G000090' => 'cla', 'ClCG07G000100' => 'cla', 'COL.COLO4_09143' => 'col', 'COL.COLO4_25124' => 'col', 'Cpa.g.sc16.34' => 'cpa', 'Cpa.g.sc3504.1' => 'cpa', 'Cpa.g.sc60.37' => 'cpa', 'CsaV3_6G018520' => 'csa', 'CsaV3_6G036860' => 'csa', 'CSS0001072' => 'camsi', 'CSS0020208' => 'camsi', 'CSS0021253' => 'camsi', 'CSS0022190' => 'camsi', 'CSS0036150' => 'camsi', 'CSS0040442' => 'camsi', 'CSS0042300' => 'camsi', 'CSS0045298' => 'camsi', 'DCAR_012449' => 'dca', 'DCAR_018405' => 'dca', 'DCAR_024573' => 'dca', 'DCAR_030591' => 'dca', 'Dinv16926' => 'din', 'Dinv32963' => 'din', 'Dinv38382' => 'din', 'Dinv38383' => 'din', 'Duzib133G0974' => 'dzi', 'Duzib138G1867' => 'dzi', 'Duzib211G0420' => 'dzi', 'Duzib212G0930' => 'dzi', 'ECA234G1645' => 'eca', 'ECA247G3467' => 'eca', 'ECA248G1703' => 'eca', 'EL10Ac3g06327' => 'bvu', 'EL10Ac7g17204' => 'bvu', 'Eucgr.A00855' => 'egr', 'Eucgr.A00858' => 'egr', 'Eucgr.H01520' => 'egr', 'Eucgr.H03604' => 'egr', 'Eucgr.L03465' => 'egr', 'Eucgr.L03466' => 'egr', 'FAN01G0988' => 'fan', 'FAN02G3892' => 'fan', 'FAN05G3381' => 'fan', 'FAN07G0967' => 'fan', 'FAN07G1493' => 'fan', 'FAN08G3125' => 'fan', 'FAN09G0402' => 'fan', 'FAN12G2594' => 'fan', 'FAN12G3879' => 'fan', 'FAN14G1546' => 'fan', 'FAN15G3626' => 'fan', 'FAN17G0588' => 'fan', 'FAN17G0609' => 'fan', 'FAN18G2817' => 'fan', 'FAN19G1305' => 'fan', 'FAN20G1787' => 'fan', 'FAN22G0073' => 'fan', 'FAN22G0352' => 'fan', 'FAN22G0368' => 'fan', 'FAN22G2273' => 'fan', 'FAN24G1998' => 'fan', 'FAN27G1317' => 'fan', 'FvH4_2g23980' => 'fve', 'FvH4_4g14380' => 'fve', 'FvH4_4g14390' => 'fve', 'FvH4_6g09250' => 'fve', 'Glyma.03G151100' => 'gma', 'Glyma.04G122550' => 'gma', 'Glyma.05G001600' => 'gma', 'Glyma.09G270766' => 'gma', 'Glyma.09G270832' => 'gma', 'Glyma.13G209800' => 'gma', 'Glyma.15G102800' => 'gma', 'Glyma.18G218900' => 'gma', 'Glyma.19G001500' => 'gma', 'Glyma.19G153600' => 'gma', 'Gohir.A02G028600' => 'ghi', 'Gohir.A08G045000' => 'ghi', 'Gohir.A11G120500' => 'ghi', 'Gohir.A12G006200' => 'ghi', 'Gohir.A12G006250' => 'ghi', 'Gohir.D02G036300' => 'ghi', 'Gohir.D08G054700' => 'ghi', 'Gohir.D11G125600' => 'ghi', 'Gohir.D12G005700' => 'ghi', 'Gorai.004G055200' => 'gra', 'Gorai.005G040400' => 'gra', 'Gorai.007G134500' => 'gra', 'Gorai.008G005500' => 'gra', 'GSVIVG01011094001' => 'vvi', 'GSVIVG01017879001' => 'vvi', 'GSVIVG01025988001' => 'vvi', 'GSVIVG01029847001' => 'vvi', 'HanXRQChr10g0282901' => 'han', 'HanXRQChr10g0310371' => 'han', 'HanXRQChr10g0315041' => 'han', 'HanXRQChr11g0327651' => 'han', 'HanXRQChr12g0359391' => 'han', 'Haze_00972' => 'cav', 'Haze_00973' => 'cav', 'Haze_00974' => 'cav', 'Haze_04747' => 'cav', 'Haze_04749' => 'cav', 'Haze_04750' => 'cav', 'Haze_21217' => 'cav', 'Hma1.2p1_1037F.1_g250680' => 'hma', 'Hma1.2p1_1644F.1_g295320' => 'hma', 'HPP92_011322' => 'vpl', 'HPP92_011323' => 'vpl', 'HPP92_011324' => 'vpl', 'HPP92_011325' => 'vpl', 'HPP92_011326' => 'vpl', 'Hund12205' => 'sun', 'Hund17957' => 'sun', 'Lalb_Chr06g0176771' => 'lal', 'Lalb_Chr18g0056021' => 'lal', 'Lalb_Chr18g0056031' => 'lal', 'Lalb_Chr18g0056041' => 'lal', 'Lalb_Chr20g0107751' => 'lal', 'Lalb_Chr20g0118371' => 'lal', 'Lj1g0010239' => 'lja', 'Lj1g0017101' => 'lja', 'Lj2A1178G40' => 'lonja', 'Lj2A54G84' => 'lonja', 'Lj2g0015248' => 'lja', 'Lj3A761T51' => 'lonja', 'Lj6g0018116' => 'lja', 'Lsat_1_v5_gn_4_136040' => 'lsa', 'Lsat_1_v5_gn_5_187461' => 'lsa', 'Lsat_1_v5_gn_5_77001' => 'lsa', 'Lsat_1_v5_gn_9_4461' => 'lsa', 'Manes.01G210100' => 'mes', 'Manes.03G185600' => 'mes', 'Manes.05G073300' => 'mes', 'Manes.09G120300' => 'mes', 'Manes.15G022100' => 'mes', 'Mapoly0096s0053' => 'mpo', 'MBI03_g14058_MAGBIO' => 'mbi', 'MBI03_g33876_MAGBIO' => 'mbi', 'MBI03_g36854_MAGBIO' => 'mbi', 'MBI17_g11997_MAGBIO' => 'mbi', 'MD03G1269000' => 'mdo', 'MD04G1179600' => 'mdo', 'MD11G1289800' => 'mdo', 'MD12G1194700' => 'mdo', 'MD13G1182100' => 'mdo', 'MD13G1182200' => 'mdo', 'MD16G1182600' => 'mdo', 'Medtr2g021400' => 'mtr', 'Medtr2g021470' => 'mtr', 'Medtr2g105810' => 'mtr', 'Medtr3g033580' => 'mtr', 'Medtr6g007970' => 'mtr', 'Medtr7g056330' => 'mtr', 'Medtr7g074290' => 'mtr', 'Medtr7g074380' => 'mtr', 'Medtr7g094550' => 'mtr', 'Medtr8g069995' => 'mtr', 'MELO3C014345.2' => 'cme', 'MELO3C021395.2' => 'cme', 'Migut.D00262' => 'egut', 'Migut.G00257' => 'egut', 'MSTRG.21575' => 'ama', 'MSTRG.3985' => 'ama', 'Nitab4.5_0000295g0140' => 'nta', 'Nitab4.5_0000732g0140' => 'nta', 'Nitab4.5_0003162g0020' => 'nta', 'Nitab4.5_0006180g0090' => 'nta', 'Nitab4.5_0006390g0010' => 'nta', 'Nitab4.5_0007392g0040' => 'nta', 'Nn1g02140' => 'nnu', 'Nn4g26168' => 'nnu', 'Nn5g26754' => 'nnu', 'Oeu001433.1' => 'oeu', 'Oeu010299.2' => 'oeu', 'Oeu011171.1' => 'oeu', 'Oeu037675.1' => 'oeu', 'Oeu038359.1' => 'oeu', 'Oeu063834.1' => 'oeu', 'Oeu063835.1' => 'oeu', 'Os05g0312000' => 'osa', 'Os07g0211101' => 'osa', 'Os07g0211200' => 'osa', 'Os07g0681500' => 'osa', 'Peaxi162Scf00095g01015' => 'pax', 'Peaxi162Scf00104g00329' => 'pax', 'Peaxi162Scf00161g00137' => 'pax', 'PGR004G1665' => 'pgr', 'PGR031G2937' => 'pgr', 'PGR119G2145' => 'pgr', 'PGSC0003DMG400004351' => 'stu', 'PGSC0003DMG400014625' => 'stu', 'PGSC0003DMG401000943' => 'stu', 'Phvul.001G148600' => 'pvu', 'Phvul.004G001700' => 'pvu', 'Phvul.006G154900' => 'pvu', 'Phvul.008G078200' => 'pvu', 'Phvul.011G136500' => 'pvu', 'Potri.002G215600' => 'ptr', 'Potri.008G201600' => 'ptr', 'Potri.014G138400' => 'ptr', 'Potri.016G142500' => 'ptr', 'Pp3c16_10580' => 'ppa', 'Pp3c5_25280' => 'ppa', 'Prupe.1G150000' => 'ppe', 'Prupe.1G150100' => 'ppe', 'Prupe.6G299600' => 'ppe', 'Prupe.8G245000' => 'ppe', 'Psat0s4927g0040' => 'psa', 'Psat1g052080' => 'psa', 'Psat1g183800' => 'psa', 'Psat3g113840' => 'psa', 'Psat3g126120' => 'psa', 'Psat3g126160' => 'psa', 'Psat3g158760' => 'psa', 'Psat3g158840' => 'psa', 'PSO170G2858' => 'pso', 'PSO339G0606' => 'pso', 'PSO384G4709' => 'pso', 'PSO407G0334' => 'pso', 'QL04p040276' => 'qlo', 'QL06p005458' => 'qlo', 'QL06p005472' => 'qlo', 'QL07p030546' => 'qlo', 'QL07p031519' => 'qlo', 'QL09p050949' => 'qlo', 'QL09p050966' => 'qlo', 'QL09p051067' => 'qlo', 'QL12p022706' => 'qlo', 'RcHm_v2.0_Chr2g0119601' => 'rch', 'RcHm_v2.0_Chr3g0459591' => 'rch', 'RcHm_v2.0_Chr4g0418521' => 'rch', 'RcHm_v2.0_Chr4g0418531' => 'rch', 'RcHm_v2.0_Chr4g0418541' => 'rch', 'RcHm_v2.0_Chr6g0291641' => 'rch', 'Rhsim01G0086300' => 'rsi', 'Rhsim01G0276300' => 'rsi', 'Rhsim01G0276500' => 'rsi', 'Rhsim04G0207700' => 'rsi', 'Rhsim05G0234500' => 'rsi', 'Rhsim13G0022400' => 'rsi', 'Sabra02G0167900' => 'sbr', 'Sabra04G0158500' => 'sbr', 'Sabra08G0159800' => 'sbr', 'Sabra10G0011500' => 'sbr', 'Sabra14G0104400' => 'sbr', 'SalBow2G2440' => 'sbo', 'SalBow4G2265' => 'sbo', 'Sc02g0000060' => 'sci', 'Sc05g0005020' => 'sci', 'Sc13g0003890' => 'sci', 'Sed0014865' => 'sed', 'Sed0017224' => 'sed', 'Sed0026391' => 'sed', 'SEGI_00063' => 'sgi', 'SEGI_10967' => 'sgi', 'SEGI_17510' => 'sgi', 'SEGI_24396' => 'sgi', 'SEGI_39719' => 'sgi', 'SEGI_41392' => 'sgi', 'SGA_v2.0_scaffold11G05794' => 'sas', 'SGA_v2.0_scaffold142G35607' => 'sas', 'SGA_v2.0_scaffold1G00447' => 'sas', 'SHI15388' => 'shi', 'SHI15394' => 'shi', 'SHI15396' => 'shi', 'SHI15399' => 'shi', 'SMO343G0151' => 'smo', 'SMO367G1118' => 'smo', 'Solyc01g080200.3' => 'sly', 'Solyc06g008960.3' => 'sly', 'Solyc09g064780.3' => 'sly', 'Sopen01g031980' => 'spe', 'Sopen06g003710' => 'spe', 'Sopen09g026460' => 'spe', 'Sp3g21240' => 'spa', 'Sp4g30030' => 'spa', 'TAR365G0022' => 'tar', 'TAR365G1023' => 'tar', 'TAR365G1253' => 'tar', 'TAR623G0078' => 'tar', 'TAR623G1721' => 'tar', 'TAR633G0959' => 'tar', 'THA.LOC104802225' => 'tha', 'THA.LOC104804769' => 'tha', 'THA.LOC104808660' => 'tha', 'THA.LOC104812792' => 'tha', 'Thecc.01G284000' => 'tca', 'Thecc.04G220600' => 'tca', 'Thecc.05G268900' => 'tca', 'Thecc.08G171100' => 'tca', 'Thhalv10001284m.g' => 'esa', 'Thhalv10019912m.g' => 'esa', 'TPR.G14189' => 'tpr', 'TPR.G18110' => 'tpr', 'TPR.G18130' => 'tpr', 'TPR.G18131' => 'tpr', 'TPR.G18140' => 'tpr', 'TPR.G24282' => 'tpr', 'TPR.G25221' => 'tpr', 'TPR.G29267' => 'tpr', 'TPR.G35315' => 'tpr', 'TPR.G36173' => 'tpr', 'TWI09G0794' => 'twi', 'TWI59G1348' => 'twi', 'TWI74G0430' => 'twi', 'unitig_26.g8940' => 'ugi', 'unitig_749.g13744' => 'ugi', 'unitig_749.g13745' => 'ugi', 'vmacro08269' => 'vma', 'vmacro14937' => 'vma', 'vmacro20401' => 'vma', 'VMungo0464G1349' => 'vmu', 'VMungo0540G0289' => 'vmu', 'VMungo1215G1590' => 'vmu', 'VMungo1309G0221' => 'vmu', 'VMungo1309G2815' => 'vmu', 'VMungo1383G0239' => 'vmu', 'VMungo1383G2910' => 'vmu', 'Zm00001eb095270' => 'zma', 'Zm00001eb095280' => 'zma', 'Zm00001eb111630' => 'zma', 'Zm00001eb237080' => 'zma', 'Zm00001eb273740' => 'zma', 'Zm00001eb285040' => 'zma', 'Zm00001eb330790' => 'zma', 'Zm00001eb337380' => 'zma' ) $gf_id = 'HOM05D001484' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001484' ) $data_identifier = 'HOM05D001484' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 2, 'aly' => (int) 2, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 22, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 7, 'hma' => (int) 2, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 7, 'mtr' => (int) 10, 'cme' => (int) 2, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 4, 'ppa' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 4, 'qlo' => (int) 9, 'rch' => (int) 6, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 10, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 7, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb337380' $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' => 'HOM05D001484', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p31500' => 'bna', 'A05p00020' => 'bna', 'A07p08820' => 'bna', 'Aa31LG4G3300' => 'aar', 'Aa31LG8G10030' => 'aar', 'Actinidia00731' => 'ach', 'Actinidia11473' => 'ach', 'Actinidia23469' => 'ach', 'Actinidia24318' => 'ach', 'Actinidia40196' => 'ach', 'Actinidia40197' => 'ach', 'Actinidia40198' => 'ach', 'Ah.08g212990' => 'amhyb', 'Ah.15g091720' => 'amhyb', 'AL3G38260' => 'aly', 'AL4G47710' => 'aly', 'Aqoxy2G00671' => 'aox', 'Aqoxy2G03236' => 'aox', 'arahy.Tifrunner.gnm1.ann1.05IDCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KR684' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATY3SJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK6QJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6APGL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IDT7Z9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM073U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ0R87' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LE7RV4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT4QRX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V5ENPK' => 'arhy', 'AT2G48110' => 'ath', 'AT3G23590' => 'ath', 'ATR0626G186' => 'atr', 'ATR1127G141' => 'atr', 'Atru.chr4.2583' => 'acertr', 'Atru.chr5.1358' => 'acertr', 'Atru.chr5.1359' => 'acertr', 'Atru.chr8.46' => 'acertr', 'AUR62002640' => 'cqu', 'AUR62030055' => 'cqu', 'AUR62033713' => 'cqu', 'AUR62033714' => 'cqu', 'AUR62036795' => 'cqu', 'AUR62039891' => 'cqu', 'BcaB02g08737' => 'bca', 'BcaB04g20441' => 'bca', 'BcaB06g26509' => 'bca', 'BcaB06g26510' => 'bca', 'BcaB06g26511' => 'bca', 'BcaB06g26512' => 'bca', 'BcaB06g26513' => 'bca', 'BcaC02g12564' => 'bca', 'BcaC02g12565' => 'bca', 'BcaC02g12794' => 'bca', 'BcaC02g12795' => 'bca', 'BcaC02g12796' => 'bca', 'BcaC06g35541' => 'bca', 'BNapus_Darmor_BZH_scaffold_188p00080' => 'bna', 'BNapus_Darmor_BZH_scaffold_188p00090' => 'bna', 'BolC1t03972H' => 'bol', 'BolC1t03973H' => 'bol', 'BolC4t21680H' => 'bol', 'BolC7t41863H' => 'bol', 'BolSC55t61227H' => 'bol', 'BolSC55t61228H' => 'bol', 'BraA01t03278Z' => 'bra', 'BraA05t18998Z' => 'bra', 'BraA07t28673Z' => 'bra', 'C01p40150' => 'bna', 'C05p12370' => 'bna', 'C07p13680' => 'bna', 'CAN.G1006.16' => 'can', 'CAN.G1006.17' => 'can', 'CAN.G1170.2' => 'can', 'CAN.G962.7' => 'can', 'CANSAT25G2179' => 'cansat', 'CANSAT78G1573' => 'cansat', 'CARHR099510' => 'chi', 'CARHR143510' => 'chi', 'Carub.0003s2380' => 'cru', 'Carub.0004s3082' => 'cru', 'Ca_00614_v3' => 'car', 'Ca_07801_v3' => 'car', 'Ca_08567_v3' => 'car', 'Ca_09571_v3' => 'car', 'CBR_g19290' => 'cbr', 'Cc01_g19770' => 'ccan', 'Cc03_g03030' => 'ccan', 'CDE07G0968' => 'cde', 'CDE09G1441' => 'cde', 'Cfa006103' => 'cfa', 'Cfa015573' => 'cfa', 'Cfa016988' => 'cfa', 'Ciclev10006738m.g' => 'ccl', 'Ciclev10010920m.g' => 'ccl', 'Ciclev10018517m.g' => 'ccl', 'CiPaw.01G159200' => 'cil', 'CiPaw.02G091000' => 'cil', 'CiPaw.02G091100' => 'cil', 'CiPaw.08G103100' => 'cil', 'CiPaw.09G224900' => 'cil', 'ClCG06G005740' => 'cla', 'ClCG07G000090' => 'cla', 'ClCG07G000100' => 'cla', 'COL.COLO4_09143' => 'col', 'COL.COLO4_25124' => 'col', 'Cpa.g.sc16.34' => 'cpa', 'Cpa.g.sc3504.1' => 'cpa', 'Cpa.g.sc60.37' => 'cpa', 'CsaV3_6G018520' => 'csa', 'CsaV3_6G036860' => 'csa', 'CSS0001072' => 'camsi', 'CSS0020208' => 'camsi', 'CSS0021253' => 'camsi', 'CSS0022190' => 'camsi', 'CSS0036150' => 'camsi', 'CSS0040442' => 'camsi', 'CSS0042300' => 'camsi', 'CSS0045298' => 'camsi', 'DCAR_012449' => 'dca', 'DCAR_018405' => 'dca', 'DCAR_024573' => 'dca', 'DCAR_030591' => 'dca', 'Dinv16926' => 'din', 'Dinv32963' => 'din', 'Dinv38382' => 'din', 'Dinv38383' => 'din', 'Duzib133G0974' => 'dzi', 'Duzib138G1867' => 'dzi', 'Duzib211G0420' => 'dzi', 'Duzib212G0930' => 'dzi', 'ECA234G1645' => 'eca', 'ECA247G3467' => 'eca', 'ECA248G1703' => 'eca', 'EL10Ac3g06327' => 'bvu', 'EL10Ac7g17204' => 'bvu', 'Eucgr.A00855' => 'egr', 'Eucgr.A00858' => 'egr', 'Eucgr.H01520' => 'egr', 'Eucgr.H03604' => 'egr', 'Eucgr.L03465' => 'egr', 'Eucgr.L03466' => 'egr', 'FAN01G0988' => 'fan', 'FAN02G3892' => 'fan', 'FAN05G3381' => 'fan', 'FAN07G0967' => 'fan', 'FAN07G1493' => 'fan', 'FAN08G3125' => 'fan', 'FAN09G0402' => 'fan', 'FAN12G2594' => 'fan', 'FAN12G3879' => 'fan', 'FAN14G1546' => 'fan', 'FAN15G3626' => 'fan', 'FAN17G0588' => 'fan', 'FAN17G0609' => 'fan', 'FAN18G2817' => 'fan', 'FAN19G1305' => 'fan', 'FAN20G1787' => 'fan', 'FAN22G0073' => 'fan', 'FAN22G0352' => 'fan', 'FAN22G0368' => 'fan', 'FAN22G2273' => 'fan', 'FAN24G1998' => 'fan', 'FAN27G1317' => 'fan', 'FvH4_2g23980' => 'fve', 'FvH4_4g14380' => 'fve', 'FvH4_4g14390' => 'fve', 'FvH4_6g09250' => 'fve', 'Glyma.03G151100' => 'gma', 'Glyma.04G122550' => 'gma', 'Glyma.05G001600' => 'gma', 'Glyma.09G270766' => 'gma', 'Glyma.09G270832' => 'gma', 'Glyma.13G209800' => 'gma', 'Glyma.15G102800' => 'gma', 'Glyma.18G218900' => 'gma', 'Glyma.19G001500' => 'gma', 'Glyma.19G153600' => 'gma', 'Gohir.A02G028600' => 'ghi', 'Gohir.A08G045000' => 'ghi', 'Gohir.A11G120500' => 'ghi', 'Gohir.A12G006200' => 'ghi', 'Gohir.A12G006250' => 'ghi', 'Gohir.D02G036300' => 'ghi', 'Gohir.D08G054700' => 'ghi', 'Gohir.D11G125600' => 'ghi', 'Gohir.D12G005700' => 'ghi', 'Gorai.004G055200' => 'gra', 'Gorai.005G040400' => 'gra', 'Gorai.007G134500' => 'gra', 'Gorai.008G005500' => 'gra', 'GSVIVG01011094001' => 'vvi', 'GSVIVG01017879001' => 'vvi', 'GSVIVG01025988001' => 'vvi', 'GSVIVG01029847001' => 'vvi', 'HanXRQChr10g0282901' => 'han', 'HanXRQChr10g0310371' => 'han', 'HanXRQChr10g0315041' => 'han', 'HanXRQChr11g0327651' => 'han', 'HanXRQChr12g0359391' => 'han', 'Haze_00972' => 'cav', 'Haze_00973' => 'cav', 'Haze_00974' => 'cav', 'Haze_04747' => 'cav', 'Haze_04749' => 'cav', 'Haze_04750' => 'cav', 'Haze_21217' => 'cav', 'Hma1.2p1_1037F.1_g250680' => 'hma', 'Hma1.2p1_1644F.1_g295320' => 'hma', 'HPP92_011322' => 'vpl', 'HPP92_011323' => 'vpl', 'HPP92_011324' => 'vpl', 'HPP92_011325' => 'vpl', 'HPP92_011326' => 'vpl', 'Hund12205' => 'sun', 'Hund17957' => 'sun', 'Lalb_Chr06g0176771' => 'lal', 'Lalb_Chr18g0056021' => 'lal', 'Lalb_Chr18g0056031' => 'lal', 'Lalb_Chr18g0056041' => 'lal', 'Lalb_Chr20g0107751' => 'lal', 'Lalb_Chr20g0118371' => 'lal', 'Lj1g0010239' => 'lja', 'Lj1g0017101' => 'lja', 'Lj2A1178G40' => 'lonja', 'Lj2A54G84' => 'lonja', 'Lj2g0015248' => 'lja', 'Lj3A761T51' => 'lonja', 'Lj6g0018116' => 'lja', 'Lsat_1_v5_gn_4_136040' => 'lsa', 'Lsat_1_v5_gn_5_187461' => 'lsa', 'Lsat_1_v5_gn_5_77001' => 'lsa', 'Lsat_1_v5_gn_9_4461' => 'lsa', 'Manes.01G210100' => 'mes', 'Manes.03G185600' => 'mes', 'Manes.05G073300' => 'mes', 'Manes.09G120300' => 'mes', 'Manes.15G022100' => 'mes', 'Mapoly0096s0053' => 'mpo', 'MBI03_g14058_MAGBIO' => 'mbi', 'MBI03_g33876_MAGBIO' => 'mbi', 'MBI03_g36854_MAGBIO' => 'mbi', 'MBI17_g11997_MAGBIO' => 'mbi', 'MD03G1269000' => 'mdo', 'MD04G1179600' => 'mdo', 'MD11G1289800' => 'mdo', 'MD12G1194700' => 'mdo', 'MD13G1182100' => 'mdo', 'MD13G1182200' => 'mdo', 'MD16G1182600' => 'mdo', 'Medtr2g021400' => 'mtr', 'Medtr2g021470' => 'mtr', 'Medtr2g105810' => 'mtr', 'Medtr3g033580' => 'mtr', 'Medtr6g007970' => 'mtr', 'Medtr7g056330' => 'mtr', 'Medtr7g074290' => 'mtr', 'Medtr7g074380' => 'mtr', 'Medtr7g094550' => 'mtr', 'Medtr8g069995' => 'mtr', 'MELO3C014345.2' => 'cme', 'MELO3C021395.2' => 'cme', 'Migut.D00262' => 'egut', 'Migut.G00257' => 'egut', 'MSTRG.21575' => 'ama', 'MSTRG.3985' => 'ama', 'Nitab4.5_0000295g0140' => 'nta', 'Nitab4.5_0000732g0140' => 'nta', 'Nitab4.5_0003162g0020' => 'nta', 'Nitab4.5_0006180g0090' => 'nta', 'Nitab4.5_0006390g0010' => 'nta', 'Nitab4.5_0007392g0040' => 'nta', 'Nn1g02140' => 'nnu', 'Nn4g26168' => 'nnu', 'Nn5g26754' => 'nnu', 'Oeu001433.1' => 'oeu', 'Oeu010299.2' => 'oeu', 'Oeu011171.1' => 'oeu', 'Oeu037675.1' => 'oeu', 'Oeu038359.1' => 'oeu', 'Oeu063834.1' => 'oeu', 'Oeu063835.1' => 'oeu', 'Os05g0312000' => 'osa', 'Os07g0211101' => 'osa', 'Os07g0211200' => 'osa', 'Os07g0681500' => 'osa', 'Peaxi162Scf00095g01015' => 'pax', 'Peaxi162Scf00104g00329' => 'pax', 'Peaxi162Scf00161g00137' => 'pax', 'PGR004G1665' => 'pgr', 'PGR031G2937' => 'pgr', 'PGR119G2145' => 'pgr', 'PGSC0003DMG400004351' => 'stu', 'PGSC0003DMG400014625' => 'stu', 'PGSC0003DMG401000943' => 'stu', 'Phvul.001G148600' => 'pvu', 'Phvul.004G001700' => 'pvu', 'Phvul.006G154900' => 'pvu', 'Phvul.008G078200' => 'pvu', 'Phvul.011G136500' => 'pvu', 'Potri.002G215600' => 'ptr', 'Potri.008G201600' => 'ptr', 'Potri.014G138400' => 'ptr', 'Potri.016G142500' => 'ptr', 'Pp3c16_10580' => 'ppa', 'Pp3c5_25280' => 'ppa', 'Prupe.1G150000' => 'ppe', 'Prupe.1G150100' => 'ppe', 'Prupe.6G299600' => 'ppe', 'Prupe.8G245000' => 'ppe', 'Psat0s4927g0040' => 'psa', 'Psat1g052080' => 'psa', 'Psat1g183800' => 'psa', 'Psat3g113840' => 'psa', 'Psat3g126120' => 'psa', 'Psat3g126160' => 'psa', 'Psat3g158760' => 'psa', 'Psat3g158840' => 'psa', 'PSO170G2858' => 'pso', 'PSO339G0606' => 'pso', 'PSO384G4709' => 'pso', 'PSO407G0334' => 'pso', 'QL04p040276' => 'qlo', 'QL06p005458' => 'qlo', 'QL06p005472' => 'qlo', 'QL07p030546' => 'qlo', 'QL07p031519' => 'qlo', 'QL09p050949' => 'qlo', 'QL09p050966' => 'qlo', 'QL09p051067' => 'qlo', 'QL12p022706' => 'qlo', 'RcHm_v2.0_Chr2g0119601' => 'rch', 'RcHm_v2.0_Chr3g0459591' => 'rch', 'RcHm_v2.0_Chr4g0418521' => 'rch', 'RcHm_v2.0_Chr4g0418531' => 'rch', 'RcHm_v2.0_Chr4g0418541' => 'rch', 'RcHm_v2.0_Chr6g0291641' => 'rch', 'Rhsim01G0086300' => 'rsi', 'Rhsim01G0276300' => 'rsi', 'Rhsim01G0276500' => 'rsi', 'Rhsim04G0207700' => 'rsi', 'Rhsim05G0234500' => 'rsi', 'Rhsim13G0022400' => 'rsi', 'Sabra02G0167900' => 'sbr', 'Sabra04G0158500' => 'sbr', 'Sabra08G0159800' => 'sbr', 'Sabra10G0011500' => 'sbr', 'Sabra14G0104400' => 'sbr', 'SalBow2G2440' => 'sbo', 'SalBow4G2265' => 'sbo', 'Sc02g0000060' => 'sci', 'Sc05g0005020' => 'sci', 'Sc13g0003890' => 'sci', 'Sed0014865' => 'sed', 'Sed0017224' => 'sed', 'Sed0026391' => 'sed', 'SEGI_00063' => 'sgi', 'SEGI_10967' => 'sgi', 'SEGI_17510' => 'sgi', 'SEGI_24396' => 'sgi', 'SEGI_39719' => 'sgi', 'SEGI_41392' => 'sgi', 'SGA_v2.0_scaffold11G05794' => 'sas', 'SGA_v2.0_scaffold142G35607' => 'sas', 'SGA_v2.0_scaffold1G00447' => 'sas', 'SHI15388' => 'shi', 'SHI15394' => 'shi', 'SHI15396' => 'shi', 'SHI15399' => 'shi', 'SMO343G0151' => 'smo', 'SMO367G1118' => 'smo', 'Solyc01g080200.3' => 'sly', 'Solyc06g008960.3' => 'sly', 'Solyc09g064780.3' => 'sly', 'Sopen01g031980' => 'spe', 'Sopen06g003710' => 'spe', 'Sopen09g026460' => 'spe', 'Sp3g21240' => 'spa', 'Sp4g30030' => 'spa', 'TAR365G0022' => 'tar', 'TAR365G1023' => 'tar', 'TAR365G1253' => 'tar', 'TAR623G0078' => 'tar', 'TAR623G1721' => 'tar', 'TAR633G0959' => 'tar', 'THA.LOC104802225' => 'tha', 'THA.LOC104804769' => 'tha', 'THA.LOC104808660' => 'tha', 'THA.LOC104812792' => 'tha', 'Thecc.01G284000' => 'tca', 'Thecc.04G220600' => 'tca', 'Thecc.05G268900' => 'tca', 'Thecc.08G171100' => 'tca', 'Thhalv10001284m.g' => 'esa', 'Thhalv10019912m.g' => 'esa', 'TPR.G14189' => 'tpr', 'TPR.G18110' => 'tpr', 'TPR.G18130' => 'tpr', 'TPR.G18131' => 'tpr', 'TPR.G18140' => 'tpr', 'TPR.G24282' => 'tpr', 'TPR.G25221' => 'tpr', 'TPR.G29267' => 'tpr', 'TPR.G35315' => 'tpr', 'TPR.G36173' => 'tpr', 'TWI09G0794' => 'twi', 'TWI59G1348' => 'twi', 'TWI74G0430' => 'twi', 'unitig_26.g8940' => 'ugi', 'unitig_749.g13744' => 'ugi', 'unitig_749.g13745' => 'ugi', 'vmacro08269' => 'vma', 'vmacro14937' => 'vma', 'vmacro20401' => 'vma', 'VMungo0464G1349' => 'vmu', 'VMungo0540G0289' => 'vmu', 'VMungo1215G1590' => 'vmu', 'VMungo1309G0221' => 'vmu', 'VMungo1309G2815' => 'vmu', 'VMungo1383G0239' => 'vmu', 'VMungo1383G2910' => 'vmu', 'Zm00001eb095270' => 'zma', 'Zm00001eb095280' => 'zma', 'Zm00001eb111630' => 'zma', 'Zm00001eb237080' => 'zma', 'Zm00001eb273740' => 'zma', 'Zm00001eb285040' => 'zma', 'Zm00001eb330790' => 'zma', 'Zm00001eb337380' => 'zma' ), 'gf_id' => 'HOM05D001484', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001484' ), 'data_identifier' => 'HOM05D001484', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001484', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p31500' => 'bna', 'A05p00020' => 'bna', 'A07p08820' => 'bna', 'Aa31LG4G3300' => 'aar', 'Aa31LG8G10030' => 'aar', 'Actinidia00731' => 'ach', 'Actinidia11473' => 'ach', 'Actinidia23469' => 'ach', 'Actinidia24318' => 'ach', 'Actinidia40196' => 'ach', 'Actinidia40197' => 'ach', 'Actinidia40198' => 'ach', 'Ah.08g212990' => 'amhyb', 'Ah.15g091720' => 'amhyb', 'AL3G38260' => 'aly', 'AL4G47710' => 'aly', 'Aqoxy2G00671' => 'aox', 'Aqoxy2G03236' => 'aox', 'arahy.Tifrunner.gnm1.ann1.05IDCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KR684' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATY3SJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK6QJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6APGL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IDT7Z9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM073U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ0R87' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LE7RV4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT4QRX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V5ENPK' => 'arhy', 'AT2G48110' => 'ath', 'AT3G23590' => 'ath', 'ATR0626G186' => 'atr', 'ATR1127G141' => 'atr', 'Atru.chr4.2583' => 'acertr', 'Atru.chr5.1358' => 'acertr', 'Atru.chr5.1359' => 'acertr', 'Atru.chr8.46' => 'acertr', 'AUR62002640' => 'cqu', 'AUR62030055' => 'cqu', 'AUR62033713' => 'cqu', 'AUR62033714' => 'cqu', 'AUR62036795' => 'cqu', 'AUR62039891' => 'cqu', 'BcaB02g08737' => 'bca', 'BcaB04g20441' => 'bca', 'BcaB06g26509' => 'bca', 'BcaB06g26510' => 'bca', 'BcaB06g26511' => 'bca', 'BcaB06g26512' => 'bca', 'BcaB06g26513' => 'bca', 'BcaC02g12564' => 'bca', 'BcaC02g12565' => 'bca', 'BcaC02g12794' => 'bca', 'BcaC02g12795' => 'bca', 'BcaC02g12796' => 'bca', 'BcaC06g35541' => 'bca', 'BNapus_Darmor_BZH_scaffold_188p00080' => 'bna', 'BNapus_Darmor_BZH_scaffold_188p00090' => 'bna', 'BolC1t03972H' => 'bol', 'BolC1t03973H' => 'bol', 'BolC4t21680H' => 'bol', 'BolC7t41863H' => 'bol', 'BolSC55t61227H' => 'bol', 'BolSC55t61228H' => 'bol', 'BraA01t03278Z' => 'bra', 'BraA05t18998Z' => 'bra', 'BraA07t28673Z' => 'bra', 'C01p40150' => 'bna', 'C05p12370' => 'bna', 'C07p13680' => 'bna', 'CAN.G1006.16' => 'can', 'CAN.G1006.17' => 'can', 'CAN.G1170.2' => 'can', 'CAN.G962.7' => 'can', 'CANSAT25G2179' => 'cansat', 'CANSAT78G1573' => 'cansat', 'CARHR099510' => 'chi', 'CARHR143510' => 'chi', 'Carub.0003s2380' => 'cru', 'Carub.0004s3082' => 'cru', 'Ca_00614_v3' => 'car', 'Ca_07801_v3' => 'car', 'Ca_08567_v3' => 'car', 'Ca_09571_v3' => 'car', 'CBR_g19290' => 'cbr', 'Cc01_g19770' => 'ccan', 'Cc03_g03030' => 'ccan', 'CDE07G0968' => 'cde', 'CDE09G1441' => 'cde', 'Cfa006103' => 'cfa', 'Cfa015573' => 'cfa', 'Cfa016988' => 'cfa', 'Ciclev10006738m.g' => 'ccl', 'Ciclev10010920m.g' => 'ccl', 'Ciclev10018517m.g' => 'ccl', 'CiPaw.01G159200' => 'cil', 'CiPaw.02G091000' => 'cil', 'CiPaw.02G091100' => 'cil', 'CiPaw.08G103100' => 'cil', 'CiPaw.09G224900' => 'cil', 'ClCG06G005740' => 'cla', 'ClCG07G000090' => 'cla', 'ClCG07G000100' => 'cla', 'COL.COLO4_09143' => 'col', 'COL.COLO4_25124' => 'col', 'Cpa.g.sc16.34' => 'cpa', 'Cpa.g.sc3504.1' => 'cpa', 'Cpa.g.sc60.37' => 'cpa', 'CsaV3_6G018520' => 'csa', 'CsaV3_6G036860' => 'csa', 'CSS0001072' => 'camsi', 'CSS0020208' => 'camsi', 'CSS0021253' => 'camsi', 'CSS0022190' => 'camsi', 'CSS0036150' => 'camsi', 'CSS0040442' => 'camsi', 'CSS0042300' => 'camsi', 'CSS0045298' => 'camsi', 'DCAR_012449' => 'dca', 'DCAR_018405' => 'dca', 'DCAR_024573' => 'dca', 'DCAR_030591' => 'dca', 'Dinv16926' => 'din', 'Dinv32963' => 'din', 'Dinv38382' => 'din', 'Dinv38383' => 'din', 'Duzib133G0974' => 'dzi', 'Duzib138G1867' => 'dzi', 'Duzib211G0420' => 'dzi', 'Duzib212G0930' => 'dzi', 'ECA234G1645' => 'eca', 'ECA247G3467' => 'eca', 'ECA248G1703' => 'eca', 'EL10Ac3g06327' => 'bvu', 'EL10Ac7g17204' => 'bvu', 'Eucgr.A00855' => 'egr', 'Eucgr.A00858' => 'egr', 'Eucgr.H01520' => 'egr', 'Eucgr.H03604' => 'egr', 'Eucgr.L03465' => 'egr', 'Eucgr.L03466' => 'egr', 'FAN01G0988' => 'fan', 'FAN02G3892' => 'fan', 'FAN05G3381' => 'fan', 'FAN07G0967' => 'fan', 'FAN07G1493' => 'fan', 'FAN08G3125' => 'fan', 'FAN09G0402' => 'fan', 'FAN12G2594' => 'fan', 'FAN12G3879' => 'fan', 'FAN14G1546' => 'fan', 'FAN15G3626' => 'fan', 'FAN17G0588' => 'fan', 'FAN17G0609' => 'fan', 'FAN18G2817' => 'fan', 'FAN19G1305' => 'fan', 'FAN20G1787' => 'fan', 'FAN22G0073' => 'fan', 'FAN22G0352' => 'fan', 'FAN22G0368' => 'fan', 'FAN22G2273' => 'fan', 'FAN24G1998' => 'fan', 'FAN27G1317' => 'fan', 'FvH4_2g23980' => 'fve', 'FvH4_4g14380' => 'fve', 'FvH4_4g14390' => 'fve', 'FvH4_6g09250' => 'fve', 'Glyma.03G151100' => 'gma', 'Glyma.04G122550' => 'gma', 'Glyma.05G001600' => 'gma', 'Glyma.09G270766' => 'gma', 'Glyma.09G270832' => 'gma', 'Glyma.13G209800' => 'gma', 'Glyma.15G102800' => 'gma', 'Glyma.18G218900' => 'gma', 'Glyma.19G001500' => 'gma', 'Glyma.19G153600' => 'gma', 'Gohir.A02G028600' => 'ghi', 'Gohir.A08G045000' => 'ghi', 'Gohir.A11G120500' => 'ghi', 'Gohir.A12G006200' => 'ghi', 'Gohir.A12G006250' => 'ghi', 'Gohir.D02G036300' => 'ghi', 'Gohir.D08G054700' => 'ghi', 'Gohir.D11G125600' => 'ghi', 'Gohir.D12G005700' => 'ghi', 'Gorai.004G055200' => 'gra', 'Gorai.005G040400' => 'gra', 'Gorai.007G134500' => 'gra', 'Gorai.008G005500' => 'gra', 'GSVIVG01011094001' => 'vvi', 'GSVIVG01017879001' => 'vvi', 'GSVIVG01025988001' => 'vvi', 'GSVIVG01029847001' => 'vvi', 'HanXRQChr10g0282901' => 'han', 'HanXRQChr10g0310371' => 'han', 'HanXRQChr10g0315041' => 'han', 'HanXRQChr11g0327651' => 'han', 'HanXRQChr12g0359391' => 'han', 'Haze_00972' => 'cav', 'Haze_00973' => 'cav', 'Haze_00974' => 'cav', 'Haze_04747' => 'cav', 'Haze_04749' => 'cav', 'Haze_04750' => 'cav', 'Haze_21217' => 'cav', 'Hma1.2p1_1037F.1_g250680' => 'hma', 'Hma1.2p1_1644F.1_g295320' => 'hma', 'HPP92_011322' => 'vpl', 'HPP92_011323' => 'vpl', 'HPP92_011324' => 'vpl', 'HPP92_011325' => 'vpl', 'HPP92_011326' => 'vpl', 'Hund12205' => 'sun', 'Hund17957' => 'sun', 'Lalb_Chr06g0176771' => 'lal', 'Lalb_Chr18g0056021' => 'lal', 'Lalb_Chr18g0056031' => 'lal', 'Lalb_Chr18g0056041' => 'lal', 'Lalb_Chr20g0107751' => 'lal', 'Lalb_Chr20g0118371' => 'lal', 'Lj1g0010239' => 'lja', 'Lj1g0017101' => 'lja', 'Lj2A1178G40' => 'lonja', 'Lj2A54G84' => 'lonja', 'Lj2g0015248' => 'lja', 'Lj3A761T51' => 'lonja', 'Lj6g0018116' => 'lja', 'Lsat_1_v5_gn_4_136040' => 'lsa', 'Lsat_1_v5_gn_5_187461' => 'lsa', 'Lsat_1_v5_gn_5_77001' => 'lsa', 'Lsat_1_v5_gn_9_4461' => 'lsa', 'Manes.01G210100' => 'mes', 'Manes.03G185600' => 'mes', 'Manes.05G073300' => 'mes', 'Manes.09G120300' => 'mes', 'Manes.15G022100' => 'mes', 'Mapoly0096s0053' => 'mpo', 'MBI03_g14058_MAGBIO' => 'mbi', 'MBI03_g33876_MAGBIO' => 'mbi', 'MBI03_g36854_MAGBIO' => 'mbi', 'MBI17_g11997_MAGBIO' => 'mbi', 'MD03G1269000' => 'mdo', 'MD04G1179600' => 'mdo', 'MD11G1289800' => 'mdo', 'MD12G1194700' => 'mdo', 'MD13G1182100' => 'mdo', 'MD13G1182200' => 'mdo', 'MD16G1182600' => 'mdo', 'Medtr2g021400' => 'mtr', 'Medtr2g021470' => 'mtr', 'Medtr2g105810' => 'mtr', 'Medtr3g033580' => 'mtr', 'Medtr6g007970' => 'mtr', 'Medtr7g056330' => 'mtr', 'Medtr7g074290' => 'mtr', 'Medtr7g074380' => 'mtr', 'Medtr7g094550' => 'mtr', 'Medtr8g069995' => 'mtr', 'MELO3C014345.2' => 'cme', 'MELO3C021395.2' => 'cme', 'Migut.D00262' => 'egut', 'Migut.G00257' => 'egut', 'MSTRG.21575' => 'ama', 'MSTRG.3985' => 'ama', 'Nitab4.5_0000295g0140' => 'nta', 'Nitab4.5_0000732g0140' => 'nta', 'Nitab4.5_0003162g0020' => 'nta', 'Nitab4.5_0006180g0090' => 'nta', 'Nitab4.5_0006390g0010' => 'nta', 'Nitab4.5_0007392g0040' => 'nta', 'Nn1g02140' => 'nnu', 'Nn4g26168' => 'nnu', 'Nn5g26754' => 'nnu', 'Oeu001433.1' => 'oeu', 'Oeu010299.2' => 'oeu', 'Oeu011171.1' => 'oeu', 'Oeu037675.1' => 'oeu', 'Oeu038359.1' => 'oeu', 'Oeu063834.1' => 'oeu', 'Oeu063835.1' => 'oeu', 'Os05g0312000' => 'osa', 'Os07g0211101' => 'osa', 'Os07g0211200' => 'osa', 'Os07g0681500' => 'osa', 'Peaxi162Scf00095g01015' => 'pax', 'Peaxi162Scf00104g00329' => 'pax', 'Peaxi162Scf00161g00137' => 'pax', 'PGR004G1665' => 'pgr', 'PGR031G2937' => 'pgr', 'PGR119G2145' => 'pgr', 'PGSC0003DMG400004351' => 'stu', 'PGSC0003DMG400014625' => 'stu', 'PGSC0003DMG401000943' => 'stu', 'Phvul.001G148600' => 'pvu', 'Phvul.004G001700' => 'pvu', 'Phvul.006G154900' => 'pvu', 'Phvul.008G078200' => 'pvu', 'Phvul.011G136500' => 'pvu', 'Potri.002G215600' => 'ptr', 'Potri.008G201600' => 'ptr', 'Potri.014G138400' => 'ptr', 'Potri.016G142500' => 'ptr', 'Pp3c16_10580' => 'ppa', 'Pp3c5_25280' => 'ppa', 'Prupe.1G150000' => 'ppe', 'Prupe.1G150100' => 'ppe', 'Prupe.6G299600' => 'ppe', 'Prupe.8G245000' => 'ppe', 'Psat0s4927g0040' => 'psa', 'Psat1g052080' => 'psa', 'Psat1g183800' => 'psa', 'Psat3g113840' => 'psa', 'Psat3g126120' => 'psa', 'Psat3g126160' => 'psa', 'Psat3g158760' => 'psa', 'Psat3g158840' => 'psa', 'PSO170G2858' => 'pso', 'PSO339G0606' => 'pso', 'PSO384G4709' => 'pso', 'PSO407G0334' => 'pso', 'QL04p040276' => 'qlo', 'QL06p005458' => 'qlo', 'QL06p005472' => 'qlo', 'QL07p030546' => 'qlo', 'QL07p031519' => 'qlo', 'QL09p050949' => 'qlo', 'QL09p050966' => 'qlo', 'QL09p051067' => 'qlo', 'QL12p022706' => 'qlo', 'RcHm_v2.0_Chr2g0119601' => 'rch', 'RcHm_v2.0_Chr3g0459591' => 'rch', 'RcHm_v2.0_Chr4g0418521' => 'rch', 'RcHm_v2.0_Chr4g0418531' => 'rch', 'RcHm_v2.0_Chr4g0418541' => 'rch', 'RcHm_v2.0_Chr6g0291641' => 'rch', 'Rhsim01G0086300' => 'rsi', 'Rhsim01G0276300' => 'rsi', 'Rhsim01G0276500' => 'rsi', 'Rhsim04G0207700' => 'rsi', 'Rhsim05G0234500' => 'rsi', 'Rhsim13G0022400' => 'rsi', 'Sabra02G0167900' => 'sbr', 'Sabra04G0158500' => 'sbr', 'Sabra08G0159800' => 'sbr', 'Sabra10G0011500' => 'sbr', 'Sabra14G0104400' => 'sbr', 'SalBow2G2440' => 'sbo', 'SalBow4G2265' => 'sbo', 'Sc02g0000060' => 'sci', 'Sc05g0005020' => 'sci', 'Sc13g0003890' => 'sci', 'Sed0014865' => 'sed', 'Sed0017224' => 'sed', 'Sed0026391' => 'sed', 'SEGI_00063' => 'sgi', 'SEGI_10967' => 'sgi', 'SEGI_17510' => 'sgi', 'SEGI_24396' => 'sgi', 'SEGI_39719' => 'sgi', 'SEGI_41392' => 'sgi', 'SGA_v2.0_scaffold11G05794' => 'sas', 'SGA_v2.0_scaffold142G35607' => 'sas', 'SGA_v2.0_scaffold1G00447' => 'sas', 'SHI15388' => 'shi', 'SHI15394' => 'shi', 'SHI15396' => 'shi', 'SHI15399' => 'shi', 'SMO343G0151' => 'smo', 'SMO367G1118' => 'smo', 'Solyc01g080200.3' => 'sly', 'Solyc06g008960.3' => 'sly', 'Solyc09g064780.3' => 'sly', 'Sopen01g031980' => 'spe', 'Sopen06g003710' => 'spe', 'Sopen09g026460' => 'spe', 'Sp3g21240' => 'spa', 'Sp4g30030' => 'spa', 'TAR365G0022' => 'tar', 'TAR365G1023' => 'tar', 'TAR365G1253' => 'tar', 'TAR623G0078' => 'tar', 'TAR623G1721' => 'tar', 'TAR633G0959' => 'tar', 'THA.LOC104802225' => 'tha', 'THA.LOC104804769' => 'tha', 'THA.LOC104808660' => 'tha', 'THA.LOC104812792' => 'tha', 'Thecc.01G284000' => 'tca', 'Thecc.04G220600' => 'tca', 'Thecc.05G268900' => 'tca', 'Thecc.08G171100' => 'tca', 'Thhalv10001284m.g' => 'esa', 'Thhalv10019912m.g' => 'esa', 'TPR.G14189' => 'tpr', 'TPR.G18110' => 'tpr', 'TPR.G18130' => 'tpr', 'TPR.G18131' => 'tpr', 'TPR.G18140' => 'tpr', 'TPR.G24282' => 'tpr', 'TPR.G25221' => 'tpr', 'TPR.G29267' => 'tpr', 'TPR.G35315' => 'tpr', 'TPR.G36173' => 'tpr', 'TWI09G0794' => 'twi', 'TWI59G1348' => 'twi', 'TWI74G0430' => 'twi', 'unitig_26.g8940' => 'ugi', 'unitig_749.g13744' => 'ugi', 'unitig_749.g13745' => 'ugi', 'vmacro08269' => 'vma', 'vmacro14937' => 'vma', 'vmacro20401' => 'vma', 'VMungo0464G1349' => 'vmu', 'VMungo0540G0289' => 'vmu', 'VMungo1215G1590' => 'vmu', 'VMungo1309G0221' => 'vmu', 'VMungo1309G2815' => 'vmu', 'VMungo1383G0239' => 'vmu', 'VMungo1383G2910' => 'vmu', 'Zm00001eb095270' => 'zma', 'Zm00001eb095280' => 'zma', 'Zm00001eb111630' => 'zma', 'Zm00001eb237080' => 'zma', 'Zm00001eb273740' => 'zma', 'Zm00001eb285040' => 'zma', 'Zm00001eb330790' => 'zma', 'Zm00001eb337380' => 'zma' ) $gf_id = 'HOM05D001484' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001484' ) $data_identifier = 'HOM05D001484' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 2, 'aly' => (int) 2, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 22, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 7, 'hma' => (int) 2, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 7, 'mtr' => (int) 10, 'cme' => (int) 2, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 4, 'ppa' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 4, 'qlo' => (int) 9, 'rch' => (int) 6, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 10, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 7, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb337380' $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' => 'HOM05D001484', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p31500' => 'bna', 'A05p00020' => 'bna', 'A07p08820' => 'bna', 'Aa31LG4G3300' => 'aar', 'Aa31LG8G10030' => 'aar', 'Actinidia00731' => 'ach', 'Actinidia11473' => 'ach', 'Actinidia23469' => 'ach', 'Actinidia24318' => 'ach', 'Actinidia40196' => 'ach', 'Actinidia40197' => 'ach', 'Actinidia40198' => 'ach', 'Ah.08g212990' => 'amhyb', 'Ah.15g091720' => 'amhyb', 'AL3G38260' => 'aly', 'AL4G47710' => 'aly', 'Aqoxy2G00671' => 'aox', 'Aqoxy2G03236' => 'aox', 'arahy.Tifrunner.gnm1.ann1.05IDCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KR684' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATY3SJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK6QJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6APGL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IDT7Z9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM073U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ0R87' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LE7RV4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT4QRX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V5ENPK' => 'arhy', 'AT2G48110' => 'ath', 'AT3G23590' => 'ath', 'ATR0626G186' => 'atr', 'ATR1127G141' => 'atr', 'Atru.chr4.2583' => 'acertr', 'Atru.chr5.1358' => 'acertr', 'Atru.chr5.1359' => 'acertr', 'Atru.chr8.46' => 'acertr', 'AUR62002640' => 'cqu', 'AUR62030055' => 'cqu', 'AUR62033713' => 'cqu', 'AUR62033714' => 'cqu', 'AUR62036795' => 'cqu', 'AUR62039891' => 'cqu', 'BcaB02g08737' => 'bca', 'BcaB04g20441' => 'bca', 'BcaB06g26509' => 'bca', 'BcaB06g26510' => 'bca', 'BcaB06g26511' => 'bca', 'BcaB06g26512' => 'bca', 'BcaB06g26513' => 'bca', 'BcaC02g12564' => 'bca', 'BcaC02g12565' => 'bca', 'BcaC02g12794' => 'bca', 'BcaC02g12795' => 'bca', 'BcaC02g12796' => 'bca', 'BcaC06g35541' => 'bca', 'BNapus_Darmor_BZH_scaffold_188p00080' => 'bna', 'BNapus_Darmor_BZH_scaffold_188p00090' => 'bna', 'BolC1t03972H' => 'bol', 'BolC1t03973H' => 'bol', 'BolC4t21680H' => 'bol', 'BolC7t41863H' => 'bol', 'BolSC55t61227H' => 'bol', 'BolSC55t61228H' => 'bol', 'BraA01t03278Z' => 'bra', 'BraA05t18998Z' => 'bra', 'BraA07t28673Z' => 'bra', 'C01p40150' => 'bna', 'C05p12370' => 'bna', 'C07p13680' => 'bna', 'CAN.G1006.16' => 'can', 'CAN.G1006.17' => 'can', 'CAN.G1170.2' => 'can', 'CAN.G962.7' => 'can', 'CANSAT25G2179' => 'cansat', 'CANSAT78G1573' => 'cansat', 'CARHR099510' => 'chi', 'CARHR143510' => 'chi', 'Carub.0003s2380' => 'cru', 'Carub.0004s3082' => 'cru', 'Ca_00614_v3' => 'car', 'Ca_07801_v3' => 'car', 'Ca_08567_v3' => 'car', 'Ca_09571_v3' => 'car', 'CBR_g19290' => 'cbr', 'Cc01_g19770' => 'ccan', 'Cc03_g03030' => 'ccan', 'CDE07G0968' => 'cde', 'CDE09G1441' => 'cde', 'Cfa006103' => 'cfa', 'Cfa015573' => 'cfa', 'Cfa016988' => 'cfa', 'Ciclev10006738m.g' => 'ccl', 'Ciclev10010920m.g' => 'ccl', 'Ciclev10018517m.g' => 'ccl', 'CiPaw.01G159200' => 'cil', 'CiPaw.02G091000' => 'cil', 'CiPaw.02G091100' => 'cil', 'CiPaw.08G103100' => 'cil', 'CiPaw.09G224900' => 'cil', 'ClCG06G005740' => 'cla', 'ClCG07G000090' => 'cla', 'ClCG07G000100' => 'cla', 'COL.COLO4_09143' => 'col', 'COL.COLO4_25124' => 'col', 'Cpa.g.sc16.34' => 'cpa', 'Cpa.g.sc3504.1' => 'cpa', 'Cpa.g.sc60.37' => 'cpa', 'CsaV3_6G018520' => 'csa', 'CsaV3_6G036860' => 'csa', 'CSS0001072' => 'camsi', 'CSS0020208' => 'camsi', 'CSS0021253' => 'camsi', 'CSS0022190' => 'camsi', 'CSS0036150' => 'camsi', 'CSS0040442' => 'camsi', 'CSS0042300' => 'camsi', 'CSS0045298' => 'camsi', 'DCAR_012449' => 'dca', 'DCAR_018405' => 'dca', 'DCAR_024573' => 'dca', 'DCAR_030591' => 'dca', 'Dinv16926' => 'din', 'Dinv32963' => 'din', 'Dinv38382' => 'din', 'Dinv38383' => 'din', 'Duzib133G0974' => 'dzi', 'Duzib138G1867' => 'dzi', 'Duzib211G0420' => 'dzi', 'Duzib212G0930' => 'dzi', 'ECA234G1645' => 'eca', 'ECA247G3467' => 'eca', 'ECA248G1703' => 'eca', 'EL10Ac3g06327' => 'bvu', 'EL10Ac7g17204' => 'bvu', 'Eucgr.A00855' => 'egr', 'Eucgr.A00858' => 'egr', 'Eucgr.H01520' => 'egr', 'Eucgr.H03604' => 'egr', 'Eucgr.L03465' => 'egr', 'Eucgr.L03466' => 'egr', 'FAN01G0988' => 'fan', 'FAN02G3892' => 'fan', 'FAN05G3381' => 'fan', 'FAN07G0967' => 'fan', 'FAN07G1493' => 'fan', 'FAN08G3125' => 'fan', 'FAN09G0402' => 'fan', 'FAN12G2594' => 'fan', 'FAN12G3879' => 'fan', 'FAN14G1546' => 'fan', 'FAN15G3626' => 'fan', 'FAN17G0588' => 'fan', 'FAN17G0609' => 'fan', 'FAN18G2817' => 'fan', 'FAN19G1305' => 'fan', 'FAN20G1787' => 'fan', 'FAN22G0073' => 'fan', 'FAN22G0352' => 'fan', 'FAN22G0368' => 'fan', 'FAN22G2273' => 'fan', 'FAN24G1998' => 'fan', 'FAN27G1317' => 'fan', 'FvH4_2g23980' => 'fve', 'FvH4_4g14380' => 'fve', 'FvH4_4g14390' => 'fve', 'FvH4_6g09250' => 'fve', 'Glyma.03G151100' => 'gma', 'Glyma.04G122550' => 'gma', 'Glyma.05G001600' => 'gma', 'Glyma.09G270766' => 'gma', 'Glyma.09G270832' => 'gma', 'Glyma.13G209800' => 'gma', 'Glyma.15G102800' => 'gma', 'Glyma.18G218900' => 'gma', 'Glyma.19G001500' => 'gma', 'Glyma.19G153600' => 'gma', 'Gohir.A02G028600' => 'ghi', 'Gohir.A08G045000' => 'ghi', 'Gohir.A11G120500' => 'ghi', 'Gohir.A12G006200' => 'ghi', 'Gohir.A12G006250' => 'ghi', 'Gohir.D02G036300' => 'ghi', 'Gohir.D08G054700' => 'ghi', 'Gohir.D11G125600' => 'ghi', 'Gohir.D12G005700' => 'ghi', 'Gorai.004G055200' => 'gra', 'Gorai.005G040400' => 'gra', 'Gorai.007G134500' => 'gra', 'Gorai.008G005500' => 'gra', 'GSVIVG01011094001' => 'vvi', 'GSVIVG01017879001' => 'vvi', 'GSVIVG01025988001' => 'vvi', 'GSVIVG01029847001' => 'vvi', 'HanXRQChr10g0282901' => 'han', 'HanXRQChr10g0310371' => 'han', 'HanXRQChr10g0315041' => 'han', 'HanXRQChr11g0327651' => 'han', 'HanXRQChr12g0359391' => 'han', 'Haze_00972' => 'cav', 'Haze_00973' => 'cav', 'Haze_00974' => 'cav', 'Haze_04747' => 'cav', 'Haze_04749' => 'cav', 'Haze_04750' => 'cav', 'Haze_21217' => 'cav', 'Hma1.2p1_1037F.1_g250680' => 'hma', 'Hma1.2p1_1644F.1_g295320' => 'hma', 'HPP92_011322' => 'vpl', 'HPP92_011323' => 'vpl', 'HPP92_011324' => 'vpl', 'HPP92_011325' => 'vpl', 'HPP92_011326' => 'vpl', 'Hund12205' => 'sun', 'Hund17957' => 'sun', 'Lalb_Chr06g0176771' => 'lal', 'Lalb_Chr18g0056021' => 'lal', 'Lalb_Chr18g0056031' => 'lal', 'Lalb_Chr18g0056041' => 'lal', 'Lalb_Chr20g0107751' => 'lal', 'Lalb_Chr20g0118371' => 'lal', 'Lj1g0010239' => 'lja', 'Lj1g0017101' => 'lja', 'Lj2A1178G40' => 'lonja', 'Lj2A54G84' => 'lonja', 'Lj2g0015248' => 'lja', 'Lj3A761T51' => 'lonja', 'Lj6g0018116' => 'lja', 'Lsat_1_v5_gn_4_136040' => 'lsa', 'Lsat_1_v5_gn_5_187461' => 'lsa', 'Lsat_1_v5_gn_5_77001' => 'lsa', 'Lsat_1_v5_gn_9_4461' => 'lsa', 'Manes.01G210100' => 'mes', 'Manes.03G185600' => 'mes', 'Manes.05G073300' => 'mes', 'Manes.09G120300' => 'mes', 'Manes.15G022100' => 'mes', 'Mapoly0096s0053' => 'mpo', 'MBI03_g14058_MAGBIO' => 'mbi', 'MBI03_g33876_MAGBIO' => 'mbi', 'MBI03_g36854_MAGBIO' => 'mbi', 'MBI17_g11997_MAGBIO' => 'mbi', 'MD03G1269000' => 'mdo', 'MD04G1179600' => 'mdo', 'MD11G1289800' => 'mdo', 'MD12G1194700' => 'mdo', 'MD13G1182100' => 'mdo', 'MD13G1182200' => 'mdo', 'MD16G1182600' => 'mdo', 'Medtr2g021400' => 'mtr', 'Medtr2g021470' => 'mtr', 'Medtr2g105810' => 'mtr', 'Medtr3g033580' => 'mtr', 'Medtr6g007970' => 'mtr', 'Medtr7g056330' => 'mtr', 'Medtr7g074290' => 'mtr', 'Medtr7g074380' => 'mtr', 'Medtr7g094550' => 'mtr', 'Medtr8g069995' => 'mtr', 'MELO3C014345.2' => 'cme', 'MELO3C021395.2' => 'cme', 'Migut.D00262' => 'egut', 'Migut.G00257' => 'egut', 'MSTRG.21575' => 'ama', 'MSTRG.3985' => 'ama', 'Nitab4.5_0000295g0140' => 'nta', 'Nitab4.5_0000732g0140' => 'nta', 'Nitab4.5_0003162g0020' => 'nta', 'Nitab4.5_0006180g0090' => 'nta', 'Nitab4.5_0006390g0010' => 'nta', 'Nitab4.5_0007392g0040' => 'nta', 'Nn1g02140' => 'nnu', 'Nn4g26168' => 'nnu', 'Nn5g26754' => 'nnu', 'Oeu001433.1' => 'oeu', 'Oeu010299.2' => 'oeu', 'Oeu011171.1' => 'oeu', 'Oeu037675.1' => 'oeu', 'Oeu038359.1' => 'oeu', 'Oeu063834.1' => 'oeu', 'Oeu063835.1' => 'oeu', 'Os05g0312000' => 'osa', 'Os07g0211101' => 'osa', 'Os07g0211200' => 'osa', 'Os07g0681500' => 'osa', 'Peaxi162Scf00095g01015' => 'pax', 'Peaxi162Scf00104g00329' => 'pax', 'Peaxi162Scf00161g00137' => 'pax', 'PGR004G1665' => 'pgr', 'PGR031G2937' => 'pgr', 'PGR119G2145' => 'pgr', 'PGSC0003DMG400004351' => 'stu', 'PGSC0003DMG400014625' => 'stu', 'PGSC0003DMG401000943' => 'stu', 'Phvul.001G148600' => 'pvu', 'Phvul.004G001700' => 'pvu', 'Phvul.006G154900' => 'pvu', 'Phvul.008G078200' => 'pvu', 'Phvul.011G136500' => 'pvu', 'Potri.002G215600' => 'ptr', 'Potri.008G201600' => 'ptr', 'Potri.014G138400' => 'ptr', 'Potri.016G142500' => 'ptr', 'Pp3c16_10580' => 'ppa', 'Pp3c5_25280' => 'ppa', 'Prupe.1G150000' => 'ppe', 'Prupe.1G150100' => 'ppe', 'Prupe.6G299600' => 'ppe', 'Prupe.8G245000' => 'ppe', 'Psat0s4927g0040' => 'psa', 'Psat1g052080' => 'psa', 'Psat1g183800' => 'psa', 'Psat3g113840' => 'psa', 'Psat3g126120' => 'psa', 'Psat3g126160' => 'psa', 'Psat3g158760' => 'psa', 'Psat3g158840' => 'psa', 'PSO170G2858' => 'pso', 'PSO339G0606' => 'pso', 'PSO384G4709' => 'pso', 'PSO407G0334' => 'pso', 'QL04p040276' => 'qlo', 'QL06p005458' => 'qlo', 'QL06p005472' => 'qlo', 'QL07p030546' => 'qlo', 'QL07p031519' => 'qlo', 'QL09p050949' => 'qlo', 'QL09p050966' => 'qlo', 'QL09p051067' => 'qlo', 'QL12p022706' => 'qlo', 'RcHm_v2.0_Chr2g0119601' => 'rch', 'RcHm_v2.0_Chr3g0459591' => 'rch', 'RcHm_v2.0_Chr4g0418521' => 'rch', 'RcHm_v2.0_Chr4g0418531' => 'rch', 'RcHm_v2.0_Chr4g0418541' => 'rch', 'RcHm_v2.0_Chr6g0291641' => 'rch', 'Rhsim01G0086300' => 'rsi', 'Rhsim01G0276300' => 'rsi', 'Rhsim01G0276500' => 'rsi', 'Rhsim04G0207700' => 'rsi', 'Rhsim05G0234500' => 'rsi', 'Rhsim13G0022400' => 'rsi', 'Sabra02G0167900' => 'sbr', 'Sabra04G0158500' => 'sbr', 'Sabra08G0159800' => 'sbr', 'Sabra10G0011500' => 'sbr', 'Sabra14G0104400' => 'sbr', 'SalBow2G2440' => 'sbo', 'SalBow4G2265' => 'sbo', 'Sc02g0000060' => 'sci', 'Sc05g0005020' => 'sci', 'Sc13g0003890' => 'sci', 'Sed0014865' => 'sed', 'Sed0017224' => 'sed', 'Sed0026391' => 'sed', 'SEGI_00063' => 'sgi', 'SEGI_10967' => 'sgi', 'SEGI_17510' => 'sgi', 'SEGI_24396' => 'sgi', 'SEGI_39719' => 'sgi', 'SEGI_41392' => 'sgi', 'SGA_v2.0_scaffold11G05794' => 'sas', 'SGA_v2.0_scaffold142G35607' => 'sas', 'SGA_v2.0_scaffold1G00447' => 'sas', 'SHI15388' => 'shi', 'SHI15394' => 'shi', 'SHI15396' => 'shi', 'SHI15399' => 'shi', 'SMO343G0151' => 'smo', 'SMO367G1118' => 'smo', 'Solyc01g080200.3' => 'sly', 'Solyc06g008960.3' => 'sly', 'Solyc09g064780.3' => 'sly', 'Sopen01g031980' => 'spe', 'Sopen06g003710' => 'spe', 'Sopen09g026460' => 'spe', 'Sp3g21240' => 'spa', 'Sp4g30030' => 'spa', 'TAR365G0022' => 'tar', 'TAR365G1023' => 'tar', 'TAR365G1253' => 'tar', 'TAR623G0078' => 'tar', 'TAR623G1721' => 'tar', 'TAR633G0959' => 'tar', 'THA.LOC104802225' => 'tha', 'THA.LOC104804769' => 'tha', 'THA.LOC104808660' => 'tha', 'THA.LOC104812792' => 'tha', 'Thecc.01G284000' => 'tca', 'Thecc.04G220600' => 'tca', 'Thecc.05G268900' => 'tca', 'Thecc.08G171100' => 'tca', 'Thhalv10001284m.g' => 'esa', 'Thhalv10019912m.g' => 'esa', 'TPR.G14189' => 'tpr', 'TPR.G18110' => 'tpr', 'TPR.G18130' => 'tpr', 'TPR.G18131' => 'tpr', 'TPR.G18140' => 'tpr', 'TPR.G24282' => 'tpr', 'TPR.G25221' => 'tpr', 'TPR.G29267' => 'tpr', 'TPR.G35315' => 'tpr', 'TPR.G36173' => 'tpr', 'TWI09G0794' => 'twi', 'TWI59G1348' => 'twi', 'TWI74G0430' => 'twi', 'unitig_26.g8940' => 'ugi', 'unitig_749.g13744' => 'ugi', 'unitig_749.g13745' => 'ugi', 'vmacro08269' => 'vma', 'vmacro14937' => 'vma', 'vmacro20401' => 'vma', 'VMungo0464G1349' => 'vmu', 'VMungo0540G0289' => 'vmu', 'VMungo1215G1590' => 'vmu', 'VMungo1309G0221' => 'vmu', 'VMungo1309G2815' => 'vmu', 'VMungo1383G0239' => 'vmu', 'VMungo1383G2910' => 'vmu', 'Zm00001eb095270' => 'zma', 'Zm00001eb095280' => 'zma', 'Zm00001eb111630' => 'zma', 'Zm00001eb237080' => 'zma', 'Zm00001eb273740' => 'zma', 'Zm00001eb285040' => 'zma', 'Zm00001eb330790' => 'zma', 'Zm00001eb337380' => 'zma' ), 'gf_id' => 'HOM05D001484', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001484' ), 'data_identifier' => 'HOM05D001484', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001484', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p31500' => 'bna', 'A05p00020' => 'bna', 'A07p08820' => 'bna', 'Aa31LG4G3300' => 'aar', 'Aa31LG8G10030' => 'aar', 'Actinidia00731' => 'ach', 'Actinidia11473' => 'ach', 'Actinidia23469' => 'ach', 'Actinidia24318' => 'ach', 'Actinidia40196' => 'ach', 'Actinidia40197' => 'ach', 'Actinidia40198' => 'ach', 'Ah.08g212990' => 'amhyb', 'Ah.15g091720' => 'amhyb', 'AL3G38260' => 'aly', 'AL4G47710' => 'aly', 'Aqoxy2G00671' => 'aox', 'Aqoxy2G03236' => 'aox', 'arahy.Tifrunner.gnm1.ann1.05IDCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KR684' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATY3SJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK6QJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6APGL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IDT7Z9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM073U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ0R87' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LE7RV4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT4QRX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V5ENPK' => 'arhy', 'AT2G48110' => 'ath', 'AT3G23590' => 'ath', 'ATR0626G186' => 'atr', 'ATR1127G141' => 'atr', 'Atru.chr4.2583' => 'acertr', 'Atru.chr5.1358' => 'acertr', 'Atru.chr5.1359' => 'acertr', 'Atru.chr8.46' => 'acertr', 'AUR62002640' => 'cqu', 'AUR62030055' => 'cqu', 'AUR62033713' => 'cqu', 'AUR62033714' => 'cqu', 'AUR62036795' => 'cqu', 'AUR62039891' => 'cqu', 'BcaB02g08737' => 'bca', 'BcaB04g20441' => 'bca', 'BcaB06g26509' => 'bca', 'BcaB06g26510' => 'bca', 'BcaB06g26511' => 'bca', 'BcaB06g26512' => 'bca', 'BcaB06g26513' => 'bca', 'BcaC02g12564' => 'bca', 'BcaC02g12565' => 'bca', 'BcaC02g12794' => 'bca', 'BcaC02g12795' => 'bca', 'BcaC02g12796' => 'bca', 'BcaC06g35541' => 'bca', 'BNapus_Darmor_BZH_scaffold_188p00080' => 'bna', 'BNapus_Darmor_BZH_scaffold_188p00090' => 'bna', 'BolC1t03972H' => 'bol', 'BolC1t03973H' => 'bol', 'BolC4t21680H' => 'bol', 'BolC7t41863H' => 'bol', 'BolSC55t61227H' => 'bol', 'BolSC55t61228H' => 'bol', 'BraA01t03278Z' => 'bra', 'BraA05t18998Z' => 'bra', 'BraA07t28673Z' => 'bra', 'C01p40150' => 'bna', 'C05p12370' => 'bna', 'C07p13680' => 'bna', 'CAN.G1006.16' => 'can', 'CAN.G1006.17' => 'can', 'CAN.G1170.2' => 'can', 'CAN.G962.7' => 'can', 'CANSAT25G2179' => 'cansat', 'CANSAT78G1573' => 'cansat', 'CARHR099510' => 'chi', 'CARHR143510' => 'chi', 'Carub.0003s2380' => 'cru', 'Carub.0004s3082' => 'cru', 'Ca_00614_v3' => 'car', 'Ca_07801_v3' => 'car', 'Ca_08567_v3' => 'car', 'Ca_09571_v3' => 'car', 'CBR_g19290' => 'cbr', 'Cc01_g19770' => 'ccan', 'Cc03_g03030' => 'ccan', 'CDE07G0968' => 'cde', 'CDE09G1441' => 'cde', 'Cfa006103' => 'cfa', 'Cfa015573' => 'cfa', 'Cfa016988' => 'cfa', 'Ciclev10006738m.g' => 'ccl', 'Ciclev10010920m.g' => 'ccl', 'Ciclev10018517m.g' => 'ccl', 'CiPaw.01G159200' => 'cil', 'CiPaw.02G091000' => 'cil', 'CiPaw.02G091100' => 'cil', 'CiPaw.08G103100' => 'cil', 'CiPaw.09G224900' => 'cil', 'ClCG06G005740' => 'cla', 'ClCG07G000090' => 'cla', 'ClCG07G000100' => 'cla', 'COL.COLO4_09143' => 'col', 'COL.COLO4_25124' => 'col', 'Cpa.g.sc16.34' => 'cpa', 'Cpa.g.sc3504.1' => 'cpa', 'Cpa.g.sc60.37' => 'cpa', 'CsaV3_6G018520' => 'csa', 'CsaV3_6G036860' => 'csa', 'CSS0001072' => 'camsi', 'CSS0020208' => 'camsi', 'CSS0021253' => 'camsi', 'CSS0022190' => 'camsi', 'CSS0036150' => 'camsi', 'CSS0040442' => 'camsi', 'CSS0042300' => 'camsi', 'CSS0045298' => 'camsi', 'DCAR_012449' => 'dca', 'DCAR_018405' => 'dca', 'DCAR_024573' => 'dca', 'DCAR_030591' => 'dca', 'Dinv16926' => 'din', 'Dinv32963' => 'din', 'Dinv38382' => 'din', 'Dinv38383' => 'din', 'Duzib133G0974' => 'dzi', 'Duzib138G1867' => 'dzi', 'Duzib211G0420' => 'dzi', 'Duzib212G0930' => 'dzi', 'ECA234G1645' => 'eca', 'ECA247G3467' => 'eca', 'ECA248G1703' => 'eca', 'EL10Ac3g06327' => 'bvu', 'EL10Ac7g17204' => 'bvu', 'Eucgr.A00855' => 'egr', 'Eucgr.A00858' => 'egr', 'Eucgr.H01520' => 'egr', 'Eucgr.H03604' => 'egr', 'Eucgr.L03465' => 'egr', 'Eucgr.L03466' => 'egr', 'FAN01G0988' => 'fan', 'FAN02G3892' => 'fan', 'FAN05G3381' => 'fan', 'FAN07G0967' => 'fan', 'FAN07G1493' => 'fan', 'FAN08G3125' => 'fan', 'FAN09G0402' => 'fan', 'FAN12G2594' => 'fan', 'FAN12G3879' => 'fan', 'FAN14G1546' => 'fan', 'FAN15G3626' => 'fan', 'FAN17G0588' => 'fan', 'FAN17G0609' => 'fan', 'FAN18G2817' => 'fan', 'FAN19G1305' => 'fan', 'FAN20G1787' => 'fan', 'FAN22G0073' => 'fan', 'FAN22G0352' => 'fan', 'FAN22G0368' => 'fan', 'FAN22G2273' => 'fan', 'FAN24G1998' => 'fan', 'FAN27G1317' => 'fan', 'FvH4_2g23980' => 'fve', 'FvH4_4g14380' => 'fve', 'FvH4_4g14390' => 'fve', 'FvH4_6g09250' => 'fve', 'Glyma.03G151100' => 'gma', 'Glyma.04G122550' => 'gma', 'Glyma.05G001600' => 'gma', 'Glyma.09G270766' => 'gma', 'Glyma.09G270832' => 'gma', 'Glyma.13G209800' => 'gma', 'Glyma.15G102800' => 'gma', 'Glyma.18G218900' => 'gma', 'Glyma.19G001500' => 'gma', 'Glyma.19G153600' => 'gma', 'Gohir.A02G028600' => 'ghi', 'Gohir.A08G045000' => 'ghi', 'Gohir.A11G120500' => 'ghi', 'Gohir.A12G006200' => 'ghi', 'Gohir.A12G006250' => 'ghi', 'Gohir.D02G036300' => 'ghi', 'Gohir.D08G054700' => 'ghi', 'Gohir.D11G125600' => 'ghi', 'Gohir.D12G005700' => 'ghi', 'Gorai.004G055200' => 'gra', 'Gorai.005G040400' => 'gra', 'Gorai.007G134500' => 'gra', 'Gorai.008G005500' => 'gra', 'GSVIVG01011094001' => 'vvi', 'GSVIVG01017879001' => 'vvi', 'GSVIVG01025988001' => 'vvi', 'GSVIVG01029847001' => 'vvi', 'HanXRQChr10g0282901' => 'han', 'HanXRQChr10g0310371' => 'han', 'HanXRQChr10g0315041' => 'han', 'HanXRQChr11g0327651' => 'han', 'HanXRQChr12g0359391' => 'han', 'Haze_00972' => 'cav', 'Haze_00973' => 'cav', 'Haze_00974' => 'cav', 'Haze_04747' => 'cav', 'Haze_04749' => 'cav', 'Haze_04750' => 'cav', 'Haze_21217' => 'cav', 'Hma1.2p1_1037F.1_g250680' => 'hma', 'Hma1.2p1_1644F.1_g295320' => 'hma', 'HPP92_011322' => 'vpl', 'HPP92_011323' => 'vpl', 'HPP92_011324' => 'vpl', 'HPP92_011325' => 'vpl', 'HPP92_011326' => 'vpl', 'Hund12205' => 'sun', 'Hund17957' => 'sun', 'Lalb_Chr06g0176771' => 'lal', 'Lalb_Chr18g0056021' => 'lal', 'Lalb_Chr18g0056031' => 'lal', 'Lalb_Chr18g0056041' => 'lal', 'Lalb_Chr20g0107751' => 'lal', 'Lalb_Chr20g0118371' => 'lal', 'Lj1g0010239' => 'lja', 'Lj1g0017101' => 'lja', 'Lj2A1178G40' => 'lonja', 'Lj2A54G84' => 'lonja', 'Lj2g0015248' => 'lja', 'Lj3A761T51' => 'lonja', 'Lj6g0018116' => 'lja', 'Lsat_1_v5_gn_4_136040' => 'lsa', 'Lsat_1_v5_gn_5_187461' => 'lsa', 'Lsat_1_v5_gn_5_77001' => 'lsa', 'Lsat_1_v5_gn_9_4461' => 'lsa', 'Manes.01G210100' => 'mes', 'Manes.03G185600' => 'mes', 'Manes.05G073300' => 'mes', 'Manes.09G120300' => 'mes', 'Manes.15G022100' => 'mes', 'Mapoly0096s0053' => 'mpo', 'MBI03_g14058_MAGBIO' => 'mbi', 'MBI03_g33876_MAGBIO' => 'mbi', 'MBI03_g36854_MAGBIO' => 'mbi', 'MBI17_g11997_MAGBIO' => 'mbi', 'MD03G1269000' => 'mdo', 'MD04G1179600' => 'mdo', 'MD11G1289800' => 'mdo', 'MD12G1194700' => 'mdo', 'MD13G1182100' => 'mdo', 'MD13G1182200' => 'mdo', 'MD16G1182600' => 'mdo', 'Medtr2g021400' => 'mtr', 'Medtr2g021470' => 'mtr', 'Medtr2g105810' => 'mtr', 'Medtr3g033580' => 'mtr', 'Medtr6g007970' => 'mtr', 'Medtr7g056330' => 'mtr', 'Medtr7g074290' => 'mtr', 'Medtr7g074380' => 'mtr', 'Medtr7g094550' => 'mtr', 'Medtr8g069995' => 'mtr', 'MELO3C014345.2' => 'cme', 'MELO3C021395.2' => 'cme', 'Migut.D00262' => 'egut', 'Migut.G00257' => 'egut', 'MSTRG.21575' => 'ama', 'MSTRG.3985' => 'ama', 'Nitab4.5_0000295g0140' => 'nta', 'Nitab4.5_0000732g0140' => 'nta', 'Nitab4.5_0003162g0020' => 'nta', 'Nitab4.5_0006180g0090' => 'nta', 'Nitab4.5_0006390g0010' => 'nta', 'Nitab4.5_0007392g0040' => 'nta', 'Nn1g02140' => 'nnu', 'Nn4g26168' => 'nnu', 'Nn5g26754' => 'nnu', 'Oeu001433.1' => 'oeu', 'Oeu010299.2' => 'oeu', 'Oeu011171.1' => 'oeu', 'Oeu037675.1' => 'oeu', 'Oeu038359.1' => 'oeu', 'Oeu063834.1' => 'oeu', 'Oeu063835.1' => 'oeu', 'Os05g0312000' => 'osa', 'Os07g0211101' => 'osa', 'Os07g0211200' => 'osa', 'Os07g0681500' => 'osa', 'Peaxi162Scf00095g01015' => 'pax', 'Peaxi162Scf00104g00329' => 'pax', 'Peaxi162Scf00161g00137' => 'pax', 'PGR004G1665' => 'pgr', 'PGR031G2937' => 'pgr', 'PGR119G2145' => 'pgr', 'PGSC0003DMG400004351' => 'stu', 'PGSC0003DMG400014625' => 'stu', 'PGSC0003DMG401000943' => 'stu', 'Phvul.001G148600' => 'pvu', 'Phvul.004G001700' => 'pvu', 'Phvul.006G154900' => 'pvu', 'Phvul.008G078200' => 'pvu', 'Phvul.011G136500' => 'pvu', 'Potri.002G215600' => 'ptr', 'Potri.008G201600' => 'ptr', 'Potri.014G138400' => 'ptr', 'Potri.016G142500' => 'ptr', 'Pp3c16_10580' => 'ppa', 'Pp3c5_25280' => 'ppa', 'Prupe.1G150000' => 'ppe', 'Prupe.1G150100' => 'ppe', 'Prupe.6G299600' => 'ppe', 'Prupe.8G245000' => 'ppe', 'Psat0s4927g0040' => 'psa', 'Psat1g052080' => 'psa', 'Psat1g183800' => 'psa', 'Psat3g113840' => 'psa', 'Psat3g126120' => 'psa', 'Psat3g126160' => 'psa', 'Psat3g158760' => 'psa', 'Psat3g158840' => 'psa', 'PSO170G2858' => 'pso', 'PSO339G0606' => 'pso', 'PSO384G4709' => 'pso', 'PSO407G0334' => 'pso', 'QL04p040276' => 'qlo', 'QL06p005458' => 'qlo', 'QL06p005472' => 'qlo', 'QL07p030546' => 'qlo', 'QL07p031519' => 'qlo', 'QL09p050949' => 'qlo', 'QL09p050966' => 'qlo', 'QL09p051067' => 'qlo', 'QL12p022706' => 'qlo', 'RcHm_v2.0_Chr2g0119601' => 'rch', 'RcHm_v2.0_Chr3g0459591' => 'rch', 'RcHm_v2.0_Chr4g0418521' => 'rch', 'RcHm_v2.0_Chr4g0418531' => 'rch', 'RcHm_v2.0_Chr4g0418541' => 'rch', 'RcHm_v2.0_Chr6g0291641' => 'rch', 'Rhsim01G0086300' => 'rsi', 'Rhsim01G0276300' => 'rsi', 'Rhsim01G0276500' => 'rsi', 'Rhsim04G0207700' => 'rsi', 'Rhsim05G0234500' => 'rsi', 'Rhsim13G0022400' => 'rsi', 'Sabra02G0167900' => 'sbr', 'Sabra04G0158500' => 'sbr', 'Sabra08G0159800' => 'sbr', 'Sabra10G0011500' => 'sbr', 'Sabra14G0104400' => 'sbr', 'SalBow2G2440' => 'sbo', 'SalBow4G2265' => 'sbo', 'Sc02g0000060' => 'sci', 'Sc05g0005020' => 'sci', 'Sc13g0003890' => 'sci', 'Sed0014865' => 'sed', 'Sed0017224' => 'sed', 'Sed0026391' => 'sed', 'SEGI_00063' => 'sgi', 'SEGI_10967' => 'sgi', 'SEGI_17510' => 'sgi', 'SEGI_24396' => 'sgi', 'SEGI_39719' => 'sgi', 'SEGI_41392' => 'sgi', 'SGA_v2.0_scaffold11G05794' => 'sas', 'SGA_v2.0_scaffold142G35607' => 'sas', 'SGA_v2.0_scaffold1G00447' => 'sas', 'SHI15388' => 'shi', 'SHI15394' => 'shi', 'SHI15396' => 'shi', 'SHI15399' => 'shi', 'SMO343G0151' => 'smo', 'SMO367G1118' => 'smo', 'Solyc01g080200.3' => 'sly', 'Solyc06g008960.3' => 'sly', 'Solyc09g064780.3' => 'sly', 'Sopen01g031980' => 'spe', 'Sopen06g003710' => 'spe', 'Sopen09g026460' => 'spe', 'Sp3g21240' => 'spa', 'Sp4g30030' => 'spa', 'TAR365G0022' => 'tar', 'TAR365G1023' => 'tar', 'TAR365G1253' => 'tar', 'TAR623G0078' => 'tar', 'TAR623G1721' => 'tar', 'TAR633G0959' => 'tar', 'THA.LOC104802225' => 'tha', 'THA.LOC104804769' => 'tha', 'THA.LOC104808660' => 'tha', 'THA.LOC104812792' => 'tha', 'Thecc.01G284000' => 'tca', 'Thecc.04G220600' => 'tca', 'Thecc.05G268900' => 'tca', 'Thecc.08G171100' => 'tca', 'Thhalv10001284m.g' => 'esa', 'Thhalv10019912m.g' => 'esa', 'TPR.G14189' => 'tpr', 'TPR.G18110' => 'tpr', 'TPR.G18130' => 'tpr', 'TPR.G18131' => 'tpr', 'TPR.G18140' => 'tpr', 'TPR.G24282' => 'tpr', 'TPR.G25221' => 'tpr', 'TPR.G29267' => 'tpr', 'TPR.G35315' => 'tpr', 'TPR.G36173' => 'tpr', 'TWI09G0794' => 'twi', 'TWI59G1348' => 'twi', 'TWI74G0430' => 'twi', 'unitig_26.g8940' => 'ugi', 'unitig_749.g13744' => 'ugi', 'unitig_749.g13745' => 'ugi', 'vmacro08269' => 'vma', 'vmacro14937' => 'vma', 'vmacro20401' => 'vma', 'VMungo0464G1349' => 'vmu', 'VMungo0540G0289' => 'vmu', 'VMungo1215G1590' => 'vmu', 'VMungo1309G0221' => 'vmu', 'VMungo1309G2815' => 'vmu', 'VMungo1383G0239' => 'vmu', 'VMungo1383G2910' => 'vmu', 'Zm00001eb095270' => 'zma', 'Zm00001eb095280' => 'zma', 'Zm00001eb111630' => 'zma', 'Zm00001eb237080' => 'zma', 'Zm00001eb273740' => 'zma', 'Zm00001eb285040' => 'zma', 'Zm00001eb330790' => 'zma', 'Zm00001eb337380' => 'zma' ) $gf_id = 'HOM05D001484' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001484' ) $data_identifier = 'HOM05D001484' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 2, 'aly' => (int) 2, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 22, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 7, 'hma' => (int) 2, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 7, 'mtr' => (int) 10, 'cme' => (int) 2, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 4, 'ppa' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 4, 'qlo' => (int) 9, 'rch' => (int) 6, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 10, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 7, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb337380' $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' => 'HOM05D001484', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p31500' => 'bna', 'A05p00020' => 'bna', 'A07p08820' => 'bna', 'Aa31LG4G3300' => 'aar', 'Aa31LG8G10030' => 'aar', 'Actinidia00731' => 'ach', 'Actinidia11473' => 'ach', 'Actinidia23469' => 'ach', 'Actinidia24318' => 'ach', 'Actinidia40196' => 'ach', 'Actinidia40197' => 'ach', 'Actinidia40198' => 'ach', 'Ah.08g212990' => 'amhyb', 'Ah.15g091720' => 'amhyb', 'AL3G38260' => 'aly', 'AL4G47710' => 'aly', 'Aqoxy2G00671' => 'aox', 'Aqoxy2G03236' => 'aox', 'arahy.Tifrunner.gnm1.ann1.05IDCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KR684' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATY3SJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK6QJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6APGL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IDT7Z9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM073U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ0R87' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LE7RV4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT4QRX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V5ENPK' => 'arhy', 'AT2G48110' => 'ath', 'AT3G23590' => 'ath', 'ATR0626G186' => 'atr', 'ATR1127G141' => 'atr', 'Atru.chr4.2583' => 'acertr', 'Atru.chr5.1358' => 'acertr', 'Atru.chr5.1359' => 'acertr', 'Atru.chr8.46' => 'acertr', 'AUR62002640' => 'cqu', 'AUR62030055' => 'cqu', 'AUR62033713' => 'cqu', 'AUR62033714' => 'cqu', 'AUR62036795' => 'cqu', 'AUR62039891' => 'cqu', 'BcaB02g08737' => 'bca', 'BcaB04g20441' => 'bca', 'BcaB06g26509' => 'bca', 'BcaB06g26510' => 'bca', 'BcaB06g26511' => 'bca', 'BcaB06g26512' => 'bca', 'BcaB06g26513' => 'bca', 'BcaC02g12564' => 'bca', 'BcaC02g12565' => 'bca', 'BcaC02g12794' => 'bca', 'BcaC02g12795' => 'bca', 'BcaC02g12796' => 'bca', 'BcaC06g35541' => 'bca', 'BNapus_Darmor_BZH_scaffold_188p00080' => 'bna', 'BNapus_Darmor_BZH_scaffold_188p00090' => 'bna', 'BolC1t03972H' => 'bol', 'BolC1t03973H' => 'bol', 'BolC4t21680H' => 'bol', 'BolC7t41863H' => 'bol', 'BolSC55t61227H' => 'bol', 'BolSC55t61228H' => 'bol', 'BraA01t03278Z' => 'bra', 'BraA05t18998Z' => 'bra', 'BraA07t28673Z' => 'bra', 'C01p40150' => 'bna', 'C05p12370' => 'bna', 'C07p13680' => 'bna', 'CAN.G1006.16' => 'can', 'CAN.G1006.17' => 'can', 'CAN.G1170.2' => 'can', 'CAN.G962.7' => 'can', 'CANSAT25G2179' => 'cansat', 'CANSAT78G1573' => 'cansat', 'CARHR099510' => 'chi', 'CARHR143510' => 'chi', 'Carub.0003s2380' => 'cru', 'Carub.0004s3082' => 'cru', 'Ca_00614_v3' => 'car', 'Ca_07801_v3' => 'car', 'Ca_08567_v3' => 'car', 'Ca_09571_v3' => 'car', 'CBR_g19290' => 'cbr', 'Cc01_g19770' => 'ccan', 'Cc03_g03030' => 'ccan', 'CDE07G0968' => 'cde', 'CDE09G1441' => 'cde', 'Cfa006103' => 'cfa', 'Cfa015573' => 'cfa', 'Cfa016988' => 'cfa', 'Ciclev10006738m.g' => 'ccl', 'Ciclev10010920m.g' => 'ccl', 'Ciclev10018517m.g' => 'ccl', 'CiPaw.01G159200' => 'cil', 'CiPaw.02G091000' => 'cil', 'CiPaw.02G091100' => 'cil', 'CiPaw.08G103100' => 'cil', 'CiPaw.09G224900' => 'cil', 'ClCG06G005740' => 'cla', 'ClCG07G000090' => 'cla', 'ClCG07G000100' => 'cla', 'COL.COLO4_09143' => 'col', 'COL.COLO4_25124' => 'col', 'Cpa.g.sc16.34' => 'cpa', 'Cpa.g.sc3504.1' => 'cpa', 'Cpa.g.sc60.37' => 'cpa', 'CsaV3_6G018520' => 'csa', 'CsaV3_6G036860' => 'csa', 'CSS0001072' => 'camsi', 'CSS0020208' => 'camsi', 'CSS0021253' => 'camsi', 'CSS0022190' => 'camsi', 'CSS0036150' => 'camsi', 'CSS0040442' => 'camsi', 'CSS0042300' => 'camsi', 'CSS0045298' => 'camsi', 'DCAR_012449' => 'dca', 'DCAR_018405' => 'dca', 'DCAR_024573' => 'dca', 'DCAR_030591' => 'dca', 'Dinv16926' => 'din', 'Dinv32963' => 'din', 'Dinv38382' => 'din', 'Dinv38383' => 'din', 'Duzib133G0974' => 'dzi', 'Duzib138G1867' => 'dzi', 'Duzib211G0420' => 'dzi', 'Duzib212G0930' => 'dzi', 'ECA234G1645' => 'eca', 'ECA247G3467' => 'eca', 'ECA248G1703' => 'eca', 'EL10Ac3g06327' => 'bvu', 'EL10Ac7g17204' => 'bvu', 'Eucgr.A00855' => 'egr', 'Eucgr.A00858' => 'egr', 'Eucgr.H01520' => 'egr', 'Eucgr.H03604' => 'egr', 'Eucgr.L03465' => 'egr', 'Eucgr.L03466' => 'egr', 'FAN01G0988' => 'fan', 'FAN02G3892' => 'fan', 'FAN05G3381' => 'fan', 'FAN07G0967' => 'fan', 'FAN07G1493' => 'fan', 'FAN08G3125' => 'fan', 'FAN09G0402' => 'fan', 'FAN12G2594' => 'fan', 'FAN12G3879' => 'fan', 'FAN14G1546' => 'fan', 'FAN15G3626' => 'fan', 'FAN17G0588' => 'fan', 'FAN17G0609' => 'fan', 'FAN18G2817' => 'fan', 'FAN19G1305' => 'fan', 'FAN20G1787' => 'fan', 'FAN22G0073' => 'fan', 'FAN22G0352' => 'fan', 'FAN22G0368' => 'fan', 'FAN22G2273' => 'fan', 'FAN24G1998' => 'fan', 'FAN27G1317' => 'fan', 'FvH4_2g23980' => 'fve', 'FvH4_4g14380' => 'fve', 'FvH4_4g14390' => 'fve', 'FvH4_6g09250' => 'fve', 'Glyma.03G151100' => 'gma', 'Glyma.04G122550' => 'gma', 'Glyma.05G001600' => 'gma', 'Glyma.09G270766' => 'gma', 'Glyma.09G270832' => 'gma', 'Glyma.13G209800' => 'gma', 'Glyma.15G102800' => 'gma', 'Glyma.18G218900' => 'gma', 'Glyma.19G001500' => 'gma', 'Glyma.19G153600' => 'gma', 'Gohir.A02G028600' => 'ghi', 'Gohir.A08G045000' => 'ghi', 'Gohir.A11G120500' => 'ghi', 'Gohir.A12G006200' => 'ghi', 'Gohir.A12G006250' => 'ghi', 'Gohir.D02G036300' => 'ghi', 'Gohir.D08G054700' => 'ghi', 'Gohir.D11G125600' => 'ghi', 'Gohir.D12G005700' => 'ghi', 'Gorai.004G055200' => 'gra', 'Gorai.005G040400' => 'gra', 'Gorai.007G134500' => 'gra', 'Gorai.008G005500' => 'gra', 'GSVIVG01011094001' => 'vvi', 'GSVIVG01017879001' => 'vvi', 'GSVIVG01025988001' => 'vvi', 'GSVIVG01029847001' => 'vvi', 'HanXRQChr10g0282901' => 'han', 'HanXRQChr10g0310371' => 'han', 'HanXRQChr10g0315041' => 'han', 'HanXRQChr11g0327651' => 'han', 'HanXRQChr12g0359391' => 'han', 'Haze_00972' => 'cav', 'Haze_00973' => 'cav', 'Haze_00974' => 'cav', 'Haze_04747' => 'cav', 'Haze_04749' => 'cav', 'Haze_04750' => 'cav', 'Haze_21217' => 'cav', 'Hma1.2p1_1037F.1_g250680' => 'hma', 'Hma1.2p1_1644F.1_g295320' => 'hma', 'HPP92_011322' => 'vpl', 'HPP92_011323' => 'vpl', 'HPP92_011324' => 'vpl', 'HPP92_011325' => 'vpl', 'HPP92_011326' => 'vpl', 'Hund12205' => 'sun', 'Hund17957' => 'sun', 'Lalb_Chr06g0176771' => 'lal', 'Lalb_Chr18g0056021' => 'lal', 'Lalb_Chr18g0056031' => 'lal', 'Lalb_Chr18g0056041' => 'lal', 'Lalb_Chr20g0107751' => 'lal', 'Lalb_Chr20g0118371' => 'lal', 'Lj1g0010239' => 'lja', 'Lj1g0017101' => 'lja', 'Lj2A1178G40' => 'lonja', 'Lj2A54G84' => 'lonja', 'Lj2g0015248' => 'lja', 'Lj3A761T51' => 'lonja', 'Lj6g0018116' => 'lja', 'Lsat_1_v5_gn_4_136040' => 'lsa', 'Lsat_1_v5_gn_5_187461' => 'lsa', 'Lsat_1_v5_gn_5_77001' => 'lsa', 'Lsat_1_v5_gn_9_4461' => 'lsa', 'Manes.01G210100' => 'mes', 'Manes.03G185600' => 'mes', 'Manes.05G073300' => 'mes', 'Manes.09G120300' => 'mes', 'Manes.15G022100' => 'mes', 'Mapoly0096s0053' => 'mpo', 'MBI03_g14058_MAGBIO' => 'mbi', 'MBI03_g33876_MAGBIO' => 'mbi', 'MBI03_g36854_MAGBIO' => 'mbi', 'MBI17_g11997_MAGBIO' => 'mbi', 'MD03G1269000' => 'mdo', 'MD04G1179600' => 'mdo', 'MD11G1289800' => 'mdo', 'MD12G1194700' => 'mdo', 'MD13G1182100' => 'mdo', 'MD13G1182200' => 'mdo', 'MD16G1182600' => 'mdo', 'Medtr2g021400' => 'mtr', 'Medtr2g021470' => 'mtr', 'Medtr2g105810' => 'mtr', 'Medtr3g033580' => 'mtr', 'Medtr6g007970' => 'mtr', 'Medtr7g056330' => 'mtr', 'Medtr7g074290' => 'mtr', 'Medtr7g074380' => 'mtr', 'Medtr7g094550' => 'mtr', 'Medtr8g069995' => 'mtr', 'MELO3C014345.2' => 'cme', 'MELO3C021395.2' => 'cme', 'Migut.D00262' => 'egut', 'Migut.G00257' => 'egut', 'MSTRG.21575' => 'ama', 'MSTRG.3985' => 'ama', 'Nitab4.5_0000295g0140' => 'nta', 'Nitab4.5_0000732g0140' => 'nta', 'Nitab4.5_0003162g0020' => 'nta', 'Nitab4.5_0006180g0090' => 'nta', 'Nitab4.5_0006390g0010' => 'nta', 'Nitab4.5_0007392g0040' => 'nta', 'Nn1g02140' => 'nnu', 'Nn4g26168' => 'nnu', 'Nn5g26754' => 'nnu', 'Oeu001433.1' => 'oeu', 'Oeu010299.2' => 'oeu', 'Oeu011171.1' => 'oeu', 'Oeu037675.1' => 'oeu', 'Oeu038359.1' => 'oeu', 'Oeu063834.1' => 'oeu', 'Oeu063835.1' => 'oeu', 'Os05g0312000' => 'osa', 'Os07g0211101' => 'osa', 'Os07g0211200' => 'osa', 'Os07g0681500' => 'osa', 'Peaxi162Scf00095g01015' => 'pax', 'Peaxi162Scf00104g00329' => 'pax', 'Peaxi162Scf00161g00137' => 'pax', 'PGR004G1665' => 'pgr', 'PGR031G2937' => 'pgr', 'PGR119G2145' => 'pgr', 'PGSC0003DMG400004351' => 'stu', 'PGSC0003DMG400014625' => 'stu', 'PGSC0003DMG401000943' => 'stu', 'Phvul.001G148600' => 'pvu', 'Phvul.004G001700' => 'pvu', 'Phvul.006G154900' => 'pvu', 'Phvul.008G078200' => 'pvu', 'Phvul.011G136500' => 'pvu', 'Potri.002G215600' => 'ptr', 'Potri.008G201600' => 'ptr', 'Potri.014G138400' => 'ptr', 'Potri.016G142500' => 'ptr', 'Pp3c16_10580' => 'ppa', 'Pp3c5_25280' => 'ppa', 'Prupe.1G150000' => 'ppe', 'Prupe.1G150100' => 'ppe', 'Prupe.6G299600' => 'ppe', 'Prupe.8G245000' => 'ppe', 'Psat0s4927g0040' => 'psa', 'Psat1g052080' => 'psa', 'Psat1g183800' => 'psa', 'Psat3g113840' => 'psa', 'Psat3g126120' => 'psa', 'Psat3g126160' => 'psa', 'Psat3g158760' => 'psa', 'Psat3g158840' => 'psa', 'PSO170G2858' => 'pso', 'PSO339G0606' => 'pso', 'PSO384G4709' => 'pso', 'PSO407G0334' => 'pso', 'QL04p040276' => 'qlo', 'QL06p005458' => 'qlo', 'QL06p005472' => 'qlo', 'QL07p030546' => 'qlo', 'QL07p031519' => 'qlo', 'QL09p050949' => 'qlo', 'QL09p050966' => 'qlo', 'QL09p051067' => 'qlo', 'QL12p022706' => 'qlo', 'RcHm_v2.0_Chr2g0119601' => 'rch', 'RcHm_v2.0_Chr3g0459591' => 'rch', 'RcHm_v2.0_Chr4g0418521' => 'rch', 'RcHm_v2.0_Chr4g0418531' => 'rch', 'RcHm_v2.0_Chr4g0418541' => 'rch', 'RcHm_v2.0_Chr6g0291641' => 'rch', 'Rhsim01G0086300' => 'rsi', 'Rhsim01G0276300' => 'rsi', 'Rhsim01G0276500' => 'rsi', 'Rhsim04G0207700' => 'rsi', 'Rhsim05G0234500' => 'rsi', 'Rhsim13G0022400' => 'rsi', 'Sabra02G0167900' => 'sbr', 'Sabra04G0158500' => 'sbr', 'Sabra08G0159800' => 'sbr', 'Sabra10G0011500' => 'sbr', 'Sabra14G0104400' => 'sbr', 'SalBow2G2440' => 'sbo', 'SalBow4G2265' => 'sbo', 'Sc02g0000060' => 'sci', 'Sc05g0005020' => 'sci', 'Sc13g0003890' => 'sci', 'Sed0014865' => 'sed', 'Sed0017224' => 'sed', 'Sed0026391' => 'sed', 'SEGI_00063' => 'sgi', 'SEGI_10967' => 'sgi', 'SEGI_17510' => 'sgi', 'SEGI_24396' => 'sgi', 'SEGI_39719' => 'sgi', 'SEGI_41392' => 'sgi', 'SGA_v2.0_scaffold11G05794' => 'sas', 'SGA_v2.0_scaffold142G35607' => 'sas', 'SGA_v2.0_scaffold1G00447' => 'sas', 'SHI15388' => 'shi', 'SHI15394' => 'shi', 'SHI15396' => 'shi', 'SHI15399' => 'shi', 'SMO343G0151' => 'smo', 'SMO367G1118' => 'smo', 'Solyc01g080200.3' => 'sly', 'Solyc06g008960.3' => 'sly', 'Solyc09g064780.3' => 'sly', 'Sopen01g031980' => 'spe', 'Sopen06g003710' => 'spe', 'Sopen09g026460' => 'spe', 'Sp3g21240' => 'spa', 'Sp4g30030' => 'spa', 'TAR365G0022' => 'tar', 'TAR365G1023' => 'tar', 'TAR365G1253' => 'tar', 'TAR623G0078' => 'tar', 'TAR623G1721' => 'tar', 'TAR633G0959' => 'tar', 'THA.LOC104802225' => 'tha', 'THA.LOC104804769' => 'tha', 'THA.LOC104808660' => 'tha', 'THA.LOC104812792' => 'tha', 'Thecc.01G284000' => 'tca', 'Thecc.04G220600' => 'tca', 'Thecc.05G268900' => 'tca', 'Thecc.08G171100' => 'tca', 'Thhalv10001284m.g' => 'esa', 'Thhalv10019912m.g' => 'esa', 'TPR.G14189' => 'tpr', 'TPR.G18110' => 'tpr', 'TPR.G18130' => 'tpr', 'TPR.G18131' => 'tpr', 'TPR.G18140' => 'tpr', 'TPR.G24282' => 'tpr', 'TPR.G25221' => 'tpr', 'TPR.G29267' => 'tpr', 'TPR.G35315' => 'tpr', 'TPR.G36173' => 'tpr', 'TWI09G0794' => 'twi', 'TWI59G1348' => 'twi', 'TWI74G0430' => 'twi', 'unitig_26.g8940' => 'ugi', 'unitig_749.g13744' => 'ugi', 'unitig_749.g13745' => 'ugi', 'vmacro08269' => 'vma', 'vmacro14937' => 'vma', 'vmacro20401' => 'vma', 'VMungo0464G1349' => 'vmu', 'VMungo0540G0289' => 'vmu', 'VMungo1215G1590' => 'vmu', 'VMungo1309G0221' => 'vmu', 'VMungo1309G2815' => 'vmu', 'VMungo1383G0239' => 'vmu', 'VMungo1383G2910' => 'vmu', 'Zm00001eb095270' => 'zma', 'Zm00001eb095280' => 'zma', 'Zm00001eb111630' => 'zma', 'Zm00001eb237080' => 'zma', 'Zm00001eb273740' => 'zma', 'Zm00001eb285040' => 'zma', 'Zm00001eb330790' => 'zma', 'Zm00001eb337380' => 'zma' ), 'gf_id' => 'HOM05D001484', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001484' ), 'data_identifier' => 'HOM05D001484', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001484', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p31500' => 'bna', 'A05p00020' => 'bna', 'A07p08820' => 'bna', 'Aa31LG4G3300' => 'aar', 'Aa31LG8G10030' => 'aar', 'Actinidia00731' => 'ach', 'Actinidia11473' => 'ach', 'Actinidia23469' => 'ach', 'Actinidia24318' => 'ach', 'Actinidia40196' => 'ach', 'Actinidia40197' => 'ach', 'Actinidia40198' => 'ach', 'Ah.08g212990' => 'amhyb', 'Ah.15g091720' => 'amhyb', 'AL3G38260' => 'aly', 'AL4G47710' => 'aly', 'Aqoxy2G00671' => 'aox', 'Aqoxy2G03236' => 'aox', 'arahy.Tifrunner.gnm1.ann1.05IDCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KR684' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATY3SJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK6QJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6APGL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IDT7Z9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM073U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ0R87' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LE7RV4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT4QRX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V5ENPK' => 'arhy', 'AT2G48110' => 'ath', 'AT3G23590' => 'ath', 'ATR0626G186' => 'atr', 'ATR1127G141' => 'atr', 'Atru.chr4.2583' => 'acertr', 'Atru.chr5.1358' => 'acertr', 'Atru.chr5.1359' => 'acertr', 'Atru.chr8.46' => 'acertr', 'AUR62002640' => 'cqu', 'AUR62030055' => 'cqu', 'AUR62033713' => 'cqu', 'AUR62033714' => 'cqu', 'AUR62036795' => 'cqu', 'AUR62039891' => 'cqu', 'BcaB02g08737' => 'bca', 'BcaB04g20441' => 'bca', 'BcaB06g26509' => 'bca', 'BcaB06g26510' => 'bca', 'BcaB06g26511' => 'bca', 'BcaB06g26512' => 'bca', 'BcaB06g26513' => 'bca', 'BcaC02g12564' => 'bca', 'BcaC02g12565' => 'bca', 'BcaC02g12794' => 'bca', 'BcaC02g12795' => 'bca', 'BcaC02g12796' => 'bca', 'BcaC06g35541' => 'bca', 'BNapus_Darmor_BZH_scaffold_188p00080' => 'bna', 'BNapus_Darmor_BZH_scaffold_188p00090' => 'bna', 'BolC1t03972H' => 'bol', 'BolC1t03973H' => 'bol', 'BolC4t21680H' => 'bol', 'BolC7t41863H' => 'bol', 'BolSC55t61227H' => 'bol', 'BolSC55t61228H' => 'bol', 'BraA01t03278Z' => 'bra', 'BraA05t18998Z' => 'bra', 'BraA07t28673Z' => 'bra', 'C01p40150' => 'bna', 'C05p12370' => 'bna', 'C07p13680' => 'bna', 'CAN.G1006.16' => 'can', 'CAN.G1006.17' => 'can', 'CAN.G1170.2' => 'can', 'CAN.G962.7' => 'can', 'CANSAT25G2179' => 'cansat', 'CANSAT78G1573' => 'cansat', 'CARHR099510' => 'chi', 'CARHR143510' => 'chi', 'Carub.0003s2380' => 'cru', 'Carub.0004s3082' => 'cru', 'Ca_00614_v3' => 'car', 'Ca_07801_v3' => 'car', 'Ca_08567_v3' => 'car', 'Ca_09571_v3' => 'car', 'CBR_g19290' => 'cbr', 'Cc01_g19770' => 'ccan', 'Cc03_g03030' => 'ccan', 'CDE07G0968' => 'cde', 'CDE09G1441' => 'cde', 'Cfa006103' => 'cfa', 'Cfa015573' => 'cfa', 'Cfa016988' => 'cfa', 'Ciclev10006738m.g' => 'ccl', 'Ciclev10010920m.g' => 'ccl', 'Ciclev10018517m.g' => 'ccl', 'CiPaw.01G159200' => 'cil', 'CiPaw.02G091000' => 'cil', 'CiPaw.02G091100' => 'cil', 'CiPaw.08G103100' => 'cil', 'CiPaw.09G224900' => 'cil', 'ClCG06G005740' => 'cla', 'ClCG07G000090' => 'cla', 'ClCG07G000100' => 'cla', 'COL.COLO4_09143' => 'col', 'COL.COLO4_25124' => 'col', 'Cpa.g.sc16.34' => 'cpa', 'Cpa.g.sc3504.1' => 'cpa', 'Cpa.g.sc60.37' => 'cpa', 'CsaV3_6G018520' => 'csa', 'CsaV3_6G036860' => 'csa', 'CSS0001072' => 'camsi', 'CSS0020208' => 'camsi', 'CSS0021253' => 'camsi', 'CSS0022190' => 'camsi', 'CSS0036150' => 'camsi', 'CSS0040442' => 'camsi', 'CSS0042300' => 'camsi', 'CSS0045298' => 'camsi', 'DCAR_012449' => 'dca', 'DCAR_018405' => 'dca', 'DCAR_024573' => 'dca', 'DCAR_030591' => 'dca', 'Dinv16926' => 'din', 'Dinv32963' => 'din', 'Dinv38382' => 'din', 'Dinv38383' => 'din', 'Duzib133G0974' => 'dzi', 'Duzib138G1867' => 'dzi', 'Duzib211G0420' => 'dzi', 'Duzib212G0930' => 'dzi', 'ECA234G1645' => 'eca', 'ECA247G3467' => 'eca', 'ECA248G1703' => 'eca', 'EL10Ac3g06327' => 'bvu', 'EL10Ac7g17204' => 'bvu', 'Eucgr.A00855' => 'egr', 'Eucgr.A00858' => 'egr', 'Eucgr.H01520' => 'egr', 'Eucgr.H03604' => 'egr', 'Eucgr.L03465' => 'egr', 'Eucgr.L03466' => 'egr', 'FAN01G0988' => 'fan', 'FAN02G3892' => 'fan', 'FAN05G3381' => 'fan', 'FAN07G0967' => 'fan', 'FAN07G1493' => 'fan', 'FAN08G3125' => 'fan', 'FAN09G0402' => 'fan', 'FAN12G2594' => 'fan', 'FAN12G3879' => 'fan', 'FAN14G1546' => 'fan', 'FAN15G3626' => 'fan', 'FAN17G0588' => 'fan', 'FAN17G0609' => 'fan', 'FAN18G2817' => 'fan', 'FAN19G1305' => 'fan', 'FAN20G1787' => 'fan', 'FAN22G0073' => 'fan', 'FAN22G0352' => 'fan', 'FAN22G0368' => 'fan', 'FAN22G2273' => 'fan', 'FAN24G1998' => 'fan', 'FAN27G1317' => 'fan', 'FvH4_2g23980' => 'fve', 'FvH4_4g14380' => 'fve', 'FvH4_4g14390' => 'fve', 'FvH4_6g09250' => 'fve', 'Glyma.03G151100' => 'gma', 'Glyma.04G122550' => 'gma', 'Glyma.05G001600' => 'gma', 'Glyma.09G270766' => 'gma', 'Glyma.09G270832' => 'gma', 'Glyma.13G209800' => 'gma', 'Glyma.15G102800' => 'gma', 'Glyma.18G218900' => 'gma', 'Glyma.19G001500' => 'gma', 'Glyma.19G153600' => 'gma', 'Gohir.A02G028600' => 'ghi', 'Gohir.A08G045000' => 'ghi', 'Gohir.A11G120500' => 'ghi', 'Gohir.A12G006200' => 'ghi', 'Gohir.A12G006250' => 'ghi', 'Gohir.D02G036300' => 'ghi', 'Gohir.D08G054700' => 'ghi', 'Gohir.D11G125600' => 'ghi', 'Gohir.D12G005700' => 'ghi', 'Gorai.004G055200' => 'gra', 'Gorai.005G040400' => 'gra', 'Gorai.007G134500' => 'gra', 'Gorai.008G005500' => 'gra', 'GSVIVG01011094001' => 'vvi', 'GSVIVG01017879001' => 'vvi', 'GSVIVG01025988001' => 'vvi', 'GSVIVG01029847001' => 'vvi', 'HanXRQChr10g0282901' => 'han', 'HanXRQChr10g0310371' => 'han', 'HanXRQChr10g0315041' => 'han', 'HanXRQChr11g0327651' => 'han', 'HanXRQChr12g0359391' => 'han', 'Haze_00972' => 'cav', 'Haze_00973' => 'cav', 'Haze_00974' => 'cav', 'Haze_04747' => 'cav', 'Haze_04749' => 'cav', 'Haze_04750' => 'cav', 'Haze_21217' => 'cav', 'Hma1.2p1_1037F.1_g250680' => 'hma', 'Hma1.2p1_1644F.1_g295320' => 'hma', 'HPP92_011322' => 'vpl', 'HPP92_011323' => 'vpl', 'HPP92_011324' => 'vpl', 'HPP92_011325' => 'vpl', 'HPP92_011326' => 'vpl', 'Hund12205' => 'sun', 'Hund17957' => 'sun', 'Lalb_Chr06g0176771' => 'lal', 'Lalb_Chr18g0056021' => 'lal', 'Lalb_Chr18g0056031' => 'lal', 'Lalb_Chr18g0056041' => 'lal', 'Lalb_Chr20g0107751' => 'lal', 'Lalb_Chr20g0118371' => 'lal', 'Lj1g0010239' => 'lja', 'Lj1g0017101' => 'lja', 'Lj2A1178G40' => 'lonja', 'Lj2A54G84' => 'lonja', 'Lj2g0015248' => 'lja', 'Lj3A761T51' => 'lonja', 'Lj6g0018116' => 'lja', 'Lsat_1_v5_gn_4_136040' => 'lsa', 'Lsat_1_v5_gn_5_187461' => 'lsa', 'Lsat_1_v5_gn_5_77001' => 'lsa', 'Lsat_1_v5_gn_9_4461' => 'lsa', 'Manes.01G210100' => 'mes', 'Manes.03G185600' => 'mes', 'Manes.05G073300' => 'mes', 'Manes.09G120300' => 'mes', 'Manes.15G022100' => 'mes', 'Mapoly0096s0053' => 'mpo', 'MBI03_g14058_MAGBIO' => 'mbi', 'MBI03_g33876_MAGBIO' => 'mbi', 'MBI03_g36854_MAGBIO' => 'mbi', 'MBI17_g11997_MAGBIO' => 'mbi', 'MD03G1269000' => 'mdo', 'MD04G1179600' => 'mdo', 'MD11G1289800' => 'mdo', 'MD12G1194700' => 'mdo', 'MD13G1182100' => 'mdo', 'MD13G1182200' => 'mdo', 'MD16G1182600' => 'mdo', 'Medtr2g021400' => 'mtr', 'Medtr2g021470' => 'mtr', 'Medtr2g105810' => 'mtr', 'Medtr3g033580' => 'mtr', 'Medtr6g007970' => 'mtr', 'Medtr7g056330' => 'mtr', 'Medtr7g074290' => 'mtr', 'Medtr7g074380' => 'mtr', 'Medtr7g094550' => 'mtr', 'Medtr8g069995' => 'mtr', 'MELO3C014345.2' => 'cme', 'MELO3C021395.2' => 'cme', 'Migut.D00262' => 'egut', 'Migut.G00257' => 'egut', 'MSTRG.21575' => 'ama', 'MSTRG.3985' => 'ama', 'Nitab4.5_0000295g0140' => 'nta', 'Nitab4.5_0000732g0140' => 'nta', 'Nitab4.5_0003162g0020' => 'nta', 'Nitab4.5_0006180g0090' => 'nta', 'Nitab4.5_0006390g0010' => 'nta', 'Nitab4.5_0007392g0040' => 'nta', 'Nn1g02140' => 'nnu', 'Nn4g26168' => 'nnu', 'Nn5g26754' => 'nnu', 'Oeu001433.1' => 'oeu', 'Oeu010299.2' => 'oeu', 'Oeu011171.1' => 'oeu', 'Oeu037675.1' => 'oeu', 'Oeu038359.1' => 'oeu', 'Oeu063834.1' => 'oeu', 'Oeu063835.1' => 'oeu', 'Os05g0312000' => 'osa', 'Os07g0211101' => 'osa', 'Os07g0211200' => 'osa', 'Os07g0681500' => 'osa', 'Peaxi162Scf00095g01015' => 'pax', 'Peaxi162Scf00104g00329' => 'pax', 'Peaxi162Scf00161g00137' => 'pax', 'PGR004G1665' => 'pgr', 'PGR031G2937' => 'pgr', 'PGR119G2145' => 'pgr', 'PGSC0003DMG400004351' => 'stu', 'PGSC0003DMG400014625' => 'stu', 'PGSC0003DMG401000943' => 'stu', 'Phvul.001G148600' => 'pvu', 'Phvul.004G001700' => 'pvu', 'Phvul.006G154900' => 'pvu', 'Phvul.008G078200' => 'pvu', 'Phvul.011G136500' => 'pvu', 'Potri.002G215600' => 'ptr', 'Potri.008G201600' => 'ptr', 'Potri.014G138400' => 'ptr', 'Potri.016G142500' => 'ptr', 'Pp3c16_10580' => 'ppa', 'Pp3c5_25280' => 'ppa', 'Prupe.1G150000' => 'ppe', 'Prupe.1G150100' => 'ppe', 'Prupe.6G299600' => 'ppe', 'Prupe.8G245000' => 'ppe', 'Psat0s4927g0040' => 'psa', 'Psat1g052080' => 'psa', 'Psat1g183800' => 'psa', 'Psat3g113840' => 'psa', 'Psat3g126120' => 'psa', 'Psat3g126160' => 'psa', 'Psat3g158760' => 'psa', 'Psat3g158840' => 'psa', 'PSO170G2858' => 'pso', 'PSO339G0606' => 'pso', 'PSO384G4709' => 'pso', 'PSO407G0334' => 'pso', 'QL04p040276' => 'qlo', 'QL06p005458' => 'qlo', 'QL06p005472' => 'qlo', 'QL07p030546' => 'qlo', 'QL07p031519' => 'qlo', 'QL09p050949' => 'qlo', 'QL09p050966' => 'qlo', 'QL09p051067' => 'qlo', 'QL12p022706' => 'qlo', 'RcHm_v2.0_Chr2g0119601' => 'rch', 'RcHm_v2.0_Chr3g0459591' => 'rch', 'RcHm_v2.0_Chr4g0418521' => 'rch', 'RcHm_v2.0_Chr4g0418531' => 'rch', 'RcHm_v2.0_Chr4g0418541' => 'rch', 'RcHm_v2.0_Chr6g0291641' => 'rch', 'Rhsim01G0086300' => 'rsi', 'Rhsim01G0276300' => 'rsi', 'Rhsim01G0276500' => 'rsi', 'Rhsim04G0207700' => 'rsi', 'Rhsim05G0234500' => 'rsi', 'Rhsim13G0022400' => 'rsi', 'Sabra02G0167900' => 'sbr', 'Sabra04G0158500' => 'sbr', 'Sabra08G0159800' => 'sbr', 'Sabra10G0011500' => 'sbr', 'Sabra14G0104400' => 'sbr', 'SalBow2G2440' => 'sbo', 'SalBow4G2265' => 'sbo', 'Sc02g0000060' => 'sci', 'Sc05g0005020' => 'sci', 'Sc13g0003890' => 'sci', 'Sed0014865' => 'sed', 'Sed0017224' => 'sed', 'Sed0026391' => 'sed', 'SEGI_00063' => 'sgi', 'SEGI_10967' => 'sgi', 'SEGI_17510' => 'sgi', 'SEGI_24396' => 'sgi', 'SEGI_39719' => 'sgi', 'SEGI_41392' => 'sgi', 'SGA_v2.0_scaffold11G05794' => 'sas', 'SGA_v2.0_scaffold142G35607' => 'sas', 'SGA_v2.0_scaffold1G00447' => 'sas', 'SHI15388' => 'shi', 'SHI15394' => 'shi', 'SHI15396' => 'shi', 'SHI15399' => 'shi', 'SMO343G0151' => 'smo', 'SMO367G1118' => 'smo', 'Solyc01g080200.3' => 'sly', 'Solyc06g008960.3' => 'sly', 'Solyc09g064780.3' => 'sly', 'Sopen01g031980' => 'spe', 'Sopen06g003710' => 'spe', 'Sopen09g026460' => 'spe', 'Sp3g21240' => 'spa', 'Sp4g30030' => 'spa', 'TAR365G0022' => 'tar', 'TAR365G1023' => 'tar', 'TAR365G1253' => 'tar', 'TAR623G0078' => 'tar', 'TAR623G1721' => 'tar', 'TAR633G0959' => 'tar', 'THA.LOC104802225' => 'tha', 'THA.LOC104804769' => 'tha', 'THA.LOC104808660' => 'tha', 'THA.LOC104812792' => 'tha', 'Thecc.01G284000' => 'tca', 'Thecc.04G220600' => 'tca', 'Thecc.05G268900' => 'tca', 'Thecc.08G171100' => 'tca', 'Thhalv10001284m.g' => 'esa', 'Thhalv10019912m.g' => 'esa', 'TPR.G14189' => 'tpr', 'TPR.G18110' => 'tpr', 'TPR.G18130' => 'tpr', 'TPR.G18131' => 'tpr', 'TPR.G18140' => 'tpr', 'TPR.G24282' => 'tpr', 'TPR.G25221' => 'tpr', 'TPR.G29267' => 'tpr', 'TPR.G35315' => 'tpr', 'TPR.G36173' => 'tpr', 'TWI09G0794' => 'twi', 'TWI59G1348' => 'twi', 'TWI74G0430' => 'twi', 'unitig_26.g8940' => 'ugi', 'unitig_749.g13744' => 'ugi', 'unitig_749.g13745' => 'ugi', 'vmacro08269' => 'vma', 'vmacro14937' => 'vma', 'vmacro20401' => 'vma', 'VMungo0464G1349' => 'vmu', 'VMungo0540G0289' => 'vmu', 'VMungo1215G1590' => 'vmu', 'VMungo1309G0221' => 'vmu', 'VMungo1309G2815' => 'vmu', 'VMungo1383G0239' => 'vmu', 'VMungo1383G2910' => 'vmu', 'Zm00001eb095270' => 'zma', 'Zm00001eb095280' => 'zma', 'Zm00001eb111630' => 'zma', 'Zm00001eb237080' => 'zma', 'Zm00001eb273740' => 'zma', 'Zm00001eb285040' => 'zma', 'Zm00001eb330790' => 'zma', 'Zm00001eb337380' => 'zma' ) $gf_id = 'HOM05D001484' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001484' ) $data_identifier = 'HOM05D001484' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 2, 'aly' => (int) 2, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 22, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 7, 'hma' => (int) 2, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 7, 'mtr' => (int) 10, 'cme' => (int) 2, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 4, 'ppa' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 4, 'qlo' => (int) 9, 'rch' => (int) 6, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 10, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 7, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb337380' $species_info = array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ) $local_species = 'aox' $disabled = '' $selected = '' $num_hits = (int) 0include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001484', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p31500' => 'bna', 'A05p00020' => 'bna', 'A07p08820' => 'bna', 'Aa31LG4G3300' => 'aar', 'Aa31LG8G10030' => 'aar', 'Actinidia00731' => 'ach', 'Actinidia11473' => 'ach', 'Actinidia23469' => 'ach', 'Actinidia24318' => 'ach', 'Actinidia40196' => 'ach', 'Actinidia40197' => 'ach', 'Actinidia40198' => 'ach', 'Ah.08g212990' => 'amhyb', 'Ah.15g091720' => 'amhyb', 'AL3G38260' => 'aly', 'AL4G47710' => 'aly', 'Aqoxy2G00671' => 'aox', 'Aqoxy2G03236' => 'aox', 'arahy.Tifrunner.gnm1.ann1.05IDCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KR684' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATY3SJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK6QJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6APGL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IDT7Z9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM073U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ0R87' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LE7RV4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT4QRX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V5ENPK' => 'arhy', 'AT2G48110' => 'ath', 'AT3G23590' => 'ath', 'ATR0626G186' => 'atr', 'ATR1127G141' => 'atr', 'Atru.chr4.2583' => 'acertr', 'Atru.chr5.1358' => 'acertr', 'Atru.chr5.1359' => 'acertr', 'Atru.chr8.46' => 'acertr', 'AUR62002640' => 'cqu', 'AUR62030055' => 'cqu', 'AUR62033713' => 'cqu', 'AUR62033714' => 'cqu', 'AUR62036795' => 'cqu', 'AUR62039891' => 'cqu', 'BcaB02g08737' => 'bca', 'BcaB04g20441' => 'bca', 'BcaB06g26509' => 'bca', 'BcaB06g26510' => 'bca', 'BcaB06g26511' => 'bca', 'BcaB06g26512' => 'bca', 'BcaB06g26513' => 'bca', 'BcaC02g12564' => 'bca', 'BcaC02g12565' => 'bca', 'BcaC02g12794' => 'bca', 'BcaC02g12795' => 'bca', 'BcaC02g12796' => 'bca', 'BcaC06g35541' => 'bca', 'BNapus_Darmor_BZH_scaffold_188p00080' => 'bna', 'BNapus_Darmor_BZH_scaffold_188p00090' => 'bna', 'BolC1t03972H' => 'bol', 'BolC1t03973H' => 'bol', 'BolC4t21680H' => 'bol', 'BolC7t41863H' => 'bol', 'BolSC55t61227H' => 'bol', 'BolSC55t61228H' => 'bol', 'BraA01t03278Z' => 'bra', 'BraA05t18998Z' => 'bra', 'BraA07t28673Z' => 'bra', 'C01p40150' => 'bna', 'C05p12370' => 'bna', 'C07p13680' => 'bna', 'CAN.G1006.16' => 'can', 'CAN.G1006.17' => 'can', 'CAN.G1170.2' => 'can', 'CAN.G962.7' => 'can', 'CANSAT25G2179' => 'cansat', 'CANSAT78G1573' => 'cansat', 'CARHR099510' => 'chi', 'CARHR143510' => 'chi', 'Carub.0003s2380' => 'cru', 'Carub.0004s3082' => 'cru', 'Ca_00614_v3' => 'car', 'Ca_07801_v3' => 'car', 'Ca_08567_v3' => 'car', 'Ca_09571_v3' => 'car', 'CBR_g19290' => 'cbr', 'Cc01_g19770' => 'ccan', 'Cc03_g03030' => 'ccan', 'CDE07G0968' => 'cde', 'CDE09G1441' => 'cde', 'Cfa006103' => 'cfa', 'Cfa015573' => 'cfa', 'Cfa016988' => 'cfa', 'Ciclev10006738m.g' => 'ccl', 'Ciclev10010920m.g' => 'ccl', 'Ciclev10018517m.g' => 'ccl', 'CiPaw.01G159200' => 'cil', 'CiPaw.02G091000' => 'cil', 'CiPaw.02G091100' => 'cil', 'CiPaw.08G103100' => 'cil', 'CiPaw.09G224900' => 'cil', 'ClCG06G005740' => 'cla', 'ClCG07G000090' => 'cla', 'ClCG07G000100' => 'cla', 'COL.COLO4_09143' => 'col', 'COL.COLO4_25124' => 'col', 'Cpa.g.sc16.34' => 'cpa', 'Cpa.g.sc3504.1' => 'cpa', 'Cpa.g.sc60.37' => 'cpa', 'CsaV3_6G018520' => 'csa', 'CsaV3_6G036860' => 'csa', 'CSS0001072' => 'camsi', 'CSS0020208' => 'camsi', 'CSS0021253' => 'camsi', 'CSS0022190' => 'camsi', 'CSS0036150' => 'camsi', 'CSS0040442' => 'camsi', 'CSS0042300' => 'camsi', 'CSS0045298' => 'camsi', 'DCAR_012449' => 'dca', 'DCAR_018405' => 'dca', 'DCAR_024573' => 'dca', 'DCAR_030591' => 'dca', 'Dinv16926' => 'din', 'Dinv32963' => 'din', 'Dinv38382' => 'din', 'Dinv38383' => 'din', 'Duzib133G0974' => 'dzi', 'Duzib138G1867' => 'dzi', 'Duzib211G0420' => 'dzi', 'Duzib212G0930' => 'dzi', 'ECA234G1645' => 'eca', 'ECA247G3467' => 'eca', 'ECA248G1703' => 'eca', 'EL10Ac3g06327' => 'bvu', 'EL10Ac7g17204' => 'bvu', 'Eucgr.A00855' => 'egr', 'Eucgr.A00858' => 'egr', 'Eucgr.H01520' => 'egr', 'Eucgr.H03604' => 'egr', 'Eucgr.L03465' => 'egr', 'Eucgr.L03466' => 'egr', 'FAN01G0988' => 'fan', 'FAN02G3892' => 'fan', 'FAN05G3381' => 'fan', 'FAN07G0967' => 'fan', 'FAN07G1493' => 'fan', 'FAN08G3125' => 'fan', 'FAN09G0402' => 'fan', 'FAN12G2594' => 'fan', 'FAN12G3879' => 'fan', 'FAN14G1546' => 'fan', 'FAN15G3626' => 'fan', 'FAN17G0588' => 'fan', 'FAN17G0609' => 'fan', 'FAN18G2817' => 'fan', 'FAN19G1305' => 'fan', 'FAN20G1787' => 'fan', 'FAN22G0073' => 'fan', 'FAN22G0352' => 'fan', 'FAN22G0368' => 'fan', 'FAN22G2273' => 'fan', 'FAN24G1998' => 'fan', 'FAN27G1317' => 'fan', 'FvH4_2g23980' => 'fve', 'FvH4_4g14380' => 'fve', 'FvH4_4g14390' => 'fve', 'FvH4_6g09250' => 'fve', 'Glyma.03G151100' => 'gma', 'Glyma.04G122550' => 'gma', 'Glyma.05G001600' => 'gma', 'Glyma.09G270766' => 'gma', 'Glyma.09G270832' => 'gma', 'Glyma.13G209800' => 'gma', 'Glyma.15G102800' => 'gma', 'Glyma.18G218900' => 'gma', 'Glyma.19G001500' => 'gma', 'Glyma.19G153600' => 'gma', 'Gohir.A02G028600' => 'ghi', 'Gohir.A08G045000' => 'ghi', 'Gohir.A11G120500' => 'ghi', 'Gohir.A12G006200' => 'ghi', 'Gohir.A12G006250' => 'ghi', 'Gohir.D02G036300' => 'ghi', 'Gohir.D08G054700' => 'ghi', 'Gohir.D11G125600' => 'ghi', 'Gohir.D12G005700' => 'ghi', 'Gorai.004G055200' => 'gra', 'Gorai.005G040400' => 'gra', 'Gorai.007G134500' => 'gra', 'Gorai.008G005500' => 'gra', 'GSVIVG01011094001' => 'vvi', 'GSVIVG01017879001' => 'vvi', 'GSVIVG01025988001' => 'vvi', 'GSVIVG01029847001' => 'vvi', 'HanXRQChr10g0282901' => 'han', 'HanXRQChr10g0310371' => 'han', 'HanXRQChr10g0315041' => 'han', 'HanXRQChr11g0327651' => 'han', 'HanXRQChr12g0359391' => 'han', 'Haze_00972' => 'cav', 'Haze_00973' => 'cav', 'Haze_00974' => 'cav', 'Haze_04747' => 'cav', 'Haze_04749' => 'cav', 'Haze_04750' => 'cav', 'Haze_21217' => 'cav', 'Hma1.2p1_1037F.1_g250680' => 'hma', 'Hma1.2p1_1644F.1_g295320' => 'hma', 'HPP92_011322' => 'vpl', 'HPP92_011323' => 'vpl', 'HPP92_011324' => 'vpl', 'HPP92_011325' => 'vpl', 'HPP92_011326' => 'vpl', 'Hund12205' => 'sun', 'Hund17957' => 'sun', 'Lalb_Chr06g0176771' => 'lal', 'Lalb_Chr18g0056021' => 'lal', 'Lalb_Chr18g0056031' => 'lal', 'Lalb_Chr18g0056041' => 'lal', 'Lalb_Chr20g0107751' => 'lal', 'Lalb_Chr20g0118371' => 'lal', 'Lj1g0010239' => 'lja', 'Lj1g0017101' => 'lja', 'Lj2A1178G40' => 'lonja', 'Lj2A54G84' => 'lonja', 'Lj2g0015248' => 'lja', 'Lj3A761T51' => 'lonja', 'Lj6g0018116' => 'lja', 'Lsat_1_v5_gn_4_136040' => 'lsa', 'Lsat_1_v5_gn_5_187461' => 'lsa', 'Lsat_1_v5_gn_5_77001' => 'lsa', 'Lsat_1_v5_gn_9_4461' => 'lsa', 'Manes.01G210100' => 'mes', 'Manes.03G185600' => 'mes', 'Manes.05G073300' => 'mes', 'Manes.09G120300' => 'mes', 'Manes.15G022100' => 'mes', 'Mapoly0096s0053' => 'mpo', 'MBI03_g14058_MAGBIO' => 'mbi', 'MBI03_g33876_MAGBIO' => 'mbi', 'MBI03_g36854_MAGBIO' => 'mbi', 'MBI17_g11997_MAGBIO' => 'mbi', 'MD03G1269000' => 'mdo', 'MD04G1179600' => 'mdo', 'MD11G1289800' => 'mdo', 'MD12G1194700' => 'mdo', 'MD13G1182100' => 'mdo', 'MD13G1182200' => 'mdo', 'MD16G1182600' => 'mdo', 'Medtr2g021400' => 'mtr', 'Medtr2g021470' => 'mtr', 'Medtr2g105810' => 'mtr', 'Medtr3g033580' => 'mtr', 'Medtr6g007970' => 'mtr', 'Medtr7g056330' => 'mtr', 'Medtr7g074290' => 'mtr', 'Medtr7g074380' => 'mtr', 'Medtr7g094550' => 'mtr', 'Medtr8g069995' => 'mtr', 'MELO3C014345.2' => 'cme', 'MELO3C021395.2' => 'cme', 'Migut.D00262' => 'egut', 'Migut.G00257' => 'egut', 'MSTRG.21575' => 'ama', 'MSTRG.3985' => 'ama', 'Nitab4.5_0000295g0140' => 'nta', 'Nitab4.5_0000732g0140' => 'nta', 'Nitab4.5_0003162g0020' => 'nta', 'Nitab4.5_0006180g0090' => 'nta', 'Nitab4.5_0006390g0010' => 'nta', 'Nitab4.5_0007392g0040' => 'nta', 'Nn1g02140' => 'nnu', 'Nn4g26168' => 'nnu', 'Nn5g26754' => 'nnu', 'Oeu001433.1' => 'oeu', 'Oeu010299.2' => 'oeu', 'Oeu011171.1' => 'oeu', 'Oeu037675.1' => 'oeu', 'Oeu038359.1' => 'oeu', 'Oeu063834.1' => 'oeu', 'Oeu063835.1' => 'oeu', 'Os05g0312000' => 'osa', 'Os07g0211101' => 'osa', 'Os07g0211200' => 'osa', 'Os07g0681500' => 'osa', 'Peaxi162Scf00095g01015' => 'pax', 'Peaxi162Scf00104g00329' => 'pax', 'Peaxi162Scf00161g00137' => 'pax', 'PGR004G1665' => 'pgr', 'PGR031G2937' => 'pgr', 'PGR119G2145' => 'pgr', 'PGSC0003DMG400004351' => 'stu', 'PGSC0003DMG400014625' => 'stu', 'PGSC0003DMG401000943' => 'stu', 'Phvul.001G148600' => 'pvu', 'Phvul.004G001700' => 'pvu', 'Phvul.006G154900' => 'pvu', 'Phvul.008G078200' => 'pvu', 'Phvul.011G136500' => 'pvu', 'Potri.002G215600' => 'ptr', 'Potri.008G201600' => 'ptr', 'Potri.014G138400' => 'ptr', 'Potri.016G142500' => 'ptr', 'Pp3c16_10580' => 'ppa', 'Pp3c5_25280' => 'ppa', 'Prupe.1G150000' => 'ppe', 'Prupe.1G150100' => 'ppe', 'Prupe.6G299600' => 'ppe', 'Prupe.8G245000' => 'ppe', 'Psat0s4927g0040' => 'psa', 'Psat1g052080' => 'psa', 'Psat1g183800' => 'psa', 'Psat3g113840' => 'psa', 'Psat3g126120' => 'psa', 'Psat3g126160' => 'psa', 'Psat3g158760' => 'psa', 'Psat3g158840' => 'psa', 'PSO170G2858' => 'pso', 'PSO339G0606' => 'pso', 'PSO384G4709' => 'pso', 'PSO407G0334' => 'pso', 'QL04p040276' => 'qlo', 'QL06p005458' => 'qlo', 'QL06p005472' => 'qlo', 'QL07p030546' => 'qlo', 'QL07p031519' => 'qlo', 'QL09p050949' => 'qlo', 'QL09p050966' => 'qlo', 'QL09p051067' => 'qlo', 'QL12p022706' => 'qlo', 'RcHm_v2.0_Chr2g0119601' => 'rch', 'RcHm_v2.0_Chr3g0459591' => 'rch', 'RcHm_v2.0_Chr4g0418521' => 'rch', 'RcHm_v2.0_Chr4g0418531' => 'rch', 'RcHm_v2.0_Chr4g0418541' => 'rch', 'RcHm_v2.0_Chr6g0291641' => 'rch', 'Rhsim01G0086300' => 'rsi', 'Rhsim01G0276300' => 'rsi', 'Rhsim01G0276500' => 'rsi', 'Rhsim04G0207700' => 'rsi', 'Rhsim05G0234500' => 'rsi', 'Rhsim13G0022400' => 'rsi', 'Sabra02G0167900' => 'sbr', 'Sabra04G0158500' => 'sbr', 'Sabra08G0159800' => 'sbr', 'Sabra10G0011500' => 'sbr', 'Sabra14G0104400' => 'sbr', 'SalBow2G2440' => 'sbo', 'SalBow4G2265' => 'sbo', 'Sc02g0000060' => 'sci', 'Sc05g0005020' => 'sci', 'Sc13g0003890' => 'sci', 'Sed0014865' => 'sed', 'Sed0017224' => 'sed', 'Sed0026391' => 'sed', 'SEGI_00063' => 'sgi', 'SEGI_10967' => 'sgi', 'SEGI_17510' => 'sgi', 'SEGI_24396' => 'sgi', 'SEGI_39719' => 'sgi', 'SEGI_41392' => 'sgi', 'SGA_v2.0_scaffold11G05794' => 'sas', 'SGA_v2.0_scaffold142G35607' => 'sas', 'SGA_v2.0_scaffold1G00447' => 'sas', 'SHI15388' => 'shi', 'SHI15394' => 'shi', 'SHI15396' => 'shi', 'SHI15399' => 'shi', 'SMO343G0151' => 'smo', 'SMO367G1118' => 'smo', 'Solyc01g080200.3' => 'sly', 'Solyc06g008960.3' => 'sly', 'Solyc09g064780.3' => 'sly', 'Sopen01g031980' => 'spe', 'Sopen06g003710' => 'spe', 'Sopen09g026460' => 'spe', 'Sp3g21240' => 'spa', 'Sp4g30030' => 'spa', 'TAR365G0022' => 'tar', 'TAR365G1023' => 'tar', 'TAR365G1253' => 'tar', 'TAR623G0078' => 'tar', 'TAR623G1721' => 'tar', 'TAR633G0959' => 'tar', 'THA.LOC104802225' => 'tha', 'THA.LOC104804769' => 'tha', 'THA.LOC104808660' => 'tha', 'THA.LOC104812792' => 'tha', 'Thecc.01G284000' => 'tca', 'Thecc.04G220600' => 'tca', 'Thecc.05G268900' => 'tca', 'Thecc.08G171100' => 'tca', 'Thhalv10001284m.g' => 'esa', 'Thhalv10019912m.g' => 'esa', 'TPR.G14189' => 'tpr', 'TPR.G18110' => 'tpr', 'TPR.G18130' => 'tpr', 'TPR.G18131' => 'tpr', 'TPR.G18140' => 'tpr', 'TPR.G24282' => 'tpr', 'TPR.G25221' => 'tpr', 'TPR.G29267' => 'tpr', 'TPR.G35315' => 'tpr', 'TPR.G36173' => 'tpr', 'TWI09G0794' => 'twi', 'TWI59G1348' => 'twi', 'TWI74G0430' => 'twi', 'unitig_26.g8940' => 'ugi', 'unitig_749.g13744' => 'ugi', 'unitig_749.g13745' => 'ugi', 'vmacro08269' => 'vma', 'vmacro14937' => 'vma', 'vmacro20401' => 'vma', 'VMungo0464G1349' => 'vmu', 'VMungo0540G0289' => 'vmu', 'VMungo1215G1590' => 'vmu', 'VMungo1309G0221' => 'vmu', 'VMungo1309G2815' => 'vmu', 'VMungo1383G0239' => 'vmu', 'VMungo1383G2910' => 'vmu', 'Zm00001eb095270' => 'zma', 'Zm00001eb095280' => 'zma', 'Zm00001eb111630' => 'zma', 'Zm00001eb237080' => 'zma', 'Zm00001eb273740' => 'zma', 'Zm00001eb285040' => 'zma', 'Zm00001eb330790' => 'zma', 'Zm00001eb337380' => 'zma' ), 'gf_id' => 'HOM05D001484', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001484' ), 'data_identifier' => 'HOM05D001484', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001484', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p31500' => 'bna', 'A05p00020' => 'bna', 'A07p08820' => 'bna', 'Aa31LG4G3300' => 'aar', 'Aa31LG8G10030' => 'aar', 'Actinidia00731' => 'ach', 'Actinidia11473' => 'ach', 'Actinidia23469' => 'ach', 'Actinidia24318' => 'ach', 'Actinidia40196' => 'ach', 'Actinidia40197' => 'ach', 'Actinidia40198' => 'ach', 'Ah.08g212990' => 'amhyb', 'Ah.15g091720' => 'amhyb', 'AL3G38260' => 'aly', 'AL4G47710' => 'aly', 'Aqoxy2G00671' => 'aox', 'Aqoxy2G03236' => 'aox', 'arahy.Tifrunner.gnm1.ann1.05IDCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KR684' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATY3SJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK6QJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6APGL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IDT7Z9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM073U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ0R87' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LE7RV4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT4QRX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V5ENPK' => 'arhy', 'AT2G48110' => 'ath', 'AT3G23590' => 'ath', 'ATR0626G186' => 'atr', 'ATR1127G141' => 'atr', 'Atru.chr4.2583' => 'acertr', 'Atru.chr5.1358' => 'acertr', 'Atru.chr5.1359' => 'acertr', 'Atru.chr8.46' => 'acertr', 'AUR62002640' => 'cqu', 'AUR62030055' => 'cqu', 'AUR62033713' => 'cqu', 'AUR62033714' => 'cqu', 'AUR62036795' => 'cqu', 'AUR62039891' => 'cqu', 'BcaB02g08737' => 'bca', 'BcaB04g20441' => 'bca', 'BcaB06g26509' => 'bca', 'BcaB06g26510' => 'bca', 'BcaB06g26511' => 'bca', 'BcaB06g26512' => 'bca', 'BcaB06g26513' => 'bca', 'BcaC02g12564' => 'bca', 'BcaC02g12565' => 'bca', 'BcaC02g12794' => 'bca', 'BcaC02g12795' => 'bca', 'BcaC02g12796' => 'bca', 'BcaC06g35541' => 'bca', 'BNapus_Darmor_BZH_scaffold_188p00080' => 'bna', 'BNapus_Darmor_BZH_scaffold_188p00090' => 'bna', 'BolC1t03972H' => 'bol', 'BolC1t03973H' => 'bol', 'BolC4t21680H' => 'bol', 'BolC7t41863H' => 'bol', 'BolSC55t61227H' => 'bol', 'BolSC55t61228H' => 'bol', 'BraA01t03278Z' => 'bra', 'BraA05t18998Z' => 'bra', 'BraA07t28673Z' => 'bra', 'C01p40150' => 'bna', 'C05p12370' => 'bna', 'C07p13680' => 'bna', 'CAN.G1006.16' => 'can', 'CAN.G1006.17' => 'can', 'CAN.G1170.2' => 'can', 'CAN.G962.7' => 'can', 'CANSAT25G2179' => 'cansat', 'CANSAT78G1573' => 'cansat', 'CARHR099510' => 'chi', 'CARHR143510' => 'chi', 'Carub.0003s2380' => 'cru', 'Carub.0004s3082' => 'cru', 'Ca_00614_v3' => 'car', 'Ca_07801_v3' => 'car', 'Ca_08567_v3' => 'car', 'Ca_09571_v3' => 'car', 'CBR_g19290' => 'cbr', 'Cc01_g19770' => 'ccan', 'Cc03_g03030' => 'ccan', 'CDE07G0968' => 'cde', 'CDE09G1441' => 'cde', 'Cfa006103' => 'cfa', 'Cfa015573' => 'cfa', 'Cfa016988' => 'cfa', 'Ciclev10006738m.g' => 'ccl', 'Ciclev10010920m.g' => 'ccl', 'Ciclev10018517m.g' => 'ccl', 'CiPaw.01G159200' => 'cil', 'CiPaw.02G091000' => 'cil', 'CiPaw.02G091100' => 'cil', 'CiPaw.08G103100' => 'cil', 'CiPaw.09G224900' => 'cil', 'ClCG06G005740' => 'cla', 'ClCG07G000090' => 'cla', 'ClCG07G000100' => 'cla', 'COL.COLO4_09143' => 'col', 'COL.COLO4_25124' => 'col', 'Cpa.g.sc16.34' => 'cpa', 'Cpa.g.sc3504.1' => 'cpa', 'Cpa.g.sc60.37' => 'cpa', 'CsaV3_6G018520' => 'csa', 'CsaV3_6G036860' => 'csa', 'CSS0001072' => 'camsi', 'CSS0020208' => 'camsi', 'CSS0021253' => 'camsi', 'CSS0022190' => 'camsi', 'CSS0036150' => 'camsi', 'CSS0040442' => 'camsi', 'CSS0042300' => 'camsi', 'CSS0045298' => 'camsi', 'DCAR_012449' => 'dca', 'DCAR_018405' => 'dca', 'DCAR_024573' => 'dca', 'DCAR_030591' => 'dca', 'Dinv16926' => 'din', 'Dinv32963' => 'din', 'Dinv38382' => 'din', 'Dinv38383' => 'din', 'Duzib133G0974' => 'dzi', 'Duzib138G1867' => 'dzi', 'Duzib211G0420' => 'dzi', 'Duzib212G0930' => 'dzi', 'ECA234G1645' => 'eca', 'ECA247G3467' => 'eca', 'ECA248G1703' => 'eca', 'EL10Ac3g06327' => 'bvu', 'EL10Ac7g17204' => 'bvu', 'Eucgr.A00855' => 'egr', 'Eucgr.A00858' => 'egr', 'Eucgr.H01520' => 'egr', 'Eucgr.H03604' => 'egr', 'Eucgr.L03465' => 'egr', 'Eucgr.L03466' => 'egr', 'FAN01G0988' => 'fan', 'FAN02G3892' => 'fan', 'FAN05G3381' => 'fan', 'FAN07G0967' => 'fan', 'FAN07G1493' => 'fan', 'FAN08G3125' => 'fan', 'FAN09G0402' => 'fan', 'FAN12G2594' => 'fan', 'FAN12G3879' => 'fan', 'FAN14G1546' => 'fan', 'FAN15G3626' => 'fan', 'FAN17G0588' => 'fan', 'FAN17G0609' => 'fan', 'FAN18G2817' => 'fan', 'FAN19G1305' => 'fan', 'FAN20G1787' => 'fan', 'FAN22G0073' => 'fan', 'FAN22G0352' => 'fan', 'FAN22G0368' => 'fan', 'FAN22G2273' => 'fan', 'FAN24G1998' => 'fan', 'FAN27G1317' => 'fan', 'FvH4_2g23980' => 'fve', 'FvH4_4g14380' => 'fve', 'FvH4_4g14390' => 'fve', 'FvH4_6g09250' => 'fve', 'Glyma.03G151100' => 'gma', 'Glyma.04G122550' => 'gma', 'Glyma.05G001600' => 'gma', 'Glyma.09G270766' => 'gma', 'Glyma.09G270832' => 'gma', 'Glyma.13G209800' => 'gma', 'Glyma.15G102800' => 'gma', 'Glyma.18G218900' => 'gma', 'Glyma.19G001500' => 'gma', 'Glyma.19G153600' => 'gma', 'Gohir.A02G028600' => 'ghi', 'Gohir.A08G045000' => 'ghi', 'Gohir.A11G120500' => 'ghi', 'Gohir.A12G006200' => 'ghi', 'Gohir.A12G006250' => 'ghi', 'Gohir.D02G036300' => 'ghi', 'Gohir.D08G054700' => 'ghi', 'Gohir.D11G125600' => 'ghi', 'Gohir.D12G005700' => 'ghi', 'Gorai.004G055200' => 'gra', 'Gorai.005G040400' => 'gra', 'Gorai.007G134500' => 'gra', 'Gorai.008G005500' => 'gra', 'GSVIVG01011094001' => 'vvi', 'GSVIVG01017879001' => 'vvi', 'GSVIVG01025988001' => 'vvi', 'GSVIVG01029847001' => 'vvi', 'HanXRQChr10g0282901' => 'han', 'HanXRQChr10g0310371' => 'han', 'HanXRQChr10g0315041' => 'han', 'HanXRQChr11g0327651' => 'han', 'HanXRQChr12g0359391' => 'han', 'Haze_00972' => 'cav', 'Haze_00973' => 'cav', 'Haze_00974' => 'cav', 'Haze_04747' => 'cav', 'Haze_04749' => 'cav', 'Haze_04750' => 'cav', 'Haze_21217' => 'cav', 'Hma1.2p1_1037F.1_g250680' => 'hma', 'Hma1.2p1_1644F.1_g295320' => 'hma', 'HPP92_011322' => 'vpl', 'HPP92_011323' => 'vpl', 'HPP92_011324' => 'vpl', 'HPP92_011325' => 'vpl', 'HPP92_011326' => 'vpl', 'Hund12205' => 'sun', 'Hund17957' => 'sun', 'Lalb_Chr06g0176771' => 'lal', 'Lalb_Chr18g0056021' => 'lal', 'Lalb_Chr18g0056031' => 'lal', 'Lalb_Chr18g0056041' => 'lal', 'Lalb_Chr20g0107751' => 'lal', 'Lalb_Chr20g0118371' => 'lal', 'Lj1g0010239' => 'lja', 'Lj1g0017101' => 'lja', 'Lj2A1178G40' => 'lonja', 'Lj2A54G84' => 'lonja', 'Lj2g0015248' => 'lja', 'Lj3A761T51' => 'lonja', 'Lj6g0018116' => 'lja', 'Lsat_1_v5_gn_4_136040' => 'lsa', 'Lsat_1_v5_gn_5_187461' => 'lsa', 'Lsat_1_v5_gn_5_77001' => 'lsa', 'Lsat_1_v5_gn_9_4461' => 'lsa', 'Manes.01G210100' => 'mes', 'Manes.03G185600' => 'mes', 'Manes.05G073300' => 'mes', 'Manes.09G120300' => 'mes', 'Manes.15G022100' => 'mes', 'Mapoly0096s0053' => 'mpo', 'MBI03_g14058_MAGBIO' => 'mbi', 'MBI03_g33876_MAGBIO' => 'mbi', 'MBI03_g36854_MAGBIO' => 'mbi', 'MBI17_g11997_MAGBIO' => 'mbi', 'MD03G1269000' => 'mdo', 'MD04G1179600' => 'mdo', 'MD11G1289800' => 'mdo', 'MD12G1194700' => 'mdo', 'MD13G1182100' => 'mdo', 'MD13G1182200' => 'mdo', 'MD16G1182600' => 'mdo', 'Medtr2g021400' => 'mtr', 'Medtr2g021470' => 'mtr', 'Medtr2g105810' => 'mtr', 'Medtr3g033580' => 'mtr', 'Medtr6g007970' => 'mtr', 'Medtr7g056330' => 'mtr', 'Medtr7g074290' => 'mtr', 'Medtr7g074380' => 'mtr', 'Medtr7g094550' => 'mtr', 'Medtr8g069995' => 'mtr', 'MELO3C014345.2' => 'cme', 'MELO3C021395.2' => 'cme', 'Migut.D00262' => 'egut', 'Migut.G00257' => 'egut', 'MSTRG.21575' => 'ama', 'MSTRG.3985' => 'ama', 'Nitab4.5_0000295g0140' => 'nta', 'Nitab4.5_0000732g0140' => 'nta', 'Nitab4.5_0003162g0020' => 'nta', 'Nitab4.5_0006180g0090' => 'nta', 'Nitab4.5_0006390g0010' => 'nta', 'Nitab4.5_0007392g0040' => 'nta', 'Nn1g02140' => 'nnu', 'Nn4g26168' => 'nnu', 'Nn5g26754' => 'nnu', 'Oeu001433.1' => 'oeu', 'Oeu010299.2' => 'oeu', 'Oeu011171.1' => 'oeu', 'Oeu037675.1' => 'oeu', 'Oeu038359.1' => 'oeu', 'Oeu063834.1' => 'oeu', 'Oeu063835.1' => 'oeu', 'Os05g0312000' => 'osa', 'Os07g0211101' => 'osa', 'Os07g0211200' => 'osa', 'Os07g0681500' => 'osa', 'Peaxi162Scf00095g01015' => 'pax', 'Peaxi162Scf00104g00329' => 'pax', 'Peaxi162Scf00161g00137' => 'pax', 'PGR004G1665' => 'pgr', 'PGR031G2937' => 'pgr', 'PGR119G2145' => 'pgr', 'PGSC0003DMG400004351' => 'stu', 'PGSC0003DMG400014625' => 'stu', 'PGSC0003DMG401000943' => 'stu', 'Phvul.001G148600' => 'pvu', 'Phvul.004G001700' => 'pvu', 'Phvul.006G154900' => 'pvu', 'Phvul.008G078200' => 'pvu', 'Phvul.011G136500' => 'pvu', 'Potri.002G215600' => 'ptr', 'Potri.008G201600' => 'ptr', 'Potri.014G138400' => 'ptr', 'Potri.016G142500' => 'ptr', 'Pp3c16_10580' => 'ppa', 'Pp3c5_25280' => 'ppa', 'Prupe.1G150000' => 'ppe', 'Prupe.1G150100' => 'ppe', 'Prupe.6G299600' => 'ppe', 'Prupe.8G245000' => 'ppe', 'Psat0s4927g0040' => 'psa', 'Psat1g052080' => 'psa', 'Psat1g183800' => 'psa', 'Psat3g113840' => 'psa', 'Psat3g126120' => 'psa', 'Psat3g126160' => 'psa', 'Psat3g158760' => 'psa', 'Psat3g158840' => 'psa', 'PSO170G2858' => 'pso', 'PSO339G0606' => 'pso', 'PSO384G4709' => 'pso', 'PSO407G0334' => 'pso', 'QL04p040276' => 'qlo', 'QL06p005458' => 'qlo', 'QL06p005472' => 'qlo', 'QL07p030546' => 'qlo', 'QL07p031519' => 'qlo', 'QL09p050949' => 'qlo', 'QL09p050966' => 'qlo', 'QL09p051067' => 'qlo', 'QL12p022706' => 'qlo', 'RcHm_v2.0_Chr2g0119601' => 'rch', 'RcHm_v2.0_Chr3g0459591' => 'rch', 'RcHm_v2.0_Chr4g0418521' => 'rch', 'RcHm_v2.0_Chr4g0418531' => 'rch', 'RcHm_v2.0_Chr4g0418541' => 'rch', 'RcHm_v2.0_Chr6g0291641' => 'rch', 'Rhsim01G0086300' => 'rsi', 'Rhsim01G0276300' => 'rsi', 'Rhsim01G0276500' => 'rsi', 'Rhsim04G0207700' => 'rsi', 'Rhsim05G0234500' => 'rsi', 'Rhsim13G0022400' => 'rsi', 'Sabra02G0167900' => 'sbr', 'Sabra04G0158500' => 'sbr', 'Sabra08G0159800' => 'sbr', 'Sabra10G0011500' => 'sbr', 'Sabra14G0104400' => 'sbr', 'SalBow2G2440' => 'sbo', 'SalBow4G2265' => 'sbo', 'Sc02g0000060' => 'sci', 'Sc05g0005020' => 'sci', 'Sc13g0003890' => 'sci', 'Sed0014865' => 'sed', 'Sed0017224' => 'sed', 'Sed0026391' => 'sed', 'SEGI_00063' => 'sgi', 'SEGI_10967' => 'sgi', 'SEGI_17510' => 'sgi', 'SEGI_24396' => 'sgi', 'SEGI_39719' => 'sgi', 'SEGI_41392' => 'sgi', 'SGA_v2.0_scaffold11G05794' => 'sas', 'SGA_v2.0_scaffold142G35607' => 'sas', 'SGA_v2.0_scaffold1G00447' => 'sas', 'SHI15388' => 'shi', 'SHI15394' => 'shi', 'SHI15396' => 'shi', 'SHI15399' => 'shi', 'SMO343G0151' => 'smo', 'SMO367G1118' => 'smo', 'Solyc01g080200.3' => 'sly', 'Solyc06g008960.3' => 'sly', 'Solyc09g064780.3' => 'sly', 'Sopen01g031980' => 'spe', 'Sopen06g003710' => 'spe', 'Sopen09g026460' => 'spe', 'Sp3g21240' => 'spa', 'Sp4g30030' => 'spa', 'TAR365G0022' => 'tar', 'TAR365G1023' => 'tar', 'TAR365G1253' => 'tar', 'TAR623G0078' => 'tar', 'TAR623G1721' => 'tar', 'TAR633G0959' => 'tar', 'THA.LOC104802225' => 'tha', 'THA.LOC104804769' => 'tha', 'THA.LOC104808660' => 'tha', 'THA.LOC104812792' => 'tha', 'Thecc.01G284000' => 'tca', 'Thecc.04G220600' => 'tca', 'Thecc.05G268900' => 'tca', 'Thecc.08G171100' => 'tca', 'Thhalv10001284m.g' => 'esa', 'Thhalv10019912m.g' => 'esa', 'TPR.G14189' => 'tpr', 'TPR.G18110' => 'tpr', 'TPR.G18130' => 'tpr', 'TPR.G18131' => 'tpr', 'TPR.G18140' => 'tpr', 'TPR.G24282' => 'tpr', 'TPR.G25221' => 'tpr', 'TPR.G29267' => 'tpr', 'TPR.G35315' => 'tpr', 'TPR.G36173' => 'tpr', 'TWI09G0794' => 'twi', 'TWI59G1348' => 'twi', 'TWI74G0430' => 'twi', 'unitig_26.g8940' => 'ugi', 'unitig_749.g13744' => 'ugi', 'unitig_749.g13745' => 'ugi', 'vmacro08269' => 'vma', 'vmacro14937' => 'vma', 'vmacro20401' => 'vma', 'VMungo0464G1349' => 'vmu', 'VMungo0540G0289' => 'vmu', 'VMungo1215G1590' => 'vmu', 'VMungo1309G0221' => 'vmu', 'VMungo1309G2815' => 'vmu', 'VMungo1383G0239' => 'vmu', 'VMungo1383G2910' => 'vmu', 'Zm00001eb095270' => 'zma', 'Zm00001eb095280' => 'zma', 'Zm00001eb111630' => 'zma', 'Zm00001eb237080' => 'zma', 'Zm00001eb273740' => 'zma', 'Zm00001eb285040' => 'zma', 'Zm00001eb330790' => 'zma', 'Zm00001eb337380' => 'zma' ) $gf_id = 'HOM05D001484' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001484' ) $data_identifier = 'HOM05D001484' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 2, 'aly' => (int) 2, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 22, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 7, 'hma' => (int) 2, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 7, 'mtr' => (int) 10, 'cme' => (int) 2, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 4, 'ppa' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 4, 'qlo' => (int) 9, 'rch' => (int) 6, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 10, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 7, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb337380' $species_info = array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ) $local_species = 'aox' $disabled = '' $selected = '' $num_hits = (int) 0
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001484', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p31500' => 'bna', 'A05p00020' => 'bna', 'A07p08820' => 'bna', 'Aa31LG4G3300' => 'aar', 'Aa31LG8G10030' => 'aar', 'Actinidia00731' => 'ach', 'Actinidia11473' => 'ach', 'Actinidia23469' => 'ach', 'Actinidia24318' => 'ach', 'Actinidia40196' => 'ach', 'Actinidia40197' => 'ach', 'Actinidia40198' => 'ach', 'Ah.08g212990' => 'amhyb', 'Ah.15g091720' => 'amhyb', 'AL3G38260' => 'aly', 'AL4G47710' => 'aly', 'Aqoxy2G00671' => 'aox', 'Aqoxy2G03236' => 'aox', 'arahy.Tifrunner.gnm1.ann1.05IDCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KR684' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATY3SJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK6QJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6APGL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IDT7Z9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM073U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ0R87' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LE7RV4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT4QRX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V5ENPK' => 'arhy', 'AT2G48110' => 'ath', 'AT3G23590' => 'ath', 'ATR0626G186' => 'atr', 'ATR1127G141' => 'atr', 'Atru.chr4.2583' => 'acertr', 'Atru.chr5.1358' => 'acertr', 'Atru.chr5.1359' => 'acertr', 'Atru.chr8.46' => 'acertr', 'AUR62002640' => 'cqu', 'AUR62030055' => 'cqu', 'AUR62033713' => 'cqu', 'AUR62033714' => 'cqu', 'AUR62036795' => 'cqu', 'AUR62039891' => 'cqu', 'BcaB02g08737' => 'bca', 'BcaB04g20441' => 'bca', 'BcaB06g26509' => 'bca', 'BcaB06g26510' => 'bca', 'BcaB06g26511' => 'bca', 'BcaB06g26512' => 'bca', 'BcaB06g26513' => 'bca', 'BcaC02g12564' => 'bca', 'BcaC02g12565' => 'bca', 'BcaC02g12794' => 'bca', 'BcaC02g12795' => 'bca', 'BcaC02g12796' => 'bca', 'BcaC06g35541' => 'bca', 'BNapus_Darmor_BZH_scaffold_188p00080' => 'bna', 'BNapus_Darmor_BZH_scaffold_188p00090' => 'bna', 'BolC1t03972H' => 'bol', 'BolC1t03973H' => 'bol', 'BolC4t21680H' => 'bol', 'BolC7t41863H' => 'bol', 'BolSC55t61227H' => 'bol', 'BolSC55t61228H' => 'bol', 'BraA01t03278Z' => 'bra', 'BraA05t18998Z' => 'bra', 'BraA07t28673Z' => 'bra', 'C01p40150' => 'bna', 'C05p12370' => 'bna', 'C07p13680' => 'bna', 'CAN.G1006.16' => 'can', 'CAN.G1006.17' => 'can', 'CAN.G1170.2' => 'can', 'CAN.G962.7' => 'can', 'CANSAT25G2179' => 'cansat', 'CANSAT78G1573' => 'cansat', 'CARHR099510' => 'chi', 'CARHR143510' => 'chi', 'Carub.0003s2380' => 'cru', 'Carub.0004s3082' => 'cru', 'Ca_00614_v3' => 'car', 'Ca_07801_v3' => 'car', 'Ca_08567_v3' => 'car', 'Ca_09571_v3' => 'car', 'CBR_g19290' => 'cbr', 'Cc01_g19770' => 'ccan', 'Cc03_g03030' => 'ccan', 'CDE07G0968' => 'cde', 'CDE09G1441' => 'cde', 'Cfa006103' => 'cfa', 'Cfa015573' => 'cfa', 'Cfa016988' => 'cfa', 'Ciclev10006738m.g' => 'ccl', 'Ciclev10010920m.g' => 'ccl', 'Ciclev10018517m.g' => 'ccl', 'CiPaw.01G159200' => 'cil', 'CiPaw.02G091000' => 'cil', 'CiPaw.02G091100' => 'cil', 'CiPaw.08G103100' => 'cil', 'CiPaw.09G224900' => 'cil', 'ClCG06G005740' => 'cla', 'ClCG07G000090' => 'cla', 'ClCG07G000100' => 'cla', 'COL.COLO4_09143' => 'col', 'COL.COLO4_25124' => 'col', 'Cpa.g.sc16.34' => 'cpa', 'Cpa.g.sc3504.1' => 'cpa', 'Cpa.g.sc60.37' => 'cpa', 'CsaV3_6G018520' => 'csa', 'CsaV3_6G036860' => 'csa', 'CSS0001072' => 'camsi', 'CSS0020208' => 'camsi', 'CSS0021253' => 'camsi', 'CSS0022190' => 'camsi', 'CSS0036150' => 'camsi', 'CSS0040442' => 'camsi', 'CSS0042300' => 'camsi', 'CSS0045298' => 'camsi', 'DCAR_012449' => 'dca', 'DCAR_018405' => 'dca', 'DCAR_024573' => 'dca', 'DCAR_030591' => 'dca', 'Dinv16926' => 'din', 'Dinv32963' => 'din', 'Dinv38382' => 'din', 'Dinv38383' => 'din', 'Duzib133G0974' => 'dzi', 'Duzib138G1867' => 'dzi', 'Duzib211G0420' => 'dzi', 'Duzib212G0930' => 'dzi', 'ECA234G1645' => 'eca', 'ECA247G3467' => 'eca', 'ECA248G1703' => 'eca', 'EL10Ac3g06327' => 'bvu', 'EL10Ac7g17204' => 'bvu', 'Eucgr.A00855' => 'egr', 'Eucgr.A00858' => 'egr', 'Eucgr.H01520' => 'egr', 'Eucgr.H03604' => 'egr', 'Eucgr.L03465' => 'egr', 'Eucgr.L03466' => 'egr', 'FAN01G0988' => 'fan', 'FAN02G3892' => 'fan', 'FAN05G3381' => 'fan', 'FAN07G0967' => 'fan', 'FAN07G1493' => 'fan', 'FAN08G3125' => 'fan', 'FAN09G0402' => 'fan', 'FAN12G2594' => 'fan', 'FAN12G3879' => 'fan', 'FAN14G1546' => 'fan', 'FAN15G3626' => 'fan', 'FAN17G0588' => 'fan', 'FAN17G0609' => 'fan', 'FAN18G2817' => 'fan', 'FAN19G1305' => 'fan', 'FAN20G1787' => 'fan', 'FAN22G0073' => 'fan', 'FAN22G0352' => 'fan', 'FAN22G0368' => 'fan', 'FAN22G2273' => 'fan', 'FAN24G1998' => 'fan', 'FAN27G1317' => 'fan', 'FvH4_2g23980' => 'fve', 'FvH4_4g14380' => 'fve', 'FvH4_4g14390' => 'fve', 'FvH4_6g09250' => 'fve', 'Glyma.03G151100' => 'gma', 'Glyma.04G122550' => 'gma', 'Glyma.05G001600' => 'gma', 'Glyma.09G270766' => 'gma', 'Glyma.09G270832' => 'gma', 'Glyma.13G209800' => 'gma', 'Glyma.15G102800' => 'gma', 'Glyma.18G218900' => 'gma', 'Glyma.19G001500' => 'gma', 'Glyma.19G153600' => 'gma', 'Gohir.A02G028600' => 'ghi', 'Gohir.A08G045000' => 'ghi', 'Gohir.A11G120500' => 'ghi', 'Gohir.A12G006200' => 'ghi', 'Gohir.A12G006250' => 'ghi', 'Gohir.D02G036300' => 'ghi', 'Gohir.D08G054700' => 'ghi', 'Gohir.D11G125600' => 'ghi', 'Gohir.D12G005700' => 'ghi', 'Gorai.004G055200' => 'gra', 'Gorai.005G040400' => 'gra', 'Gorai.007G134500' => 'gra', 'Gorai.008G005500' => 'gra', 'GSVIVG01011094001' => 'vvi', 'GSVIVG01017879001' => 'vvi', 'GSVIVG01025988001' => 'vvi', 'GSVIVG01029847001' => 'vvi', 'HanXRQChr10g0282901' => 'han', 'HanXRQChr10g0310371' => 'han', 'HanXRQChr10g0315041' => 'han', 'HanXRQChr11g0327651' => 'han', 'HanXRQChr12g0359391' => 'han', 'Haze_00972' => 'cav', 'Haze_00973' => 'cav', 'Haze_00974' => 'cav', 'Haze_04747' => 'cav', 'Haze_04749' => 'cav', 'Haze_04750' => 'cav', 'Haze_21217' => 'cav', 'Hma1.2p1_1037F.1_g250680' => 'hma', 'Hma1.2p1_1644F.1_g295320' => 'hma', 'HPP92_011322' => 'vpl', 'HPP92_011323' => 'vpl', 'HPP92_011324' => 'vpl', 'HPP92_011325' => 'vpl', 'HPP92_011326' => 'vpl', 'Hund12205' => 'sun', 'Hund17957' => 'sun', 'Lalb_Chr06g0176771' => 'lal', 'Lalb_Chr18g0056021' => 'lal', 'Lalb_Chr18g0056031' => 'lal', 'Lalb_Chr18g0056041' => 'lal', 'Lalb_Chr20g0107751' => 'lal', 'Lalb_Chr20g0118371' => 'lal', 'Lj1g0010239' => 'lja', 'Lj1g0017101' => 'lja', 'Lj2A1178G40' => 'lonja', 'Lj2A54G84' => 'lonja', 'Lj2g0015248' => 'lja', 'Lj3A761T51' => 'lonja', 'Lj6g0018116' => 'lja', 'Lsat_1_v5_gn_4_136040' => 'lsa', 'Lsat_1_v5_gn_5_187461' => 'lsa', 'Lsat_1_v5_gn_5_77001' => 'lsa', 'Lsat_1_v5_gn_9_4461' => 'lsa', 'Manes.01G210100' => 'mes', 'Manes.03G185600' => 'mes', 'Manes.05G073300' => 'mes', 'Manes.09G120300' => 'mes', 'Manes.15G022100' => 'mes', 'Mapoly0096s0053' => 'mpo', 'MBI03_g14058_MAGBIO' => 'mbi', 'MBI03_g33876_MAGBIO' => 'mbi', 'MBI03_g36854_MAGBIO' => 'mbi', 'MBI17_g11997_MAGBIO' => 'mbi', 'MD03G1269000' => 'mdo', 'MD04G1179600' => 'mdo', 'MD11G1289800' => 'mdo', 'MD12G1194700' => 'mdo', 'MD13G1182100' => 'mdo', 'MD13G1182200' => 'mdo', 'MD16G1182600' => 'mdo', 'Medtr2g021400' => 'mtr', 'Medtr2g021470' => 'mtr', 'Medtr2g105810' => 'mtr', 'Medtr3g033580' => 'mtr', 'Medtr6g007970' => 'mtr', 'Medtr7g056330' => 'mtr', 'Medtr7g074290' => 'mtr', 'Medtr7g074380' => 'mtr', 'Medtr7g094550' => 'mtr', 'Medtr8g069995' => 'mtr', 'MELO3C014345.2' => 'cme', 'MELO3C021395.2' => 'cme', 'Migut.D00262' => 'egut', 'Migut.G00257' => 'egut', 'MSTRG.21575' => 'ama', 'MSTRG.3985' => 'ama', 'Nitab4.5_0000295g0140' => 'nta', 'Nitab4.5_0000732g0140' => 'nta', 'Nitab4.5_0003162g0020' => 'nta', 'Nitab4.5_0006180g0090' => 'nta', 'Nitab4.5_0006390g0010' => 'nta', 'Nitab4.5_0007392g0040' => 'nta', 'Nn1g02140' => 'nnu', 'Nn4g26168' => 'nnu', 'Nn5g26754' => 'nnu', 'Oeu001433.1' => 'oeu', 'Oeu010299.2' => 'oeu', 'Oeu011171.1' => 'oeu', 'Oeu037675.1' => 'oeu', 'Oeu038359.1' => 'oeu', 'Oeu063834.1' => 'oeu', 'Oeu063835.1' => 'oeu', 'Os05g0312000' => 'osa', 'Os07g0211101' => 'osa', 'Os07g0211200' => 'osa', 'Os07g0681500' => 'osa', 'Peaxi162Scf00095g01015' => 'pax', 'Peaxi162Scf00104g00329' => 'pax', 'Peaxi162Scf00161g00137' => 'pax', 'PGR004G1665' => 'pgr', 'PGR031G2937' => 'pgr', 'PGR119G2145' => 'pgr', 'PGSC0003DMG400004351' => 'stu', 'PGSC0003DMG400014625' => 'stu', 'PGSC0003DMG401000943' => 'stu', 'Phvul.001G148600' => 'pvu', 'Phvul.004G001700' => 'pvu', 'Phvul.006G154900' => 'pvu', 'Phvul.008G078200' => 'pvu', 'Phvul.011G136500' => 'pvu', 'Potri.002G215600' => 'ptr', 'Potri.008G201600' => 'ptr', 'Potri.014G138400' => 'ptr', 'Potri.016G142500' => 'ptr', 'Pp3c16_10580' => 'ppa', 'Pp3c5_25280' => 'ppa', 'Prupe.1G150000' => 'ppe', 'Prupe.1G150100' => 'ppe', 'Prupe.6G299600' => 'ppe', 'Prupe.8G245000' => 'ppe', 'Psat0s4927g0040' => 'psa', 'Psat1g052080' => 'psa', 'Psat1g183800' => 'psa', 'Psat3g113840' => 'psa', 'Psat3g126120' => 'psa', 'Psat3g126160' => 'psa', 'Psat3g158760' => 'psa', 'Psat3g158840' => 'psa', 'PSO170G2858' => 'pso', 'PSO339G0606' => 'pso', 'PSO384G4709' => 'pso', 'PSO407G0334' => 'pso', 'QL04p040276' => 'qlo', 'QL06p005458' => 'qlo', 'QL06p005472' => 'qlo', 'QL07p030546' => 'qlo', 'QL07p031519' => 'qlo', 'QL09p050949' => 'qlo', 'QL09p050966' => 'qlo', 'QL09p051067' => 'qlo', 'QL12p022706' => 'qlo', 'RcHm_v2.0_Chr2g0119601' => 'rch', 'RcHm_v2.0_Chr3g0459591' => 'rch', 'RcHm_v2.0_Chr4g0418521' => 'rch', 'RcHm_v2.0_Chr4g0418531' => 'rch', 'RcHm_v2.0_Chr4g0418541' => 'rch', 'RcHm_v2.0_Chr6g0291641' => 'rch', 'Rhsim01G0086300' => 'rsi', 'Rhsim01G0276300' => 'rsi', 'Rhsim01G0276500' => 'rsi', 'Rhsim04G0207700' => 'rsi', 'Rhsim05G0234500' => 'rsi', 'Rhsim13G0022400' => 'rsi', 'Sabra02G0167900' => 'sbr', 'Sabra04G0158500' => 'sbr', 'Sabra08G0159800' => 'sbr', 'Sabra10G0011500' => 'sbr', 'Sabra14G0104400' => 'sbr', 'SalBow2G2440' => 'sbo', 'SalBow4G2265' => 'sbo', 'Sc02g0000060' => 'sci', 'Sc05g0005020' => 'sci', 'Sc13g0003890' => 'sci', 'Sed0014865' => 'sed', 'Sed0017224' => 'sed', 'Sed0026391' => 'sed', 'SEGI_00063' => 'sgi', 'SEGI_10967' => 'sgi', 'SEGI_17510' => 'sgi', 'SEGI_24396' => 'sgi', 'SEGI_39719' => 'sgi', 'SEGI_41392' => 'sgi', 'SGA_v2.0_scaffold11G05794' => 'sas', 'SGA_v2.0_scaffold142G35607' => 'sas', 'SGA_v2.0_scaffold1G00447' => 'sas', 'SHI15388' => 'shi', 'SHI15394' => 'shi', 'SHI15396' => 'shi', 'SHI15399' => 'shi', 'SMO343G0151' => 'smo', 'SMO367G1118' => 'smo', 'Solyc01g080200.3' => 'sly', 'Solyc06g008960.3' => 'sly', 'Solyc09g064780.3' => 'sly', 'Sopen01g031980' => 'spe', 'Sopen06g003710' => 'spe', 'Sopen09g026460' => 'spe', 'Sp3g21240' => 'spa', 'Sp4g30030' => 'spa', 'TAR365G0022' => 'tar', 'TAR365G1023' => 'tar', 'TAR365G1253' => 'tar', 'TAR623G0078' => 'tar', 'TAR623G1721' => 'tar', 'TAR633G0959' => 'tar', 'THA.LOC104802225' => 'tha', 'THA.LOC104804769' => 'tha', 'THA.LOC104808660' => 'tha', 'THA.LOC104812792' => 'tha', 'Thecc.01G284000' => 'tca', 'Thecc.04G220600' => 'tca', 'Thecc.05G268900' => 'tca', 'Thecc.08G171100' => 'tca', 'Thhalv10001284m.g' => 'esa', 'Thhalv10019912m.g' => 'esa', 'TPR.G14189' => 'tpr', 'TPR.G18110' => 'tpr', 'TPR.G18130' => 'tpr', 'TPR.G18131' => 'tpr', 'TPR.G18140' => 'tpr', 'TPR.G24282' => 'tpr', 'TPR.G25221' => 'tpr', 'TPR.G29267' => 'tpr', 'TPR.G35315' => 'tpr', 'TPR.G36173' => 'tpr', 'TWI09G0794' => 'twi', 'TWI59G1348' => 'twi', 'TWI74G0430' => 'twi', 'unitig_26.g8940' => 'ugi', 'unitig_749.g13744' => 'ugi', 'unitig_749.g13745' => 'ugi', 'vmacro08269' => 'vma', 'vmacro14937' => 'vma', 'vmacro20401' => 'vma', 'VMungo0464G1349' => 'vmu', 'VMungo0540G0289' => 'vmu', 'VMungo1215G1590' => 'vmu', 'VMungo1309G0221' => 'vmu', 'VMungo1309G2815' => 'vmu', 'VMungo1383G0239' => 'vmu', 'VMungo1383G2910' => 'vmu', 'Zm00001eb095270' => 'zma', 'Zm00001eb095280' => 'zma', 'Zm00001eb111630' => 'zma', 'Zm00001eb237080' => 'zma', 'Zm00001eb273740' => 'zma', 'Zm00001eb285040' => 'zma', 'Zm00001eb330790' => 'zma', 'Zm00001eb337380' => 'zma' ), 'gf_id' => 'HOM05D001484', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001484' ), 'data_identifier' => 'HOM05D001484', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001484', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p31500' => 'bna', 'A05p00020' => 'bna', 'A07p08820' => 'bna', 'Aa31LG4G3300' => 'aar', 'Aa31LG8G10030' => 'aar', 'Actinidia00731' => 'ach', 'Actinidia11473' => 'ach', 'Actinidia23469' => 'ach', 'Actinidia24318' => 'ach', 'Actinidia40196' => 'ach', 'Actinidia40197' => 'ach', 'Actinidia40198' => 'ach', 'Ah.08g212990' => 'amhyb', 'Ah.15g091720' => 'amhyb', 'AL3G38260' => 'aly', 'AL4G47710' => 'aly', 'Aqoxy2G00671' => 'aox', 'Aqoxy2G03236' => 'aox', 'arahy.Tifrunner.gnm1.ann1.05IDCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KR684' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATY3SJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK6QJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6APGL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IDT7Z9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM073U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ0R87' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LE7RV4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT4QRX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V5ENPK' => 'arhy', 'AT2G48110' => 'ath', 'AT3G23590' => 'ath', 'ATR0626G186' => 'atr', 'ATR1127G141' => 'atr', 'Atru.chr4.2583' => 'acertr', 'Atru.chr5.1358' => 'acertr', 'Atru.chr5.1359' => 'acertr', 'Atru.chr8.46' => 'acertr', 'AUR62002640' => 'cqu', 'AUR62030055' => 'cqu', 'AUR62033713' => 'cqu', 'AUR62033714' => 'cqu', 'AUR62036795' => 'cqu', 'AUR62039891' => 'cqu', 'BcaB02g08737' => 'bca', 'BcaB04g20441' => 'bca', 'BcaB06g26509' => 'bca', 'BcaB06g26510' => 'bca', 'BcaB06g26511' => 'bca', 'BcaB06g26512' => 'bca', 'BcaB06g26513' => 'bca', 'BcaC02g12564' => 'bca', 'BcaC02g12565' => 'bca', 'BcaC02g12794' => 'bca', 'BcaC02g12795' => 'bca', 'BcaC02g12796' => 'bca', 'BcaC06g35541' => 'bca', 'BNapus_Darmor_BZH_scaffold_188p00080' => 'bna', 'BNapus_Darmor_BZH_scaffold_188p00090' => 'bna', 'BolC1t03972H' => 'bol', 'BolC1t03973H' => 'bol', 'BolC4t21680H' => 'bol', 'BolC7t41863H' => 'bol', 'BolSC55t61227H' => 'bol', 'BolSC55t61228H' => 'bol', 'BraA01t03278Z' => 'bra', 'BraA05t18998Z' => 'bra', 'BraA07t28673Z' => 'bra', 'C01p40150' => 'bna', 'C05p12370' => 'bna', 'C07p13680' => 'bna', 'CAN.G1006.16' => 'can', 'CAN.G1006.17' => 'can', 'CAN.G1170.2' => 'can', 'CAN.G962.7' => 'can', 'CANSAT25G2179' => 'cansat', 'CANSAT78G1573' => 'cansat', 'CARHR099510' => 'chi', 'CARHR143510' => 'chi', 'Carub.0003s2380' => 'cru', 'Carub.0004s3082' => 'cru', 'Ca_00614_v3' => 'car', 'Ca_07801_v3' => 'car', 'Ca_08567_v3' => 'car', 'Ca_09571_v3' => 'car', 'CBR_g19290' => 'cbr', 'Cc01_g19770' => 'ccan', 'Cc03_g03030' => 'ccan', 'CDE07G0968' => 'cde', 'CDE09G1441' => 'cde', 'Cfa006103' => 'cfa', 'Cfa015573' => 'cfa', 'Cfa016988' => 'cfa', 'Ciclev10006738m.g' => 'ccl', 'Ciclev10010920m.g' => 'ccl', 'Ciclev10018517m.g' => 'ccl', 'CiPaw.01G159200' => 'cil', 'CiPaw.02G091000' => 'cil', 'CiPaw.02G091100' => 'cil', 'CiPaw.08G103100' => 'cil', 'CiPaw.09G224900' => 'cil', 'ClCG06G005740' => 'cla', 'ClCG07G000090' => 'cla', 'ClCG07G000100' => 'cla', 'COL.COLO4_09143' => 'col', 'COL.COLO4_25124' => 'col', 'Cpa.g.sc16.34' => 'cpa', 'Cpa.g.sc3504.1' => 'cpa', 'Cpa.g.sc60.37' => 'cpa', 'CsaV3_6G018520' => 'csa', 'CsaV3_6G036860' => 'csa', 'CSS0001072' => 'camsi', 'CSS0020208' => 'camsi', 'CSS0021253' => 'camsi', 'CSS0022190' => 'camsi', 'CSS0036150' => 'camsi', 'CSS0040442' => 'camsi', 'CSS0042300' => 'camsi', 'CSS0045298' => 'camsi', 'DCAR_012449' => 'dca', 'DCAR_018405' => 'dca', 'DCAR_024573' => 'dca', 'DCAR_030591' => 'dca', 'Dinv16926' => 'din', 'Dinv32963' => 'din', 'Dinv38382' => 'din', 'Dinv38383' => 'din', 'Duzib133G0974' => 'dzi', 'Duzib138G1867' => 'dzi', 'Duzib211G0420' => 'dzi', 'Duzib212G0930' => 'dzi', 'ECA234G1645' => 'eca', 'ECA247G3467' => 'eca', 'ECA248G1703' => 'eca', 'EL10Ac3g06327' => 'bvu', 'EL10Ac7g17204' => 'bvu', 'Eucgr.A00855' => 'egr', 'Eucgr.A00858' => 'egr', 'Eucgr.H01520' => 'egr', 'Eucgr.H03604' => 'egr', 'Eucgr.L03465' => 'egr', 'Eucgr.L03466' => 'egr', 'FAN01G0988' => 'fan', 'FAN02G3892' => 'fan', 'FAN05G3381' => 'fan', 'FAN07G0967' => 'fan', 'FAN07G1493' => 'fan', 'FAN08G3125' => 'fan', 'FAN09G0402' => 'fan', 'FAN12G2594' => 'fan', 'FAN12G3879' => 'fan', 'FAN14G1546' => 'fan', 'FAN15G3626' => 'fan', 'FAN17G0588' => 'fan', 'FAN17G0609' => 'fan', 'FAN18G2817' => 'fan', 'FAN19G1305' => 'fan', 'FAN20G1787' => 'fan', 'FAN22G0073' => 'fan', 'FAN22G0352' => 'fan', 'FAN22G0368' => 'fan', 'FAN22G2273' => 'fan', 'FAN24G1998' => 'fan', 'FAN27G1317' => 'fan', 'FvH4_2g23980' => 'fve', 'FvH4_4g14380' => 'fve', 'FvH4_4g14390' => 'fve', 'FvH4_6g09250' => 'fve', 'Glyma.03G151100' => 'gma', 'Glyma.04G122550' => 'gma', 'Glyma.05G001600' => 'gma', 'Glyma.09G270766' => 'gma', 'Glyma.09G270832' => 'gma', 'Glyma.13G209800' => 'gma', 'Glyma.15G102800' => 'gma', 'Glyma.18G218900' => 'gma', 'Glyma.19G001500' => 'gma', 'Glyma.19G153600' => 'gma', 'Gohir.A02G028600' => 'ghi', 'Gohir.A08G045000' => 'ghi', 'Gohir.A11G120500' => 'ghi', 'Gohir.A12G006200' => 'ghi', 'Gohir.A12G006250' => 'ghi', 'Gohir.D02G036300' => 'ghi', 'Gohir.D08G054700' => 'ghi', 'Gohir.D11G125600' => 'ghi', 'Gohir.D12G005700' => 'ghi', 'Gorai.004G055200' => 'gra', 'Gorai.005G040400' => 'gra', 'Gorai.007G134500' => 'gra', 'Gorai.008G005500' => 'gra', 'GSVIVG01011094001' => 'vvi', 'GSVIVG01017879001' => 'vvi', 'GSVIVG01025988001' => 'vvi', 'GSVIVG01029847001' => 'vvi', 'HanXRQChr10g0282901' => 'han', 'HanXRQChr10g0310371' => 'han', 'HanXRQChr10g0315041' => 'han', 'HanXRQChr11g0327651' => 'han', 'HanXRQChr12g0359391' => 'han', 'Haze_00972' => 'cav', 'Haze_00973' => 'cav', 'Haze_00974' => 'cav', 'Haze_04747' => 'cav', 'Haze_04749' => 'cav', 'Haze_04750' => 'cav', 'Haze_21217' => 'cav', 'Hma1.2p1_1037F.1_g250680' => 'hma', 'Hma1.2p1_1644F.1_g295320' => 'hma', 'HPP92_011322' => 'vpl', 'HPP92_011323' => 'vpl', 'HPP92_011324' => 'vpl', 'HPP92_011325' => 'vpl', 'HPP92_011326' => 'vpl', 'Hund12205' => 'sun', 'Hund17957' => 'sun', 'Lalb_Chr06g0176771' => 'lal', 'Lalb_Chr18g0056021' => 'lal', 'Lalb_Chr18g0056031' => 'lal', 'Lalb_Chr18g0056041' => 'lal', 'Lalb_Chr20g0107751' => 'lal', 'Lalb_Chr20g0118371' => 'lal', 'Lj1g0010239' => 'lja', 'Lj1g0017101' => 'lja', 'Lj2A1178G40' => 'lonja', 'Lj2A54G84' => 'lonja', 'Lj2g0015248' => 'lja', 'Lj3A761T51' => 'lonja', 'Lj6g0018116' => 'lja', 'Lsat_1_v5_gn_4_136040' => 'lsa', 'Lsat_1_v5_gn_5_187461' => 'lsa', 'Lsat_1_v5_gn_5_77001' => 'lsa', 'Lsat_1_v5_gn_9_4461' => 'lsa', 'Manes.01G210100' => 'mes', 'Manes.03G185600' => 'mes', 'Manes.05G073300' => 'mes', 'Manes.09G120300' => 'mes', 'Manes.15G022100' => 'mes', 'Mapoly0096s0053' => 'mpo', 'MBI03_g14058_MAGBIO' => 'mbi', 'MBI03_g33876_MAGBIO' => 'mbi', 'MBI03_g36854_MAGBIO' => 'mbi', 'MBI17_g11997_MAGBIO' => 'mbi', 'MD03G1269000' => 'mdo', 'MD04G1179600' => 'mdo', 'MD11G1289800' => 'mdo', 'MD12G1194700' => 'mdo', 'MD13G1182100' => 'mdo', 'MD13G1182200' => 'mdo', 'MD16G1182600' => 'mdo', 'Medtr2g021400' => 'mtr', 'Medtr2g021470' => 'mtr', 'Medtr2g105810' => 'mtr', 'Medtr3g033580' => 'mtr', 'Medtr6g007970' => 'mtr', 'Medtr7g056330' => 'mtr', 'Medtr7g074290' => 'mtr', 'Medtr7g074380' => 'mtr', 'Medtr7g094550' => 'mtr', 'Medtr8g069995' => 'mtr', 'MELO3C014345.2' => 'cme', 'MELO3C021395.2' => 'cme', 'Migut.D00262' => 'egut', 'Migut.G00257' => 'egut', 'MSTRG.21575' => 'ama', 'MSTRG.3985' => 'ama', 'Nitab4.5_0000295g0140' => 'nta', 'Nitab4.5_0000732g0140' => 'nta', 'Nitab4.5_0003162g0020' => 'nta', 'Nitab4.5_0006180g0090' => 'nta', 'Nitab4.5_0006390g0010' => 'nta', 'Nitab4.5_0007392g0040' => 'nta', 'Nn1g02140' => 'nnu', 'Nn4g26168' => 'nnu', 'Nn5g26754' => 'nnu', 'Oeu001433.1' => 'oeu', 'Oeu010299.2' => 'oeu', 'Oeu011171.1' => 'oeu', 'Oeu037675.1' => 'oeu', 'Oeu038359.1' => 'oeu', 'Oeu063834.1' => 'oeu', 'Oeu063835.1' => 'oeu', 'Os05g0312000' => 'osa', 'Os07g0211101' => 'osa', 'Os07g0211200' => 'osa', 'Os07g0681500' => 'osa', 'Peaxi162Scf00095g01015' => 'pax', 'Peaxi162Scf00104g00329' => 'pax', 'Peaxi162Scf00161g00137' => 'pax', 'PGR004G1665' => 'pgr', 'PGR031G2937' => 'pgr', 'PGR119G2145' => 'pgr', 'PGSC0003DMG400004351' => 'stu', 'PGSC0003DMG400014625' => 'stu', 'PGSC0003DMG401000943' => 'stu', 'Phvul.001G148600' => 'pvu', 'Phvul.004G001700' => 'pvu', 'Phvul.006G154900' => 'pvu', 'Phvul.008G078200' => 'pvu', 'Phvul.011G136500' => 'pvu', 'Potri.002G215600' => 'ptr', 'Potri.008G201600' => 'ptr', 'Potri.014G138400' => 'ptr', 'Potri.016G142500' => 'ptr', 'Pp3c16_10580' => 'ppa', 'Pp3c5_25280' => 'ppa', 'Prupe.1G150000' => 'ppe', 'Prupe.1G150100' => 'ppe', 'Prupe.6G299600' => 'ppe', 'Prupe.8G245000' => 'ppe', 'Psat0s4927g0040' => 'psa', 'Psat1g052080' => 'psa', 'Psat1g183800' => 'psa', 'Psat3g113840' => 'psa', 'Psat3g126120' => 'psa', 'Psat3g126160' => 'psa', 'Psat3g158760' => 'psa', 'Psat3g158840' => 'psa', 'PSO170G2858' => 'pso', 'PSO339G0606' => 'pso', 'PSO384G4709' => 'pso', 'PSO407G0334' => 'pso', 'QL04p040276' => 'qlo', 'QL06p005458' => 'qlo', 'QL06p005472' => 'qlo', 'QL07p030546' => 'qlo', 'QL07p031519' => 'qlo', 'QL09p050949' => 'qlo', 'QL09p050966' => 'qlo', 'QL09p051067' => 'qlo', 'QL12p022706' => 'qlo', 'RcHm_v2.0_Chr2g0119601' => 'rch', 'RcHm_v2.0_Chr3g0459591' => 'rch', 'RcHm_v2.0_Chr4g0418521' => 'rch', 'RcHm_v2.0_Chr4g0418531' => 'rch', 'RcHm_v2.0_Chr4g0418541' => 'rch', 'RcHm_v2.0_Chr6g0291641' => 'rch', 'Rhsim01G0086300' => 'rsi', 'Rhsim01G0276300' => 'rsi', 'Rhsim01G0276500' => 'rsi', 'Rhsim04G0207700' => 'rsi', 'Rhsim05G0234500' => 'rsi', 'Rhsim13G0022400' => 'rsi', 'Sabra02G0167900' => 'sbr', 'Sabra04G0158500' => 'sbr', 'Sabra08G0159800' => 'sbr', 'Sabra10G0011500' => 'sbr', 'Sabra14G0104400' => 'sbr', 'SalBow2G2440' => 'sbo', 'SalBow4G2265' => 'sbo', 'Sc02g0000060' => 'sci', 'Sc05g0005020' => 'sci', 'Sc13g0003890' => 'sci', 'Sed0014865' => 'sed', 'Sed0017224' => 'sed', 'Sed0026391' => 'sed', 'SEGI_00063' => 'sgi', 'SEGI_10967' => 'sgi', 'SEGI_17510' => 'sgi', 'SEGI_24396' => 'sgi', 'SEGI_39719' => 'sgi', 'SEGI_41392' => 'sgi', 'SGA_v2.0_scaffold11G05794' => 'sas', 'SGA_v2.0_scaffold142G35607' => 'sas', 'SGA_v2.0_scaffold1G00447' => 'sas', 'SHI15388' => 'shi', 'SHI15394' => 'shi', 'SHI15396' => 'shi', 'SHI15399' => 'shi', 'SMO343G0151' => 'smo', 'SMO367G1118' => 'smo', 'Solyc01g080200.3' => 'sly', 'Solyc06g008960.3' => 'sly', 'Solyc09g064780.3' => 'sly', 'Sopen01g031980' => 'spe', 'Sopen06g003710' => 'spe', 'Sopen09g026460' => 'spe', 'Sp3g21240' => 'spa', 'Sp4g30030' => 'spa', 'TAR365G0022' => 'tar', 'TAR365G1023' => 'tar', 'TAR365G1253' => 'tar', 'TAR623G0078' => 'tar', 'TAR623G1721' => 'tar', 'TAR633G0959' => 'tar', 'THA.LOC104802225' => 'tha', 'THA.LOC104804769' => 'tha', 'THA.LOC104808660' => 'tha', 'THA.LOC104812792' => 'tha', 'Thecc.01G284000' => 'tca', 'Thecc.04G220600' => 'tca', 'Thecc.05G268900' => 'tca', 'Thecc.08G171100' => 'tca', 'Thhalv10001284m.g' => 'esa', 'Thhalv10019912m.g' => 'esa', 'TPR.G14189' => 'tpr', 'TPR.G18110' => 'tpr', 'TPR.G18130' => 'tpr', 'TPR.G18131' => 'tpr', 'TPR.G18140' => 'tpr', 'TPR.G24282' => 'tpr', 'TPR.G25221' => 'tpr', 'TPR.G29267' => 'tpr', 'TPR.G35315' => 'tpr', 'TPR.G36173' => 'tpr', 'TWI09G0794' => 'twi', 'TWI59G1348' => 'twi', 'TWI74G0430' => 'twi', 'unitig_26.g8940' => 'ugi', 'unitig_749.g13744' => 'ugi', 'unitig_749.g13745' => 'ugi', 'vmacro08269' => 'vma', 'vmacro14937' => 'vma', 'vmacro20401' => 'vma', 'VMungo0464G1349' => 'vmu', 'VMungo0540G0289' => 'vmu', 'VMungo1215G1590' => 'vmu', 'VMungo1309G0221' => 'vmu', 'VMungo1309G2815' => 'vmu', 'VMungo1383G0239' => 'vmu', 'VMungo1383G2910' => 'vmu', 'Zm00001eb095270' => 'zma', 'Zm00001eb095280' => 'zma', 'Zm00001eb111630' => 'zma', 'Zm00001eb237080' => 'zma', 'Zm00001eb273740' => 'zma', 'Zm00001eb285040' => 'zma', 'Zm00001eb330790' => 'zma', 'Zm00001eb337380' => 'zma' ) $gf_id = 'HOM05D001484' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001484' ) $data_identifier = 'HOM05D001484' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 2, 'aly' => (int) 2, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 22, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 7, 'hma' => (int) 2, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 7, 'mtr' => (int) 10, 'cme' => (int) 2, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 4, 'ppa' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 4, 'qlo' => (int) 9, 'rch' => (int) 6, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 10, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 7, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb337380' $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' => 'HOM05D001484', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p31500' => 'bna', 'A05p00020' => 'bna', 'A07p08820' => 'bna', 'Aa31LG4G3300' => 'aar', 'Aa31LG8G10030' => 'aar', 'Actinidia00731' => 'ach', 'Actinidia11473' => 'ach', 'Actinidia23469' => 'ach', 'Actinidia24318' => 'ach', 'Actinidia40196' => 'ach', 'Actinidia40197' => 'ach', 'Actinidia40198' => 'ach', 'Ah.08g212990' => 'amhyb', 'Ah.15g091720' => 'amhyb', 'AL3G38260' => 'aly', 'AL4G47710' => 'aly', 'Aqoxy2G00671' => 'aox', 'Aqoxy2G03236' => 'aox', 'arahy.Tifrunner.gnm1.ann1.05IDCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KR684' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATY3SJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK6QJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6APGL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IDT7Z9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM073U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ0R87' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LE7RV4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT4QRX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V5ENPK' => 'arhy', 'AT2G48110' => 'ath', 'AT3G23590' => 'ath', 'ATR0626G186' => 'atr', 'ATR1127G141' => 'atr', 'Atru.chr4.2583' => 'acertr', 'Atru.chr5.1358' => 'acertr', 'Atru.chr5.1359' => 'acertr', 'Atru.chr8.46' => 'acertr', 'AUR62002640' => 'cqu', 'AUR62030055' => 'cqu', 'AUR62033713' => 'cqu', 'AUR62033714' => 'cqu', 'AUR62036795' => 'cqu', 'AUR62039891' => 'cqu', 'BcaB02g08737' => 'bca', 'BcaB04g20441' => 'bca', 'BcaB06g26509' => 'bca', 'BcaB06g26510' => 'bca', 'BcaB06g26511' => 'bca', 'BcaB06g26512' => 'bca', 'BcaB06g26513' => 'bca', 'BcaC02g12564' => 'bca', 'BcaC02g12565' => 'bca', 'BcaC02g12794' => 'bca', 'BcaC02g12795' => 'bca', 'BcaC02g12796' => 'bca', 'BcaC06g35541' => 'bca', 'BNapus_Darmor_BZH_scaffold_188p00080' => 'bna', 'BNapus_Darmor_BZH_scaffold_188p00090' => 'bna', 'BolC1t03972H' => 'bol', 'BolC1t03973H' => 'bol', 'BolC4t21680H' => 'bol', 'BolC7t41863H' => 'bol', 'BolSC55t61227H' => 'bol', 'BolSC55t61228H' => 'bol', 'BraA01t03278Z' => 'bra', 'BraA05t18998Z' => 'bra', 'BraA07t28673Z' => 'bra', 'C01p40150' => 'bna', 'C05p12370' => 'bna', 'C07p13680' => 'bna', 'CAN.G1006.16' => 'can', 'CAN.G1006.17' => 'can', 'CAN.G1170.2' => 'can', 'CAN.G962.7' => 'can', 'CANSAT25G2179' => 'cansat', 'CANSAT78G1573' => 'cansat', 'CARHR099510' => 'chi', 'CARHR143510' => 'chi', 'Carub.0003s2380' => 'cru', 'Carub.0004s3082' => 'cru', 'Ca_00614_v3' => 'car', 'Ca_07801_v3' => 'car', 'Ca_08567_v3' => 'car', 'Ca_09571_v3' => 'car', 'CBR_g19290' => 'cbr', 'Cc01_g19770' => 'ccan', 'Cc03_g03030' => 'ccan', 'CDE07G0968' => 'cde', 'CDE09G1441' => 'cde', 'Cfa006103' => 'cfa', 'Cfa015573' => 'cfa', 'Cfa016988' => 'cfa', 'Ciclev10006738m.g' => 'ccl', 'Ciclev10010920m.g' => 'ccl', 'Ciclev10018517m.g' => 'ccl', 'CiPaw.01G159200' => 'cil', 'CiPaw.02G091000' => 'cil', 'CiPaw.02G091100' => 'cil', 'CiPaw.08G103100' => 'cil', 'CiPaw.09G224900' => 'cil', 'ClCG06G005740' => 'cla', 'ClCG07G000090' => 'cla', 'ClCG07G000100' => 'cla', 'COL.COLO4_09143' => 'col', 'COL.COLO4_25124' => 'col', 'Cpa.g.sc16.34' => 'cpa', 'Cpa.g.sc3504.1' => 'cpa', 'Cpa.g.sc60.37' => 'cpa', 'CsaV3_6G018520' => 'csa', 'CsaV3_6G036860' => 'csa', 'CSS0001072' => 'camsi', 'CSS0020208' => 'camsi', 'CSS0021253' => 'camsi', 'CSS0022190' => 'camsi', 'CSS0036150' => 'camsi', 'CSS0040442' => 'camsi', 'CSS0042300' => 'camsi', 'CSS0045298' => 'camsi', 'DCAR_012449' => 'dca', 'DCAR_018405' => 'dca', 'DCAR_024573' => 'dca', 'DCAR_030591' => 'dca', 'Dinv16926' => 'din', 'Dinv32963' => 'din', 'Dinv38382' => 'din', 'Dinv38383' => 'din', 'Duzib133G0974' => 'dzi', 'Duzib138G1867' => 'dzi', 'Duzib211G0420' => 'dzi', 'Duzib212G0930' => 'dzi', 'ECA234G1645' => 'eca', 'ECA247G3467' => 'eca', 'ECA248G1703' => 'eca', 'EL10Ac3g06327' => 'bvu', 'EL10Ac7g17204' => 'bvu', 'Eucgr.A00855' => 'egr', 'Eucgr.A00858' => 'egr', 'Eucgr.H01520' => 'egr', 'Eucgr.H03604' => 'egr', 'Eucgr.L03465' => 'egr', 'Eucgr.L03466' => 'egr', 'FAN01G0988' => 'fan', 'FAN02G3892' => 'fan', 'FAN05G3381' => 'fan', 'FAN07G0967' => 'fan', 'FAN07G1493' => 'fan', 'FAN08G3125' => 'fan', 'FAN09G0402' => 'fan', 'FAN12G2594' => 'fan', 'FAN12G3879' => 'fan', 'FAN14G1546' => 'fan', 'FAN15G3626' => 'fan', 'FAN17G0588' => 'fan', 'FAN17G0609' => 'fan', 'FAN18G2817' => 'fan', 'FAN19G1305' => 'fan', 'FAN20G1787' => 'fan', 'FAN22G0073' => 'fan', 'FAN22G0352' => 'fan', 'FAN22G0368' => 'fan', 'FAN22G2273' => 'fan', 'FAN24G1998' => 'fan', 'FAN27G1317' => 'fan', 'FvH4_2g23980' => 'fve', 'FvH4_4g14380' => 'fve', 'FvH4_4g14390' => 'fve', 'FvH4_6g09250' => 'fve', 'Glyma.03G151100' => 'gma', 'Glyma.04G122550' => 'gma', 'Glyma.05G001600' => 'gma', 'Glyma.09G270766' => 'gma', 'Glyma.09G270832' => 'gma', 'Glyma.13G209800' => 'gma', 'Glyma.15G102800' => 'gma', 'Glyma.18G218900' => 'gma', 'Glyma.19G001500' => 'gma', 'Glyma.19G153600' => 'gma', 'Gohir.A02G028600' => 'ghi', 'Gohir.A08G045000' => 'ghi', 'Gohir.A11G120500' => 'ghi', 'Gohir.A12G006200' => 'ghi', 'Gohir.A12G006250' => 'ghi', 'Gohir.D02G036300' => 'ghi', 'Gohir.D08G054700' => 'ghi', 'Gohir.D11G125600' => 'ghi', 'Gohir.D12G005700' => 'ghi', 'Gorai.004G055200' => 'gra', 'Gorai.005G040400' => 'gra', 'Gorai.007G134500' => 'gra', 'Gorai.008G005500' => 'gra', 'GSVIVG01011094001' => 'vvi', 'GSVIVG01017879001' => 'vvi', 'GSVIVG01025988001' => 'vvi', 'GSVIVG01029847001' => 'vvi', 'HanXRQChr10g0282901' => 'han', 'HanXRQChr10g0310371' => 'han', 'HanXRQChr10g0315041' => 'han', 'HanXRQChr11g0327651' => 'han', 'HanXRQChr12g0359391' => 'han', 'Haze_00972' => 'cav', 'Haze_00973' => 'cav', 'Haze_00974' => 'cav', 'Haze_04747' => 'cav', 'Haze_04749' => 'cav', 'Haze_04750' => 'cav', 'Haze_21217' => 'cav', 'Hma1.2p1_1037F.1_g250680' => 'hma', 'Hma1.2p1_1644F.1_g295320' => 'hma', 'HPP92_011322' => 'vpl', 'HPP92_011323' => 'vpl', 'HPP92_011324' => 'vpl', 'HPP92_011325' => 'vpl', 'HPP92_011326' => 'vpl', 'Hund12205' => 'sun', 'Hund17957' => 'sun', 'Lalb_Chr06g0176771' => 'lal', 'Lalb_Chr18g0056021' => 'lal', 'Lalb_Chr18g0056031' => 'lal', 'Lalb_Chr18g0056041' => 'lal', 'Lalb_Chr20g0107751' => 'lal', 'Lalb_Chr20g0118371' => 'lal', 'Lj1g0010239' => 'lja', 'Lj1g0017101' => 'lja', 'Lj2A1178G40' => 'lonja', 'Lj2A54G84' => 'lonja', 'Lj2g0015248' => 'lja', 'Lj3A761T51' => 'lonja', 'Lj6g0018116' => 'lja', 'Lsat_1_v5_gn_4_136040' => 'lsa', 'Lsat_1_v5_gn_5_187461' => 'lsa', 'Lsat_1_v5_gn_5_77001' => 'lsa', 'Lsat_1_v5_gn_9_4461' => 'lsa', 'Manes.01G210100' => 'mes', 'Manes.03G185600' => 'mes', 'Manes.05G073300' => 'mes', 'Manes.09G120300' => 'mes', 'Manes.15G022100' => 'mes', 'Mapoly0096s0053' => 'mpo', 'MBI03_g14058_MAGBIO' => 'mbi', 'MBI03_g33876_MAGBIO' => 'mbi', 'MBI03_g36854_MAGBIO' => 'mbi', 'MBI17_g11997_MAGBIO' => 'mbi', 'MD03G1269000' => 'mdo', 'MD04G1179600' => 'mdo', 'MD11G1289800' => 'mdo', 'MD12G1194700' => 'mdo', 'MD13G1182100' => 'mdo', 'MD13G1182200' => 'mdo', 'MD16G1182600' => 'mdo', 'Medtr2g021400' => 'mtr', 'Medtr2g021470' => 'mtr', 'Medtr2g105810' => 'mtr', 'Medtr3g033580' => 'mtr', 'Medtr6g007970' => 'mtr', 'Medtr7g056330' => 'mtr', 'Medtr7g074290' => 'mtr', 'Medtr7g074380' => 'mtr', 'Medtr7g094550' => 'mtr', 'Medtr8g069995' => 'mtr', 'MELO3C014345.2' => 'cme', 'MELO3C021395.2' => 'cme', 'Migut.D00262' => 'egut', 'Migut.G00257' => 'egut', 'MSTRG.21575' => 'ama', 'MSTRG.3985' => 'ama', 'Nitab4.5_0000295g0140' => 'nta', 'Nitab4.5_0000732g0140' => 'nta', 'Nitab4.5_0003162g0020' => 'nta', 'Nitab4.5_0006180g0090' => 'nta', 'Nitab4.5_0006390g0010' => 'nta', 'Nitab4.5_0007392g0040' => 'nta', 'Nn1g02140' => 'nnu', 'Nn4g26168' => 'nnu', 'Nn5g26754' => 'nnu', 'Oeu001433.1' => 'oeu', 'Oeu010299.2' => 'oeu', 'Oeu011171.1' => 'oeu', 'Oeu037675.1' => 'oeu', 'Oeu038359.1' => 'oeu', 'Oeu063834.1' => 'oeu', 'Oeu063835.1' => 'oeu', 'Os05g0312000' => 'osa', 'Os07g0211101' => 'osa', 'Os07g0211200' => 'osa', 'Os07g0681500' => 'osa', 'Peaxi162Scf00095g01015' => 'pax', 'Peaxi162Scf00104g00329' => 'pax', 'Peaxi162Scf00161g00137' => 'pax', 'PGR004G1665' => 'pgr', 'PGR031G2937' => 'pgr', 'PGR119G2145' => 'pgr', 'PGSC0003DMG400004351' => 'stu', 'PGSC0003DMG400014625' => 'stu', 'PGSC0003DMG401000943' => 'stu', 'Phvul.001G148600' => 'pvu', 'Phvul.004G001700' => 'pvu', 'Phvul.006G154900' => 'pvu', 'Phvul.008G078200' => 'pvu', 'Phvul.011G136500' => 'pvu', 'Potri.002G215600' => 'ptr', 'Potri.008G201600' => 'ptr', 'Potri.014G138400' => 'ptr', 'Potri.016G142500' => 'ptr', 'Pp3c16_10580' => 'ppa', 'Pp3c5_25280' => 'ppa', 'Prupe.1G150000' => 'ppe', 'Prupe.1G150100' => 'ppe', 'Prupe.6G299600' => 'ppe', 'Prupe.8G245000' => 'ppe', 'Psat0s4927g0040' => 'psa', 'Psat1g052080' => 'psa', 'Psat1g183800' => 'psa', 'Psat3g113840' => 'psa', 'Psat3g126120' => 'psa', 'Psat3g126160' => 'psa', 'Psat3g158760' => 'psa', 'Psat3g158840' => 'psa', 'PSO170G2858' => 'pso', 'PSO339G0606' => 'pso', 'PSO384G4709' => 'pso', 'PSO407G0334' => 'pso', 'QL04p040276' => 'qlo', 'QL06p005458' => 'qlo', 'QL06p005472' => 'qlo', 'QL07p030546' => 'qlo', 'QL07p031519' => 'qlo', 'QL09p050949' => 'qlo', 'QL09p050966' => 'qlo', 'QL09p051067' => 'qlo', 'QL12p022706' => 'qlo', 'RcHm_v2.0_Chr2g0119601' => 'rch', 'RcHm_v2.0_Chr3g0459591' => 'rch', 'RcHm_v2.0_Chr4g0418521' => 'rch', 'RcHm_v2.0_Chr4g0418531' => 'rch', 'RcHm_v2.0_Chr4g0418541' => 'rch', 'RcHm_v2.0_Chr6g0291641' => 'rch', 'Rhsim01G0086300' => 'rsi', 'Rhsim01G0276300' => 'rsi', 'Rhsim01G0276500' => 'rsi', 'Rhsim04G0207700' => 'rsi', 'Rhsim05G0234500' => 'rsi', 'Rhsim13G0022400' => 'rsi', 'Sabra02G0167900' => 'sbr', 'Sabra04G0158500' => 'sbr', 'Sabra08G0159800' => 'sbr', 'Sabra10G0011500' => 'sbr', 'Sabra14G0104400' => 'sbr', 'SalBow2G2440' => 'sbo', 'SalBow4G2265' => 'sbo', 'Sc02g0000060' => 'sci', 'Sc05g0005020' => 'sci', 'Sc13g0003890' => 'sci', 'Sed0014865' => 'sed', 'Sed0017224' => 'sed', 'Sed0026391' => 'sed', 'SEGI_00063' => 'sgi', 'SEGI_10967' => 'sgi', 'SEGI_17510' => 'sgi', 'SEGI_24396' => 'sgi', 'SEGI_39719' => 'sgi', 'SEGI_41392' => 'sgi', 'SGA_v2.0_scaffold11G05794' => 'sas', 'SGA_v2.0_scaffold142G35607' => 'sas', 'SGA_v2.0_scaffold1G00447' => 'sas', 'SHI15388' => 'shi', 'SHI15394' => 'shi', 'SHI15396' => 'shi', 'SHI15399' => 'shi', 'SMO343G0151' => 'smo', 'SMO367G1118' => 'smo', 'Solyc01g080200.3' => 'sly', 'Solyc06g008960.3' => 'sly', 'Solyc09g064780.3' => 'sly', 'Sopen01g031980' => 'spe', 'Sopen06g003710' => 'spe', 'Sopen09g026460' => 'spe', 'Sp3g21240' => 'spa', 'Sp4g30030' => 'spa', 'TAR365G0022' => 'tar', 'TAR365G1023' => 'tar', 'TAR365G1253' => 'tar', 'TAR623G0078' => 'tar', 'TAR623G1721' => 'tar', 'TAR633G0959' => 'tar', 'THA.LOC104802225' => 'tha', 'THA.LOC104804769' => 'tha', 'THA.LOC104808660' => 'tha', 'THA.LOC104812792' => 'tha', 'Thecc.01G284000' => 'tca', 'Thecc.04G220600' => 'tca', 'Thecc.05G268900' => 'tca', 'Thecc.08G171100' => 'tca', 'Thhalv10001284m.g' => 'esa', 'Thhalv10019912m.g' => 'esa', 'TPR.G14189' => 'tpr', 'TPR.G18110' => 'tpr', 'TPR.G18130' => 'tpr', 'TPR.G18131' => 'tpr', 'TPR.G18140' => 'tpr', 'TPR.G24282' => 'tpr', 'TPR.G25221' => 'tpr', 'TPR.G29267' => 'tpr', 'TPR.G35315' => 'tpr', 'TPR.G36173' => 'tpr', 'TWI09G0794' => 'twi', 'TWI59G1348' => 'twi', 'TWI74G0430' => 'twi', 'unitig_26.g8940' => 'ugi', 'unitig_749.g13744' => 'ugi', 'unitig_749.g13745' => 'ugi', 'vmacro08269' => 'vma', 'vmacro14937' => 'vma', 'vmacro20401' => 'vma', 'VMungo0464G1349' => 'vmu', 'VMungo0540G0289' => 'vmu', 'VMungo1215G1590' => 'vmu', 'VMungo1309G0221' => 'vmu', 'VMungo1309G2815' => 'vmu', 'VMungo1383G0239' => 'vmu', 'VMungo1383G2910' => 'vmu', 'Zm00001eb095270' => 'zma', 'Zm00001eb095280' => 'zma', 'Zm00001eb111630' => 'zma', 'Zm00001eb237080' => 'zma', 'Zm00001eb273740' => 'zma', 'Zm00001eb285040' => 'zma', 'Zm00001eb330790' => 'zma', 'Zm00001eb337380' => 'zma' ), 'gf_id' => 'HOM05D001484', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001484' ), 'data_identifier' => 'HOM05D001484', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001484', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p31500' => 'bna', 'A05p00020' => 'bna', 'A07p08820' => 'bna', 'Aa31LG4G3300' => 'aar', 'Aa31LG8G10030' => 'aar', 'Actinidia00731' => 'ach', 'Actinidia11473' => 'ach', 'Actinidia23469' => 'ach', 'Actinidia24318' => 'ach', 'Actinidia40196' => 'ach', 'Actinidia40197' => 'ach', 'Actinidia40198' => 'ach', 'Ah.08g212990' => 'amhyb', 'Ah.15g091720' => 'amhyb', 'AL3G38260' => 'aly', 'AL4G47710' => 'aly', 'Aqoxy2G00671' => 'aox', 'Aqoxy2G03236' => 'aox', 'arahy.Tifrunner.gnm1.ann1.05IDCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KR684' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATY3SJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK6QJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6APGL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IDT7Z9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM073U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ0R87' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LE7RV4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT4QRX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V5ENPK' => 'arhy', 'AT2G48110' => 'ath', 'AT3G23590' => 'ath', 'ATR0626G186' => 'atr', 'ATR1127G141' => 'atr', 'Atru.chr4.2583' => 'acertr', 'Atru.chr5.1358' => 'acertr', 'Atru.chr5.1359' => 'acertr', 'Atru.chr8.46' => 'acertr', 'AUR62002640' => 'cqu', 'AUR62030055' => 'cqu', 'AUR62033713' => 'cqu', 'AUR62033714' => 'cqu', 'AUR62036795' => 'cqu', 'AUR62039891' => 'cqu', 'BcaB02g08737' => 'bca', 'BcaB04g20441' => 'bca', 'BcaB06g26509' => 'bca', 'BcaB06g26510' => 'bca', 'BcaB06g26511' => 'bca', 'BcaB06g26512' => 'bca', 'BcaB06g26513' => 'bca', 'BcaC02g12564' => 'bca', 'BcaC02g12565' => 'bca', 'BcaC02g12794' => 'bca', 'BcaC02g12795' => 'bca', 'BcaC02g12796' => 'bca', 'BcaC06g35541' => 'bca', 'BNapus_Darmor_BZH_scaffold_188p00080' => 'bna', 'BNapus_Darmor_BZH_scaffold_188p00090' => 'bna', 'BolC1t03972H' => 'bol', 'BolC1t03973H' => 'bol', 'BolC4t21680H' => 'bol', 'BolC7t41863H' => 'bol', 'BolSC55t61227H' => 'bol', 'BolSC55t61228H' => 'bol', 'BraA01t03278Z' => 'bra', 'BraA05t18998Z' => 'bra', 'BraA07t28673Z' => 'bra', 'C01p40150' => 'bna', 'C05p12370' => 'bna', 'C07p13680' => 'bna', 'CAN.G1006.16' => 'can', 'CAN.G1006.17' => 'can', 'CAN.G1170.2' => 'can', 'CAN.G962.7' => 'can', 'CANSAT25G2179' => 'cansat', 'CANSAT78G1573' => 'cansat', 'CARHR099510' => 'chi', 'CARHR143510' => 'chi', 'Carub.0003s2380' => 'cru', 'Carub.0004s3082' => 'cru', 'Ca_00614_v3' => 'car', 'Ca_07801_v3' => 'car', 'Ca_08567_v3' => 'car', 'Ca_09571_v3' => 'car', 'CBR_g19290' => 'cbr', 'Cc01_g19770' => 'ccan', 'Cc03_g03030' => 'ccan', 'CDE07G0968' => 'cde', 'CDE09G1441' => 'cde', 'Cfa006103' => 'cfa', 'Cfa015573' => 'cfa', 'Cfa016988' => 'cfa', 'Ciclev10006738m.g' => 'ccl', 'Ciclev10010920m.g' => 'ccl', 'Ciclev10018517m.g' => 'ccl', 'CiPaw.01G159200' => 'cil', 'CiPaw.02G091000' => 'cil', 'CiPaw.02G091100' => 'cil', 'CiPaw.08G103100' => 'cil', 'CiPaw.09G224900' => 'cil', 'ClCG06G005740' => 'cla', 'ClCG07G000090' => 'cla', 'ClCG07G000100' => 'cla', 'COL.COLO4_09143' => 'col', 'COL.COLO4_25124' => 'col', 'Cpa.g.sc16.34' => 'cpa', 'Cpa.g.sc3504.1' => 'cpa', 'Cpa.g.sc60.37' => 'cpa', 'CsaV3_6G018520' => 'csa', 'CsaV3_6G036860' => 'csa', 'CSS0001072' => 'camsi', 'CSS0020208' => 'camsi', 'CSS0021253' => 'camsi', 'CSS0022190' => 'camsi', 'CSS0036150' => 'camsi', 'CSS0040442' => 'camsi', 'CSS0042300' => 'camsi', 'CSS0045298' => 'camsi', 'DCAR_012449' => 'dca', 'DCAR_018405' => 'dca', 'DCAR_024573' => 'dca', 'DCAR_030591' => 'dca', 'Dinv16926' => 'din', 'Dinv32963' => 'din', 'Dinv38382' => 'din', 'Dinv38383' => 'din', 'Duzib133G0974' => 'dzi', 'Duzib138G1867' => 'dzi', 'Duzib211G0420' => 'dzi', 'Duzib212G0930' => 'dzi', 'ECA234G1645' => 'eca', 'ECA247G3467' => 'eca', 'ECA248G1703' => 'eca', 'EL10Ac3g06327' => 'bvu', 'EL10Ac7g17204' => 'bvu', 'Eucgr.A00855' => 'egr', 'Eucgr.A00858' => 'egr', 'Eucgr.H01520' => 'egr', 'Eucgr.H03604' => 'egr', 'Eucgr.L03465' => 'egr', 'Eucgr.L03466' => 'egr', 'FAN01G0988' => 'fan', 'FAN02G3892' => 'fan', 'FAN05G3381' => 'fan', 'FAN07G0967' => 'fan', 'FAN07G1493' => 'fan', 'FAN08G3125' => 'fan', 'FAN09G0402' => 'fan', 'FAN12G2594' => 'fan', 'FAN12G3879' => 'fan', 'FAN14G1546' => 'fan', 'FAN15G3626' => 'fan', 'FAN17G0588' => 'fan', 'FAN17G0609' => 'fan', 'FAN18G2817' => 'fan', 'FAN19G1305' => 'fan', 'FAN20G1787' => 'fan', 'FAN22G0073' => 'fan', 'FAN22G0352' => 'fan', 'FAN22G0368' => 'fan', 'FAN22G2273' => 'fan', 'FAN24G1998' => 'fan', 'FAN27G1317' => 'fan', 'FvH4_2g23980' => 'fve', 'FvH4_4g14380' => 'fve', 'FvH4_4g14390' => 'fve', 'FvH4_6g09250' => 'fve', 'Glyma.03G151100' => 'gma', 'Glyma.04G122550' => 'gma', 'Glyma.05G001600' => 'gma', 'Glyma.09G270766' => 'gma', 'Glyma.09G270832' => 'gma', 'Glyma.13G209800' => 'gma', 'Glyma.15G102800' => 'gma', 'Glyma.18G218900' => 'gma', 'Glyma.19G001500' => 'gma', 'Glyma.19G153600' => 'gma', 'Gohir.A02G028600' => 'ghi', 'Gohir.A08G045000' => 'ghi', 'Gohir.A11G120500' => 'ghi', 'Gohir.A12G006200' => 'ghi', 'Gohir.A12G006250' => 'ghi', 'Gohir.D02G036300' => 'ghi', 'Gohir.D08G054700' => 'ghi', 'Gohir.D11G125600' => 'ghi', 'Gohir.D12G005700' => 'ghi', 'Gorai.004G055200' => 'gra', 'Gorai.005G040400' => 'gra', 'Gorai.007G134500' => 'gra', 'Gorai.008G005500' => 'gra', 'GSVIVG01011094001' => 'vvi', 'GSVIVG01017879001' => 'vvi', 'GSVIVG01025988001' => 'vvi', 'GSVIVG01029847001' => 'vvi', 'HanXRQChr10g0282901' => 'han', 'HanXRQChr10g0310371' => 'han', 'HanXRQChr10g0315041' => 'han', 'HanXRQChr11g0327651' => 'han', 'HanXRQChr12g0359391' => 'han', 'Haze_00972' => 'cav', 'Haze_00973' => 'cav', 'Haze_00974' => 'cav', 'Haze_04747' => 'cav', 'Haze_04749' => 'cav', 'Haze_04750' => 'cav', 'Haze_21217' => 'cav', 'Hma1.2p1_1037F.1_g250680' => 'hma', 'Hma1.2p1_1644F.1_g295320' => 'hma', 'HPP92_011322' => 'vpl', 'HPP92_011323' => 'vpl', 'HPP92_011324' => 'vpl', 'HPP92_011325' => 'vpl', 'HPP92_011326' => 'vpl', 'Hund12205' => 'sun', 'Hund17957' => 'sun', 'Lalb_Chr06g0176771' => 'lal', 'Lalb_Chr18g0056021' => 'lal', 'Lalb_Chr18g0056031' => 'lal', 'Lalb_Chr18g0056041' => 'lal', 'Lalb_Chr20g0107751' => 'lal', 'Lalb_Chr20g0118371' => 'lal', 'Lj1g0010239' => 'lja', 'Lj1g0017101' => 'lja', 'Lj2A1178G40' => 'lonja', 'Lj2A54G84' => 'lonja', 'Lj2g0015248' => 'lja', 'Lj3A761T51' => 'lonja', 'Lj6g0018116' => 'lja', 'Lsat_1_v5_gn_4_136040' => 'lsa', 'Lsat_1_v5_gn_5_187461' => 'lsa', 'Lsat_1_v5_gn_5_77001' => 'lsa', 'Lsat_1_v5_gn_9_4461' => 'lsa', 'Manes.01G210100' => 'mes', 'Manes.03G185600' => 'mes', 'Manes.05G073300' => 'mes', 'Manes.09G120300' => 'mes', 'Manes.15G022100' => 'mes', 'Mapoly0096s0053' => 'mpo', 'MBI03_g14058_MAGBIO' => 'mbi', 'MBI03_g33876_MAGBIO' => 'mbi', 'MBI03_g36854_MAGBIO' => 'mbi', 'MBI17_g11997_MAGBIO' => 'mbi', 'MD03G1269000' => 'mdo', 'MD04G1179600' => 'mdo', 'MD11G1289800' => 'mdo', 'MD12G1194700' => 'mdo', 'MD13G1182100' => 'mdo', 'MD13G1182200' => 'mdo', 'MD16G1182600' => 'mdo', 'Medtr2g021400' => 'mtr', 'Medtr2g021470' => 'mtr', 'Medtr2g105810' => 'mtr', 'Medtr3g033580' => 'mtr', 'Medtr6g007970' => 'mtr', 'Medtr7g056330' => 'mtr', 'Medtr7g074290' => 'mtr', 'Medtr7g074380' => 'mtr', 'Medtr7g094550' => 'mtr', 'Medtr8g069995' => 'mtr', 'MELO3C014345.2' => 'cme', 'MELO3C021395.2' => 'cme', 'Migut.D00262' => 'egut', 'Migut.G00257' => 'egut', 'MSTRG.21575' => 'ama', 'MSTRG.3985' => 'ama', 'Nitab4.5_0000295g0140' => 'nta', 'Nitab4.5_0000732g0140' => 'nta', 'Nitab4.5_0003162g0020' => 'nta', 'Nitab4.5_0006180g0090' => 'nta', 'Nitab4.5_0006390g0010' => 'nta', 'Nitab4.5_0007392g0040' => 'nta', 'Nn1g02140' => 'nnu', 'Nn4g26168' => 'nnu', 'Nn5g26754' => 'nnu', 'Oeu001433.1' => 'oeu', 'Oeu010299.2' => 'oeu', 'Oeu011171.1' => 'oeu', 'Oeu037675.1' => 'oeu', 'Oeu038359.1' => 'oeu', 'Oeu063834.1' => 'oeu', 'Oeu063835.1' => 'oeu', 'Os05g0312000' => 'osa', 'Os07g0211101' => 'osa', 'Os07g0211200' => 'osa', 'Os07g0681500' => 'osa', 'Peaxi162Scf00095g01015' => 'pax', 'Peaxi162Scf00104g00329' => 'pax', 'Peaxi162Scf00161g00137' => 'pax', 'PGR004G1665' => 'pgr', 'PGR031G2937' => 'pgr', 'PGR119G2145' => 'pgr', 'PGSC0003DMG400004351' => 'stu', 'PGSC0003DMG400014625' => 'stu', 'PGSC0003DMG401000943' => 'stu', 'Phvul.001G148600' => 'pvu', 'Phvul.004G001700' => 'pvu', 'Phvul.006G154900' => 'pvu', 'Phvul.008G078200' => 'pvu', 'Phvul.011G136500' => 'pvu', 'Potri.002G215600' => 'ptr', 'Potri.008G201600' => 'ptr', 'Potri.014G138400' => 'ptr', 'Potri.016G142500' => 'ptr', 'Pp3c16_10580' => 'ppa', 'Pp3c5_25280' => 'ppa', 'Prupe.1G150000' => 'ppe', 'Prupe.1G150100' => 'ppe', 'Prupe.6G299600' => 'ppe', 'Prupe.8G245000' => 'ppe', 'Psat0s4927g0040' => 'psa', 'Psat1g052080' => 'psa', 'Psat1g183800' => 'psa', 'Psat3g113840' => 'psa', 'Psat3g126120' => 'psa', 'Psat3g126160' => 'psa', 'Psat3g158760' => 'psa', 'Psat3g158840' => 'psa', 'PSO170G2858' => 'pso', 'PSO339G0606' => 'pso', 'PSO384G4709' => 'pso', 'PSO407G0334' => 'pso', 'QL04p040276' => 'qlo', 'QL06p005458' => 'qlo', 'QL06p005472' => 'qlo', 'QL07p030546' => 'qlo', 'QL07p031519' => 'qlo', 'QL09p050949' => 'qlo', 'QL09p050966' => 'qlo', 'QL09p051067' => 'qlo', 'QL12p022706' => 'qlo', 'RcHm_v2.0_Chr2g0119601' => 'rch', 'RcHm_v2.0_Chr3g0459591' => 'rch', 'RcHm_v2.0_Chr4g0418521' => 'rch', 'RcHm_v2.0_Chr4g0418531' => 'rch', 'RcHm_v2.0_Chr4g0418541' => 'rch', 'RcHm_v2.0_Chr6g0291641' => 'rch', 'Rhsim01G0086300' => 'rsi', 'Rhsim01G0276300' => 'rsi', 'Rhsim01G0276500' => 'rsi', 'Rhsim04G0207700' => 'rsi', 'Rhsim05G0234500' => 'rsi', 'Rhsim13G0022400' => 'rsi', 'Sabra02G0167900' => 'sbr', 'Sabra04G0158500' => 'sbr', 'Sabra08G0159800' => 'sbr', 'Sabra10G0011500' => 'sbr', 'Sabra14G0104400' => 'sbr', 'SalBow2G2440' => 'sbo', 'SalBow4G2265' => 'sbo', 'Sc02g0000060' => 'sci', 'Sc05g0005020' => 'sci', 'Sc13g0003890' => 'sci', 'Sed0014865' => 'sed', 'Sed0017224' => 'sed', 'Sed0026391' => 'sed', 'SEGI_00063' => 'sgi', 'SEGI_10967' => 'sgi', 'SEGI_17510' => 'sgi', 'SEGI_24396' => 'sgi', 'SEGI_39719' => 'sgi', 'SEGI_41392' => 'sgi', 'SGA_v2.0_scaffold11G05794' => 'sas', 'SGA_v2.0_scaffold142G35607' => 'sas', 'SGA_v2.0_scaffold1G00447' => 'sas', 'SHI15388' => 'shi', 'SHI15394' => 'shi', 'SHI15396' => 'shi', 'SHI15399' => 'shi', 'SMO343G0151' => 'smo', 'SMO367G1118' => 'smo', 'Solyc01g080200.3' => 'sly', 'Solyc06g008960.3' => 'sly', 'Solyc09g064780.3' => 'sly', 'Sopen01g031980' => 'spe', 'Sopen06g003710' => 'spe', 'Sopen09g026460' => 'spe', 'Sp3g21240' => 'spa', 'Sp4g30030' => 'spa', 'TAR365G0022' => 'tar', 'TAR365G1023' => 'tar', 'TAR365G1253' => 'tar', 'TAR623G0078' => 'tar', 'TAR623G1721' => 'tar', 'TAR633G0959' => 'tar', 'THA.LOC104802225' => 'tha', 'THA.LOC104804769' => 'tha', 'THA.LOC104808660' => 'tha', 'THA.LOC104812792' => 'tha', 'Thecc.01G284000' => 'tca', 'Thecc.04G220600' => 'tca', 'Thecc.05G268900' => 'tca', 'Thecc.08G171100' => 'tca', 'Thhalv10001284m.g' => 'esa', 'Thhalv10019912m.g' => 'esa', 'TPR.G14189' => 'tpr', 'TPR.G18110' => 'tpr', 'TPR.G18130' => 'tpr', 'TPR.G18131' => 'tpr', 'TPR.G18140' => 'tpr', 'TPR.G24282' => 'tpr', 'TPR.G25221' => 'tpr', 'TPR.G29267' => 'tpr', 'TPR.G35315' => 'tpr', 'TPR.G36173' => 'tpr', 'TWI09G0794' => 'twi', 'TWI59G1348' => 'twi', 'TWI74G0430' => 'twi', 'unitig_26.g8940' => 'ugi', 'unitig_749.g13744' => 'ugi', 'unitig_749.g13745' => 'ugi', 'vmacro08269' => 'vma', 'vmacro14937' => 'vma', 'vmacro20401' => 'vma', 'VMungo0464G1349' => 'vmu', 'VMungo0540G0289' => 'vmu', 'VMungo1215G1590' => 'vmu', 'VMungo1309G0221' => 'vmu', 'VMungo1309G2815' => 'vmu', 'VMungo1383G0239' => 'vmu', 'VMungo1383G2910' => 'vmu', 'Zm00001eb095270' => 'zma', 'Zm00001eb095280' => 'zma', 'Zm00001eb111630' => 'zma', 'Zm00001eb237080' => 'zma', 'Zm00001eb273740' => 'zma', 'Zm00001eb285040' => 'zma', 'Zm00001eb330790' => 'zma', 'Zm00001eb337380' => 'zma' ) $gf_id = 'HOM05D001484' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001484' ) $data_identifier = 'HOM05D001484' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 2, 'aly' => (int) 2, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 22, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 7, 'hma' => (int) 2, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 7, 'mtr' => (int) 10, 'cme' => (int) 2, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 4, 'ppa' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 4, 'qlo' => (int) 9, 'rch' => (int) 6, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 10, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 7, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb337380' $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' => 'HOM05D001484', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p31500' => 'bna', 'A05p00020' => 'bna', 'A07p08820' => 'bna', 'Aa31LG4G3300' => 'aar', 'Aa31LG8G10030' => 'aar', 'Actinidia00731' => 'ach', 'Actinidia11473' => 'ach', 'Actinidia23469' => 'ach', 'Actinidia24318' => 'ach', 'Actinidia40196' => 'ach', 'Actinidia40197' => 'ach', 'Actinidia40198' => 'ach', 'Ah.08g212990' => 'amhyb', 'Ah.15g091720' => 'amhyb', 'AL3G38260' => 'aly', 'AL4G47710' => 'aly', 'Aqoxy2G00671' => 'aox', 'Aqoxy2G03236' => 'aox', 'arahy.Tifrunner.gnm1.ann1.05IDCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KR684' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATY3SJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK6QJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6APGL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IDT7Z9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM073U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ0R87' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LE7RV4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT4QRX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V5ENPK' => 'arhy', 'AT2G48110' => 'ath', 'AT3G23590' => 'ath', 'ATR0626G186' => 'atr', 'ATR1127G141' => 'atr', 'Atru.chr4.2583' => 'acertr', 'Atru.chr5.1358' => 'acertr', 'Atru.chr5.1359' => 'acertr', 'Atru.chr8.46' => 'acertr', 'AUR62002640' => 'cqu', 'AUR62030055' => 'cqu', 'AUR62033713' => 'cqu', 'AUR62033714' => 'cqu', 'AUR62036795' => 'cqu', 'AUR62039891' => 'cqu', 'BcaB02g08737' => 'bca', 'BcaB04g20441' => 'bca', 'BcaB06g26509' => 'bca', 'BcaB06g26510' => 'bca', 'BcaB06g26511' => 'bca', 'BcaB06g26512' => 'bca', 'BcaB06g26513' => 'bca', 'BcaC02g12564' => 'bca', 'BcaC02g12565' => 'bca', 'BcaC02g12794' => 'bca', 'BcaC02g12795' => 'bca', 'BcaC02g12796' => 'bca', 'BcaC06g35541' => 'bca', 'BNapus_Darmor_BZH_scaffold_188p00080' => 'bna', 'BNapus_Darmor_BZH_scaffold_188p00090' => 'bna', 'BolC1t03972H' => 'bol', 'BolC1t03973H' => 'bol', 'BolC4t21680H' => 'bol', 'BolC7t41863H' => 'bol', 'BolSC55t61227H' => 'bol', 'BolSC55t61228H' => 'bol', 'BraA01t03278Z' => 'bra', 'BraA05t18998Z' => 'bra', 'BraA07t28673Z' => 'bra', 'C01p40150' => 'bna', 'C05p12370' => 'bna', 'C07p13680' => 'bna', 'CAN.G1006.16' => 'can', 'CAN.G1006.17' => 'can', 'CAN.G1170.2' => 'can', 'CAN.G962.7' => 'can', 'CANSAT25G2179' => 'cansat', 'CANSAT78G1573' => 'cansat', 'CARHR099510' => 'chi', 'CARHR143510' => 'chi', 'Carub.0003s2380' => 'cru', 'Carub.0004s3082' => 'cru', 'Ca_00614_v3' => 'car', 'Ca_07801_v3' => 'car', 'Ca_08567_v3' => 'car', 'Ca_09571_v3' => 'car', 'CBR_g19290' => 'cbr', 'Cc01_g19770' => 'ccan', 'Cc03_g03030' => 'ccan', 'CDE07G0968' => 'cde', 'CDE09G1441' => 'cde', 'Cfa006103' => 'cfa', 'Cfa015573' => 'cfa', 'Cfa016988' => 'cfa', 'Ciclev10006738m.g' => 'ccl', 'Ciclev10010920m.g' => 'ccl', 'Ciclev10018517m.g' => 'ccl', 'CiPaw.01G159200' => 'cil', 'CiPaw.02G091000' => 'cil', 'CiPaw.02G091100' => 'cil', 'CiPaw.08G103100' => 'cil', 'CiPaw.09G224900' => 'cil', 'ClCG06G005740' => 'cla', 'ClCG07G000090' => 'cla', 'ClCG07G000100' => 'cla', 'COL.COLO4_09143' => 'col', 'COL.COLO4_25124' => 'col', 'Cpa.g.sc16.34' => 'cpa', 'Cpa.g.sc3504.1' => 'cpa', 'Cpa.g.sc60.37' => 'cpa', 'CsaV3_6G018520' => 'csa', 'CsaV3_6G036860' => 'csa', 'CSS0001072' => 'camsi', 'CSS0020208' => 'camsi', 'CSS0021253' => 'camsi', 'CSS0022190' => 'camsi', 'CSS0036150' => 'camsi', 'CSS0040442' => 'camsi', 'CSS0042300' => 'camsi', 'CSS0045298' => 'camsi', 'DCAR_012449' => 'dca', 'DCAR_018405' => 'dca', 'DCAR_024573' => 'dca', 'DCAR_030591' => 'dca', 'Dinv16926' => 'din', 'Dinv32963' => 'din', 'Dinv38382' => 'din', 'Dinv38383' => 'din', 'Duzib133G0974' => 'dzi', 'Duzib138G1867' => 'dzi', 'Duzib211G0420' => 'dzi', 'Duzib212G0930' => 'dzi', 'ECA234G1645' => 'eca', 'ECA247G3467' => 'eca', 'ECA248G1703' => 'eca', 'EL10Ac3g06327' => 'bvu', 'EL10Ac7g17204' => 'bvu', 'Eucgr.A00855' => 'egr', 'Eucgr.A00858' => 'egr', 'Eucgr.H01520' => 'egr', 'Eucgr.H03604' => 'egr', 'Eucgr.L03465' => 'egr', 'Eucgr.L03466' => 'egr', 'FAN01G0988' => 'fan', 'FAN02G3892' => 'fan', 'FAN05G3381' => 'fan', 'FAN07G0967' => 'fan', 'FAN07G1493' => 'fan', 'FAN08G3125' => 'fan', 'FAN09G0402' => 'fan', 'FAN12G2594' => 'fan', 'FAN12G3879' => 'fan', 'FAN14G1546' => 'fan', 'FAN15G3626' => 'fan', 'FAN17G0588' => 'fan', 'FAN17G0609' => 'fan', 'FAN18G2817' => 'fan', 'FAN19G1305' => 'fan', 'FAN20G1787' => 'fan', 'FAN22G0073' => 'fan', 'FAN22G0352' => 'fan', 'FAN22G0368' => 'fan', 'FAN22G2273' => 'fan', 'FAN24G1998' => 'fan', 'FAN27G1317' => 'fan', 'FvH4_2g23980' => 'fve', 'FvH4_4g14380' => 'fve', 'FvH4_4g14390' => 'fve', 'FvH4_6g09250' => 'fve', 'Glyma.03G151100' => 'gma', 'Glyma.04G122550' => 'gma', 'Glyma.05G001600' => 'gma', 'Glyma.09G270766' => 'gma', 'Glyma.09G270832' => 'gma', 'Glyma.13G209800' => 'gma', 'Glyma.15G102800' => 'gma', 'Glyma.18G218900' => 'gma', 'Glyma.19G001500' => 'gma', 'Glyma.19G153600' => 'gma', 'Gohir.A02G028600' => 'ghi', 'Gohir.A08G045000' => 'ghi', 'Gohir.A11G120500' => 'ghi', 'Gohir.A12G006200' => 'ghi', 'Gohir.A12G006250' => 'ghi', 'Gohir.D02G036300' => 'ghi', 'Gohir.D08G054700' => 'ghi', 'Gohir.D11G125600' => 'ghi', 'Gohir.D12G005700' => 'ghi', 'Gorai.004G055200' => 'gra', 'Gorai.005G040400' => 'gra', 'Gorai.007G134500' => 'gra', 'Gorai.008G005500' => 'gra', 'GSVIVG01011094001' => 'vvi', 'GSVIVG01017879001' => 'vvi', 'GSVIVG01025988001' => 'vvi', 'GSVIVG01029847001' => 'vvi', 'HanXRQChr10g0282901' => 'han', 'HanXRQChr10g0310371' => 'han', 'HanXRQChr10g0315041' => 'han', 'HanXRQChr11g0327651' => 'han', 'HanXRQChr12g0359391' => 'han', 'Haze_00972' => 'cav', 'Haze_00973' => 'cav', 'Haze_00974' => 'cav', 'Haze_04747' => 'cav', 'Haze_04749' => 'cav', 'Haze_04750' => 'cav', 'Haze_21217' => 'cav', 'Hma1.2p1_1037F.1_g250680' => 'hma', 'Hma1.2p1_1644F.1_g295320' => 'hma', 'HPP92_011322' => 'vpl', 'HPP92_011323' => 'vpl', 'HPP92_011324' => 'vpl', 'HPP92_011325' => 'vpl', 'HPP92_011326' => 'vpl', 'Hund12205' => 'sun', 'Hund17957' => 'sun', 'Lalb_Chr06g0176771' => 'lal', 'Lalb_Chr18g0056021' => 'lal', 'Lalb_Chr18g0056031' => 'lal', 'Lalb_Chr18g0056041' => 'lal', 'Lalb_Chr20g0107751' => 'lal', 'Lalb_Chr20g0118371' => 'lal', 'Lj1g0010239' => 'lja', 'Lj1g0017101' => 'lja', 'Lj2A1178G40' => 'lonja', 'Lj2A54G84' => 'lonja', 'Lj2g0015248' => 'lja', 'Lj3A761T51' => 'lonja', 'Lj6g0018116' => 'lja', 'Lsat_1_v5_gn_4_136040' => 'lsa', 'Lsat_1_v5_gn_5_187461' => 'lsa', 'Lsat_1_v5_gn_5_77001' => 'lsa', 'Lsat_1_v5_gn_9_4461' => 'lsa', 'Manes.01G210100' => 'mes', 'Manes.03G185600' => 'mes', 'Manes.05G073300' => 'mes', 'Manes.09G120300' => 'mes', 'Manes.15G022100' => 'mes', 'Mapoly0096s0053' => 'mpo', 'MBI03_g14058_MAGBIO' => 'mbi', 'MBI03_g33876_MAGBIO' => 'mbi', 'MBI03_g36854_MAGBIO' => 'mbi', 'MBI17_g11997_MAGBIO' => 'mbi', 'MD03G1269000' => 'mdo', 'MD04G1179600' => 'mdo', 'MD11G1289800' => 'mdo', 'MD12G1194700' => 'mdo', 'MD13G1182100' => 'mdo', 'MD13G1182200' => 'mdo', 'MD16G1182600' => 'mdo', 'Medtr2g021400' => 'mtr', 'Medtr2g021470' => 'mtr', 'Medtr2g105810' => 'mtr', 'Medtr3g033580' => 'mtr', 'Medtr6g007970' => 'mtr', 'Medtr7g056330' => 'mtr', 'Medtr7g074290' => 'mtr', 'Medtr7g074380' => 'mtr', 'Medtr7g094550' => 'mtr', 'Medtr8g069995' => 'mtr', 'MELO3C014345.2' => 'cme', 'MELO3C021395.2' => 'cme', 'Migut.D00262' => 'egut', 'Migut.G00257' => 'egut', 'MSTRG.21575' => 'ama', 'MSTRG.3985' => 'ama', 'Nitab4.5_0000295g0140' => 'nta', 'Nitab4.5_0000732g0140' => 'nta', 'Nitab4.5_0003162g0020' => 'nta', 'Nitab4.5_0006180g0090' => 'nta', 'Nitab4.5_0006390g0010' => 'nta', 'Nitab4.5_0007392g0040' => 'nta', 'Nn1g02140' => 'nnu', 'Nn4g26168' => 'nnu', 'Nn5g26754' => 'nnu', 'Oeu001433.1' => 'oeu', 'Oeu010299.2' => 'oeu', 'Oeu011171.1' => 'oeu', 'Oeu037675.1' => 'oeu', 'Oeu038359.1' => 'oeu', 'Oeu063834.1' => 'oeu', 'Oeu063835.1' => 'oeu', 'Os05g0312000' => 'osa', 'Os07g0211101' => 'osa', 'Os07g0211200' => 'osa', 'Os07g0681500' => 'osa', 'Peaxi162Scf00095g01015' => 'pax', 'Peaxi162Scf00104g00329' => 'pax', 'Peaxi162Scf00161g00137' => 'pax', 'PGR004G1665' => 'pgr', 'PGR031G2937' => 'pgr', 'PGR119G2145' => 'pgr', 'PGSC0003DMG400004351' => 'stu', 'PGSC0003DMG400014625' => 'stu', 'PGSC0003DMG401000943' => 'stu', 'Phvul.001G148600' => 'pvu', 'Phvul.004G001700' => 'pvu', 'Phvul.006G154900' => 'pvu', 'Phvul.008G078200' => 'pvu', 'Phvul.011G136500' => 'pvu', 'Potri.002G215600' => 'ptr', 'Potri.008G201600' => 'ptr', 'Potri.014G138400' => 'ptr', 'Potri.016G142500' => 'ptr', 'Pp3c16_10580' => 'ppa', 'Pp3c5_25280' => 'ppa', 'Prupe.1G150000' => 'ppe', 'Prupe.1G150100' => 'ppe', 'Prupe.6G299600' => 'ppe', 'Prupe.8G245000' => 'ppe', 'Psat0s4927g0040' => 'psa', 'Psat1g052080' => 'psa', 'Psat1g183800' => 'psa', 'Psat3g113840' => 'psa', 'Psat3g126120' => 'psa', 'Psat3g126160' => 'psa', 'Psat3g158760' => 'psa', 'Psat3g158840' => 'psa', 'PSO170G2858' => 'pso', 'PSO339G0606' => 'pso', 'PSO384G4709' => 'pso', 'PSO407G0334' => 'pso', 'QL04p040276' => 'qlo', 'QL06p005458' => 'qlo', 'QL06p005472' => 'qlo', 'QL07p030546' => 'qlo', 'QL07p031519' => 'qlo', 'QL09p050949' => 'qlo', 'QL09p050966' => 'qlo', 'QL09p051067' => 'qlo', 'QL12p022706' => 'qlo', 'RcHm_v2.0_Chr2g0119601' => 'rch', 'RcHm_v2.0_Chr3g0459591' => 'rch', 'RcHm_v2.0_Chr4g0418521' => 'rch', 'RcHm_v2.0_Chr4g0418531' => 'rch', 'RcHm_v2.0_Chr4g0418541' => 'rch', 'RcHm_v2.0_Chr6g0291641' => 'rch', 'Rhsim01G0086300' => 'rsi', 'Rhsim01G0276300' => 'rsi', 'Rhsim01G0276500' => 'rsi', 'Rhsim04G0207700' => 'rsi', 'Rhsim05G0234500' => 'rsi', 'Rhsim13G0022400' => 'rsi', 'Sabra02G0167900' => 'sbr', 'Sabra04G0158500' => 'sbr', 'Sabra08G0159800' => 'sbr', 'Sabra10G0011500' => 'sbr', 'Sabra14G0104400' => 'sbr', 'SalBow2G2440' => 'sbo', 'SalBow4G2265' => 'sbo', 'Sc02g0000060' => 'sci', 'Sc05g0005020' => 'sci', 'Sc13g0003890' => 'sci', 'Sed0014865' => 'sed', 'Sed0017224' => 'sed', 'Sed0026391' => 'sed', 'SEGI_00063' => 'sgi', 'SEGI_10967' => 'sgi', 'SEGI_17510' => 'sgi', 'SEGI_24396' => 'sgi', 'SEGI_39719' => 'sgi', 'SEGI_41392' => 'sgi', 'SGA_v2.0_scaffold11G05794' => 'sas', 'SGA_v2.0_scaffold142G35607' => 'sas', 'SGA_v2.0_scaffold1G00447' => 'sas', 'SHI15388' => 'shi', 'SHI15394' => 'shi', 'SHI15396' => 'shi', 'SHI15399' => 'shi', 'SMO343G0151' => 'smo', 'SMO367G1118' => 'smo', 'Solyc01g080200.3' => 'sly', 'Solyc06g008960.3' => 'sly', 'Solyc09g064780.3' => 'sly', 'Sopen01g031980' => 'spe', 'Sopen06g003710' => 'spe', 'Sopen09g026460' => 'spe', 'Sp3g21240' => 'spa', 'Sp4g30030' => 'spa', 'TAR365G0022' => 'tar', 'TAR365G1023' => 'tar', 'TAR365G1253' => 'tar', 'TAR623G0078' => 'tar', 'TAR623G1721' => 'tar', 'TAR633G0959' => 'tar', 'THA.LOC104802225' => 'tha', 'THA.LOC104804769' => 'tha', 'THA.LOC104808660' => 'tha', 'THA.LOC104812792' => 'tha', 'Thecc.01G284000' => 'tca', 'Thecc.04G220600' => 'tca', 'Thecc.05G268900' => 'tca', 'Thecc.08G171100' => 'tca', 'Thhalv10001284m.g' => 'esa', 'Thhalv10019912m.g' => 'esa', 'TPR.G14189' => 'tpr', 'TPR.G18110' => 'tpr', 'TPR.G18130' => 'tpr', 'TPR.G18131' => 'tpr', 'TPR.G18140' => 'tpr', 'TPR.G24282' => 'tpr', 'TPR.G25221' => 'tpr', 'TPR.G29267' => 'tpr', 'TPR.G35315' => 'tpr', 'TPR.G36173' => 'tpr', 'TWI09G0794' => 'twi', 'TWI59G1348' => 'twi', 'TWI74G0430' => 'twi', 'unitig_26.g8940' => 'ugi', 'unitig_749.g13744' => 'ugi', 'unitig_749.g13745' => 'ugi', 'vmacro08269' => 'vma', 'vmacro14937' => 'vma', 'vmacro20401' => 'vma', 'VMungo0464G1349' => 'vmu', 'VMungo0540G0289' => 'vmu', 'VMungo1215G1590' => 'vmu', 'VMungo1309G0221' => 'vmu', 'VMungo1309G2815' => 'vmu', 'VMungo1383G0239' => 'vmu', 'VMungo1383G2910' => 'vmu', 'Zm00001eb095270' => 'zma', 'Zm00001eb095280' => 'zma', 'Zm00001eb111630' => 'zma', 'Zm00001eb237080' => 'zma', 'Zm00001eb273740' => 'zma', 'Zm00001eb285040' => 'zma', 'Zm00001eb330790' => 'zma', 'Zm00001eb337380' => 'zma' ), 'gf_id' => 'HOM05D001484', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001484' ), 'data_identifier' => 'HOM05D001484', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001484', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p31500' => 'bna', 'A05p00020' => 'bna', 'A07p08820' => 'bna', 'Aa31LG4G3300' => 'aar', 'Aa31LG8G10030' => 'aar', 'Actinidia00731' => 'ach', 'Actinidia11473' => 'ach', 'Actinidia23469' => 'ach', 'Actinidia24318' => 'ach', 'Actinidia40196' => 'ach', 'Actinidia40197' => 'ach', 'Actinidia40198' => 'ach', 'Ah.08g212990' => 'amhyb', 'Ah.15g091720' => 'amhyb', 'AL3G38260' => 'aly', 'AL4G47710' => 'aly', 'Aqoxy2G00671' => 'aox', 'Aqoxy2G03236' => 'aox', 'arahy.Tifrunner.gnm1.ann1.05IDCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KR684' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATY3SJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK6QJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6APGL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IDT7Z9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM073U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ0R87' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LE7RV4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT4QRX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V5ENPK' => 'arhy', 'AT2G48110' => 'ath', 'AT3G23590' => 'ath', 'ATR0626G186' => 'atr', 'ATR1127G141' => 'atr', 'Atru.chr4.2583' => 'acertr', 'Atru.chr5.1358' => 'acertr', 'Atru.chr5.1359' => 'acertr', 'Atru.chr8.46' => 'acertr', 'AUR62002640' => 'cqu', 'AUR62030055' => 'cqu', 'AUR62033713' => 'cqu', 'AUR62033714' => 'cqu', 'AUR62036795' => 'cqu', 'AUR62039891' => 'cqu', 'BcaB02g08737' => 'bca', 'BcaB04g20441' => 'bca', 'BcaB06g26509' => 'bca', 'BcaB06g26510' => 'bca', 'BcaB06g26511' => 'bca', 'BcaB06g26512' => 'bca', 'BcaB06g26513' => 'bca', 'BcaC02g12564' => 'bca', 'BcaC02g12565' => 'bca', 'BcaC02g12794' => 'bca', 'BcaC02g12795' => 'bca', 'BcaC02g12796' => 'bca', 'BcaC06g35541' => 'bca', 'BNapus_Darmor_BZH_scaffold_188p00080' => 'bna', 'BNapus_Darmor_BZH_scaffold_188p00090' => 'bna', 'BolC1t03972H' => 'bol', 'BolC1t03973H' => 'bol', 'BolC4t21680H' => 'bol', 'BolC7t41863H' => 'bol', 'BolSC55t61227H' => 'bol', 'BolSC55t61228H' => 'bol', 'BraA01t03278Z' => 'bra', 'BraA05t18998Z' => 'bra', 'BraA07t28673Z' => 'bra', 'C01p40150' => 'bna', 'C05p12370' => 'bna', 'C07p13680' => 'bna', 'CAN.G1006.16' => 'can', 'CAN.G1006.17' => 'can', 'CAN.G1170.2' => 'can', 'CAN.G962.7' => 'can', 'CANSAT25G2179' => 'cansat', 'CANSAT78G1573' => 'cansat', 'CARHR099510' => 'chi', 'CARHR143510' => 'chi', 'Carub.0003s2380' => 'cru', 'Carub.0004s3082' => 'cru', 'Ca_00614_v3' => 'car', 'Ca_07801_v3' => 'car', 'Ca_08567_v3' => 'car', 'Ca_09571_v3' => 'car', 'CBR_g19290' => 'cbr', 'Cc01_g19770' => 'ccan', 'Cc03_g03030' => 'ccan', 'CDE07G0968' => 'cde', 'CDE09G1441' => 'cde', 'Cfa006103' => 'cfa', 'Cfa015573' => 'cfa', 'Cfa016988' => 'cfa', 'Ciclev10006738m.g' => 'ccl', 'Ciclev10010920m.g' => 'ccl', 'Ciclev10018517m.g' => 'ccl', 'CiPaw.01G159200' => 'cil', 'CiPaw.02G091000' => 'cil', 'CiPaw.02G091100' => 'cil', 'CiPaw.08G103100' => 'cil', 'CiPaw.09G224900' => 'cil', 'ClCG06G005740' => 'cla', 'ClCG07G000090' => 'cla', 'ClCG07G000100' => 'cla', 'COL.COLO4_09143' => 'col', 'COL.COLO4_25124' => 'col', 'Cpa.g.sc16.34' => 'cpa', 'Cpa.g.sc3504.1' => 'cpa', 'Cpa.g.sc60.37' => 'cpa', 'CsaV3_6G018520' => 'csa', 'CsaV3_6G036860' => 'csa', 'CSS0001072' => 'camsi', 'CSS0020208' => 'camsi', 'CSS0021253' => 'camsi', 'CSS0022190' => 'camsi', 'CSS0036150' => 'camsi', 'CSS0040442' => 'camsi', 'CSS0042300' => 'camsi', 'CSS0045298' => 'camsi', 'DCAR_012449' => 'dca', 'DCAR_018405' => 'dca', 'DCAR_024573' => 'dca', 'DCAR_030591' => 'dca', 'Dinv16926' => 'din', 'Dinv32963' => 'din', 'Dinv38382' => 'din', 'Dinv38383' => 'din', 'Duzib133G0974' => 'dzi', 'Duzib138G1867' => 'dzi', 'Duzib211G0420' => 'dzi', 'Duzib212G0930' => 'dzi', 'ECA234G1645' => 'eca', 'ECA247G3467' => 'eca', 'ECA248G1703' => 'eca', 'EL10Ac3g06327' => 'bvu', 'EL10Ac7g17204' => 'bvu', 'Eucgr.A00855' => 'egr', 'Eucgr.A00858' => 'egr', 'Eucgr.H01520' => 'egr', 'Eucgr.H03604' => 'egr', 'Eucgr.L03465' => 'egr', 'Eucgr.L03466' => 'egr', 'FAN01G0988' => 'fan', 'FAN02G3892' => 'fan', 'FAN05G3381' => 'fan', 'FAN07G0967' => 'fan', 'FAN07G1493' => 'fan', 'FAN08G3125' => 'fan', 'FAN09G0402' => 'fan', 'FAN12G2594' => 'fan', 'FAN12G3879' => 'fan', 'FAN14G1546' => 'fan', 'FAN15G3626' => 'fan', 'FAN17G0588' => 'fan', 'FAN17G0609' => 'fan', 'FAN18G2817' => 'fan', 'FAN19G1305' => 'fan', 'FAN20G1787' => 'fan', 'FAN22G0073' => 'fan', 'FAN22G0352' => 'fan', 'FAN22G0368' => 'fan', 'FAN22G2273' => 'fan', 'FAN24G1998' => 'fan', 'FAN27G1317' => 'fan', 'FvH4_2g23980' => 'fve', 'FvH4_4g14380' => 'fve', 'FvH4_4g14390' => 'fve', 'FvH4_6g09250' => 'fve', 'Glyma.03G151100' => 'gma', 'Glyma.04G122550' => 'gma', 'Glyma.05G001600' => 'gma', 'Glyma.09G270766' => 'gma', 'Glyma.09G270832' => 'gma', 'Glyma.13G209800' => 'gma', 'Glyma.15G102800' => 'gma', 'Glyma.18G218900' => 'gma', 'Glyma.19G001500' => 'gma', 'Glyma.19G153600' => 'gma', 'Gohir.A02G028600' => 'ghi', 'Gohir.A08G045000' => 'ghi', 'Gohir.A11G120500' => 'ghi', 'Gohir.A12G006200' => 'ghi', 'Gohir.A12G006250' => 'ghi', 'Gohir.D02G036300' => 'ghi', 'Gohir.D08G054700' => 'ghi', 'Gohir.D11G125600' => 'ghi', 'Gohir.D12G005700' => 'ghi', 'Gorai.004G055200' => 'gra', 'Gorai.005G040400' => 'gra', 'Gorai.007G134500' => 'gra', 'Gorai.008G005500' => 'gra', 'GSVIVG01011094001' => 'vvi', 'GSVIVG01017879001' => 'vvi', 'GSVIVG01025988001' => 'vvi', 'GSVIVG01029847001' => 'vvi', 'HanXRQChr10g0282901' => 'han', 'HanXRQChr10g0310371' => 'han', 'HanXRQChr10g0315041' => 'han', 'HanXRQChr11g0327651' => 'han', 'HanXRQChr12g0359391' => 'han', 'Haze_00972' => 'cav', 'Haze_00973' => 'cav', 'Haze_00974' => 'cav', 'Haze_04747' => 'cav', 'Haze_04749' => 'cav', 'Haze_04750' => 'cav', 'Haze_21217' => 'cav', 'Hma1.2p1_1037F.1_g250680' => 'hma', 'Hma1.2p1_1644F.1_g295320' => 'hma', 'HPP92_011322' => 'vpl', 'HPP92_011323' => 'vpl', 'HPP92_011324' => 'vpl', 'HPP92_011325' => 'vpl', 'HPP92_011326' => 'vpl', 'Hund12205' => 'sun', 'Hund17957' => 'sun', 'Lalb_Chr06g0176771' => 'lal', 'Lalb_Chr18g0056021' => 'lal', 'Lalb_Chr18g0056031' => 'lal', 'Lalb_Chr18g0056041' => 'lal', 'Lalb_Chr20g0107751' => 'lal', 'Lalb_Chr20g0118371' => 'lal', 'Lj1g0010239' => 'lja', 'Lj1g0017101' => 'lja', 'Lj2A1178G40' => 'lonja', 'Lj2A54G84' => 'lonja', 'Lj2g0015248' => 'lja', 'Lj3A761T51' => 'lonja', 'Lj6g0018116' => 'lja', 'Lsat_1_v5_gn_4_136040' => 'lsa', 'Lsat_1_v5_gn_5_187461' => 'lsa', 'Lsat_1_v5_gn_5_77001' => 'lsa', 'Lsat_1_v5_gn_9_4461' => 'lsa', 'Manes.01G210100' => 'mes', 'Manes.03G185600' => 'mes', 'Manes.05G073300' => 'mes', 'Manes.09G120300' => 'mes', 'Manes.15G022100' => 'mes', 'Mapoly0096s0053' => 'mpo', 'MBI03_g14058_MAGBIO' => 'mbi', 'MBI03_g33876_MAGBIO' => 'mbi', 'MBI03_g36854_MAGBIO' => 'mbi', 'MBI17_g11997_MAGBIO' => 'mbi', 'MD03G1269000' => 'mdo', 'MD04G1179600' => 'mdo', 'MD11G1289800' => 'mdo', 'MD12G1194700' => 'mdo', 'MD13G1182100' => 'mdo', 'MD13G1182200' => 'mdo', 'MD16G1182600' => 'mdo', 'Medtr2g021400' => 'mtr', 'Medtr2g021470' => 'mtr', 'Medtr2g105810' => 'mtr', 'Medtr3g033580' => 'mtr', 'Medtr6g007970' => 'mtr', 'Medtr7g056330' => 'mtr', 'Medtr7g074290' => 'mtr', 'Medtr7g074380' => 'mtr', 'Medtr7g094550' => 'mtr', 'Medtr8g069995' => 'mtr', 'MELO3C014345.2' => 'cme', 'MELO3C021395.2' => 'cme', 'Migut.D00262' => 'egut', 'Migut.G00257' => 'egut', 'MSTRG.21575' => 'ama', 'MSTRG.3985' => 'ama', 'Nitab4.5_0000295g0140' => 'nta', 'Nitab4.5_0000732g0140' => 'nta', 'Nitab4.5_0003162g0020' => 'nta', 'Nitab4.5_0006180g0090' => 'nta', 'Nitab4.5_0006390g0010' => 'nta', 'Nitab4.5_0007392g0040' => 'nta', 'Nn1g02140' => 'nnu', 'Nn4g26168' => 'nnu', 'Nn5g26754' => 'nnu', 'Oeu001433.1' => 'oeu', 'Oeu010299.2' => 'oeu', 'Oeu011171.1' => 'oeu', 'Oeu037675.1' => 'oeu', 'Oeu038359.1' => 'oeu', 'Oeu063834.1' => 'oeu', 'Oeu063835.1' => 'oeu', 'Os05g0312000' => 'osa', 'Os07g0211101' => 'osa', 'Os07g0211200' => 'osa', 'Os07g0681500' => 'osa', 'Peaxi162Scf00095g01015' => 'pax', 'Peaxi162Scf00104g00329' => 'pax', 'Peaxi162Scf00161g00137' => 'pax', 'PGR004G1665' => 'pgr', 'PGR031G2937' => 'pgr', 'PGR119G2145' => 'pgr', 'PGSC0003DMG400004351' => 'stu', 'PGSC0003DMG400014625' => 'stu', 'PGSC0003DMG401000943' => 'stu', 'Phvul.001G148600' => 'pvu', 'Phvul.004G001700' => 'pvu', 'Phvul.006G154900' => 'pvu', 'Phvul.008G078200' => 'pvu', 'Phvul.011G136500' => 'pvu', 'Potri.002G215600' => 'ptr', 'Potri.008G201600' => 'ptr', 'Potri.014G138400' => 'ptr', 'Potri.016G142500' => 'ptr', 'Pp3c16_10580' => 'ppa', 'Pp3c5_25280' => 'ppa', 'Prupe.1G150000' => 'ppe', 'Prupe.1G150100' => 'ppe', 'Prupe.6G299600' => 'ppe', 'Prupe.8G245000' => 'ppe', 'Psat0s4927g0040' => 'psa', 'Psat1g052080' => 'psa', 'Psat1g183800' => 'psa', 'Psat3g113840' => 'psa', 'Psat3g126120' => 'psa', 'Psat3g126160' => 'psa', 'Psat3g158760' => 'psa', 'Psat3g158840' => 'psa', 'PSO170G2858' => 'pso', 'PSO339G0606' => 'pso', 'PSO384G4709' => 'pso', 'PSO407G0334' => 'pso', 'QL04p040276' => 'qlo', 'QL06p005458' => 'qlo', 'QL06p005472' => 'qlo', 'QL07p030546' => 'qlo', 'QL07p031519' => 'qlo', 'QL09p050949' => 'qlo', 'QL09p050966' => 'qlo', 'QL09p051067' => 'qlo', 'QL12p022706' => 'qlo', 'RcHm_v2.0_Chr2g0119601' => 'rch', 'RcHm_v2.0_Chr3g0459591' => 'rch', 'RcHm_v2.0_Chr4g0418521' => 'rch', 'RcHm_v2.0_Chr4g0418531' => 'rch', 'RcHm_v2.0_Chr4g0418541' => 'rch', 'RcHm_v2.0_Chr6g0291641' => 'rch', 'Rhsim01G0086300' => 'rsi', 'Rhsim01G0276300' => 'rsi', 'Rhsim01G0276500' => 'rsi', 'Rhsim04G0207700' => 'rsi', 'Rhsim05G0234500' => 'rsi', 'Rhsim13G0022400' => 'rsi', 'Sabra02G0167900' => 'sbr', 'Sabra04G0158500' => 'sbr', 'Sabra08G0159800' => 'sbr', 'Sabra10G0011500' => 'sbr', 'Sabra14G0104400' => 'sbr', 'SalBow2G2440' => 'sbo', 'SalBow4G2265' => 'sbo', 'Sc02g0000060' => 'sci', 'Sc05g0005020' => 'sci', 'Sc13g0003890' => 'sci', 'Sed0014865' => 'sed', 'Sed0017224' => 'sed', 'Sed0026391' => 'sed', 'SEGI_00063' => 'sgi', 'SEGI_10967' => 'sgi', 'SEGI_17510' => 'sgi', 'SEGI_24396' => 'sgi', 'SEGI_39719' => 'sgi', 'SEGI_41392' => 'sgi', 'SGA_v2.0_scaffold11G05794' => 'sas', 'SGA_v2.0_scaffold142G35607' => 'sas', 'SGA_v2.0_scaffold1G00447' => 'sas', 'SHI15388' => 'shi', 'SHI15394' => 'shi', 'SHI15396' => 'shi', 'SHI15399' => 'shi', 'SMO343G0151' => 'smo', 'SMO367G1118' => 'smo', 'Solyc01g080200.3' => 'sly', 'Solyc06g008960.3' => 'sly', 'Solyc09g064780.3' => 'sly', 'Sopen01g031980' => 'spe', 'Sopen06g003710' => 'spe', 'Sopen09g026460' => 'spe', 'Sp3g21240' => 'spa', 'Sp4g30030' => 'spa', 'TAR365G0022' => 'tar', 'TAR365G1023' => 'tar', 'TAR365G1253' => 'tar', 'TAR623G0078' => 'tar', 'TAR623G1721' => 'tar', 'TAR633G0959' => 'tar', 'THA.LOC104802225' => 'tha', 'THA.LOC104804769' => 'tha', 'THA.LOC104808660' => 'tha', 'THA.LOC104812792' => 'tha', 'Thecc.01G284000' => 'tca', 'Thecc.04G220600' => 'tca', 'Thecc.05G268900' => 'tca', 'Thecc.08G171100' => 'tca', 'Thhalv10001284m.g' => 'esa', 'Thhalv10019912m.g' => 'esa', 'TPR.G14189' => 'tpr', 'TPR.G18110' => 'tpr', 'TPR.G18130' => 'tpr', 'TPR.G18131' => 'tpr', 'TPR.G18140' => 'tpr', 'TPR.G24282' => 'tpr', 'TPR.G25221' => 'tpr', 'TPR.G29267' => 'tpr', 'TPR.G35315' => 'tpr', 'TPR.G36173' => 'tpr', 'TWI09G0794' => 'twi', 'TWI59G1348' => 'twi', 'TWI74G0430' => 'twi', 'unitig_26.g8940' => 'ugi', 'unitig_749.g13744' => 'ugi', 'unitig_749.g13745' => 'ugi', 'vmacro08269' => 'vma', 'vmacro14937' => 'vma', 'vmacro20401' => 'vma', 'VMungo0464G1349' => 'vmu', 'VMungo0540G0289' => 'vmu', 'VMungo1215G1590' => 'vmu', 'VMungo1309G0221' => 'vmu', 'VMungo1309G2815' => 'vmu', 'VMungo1383G0239' => 'vmu', 'VMungo1383G2910' => 'vmu', 'Zm00001eb095270' => 'zma', 'Zm00001eb095280' => 'zma', 'Zm00001eb111630' => 'zma', 'Zm00001eb237080' => 'zma', 'Zm00001eb273740' => 'zma', 'Zm00001eb285040' => 'zma', 'Zm00001eb330790' => 'zma', 'Zm00001eb337380' => 'zma' ) $gf_id = 'HOM05D001484' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001484' ) $data_identifier = 'HOM05D001484' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 2, 'aly' => (int) 2, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 22, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 7, 'hma' => (int) 2, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 7, 'mtr' => (int) 10, 'cme' => (int) 2, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 4, 'ppa' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 4, 'qlo' => (int) 9, 'rch' => (int) 6, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 10, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 7, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb337380' $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' => 'HOM05D001484', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p31500' => 'bna', 'A05p00020' => 'bna', 'A07p08820' => 'bna', 'Aa31LG4G3300' => 'aar', 'Aa31LG8G10030' => 'aar', 'Actinidia00731' => 'ach', 'Actinidia11473' => 'ach', 'Actinidia23469' => 'ach', 'Actinidia24318' => 'ach', 'Actinidia40196' => 'ach', 'Actinidia40197' => 'ach', 'Actinidia40198' => 'ach', 'Ah.08g212990' => 'amhyb', 'Ah.15g091720' => 'amhyb', 'AL3G38260' => 'aly', 'AL4G47710' => 'aly', 'Aqoxy2G00671' => 'aox', 'Aqoxy2G03236' => 'aox', 'arahy.Tifrunner.gnm1.ann1.05IDCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KR684' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATY3SJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK6QJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6APGL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IDT7Z9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM073U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ0R87' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LE7RV4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT4QRX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V5ENPK' => 'arhy', 'AT2G48110' => 'ath', 'AT3G23590' => 'ath', 'ATR0626G186' => 'atr', 'ATR1127G141' => 'atr', 'Atru.chr4.2583' => 'acertr', 'Atru.chr5.1358' => 'acertr', 'Atru.chr5.1359' => 'acertr', 'Atru.chr8.46' => 'acertr', 'AUR62002640' => 'cqu', 'AUR62030055' => 'cqu', 'AUR62033713' => 'cqu', 'AUR62033714' => 'cqu', 'AUR62036795' => 'cqu', 'AUR62039891' => 'cqu', 'BcaB02g08737' => 'bca', 'BcaB04g20441' => 'bca', 'BcaB06g26509' => 'bca', 'BcaB06g26510' => 'bca', 'BcaB06g26511' => 'bca', 'BcaB06g26512' => 'bca', 'BcaB06g26513' => 'bca', 'BcaC02g12564' => 'bca', 'BcaC02g12565' => 'bca', 'BcaC02g12794' => 'bca', 'BcaC02g12795' => 'bca', 'BcaC02g12796' => 'bca', 'BcaC06g35541' => 'bca', 'BNapus_Darmor_BZH_scaffold_188p00080' => 'bna', 'BNapus_Darmor_BZH_scaffold_188p00090' => 'bna', 'BolC1t03972H' => 'bol', 'BolC1t03973H' => 'bol', 'BolC4t21680H' => 'bol', 'BolC7t41863H' => 'bol', 'BolSC55t61227H' => 'bol', 'BolSC55t61228H' => 'bol', 'BraA01t03278Z' => 'bra', 'BraA05t18998Z' => 'bra', 'BraA07t28673Z' => 'bra', 'C01p40150' => 'bna', 'C05p12370' => 'bna', 'C07p13680' => 'bna', 'CAN.G1006.16' => 'can', 'CAN.G1006.17' => 'can', 'CAN.G1170.2' => 'can', 'CAN.G962.7' => 'can', 'CANSAT25G2179' => 'cansat', 'CANSAT78G1573' => 'cansat', 'CARHR099510' => 'chi', 'CARHR143510' => 'chi', 'Carub.0003s2380' => 'cru', 'Carub.0004s3082' => 'cru', 'Ca_00614_v3' => 'car', 'Ca_07801_v3' => 'car', 'Ca_08567_v3' => 'car', 'Ca_09571_v3' => 'car', 'CBR_g19290' => 'cbr', 'Cc01_g19770' => 'ccan', 'Cc03_g03030' => 'ccan', 'CDE07G0968' => 'cde', 'CDE09G1441' => 'cde', 'Cfa006103' => 'cfa', 'Cfa015573' => 'cfa', 'Cfa016988' => 'cfa', 'Ciclev10006738m.g' => 'ccl', 'Ciclev10010920m.g' => 'ccl', 'Ciclev10018517m.g' => 'ccl', 'CiPaw.01G159200' => 'cil', 'CiPaw.02G091000' => 'cil', 'CiPaw.02G091100' => 'cil', 'CiPaw.08G103100' => 'cil', 'CiPaw.09G224900' => 'cil', 'ClCG06G005740' => 'cla', 'ClCG07G000090' => 'cla', 'ClCG07G000100' => 'cla', 'COL.COLO4_09143' => 'col', 'COL.COLO4_25124' => 'col', 'Cpa.g.sc16.34' => 'cpa', 'Cpa.g.sc3504.1' => 'cpa', 'Cpa.g.sc60.37' => 'cpa', 'CsaV3_6G018520' => 'csa', 'CsaV3_6G036860' => 'csa', 'CSS0001072' => 'camsi', 'CSS0020208' => 'camsi', 'CSS0021253' => 'camsi', 'CSS0022190' => 'camsi', 'CSS0036150' => 'camsi', 'CSS0040442' => 'camsi', 'CSS0042300' => 'camsi', 'CSS0045298' => 'camsi', 'DCAR_012449' => 'dca', 'DCAR_018405' => 'dca', 'DCAR_024573' => 'dca', 'DCAR_030591' => 'dca', 'Dinv16926' => 'din', 'Dinv32963' => 'din', 'Dinv38382' => 'din', 'Dinv38383' => 'din', 'Duzib133G0974' => 'dzi', 'Duzib138G1867' => 'dzi', 'Duzib211G0420' => 'dzi', 'Duzib212G0930' => 'dzi', 'ECA234G1645' => 'eca', 'ECA247G3467' => 'eca', 'ECA248G1703' => 'eca', 'EL10Ac3g06327' => 'bvu', 'EL10Ac7g17204' => 'bvu', 'Eucgr.A00855' => 'egr', 'Eucgr.A00858' => 'egr', 'Eucgr.H01520' => 'egr', 'Eucgr.H03604' => 'egr', 'Eucgr.L03465' => 'egr', 'Eucgr.L03466' => 'egr', 'FAN01G0988' => 'fan', 'FAN02G3892' => 'fan', 'FAN05G3381' => 'fan', 'FAN07G0967' => 'fan', 'FAN07G1493' => 'fan', 'FAN08G3125' => 'fan', 'FAN09G0402' => 'fan', 'FAN12G2594' => 'fan', 'FAN12G3879' => 'fan', 'FAN14G1546' => 'fan', 'FAN15G3626' => 'fan', 'FAN17G0588' => 'fan', 'FAN17G0609' => 'fan', 'FAN18G2817' => 'fan', 'FAN19G1305' => 'fan', 'FAN20G1787' => 'fan', 'FAN22G0073' => 'fan', 'FAN22G0352' => 'fan', 'FAN22G0368' => 'fan', 'FAN22G2273' => 'fan', 'FAN24G1998' => 'fan', 'FAN27G1317' => 'fan', 'FvH4_2g23980' => 'fve', 'FvH4_4g14380' => 'fve', 'FvH4_4g14390' => 'fve', 'FvH4_6g09250' => 'fve', 'Glyma.03G151100' => 'gma', 'Glyma.04G122550' => 'gma', 'Glyma.05G001600' => 'gma', 'Glyma.09G270766' => 'gma', 'Glyma.09G270832' => 'gma', 'Glyma.13G209800' => 'gma', 'Glyma.15G102800' => 'gma', 'Glyma.18G218900' => 'gma', 'Glyma.19G001500' => 'gma', 'Glyma.19G153600' => 'gma', 'Gohir.A02G028600' => 'ghi', 'Gohir.A08G045000' => 'ghi', 'Gohir.A11G120500' => 'ghi', 'Gohir.A12G006200' => 'ghi', 'Gohir.A12G006250' => 'ghi', 'Gohir.D02G036300' => 'ghi', 'Gohir.D08G054700' => 'ghi', 'Gohir.D11G125600' => 'ghi', 'Gohir.D12G005700' => 'ghi', 'Gorai.004G055200' => 'gra', 'Gorai.005G040400' => 'gra', 'Gorai.007G134500' => 'gra', 'Gorai.008G005500' => 'gra', 'GSVIVG01011094001' => 'vvi', 'GSVIVG01017879001' => 'vvi', 'GSVIVG01025988001' => 'vvi', 'GSVIVG01029847001' => 'vvi', 'HanXRQChr10g0282901' => 'han', 'HanXRQChr10g0310371' => 'han', 'HanXRQChr10g0315041' => 'han', 'HanXRQChr11g0327651' => 'han', 'HanXRQChr12g0359391' => 'han', 'Haze_00972' => 'cav', 'Haze_00973' => 'cav', 'Haze_00974' => 'cav', 'Haze_04747' => 'cav', 'Haze_04749' => 'cav', 'Haze_04750' => 'cav', 'Haze_21217' => 'cav', 'Hma1.2p1_1037F.1_g250680' => 'hma', 'Hma1.2p1_1644F.1_g295320' => 'hma', 'HPP92_011322' => 'vpl', 'HPP92_011323' => 'vpl', 'HPP92_011324' => 'vpl', 'HPP92_011325' => 'vpl', 'HPP92_011326' => 'vpl', 'Hund12205' => 'sun', 'Hund17957' => 'sun', 'Lalb_Chr06g0176771' => 'lal', 'Lalb_Chr18g0056021' => 'lal', 'Lalb_Chr18g0056031' => 'lal', 'Lalb_Chr18g0056041' => 'lal', 'Lalb_Chr20g0107751' => 'lal', 'Lalb_Chr20g0118371' => 'lal', 'Lj1g0010239' => 'lja', 'Lj1g0017101' => 'lja', 'Lj2A1178G40' => 'lonja', 'Lj2A54G84' => 'lonja', 'Lj2g0015248' => 'lja', 'Lj3A761T51' => 'lonja', 'Lj6g0018116' => 'lja', 'Lsat_1_v5_gn_4_136040' => 'lsa', 'Lsat_1_v5_gn_5_187461' => 'lsa', 'Lsat_1_v5_gn_5_77001' => 'lsa', 'Lsat_1_v5_gn_9_4461' => 'lsa', 'Manes.01G210100' => 'mes', 'Manes.03G185600' => 'mes', 'Manes.05G073300' => 'mes', 'Manes.09G120300' => 'mes', 'Manes.15G022100' => 'mes', 'Mapoly0096s0053' => 'mpo', 'MBI03_g14058_MAGBIO' => 'mbi', 'MBI03_g33876_MAGBIO' => 'mbi', 'MBI03_g36854_MAGBIO' => 'mbi', 'MBI17_g11997_MAGBIO' => 'mbi', 'MD03G1269000' => 'mdo', 'MD04G1179600' => 'mdo', 'MD11G1289800' => 'mdo', 'MD12G1194700' => 'mdo', 'MD13G1182100' => 'mdo', 'MD13G1182200' => 'mdo', 'MD16G1182600' => 'mdo', 'Medtr2g021400' => 'mtr', 'Medtr2g021470' => 'mtr', 'Medtr2g105810' => 'mtr', 'Medtr3g033580' => 'mtr', 'Medtr6g007970' => 'mtr', 'Medtr7g056330' => 'mtr', 'Medtr7g074290' => 'mtr', 'Medtr7g074380' => 'mtr', 'Medtr7g094550' => 'mtr', 'Medtr8g069995' => 'mtr', 'MELO3C014345.2' => 'cme', 'MELO3C021395.2' => 'cme', 'Migut.D00262' => 'egut', 'Migut.G00257' => 'egut', 'MSTRG.21575' => 'ama', 'MSTRG.3985' => 'ama', 'Nitab4.5_0000295g0140' => 'nta', 'Nitab4.5_0000732g0140' => 'nta', 'Nitab4.5_0003162g0020' => 'nta', 'Nitab4.5_0006180g0090' => 'nta', 'Nitab4.5_0006390g0010' => 'nta', 'Nitab4.5_0007392g0040' => 'nta', 'Nn1g02140' => 'nnu', 'Nn4g26168' => 'nnu', 'Nn5g26754' => 'nnu', 'Oeu001433.1' => 'oeu', 'Oeu010299.2' => 'oeu', 'Oeu011171.1' => 'oeu', 'Oeu037675.1' => 'oeu', 'Oeu038359.1' => 'oeu', 'Oeu063834.1' => 'oeu', 'Oeu063835.1' => 'oeu', 'Os05g0312000' => 'osa', 'Os07g0211101' => 'osa', 'Os07g0211200' => 'osa', 'Os07g0681500' => 'osa', 'Peaxi162Scf00095g01015' => 'pax', 'Peaxi162Scf00104g00329' => 'pax', 'Peaxi162Scf00161g00137' => 'pax', 'PGR004G1665' => 'pgr', 'PGR031G2937' => 'pgr', 'PGR119G2145' => 'pgr', 'PGSC0003DMG400004351' => 'stu', 'PGSC0003DMG400014625' => 'stu', 'PGSC0003DMG401000943' => 'stu', 'Phvul.001G148600' => 'pvu', 'Phvul.004G001700' => 'pvu', 'Phvul.006G154900' => 'pvu', 'Phvul.008G078200' => 'pvu', 'Phvul.011G136500' => 'pvu', 'Potri.002G215600' => 'ptr', 'Potri.008G201600' => 'ptr', 'Potri.014G138400' => 'ptr', 'Potri.016G142500' => 'ptr', 'Pp3c16_10580' => 'ppa', 'Pp3c5_25280' => 'ppa', 'Prupe.1G150000' => 'ppe', 'Prupe.1G150100' => 'ppe', 'Prupe.6G299600' => 'ppe', 'Prupe.8G245000' => 'ppe', 'Psat0s4927g0040' => 'psa', 'Psat1g052080' => 'psa', 'Psat1g183800' => 'psa', 'Psat3g113840' => 'psa', 'Psat3g126120' => 'psa', 'Psat3g126160' => 'psa', 'Psat3g158760' => 'psa', 'Psat3g158840' => 'psa', 'PSO170G2858' => 'pso', 'PSO339G0606' => 'pso', 'PSO384G4709' => 'pso', 'PSO407G0334' => 'pso', 'QL04p040276' => 'qlo', 'QL06p005458' => 'qlo', 'QL06p005472' => 'qlo', 'QL07p030546' => 'qlo', 'QL07p031519' => 'qlo', 'QL09p050949' => 'qlo', 'QL09p050966' => 'qlo', 'QL09p051067' => 'qlo', 'QL12p022706' => 'qlo', 'RcHm_v2.0_Chr2g0119601' => 'rch', 'RcHm_v2.0_Chr3g0459591' => 'rch', 'RcHm_v2.0_Chr4g0418521' => 'rch', 'RcHm_v2.0_Chr4g0418531' => 'rch', 'RcHm_v2.0_Chr4g0418541' => 'rch', 'RcHm_v2.0_Chr6g0291641' => 'rch', 'Rhsim01G0086300' => 'rsi', 'Rhsim01G0276300' => 'rsi', 'Rhsim01G0276500' => 'rsi', 'Rhsim04G0207700' => 'rsi', 'Rhsim05G0234500' => 'rsi', 'Rhsim13G0022400' => 'rsi', 'Sabra02G0167900' => 'sbr', 'Sabra04G0158500' => 'sbr', 'Sabra08G0159800' => 'sbr', 'Sabra10G0011500' => 'sbr', 'Sabra14G0104400' => 'sbr', 'SalBow2G2440' => 'sbo', 'SalBow4G2265' => 'sbo', 'Sc02g0000060' => 'sci', 'Sc05g0005020' => 'sci', 'Sc13g0003890' => 'sci', 'Sed0014865' => 'sed', 'Sed0017224' => 'sed', 'Sed0026391' => 'sed', 'SEGI_00063' => 'sgi', 'SEGI_10967' => 'sgi', 'SEGI_17510' => 'sgi', 'SEGI_24396' => 'sgi', 'SEGI_39719' => 'sgi', 'SEGI_41392' => 'sgi', 'SGA_v2.0_scaffold11G05794' => 'sas', 'SGA_v2.0_scaffold142G35607' => 'sas', 'SGA_v2.0_scaffold1G00447' => 'sas', 'SHI15388' => 'shi', 'SHI15394' => 'shi', 'SHI15396' => 'shi', 'SHI15399' => 'shi', 'SMO343G0151' => 'smo', 'SMO367G1118' => 'smo', 'Solyc01g080200.3' => 'sly', 'Solyc06g008960.3' => 'sly', 'Solyc09g064780.3' => 'sly', 'Sopen01g031980' => 'spe', 'Sopen06g003710' => 'spe', 'Sopen09g026460' => 'spe', 'Sp3g21240' => 'spa', 'Sp4g30030' => 'spa', 'TAR365G0022' => 'tar', 'TAR365G1023' => 'tar', 'TAR365G1253' => 'tar', 'TAR623G0078' => 'tar', 'TAR623G1721' => 'tar', 'TAR633G0959' => 'tar', 'THA.LOC104802225' => 'tha', 'THA.LOC104804769' => 'tha', 'THA.LOC104808660' => 'tha', 'THA.LOC104812792' => 'tha', 'Thecc.01G284000' => 'tca', 'Thecc.04G220600' => 'tca', 'Thecc.05G268900' => 'tca', 'Thecc.08G171100' => 'tca', 'Thhalv10001284m.g' => 'esa', 'Thhalv10019912m.g' => 'esa', 'TPR.G14189' => 'tpr', 'TPR.G18110' => 'tpr', 'TPR.G18130' => 'tpr', 'TPR.G18131' => 'tpr', 'TPR.G18140' => 'tpr', 'TPR.G24282' => 'tpr', 'TPR.G25221' => 'tpr', 'TPR.G29267' => 'tpr', 'TPR.G35315' => 'tpr', 'TPR.G36173' => 'tpr', 'TWI09G0794' => 'twi', 'TWI59G1348' => 'twi', 'TWI74G0430' => 'twi', 'unitig_26.g8940' => 'ugi', 'unitig_749.g13744' => 'ugi', 'unitig_749.g13745' => 'ugi', 'vmacro08269' => 'vma', 'vmacro14937' => 'vma', 'vmacro20401' => 'vma', 'VMungo0464G1349' => 'vmu', 'VMungo0540G0289' => 'vmu', 'VMungo1215G1590' => 'vmu', 'VMungo1309G0221' => 'vmu', 'VMungo1309G2815' => 'vmu', 'VMungo1383G0239' => 'vmu', 'VMungo1383G2910' => 'vmu', 'Zm00001eb095270' => 'zma', 'Zm00001eb095280' => 'zma', 'Zm00001eb111630' => 'zma', 'Zm00001eb237080' => 'zma', 'Zm00001eb273740' => 'zma', 'Zm00001eb285040' => 'zma', 'Zm00001eb330790' => 'zma', 'Zm00001eb337380' => 'zma' ), 'gf_id' => 'HOM05D001484', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001484' ), 'data_identifier' => 'HOM05D001484', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001484', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p31500' => 'bna', 'A05p00020' => 'bna', 'A07p08820' => 'bna', 'Aa31LG4G3300' => 'aar', 'Aa31LG8G10030' => 'aar', 'Actinidia00731' => 'ach', 'Actinidia11473' => 'ach', 'Actinidia23469' => 'ach', 'Actinidia24318' => 'ach', 'Actinidia40196' => 'ach', 'Actinidia40197' => 'ach', 'Actinidia40198' => 'ach', 'Ah.08g212990' => 'amhyb', 'Ah.15g091720' => 'amhyb', 'AL3G38260' => 'aly', 'AL4G47710' => 'aly', 'Aqoxy2G00671' => 'aox', 'Aqoxy2G03236' => 'aox', 'arahy.Tifrunner.gnm1.ann1.05IDCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KR684' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATY3SJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK6QJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6APGL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IDT7Z9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM073U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ0R87' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LE7RV4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT4QRX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V5ENPK' => 'arhy', 'AT2G48110' => 'ath', 'AT3G23590' => 'ath', 'ATR0626G186' => 'atr', 'ATR1127G141' => 'atr', 'Atru.chr4.2583' => 'acertr', 'Atru.chr5.1358' => 'acertr', 'Atru.chr5.1359' => 'acertr', 'Atru.chr8.46' => 'acertr', 'AUR62002640' => 'cqu', 'AUR62030055' => 'cqu', 'AUR62033713' => 'cqu', 'AUR62033714' => 'cqu', 'AUR62036795' => 'cqu', 'AUR62039891' => 'cqu', 'BcaB02g08737' => 'bca', 'BcaB04g20441' => 'bca', 'BcaB06g26509' => 'bca', 'BcaB06g26510' => 'bca', 'BcaB06g26511' => 'bca', 'BcaB06g26512' => 'bca', 'BcaB06g26513' => 'bca', 'BcaC02g12564' => 'bca', 'BcaC02g12565' => 'bca', 'BcaC02g12794' => 'bca', 'BcaC02g12795' => 'bca', 'BcaC02g12796' => 'bca', 'BcaC06g35541' => 'bca', 'BNapus_Darmor_BZH_scaffold_188p00080' => 'bna', 'BNapus_Darmor_BZH_scaffold_188p00090' => 'bna', 'BolC1t03972H' => 'bol', 'BolC1t03973H' => 'bol', 'BolC4t21680H' => 'bol', 'BolC7t41863H' => 'bol', 'BolSC55t61227H' => 'bol', 'BolSC55t61228H' => 'bol', 'BraA01t03278Z' => 'bra', 'BraA05t18998Z' => 'bra', 'BraA07t28673Z' => 'bra', 'C01p40150' => 'bna', 'C05p12370' => 'bna', 'C07p13680' => 'bna', 'CAN.G1006.16' => 'can', 'CAN.G1006.17' => 'can', 'CAN.G1170.2' => 'can', 'CAN.G962.7' => 'can', 'CANSAT25G2179' => 'cansat', 'CANSAT78G1573' => 'cansat', 'CARHR099510' => 'chi', 'CARHR143510' => 'chi', 'Carub.0003s2380' => 'cru', 'Carub.0004s3082' => 'cru', 'Ca_00614_v3' => 'car', 'Ca_07801_v3' => 'car', 'Ca_08567_v3' => 'car', 'Ca_09571_v3' => 'car', 'CBR_g19290' => 'cbr', 'Cc01_g19770' => 'ccan', 'Cc03_g03030' => 'ccan', 'CDE07G0968' => 'cde', 'CDE09G1441' => 'cde', 'Cfa006103' => 'cfa', 'Cfa015573' => 'cfa', 'Cfa016988' => 'cfa', 'Ciclev10006738m.g' => 'ccl', 'Ciclev10010920m.g' => 'ccl', 'Ciclev10018517m.g' => 'ccl', 'CiPaw.01G159200' => 'cil', 'CiPaw.02G091000' => 'cil', 'CiPaw.02G091100' => 'cil', 'CiPaw.08G103100' => 'cil', 'CiPaw.09G224900' => 'cil', 'ClCG06G005740' => 'cla', 'ClCG07G000090' => 'cla', 'ClCG07G000100' => 'cla', 'COL.COLO4_09143' => 'col', 'COL.COLO4_25124' => 'col', 'Cpa.g.sc16.34' => 'cpa', 'Cpa.g.sc3504.1' => 'cpa', 'Cpa.g.sc60.37' => 'cpa', 'CsaV3_6G018520' => 'csa', 'CsaV3_6G036860' => 'csa', 'CSS0001072' => 'camsi', 'CSS0020208' => 'camsi', 'CSS0021253' => 'camsi', 'CSS0022190' => 'camsi', 'CSS0036150' => 'camsi', 'CSS0040442' => 'camsi', 'CSS0042300' => 'camsi', 'CSS0045298' => 'camsi', 'DCAR_012449' => 'dca', 'DCAR_018405' => 'dca', 'DCAR_024573' => 'dca', 'DCAR_030591' => 'dca', 'Dinv16926' => 'din', 'Dinv32963' => 'din', 'Dinv38382' => 'din', 'Dinv38383' => 'din', 'Duzib133G0974' => 'dzi', 'Duzib138G1867' => 'dzi', 'Duzib211G0420' => 'dzi', 'Duzib212G0930' => 'dzi', 'ECA234G1645' => 'eca', 'ECA247G3467' => 'eca', 'ECA248G1703' => 'eca', 'EL10Ac3g06327' => 'bvu', 'EL10Ac7g17204' => 'bvu', 'Eucgr.A00855' => 'egr', 'Eucgr.A00858' => 'egr', 'Eucgr.H01520' => 'egr', 'Eucgr.H03604' => 'egr', 'Eucgr.L03465' => 'egr', 'Eucgr.L03466' => 'egr', 'FAN01G0988' => 'fan', 'FAN02G3892' => 'fan', 'FAN05G3381' => 'fan', 'FAN07G0967' => 'fan', 'FAN07G1493' => 'fan', 'FAN08G3125' => 'fan', 'FAN09G0402' => 'fan', 'FAN12G2594' => 'fan', 'FAN12G3879' => 'fan', 'FAN14G1546' => 'fan', 'FAN15G3626' => 'fan', 'FAN17G0588' => 'fan', 'FAN17G0609' => 'fan', 'FAN18G2817' => 'fan', 'FAN19G1305' => 'fan', 'FAN20G1787' => 'fan', 'FAN22G0073' => 'fan', 'FAN22G0352' => 'fan', 'FAN22G0368' => 'fan', 'FAN22G2273' => 'fan', 'FAN24G1998' => 'fan', 'FAN27G1317' => 'fan', 'FvH4_2g23980' => 'fve', 'FvH4_4g14380' => 'fve', 'FvH4_4g14390' => 'fve', 'FvH4_6g09250' => 'fve', 'Glyma.03G151100' => 'gma', 'Glyma.04G122550' => 'gma', 'Glyma.05G001600' => 'gma', 'Glyma.09G270766' => 'gma', 'Glyma.09G270832' => 'gma', 'Glyma.13G209800' => 'gma', 'Glyma.15G102800' => 'gma', 'Glyma.18G218900' => 'gma', 'Glyma.19G001500' => 'gma', 'Glyma.19G153600' => 'gma', 'Gohir.A02G028600' => 'ghi', 'Gohir.A08G045000' => 'ghi', 'Gohir.A11G120500' => 'ghi', 'Gohir.A12G006200' => 'ghi', 'Gohir.A12G006250' => 'ghi', 'Gohir.D02G036300' => 'ghi', 'Gohir.D08G054700' => 'ghi', 'Gohir.D11G125600' => 'ghi', 'Gohir.D12G005700' => 'ghi', 'Gorai.004G055200' => 'gra', 'Gorai.005G040400' => 'gra', 'Gorai.007G134500' => 'gra', 'Gorai.008G005500' => 'gra', 'GSVIVG01011094001' => 'vvi', 'GSVIVG01017879001' => 'vvi', 'GSVIVG01025988001' => 'vvi', 'GSVIVG01029847001' => 'vvi', 'HanXRQChr10g0282901' => 'han', 'HanXRQChr10g0310371' => 'han', 'HanXRQChr10g0315041' => 'han', 'HanXRQChr11g0327651' => 'han', 'HanXRQChr12g0359391' => 'han', 'Haze_00972' => 'cav', 'Haze_00973' => 'cav', 'Haze_00974' => 'cav', 'Haze_04747' => 'cav', 'Haze_04749' => 'cav', 'Haze_04750' => 'cav', 'Haze_21217' => 'cav', 'Hma1.2p1_1037F.1_g250680' => 'hma', 'Hma1.2p1_1644F.1_g295320' => 'hma', 'HPP92_011322' => 'vpl', 'HPP92_011323' => 'vpl', 'HPP92_011324' => 'vpl', 'HPP92_011325' => 'vpl', 'HPP92_011326' => 'vpl', 'Hund12205' => 'sun', 'Hund17957' => 'sun', 'Lalb_Chr06g0176771' => 'lal', 'Lalb_Chr18g0056021' => 'lal', 'Lalb_Chr18g0056031' => 'lal', 'Lalb_Chr18g0056041' => 'lal', 'Lalb_Chr20g0107751' => 'lal', 'Lalb_Chr20g0118371' => 'lal', 'Lj1g0010239' => 'lja', 'Lj1g0017101' => 'lja', 'Lj2A1178G40' => 'lonja', 'Lj2A54G84' => 'lonja', 'Lj2g0015248' => 'lja', 'Lj3A761T51' => 'lonja', 'Lj6g0018116' => 'lja', 'Lsat_1_v5_gn_4_136040' => 'lsa', 'Lsat_1_v5_gn_5_187461' => 'lsa', 'Lsat_1_v5_gn_5_77001' => 'lsa', 'Lsat_1_v5_gn_9_4461' => 'lsa', 'Manes.01G210100' => 'mes', 'Manes.03G185600' => 'mes', 'Manes.05G073300' => 'mes', 'Manes.09G120300' => 'mes', 'Manes.15G022100' => 'mes', 'Mapoly0096s0053' => 'mpo', 'MBI03_g14058_MAGBIO' => 'mbi', 'MBI03_g33876_MAGBIO' => 'mbi', 'MBI03_g36854_MAGBIO' => 'mbi', 'MBI17_g11997_MAGBIO' => 'mbi', 'MD03G1269000' => 'mdo', 'MD04G1179600' => 'mdo', 'MD11G1289800' => 'mdo', 'MD12G1194700' => 'mdo', 'MD13G1182100' => 'mdo', 'MD13G1182200' => 'mdo', 'MD16G1182600' => 'mdo', 'Medtr2g021400' => 'mtr', 'Medtr2g021470' => 'mtr', 'Medtr2g105810' => 'mtr', 'Medtr3g033580' => 'mtr', 'Medtr6g007970' => 'mtr', 'Medtr7g056330' => 'mtr', 'Medtr7g074290' => 'mtr', 'Medtr7g074380' => 'mtr', 'Medtr7g094550' => 'mtr', 'Medtr8g069995' => 'mtr', 'MELO3C014345.2' => 'cme', 'MELO3C021395.2' => 'cme', 'Migut.D00262' => 'egut', 'Migut.G00257' => 'egut', 'MSTRG.21575' => 'ama', 'MSTRG.3985' => 'ama', 'Nitab4.5_0000295g0140' => 'nta', 'Nitab4.5_0000732g0140' => 'nta', 'Nitab4.5_0003162g0020' => 'nta', 'Nitab4.5_0006180g0090' => 'nta', 'Nitab4.5_0006390g0010' => 'nta', 'Nitab4.5_0007392g0040' => 'nta', 'Nn1g02140' => 'nnu', 'Nn4g26168' => 'nnu', 'Nn5g26754' => 'nnu', 'Oeu001433.1' => 'oeu', 'Oeu010299.2' => 'oeu', 'Oeu011171.1' => 'oeu', 'Oeu037675.1' => 'oeu', 'Oeu038359.1' => 'oeu', 'Oeu063834.1' => 'oeu', 'Oeu063835.1' => 'oeu', 'Os05g0312000' => 'osa', 'Os07g0211101' => 'osa', 'Os07g0211200' => 'osa', 'Os07g0681500' => 'osa', 'Peaxi162Scf00095g01015' => 'pax', 'Peaxi162Scf00104g00329' => 'pax', 'Peaxi162Scf00161g00137' => 'pax', 'PGR004G1665' => 'pgr', 'PGR031G2937' => 'pgr', 'PGR119G2145' => 'pgr', 'PGSC0003DMG400004351' => 'stu', 'PGSC0003DMG400014625' => 'stu', 'PGSC0003DMG401000943' => 'stu', 'Phvul.001G148600' => 'pvu', 'Phvul.004G001700' => 'pvu', 'Phvul.006G154900' => 'pvu', 'Phvul.008G078200' => 'pvu', 'Phvul.011G136500' => 'pvu', 'Potri.002G215600' => 'ptr', 'Potri.008G201600' => 'ptr', 'Potri.014G138400' => 'ptr', 'Potri.016G142500' => 'ptr', 'Pp3c16_10580' => 'ppa', 'Pp3c5_25280' => 'ppa', 'Prupe.1G150000' => 'ppe', 'Prupe.1G150100' => 'ppe', 'Prupe.6G299600' => 'ppe', 'Prupe.8G245000' => 'ppe', 'Psat0s4927g0040' => 'psa', 'Psat1g052080' => 'psa', 'Psat1g183800' => 'psa', 'Psat3g113840' => 'psa', 'Psat3g126120' => 'psa', 'Psat3g126160' => 'psa', 'Psat3g158760' => 'psa', 'Psat3g158840' => 'psa', 'PSO170G2858' => 'pso', 'PSO339G0606' => 'pso', 'PSO384G4709' => 'pso', 'PSO407G0334' => 'pso', 'QL04p040276' => 'qlo', 'QL06p005458' => 'qlo', 'QL06p005472' => 'qlo', 'QL07p030546' => 'qlo', 'QL07p031519' => 'qlo', 'QL09p050949' => 'qlo', 'QL09p050966' => 'qlo', 'QL09p051067' => 'qlo', 'QL12p022706' => 'qlo', 'RcHm_v2.0_Chr2g0119601' => 'rch', 'RcHm_v2.0_Chr3g0459591' => 'rch', 'RcHm_v2.0_Chr4g0418521' => 'rch', 'RcHm_v2.0_Chr4g0418531' => 'rch', 'RcHm_v2.0_Chr4g0418541' => 'rch', 'RcHm_v2.0_Chr6g0291641' => 'rch', 'Rhsim01G0086300' => 'rsi', 'Rhsim01G0276300' => 'rsi', 'Rhsim01G0276500' => 'rsi', 'Rhsim04G0207700' => 'rsi', 'Rhsim05G0234500' => 'rsi', 'Rhsim13G0022400' => 'rsi', 'Sabra02G0167900' => 'sbr', 'Sabra04G0158500' => 'sbr', 'Sabra08G0159800' => 'sbr', 'Sabra10G0011500' => 'sbr', 'Sabra14G0104400' => 'sbr', 'SalBow2G2440' => 'sbo', 'SalBow4G2265' => 'sbo', 'Sc02g0000060' => 'sci', 'Sc05g0005020' => 'sci', 'Sc13g0003890' => 'sci', 'Sed0014865' => 'sed', 'Sed0017224' => 'sed', 'Sed0026391' => 'sed', 'SEGI_00063' => 'sgi', 'SEGI_10967' => 'sgi', 'SEGI_17510' => 'sgi', 'SEGI_24396' => 'sgi', 'SEGI_39719' => 'sgi', 'SEGI_41392' => 'sgi', 'SGA_v2.0_scaffold11G05794' => 'sas', 'SGA_v2.0_scaffold142G35607' => 'sas', 'SGA_v2.0_scaffold1G00447' => 'sas', 'SHI15388' => 'shi', 'SHI15394' => 'shi', 'SHI15396' => 'shi', 'SHI15399' => 'shi', 'SMO343G0151' => 'smo', 'SMO367G1118' => 'smo', 'Solyc01g080200.3' => 'sly', 'Solyc06g008960.3' => 'sly', 'Solyc09g064780.3' => 'sly', 'Sopen01g031980' => 'spe', 'Sopen06g003710' => 'spe', 'Sopen09g026460' => 'spe', 'Sp3g21240' => 'spa', 'Sp4g30030' => 'spa', 'TAR365G0022' => 'tar', 'TAR365G1023' => 'tar', 'TAR365G1253' => 'tar', 'TAR623G0078' => 'tar', 'TAR623G1721' => 'tar', 'TAR633G0959' => 'tar', 'THA.LOC104802225' => 'tha', 'THA.LOC104804769' => 'tha', 'THA.LOC104808660' => 'tha', 'THA.LOC104812792' => 'tha', 'Thecc.01G284000' => 'tca', 'Thecc.04G220600' => 'tca', 'Thecc.05G268900' => 'tca', 'Thecc.08G171100' => 'tca', 'Thhalv10001284m.g' => 'esa', 'Thhalv10019912m.g' => 'esa', 'TPR.G14189' => 'tpr', 'TPR.G18110' => 'tpr', 'TPR.G18130' => 'tpr', 'TPR.G18131' => 'tpr', 'TPR.G18140' => 'tpr', 'TPR.G24282' => 'tpr', 'TPR.G25221' => 'tpr', 'TPR.G29267' => 'tpr', 'TPR.G35315' => 'tpr', 'TPR.G36173' => 'tpr', 'TWI09G0794' => 'twi', 'TWI59G1348' => 'twi', 'TWI74G0430' => 'twi', 'unitig_26.g8940' => 'ugi', 'unitig_749.g13744' => 'ugi', 'unitig_749.g13745' => 'ugi', 'vmacro08269' => 'vma', 'vmacro14937' => 'vma', 'vmacro20401' => 'vma', 'VMungo0464G1349' => 'vmu', 'VMungo0540G0289' => 'vmu', 'VMungo1215G1590' => 'vmu', 'VMungo1309G0221' => 'vmu', 'VMungo1309G2815' => 'vmu', 'VMungo1383G0239' => 'vmu', 'VMungo1383G2910' => 'vmu', 'Zm00001eb095270' => 'zma', 'Zm00001eb095280' => 'zma', 'Zm00001eb111630' => 'zma', 'Zm00001eb237080' => 'zma', 'Zm00001eb273740' => 'zma', 'Zm00001eb285040' => 'zma', 'Zm00001eb330790' => 'zma', 'Zm00001eb337380' => 'zma' ) $gf_id = 'HOM05D001484' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001484' ) $data_identifier = 'HOM05D001484' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 2, 'aly' => (int) 2, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 22, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 7, 'hma' => (int) 2, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 7, 'mtr' => (int) 10, 'cme' => (int) 2, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 4, 'ppa' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 4, 'qlo' => (int) 9, 'rch' => (int) 6, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 10, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 7, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb337380' $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' => 'HOM05D001484', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p31500' => 'bna', 'A05p00020' => 'bna', 'A07p08820' => 'bna', 'Aa31LG4G3300' => 'aar', 'Aa31LG8G10030' => 'aar', 'Actinidia00731' => 'ach', 'Actinidia11473' => 'ach', 'Actinidia23469' => 'ach', 'Actinidia24318' => 'ach', 'Actinidia40196' => 'ach', 'Actinidia40197' => 'ach', 'Actinidia40198' => 'ach', 'Ah.08g212990' => 'amhyb', 'Ah.15g091720' => 'amhyb', 'AL3G38260' => 'aly', 'AL4G47710' => 'aly', 'Aqoxy2G00671' => 'aox', 'Aqoxy2G03236' => 'aox', 'arahy.Tifrunner.gnm1.ann1.05IDCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KR684' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATY3SJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK6QJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6APGL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IDT7Z9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM073U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ0R87' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LE7RV4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT4QRX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V5ENPK' => 'arhy', 'AT2G48110' => 'ath', 'AT3G23590' => 'ath', 'ATR0626G186' => 'atr', 'ATR1127G141' => 'atr', 'Atru.chr4.2583' => 'acertr', 'Atru.chr5.1358' => 'acertr', 'Atru.chr5.1359' => 'acertr', 'Atru.chr8.46' => 'acertr', 'AUR62002640' => 'cqu', 'AUR62030055' => 'cqu', 'AUR62033713' => 'cqu', 'AUR62033714' => 'cqu', 'AUR62036795' => 'cqu', 'AUR62039891' => 'cqu', 'BcaB02g08737' => 'bca', 'BcaB04g20441' => 'bca', 'BcaB06g26509' => 'bca', 'BcaB06g26510' => 'bca', 'BcaB06g26511' => 'bca', 'BcaB06g26512' => 'bca', 'BcaB06g26513' => 'bca', 'BcaC02g12564' => 'bca', 'BcaC02g12565' => 'bca', 'BcaC02g12794' => 'bca', 'BcaC02g12795' => 'bca', 'BcaC02g12796' => 'bca', 'BcaC06g35541' => 'bca', 'BNapus_Darmor_BZH_scaffold_188p00080' => 'bna', 'BNapus_Darmor_BZH_scaffold_188p00090' => 'bna', 'BolC1t03972H' => 'bol', 'BolC1t03973H' => 'bol', 'BolC4t21680H' => 'bol', 'BolC7t41863H' => 'bol', 'BolSC55t61227H' => 'bol', 'BolSC55t61228H' => 'bol', 'BraA01t03278Z' => 'bra', 'BraA05t18998Z' => 'bra', 'BraA07t28673Z' => 'bra', 'C01p40150' => 'bna', 'C05p12370' => 'bna', 'C07p13680' => 'bna', 'CAN.G1006.16' => 'can', 'CAN.G1006.17' => 'can', 'CAN.G1170.2' => 'can', 'CAN.G962.7' => 'can', 'CANSAT25G2179' => 'cansat', 'CANSAT78G1573' => 'cansat', 'CARHR099510' => 'chi', 'CARHR143510' => 'chi', 'Carub.0003s2380' => 'cru', 'Carub.0004s3082' => 'cru', 'Ca_00614_v3' => 'car', 'Ca_07801_v3' => 'car', 'Ca_08567_v3' => 'car', 'Ca_09571_v3' => 'car', 'CBR_g19290' => 'cbr', 'Cc01_g19770' => 'ccan', 'Cc03_g03030' => 'ccan', 'CDE07G0968' => 'cde', 'CDE09G1441' => 'cde', 'Cfa006103' => 'cfa', 'Cfa015573' => 'cfa', 'Cfa016988' => 'cfa', 'Ciclev10006738m.g' => 'ccl', 'Ciclev10010920m.g' => 'ccl', 'Ciclev10018517m.g' => 'ccl', 'CiPaw.01G159200' => 'cil', 'CiPaw.02G091000' => 'cil', 'CiPaw.02G091100' => 'cil', 'CiPaw.08G103100' => 'cil', 'CiPaw.09G224900' => 'cil', 'ClCG06G005740' => 'cla', 'ClCG07G000090' => 'cla', 'ClCG07G000100' => 'cla', 'COL.COLO4_09143' => 'col', 'COL.COLO4_25124' => 'col', 'Cpa.g.sc16.34' => 'cpa', 'Cpa.g.sc3504.1' => 'cpa', 'Cpa.g.sc60.37' => 'cpa', 'CsaV3_6G018520' => 'csa', 'CsaV3_6G036860' => 'csa', 'CSS0001072' => 'camsi', 'CSS0020208' => 'camsi', 'CSS0021253' => 'camsi', 'CSS0022190' => 'camsi', 'CSS0036150' => 'camsi', 'CSS0040442' => 'camsi', 'CSS0042300' => 'camsi', 'CSS0045298' => 'camsi', 'DCAR_012449' => 'dca', 'DCAR_018405' => 'dca', 'DCAR_024573' => 'dca', 'DCAR_030591' => 'dca', 'Dinv16926' => 'din', 'Dinv32963' => 'din', 'Dinv38382' => 'din', 'Dinv38383' => 'din', 'Duzib133G0974' => 'dzi', 'Duzib138G1867' => 'dzi', 'Duzib211G0420' => 'dzi', 'Duzib212G0930' => 'dzi', 'ECA234G1645' => 'eca', 'ECA247G3467' => 'eca', 'ECA248G1703' => 'eca', 'EL10Ac3g06327' => 'bvu', 'EL10Ac7g17204' => 'bvu', 'Eucgr.A00855' => 'egr', 'Eucgr.A00858' => 'egr', 'Eucgr.H01520' => 'egr', 'Eucgr.H03604' => 'egr', 'Eucgr.L03465' => 'egr', 'Eucgr.L03466' => 'egr', 'FAN01G0988' => 'fan', 'FAN02G3892' => 'fan', 'FAN05G3381' => 'fan', 'FAN07G0967' => 'fan', 'FAN07G1493' => 'fan', 'FAN08G3125' => 'fan', 'FAN09G0402' => 'fan', 'FAN12G2594' => 'fan', 'FAN12G3879' => 'fan', 'FAN14G1546' => 'fan', 'FAN15G3626' => 'fan', 'FAN17G0588' => 'fan', 'FAN17G0609' => 'fan', 'FAN18G2817' => 'fan', 'FAN19G1305' => 'fan', 'FAN20G1787' => 'fan', 'FAN22G0073' => 'fan', 'FAN22G0352' => 'fan', 'FAN22G0368' => 'fan', 'FAN22G2273' => 'fan', 'FAN24G1998' => 'fan', 'FAN27G1317' => 'fan', 'FvH4_2g23980' => 'fve', 'FvH4_4g14380' => 'fve', 'FvH4_4g14390' => 'fve', 'FvH4_6g09250' => 'fve', 'Glyma.03G151100' => 'gma', 'Glyma.04G122550' => 'gma', 'Glyma.05G001600' => 'gma', 'Glyma.09G270766' => 'gma', 'Glyma.09G270832' => 'gma', 'Glyma.13G209800' => 'gma', 'Glyma.15G102800' => 'gma', 'Glyma.18G218900' => 'gma', 'Glyma.19G001500' => 'gma', 'Glyma.19G153600' => 'gma', 'Gohir.A02G028600' => 'ghi', 'Gohir.A08G045000' => 'ghi', 'Gohir.A11G120500' => 'ghi', 'Gohir.A12G006200' => 'ghi', 'Gohir.A12G006250' => 'ghi', 'Gohir.D02G036300' => 'ghi', 'Gohir.D08G054700' => 'ghi', 'Gohir.D11G125600' => 'ghi', 'Gohir.D12G005700' => 'ghi', 'Gorai.004G055200' => 'gra', 'Gorai.005G040400' => 'gra', 'Gorai.007G134500' => 'gra', 'Gorai.008G005500' => 'gra', 'GSVIVG01011094001' => 'vvi', 'GSVIVG01017879001' => 'vvi', 'GSVIVG01025988001' => 'vvi', 'GSVIVG01029847001' => 'vvi', 'HanXRQChr10g0282901' => 'han', 'HanXRQChr10g0310371' => 'han', 'HanXRQChr10g0315041' => 'han', 'HanXRQChr11g0327651' => 'han', 'HanXRQChr12g0359391' => 'han', 'Haze_00972' => 'cav', 'Haze_00973' => 'cav', 'Haze_00974' => 'cav', 'Haze_04747' => 'cav', 'Haze_04749' => 'cav', 'Haze_04750' => 'cav', 'Haze_21217' => 'cav', 'Hma1.2p1_1037F.1_g250680' => 'hma', 'Hma1.2p1_1644F.1_g295320' => 'hma', 'HPP92_011322' => 'vpl', 'HPP92_011323' => 'vpl', 'HPP92_011324' => 'vpl', 'HPP92_011325' => 'vpl', 'HPP92_011326' => 'vpl', 'Hund12205' => 'sun', 'Hund17957' => 'sun', 'Lalb_Chr06g0176771' => 'lal', 'Lalb_Chr18g0056021' => 'lal', 'Lalb_Chr18g0056031' => 'lal', 'Lalb_Chr18g0056041' => 'lal', 'Lalb_Chr20g0107751' => 'lal', 'Lalb_Chr20g0118371' => 'lal', 'Lj1g0010239' => 'lja', 'Lj1g0017101' => 'lja', 'Lj2A1178G40' => 'lonja', 'Lj2A54G84' => 'lonja', 'Lj2g0015248' => 'lja', 'Lj3A761T51' => 'lonja', 'Lj6g0018116' => 'lja', 'Lsat_1_v5_gn_4_136040' => 'lsa', 'Lsat_1_v5_gn_5_187461' => 'lsa', 'Lsat_1_v5_gn_5_77001' => 'lsa', 'Lsat_1_v5_gn_9_4461' => 'lsa', 'Manes.01G210100' => 'mes', 'Manes.03G185600' => 'mes', 'Manes.05G073300' => 'mes', 'Manes.09G120300' => 'mes', 'Manes.15G022100' => 'mes', 'Mapoly0096s0053' => 'mpo', 'MBI03_g14058_MAGBIO' => 'mbi', 'MBI03_g33876_MAGBIO' => 'mbi', 'MBI03_g36854_MAGBIO' => 'mbi', 'MBI17_g11997_MAGBIO' => 'mbi', 'MD03G1269000' => 'mdo', 'MD04G1179600' => 'mdo', 'MD11G1289800' => 'mdo', 'MD12G1194700' => 'mdo', 'MD13G1182100' => 'mdo', 'MD13G1182200' => 'mdo', 'MD16G1182600' => 'mdo', 'Medtr2g021400' => 'mtr', 'Medtr2g021470' => 'mtr', 'Medtr2g105810' => 'mtr', 'Medtr3g033580' => 'mtr', 'Medtr6g007970' => 'mtr', 'Medtr7g056330' => 'mtr', 'Medtr7g074290' => 'mtr', 'Medtr7g074380' => 'mtr', 'Medtr7g094550' => 'mtr', 'Medtr8g069995' => 'mtr', 'MELO3C014345.2' => 'cme', 'MELO3C021395.2' => 'cme', 'Migut.D00262' => 'egut', 'Migut.G00257' => 'egut', 'MSTRG.21575' => 'ama', 'MSTRG.3985' => 'ama', 'Nitab4.5_0000295g0140' => 'nta', 'Nitab4.5_0000732g0140' => 'nta', 'Nitab4.5_0003162g0020' => 'nta', 'Nitab4.5_0006180g0090' => 'nta', 'Nitab4.5_0006390g0010' => 'nta', 'Nitab4.5_0007392g0040' => 'nta', 'Nn1g02140' => 'nnu', 'Nn4g26168' => 'nnu', 'Nn5g26754' => 'nnu', 'Oeu001433.1' => 'oeu', 'Oeu010299.2' => 'oeu', 'Oeu011171.1' => 'oeu', 'Oeu037675.1' => 'oeu', 'Oeu038359.1' => 'oeu', 'Oeu063834.1' => 'oeu', 'Oeu063835.1' => 'oeu', 'Os05g0312000' => 'osa', 'Os07g0211101' => 'osa', 'Os07g0211200' => 'osa', 'Os07g0681500' => 'osa', 'Peaxi162Scf00095g01015' => 'pax', 'Peaxi162Scf00104g00329' => 'pax', 'Peaxi162Scf00161g00137' => 'pax', 'PGR004G1665' => 'pgr', 'PGR031G2937' => 'pgr', 'PGR119G2145' => 'pgr', 'PGSC0003DMG400004351' => 'stu', 'PGSC0003DMG400014625' => 'stu', 'PGSC0003DMG401000943' => 'stu', 'Phvul.001G148600' => 'pvu', 'Phvul.004G001700' => 'pvu', 'Phvul.006G154900' => 'pvu', 'Phvul.008G078200' => 'pvu', 'Phvul.011G136500' => 'pvu', 'Potri.002G215600' => 'ptr', 'Potri.008G201600' => 'ptr', 'Potri.014G138400' => 'ptr', 'Potri.016G142500' => 'ptr', 'Pp3c16_10580' => 'ppa', 'Pp3c5_25280' => 'ppa', 'Prupe.1G150000' => 'ppe', 'Prupe.1G150100' => 'ppe', 'Prupe.6G299600' => 'ppe', 'Prupe.8G245000' => 'ppe', 'Psat0s4927g0040' => 'psa', 'Psat1g052080' => 'psa', 'Psat1g183800' => 'psa', 'Psat3g113840' => 'psa', 'Psat3g126120' => 'psa', 'Psat3g126160' => 'psa', 'Psat3g158760' => 'psa', 'Psat3g158840' => 'psa', 'PSO170G2858' => 'pso', 'PSO339G0606' => 'pso', 'PSO384G4709' => 'pso', 'PSO407G0334' => 'pso', 'QL04p040276' => 'qlo', 'QL06p005458' => 'qlo', 'QL06p005472' => 'qlo', 'QL07p030546' => 'qlo', 'QL07p031519' => 'qlo', 'QL09p050949' => 'qlo', 'QL09p050966' => 'qlo', 'QL09p051067' => 'qlo', 'QL12p022706' => 'qlo', 'RcHm_v2.0_Chr2g0119601' => 'rch', 'RcHm_v2.0_Chr3g0459591' => 'rch', 'RcHm_v2.0_Chr4g0418521' => 'rch', 'RcHm_v2.0_Chr4g0418531' => 'rch', 'RcHm_v2.0_Chr4g0418541' => 'rch', 'RcHm_v2.0_Chr6g0291641' => 'rch', 'Rhsim01G0086300' => 'rsi', 'Rhsim01G0276300' => 'rsi', 'Rhsim01G0276500' => 'rsi', 'Rhsim04G0207700' => 'rsi', 'Rhsim05G0234500' => 'rsi', 'Rhsim13G0022400' => 'rsi', 'Sabra02G0167900' => 'sbr', 'Sabra04G0158500' => 'sbr', 'Sabra08G0159800' => 'sbr', 'Sabra10G0011500' => 'sbr', 'Sabra14G0104400' => 'sbr', 'SalBow2G2440' => 'sbo', 'SalBow4G2265' => 'sbo', 'Sc02g0000060' => 'sci', 'Sc05g0005020' => 'sci', 'Sc13g0003890' => 'sci', 'Sed0014865' => 'sed', 'Sed0017224' => 'sed', 'Sed0026391' => 'sed', 'SEGI_00063' => 'sgi', 'SEGI_10967' => 'sgi', 'SEGI_17510' => 'sgi', 'SEGI_24396' => 'sgi', 'SEGI_39719' => 'sgi', 'SEGI_41392' => 'sgi', 'SGA_v2.0_scaffold11G05794' => 'sas', 'SGA_v2.0_scaffold142G35607' => 'sas', 'SGA_v2.0_scaffold1G00447' => 'sas', 'SHI15388' => 'shi', 'SHI15394' => 'shi', 'SHI15396' => 'shi', 'SHI15399' => 'shi', 'SMO343G0151' => 'smo', 'SMO367G1118' => 'smo', 'Solyc01g080200.3' => 'sly', 'Solyc06g008960.3' => 'sly', 'Solyc09g064780.3' => 'sly', 'Sopen01g031980' => 'spe', 'Sopen06g003710' => 'spe', 'Sopen09g026460' => 'spe', 'Sp3g21240' => 'spa', 'Sp4g30030' => 'spa', 'TAR365G0022' => 'tar', 'TAR365G1023' => 'tar', 'TAR365G1253' => 'tar', 'TAR623G0078' => 'tar', 'TAR623G1721' => 'tar', 'TAR633G0959' => 'tar', 'THA.LOC104802225' => 'tha', 'THA.LOC104804769' => 'tha', 'THA.LOC104808660' => 'tha', 'THA.LOC104812792' => 'tha', 'Thecc.01G284000' => 'tca', 'Thecc.04G220600' => 'tca', 'Thecc.05G268900' => 'tca', 'Thecc.08G171100' => 'tca', 'Thhalv10001284m.g' => 'esa', 'Thhalv10019912m.g' => 'esa', 'TPR.G14189' => 'tpr', 'TPR.G18110' => 'tpr', 'TPR.G18130' => 'tpr', 'TPR.G18131' => 'tpr', 'TPR.G18140' => 'tpr', 'TPR.G24282' => 'tpr', 'TPR.G25221' => 'tpr', 'TPR.G29267' => 'tpr', 'TPR.G35315' => 'tpr', 'TPR.G36173' => 'tpr', 'TWI09G0794' => 'twi', 'TWI59G1348' => 'twi', 'TWI74G0430' => 'twi', 'unitig_26.g8940' => 'ugi', 'unitig_749.g13744' => 'ugi', 'unitig_749.g13745' => 'ugi', 'vmacro08269' => 'vma', 'vmacro14937' => 'vma', 'vmacro20401' => 'vma', 'VMungo0464G1349' => 'vmu', 'VMungo0540G0289' => 'vmu', 'VMungo1215G1590' => 'vmu', 'VMungo1309G0221' => 'vmu', 'VMungo1309G2815' => 'vmu', 'VMungo1383G0239' => 'vmu', 'VMungo1383G2910' => 'vmu', 'Zm00001eb095270' => 'zma', 'Zm00001eb095280' => 'zma', 'Zm00001eb111630' => 'zma', 'Zm00001eb237080' => 'zma', 'Zm00001eb273740' => 'zma', 'Zm00001eb285040' => 'zma', 'Zm00001eb330790' => 'zma', 'Zm00001eb337380' => 'zma' ), 'gf_id' => 'HOM05D001484', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001484' ), 'data_identifier' => 'HOM05D001484', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001484', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p31500' => 'bna', 'A05p00020' => 'bna', 'A07p08820' => 'bna', 'Aa31LG4G3300' => 'aar', 'Aa31LG8G10030' => 'aar', 'Actinidia00731' => 'ach', 'Actinidia11473' => 'ach', 'Actinidia23469' => 'ach', 'Actinidia24318' => 'ach', 'Actinidia40196' => 'ach', 'Actinidia40197' => 'ach', 'Actinidia40198' => 'ach', 'Ah.08g212990' => 'amhyb', 'Ah.15g091720' => 'amhyb', 'AL3G38260' => 'aly', 'AL4G47710' => 'aly', 'Aqoxy2G00671' => 'aox', 'Aqoxy2G03236' => 'aox', 'arahy.Tifrunner.gnm1.ann1.05IDCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KR684' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATY3SJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK6QJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6APGL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IDT7Z9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM073U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ0R87' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LE7RV4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT4QRX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V5ENPK' => 'arhy', 'AT2G48110' => 'ath', 'AT3G23590' => 'ath', 'ATR0626G186' => 'atr', 'ATR1127G141' => 'atr', 'Atru.chr4.2583' => 'acertr', 'Atru.chr5.1358' => 'acertr', 'Atru.chr5.1359' => 'acertr', 'Atru.chr8.46' => 'acertr', 'AUR62002640' => 'cqu', 'AUR62030055' => 'cqu', 'AUR62033713' => 'cqu', 'AUR62033714' => 'cqu', 'AUR62036795' => 'cqu', 'AUR62039891' => 'cqu', 'BcaB02g08737' => 'bca', 'BcaB04g20441' => 'bca', 'BcaB06g26509' => 'bca', 'BcaB06g26510' => 'bca', 'BcaB06g26511' => 'bca', 'BcaB06g26512' => 'bca', 'BcaB06g26513' => 'bca', 'BcaC02g12564' => 'bca', 'BcaC02g12565' => 'bca', 'BcaC02g12794' => 'bca', 'BcaC02g12795' => 'bca', 'BcaC02g12796' => 'bca', 'BcaC06g35541' => 'bca', 'BNapus_Darmor_BZH_scaffold_188p00080' => 'bna', 'BNapus_Darmor_BZH_scaffold_188p00090' => 'bna', 'BolC1t03972H' => 'bol', 'BolC1t03973H' => 'bol', 'BolC4t21680H' => 'bol', 'BolC7t41863H' => 'bol', 'BolSC55t61227H' => 'bol', 'BolSC55t61228H' => 'bol', 'BraA01t03278Z' => 'bra', 'BraA05t18998Z' => 'bra', 'BraA07t28673Z' => 'bra', 'C01p40150' => 'bna', 'C05p12370' => 'bna', 'C07p13680' => 'bna', 'CAN.G1006.16' => 'can', 'CAN.G1006.17' => 'can', 'CAN.G1170.2' => 'can', 'CAN.G962.7' => 'can', 'CANSAT25G2179' => 'cansat', 'CANSAT78G1573' => 'cansat', 'CARHR099510' => 'chi', 'CARHR143510' => 'chi', 'Carub.0003s2380' => 'cru', 'Carub.0004s3082' => 'cru', 'Ca_00614_v3' => 'car', 'Ca_07801_v3' => 'car', 'Ca_08567_v3' => 'car', 'Ca_09571_v3' => 'car', 'CBR_g19290' => 'cbr', 'Cc01_g19770' => 'ccan', 'Cc03_g03030' => 'ccan', 'CDE07G0968' => 'cde', 'CDE09G1441' => 'cde', 'Cfa006103' => 'cfa', 'Cfa015573' => 'cfa', 'Cfa016988' => 'cfa', 'Ciclev10006738m.g' => 'ccl', 'Ciclev10010920m.g' => 'ccl', 'Ciclev10018517m.g' => 'ccl', 'CiPaw.01G159200' => 'cil', 'CiPaw.02G091000' => 'cil', 'CiPaw.02G091100' => 'cil', 'CiPaw.08G103100' => 'cil', 'CiPaw.09G224900' => 'cil', 'ClCG06G005740' => 'cla', 'ClCG07G000090' => 'cla', 'ClCG07G000100' => 'cla', 'COL.COLO4_09143' => 'col', 'COL.COLO4_25124' => 'col', 'Cpa.g.sc16.34' => 'cpa', 'Cpa.g.sc3504.1' => 'cpa', 'Cpa.g.sc60.37' => 'cpa', 'CsaV3_6G018520' => 'csa', 'CsaV3_6G036860' => 'csa', 'CSS0001072' => 'camsi', 'CSS0020208' => 'camsi', 'CSS0021253' => 'camsi', 'CSS0022190' => 'camsi', 'CSS0036150' => 'camsi', 'CSS0040442' => 'camsi', 'CSS0042300' => 'camsi', 'CSS0045298' => 'camsi', 'DCAR_012449' => 'dca', 'DCAR_018405' => 'dca', 'DCAR_024573' => 'dca', 'DCAR_030591' => 'dca', 'Dinv16926' => 'din', 'Dinv32963' => 'din', 'Dinv38382' => 'din', 'Dinv38383' => 'din', 'Duzib133G0974' => 'dzi', 'Duzib138G1867' => 'dzi', 'Duzib211G0420' => 'dzi', 'Duzib212G0930' => 'dzi', 'ECA234G1645' => 'eca', 'ECA247G3467' => 'eca', 'ECA248G1703' => 'eca', 'EL10Ac3g06327' => 'bvu', 'EL10Ac7g17204' => 'bvu', 'Eucgr.A00855' => 'egr', 'Eucgr.A00858' => 'egr', 'Eucgr.H01520' => 'egr', 'Eucgr.H03604' => 'egr', 'Eucgr.L03465' => 'egr', 'Eucgr.L03466' => 'egr', 'FAN01G0988' => 'fan', 'FAN02G3892' => 'fan', 'FAN05G3381' => 'fan', 'FAN07G0967' => 'fan', 'FAN07G1493' => 'fan', 'FAN08G3125' => 'fan', 'FAN09G0402' => 'fan', 'FAN12G2594' => 'fan', 'FAN12G3879' => 'fan', 'FAN14G1546' => 'fan', 'FAN15G3626' => 'fan', 'FAN17G0588' => 'fan', 'FAN17G0609' => 'fan', 'FAN18G2817' => 'fan', 'FAN19G1305' => 'fan', 'FAN20G1787' => 'fan', 'FAN22G0073' => 'fan', 'FAN22G0352' => 'fan', 'FAN22G0368' => 'fan', 'FAN22G2273' => 'fan', 'FAN24G1998' => 'fan', 'FAN27G1317' => 'fan', 'FvH4_2g23980' => 'fve', 'FvH4_4g14380' => 'fve', 'FvH4_4g14390' => 'fve', 'FvH4_6g09250' => 'fve', 'Glyma.03G151100' => 'gma', 'Glyma.04G122550' => 'gma', 'Glyma.05G001600' => 'gma', 'Glyma.09G270766' => 'gma', 'Glyma.09G270832' => 'gma', 'Glyma.13G209800' => 'gma', 'Glyma.15G102800' => 'gma', 'Glyma.18G218900' => 'gma', 'Glyma.19G001500' => 'gma', 'Glyma.19G153600' => 'gma', 'Gohir.A02G028600' => 'ghi', 'Gohir.A08G045000' => 'ghi', 'Gohir.A11G120500' => 'ghi', 'Gohir.A12G006200' => 'ghi', 'Gohir.A12G006250' => 'ghi', 'Gohir.D02G036300' => 'ghi', 'Gohir.D08G054700' => 'ghi', 'Gohir.D11G125600' => 'ghi', 'Gohir.D12G005700' => 'ghi', 'Gorai.004G055200' => 'gra', 'Gorai.005G040400' => 'gra', 'Gorai.007G134500' => 'gra', 'Gorai.008G005500' => 'gra', 'GSVIVG01011094001' => 'vvi', 'GSVIVG01017879001' => 'vvi', 'GSVIVG01025988001' => 'vvi', 'GSVIVG01029847001' => 'vvi', 'HanXRQChr10g0282901' => 'han', 'HanXRQChr10g0310371' => 'han', 'HanXRQChr10g0315041' => 'han', 'HanXRQChr11g0327651' => 'han', 'HanXRQChr12g0359391' => 'han', 'Haze_00972' => 'cav', 'Haze_00973' => 'cav', 'Haze_00974' => 'cav', 'Haze_04747' => 'cav', 'Haze_04749' => 'cav', 'Haze_04750' => 'cav', 'Haze_21217' => 'cav', 'Hma1.2p1_1037F.1_g250680' => 'hma', 'Hma1.2p1_1644F.1_g295320' => 'hma', 'HPP92_011322' => 'vpl', 'HPP92_011323' => 'vpl', 'HPP92_011324' => 'vpl', 'HPP92_011325' => 'vpl', 'HPP92_011326' => 'vpl', 'Hund12205' => 'sun', 'Hund17957' => 'sun', 'Lalb_Chr06g0176771' => 'lal', 'Lalb_Chr18g0056021' => 'lal', 'Lalb_Chr18g0056031' => 'lal', 'Lalb_Chr18g0056041' => 'lal', 'Lalb_Chr20g0107751' => 'lal', 'Lalb_Chr20g0118371' => 'lal', 'Lj1g0010239' => 'lja', 'Lj1g0017101' => 'lja', 'Lj2A1178G40' => 'lonja', 'Lj2A54G84' => 'lonja', 'Lj2g0015248' => 'lja', 'Lj3A761T51' => 'lonja', 'Lj6g0018116' => 'lja', 'Lsat_1_v5_gn_4_136040' => 'lsa', 'Lsat_1_v5_gn_5_187461' => 'lsa', 'Lsat_1_v5_gn_5_77001' => 'lsa', 'Lsat_1_v5_gn_9_4461' => 'lsa', 'Manes.01G210100' => 'mes', 'Manes.03G185600' => 'mes', 'Manes.05G073300' => 'mes', 'Manes.09G120300' => 'mes', 'Manes.15G022100' => 'mes', 'Mapoly0096s0053' => 'mpo', 'MBI03_g14058_MAGBIO' => 'mbi', 'MBI03_g33876_MAGBIO' => 'mbi', 'MBI03_g36854_MAGBIO' => 'mbi', 'MBI17_g11997_MAGBIO' => 'mbi', 'MD03G1269000' => 'mdo', 'MD04G1179600' => 'mdo', 'MD11G1289800' => 'mdo', 'MD12G1194700' => 'mdo', 'MD13G1182100' => 'mdo', 'MD13G1182200' => 'mdo', 'MD16G1182600' => 'mdo', 'Medtr2g021400' => 'mtr', 'Medtr2g021470' => 'mtr', 'Medtr2g105810' => 'mtr', 'Medtr3g033580' => 'mtr', 'Medtr6g007970' => 'mtr', 'Medtr7g056330' => 'mtr', 'Medtr7g074290' => 'mtr', 'Medtr7g074380' => 'mtr', 'Medtr7g094550' => 'mtr', 'Medtr8g069995' => 'mtr', 'MELO3C014345.2' => 'cme', 'MELO3C021395.2' => 'cme', 'Migut.D00262' => 'egut', 'Migut.G00257' => 'egut', 'MSTRG.21575' => 'ama', 'MSTRG.3985' => 'ama', 'Nitab4.5_0000295g0140' => 'nta', 'Nitab4.5_0000732g0140' => 'nta', 'Nitab4.5_0003162g0020' => 'nta', 'Nitab4.5_0006180g0090' => 'nta', 'Nitab4.5_0006390g0010' => 'nta', 'Nitab4.5_0007392g0040' => 'nta', 'Nn1g02140' => 'nnu', 'Nn4g26168' => 'nnu', 'Nn5g26754' => 'nnu', 'Oeu001433.1' => 'oeu', 'Oeu010299.2' => 'oeu', 'Oeu011171.1' => 'oeu', 'Oeu037675.1' => 'oeu', 'Oeu038359.1' => 'oeu', 'Oeu063834.1' => 'oeu', 'Oeu063835.1' => 'oeu', 'Os05g0312000' => 'osa', 'Os07g0211101' => 'osa', 'Os07g0211200' => 'osa', 'Os07g0681500' => 'osa', 'Peaxi162Scf00095g01015' => 'pax', 'Peaxi162Scf00104g00329' => 'pax', 'Peaxi162Scf00161g00137' => 'pax', 'PGR004G1665' => 'pgr', 'PGR031G2937' => 'pgr', 'PGR119G2145' => 'pgr', 'PGSC0003DMG400004351' => 'stu', 'PGSC0003DMG400014625' => 'stu', 'PGSC0003DMG401000943' => 'stu', 'Phvul.001G148600' => 'pvu', 'Phvul.004G001700' => 'pvu', 'Phvul.006G154900' => 'pvu', 'Phvul.008G078200' => 'pvu', 'Phvul.011G136500' => 'pvu', 'Potri.002G215600' => 'ptr', 'Potri.008G201600' => 'ptr', 'Potri.014G138400' => 'ptr', 'Potri.016G142500' => 'ptr', 'Pp3c16_10580' => 'ppa', 'Pp3c5_25280' => 'ppa', 'Prupe.1G150000' => 'ppe', 'Prupe.1G150100' => 'ppe', 'Prupe.6G299600' => 'ppe', 'Prupe.8G245000' => 'ppe', 'Psat0s4927g0040' => 'psa', 'Psat1g052080' => 'psa', 'Psat1g183800' => 'psa', 'Psat3g113840' => 'psa', 'Psat3g126120' => 'psa', 'Psat3g126160' => 'psa', 'Psat3g158760' => 'psa', 'Psat3g158840' => 'psa', 'PSO170G2858' => 'pso', 'PSO339G0606' => 'pso', 'PSO384G4709' => 'pso', 'PSO407G0334' => 'pso', 'QL04p040276' => 'qlo', 'QL06p005458' => 'qlo', 'QL06p005472' => 'qlo', 'QL07p030546' => 'qlo', 'QL07p031519' => 'qlo', 'QL09p050949' => 'qlo', 'QL09p050966' => 'qlo', 'QL09p051067' => 'qlo', 'QL12p022706' => 'qlo', 'RcHm_v2.0_Chr2g0119601' => 'rch', 'RcHm_v2.0_Chr3g0459591' => 'rch', 'RcHm_v2.0_Chr4g0418521' => 'rch', 'RcHm_v2.0_Chr4g0418531' => 'rch', 'RcHm_v2.0_Chr4g0418541' => 'rch', 'RcHm_v2.0_Chr6g0291641' => 'rch', 'Rhsim01G0086300' => 'rsi', 'Rhsim01G0276300' => 'rsi', 'Rhsim01G0276500' => 'rsi', 'Rhsim04G0207700' => 'rsi', 'Rhsim05G0234500' => 'rsi', 'Rhsim13G0022400' => 'rsi', 'Sabra02G0167900' => 'sbr', 'Sabra04G0158500' => 'sbr', 'Sabra08G0159800' => 'sbr', 'Sabra10G0011500' => 'sbr', 'Sabra14G0104400' => 'sbr', 'SalBow2G2440' => 'sbo', 'SalBow4G2265' => 'sbo', 'Sc02g0000060' => 'sci', 'Sc05g0005020' => 'sci', 'Sc13g0003890' => 'sci', 'Sed0014865' => 'sed', 'Sed0017224' => 'sed', 'Sed0026391' => 'sed', 'SEGI_00063' => 'sgi', 'SEGI_10967' => 'sgi', 'SEGI_17510' => 'sgi', 'SEGI_24396' => 'sgi', 'SEGI_39719' => 'sgi', 'SEGI_41392' => 'sgi', 'SGA_v2.0_scaffold11G05794' => 'sas', 'SGA_v2.0_scaffold142G35607' => 'sas', 'SGA_v2.0_scaffold1G00447' => 'sas', 'SHI15388' => 'shi', 'SHI15394' => 'shi', 'SHI15396' => 'shi', 'SHI15399' => 'shi', 'SMO343G0151' => 'smo', 'SMO367G1118' => 'smo', 'Solyc01g080200.3' => 'sly', 'Solyc06g008960.3' => 'sly', 'Solyc09g064780.3' => 'sly', 'Sopen01g031980' => 'spe', 'Sopen06g003710' => 'spe', 'Sopen09g026460' => 'spe', 'Sp3g21240' => 'spa', 'Sp4g30030' => 'spa', 'TAR365G0022' => 'tar', 'TAR365G1023' => 'tar', 'TAR365G1253' => 'tar', 'TAR623G0078' => 'tar', 'TAR623G1721' => 'tar', 'TAR633G0959' => 'tar', 'THA.LOC104802225' => 'tha', 'THA.LOC104804769' => 'tha', 'THA.LOC104808660' => 'tha', 'THA.LOC104812792' => 'tha', 'Thecc.01G284000' => 'tca', 'Thecc.04G220600' => 'tca', 'Thecc.05G268900' => 'tca', 'Thecc.08G171100' => 'tca', 'Thhalv10001284m.g' => 'esa', 'Thhalv10019912m.g' => 'esa', 'TPR.G14189' => 'tpr', 'TPR.G18110' => 'tpr', 'TPR.G18130' => 'tpr', 'TPR.G18131' => 'tpr', 'TPR.G18140' => 'tpr', 'TPR.G24282' => 'tpr', 'TPR.G25221' => 'tpr', 'TPR.G29267' => 'tpr', 'TPR.G35315' => 'tpr', 'TPR.G36173' => 'tpr', 'TWI09G0794' => 'twi', 'TWI59G1348' => 'twi', 'TWI74G0430' => 'twi', 'unitig_26.g8940' => 'ugi', 'unitig_749.g13744' => 'ugi', 'unitig_749.g13745' => 'ugi', 'vmacro08269' => 'vma', 'vmacro14937' => 'vma', 'vmacro20401' => 'vma', 'VMungo0464G1349' => 'vmu', 'VMungo0540G0289' => 'vmu', 'VMungo1215G1590' => 'vmu', 'VMungo1309G0221' => 'vmu', 'VMungo1309G2815' => 'vmu', 'VMungo1383G0239' => 'vmu', 'VMungo1383G2910' => 'vmu', 'Zm00001eb095270' => 'zma', 'Zm00001eb095280' => 'zma', 'Zm00001eb111630' => 'zma', 'Zm00001eb237080' => 'zma', 'Zm00001eb273740' => 'zma', 'Zm00001eb285040' => 'zma', 'Zm00001eb330790' => 'zma', 'Zm00001eb337380' => 'zma' ) $gf_id = 'HOM05D001484' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001484' ) $data_identifier = 'HOM05D001484' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 2, 'aly' => (int) 2, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 22, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 7, 'hma' => (int) 2, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 7, 'mtr' => (int) 10, 'cme' => (int) 2, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 4, 'ppa' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 4, 'qlo' => (int) 9, 'rch' => (int) 6, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 10, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 7, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb337380' $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' => 'HOM05D001484', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p31500' => 'bna', 'A05p00020' => 'bna', 'A07p08820' => 'bna', 'Aa31LG4G3300' => 'aar', 'Aa31LG8G10030' => 'aar', 'Actinidia00731' => 'ach', 'Actinidia11473' => 'ach', 'Actinidia23469' => 'ach', 'Actinidia24318' => 'ach', 'Actinidia40196' => 'ach', 'Actinidia40197' => 'ach', 'Actinidia40198' => 'ach', 'Ah.08g212990' => 'amhyb', 'Ah.15g091720' => 'amhyb', 'AL3G38260' => 'aly', 'AL4G47710' => 'aly', 'Aqoxy2G00671' => 'aox', 'Aqoxy2G03236' => 'aox', 'arahy.Tifrunner.gnm1.ann1.05IDCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KR684' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATY3SJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK6QJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6APGL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IDT7Z9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM073U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ0R87' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LE7RV4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT4QRX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V5ENPK' => 'arhy', 'AT2G48110' => 'ath', 'AT3G23590' => 'ath', 'ATR0626G186' => 'atr', 'ATR1127G141' => 'atr', 'Atru.chr4.2583' => 'acertr', 'Atru.chr5.1358' => 'acertr', 'Atru.chr5.1359' => 'acertr', 'Atru.chr8.46' => 'acertr', 'AUR62002640' => 'cqu', 'AUR62030055' => 'cqu', 'AUR62033713' => 'cqu', 'AUR62033714' => 'cqu', 'AUR62036795' => 'cqu', 'AUR62039891' => 'cqu', 'BcaB02g08737' => 'bca', 'BcaB04g20441' => 'bca', 'BcaB06g26509' => 'bca', 'BcaB06g26510' => 'bca', 'BcaB06g26511' => 'bca', 'BcaB06g26512' => 'bca', 'BcaB06g26513' => 'bca', 'BcaC02g12564' => 'bca', 'BcaC02g12565' => 'bca', 'BcaC02g12794' => 'bca', 'BcaC02g12795' => 'bca', 'BcaC02g12796' => 'bca', 'BcaC06g35541' => 'bca', 'BNapus_Darmor_BZH_scaffold_188p00080' => 'bna', 'BNapus_Darmor_BZH_scaffold_188p00090' => 'bna', 'BolC1t03972H' => 'bol', 'BolC1t03973H' => 'bol', 'BolC4t21680H' => 'bol', 'BolC7t41863H' => 'bol', 'BolSC55t61227H' => 'bol', 'BolSC55t61228H' => 'bol', 'BraA01t03278Z' => 'bra', 'BraA05t18998Z' => 'bra', 'BraA07t28673Z' => 'bra', 'C01p40150' => 'bna', 'C05p12370' => 'bna', 'C07p13680' => 'bna', 'CAN.G1006.16' => 'can', 'CAN.G1006.17' => 'can', 'CAN.G1170.2' => 'can', 'CAN.G962.7' => 'can', 'CANSAT25G2179' => 'cansat', 'CANSAT78G1573' => 'cansat', 'CARHR099510' => 'chi', 'CARHR143510' => 'chi', 'Carub.0003s2380' => 'cru', 'Carub.0004s3082' => 'cru', 'Ca_00614_v3' => 'car', 'Ca_07801_v3' => 'car', 'Ca_08567_v3' => 'car', 'Ca_09571_v3' => 'car', 'CBR_g19290' => 'cbr', 'Cc01_g19770' => 'ccan', 'Cc03_g03030' => 'ccan', 'CDE07G0968' => 'cde', 'CDE09G1441' => 'cde', 'Cfa006103' => 'cfa', 'Cfa015573' => 'cfa', 'Cfa016988' => 'cfa', 'Ciclev10006738m.g' => 'ccl', 'Ciclev10010920m.g' => 'ccl', 'Ciclev10018517m.g' => 'ccl', 'CiPaw.01G159200' => 'cil', 'CiPaw.02G091000' => 'cil', 'CiPaw.02G091100' => 'cil', 'CiPaw.08G103100' => 'cil', 'CiPaw.09G224900' => 'cil', 'ClCG06G005740' => 'cla', 'ClCG07G000090' => 'cla', 'ClCG07G000100' => 'cla', 'COL.COLO4_09143' => 'col', 'COL.COLO4_25124' => 'col', 'Cpa.g.sc16.34' => 'cpa', 'Cpa.g.sc3504.1' => 'cpa', 'Cpa.g.sc60.37' => 'cpa', 'CsaV3_6G018520' => 'csa', 'CsaV3_6G036860' => 'csa', 'CSS0001072' => 'camsi', 'CSS0020208' => 'camsi', 'CSS0021253' => 'camsi', 'CSS0022190' => 'camsi', 'CSS0036150' => 'camsi', 'CSS0040442' => 'camsi', 'CSS0042300' => 'camsi', 'CSS0045298' => 'camsi', 'DCAR_012449' => 'dca', 'DCAR_018405' => 'dca', 'DCAR_024573' => 'dca', 'DCAR_030591' => 'dca', 'Dinv16926' => 'din', 'Dinv32963' => 'din', 'Dinv38382' => 'din', 'Dinv38383' => 'din', 'Duzib133G0974' => 'dzi', 'Duzib138G1867' => 'dzi', 'Duzib211G0420' => 'dzi', 'Duzib212G0930' => 'dzi', 'ECA234G1645' => 'eca', 'ECA247G3467' => 'eca', 'ECA248G1703' => 'eca', 'EL10Ac3g06327' => 'bvu', 'EL10Ac7g17204' => 'bvu', 'Eucgr.A00855' => 'egr', 'Eucgr.A00858' => 'egr', 'Eucgr.H01520' => 'egr', 'Eucgr.H03604' => 'egr', 'Eucgr.L03465' => 'egr', 'Eucgr.L03466' => 'egr', 'FAN01G0988' => 'fan', 'FAN02G3892' => 'fan', 'FAN05G3381' => 'fan', 'FAN07G0967' => 'fan', 'FAN07G1493' => 'fan', 'FAN08G3125' => 'fan', 'FAN09G0402' => 'fan', 'FAN12G2594' => 'fan', 'FAN12G3879' => 'fan', 'FAN14G1546' => 'fan', 'FAN15G3626' => 'fan', 'FAN17G0588' => 'fan', 'FAN17G0609' => 'fan', 'FAN18G2817' => 'fan', 'FAN19G1305' => 'fan', 'FAN20G1787' => 'fan', 'FAN22G0073' => 'fan', 'FAN22G0352' => 'fan', 'FAN22G0368' => 'fan', 'FAN22G2273' => 'fan', 'FAN24G1998' => 'fan', 'FAN27G1317' => 'fan', 'FvH4_2g23980' => 'fve', 'FvH4_4g14380' => 'fve', 'FvH4_4g14390' => 'fve', 'FvH4_6g09250' => 'fve', 'Glyma.03G151100' => 'gma', 'Glyma.04G122550' => 'gma', 'Glyma.05G001600' => 'gma', 'Glyma.09G270766' => 'gma', 'Glyma.09G270832' => 'gma', 'Glyma.13G209800' => 'gma', 'Glyma.15G102800' => 'gma', 'Glyma.18G218900' => 'gma', 'Glyma.19G001500' => 'gma', 'Glyma.19G153600' => 'gma', 'Gohir.A02G028600' => 'ghi', 'Gohir.A08G045000' => 'ghi', 'Gohir.A11G120500' => 'ghi', 'Gohir.A12G006200' => 'ghi', 'Gohir.A12G006250' => 'ghi', 'Gohir.D02G036300' => 'ghi', 'Gohir.D08G054700' => 'ghi', 'Gohir.D11G125600' => 'ghi', 'Gohir.D12G005700' => 'ghi', 'Gorai.004G055200' => 'gra', 'Gorai.005G040400' => 'gra', 'Gorai.007G134500' => 'gra', 'Gorai.008G005500' => 'gra', 'GSVIVG01011094001' => 'vvi', 'GSVIVG01017879001' => 'vvi', 'GSVIVG01025988001' => 'vvi', 'GSVIVG01029847001' => 'vvi', 'HanXRQChr10g0282901' => 'han', 'HanXRQChr10g0310371' => 'han', 'HanXRQChr10g0315041' => 'han', 'HanXRQChr11g0327651' => 'han', 'HanXRQChr12g0359391' => 'han', 'Haze_00972' => 'cav', 'Haze_00973' => 'cav', 'Haze_00974' => 'cav', 'Haze_04747' => 'cav', 'Haze_04749' => 'cav', 'Haze_04750' => 'cav', 'Haze_21217' => 'cav', 'Hma1.2p1_1037F.1_g250680' => 'hma', 'Hma1.2p1_1644F.1_g295320' => 'hma', 'HPP92_011322' => 'vpl', 'HPP92_011323' => 'vpl', 'HPP92_011324' => 'vpl', 'HPP92_011325' => 'vpl', 'HPP92_011326' => 'vpl', 'Hund12205' => 'sun', 'Hund17957' => 'sun', 'Lalb_Chr06g0176771' => 'lal', 'Lalb_Chr18g0056021' => 'lal', 'Lalb_Chr18g0056031' => 'lal', 'Lalb_Chr18g0056041' => 'lal', 'Lalb_Chr20g0107751' => 'lal', 'Lalb_Chr20g0118371' => 'lal', 'Lj1g0010239' => 'lja', 'Lj1g0017101' => 'lja', 'Lj2A1178G40' => 'lonja', 'Lj2A54G84' => 'lonja', 'Lj2g0015248' => 'lja', 'Lj3A761T51' => 'lonja', 'Lj6g0018116' => 'lja', 'Lsat_1_v5_gn_4_136040' => 'lsa', 'Lsat_1_v5_gn_5_187461' => 'lsa', 'Lsat_1_v5_gn_5_77001' => 'lsa', 'Lsat_1_v5_gn_9_4461' => 'lsa', 'Manes.01G210100' => 'mes', 'Manes.03G185600' => 'mes', 'Manes.05G073300' => 'mes', 'Manes.09G120300' => 'mes', 'Manes.15G022100' => 'mes', 'Mapoly0096s0053' => 'mpo', 'MBI03_g14058_MAGBIO' => 'mbi', 'MBI03_g33876_MAGBIO' => 'mbi', 'MBI03_g36854_MAGBIO' => 'mbi', 'MBI17_g11997_MAGBIO' => 'mbi', 'MD03G1269000' => 'mdo', 'MD04G1179600' => 'mdo', 'MD11G1289800' => 'mdo', 'MD12G1194700' => 'mdo', 'MD13G1182100' => 'mdo', 'MD13G1182200' => 'mdo', 'MD16G1182600' => 'mdo', 'Medtr2g021400' => 'mtr', 'Medtr2g021470' => 'mtr', 'Medtr2g105810' => 'mtr', 'Medtr3g033580' => 'mtr', 'Medtr6g007970' => 'mtr', 'Medtr7g056330' => 'mtr', 'Medtr7g074290' => 'mtr', 'Medtr7g074380' => 'mtr', 'Medtr7g094550' => 'mtr', 'Medtr8g069995' => 'mtr', 'MELO3C014345.2' => 'cme', 'MELO3C021395.2' => 'cme', 'Migut.D00262' => 'egut', 'Migut.G00257' => 'egut', 'MSTRG.21575' => 'ama', 'MSTRG.3985' => 'ama', 'Nitab4.5_0000295g0140' => 'nta', 'Nitab4.5_0000732g0140' => 'nta', 'Nitab4.5_0003162g0020' => 'nta', 'Nitab4.5_0006180g0090' => 'nta', 'Nitab4.5_0006390g0010' => 'nta', 'Nitab4.5_0007392g0040' => 'nta', 'Nn1g02140' => 'nnu', 'Nn4g26168' => 'nnu', 'Nn5g26754' => 'nnu', 'Oeu001433.1' => 'oeu', 'Oeu010299.2' => 'oeu', 'Oeu011171.1' => 'oeu', 'Oeu037675.1' => 'oeu', 'Oeu038359.1' => 'oeu', 'Oeu063834.1' => 'oeu', 'Oeu063835.1' => 'oeu', 'Os05g0312000' => 'osa', 'Os07g0211101' => 'osa', 'Os07g0211200' => 'osa', 'Os07g0681500' => 'osa', 'Peaxi162Scf00095g01015' => 'pax', 'Peaxi162Scf00104g00329' => 'pax', 'Peaxi162Scf00161g00137' => 'pax', 'PGR004G1665' => 'pgr', 'PGR031G2937' => 'pgr', 'PGR119G2145' => 'pgr', 'PGSC0003DMG400004351' => 'stu', 'PGSC0003DMG400014625' => 'stu', 'PGSC0003DMG401000943' => 'stu', 'Phvul.001G148600' => 'pvu', 'Phvul.004G001700' => 'pvu', 'Phvul.006G154900' => 'pvu', 'Phvul.008G078200' => 'pvu', 'Phvul.011G136500' => 'pvu', 'Potri.002G215600' => 'ptr', 'Potri.008G201600' => 'ptr', 'Potri.014G138400' => 'ptr', 'Potri.016G142500' => 'ptr', 'Pp3c16_10580' => 'ppa', 'Pp3c5_25280' => 'ppa', 'Prupe.1G150000' => 'ppe', 'Prupe.1G150100' => 'ppe', 'Prupe.6G299600' => 'ppe', 'Prupe.8G245000' => 'ppe', 'Psat0s4927g0040' => 'psa', 'Psat1g052080' => 'psa', 'Psat1g183800' => 'psa', 'Psat3g113840' => 'psa', 'Psat3g126120' => 'psa', 'Psat3g126160' => 'psa', 'Psat3g158760' => 'psa', 'Psat3g158840' => 'psa', 'PSO170G2858' => 'pso', 'PSO339G0606' => 'pso', 'PSO384G4709' => 'pso', 'PSO407G0334' => 'pso', 'QL04p040276' => 'qlo', 'QL06p005458' => 'qlo', 'QL06p005472' => 'qlo', 'QL07p030546' => 'qlo', 'QL07p031519' => 'qlo', 'QL09p050949' => 'qlo', 'QL09p050966' => 'qlo', 'QL09p051067' => 'qlo', 'QL12p022706' => 'qlo', 'RcHm_v2.0_Chr2g0119601' => 'rch', 'RcHm_v2.0_Chr3g0459591' => 'rch', 'RcHm_v2.0_Chr4g0418521' => 'rch', 'RcHm_v2.0_Chr4g0418531' => 'rch', 'RcHm_v2.0_Chr4g0418541' => 'rch', 'RcHm_v2.0_Chr6g0291641' => 'rch', 'Rhsim01G0086300' => 'rsi', 'Rhsim01G0276300' => 'rsi', 'Rhsim01G0276500' => 'rsi', 'Rhsim04G0207700' => 'rsi', 'Rhsim05G0234500' => 'rsi', 'Rhsim13G0022400' => 'rsi', 'Sabra02G0167900' => 'sbr', 'Sabra04G0158500' => 'sbr', 'Sabra08G0159800' => 'sbr', 'Sabra10G0011500' => 'sbr', 'Sabra14G0104400' => 'sbr', 'SalBow2G2440' => 'sbo', 'SalBow4G2265' => 'sbo', 'Sc02g0000060' => 'sci', 'Sc05g0005020' => 'sci', 'Sc13g0003890' => 'sci', 'Sed0014865' => 'sed', 'Sed0017224' => 'sed', 'Sed0026391' => 'sed', 'SEGI_00063' => 'sgi', 'SEGI_10967' => 'sgi', 'SEGI_17510' => 'sgi', 'SEGI_24396' => 'sgi', 'SEGI_39719' => 'sgi', 'SEGI_41392' => 'sgi', 'SGA_v2.0_scaffold11G05794' => 'sas', 'SGA_v2.0_scaffold142G35607' => 'sas', 'SGA_v2.0_scaffold1G00447' => 'sas', 'SHI15388' => 'shi', 'SHI15394' => 'shi', 'SHI15396' => 'shi', 'SHI15399' => 'shi', 'SMO343G0151' => 'smo', 'SMO367G1118' => 'smo', 'Solyc01g080200.3' => 'sly', 'Solyc06g008960.3' => 'sly', 'Solyc09g064780.3' => 'sly', 'Sopen01g031980' => 'spe', 'Sopen06g003710' => 'spe', 'Sopen09g026460' => 'spe', 'Sp3g21240' => 'spa', 'Sp4g30030' => 'spa', 'TAR365G0022' => 'tar', 'TAR365G1023' => 'tar', 'TAR365G1253' => 'tar', 'TAR623G0078' => 'tar', 'TAR623G1721' => 'tar', 'TAR633G0959' => 'tar', 'THA.LOC104802225' => 'tha', 'THA.LOC104804769' => 'tha', 'THA.LOC104808660' => 'tha', 'THA.LOC104812792' => 'tha', 'Thecc.01G284000' => 'tca', 'Thecc.04G220600' => 'tca', 'Thecc.05G268900' => 'tca', 'Thecc.08G171100' => 'tca', 'Thhalv10001284m.g' => 'esa', 'Thhalv10019912m.g' => 'esa', 'TPR.G14189' => 'tpr', 'TPR.G18110' => 'tpr', 'TPR.G18130' => 'tpr', 'TPR.G18131' => 'tpr', 'TPR.G18140' => 'tpr', 'TPR.G24282' => 'tpr', 'TPR.G25221' => 'tpr', 'TPR.G29267' => 'tpr', 'TPR.G35315' => 'tpr', 'TPR.G36173' => 'tpr', 'TWI09G0794' => 'twi', 'TWI59G1348' => 'twi', 'TWI74G0430' => 'twi', 'unitig_26.g8940' => 'ugi', 'unitig_749.g13744' => 'ugi', 'unitig_749.g13745' => 'ugi', 'vmacro08269' => 'vma', 'vmacro14937' => 'vma', 'vmacro20401' => 'vma', 'VMungo0464G1349' => 'vmu', 'VMungo0540G0289' => 'vmu', 'VMungo1215G1590' => 'vmu', 'VMungo1309G0221' => 'vmu', 'VMungo1309G2815' => 'vmu', 'VMungo1383G0239' => 'vmu', 'VMungo1383G2910' => 'vmu', 'Zm00001eb095270' => 'zma', 'Zm00001eb095280' => 'zma', 'Zm00001eb111630' => 'zma', 'Zm00001eb237080' => 'zma', 'Zm00001eb273740' => 'zma', 'Zm00001eb285040' => 'zma', 'Zm00001eb330790' => 'zma', 'Zm00001eb337380' => 'zma' ), 'gf_id' => 'HOM05D001484', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001484' ), 'data_identifier' => 'HOM05D001484', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001484', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p31500' => 'bna', 'A05p00020' => 'bna', 'A07p08820' => 'bna', 'Aa31LG4G3300' => 'aar', 'Aa31LG8G10030' => 'aar', 'Actinidia00731' => 'ach', 'Actinidia11473' => 'ach', 'Actinidia23469' => 'ach', 'Actinidia24318' => 'ach', 'Actinidia40196' => 'ach', 'Actinidia40197' => 'ach', 'Actinidia40198' => 'ach', 'Ah.08g212990' => 'amhyb', 'Ah.15g091720' => 'amhyb', 'AL3G38260' => 'aly', 'AL4G47710' => 'aly', 'Aqoxy2G00671' => 'aox', 'Aqoxy2G03236' => 'aox', 'arahy.Tifrunner.gnm1.ann1.05IDCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KR684' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATY3SJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK6QJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6APGL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IDT7Z9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM073U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ0R87' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LE7RV4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT4QRX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V5ENPK' => 'arhy', 'AT2G48110' => 'ath', 'AT3G23590' => 'ath', 'ATR0626G186' => 'atr', 'ATR1127G141' => 'atr', 'Atru.chr4.2583' => 'acertr', 'Atru.chr5.1358' => 'acertr', 'Atru.chr5.1359' => 'acertr', 'Atru.chr8.46' => 'acertr', 'AUR62002640' => 'cqu', 'AUR62030055' => 'cqu', 'AUR62033713' => 'cqu', 'AUR62033714' => 'cqu', 'AUR62036795' => 'cqu', 'AUR62039891' => 'cqu', 'BcaB02g08737' => 'bca', 'BcaB04g20441' => 'bca', 'BcaB06g26509' => 'bca', 'BcaB06g26510' => 'bca', 'BcaB06g26511' => 'bca', 'BcaB06g26512' => 'bca', 'BcaB06g26513' => 'bca', 'BcaC02g12564' => 'bca', 'BcaC02g12565' => 'bca', 'BcaC02g12794' => 'bca', 'BcaC02g12795' => 'bca', 'BcaC02g12796' => 'bca', 'BcaC06g35541' => 'bca', 'BNapus_Darmor_BZH_scaffold_188p00080' => 'bna', 'BNapus_Darmor_BZH_scaffold_188p00090' => 'bna', 'BolC1t03972H' => 'bol', 'BolC1t03973H' => 'bol', 'BolC4t21680H' => 'bol', 'BolC7t41863H' => 'bol', 'BolSC55t61227H' => 'bol', 'BolSC55t61228H' => 'bol', 'BraA01t03278Z' => 'bra', 'BraA05t18998Z' => 'bra', 'BraA07t28673Z' => 'bra', 'C01p40150' => 'bna', 'C05p12370' => 'bna', 'C07p13680' => 'bna', 'CAN.G1006.16' => 'can', 'CAN.G1006.17' => 'can', 'CAN.G1170.2' => 'can', 'CAN.G962.7' => 'can', 'CANSAT25G2179' => 'cansat', 'CANSAT78G1573' => 'cansat', 'CARHR099510' => 'chi', 'CARHR143510' => 'chi', 'Carub.0003s2380' => 'cru', 'Carub.0004s3082' => 'cru', 'Ca_00614_v3' => 'car', 'Ca_07801_v3' => 'car', 'Ca_08567_v3' => 'car', 'Ca_09571_v3' => 'car', 'CBR_g19290' => 'cbr', 'Cc01_g19770' => 'ccan', 'Cc03_g03030' => 'ccan', 'CDE07G0968' => 'cde', 'CDE09G1441' => 'cde', 'Cfa006103' => 'cfa', 'Cfa015573' => 'cfa', 'Cfa016988' => 'cfa', 'Ciclev10006738m.g' => 'ccl', 'Ciclev10010920m.g' => 'ccl', 'Ciclev10018517m.g' => 'ccl', 'CiPaw.01G159200' => 'cil', 'CiPaw.02G091000' => 'cil', 'CiPaw.02G091100' => 'cil', 'CiPaw.08G103100' => 'cil', 'CiPaw.09G224900' => 'cil', 'ClCG06G005740' => 'cla', 'ClCG07G000090' => 'cla', 'ClCG07G000100' => 'cla', 'COL.COLO4_09143' => 'col', 'COL.COLO4_25124' => 'col', 'Cpa.g.sc16.34' => 'cpa', 'Cpa.g.sc3504.1' => 'cpa', 'Cpa.g.sc60.37' => 'cpa', 'CsaV3_6G018520' => 'csa', 'CsaV3_6G036860' => 'csa', 'CSS0001072' => 'camsi', 'CSS0020208' => 'camsi', 'CSS0021253' => 'camsi', 'CSS0022190' => 'camsi', 'CSS0036150' => 'camsi', 'CSS0040442' => 'camsi', 'CSS0042300' => 'camsi', 'CSS0045298' => 'camsi', 'DCAR_012449' => 'dca', 'DCAR_018405' => 'dca', 'DCAR_024573' => 'dca', 'DCAR_030591' => 'dca', 'Dinv16926' => 'din', 'Dinv32963' => 'din', 'Dinv38382' => 'din', 'Dinv38383' => 'din', 'Duzib133G0974' => 'dzi', 'Duzib138G1867' => 'dzi', 'Duzib211G0420' => 'dzi', 'Duzib212G0930' => 'dzi', 'ECA234G1645' => 'eca', 'ECA247G3467' => 'eca', 'ECA248G1703' => 'eca', 'EL10Ac3g06327' => 'bvu', 'EL10Ac7g17204' => 'bvu', 'Eucgr.A00855' => 'egr', 'Eucgr.A00858' => 'egr', 'Eucgr.H01520' => 'egr', 'Eucgr.H03604' => 'egr', 'Eucgr.L03465' => 'egr', 'Eucgr.L03466' => 'egr', 'FAN01G0988' => 'fan', 'FAN02G3892' => 'fan', 'FAN05G3381' => 'fan', 'FAN07G0967' => 'fan', 'FAN07G1493' => 'fan', 'FAN08G3125' => 'fan', 'FAN09G0402' => 'fan', 'FAN12G2594' => 'fan', 'FAN12G3879' => 'fan', 'FAN14G1546' => 'fan', 'FAN15G3626' => 'fan', 'FAN17G0588' => 'fan', 'FAN17G0609' => 'fan', 'FAN18G2817' => 'fan', 'FAN19G1305' => 'fan', 'FAN20G1787' => 'fan', 'FAN22G0073' => 'fan', 'FAN22G0352' => 'fan', 'FAN22G0368' => 'fan', 'FAN22G2273' => 'fan', 'FAN24G1998' => 'fan', 'FAN27G1317' => 'fan', 'FvH4_2g23980' => 'fve', 'FvH4_4g14380' => 'fve', 'FvH4_4g14390' => 'fve', 'FvH4_6g09250' => 'fve', 'Glyma.03G151100' => 'gma', 'Glyma.04G122550' => 'gma', 'Glyma.05G001600' => 'gma', 'Glyma.09G270766' => 'gma', 'Glyma.09G270832' => 'gma', 'Glyma.13G209800' => 'gma', 'Glyma.15G102800' => 'gma', 'Glyma.18G218900' => 'gma', 'Glyma.19G001500' => 'gma', 'Glyma.19G153600' => 'gma', 'Gohir.A02G028600' => 'ghi', 'Gohir.A08G045000' => 'ghi', 'Gohir.A11G120500' => 'ghi', 'Gohir.A12G006200' => 'ghi', 'Gohir.A12G006250' => 'ghi', 'Gohir.D02G036300' => 'ghi', 'Gohir.D08G054700' => 'ghi', 'Gohir.D11G125600' => 'ghi', 'Gohir.D12G005700' => 'ghi', 'Gorai.004G055200' => 'gra', 'Gorai.005G040400' => 'gra', 'Gorai.007G134500' => 'gra', 'Gorai.008G005500' => 'gra', 'GSVIVG01011094001' => 'vvi', 'GSVIVG01017879001' => 'vvi', 'GSVIVG01025988001' => 'vvi', 'GSVIVG01029847001' => 'vvi', 'HanXRQChr10g0282901' => 'han', 'HanXRQChr10g0310371' => 'han', 'HanXRQChr10g0315041' => 'han', 'HanXRQChr11g0327651' => 'han', 'HanXRQChr12g0359391' => 'han', 'Haze_00972' => 'cav', 'Haze_00973' => 'cav', 'Haze_00974' => 'cav', 'Haze_04747' => 'cav', 'Haze_04749' => 'cav', 'Haze_04750' => 'cav', 'Haze_21217' => 'cav', 'Hma1.2p1_1037F.1_g250680' => 'hma', 'Hma1.2p1_1644F.1_g295320' => 'hma', 'HPP92_011322' => 'vpl', 'HPP92_011323' => 'vpl', 'HPP92_011324' => 'vpl', 'HPP92_011325' => 'vpl', 'HPP92_011326' => 'vpl', 'Hund12205' => 'sun', 'Hund17957' => 'sun', 'Lalb_Chr06g0176771' => 'lal', 'Lalb_Chr18g0056021' => 'lal', 'Lalb_Chr18g0056031' => 'lal', 'Lalb_Chr18g0056041' => 'lal', 'Lalb_Chr20g0107751' => 'lal', 'Lalb_Chr20g0118371' => 'lal', 'Lj1g0010239' => 'lja', 'Lj1g0017101' => 'lja', 'Lj2A1178G40' => 'lonja', 'Lj2A54G84' => 'lonja', 'Lj2g0015248' => 'lja', 'Lj3A761T51' => 'lonja', 'Lj6g0018116' => 'lja', 'Lsat_1_v5_gn_4_136040' => 'lsa', 'Lsat_1_v5_gn_5_187461' => 'lsa', 'Lsat_1_v5_gn_5_77001' => 'lsa', 'Lsat_1_v5_gn_9_4461' => 'lsa', 'Manes.01G210100' => 'mes', 'Manes.03G185600' => 'mes', 'Manes.05G073300' => 'mes', 'Manes.09G120300' => 'mes', 'Manes.15G022100' => 'mes', 'Mapoly0096s0053' => 'mpo', 'MBI03_g14058_MAGBIO' => 'mbi', 'MBI03_g33876_MAGBIO' => 'mbi', 'MBI03_g36854_MAGBIO' => 'mbi', 'MBI17_g11997_MAGBIO' => 'mbi', 'MD03G1269000' => 'mdo', 'MD04G1179600' => 'mdo', 'MD11G1289800' => 'mdo', 'MD12G1194700' => 'mdo', 'MD13G1182100' => 'mdo', 'MD13G1182200' => 'mdo', 'MD16G1182600' => 'mdo', 'Medtr2g021400' => 'mtr', 'Medtr2g021470' => 'mtr', 'Medtr2g105810' => 'mtr', 'Medtr3g033580' => 'mtr', 'Medtr6g007970' => 'mtr', 'Medtr7g056330' => 'mtr', 'Medtr7g074290' => 'mtr', 'Medtr7g074380' => 'mtr', 'Medtr7g094550' => 'mtr', 'Medtr8g069995' => 'mtr', 'MELO3C014345.2' => 'cme', 'MELO3C021395.2' => 'cme', 'Migut.D00262' => 'egut', 'Migut.G00257' => 'egut', 'MSTRG.21575' => 'ama', 'MSTRG.3985' => 'ama', 'Nitab4.5_0000295g0140' => 'nta', 'Nitab4.5_0000732g0140' => 'nta', 'Nitab4.5_0003162g0020' => 'nta', 'Nitab4.5_0006180g0090' => 'nta', 'Nitab4.5_0006390g0010' => 'nta', 'Nitab4.5_0007392g0040' => 'nta', 'Nn1g02140' => 'nnu', 'Nn4g26168' => 'nnu', 'Nn5g26754' => 'nnu', 'Oeu001433.1' => 'oeu', 'Oeu010299.2' => 'oeu', 'Oeu011171.1' => 'oeu', 'Oeu037675.1' => 'oeu', 'Oeu038359.1' => 'oeu', 'Oeu063834.1' => 'oeu', 'Oeu063835.1' => 'oeu', 'Os05g0312000' => 'osa', 'Os07g0211101' => 'osa', 'Os07g0211200' => 'osa', 'Os07g0681500' => 'osa', 'Peaxi162Scf00095g01015' => 'pax', 'Peaxi162Scf00104g00329' => 'pax', 'Peaxi162Scf00161g00137' => 'pax', 'PGR004G1665' => 'pgr', 'PGR031G2937' => 'pgr', 'PGR119G2145' => 'pgr', 'PGSC0003DMG400004351' => 'stu', 'PGSC0003DMG400014625' => 'stu', 'PGSC0003DMG401000943' => 'stu', 'Phvul.001G148600' => 'pvu', 'Phvul.004G001700' => 'pvu', 'Phvul.006G154900' => 'pvu', 'Phvul.008G078200' => 'pvu', 'Phvul.011G136500' => 'pvu', 'Potri.002G215600' => 'ptr', 'Potri.008G201600' => 'ptr', 'Potri.014G138400' => 'ptr', 'Potri.016G142500' => 'ptr', 'Pp3c16_10580' => 'ppa', 'Pp3c5_25280' => 'ppa', 'Prupe.1G150000' => 'ppe', 'Prupe.1G150100' => 'ppe', 'Prupe.6G299600' => 'ppe', 'Prupe.8G245000' => 'ppe', 'Psat0s4927g0040' => 'psa', 'Psat1g052080' => 'psa', 'Psat1g183800' => 'psa', 'Psat3g113840' => 'psa', 'Psat3g126120' => 'psa', 'Psat3g126160' => 'psa', 'Psat3g158760' => 'psa', 'Psat3g158840' => 'psa', 'PSO170G2858' => 'pso', 'PSO339G0606' => 'pso', 'PSO384G4709' => 'pso', 'PSO407G0334' => 'pso', 'QL04p040276' => 'qlo', 'QL06p005458' => 'qlo', 'QL06p005472' => 'qlo', 'QL07p030546' => 'qlo', 'QL07p031519' => 'qlo', 'QL09p050949' => 'qlo', 'QL09p050966' => 'qlo', 'QL09p051067' => 'qlo', 'QL12p022706' => 'qlo', 'RcHm_v2.0_Chr2g0119601' => 'rch', 'RcHm_v2.0_Chr3g0459591' => 'rch', 'RcHm_v2.0_Chr4g0418521' => 'rch', 'RcHm_v2.0_Chr4g0418531' => 'rch', 'RcHm_v2.0_Chr4g0418541' => 'rch', 'RcHm_v2.0_Chr6g0291641' => 'rch', 'Rhsim01G0086300' => 'rsi', 'Rhsim01G0276300' => 'rsi', 'Rhsim01G0276500' => 'rsi', 'Rhsim04G0207700' => 'rsi', 'Rhsim05G0234500' => 'rsi', 'Rhsim13G0022400' => 'rsi', 'Sabra02G0167900' => 'sbr', 'Sabra04G0158500' => 'sbr', 'Sabra08G0159800' => 'sbr', 'Sabra10G0011500' => 'sbr', 'Sabra14G0104400' => 'sbr', 'SalBow2G2440' => 'sbo', 'SalBow4G2265' => 'sbo', 'Sc02g0000060' => 'sci', 'Sc05g0005020' => 'sci', 'Sc13g0003890' => 'sci', 'Sed0014865' => 'sed', 'Sed0017224' => 'sed', 'Sed0026391' => 'sed', 'SEGI_00063' => 'sgi', 'SEGI_10967' => 'sgi', 'SEGI_17510' => 'sgi', 'SEGI_24396' => 'sgi', 'SEGI_39719' => 'sgi', 'SEGI_41392' => 'sgi', 'SGA_v2.0_scaffold11G05794' => 'sas', 'SGA_v2.0_scaffold142G35607' => 'sas', 'SGA_v2.0_scaffold1G00447' => 'sas', 'SHI15388' => 'shi', 'SHI15394' => 'shi', 'SHI15396' => 'shi', 'SHI15399' => 'shi', 'SMO343G0151' => 'smo', 'SMO367G1118' => 'smo', 'Solyc01g080200.3' => 'sly', 'Solyc06g008960.3' => 'sly', 'Solyc09g064780.3' => 'sly', 'Sopen01g031980' => 'spe', 'Sopen06g003710' => 'spe', 'Sopen09g026460' => 'spe', 'Sp3g21240' => 'spa', 'Sp4g30030' => 'spa', 'TAR365G0022' => 'tar', 'TAR365G1023' => 'tar', 'TAR365G1253' => 'tar', 'TAR623G0078' => 'tar', 'TAR623G1721' => 'tar', 'TAR633G0959' => 'tar', 'THA.LOC104802225' => 'tha', 'THA.LOC104804769' => 'tha', 'THA.LOC104808660' => 'tha', 'THA.LOC104812792' => 'tha', 'Thecc.01G284000' => 'tca', 'Thecc.04G220600' => 'tca', 'Thecc.05G268900' => 'tca', 'Thecc.08G171100' => 'tca', 'Thhalv10001284m.g' => 'esa', 'Thhalv10019912m.g' => 'esa', 'TPR.G14189' => 'tpr', 'TPR.G18110' => 'tpr', 'TPR.G18130' => 'tpr', 'TPR.G18131' => 'tpr', 'TPR.G18140' => 'tpr', 'TPR.G24282' => 'tpr', 'TPR.G25221' => 'tpr', 'TPR.G29267' => 'tpr', 'TPR.G35315' => 'tpr', 'TPR.G36173' => 'tpr', 'TWI09G0794' => 'twi', 'TWI59G1348' => 'twi', 'TWI74G0430' => 'twi', 'unitig_26.g8940' => 'ugi', 'unitig_749.g13744' => 'ugi', 'unitig_749.g13745' => 'ugi', 'vmacro08269' => 'vma', 'vmacro14937' => 'vma', 'vmacro20401' => 'vma', 'VMungo0464G1349' => 'vmu', 'VMungo0540G0289' => 'vmu', 'VMungo1215G1590' => 'vmu', 'VMungo1309G0221' => 'vmu', 'VMungo1309G2815' => 'vmu', 'VMungo1383G0239' => 'vmu', 'VMungo1383G2910' => 'vmu', 'Zm00001eb095270' => 'zma', 'Zm00001eb095280' => 'zma', 'Zm00001eb111630' => 'zma', 'Zm00001eb237080' => 'zma', 'Zm00001eb273740' => 'zma', 'Zm00001eb285040' => 'zma', 'Zm00001eb330790' => 'zma', 'Zm00001eb337380' => 'zma' ) $gf_id = 'HOM05D001484' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001484' ) $data_identifier = 'HOM05D001484' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 2, 'aly' => (int) 2, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 22, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 7, 'hma' => (int) 2, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 7, 'mtr' => (int) 10, 'cme' => (int) 2, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 4, 'ppa' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 4, 'qlo' => (int) 9, 'rch' => (int) 6, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 10, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 7, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb337380' $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' => 'HOM05D001484', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p31500' => 'bna', 'A05p00020' => 'bna', 'A07p08820' => 'bna', 'Aa31LG4G3300' => 'aar', 'Aa31LG8G10030' => 'aar', 'Actinidia00731' => 'ach', 'Actinidia11473' => 'ach', 'Actinidia23469' => 'ach', 'Actinidia24318' => 'ach', 'Actinidia40196' => 'ach', 'Actinidia40197' => 'ach', 'Actinidia40198' => 'ach', 'Ah.08g212990' => 'amhyb', 'Ah.15g091720' => 'amhyb', 'AL3G38260' => 'aly', 'AL4G47710' => 'aly', 'Aqoxy2G00671' => 'aox', 'Aqoxy2G03236' => 'aox', 'arahy.Tifrunner.gnm1.ann1.05IDCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KR684' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATY3SJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK6QJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6APGL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IDT7Z9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM073U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ0R87' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LE7RV4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT4QRX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V5ENPK' => 'arhy', 'AT2G48110' => 'ath', 'AT3G23590' => 'ath', 'ATR0626G186' => 'atr', 'ATR1127G141' => 'atr', 'Atru.chr4.2583' => 'acertr', 'Atru.chr5.1358' => 'acertr', 'Atru.chr5.1359' => 'acertr', 'Atru.chr8.46' => 'acertr', 'AUR62002640' => 'cqu', 'AUR62030055' => 'cqu', 'AUR62033713' => 'cqu', 'AUR62033714' => 'cqu', 'AUR62036795' => 'cqu', 'AUR62039891' => 'cqu', 'BcaB02g08737' => 'bca', 'BcaB04g20441' => 'bca', 'BcaB06g26509' => 'bca', 'BcaB06g26510' => 'bca', 'BcaB06g26511' => 'bca', 'BcaB06g26512' => 'bca', 'BcaB06g26513' => 'bca', 'BcaC02g12564' => 'bca', 'BcaC02g12565' => 'bca', 'BcaC02g12794' => 'bca', 'BcaC02g12795' => 'bca', 'BcaC02g12796' => 'bca', 'BcaC06g35541' => 'bca', 'BNapus_Darmor_BZH_scaffold_188p00080' => 'bna', 'BNapus_Darmor_BZH_scaffold_188p00090' => 'bna', 'BolC1t03972H' => 'bol', 'BolC1t03973H' => 'bol', 'BolC4t21680H' => 'bol', 'BolC7t41863H' => 'bol', 'BolSC55t61227H' => 'bol', 'BolSC55t61228H' => 'bol', 'BraA01t03278Z' => 'bra', 'BraA05t18998Z' => 'bra', 'BraA07t28673Z' => 'bra', 'C01p40150' => 'bna', 'C05p12370' => 'bna', 'C07p13680' => 'bna', 'CAN.G1006.16' => 'can', 'CAN.G1006.17' => 'can', 'CAN.G1170.2' => 'can', 'CAN.G962.7' => 'can', 'CANSAT25G2179' => 'cansat', 'CANSAT78G1573' => 'cansat', 'CARHR099510' => 'chi', 'CARHR143510' => 'chi', 'Carub.0003s2380' => 'cru', 'Carub.0004s3082' => 'cru', 'Ca_00614_v3' => 'car', 'Ca_07801_v3' => 'car', 'Ca_08567_v3' => 'car', 'Ca_09571_v3' => 'car', 'CBR_g19290' => 'cbr', 'Cc01_g19770' => 'ccan', 'Cc03_g03030' => 'ccan', 'CDE07G0968' => 'cde', 'CDE09G1441' => 'cde', 'Cfa006103' => 'cfa', 'Cfa015573' => 'cfa', 'Cfa016988' => 'cfa', 'Ciclev10006738m.g' => 'ccl', 'Ciclev10010920m.g' => 'ccl', 'Ciclev10018517m.g' => 'ccl', 'CiPaw.01G159200' => 'cil', 'CiPaw.02G091000' => 'cil', 'CiPaw.02G091100' => 'cil', 'CiPaw.08G103100' => 'cil', 'CiPaw.09G224900' => 'cil', 'ClCG06G005740' => 'cla', 'ClCG07G000090' => 'cla', 'ClCG07G000100' => 'cla', 'COL.COLO4_09143' => 'col', 'COL.COLO4_25124' => 'col', 'Cpa.g.sc16.34' => 'cpa', 'Cpa.g.sc3504.1' => 'cpa', 'Cpa.g.sc60.37' => 'cpa', 'CsaV3_6G018520' => 'csa', 'CsaV3_6G036860' => 'csa', 'CSS0001072' => 'camsi', 'CSS0020208' => 'camsi', 'CSS0021253' => 'camsi', 'CSS0022190' => 'camsi', 'CSS0036150' => 'camsi', 'CSS0040442' => 'camsi', 'CSS0042300' => 'camsi', 'CSS0045298' => 'camsi', 'DCAR_012449' => 'dca', 'DCAR_018405' => 'dca', 'DCAR_024573' => 'dca', 'DCAR_030591' => 'dca', 'Dinv16926' => 'din', 'Dinv32963' => 'din', 'Dinv38382' => 'din', 'Dinv38383' => 'din', 'Duzib133G0974' => 'dzi', 'Duzib138G1867' => 'dzi', 'Duzib211G0420' => 'dzi', 'Duzib212G0930' => 'dzi', 'ECA234G1645' => 'eca', 'ECA247G3467' => 'eca', 'ECA248G1703' => 'eca', 'EL10Ac3g06327' => 'bvu', 'EL10Ac7g17204' => 'bvu', 'Eucgr.A00855' => 'egr', 'Eucgr.A00858' => 'egr', 'Eucgr.H01520' => 'egr', 'Eucgr.H03604' => 'egr', 'Eucgr.L03465' => 'egr', 'Eucgr.L03466' => 'egr', 'FAN01G0988' => 'fan', 'FAN02G3892' => 'fan', 'FAN05G3381' => 'fan', 'FAN07G0967' => 'fan', 'FAN07G1493' => 'fan', 'FAN08G3125' => 'fan', 'FAN09G0402' => 'fan', 'FAN12G2594' => 'fan', 'FAN12G3879' => 'fan', 'FAN14G1546' => 'fan', 'FAN15G3626' => 'fan', 'FAN17G0588' => 'fan', 'FAN17G0609' => 'fan', 'FAN18G2817' => 'fan', 'FAN19G1305' => 'fan', 'FAN20G1787' => 'fan', 'FAN22G0073' => 'fan', 'FAN22G0352' => 'fan', 'FAN22G0368' => 'fan', 'FAN22G2273' => 'fan', 'FAN24G1998' => 'fan', 'FAN27G1317' => 'fan', 'FvH4_2g23980' => 'fve', 'FvH4_4g14380' => 'fve', 'FvH4_4g14390' => 'fve', 'FvH4_6g09250' => 'fve', 'Glyma.03G151100' => 'gma', 'Glyma.04G122550' => 'gma', 'Glyma.05G001600' => 'gma', 'Glyma.09G270766' => 'gma', 'Glyma.09G270832' => 'gma', 'Glyma.13G209800' => 'gma', 'Glyma.15G102800' => 'gma', 'Glyma.18G218900' => 'gma', 'Glyma.19G001500' => 'gma', 'Glyma.19G153600' => 'gma', 'Gohir.A02G028600' => 'ghi', 'Gohir.A08G045000' => 'ghi', 'Gohir.A11G120500' => 'ghi', 'Gohir.A12G006200' => 'ghi', 'Gohir.A12G006250' => 'ghi', 'Gohir.D02G036300' => 'ghi', 'Gohir.D08G054700' => 'ghi', 'Gohir.D11G125600' => 'ghi', 'Gohir.D12G005700' => 'ghi', 'Gorai.004G055200' => 'gra', 'Gorai.005G040400' => 'gra', 'Gorai.007G134500' => 'gra', 'Gorai.008G005500' => 'gra', 'GSVIVG01011094001' => 'vvi', 'GSVIVG01017879001' => 'vvi', 'GSVIVG01025988001' => 'vvi', 'GSVIVG01029847001' => 'vvi', 'HanXRQChr10g0282901' => 'han', 'HanXRQChr10g0310371' => 'han', 'HanXRQChr10g0315041' => 'han', 'HanXRQChr11g0327651' => 'han', 'HanXRQChr12g0359391' => 'han', 'Haze_00972' => 'cav', 'Haze_00973' => 'cav', 'Haze_00974' => 'cav', 'Haze_04747' => 'cav', 'Haze_04749' => 'cav', 'Haze_04750' => 'cav', 'Haze_21217' => 'cav', 'Hma1.2p1_1037F.1_g250680' => 'hma', 'Hma1.2p1_1644F.1_g295320' => 'hma', 'HPP92_011322' => 'vpl', 'HPP92_011323' => 'vpl', 'HPP92_011324' => 'vpl', 'HPP92_011325' => 'vpl', 'HPP92_011326' => 'vpl', 'Hund12205' => 'sun', 'Hund17957' => 'sun', 'Lalb_Chr06g0176771' => 'lal', 'Lalb_Chr18g0056021' => 'lal', 'Lalb_Chr18g0056031' => 'lal', 'Lalb_Chr18g0056041' => 'lal', 'Lalb_Chr20g0107751' => 'lal', 'Lalb_Chr20g0118371' => 'lal', 'Lj1g0010239' => 'lja', 'Lj1g0017101' => 'lja', 'Lj2A1178G40' => 'lonja', 'Lj2A54G84' => 'lonja', 'Lj2g0015248' => 'lja', 'Lj3A761T51' => 'lonja', 'Lj6g0018116' => 'lja', 'Lsat_1_v5_gn_4_136040' => 'lsa', 'Lsat_1_v5_gn_5_187461' => 'lsa', 'Lsat_1_v5_gn_5_77001' => 'lsa', 'Lsat_1_v5_gn_9_4461' => 'lsa', 'Manes.01G210100' => 'mes', 'Manes.03G185600' => 'mes', 'Manes.05G073300' => 'mes', 'Manes.09G120300' => 'mes', 'Manes.15G022100' => 'mes', 'Mapoly0096s0053' => 'mpo', 'MBI03_g14058_MAGBIO' => 'mbi', 'MBI03_g33876_MAGBIO' => 'mbi', 'MBI03_g36854_MAGBIO' => 'mbi', 'MBI17_g11997_MAGBIO' => 'mbi', 'MD03G1269000' => 'mdo', 'MD04G1179600' => 'mdo', 'MD11G1289800' => 'mdo', 'MD12G1194700' => 'mdo', 'MD13G1182100' => 'mdo', 'MD13G1182200' => 'mdo', 'MD16G1182600' => 'mdo', 'Medtr2g021400' => 'mtr', 'Medtr2g021470' => 'mtr', 'Medtr2g105810' => 'mtr', 'Medtr3g033580' => 'mtr', 'Medtr6g007970' => 'mtr', 'Medtr7g056330' => 'mtr', 'Medtr7g074290' => 'mtr', 'Medtr7g074380' => 'mtr', 'Medtr7g094550' => 'mtr', 'Medtr8g069995' => 'mtr', 'MELO3C014345.2' => 'cme', 'MELO3C021395.2' => 'cme', 'Migut.D00262' => 'egut', 'Migut.G00257' => 'egut', 'MSTRG.21575' => 'ama', 'MSTRG.3985' => 'ama', 'Nitab4.5_0000295g0140' => 'nta', 'Nitab4.5_0000732g0140' => 'nta', 'Nitab4.5_0003162g0020' => 'nta', 'Nitab4.5_0006180g0090' => 'nta', 'Nitab4.5_0006390g0010' => 'nta', 'Nitab4.5_0007392g0040' => 'nta', 'Nn1g02140' => 'nnu', 'Nn4g26168' => 'nnu', 'Nn5g26754' => 'nnu', 'Oeu001433.1' => 'oeu', 'Oeu010299.2' => 'oeu', 'Oeu011171.1' => 'oeu', 'Oeu037675.1' => 'oeu', 'Oeu038359.1' => 'oeu', 'Oeu063834.1' => 'oeu', 'Oeu063835.1' => 'oeu', 'Os05g0312000' => 'osa', 'Os07g0211101' => 'osa', 'Os07g0211200' => 'osa', 'Os07g0681500' => 'osa', 'Peaxi162Scf00095g01015' => 'pax', 'Peaxi162Scf00104g00329' => 'pax', 'Peaxi162Scf00161g00137' => 'pax', 'PGR004G1665' => 'pgr', 'PGR031G2937' => 'pgr', 'PGR119G2145' => 'pgr', 'PGSC0003DMG400004351' => 'stu', 'PGSC0003DMG400014625' => 'stu', 'PGSC0003DMG401000943' => 'stu', 'Phvul.001G148600' => 'pvu', 'Phvul.004G001700' => 'pvu', 'Phvul.006G154900' => 'pvu', 'Phvul.008G078200' => 'pvu', 'Phvul.011G136500' => 'pvu', 'Potri.002G215600' => 'ptr', 'Potri.008G201600' => 'ptr', 'Potri.014G138400' => 'ptr', 'Potri.016G142500' => 'ptr', 'Pp3c16_10580' => 'ppa', 'Pp3c5_25280' => 'ppa', 'Prupe.1G150000' => 'ppe', 'Prupe.1G150100' => 'ppe', 'Prupe.6G299600' => 'ppe', 'Prupe.8G245000' => 'ppe', 'Psat0s4927g0040' => 'psa', 'Psat1g052080' => 'psa', 'Psat1g183800' => 'psa', 'Psat3g113840' => 'psa', 'Psat3g126120' => 'psa', 'Psat3g126160' => 'psa', 'Psat3g158760' => 'psa', 'Psat3g158840' => 'psa', 'PSO170G2858' => 'pso', 'PSO339G0606' => 'pso', 'PSO384G4709' => 'pso', 'PSO407G0334' => 'pso', 'QL04p040276' => 'qlo', 'QL06p005458' => 'qlo', 'QL06p005472' => 'qlo', 'QL07p030546' => 'qlo', 'QL07p031519' => 'qlo', 'QL09p050949' => 'qlo', 'QL09p050966' => 'qlo', 'QL09p051067' => 'qlo', 'QL12p022706' => 'qlo', 'RcHm_v2.0_Chr2g0119601' => 'rch', 'RcHm_v2.0_Chr3g0459591' => 'rch', 'RcHm_v2.0_Chr4g0418521' => 'rch', 'RcHm_v2.0_Chr4g0418531' => 'rch', 'RcHm_v2.0_Chr4g0418541' => 'rch', 'RcHm_v2.0_Chr6g0291641' => 'rch', 'Rhsim01G0086300' => 'rsi', 'Rhsim01G0276300' => 'rsi', 'Rhsim01G0276500' => 'rsi', 'Rhsim04G0207700' => 'rsi', 'Rhsim05G0234500' => 'rsi', 'Rhsim13G0022400' => 'rsi', 'Sabra02G0167900' => 'sbr', 'Sabra04G0158500' => 'sbr', 'Sabra08G0159800' => 'sbr', 'Sabra10G0011500' => 'sbr', 'Sabra14G0104400' => 'sbr', 'SalBow2G2440' => 'sbo', 'SalBow4G2265' => 'sbo', 'Sc02g0000060' => 'sci', 'Sc05g0005020' => 'sci', 'Sc13g0003890' => 'sci', 'Sed0014865' => 'sed', 'Sed0017224' => 'sed', 'Sed0026391' => 'sed', 'SEGI_00063' => 'sgi', 'SEGI_10967' => 'sgi', 'SEGI_17510' => 'sgi', 'SEGI_24396' => 'sgi', 'SEGI_39719' => 'sgi', 'SEGI_41392' => 'sgi', 'SGA_v2.0_scaffold11G05794' => 'sas', 'SGA_v2.0_scaffold142G35607' => 'sas', 'SGA_v2.0_scaffold1G00447' => 'sas', 'SHI15388' => 'shi', 'SHI15394' => 'shi', 'SHI15396' => 'shi', 'SHI15399' => 'shi', 'SMO343G0151' => 'smo', 'SMO367G1118' => 'smo', 'Solyc01g080200.3' => 'sly', 'Solyc06g008960.3' => 'sly', 'Solyc09g064780.3' => 'sly', 'Sopen01g031980' => 'spe', 'Sopen06g003710' => 'spe', 'Sopen09g026460' => 'spe', 'Sp3g21240' => 'spa', 'Sp4g30030' => 'spa', 'TAR365G0022' => 'tar', 'TAR365G1023' => 'tar', 'TAR365G1253' => 'tar', 'TAR623G0078' => 'tar', 'TAR623G1721' => 'tar', 'TAR633G0959' => 'tar', 'THA.LOC104802225' => 'tha', 'THA.LOC104804769' => 'tha', 'THA.LOC104808660' => 'tha', 'THA.LOC104812792' => 'tha', 'Thecc.01G284000' => 'tca', 'Thecc.04G220600' => 'tca', 'Thecc.05G268900' => 'tca', 'Thecc.08G171100' => 'tca', 'Thhalv10001284m.g' => 'esa', 'Thhalv10019912m.g' => 'esa', 'TPR.G14189' => 'tpr', 'TPR.G18110' => 'tpr', 'TPR.G18130' => 'tpr', 'TPR.G18131' => 'tpr', 'TPR.G18140' => 'tpr', 'TPR.G24282' => 'tpr', 'TPR.G25221' => 'tpr', 'TPR.G29267' => 'tpr', 'TPR.G35315' => 'tpr', 'TPR.G36173' => 'tpr', 'TWI09G0794' => 'twi', 'TWI59G1348' => 'twi', 'TWI74G0430' => 'twi', 'unitig_26.g8940' => 'ugi', 'unitig_749.g13744' => 'ugi', 'unitig_749.g13745' => 'ugi', 'vmacro08269' => 'vma', 'vmacro14937' => 'vma', 'vmacro20401' => 'vma', 'VMungo0464G1349' => 'vmu', 'VMungo0540G0289' => 'vmu', 'VMungo1215G1590' => 'vmu', 'VMungo1309G0221' => 'vmu', 'VMungo1309G2815' => 'vmu', 'VMungo1383G0239' => 'vmu', 'VMungo1383G2910' => 'vmu', 'Zm00001eb095270' => 'zma', 'Zm00001eb095280' => 'zma', 'Zm00001eb111630' => 'zma', 'Zm00001eb237080' => 'zma', 'Zm00001eb273740' => 'zma', 'Zm00001eb285040' => 'zma', 'Zm00001eb330790' => 'zma', 'Zm00001eb337380' => 'zma' ), 'gf_id' => 'HOM05D001484', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001484' ), 'data_identifier' => 'HOM05D001484', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001484', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p31500' => 'bna', 'A05p00020' => 'bna', 'A07p08820' => 'bna', 'Aa31LG4G3300' => 'aar', 'Aa31LG8G10030' => 'aar', 'Actinidia00731' => 'ach', 'Actinidia11473' => 'ach', 'Actinidia23469' => 'ach', 'Actinidia24318' => 'ach', 'Actinidia40196' => 'ach', 'Actinidia40197' => 'ach', 'Actinidia40198' => 'ach', 'Ah.08g212990' => 'amhyb', 'Ah.15g091720' => 'amhyb', 'AL3G38260' => 'aly', 'AL4G47710' => 'aly', 'Aqoxy2G00671' => 'aox', 'Aqoxy2G03236' => 'aox', 'arahy.Tifrunner.gnm1.ann1.05IDCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KR684' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATY3SJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK6QJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6APGL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IDT7Z9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM073U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ0R87' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LE7RV4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT4QRX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V5ENPK' => 'arhy', 'AT2G48110' => 'ath', 'AT3G23590' => 'ath', 'ATR0626G186' => 'atr', 'ATR1127G141' => 'atr', 'Atru.chr4.2583' => 'acertr', 'Atru.chr5.1358' => 'acertr', 'Atru.chr5.1359' => 'acertr', 'Atru.chr8.46' => 'acertr', 'AUR62002640' => 'cqu', 'AUR62030055' => 'cqu', 'AUR62033713' => 'cqu', 'AUR62033714' => 'cqu', 'AUR62036795' => 'cqu', 'AUR62039891' => 'cqu', 'BcaB02g08737' => 'bca', 'BcaB04g20441' => 'bca', 'BcaB06g26509' => 'bca', 'BcaB06g26510' => 'bca', 'BcaB06g26511' => 'bca', 'BcaB06g26512' => 'bca', 'BcaB06g26513' => 'bca', 'BcaC02g12564' => 'bca', 'BcaC02g12565' => 'bca', 'BcaC02g12794' => 'bca', 'BcaC02g12795' => 'bca', 'BcaC02g12796' => 'bca', 'BcaC06g35541' => 'bca', 'BNapus_Darmor_BZH_scaffold_188p00080' => 'bna', 'BNapus_Darmor_BZH_scaffold_188p00090' => 'bna', 'BolC1t03972H' => 'bol', 'BolC1t03973H' => 'bol', 'BolC4t21680H' => 'bol', 'BolC7t41863H' => 'bol', 'BolSC55t61227H' => 'bol', 'BolSC55t61228H' => 'bol', 'BraA01t03278Z' => 'bra', 'BraA05t18998Z' => 'bra', 'BraA07t28673Z' => 'bra', 'C01p40150' => 'bna', 'C05p12370' => 'bna', 'C07p13680' => 'bna', 'CAN.G1006.16' => 'can', 'CAN.G1006.17' => 'can', 'CAN.G1170.2' => 'can', 'CAN.G962.7' => 'can', 'CANSAT25G2179' => 'cansat', 'CANSAT78G1573' => 'cansat', 'CARHR099510' => 'chi', 'CARHR143510' => 'chi', 'Carub.0003s2380' => 'cru', 'Carub.0004s3082' => 'cru', 'Ca_00614_v3' => 'car', 'Ca_07801_v3' => 'car', 'Ca_08567_v3' => 'car', 'Ca_09571_v3' => 'car', 'CBR_g19290' => 'cbr', 'Cc01_g19770' => 'ccan', 'Cc03_g03030' => 'ccan', 'CDE07G0968' => 'cde', 'CDE09G1441' => 'cde', 'Cfa006103' => 'cfa', 'Cfa015573' => 'cfa', 'Cfa016988' => 'cfa', 'Ciclev10006738m.g' => 'ccl', 'Ciclev10010920m.g' => 'ccl', 'Ciclev10018517m.g' => 'ccl', 'CiPaw.01G159200' => 'cil', 'CiPaw.02G091000' => 'cil', 'CiPaw.02G091100' => 'cil', 'CiPaw.08G103100' => 'cil', 'CiPaw.09G224900' => 'cil', 'ClCG06G005740' => 'cla', 'ClCG07G000090' => 'cla', 'ClCG07G000100' => 'cla', 'COL.COLO4_09143' => 'col', 'COL.COLO4_25124' => 'col', 'Cpa.g.sc16.34' => 'cpa', 'Cpa.g.sc3504.1' => 'cpa', 'Cpa.g.sc60.37' => 'cpa', 'CsaV3_6G018520' => 'csa', 'CsaV3_6G036860' => 'csa', 'CSS0001072' => 'camsi', 'CSS0020208' => 'camsi', 'CSS0021253' => 'camsi', 'CSS0022190' => 'camsi', 'CSS0036150' => 'camsi', 'CSS0040442' => 'camsi', 'CSS0042300' => 'camsi', 'CSS0045298' => 'camsi', 'DCAR_012449' => 'dca', 'DCAR_018405' => 'dca', 'DCAR_024573' => 'dca', 'DCAR_030591' => 'dca', 'Dinv16926' => 'din', 'Dinv32963' => 'din', 'Dinv38382' => 'din', 'Dinv38383' => 'din', 'Duzib133G0974' => 'dzi', 'Duzib138G1867' => 'dzi', 'Duzib211G0420' => 'dzi', 'Duzib212G0930' => 'dzi', 'ECA234G1645' => 'eca', 'ECA247G3467' => 'eca', 'ECA248G1703' => 'eca', 'EL10Ac3g06327' => 'bvu', 'EL10Ac7g17204' => 'bvu', 'Eucgr.A00855' => 'egr', 'Eucgr.A00858' => 'egr', 'Eucgr.H01520' => 'egr', 'Eucgr.H03604' => 'egr', 'Eucgr.L03465' => 'egr', 'Eucgr.L03466' => 'egr', 'FAN01G0988' => 'fan', 'FAN02G3892' => 'fan', 'FAN05G3381' => 'fan', 'FAN07G0967' => 'fan', 'FAN07G1493' => 'fan', 'FAN08G3125' => 'fan', 'FAN09G0402' => 'fan', 'FAN12G2594' => 'fan', 'FAN12G3879' => 'fan', 'FAN14G1546' => 'fan', 'FAN15G3626' => 'fan', 'FAN17G0588' => 'fan', 'FAN17G0609' => 'fan', 'FAN18G2817' => 'fan', 'FAN19G1305' => 'fan', 'FAN20G1787' => 'fan', 'FAN22G0073' => 'fan', 'FAN22G0352' => 'fan', 'FAN22G0368' => 'fan', 'FAN22G2273' => 'fan', 'FAN24G1998' => 'fan', 'FAN27G1317' => 'fan', 'FvH4_2g23980' => 'fve', 'FvH4_4g14380' => 'fve', 'FvH4_4g14390' => 'fve', 'FvH4_6g09250' => 'fve', 'Glyma.03G151100' => 'gma', 'Glyma.04G122550' => 'gma', 'Glyma.05G001600' => 'gma', 'Glyma.09G270766' => 'gma', 'Glyma.09G270832' => 'gma', 'Glyma.13G209800' => 'gma', 'Glyma.15G102800' => 'gma', 'Glyma.18G218900' => 'gma', 'Glyma.19G001500' => 'gma', 'Glyma.19G153600' => 'gma', 'Gohir.A02G028600' => 'ghi', 'Gohir.A08G045000' => 'ghi', 'Gohir.A11G120500' => 'ghi', 'Gohir.A12G006200' => 'ghi', 'Gohir.A12G006250' => 'ghi', 'Gohir.D02G036300' => 'ghi', 'Gohir.D08G054700' => 'ghi', 'Gohir.D11G125600' => 'ghi', 'Gohir.D12G005700' => 'ghi', 'Gorai.004G055200' => 'gra', 'Gorai.005G040400' => 'gra', 'Gorai.007G134500' => 'gra', 'Gorai.008G005500' => 'gra', 'GSVIVG01011094001' => 'vvi', 'GSVIVG01017879001' => 'vvi', 'GSVIVG01025988001' => 'vvi', 'GSVIVG01029847001' => 'vvi', 'HanXRQChr10g0282901' => 'han', 'HanXRQChr10g0310371' => 'han', 'HanXRQChr10g0315041' => 'han', 'HanXRQChr11g0327651' => 'han', 'HanXRQChr12g0359391' => 'han', 'Haze_00972' => 'cav', 'Haze_00973' => 'cav', 'Haze_00974' => 'cav', 'Haze_04747' => 'cav', 'Haze_04749' => 'cav', 'Haze_04750' => 'cav', 'Haze_21217' => 'cav', 'Hma1.2p1_1037F.1_g250680' => 'hma', 'Hma1.2p1_1644F.1_g295320' => 'hma', 'HPP92_011322' => 'vpl', 'HPP92_011323' => 'vpl', 'HPP92_011324' => 'vpl', 'HPP92_011325' => 'vpl', 'HPP92_011326' => 'vpl', 'Hund12205' => 'sun', 'Hund17957' => 'sun', 'Lalb_Chr06g0176771' => 'lal', 'Lalb_Chr18g0056021' => 'lal', 'Lalb_Chr18g0056031' => 'lal', 'Lalb_Chr18g0056041' => 'lal', 'Lalb_Chr20g0107751' => 'lal', 'Lalb_Chr20g0118371' => 'lal', 'Lj1g0010239' => 'lja', 'Lj1g0017101' => 'lja', 'Lj2A1178G40' => 'lonja', 'Lj2A54G84' => 'lonja', 'Lj2g0015248' => 'lja', 'Lj3A761T51' => 'lonja', 'Lj6g0018116' => 'lja', 'Lsat_1_v5_gn_4_136040' => 'lsa', 'Lsat_1_v5_gn_5_187461' => 'lsa', 'Lsat_1_v5_gn_5_77001' => 'lsa', 'Lsat_1_v5_gn_9_4461' => 'lsa', 'Manes.01G210100' => 'mes', 'Manes.03G185600' => 'mes', 'Manes.05G073300' => 'mes', 'Manes.09G120300' => 'mes', 'Manes.15G022100' => 'mes', 'Mapoly0096s0053' => 'mpo', 'MBI03_g14058_MAGBIO' => 'mbi', 'MBI03_g33876_MAGBIO' => 'mbi', 'MBI03_g36854_MAGBIO' => 'mbi', 'MBI17_g11997_MAGBIO' => 'mbi', 'MD03G1269000' => 'mdo', 'MD04G1179600' => 'mdo', 'MD11G1289800' => 'mdo', 'MD12G1194700' => 'mdo', 'MD13G1182100' => 'mdo', 'MD13G1182200' => 'mdo', 'MD16G1182600' => 'mdo', 'Medtr2g021400' => 'mtr', 'Medtr2g021470' => 'mtr', 'Medtr2g105810' => 'mtr', 'Medtr3g033580' => 'mtr', 'Medtr6g007970' => 'mtr', 'Medtr7g056330' => 'mtr', 'Medtr7g074290' => 'mtr', 'Medtr7g074380' => 'mtr', 'Medtr7g094550' => 'mtr', 'Medtr8g069995' => 'mtr', 'MELO3C014345.2' => 'cme', 'MELO3C021395.2' => 'cme', 'Migut.D00262' => 'egut', 'Migut.G00257' => 'egut', 'MSTRG.21575' => 'ama', 'MSTRG.3985' => 'ama', 'Nitab4.5_0000295g0140' => 'nta', 'Nitab4.5_0000732g0140' => 'nta', 'Nitab4.5_0003162g0020' => 'nta', 'Nitab4.5_0006180g0090' => 'nta', 'Nitab4.5_0006390g0010' => 'nta', 'Nitab4.5_0007392g0040' => 'nta', 'Nn1g02140' => 'nnu', 'Nn4g26168' => 'nnu', 'Nn5g26754' => 'nnu', 'Oeu001433.1' => 'oeu', 'Oeu010299.2' => 'oeu', 'Oeu011171.1' => 'oeu', 'Oeu037675.1' => 'oeu', 'Oeu038359.1' => 'oeu', 'Oeu063834.1' => 'oeu', 'Oeu063835.1' => 'oeu', 'Os05g0312000' => 'osa', 'Os07g0211101' => 'osa', 'Os07g0211200' => 'osa', 'Os07g0681500' => 'osa', 'Peaxi162Scf00095g01015' => 'pax', 'Peaxi162Scf00104g00329' => 'pax', 'Peaxi162Scf00161g00137' => 'pax', 'PGR004G1665' => 'pgr', 'PGR031G2937' => 'pgr', 'PGR119G2145' => 'pgr', 'PGSC0003DMG400004351' => 'stu', 'PGSC0003DMG400014625' => 'stu', 'PGSC0003DMG401000943' => 'stu', 'Phvul.001G148600' => 'pvu', 'Phvul.004G001700' => 'pvu', 'Phvul.006G154900' => 'pvu', 'Phvul.008G078200' => 'pvu', 'Phvul.011G136500' => 'pvu', 'Potri.002G215600' => 'ptr', 'Potri.008G201600' => 'ptr', 'Potri.014G138400' => 'ptr', 'Potri.016G142500' => 'ptr', 'Pp3c16_10580' => 'ppa', 'Pp3c5_25280' => 'ppa', 'Prupe.1G150000' => 'ppe', 'Prupe.1G150100' => 'ppe', 'Prupe.6G299600' => 'ppe', 'Prupe.8G245000' => 'ppe', 'Psat0s4927g0040' => 'psa', 'Psat1g052080' => 'psa', 'Psat1g183800' => 'psa', 'Psat3g113840' => 'psa', 'Psat3g126120' => 'psa', 'Psat3g126160' => 'psa', 'Psat3g158760' => 'psa', 'Psat3g158840' => 'psa', 'PSO170G2858' => 'pso', 'PSO339G0606' => 'pso', 'PSO384G4709' => 'pso', 'PSO407G0334' => 'pso', 'QL04p040276' => 'qlo', 'QL06p005458' => 'qlo', 'QL06p005472' => 'qlo', 'QL07p030546' => 'qlo', 'QL07p031519' => 'qlo', 'QL09p050949' => 'qlo', 'QL09p050966' => 'qlo', 'QL09p051067' => 'qlo', 'QL12p022706' => 'qlo', 'RcHm_v2.0_Chr2g0119601' => 'rch', 'RcHm_v2.0_Chr3g0459591' => 'rch', 'RcHm_v2.0_Chr4g0418521' => 'rch', 'RcHm_v2.0_Chr4g0418531' => 'rch', 'RcHm_v2.0_Chr4g0418541' => 'rch', 'RcHm_v2.0_Chr6g0291641' => 'rch', 'Rhsim01G0086300' => 'rsi', 'Rhsim01G0276300' => 'rsi', 'Rhsim01G0276500' => 'rsi', 'Rhsim04G0207700' => 'rsi', 'Rhsim05G0234500' => 'rsi', 'Rhsim13G0022400' => 'rsi', 'Sabra02G0167900' => 'sbr', 'Sabra04G0158500' => 'sbr', 'Sabra08G0159800' => 'sbr', 'Sabra10G0011500' => 'sbr', 'Sabra14G0104400' => 'sbr', 'SalBow2G2440' => 'sbo', 'SalBow4G2265' => 'sbo', 'Sc02g0000060' => 'sci', 'Sc05g0005020' => 'sci', 'Sc13g0003890' => 'sci', 'Sed0014865' => 'sed', 'Sed0017224' => 'sed', 'Sed0026391' => 'sed', 'SEGI_00063' => 'sgi', 'SEGI_10967' => 'sgi', 'SEGI_17510' => 'sgi', 'SEGI_24396' => 'sgi', 'SEGI_39719' => 'sgi', 'SEGI_41392' => 'sgi', 'SGA_v2.0_scaffold11G05794' => 'sas', 'SGA_v2.0_scaffold142G35607' => 'sas', 'SGA_v2.0_scaffold1G00447' => 'sas', 'SHI15388' => 'shi', 'SHI15394' => 'shi', 'SHI15396' => 'shi', 'SHI15399' => 'shi', 'SMO343G0151' => 'smo', 'SMO367G1118' => 'smo', 'Solyc01g080200.3' => 'sly', 'Solyc06g008960.3' => 'sly', 'Solyc09g064780.3' => 'sly', 'Sopen01g031980' => 'spe', 'Sopen06g003710' => 'spe', 'Sopen09g026460' => 'spe', 'Sp3g21240' => 'spa', 'Sp4g30030' => 'spa', 'TAR365G0022' => 'tar', 'TAR365G1023' => 'tar', 'TAR365G1253' => 'tar', 'TAR623G0078' => 'tar', 'TAR623G1721' => 'tar', 'TAR633G0959' => 'tar', 'THA.LOC104802225' => 'tha', 'THA.LOC104804769' => 'tha', 'THA.LOC104808660' => 'tha', 'THA.LOC104812792' => 'tha', 'Thecc.01G284000' => 'tca', 'Thecc.04G220600' => 'tca', 'Thecc.05G268900' => 'tca', 'Thecc.08G171100' => 'tca', 'Thhalv10001284m.g' => 'esa', 'Thhalv10019912m.g' => 'esa', 'TPR.G14189' => 'tpr', 'TPR.G18110' => 'tpr', 'TPR.G18130' => 'tpr', 'TPR.G18131' => 'tpr', 'TPR.G18140' => 'tpr', 'TPR.G24282' => 'tpr', 'TPR.G25221' => 'tpr', 'TPR.G29267' => 'tpr', 'TPR.G35315' => 'tpr', 'TPR.G36173' => 'tpr', 'TWI09G0794' => 'twi', 'TWI59G1348' => 'twi', 'TWI74G0430' => 'twi', 'unitig_26.g8940' => 'ugi', 'unitig_749.g13744' => 'ugi', 'unitig_749.g13745' => 'ugi', 'vmacro08269' => 'vma', 'vmacro14937' => 'vma', 'vmacro20401' => 'vma', 'VMungo0464G1349' => 'vmu', 'VMungo0540G0289' => 'vmu', 'VMungo1215G1590' => 'vmu', 'VMungo1309G0221' => 'vmu', 'VMungo1309G2815' => 'vmu', 'VMungo1383G0239' => 'vmu', 'VMungo1383G2910' => 'vmu', 'Zm00001eb095270' => 'zma', 'Zm00001eb095280' => 'zma', 'Zm00001eb111630' => 'zma', 'Zm00001eb237080' => 'zma', 'Zm00001eb273740' => 'zma', 'Zm00001eb285040' => 'zma', 'Zm00001eb330790' => 'zma', 'Zm00001eb337380' => 'zma' ) $gf_id = 'HOM05D001484' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001484' ) $data_identifier = 'HOM05D001484' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 2, 'aly' => (int) 2, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 22, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 7, 'hma' => (int) 2, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 7, 'mtr' => (int) 10, 'cme' => (int) 2, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 4, 'ppa' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 4, 'qlo' => (int) 9, 'rch' => (int) 6, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 10, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 7, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb337380' $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' => 'HOM05D001484', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p31500' => 'bna', 'A05p00020' => 'bna', 'A07p08820' => 'bna', 'Aa31LG4G3300' => 'aar', 'Aa31LG8G10030' => 'aar', 'Actinidia00731' => 'ach', 'Actinidia11473' => 'ach', 'Actinidia23469' => 'ach', 'Actinidia24318' => 'ach', 'Actinidia40196' => 'ach', 'Actinidia40197' => 'ach', 'Actinidia40198' => 'ach', 'Ah.08g212990' => 'amhyb', 'Ah.15g091720' => 'amhyb', 'AL3G38260' => 'aly', 'AL4G47710' => 'aly', 'Aqoxy2G00671' => 'aox', 'Aqoxy2G03236' => 'aox', 'arahy.Tifrunner.gnm1.ann1.05IDCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KR684' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATY3SJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK6QJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6APGL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IDT7Z9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM073U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ0R87' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LE7RV4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT4QRX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V5ENPK' => 'arhy', 'AT2G48110' => 'ath', 'AT3G23590' => 'ath', 'ATR0626G186' => 'atr', 'ATR1127G141' => 'atr', 'Atru.chr4.2583' => 'acertr', 'Atru.chr5.1358' => 'acertr', 'Atru.chr5.1359' => 'acertr', 'Atru.chr8.46' => 'acertr', 'AUR62002640' => 'cqu', 'AUR62030055' => 'cqu', 'AUR62033713' => 'cqu', 'AUR62033714' => 'cqu', 'AUR62036795' => 'cqu', 'AUR62039891' => 'cqu', 'BcaB02g08737' => 'bca', 'BcaB04g20441' => 'bca', 'BcaB06g26509' => 'bca', 'BcaB06g26510' => 'bca', 'BcaB06g26511' => 'bca', 'BcaB06g26512' => 'bca', 'BcaB06g26513' => 'bca', 'BcaC02g12564' => 'bca', 'BcaC02g12565' => 'bca', 'BcaC02g12794' => 'bca', 'BcaC02g12795' => 'bca', 'BcaC02g12796' => 'bca', 'BcaC06g35541' => 'bca', 'BNapus_Darmor_BZH_scaffold_188p00080' => 'bna', 'BNapus_Darmor_BZH_scaffold_188p00090' => 'bna', 'BolC1t03972H' => 'bol', 'BolC1t03973H' => 'bol', 'BolC4t21680H' => 'bol', 'BolC7t41863H' => 'bol', 'BolSC55t61227H' => 'bol', 'BolSC55t61228H' => 'bol', 'BraA01t03278Z' => 'bra', 'BraA05t18998Z' => 'bra', 'BraA07t28673Z' => 'bra', 'C01p40150' => 'bna', 'C05p12370' => 'bna', 'C07p13680' => 'bna', 'CAN.G1006.16' => 'can', 'CAN.G1006.17' => 'can', 'CAN.G1170.2' => 'can', 'CAN.G962.7' => 'can', 'CANSAT25G2179' => 'cansat', 'CANSAT78G1573' => 'cansat', 'CARHR099510' => 'chi', 'CARHR143510' => 'chi', 'Carub.0003s2380' => 'cru', 'Carub.0004s3082' => 'cru', 'Ca_00614_v3' => 'car', 'Ca_07801_v3' => 'car', 'Ca_08567_v3' => 'car', 'Ca_09571_v3' => 'car', 'CBR_g19290' => 'cbr', 'Cc01_g19770' => 'ccan', 'Cc03_g03030' => 'ccan', 'CDE07G0968' => 'cde', 'CDE09G1441' => 'cde', 'Cfa006103' => 'cfa', 'Cfa015573' => 'cfa', 'Cfa016988' => 'cfa', 'Ciclev10006738m.g' => 'ccl', 'Ciclev10010920m.g' => 'ccl', 'Ciclev10018517m.g' => 'ccl', 'CiPaw.01G159200' => 'cil', 'CiPaw.02G091000' => 'cil', 'CiPaw.02G091100' => 'cil', 'CiPaw.08G103100' => 'cil', 'CiPaw.09G224900' => 'cil', 'ClCG06G005740' => 'cla', 'ClCG07G000090' => 'cla', 'ClCG07G000100' => 'cla', 'COL.COLO4_09143' => 'col', 'COL.COLO4_25124' => 'col', 'Cpa.g.sc16.34' => 'cpa', 'Cpa.g.sc3504.1' => 'cpa', 'Cpa.g.sc60.37' => 'cpa', 'CsaV3_6G018520' => 'csa', 'CsaV3_6G036860' => 'csa', 'CSS0001072' => 'camsi', 'CSS0020208' => 'camsi', 'CSS0021253' => 'camsi', 'CSS0022190' => 'camsi', 'CSS0036150' => 'camsi', 'CSS0040442' => 'camsi', 'CSS0042300' => 'camsi', 'CSS0045298' => 'camsi', 'DCAR_012449' => 'dca', 'DCAR_018405' => 'dca', 'DCAR_024573' => 'dca', 'DCAR_030591' => 'dca', 'Dinv16926' => 'din', 'Dinv32963' => 'din', 'Dinv38382' => 'din', 'Dinv38383' => 'din', 'Duzib133G0974' => 'dzi', 'Duzib138G1867' => 'dzi', 'Duzib211G0420' => 'dzi', 'Duzib212G0930' => 'dzi', 'ECA234G1645' => 'eca', 'ECA247G3467' => 'eca', 'ECA248G1703' => 'eca', 'EL10Ac3g06327' => 'bvu', 'EL10Ac7g17204' => 'bvu', 'Eucgr.A00855' => 'egr', 'Eucgr.A00858' => 'egr', 'Eucgr.H01520' => 'egr', 'Eucgr.H03604' => 'egr', 'Eucgr.L03465' => 'egr', 'Eucgr.L03466' => 'egr', 'FAN01G0988' => 'fan', 'FAN02G3892' => 'fan', 'FAN05G3381' => 'fan', 'FAN07G0967' => 'fan', 'FAN07G1493' => 'fan', 'FAN08G3125' => 'fan', 'FAN09G0402' => 'fan', 'FAN12G2594' => 'fan', 'FAN12G3879' => 'fan', 'FAN14G1546' => 'fan', 'FAN15G3626' => 'fan', 'FAN17G0588' => 'fan', 'FAN17G0609' => 'fan', 'FAN18G2817' => 'fan', 'FAN19G1305' => 'fan', 'FAN20G1787' => 'fan', 'FAN22G0073' => 'fan', 'FAN22G0352' => 'fan', 'FAN22G0368' => 'fan', 'FAN22G2273' => 'fan', 'FAN24G1998' => 'fan', 'FAN27G1317' => 'fan', 'FvH4_2g23980' => 'fve', 'FvH4_4g14380' => 'fve', 'FvH4_4g14390' => 'fve', 'FvH4_6g09250' => 'fve', 'Glyma.03G151100' => 'gma', 'Glyma.04G122550' => 'gma', 'Glyma.05G001600' => 'gma', 'Glyma.09G270766' => 'gma', 'Glyma.09G270832' => 'gma', 'Glyma.13G209800' => 'gma', 'Glyma.15G102800' => 'gma', 'Glyma.18G218900' => 'gma', 'Glyma.19G001500' => 'gma', 'Glyma.19G153600' => 'gma', 'Gohir.A02G028600' => 'ghi', 'Gohir.A08G045000' => 'ghi', 'Gohir.A11G120500' => 'ghi', 'Gohir.A12G006200' => 'ghi', 'Gohir.A12G006250' => 'ghi', 'Gohir.D02G036300' => 'ghi', 'Gohir.D08G054700' => 'ghi', 'Gohir.D11G125600' => 'ghi', 'Gohir.D12G005700' => 'ghi', 'Gorai.004G055200' => 'gra', 'Gorai.005G040400' => 'gra', 'Gorai.007G134500' => 'gra', 'Gorai.008G005500' => 'gra', 'GSVIVG01011094001' => 'vvi', 'GSVIVG01017879001' => 'vvi', 'GSVIVG01025988001' => 'vvi', 'GSVIVG01029847001' => 'vvi', 'HanXRQChr10g0282901' => 'han', 'HanXRQChr10g0310371' => 'han', 'HanXRQChr10g0315041' => 'han', 'HanXRQChr11g0327651' => 'han', 'HanXRQChr12g0359391' => 'han', 'Haze_00972' => 'cav', 'Haze_00973' => 'cav', 'Haze_00974' => 'cav', 'Haze_04747' => 'cav', 'Haze_04749' => 'cav', 'Haze_04750' => 'cav', 'Haze_21217' => 'cav', 'Hma1.2p1_1037F.1_g250680' => 'hma', 'Hma1.2p1_1644F.1_g295320' => 'hma', 'HPP92_011322' => 'vpl', 'HPP92_011323' => 'vpl', 'HPP92_011324' => 'vpl', 'HPP92_011325' => 'vpl', 'HPP92_011326' => 'vpl', 'Hund12205' => 'sun', 'Hund17957' => 'sun', 'Lalb_Chr06g0176771' => 'lal', 'Lalb_Chr18g0056021' => 'lal', 'Lalb_Chr18g0056031' => 'lal', 'Lalb_Chr18g0056041' => 'lal', 'Lalb_Chr20g0107751' => 'lal', 'Lalb_Chr20g0118371' => 'lal', 'Lj1g0010239' => 'lja', 'Lj1g0017101' => 'lja', 'Lj2A1178G40' => 'lonja', 'Lj2A54G84' => 'lonja', 'Lj2g0015248' => 'lja', 'Lj3A761T51' => 'lonja', 'Lj6g0018116' => 'lja', 'Lsat_1_v5_gn_4_136040' => 'lsa', 'Lsat_1_v5_gn_5_187461' => 'lsa', 'Lsat_1_v5_gn_5_77001' => 'lsa', 'Lsat_1_v5_gn_9_4461' => 'lsa', 'Manes.01G210100' => 'mes', 'Manes.03G185600' => 'mes', 'Manes.05G073300' => 'mes', 'Manes.09G120300' => 'mes', 'Manes.15G022100' => 'mes', 'Mapoly0096s0053' => 'mpo', 'MBI03_g14058_MAGBIO' => 'mbi', 'MBI03_g33876_MAGBIO' => 'mbi', 'MBI03_g36854_MAGBIO' => 'mbi', 'MBI17_g11997_MAGBIO' => 'mbi', 'MD03G1269000' => 'mdo', 'MD04G1179600' => 'mdo', 'MD11G1289800' => 'mdo', 'MD12G1194700' => 'mdo', 'MD13G1182100' => 'mdo', 'MD13G1182200' => 'mdo', 'MD16G1182600' => 'mdo', 'Medtr2g021400' => 'mtr', 'Medtr2g021470' => 'mtr', 'Medtr2g105810' => 'mtr', 'Medtr3g033580' => 'mtr', 'Medtr6g007970' => 'mtr', 'Medtr7g056330' => 'mtr', 'Medtr7g074290' => 'mtr', 'Medtr7g074380' => 'mtr', 'Medtr7g094550' => 'mtr', 'Medtr8g069995' => 'mtr', 'MELO3C014345.2' => 'cme', 'MELO3C021395.2' => 'cme', 'Migut.D00262' => 'egut', 'Migut.G00257' => 'egut', 'MSTRG.21575' => 'ama', 'MSTRG.3985' => 'ama', 'Nitab4.5_0000295g0140' => 'nta', 'Nitab4.5_0000732g0140' => 'nta', 'Nitab4.5_0003162g0020' => 'nta', 'Nitab4.5_0006180g0090' => 'nta', 'Nitab4.5_0006390g0010' => 'nta', 'Nitab4.5_0007392g0040' => 'nta', 'Nn1g02140' => 'nnu', 'Nn4g26168' => 'nnu', 'Nn5g26754' => 'nnu', 'Oeu001433.1' => 'oeu', 'Oeu010299.2' => 'oeu', 'Oeu011171.1' => 'oeu', 'Oeu037675.1' => 'oeu', 'Oeu038359.1' => 'oeu', 'Oeu063834.1' => 'oeu', 'Oeu063835.1' => 'oeu', 'Os05g0312000' => 'osa', 'Os07g0211101' => 'osa', 'Os07g0211200' => 'osa', 'Os07g0681500' => 'osa', 'Peaxi162Scf00095g01015' => 'pax', 'Peaxi162Scf00104g00329' => 'pax', 'Peaxi162Scf00161g00137' => 'pax', 'PGR004G1665' => 'pgr', 'PGR031G2937' => 'pgr', 'PGR119G2145' => 'pgr', 'PGSC0003DMG400004351' => 'stu', 'PGSC0003DMG400014625' => 'stu', 'PGSC0003DMG401000943' => 'stu', 'Phvul.001G148600' => 'pvu', 'Phvul.004G001700' => 'pvu', 'Phvul.006G154900' => 'pvu', 'Phvul.008G078200' => 'pvu', 'Phvul.011G136500' => 'pvu', 'Potri.002G215600' => 'ptr', 'Potri.008G201600' => 'ptr', 'Potri.014G138400' => 'ptr', 'Potri.016G142500' => 'ptr', 'Pp3c16_10580' => 'ppa', 'Pp3c5_25280' => 'ppa', 'Prupe.1G150000' => 'ppe', 'Prupe.1G150100' => 'ppe', 'Prupe.6G299600' => 'ppe', 'Prupe.8G245000' => 'ppe', 'Psat0s4927g0040' => 'psa', 'Psat1g052080' => 'psa', 'Psat1g183800' => 'psa', 'Psat3g113840' => 'psa', 'Psat3g126120' => 'psa', 'Psat3g126160' => 'psa', 'Psat3g158760' => 'psa', 'Psat3g158840' => 'psa', 'PSO170G2858' => 'pso', 'PSO339G0606' => 'pso', 'PSO384G4709' => 'pso', 'PSO407G0334' => 'pso', 'QL04p040276' => 'qlo', 'QL06p005458' => 'qlo', 'QL06p005472' => 'qlo', 'QL07p030546' => 'qlo', 'QL07p031519' => 'qlo', 'QL09p050949' => 'qlo', 'QL09p050966' => 'qlo', 'QL09p051067' => 'qlo', 'QL12p022706' => 'qlo', 'RcHm_v2.0_Chr2g0119601' => 'rch', 'RcHm_v2.0_Chr3g0459591' => 'rch', 'RcHm_v2.0_Chr4g0418521' => 'rch', 'RcHm_v2.0_Chr4g0418531' => 'rch', 'RcHm_v2.0_Chr4g0418541' => 'rch', 'RcHm_v2.0_Chr6g0291641' => 'rch', 'Rhsim01G0086300' => 'rsi', 'Rhsim01G0276300' => 'rsi', 'Rhsim01G0276500' => 'rsi', 'Rhsim04G0207700' => 'rsi', 'Rhsim05G0234500' => 'rsi', 'Rhsim13G0022400' => 'rsi', 'Sabra02G0167900' => 'sbr', 'Sabra04G0158500' => 'sbr', 'Sabra08G0159800' => 'sbr', 'Sabra10G0011500' => 'sbr', 'Sabra14G0104400' => 'sbr', 'SalBow2G2440' => 'sbo', 'SalBow4G2265' => 'sbo', 'Sc02g0000060' => 'sci', 'Sc05g0005020' => 'sci', 'Sc13g0003890' => 'sci', 'Sed0014865' => 'sed', 'Sed0017224' => 'sed', 'Sed0026391' => 'sed', 'SEGI_00063' => 'sgi', 'SEGI_10967' => 'sgi', 'SEGI_17510' => 'sgi', 'SEGI_24396' => 'sgi', 'SEGI_39719' => 'sgi', 'SEGI_41392' => 'sgi', 'SGA_v2.0_scaffold11G05794' => 'sas', 'SGA_v2.0_scaffold142G35607' => 'sas', 'SGA_v2.0_scaffold1G00447' => 'sas', 'SHI15388' => 'shi', 'SHI15394' => 'shi', 'SHI15396' => 'shi', 'SHI15399' => 'shi', 'SMO343G0151' => 'smo', 'SMO367G1118' => 'smo', 'Solyc01g080200.3' => 'sly', 'Solyc06g008960.3' => 'sly', 'Solyc09g064780.3' => 'sly', 'Sopen01g031980' => 'spe', 'Sopen06g003710' => 'spe', 'Sopen09g026460' => 'spe', 'Sp3g21240' => 'spa', 'Sp4g30030' => 'spa', 'TAR365G0022' => 'tar', 'TAR365G1023' => 'tar', 'TAR365G1253' => 'tar', 'TAR623G0078' => 'tar', 'TAR623G1721' => 'tar', 'TAR633G0959' => 'tar', 'THA.LOC104802225' => 'tha', 'THA.LOC104804769' => 'tha', 'THA.LOC104808660' => 'tha', 'THA.LOC104812792' => 'tha', 'Thecc.01G284000' => 'tca', 'Thecc.04G220600' => 'tca', 'Thecc.05G268900' => 'tca', 'Thecc.08G171100' => 'tca', 'Thhalv10001284m.g' => 'esa', 'Thhalv10019912m.g' => 'esa', 'TPR.G14189' => 'tpr', 'TPR.G18110' => 'tpr', 'TPR.G18130' => 'tpr', 'TPR.G18131' => 'tpr', 'TPR.G18140' => 'tpr', 'TPR.G24282' => 'tpr', 'TPR.G25221' => 'tpr', 'TPR.G29267' => 'tpr', 'TPR.G35315' => 'tpr', 'TPR.G36173' => 'tpr', 'TWI09G0794' => 'twi', 'TWI59G1348' => 'twi', 'TWI74G0430' => 'twi', 'unitig_26.g8940' => 'ugi', 'unitig_749.g13744' => 'ugi', 'unitig_749.g13745' => 'ugi', 'vmacro08269' => 'vma', 'vmacro14937' => 'vma', 'vmacro20401' => 'vma', 'VMungo0464G1349' => 'vmu', 'VMungo0540G0289' => 'vmu', 'VMungo1215G1590' => 'vmu', 'VMungo1309G0221' => 'vmu', 'VMungo1309G2815' => 'vmu', 'VMungo1383G0239' => 'vmu', 'VMungo1383G2910' => 'vmu', 'Zm00001eb095270' => 'zma', 'Zm00001eb095280' => 'zma', 'Zm00001eb111630' => 'zma', 'Zm00001eb237080' => 'zma', 'Zm00001eb273740' => 'zma', 'Zm00001eb285040' => 'zma', 'Zm00001eb330790' => 'zma', 'Zm00001eb337380' => 'zma' ), 'gf_id' => 'HOM05D001484', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001484' ), 'data_identifier' => 'HOM05D001484', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001484', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p31500' => 'bna', 'A05p00020' => 'bna', 'A07p08820' => 'bna', 'Aa31LG4G3300' => 'aar', 'Aa31LG8G10030' => 'aar', 'Actinidia00731' => 'ach', 'Actinidia11473' => 'ach', 'Actinidia23469' => 'ach', 'Actinidia24318' => 'ach', 'Actinidia40196' => 'ach', 'Actinidia40197' => 'ach', 'Actinidia40198' => 'ach', 'Ah.08g212990' => 'amhyb', 'Ah.15g091720' => 'amhyb', 'AL3G38260' => 'aly', 'AL4G47710' => 'aly', 'Aqoxy2G00671' => 'aox', 'Aqoxy2G03236' => 'aox', 'arahy.Tifrunner.gnm1.ann1.05IDCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KR684' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATY3SJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK6QJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6APGL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IDT7Z9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM073U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ0R87' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LE7RV4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT4QRX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V5ENPK' => 'arhy', 'AT2G48110' => 'ath', 'AT3G23590' => 'ath', 'ATR0626G186' => 'atr', 'ATR1127G141' => 'atr', 'Atru.chr4.2583' => 'acertr', 'Atru.chr5.1358' => 'acertr', 'Atru.chr5.1359' => 'acertr', 'Atru.chr8.46' => 'acertr', 'AUR62002640' => 'cqu', 'AUR62030055' => 'cqu', 'AUR62033713' => 'cqu', 'AUR62033714' => 'cqu', 'AUR62036795' => 'cqu', 'AUR62039891' => 'cqu', 'BcaB02g08737' => 'bca', 'BcaB04g20441' => 'bca', 'BcaB06g26509' => 'bca', 'BcaB06g26510' => 'bca', 'BcaB06g26511' => 'bca', 'BcaB06g26512' => 'bca', 'BcaB06g26513' => 'bca', 'BcaC02g12564' => 'bca', 'BcaC02g12565' => 'bca', 'BcaC02g12794' => 'bca', 'BcaC02g12795' => 'bca', 'BcaC02g12796' => 'bca', 'BcaC06g35541' => 'bca', 'BNapus_Darmor_BZH_scaffold_188p00080' => 'bna', 'BNapus_Darmor_BZH_scaffold_188p00090' => 'bna', 'BolC1t03972H' => 'bol', 'BolC1t03973H' => 'bol', 'BolC4t21680H' => 'bol', 'BolC7t41863H' => 'bol', 'BolSC55t61227H' => 'bol', 'BolSC55t61228H' => 'bol', 'BraA01t03278Z' => 'bra', 'BraA05t18998Z' => 'bra', 'BraA07t28673Z' => 'bra', 'C01p40150' => 'bna', 'C05p12370' => 'bna', 'C07p13680' => 'bna', 'CAN.G1006.16' => 'can', 'CAN.G1006.17' => 'can', 'CAN.G1170.2' => 'can', 'CAN.G962.7' => 'can', 'CANSAT25G2179' => 'cansat', 'CANSAT78G1573' => 'cansat', 'CARHR099510' => 'chi', 'CARHR143510' => 'chi', 'Carub.0003s2380' => 'cru', 'Carub.0004s3082' => 'cru', 'Ca_00614_v3' => 'car', 'Ca_07801_v3' => 'car', 'Ca_08567_v3' => 'car', 'Ca_09571_v3' => 'car', 'CBR_g19290' => 'cbr', 'Cc01_g19770' => 'ccan', 'Cc03_g03030' => 'ccan', 'CDE07G0968' => 'cde', 'CDE09G1441' => 'cde', 'Cfa006103' => 'cfa', 'Cfa015573' => 'cfa', 'Cfa016988' => 'cfa', 'Ciclev10006738m.g' => 'ccl', 'Ciclev10010920m.g' => 'ccl', 'Ciclev10018517m.g' => 'ccl', 'CiPaw.01G159200' => 'cil', 'CiPaw.02G091000' => 'cil', 'CiPaw.02G091100' => 'cil', 'CiPaw.08G103100' => 'cil', 'CiPaw.09G224900' => 'cil', 'ClCG06G005740' => 'cla', 'ClCG07G000090' => 'cla', 'ClCG07G000100' => 'cla', 'COL.COLO4_09143' => 'col', 'COL.COLO4_25124' => 'col', 'Cpa.g.sc16.34' => 'cpa', 'Cpa.g.sc3504.1' => 'cpa', 'Cpa.g.sc60.37' => 'cpa', 'CsaV3_6G018520' => 'csa', 'CsaV3_6G036860' => 'csa', 'CSS0001072' => 'camsi', 'CSS0020208' => 'camsi', 'CSS0021253' => 'camsi', 'CSS0022190' => 'camsi', 'CSS0036150' => 'camsi', 'CSS0040442' => 'camsi', 'CSS0042300' => 'camsi', 'CSS0045298' => 'camsi', 'DCAR_012449' => 'dca', 'DCAR_018405' => 'dca', 'DCAR_024573' => 'dca', 'DCAR_030591' => 'dca', 'Dinv16926' => 'din', 'Dinv32963' => 'din', 'Dinv38382' => 'din', 'Dinv38383' => 'din', 'Duzib133G0974' => 'dzi', 'Duzib138G1867' => 'dzi', 'Duzib211G0420' => 'dzi', 'Duzib212G0930' => 'dzi', 'ECA234G1645' => 'eca', 'ECA247G3467' => 'eca', 'ECA248G1703' => 'eca', 'EL10Ac3g06327' => 'bvu', 'EL10Ac7g17204' => 'bvu', 'Eucgr.A00855' => 'egr', 'Eucgr.A00858' => 'egr', 'Eucgr.H01520' => 'egr', 'Eucgr.H03604' => 'egr', 'Eucgr.L03465' => 'egr', 'Eucgr.L03466' => 'egr', 'FAN01G0988' => 'fan', 'FAN02G3892' => 'fan', 'FAN05G3381' => 'fan', 'FAN07G0967' => 'fan', 'FAN07G1493' => 'fan', 'FAN08G3125' => 'fan', 'FAN09G0402' => 'fan', 'FAN12G2594' => 'fan', 'FAN12G3879' => 'fan', 'FAN14G1546' => 'fan', 'FAN15G3626' => 'fan', 'FAN17G0588' => 'fan', 'FAN17G0609' => 'fan', 'FAN18G2817' => 'fan', 'FAN19G1305' => 'fan', 'FAN20G1787' => 'fan', 'FAN22G0073' => 'fan', 'FAN22G0352' => 'fan', 'FAN22G0368' => 'fan', 'FAN22G2273' => 'fan', 'FAN24G1998' => 'fan', 'FAN27G1317' => 'fan', 'FvH4_2g23980' => 'fve', 'FvH4_4g14380' => 'fve', 'FvH4_4g14390' => 'fve', 'FvH4_6g09250' => 'fve', 'Glyma.03G151100' => 'gma', 'Glyma.04G122550' => 'gma', 'Glyma.05G001600' => 'gma', 'Glyma.09G270766' => 'gma', 'Glyma.09G270832' => 'gma', 'Glyma.13G209800' => 'gma', 'Glyma.15G102800' => 'gma', 'Glyma.18G218900' => 'gma', 'Glyma.19G001500' => 'gma', 'Glyma.19G153600' => 'gma', 'Gohir.A02G028600' => 'ghi', 'Gohir.A08G045000' => 'ghi', 'Gohir.A11G120500' => 'ghi', 'Gohir.A12G006200' => 'ghi', 'Gohir.A12G006250' => 'ghi', 'Gohir.D02G036300' => 'ghi', 'Gohir.D08G054700' => 'ghi', 'Gohir.D11G125600' => 'ghi', 'Gohir.D12G005700' => 'ghi', 'Gorai.004G055200' => 'gra', 'Gorai.005G040400' => 'gra', 'Gorai.007G134500' => 'gra', 'Gorai.008G005500' => 'gra', 'GSVIVG01011094001' => 'vvi', 'GSVIVG01017879001' => 'vvi', 'GSVIVG01025988001' => 'vvi', 'GSVIVG01029847001' => 'vvi', 'HanXRQChr10g0282901' => 'han', 'HanXRQChr10g0310371' => 'han', 'HanXRQChr10g0315041' => 'han', 'HanXRQChr11g0327651' => 'han', 'HanXRQChr12g0359391' => 'han', 'Haze_00972' => 'cav', 'Haze_00973' => 'cav', 'Haze_00974' => 'cav', 'Haze_04747' => 'cav', 'Haze_04749' => 'cav', 'Haze_04750' => 'cav', 'Haze_21217' => 'cav', 'Hma1.2p1_1037F.1_g250680' => 'hma', 'Hma1.2p1_1644F.1_g295320' => 'hma', 'HPP92_011322' => 'vpl', 'HPP92_011323' => 'vpl', 'HPP92_011324' => 'vpl', 'HPP92_011325' => 'vpl', 'HPP92_011326' => 'vpl', 'Hund12205' => 'sun', 'Hund17957' => 'sun', 'Lalb_Chr06g0176771' => 'lal', 'Lalb_Chr18g0056021' => 'lal', 'Lalb_Chr18g0056031' => 'lal', 'Lalb_Chr18g0056041' => 'lal', 'Lalb_Chr20g0107751' => 'lal', 'Lalb_Chr20g0118371' => 'lal', 'Lj1g0010239' => 'lja', 'Lj1g0017101' => 'lja', 'Lj2A1178G40' => 'lonja', 'Lj2A54G84' => 'lonja', 'Lj2g0015248' => 'lja', 'Lj3A761T51' => 'lonja', 'Lj6g0018116' => 'lja', 'Lsat_1_v5_gn_4_136040' => 'lsa', 'Lsat_1_v5_gn_5_187461' => 'lsa', 'Lsat_1_v5_gn_5_77001' => 'lsa', 'Lsat_1_v5_gn_9_4461' => 'lsa', 'Manes.01G210100' => 'mes', 'Manes.03G185600' => 'mes', 'Manes.05G073300' => 'mes', 'Manes.09G120300' => 'mes', 'Manes.15G022100' => 'mes', 'Mapoly0096s0053' => 'mpo', 'MBI03_g14058_MAGBIO' => 'mbi', 'MBI03_g33876_MAGBIO' => 'mbi', 'MBI03_g36854_MAGBIO' => 'mbi', 'MBI17_g11997_MAGBIO' => 'mbi', 'MD03G1269000' => 'mdo', 'MD04G1179600' => 'mdo', 'MD11G1289800' => 'mdo', 'MD12G1194700' => 'mdo', 'MD13G1182100' => 'mdo', 'MD13G1182200' => 'mdo', 'MD16G1182600' => 'mdo', 'Medtr2g021400' => 'mtr', 'Medtr2g021470' => 'mtr', 'Medtr2g105810' => 'mtr', 'Medtr3g033580' => 'mtr', 'Medtr6g007970' => 'mtr', 'Medtr7g056330' => 'mtr', 'Medtr7g074290' => 'mtr', 'Medtr7g074380' => 'mtr', 'Medtr7g094550' => 'mtr', 'Medtr8g069995' => 'mtr', 'MELO3C014345.2' => 'cme', 'MELO3C021395.2' => 'cme', 'Migut.D00262' => 'egut', 'Migut.G00257' => 'egut', 'MSTRG.21575' => 'ama', 'MSTRG.3985' => 'ama', 'Nitab4.5_0000295g0140' => 'nta', 'Nitab4.5_0000732g0140' => 'nta', 'Nitab4.5_0003162g0020' => 'nta', 'Nitab4.5_0006180g0090' => 'nta', 'Nitab4.5_0006390g0010' => 'nta', 'Nitab4.5_0007392g0040' => 'nta', 'Nn1g02140' => 'nnu', 'Nn4g26168' => 'nnu', 'Nn5g26754' => 'nnu', 'Oeu001433.1' => 'oeu', 'Oeu010299.2' => 'oeu', 'Oeu011171.1' => 'oeu', 'Oeu037675.1' => 'oeu', 'Oeu038359.1' => 'oeu', 'Oeu063834.1' => 'oeu', 'Oeu063835.1' => 'oeu', 'Os05g0312000' => 'osa', 'Os07g0211101' => 'osa', 'Os07g0211200' => 'osa', 'Os07g0681500' => 'osa', 'Peaxi162Scf00095g01015' => 'pax', 'Peaxi162Scf00104g00329' => 'pax', 'Peaxi162Scf00161g00137' => 'pax', 'PGR004G1665' => 'pgr', 'PGR031G2937' => 'pgr', 'PGR119G2145' => 'pgr', 'PGSC0003DMG400004351' => 'stu', 'PGSC0003DMG400014625' => 'stu', 'PGSC0003DMG401000943' => 'stu', 'Phvul.001G148600' => 'pvu', 'Phvul.004G001700' => 'pvu', 'Phvul.006G154900' => 'pvu', 'Phvul.008G078200' => 'pvu', 'Phvul.011G136500' => 'pvu', 'Potri.002G215600' => 'ptr', 'Potri.008G201600' => 'ptr', 'Potri.014G138400' => 'ptr', 'Potri.016G142500' => 'ptr', 'Pp3c16_10580' => 'ppa', 'Pp3c5_25280' => 'ppa', 'Prupe.1G150000' => 'ppe', 'Prupe.1G150100' => 'ppe', 'Prupe.6G299600' => 'ppe', 'Prupe.8G245000' => 'ppe', 'Psat0s4927g0040' => 'psa', 'Psat1g052080' => 'psa', 'Psat1g183800' => 'psa', 'Psat3g113840' => 'psa', 'Psat3g126120' => 'psa', 'Psat3g126160' => 'psa', 'Psat3g158760' => 'psa', 'Psat3g158840' => 'psa', 'PSO170G2858' => 'pso', 'PSO339G0606' => 'pso', 'PSO384G4709' => 'pso', 'PSO407G0334' => 'pso', 'QL04p040276' => 'qlo', 'QL06p005458' => 'qlo', 'QL06p005472' => 'qlo', 'QL07p030546' => 'qlo', 'QL07p031519' => 'qlo', 'QL09p050949' => 'qlo', 'QL09p050966' => 'qlo', 'QL09p051067' => 'qlo', 'QL12p022706' => 'qlo', 'RcHm_v2.0_Chr2g0119601' => 'rch', 'RcHm_v2.0_Chr3g0459591' => 'rch', 'RcHm_v2.0_Chr4g0418521' => 'rch', 'RcHm_v2.0_Chr4g0418531' => 'rch', 'RcHm_v2.0_Chr4g0418541' => 'rch', 'RcHm_v2.0_Chr6g0291641' => 'rch', 'Rhsim01G0086300' => 'rsi', 'Rhsim01G0276300' => 'rsi', 'Rhsim01G0276500' => 'rsi', 'Rhsim04G0207700' => 'rsi', 'Rhsim05G0234500' => 'rsi', 'Rhsim13G0022400' => 'rsi', 'Sabra02G0167900' => 'sbr', 'Sabra04G0158500' => 'sbr', 'Sabra08G0159800' => 'sbr', 'Sabra10G0011500' => 'sbr', 'Sabra14G0104400' => 'sbr', 'SalBow2G2440' => 'sbo', 'SalBow4G2265' => 'sbo', 'Sc02g0000060' => 'sci', 'Sc05g0005020' => 'sci', 'Sc13g0003890' => 'sci', 'Sed0014865' => 'sed', 'Sed0017224' => 'sed', 'Sed0026391' => 'sed', 'SEGI_00063' => 'sgi', 'SEGI_10967' => 'sgi', 'SEGI_17510' => 'sgi', 'SEGI_24396' => 'sgi', 'SEGI_39719' => 'sgi', 'SEGI_41392' => 'sgi', 'SGA_v2.0_scaffold11G05794' => 'sas', 'SGA_v2.0_scaffold142G35607' => 'sas', 'SGA_v2.0_scaffold1G00447' => 'sas', 'SHI15388' => 'shi', 'SHI15394' => 'shi', 'SHI15396' => 'shi', 'SHI15399' => 'shi', 'SMO343G0151' => 'smo', 'SMO367G1118' => 'smo', 'Solyc01g080200.3' => 'sly', 'Solyc06g008960.3' => 'sly', 'Solyc09g064780.3' => 'sly', 'Sopen01g031980' => 'spe', 'Sopen06g003710' => 'spe', 'Sopen09g026460' => 'spe', 'Sp3g21240' => 'spa', 'Sp4g30030' => 'spa', 'TAR365G0022' => 'tar', 'TAR365G1023' => 'tar', 'TAR365G1253' => 'tar', 'TAR623G0078' => 'tar', 'TAR623G1721' => 'tar', 'TAR633G0959' => 'tar', 'THA.LOC104802225' => 'tha', 'THA.LOC104804769' => 'tha', 'THA.LOC104808660' => 'tha', 'THA.LOC104812792' => 'tha', 'Thecc.01G284000' => 'tca', 'Thecc.04G220600' => 'tca', 'Thecc.05G268900' => 'tca', 'Thecc.08G171100' => 'tca', 'Thhalv10001284m.g' => 'esa', 'Thhalv10019912m.g' => 'esa', 'TPR.G14189' => 'tpr', 'TPR.G18110' => 'tpr', 'TPR.G18130' => 'tpr', 'TPR.G18131' => 'tpr', 'TPR.G18140' => 'tpr', 'TPR.G24282' => 'tpr', 'TPR.G25221' => 'tpr', 'TPR.G29267' => 'tpr', 'TPR.G35315' => 'tpr', 'TPR.G36173' => 'tpr', 'TWI09G0794' => 'twi', 'TWI59G1348' => 'twi', 'TWI74G0430' => 'twi', 'unitig_26.g8940' => 'ugi', 'unitig_749.g13744' => 'ugi', 'unitig_749.g13745' => 'ugi', 'vmacro08269' => 'vma', 'vmacro14937' => 'vma', 'vmacro20401' => 'vma', 'VMungo0464G1349' => 'vmu', 'VMungo0540G0289' => 'vmu', 'VMungo1215G1590' => 'vmu', 'VMungo1309G0221' => 'vmu', 'VMungo1309G2815' => 'vmu', 'VMungo1383G0239' => 'vmu', 'VMungo1383G2910' => 'vmu', 'Zm00001eb095270' => 'zma', 'Zm00001eb095280' => 'zma', 'Zm00001eb111630' => 'zma', 'Zm00001eb237080' => 'zma', 'Zm00001eb273740' => 'zma', 'Zm00001eb285040' => 'zma', 'Zm00001eb330790' => 'zma', 'Zm00001eb337380' => 'zma' ) $gf_id = 'HOM05D001484' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001484' ) $data_identifier = 'HOM05D001484' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 2, 'aly' => (int) 2, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 22, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 7, 'hma' => (int) 2, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 7, 'mtr' => (int) 10, 'cme' => (int) 2, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 4, 'ppa' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 4, 'qlo' => (int) 9, 'rch' => (int) 6, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 10, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 7, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb337380' $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' => 'HOM05D001484', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p31500' => 'bna', 'A05p00020' => 'bna', 'A07p08820' => 'bna', 'Aa31LG4G3300' => 'aar', 'Aa31LG8G10030' => 'aar', 'Actinidia00731' => 'ach', 'Actinidia11473' => 'ach', 'Actinidia23469' => 'ach', 'Actinidia24318' => 'ach', 'Actinidia40196' => 'ach', 'Actinidia40197' => 'ach', 'Actinidia40198' => 'ach', 'Ah.08g212990' => 'amhyb', 'Ah.15g091720' => 'amhyb', 'AL3G38260' => 'aly', 'AL4G47710' => 'aly', 'Aqoxy2G00671' => 'aox', 'Aqoxy2G03236' => 'aox', 'arahy.Tifrunner.gnm1.ann1.05IDCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KR684' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATY3SJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK6QJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6APGL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IDT7Z9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM073U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ0R87' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LE7RV4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT4QRX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V5ENPK' => 'arhy', 'AT2G48110' => 'ath', 'AT3G23590' => 'ath', 'ATR0626G186' => 'atr', 'ATR1127G141' => 'atr', 'Atru.chr4.2583' => 'acertr', 'Atru.chr5.1358' => 'acertr', 'Atru.chr5.1359' => 'acertr', 'Atru.chr8.46' => 'acertr', 'AUR62002640' => 'cqu', 'AUR62030055' => 'cqu', 'AUR62033713' => 'cqu', 'AUR62033714' => 'cqu', 'AUR62036795' => 'cqu', 'AUR62039891' => 'cqu', 'BcaB02g08737' => 'bca', 'BcaB04g20441' => 'bca', 'BcaB06g26509' => 'bca', 'BcaB06g26510' => 'bca', 'BcaB06g26511' => 'bca', 'BcaB06g26512' => 'bca', 'BcaB06g26513' => 'bca', 'BcaC02g12564' => 'bca', 'BcaC02g12565' => 'bca', 'BcaC02g12794' => 'bca', 'BcaC02g12795' => 'bca', 'BcaC02g12796' => 'bca', 'BcaC06g35541' => 'bca', 'BNapus_Darmor_BZH_scaffold_188p00080' => 'bna', 'BNapus_Darmor_BZH_scaffold_188p00090' => 'bna', 'BolC1t03972H' => 'bol', 'BolC1t03973H' => 'bol', 'BolC4t21680H' => 'bol', 'BolC7t41863H' => 'bol', 'BolSC55t61227H' => 'bol', 'BolSC55t61228H' => 'bol', 'BraA01t03278Z' => 'bra', 'BraA05t18998Z' => 'bra', 'BraA07t28673Z' => 'bra', 'C01p40150' => 'bna', 'C05p12370' => 'bna', 'C07p13680' => 'bna', 'CAN.G1006.16' => 'can', 'CAN.G1006.17' => 'can', 'CAN.G1170.2' => 'can', 'CAN.G962.7' => 'can', 'CANSAT25G2179' => 'cansat', 'CANSAT78G1573' => 'cansat', 'CARHR099510' => 'chi', 'CARHR143510' => 'chi', 'Carub.0003s2380' => 'cru', 'Carub.0004s3082' => 'cru', 'Ca_00614_v3' => 'car', 'Ca_07801_v3' => 'car', 'Ca_08567_v3' => 'car', 'Ca_09571_v3' => 'car', 'CBR_g19290' => 'cbr', 'Cc01_g19770' => 'ccan', 'Cc03_g03030' => 'ccan', 'CDE07G0968' => 'cde', 'CDE09G1441' => 'cde', 'Cfa006103' => 'cfa', 'Cfa015573' => 'cfa', 'Cfa016988' => 'cfa', 'Ciclev10006738m.g' => 'ccl', 'Ciclev10010920m.g' => 'ccl', 'Ciclev10018517m.g' => 'ccl', 'CiPaw.01G159200' => 'cil', 'CiPaw.02G091000' => 'cil', 'CiPaw.02G091100' => 'cil', 'CiPaw.08G103100' => 'cil', 'CiPaw.09G224900' => 'cil', 'ClCG06G005740' => 'cla', 'ClCG07G000090' => 'cla', 'ClCG07G000100' => 'cla', 'COL.COLO4_09143' => 'col', 'COL.COLO4_25124' => 'col', 'Cpa.g.sc16.34' => 'cpa', 'Cpa.g.sc3504.1' => 'cpa', 'Cpa.g.sc60.37' => 'cpa', 'CsaV3_6G018520' => 'csa', 'CsaV3_6G036860' => 'csa', 'CSS0001072' => 'camsi', 'CSS0020208' => 'camsi', 'CSS0021253' => 'camsi', 'CSS0022190' => 'camsi', 'CSS0036150' => 'camsi', 'CSS0040442' => 'camsi', 'CSS0042300' => 'camsi', 'CSS0045298' => 'camsi', 'DCAR_012449' => 'dca', 'DCAR_018405' => 'dca', 'DCAR_024573' => 'dca', 'DCAR_030591' => 'dca', 'Dinv16926' => 'din', 'Dinv32963' => 'din', 'Dinv38382' => 'din', 'Dinv38383' => 'din', 'Duzib133G0974' => 'dzi', 'Duzib138G1867' => 'dzi', 'Duzib211G0420' => 'dzi', 'Duzib212G0930' => 'dzi', 'ECA234G1645' => 'eca', 'ECA247G3467' => 'eca', 'ECA248G1703' => 'eca', 'EL10Ac3g06327' => 'bvu', 'EL10Ac7g17204' => 'bvu', 'Eucgr.A00855' => 'egr', 'Eucgr.A00858' => 'egr', 'Eucgr.H01520' => 'egr', 'Eucgr.H03604' => 'egr', 'Eucgr.L03465' => 'egr', 'Eucgr.L03466' => 'egr', 'FAN01G0988' => 'fan', 'FAN02G3892' => 'fan', 'FAN05G3381' => 'fan', 'FAN07G0967' => 'fan', 'FAN07G1493' => 'fan', 'FAN08G3125' => 'fan', 'FAN09G0402' => 'fan', 'FAN12G2594' => 'fan', 'FAN12G3879' => 'fan', 'FAN14G1546' => 'fan', 'FAN15G3626' => 'fan', 'FAN17G0588' => 'fan', 'FAN17G0609' => 'fan', 'FAN18G2817' => 'fan', 'FAN19G1305' => 'fan', 'FAN20G1787' => 'fan', 'FAN22G0073' => 'fan', 'FAN22G0352' => 'fan', 'FAN22G0368' => 'fan', 'FAN22G2273' => 'fan', 'FAN24G1998' => 'fan', 'FAN27G1317' => 'fan', 'FvH4_2g23980' => 'fve', 'FvH4_4g14380' => 'fve', 'FvH4_4g14390' => 'fve', 'FvH4_6g09250' => 'fve', 'Glyma.03G151100' => 'gma', 'Glyma.04G122550' => 'gma', 'Glyma.05G001600' => 'gma', 'Glyma.09G270766' => 'gma', 'Glyma.09G270832' => 'gma', 'Glyma.13G209800' => 'gma', 'Glyma.15G102800' => 'gma', 'Glyma.18G218900' => 'gma', 'Glyma.19G001500' => 'gma', 'Glyma.19G153600' => 'gma', 'Gohir.A02G028600' => 'ghi', 'Gohir.A08G045000' => 'ghi', 'Gohir.A11G120500' => 'ghi', 'Gohir.A12G006200' => 'ghi', 'Gohir.A12G006250' => 'ghi', 'Gohir.D02G036300' => 'ghi', 'Gohir.D08G054700' => 'ghi', 'Gohir.D11G125600' => 'ghi', 'Gohir.D12G005700' => 'ghi', 'Gorai.004G055200' => 'gra', 'Gorai.005G040400' => 'gra', 'Gorai.007G134500' => 'gra', 'Gorai.008G005500' => 'gra', 'GSVIVG01011094001' => 'vvi', 'GSVIVG01017879001' => 'vvi', 'GSVIVG01025988001' => 'vvi', 'GSVIVG01029847001' => 'vvi', 'HanXRQChr10g0282901' => 'han', 'HanXRQChr10g0310371' => 'han', 'HanXRQChr10g0315041' => 'han', 'HanXRQChr11g0327651' => 'han', 'HanXRQChr12g0359391' => 'han', 'Haze_00972' => 'cav', 'Haze_00973' => 'cav', 'Haze_00974' => 'cav', 'Haze_04747' => 'cav', 'Haze_04749' => 'cav', 'Haze_04750' => 'cav', 'Haze_21217' => 'cav', 'Hma1.2p1_1037F.1_g250680' => 'hma', 'Hma1.2p1_1644F.1_g295320' => 'hma', 'HPP92_011322' => 'vpl', 'HPP92_011323' => 'vpl', 'HPP92_011324' => 'vpl', 'HPP92_011325' => 'vpl', 'HPP92_011326' => 'vpl', 'Hund12205' => 'sun', 'Hund17957' => 'sun', 'Lalb_Chr06g0176771' => 'lal', 'Lalb_Chr18g0056021' => 'lal', 'Lalb_Chr18g0056031' => 'lal', 'Lalb_Chr18g0056041' => 'lal', 'Lalb_Chr20g0107751' => 'lal', 'Lalb_Chr20g0118371' => 'lal', 'Lj1g0010239' => 'lja', 'Lj1g0017101' => 'lja', 'Lj2A1178G40' => 'lonja', 'Lj2A54G84' => 'lonja', 'Lj2g0015248' => 'lja', 'Lj3A761T51' => 'lonja', 'Lj6g0018116' => 'lja', 'Lsat_1_v5_gn_4_136040' => 'lsa', 'Lsat_1_v5_gn_5_187461' => 'lsa', 'Lsat_1_v5_gn_5_77001' => 'lsa', 'Lsat_1_v5_gn_9_4461' => 'lsa', 'Manes.01G210100' => 'mes', 'Manes.03G185600' => 'mes', 'Manes.05G073300' => 'mes', 'Manes.09G120300' => 'mes', 'Manes.15G022100' => 'mes', 'Mapoly0096s0053' => 'mpo', 'MBI03_g14058_MAGBIO' => 'mbi', 'MBI03_g33876_MAGBIO' => 'mbi', 'MBI03_g36854_MAGBIO' => 'mbi', 'MBI17_g11997_MAGBIO' => 'mbi', 'MD03G1269000' => 'mdo', 'MD04G1179600' => 'mdo', 'MD11G1289800' => 'mdo', 'MD12G1194700' => 'mdo', 'MD13G1182100' => 'mdo', 'MD13G1182200' => 'mdo', 'MD16G1182600' => 'mdo', 'Medtr2g021400' => 'mtr', 'Medtr2g021470' => 'mtr', 'Medtr2g105810' => 'mtr', 'Medtr3g033580' => 'mtr', 'Medtr6g007970' => 'mtr', 'Medtr7g056330' => 'mtr', 'Medtr7g074290' => 'mtr', 'Medtr7g074380' => 'mtr', 'Medtr7g094550' => 'mtr', 'Medtr8g069995' => 'mtr', 'MELO3C014345.2' => 'cme', 'MELO3C021395.2' => 'cme', 'Migut.D00262' => 'egut', 'Migut.G00257' => 'egut', 'MSTRG.21575' => 'ama', 'MSTRG.3985' => 'ama', 'Nitab4.5_0000295g0140' => 'nta', 'Nitab4.5_0000732g0140' => 'nta', 'Nitab4.5_0003162g0020' => 'nta', 'Nitab4.5_0006180g0090' => 'nta', 'Nitab4.5_0006390g0010' => 'nta', 'Nitab4.5_0007392g0040' => 'nta', 'Nn1g02140' => 'nnu', 'Nn4g26168' => 'nnu', 'Nn5g26754' => 'nnu', 'Oeu001433.1' => 'oeu', 'Oeu010299.2' => 'oeu', 'Oeu011171.1' => 'oeu', 'Oeu037675.1' => 'oeu', 'Oeu038359.1' => 'oeu', 'Oeu063834.1' => 'oeu', 'Oeu063835.1' => 'oeu', 'Os05g0312000' => 'osa', 'Os07g0211101' => 'osa', 'Os07g0211200' => 'osa', 'Os07g0681500' => 'osa', 'Peaxi162Scf00095g01015' => 'pax', 'Peaxi162Scf00104g00329' => 'pax', 'Peaxi162Scf00161g00137' => 'pax', 'PGR004G1665' => 'pgr', 'PGR031G2937' => 'pgr', 'PGR119G2145' => 'pgr', 'PGSC0003DMG400004351' => 'stu', 'PGSC0003DMG400014625' => 'stu', 'PGSC0003DMG401000943' => 'stu', 'Phvul.001G148600' => 'pvu', 'Phvul.004G001700' => 'pvu', 'Phvul.006G154900' => 'pvu', 'Phvul.008G078200' => 'pvu', 'Phvul.011G136500' => 'pvu', 'Potri.002G215600' => 'ptr', 'Potri.008G201600' => 'ptr', 'Potri.014G138400' => 'ptr', 'Potri.016G142500' => 'ptr', 'Pp3c16_10580' => 'ppa', 'Pp3c5_25280' => 'ppa', 'Prupe.1G150000' => 'ppe', 'Prupe.1G150100' => 'ppe', 'Prupe.6G299600' => 'ppe', 'Prupe.8G245000' => 'ppe', 'Psat0s4927g0040' => 'psa', 'Psat1g052080' => 'psa', 'Psat1g183800' => 'psa', 'Psat3g113840' => 'psa', 'Psat3g126120' => 'psa', 'Psat3g126160' => 'psa', 'Psat3g158760' => 'psa', 'Psat3g158840' => 'psa', 'PSO170G2858' => 'pso', 'PSO339G0606' => 'pso', 'PSO384G4709' => 'pso', 'PSO407G0334' => 'pso', 'QL04p040276' => 'qlo', 'QL06p005458' => 'qlo', 'QL06p005472' => 'qlo', 'QL07p030546' => 'qlo', 'QL07p031519' => 'qlo', 'QL09p050949' => 'qlo', 'QL09p050966' => 'qlo', 'QL09p051067' => 'qlo', 'QL12p022706' => 'qlo', 'RcHm_v2.0_Chr2g0119601' => 'rch', 'RcHm_v2.0_Chr3g0459591' => 'rch', 'RcHm_v2.0_Chr4g0418521' => 'rch', 'RcHm_v2.0_Chr4g0418531' => 'rch', 'RcHm_v2.0_Chr4g0418541' => 'rch', 'RcHm_v2.0_Chr6g0291641' => 'rch', 'Rhsim01G0086300' => 'rsi', 'Rhsim01G0276300' => 'rsi', 'Rhsim01G0276500' => 'rsi', 'Rhsim04G0207700' => 'rsi', 'Rhsim05G0234500' => 'rsi', 'Rhsim13G0022400' => 'rsi', 'Sabra02G0167900' => 'sbr', 'Sabra04G0158500' => 'sbr', 'Sabra08G0159800' => 'sbr', 'Sabra10G0011500' => 'sbr', 'Sabra14G0104400' => 'sbr', 'SalBow2G2440' => 'sbo', 'SalBow4G2265' => 'sbo', 'Sc02g0000060' => 'sci', 'Sc05g0005020' => 'sci', 'Sc13g0003890' => 'sci', 'Sed0014865' => 'sed', 'Sed0017224' => 'sed', 'Sed0026391' => 'sed', 'SEGI_00063' => 'sgi', 'SEGI_10967' => 'sgi', 'SEGI_17510' => 'sgi', 'SEGI_24396' => 'sgi', 'SEGI_39719' => 'sgi', 'SEGI_41392' => 'sgi', 'SGA_v2.0_scaffold11G05794' => 'sas', 'SGA_v2.0_scaffold142G35607' => 'sas', 'SGA_v2.0_scaffold1G00447' => 'sas', 'SHI15388' => 'shi', 'SHI15394' => 'shi', 'SHI15396' => 'shi', 'SHI15399' => 'shi', 'SMO343G0151' => 'smo', 'SMO367G1118' => 'smo', 'Solyc01g080200.3' => 'sly', 'Solyc06g008960.3' => 'sly', 'Solyc09g064780.3' => 'sly', 'Sopen01g031980' => 'spe', 'Sopen06g003710' => 'spe', 'Sopen09g026460' => 'spe', 'Sp3g21240' => 'spa', 'Sp4g30030' => 'spa', 'TAR365G0022' => 'tar', 'TAR365G1023' => 'tar', 'TAR365G1253' => 'tar', 'TAR623G0078' => 'tar', 'TAR623G1721' => 'tar', 'TAR633G0959' => 'tar', 'THA.LOC104802225' => 'tha', 'THA.LOC104804769' => 'tha', 'THA.LOC104808660' => 'tha', 'THA.LOC104812792' => 'tha', 'Thecc.01G284000' => 'tca', 'Thecc.04G220600' => 'tca', 'Thecc.05G268900' => 'tca', 'Thecc.08G171100' => 'tca', 'Thhalv10001284m.g' => 'esa', 'Thhalv10019912m.g' => 'esa', 'TPR.G14189' => 'tpr', 'TPR.G18110' => 'tpr', 'TPR.G18130' => 'tpr', 'TPR.G18131' => 'tpr', 'TPR.G18140' => 'tpr', 'TPR.G24282' => 'tpr', 'TPR.G25221' => 'tpr', 'TPR.G29267' => 'tpr', 'TPR.G35315' => 'tpr', 'TPR.G36173' => 'tpr', 'TWI09G0794' => 'twi', 'TWI59G1348' => 'twi', 'TWI74G0430' => 'twi', 'unitig_26.g8940' => 'ugi', 'unitig_749.g13744' => 'ugi', 'unitig_749.g13745' => 'ugi', 'vmacro08269' => 'vma', 'vmacro14937' => 'vma', 'vmacro20401' => 'vma', 'VMungo0464G1349' => 'vmu', 'VMungo0540G0289' => 'vmu', 'VMungo1215G1590' => 'vmu', 'VMungo1309G0221' => 'vmu', 'VMungo1309G2815' => 'vmu', 'VMungo1383G0239' => 'vmu', 'VMungo1383G2910' => 'vmu', 'Zm00001eb095270' => 'zma', 'Zm00001eb095280' => 'zma', 'Zm00001eb111630' => 'zma', 'Zm00001eb237080' => 'zma', 'Zm00001eb273740' => 'zma', 'Zm00001eb285040' => 'zma', 'Zm00001eb330790' => 'zma', 'Zm00001eb337380' => 'zma' ), 'gf_id' => 'HOM05D001484', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001484' ), 'data_identifier' => 'HOM05D001484', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001484', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p31500' => 'bna', 'A05p00020' => 'bna', 'A07p08820' => 'bna', 'Aa31LG4G3300' => 'aar', 'Aa31LG8G10030' => 'aar', 'Actinidia00731' => 'ach', 'Actinidia11473' => 'ach', 'Actinidia23469' => 'ach', 'Actinidia24318' => 'ach', 'Actinidia40196' => 'ach', 'Actinidia40197' => 'ach', 'Actinidia40198' => 'ach', 'Ah.08g212990' => 'amhyb', 'Ah.15g091720' => 'amhyb', 'AL3G38260' => 'aly', 'AL4G47710' => 'aly', 'Aqoxy2G00671' => 'aox', 'Aqoxy2G03236' => 'aox', 'arahy.Tifrunner.gnm1.ann1.05IDCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KR684' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATY3SJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK6QJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6APGL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IDT7Z9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM073U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ0R87' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LE7RV4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT4QRX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V5ENPK' => 'arhy', 'AT2G48110' => 'ath', 'AT3G23590' => 'ath', 'ATR0626G186' => 'atr', 'ATR1127G141' => 'atr', 'Atru.chr4.2583' => 'acertr', 'Atru.chr5.1358' => 'acertr', 'Atru.chr5.1359' => 'acertr', 'Atru.chr8.46' => 'acertr', 'AUR62002640' => 'cqu', 'AUR62030055' => 'cqu', 'AUR62033713' => 'cqu', 'AUR62033714' => 'cqu', 'AUR62036795' => 'cqu', 'AUR62039891' => 'cqu', 'BcaB02g08737' => 'bca', 'BcaB04g20441' => 'bca', 'BcaB06g26509' => 'bca', 'BcaB06g26510' => 'bca', 'BcaB06g26511' => 'bca', 'BcaB06g26512' => 'bca', 'BcaB06g26513' => 'bca', 'BcaC02g12564' => 'bca', 'BcaC02g12565' => 'bca', 'BcaC02g12794' => 'bca', 'BcaC02g12795' => 'bca', 'BcaC02g12796' => 'bca', 'BcaC06g35541' => 'bca', 'BNapus_Darmor_BZH_scaffold_188p00080' => 'bna', 'BNapus_Darmor_BZH_scaffold_188p00090' => 'bna', 'BolC1t03972H' => 'bol', 'BolC1t03973H' => 'bol', 'BolC4t21680H' => 'bol', 'BolC7t41863H' => 'bol', 'BolSC55t61227H' => 'bol', 'BolSC55t61228H' => 'bol', 'BraA01t03278Z' => 'bra', 'BraA05t18998Z' => 'bra', 'BraA07t28673Z' => 'bra', 'C01p40150' => 'bna', 'C05p12370' => 'bna', 'C07p13680' => 'bna', 'CAN.G1006.16' => 'can', 'CAN.G1006.17' => 'can', 'CAN.G1170.2' => 'can', 'CAN.G962.7' => 'can', 'CANSAT25G2179' => 'cansat', 'CANSAT78G1573' => 'cansat', 'CARHR099510' => 'chi', 'CARHR143510' => 'chi', 'Carub.0003s2380' => 'cru', 'Carub.0004s3082' => 'cru', 'Ca_00614_v3' => 'car', 'Ca_07801_v3' => 'car', 'Ca_08567_v3' => 'car', 'Ca_09571_v3' => 'car', 'CBR_g19290' => 'cbr', 'Cc01_g19770' => 'ccan', 'Cc03_g03030' => 'ccan', 'CDE07G0968' => 'cde', 'CDE09G1441' => 'cde', 'Cfa006103' => 'cfa', 'Cfa015573' => 'cfa', 'Cfa016988' => 'cfa', 'Ciclev10006738m.g' => 'ccl', 'Ciclev10010920m.g' => 'ccl', 'Ciclev10018517m.g' => 'ccl', 'CiPaw.01G159200' => 'cil', 'CiPaw.02G091000' => 'cil', 'CiPaw.02G091100' => 'cil', 'CiPaw.08G103100' => 'cil', 'CiPaw.09G224900' => 'cil', 'ClCG06G005740' => 'cla', 'ClCG07G000090' => 'cla', 'ClCG07G000100' => 'cla', 'COL.COLO4_09143' => 'col', 'COL.COLO4_25124' => 'col', 'Cpa.g.sc16.34' => 'cpa', 'Cpa.g.sc3504.1' => 'cpa', 'Cpa.g.sc60.37' => 'cpa', 'CsaV3_6G018520' => 'csa', 'CsaV3_6G036860' => 'csa', 'CSS0001072' => 'camsi', 'CSS0020208' => 'camsi', 'CSS0021253' => 'camsi', 'CSS0022190' => 'camsi', 'CSS0036150' => 'camsi', 'CSS0040442' => 'camsi', 'CSS0042300' => 'camsi', 'CSS0045298' => 'camsi', 'DCAR_012449' => 'dca', 'DCAR_018405' => 'dca', 'DCAR_024573' => 'dca', 'DCAR_030591' => 'dca', 'Dinv16926' => 'din', 'Dinv32963' => 'din', 'Dinv38382' => 'din', 'Dinv38383' => 'din', 'Duzib133G0974' => 'dzi', 'Duzib138G1867' => 'dzi', 'Duzib211G0420' => 'dzi', 'Duzib212G0930' => 'dzi', 'ECA234G1645' => 'eca', 'ECA247G3467' => 'eca', 'ECA248G1703' => 'eca', 'EL10Ac3g06327' => 'bvu', 'EL10Ac7g17204' => 'bvu', 'Eucgr.A00855' => 'egr', 'Eucgr.A00858' => 'egr', 'Eucgr.H01520' => 'egr', 'Eucgr.H03604' => 'egr', 'Eucgr.L03465' => 'egr', 'Eucgr.L03466' => 'egr', 'FAN01G0988' => 'fan', 'FAN02G3892' => 'fan', 'FAN05G3381' => 'fan', 'FAN07G0967' => 'fan', 'FAN07G1493' => 'fan', 'FAN08G3125' => 'fan', 'FAN09G0402' => 'fan', 'FAN12G2594' => 'fan', 'FAN12G3879' => 'fan', 'FAN14G1546' => 'fan', 'FAN15G3626' => 'fan', 'FAN17G0588' => 'fan', 'FAN17G0609' => 'fan', 'FAN18G2817' => 'fan', 'FAN19G1305' => 'fan', 'FAN20G1787' => 'fan', 'FAN22G0073' => 'fan', 'FAN22G0352' => 'fan', 'FAN22G0368' => 'fan', 'FAN22G2273' => 'fan', 'FAN24G1998' => 'fan', 'FAN27G1317' => 'fan', 'FvH4_2g23980' => 'fve', 'FvH4_4g14380' => 'fve', 'FvH4_4g14390' => 'fve', 'FvH4_6g09250' => 'fve', 'Glyma.03G151100' => 'gma', 'Glyma.04G122550' => 'gma', 'Glyma.05G001600' => 'gma', 'Glyma.09G270766' => 'gma', 'Glyma.09G270832' => 'gma', 'Glyma.13G209800' => 'gma', 'Glyma.15G102800' => 'gma', 'Glyma.18G218900' => 'gma', 'Glyma.19G001500' => 'gma', 'Glyma.19G153600' => 'gma', 'Gohir.A02G028600' => 'ghi', 'Gohir.A08G045000' => 'ghi', 'Gohir.A11G120500' => 'ghi', 'Gohir.A12G006200' => 'ghi', 'Gohir.A12G006250' => 'ghi', 'Gohir.D02G036300' => 'ghi', 'Gohir.D08G054700' => 'ghi', 'Gohir.D11G125600' => 'ghi', 'Gohir.D12G005700' => 'ghi', 'Gorai.004G055200' => 'gra', 'Gorai.005G040400' => 'gra', 'Gorai.007G134500' => 'gra', 'Gorai.008G005500' => 'gra', 'GSVIVG01011094001' => 'vvi', 'GSVIVG01017879001' => 'vvi', 'GSVIVG01025988001' => 'vvi', 'GSVIVG01029847001' => 'vvi', 'HanXRQChr10g0282901' => 'han', 'HanXRQChr10g0310371' => 'han', 'HanXRQChr10g0315041' => 'han', 'HanXRQChr11g0327651' => 'han', 'HanXRQChr12g0359391' => 'han', 'Haze_00972' => 'cav', 'Haze_00973' => 'cav', 'Haze_00974' => 'cav', 'Haze_04747' => 'cav', 'Haze_04749' => 'cav', 'Haze_04750' => 'cav', 'Haze_21217' => 'cav', 'Hma1.2p1_1037F.1_g250680' => 'hma', 'Hma1.2p1_1644F.1_g295320' => 'hma', 'HPP92_011322' => 'vpl', 'HPP92_011323' => 'vpl', 'HPP92_011324' => 'vpl', 'HPP92_011325' => 'vpl', 'HPP92_011326' => 'vpl', 'Hund12205' => 'sun', 'Hund17957' => 'sun', 'Lalb_Chr06g0176771' => 'lal', 'Lalb_Chr18g0056021' => 'lal', 'Lalb_Chr18g0056031' => 'lal', 'Lalb_Chr18g0056041' => 'lal', 'Lalb_Chr20g0107751' => 'lal', 'Lalb_Chr20g0118371' => 'lal', 'Lj1g0010239' => 'lja', 'Lj1g0017101' => 'lja', 'Lj2A1178G40' => 'lonja', 'Lj2A54G84' => 'lonja', 'Lj2g0015248' => 'lja', 'Lj3A761T51' => 'lonja', 'Lj6g0018116' => 'lja', 'Lsat_1_v5_gn_4_136040' => 'lsa', 'Lsat_1_v5_gn_5_187461' => 'lsa', 'Lsat_1_v5_gn_5_77001' => 'lsa', 'Lsat_1_v5_gn_9_4461' => 'lsa', 'Manes.01G210100' => 'mes', 'Manes.03G185600' => 'mes', 'Manes.05G073300' => 'mes', 'Manes.09G120300' => 'mes', 'Manes.15G022100' => 'mes', 'Mapoly0096s0053' => 'mpo', 'MBI03_g14058_MAGBIO' => 'mbi', 'MBI03_g33876_MAGBIO' => 'mbi', 'MBI03_g36854_MAGBIO' => 'mbi', 'MBI17_g11997_MAGBIO' => 'mbi', 'MD03G1269000' => 'mdo', 'MD04G1179600' => 'mdo', 'MD11G1289800' => 'mdo', 'MD12G1194700' => 'mdo', 'MD13G1182100' => 'mdo', 'MD13G1182200' => 'mdo', 'MD16G1182600' => 'mdo', 'Medtr2g021400' => 'mtr', 'Medtr2g021470' => 'mtr', 'Medtr2g105810' => 'mtr', 'Medtr3g033580' => 'mtr', 'Medtr6g007970' => 'mtr', 'Medtr7g056330' => 'mtr', 'Medtr7g074290' => 'mtr', 'Medtr7g074380' => 'mtr', 'Medtr7g094550' => 'mtr', 'Medtr8g069995' => 'mtr', 'MELO3C014345.2' => 'cme', 'MELO3C021395.2' => 'cme', 'Migut.D00262' => 'egut', 'Migut.G00257' => 'egut', 'MSTRG.21575' => 'ama', 'MSTRG.3985' => 'ama', 'Nitab4.5_0000295g0140' => 'nta', 'Nitab4.5_0000732g0140' => 'nta', 'Nitab4.5_0003162g0020' => 'nta', 'Nitab4.5_0006180g0090' => 'nta', 'Nitab4.5_0006390g0010' => 'nta', 'Nitab4.5_0007392g0040' => 'nta', 'Nn1g02140' => 'nnu', 'Nn4g26168' => 'nnu', 'Nn5g26754' => 'nnu', 'Oeu001433.1' => 'oeu', 'Oeu010299.2' => 'oeu', 'Oeu011171.1' => 'oeu', 'Oeu037675.1' => 'oeu', 'Oeu038359.1' => 'oeu', 'Oeu063834.1' => 'oeu', 'Oeu063835.1' => 'oeu', 'Os05g0312000' => 'osa', 'Os07g0211101' => 'osa', 'Os07g0211200' => 'osa', 'Os07g0681500' => 'osa', 'Peaxi162Scf00095g01015' => 'pax', 'Peaxi162Scf00104g00329' => 'pax', 'Peaxi162Scf00161g00137' => 'pax', 'PGR004G1665' => 'pgr', 'PGR031G2937' => 'pgr', 'PGR119G2145' => 'pgr', 'PGSC0003DMG400004351' => 'stu', 'PGSC0003DMG400014625' => 'stu', 'PGSC0003DMG401000943' => 'stu', 'Phvul.001G148600' => 'pvu', 'Phvul.004G001700' => 'pvu', 'Phvul.006G154900' => 'pvu', 'Phvul.008G078200' => 'pvu', 'Phvul.011G136500' => 'pvu', 'Potri.002G215600' => 'ptr', 'Potri.008G201600' => 'ptr', 'Potri.014G138400' => 'ptr', 'Potri.016G142500' => 'ptr', 'Pp3c16_10580' => 'ppa', 'Pp3c5_25280' => 'ppa', 'Prupe.1G150000' => 'ppe', 'Prupe.1G150100' => 'ppe', 'Prupe.6G299600' => 'ppe', 'Prupe.8G245000' => 'ppe', 'Psat0s4927g0040' => 'psa', 'Psat1g052080' => 'psa', 'Psat1g183800' => 'psa', 'Psat3g113840' => 'psa', 'Psat3g126120' => 'psa', 'Psat3g126160' => 'psa', 'Psat3g158760' => 'psa', 'Psat3g158840' => 'psa', 'PSO170G2858' => 'pso', 'PSO339G0606' => 'pso', 'PSO384G4709' => 'pso', 'PSO407G0334' => 'pso', 'QL04p040276' => 'qlo', 'QL06p005458' => 'qlo', 'QL06p005472' => 'qlo', 'QL07p030546' => 'qlo', 'QL07p031519' => 'qlo', 'QL09p050949' => 'qlo', 'QL09p050966' => 'qlo', 'QL09p051067' => 'qlo', 'QL12p022706' => 'qlo', 'RcHm_v2.0_Chr2g0119601' => 'rch', 'RcHm_v2.0_Chr3g0459591' => 'rch', 'RcHm_v2.0_Chr4g0418521' => 'rch', 'RcHm_v2.0_Chr4g0418531' => 'rch', 'RcHm_v2.0_Chr4g0418541' => 'rch', 'RcHm_v2.0_Chr6g0291641' => 'rch', 'Rhsim01G0086300' => 'rsi', 'Rhsim01G0276300' => 'rsi', 'Rhsim01G0276500' => 'rsi', 'Rhsim04G0207700' => 'rsi', 'Rhsim05G0234500' => 'rsi', 'Rhsim13G0022400' => 'rsi', 'Sabra02G0167900' => 'sbr', 'Sabra04G0158500' => 'sbr', 'Sabra08G0159800' => 'sbr', 'Sabra10G0011500' => 'sbr', 'Sabra14G0104400' => 'sbr', 'SalBow2G2440' => 'sbo', 'SalBow4G2265' => 'sbo', 'Sc02g0000060' => 'sci', 'Sc05g0005020' => 'sci', 'Sc13g0003890' => 'sci', 'Sed0014865' => 'sed', 'Sed0017224' => 'sed', 'Sed0026391' => 'sed', 'SEGI_00063' => 'sgi', 'SEGI_10967' => 'sgi', 'SEGI_17510' => 'sgi', 'SEGI_24396' => 'sgi', 'SEGI_39719' => 'sgi', 'SEGI_41392' => 'sgi', 'SGA_v2.0_scaffold11G05794' => 'sas', 'SGA_v2.0_scaffold142G35607' => 'sas', 'SGA_v2.0_scaffold1G00447' => 'sas', 'SHI15388' => 'shi', 'SHI15394' => 'shi', 'SHI15396' => 'shi', 'SHI15399' => 'shi', 'SMO343G0151' => 'smo', 'SMO367G1118' => 'smo', 'Solyc01g080200.3' => 'sly', 'Solyc06g008960.3' => 'sly', 'Solyc09g064780.3' => 'sly', 'Sopen01g031980' => 'spe', 'Sopen06g003710' => 'spe', 'Sopen09g026460' => 'spe', 'Sp3g21240' => 'spa', 'Sp4g30030' => 'spa', 'TAR365G0022' => 'tar', 'TAR365G1023' => 'tar', 'TAR365G1253' => 'tar', 'TAR623G0078' => 'tar', 'TAR623G1721' => 'tar', 'TAR633G0959' => 'tar', 'THA.LOC104802225' => 'tha', 'THA.LOC104804769' => 'tha', 'THA.LOC104808660' => 'tha', 'THA.LOC104812792' => 'tha', 'Thecc.01G284000' => 'tca', 'Thecc.04G220600' => 'tca', 'Thecc.05G268900' => 'tca', 'Thecc.08G171100' => 'tca', 'Thhalv10001284m.g' => 'esa', 'Thhalv10019912m.g' => 'esa', 'TPR.G14189' => 'tpr', 'TPR.G18110' => 'tpr', 'TPR.G18130' => 'tpr', 'TPR.G18131' => 'tpr', 'TPR.G18140' => 'tpr', 'TPR.G24282' => 'tpr', 'TPR.G25221' => 'tpr', 'TPR.G29267' => 'tpr', 'TPR.G35315' => 'tpr', 'TPR.G36173' => 'tpr', 'TWI09G0794' => 'twi', 'TWI59G1348' => 'twi', 'TWI74G0430' => 'twi', 'unitig_26.g8940' => 'ugi', 'unitig_749.g13744' => 'ugi', 'unitig_749.g13745' => 'ugi', 'vmacro08269' => 'vma', 'vmacro14937' => 'vma', 'vmacro20401' => 'vma', 'VMungo0464G1349' => 'vmu', 'VMungo0540G0289' => 'vmu', 'VMungo1215G1590' => 'vmu', 'VMungo1309G0221' => 'vmu', 'VMungo1309G2815' => 'vmu', 'VMungo1383G0239' => 'vmu', 'VMungo1383G2910' => 'vmu', 'Zm00001eb095270' => 'zma', 'Zm00001eb095280' => 'zma', 'Zm00001eb111630' => 'zma', 'Zm00001eb237080' => 'zma', 'Zm00001eb273740' => 'zma', 'Zm00001eb285040' => 'zma', 'Zm00001eb330790' => 'zma', 'Zm00001eb337380' => 'zma' ) $gf_id = 'HOM05D001484' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001484' ) $data_identifier = 'HOM05D001484' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 2, 'aly' => (int) 2, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 22, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 7, 'hma' => (int) 2, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 7, 'mtr' => (int) 10, 'cme' => (int) 2, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 4, 'ppa' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 4, 'qlo' => (int) 9, 'rch' => (int) 6, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 10, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 7, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb337380' $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' => 'HOM05D001484', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p31500' => 'bna', 'A05p00020' => 'bna', 'A07p08820' => 'bna', 'Aa31LG4G3300' => 'aar', 'Aa31LG8G10030' => 'aar', 'Actinidia00731' => 'ach', 'Actinidia11473' => 'ach', 'Actinidia23469' => 'ach', 'Actinidia24318' => 'ach', 'Actinidia40196' => 'ach', 'Actinidia40197' => 'ach', 'Actinidia40198' => 'ach', 'Ah.08g212990' => 'amhyb', 'Ah.15g091720' => 'amhyb', 'AL3G38260' => 'aly', 'AL4G47710' => 'aly', 'Aqoxy2G00671' => 'aox', 'Aqoxy2G03236' => 'aox', 'arahy.Tifrunner.gnm1.ann1.05IDCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KR684' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATY3SJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK6QJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6APGL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IDT7Z9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM073U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ0R87' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LE7RV4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT4QRX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V5ENPK' => 'arhy', 'AT2G48110' => 'ath', 'AT3G23590' => 'ath', 'ATR0626G186' => 'atr', 'ATR1127G141' => 'atr', 'Atru.chr4.2583' => 'acertr', 'Atru.chr5.1358' => 'acertr', 'Atru.chr5.1359' => 'acertr', 'Atru.chr8.46' => 'acertr', 'AUR62002640' => 'cqu', 'AUR62030055' => 'cqu', 'AUR62033713' => 'cqu', 'AUR62033714' => 'cqu', 'AUR62036795' => 'cqu', 'AUR62039891' => 'cqu', 'BcaB02g08737' => 'bca', 'BcaB04g20441' => 'bca', 'BcaB06g26509' => 'bca', 'BcaB06g26510' => 'bca', 'BcaB06g26511' => 'bca', 'BcaB06g26512' => 'bca', 'BcaB06g26513' => 'bca', 'BcaC02g12564' => 'bca', 'BcaC02g12565' => 'bca', 'BcaC02g12794' => 'bca', 'BcaC02g12795' => 'bca', 'BcaC02g12796' => 'bca', 'BcaC06g35541' => 'bca', 'BNapus_Darmor_BZH_scaffold_188p00080' => 'bna', 'BNapus_Darmor_BZH_scaffold_188p00090' => 'bna', 'BolC1t03972H' => 'bol', 'BolC1t03973H' => 'bol', 'BolC4t21680H' => 'bol', 'BolC7t41863H' => 'bol', 'BolSC55t61227H' => 'bol', 'BolSC55t61228H' => 'bol', 'BraA01t03278Z' => 'bra', 'BraA05t18998Z' => 'bra', 'BraA07t28673Z' => 'bra', 'C01p40150' => 'bna', 'C05p12370' => 'bna', 'C07p13680' => 'bna', 'CAN.G1006.16' => 'can', 'CAN.G1006.17' => 'can', 'CAN.G1170.2' => 'can', 'CAN.G962.7' => 'can', 'CANSAT25G2179' => 'cansat', 'CANSAT78G1573' => 'cansat', 'CARHR099510' => 'chi', 'CARHR143510' => 'chi', 'Carub.0003s2380' => 'cru', 'Carub.0004s3082' => 'cru', 'Ca_00614_v3' => 'car', 'Ca_07801_v3' => 'car', 'Ca_08567_v3' => 'car', 'Ca_09571_v3' => 'car', 'CBR_g19290' => 'cbr', 'Cc01_g19770' => 'ccan', 'Cc03_g03030' => 'ccan', 'CDE07G0968' => 'cde', 'CDE09G1441' => 'cde', 'Cfa006103' => 'cfa', 'Cfa015573' => 'cfa', 'Cfa016988' => 'cfa', 'Ciclev10006738m.g' => 'ccl', 'Ciclev10010920m.g' => 'ccl', 'Ciclev10018517m.g' => 'ccl', 'CiPaw.01G159200' => 'cil', 'CiPaw.02G091000' => 'cil', 'CiPaw.02G091100' => 'cil', 'CiPaw.08G103100' => 'cil', 'CiPaw.09G224900' => 'cil', 'ClCG06G005740' => 'cla', 'ClCG07G000090' => 'cla', 'ClCG07G000100' => 'cla', 'COL.COLO4_09143' => 'col', 'COL.COLO4_25124' => 'col', 'Cpa.g.sc16.34' => 'cpa', 'Cpa.g.sc3504.1' => 'cpa', 'Cpa.g.sc60.37' => 'cpa', 'CsaV3_6G018520' => 'csa', 'CsaV3_6G036860' => 'csa', 'CSS0001072' => 'camsi', 'CSS0020208' => 'camsi', 'CSS0021253' => 'camsi', 'CSS0022190' => 'camsi', 'CSS0036150' => 'camsi', 'CSS0040442' => 'camsi', 'CSS0042300' => 'camsi', 'CSS0045298' => 'camsi', 'DCAR_012449' => 'dca', 'DCAR_018405' => 'dca', 'DCAR_024573' => 'dca', 'DCAR_030591' => 'dca', 'Dinv16926' => 'din', 'Dinv32963' => 'din', 'Dinv38382' => 'din', 'Dinv38383' => 'din', 'Duzib133G0974' => 'dzi', 'Duzib138G1867' => 'dzi', 'Duzib211G0420' => 'dzi', 'Duzib212G0930' => 'dzi', 'ECA234G1645' => 'eca', 'ECA247G3467' => 'eca', 'ECA248G1703' => 'eca', 'EL10Ac3g06327' => 'bvu', 'EL10Ac7g17204' => 'bvu', 'Eucgr.A00855' => 'egr', 'Eucgr.A00858' => 'egr', 'Eucgr.H01520' => 'egr', 'Eucgr.H03604' => 'egr', 'Eucgr.L03465' => 'egr', 'Eucgr.L03466' => 'egr', 'FAN01G0988' => 'fan', 'FAN02G3892' => 'fan', 'FAN05G3381' => 'fan', 'FAN07G0967' => 'fan', 'FAN07G1493' => 'fan', 'FAN08G3125' => 'fan', 'FAN09G0402' => 'fan', 'FAN12G2594' => 'fan', 'FAN12G3879' => 'fan', 'FAN14G1546' => 'fan', 'FAN15G3626' => 'fan', 'FAN17G0588' => 'fan', 'FAN17G0609' => 'fan', 'FAN18G2817' => 'fan', 'FAN19G1305' => 'fan', 'FAN20G1787' => 'fan', 'FAN22G0073' => 'fan', 'FAN22G0352' => 'fan', 'FAN22G0368' => 'fan', 'FAN22G2273' => 'fan', 'FAN24G1998' => 'fan', 'FAN27G1317' => 'fan', 'FvH4_2g23980' => 'fve', 'FvH4_4g14380' => 'fve', 'FvH4_4g14390' => 'fve', 'FvH4_6g09250' => 'fve', 'Glyma.03G151100' => 'gma', 'Glyma.04G122550' => 'gma', 'Glyma.05G001600' => 'gma', 'Glyma.09G270766' => 'gma', 'Glyma.09G270832' => 'gma', 'Glyma.13G209800' => 'gma', 'Glyma.15G102800' => 'gma', 'Glyma.18G218900' => 'gma', 'Glyma.19G001500' => 'gma', 'Glyma.19G153600' => 'gma', 'Gohir.A02G028600' => 'ghi', 'Gohir.A08G045000' => 'ghi', 'Gohir.A11G120500' => 'ghi', 'Gohir.A12G006200' => 'ghi', 'Gohir.A12G006250' => 'ghi', 'Gohir.D02G036300' => 'ghi', 'Gohir.D08G054700' => 'ghi', 'Gohir.D11G125600' => 'ghi', 'Gohir.D12G005700' => 'ghi', 'Gorai.004G055200' => 'gra', 'Gorai.005G040400' => 'gra', 'Gorai.007G134500' => 'gra', 'Gorai.008G005500' => 'gra', 'GSVIVG01011094001' => 'vvi', 'GSVIVG01017879001' => 'vvi', 'GSVIVG01025988001' => 'vvi', 'GSVIVG01029847001' => 'vvi', 'HanXRQChr10g0282901' => 'han', 'HanXRQChr10g0310371' => 'han', 'HanXRQChr10g0315041' => 'han', 'HanXRQChr11g0327651' => 'han', 'HanXRQChr12g0359391' => 'han', 'Haze_00972' => 'cav', 'Haze_00973' => 'cav', 'Haze_00974' => 'cav', 'Haze_04747' => 'cav', 'Haze_04749' => 'cav', 'Haze_04750' => 'cav', 'Haze_21217' => 'cav', 'Hma1.2p1_1037F.1_g250680' => 'hma', 'Hma1.2p1_1644F.1_g295320' => 'hma', 'HPP92_011322' => 'vpl', 'HPP92_011323' => 'vpl', 'HPP92_011324' => 'vpl', 'HPP92_011325' => 'vpl', 'HPP92_011326' => 'vpl', 'Hund12205' => 'sun', 'Hund17957' => 'sun', 'Lalb_Chr06g0176771' => 'lal', 'Lalb_Chr18g0056021' => 'lal', 'Lalb_Chr18g0056031' => 'lal', 'Lalb_Chr18g0056041' => 'lal', 'Lalb_Chr20g0107751' => 'lal', 'Lalb_Chr20g0118371' => 'lal', 'Lj1g0010239' => 'lja', 'Lj1g0017101' => 'lja', 'Lj2A1178G40' => 'lonja', 'Lj2A54G84' => 'lonja', 'Lj2g0015248' => 'lja', 'Lj3A761T51' => 'lonja', 'Lj6g0018116' => 'lja', 'Lsat_1_v5_gn_4_136040' => 'lsa', 'Lsat_1_v5_gn_5_187461' => 'lsa', 'Lsat_1_v5_gn_5_77001' => 'lsa', 'Lsat_1_v5_gn_9_4461' => 'lsa', 'Manes.01G210100' => 'mes', 'Manes.03G185600' => 'mes', 'Manes.05G073300' => 'mes', 'Manes.09G120300' => 'mes', 'Manes.15G022100' => 'mes', 'Mapoly0096s0053' => 'mpo', 'MBI03_g14058_MAGBIO' => 'mbi', 'MBI03_g33876_MAGBIO' => 'mbi', 'MBI03_g36854_MAGBIO' => 'mbi', 'MBI17_g11997_MAGBIO' => 'mbi', 'MD03G1269000' => 'mdo', 'MD04G1179600' => 'mdo', 'MD11G1289800' => 'mdo', 'MD12G1194700' => 'mdo', 'MD13G1182100' => 'mdo', 'MD13G1182200' => 'mdo', 'MD16G1182600' => 'mdo', 'Medtr2g021400' => 'mtr', 'Medtr2g021470' => 'mtr', 'Medtr2g105810' => 'mtr', 'Medtr3g033580' => 'mtr', 'Medtr6g007970' => 'mtr', 'Medtr7g056330' => 'mtr', 'Medtr7g074290' => 'mtr', 'Medtr7g074380' => 'mtr', 'Medtr7g094550' => 'mtr', 'Medtr8g069995' => 'mtr', 'MELO3C014345.2' => 'cme', 'MELO3C021395.2' => 'cme', 'Migut.D00262' => 'egut', 'Migut.G00257' => 'egut', 'MSTRG.21575' => 'ama', 'MSTRG.3985' => 'ama', 'Nitab4.5_0000295g0140' => 'nta', 'Nitab4.5_0000732g0140' => 'nta', 'Nitab4.5_0003162g0020' => 'nta', 'Nitab4.5_0006180g0090' => 'nta', 'Nitab4.5_0006390g0010' => 'nta', 'Nitab4.5_0007392g0040' => 'nta', 'Nn1g02140' => 'nnu', 'Nn4g26168' => 'nnu', 'Nn5g26754' => 'nnu', 'Oeu001433.1' => 'oeu', 'Oeu010299.2' => 'oeu', 'Oeu011171.1' => 'oeu', 'Oeu037675.1' => 'oeu', 'Oeu038359.1' => 'oeu', 'Oeu063834.1' => 'oeu', 'Oeu063835.1' => 'oeu', 'Os05g0312000' => 'osa', 'Os07g0211101' => 'osa', 'Os07g0211200' => 'osa', 'Os07g0681500' => 'osa', 'Peaxi162Scf00095g01015' => 'pax', 'Peaxi162Scf00104g00329' => 'pax', 'Peaxi162Scf00161g00137' => 'pax', 'PGR004G1665' => 'pgr', 'PGR031G2937' => 'pgr', 'PGR119G2145' => 'pgr', 'PGSC0003DMG400004351' => 'stu', 'PGSC0003DMG400014625' => 'stu', 'PGSC0003DMG401000943' => 'stu', 'Phvul.001G148600' => 'pvu', 'Phvul.004G001700' => 'pvu', 'Phvul.006G154900' => 'pvu', 'Phvul.008G078200' => 'pvu', 'Phvul.011G136500' => 'pvu', 'Potri.002G215600' => 'ptr', 'Potri.008G201600' => 'ptr', 'Potri.014G138400' => 'ptr', 'Potri.016G142500' => 'ptr', 'Pp3c16_10580' => 'ppa', 'Pp3c5_25280' => 'ppa', 'Prupe.1G150000' => 'ppe', 'Prupe.1G150100' => 'ppe', 'Prupe.6G299600' => 'ppe', 'Prupe.8G245000' => 'ppe', 'Psat0s4927g0040' => 'psa', 'Psat1g052080' => 'psa', 'Psat1g183800' => 'psa', 'Psat3g113840' => 'psa', 'Psat3g126120' => 'psa', 'Psat3g126160' => 'psa', 'Psat3g158760' => 'psa', 'Psat3g158840' => 'psa', 'PSO170G2858' => 'pso', 'PSO339G0606' => 'pso', 'PSO384G4709' => 'pso', 'PSO407G0334' => 'pso', 'QL04p040276' => 'qlo', 'QL06p005458' => 'qlo', 'QL06p005472' => 'qlo', 'QL07p030546' => 'qlo', 'QL07p031519' => 'qlo', 'QL09p050949' => 'qlo', 'QL09p050966' => 'qlo', 'QL09p051067' => 'qlo', 'QL12p022706' => 'qlo', 'RcHm_v2.0_Chr2g0119601' => 'rch', 'RcHm_v2.0_Chr3g0459591' => 'rch', 'RcHm_v2.0_Chr4g0418521' => 'rch', 'RcHm_v2.0_Chr4g0418531' => 'rch', 'RcHm_v2.0_Chr4g0418541' => 'rch', 'RcHm_v2.0_Chr6g0291641' => 'rch', 'Rhsim01G0086300' => 'rsi', 'Rhsim01G0276300' => 'rsi', 'Rhsim01G0276500' => 'rsi', 'Rhsim04G0207700' => 'rsi', 'Rhsim05G0234500' => 'rsi', 'Rhsim13G0022400' => 'rsi', 'Sabra02G0167900' => 'sbr', 'Sabra04G0158500' => 'sbr', 'Sabra08G0159800' => 'sbr', 'Sabra10G0011500' => 'sbr', 'Sabra14G0104400' => 'sbr', 'SalBow2G2440' => 'sbo', 'SalBow4G2265' => 'sbo', 'Sc02g0000060' => 'sci', 'Sc05g0005020' => 'sci', 'Sc13g0003890' => 'sci', 'Sed0014865' => 'sed', 'Sed0017224' => 'sed', 'Sed0026391' => 'sed', 'SEGI_00063' => 'sgi', 'SEGI_10967' => 'sgi', 'SEGI_17510' => 'sgi', 'SEGI_24396' => 'sgi', 'SEGI_39719' => 'sgi', 'SEGI_41392' => 'sgi', 'SGA_v2.0_scaffold11G05794' => 'sas', 'SGA_v2.0_scaffold142G35607' => 'sas', 'SGA_v2.0_scaffold1G00447' => 'sas', 'SHI15388' => 'shi', 'SHI15394' => 'shi', 'SHI15396' => 'shi', 'SHI15399' => 'shi', 'SMO343G0151' => 'smo', 'SMO367G1118' => 'smo', 'Solyc01g080200.3' => 'sly', 'Solyc06g008960.3' => 'sly', 'Solyc09g064780.3' => 'sly', 'Sopen01g031980' => 'spe', 'Sopen06g003710' => 'spe', 'Sopen09g026460' => 'spe', 'Sp3g21240' => 'spa', 'Sp4g30030' => 'spa', 'TAR365G0022' => 'tar', 'TAR365G1023' => 'tar', 'TAR365G1253' => 'tar', 'TAR623G0078' => 'tar', 'TAR623G1721' => 'tar', 'TAR633G0959' => 'tar', 'THA.LOC104802225' => 'tha', 'THA.LOC104804769' => 'tha', 'THA.LOC104808660' => 'tha', 'THA.LOC104812792' => 'tha', 'Thecc.01G284000' => 'tca', 'Thecc.04G220600' => 'tca', 'Thecc.05G268900' => 'tca', 'Thecc.08G171100' => 'tca', 'Thhalv10001284m.g' => 'esa', 'Thhalv10019912m.g' => 'esa', 'TPR.G14189' => 'tpr', 'TPR.G18110' => 'tpr', 'TPR.G18130' => 'tpr', 'TPR.G18131' => 'tpr', 'TPR.G18140' => 'tpr', 'TPR.G24282' => 'tpr', 'TPR.G25221' => 'tpr', 'TPR.G29267' => 'tpr', 'TPR.G35315' => 'tpr', 'TPR.G36173' => 'tpr', 'TWI09G0794' => 'twi', 'TWI59G1348' => 'twi', 'TWI74G0430' => 'twi', 'unitig_26.g8940' => 'ugi', 'unitig_749.g13744' => 'ugi', 'unitig_749.g13745' => 'ugi', 'vmacro08269' => 'vma', 'vmacro14937' => 'vma', 'vmacro20401' => 'vma', 'VMungo0464G1349' => 'vmu', 'VMungo0540G0289' => 'vmu', 'VMungo1215G1590' => 'vmu', 'VMungo1309G0221' => 'vmu', 'VMungo1309G2815' => 'vmu', 'VMungo1383G0239' => 'vmu', 'VMungo1383G2910' => 'vmu', 'Zm00001eb095270' => 'zma', 'Zm00001eb095280' => 'zma', 'Zm00001eb111630' => 'zma', 'Zm00001eb237080' => 'zma', 'Zm00001eb273740' => 'zma', 'Zm00001eb285040' => 'zma', 'Zm00001eb330790' => 'zma', 'Zm00001eb337380' => 'zma' ), 'gf_id' => 'HOM05D001484', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001484' ), 'data_identifier' => 'HOM05D001484', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001484', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p31500' => 'bna', 'A05p00020' => 'bna', 'A07p08820' => 'bna', 'Aa31LG4G3300' => 'aar', 'Aa31LG8G10030' => 'aar', 'Actinidia00731' => 'ach', 'Actinidia11473' => 'ach', 'Actinidia23469' => 'ach', 'Actinidia24318' => 'ach', 'Actinidia40196' => 'ach', 'Actinidia40197' => 'ach', 'Actinidia40198' => 'ach', 'Ah.08g212990' => 'amhyb', 'Ah.15g091720' => 'amhyb', 'AL3G38260' => 'aly', 'AL4G47710' => 'aly', 'Aqoxy2G00671' => 'aox', 'Aqoxy2G03236' => 'aox', 'arahy.Tifrunner.gnm1.ann1.05IDCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KR684' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATY3SJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK6QJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6APGL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IDT7Z9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM073U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ0R87' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LE7RV4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT4QRX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V5ENPK' => 'arhy', 'AT2G48110' => 'ath', 'AT3G23590' => 'ath', 'ATR0626G186' => 'atr', 'ATR1127G141' => 'atr', 'Atru.chr4.2583' => 'acertr', 'Atru.chr5.1358' => 'acertr', 'Atru.chr5.1359' => 'acertr', 'Atru.chr8.46' => 'acertr', 'AUR62002640' => 'cqu', 'AUR62030055' => 'cqu', 'AUR62033713' => 'cqu', 'AUR62033714' => 'cqu', 'AUR62036795' => 'cqu', 'AUR62039891' => 'cqu', 'BcaB02g08737' => 'bca', 'BcaB04g20441' => 'bca', 'BcaB06g26509' => 'bca', 'BcaB06g26510' => 'bca', 'BcaB06g26511' => 'bca', 'BcaB06g26512' => 'bca', 'BcaB06g26513' => 'bca', 'BcaC02g12564' => 'bca', 'BcaC02g12565' => 'bca', 'BcaC02g12794' => 'bca', 'BcaC02g12795' => 'bca', 'BcaC02g12796' => 'bca', 'BcaC06g35541' => 'bca', 'BNapus_Darmor_BZH_scaffold_188p00080' => 'bna', 'BNapus_Darmor_BZH_scaffold_188p00090' => 'bna', 'BolC1t03972H' => 'bol', 'BolC1t03973H' => 'bol', 'BolC4t21680H' => 'bol', 'BolC7t41863H' => 'bol', 'BolSC55t61227H' => 'bol', 'BolSC55t61228H' => 'bol', 'BraA01t03278Z' => 'bra', 'BraA05t18998Z' => 'bra', 'BraA07t28673Z' => 'bra', 'C01p40150' => 'bna', 'C05p12370' => 'bna', 'C07p13680' => 'bna', 'CAN.G1006.16' => 'can', 'CAN.G1006.17' => 'can', 'CAN.G1170.2' => 'can', 'CAN.G962.7' => 'can', 'CANSAT25G2179' => 'cansat', 'CANSAT78G1573' => 'cansat', 'CARHR099510' => 'chi', 'CARHR143510' => 'chi', 'Carub.0003s2380' => 'cru', 'Carub.0004s3082' => 'cru', 'Ca_00614_v3' => 'car', 'Ca_07801_v3' => 'car', 'Ca_08567_v3' => 'car', 'Ca_09571_v3' => 'car', 'CBR_g19290' => 'cbr', 'Cc01_g19770' => 'ccan', 'Cc03_g03030' => 'ccan', 'CDE07G0968' => 'cde', 'CDE09G1441' => 'cde', 'Cfa006103' => 'cfa', 'Cfa015573' => 'cfa', 'Cfa016988' => 'cfa', 'Ciclev10006738m.g' => 'ccl', 'Ciclev10010920m.g' => 'ccl', 'Ciclev10018517m.g' => 'ccl', 'CiPaw.01G159200' => 'cil', 'CiPaw.02G091000' => 'cil', 'CiPaw.02G091100' => 'cil', 'CiPaw.08G103100' => 'cil', 'CiPaw.09G224900' => 'cil', 'ClCG06G005740' => 'cla', 'ClCG07G000090' => 'cla', 'ClCG07G000100' => 'cla', 'COL.COLO4_09143' => 'col', 'COL.COLO4_25124' => 'col', 'Cpa.g.sc16.34' => 'cpa', 'Cpa.g.sc3504.1' => 'cpa', 'Cpa.g.sc60.37' => 'cpa', 'CsaV3_6G018520' => 'csa', 'CsaV3_6G036860' => 'csa', 'CSS0001072' => 'camsi', 'CSS0020208' => 'camsi', 'CSS0021253' => 'camsi', 'CSS0022190' => 'camsi', 'CSS0036150' => 'camsi', 'CSS0040442' => 'camsi', 'CSS0042300' => 'camsi', 'CSS0045298' => 'camsi', 'DCAR_012449' => 'dca', 'DCAR_018405' => 'dca', 'DCAR_024573' => 'dca', 'DCAR_030591' => 'dca', 'Dinv16926' => 'din', 'Dinv32963' => 'din', 'Dinv38382' => 'din', 'Dinv38383' => 'din', 'Duzib133G0974' => 'dzi', 'Duzib138G1867' => 'dzi', 'Duzib211G0420' => 'dzi', 'Duzib212G0930' => 'dzi', 'ECA234G1645' => 'eca', 'ECA247G3467' => 'eca', 'ECA248G1703' => 'eca', 'EL10Ac3g06327' => 'bvu', 'EL10Ac7g17204' => 'bvu', 'Eucgr.A00855' => 'egr', 'Eucgr.A00858' => 'egr', 'Eucgr.H01520' => 'egr', 'Eucgr.H03604' => 'egr', 'Eucgr.L03465' => 'egr', 'Eucgr.L03466' => 'egr', 'FAN01G0988' => 'fan', 'FAN02G3892' => 'fan', 'FAN05G3381' => 'fan', 'FAN07G0967' => 'fan', 'FAN07G1493' => 'fan', 'FAN08G3125' => 'fan', 'FAN09G0402' => 'fan', 'FAN12G2594' => 'fan', 'FAN12G3879' => 'fan', 'FAN14G1546' => 'fan', 'FAN15G3626' => 'fan', 'FAN17G0588' => 'fan', 'FAN17G0609' => 'fan', 'FAN18G2817' => 'fan', 'FAN19G1305' => 'fan', 'FAN20G1787' => 'fan', 'FAN22G0073' => 'fan', 'FAN22G0352' => 'fan', 'FAN22G0368' => 'fan', 'FAN22G2273' => 'fan', 'FAN24G1998' => 'fan', 'FAN27G1317' => 'fan', 'FvH4_2g23980' => 'fve', 'FvH4_4g14380' => 'fve', 'FvH4_4g14390' => 'fve', 'FvH4_6g09250' => 'fve', 'Glyma.03G151100' => 'gma', 'Glyma.04G122550' => 'gma', 'Glyma.05G001600' => 'gma', 'Glyma.09G270766' => 'gma', 'Glyma.09G270832' => 'gma', 'Glyma.13G209800' => 'gma', 'Glyma.15G102800' => 'gma', 'Glyma.18G218900' => 'gma', 'Glyma.19G001500' => 'gma', 'Glyma.19G153600' => 'gma', 'Gohir.A02G028600' => 'ghi', 'Gohir.A08G045000' => 'ghi', 'Gohir.A11G120500' => 'ghi', 'Gohir.A12G006200' => 'ghi', 'Gohir.A12G006250' => 'ghi', 'Gohir.D02G036300' => 'ghi', 'Gohir.D08G054700' => 'ghi', 'Gohir.D11G125600' => 'ghi', 'Gohir.D12G005700' => 'ghi', 'Gorai.004G055200' => 'gra', 'Gorai.005G040400' => 'gra', 'Gorai.007G134500' => 'gra', 'Gorai.008G005500' => 'gra', 'GSVIVG01011094001' => 'vvi', 'GSVIVG01017879001' => 'vvi', 'GSVIVG01025988001' => 'vvi', 'GSVIVG01029847001' => 'vvi', 'HanXRQChr10g0282901' => 'han', 'HanXRQChr10g0310371' => 'han', 'HanXRQChr10g0315041' => 'han', 'HanXRQChr11g0327651' => 'han', 'HanXRQChr12g0359391' => 'han', 'Haze_00972' => 'cav', 'Haze_00973' => 'cav', 'Haze_00974' => 'cav', 'Haze_04747' => 'cav', 'Haze_04749' => 'cav', 'Haze_04750' => 'cav', 'Haze_21217' => 'cav', 'Hma1.2p1_1037F.1_g250680' => 'hma', 'Hma1.2p1_1644F.1_g295320' => 'hma', 'HPP92_011322' => 'vpl', 'HPP92_011323' => 'vpl', 'HPP92_011324' => 'vpl', 'HPP92_011325' => 'vpl', 'HPP92_011326' => 'vpl', 'Hund12205' => 'sun', 'Hund17957' => 'sun', 'Lalb_Chr06g0176771' => 'lal', 'Lalb_Chr18g0056021' => 'lal', 'Lalb_Chr18g0056031' => 'lal', 'Lalb_Chr18g0056041' => 'lal', 'Lalb_Chr20g0107751' => 'lal', 'Lalb_Chr20g0118371' => 'lal', 'Lj1g0010239' => 'lja', 'Lj1g0017101' => 'lja', 'Lj2A1178G40' => 'lonja', 'Lj2A54G84' => 'lonja', 'Lj2g0015248' => 'lja', 'Lj3A761T51' => 'lonja', 'Lj6g0018116' => 'lja', 'Lsat_1_v5_gn_4_136040' => 'lsa', 'Lsat_1_v5_gn_5_187461' => 'lsa', 'Lsat_1_v5_gn_5_77001' => 'lsa', 'Lsat_1_v5_gn_9_4461' => 'lsa', 'Manes.01G210100' => 'mes', 'Manes.03G185600' => 'mes', 'Manes.05G073300' => 'mes', 'Manes.09G120300' => 'mes', 'Manes.15G022100' => 'mes', 'Mapoly0096s0053' => 'mpo', 'MBI03_g14058_MAGBIO' => 'mbi', 'MBI03_g33876_MAGBIO' => 'mbi', 'MBI03_g36854_MAGBIO' => 'mbi', 'MBI17_g11997_MAGBIO' => 'mbi', 'MD03G1269000' => 'mdo', 'MD04G1179600' => 'mdo', 'MD11G1289800' => 'mdo', 'MD12G1194700' => 'mdo', 'MD13G1182100' => 'mdo', 'MD13G1182200' => 'mdo', 'MD16G1182600' => 'mdo', 'Medtr2g021400' => 'mtr', 'Medtr2g021470' => 'mtr', 'Medtr2g105810' => 'mtr', 'Medtr3g033580' => 'mtr', 'Medtr6g007970' => 'mtr', 'Medtr7g056330' => 'mtr', 'Medtr7g074290' => 'mtr', 'Medtr7g074380' => 'mtr', 'Medtr7g094550' => 'mtr', 'Medtr8g069995' => 'mtr', 'MELO3C014345.2' => 'cme', 'MELO3C021395.2' => 'cme', 'Migut.D00262' => 'egut', 'Migut.G00257' => 'egut', 'MSTRG.21575' => 'ama', 'MSTRG.3985' => 'ama', 'Nitab4.5_0000295g0140' => 'nta', 'Nitab4.5_0000732g0140' => 'nta', 'Nitab4.5_0003162g0020' => 'nta', 'Nitab4.5_0006180g0090' => 'nta', 'Nitab4.5_0006390g0010' => 'nta', 'Nitab4.5_0007392g0040' => 'nta', 'Nn1g02140' => 'nnu', 'Nn4g26168' => 'nnu', 'Nn5g26754' => 'nnu', 'Oeu001433.1' => 'oeu', 'Oeu010299.2' => 'oeu', 'Oeu011171.1' => 'oeu', 'Oeu037675.1' => 'oeu', 'Oeu038359.1' => 'oeu', 'Oeu063834.1' => 'oeu', 'Oeu063835.1' => 'oeu', 'Os05g0312000' => 'osa', 'Os07g0211101' => 'osa', 'Os07g0211200' => 'osa', 'Os07g0681500' => 'osa', 'Peaxi162Scf00095g01015' => 'pax', 'Peaxi162Scf00104g00329' => 'pax', 'Peaxi162Scf00161g00137' => 'pax', 'PGR004G1665' => 'pgr', 'PGR031G2937' => 'pgr', 'PGR119G2145' => 'pgr', 'PGSC0003DMG400004351' => 'stu', 'PGSC0003DMG400014625' => 'stu', 'PGSC0003DMG401000943' => 'stu', 'Phvul.001G148600' => 'pvu', 'Phvul.004G001700' => 'pvu', 'Phvul.006G154900' => 'pvu', 'Phvul.008G078200' => 'pvu', 'Phvul.011G136500' => 'pvu', 'Potri.002G215600' => 'ptr', 'Potri.008G201600' => 'ptr', 'Potri.014G138400' => 'ptr', 'Potri.016G142500' => 'ptr', 'Pp3c16_10580' => 'ppa', 'Pp3c5_25280' => 'ppa', 'Prupe.1G150000' => 'ppe', 'Prupe.1G150100' => 'ppe', 'Prupe.6G299600' => 'ppe', 'Prupe.8G245000' => 'ppe', 'Psat0s4927g0040' => 'psa', 'Psat1g052080' => 'psa', 'Psat1g183800' => 'psa', 'Psat3g113840' => 'psa', 'Psat3g126120' => 'psa', 'Psat3g126160' => 'psa', 'Psat3g158760' => 'psa', 'Psat3g158840' => 'psa', 'PSO170G2858' => 'pso', 'PSO339G0606' => 'pso', 'PSO384G4709' => 'pso', 'PSO407G0334' => 'pso', 'QL04p040276' => 'qlo', 'QL06p005458' => 'qlo', 'QL06p005472' => 'qlo', 'QL07p030546' => 'qlo', 'QL07p031519' => 'qlo', 'QL09p050949' => 'qlo', 'QL09p050966' => 'qlo', 'QL09p051067' => 'qlo', 'QL12p022706' => 'qlo', 'RcHm_v2.0_Chr2g0119601' => 'rch', 'RcHm_v2.0_Chr3g0459591' => 'rch', 'RcHm_v2.0_Chr4g0418521' => 'rch', 'RcHm_v2.0_Chr4g0418531' => 'rch', 'RcHm_v2.0_Chr4g0418541' => 'rch', 'RcHm_v2.0_Chr6g0291641' => 'rch', 'Rhsim01G0086300' => 'rsi', 'Rhsim01G0276300' => 'rsi', 'Rhsim01G0276500' => 'rsi', 'Rhsim04G0207700' => 'rsi', 'Rhsim05G0234500' => 'rsi', 'Rhsim13G0022400' => 'rsi', 'Sabra02G0167900' => 'sbr', 'Sabra04G0158500' => 'sbr', 'Sabra08G0159800' => 'sbr', 'Sabra10G0011500' => 'sbr', 'Sabra14G0104400' => 'sbr', 'SalBow2G2440' => 'sbo', 'SalBow4G2265' => 'sbo', 'Sc02g0000060' => 'sci', 'Sc05g0005020' => 'sci', 'Sc13g0003890' => 'sci', 'Sed0014865' => 'sed', 'Sed0017224' => 'sed', 'Sed0026391' => 'sed', 'SEGI_00063' => 'sgi', 'SEGI_10967' => 'sgi', 'SEGI_17510' => 'sgi', 'SEGI_24396' => 'sgi', 'SEGI_39719' => 'sgi', 'SEGI_41392' => 'sgi', 'SGA_v2.0_scaffold11G05794' => 'sas', 'SGA_v2.0_scaffold142G35607' => 'sas', 'SGA_v2.0_scaffold1G00447' => 'sas', 'SHI15388' => 'shi', 'SHI15394' => 'shi', 'SHI15396' => 'shi', 'SHI15399' => 'shi', 'SMO343G0151' => 'smo', 'SMO367G1118' => 'smo', 'Solyc01g080200.3' => 'sly', 'Solyc06g008960.3' => 'sly', 'Solyc09g064780.3' => 'sly', 'Sopen01g031980' => 'spe', 'Sopen06g003710' => 'spe', 'Sopen09g026460' => 'spe', 'Sp3g21240' => 'spa', 'Sp4g30030' => 'spa', 'TAR365G0022' => 'tar', 'TAR365G1023' => 'tar', 'TAR365G1253' => 'tar', 'TAR623G0078' => 'tar', 'TAR623G1721' => 'tar', 'TAR633G0959' => 'tar', 'THA.LOC104802225' => 'tha', 'THA.LOC104804769' => 'tha', 'THA.LOC104808660' => 'tha', 'THA.LOC104812792' => 'tha', 'Thecc.01G284000' => 'tca', 'Thecc.04G220600' => 'tca', 'Thecc.05G268900' => 'tca', 'Thecc.08G171100' => 'tca', 'Thhalv10001284m.g' => 'esa', 'Thhalv10019912m.g' => 'esa', 'TPR.G14189' => 'tpr', 'TPR.G18110' => 'tpr', 'TPR.G18130' => 'tpr', 'TPR.G18131' => 'tpr', 'TPR.G18140' => 'tpr', 'TPR.G24282' => 'tpr', 'TPR.G25221' => 'tpr', 'TPR.G29267' => 'tpr', 'TPR.G35315' => 'tpr', 'TPR.G36173' => 'tpr', 'TWI09G0794' => 'twi', 'TWI59G1348' => 'twi', 'TWI74G0430' => 'twi', 'unitig_26.g8940' => 'ugi', 'unitig_749.g13744' => 'ugi', 'unitig_749.g13745' => 'ugi', 'vmacro08269' => 'vma', 'vmacro14937' => 'vma', 'vmacro20401' => 'vma', 'VMungo0464G1349' => 'vmu', 'VMungo0540G0289' => 'vmu', 'VMungo1215G1590' => 'vmu', 'VMungo1309G0221' => 'vmu', 'VMungo1309G2815' => 'vmu', 'VMungo1383G0239' => 'vmu', 'VMungo1383G2910' => 'vmu', 'Zm00001eb095270' => 'zma', 'Zm00001eb095280' => 'zma', 'Zm00001eb111630' => 'zma', 'Zm00001eb237080' => 'zma', 'Zm00001eb273740' => 'zma', 'Zm00001eb285040' => 'zma', 'Zm00001eb330790' => 'zma', 'Zm00001eb337380' => 'zma' ) $gf_id = 'HOM05D001484' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001484' ) $data_identifier = 'HOM05D001484' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 2, 'aly' => (int) 2, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 22, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 7, 'hma' => (int) 2, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 7, 'mtr' => (int) 10, 'cme' => (int) 2, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 4, 'ppa' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 4, 'qlo' => (int) 9, 'rch' => (int) 6, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 10, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 7, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb337380' $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' => 'HOM05D001484', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p31500' => 'bna', 'A05p00020' => 'bna', 'A07p08820' => 'bna', 'Aa31LG4G3300' => 'aar', 'Aa31LG8G10030' => 'aar', 'Actinidia00731' => 'ach', 'Actinidia11473' => 'ach', 'Actinidia23469' => 'ach', 'Actinidia24318' => 'ach', 'Actinidia40196' => 'ach', 'Actinidia40197' => 'ach', 'Actinidia40198' => 'ach', 'Ah.08g212990' => 'amhyb', 'Ah.15g091720' => 'amhyb', 'AL3G38260' => 'aly', 'AL4G47710' => 'aly', 'Aqoxy2G00671' => 'aox', 'Aqoxy2G03236' => 'aox', 'arahy.Tifrunner.gnm1.ann1.05IDCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KR684' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATY3SJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK6QJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6APGL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IDT7Z9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM073U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ0R87' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LE7RV4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT4QRX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V5ENPK' => 'arhy', 'AT2G48110' => 'ath', 'AT3G23590' => 'ath', 'ATR0626G186' => 'atr', 'ATR1127G141' => 'atr', 'Atru.chr4.2583' => 'acertr', 'Atru.chr5.1358' => 'acertr', 'Atru.chr5.1359' => 'acertr', 'Atru.chr8.46' => 'acertr', 'AUR62002640' => 'cqu', 'AUR62030055' => 'cqu', 'AUR62033713' => 'cqu', 'AUR62033714' => 'cqu', 'AUR62036795' => 'cqu', 'AUR62039891' => 'cqu', 'BcaB02g08737' => 'bca', 'BcaB04g20441' => 'bca', 'BcaB06g26509' => 'bca', 'BcaB06g26510' => 'bca', 'BcaB06g26511' => 'bca', 'BcaB06g26512' => 'bca', 'BcaB06g26513' => 'bca', 'BcaC02g12564' => 'bca', 'BcaC02g12565' => 'bca', 'BcaC02g12794' => 'bca', 'BcaC02g12795' => 'bca', 'BcaC02g12796' => 'bca', 'BcaC06g35541' => 'bca', 'BNapus_Darmor_BZH_scaffold_188p00080' => 'bna', 'BNapus_Darmor_BZH_scaffold_188p00090' => 'bna', 'BolC1t03972H' => 'bol', 'BolC1t03973H' => 'bol', 'BolC4t21680H' => 'bol', 'BolC7t41863H' => 'bol', 'BolSC55t61227H' => 'bol', 'BolSC55t61228H' => 'bol', 'BraA01t03278Z' => 'bra', 'BraA05t18998Z' => 'bra', 'BraA07t28673Z' => 'bra', 'C01p40150' => 'bna', 'C05p12370' => 'bna', 'C07p13680' => 'bna', 'CAN.G1006.16' => 'can', 'CAN.G1006.17' => 'can', 'CAN.G1170.2' => 'can', 'CAN.G962.7' => 'can', 'CANSAT25G2179' => 'cansat', 'CANSAT78G1573' => 'cansat', 'CARHR099510' => 'chi', 'CARHR143510' => 'chi', 'Carub.0003s2380' => 'cru', 'Carub.0004s3082' => 'cru', 'Ca_00614_v3' => 'car', 'Ca_07801_v3' => 'car', 'Ca_08567_v3' => 'car', 'Ca_09571_v3' => 'car', 'CBR_g19290' => 'cbr', 'Cc01_g19770' => 'ccan', 'Cc03_g03030' => 'ccan', 'CDE07G0968' => 'cde', 'CDE09G1441' => 'cde', 'Cfa006103' => 'cfa', 'Cfa015573' => 'cfa', 'Cfa016988' => 'cfa', 'Ciclev10006738m.g' => 'ccl', 'Ciclev10010920m.g' => 'ccl', 'Ciclev10018517m.g' => 'ccl', 'CiPaw.01G159200' => 'cil', 'CiPaw.02G091000' => 'cil', 'CiPaw.02G091100' => 'cil', 'CiPaw.08G103100' => 'cil', 'CiPaw.09G224900' => 'cil', 'ClCG06G005740' => 'cla', 'ClCG07G000090' => 'cla', 'ClCG07G000100' => 'cla', 'COL.COLO4_09143' => 'col', 'COL.COLO4_25124' => 'col', 'Cpa.g.sc16.34' => 'cpa', 'Cpa.g.sc3504.1' => 'cpa', 'Cpa.g.sc60.37' => 'cpa', 'CsaV3_6G018520' => 'csa', 'CsaV3_6G036860' => 'csa', 'CSS0001072' => 'camsi', 'CSS0020208' => 'camsi', 'CSS0021253' => 'camsi', 'CSS0022190' => 'camsi', 'CSS0036150' => 'camsi', 'CSS0040442' => 'camsi', 'CSS0042300' => 'camsi', 'CSS0045298' => 'camsi', 'DCAR_012449' => 'dca', 'DCAR_018405' => 'dca', 'DCAR_024573' => 'dca', 'DCAR_030591' => 'dca', 'Dinv16926' => 'din', 'Dinv32963' => 'din', 'Dinv38382' => 'din', 'Dinv38383' => 'din', 'Duzib133G0974' => 'dzi', 'Duzib138G1867' => 'dzi', 'Duzib211G0420' => 'dzi', 'Duzib212G0930' => 'dzi', 'ECA234G1645' => 'eca', 'ECA247G3467' => 'eca', 'ECA248G1703' => 'eca', 'EL10Ac3g06327' => 'bvu', 'EL10Ac7g17204' => 'bvu', 'Eucgr.A00855' => 'egr', 'Eucgr.A00858' => 'egr', 'Eucgr.H01520' => 'egr', 'Eucgr.H03604' => 'egr', 'Eucgr.L03465' => 'egr', 'Eucgr.L03466' => 'egr', 'FAN01G0988' => 'fan', 'FAN02G3892' => 'fan', 'FAN05G3381' => 'fan', 'FAN07G0967' => 'fan', 'FAN07G1493' => 'fan', 'FAN08G3125' => 'fan', 'FAN09G0402' => 'fan', 'FAN12G2594' => 'fan', 'FAN12G3879' => 'fan', 'FAN14G1546' => 'fan', 'FAN15G3626' => 'fan', 'FAN17G0588' => 'fan', 'FAN17G0609' => 'fan', 'FAN18G2817' => 'fan', 'FAN19G1305' => 'fan', 'FAN20G1787' => 'fan', 'FAN22G0073' => 'fan', 'FAN22G0352' => 'fan', 'FAN22G0368' => 'fan', 'FAN22G2273' => 'fan', 'FAN24G1998' => 'fan', 'FAN27G1317' => 'fan', 'FvH4_2g23980' => 'fve', 'FvH4_4g14380' => 'fve', 'FvH4_4g14390' => 'fve', 'FvH4_6g09250' => 'fve', 'Glyma.03G151100' => 'gma', 'Glyma.04G122550' => 'gma', 'Glyma.05G001600' => 'gma', 'Glyma.09G270766' => 'gma', 'Glyma.09G270832' => 'gma', 'Glyma.13G209800' => 'gma', 'Glyma.15G102800' => 'gma', 'Glyma.18G218900' => 'gma', 'Glyma.19G001500' => 'gma', 'Glyma.19G153600' => 'gma', 'Gohir.A02G028600' => 'ghi', 'Gohir.A08G045000' => 'ghi', 'Gohir.A11G120500' => 'ghi', 'Gohir.A12G006200' => 'ghi', 'Gohir.A12G006250' => 'ghi', 'Gohir.D02G036300' => 'ghi', 'Gohir.D08G054700' => 'ghi', 'Gohir.D11G125600' => 'ghi', 'Gohir.D12G005700' => 'ghi', 'Gorai.004G055200' => 'gra', 'Gorai.005G040400' => 'gra', 'Gorai.007G134500' => 'gra', 'Gorai.008G005500' => 'gra', 'GSVIVG01011094001' => 'vvi', 'GSVIVG01017879001' => 'vvi', 'GSVIVG01025988001' => 'vvi', 'GSVIVG01029847001' => 'vvi', 'HanXRQChr10g0282901' => 'han', 'HanXRQChr10g0310371' => 'han', 'HanXRQChr10g0315041' => 'han', 'HanXRQChr11g0327651' => 'han', 'HanXRQChr12g0359391' => 'han', 'Haze_00972' => 'cav', 'Haze_00973' => 'cav', 'Haze_00974' => 'cav', 'Haze_04747' => 'cav', 'Haze_04749' => 'cav', 'Haze_04750' => 'cav', 'Haze_21217' => 'cav', 'Hma1.2p1_1037F.1_g250680' => 'hma', 'Hma1.2p1_1644F.1_g295320' => 'hma', 'HPP92_011322' => 'vpl', 'HPP92_011323' => 'vpl', 'HPP92_011324' => 'vpl', 'HPP92_011325' => 'vpl', 'HPP92_011326' => 'vpl', 'Hund12205' => 'sun', 'Hund17957' => 'sun', 'Lalb_Chr06g0176771' => 'lal', 'Lalb_Chr18g0056021' => 'lal', 'Lalb_Chr18g0056031' => 'lal', 'Lalb_Chr18g0056041' => 'lal', 'Lalb_Chr20g0107751' => 'lal', 'Lalb_Chr20g0118371' => 'lal', 'Lj1g0010239' => 'lja', 'Lj1g0017101' => 'lja', 'Lj2A1178G40' => 'lonja', 'Lj2A54G84' => 'lonja', 'Lj2g0015248' => 'lja', 'Lj3A761T51' => 'lonja', 'Lj6g0018116' => 'lja', 'Lsat_1_v5_gn_4_136040' => 'lsa', 'Lsat_1_v5_gn_5_187461' => 'lsa', 'Lsat_1_v5_gn_5_77001' => 'lsa', 'Lsat_1_v5_gn_9_4461' => 'lsa', 'Manes.01G210100' => 'mes', 'Manes.03G185600' => 'mes', 'Manes.05G073300' => 'mes', 'Manes.09G120300' => 'mes', 'Manes.15G022100' => 'mes', 'Mapoly0096s0053' => 'mpo', 'MBI03_g14058_MAGBIO' => 'mbi', 'MBI03_g33876_MAGBIO' => 'mbi', 'MBI03_g36854_MAGBIO' => 'mbi', 'MBI17_g11997_MAGBIO' => 'mbi', 'MD03G1269000' => 'mdo', 'MD04G1179600' => 'mdo', 'MD11G1289800' => 'mdo', 'MD12G1194700' => 'mdo', 'MD13G1182100' => 'mdo', 'MD13G1182200' => 'mdo', 'MD16G1182600' => 'mdo', 'Medtr2g021400' => 'mtr', 'Medtr2g021470' => 'mtr', 'Medtr2g105810' => 'mtr', 'Medtr3g033580' => 'mtr', 'Medtr6g007970' => 'mtr', 'Medtr7g056330' => 'mtr', 'Medtr7g074290' => 'mtr', 'Medtr7g074380' => 'mtr', 'Medtr7g094550' => 'mtr', 'Medtr8g069995' => 'mtr', 'MELO3C014345.2' => 'cme', 'MELO3C021395.2' => 'cme', 'Migut.D00262' => 'egut', 'Migut.G00257' => 'egut', 'MSTRG.21575' => 'ama', 'MSTRG.3985' => 'ama', 'Nitab4.5_0000295g0140' => 'nta', 'Nitab4.5_0000732g0140' => 'nta', 'Nitab4.5_0003162g0020' => 'nta', 'Nitab4.5_0006180g0090' => 'nta', 'Nitab4.5_0006390g0010' => 'nta', 'Nitab4.5_0007392g0040' => 'nta', 'Nn1g02140' => 'nnu', 'Nn4g26168' => 'nnu', 'Nn5g26754' => 'nnu', 'Oeu001433.1' => 'oeu', 'Oeu010299.2' => 'oeu', 'Oeu011171.1' => 'oeu', 'Oeu037675.1' => 'oeu', 'Oeu038359.1' => 'oeu', 'Oeu063834.1' => 'oeu', 'Oeu063835.1' => 'oeu', 'Os05g0312000' => 'osa', 'Os07g0211101' => 'osa', 'Os07g0211200' => 'osa', 'Os07g0681500' => 'osa', 'Peaxi162Scf00095g01015' => 'pax', 'Peaxi162Scf00104g00329' => 'pax', 'Peaxi162Scf00161g00137' => 'pax', 'PGR004G1665' => 'pgr', 'PGR031G2937' => 'pgr', 'PGR119G2145' => 'pgr', 'PGSC0003DMG400004351' => 'stu', 'PGSC0003DMG400014625' => 'stu', 'PGSC0003DMG401000943' => 'stu', 'Phvul.001G148600' => 'pvu', 'Phvul.004G001700' => 'pvu', 'Phvul.006G154900' => 'pvu', 'Phvul.008G078200' => 'pvu', 'Phvul.011G136500' => 'pvu', 'Potri.002G215600' => 'ptr', 'Potri.008G201600' => 'ptr', 'Potri.014G138400' => 'ptr', 'Potri.016G142500' => 'ptr', 'Pp3c16_10580' => 'ppa', 'Pp3c5_25280' => 'ppa', 'Prupe.1G150000' => 'ppe', 'Prupe.1G150100' => 'ppe', 'Prupe.6G299600' => 'ppe', 'Prupe.8G245000' => 'ppe', 'Psat0s4927g0040' => 'psa', 'Psat1g052080' => 'psa', 'Psat1g183800' => 'psa', 'Psat3g113840' => 'psa', 'Psat3g126120' => 'psa', 'Psat3g126160' => 'psa', 'Psat3g158760' => 'psa', 'Psat3g158840' => 'psa', 'PSO170G2858' => 'pso', 'PSO339G0606' => 'pso', 'PSO384G4709' => 'pso', 'PSO407G0334' => 'pso', 'QL04p040276' => 'qlo', 'QL06p005458' => 'qlo', 'QL06p005472' => 'qlo', 'QL07p030546' => 'qlo', 'QL07p031519' => 'qlo', 'QL09p050949' => 'qlo', 'QL09p050966' => 'qlo', 'QL09p051067' => 'qlo', 'QL12p022706' => 'qlo', 'RcHm_v2.0_Chr2g0119601' => 'rch', 'RcHm_v2.0_Chr3g0459591' => 'rch', 'RcHm_v2.0_Chr4g0418521' => 'rch', 'RcHm_v2.0_Chr4g0418531' => 'rch', 'RcHm_v2.0_Chr4g0418541' => 'rch', 'RcHm_v2.0_Chr6g0291641' => 'rch', 'Rhsim01G0086300' => 'rsi', 'Rhsim01G0276300' => 'rsi', 'Rhsim01G0276500' => 'rsi', 'Rhsim04G0207700' => 'rsi', 'Rhsim05G0234500' => 'rsi', 'Rhsim13G0022400' => 'rsi', 'Sabra02G0167900' => 'sbr', 'Sabra04G0158500' => 'sbr', 'Sabra08G0159800' => 'sbr', 'Sabra10G0011500' => 'sbr', 'Sabra14G0104400' => 'sbr', 'SalBow2G2440' => 'sbo', 'SalBow4G2265' => 'sbo', 'Sc02g0000060' => 'sci', 'Sc05g0005020' => 'sci', 'Sc13g0003890' => 'sci', 'Sed0014865' => 'sed', 'Sed0017224' => 'sed', 'Sed0026391' => 'sed', 'SEGI_00063' => 'sgi', 'SEGI_10967' => 'sgi', 'SEGI_17510' => 'sgi', 'SEGI_24396' => 'sgi', 'SEGI_39719' => 'sgi', 'SEGI_41392' => 'sgi', 'SGA_v2.0_scaffold11G05794' => 'sas', 'SGA_v2.0_scaffold142G35607' => 'sas', 'SGA_v2.0_scaffold1G00447' => 'sas', 'SHI15388' => 'shi', 'SHI15394' => 'shi', 'SHI15396' => 'shi', 'SHI15399' => 'shi', 'SMO343G0151' => 'smo', 'SMO367G1118' => 'smo', 'Solyc01g080200.3' => 'sly', 'Solyc06g008960.3' => 'sly', 'Solyc09g064780.3' => 'sly', 'Sopen01g031980' => 'spe', 'Sopen06g003710' => 'spe', 'Sopen09g026460' => 'spe', 'Sp3g21240' => 'spa', 'Sp4g30030' => 'spa', 'TAR365G0022' => 'tar', 'TAR365G1023' => 'tar', 'TAR365G1253' => 'tar', 'TAR623G0078' => 'tar', 'TAR623G1721' => 'tar', 'TAR633G0959' => 'tar', 'THA.LOC104802225' => 'tha', 'THA.LOC104804769' => 'tha', 'THA.LOC104808660' => 'tha', 'THA.LOC104812792' => 'tha', 'Thecc.01G284000' => 'tca', 'Thecc.04G220600' => 'tca', 'Thecc.05G268900' => 'tca', 'Thecc.08G171100' => 'tca', 'Thhalv10001284m.g' => 'esa', 'Thhalv10019912m.g' => 'esa', 'TPR.G14189' => 'tpr', 'TPR.G18110' => 'tpr', 'TPR.G18130' => 'tpr', 'TPR.G18131' => 'tpr', 'TPR.G18140' => 'tpr', 'TPR.G24282' => 'tpr', 'TPR.G25221' => 'tpr', 'TPR.G29267' => 'tpr', 'TPR.G35315' => 'tpr', 'TPR.G36173' => 'tpr', 'TWI09G0794' => 'twi', 'TWI59G1348' => 'twi', 'TWI74G0430' => 'twi', 'unitig_26.g8940' => 'ugi', 'unitig_749.g13744' => 'ugi', 'unitig_749.g13745' => 'ugi', 'vmacro08269' => 'vma', 'vmacro14937' => 'vma', 'vmacro20401' => 'vma', 'VMungo0464G1349' => 'vmu', 'VMungo0540G0289' => 'vmu', 'VMungo1215G1590' => 'vmu', 'VMungo1309G0221' => 'vmu', 'VMungo1309G2815' => 'vmu', 'VMungo1383G0239' => 'vmu', 'VMungo1383G2910' => 'vmu', 'Zm00001eb095270' => 'zma', 'Zm00001eb095280' => 'zma', 'Zm00001eb111630' => 'zma', 'Zm00001eb237080' => 'zma', 'Zm00001eb273740' => 'zma', 'Zm00001eb285040' => 'zma', 'Zm00001eb330790' => 'zma', 'Zm00001eb337380' => 'zma' ), 'gf_id' => 'HOM05D001484', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001484' ), 'data_identifier' => 'HOM05D001484', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001484', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p31500' => 'bna', 'A05p00020' => 'bna', 'A07p08820' => 'bna', 'Aa31LG4G3300' => 'aar', 'Aa31LG8G10030' => 'aar', 'Actinidia00731' => 'ach', 'Actinidia11473' => 'ach', 'Actinidia23469' => 'ach', 'Actinidia24318' => 'ach', 'Actinidia40196' => 'ach', 'Actinidia40197' => 'ach', 'Actinidia40198' => 'ach', 'Ah.08g212990' => 'amhyb', 'Ah.15g091720' => 'amhyb', 'AL3G38260' => 'aly', 'AL4G47710' => 'aly', 'Aqoxy2G00671' => 'aox', 'Aqoxy2G03236' => 'aox', 'arahy.Tifrunner.gnm1.ann1.05IDCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KR684' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATY3SJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK6QJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6APGL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IDT7Z9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM073U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ0R87' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LE7RV4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT4QRX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V5ENPK' => 'arhy', 'AT2G48110' => 'ath', 'AT3G23590' => 'ath', 'ATR0626G186' => 'atr', 'ATR1127G141' => 'atr', 'Atru.chr4.2583' => 'acertr', 'Atru.chr5.1358' => 'acertr', 'Atru.chr5.1359' => 'acertr', 'Atru.chr8.46' => 'acertr', 'AUR62002640' => 'cqu', 'AUR62030055' => 'cqu', 'AUR62033713' => 'cqu', 'AUR62033714' => 'cqu', 'AUR62036795' => 'cqu', 'AUR62039891' => 'cqu', 'BcaB02g08737' => 'bca', 'BcaB04g20441' => 'bca', 'BcaB06g26509' => 'bca', 'BcaB06g26510' => 'bca', 'BcaB06g26511' => 'bca', 'BcaB06g26512' => 'bca', 'BcaB06g26513' => 'bca', 'BcaC02g12564' => 'bca', 'BcaC02g12565' => 'bca', 'BcaC02g12794' => 'bca', 'BcaC02g12795' => 'bca', 'BcaC02g12796' => 'bca', 'BcaC06g35541' => 'bca', 'BNapus_Darmor_BZH_scaffold_188p00080' => 'bna', 'BNapus_Darmor_BZH_scaffold_188p00090' => 'bna', 'BolC1t03972H' => 'bol', 'BolC1t03973H' => 'bol', 'BolC4t21680H' => 'bol', 'BolC7t41863H' => 'bol', 'BolSC55t61227H' => 'bol', 'BolSC55t61228H' => 'bol', 'BraA01t03278Z' => 'bra', 'BraA05t18998Z' => 'bra', 'BraA07t28673Z' => 'bra', 'C01p40150' => 'bna', 'C05p12370' => 'bna', 'C07p13680' => 'bna', 'CAN.G1006.16' => 'can', 'CAN.G1006.17' => 'can', 'CAN.G1170.2' => 'can', 'CAN.G962.7' => 'can', 'CANSAT25G2179' => 'cansat', 'CANSAT78G1573' => 'cansat', 'CARHR099510' => 'chi', 'CARHR143510' => 'chi', 'Carub.0003s2380' => 'cru', 'Carub.0004s3082' => 'cru', 'Ca_00614_v3' => 'car', 'Ca_07801_v3' => 'car', 'Ca_08567_v3' => 'car', 'Ca_09571_v3' => 'car', 'CBR_g19290' => 'cbr', 'Cc01_g19770' => 'ccan', 'Cc03_g03030' => 'ccan', 'CDE07G0968' => 'cde', 'CDE09G1441' => 'cde', 'Cfa006103' => 'cfa', 'Cfa015573' => 'cfa', 'Cfa016988' => 'cfa', 'Ciclev10006738m.g' => 'ccl', 'Ciclev10010920m.g' => 'ccl', 'Ciclev10018517m.g' => 'ccl', 'CiPaw.01G159200' => 'cil', 'CiPaw.02G091000' => 'cil', 'CiPaw.02G091100' => 'cil', 'CiPaw.08G103100' => 'cil', 'CiPaw.09G224900' => 'cil', 'ClCG06G005740' => 'cla', 'ClCG07G000090' => 'cla', 'ClCG07G000100' => 'cla', 'COL.COLO4_09143' => 'col', 'COL.COLO4_25124' => 'col', 'Cpa.g.sc16.34' => 'cpa', 'Cpa.g.sc3504.1' => 'cpa', 'Cpa.g.sc60.37' => 'cpa', 'CsaV3_6G018520' => 'csa', 'CsaV3_6G036860' => 'csa', 'CSS0001072' => 'camsi', 'CSS0020208' => 'camsi', 'CSS0021253' => 'camsi', 'CSS0022190' => 'camsi', 'CSS0036150' => 'camsi', 'CSS0040442' => 'camsi', 'CSS0042300' => 'camsi', 'CSS0045298' => 'camsi', 'DCAR_012449' => 'dca', 'DCAR_018405' => 'dca', 'DCAR_024573' => 'dca', 'DCAR_030591' => 'dca', 'Dinv16926' => 'din', 'Dinv32963' => 'din', 'Dinv38382' => 'din', 'Dinv38383' => 'din', 'Duzib133G0974' => 'dzi', 'Duzib138G1867' => 'dzi', 'Duzib211G0420' => 'dzi', 'Duzib212G0930' => 'dzi', 'ECA234G1645' => 'eca', 'ECA247G3467' => 'eca', 'ECA248G1703' => 'eca', 'EL10Ac3g06327' => 'bvu', 'EL10Ac7g17204' => 'bvu', 'Eucgr.A00855' => 'egr', 'Eucgr.A00858' => 'egr', 'Eucgr.H01520' => 'egr', 'Eucgr.H03604' => 'egr', 'Eucgr.L03465' => 'egr', 'Eucgr.L03466' => 'egr', 'FAN01G0988' => 'fan', 'FAN02G3892' => 'fan', 'FAN05G3381' => 'fan', 'FAN07G0967' => 'fan', 'FAN07G1493' => 'fan', 'FAN08G3125' => 'fan', 'FAN09G0402' => 'fan', 'FAN12G2594' => 'fan', 'FAN12G3879' => 'fan', 'FAN14G1546' => 'fan', 'FAN15G3626' => 'fan', 'FAN17G0588' => 'fan', 'FAN17G0609' => 'fan', 'FAN18G2817' => 'fan', 'FAN19G1305' => 'fan', 'FAN20G1787' => 'fan', 'FAN22G0073' => 'fan', 'FAN22G0352' => 'fan', 'FAN22G0368' => 'fan', 'FAN22G2273' => 'fan', 'FAN24G1998' => 'fan', 'FAN27G1317' => 'fan', 'FvH4_2g23980' => 'fve', 'FvH4_4g14380' => 'fve', 'FvH4_4g14390' => 'fve', 'FvH4_6g09250' => 'fve', 'Glyma.03G151100' => 'gma', 'Glyma.04G122550' => 'gma', 'Glyma.05G001600' => 'gma', 'Glyma.09G270766' => 'gma', 'Glyma.09G270832' => 'gma', 'Glyma.13G209800' => 'gma', 'Glyma.15G102800' => 'gma', 'Glyma.18G218900' => 'gma', 'Glyma.19G001500' => 'gma', 'Glyma.19G153600' => 'gma', 'Gohir.A02G028600' => 'ghi', 'Gohir.A08G045000' => 'ghi', 'Gohir.A11G120500' => 'ghi', 'Gohir.A12G006200' => 'ghi', 'Gohir.A12G006250' => 'ghi', 'Gohir.D02G036300' => 'ghi', 'Gohir.D08G054700' => 'ghi', 'Gohir.D11G125600' => 'ghi', 'Gohir.D12G005700' => 'ghi', 'Gorai.004G055200' => 'gra', 'Gorai.005G040400' => 'gra', 'Gorai.007G134500' => 'gra', 'Gorai.008G005500' => 'gra', 'GSVIVG01011094001' => 'vvi', 'GSVIVG01017879001' => 'vvi', 'GSVIVG01025988001' => 'vvi', 'GSVIVG01029847001' => 'vvi', 'HanXRQChr10g0282901' => 'han', 'HanXRQChr10g0310371' => 'han', 'HanXRQChr10g0315041' => 'han', 'HanXRQChr11g0327651' => 'han', 'HanXRQChr12g0359391' => 'han', 'Haze_00972' => 'cav', 'Haze_00973' => 'cav', 'Haze_00974' => 'cav', 'Haze_04747' => 'cav', 'Haze_04749' => 'cav', 'Haze_04750' => 'cav', 'Haze_21217' => 'cav', 'Hma1.2p1_1037F.1_g250680' => 'hma', 'Hma1.2p1_1644F.1_g295320' => 'hma', 'HPP92_011322' => 'vpl', 'HPP92_011323' => 'vpl', 'HPP92_011324' => 'vpl', 'HPP92_011325' => 'vpl', 'HPP92_011326' => 'vpl', 'Hund12205' => 'sun', 'Hund17957' => 'sun', 'Lalb_Chr06g0176771' => 'lal', 'Lalb_Chr18g0056021' => 'lal', 'Lalb_Chr18g0056031' => 'lal', 'Lalb_Chr18g0056041' => 'lal', 'Lalb_Chr20g0107751' => 'lal', 'Lalb_Chr20g0118371' => 'lal', 'Lj1g0010239' => 'lja', 'Lj1g0017101' => 'lja', 'Lj2A1178G40' => 'lonja', 'Lj2A54G84' => 'lonja', 'Lj2g0015248' => 'lja', 'Lj3A761T51' => 'lonja', 'Lj6g0018116' => 'lja', 'Lsat_1_v5_gn_4_136040' => 'lsa', 'Lsat_1_v5_gn_5_187461' => 'lsa', 'Lsat_1_v5_gn_5_77001' => 'lsa', 'Lsat_1_v5_gn_9_4461' => 'lsa', 'Manes.01G210100' => 'mes', 'Manes.03G185600' => 'mes', 'Manes.05G073300' => 'mes', 'Manes.09G120300' => 'mes', 'Manes.15G022100' => 'mes', 'Mapoly0096s0053' => 'mpo', 'MBI03_g14058_MAGBIO' => 'mbi', 'MBI03_g33876_MAGBIO' => 'mbi', 'MBI03_g36854_MAGBIO' => 'mbi', 'MBI17_g11997_MAGBIO' => 'mbi', 'MD03G1269000' => 'mdo', 'MD04G1179600' => 'mdo', 'MD11G1289800' => 'mdo', 'MD12G1194700' => 'mdo', 'MD13G1182100' => 'mdo', 'MD13G1182200' => 'mdo', 'MD16G1182600' => 'mdo', 'Medtr2g021400' => 'mtr', 'Medtr2g021470' => 'mtr', 'Medtr2g105810' => 'mtr', 'Medtr3g033580' => 'mtr', 'Medtr6g007970' => 'mtr', 'Medtr7g056330' => 'mtr', 'Medtr7g074290' => 'mtr', 'Medtr7g074380' => 'mtr', 'Medtr7g094550' => 'mtr', 'Medtr8g069995' => 'mtr', 'MELO3C014345.2' => 'cme', 'MELO3C021395.2' => 'cme', 'Migut.D00262' => 'egut', 'Migut.G00257' => 'egut', 'MSTRG.21575' => 'ama', 'MSTRG.3985' => 'ama', 'Nitab4.5_0000295g0140' => 'nta', 'Nitab4.5_0000732g0140' => 'nta', 'Nitab4.5_0003162g0020' => 'nta', 'Nitab4.5_0006180g0090' => 'nta', 'Nitab4.5_0006390g0010' => 'nta', 'Nitab4.5_0007392g0040' => 'nta', 'Nn1g02140' => 'nnu', 'Nn4g26168' => 'nnu', 'Nn5g26754' => 'nnu', 'Oeu001433.1' => 'oeu', 'Oeu010299.2' => 'oeu', 'Oeu011171.1' => 'oeu', 'Oeu037675.1' => 'oeu', 'Oeu038359.1' => 'oeu', 'Oeu063834.1' => 'oeu', 'Oeu063835.1' => 'oeu', 'Os05g0312000' => 'osa', 'Os07g0211101' => 'osa', 'Os07g0211200' => 'osa', 'Os07g0681500' => 'osa', 'Peaxi162Scf00095g01015' => 'pax', 'Peaxi162Scf00104g00329' => 'pax', 'Peaxi162Scf00161g00137' => 'pax', 'PGR004G1665' => 'pgr', 'PGR031G2937' => 'pgr', 'PGR119G2145' => 'pgr', 'PGSC0003DMG400004351' => 'stu', 'PGSC0003DMG400014625' => 'stu', 'PGSC0003DMG401000943' => 'stu', 'Phvul.001G148600' => 'pvu', 'Phvul.004G001700' => 'pvu', 'Phvul.006G154900' => 'pvu', 'Phvul.008G078200' => 'pvu', 'Phvul.011G136500' => 'pvu', 'Potri.002G215600' => 'ptr', 'Potri.008G201600' => 'ptr', 'Potri.014G138400' => 'ptr', 'Potri.016G142500' => 'ptr', 'Pp3c16_10580' => 'ppa', 'Pp3c5_25280' => 'ppa', 'Prupe.1G150000' => 'ppe', 'Prupe.1G150100' => 'ppe', 'Prupe.6G299600' => 'ppe', 'Prupe.8G245000' => 'ppe', 'Psat0s4927g0040' => 'psa', 'Psat1g052080' => 'psa', 'Psat1g183800' => 'psa', 'Psat3g113840' => 'psa', 'Psat3g126120' => 'psa', 'Psat3g126160' => 'psa', 'Psat3g158760' => 'psa', 'Psat3g158840' => 'psa', 'PSO170G2858' => 'pso', 'PSO339G0606' => 'pso', 'PSO384G4709' => 'pso', 'PSO407G0334' => 'pso', 'QL04p040276' => 'qlo', 'QL06p005458' => 'qlo', 'QL06p005472' => 'qlo', 'QL07p030546' => 'qlo', 'QL07p031519' => 'qlo', 'QL09p050949' => 'qlo', 'QL09p050966' => 'qlo', 'QL09p051067' => 'qlo', 'QL12p022706' => 'qlo', 'RcHm_v2.0_Chr2g0119601' => 'rch', 'RcHm_v2.0_Chr3g0459591' => 'rch', 'RcHm_v2.0_Chr4g0418521' => 'rch', 'RcHm_v2.0_Chr4g0418531' => 'rch', 'RcHm_v2.0_Chr4g0418541' => 'rch', 'RcHm_v2.0_Chr6g0291641' => 'rch', 'Rhsim01G0086300' => 'rsi', 'Rhsim01G0276300' => 'rsi', 'Rhsim01G0276500' => 'rsi', 'Rhsim04G0207700' => 'rsi', 'Rhsim05G0234500' => 'rsi', 'Rhsim13G0022400' => 'rsi', 'Sabra02G0167900' => 'sbr', 'Sabra04G0158500' => 'sbr', 'Sabra08G0159800' => 'sbr', 'Sabra10G0011500' => 'sbr', 'Sabra14G0104400' => 'sbr', 'SalBow2G2440' => 'sbo', 'SalBow4G2265' => 'sbo', 'Sc02g0000060' => 'sci', 'Sc05g0005020' => 'sci', 'Sc13g0003890' => 'sci', 'Sed0014865' => 'sed', 'Sed0017224' => 'sed', 'Sed0026391' => 'sed', 'SEGI_00063' => 'sgi', 'SEGI_10967' => 'sgi', 'SEGI_17510' => 'sgi', 'SEGI_24396' => 'sgi', 'SEGI_39719' => 'sgi', 'SEGI_41392' => 'sgi', 'SGA_v2.0_scaffold11G05794' => 'sas', 'SGA_v2.0_scaffold142G35607' => 'sas', 'SGA_v2.0_scaffold1G00447' => 'sas', 'SHI15388' => 'shi', 'SHI15394' => 'shi', 'SHI15396' => 'shi', 'SHI15399' => 'shi', 'SMO343G0151' => 'smo', 'SMO367G1118' => 'smo', 'Solyc01g080200.3' => 'sly', 'Solyc06g008960.3' => 'sly', 'Solyc09g064780.3' => 'sly', 'Sopen01g031980' => 'spe', 'Sopen06g003710' => 'spe', 'Sopen09g026460' => 'spe', 'Sp3g21240' => 'spa', 'Sp4g30030' => 'spa', 'TAR365G0022' => 'tar', 'TAR365G1023' => 'tar', 'TAR365G1253' => 'tar', 'TAR623G0078' => 'tar', 'TAR623G1721' => 'tar', 'TAR633G0959' => 'tar', 'THA.LOC104802225' => 'tha', 'THA.LOC104804769' => 'tha', 'THA.LOC104808660' => 'tha', 'THA.LOC104812792' => 'tha', 'Thecc.01G284000' => 'tca', 'Thecc.04G220600' => 'tca', 'Thecc.05G268900' => 'tca', 'Thecc.08G171100' => 'tca', 'Thhalv10001284m.g' => 'esa', 'Thhalv10019912m.g' => 'esa', 'TPR.G14189' => 'tpr', 'TPR.G18110' => 'tpr', 'TPR.G18130' => 'tpr', 'TPR.G18131' => 'tpr', 'TPR.G18140' => 'tpr', 'TPR.G24282' => 'tpr', 'TPR.G25221' => 'tpr', 'TPR.G29267' => 'tpr', 'TPR.G35315' => 'tpr', 'TPR.G36173' => 'tpr', 'TWI09G0794' => 'twi', 'TWI59G1348' => 'twi', 'TWI74G0430' => 'twi', 'unitig_26.g8940' => 'ugi', 'unitig_749.g13744' => 'ugi', 'unitig_749.g13745' => 'ugi', 'vmacro08269' => 'vma', 'vmacro14937' => 'vma', 'vmacro20401' => 'vma', 'VMungo0464G1349' => 'vmu', 'VMungo0540G0289' => 'vmu', 'VMungo1215G1590' => 'vmu', 'VMungo1309G0221' => 'vmu', 'VMungo1309G2815' => 'vmu', 'VMungo1383G0239' => 'vmu', 'VMungo1383G2910' => 'vmu', 'Zm00001eb095270' => 'zma', 'Zm00001eb095280' => 'zma', 'Zm00001eb111630' => 'zma', 'Zm00001eb237080' => 'zma', 'Zm00001eb273740' => 'zma', 'Zm00001eb285040' => 'zma', 'Zm00001eb330790' => 'zma', 'Zm00001eb337380' => 'zma' ) $gf_id = 'HOM05D001484' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001484' ) $data_identifier = 'HOM05D001484' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 2, 'aly' => (int) 2, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 22, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 7, 'hma' => (int) 2, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 7, 'mtr' => (int) 10, 'cme' => (int) 2, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 4, 'ppa' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 4, 'qlo' => (int) 9, 'rch' => (int) 6, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 10, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 7, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb337380' $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' => 'HOM05D001484', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p31500' => 'bna', 'A05p00020' => 'bna', 'A07p08820' => 'bna', 'Aa31LG4G3300' => 'aar', 'Aa31LG8G10030' => 'aar', 'Actinidia00731' => 'ach', 'Actinidia11473' => 'ach', 'Actinidia23469' => 'ach', 'Actinidia24318' => 'ach', 'Actinidia40196' => 'ach', 'Actinidia40197' => 'ach', 'Actinidia40198' => 'ach', 'Ah.08g212990' => 'amhyb', 'Ah.15g091720' => 'amhyb', 'AL3G38260' => 'aly', 'AL4G47710' => 'aly', 'Aqoxy2G00671' => 'aox', 'Aqoxy2G03236' => 'aox', 'arahy.Tifrunner.gnm1.ann1.05IDCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KR684' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATY3SJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK6QJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6APGL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IDT7Z9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM073U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ0R87' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LE7RV4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT4QRX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V5ENPK' => 'arhy', 'AT2G48110' => 'ath', 'AT3G23590' => 'ath', 'ATR0626G186' => 'atr', 'ATR1127G141' => 'atr', 'Atru.chr4.2583' => 'acertr', 'Atru.chr5.1358' => 'acertr', 'Atru.chr5.1359' => 'acertr', 'Atru.chr8.46' => 'acertr', 'AUR62002640' => 'cqu', 'AUR62030055' => 'cqu', 'AUR62033713' => 'cqu', 'AUR62033714' => 'cqu', 'AUR62036795' => 'cqu', 'AUR62039891' => 'cqu', 'BcaB02g08737' => 'bca', 'BcaB04g20441' => 'bca', 'BcaB06g26509' => 'bca', 'BcaB06g26510' => 'bca', 'BcaB06g26511' => 'bca', 'BcaB06g26512' => 'bca', 'BcaB06g26513' => 'bca', 'BcaC02g12564' => 'bca', 'BcaC02g12565' => 'bca', 'BcaC02g12794' => 'bca', 'BcaC02g12795' => 'bca', 'BcaC02g12796' => 'bca', 'BcaC06g35541' => 'bca', 'BNapus_Darmor_BZH_scaffold_188p00080' => 'bna', 'BNapus_Darmor_BZH_scaffold_188p00090' => 'bna', 'BolC1t03972H' => 'bol', 'BolC1t03973H' => 'bol', 'BolC4t21680H' => 'bol', 'BolC7t41863H' => 'bol', 'BolSC55t61227H' => 'bol', 'BolSC55t61228H' => 'bol', 'BraA01t03278Z' => 'bra', 'BraA05t18998Z' => 'bra', 'BraA07t28673Z' => 'bra', 'C01p40150' => 'bna', 'C05p12370' => 'bna', 'C07p13680' => 'bna', 'CAN.G1006.16' => 'can', 'CAN.G1006.17' => 'can', 'CAN.G1170.2' => 'can', 'CAN.G962.7' => 'can', 'CANSAT25G2179' => 'cansat', 'CANSAT78G1573' => 'cansat', 'CARHR099510' => 'chi', 'CARHR143510' => 'chi', 'Carub.0003s2380' => 'cru', 'Carub.0004s3082' => 'cru', 'Ca_00614_v3' => 'car', 'Ca_07801_v3' => 'car', 'Ca_08567_v3' => 'car', 'Ca_09571_v3' => 'car', 'CBR_g19290' => 'cbr', 'Cc01_g19770' => 'ccan', 'Cc03_g03030' => 'ccan', 'CDE07G0968' => 'cde', 'CDE09G1441' => 'cde', 'Cfa006103' => 'cfa', 'Cfa015573' => 'cfa', 'Cfa016988' => 'cfa', 'Ciclev10006738m.g' => 'ccl', 'Ciclev10010920m.g' => 'ccl', 'Ciclev10018517m.g' => 'ccl', 'CiPaw.01G159200' => 'cil', 'CiPaw.02G091000' => 'cil', 'CiPaw.02G091100' => 'cil', 'CiPaw.08G103100' => 'cil', 'CiPaw.09G224900' => 'cil', 'ClCG06G005740' => 'cla', 'ClCG07G000090' => 'cla', 'ClCG07G000100' => 'cla', 'COL.COLO4_09143' => 'col', 'COL.COLO4_25124' => 'col', 'Cpa.g.sc16.34' => 'cpa', 'Cpa.g.sc3504.1' => 'cpa', 'Cpa.g.sc60.37' => 'cpa', 'CsaV3_6G018520' => 'csa', 'CsaV3_6G036860' => 'csa', 'CSS0001072' => 'camsi', 'CSS0020208' => 'camsi', 'CSS0021253' => 'camsi', 'CSS0022190' => 'camsi', 'CSS0036150' => 'camsi', 'CSS0040442' => 'camsi', 'CSS0042300' => 'camsi', 'CSS0045298' => 'camsi', 'DCAR_012449' => 'dca', 'DCAR_018405' => 'dca', 'DCAR_024573' => 'dca', 'DCAR_030591' => 'dca', 'Dinv16926' => 'din', 'Dinv32963' => 'din', 'Dinv38382' => 'din', 'Dinv38383' => 'din', 'Duzib133G0974' => 'dzi', 'Duzib138G1867' => 'dzi', 'Duzib211G0420' => 'dzi', 'Duzib212G0930' => 'dzi', 'ECA234G1645' => 'eca', 'ECA247G3467' => 'eca', 'ECA248G1703' => 'eca', 'EL10Ac3g06327' => 'bvu', 'EL10Ac7g17204' => 'bvu', 'Eucgr.A00855' => 'egr', 'Eucgr.A00858' => 'egr', 'Eucgr.H01520' => 'egr', 'Eucgr.H03604' => 'egr', 'Eucgr.L03465' => 'egr', 'Eucgr.L03466' => 'egr', 'FAN01G0988' => 'fan', 'FAN02G3892' => 'fan', 'FAN05G3381' => 'fan', 'FAN07G0967' => 'fan', 'FAN07G1493' => 'fan', 'FAN08G3125' => 'fan', 'FAN09G0402' => 'fan', 'FAN12G2594' => 'fan', 'FAN12G3879' => 'fan', 'FAN14G1546' => 'fan', 'FAN15G3626' => 'fan', 'FAN17G0588' => 'fan', 'FAN17G0609' => 'fan', 'FAN18G2817' => 'fan', 'FAN19G1305' => 'fan', 'FAN20G1787' => 'fan', 'FAN22G0073' => 'fan', 'FAN22G0352' => 'fan', 'FAN22G0368' => 'fan', 'FAN22G2273' => 'fan', 'FAN24G1998' => 'fan', 'FAN27G1317' => 'fan', 'FvH4_2g23980' => 'fve', 'FvH4_4g14380' => 'fve', 'FvH4_4g14390' => 'fve', 'FvH4_6g09250' => 'fve', 'Glyma.03G151100' => 'gma', 'Glyma.04G122550' => 'gma', 'Glyma.05G001600' => 'gma', 'Glyma.09G270766' => 'gma', 'Glyma.09G270832' => 'gma', 'Glyma.13G209800' => 'gma', 'Glyma.15G102800' => 'gma', 'Glyma.18G218900' => 'gma', 'Glyma.19G001500' => 'gma', 'Glyma.19G153600' => 'gma', 'Gohir.A02G028600' => 'ghi', 'Gohir.A08G045000' => 'ghi', 'Gohir.A11G120500' => 'ghi', 'Gohir.A12G006200' => 'ghi', 'Gohir.A12G006250' => 'ghi', 'Gohir.D02G036300' => 'ghi', 'Gohir.D08G054700' => 'ghi', 'Gohir.D11G125600' => 'ghi', 'Gohir.D12G005700' => 'ghi', 'Gorai.004G055200' => 'gra', 'Gorai.005G040400' => 'gra', 'Gorai.007G134500' => 'gra', 'Gorai.008G005500' => 'gra', 'GSVIVG01011094001' => 'vvi', 'GSVIVG01017879001' => 'vvi', 'GSVIVG01025988001' => 'vvi', 'GSVIVG01029847001' => 'vvi', 'HanXRQChr10g0282901' => 'han', 'HanXRQChr10g0310371' => 'han', 'HanXRQChr10g0315041' => 'han', 'HanXRQChr11g0327651' => 'han', 'HanXRQChr12g0359391' => 'han', 'Haze_00972' => 'cav', 'Haze_00973' => 'cav', 'Haze_00974' => 'cav', 'Haze_04747' => 'cav', 'Haze_04749' => 'cav', 'Haze_04750' => 'cav', 'Haze_21217' => 'cav', 'Hma1.2p1_1037F.1_g250680' => 'hma', 'Hma1.2p1_1644F.1_g295320' => 'hma', 'HPP92_011322' => 'vpl', 'HPP92_011323' => 'vpl', 'HPP92_011324' => 'vpl', 'HPP92_011325' => 'vpl', 'HPP92_011326' => 'vpl', 'Hund12205' => 'sun', 'Hund17957' => 'sun', 'Lalb_Chr06g0176771' => 'lal', 'Lalb_Chr18g0056021' => 'lal', 'Lalb_Chr18g0056031' => 'lal', 'Lalb_Chr18g0056041' => 'lal', 'Lalb_Chr20g0107751' => 'lal', 'Lalb_Chr20g0118371' => 'lal', 'Lj1g0010239' => 'lja', 'Lj1g0017101' => 'lja', 'Lj2A1178G40' => 'lonja', 'Lj2A54G84' => 'lonja', 'Lj2g0015248' => 'lja', 'Lj3A761T51' => 'lonja', 'Lj6g0018116' => 'lja', 'Lsat_1_v5_gn_4_136040' => 'lsa', 'Lsat_1_v5_gn_5_187461' => 'lsa', 'Lsat_1_v5_gn_5_77001' => 'lsa', 'Lsat_1_v5_gn_9_4461' => 'lsa', 'Manes.01G210100' => 'mes', 'Manes.03G185600' => 'mes', 'Manes.05G073300' => 'mes', 'Manes.09G120300' => 'mes', 'Manes.15G022100' => 'mes', 'Mapoly0096s0053' => 'mpo', 'MBI03_g14058_MAGBIO' => 'mbi', 'MBI03_g33876_MAGBIO' => 'mbi', 'MBI03_g36854_MAGBIO' => 'mbi', 'MBI17_g11997_MAGBIO' => 'mbi', 'MD03G1269000' => 'mdo', 'MD04G1179600' => 'mdo', 'MD11G1289800' => 'mdo', 'MD12G1194700' => 'mdo', 'MD13G1182100' => 'mdo', 'MD13G1182200' => 'mdo', 'MD16G1182600' => 'mdo', 'Medtr2g021400' => 'mtr', 'Medtr2g021470' => 'mtr', 'Medtr2g105810' => 'mtr', 'Medtr3g033580' => 'mtr', 'Medtr6g007970' => 'mtr', 'Medtr7g056330' => 'mtr', 'Medtr7g074290' => 'mtr', 'Medtr7g074380' => 'mtr', 'Medtr7g094550' => 'mtr', 'Medtr8g069995' => 'mtr', 'MELO3C014345.2' => 'cme', 'MELO3C021395.2' => 'cme', 'Migut.D00262' => 'egut', 'Migut.G00257' => 'egut', 'MSTRG.21575' => 'ama', 'MSTRG.3985' => 'ama', 'Nitab4.5_0000295g0140' => 'nta', 'Nitab4.5_0000732g0140' => 'nta', 'Nitab4.5_0003162g0020' => 'nta', 'Nitab4.5_0006180g0090' => 'nta', 'Nitab4.5_0006390g0010' => 'nta', 'Nitab4.5_0007392g0040' => 'nta', 'Nn1g02140' => 'nnu', 'Nn4g26168' => 'nnu', 'Nn5g26754' => 'nnu', 'Oeu001433.1' => 'oeu', 'Oeu010299.2' => 'oeu', 'Oeu011171.1' => 'oeu', 'Oeu037675.1' => 'oeu', 'Oeu038359.1' => 'oeu', 'Oeu063834.1' => 'oeu', 'Oeu063835.1' => 'oeu', 'Os05g0312000' => 'osa', 'Os07g0211101' => 'osa', 'Os07g0211200' => 'osa', 'Os07g0681500' => 'osa', 'Peaxi162Scf00095g01015' => 'pax', 'Peaxi162Scf00104g00329' => 'pax', 'Peaxi162Scf00161g00137' => 'pax', 'PGR004G1665' => 'pgr', 'PGR031G2937' => 'pgr', 'PGR119G2145' => 'pgr', 'PGSC0003DMG400004351' => 'stu', 'PGSC0003DMG400014625' => 'stu', 'PGSC0003DMG401000943' => 'stu', 'Phvul.001G148600' => 'pvu', 'Phvul.004G001700' => 'pvu', 'Phvul.006G154900' => 'pvu', 'Phvul.008G078200' => 'pvu', 'Phvul.011G136500' => 'pvu', 'Potri.002G215600' => 'ptr', 'Potri.008G201600' => 'ptr', 'Potri.014G138400' => 'ptr', 'Potri.016G142500' => 'ptr', 'Pp3c16_10580' => 'ppa', 'Pp3c5_25280' => 'ppa', 'Prupe.1G150000' => 'ppe', 'Prupe.1G150100' => 'ppe', 'Prupe.6G299600' => 'ppe', 'Prupe.8G245000' => 'ppe', 'Psat0s4927g0040' => 'psa', 'Psat1g052080' => 'psa', 'Psat1g183800' => 'psa', 'Psat3g113840' => 'psa', 'Psat3g126120' => 'psa', 'Psat3g126160' => 'psa', 'Psat3g158760' => 'psa', 'Psat3g158840' => 'psa', 'PSO170G2858' => 'pso', 'PSO339G0606' => 'pso', 'PSO384G4709' => 'pso', 'PSO407G0334' => 'pso', 'QL04p040276' => 'qlo', 'QL06p005458' => 'qlo', 'QL06p005472' => 'qlo', 'QL07p030546' => 'qlo', 'QL07p031519' => 'qlo', 'QL09p050949' => 'qlo', 'QL09p050966' => 'qlo', 'QL09p051067' => 'qlo', 'QL12p022706' => 'qlo', 'RcHm_v2.0_Chr2g0119601' => 'rch', 'RcHm_v2.0_Chr3g0459591' => 'rch', 'RcHm_v2.0_Chr4g0418521' => 'rch', 'RcHm_v2.0_Chr4g0418531' => 'rch', 'RcHm_v2.0_Chr4g0418541' => 'rch', 'RcHm_v2.0_Chr6g0291641' => 'rch', 'Rhsim01G0086300' => 'rsi', 'Rhsim01G0276300' => 'rsi', 'Rhsim01G0276500' => 'rsi', 'Rhsim04G0207700' => 'rsi', 'Rhsim05G0234500' => 'rsi', 'Rhsim13G0022400' => 'rsi', 'Sabra02G0167900' => 'sbr', 'Sabra04G0158500' => 'sbr', 'Sabra08G0159800' => 'sbr', 'Sabra10G0011500' => 'sbr', 'Sabra14G0104400' => 'sbr', 'SalBow2G2440' => 'sbo', 'SalBow4G2265' => 'sbo', 'Sc02g0000060' => 'sci', 'Sc05g0005020' => 'sci', 'Sc13g0003890' => 'sci', 'Sed0014865' => 'sed', 'Sed0017224' => 'sed', 'Sed0026391' => 'sed', 'SEGI_00063' => 'sgi', 'SEGI_10967' => 'sgi', 'SEGI_17510' => 'sgi', 'SEGI_24396' => 'sgi', 'SEGI_39719' => 'sgi', 'SEGI_41392' => 'sgi', 'SGA_v2.0_scaffold11G05794' => 'sas', 'SGA_v2.0_scaffold142G35607' => 'sas', 'SGA_v2.0_scaffold1G00447' => 'sas', 'SHI15388' => 'shi', 'SHI15394' => 'shi', 'SHI15396' => 'shi', 'SHI15399' => 'shi', 'SMO343G0151' => 'smo', 'SMO367G1118' => 'smo', 'Solyc01g080200.3' => 'sly', 'Solyc06g008960.3' => 'sly', 'Solyc09g064780.3' => 'sly', 'Sopen01g031980' => 'spe', 'Sopen06g003710' => 'spe', 'Sopen09g026460' => 'spe', 'Sp3g21240' => 'spa', 'Sp4g30030' => 'spa', 'TAR365G0022' => 'tar', 'TAR365G1023' => 'tar', 'TAR365G1253' => 'tar', 'TAR623G0078' => 'tar', 'TAR623G1721' => 'tar', 'TAR633G0959' => 'tar', 'THA.LOC104802225' => 'tha', 'THA.LOC104804769' => 'tha', 'THA.LOC104808660' => 'tha', 'THA.LOC104812792' => 'tha', 'Thecc.01G284000' => 'tca', 'Thecc.04G220600' => 'tca', 'Thecc.05G268900' => 'tca', 'Thecc.08G171100' => 'tca', 'Thhalv10001284m.g' => 'esa', 'Thhalv10019912m.g' => 'esa', 'TPR.G14189' => 'tpr', 'TPR.G18110' => 'tpr', 'TPR.G18130' => 'tpr', 'TPR.G18131' => 'tpr', 'TPR.G18140' => 'tpr', 'TPR.G24282' => 'tpr', 'TPR.G25221' => 'tpr', 'TPR.G29267' => 'tpr', 'TPR.G35315' => 'tpr', 'TPR.G36173' => 'tpr', 'TWI09G0794' => 'twi', 'TWI59G1348' => 'twi', 'TWI74G0430' => 'twi', 'unitig_26.g8940' => 'ugi', 'unitig_749.g13744' => 'ugi', 'unitig_749.g13745' => 'ugi', 'vmacro08269' => 'vma', 'vmacro14937' => 'vma', 'vmacro20401' => 'vma', 'VMungo0464G1349' => 'vmu', 'VMungo0540G0289' => 'vmu', 'VMungo1215G1590' => 'vmu', 'VMungo1309G0221' => 'vmu', 'VMungo1309G2815' => 'vmu', 'VMungo1383G0239' => 'vmu', 'VMungo1383G2910' => 'vmu', 'Zm00001eb095270' => 'zma', 'Zm00001eb095280' => 'zma', 'Zm00001eb111630' => 'zma', 'Zm00001eb237080' => 'zma', 'Zm00001eb273740' => 'zma', 'Zm00001eb285040' => 'zma', 'Zm00001eb330790' => 'zma', 'Zm00001eb337380' => 'zma' ), 'gf_id' => 'HOM05D001484', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001484' ), 'data_identifier' => 'HOM05D001484', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001484', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p31500' => 'bna', 'A05p00020' => 'bna', 'A07p08820' => 'bna', 'Aa31LG4G3300' => 'aar', 'Aa31LG8G10030' => 'aar', 'Actinidia00731' => 'ach', 'Actinidia11473' => 'ach', 'Actinidia23469' => 'ach', 'Actinidia24318' => 'ach', 'Actinidia40196' => 'ach', 'Actinidia40197' => 'ach', 'Actinidia40198' => 'ach', 'Ah.08g212990' => 'amhyb', 'Ah.15g091720' => 'amhyb', 'AL3G38260' => 'aly', 'AL4G47710' => 'aly', 'Aqoxy2G00671' => 'aox', 'Aqoxy2G03236' => 'aox', 'arahy.Tifrunner.gnm1.ann1.05IDCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KR684' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATY3SJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK6QJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6APGL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IDT7Z9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM073U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ0R87' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LE7RV4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT4QRX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V5ENPK' => 'arhy', 'AT2G48110' => 'ath', 'AT3G23590' => 'ath', 'ATR0626G186' => 'atr', 'ATR1127G141' => 'atr', 'Atru.chr4.2583' => 'acertr', 'Atru.chr5.1358' => 'acertr', 'Atru.chr5.1359' => 'acertr', 'Atru.chr8.46' => 'acertr', 'AUR62002640' => 'cqu', 'AUR62030055' => 'cqu', 'AUR62033713' => 'cqu', 'AUR62033714' => 'cqu', 'AUR62036795' => 'cqu', 'AUR62039891' => 'cqu', 'BcaB02g08737' => 'bca', 'BcaB04g20441' => 'bca', 'BcaB06g26509' => 'bca', 'BcaB06g26510' => 'bca', 'BcaB06g26511' => 'bca', 'BcaB06g26512' => 'bca', 'BcaB06g26513' => 'bca', 'BcaC02g12564' => 'bca', 'BcaC02g12565' => 'bca', 'BcaC02g12794' => 'bca', 'BcaC02g12795' => 'bca', 'BcaC02g12796' => 'bca', 'BcaC06g35541' => 'bca', 'BNapus_Darmor_BZH_scaffold_188p00080' => 'bna', 'BNapus_Darmor_BZH_scaffold_188p00090' => 'bna', 'BolC1t03972H' => 'bol', 'BolC1t03973H' => 'bol', 'BolC4t21680H' => 'bol', 'BolC7t41863H' => 'bol', 'BolSC55t61227H' => 'bol', 'BolSC55t61228H' => 'bol', 'BraA01t03278Z' => 'bra', 'BraA05t18998Z' => 'bra', 'BraA07t28673Z' => 'bra', 'C01p40150' => 'bna', 'C05p12370' => 'bna', 'C07p13680' => 'bna', 'CAN.G1006.16' => 'can', 'CAN.G1006.17' => 'can', 'CAN.G1170.2' => 'can', 'CAN.G962.7' => 'can', 'CANSAT25G2179' => 'cansat', 'CANSAT78G1573' => 'cansat', 'CARHR099510' => 'chi', 'CARHR143510' => 'chi', 'Carub.0003s2380' => 'cru', 'Carub.0004s3082' => 'cru', 'Ca_00614_v3' => 'car', 'Ca_07801_v3' => 'car', 'Ca_08567_v3' => 'car', 'Ca_09571_v3' => 'car', 'CBR_g19290' => 'cbr', 'Cc01_g19770' => 'ccan', 'Cc03_g03030' => 'ccan', 'CDE07G0968' => 'cde', 'CDE09G1441' => 'cde', 'Cfa006103' => 'cfa', 'Cfa015573' => 'cfa', 'Cfa016988' => 'cfa', 'Ciclev10006738m.g' => 'ccl', 'Ciclev10010920m.g' => 'ccl', 'Ciclev10018517m.g' => 'ccl', 'CiPaw.01G159200' => 'cil', 'CiPaw.02G091000' => 'cil', 'CiPaw.02G091100' => 'cil', 'CiPaw.08G103100' => 'cil', 'CiPaw.09G224900' => 'cil', 'ClCG06G005740' => 'cla', 'ClCG07G000090' => 'cla', 'ClCG07G000100' => 'cla', 'COL.COLO4_09143' => 'col', 'COL.COLO4_25124' => 'col', 'Cpa.g.sc16.34' => 'cpa', 'Cpa.g.sc3504.1' => 'cpa', 'Cpa.g.sc60.37' => 'cpa', 'CsaV3_6G018520' => 'csa', 'CsaV3_6G036860' => 'csa', 'CSS0001072' => 'camsi', 'CSS0020208' => 'camsi', 'CSS0021253' => 'camsi', 'CSS0022190' => 'camsi', 'CSS0036150' => 'camsi', 'CSS0040442' => 'camsi', 'CSS0042300' => 'camsi', 'CSS0045298' => 'camsi', 'DCAR_012449' => 'dca', 'DCAR_018405' => 'dca', 'DCAR_024573' => 'dca', 'DCAR_030591' => 'dca', 'Dinv16926' => 'din', 'Dinv32963' => 'din', 'Dinv38382' => 'din', 'Dinv38383' => 'din', 'Duzib133G0974' => 'dzi', 'Duzib138G1867' => 'dzi', 'Duzib211G0420' => 'dzi', 'Duzib212G0930' => 'dzi', 'ECA234G1645' => 'eca', 'ECA247G3467' => 'eca', 'ECA248G1703' => 'eca', 'EL10Ac3g06327' => 'bvu', 'EL10Ac7g17204' => 'bvu', 'Eucgr.A00855' => 'egr', 'Eucgr.A00858' => 'egr', 'Eucgr.H01520' => 'egr', 'Eucgr.H03604' => 'egr', 'Eucgr.L03465' => 'egr', 'Eucgr.L03466' => 'egr', 'FAN01G0988' => 'fan', 'FAN02G3892' => 'fan', 'FAN05G3381' => 'fan', 'FAN07G0967' => 'fan', 'FAN07G1493' => 'fan', 'FAN08G3125' => 'fan', 'FAN09G0402' => 'fan', 'FAN12G2594' => 'fan', 'FAN12G3879' => 'fan', 'FAN14G1546' => 'fan', 'FAN15G3626' => 'fan', 'FAN17G0588' => 'fan', 'FAN17G0609' => 'fan', 'FAN18G2817' => 'fan', 'FAN19G1305' => 'fan', 'FAN20G1787' => 'fan', 'FAN22G0073' => 'fan', 'FAN22G0352' => 'fan', 'FAN22G0368' => 'fan', 'FAN22G2273' => 'fan', 'FAN24G1998' => 'fan', 'FAN27G1317' => 'fan', 'FvH4_2g23980' => 'fve', 'FvH4_4g14380' => 'fve', 'FvH4_4g14390' => 'fve', 'FvH4_6g09250' => 'fve', 'Glyma.03G151100' => 'gma', 'Glyma.04G122550' => 'gma', 'Glyma.05G001600' => 'gma', 'Glyma.09G270766' => 'gma', 'Glyma.09G270832' => 'gma', 'Glyma.13G209800' => 'gma', 'Glyma.15G102800' => 'gma', 'Glyma.18G218900' => 'gma', 'Glyma.19G001500' => 'gma', 'Glyma.19G153600' => 'gma', 'Gohir.A02G028600' => 'ghi', 'Gohir.A08G045000' => 'ghi', 'Gohir.A11G120500' => 'ghi', 'Gohir.A12G006200' => 'ghi', 'Gohir.A12G006250' => 'ghi', 'Gohir.D02G036300' => 'ghi', 'Gohir.D08G054700' => 'ghi', 'Gohir.D11G125600' => 'ghi', 'Gohir.D12G005700' => 'ghi', 'Gorai.004G055200' => 'gra', 'Gorai.005G040400' => 'gra', 'Gorai.007G134500' => 'gra', 'Gorai.008G005500' => 'gra', 'GSVIVG01011094001' => 'vvi', 'GSVIVG01017879001' => 'vvi', 'GSVIVG01025988001' => 'vvi', 'GSVIVG01029847001' => 'vvi', 'HanXRQChr10g0282901' => 'han', 'HanXRQChr10g0310371' => 'han', 'HanXRQChr10g0315041' => 'han', 'HanXRQChr11g0327651' => 'han', 'HanXRQChr12g0359391' => 'han', 'Haze_00972' => 'cav', 'Haze_00973' => 'cav', 'Haze_00974' => 'cav', 'Haze_04747' => 'cav', 'Haze_04749' => 'cav', 'Haze_04750' => 'cav', 'Haze_21217' => 'cav', 'Hma1.2p1_1037F.1_g250680' => 'hma', 'Hma1.2p1_1644F.1_g295320' => 'hma', 'HPP92_011322' => 'vpl', 'HPP92_011323' => 'vpl', 'HPP92_011324' => 'vpl', 'HPP92_011325' => 'vpl', 'HPP92_011326' => 'vpl', 'Hund12205' => 'sun', 'Hund17957' => 'sun', 'Lalb_Chr06g0176771' => 'lal', 'Lalb_Chr18g0056021' => 'lal', 'Lalb_Chr18g0056031' => 'lal', 'Lalb_Chr18g0056041' => 'lal', 'Lalb_Chr20g0107751' => 'lal', 'Lalb_Chr20g0118371' => 'lal', 'Lj1g0010239' => 'lja', 'Lj1g0017101' => 'lja', 'Lj2A1178G40' => 'lonja', 'Lj2A54G84' => 'lonja', 'Lj2g0015248' => 'lja', 'Lj3A761T51' => 'lonja', 'Lj6g0018116' => 'lja', 'Lsat_1_v5_gn_4_136040' => 'lsa', 'Lsat_1_v5_gn_5_187461' => 'lsa', 'Lsat_1_v5_gn_5_77001' => 'lsa', 'Lsat_1_v5_gn_9_4461' => 'lsa', 'Manes.01G210100' => 'mes', 'Manes.03G185600' => 'mes', 'Manes.05G073300' => 'mes', 'Manes.09G120300' => 'mes', 'Manes.15G022100' => 'mes', 'Mapoly0096s0053' => 'mpo', 'MBI03_g14058_MAGBIO' => 'mbi', 'MBI03_g33876_MAGBIO' => 'mbi', 'MBI03_g36854_MAGBIO' => 'mbi', 'MBI17_g11997_MAGBIO' => 'mbi', 'MD03G1269000' => 'mdo', 'MD04G1179600' => 'mdo', 'MD11G1289800' => 'mdo', 'MD12G1194700' => 'mdo', 'MD13G1182100' => 'mdo', 'MD13G1182200' => 'mdo', 'MD16G1182600' => 'mdo', 'Medtr2g021400' => 'mtr', 'Medtr2g021470' => 'mtr', 'Medtr2g105810' => 'mtr', 'Medtr3g033580' => 'mtr', 'Medtr6g007970' => 'mtr', 'Medtr7g056330' => 'mtr', 'Medtr7g074290' => 'mtr', 'Medtr7g074380' => 'mtr', 'Medtr7g094550' => 'mtr', 'Medtr8g069995' => 'mtr', 'MELO3C014345.2' => 'cme', 'MELO3C021395.2' => 'cme', 'Migut.D00262' => 'egut', 'Migut.G00257' => 'egut', 'MSTRG.21575' => 'ama', 'MSTRG.3985' => 'ama', 'Nitab4.5_0000295g0140' => 'nta', 'Nitab4.5_0000732g0140' => 'nta', 'Nitab4.5_0003162g0020' => 'nta', 'Nitab4.5_0006180g0090' => 'nta', 'Nitab4.5_0006390g0010' => 'nta', 'Nitab4.5_0007392g0040' => 'nta', 'Nn1g02140' => 'nnu', 'Nn4g26168' => 'nnu', 'Nn5g26754' => 'nnu', 'Oeu001433.1' => 'oeu', 'Oeu010299.2' => 'oeu', 'Oeu011171.1' => 'oeu', 'Oeu037675.1' => 'oeu', 'Oeu038359.1' => 'oeu', 'Oeu063834.1' => 'oeu', 'Oeu063835.1' => 'oeu', 'Os05g0312000' => 'osa', 'Os07g0211101' => 'osa', 'Os07g0211200' => 'osa', 'Os07g0681500' => 'osa', 'Peaxi162Scf00095g01015' => 'pax', 'Peaxi162Scf00104g00329' => 'pax', 'Peaxi162Scf00161g00137' => 'pax', 'PGR004G1665' => 'pgr', 'PGR031G2937' => 'pgr', 'PGR119G2145' => 'pgr', 'PGSC0003DMG400004351' => 'stu', 'PGSC0003DMG400014625' => 'stu', 'PGSC0003DMG401000943' => 'stu', 'Phvul.001G148600' => 'pvu', 'Phvul.004G001700' => 'pvu', 'Phvul.006G154900' => 'pvu', 'Phvul.008G078200' => 'pvu', 'Phvul.011G136500' => 'pvu', 'Potri.002G215600' => 'ptr', 'Potri.008G201600' => 'ptr', 'Potri.014G138400' => 'ptr', 'Potri.016G142500' => 'ptr', 'Pp3c16_10580' => 'ppa', 'Pp3c5_25280' => 'ppa', 'Prupe.1G150000' => 'ppe', 'Prupe.1G150100' => 'ppe', 'Prupe.6G299600' => 'ppe', 'Prupe.8G245000' => 'ppe', 'Psat0s4927g0040' => 'psa', 'Psat1g052080' => 'psa', 'Psat1g183800' => 'psa', 'Psat3g113840' => 'psa', 'Psat3g126120' => 'psa', 'Psat3g126160' => 'psa', 'Psat3g158760' => 'psa', 'Psat3g158840' => 'psa', 'PSO170G2858' => 'pso', 'PSO339G0606' => 'pso', 'PSO384G4709' => 'pso', 'PSO407G0334' => 'pso', 'QL04p040276' => 'qlo', 'QL06p005458' => 'qlo', 'QL06p005472' => 'qlo', 'QL07p030546' => 'qlo', 'QL07p031519' => 'qlo', 'QL09p050949' => 'qlo', 'QL09p050966' => 'qlo', 'QL09p051067' => 'qlo', 'QL12p022706' => 'qlo', 'RcHm_v2.0_Chr2g0119601' => 'rch', 'RcHm_v2.0_Chr3g0459591' => 'rch', 'RcHm_v2.0_Chr4g0418521' => 'rch', 'RcHm_v2.0_Chr4g0418531' => 'rch', 'RcHm_v2.0_Chr4g0418541' => 'rch', 'RcHm_v2.0_Chr6g0291641' => 'rch', 'Rhsim01G0086300' => 'rsi', 'Rhsim01G0276300' => 'rsi', 'Rhsim01G0276500' => 'rsi', 'Rhsim04G0207700' => 'rsi', 'Rhsim05G0234500' => 'rsi', 'Rhsim13G0022400' => 'rsi', 'Sabra02G0167900' => 'sbr', 'Sabra04G0158500' => 'sbr', 'Sabra08G0159800' => 'sbr', 'Sabra10G0011500' => 'sbr', 'Sabra14G0104400' => 'sbr', 'SalBow2G2440' => 'sbo', 'SalBow4G2265' => 'sbo', 'Sc02g0000060' => 'sci', 'Sc05g0005020' => 'sci', 'Sc13g0003890' => 'sci', 'Sed0014865' => 'sed', 'Sed0017224' => 'sed', 'Sed0026391' => 'sed', 'SEGI_00063' => 'sgi', 'SEGI_10967' => 'sgi', 'SEGI_17510' => 'sgi', 'SEGI_24396' => 'sgi', 'SEGI_39719' => 'sgi', 'SEGI_41392' => 'sgi', 'SGA_v2.0_scaffold11G05794' => 'sas', 'SGA_v2.0_scaffold142G35607' => 'sas', 'SGA_v2.0_scaffold1G00447' => 'sas', 'SHI15388' => 'shi', 'SHI15394' => 'shi', 'SHI15396' => 'shi', 'SHI15399' => 'shi', 'SMO343G0151' => 'smo', 'SMO367G1118' => 'smo', 'Solyc01g080200.3' => 'sly', 'Solyc06g008960.3' => 'sly', 'Solyc09g064780.3' => 'sly', 'Sopen01g031980' => 'spe', 'Sopen06g003710' => 'spe', 'Sopen09g026460' => 'spe', 'Sp3g21240' => 'spa', 'Sp4g30030' => 'spa', 'TAR365G0022' => 'tar', 'TAR365G1023' => 'tar', 'TAR365G1253' => 'tar', 'TAR623G0078' => 'tar', 'TAR623G1721' => 'tar', 'TAR633G0959' => 'tar', 'THA.LOC104802225' => 'tha', 'THA.LOC104804769' => 'tha', 'THA.LOC104808660' => 'tha', 'THA.LOC104812792' => 'tha', 'Thecc.01G284000' => 'tca', 'Thecc.04G220600' => 'tca', 'Thecc.05G268900' => 'tca', 'Thecc.08G171100' => 'tca', 'Thhalv10001284m.g' => 'esa', 'Thhalv10019912m.g' => 'esa', 'TPR.G14189' => 'tpr', 'TPR.G18110' => 'tpr', 'TPR.G18130' => 'tpr', 'TPR.G18131' => 'tpr', 'TPR.G18140' => 'tpr', 'TPR.G24282' => 'tpr', 'TPR.G25221' => 'tpr', 'TPR.G29267' => 'tpr', 'TPR.G35315' => 'tpr', 'TPR.G36173' => 'tpr', 'TWI09G0794' => 'twi', 'TWI59G1348' => 'twi', 'TWI74G0430' => 'twi', 'unitig_26.g8940' => 'ugi', 'unitig_749.g13744' => 'ugi', 'unitig_749.g13745' => 'ugi', 'vmacro08269' => 'vma', 'vmacro14937' => 'vma', 'vmacro20401' => 'vma', 'VMungo0464G1349' => 'vmu', 'VMungo0540G0289' => 'vmu', 'VMungo1215G1590' => 'vmu', 'VMungo1309G0221' => 'vmu', 'VMungo1309G2815' => 'vmu', 'VMungo1383G0239' => 'vmu', 'VMungo1383G2910' => 'vmu', 'Zm00001eb095270' => 'zma', 'Zm00001eb095280' => 'zma', 'Zm00001eb111630' => 'zma', 'Zm00001eb237080' => 'zma', 'Zm00001eb273740' => 'zma', 'Zm00001eb285040' => 'zma', 'Zm00001eb330790' => 'zma', 'Zm00001eb337380' => 'zma' ) $gf_id = 'HOM05D001484' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001484' ) $data_identifier = 'HOM05D001484' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 2, 'aly' => (int) 2, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 22, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 7, 'hma' => (int) 2, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 7, 'mtr' => (int) 10, 'cme' => (int) 2, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 4, 'ppa' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 4, 'qlo' => (int) 9, 'rch' => (int) 6, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 10, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 7, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb337380' $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' => 'HOM05D001484', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p31500' => 'bna', 'A05p00020' => 'bna', 'A07p08820' => 'bna', 'Aa31LG4G3300' => 'aar', 'Aa31LG8G10030' => 'aar', 'Actinidia00731' => 'ach', 'Actinidia11473' => 'ach', 'Actinidia23469' => 'ach', 'Actinidia24318' => 'ach', 'Actinidia40196' => 'ach', 'Actinidia40197' => 'ach', 'Actinidia40198' => 'ach', 'Ah.08g212990' => 'amhyb', 'Ah.15g091720' => 'amhyb', 'AL3G38260' => 'aly', 'AL4G47710' => 'aly', 'Aqoxy2G00671' => 'aox', 'Aqoxy2G03236' => 'aox', 'arahy.Tifrunner.gnm1.ann1.05IDCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KR684' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATY3SJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK6QJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6APGL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IDT7Z9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM073U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ0R87' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LE7RV4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT4QRX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V5ENPK' => 'arhy', 'AT2G48110' => 'ath', 'AT3G23590' => 'ath', 'ATR0626G186' => 'atr', 'ATR1127G141' => 'atr', 'Atru.chr4.2583' => 'acertr', 'Atru.chr5.1358' => 'acertr', 'Atru.chr5.1359' => 'acertr', 'Atru.chr8.46' => 'acertr', 'AUR62002640' => 'cqu', 'AUR62030055' => 'cqu', 'AUR62033713' => 'cqu', 'AUR62033714' => 'cqu', 'AUR62036795' => 'cqu', 'AUR62039891' => 'cqu', 'BcaB02g08737' => 'bca', 'BcaB04g20441' => 'bca', 'BcaB06g26509' => 'bca', 'BcaB06g26510' => 'bca', 'BcaB06g26511' => 'bca', 'BcaB06g26512' => 'bca', 'BcaB06g26513' => 'bca', 'BcaC02g12564' => 'bca', 'BcaC02g12565' => 'bca', 'BcaC02g12794' => 'bca', 'BcaC02g12795' => 'bca', 'BcaC02g12796' => 'bca', 'BcaC06g35541' => 'bca', 'BNapus_Darmor_BZH_scaffold_188p00080' => 'bna', 'BNapus_Darmor_BZH_scaffold_188p00090' => 'bna', 'BolC1t03972H' => 'bol', 'BolC1t03973H' => 'bol', 'BolC4t21680H' => 'bol', 'BolC7t41863H' => 'bol', 'BolSC55t61227H' => 'bol', 'BolSC55t61228H' => 'bol', 'BraA01t03278Z' => 'bra', 'BraA05t18998Z' => 'bra', 'BraA07t28673Z' => 'bra', 'C01p40150' => 'bna', 'C05p12370' => 'bna', 'C07p13680' => 'bna', 'CAN.G1006.16' => 'can', 'CAN.G1006.17' => 'can', 'CAN.G1170.2' => 'can', 'CAN.G962.7' => 'can', 'CANSAT25G2179' => 'cansat', 'CANSAT78G1573' => 'cansat', 'CARHR099510' => 'chi', 'CARHR143510' => 'chi', 'Carub.0003s2380' => 'cru', 'Carub.0004s3082' => 'cru', 'Ca_00614_v3' => 'car', 'Ca_07801_v3' => 'car', 'Ca_08567_v3' => 'car', 'Ca_09571_v3' => 'car', 'CBR_g19290' => 'cbr', 'Cc01_g19770' => 'ccan', 'Cc03_g03030' => 'ccan', 'CDE07G0968' => 'cde', 'CDE09G1441' => 'cde', 'Cfa006103' => 'cfa', 'Cfa015573' => 'cfa', 'Cfa016988' => 'cfa', 'Ciclev10006738m.g' => 'ccl', 'Ciclev10010920m.g' => 'ccl', 'Ciclev10018517m.g' => 'ccl', 'CiPaw.01G159200' => 'cil', 'CiPaw.02G091000' => 'cil', 'CiPaw.02G091100' => 'cil', 'CiPaw.08G103100' => 'cil', 'CiPaw.09G224900' => 'cil', 'ClCG06G005740' => 'cla', 'ClCG07G000090' => 'cla', 'ClCG07G000100' => 'cla', 'COL.COLO4_09143' => 'col', 'COL.COLO4_25124' => 'col', 'Cpa.g.sc16.34' => 'cpa', 'Cpa.g.sc3504.1' => 'cpa', 'Cpa.g.sc60.37' => 'cpa', 'CsaV3_6G018520' => 'csa', 'CsaV3_6G036860' => 'csa', 'CSS0001072' => 'camsi', 'CSS0020208' => 'camsi', 'CSS0021253' => 'camsi', 'CSS0022190' => 'camsi', 'CSS0036150' => 'camsi', 'CSS0040442' => 'camsi', 'CSS0042300' => 'camsi', 'CSS0045298' => 'camsi', 'DCAR_012449' => 'dca', 'DCAR_018405' => 'dca', 'DCAR_024573' => 'dca', 'DCAR_030591' => 'dca', 'Dinv16926' => 'din', 'Dinv32963' => 'din', 'Dinv38382' => 'din', 'Dinv38383' => 'din', 'Duzib133G0974' => 'dzi', 'Duzib138G1867' => 'dzi', 'Duzib211G0420' => 'dzi', 'Duzib212G0930' => 'dzi', 'ECA234G1645' => 'eca', 'ECA247G3467' => 'eca', 'ECA248G1703' => 'eca', 'EL10Ac3g06327' => 'bvu', 'EL10Ac7g17204' => 'bvu', 'Eucgr.A00855' => 'egr', 'Eucgr.A00858' => 'egr', 'Eucgr.H01520' => 'egr', 'Eucgr.H03604' => 'egr', 'Eucgr.L03465' => 'egr', 'Eucgr.L03466' => 'egr', 'FAN01G0988' => 'fan', 'FAN02G3892' => 'fan', 'FAN05G3381' => 'fan', 'FAN07G0967' => 'fan', 'FAN07G1493' => 'fan', 'FAN08G3125' => 'fan', 'FAN09G0402' => 'fan', 'FAN12G2594' => 'fan', 'FAN12G3879' => 'fan', 'FAN14G1546' => 'fan', 'FAN15G3626' => 'fan', 'FAN17G0588' => 'fan', 'FAN17G0609' => 'fan', 'FAN18G2817' => 'fan', 'FAN19G1305' => 'fan', 'FAN20G1787' => 'fan', 'FAN22G0073' => 'fan', 'FAN22G0352' => 'fan', 'FAN22G0368' => 'fan', 'FAN22G2273' => 'fan', 'FAN24G1998' => 'fan', 'FAN27G1317' => 'fan', 'FvH4_2g23980' => 'fve', 'FvH4_4g14380' => 'fve', 'FvH4_4g14390' => 'fve', 'FvH4_6g09250' => 'fve', 'Glyma.03G151100' => 'gma', 'Glyma.04G122550' => 'gma', 'Glyma.05G001600' => 'gma', 'Glyma.09G270766' => 'gma', 'Glyma.09G270832' => 'gma', 'Glyma.13G209800' => 'gma', 'Glyma.15G102800' => 'gma', 'Glyma.18G218900' => 'gma', 'Glyma.19G001500' => 'gma', 'Glyma.19G153600' => 'gma', 'Gohir.A02G028600' => 'ghi', 'Gohir.A08G045000' => 'ghi', 'Gohir.A11G120500' => 'ghi', 'Gohir.A12G006200' => 'ghi', 'Gohir.A12G006250' => 'ghi', 'Gohir.D02G036300' => 'ghi', 'Gohir.D08G054700' => 'ghi', 'Gohir.D11G125600' => 'ghi', 'Gohir.D12G005700' => 'ghi', 'Gorai.004G055200' => 'gra', 'Gorai.005G040400' => 'gra', 'Gorai.007G134500' => 'gra', 'Gorai.008G005500' => 'gra', 'GSVIVG01011094001' => 'vvi', 'GSVIVG01017879001' => 'vvi', 'GSVIVG01025988001' => 'vvi', 'GSVIVG01029847001' => 'vvi', 'HanXRQChr10g0282901' => 'han', 'HanXRQChr10g0310371' => 'han', 'HanXRQChr10g0315041' => 'han', 'HanXRQChr11g0327651' => 'han', 'HanXRQChr12g0359391' => 'han', 'Haze_00972' => 'cav', 'Haze_00973' => 'cav', 'Haze_00974' => 'cav', 'Haze_04747' => 'cav', 'Haze_04749' => 'cav', 'Haze_04750' => 'cav', 'Haze_21217' => 'cav', 'Hma1.2p1_1037F.1_g250680' => 'hma', 'Hma1.2p1_1644F.1_g295320' => 'hma', 'HPP92_011322' => 'vpl', 'HPP92_011323' => 'vpl', 'HPP92_011324' => 'vpl', 'HPP92_011325' => 'vpl', 'HPP92_011326' => 'vpl', 'Hund12205' => 'sun', 'Hund17957' => 'sun', 'Lalb_Chr06g0176771' => 'lal', 'Lalb_Chr18g0056021' => 'lal', 'Lalb_Chr18g0056031' => 'lal', 'Lalb_Chr18g0056041' => 'lal', 'Lalb_Chr20g0107751' => 'lal', 'Lalb_Chr20g0118371' => 'lal', 'Lj1g0010239' => 'lja', 'Lj1g0017101' => 'lja', 'Lj2A1178G40' => 'lonja', 'Lj2A54G84' => 'lonja', 'Lj2g0015248' => 'lja', 'Lj3A761T51' => 'lonja', 'Lj6g0018116' => 'lja', 'Lsat_1_v5_gn_4_136040' => 'lsa', 'Lsat_1_v5_gn_5_187461' => 'lsa', 'Lsat_1_v5_gn_5_77001' => 'lsa', 'Lsat_1_v5_gn_9_4461' => 'lsa', 'Manes.01G210100' => 'mes', 'Manes.03G185600' => 'mes', 'Manes.05G073300' => 'mes', 'Manes.09G120300' => 'mes', 'Manes.15G022100' => 'mes', 'Mapoly0096s0053' => 'mpo', 'MBI03_g14058_MAGBIO' => 'mbi', 'MBI03_g33876_MAGBIO' => 'mbi', 'MBI03_g36854_MAGBIO' => 'mbi', 'MBI17_g11997_MAGBIO' => 'mbi', 'MD03G1269000' => 'mdo', 'MD04G1179600' => 'mdo', 'MD11G1289800' => 'mdo', 'MD12G1194700' => 'mdo', 'MD13G1182100' => 'mdo', 'MD13G1182200' => 'mdo', 'MD16G1182600' => 'mdo', 'Medtr2g021400' => 'mtr', 'Medtr2g021470' => 'mtr', 'Medtr2g105810' => 'mtr', 'Medtr3g033580' => 'mtr', 'Medtr6g007970' => 'mtr', 'Medtr7g056330' => 'mtr', 'Medtr7g074290' => 'mtr', 'Medtr7g074380' => 'mtr', 'Medtr7g094550' => 'mtr', 'Medtr8g069995' => 'mtr', 'MELO3C014345.2' => 'cme', 'MELO3C021395.2' => 'cme', 'Migut.D00262' => 'egut', 'Migut.G00257' => 'egut', 'MSTRG.21575' => 'ama', 'MSTRG.3985' => 'ama', 'Nitab4.5_0000295g0140' => 'nta', 'Nitab4.5_0000732g0140' => 'nta', 'Nitab4.5_0003162g0020' => 'nta', 'Nitab4.5_0006180g0090' => 'nta', 'Nitab4.5_0006390g0010' => 'nta', 'Nitab4.5_0007392g0040' => 'nta', 'Nn1g02140' => 'nnu', 'Nn4g26168' => 'nnu', 'Nn5g26754' => 'nnu', 'Oeu001433.1' => 'oeu', 'Oeu010299.2' => 'oeu', 'Oeu011171.1' => 'oeu', 'Oeu037675.1' => 'oeu', 'Oeu038359.1' => 'oeu', 'Oeu063834.1' => 'oeu', 'Oeu063835.1' => 'oeu', 'Os05g0312000' => 'osa', 'Os07g0211101' => 'osa', 'Os07g0211200' => 'osa', 'Os07g0681500' => 'osa', 'Peaxi162Scf00095g01015' => 'pax', 'Peaxi162Scf00104g00329' => 'pax', 'Peaxi162Scf00161g00137' => 'pax', 'PGR004G1665' => 'pgr', 'PGR031G2937' => 'pgr', 'PGR119G2145' => 'pgr', 'PGSC0003DMG400004351' => 'stu', 'PGSC0003DMG400014625' => 'stu', 'PGSC0003DMG401000943' => 'stu', 'Phvul.001G148600' => 'pvu', 'Phvul.004G001700' => 'pvu', 'Phvul.006G154900' => 'pvu', 'Phvul.008G078200' => 'pvu', 'Phvul.011G136500' => 'pvu', 'Potri.002G215600' => 'ptr', 'Potri.008G201600' => 'ptr', 'Potri.014G138400' => 'ptr', 'Potri.016G142500' => 'ptr', 'Pp3c16_10580' => 'ppa', 'Pp3c5_25280' => 'ppa', 'Prupe.1G150000' => 'ppe', 'Prupe.1G150100' => 'ppe', 'Prupe.6G299600' => 'ppe', 'Prupe.8G245000' => 'ppe', 'Psat0s4927g0040' => 'psa', 'Psat1g052080' => 'psa', 'Psat1g183800' => 'psa', 'Psat3g113840' => 'psa', 'Psat3g126120' => 'psa', 'Psat3g126160' => 'psa', 'Psat3g158760' => 'psa', 'Psat3g158840' => 'psa', 'PSO170G2858' => 'pso', 'PSO339G0606' => 'pso', 'PSO384G4709' => 'pso', 'PSO407G0334' => 'pso', 'QL04p040276' => 'qlo', 'QL06p005458' => 'qlo', 'QL06p005472' => 'qlo', 'QL07p030546' => 'qlo', 'QL07p031519' => 'qlo', 'QL09p050949' => 'qlo', 'QL09p050966' => 'qlo', 'QL09p051067' => 'qlo', 'QL12p022706' => 'qlo', 'RcHm_v2.0_Chr2g0119601' => 'rch', 'RcHm_v2.0_Chr3g0459591' => 'rch', 'RcHm_v2.0_Chr4g0418521' => 'rch', 'RcHm_v2.0_Chr4g0418531' => 'rch', 'RcHm_v2.0_Chr4g0418541' => 'rch', 'RcHm_v2.0_Chr6g0291641' => 'rch', 'Rhsim01G0086300' => 'rsi', 'Rhsim01G0276300' => 'rsi', 'Rhsim01G0276500' => 'rsi', 'Rhsim04G0207700' => 'rsi', 'Rhsim05G0234500' => 'rsi', 'Rhsim13G0022400' => 'rsi', 'Sabra02G0167900' => 'sbr', 'Sabra04G0158500' => 'sbr', 'Sabra08G0159800' => 'sbr', 'Sabra10G0011500' => 'sbr', 'Sabra14G0104400' => 'sbr', 'SalBow2G2440' => 'sbo', 'SalBow4G2265' => 'sbo', 'Sc02g0000060' => 'sci', 'Sc05g0005020' => 'sci', 'Sc13g0003890' => 'sci', 'Sed0014865' => 'sed', 'Sed0017224' => 'sed', 'Sed0026391' => 'sed', 'SEGI_00063' => 'sgi', 'SEGI_10967' => 'sgi', 'SEGI_17510' => 'sgi', 'SEGI_24396' => 'sgi', 'SEGI_39719' => 'sgi', 'SEGI_41392' => 'sgi', 'SGA_v2.0_scaffold11G05794' => 'sas', 'SGA_v2.0_scaffold142G35607' => 'sas', 'SGA_v2.0_scaffold1G00447' => 'sas', 'SHI15388' => 'shi', 'SHI15394' => 'shi', 'SHI15396' => 'shi', 'SHI15399' => 'shi', 'SMO343G0151' => 'smo', 'SMO367G1118' => 'smo', 'Solyc01g080200.3' => 'sly', 'Solyc06g008960.3' => 'sly', 'Solyc09g064780.3' => 'sly', 'Sopen01g031980' => 'spe', 'Sopen06g003710' => 'spe', 'Sopen09g026460' => 'spe', 'Sp3g21240' => 'spa', 'Sp4g30030' => 'spa', 'TAR365G0022' => 'tar', 'TAR365G1023' => 'tar', 'TAR365G1253' => 'tar', 'TAR623G0078' => 'tar', 'TAR623G1721' => 'tar', 'TAR633G0959' => 'tar', 'THA.LOC104802225' => 'tha', 'THA.LOC104804769' => 'tha', 'THA.LOC104808660' => 'tha', 'THA.LOC104812792' => 'tha', 'Thecc.01G284000' => 'tca', 'Thecc.04G220600' => 'tca', 'Thecc.05G268900' => 'tca', 'Thecc.08G171100' => 'tca', 'Thhalv10001284m.g' => 'esa', 'Thhalv10019912m.g' => 'esa', 'TPR.G14189' => 'tpr', 'TPR.G18110' => 'tpr', 'TPR.G18130' => 'tpr', 'TPR.G18131' => 'tpr', 'TPR.G18140' => 'tpr', 'TPR.G24282' => 'tpr', 'TPR.G25221' => 'tpr', 'TPR.G29267' => 'tpr', 'TPR.G35315' => 'tpr', 'TPR.G36173' => 'tpr', 'TWI09G0794' => 'twi', 'TWI59G1348' => 'twi', 'TWI74G0430' => 'twi', 'unitig_26.g8940' => 'ugi', 'unitig_749.g13744' => 'ugi', 'unitig_749.g13745' => 'ugi', 'vmacro08269' => 'vma', 'vmacro14937' => 'vma', 'vmacro20401' => 'vma', 'VMungo0464G1349' => 'vmu', 'VMungo0540G0289' => 'vmu', 'VMungo1215G1590' => 'vmu', 'VMungo1309G0221' => 'vmu', 'VMungo1309G2815' => 'vmu', 'VMungo1383G0239' => 'vmu', 'VMungo1383G2910' => 'vmu', 'Zm00001eb095270' => 'zma', 'Zm00001eb095280' => 'zma', 'Zm00001eb111630' => 'zma', 'Zm00001eb237080' => 'zma', 'Zm00001eb273740' => 'zma', 'Zm00001eb285040' => 'zma', 'Zm00001eb330790' => 'zma', 'Zm00001eb337380' => 'zma' ), 'gf_id' => 'HOM05D001484', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001484' ), 'data_identifier' => 'HOM05D001484', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001484', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p31500' => 'bna', 'A05p00020' => 'bna', 'A07p08820' => 'bna', 'Aa31LG4G3300' => 'aar', 'Aa31LG8G10030' => 'aar', 'Actinidia00731' => 'ach', 'Actinidia11473' => 'ach', 'Actinidia23469' => 'ach', 'Actinidia24318' => 'ach', 'Actinidia40196' => 'ach', 'Actinidia40197' => 'ach', 'Actinidia40198' => 'ach', 'Ah.08g212990' => 'amhyb', 'Ah.15g091720' => 'amhyb', 'AL3G38260' => 'aly', 'AL4G47710' => 'aly', 'Aqoxy2G00671' => 'aox', 'Aqoxy2G03236' => 'aox', 'arahy.Tifrunner.gnm1.ann1.05IDCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KR684' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATY3SJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK6QJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6APGL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IDT7Z9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM073U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ0R87' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LE7RV4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT4QRX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V5ENPK' => 'arhy', 'AT2G48110' => 'ath', 'AT3G23590' => 'ath', 'ATR0626G186' => 'atr', 'ATR1127G141' => 'atr', 'Atru.chr4.2583' => 'acertr', 'Atru.chr5.1358' => 'acertr', 'Atru.chr5.1359' => 'acertr', 'Atru.chr8.46' => 'acertr', 'AUR62002640' => 'cqu', 'AUR62030055' => 'cqu', 'AUR62033713' => 'cqu', 'AUR62033714' => 'cqu', 'AUR62036795' => 'cqu', 'AUR62039891' => 'cqu', 'BcaB02g08737' => 'bca', 'BcaB04g20441' => 'bca', 'BcaB06g26509' => 'bca', 'BcaB06g26510' => 'bca', 'BcaB06g26511' => 'bca', 'BcaB06g26512' => 'bca', 'BcaB06g26513' => 'bca', 'BcaC02g12564' => 'bca', 'BcaC02g12565' => 'bca', 'BcaC02g12794' => 'bca', 'BcaC02g12795' => 'bca', 'BcaC02g12796' => 'bca', 'BcaC06g35541' => 'bca', 'BNapus_Darmor_BZH_scaffold_188p00080' => 'bna', 'BNapus_Darmor_BZH_scaffold_188p00090' => 'bna', 'BolC1t03972H' => 'bol', 'BolC1t03973H' => 'bol', 'BolC4t21680H' => 'bol', 'BolC7t41863H' => 'bol', 'BolSC55t61227H' => 'bol', 'BolSC55t61228H' => 'bol', 'BraA01t03278Z' => 'bra', 'BraA05t18998Z' => 'bra', 'BraA07t28673Z' => 'bra', 'C01p40150' => 'bna', 'C05p12370' => 'bna', 'C07p13680' => 'bna', 'CAN.G1006.16' => 'can', 'CAN.G1006.17' => 'can', 'CAN.G1170.2' => 'can', 'CAN.G962.7' => 'can', 'CANSAT25G2179' => 'cansat', 'CANSAT78G1573' => 'cansat', 'CARHR099510' => 'chi', 'CARHR143510' => 'chi', 'Carub.0003s2380' => 'cru', 'Carub.0004s3082' => 'cru', 'Ca_00614_v3' => 'car', 'Ca_07801_v3' => 'car', 'Ca_08567_v3' => 'car', 'Ca_09571_v3' => 'car', 'CBR_g19290' => 'cbr', 'Cc01_g19770' => 'ccan', 'Cc03_g03030' => 'ccan', 'CDE07G0968' => 'cde', 'CDE09G1441' => 'cde', 'Cfa006103' => 'cfa', 'Cfa015573' => 'cfa', 'Cfa016988' => 'cfa', 'Ciclev10006738m.g' => 'ccl', 'Ciclev10010920m.g' => 'ccl', 'Ciclev10018517m.g' => 'ccl', 'CiPaw.01G159200' => 'cil', 'CiPaw.02G091000' => 'cil', 'CiPaw.02G091100' => 'cil', 'CiPaw.08G103100' => 'cil', 'CiPaw.09G224900' => 'cil', 'ClCG06G005740' => 'cla', 'ClCG07G000090' => 'cla', 'ClCG07G000100' => 'cla', 'COL.COLO4_09143' => 'col', 'COL.COLO4_25124' => 'col', 'Cpa.g.sc16.34' => 'cpa', 'Cpa.g.sc3504.1' => 'cpa', 'Cpa.g.sc60.37' => 'cpa', 'CsaV3_6G018520' => 'csa', 'CsaV3_6G036860' => 'csa', 'CSS0001072' => 'camsi', 'CSS0020208' => 'camsi', 'CSS0021253' => 'camsi', 'CSS0022190' => 'camsi', 'CSS0036150' => 'camsi', 'CSS0040442' => 'camsi', 'CSS0042300' => 'camsi', 'CSS0045298' => 'camsi', 'DCAR_012449' => 'dca', 'DCAR_018405' => 'dca', 'DCAR_024573' => 'dca', 'DCAR_030591' => 'dca', 'Dinv16926' => 'din', 'Dinv32963' => 'din', 'Dinv38382' => 'din', 'Dinv38383' => 'din', 'Duzib133G0974' => 'dzi', 'Duzib138G1867' => 'dzi', 'Duzib211G0420' => 'dzi', 'Duzib212G0930' => 'dzi', 'ECA234G1645' => 'eca', 'ECA247G3467' => 'eca', 'ECA248G1703' => 'eca', 'EL10Ac3g06327' => 'bvu', 'EL10Ac7g17204' => 'bvu', 'Eucgr.A00855' => 'egr', 'Eucgr.A00858' => 'egr', 'Eucgr.H01520' => 'egr', 'Eucgr.H03604' => 'egr', 'Eucgr.L03465' => 'egr', 'Eucgr.L03466' => 'egr', 'FAN01G0988' => 'fan', 'FAN02G3892' => 'fan', 'FAN05G3381' => 'fan', 'FAN07G0967' => 'fan', 'FAN07G1493' => 'fan', 'FAN08G3125' => 'fan', 'FAN09G0402' => 'fan', 'FAN12G2594' => 'fan', 'FAN12G3879' => 'fan', 'FAN14G1546' => 'fan', 'FAN15G3626' => 'fan', 'FAN17G0588' => 'fan', 'FAN17G0609' => 'fan', 'FAN18G2817' => 'fan', 'FAN19G1305' => 'fan', 'FAN20G1787' => 'fan', 'FAN22G0073' => 'fan', 'FAN22G0352' => 'fan', 'FAN22G0368' => 'fan', 'FAN22G2273' => 'fan', 'FAN24G1998' => 'fan', 'FAN27G1317' => 'fan', 'FvH4_2g23980' => 'fve', 'FvH4_4g14380' => 'fve', 'FvH4_4g14390' => 'fve', 'FvH4_6g09250' => 'fve', 'Glyma.03G151100' => 'gma', 'Glyma.04G122550' => 'gma', 'Glyma.05G001600' => 'gma', 'Glyma.09G270766' => 'gma', 'Glyma.09G270832' => 'gma', 'Glyma.13G209800' => 'gma', 'Glyma.15G102800' => 'gma', 'Glyma.18G218900' => 'gma', 'Glyma.19G001500' => 'gma', 'Glyma.19G153600' => 'gma', 'Gohir.A02G028600' => 'ghi', 'Gohir.A08G045000' => 'ghi', 'Gohir.A11G120500' => 'ghi', 'Gohir.A12G006200' => 'ghi', 'Gohir.A12G006250' => 'ghi', 'Gohir.D02G036300' => 'ghi', 'Gohir.D08G054700' => 'ghi', 'Gohir.D11G125600' => 'ghi', 'Gohir.D12G005700' => 'ghi', 'Gorai.004G055200' => 'gra', 'Gorai.005G040400' => 'gra', 'Gorai.007G134500' => 'gra', 'Gorai.008G005500' => 'gra', 'GSVIVG01011094001' => 'vvi', 'GSVIVG01017879001' => 'vvi', 'GSVIVG01025988001' => 'vvi', 'GSVIVG01029847001' => 'vvi', 'HanXRQChr10g0282901' => 'han', 'HanXRQChr10g0310371' => 'han', 'HanXRQChr10g0315041' => 'han', 'HanXRQChr11g0327651' => 'han', 'HanXRQChr12g0359391' => 'han', 'Haze_00972' => 'cav', 'Haze_00973' => 'cav', 'Haze_00974' => 'cav', 'Haze_04747' => 'cav', 'Haze_04749' => 'cav', 'Haze_04750' => 'cav', 'Haze_21217' => 'cav', 'Hma1.2p1_1037F.1_g250680' => 'hma', 'Hma1.2p1_1644F.1_g295320' => 'hma', 'HPP92_011322' => 'vpl', 'HPP92_011323' => 'vpl', 'HPP92_011324' => 'vpl', 'HPP92_011325' => 'vpl', 'HPP92_011326' => 'vpl', 'Hund12205' => 'sun', 'Hund17957' => 'sun', 'Lalb_Chr06g0176771' => 'lal', 'Lalb_Chr18g0056021' => 'lal', 'Lalb_Chr18g0056031' => 'lal', 'Lalb_Chr18g0056041' => 'lal', 'Lalb_Chr20g0107751' => 'lal', 'Lalb_Chr20g0118371' => 'lal', 'Lj1g0010239' => 'lja', 'Lj1g0017101' => 'lja', 'Lj2A1178G40' => 'lonja', 'Lj2A54G84' => 'lonja', 'Lj2g0015248' => 'lja', 'Lj3A761T51' => 'lonja', 'Lj6g0018116' => 'lja', 'Lsat_1_v5_gn_4_136040' => 'lsa', 'Lsat_1_v5_gn_5_187461' => 'lsa', 'Lsat_1_v5_gn_5_77001' => 'lsa', 'Lsat_1_v5_gn_9_4461' => 'lsa', 'Manes.01G210100' => 'mes', 'Manes.03G185600' => 'mes', 'Manes.05G073300' => 'mes', 'Manes.09G120300' => 'mes', 'Manes.15G022100' => 'mes', 'Mapoly0096s0053' => 'mpo', 'MBI03_g14058_MAGBIO' => 'mbi', 'MBI03_g33876_MAGBIO' => 'mbi', 'MBI03_g36854_MAGBIO' => 'mbi', 'MBI17_g11997_MAGBIO' => 'mbi', 'MD03G1269000' => 'mdo', 'MD04G1179600' => 'mdo', 'MD11G1289800' => 'mdo', 'MD12G1194700' => 'mdo', 'MD13G1182100' => 'mdo', 'MD13G1182200' => 'mdo', 'MD16G1182600' => 'mdo', 'Medtr2g021400' => 'mtr', 'Medtr2g021470' => 'mtr', 'Medtr2g105810' => 'mtr', 'Medtr3g033580' => 'mtr', 'Medtr6g007970' => 'mtr', 'Medtr7g056330' => 'mtr', 'Medtr7g074290' => 'mtr', 'Medtr7g074380' => 'mtr', 'Medtr7g094550' => 'mtr', 'Medtr8g069995' => 'mtr', 'MELO3C014345.2' => 'cme', 'MELO3C021395.2' => 'cme', 'Migut.D00262' => 'egut', 'Migut.G00257' => 'egut', 'MSTRG.21575' => 'ama', 'MSTRG.3985' => 'ama', 'Nitab4.5_0000295g0140' => 'nta', 'Nitab4.5_0000732g0140' => 'nta', 'Nitab4.5_0003162g0020' => 'nta', 'Nitab4.5_0006180g0090' => 'nta', 'Nitab4.5_0006390g0010' => 'nta', 'Nitab4.5_0007392g0040' => 'nta', 'Nn1g02140' => 'nnu', 'Nn4g26168' => 'nnu', 'Nn5g26754' => 'nnu', 'Oeu001433.1' => 'oeu', 'Oeu010299.2' => 'oeu', 'Oeu011171.1' => 'oeu', 'Oeu037675.1' => 'oeu', 'Oeu038359.1' => 'oeu', 'Oeu063834.1' => 'oeu', 'Oeu063835.1' => 'oeu', 'Os05g0312000' => 'osa', 'Os07g0211101' => 'osa', 'Os07g0211200' => 'osa', 'Os07g0681500' => 'osa', 'Peaxi162Scf00095g01015' => 'pax', 'Peaxi162Scf00104g00329' => 'pax', 'Peaxi162Scf00161g00137' => 'pax', 'PGR004G1665' => 'pgr', 'PGR031G2937' => 'pgr', 'PGR119G2145' => 'pgr', 'PGSC0003DMG400004351' => 'stu', 'PGSC0003DMG400014625' => 'stu', 'PGSC0003DMG401000943' => 'stu', 'Phvul.001G148600' => 'pvu', 'Phvul.004G001700' => 'pvu', 'Phvul.006G154900' => 'pvu', 'Phvul.008G078200' => 'pvu', 'Phvul.011G136500' => 'pvu', 'Potri.002G215600' => 'ptr', 'Potri.008G201600' => 'ptr', 'Potri.014G138400' => 'ptr', 'Potri.016G142500' => 'ptr', 'Pp3c16_10580' => 'ppa', 'Pp3c5_25280' => 'ppa', 'Prupe.1G150000' => 'ppe', 'Prupe.1G150100' => 'ppe', 'Prupe.6G299600' => 'ppe', 'Prupe.8G245000' => 'ppe', 'Psat0s4927g0040' => 'psa', 'Psat1g052080' => 'psa', 'Psat1g183800' => 'psa', 'Psat3g113840' => 'psa', 'Psat3g126120' => 'psa', 'Psat3g126160' => 'psa', 'Psat3g158760' => 'psa', 'Psat3g158840' => 'psa', 'PSO170G2858' => 'pso', 'PSO339G0606' => 'pso', 'PSO384G4709' => 'pso', 'PSO407G0334' => 'pso', 'QL04p040276' => 'qlo', 'QL06p005458' => 'qlo', 'QL06p005472' => 'qlo', 'QL07p030546' => 'qlo', 'QL07p031519' => 'qlo', 'QL09p050949' => 'qlo', 'QL09p050966' => 'qlo', 'QL09p051067' => 'qlo', 'QL12p022706' => 'qlo', 'RcHm_v2.0_Chr2g0119601' => 'rch', 'RcHm_v2.0_Chr3g0459591' => 'rch', 'RcHm_v2.0_Chr4g0418521' => 'rch', 'RcHm_v2.0_Chr4g0418531' => 'rch', 'RcHm_v2.0_Chr4g0418541' => 'rch', 'RcHm_v2.0_Chr6g0291641' => 'rch', 'Rhsim01G0086300' => 'rsi', 'Rhsim01G0276300' => 'rsi', 'Rhsim01G0276500' => 'rsi', 'Rhsim04G0207700' => 'rsi', 'Rhsim05G0234500' => 'rsi', 'Rhsim13G0022400' => 'rsi', 'Sabra02G0167900' => 'sbr', 'Sabra04G0158500' => 'sbr', 'Sabra08G0159800' => 'sbr', 'Sabra10G0011500' => 'sbr', 'Sabra14G0104400' => 'sbr', 'SalBow2G2440' => 'sbo', 'SalBow4G2265' => 'sbo', 'Sc02g0000060' => 'sci', 'Sc05g0005020' => 'sci', 'Sc13g0003890' => 'sci', 'Sed0014865' => 'sed', 'Sed0017224' => 'sed', 'Sed0026391' => 'sed', 'SEGI_00063' => 'sgi', 'SEGI_10967' => 'sgi', 'SEGI_17510' => 'sgi', 'SEGI_24396' => 'sgi', 'SEGI_39719' => 'sgi', 'SEGI_41392' => 'sgi', 'SGA_v2.0_scaffold11G05794' => 'sas', 'SGA_v2.0_scaffold142G35607' => 'sas', 'SGA_v2.0_scaffold1G00447' => 'sas', 'SHI15388' => 'shi', 'SHI15394' => 'shi', 'SHI15396' => 'shi', 'SHI15399' => 'shi', 'SMO343G0151' => 'smo', 'SMO367G1118' => 'smo', 'Solyc01g080200.3' => 'sly', 'Solyc06g008960.3' => 'sly', 'Solyc09g064780.3' => 'sly', 'Sopen01g031980' => 'spe', 'Sopen06g003710' => 'spe', 'Sopen09g026460' => 'spe', 'Sp3g21240' => 'spa', 'Sp4g30030' => 'spa', 'TAR365G0022' => 'tar', 'TAR365G1023' => 'tar', 'TAR365G1253' => 'tar', 'TAR623G0078' => 'tar', 'TAR623G1721' => 'tar', 'TAR633G0959' => 'tar', 'THA.LOC104802225' => 'tha', 'THA.LOC104804769' => 'tha', 'THA.LOC104808660' => 'tha', 'THA.LOC104812792' => 'tha', 'Thecc.01G284000' => 'tca', 'Thecc.04G220600' => 'tca', 'Thecc.05G268900' => 'tca', 'Thecc.08G171100' => 'tca', 'Thhalv10001284m.g' => 'esa', 'Thhalv10019912m.g' => 'esa', 'TPR.G14189' => 'tpr', 'TPR.G18110' => 'tpr', 'TPR.G18130' => 'tpr', 'TPR.G18131' => 'tpr', 'TPR.G18140' => 'tpr', 'TPR.G24282' => 'tpr', 'TPR.G25221' => 'tpr', 'TPR.G29267' => 'tpr', 'TPR.G35315' => 'tpr', 'TPR.G36173' => 'tpr', 'TWI09G0794' => 'twi', 'TWI59G1348' => 'twi', 'TWI74G0430' => 'twi', 'unitig_26.g8940' => 'ugi', 'unitig_749.g13744' => 'ugi', 'unitig_749.g13745' => 'ugi', 'vmacro08269' => 'vma', 'vmacro14937' => 'vma', 'vmacro20401' => 'vma', 'VMungo0464G1349' => 'vmu', 'VMungo0540G0289' => 'vmu', 'VMungo1215G1590' => 'vmu', 'VMungo1309G0221' => 'vmu', 'VMungo1309G2815' => 'vmu', 'VMungo1383G0239' => 'vmu', 'VMungo1383G2910' => 'vmu', 'Zm00001eb095270' => 'zma', 'Zm00001eb095280' => 'zma', 'Zm00001eb111630' => 'zma', 'Zm00001eb237080' => 'zma', 'Zm00001eb273740' => 'zma', 'Zm00001eb285040' => 'zma', 'Zm00001eb330790' => 'zma', 'Zm00001eb337380' => 'zma' ) $gf_id = 'HOM05D001484' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001484' ) $data_identifier = 'HOM05D001484' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 2, 'aly' => (int) 2, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 22, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 7, 'hma' => (int) 2, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 7, 'mtr' => (int) 10, 'cme' => (int) 2, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 4, 'ppa' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 4, 'qlo' => (int) 9, 'rch' => (int) 6, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 10, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 7, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb337380' $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' => 'HOM05D001484', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p31500' => 'bna', 'A05p00020' => 'bna', 'A07p08820' => 'bna', 'Aa31LG4G3300' => 'aar', 'Aa31LG8G10030' => 'aar', 'Actinidia00731' => 'ach', 'Actinidia11473' => 'ach', 'Actinidia23469' => 'ach', 'Actinidia24318' => 'ach', 'Actinidia40196' => 'ach', 'Actinidia40197' => 'ach', 'Actinidia40198' => 'ach', 'Ah.08g212990' => 'amhyb', 'Ah.15g091720' => 'amhyb', 'AL3G38260' => 'aly', 'AL4G47710' => 'aly', 'Aqoxy2G00671' => 'aox', 'Aqoxy2G03236' => 'aox', 'arahy.Tifrunner.gnm1.ann1.05IDCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KR684' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATY3SJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK6QJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6APGL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IDT7Z9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM073U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ0R87' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LE7RV4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT4QRX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V5ENPK' => 'arhy', 'AT2G48110' => 'ath', 'AT3G23590' => 'ath', 'ATR0626G186' => 'atr', 'ATR1127G141' => 'atr', 'Atru.chr4.2583' => 'acertr', 'Atru.chr5.1358' => 'acertr', 'Atru.chr5.1359' => 'acertr', 'Atru.chr8.46' => 'acertr', 'AUR62002640' => 'cqu', 'AUR62030055' => 'cqu', 'AUR62033713' => 'cqu', 'AUR62033714' => 'cqu', 'AUR62036795' => 'cqu', 'AUR62039891' => 'cqu', 'BcaB02g08737' => 'bca', 'BcaB04g20441' => 'bca', 'BcaB06g26509' => 'bca', 'BcaB06g26510' => 'bca', 'BcaB06g26511' => 'bca', 'BcaB06g26512' => 'bca', 'BcaB06g26513' => 'bca', 'BcaC02g12564' => 'bca', 'BcaC02g12565' => 'bca', 'BcaC02g12794' => 'bca', 'BcaC02g12795' => 'bca', 'BcaC02g12796' => 'bca', 'BcaC06g35541' => 'bca', 'BNapus_Darmor_BZH_scaffold_188p00080' => 'bna', 'BNapus_Darmor_BZH_scaffold_188p00090' => 'bna', 'BolC1t03972H' => 'bol', 'BolC1t03973H' => 'bol', 'BolC4t21680H' => 'bol', 'BolC7t41863H' => 'bol', 'BolSC55t61227H' => 'bol', 'BolSC55t61228H' => 'bol', 'BraA01t03278Z' => 'bra', 'BraA05t18998Z' => 'bra', 'BraA07t28673Z' => 'bra', 'C01p40150' => 'bna', 'C05p12370' => 'bna', 'C07p13680' => 'bna', 'CAN.G1006.16' => 'can', 'CAN.G1006.17' => 'can', 'CAN.G1170.2' => 'can', 'CAN.G962.7' => 'can', 'CANSAT25G2179' => 'cansat', 'CANSAT78G1573' => 'cansat', 'CARHR099510' => 'chi', 'CARHR143510' => 'chi', 'Carub.0003s2380' => 'cru', 'Carub.0004s3082' => 'cru', 'Ca_00614_v3' => 'car', 'Ca_07801_v3' => 'car', 'Ca_08567_v3' => 'car', 'Ca_09571_v3' => 'car', 'CBR_g19290' => 'cbr', 'Cc01_g19770' => 'ccan', 'Cc03_g03030' => 'ccan', 'CDE07G0968' => 'cde', 'CDE09G1441' => 'cde', 'Cfa006103' => 'cfa', 'Cfa015573' => 'cfa', 'Cfa016988' => 'cfa', 'Ciclev10006738m.g' => 'ccl', 'Ciclev10010920m.g' => 'ccl', 'Ciclev10018517m.g' => 'ccl', 'CiPaw.01G159200' => 'cil', 'CiPaw.02G091000' => 'cil', 'CiPaw.02G091100' => 'cil', 'CiPaw.08G103100' => 'cil', 'CiPaw.09G224900' => 'cil', 'ClCG06G005740' => 'cla', 'ClCG07G000090' => 'cla', 'ClCG07G000100' => 'cla', 'COL.COLO4_09143' => 'col', 'COL.COLO4_25124' => 'col', 'Cpa.g.sc16.34' => 'cpa', 'Cpa.g.sc3504.1' => 'cpa', 'Cpa.g.sc60.37' => 'cpa', 'CsaV3_6G018520' => 'csa', 'CsaV3_6G036860' => 'csa', 'CSS0001072' => 'camsi', 'CSS0020208' => 'camsi', 'CSS0021253' => 'camsi', 'CSS0022190' => 'camsi', 'CSS0036150' => 'camsi', 'CSS0040442' => 'camsi', 'CSS0042300' => 'camsi', 'CSS0045298' => 'camsi', 'DCAR_012449' => 'dca', 'DCAR_018405' => 'dca', 'DCAR_024573' => 'dca', 'DCAR_030591' => 'dca', 'Dinv16926' => 'din', 'Dinv32963' => 'din', 'Dinv38382' => 'din', 'Dinv38383' => 'din', 'Duzib133G0974' => 'dzi', 'Duzib138G1867' => 'dzi', 'Duzib211G0420' => 'dzi', 'Duzib212G0930' => 'dzi', 'ECA234G1645' => 'eca', 'ECA247G3467' => 'eca', 'ECA248G1703' => 'eca', 'EL10Ac3g06327' => 'bvu', 'EL10Ac7g17204' => 'bvu', 'Eucgr.A00855' => 'egr', 'Eucgr.A00858' => 'egr', 'Eucgr.H01520' => 'egr', 'Eucgr.H03604' => 'egr', 'Eucgr.L03465' => 'egr', 'Eucgr.L03466' => 'egr', 'FAN01G0988' => 'fan', 'FAN02G3892' => 'fan', 'FAN05G3381' => 'fan', 'FAN07G0967' => 'fan', 'FAN07G1493' => 'fan', 'FAN08G3125' => 'fan', 'FAN09G0402' => 'fan', 'FAN12G2594' => 'fan', 'FAN12G3879' => 'fan', 'FAN14G1546' => 'fan', 'FAN15G3626' => 'fan', 'FAN17G0588' => 'fan', 'FAN17G0609' => 'fan', 'FAN18G2817' => 'fan', 'FAN19G1305' => 'fan', 'FAN20G1787' => 'fan', 'FAN22G0073' => 'fan', 'FAN22G0352' => 'fan', 'FAN22G0368' => 'fan', 'FAN22G2273' => 'fan', 'FAN24G1998' => 'fan', 'FAN27G1317' => 'fan', 'FvH4_2g23980' => 'fve', 'FvH4_4g14380' => 'fve', 'FvH4_4g14390' => 'fve', 'FvH4_6g09250' => 'fve', 'Glyma.03G151100' => 'gma', 'Glyma.04G122550' => 'gma', 'Glyma.05G001600' => 'gma', 'Glyma.09G270766' => 'gma', 'Glyma.09G270832' => 'gma', 'Glyma.13G209800' => 'gma', 'Glyma.15G102800' => 'gma', 'Glyma.18G218900' => 'gma', 'Glyma.19G001500' => 'gma', 'Glyma.19G153600' => 'gma', 'Gohir.A02G028600' => 'ghi', 'Gohir.A08G045000' => 'ghi', 'Gohir.A11G120500' => 'ghi', 'Gohir.A12G006200' => 'ghi', 'Gohir.A12G006250' => 'ghi', 'Gohir.D02G036300' => 'ghi', 'Gohir.D08G054700' => 'ghi', 'Gohir.D11G125600' => 'ghi', 'Gohir.D12G005700' => 'ghi', 'Gorai.004G055200' => 'gra', 'Gorai.005G040400' => 'gra', 'Gorai.007G134500' => 'gra', 'Gorai.008G005500' => 'gra', 'GSVIVG01011094001' => 'vvi', 'GSVIVG01017879001' => 'vvi', 'GSVIVG01025988001' => 'vvi', 'GSVIVG01029847001' => 'vvi', 'HanXRQChr10g0282901' => 'han', 'HanXRQChr10g0310371' => 'han', 'HanXRQChr10g0315041' => 'han', 'HanXRQChr11g0327651' => 'han', 'HanXRQChr12g0359391' => 'han', 'Haze_00972' => 'cav', 'Haze_00973' => 'cav', 'Haze_00974' => 'cav', 'Haze_04747' => 'cav', 'Haze_04749' => 'cav', 'Haze_04750' => 'cav', 'Haze_21217' => 'cav', 'Hma1.2p1_1037F.1_g250680' => 'hma', 'Hma1.2p1_1644F.1_g295320' => 'hma', 'HPP92_011322' => 'vpl', 'HPP92_011323' => 'vpl', 'HPP92_011324' => 'vpl', 'HPP92_011325' => 'vpl', 'HPP92_011326' => 'vpl', 'Hund12205' => 'sun', 'Hund17957' => 'sun', 'Lalb_Chr06g0176771' => 'lal', 'Lalb_Chr18g0056021' => 'lal', 'Lalb_Chr18g0056031' => 'lal', 'Lalb_Chr18g0056041' => 'lal', 'Lalb_Chr20g0107751' => 'lal', 'Lalb_Chr20g0118371' => 'lal', 'Lj1g0010239' => 'lja', 'Lj1g0017101' => 'lja', 'Lj2A1178G40' => 'lonja', 'Lj2A54G84' => 'lonja', 'Lj2g0015248' => 'lja', 'Lj3A761T51' => 'lonja', 'Lj6g0018116' => 'lja', 'Lsat_1_v5_gn_4_136040' => 'lsa', 'Lsat_1_v5_gn_5_187461' => 'lsa', 'Lsat_1_v5_gn_5_77001' => 'lsa', 'Lsat_1_v5_gn_9_4461' => 'lsa', 'Manes.01G210100' => 'mes', 'Manes.03G185600' => 'mes', 'Manes.05G073300' => 'mes', 'Manes.09G120300' => 'mes', 'Manes.15G022100' => 'mes', 'Mapoly0096s0053' => 'mpo', 'MBI03_g14058_MAGBIO' => 'mbi', 'MBI03_g33876_MAGBIO' => 'mbi', 'MBI03_g36854_MAGBIO' => 'mbi', 'MBI17_g11997_MAGBIO' => 'mbi', 'MD03G1269000' => 'mdo', 'MD04G1179600' => 'mdo', 'MD11G1289800' => 'mdo', 'MD12G1194700' => 'mdo', 'MD13G1182100' => 'mdo', 'MD13G1182200' => 'mdo', 'MD16G1182600' => 'mdo', 'Medtr2g021400' => 'mtr', 'Medtr2g021470' => 'mtr', 'Medtr2g105810' => 'mtr', 'Medtr3g033580' => 'mtr', 'Medtr6g007970' => 'mtr', 'Medtr7g056330' => 'mtr', 'Medtr7g074290' => 'mtr', 'Medtr7g074380' => 'mtr', 'Medtr7g094550' => 'mtr', 'Medtr8g069995' => 'mtr', 'MELO3C014345.2' => 'cme', 'MELO3C021395.2' => 'cme', 'Migut.D00262' => 'egut', 'Migut.G00257' => 'egut', 'MSTRG.21575' => 'ama', 'MSTRG.3985' => 'ama', 'Nitab4.5_0000295g0140' => 'nta', 'Nitab4.5_0000732g0140' => 'nta', 'Nitab4.5_0003162g0020' => 'nta', 'Nitab4.5_0006180g0090' => 'nta', 'Nitab4.5_0006390g0010' => 'nta', 'Nitab4.5_0007392g0040' => 'nta', 'Nn1g02140' => 'nnu', 'Nn4g26168' => 'nnu', 'Nn5g26754' => 'nnu', 'Oeu001433.1' => 'oeu', 'Oeu010299.2' => 'oeu', 'Oeu011171.1' => 'oeu', 'Oeu037675.1' => 'oeu', 'Oeu038359.1' => 'oeu', 'Oeu063834.1' => 'oeu', 'Oeu063835.1' => 'oeu', 'Os05g0312000' => 'osa', 'Os07g0211101' => 'osa', 'Os07g0211200' => 'osa', 'Os07g0681500' => 'osa', 'Peaxi162Scf00095g01015' => 'pax', 'Peaxi162Scf00104g00329' => 'pax', 'Peaxi162Scf00161g00137' => 'pax', 'PGR004G1665' => 'pgr', 'PGR031G2937' => 'pgr', 'PGR119G2145' => 'pgr', 'PGSC0003DMG400004351' => 'stu', 'PGSC0003DMG400014625' => 'stu', 'PGSC0003DMG401000943' => 'stu', 'Phvul.001G148600' => 'pvu', 'Phvul.004G001700' => 'pvu', 'Phvul.006G154900' => 'pvu', 'Phvul.008G078200' => 'pvu', 'Phvul.011G136500' => 'pvu', 'Potri.002G215600' => 'ptr', 'Potri.008G201600' => 'ptr', 'Potri.014G138400' => 'ptr', 'Potri.016G142500' => 'ptr', 'Pp3c16_10580' => 'ppa', 'Pp3c5_25280' => 'ppa', 'Prupe.1G150000' => 'ppe', 'Prupe.1G150100' => 'ppe', 'Prupe.6G299600' => 'ppe', 'Prupe.8G245000' => 'ppe', 'Psat0s4927g0040' => 'psa', 'Psat1g052080' => 'psa', 'Psat1g183800' => 'psa', 'Psat3g113840' => 'psa', 'Psat3g126120' => 'psa', 'Psat3g126160' => 'psa', 'Psat3g158760' => 'psa', 'Psat3g158840' => 'psa', 'PSO170G2858' => 'pso', 'PSO339G0606' => 'pso', 'PSO384G4709' => 'pso', 'PSO407G0334' => 'pso', 'QL04p040276' => 'qlo', 'QL06p005458' => 'qlo', 'QL06p005472' => 'qlo', 'QL07p030546' => 'qlo', 'QL07p031519' => 'qlo', 'QL09p050949' => 'qlo', 'QL09p050966' => 'qlo', 'QL09p051067' => 'qlo', 'QL12p022706' => 'qlo', 'RcHm_v2.0_Chr2g0119601' => 'rch', 'RcHm_v2.0_Chr3g0459591' => 'rch', 'RcHm_v2.0_Chr4g0418521' => 'rch', 'RcHm_v2.0_Chr4g0418531' => 'rch', 'RcHm_v2.0_Chr4g0418541' => 'rch', 'RcHm_v2.0_Chr6g0291641' => 'rch', 'Rhsim01G0086300' => 'rsi', 'Rhsim01G0276300' => 'rsi', 'Rhsim01G0276500' => 'rsi', 'Rhsim04G0207700' => 'rsi', 'Rhsim05G0234500' => 'rsi', 'Rhsim13G0022400' => 'rsi', 'Sabra02G0167900' => 'sbr', 'Sabra04G0158500' => 'sbr', 'Sabra08G0159800' => 'sbr', 'Sabra10G0011500' => 'sbr', 'Sabra14G0104400' => 'sbr', 'SalBow2G2440' => 'sbo', 'SalBow4G2265' => 'sbo', 'Sc02g0000060' => 'sci', 'Sc05g0005020' => 'sci', 'Sc13g0003890' => 'sci', 'Sed0014865' => 'sed', 'Sed0017224' => 'sed', 'Sed0026391' => 'sed', 'SEGI_00063' => 'sgi', 'SEGI_10967' => 'sgi', 'SEGI_17510' => 'sgi', 'SEGI_24396' => 'sgi', 'SEGI_39719' => 'sgi', 'SEGI_41392' => 'sgi', 'SGA_v2.0_scaffold11G05794' => 'sas', 'SGA_v2.0_scaffold142G35607' => 'sas', 'SGA_v2.0_scaffold1G00447' => 'sas', 'SHI15388' => 'shi', 'SHI15394' => 'shi', 'SHI15396' => 'shi', 'SHI15399' => 'shi', 'SMO343G0151' => 'smo', 'SMO367G1118' => 'smo', 'Solyc01g080200.3' => 'sly', 'Solyc06g008960.3' => 'sly', 'Solyc09g064780.3' => 'sly', 'Sopen01g031980' => 'spe', 'Sopen06g003710' => 'spe', 'Sopen09g026460' => 'spe', 'Sp3g21240' => 'spa', 'Sp4g30030' => 'spa', 'TAR365G0022' => 'tar', 'TAR365G1023' => 'tar', 'TAR365G1253' => 'tar', 'TAR623G0078' => 'tar', 'TAR623G1721' => 'tar', 'TAR633G0959' => 'tar', 'THA.LOC104802225' => 'tha', 'THA.LOC104804769' => 'tha', 'THA.LOC104808660' => 'tha', 'THA.LOC104812792' => 'tha', 'Thecc.01G284000' => 'tca', 'Thecc.04G220600' => 'tca', 'Thecc.05G268900' => 'tca', 'Thecc.08G171100' => 'tca', 'Thhalv10001284m.g' => 'esa', 'Thhalv10019912m.g' => 'esa', 'TPR.G14189' => 'tpr', 'TPR.G18110' => 'tpr', 'TPR.G18130' => 'tpr', 'TPR.G18131' => 'tpr', 'TPR.G18140' => 'tpr', 'TPR.G24282' => 'tpr', 'TPR.G25221' => 'tpr', 'TPR.G29267' => 'tpr', 'TPR.G35315' => 'tpr', 'TPR.G36173' => 'tpr', 'TWI09G0794' => 'twi', 'TWI59G1348' => 'twi', 'TWI74G0430' => 'twi', 'unitig_26.g8940' => 'ugi', 'unitig_749.g13744' => 'ugi', 'unitig_749.g13745' => 'ugi', 'vmacro08269' => 'vma', 'vmacro14937' => 'vma', 'vmacro20401' => 'vma', 'VMungo0464G1349' => 'vmu', 'VMungo0540G0289' => 'vmu', 'VMungo1215G1590' => 'vmu', 'VMungo1309G0221' => 'vmu', 'VMungo1309G2815' => 'vmu', 'VMungo1383G0239' => 'vmu', 'VMungo1383G2910' => 'vmu', 'Zm00001eb095270' => 'zma', 'Zm00001eb095280' => 'zma', 'Zm00001eb111630' => 'zma', 'Zm00001eb237080' => 'zma', 'Zm00001eb273740' => 'zma', 'Zm00001eb285040' => 'zma', 'Zm00001eb330790' => 'zma', 'Zm00001eb337380' => 'zma' ), 'gf_id' => 'HOM05D001484', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001484' ), 'data_identifier' => 'HOM05D001484', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001484', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p31500' => 'bna', 'A05p00020' => 'bna', 'A07p08820' => 'bna', 'Aa31LG4G3300' => 'aar', 'Aa31LG8G10030' => 'aar', 'Actinidia00731' => 'ach', 'Actinidia11473' => 'ach', 'Actinidia23469' => 'ach', 'Actinidia24318' => 'ach', 'Actinidia40196' => 'ach', 'Actinidia40197' => 'ach', 'Actinidia40198' => 'ach', 'Ah.08g212990' => 'amhyb', 'Ah.15g091720' => 'amhyb', 'AL3G38260' => 'aly', 'AL4G47710' => 'aly', 'Aqoxy2G00671' => 'aox', 'Aqoxy2G03236' => 'aox', 'arahy.Tifrunner.gnm1.ann1.05IDCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KR684' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATY3SJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK6QJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6APGL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IDT7Z9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM073U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ0R87' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LE7RV4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT4QRX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V5ENPK' => 'arhy', 'AT2G48110' => 'ath', 'AT3G23590' => 'ath', 'ATR0626G186' => 'atr', 'ATR1127G141' => 'atr', 'Atru.chr4.2583' => 'acertr', 'Atru.chr5.1358' => 'acertr', 'Atru.chr5.1359' => 'acertr', 'Atru.chr8.46' => 'acertr', 'AUR62002640' => 'cqu', 'AUR62030055' => 'cqu', 'AUR62033713' => 'cqu', 'AUR62033714' => 'cqu', 'AUR62036795' => 'cqu', 'AUR62039891' => 'cqu', 'BcaB02g08737' => 'bca', 'BcaB04g20441' => 'bca', 'BcaB06g26509' => 'bca', 'BcaB06g26510' => 'bca', 'BcaB06g26511' => 'bca', 'BcaB06g26512' => 'bca', 'BcaB06g26513' => 'bca', 'BcaC02g12564' => 'bca', 'BcaC02g12565' => 'bca', 'BcaC02g12794' => 'bca', 'BcaC02g12795' => 'bca', 'BcaC02g12796' => 'bca', 'BcaC06g35541' => 'bca', 'BNapus_Darmor_BZH_scaffold_188p00080' => 'bna', 'BNapus_Darmor_BZH_scaffold_188p00090' => 'bna', 'BolC1t03972H' => 'bol', 'BolC1t03973H' => 'bol', 'BolC4t21680H' => 'bol', 'BolC7t41863H' => 'bol', 'BolSC55t61227H' => 'bol', 'BolSC55t61228H' => 'bol', 'BraA01t03278Z' => 'bra', 'BraA05t18998Z' => 'bra', 'BraA07t28673Z' => 'bra', 'C01p40150' => 'bna', 'C05p12370' => 'bna', 'C07p13680' => 'bna', 'CAN.G1006.16' => 'can', 'CAN.G1006.17' => 'can', 'CAN.G1170.2' => 'can', 'CAN.G962.7' => 'can', 'CANSAT25G2179' => 'cansat', 'CANSAT78G1573' => 'cansat', 'CARHR099510' => 'chi', 'CARHR143510' => 'chi', 'Carub.0003s2380' => 'cru', 'Carub.0004s3082' => 'cru', 'Ca_00614_v3' => 'car', 'Ca_07801_v3' => 'car', 'Ca_08567_v3' => 'car', 'Ca_09571_v3' => 'car', 'CBR_g19290' => 'cbr', 'Cc01_g19770' => 'ccan', 'Cc03_g03030' => 'ccan', 'CDE07G0968' => 'cde', 'CDE09G1441' => 'cde', 'Cfa006103' => 'cfa', 'Cfa015573' => 'cfa', 'Cfa016988' => 'cfa', 'Ciclev10006738m.g' => 'ccl', 'Ciclev10010920m.g' => 'ccl', 'Ciclev10018517m.g' => 'ccl', 'CiPaw.01G159200' => 'cil', 'CiPaw.02G091000' => 'cil', 'CiPaw.02G091100' => 'cil', 'CiPaw.08G103100' => 'cil', 'CiPaw.09G224900' => 'cil', 'ClCG06G005740' => 'cla', 'ClCG07G000090' => 'cla', 'ClCG07G000100' => 'cla', 'COL.COLO4_09143' => 'col', 'COL.COLO4_25124' => 'col', 'Cpa.g.sc16.34' => 'cpa', 'Cpa.g.sc3504.1' => 'cpa', 'Cpa.g.sc60.37' => 'cpa', 'CsaV3_6G018520' => 'csa', 'CsaV3_6G036860' => 'csa', 'CSS0001072' => 'camsi', 'CSS0020208' => 'camsi', 'CSS0021253' => 'camsi', 'CSS0022190' => 'camsi', 'CSS0036150' => 'camsi', 'CSS0040442' => 'camsi', 'CSS0042300' => 'camsi', 'CSS0045298' => 'camsi', 'DCAR_012449' => 'dca', 'DCAR_018405' => 'dca', 'DCAR_024573' => 'dca', 'DCAR_030591' => 'dca', 'Dinv16926' => 'din', 'Dinv32963' => 'din', 'Dinv38382' => 'din', 'Dinv38383' => 'din', 'Duzib133G0974' => 'dzi', 'Duzib138G1867' => 'dzi', 'Duzib211G0420' => 'dzi', 'Duzib212G0930' => 'dzi', 'ECA234G1645' => 'eca', 'ECA247G3467' => 'eca', 'ECA248G1703' => 'eca', 'EL10Ac3g06327' => 'bvu', 'EL10Ac7g17204' => 'bvu', 'Eucgr.A00855' => 'egr', 'Eucgr.A00858' => 'egr', 'Eucgr.H01520' => 'egr', 'Eucgr.H03604' => 'egr', 'Eucgr.L03465' => 'egr', 'Eucgr.L03466' => 'egr', 'FAN01G0988' => 'fan', 'FAN02G3892' => 'fan', 'FAN05G3381' => 'fan', 'FAN07G0967' => 'fan', 'FAN07G1493' => 'fan', 'FAN08G3125' => 'fan', 'FAN09G0402' => 'fan', 'FAN12G2594' => 'fan', 'FAN12G3879' => 'fan', 'FAN14G1546' => 'fan', 'FAN15G3626' => 'fan', 'FAN17G0588' => 'fan', 'FAN17G0609' => 'fan', 'FAN18G2817' => 'fan', 'FAN19G1305' => 'fan', 'FAN20G1787' => 'fan', 'FAN22G0073' => 'fan', 'FAN22G0352' => 'fan', 'FAN22G0368' => 'fan', 'FAN22G2273' => 'fan', 'FAN24G1998' => 'fan', 'FAN27G1317' => 'fan', 'FvH4_2g23980' => 'fve', 'FvH4_4g14380' => 'fve', 'FvH4_4g14390' => 'fve', 'FvH4_6g09250' => 'fve', 'Glyma.03G151100' => 'gma', 'Glyma.04G122550' => 'gma', 'Glyma.05G001600' => 'gma', 'Glyma.09G270766' => 'gma', 'Glyma.09G270832' => 'gma', 'Glyma.13G209800' => 'gma', 'Glyma.15G102800' => 'gma', 'Glyma.18G218900' => 'gma', 'Glyma.19G001500' => 'gma', 'Glyma.19G153600' => 'gma', 'Gohir.A02G028600' => 'ghi', 'Gohir.A08G045000' => 'ghi', 'Gohir.A11G120500' => 'ghi', 'Gohir.A12G006200' => 'ghi', 'Gohir.A12G006250' => 'ghi', 'Gohir.D02G036300' => 'ghi', 'Gohir.D08G054700' => 'ghi', 'Gohir.D11G125600' => 'ghi', 'Gohir.D12G005700' => 'ghi', 'Gorai.004G055200' => 'gra', 'Gorai.005G040400' => 'gra', 'Gorai.007G134500' => 'gra', 'Gorai.008G005500' => 'gra', 'GSVIVG01011094001' => 'vvi', 'GSVIVG01017879001' => 'vvi', 'GSVIVG01025988001' => 'vvi', 'GSVIVG01029847001' => 'vvi', 'HanXRQChr10g0282901' => 'han', 'HanXRQChr10g0310371' => 'han', 'HanXRQChr10g0315041' => 'han', 'HanXRQChr11g0327651' => 'han', 'HanXRQChr12g0359391' => 'han', 'Haze_00972' => 'cav', 'Haze_00973' => 'cav', 'Haze_00974' => 'cav', 'Haze_04747' => 'cav', 'Haze_04749' => 'cav', 'Haze_04750' => 'cav', 'Haze_21217' => 'cav', 'Hma1.2p1_1037F.1_g250680' => 'hma', 'Hma1.2p1_1644F.1_g295320' => 'hma', 'HPP92_011322' => 'vpl', 'HPP92_011323' => 'vpl', 'HPP92_011324' => 'vpl', 'HPP92_011325' => 'vpl', 'HPP92_011326' => 'vpl', 'Hund12205' => 'sun', 'Hund17957' => 'sun', 'Lalb_Chr06g0176771' => 'lal', 'Lalb_Chr18g0056021' => 'lal', 'Lalb_Chr18g0056031' => 'lal', 'Lalb_Chr18g0056041' => 'lal', 'Lalb_Chr20g0107751' => 'lal', 'Lalb_Chr20g0118371' => 'lal', 'Lj1g0010239' => 'lja', 'Lj1g0017101' => 'lja', 'Lj2A1178G40' => 'lonja', 'Lj2A54G84' => 'lonja', 'Lj2g0015248' => 'lja', 'Lj3A761T51' => 'lonja', 'Lj6g0018116' => 'lja', 'Lsat_1_v5_gn_4_136040' => 'lsa', 'Lsat_1_v5_gn_5_187461' => 'lsa', 'Lsat_1_v5_gn_5_77001' => 'lsa', 'Lsat_1_v5_gn_9_4461' => 'lsa', 'Manes.01G210100' => 'mes', 'Manes.03G185600' => 'mes', 'Manes.05G073300' => 'mes', 'Manes.09G120300' => 'mes', 'Manes.15G022100' => 'mes', 'Mapoly0096s0053' => 'mpo', 'MBI03_g14058_MAGBIO' => 'mbi', 'MBI03_g33876_MAGBIO' => 'mbi', 'MBI03_g36854_MAGBIO' => 'mbi', 'MBI17_g11997_MAGBIO' => 'mbi', 'MD03G1269000' => 'mdo', 'MD04G1179600' => 'mdo', 'MD11G1289800' => 'mdo', 'MD12G1194700' => 'mdo', 'MD13G1182100' => 'mdo', 'MD13G1182200' => 'mdo', 'MD16G1182600' => 'mdo', 'Medtr2g021400' => 'mtr', 'Medtr2g021470' => 'mtr', 'Medtr2g105810' => 'mtr', 'Medtr3g033580' => 'mtr', 'Medtr6g007970' => 'mtr', 'Medtr7g056330' => 'mtr', 'Medtr7g074290' => 'mtr', 'Medtr7g074380' => 'mtr', 'Medtr7g094550' => 'mtr', 'Medtr8g069995' => 'mtr', 'MELO3C014345.2' => 'cme', 'MELO3C021395.2' => 'cme', 'Migut.D00262' => 'egut', 'Migut.G00257' => 'egut', 'MSTRG.21575' => 'ama', 'MSTRG.3985' => 'ama', 'Nitab4.5_0000295g0140' => 'nta', 'Nitab4.5_0000732g0140' => 'nta', 'Nitab4.5_0003162g0020' => 'nta', 'Nitab4.5_0006180g0090' => 'nta', 'Nitab4.5_0006390g0010' => 'nta', 'Nitab4.5_0007392g0040' => 'nta', 'Nn1g02140' => 'nnu', 'Nn4g26168' => 'nnu', 'Nn5g26754' => 'nnu', 'Oeu001433.1' => 'oeu', 'Oeu010299.2' => 'oeu', 'Oeu011171.1' => 'oeu', 'Oeu037675.1' => 'oeu', 'Oeu038359.1' => 'oeu', 'Oeu063834.1' => 'oeu', 'Oeu063835.1' => 'oeu', 'Os05g0312000' => 'osa', 'Os07g0211101' => 'osa', 'Os07g0211200' => 'osa', 'Os07g0681500' => 'osa', 'Peaxi162Scf00095g01015' => 'pax', 'Peaxi162Scf00104g00329' => 'pax', 'Peaxi162Scf00161g00137' => 'pax', 'PGR004G1665' => 'pgr', 'PGR031G2937' => 'pgr', 'PGR119G2145' => 'pgr', 'PGSC0003DMG400004351' => 'stu', 'PGSC0003DMG400014625' => 'stu', 'PGSC0003DMG401000943' => 'stu', 'Phvul.001G148600' => 'pvu', 'Phvul.004G001700' => 'pvu', 'Phvul.006G154900' => 'pvu', 'Phvul.008G078200' => 'pvu', 'Phvul.011G136500' => 'pvu', 'Potri.002G215600' => 'ptr', 'Potri.008G201600' => 'ptr', 'Potri.014G138400' => 'ptr', 'Potri.016G142500' => 'ptr', 'Pp3c16_10580' => 'ppa', 'Pp3c5_25280' => 'ppa', 'Prupe.1G150000' => 'ppe', 'Prupe.1G150100' => 'ppe', 'Prupe.6G299600' => 'ppe', 'Prupe.8G245000' => 'ppe', 'Psat0s4927g0040' => 'psa', 'Psat1g052080' => 'psa', 'Psat1g183800' => 'psa', 'Psat3g113840' => 'psa', 'Psat3g126120' => 'psa', 'Psat3g126160' => 'psa', 'Psat3g158760' => 'psa', 'Psat3g158840' => 'psa', 'PSO170G2858' => 'pso', 'PSO339G0606' => 'pso', 'PSO384G4709' => 'pso', 'PSO407G0334' => 'pso', 'QL04p040276' => 'qlo', 'QL06p005458' => 'qlo', 'QL06p005472' => 'qlo', 'QL07p030546' => 'qlo', 'QL07p031519' => 'qlo', 'QL09p050949' => 'qlo', 'QL09p050966' => 'qlo', 'QL09p051067' => 'qlo', 'QL12p022706' => 'qlo', 'RcHm_v2.0_Chr2g0119601' => 'rch', 'RcHm_v2.0_Chr3g0459591' => 'rch', 'RcHm_v2.0_Chr4g0418521' => 'rch', 'RcHm_v2.0_Chr4g0418531' => 'rch', 'RcHm_v2.0_Chr4g0418541' => 'rch', 'RcHm_v2.0_Chr6g0291641' => 'rch', 'Rhsim01G0086300' => 'rsi', 'Rhsim01G0276300' => 'rsi', 'Rhsim01G0276500' => 'rsi', 'Rhsim04G0207700' => 'rsi', 'Rhsim05G0234500' => 'rsi', 'Rhsim13G0022400' => 'rsi', 'Sabra02G0167900' => 'sbr', 'Sabra04G0158500' => 'sbr', 'Sabra08G0159800' => 'sbr', 'Sabra10G0011500' => 'sbr', 'Sabra14G0104400' => 'sbr', 'SalBow2G2440' => 'sbo', 'SalBow4G2265' => 'sbo', 'Sc02g0000060' => 'sci', 'Sc05g0005020' => 'sci', 'Sc13g0003890' => 'sci', 'Sed0014865' => 'sed', 'Sed0017224' => 'sed', 'Sed0026391' => 'sed', 'SEGI_00063' => 'sgi', 'SEGI_10967' => 'sgi', 'SEGI_17510' => 'sgi', 'SEGI_24396' => 'sgi', 'SEGI_39719' => 'sgi', 'SEGI_41392' => 'sgi', 'SGA_v2.0_scaffold11G05794' => 'sas', 'SGA_v2.0_scaffold142G35607' => 'sas', 'SGA_v2.0_scaffold1G00447' => 'sas', 'SHI15388' => 'shi', 'SHI15394' => 'shi', 'SHI15396' => 'shi', 'SHI15399' => 'shi', 'SMO343G0151' => 'smo', 'SMO367G1118' => 'smo', 'Solyc01g080200.3' => 'sly', 'Solyc06g008960.3' => 'sly', 'Solyc09g064780.3' => 'sly', 'Sopen01g031980' => 'spe', 'Sopen06g003710' => 'spe', 'Sopen09g026460' => 'spe', 'Sp3g21240' => 'spa', 'Sp4g30030' => 'spa', 'TAR365G0022' => 'tar', 'TAR365G1023' => 'tar', 'TAR365G1253' => 'tar', 'TAR623G0078' => 'tar', 'TAR623G1721' => 'tar', 'TAR633G0959' => 'tar', 'THA.LOC104802225' => 'tha', 'THA.LOC104804769' => 'tha', 'THA.LOC104808660' => 'tha', 'THA.LOC104812792' => 'tha', 'Thecc.01G284000' => 'tca', 'Thecc.04G220600' => 'tca', 'Thecc.05G268900' => 'tca', 'Thecc.08G171100' => 'tca', 'Thhalv10001284m.g' => 'esa', 'Thhalv10019912m.g' => 'esa', 'TPR.G14189' => 'tpr', 'TPR.G18110' => 'tpr', 'TPR.G18130' => 'tpr', 'TPR.G18131' => 'tpr', 'TPR.G18140' => 'tpr', 'TPR.G24282' => 'tpr', 'TPR.G25221' => 'tpr', 'TPR.G29267' => 'tpr', 'TPR.G35315' => 'tpr', 'TPR.G36173' => 'tpr', 'TWI09G0794' => 'twi', 'TWI59G1348' => 'twi', 'TWI74G0430' => 'twi', 'unitig_26.g8940' => 'ugi', 'unitig_749.g13744' => 'ugi', 'unitig_749.g13745' => 'ugi', 'vmacro08269' => 'vma', 'vmacro14937' => 'vma', 'vmacro20401' => 'vma', 'VMungo0464G1349' => 'vmu', 'VMungo0540G0289' => 'vmu', 'VMungo1215G1590' => 'vmu', 'VMungo1309G0221' => 'vmu', 'VMungo1309G2815' => 'vmu', 'VMungo1383G0239' => 'vmu', 'VMungo1383G2910' => 'vmu', 'Zm00001eb095270' => 'zma', 'Zm00001eb095280' => 'zma', 'Zm00001eb111630' => 'zma', 'Zm00001eb237080' => 'zma', 'Zm00001eb273740' => 'zma', 'Zm00001eb285040' => 'zma', 'Zm00001eb330790' => 'zma', 'Zm00001eb337380' => 'zma' ) $gf_id = 'HOM05D001484' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001484' ) $data_identifier = 'HOM05D001484' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 2, 'aly' => (int) 2, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 22, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 7, 'hma' => (int) 2, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 7, 'mtr' => (int) 10, 'cme' => (int) 2, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 4, 'ppa' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 4, 'qlo' => (int) 9, 'rch' => (int) 6, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 10, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 7, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb337380' $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' => 'HOM05D001484', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p31500' => 'bna', 'A05p00020' => 'bna', 'A07p08820' => 'bna', 'Aa31LG4G3300' => 'aar', 'Aa31LG8G10030' => 'aar', 'Actinidia00731' => 'ach', 'Actinidia11473' => 'ach', 'Actinidia23469' => 'ach', 'Actinidia24318' => 'ach', 'Actinidia40196' => 'ach', 'Actinidia40197' => 'ach', 'Actinidia40198' => 'ach', 'Ah.08g212990' => 'amhyb', 'Ah.15g091720' => 'amhyb', 'AL3G38260' => 'aly', 'AL4G47710' => 'aly', 'Aqoxy2G00671' => 'aox', 'Aqoxy2G03236' => 'aox', 'arahy.Tifrunner.gnm1.ann1.05IDCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KR684' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATY3SJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK6QJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6APGL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IDT7Z9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM073U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ0R87' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LE7RV4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT4QRX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V5ENPK' => 'arhy', 'AT2G48110' => 'ath', 'AT3G23590' => 'ath', 'ATR0626G186' => 'atr', 'ATR1127G141' => 'atr', 'Atru.chr4.2583' => 'acertr', 'Atru.chr5.1358' => 'acertr', 'Atru.chr5.1359' => 'acertr', 'Atru.chr8.46' => 'acertr', 'AUR62002640' => 'cqu', 'AUR62030055' => 'cqu', 'AUR62033713' => 'cqu', 'AUR62033714' => 'cqu', 'AUR62036795' => 'cqu', 'AUR62039891' => 'cqu', 'BcaB02g08737' => 'bca', 'BcaB04g20441' => 'bca', 'BcaB06g26509' => 'bca', 'BcaB06g26510' => 'bca', 'BcaB06g26511' => 'bca', 'BcaB06g26512' => 'bca', 'BcaB06g26513' => 'bca', 'BcaC02g12564' => 'bca', 'BcaC02g12565' => 'bca', 'BcaC02g12794' => 'bca', 'BcaC02g12795' => 'bca', 'BcaC02g12796' => 'bca', 'BcaC06g35541' => 'bca', 'BNapus_Darmor_BZH_scaffold_188p00080' => 'bna', 'BNapus_Darmor_BZH_scaffold_188p00090' => 'bna', 'BolC1t03972H' => 'bol', 'BolC1t03973H' => 'bol', 'BolC4t21680H' => 'bol', 'BolC7t41863H' => 'bol', 'BolSC55t61227H' => 'bol', 'BolSC55t61228H' => 'bol', 'BraA01t03278Z' => 'bra', 'BraA05t18998Z' => 'bra', 'BraA07t28673Z' => 'bra', 'C01p40150' => 'bna', 'C05p12370' => 'bna', 'C07p13680' => 'bna', 'CAN.G1006.16' => 'can', 'CAN.G1006.17' => 'can', 'CAN.G1170.2' => 'can', 'CAN.G962.7' => 'can', 'CANSAT25G2179' => 'cansat', 'CANSAT78G1573' => 'cansat', 'CARHR099510' => 'chi', 'CARHR143510' => 'chi', 'Carub.0003s2380' => 'cru', 'Carub.0004s3082' => 'cru', 'Ca_00614_v3' => 'car', 'Ca_07801_v3' => 'car', 'Ca_08567_v3' => 'car', 'Ca_09571_v3' => 'car', 'CBR_g19290' => 'cbr', 'Cc01_g19770' => 'ccan', 'Cc03_g03030' => 'ccan', 'CDE07G0968' => 'cde', 'CDE09G1441' => 'cde', 'Cfa006103' => 'cfa', 'Cfa015573' => 'cfa', 'Cfa016988' => 'cfa', 'Ciclev10006738m.g' => 'ccl', 'Ciclev10010920m.g' => 'ccl', 'Ciclev10018517m.g' => 'ccl', 'CiPaw.01G159200' => 'cil', 'CiPaw.02G091000' => 'cil', 'CiPaw.02G091100' => 'cil', 'CiPaw.08G103100' => 'cil', 'CiPaw.09G224900' => 'cil', 'ClCG06G005740' => 'cla', 'ClCG07G000090' => 'cla', 'ClCG07G000100' => 'cla', 'COL.COLO4_09143' => 'col', 'COL.COLO4_25124' => 'col', 'Cpa.g.sc16.34' => 'cpa', 'Cpa.g.sc3504.1' => 'cpa', 'Cpa.g.sc60.37' => 'cpa', 'CsaV3_6G018520' => 'csa', 'CsaV3_6G036860' => 'csa', 'CSS0001072' => 'camsi', 'CSS0020208' => 'camsi', 'CSS0021253' => 'camsi', 'CSS0022190' => 'camsi', 'CSS0036150' => 'camsi', 'CSS0040442' => 'camsi', 'CSS0042300' => 'camsi', 'CSS0045298' => 'camsi', 'DCAR_012449' => 'dca', 'DCAR_018405' => 'dca', 'DCAR_024573' => 'dca', 'DCAR_030591' => 'dca', 'Dinv16926' => 'din', 'Dinv32963' => 'din', 'Dinv38382' => 'din', 'Dinv38383' => 'din', 'Duzib133G0974' => 'dzi', 'Duzib138G1867' => 'dzi', 'Duzib211G0420' => 'dzi', 'Duzib212G0930' => 'dzi', 'ECA234G1645' => 'eca', 'ECA247G3467' => 'eca', 'ECA248G1703' => 'eca', 'EL10Ac3g06327' => 'bvu', 'EL10Ac7g17204' => 'bvu', 'Eucgr.A00855' => 'egr', 'Eucgr.A00858' => 'egr', 'Eucgr.H01520' => 'egr', 'Eucgr.H03604' => 'egr', 'Eucgr.L03465' => 'egr', 'Eucgr.L03466' => 'egr', 'FAN01G0988' => 'fan', 'FAN02G3892' => 'fan', 'FAN05G3381' => 'fan', 'FAN07G0967' => 'fan', 'FAN07G1493' => 'fan', 'FAN08G3125' => 'fan', 'FAN09G0402' => 'fan', 'FAN12G2594' => 'fan', 'FAN12G3879' => 'fan', 'FAN14G1546' => 'fan', 'FAN15G3626' => 'fan', 'FAN17G0588' => 'fan', 'FAN17G0609' => 'fan', 'FAN18G2817' => 'fan', 'FAN19G1305' => 'fan', 'FAN20G1787' => 'fan', 'FAN22G0073' => 'fan', 'FAN22G0352' => 'fan', 'FAN22G0368' => 'fan', 'FAN22G2273' => 'fan', 'FAN24G1998' => 'fan', 'FAN27G1317' => 'fan', 'FvH4_2g23980' => 'fve', 'FvH4_4g14380' => 'fve', 'FvH4_4g14390' => 'fve', 'FvH4_6g09250' => 'fve', 'Glyma.03G151100' => 'gma', 'Glyma.04G122550' => 'gma', 'Glyma.05G001600' => 'gma', 'Glyma.09G270766' => 'gma', 'Glyma.09G270832' => 'gma', 'Glyma.13G209800' => 'gma', 'Glyma.15G102800' => 'gma', 'Glyma.18G218900' => 'gma', 'Glyma.19G001500' => 'gma', 'Glyma.19G153600' => 'gma', 'Gohir.A02G028600' => 'ghi', 'Gohir.A08G045000' => 'ghi', 'Gohir.A11G120500' => 'ghi', 'Gohir.A12G006200' => 'ghi', 'Gohir.A12G006250' => 'ghi', 'Gohir.D02G036300' => 'ghi', 'Gohir.D08G054700' => 'ghi', 'Gohir.D11G125600' => 'ghi', 'Gohir.D12G005700' => 'ghi', 'Gorai.004G055200' => 'gra', 'Gorai.005G040400' => 'gra', 'Gorai.007G134500' => 'gra', 'Gorai.008G005500' => 'gra', 'GSVIVG01011094001' => 'vvi', 'GSVIVG01017879001' => 'vvi', 'GSVIVG01025988001' => 'vvi', 'GSVIVG01029847001' => 'vvi', 'HanXRQChr10g0282901' => 'han', 'HanXRQChr10g0310371' => 'han', 'HanXRQChr10g0315041' => 'han', 'HanXRQChr11g0327651' => 'han', 'HanXRQChr12g0359391' => 'han', 'Haze_00972' => 'cav', 'Haze_00973' => 'cav', 'Haze_00974' => 'cav', 'Haze_04747' => 'cav', 'Haze_04749' => 'cav', 'Haze_04750' => 'cav', 'Haze_21217' => 'cav', 'Hma1.2p1_1037F.1_g250680' => 'hma', 'Hma1.2p1_1644F.1_g295320' => 'hma', 'HPP92_011322' => 'vpl', 'HPP92_011323' => 'vpl', 'HPP92_011324' => 'vpl', 'HPP92_011325' => 'vpl', 'HPP92_011326' => 'vpl', 'Hund12205' => 'sun', 'Hund17957' => 'sun', 'Lalb_Chr06g0176771' => 'lal', 'Lalb_Chr18g0056021' => 'lal', 'Lalb_Chr18g0056031' => 'lal', 'Lalb_Chr18g0056041' => 'lal', 'Lalb_Chr20g0107751' => 'lal', 'Lalb_Chr20g0118371' => 'lal', 'Lj1g0010239' => 'lja', 'Lj1g0017101' => 'lja', 'Lj2A1178G40' => 'lonja', 'Lj2A54G84' => 'lonja', 'Lj2g0015248' => 'lja', 'Lj3A761T51' => 'lonja', 'Lj6g0018116' => 'lja', 'Lsat_1_v5_gn_4_136040' => 'lsa', 'Lsat_1_v5_gn_5_187461' => 'lsa', 'Lsat_1_v5_gn_5_77001' => 'lsa', 'Lsat_1_v5_gn_9_4461' => 'lsa', 'Manes.01G210100' => 'mes', 'Manes.03G185600' => 'mes', 'Manes.05G073300' => 'mes', 'Manes.09G120300' => 'mes', 'Manes.15G022100' => 'mes', 'Mapoly0096s0053' => 'mpo', 'MBI03_g14058_MAGBIO' => 'mbi', 'MBI03_g33876_MAGBIO' => 'mbi', 'MBI03_g36854_MAGBIO' => 'mbi', 'MBI17_g11997_MAGBIO' => 'mbi', 'MD03G1269000' => 'mdo', 'MD04G1179600' => 'mdo', 'MD11G1289800' => 'mdo', 'MD12G1194700' => 'mdo', 'MD13G1182100' => 'mdo', 'MD13G1182200' => 'mdo', 'MD16G1182600' => 'mdo', 'Medtr2g021400' => 'mtr', 'Medtr2g021470' => 'mtr', 'Medtr2g105810' => 'mtr', 'Medtr3g033580' => 'mtr', 'Medtr6g007970' => 'mtr', 'Medtr7g056330' => 'mtr', 'Medtr7g074290' => 'mtr', 'Medtr7g074380' => 'mtr', 'Medtr7g094550' => 'mtr', 'Medtr8g069995' => 'mtr', 'MELO3C014345.2' => 'cme', 'MELO3C021395.2' => 'cme', 'Migut.D00262' => 'egut', 'Migut.G00257' => 'egut', 'MSTRG.21575' => 'ama', 'MSTRG.3985' => 'ama', 'Nitab4.5_0000295g0140' => 'nta', 'Nitab4.5_0000732g0140' => 'nta', 'Nitab4.5_0003162g0020' => 'nta', 'Nitab4.5_0006180g0090' => 'nta', 'Nitab4.5_0006390g0010' => 'nta', 'Nitab4.5_0007392g0040' => 'nta', 'Nn1g02140' => 'nnu', 'Nn4g26168' => 'nnu', 'Nn5g26754' => 'nnu', 'Oeu001433.1' => 'oeu', 'Oeu010299.2' => 'oeu', 'Oeu011171.1' => 'oeu', 'Oeu037675.1' => 'oeu', 'Oeu038359.1' => 'oeu', 'Oeu063834.1' => 'oeu', 'Oeu063835.1' => 'oeu', 'Os05g0312000' => 'osa', 'Os07g0211101' => 'osa', 'Os07g0211200' => 'osa', 'Os07g0681500' => 'osa', 'Peaxi162Scf00095g01015' => 'pax', 'Peaxi162Scf00104g00329' => 'pax', 'Peaxi162Scf00161g00137' => 'pax', 'PGR004G1665' => 'pgr', 'PGR031G2937' => 'pgr', 'PGR119G2145' => 'pgr', 'PGSC0003DMG400004351' => 'stu', 'PGSC0003DMG400014625' => 'stu', 'PGSC0003DMG401000943' => 'stu', 'Phvul.001G148600' => 'pvu', 'Phvul.004G001700' => 'pvu', 'Phvul.006G154900' => 'pvu', 'Phvul.008G078200' => 'pvu', 'Phvul.011G136500' => 'pvu', 'Potri.002G215600' => 'ptr', 'Potri.008G201600' => 'ptr', 'Potri.014G138400' => 'ptr', 'Potri.016G142500' => 'ptr', 'Pp3c16_10580' => 'ppa', 'Pp3c5_25280' => 'ppa', 'Prupe.1G150000' => 'ppe', 'Prupe.1G150100' => 'ppe', 'Prupe.6G299600' => 'ppe', 'Prupe.8G245000' => 'ppe', 'Psat0s4927g0040' => 'psa', 'Psat1g052080' => 'psa', 'Psat1g183800' => 'psa', 'Psat3g113840' => 'psa', 'Psat3g126120' => 'psa', 'Psat3g126160' => 'psa', 'Psat3g158760' => 'psa', 'Psat3g158840' => 'psa', 'PSO170G2858' => 'pso', 'PSO339G0606' => 'pso', 'PSO384G4709' => 'pso', 'PSO407G0334' => 'pso', 'QL04p040276' => 'qlo', 'QL06p005458' => 'qlo', 'QL06p005472' => 'qlo', 'QL07p030546' => 'qlo', 'QL07p031519' => 'qlo', 'QL09p050949' => 'qlo', 'QL09p050966' => 'qlo', 'QL09p051067' => 'qlo', 'QL12p022706' => 'qlo', 'RcHm_v2.0_Chr2g0119601' => 'rch', 'RcHm_v2.0_Chr3g0459591' => 'rch', 'RcHm_v2.0_Chr4g0418521' => 'rch', 'RcHm_v2.0_Chr4g0418531' => 'rch', 'RcHm_v2.0_Chr4g0418541' => 'rch', 'RcHm_v2.0_Chr6g0291641' => 'rch', 'Rhsim01G0086300' => 'rsi', 'Rhsim01G0276300' => 'rsi', 'Rhsim01G0276500' => 'rsi', 'Rhsim04G0207700' => 'rsi', 'Rhsim05G0234500' => 'rsi', 'Rhsim13G0022400' => 'rsi', 'Sabra02G0167900' => 'sbr', 'Sabra04G0158500' => 'sbr', 'Sabra08G0159800' => 'sbr', 'Sabra10G0011500' => 'sbr', 'Sabra14G0104400' => 'sbr', 'SalBow2G2440' => 'sbo', 'SalBow4G2265' => 'sbo', 'Sc02g0000060' => 'sci', 'Sc05g0005020' => 'sci', 'Sc13g0003890' => 'sci', 'Sed0014865' => 'sed', 'Sed0017224' => 'sed', 'Sed0026391' => 'sed', 'SEGI_00063' => 'sgi', 'SEGI_10967' => 'sgi', 'SEGI_17510' => 'sgi', 'SEGI_24396' => 'sgi', 'SEGI_39719' => 'sgi', 'SEGI_41392' => 'sgi', 'SGA_v2.0_scaffold11G05794' => 'sas', 'SGA_v2.0_scaffold142G35607' => 'sas', 'SGA_v2.0_scaffold1G00447' => 'sas', 'SHI15388' => 'shi', 'SHI15394' => 'shi', 'SHI15396' => 'shi', 'SHI15399' => 'shi', 'SMO343G0151' => 'smo', 'SMO367G1118' => 'smo', 'Solyc01g080200.3' => 'sly', 'Solyc06g008960.3' => 'sly', 'Solyc09g064780.3' => 'sly', 'Sopen01g031980' => 'spe', 'Sopen06g003710' => 'spe', 'Sopen09g026460' => 'spe', 'Sp3g21240' => 'spa', 'Sp4g30030' => 'spa', 'TAR365G0022' => 'tar', 'TAR365G1023' => 'tar', 'TAR365G1253' => 'tar', 'TAR623G0078' => 'tar', 'TAR623G1721' => 'tar', 'TAR633G0959' => 'tar', 'THA.LOC104802225' => 'tha', 'THA.LOC104804769' => 'tha', 'THA.LOC104808660' => 'tha', 'THA.LOC104812792' => 'tha', 'Thecc.01G284000' => 'tca', 'Thecc.04G220600' => 'tca', 'Thecc.05G268900' => 'tca', 'Thecc.08G171100' => 'tca', 'Thhalv10001284m.g' => 'esa', 'Thhalv10019912m.g' => 'esa', 'TPR.G14189' => 'tpr', 'TPR.G18110' => 'tpr', 'TPR.G18130' => 'tpr', 'TPR.G18131' => 'tpr', 'TPR.G18140' => 'tpr', 'TPR.G24282' => 'tpr', 'TPR.G25221' => 'tpr', 'TPR.G29267' => 'tpr', 'TPR.G35315' => 'tpr', 'TPR.G36173' => 'tpr', 'TWI09G0794' => 'twi', 'TWI59G1348' => 'twi', 'TWI74G0430' => 'twi', 'unitig_26.g8940' => 'ugi', 'unitig_749.g13744' => 'ugi', 'unitig_749.g13745' => 'ugi', 'vmacro08269' => 'vma', 'vmacro14937' => 'vma', 'vmacro20401' => 'vma', 'VMungo0464G1349' => 'vmu', 'VMungo0540G0289' => 'vmu', 'VMungo1215G1590' => 'vmu', 'VMungo1309G0221' => 'vmu', 'VMungo1309G2815' => 'vmu', 'VMungo1383G0239' => 'vmu', 'VMungo1383G2910' => 'vmu', 'Zm00001eb095270' => 'zma', 'Zm00001eb095280' => 'zma', 'Zm00001eb111630' => 'zma', 'Zm00001eb237080' => 'zma', 'Zm00001eb273740' => 'zma', 'Zm00001eb285040' => 'zma', 'Zm00001eb330790' => 'zma', 'Zm00001eb337380' => 'zma' ), 'gf_id' => 'HOM05D001484', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001484' ), 'data_identifier' => 'HOM05D001484', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001484', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p31500' => 'bna', 'A05p00020' => 'bna', 'A07p08820' => 'bna', 'Aa31LG4G3300' => 'aar', 'Aa31LG8G10030' => 'aar', 'Actinidia00731' => 'ach', 'Actinidia11473' => 'ach', 'Actinidia23469' => 'ach', 'Actinidia24318' => 'ach', 'Actinidia40196' => 'ach', 'Actinidia40197' => 'ach', 'Actinidia40198' => 'ach', 'Ah.08g212990' => 'amhyb', 'Ah.15g091720' => 'amhyb', 'AL3G38260' => 'aly', 'AL4G47710' => 'aly', 'Aqoxy2G00671' => 'aox', 'Aqoxy2G03236' => 'aox', 'arahy.Tifrunner.gnm1.ann1.05IDCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KR684' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATY3SJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK6QJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6APGL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IDT7Z9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM073U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ0R87' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LE7RV4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT4QRX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V5ENPK' => 'arhy', 'AT2G48110' => 'ath', 'AT3G23590' => 'ath', 'ATR0626G186' => 'atr', 'ATR1127G141' => 'atr', 'Atru.chr4.2583' => 'acertr', 'Atru.chr5.1358' => 'acertr', 'Atru.chr5.1359' => 'acertr', 'Atru.chr8.46' => 'acertr', 'AUR62002640' => 'cqu', 'AUR62030055' => 'cqu', 'AUR62033713' => 'cqu', 'AUR62033714' => 'cqu', 'AUR62036795' => 'cqu', 'AUR62039891' => 'cqu', 'BcaB02g08737' => 'bca', 'BcaB04g20441' => 'bca', 'BcaB06g26509' => 'bca', 'BcaB06g26510' => 'bca', 'BcaB06g26511' => 'bca', 'BcaB06g26512' => 'bca', 'BcaB06g26513' => 'bca', 'BcaC02g12564' => 'bca', 'BcaC02g12565' => 'bca', 'BcaC02g12794' => 'bca', 'BcaC02g12795' => 'bca', 'BcaC02g12796' => 'bca', 'BcaC06g35541' => 'bca', 'BNapus_Darmor_BZH_scaffold_188p00080' => 'bna', 'BNapus_Darmor_BZH_scaffold_188p00090' => 'bna', 'BolC1t03972H' => 'bol', 'BolC1t03973H' => 'bol', 'BolC4t21680H' => 'bol', 'BolC7t41863H' => 'bol', 'BolSC55t61227H' => 'bol', 'BolSC55t61228H' => 'bol', 'BraA01t03278Z' => 'bra', 'BraA05t18998Z' => 'bra', 'BraA07t28673Z' => 'bra', 'C01p40150' => 'bna', 'C05p12370' => 'bna', 'C07p13680' => 'bna', 'CAN.G1006.16' => 'can', 'CAN.G1006.17' => 'can', 'CAN.G1170.2' => 'can', 'CAN.G962.7' => 'can', 'CANSAT25G2179' => 'cansat', 'CANSAT78G1573' => 'cansat', 'CARHR099510' => 'chi', 'CARHR143510' => 'chi', 'Carub.0003s2380' => 'cru', 'Carub.0004s3082' => 'cru', 'Ca_00614_v3' => 'car', 'Ca_07801_v3' => 'car', 'Ca_08567_v3' => 'car', 'Ca_09571_v3' => 'car', 'CBR_g19290' => 'cbr', 'Cc01_g19770' => 'ccan', 'Cc03_g03030' => 'ccan', 'CDE07G0968' => 'cde', 'CDE09G1441' => 'cde', 'Cfa006103' => 'cfa', 'Cfa015573' => 'cfa', 'Cfa016988' => 'cfa', 'Ciclev10006738m.g' => 'ccl', 'Ciclev10010920m.g' => 'ccl', 'Ciclev10018517m.g' => 'ccl', 'CiPaw.01G159200' => 'cil', 'CiPaw.02G091000' => 'cil', 'CiPaw.02G091100' => 'cil', 'CiPaw.08G103100' => 'cil', 'CiPaw.09G224900' => 'cil', 'ClCG06G005740' => 'cla', 'ClCG07G000090' => 'cla', 'ClCG07G000100' => 'cla', 'COL.COLO4_09143' => 'col', 'COL.COLO4_25124' => 'col', 'Cpa.g.sc16.34' => 'cpa', 'Cpa.g.sc3504.1' => 'cpa', 'Cpa.g.sc60.37' => 'cpa', 'CsaV3_6G018520' => 'csa', 'CsaV3_6G036860' => 'csa', 'CSS0001072' => 'camsi', 'CSS0020208' => 'camsi', 'CSS0021253' => 'camsi', 'CSS0022190' => 'camsi', 'CSS0036150' => 'camsi', 'CSS0040442' => 'camsi', 'CSS0042300' => 'camsi', 'CSS0045298' => 'camsi', 'DCAR_012449' => 'dca', 'DCAR_018405' => 'dca', 'DCAR_024573' => 'dca', 'DCAR_030591' => 'dca', 'Dinv16926' => 'din', 'Dinv32963' => 'din', 'Dinv38382' => 'din', 'Dinv38383' => 'din', 'Duzib133G0974' => 'dzi', 'Duzib138G1867' => 'dzi', 'Duzib211G0420' => 'dzi', 'Duzib212G0930' => 'dzi', 'ECA234G1645' => 'eca', 'ECA247G3467' => 'eca', 'ECA248G1703' => 'eca', 'EL10Ac3g06327' => 'bvu', 'EL10Ac7g17204' => 'bvu', 'Eucgr.A00855' => 'egr', 'Eucgr.A00858' => 'egr', 'Eucgr.H01520' => 'egr', 'Eucgr.H03604' => 'egr', 'Eucgr.L03465' => 'egr', 'Eucgr.L03466' => 'egr', 'FAN01G0988' => 'fan', 'FAN02G3892' => 'fan', 'FAN05G3381' => 'fan', 'FAN07G0967' => 'fan', 'FAN07G1493' => 'fan', 'FAN08G3125' => 'fan', 'FAN09G0402' => 'fan', 'FAN12G2594' => 'fan', 'FAN12G3879' => 'fan', 'FAN14G1546' => 'fan', 'FAN15G3626' => 'fan', 'FAN17G0588' => 'fan', 'FAN17G0609' => 'fan', 'FAN18G2817' => 'fan', 'FAN19G1305' => 'fan', 'FAN20G1787' => 'fan', 'FAN22G0073' => 'fan', 'FAN22G0352' => 'fan', 'FAN22G0368' => 'fan', 'FAN22G2273' => 'fan', 'FAN24G1998' => 'fan', 'FAN27G1317' => 'fan', 'FvH4_2g23980' => 'fve', 'FvH4_4g14380' => 'fve', 'FvH4_4g14390' => 'fve', 'FvH4_6g09250' => 'fve', 'Glyma.03G151100' => 'gma', 'Glyma.04G122550' => 'gma', 'Glyma.05G001600' => 'gma', 'Glyma.09G270766' => 'gma', 'Glyma.09G270832' => 'gma', 'Glyma.13G209800' => 'gma', 'Glyma.15G102800' => 'gma', 'Glyma.18G218900' => 'gma', 'Glyma.19G001500' => 'gma', 'Glyma.19G153600' => 'gma', 'Gohir.A02G028600' => 'ghi', 'Gohir.A08G045000' => 'ghi', 'Gohir.A11G120500' => 'ghi', 'Gohir.A12G006200' => 'ghi', 'Gohir.A12G006250' => 'ghi', 'Gohir.D02G036300' => 'ghi', 'Gohir.D08G054700' => 'ghi', 'Gohir.D11G125600' => 'ghi', 'Gohir.D12G005700' => 'ghi', 'Gorai.004G055200' => 'gra', 'Gorai.005G040400' => 'gra', 'Gorai.007G134500' => 'gra', 'Gorai.008G005500' => 'gra', 'GSVIVG01011094001' => 'vvi', 'GSVIVG01017879001' => 'vvi', 'GSVIVG01025988001' => 'vvi', 'GSVIVG01029847001' => 'vvi', 'HanXRQChr10g0282901' => 'han', 'HanXRQChr10g0310371' => 'han', 'HanXRQChr10g0315041' => 'han', 'HanXRQChr11g0327651' => 'han', 'HanXRQChr12g0359391' => 'han', 'Haze_00972' => 'cav', 'Haze_00973' => 'cav', 'Haze_00974' => 'cav', 'Haze_04747' => 'cav', 'Haze_04749' => 'cav', 'Haze_04750' => 'cav', 'Haze_21217' => 'cav', 'Hma1.2p1_1037F.1_g250680' => 'hma', 'Hma1.2p1_1644F.1_g295320' => 'hma', 'HPP92_011322' => 'vpl', 'HPP92_011323' => 'vpl', 'HPP92_011324' => 'vpl', 'HPP92_011325' => 'vpl', 'HPP92_011326' => 'vpl', 'Hund12205' => 'sun', 'Hund17957' => 'sun', 'Lalb_Chr06g0176771' => 'lal', 'Lalb_Chr18g0056021' => 'lal', 'Lalb_Chr18g0056031' => 'lal', 'Lalb_Chr18g0056041' => 'lal', 'Lalb_Chr20g0107751' => 'lal', 'Lalb_Chr20g0118371' => 'lal', 'Lj1g0010239' => 'lja', 'Lj1g0017101' => 'lja', 'Lj2A1178G40' => 'lonja', 'Lj2A54G84' => 'lonja', 'Lj2g0015248' => 'lja', 'Lj3A761T51' => 'lonja', 'Lj6g0018116' => 'lja', 'Lsat_1_v5_gn_4_136040' => 'lsa', 'Lsat_1_v5_gn_5_187461' => 'lsa', 'Lsat_1_v5_gn_5_77001' => 'lsa', 'Lsat_1_v5_gn_9_4461' => 'lsa', 'Manes.01G210100' => 'mes', 'Manes.03G185600' => 'mes', 'Manes.05G073300' => 'mes', 'Manes.09G120300' => 'mes', 'Manes.15G022100' => 'mes', 'Mapoly0096s0053' => 'mpo', 'MBI03_g14058_MAGBIO' => 'mbi', 'MBI03_g33876_MAGBIO' => 'mbi', 'MBI03_g36854_MAGBIO' => 'mbi', 'MBI17_g11997_MAGBIO' => 'mbi', 'MD03G1269000' => 'mdo', 'MD04G1179600' => 'mdo', 'MD11G1289800' => 'mdo', 'MD12G1194700' => 'mdo', 'MD13G1182100' => 'mdo', 'MD13G1182200' => 'mdo', 'MD16G1182600' => 'mdo', 'Medtr2g021400' => 'mtr', 'Medtr2g021470' => 'mtr', 'Medtr2g105810' => 'mtr', 'Medtr3g033580' => 'mtr', 'Medtr6g007970' => 'mtr', 'Medtr7g056330' => 'mtr', 'Medtr7g074290' => 'mtr', 'Medtr7g074380' => 'mtr', 'Medtr7g094550' => 'mtr', 'Medtr8g069995' => 'mtr', 'MELO3C014345.2' => 'cme', 'MELO3C021395.2' => 'cme', 'Migut.D00262' => 'egut', 'Migut.G00257' => 'egut', 'MSTRG.21575' => 'ama', 'MSTRG.3985' => 'ama', 'Nitab4.5_0000295g0140' => 'nta', 'Nitab4.5_0000732g0140' => 'nta', 'Nitab4.5_0003162g0020' => 'nta', 'Nitab4.5_0006180g0090' => 'nta', 'Nitab4.5_0006390g0010' => 'nta', 'Nitab4.5_0007392g0040' => 'nta', 'Nn1g02140' => 'nnu', 'Nn4g26168' => 'nnu', 'Nn5g26754' => 'nnu', 'Oeu001433.1' => 'oeu', 'Oeu010299.2' => 'oeu', 'Oeu011171.1' => 'oeu', 'Oeu037675.1' => 'oeu', 'Oeu038359.1' => 'oeu', 'Oeu063834.1' => 'oeu', 'Oeu063835.1' => 'oeu', 'Os05g0312000' => 'osa', 'Os07g0211101' => 'osa', 'Os07g0211200' => 'osa', 'Os07g0681500' => 'osa', 'Peaxi162Scf00095g01015' => 'pax', 'Peaxi162Scf00104g00329' => 'pax', 'Peaxi162Scf00161g00137' => 'pax', 'PGR004G1665' => 'pgr', 'PGR031G2937' => 'pgr', 'PGR119G2145' => 'pgr', 'PGSC0003DMG400004351' => 'stu', 'PGSC0003DMG400014625' => 'stu', 'PGSC0003DMG401000943' => 'stu', 'Phvul.001G148600' => 'pvu', 'Phvul.004G001700' => 'pvu', 'Phvul.006G154900' => 'pvu', 'Phvul.008G078200' => 'pvu', 'Phvul.011G136500' => 'pvu', 'Potri.002G215600' => 'ptr', 'Potri.008G201600' => 'ptr', 'Potri.014G138400' => 'ptr', 'Potri.016G142500' => 'ptr', 'Pp3c16_10580' => 'ppa', 'Pp3c5_25280' => 'ppa', 'Prupe.1G150000' => 'ppe', 'Prupe.1G150100' => 'ppe', 'Prupe.6G299600' => 'ppe', 'Prupe.8G245000' => 'ppe', 'Psat0s4927g0040' => 'psa', 'Psat1g052080' => 'psa', 'Psat1g183800' => 'psa', 'Psat3g113840' => 'psa', 'Psat3g126120' => 'psa', 'Psat3g126160' => 'psa', 'Psat3g158760' => 'psa', 'Psat3g158840' => 'psa', 'PSO170G2858' => 'pso', 'PSO339G0606' => 'pso', 'PSO384G4709' => 'pso', 'PSO407G0334' => 'pso', 'QL04p040276' => 'qlo', 'QL06p005458' => 'qlo', 'QL06p005472' => 'qlo', 'QL07p030546' => 'qlo', 'QL07p031519' => 'qlo', 'QL09p050949' => 'qlo', 'QL09p050966' => 'qlo', 'QL09p051067' => 'qlo', 'QL12p022706' => 'qlo', 'RcHm_v2.0_Chr2g0119601' => 'rch', 'RcHm_v2.0_Chr3g0459591' => 'rch', 'RcHm_v2.0_Chr4g0418521' => 'rch', 'RcHm_v2.0_Chr4g0418531' => 'rch', 'RcHm_v2.0_Chr4g0418541' => 'rch', 'RcHm_v2.0_Chr6g0291641' => 'rch', 'Rhsim01G0086300' => 'rsi', 'Rhsim01G0276300' => 'rsi', 'Rhsim01G0276500' => 'rsi', 'Rhsim04G0207700' => 'rsi', 'Rhsim05G0234500' => 'rsi', 'Rhsim13G0022400' => 'rsi', 'Sabra02G0167900' => 'sbr', 'Sabra04G0158500' => 'sbr', 'Sabra08G0159800' => 'sbr', 'Sabra10G0011500' => 'sbr', 'Sabra14G0104400' => 'sbr', 'SalBow2G2440' => 'sbo', 'SalBow4G2265' => 'sbo', 'Sc02g0000060' => 'sci', 'Sc05g0005020' => 'sci', 'Sc13g0003890' => 'sci', 'Sed0014865' => 'sed', 'Sed0017224' => 'sed', 'Sed0026391' => 'sed', 'SEGI_00063' => 'sgi', 'SEGI_10967' => 'sgi', 'SEGI_17510' => 'sgi', 'SEGI_24396' => 'sgi', 'SEGI_39719' => 'sgi', 'SEGI_41392' => 'sgi', 'SGA_v2.0_scaffold11G05794' => 'sas', 'SGA_v2.0_scaffold142G35607' => 'sas', 'SGA_v2.0_scaffold1G00447' => 'sas', 'SHI15388' => 'shi', 'SHI15394' => 'shi', 'SHI15396' => 'shi', 'SHI15399' => 'shi', 'SMO343G0151' => 'smo', 'SMO367G1118' => 'smo', 'Solyc01g080200.3' => 'sly', 'Solyc06g008960.3' => 'sly', 'Solyc09g064780.3' => 'sly', 'Sopen01g031980' => 'spe', 'Sopen06g003710' => 'spe', 'Sopen09g026460' => 'spe', 'Sp3g21240' => 'spa', 'Sp4g30030' => 'spa', 'TAR365G0022' => 'tar', 'TAR365G1023' => 'tar', 'TAR365G1253' => 'tar', 'TAR623G0078' => 'tar', 'TAR623G1721' => 'tar', 'TAR633G0959' => 'tar', 'THA.LOC104802225' => 'tha', 'THA.LOC104804769' => 'tha', 'THA.LOC104808660' => 'tha', 'THA.LOC104812792' => 'tha', 'Thecc.01G284000' => 'tca', 'Thecc.04G220600' => 'tca', 'Thecc.05G268900' => 'tca', 'Thecc.08G171100' => 'tca', 'Thhalv10001284m.g' => 'esa', 'Thhalv10019912m.g' => 'esa', 'TPR.G14189' => 'tpr', 'TPR.G18110' => 'tpr', 'TPR.G18130' => 'tpr', 'TPR.G18131' => 'tpr', 'TPR.G18140' => 'tpr', 'TPR.G24282' => 'tpr', 'TPR.G25221' => 'tpr', 'TPR.G29267' => 'tpr', 'TPR.G35315' => 'tpr', 'TPR.G36173' => 'tpr', 'TWI09G0794' => 'twi', 'TWI59G1348' => 'twi', 'TWI74G0430' => 'twi', 'unitig_26.g8940' => 'ugi', 'unitig_749.g13744' => 'ugi', 'unitig_749.g13745' => 'ugi', 'vmacro08269' => 'vma', 'vmacro14937' => 'vma', 'vmacro20401' => 'vma', 'VMungo0464G1349' => 'vmu', 'VMungo0540G0289' => 'vmu', 'VMungo1215G1590' => 'vmu', 'VMungo1309G0221' => 'vmu', 'VMungo1309G2815' => 'vmu', 'VMungo1383G0239' => 'vmu', 'VMungo1383G2910' => 'vmu', 'Zm00001eb095270' => 'zma', 'Zm00001eb095280' => 'zma', 'Zm00001eb111630' => 'zma', 'Zm00001eb237080' => 'zma', 'Zm00001eb273740' => 'zma', 'Zm00001eb285040' => 'zma', 'Zm00001eb330790' => 'zma', 'Zm00001eb337380' => 'zma' ) $gf_id = 'HOM05D001484' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001484' ) $data_identifier = 'HOM05D001484' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 2, 'aly' => (int) 2, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 22, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 7, 'hma' => (int) 2, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 7, 'mtr' => (int) 10, 'cme' => (int) 2, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 4, 'ppa' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 4, 'qlo' => (int) 9, 'rch' => (int) 6, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 10, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 7, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb337380' $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' => 'HOM05D001484', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p31500' => 'bna', 'A05p00020' => 'bna', 'A07p08820' => 'bna', 'Aa31LG4G3300' => 'aar', 'Aa31LG8G10030' => 'aar', 'Actinidia00731' => 'ach', 'Actinidia11473' => 'ach', 'Actinidia23469' => 'ach', 'Actinidia24318' => 'ach', 'Actinidia40196' => 'ach', 'Actinidia40197' => 'ach', 'Actinidia40198' => 'ach', 'Ah.08g212990' => 'amhyb', 'Ah.15g091720' => 'amhyb', 'AL3G38260' => 'aly', 'AL4G47710' => 'aly', 'Aqoxy2G00671' => 'aox', 'Aqoxy2G03236' => 'aox', 'arahy.Tifrunner.gnm1.ann1.05IDCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KR684' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATY3SJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK6QJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6APGL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IDT7Z9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM073U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ0R87' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LE7RV4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT4QRX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V5ENPK' => 'arhy', 'AT2G48110' => 'ath', 'AT3G23590' => 'ath', 'ATR0626G186' => 'atr', 'ATR1127G141' => 'atr', 'Atru.chr4.2583' => 'acertr', 'Atru.chr5.1358' => 'acertr', 'Atru.chr5.1359' => 'acertr', 'Atru.chr8.46' => 'acertr', 'AUR62002640' => 'cqu', 'AUR62030055' => 'cqu', 'AUR62033713' => 'cqu', 'AUR62033714' => 'cqu', 'AUR62036795' => 'cqu', 'AUR62039891' => 'cqu', 'BcaB02g08737' => 'bca', 'BcaB04g20441' => 'bca', 'BcaB06g26509' => 'bca', 'BcaB06g26510' => 'bca', 'BcaB06g26511' => 'bca', 'BcaB06g26512' => 'bca', 'BcaB06g26513' => 'bca', 'BcaC02g12564' => 'bca', 'BcaC02g12565' => 'bca', 'BcaC02g12794' => 'bca', 'BcaC02g12795' => 'bca', 'BcaC02g12796' => 'bca', 'BcaC06g35541' => 'bca', 'BNapus_Darmor_BZH_scaffold_188p00080' => 'bna', 'BNapus_Darmor_BZH_scaffold_188p00090' => 'bna', 'BolC1t03972H' => 'bol', 'BolC1t03973H' => 'bol', 'BolC4t21680H' => 'bol', 'BolC7t41863H' => 'bol', 'BolSC55t61227H' => 'bol', 'BolSC55t61228H' => 'bol', 'BraA01t03278Z' => 'bra', 'BraA05t18998Z' => 'bra', 'BraA07t28673Z' => 'bra', 'C01p40150' => 'bna', 'C05p12370' => 'bna', 'C07p13680' => 'bna', 'CAN.G1006.16' => 'can', 'CAN.G1006.17' => 'can', 'CAN.G1170.2' => 'can', 'CAN.G962.7' => 'can', 'CANSAT25G2179' => 'cansat', 'CANSAT78G1573' => 'cansat', 'CARHR099510' => 'chi', 'CARHR143510' => 'chi', 'Carub.0003s2380' => 'cru', 'Carub.0004s3082' => 'cru', 'Ca_00614_v3' => 'car', 'Ca_07801_v3' => 'car', 'Ca_08567_v3' => 'car', 'Ca_09571_v3' => 'car', 'CBR_g19290' => 'cbr', 'Cc01_g19770' => 'ccan', 'Cc03_g03030' => 'ccan', 'CDE07G0968' => 'cde', 'CDE09G1441' => 'cde', 'Cfa006103' => 'cfa', 'Cfa015573' => 'cfa', 'Cfa016988' => 'cfa', 'Ciclev10006738m.g' => 'ccl', 'Ciclev10010920m.g' => 'ccl', 'Ciclev10018517m.g' => 'ccl', 'CiPaw.01G159200' => 'cil', 'CiPaw.02G091000' => 'cil', 'CiPaw.02G091100' => 'cil', 'CiPaw.08G103100' => 'cil', 'CiPaw.09G224900' => 'cil', 'ClCG06G005740' => 'cla', 'ClCG07G000090' => 'cla', 'ClCG07G000100' => 'cla', 'COL.COLO4_09143' => 'col', 'COL.COLO4_25124' => 'col', 'Cpa.g.sc16.34' => 'cpa', 'Cpa.g.sc3504.1' => 'cpa', 'Cpa.g.sc60.37' => 'cpa', 'CsaV3_6G018520' => 'csa', 'CsaV3_6G036860' => 'csa', 'CSS0001072' => 'camsi', 'CSS0020208' => 'camsi', 'CSS0021253' => 'camsi', 'CSS0022190' => 'camsi', 'CSS0036150' => 'camsi', 'CSS0040442' => 'camsi', 'CSS0042300' => 'camsi', 'CSS0045298' => 'camsi', 'DCAR_012449' => 'dca', 'DCAR_018405' => 'dca', 'DCAR_024573' => 'dca', 'DCAR_030591' => 'dca', 'Dinv16926' => 'din', 'Dinv32963' => 'din', 'Dinv38382' => 'din', 'Dinv38383' => 'din', 'Duzib133G0974' => 'dzi', 'Duzib138G1867' => 'dzi', 'Duzib211G0420' => 'dzi', 'Duzib212G0930' => 'dzi', 'ECA234G1645' => 'eca', 'ECA247G3467' => 'eca', 'ECA248G1703' => 'eca', 'EL10Ac3g06327' => 'bvu', 'EL10Ac7g17204' => 'bvu', 'Eucgr.A00855' => 'egr', 'Eucgr.A00858' => 'egr', 'Eucgr.H01520' => 'egr', 'Eucgr.H03604' => 'egr', 'Eucgr.L03465' => 'egr', 'Eucgr.L03466' => 'egr', 'FAN01G0988' => 'fan', 'FAN02G3892' => 'fan', 'FAN05G3381' => 'fan', 'FAN07G0967' => 'fan', 'FAN07G1493' => 'fan', 'FAN08G3125' => 'fan', 'FAN09G0402' => 'fan', 'FAN12G2594' => 'fan', 'FAN12G3879' => 'fan', 'FAN14G1546' => 'fan', 'FAN15G3626' => 'fan', 'FAN17G0588' => 'fan', 'FAN17G0609' => 'fan', 'FAN18G2817' => 'fan', 'FAN19G1305' => 'fan', 'FAN20G1787' => 'fan', 'FAN22G0073' => 'fan', 'FAN22G0352' => 'fan', 'FAN22G0368' => 'fan', 'FAN22G2273' => 'fan', 'FAN24G1998' => 'fan', 'FAN27G1317' => 'fan', 'FvH4_2g23980' => 'fve', 'FvH4_4g14380' => 'fve', 'FvH4_4g14390' => 'fve', 'FvH4_6g09250' => 'fve', 'Glyma.03G151100' => 'gma', 'Glyma.04G122550' => 'gma', 'Glyma.05G001600' => 'gma', 'Glyma.09G270766' => 'gma', 'Glyma.09G270832' => 'gma', 'Glyma.13G209800' => 'gma', 'Glyma.15G102800' => 'gma', 'Glyma.18G218900' => 'gma', 'Glyma.19G001500' => 'gma', 'Glyma.19G153600' => 'gma', 'Gohir.A02G028600' => 'ghi', 'Gohir.A08G045000' => 'ghi', 'Gohir.A11G120500' => 'ghi', 'Gohir.A12G006200' => 'ghi', 'Gohir.A12G006250' => 'ghi', 'Gohir.D02G036300' => 'ghi', 'Gohir.D08G054700' => 'ghi', 'Gohir.D11G125600' => 'ghi', 'Gohir.D12G005700' => 'ghi', 'Gorai.004G055200' => 'gra', 'Gorai.005G040400' => 'gra', 'Gorai.007G134500' => 'gra', 'Gorai.008G005500' => 'gra', 'GSVIVG01011094001' => 'vvi', 'GSVIVG01017879001' => 'vvi', 'GSVIVG01025988001' => 'vvi', 'GSVIVG01029847001' => 'vvi', 'HanXRQChr10g0282901' => 'han', 'HanXRQChr10g0310371' => 'han', 'HanXRQChr10g0315041' => 'han', 'HanXRQChr11g0327651' => 'han', 'HanXRQChr12g0359391' => 'han', 'Haze_00972' => 'cav', 'Haze_00973' => 'cav', 'Haze_00974' => 'cav', 'Haze_04747' => 'cav', 'Haze_04749' => 'cav', 'Haze_04750' => 'cav', 'Haze_21217' => 'cav', 'Hma1.2p1_1037F.1_g250680' => 'hma', 'Hma1.2p1_1644F.1_g295320' => 'hma', 'HPP92_011322' => 'vpl', 'HPP92_011323' => 'vpl', 'HPP92_011324' => 'vpl', 'HPP92_011325' => 'vpl', 'HPP92_011326' => 'vpl', 'Hund12205' => 'sun', 'Hund17957' => 'sun', 'Lalb_Chr06g0176771' => 'lal', 'Lalb_Chr18g0056021' => 'lal', 'Lalb_Chr18g0056031' => 'lal', 'Lalb_Chr18g0056041' => 'lal', 'Lalb_Chr20g0107751' => 'lal', 'Lalb_Chr20g0118371' => 'lal', 'Lj1g0010239' => 'lja', 'Lj1g0017101' => 'lja', 'Lj2A1178G40' => 'lonja', 'Lj2A54G84' => 'lonja', 'Lj2g0015248' => 'lja', 'Lj3A761T51' => 'lonja', 'Lj6g0018116' => 'lja', 'Lsat_1_v5_gn_4_136040' => 'lsa', 'Lsat_1_v5_gn_5_187461' => 'lsa', 'Lsat_1_v5_gn_5_77001' => 'lsa', 'Lsat_1_v5_gn_9_4461' => 'lsa', 'Manes.01G210100' => 'mes', 'Manes.03G185600' => 'mes', 'Manes.05G073300' => 'mes', 'Manes.09G120300' => 'mes', 'Manes.15G022100' => 'mes', 'Mapoly0096s0053' => 'mpo', 'MBI03_g14058_MAGBIO' => 'mbi', 'MBI03_g33876_MAGBIO' => 'mbi', 'MBI03_g36854_MAGBIO' => 'mbi', 'MBI17_g11997_MAGBIO' => 'mbi', 'MD03G1269000' => 'mdo', 'MD04G1179600' => 'mdo', 'MD11G1289800' => 'mdo', 'MD12G1194700' => 'mdo', 'MD13G1182100' => 'mdo', 'MD13G1182200' => 'mdo', 'MD16G1182600' => 'mdo', 'Medtr2g021400' => 'mtr', 'Medtr2g021470' => 'mtr', 'Medtr2g105810' => 'mtr', 'Medtr3g033580' => 'mtr', 'Medtr6g007970' => 'mtr', 'Medtr7g056330' => 'mtr', 'Medtr7g074290' => 'mtr', 'Medtr7g074380' => 'mtr', 'Medtr7g094550' => 'mtr', 'Medtr8g069995' => 'mtr', 'MELO3C014345.2' => 'cme', 'MELO3C021395.2' => 'cme', 'Migut.D00262' => 'egut', 'Migut.G00257' => 'egut', 'MSTRG.21575' => 'ama', 'MSTRG.3985' => 'ama', 'Nitab4.5_0000295g0140' => 'nta', 'Nitab4.5_0000732g0140' => 'nta', 'Nitab4.5_0003162g0020' => 'nta', 'Nitab4.5_0006180g0090' => 'nta', 'Nitab4.5_0006390g0010' => 'nta', 'Nitab4.5_0007392g0040' => 'nta', 'Nn1g02140' => 'nnu', 'Nn4g26168' => 'nnu', 'Nn5g26754' => 'nnu', 'Oeu001433.1' => 'oeu', 'Oeu010299.2' => 'oeu', 'Oeu011171.1' => 'oeu', 'Oeu037675.1' => 'oeu', 'Oeu038359.1' => 'oeu', 'Oeu063834.1' => 'oeu', 'Oeu063835.1' => 'oeu', 'Os05g0312000' => 'osa', 'Os07g0211101' => 'osa', 'Os07g0211200' => 'osa', 'Os07g0681500' => 'osa', 'Peaxi162Scf00095g01015' => 'pax', 'Peaxi162Scf00104g00329' => 'pax', 'Peaxi162Scf00161g00137' => 'pax', 'PGR004G1665' => 'pgr', 'PGR031G2937' => 'pgr', 'PGR119G2145' => 'pgr', 'PGSC0003DMG400004351' => 'stu', 'PGSC0003DMG400014625' => 'stu', 'PGSC0003DMG401000943' => 'stu', 'Phvul.001G148600' => 'pvu', 'Phvul.004G001700' => 'pvu', 'Phvul.006G154900' => 'pvu', 'Phvul.008G078200' => 'pvu', 'Phvul.011G136500' => 'pvu', 'Potri.002G215600' => 'ptr', 'Potri.008G201600' => 'ptr', 'Potri.014G138400' => 'ptr', 'Potri.016G142500' => 'ptr', 'Pp3c16_10580' => 'ppa', 'Pp3c5_25280' => 'ppa', 'Prupe.1G150000' => 'ppe', 'Prupe.1G150100' => 'ppe', 'Prupe.6G299600' => 'ppe', 'Prupe.8G245000' => 'ppe', 'Psat0s4927g0040' => 'psa', 'Psat1g052080' => 'psa', 'Psat1g183800' => 'psa', 'Psat3g113840' => 'psa', 'Psat3g126120' => 'psa', 'Psat3g126160' => 'psa', 'Psat3g158760' => 'psa', 'Psat3g158840' => 'psa', 'PSO170G2858' => 'pso', 'PSO339G0606' => 'pso', 'PSO384G4709' => 'pso', 'PSO407G0334' => 'pso', 'QL04p040276' => 'qlo', 'QL06p005458' => 'qlo', 'QL06p005472' => 'qlo', 'QL07p030546' => 'qlo', 'QL07p031519' => 'qlo', 'QL09p050949' => 'qlo', 'QL09p050966' => 'qlo', 'QL09p051067' => 'qlo', 'QL12p022706' => 'qlo', 'RcHm_v2.0_Chr2g0119601' => 'rch', 'RcHm_v2.0_Chr3g0459591' => 'rch', 'RcHm_v2.0_Chr4g0418521' => 'rch', 'RcHm_v2.0_Chr4g0418531' => 'rch', 'RcHm_v2.0_Chr4g0418541' => 'rch', 'RcHm_v2.0_Chr6g0291641' => 'rch', 'Rhsim01G0086300' => 'rsi', 'Rhsim01G0276300' => 'rsi', 'Rhsim01G0276500' => 'rsi', 'Rhsim04G0207700' => 'rsi', 'Rhsim05G0234500' => 'rsi', 'Rhsim13G0022400' => 'rsi', 'Sabra02G0167900' => 'sbr', 'Sabra04G0158500' => 'sbr', 'Sabra08G0159800' => 'sbr', 'Sabra10G0011500' => 'sbr', 'Sabra14G0104400' => 'sbr', 'SalBow2G2440' => 'sbo', 'SalBow4G2265' => 'sbo', 'Sc02g0000060' => 'sci', 'Sc05g0005020' => 'sci', 'Sc13g0003890' => 'sci', 'Sed0014865' => 'sed', 'Sed0017224' => 'sed', 'Sed0026391' => 'sed', 'SEGI_00063' => 'sgi', 'SEGI_10967' => 'sgi', 'SEGI_17510' => 'sgi', 'SEGI_24396' => 'sgi', 'SEGI_39719' => 'sgi', 'SEGI_41392' => 'sgi', 'SGA_v2.0_scaffold11G05794' => 'sas', 'SGA_v2.0_scaffold142G35607' => 'sas', 'SGA_v2.0_scaffold1G00447' => 'sas', 'SHI15388' => 'shi', 'SHI15394' => 'shi', 'SHI15396' => 'shi', 'SHI15399' => 'shi', 'SMO343G0151' => 'smo', 'SMO367G1118' => 'smo', 'Solyc01g080200.3' => 'sly', 'Solyc06g008960.3' => 'sly', 'Solyc09g064780.3' => 'sly', 'Sopen01g031980' => 'spe', 'Sopen06g003710' => 'spe', 'Sopen09g026460' => 'spe', 'Sp3g21240' => 'spa', 'Sp4g30030' => 'spa', 'TAR365G0022' => 'tar', 'TAR365G1023' => 'tar', 'TAR365G1253' => 'tar', 'TAR623G0078' => 'tar', 'TAR623G1721' => 'tar', 'TAR633G0959' => 'tar', 'THA.LOC104802225' => 'tha', 'THA.LOC104804769' => 'tha', 'THA.LOC104808660' => 'tha', 'THA.LOC104812792' => 'tha', 'Thecc.01G284000' => 'tca', 'Thecc.04G220600' => 'tca', 'Thecc.05G268900' => 'tca', 'Thecc.08G171100' => 'tca', 'Thhalv10001284m.g' => 'esa', 'Thhalv10019912m.g' => 'esa', 'TPR.G14189' => 'tpr', 'TPR.G18110' => 'tpr', 'TPR.G18130' => 'tpr', 'TPR.G18131' => 'tpr', 'TPR.G18140' => 'tpr', 'TPR.G24282' => 'tpr', 'TPR.G25221' => 'tpr', 'TPR.G29267' => 'tpr', 'TPR.G35315' => 'tpr', 'TPR.G36173' => 'tpr', 'TWI09G0794' => 'twi', 'TWI59G1348' => 'twi', 'TWI74G0430' => 'twi', 'unitig_26.g8940' => 'ugi', 'unitig_749.g13744' => 'ugi', 'unitig_749.g13745' => 'ugi', 'vmacro08269' => 'vma', 'vmacro14937' => 'vma', 'vmacro20401' => 'vma', 'VMungo0464G1349' => 'vmu', 'VMungo0540G0289' => 'vmu', 'VMungo1215G1590' => 'vmu', 'VMungo1309G0221' => 'vmu', 'VMungo1309G2815' => 'vmu', 'VMungo1383G0239' => 'vmu', 'VMungo1383G2910' => 'vmu', 'Zm00001eb095270' => 'zma', 'Zm00001eb095280' => 'zma', 'Zm00001eb111630' => 'zma', 'Zm00001eb237080' => 'zma', 'Zm00001eb273740' => 'zma', 'Zm00001eb285040' => 'zma', 'Zm00001eb330790' => 'zma', 'Zm00001eb337380' => 'zma' ), 'gf_id' => 'HOM05D001484', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001484' ), 'data_identifier' => 'HOM05D001484', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001484', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p31500' => 'bna', 'A05p00020' => 'bna', 'A07p08820' => 'bna', 'Aa31LG4G3300' => 'aar', 'Aa31LG8G10030' => 'aar', 'Actinidia00731' => 'ach', 'Actinidia11473' => 'ach', 'Actinidia23469' => 'ach', 'Actinidia24318' => 'ach', 'Actinidia40196' => 'ach', 'Actinidia40197' => 'ach', 'Actinidia40198' => 'ach', 'Ah.08g212990' => 'amhyb', 'Ah.15g091720' => 'amhyb', 'AL3G38260' => 'aly', 'AL4G47710' => 'aly', 'Aqoxy2G00671' => 'aox', 'Aqoxy2G03236' => 'aox', 'arahy.Tifrunner.gnm1.ann1.05IDCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KR684' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATY3SJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK6QJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6APGL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IDT7Z9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM073U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ0R87' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LE7RV4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT4QRX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V5ENPK' => 'arhy', 'AT2G48110' => 'ath', 'AT3G23590' => 'ath', 'ATR0626G186' => 'atr', 'ATR1127G141' => 'atr', 'Atru.chr4.2583' => 'acertr', 'Atru.chr5.1358' => 'acertr', 'Atru.chr5.1359' => 'acertr', 'Atru.chr8.46' => 'acertr', 'AUR62002640' => 'cqu', 'AUR62030055' => 'cqu', 'AUR62033713' => 'cqu', 'AUR62033714' => 'cqu', 'AUR62036795' => 'cqu', 'AUR62039891' => 'cqu', 'BcaB02g08737' => 'bca', 'BcaB04g20441' => 'bca', 'BcaB06g26509' => 'bca', 'BcaB06g26510' => 'bca', 'BcaB06g26511' => 'bca', 'BcaB06g26512' => 'bca', 'BcaB06g26513' => 'bca', 'BcaC02g12564' => 'bca', 'BcaC02g12565' => 'bca', 'BcaC02g12794' => 'bca', 'BcaC02g12795' => 'bca', 'BcaC02g12796' => 'bca', 'BcaC06g35541' => 'bca', 'BNapus_Darmor_BZH_scaffold_188p00080' => 'bna', 'BNapus_Darmor_BZH_scaffold_188p00090' => 'bna', 'BolC1t03972H' => 'bol', 'BolC1t03973H' => 'bol', 'BolC4t21680H' => 'bol', 'BolC7t41863H' => 'bol', 'BolSC55t61227H' => 'bol', 'BolSC55t61228H' => 'bol', 'BraA01t03278Z' => 'bra', 'BraA05t18998Z' => 'bra', 'BraA07t28673Z' => 'bra', 'C01p40150' => 'bna', 'C05p12370' => 'bna', 'C07p13680' => 'bna', 'CAN.G1006.16' => 'can', 'CAN.G1006.17' => 'can', 'CAN.G1170.2' => 'can', 'CAN.G962.7' => 'can', 'CANSAT25G2179' => 'cansat', 'CANSAT78G1573' => 'cansat', 'CARHR099510' => 'chi', 'CARHR143510' => 'chi', 'Carub.0003s2380' => 'cru', 'Carub.0004s3082' => 'cru', 'Ca_00614_v3' => 'car', 'Ca_07801_v3' => 'car', 'Ca_08567_v3' => 'car', 'Ca_09571_v3' => 'car', 'CBR_g19290' => 'cbr', 'Cc01_g19770' => 'ccan', 'Cc03_g03030' => 'ccan', 'CDE07G0968' => 'cde', 'CDE09G1441' => 'cde', 'Cfa006103' => 'cfa', 'Cfa015573' => 'cfa', 'Cfa016988' => 'cfa', 'Ciclev10006738m.g' => 'ccl', 'Ciclev10010920m.g' => 'ccl', 'Ciclev10018517m.g' => 'ccl', 'CiPaw.01G159200' => 'cil', 'CiPaw.02G091000' => 'cil', 'CiPaw.02G091100' => 'cil', 'CiPaw.08G103100' => 'cil', 'CiPaw.09G224900' => 'cil', 'ClCG06G005740' => 'cla', 'ClCG07G000090' => 'cla', 'ClCG07G000100' => 'cla', 'COL.COLO4_09143' => 'col', 'COL.COLO4_25124' => 'col', 'Cpa.g.sc16.34' => 'cpa', 'Cpa.g.sc3504.1' => 'cpa', 'Cpa.g.sc60.37' => 'cpa', 'CsaV3_6G018520' => 'csa', 'CsaV3_6G036860' => 'csa', 'CSS0001072' => 'camsi', 'CSS0020208' => 'camsi', 'CSS0021253' => 'camsi', 'CSS0022190' => 'camsi', 'CSS0036150' => 'camsi', 'CSS0040442' => 'camsi', 'CSS0042300' => 'camsi', 'CSS0045298' => 'camsi', 'DCAR_012449' => 'dca', 'DCAR_018405' => 'dca', 'DCAR_024573' => 'dca', 'DCAR_030591' => 'dca', 'Dinv16926' => 'din', 'Dinv32963' => 'din', 'Dinv38382' => 'din', 'Dinv38383' => 'din', 'Duzib133G0974' => 'dzi', 'Duzib138G1867' => 'dzi', 'Duzib211G0420' => 'dzi', 'Duzib212G0930' => 'dzi', 'ECA234G1645' => 'eca', 'ECA247G3467' => 'eca', 'ECA248G1703' => 'eca', 'EL10Ac3g06327' => 'bvu', 'EL10Ac7g17204' => 'bvu', 'Eucgr.A00855' => 'egr', 'Eucgr.A00858' => 'egr', 'Eucgr.H01520' => 'egr', 'Eucgr.H03604' => 'egr', 'Eucgr.L03465' => 'egr', 'Eucgr.L03466' => 'egr', 'FAN01G0988' => 'fan', 'FAN02G3892' => 'fan', 'FAN05G3381' => 'fan', 'FAN07G0967' => 'fan', 'FAN07G1493' => 'fan', 'FAN08G3125' => 'fan', 'FAN09G0402' => 'fan', 'FAN12G2594' => 'fan', 'FAN12G3879' => 'fan', 'FAN14G1546' => 'fan', 'FAN15G3626' => 'fan', 'FAN17G0588' => 'fan', 'FAN17G0609' => 'fan', 'FAN18G2817' => 'fan', 'FAN19G1305' => 'fan', 'FAN20G1787' => 'fan', 'FAN22G0073' => 'fan', 'FAN22G0352' => 'fan', 'FAN22G0368' => 'fan', 'FAN22G2273' => 'fan', 'FAN24G1998' => 'fan', 'FAN27G1317' => 'fan', 'FvH4_2g23980' => 'fve', 'FvH4_4g14380' => 'fve', 'FvH4_4g14390' => 'fve', 'FvH4_6g09250' => 'fve', 'Glyma.03G151100' => 'gma', 'Glyma.04G122550' => 'gma', 'Glyma.05G001600' => 'gma', 'Glyma.09G270766' => 'gma', 'Glyma.09G270832' => 'gma', 'Glyma.13G209800' => 'gma', 'Glyma.15G102800' => 'gma', 'Glyma.18G218900' => 'gma', 'Glyma.19G001500' => 'gma', 'Glyma.19G153600' => 'gma', 'Gohir.A02G028600' => 'ghi', 'Gohir.A08G045000' => 'ghi', 'Gohir.A11G120500' => 'ghi', 'Gohir.A12G006200' => 'ghi', 'Gohir.A12G006250' => 'ghi', 'Gohir.D02G036300' => 'ghi', 'Gohir.D08G054700' => 'ghi', 'Gohir.D11G125600' => 'ghi', 'Gohir.D12G005700' => 'ghi', 'Gorai.004G055200' => 'gra', 'Gorai.005G040400' => 'gra', 'Gorai.007G134500' => 'gra', 'Gorai.008G005500' => 'gra', 'GSVIVG01011094001' => 'vvi', 'GSVIVG01017879001' => 'vvi', 'GSVIVG01025988001' => 'vvi', 'GSVIVG01029847001' => 'vvi', 'HanXRQChr10g0282901' => 'han', 'HanXRQChr10g0310371' => 'han', 'HanXRQChr10g0315041' => 'han', 'HanXRQChr11g0327651' => 'han', 'HanXRQChr12g0359391' => 'han', 'Haze_00972' => 'cav', 'Haze_00973' => 'cav', 'Haze_00974' => 'cav', 'Haze_04747' => 'cav', 'Haze_04749' => 'cav', 'Haze_04750' => 'cav', 'Haze_21217' => 'cav', 'Hma1.2p1_1037F.1_g250680' => 'hma', 'Hma1.2p1_1644F.1_g295320' => 'hma', 'HPP92_011322' => 'vpl', 'HPP92_011323' => 'vpl', 'HPP92_011324' => 'vpl', 'HPP92_011325' => 'vpl', 'HPP92_011326' => 'vpl', 'Hund12205' => 'sun', 'Hund17957' => 'sun', 'Lalb_Chr06g0176771' => 'lal', 'Lalb_Chr18g0056021' => 'lal', 'Lalb_Chr18g0056031' => 'lal', 'Lalb_Chr18g0056041' => 'lal', 'Lalb_Chr20g0107751' => 'lal', 'Lalb_Chr20g0118371' => 'lal', 'Lj1g0010239' => 'lja', 'Lj1g0017101' => 'lja', 'Lj2A1178G40' => 'lonja', 'Lj2A54G84' => 'lonja', 'Lj2g0015248' => 'lja', 'Lj3A761T51' => 'lonja', 'Lj6g0018116' => 'lja', 'Lsat_1_v5_gn_4_136040' => 'lsa', 'Lsat_1_v5_gn_5_187461' => 'lsa', 'Lsat_1_v5_gn_5_77001' => 'lsa', 'Lsat_1_v5_gn_9_4461' => 'lsa', 'Manes.01G210100' => 'mes', 'Manes.03G185600' => 'mes', 'Manes.05G073300' => 'mes', 'Manes.09G120300' => 'mes', 'Manes.15G022100' => 'mes', 'Mapoly0096s0053' => 'mpo', 'MBI03_g14058_MAGBIO' => 'mbi', 'MBI03_g33876_MAGBIO' => 'mbi', 'MBI03_g36854_MAGBIO' => 'mbi', 'MBI17_g11997_MAGBIO' => 'mbi', 'MD03G1269000' => 'mdo', 'MD04G1179600' => 'mdo', 'MD11G1289800' => 'mdo', 'MD12G1194700' => 'mdo', 'MD13G1182100' => 'mdo', 'MD13G1182200' => 'mdo', 'MD16G1182600' => 'mdo', 'Medtr2g021400' => 'mtr', 'Medtr2g021470' => 'mtr', 'Medtr2g105810' => 'mtr', 'Medtr3g033580' => 'mtr', 'Medtr6g007970' => 'mtr', 'Medtr7g056330' => 'mtr', 'Medtr7g074290' => 'mtr', 'Medtr7g074380' => 'mtr', 'Medtr7g094550' => 'mtr', 'Medtr8g069995' => 'mtr', 'MELO3C014345.2' => 'cme', 'MELO3C021395.2' => 'cme', 'Migut.D00262' => 'egut', 'Migut.G00257' => 'egut', 'MSTRG.21575' => 'ama', 'MSTRG.3985' => 'ama', 'Nitab4.5_0000295g0140' => 'nta', 'Nitab4.5_0000732g0140' => 'nta', 'Nitab4.5_0003162g0020' => 'nta', 'Nitab4.5_0006180g0090' => 'nta', 'Nitab4.5_0006390g0010' => 'nta', 'Nitab4.5_0007392g0040' => 'nta', 'Nn1g02140' => 'nnu', 'Nn4g26168' => 'nnu', 'Nn5g26754' => 'nnu', 'Oeu001433.1' => 'oeu', 'Oeu010299.2' => 'oeu', 'Oeu011171.1' => 'oeu', 'Oeu037675.1' => 'oeu', 'Oeu038359.1' => 'oeu', 'Oeu063834.1' => 'oeu', 'Oeu063835.1' => 'oeu', 'Os05g0312000' => 'osa', 'Os07g0211101' => 'osa', 'Os07g0211200' => 'osa', 'Os07g0681500' => 'osa', 'Peaxi162Scf00095g01015' => 'pax', 'Peaxi162Scf00104g00329' => 'pax', 'Peaxi162Scf00161g00137' => 'pax', 'PGR004G1665' => 'pgr', 'PGR031G2937' => 'pgr', 'PGR119G2145' => 'pgr', 'PGSC0003DMG400004351' => 'stu', 'PGSC0003DMG400014625' => 'stu', 'PGSC0003DMG401000943' => 'stu', 'Phvul.001G148600' => 'pvu', 'Phvul.004G001700' => 'pvu', 'Phvul.006G154900' => 'pvu', 'Phvul.008G078200' => 'pvu', 'Phvul.011G136500' => 'pvu', 'Potri.002G215600' => 'ptr', 'Potri.008G201600' => 'ptr', 'Potri.014G138400' => 'ptr', 'Potri.016G142500' => 'ptr', 'Pp3c16_10580' => 'ppa', 'Pp3c5_25280' => 'ppa', 'Prupe.1G150000' => 'ppe', 'Prupe.1G150100' => 'ppe', 'Prupe.6G299600' => 'ppe', 'Prupe.8G245000' => 'ppe', 'Psat0s4927g0040' => 'psa', 'Psat1g052080' => 'psa', 'Psat1g183800' => 'psa', 'Psat3g113840' => 'psa', 'Psat3g126120' => 'psa', 'Psat3g126160' => 'psa', 'Psat3g158760' => 'psa', 'Psat3g158840' => 'psa', 'PSO170G2858' => 'pso', 'PSO339G0606' => 'pso', 'PSO384G4709' => 'pso', 'PSO407G0334' => 'pso', 'QL04p040276' => 'qlo', 'QL06p005458' => 'qlo', 'QL06p005472' => 'qlo', 'QL07p030546' => 'qlo', 'QL07p031519' => 'qlo', 'QL09p050949' => 'qlo', 'QL09p050966' => 'qlo', 'QL09p051067' => 'qlo', 'QL12p022706' => 'qlo', 'RcHm_v2.0_Chr2g0119601' => 'rch', 'RcHm_v2.0_Chr3g0459591' => 'rch', 'RcHm_v2.0_Chr4g0418521' => 'rch', 'RcHm_v2.0_Chr4g0418531' => 'rch', 'RcHm_v2.0_Chr4g0418541' => 'rch', 'RcHm_v2.0_Chr6g0291641' => 'rch', 'Rhsim01G0086300' => 'rsi', 'Rhsim01G0276300' => 'rsi', 'Rhsim01G0276500' => 'rsi', 'Rhsim04G0207700' => 'rsi', 'Rhsim05G0234500' => 'rsi', 'Rhsim13G0022400' => 'rsi', 'Sabra02G0167900' => 'sbr', 'Sabra04G0158500' => 'sbr', 'Sabra08G0159800' => 'sbr', 'Sabra10G0011500' => 'sbr', 'Sabra14G0104400' => 'sbr', 'SalBow2G2440' => 'sbo', 'SalBow4G2265' => 'sbo', 'Sc02g0000060' => 'sci', 'Sc05g0005020' => 'sci', 'Sc13g0003890' => 'sci', 'Sed0014865' => 'sed', 'Sed0017224' => 'sed', 'Sed0026391' => 'sed', 'SEGI_00063' => 'sgi', 'SEGI_10967' => 'sgi', 'SEGI_17510' => 'sgi', 'SEGI_24396' => 'sgi', 'SEGI_39719' => 'sgi', 'SEGI_41392' => 'sgi', 'SGA_v2.0_scaffold11G05794' => 'sas', 'SGA_v2.0_scaffold142G35607' => 'sas', 'SGA_v2.0_scaffold1G00447' => 'sas', 'SHI15388' => 'shi', 'SHI15394' => 'shi', 'SHI15396' => 'shi', 'SHI15399' => 'shi', 'SMO343G0151' => 'smo', 'SMO367G1118' => 'smo', 'Solyc01g080200.3' => 'sly', 'Solyc06g008960.3' => 'sly', 'Solyc09g064780.3' => 'sly', 'Sopen01g031980' => 'spe', 'Sopen06g003710' => 'spe', 'Sopen09g026460' => 'spe', 'Sp3g21240' => 'spa', 'Sp4g30030' => 'spa', 'TAR365G0022' => 'tar', 'TAR365G1023' => 'tar', 'TAR365G1253' => 'tar', 'TAR623G0078' => 'tar', 'TAR623G1721' => 'tar', 'TAR633G0959' => 'tar', 'THA.LOC104802225' => 'tha', 'THA.LOC104804769' => 'tha', 'THA.LOC104808660' => 'tha', 'THA.LOC104812792' => 'tha', 'Thecc.01G284000' => 'tca', 'Thecc.04G220600' => 'tca', 'Thecc.05G268900' => 'tca', 'Thecc.08G171100' => 'tca', 'Thhalv10001284m.g' => 'esa', 'Thhalv10019912m.g' => 'esa', 'TPR.G14189' => 'tpr', 'TPR.G18110' => 'tpr', 'TPR.G18130' => 'tpr', 'TPR.G18131' => 'tpr', 'TPR.G18140' => 'tpr', 'TPR.G24282' => 'tpr', 'TPR.G25221' => 'tpr', 'TPR.G29267' => 'tpr', 'TPR.G35315' => 'tpr', 'TPR.G36173' => 'tpr', 'TWI09G0794' => 'twi', 'TWI59G1348' => 'twi', 'TWI74G0430' => 'twi', 'unitig_26.g8940' => 'ugi', 'unitig_749.g13744' => 'ugi', 'unitig_749.g13745' => 'ugi', 'vmacro08269' => 'vma', 'vmacro14937' => 'vma', 'vmacro20401' => 'vma', 'VMungo0464G1349' => 'vmu', 'VMungo0540G0289' => 'vmu', 'VMungo1215G1590' => 'vmu', 'VMungo1309G0221' => 'vmu', 'VMungo1309G2815' => 'vmu', 'VMungo1383G0239' => 'vmu', 'VMungo1383G2910' => 'vmu', 'Zm00001eb095270' => 'zma', 'Zm00001eb095280' => 'zma', 'Zm00001eb111630' => 'zma', 'Zm00001eb237080' => 'zma', 'Zm00001eb273740' => 'zma', 'Zm00001eb285040' => 'zma', 'Zm00001eb330790' => 'zma', 'Zm00001eb337380' => 'zma' ) $gf_id = 'HOM05D001484' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001484' ) $data_identifier = 'HOM05D001484' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 2, 'aly' => (int) 2, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 22, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 7, 'hma' => (int) 2, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 7, 'mtr' => (int) 10, 'cme' => (int) 2, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 4, 'ppa' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 4, 'qlo' => (int) 9, 'rch' => (int) 6, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 10, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 7, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb337380' $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' => 'HOM05D001484', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p31500' => 'bna', 'A05p00020' => 'bna', 'A07p08820' => 'bna', 'Aa31LG4G3300' => 'aar', 'Aa31LG8G10030' => 'aar', 'Actinidia00731' => 'ach', 'Actinidia11473' => 'ach', 'Actinidia23469' => 'ach', 'Actinidia24318' => 'ach', 'Actinidia40196' => 'ach', 'Actinidia40197' => 'ach', 'Actinidia40198' => 'ach', 'Ah.08g212990' => 'amhyb', 'Ah.15g091720' => 'amhyb', 'AL3G38260' => 'aly', 'AL4G47710' => 'aly', 'Aqoxy2G00671' => 'aox', 'Aqoxy2G03236' => 'aox', 'arahy.Tifrunner.gnm1.ann1.05IDCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KR684' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATY3SJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK6QJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6APGL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IDT7Z9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM073U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ0R87' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LE7RV4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT4QRX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V5ENPK' => 'arhy', 'AT2G48110' => 'ath', 'AT3G23590' => 'ath', 'ATR0626G186' => 'atr', 'ATR1127G141' => 'atr', 'Atru.chr4.2583' => 'acertr', 'Atru.chr5.1358' => 'acertr', 'Atru.chr5.1359' => 'acertr', 'Atru.chr8.46' => 'acertr', 'AUR62002640' => 'cqu', 'AUR62030055' => 'cqu', 'AUR62033713' => 'cqu', 'AUR62033714' => 'cqu', 'AUR62036795' => 'cqu', 'AUR62039891' => 'cqu', 'BcaB02g08737' => 'bca', 'BcaB04g20441' => 'bca', 'BcaB06g26509' => 'bca', 'BcaB06g26510' => 'bca', 'BcaB06g26511' => 'bca', 'BcaB06g26512' => 'bca', 'BcaB06g26513' => 'bca', 'BcaC02g12564' => 'bca', 'BcaC02g12565' => 'bca', 'BcaC02g12794' => 'bca', 'BcaC02g12795' => 'bca', 'BcaC02g12796' => 'bca', 'BcaC06g35541' => 'bca', 'BNapus_Darmor_BZH_scaffold_188p00080' => 'bna', 'BNapus_Darmor_BZH_scaffold_188p00090' => 'bna', 'BolC1t03972H' => 'bol', 'BolC1t03973H' => 'bol', 'BolC4t21680H' => 'bol', 'BolC7t41863H' => 'bol', 'BolSC55t61227H' => 'bol', 'BolSC55t61228H' => 'bol', 'BraA01t03278Z' => 'bra', 'BraA05t18998Z' => 'bra', 'BraA07t28673Z' => 'bra', 'C01p40150' => 'bna', 'C05p12370' => 'bna', 'C07p13680' => 'bna', 'CAN.G1006.16' => 'can', 'CAN.G1006.17' => 'can', 'CAN.G1170.2' => 'can', 'CAN.G962.7' => 'can', 'CANSAT25G2179' => 'cansat', 'CANSAT78G1573' => 'cansat', 'CARHR099510' => 'chi', 'CARHR143510' => 'chi', 'Carub.0003s2380' => 'cru', 'Carub.0004s3082' => 'cru', 'Ca_00614_v3' => 'car', 'Ca_07801_v3' => 'car', 'Ca_08567_v3' => 'car', 'Ca_09571_v3' => 'car', 'CBR_g19290' => 'cbr', 'Cc01_g19770' => 'ccan', 'Cc03_g03030' => 'ccan', 'CDE07G0968' => 'cde', 'CDE09G1441' => 'cde', 'Cfa006103' => 'cfa', 'Cfa015573' => 'cfa', 'Cfa016988' => 'cfa', 'Ciclev10006738m.g' => 'ccl', 'Ciclev10010920m.g' => 'ccl', 'Ciclev10018517m.g' => 'ccl', 'CiPaw.01G159200' => 'cil', 'CiPaw.02G091000' => 'cil', 'CiPaw.02G091100' => 'cil', 'CiPaw.08G103100' => 'cil', 'CiPaw.09G224900' => 'cil', 'ClCG06G005740' => 'cla', 'ClCG07G000090' => 'cla', 'ClCG07G000100' => 'cla', 'COL.COLO4_09143' => 'col', 'COL.COLO4_25124' => 'col', 'Cpa.g.sc16.34' => 'cpa', 'Cpa.g.sc3504.1' => 'cpa', 'Cpa.g.sc60.37' => 'cpa', 'CsaV3_6G018520' => 'csa', 'CsaV3_6G036860' => 'csa', 'CSS0001072' => 'camsi', 'CSS0020208' => 'camsi', 'CSS0021253' => 'camsi', 'CSS0022190' => 'camsi', 'CSS0036150' => 'camsi', 'CSS0040442' => 'camsi', 'CSS0042300' => 'camsi', 'CSS0045298' => 'camsi', 'DCAR_012449' => 'dca', 'DCAR_018405' => 'dca', 'DCAR_024573' => 'dca', 'DCAR_030591' => 'dca', 'Dinv16926' => 'din', 'Dinv32963' => 'din', 'Dinv38382' => 'din', 'Dinv38383' => 'din', 'Duzib133G0974' => 'dzi', 'Duzib138G1867' => 'dzi', 'Duzib211G0420' => 'dzi', 'Duzib212G0930' => 'dzi', 'ECA234G1645' => 'eca', 'ECA247G3467' => 'eca', 'ECA248G1703' => 'eca', 'EL10Ac3g06327' => 'bvu', 'EL10Ac7g17204' => 'bvu', 'Eucgr.A00855' => 'egr', 'Eucgr.A00858' => 'egr', 'Eucgr.H01520' => 'egr', 'Eucgr.H03604' => 'egr', 'Eucgr.L03465' => 'egr', 'Eucgr.L03466' => 'egr', 'FAN01G0988' => 'fan', 'FAN02G3892' => 'fan', 'FAN05G3381' => 'fan', 'FAN07G0967' => 'fan', 'FAN07G1493' => 'fan', 'FAN08G3125' => 'fan', 'FAN09G0402' => 'fan', 'FAN12G2594' => 'fan', 'FAN12G3879' => 'fan', 'FAN14G1546' => 'fan', 'FAN15G3626' => 'fan', 'FAN17G0588' => 'fan', 'FAN17G0609' => 'fan', 'FAN18G2817' => 'fan', 'FAN19G1305' => 'fan', 'FAN20G1787' => 'fan', 'FAN22G0073' => 'fan', 'FAN22G0352' => 'fan', 'FAN22G0368' => 'fan', 'FAN22G2273' => 'fan', 'FAN24G1998' => 'fan', 'FAN27G1317' => 'fan', 'FvH4_2g23980' => 'fve', 'FvH4_4g14380' => 'fve', 'FvH4_4g14390' => 'fve', 'FvH4_6g09250' => 'fve', 'Glyma.03G151100' => 'gma', 'Glyma.04G122550' => 'gma', 'Glyma.05G001600' => 'gma', 'Glyma.09G270766' => 'gma', 'Glyma.09G270832' => 'gma', 'Glyma.13G209800' => 'gma', 'Glyma.15G102800' => 'gma', 'Glyma.18G218900' => 'gma', 'Glyma.19G001500' => 'gma', 'Glyma.19G153600' => 'gma', 'Gohir.A02G028600' => 'ghi', 'Gohir.A08G045000' => 'ghi', 'Gohir.A11G120500' => 'ghi', 'Gohir.A12G006200' => 'ghi', 'Gohir.A12G006250' => 'ghi', 'Gohir.D02G036300' => 'ghi', 'Gohir.D08G054700' => 'ghi', 'Gohir.D11G125600' => 'ghi', 'Gohir.D12G005700' => 'ghi', 'Gorai.004G055200' => 'gra', 'Gorai.005G040400' => 'gra', 'Gorai.007G134500' => 'gra', 'Gorai.008G005500' => 'gra', 'GSVIVG01011094001' => 'vvi', 'GSVIVG01017879001' => 'vvi', 'GSVIVG01025988001' => 'vvi', 'GSVIVG01029847001' => 'vvi', 'HanXRQChr10g0282901' => 'han', 'HanXRQChr10g0310371' => 'han', 'HanXRQChr10g0315041' => 'han', 'HanXRQChr11g0327651' => 'han', 'HanXRQChr12g0359391' => 'han', 'Haze_00972' => 'cav', 'Haze_00973' => 'cav', 'Haze_00974' => 'cav', 'Haze_04747' => 'cav', 'Haze_04749' => 'cav', 'Haze_04750' => 'cav', 'Haze_21217' => 'cav', 'Hma1.2p1_1037F.1_g250680' => 'hma', 'Hma1.2p1_1644F.1_g295320' => 'hma', 'HPP92_011322' => 'vpl', 'HPP92_011323' => 'vpl', 'HPP92_011324' => 'vpl', 'HPP92_011325' => 'vpl', 'HPP92_011326' => 'vpl', 'Hund12205' => 'sun', 'Hund17957' => 'sun', 'Lalb_Chr06g0176771' => 'lal', 'Lalb_Chr18g0056021' => 'lal', 'Lalb_Chr18g0056031' => 'lal', 'Lalb_Chr18g0056041' => 'lal', 'Lalb_Chr20g0107751' => 'lal', 'Lalb_Chr20g0118371' => 'lal', 'Lj1g0010239' => 'lja', 'Lj1g0017101' => 'lja', 'Lj2A1178G40' => 'lonja', 'Lj2A54G84' => 'lonja', 'Lj2g0015248' => 'lja', 'Lj3A761T51' => 'lonja', 'Lj6g0018116' => 'lja', 'Lsat_1_v5_gn_4_136040' => 'lsa', 'Lsat_1_v5_gn_5_187461' => 'lsa', 'Lsat_1_v5_gn_5_77001' => 'lsa', 'Lsat_1_v5_gn_9_4461' => 'lsa', 'Manes.01G210100' => 'mes', 'Manes.03G185600' => 'mes', 'Manes.05G073300' => 'mes', 'Manes.09G120300' => 'mes', 'Manes.15G022100' => 'mes', 'Mapoly0096s0053' => 'mpo', 'MBI03_g14058_MAGBIO' => 'mbi', 'MBI03_g33876_MAGBIO' => 'mbi', 'MBI03_g36854_MAGBIO' => 'mbi', 'MBI17_g11997_MAGBIO' => 'mbi', 'MD03G1269000' => 'mdo', 'MD04G1179600' => 'mdo', 'MD11G1289800' => 'mdo', 'MD12G1194700' => 'mdo', 'MD13G1182100' => 'mdo', 'MD13G1182200' => 'mdo', 'MD16G1182600' => 'mdo', 'Medtr2g021400' => 'mtr', 'Medtr2g021470' => 'mtr', 'Medtr2g105810' => 'mtr', 'Medtr3g033580' => 'mtr', 'Medtr6g007970' => 'mtr', 'Medtr7g056330' => 'mtr', 'Medtr7g074290' => 'mtr', 'Medtr7g074380' => 'mtr', 'Medtr7g094550' => 'mtr', 'Medtr8g069995' => 'mtr', 'MELO3C014345.2' => 'cme', 'MELO3C021395.2' => 'cme', 'Migut.D00262' => 'egut', 'Migut.G00257' => 'egut', 'MSTRG.21575' => 'ama', 'MSTRG.3985' => 'ama', 'Nitab4.5_0000295g0140' => 'nta', 'Nitab4.5_0000732g0140' => 'nta', 'Nitab4.5_0003162g0020' => 'nta', 'Nitab4.5_0006180g0090' => 'nta', 'Nitab4.5_0006390g0010' => 'nta', 'Nitab4.5_0007392g0040' => 'nta', 'Nn1g02140' => 'nnu', 'Nn4g26168' => 'nnu', 'Nn5g26754' => 'nnu', 'Oeu001433.1' => 'oeu', 'Oeu010299.2' => 'oeu', 'Oeu011171.1' => 'oeu', 'Oeu037675.1' => 'oeu', 'Oeu038359.1' => 'oeu', 'Oeu063834.1' => 'oeu', 'Oeu063835.1' => 'oeu', 'Os05g0312000' => 'osa', 'Os07g0211101' => 'osa', 'Os07g0211200' => 'osa', 'Os07g0681500' => 'osa', 'Peaxi162Scf00095g01015' => 'pax', 'Peaxi162Scf00104g00329' => 'pax', 'Peaxi162Scf00161g00137' => 'pax', 'PGR004G1665' => 'pgr', 'PGR031G2937' => 'pgr', 'PGR119G2145' => 'pgr', 'PGSC0003DMG400004351' => 'stu', 'PGSC0003DMG400014625' => 'stu', 'PGSC0003DMG401000943' => 'stu', 'Phvul.001G148600' => 'pvu', 'Phvul.004G001700' => 'pvu', 'Phvul.006G154900' => 'pvu', 'Phvul.008G078200' => 'pvu', 'Phvul.011G136500' => 'pvu', 'Potri.002G215600' => 'ptr', 'Potri.008G201600' => 'ptr', 'Potri.014G138400' => 'ptr', 'Potri.016G142500' => 'ptr', 'Pp3c16_10580' => 'ppa', 'Pp3c5_25280' => 'ppa', 'Prupe.1G150000' => 'ppe', 'Prupe.1G150100' => 'ppe', 'Prupe.6G299600' => 'ppe', 'Prupe.8G245000' => 'ppe', 'Psat0s4927g0040' => 'psa', 'Psat1g052080' => 'psa', 'Psat1g183800' => 'psa', 'Psat3g113840' => 'psa', 'Psat3g126120' => 'psa', 'Psat3g126160' => 'psa', 'Psat3g158760' => 'psa', 'Psat3g158840' => 'psa', 'PSO170G2858' => 'pso', 'PSO339G0606' => 'pso', 'PSO384G4709' => 'pso', 'PSO407G0334' => 'pso', 'QL04p040276' => 'qlo', 'QL06p005458' => 'qlo', 'QL06p005472' => 'qlo', 'QL07p030546' => 'qlo', 'QL07p031519' => 'qlo', 'QL09p050949' => 'qlo', 'QL09p050966' => 'qlo', 'QL09p051067' => 'qlo', 'QL12p022706' => 'qlo', 'RcHm_v2.0_Chr2g0119601' => 'rch', 'RcHm_v2.0_Chr3g0459591' => 'rch', 'RcHm_v2.0_Chr4g0418521' => 'rch', 'RcHm_v2.0_Chr4g0418531' => 'rch', 'RcHm_v2.0_Chr4g0418541' => 'rch', 'RcHm_v2.0_Chr6g0291641' => 'rch', 'Rhsim01G0086300' => 'rsi', 'Rhsim01G0276300' => 'rsi', 'Rhsim01G0276500' => 'rsi', 'Rhsim04G0207700' => 'rsi', 'Rhsim05G0234500' => 'rsi', 'Rhsim13G0022400' => 'rsi', 'Sabra02G0167900' => 'sbr', 'Sabra04G0158500' => 'sbr', 'Sabra08G0159800' => 'sbr', 'Sabra10G0011500' => 'sbr', 'Sabra14G0104400' => 'sbr', 'SalBow2G2440' => 'sbo', 'SalBow4G2265' => 'sbo', 'Sc02g0000060' => 'sci', 'Sc05g0005020' => 'sci', 'Sc13g0003890' => 'sci', 'Sed0014865' => 'sed', 'Sed0017224' => 'sed', 'Sed0026391' => 'sed', 'SEGI_00063' => 'sgi', 'SEGI_10967' => 'sgi', 'SEGI_17510' => 'sgi', 'SEGI_24396' => 'sgi', 'SEGI_39719' => 'sgi', 'SEGI_41392' => 'sgi', 'SGA_v2.0_scaffold11G05794' => 'sas', 'SGA_v2.0_scaffold142G35607' => 'sas', 'SGA_v2.0_scaffold1G00447' => 'sas', 'SHI15388' => 'shi', 'SHI15394' => 'shi', 'SHI15396' => 'shi', 'SHI15399' => 'shi', 'SMO343G0151' => 'smo', 'SMO367G1118' => 'smo', 'Solyc01g080200.3' => 'sly', 'Solyc06g008960.3' => 'sly', 'Solyc09g064780.3' => 'sly', 'Sopen01g031980' => 'spe', 'Sopen06g003710' => 'spe', 'Sopen09g026460' => 'spe', 'Sp3g21240' => 'spa', 'Sp4g30030' => 'spa', 'TAR365G0022' => 'tar', 'TAR365G1023' => 'tar', 'TAR365G1253' => 'tar', 'TAR623G0078' => 'tar', 'TAR623G1721' => 'tar', 'TAR633G0959' => 'tar', 'THA.LOC104802225' => 'tha', 'THA.LOC104804769' => 'tha', 'THA.LOC104808660' => 'tha', 'THA.LOC104812792' => 'tha', 'Thecc.01G284000' => 'tca', 'Thecc.04G220600' => 'tca', 'Thecc.05G268900' => 'tca', 'Thecc.08G171100' => 'tca', 'Thhalv10001284m.g' => 'esa', 'Thhalv10019912m.g' => 'esa', 'TPR.G14189' => 'tpr', 'TPR.G18110' => 'tpr', 'TPR.G18130' => 'tpr', 'TPR.G18131' => 'tpr', 'TPR.G18140' => 'tpr', 'TPR.G24282' => 'tpr', 'TPR.G25221' => 'tpr', 'TPR.G29267' => 'tpr', 'TPR.G35315' => 'tpr', 'TPR.G36173' => 'tpr', 'TWI09G0794' => 'twi', 'TWI59G1348' => 'twi', 'TWI74G0430' => 'twi', 'unitig_26.g8940' => 'ugi', 'unitig_749.g13744' => 'ugi', 'unitig_749.g13745' => 'ugi', 'vmacro08269' => 'vma', 'vmacro14937' => 'vma', 'vmacro20401' => 'vma', 'VMungo0464G1349' => 'vmu', 'VMungo0540G0289' => 'vmu', 'VMungo1215G1590' => 'vmu', 'VMungo1309G0221' => 'vmu', 'VMungo1309G2815' => 'vmu', 'VMungo1383G0239' => 'vmu', 'VMungo1383G2910' => 'vmu', 'Zm00001eb095270' => 'zma', 'Zm00001eb095280' => 'zma', 'Zm00001eb111630' => 'zma', 'Zm00001eb237080' => 'zma', 'Zm00001eb273740' => 'zma', 'Zm00001eb285040' => 'zma', 'Zm00001eb330790' => 'zma', 'Zm00001eb337380' => 'zma' ), 'gf_id' => 'HOM05D001484', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001484' ), 'data_identifier' => 'HOM05D001484', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001484', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p31500' => 'bna', 'A05p00020' => 'bna', 'A07p08820' => 'bna', 'Aa31LG4G3300' => 'aar', 'Aa31LG8G10030' => 'aar', 'Actinidia00731' => 'ach', 'Actinidia11473' => 'ach', 'Actinidia23469' => 'ach', 'Actinidia24318' => 'ach', 'Actinidia40196' => 'ach', 'Actinidia40197' => 'ach', 'Actinidia40198' => 'ach', 'Ah.08g212990' => 'amhyb', 'Ah.15g091720' => 'amhyb', 'AL3G38260' => 'aly', 'AL4G47710' => 'aly', 'Aqoxy2G00671' => 'aox', 'Aqoxy2G03236' => 'aox', 'arahy.Tifrunner.gnm1.ann1.05IDCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KR684' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATY3SJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK6QJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6APGL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IDT7Z9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM073U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ0R87' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LE7RV4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT4QRX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V5ENPK' => 'arhy', 'AT2G48110' => 'ath', 'AT3G23590' => 'ath', 'ATR0626G186' => 'atr', 'ATR1127G141' => 'atr', 'Atru.chr4.2583' => 'acertr', 'Atru.chr5.1358' => 'acertr', 'Atru.chr5.1359' => 'acertr', 'Atru.chr8.46' => 'acertr', 'AUR62002640' => 'cqu', 'AUR62030055' => 'cqu', 'AUR62033713' => 'cqu', 'AUR62033714' => 'cqu', 'AUR62036795' => 'cqu', 'AUR62039891' => 'cqu', 'BcaB02g08737' => 'bca', 'BcaB04g20441' => 'bca', 'BcaB06g26509' => 'bca', 'BcaB06g26510' => 'bca', 'BcaB06g26511' => 'bca', 'BcaB06g26512' => 'bca', 'BcaB06g26513' => 'bca', 'BcaC02g12564' => 'bca', 'BcaC02g12565' => 'bca', 'BcaC02g12794' => 'bca', 'BcaC02g12795' => 'bca', 'BcaC02g12796' => 'bca', 'BcaC06g35541' => 'bca', 'BNapus_Darmor_BZH_scaffold_188p00080' => 'bna', 'BNapus_Darmor_BZH_scaffold_188p00090' => 'bna', 'BolC1t03972H' => 'bol', 'BolC1t03973H' => 'bol', 'BolC4t21680H' => 'bol', 'BolC7t41863H' => 'bol', 'BolSC55t61227H' => 'bol', 'BolSC55t61228H' => 'bol', 'BraA01t03278Z' => 'bra', 'BraA05t18998Z' => 'bra', 'BraA07t28673Z' => 'bra', 'C01p40150' => 'bna', 'C05p12370' => 'bna', 'C07p13680' => 'bna', 'CAN.G1006.16' => 'can', 'CAN.G1006.17' => 'can', 'CAN.G1170.2' => 'can', 'CAN.G962.7' => 'can', 'CANSAT25G2179' => 'cansat', 'CANSAT78G1573' => 'cansat', 'CARHR099510' => 'chi', 'CARHR143510' => 'chi', 'Carub.0003s2380' => 'cru', 'Carub.0004s3082' => 'cru', 'Ca_00614_v3' => 'car', 'Ca_07801_v3' => 'car', 'Ca_08567_v3' => 'car', 'Ca_09571_v3' => 'car', 'CBR_g19290' => 'cbr', 'Cc01_g19770' => 'ccan', 'Cc03_g03030' => 'ccan', 'CDE07G0968' => 'cde', 'CDE09G1441' => 'cde', 'Cfa006103' => 'cfa', 'Cfa015573' => 'cfa', 'Cfa016988' => 'cfa', 'Ciclev10006738m.g' => 'ccl', 'Ciclev10010920m.g' => 'ccl', 'Ciclev10018517m.g' => 'ccl', 'CiPaw.01G159200' => 'cil', 'CiPaw.02G091000' => 'cil', 'CiPaw.02G091100' => 'cil', 'CiPaw.08G103100' => 'cil', 'CiPaw.09G224900' => 'cil', 'ClCG06G005740' => 'cla', 'ClCG07G000090' => 'cla', 'ClCG07G000100' => 'cla', 'COL.COLO4_09143' => 'col', 'COL.COLO4_25124' => 'col', 'Cpa.g.sc16.34' => 'cpa', 'Cpa.g.sc3504.1' => 'cpa', 'Cpa.g.sc60.37' => 'cpa', 'CsaV3_6G018520' => 'csa', 'CsaV3_6G036860' => 'csa', 'CSS0001072' => 'camsi', 'CSS0020208' => 'camsi', 'CSS0021253' => 'camsi', 'CSS0022190' => 'camsi', 'CSS0036150' => 'camsi', 'CSS0040442' => 'camsi', 'CSS0042300' => 'camsi', 'CSS0045298' => 'camsi', 'DCAR_012449' => 'dca', 'DCAR_018405' => 'dca', 'DCAR_024573' => 'dca', 'DCAR_030591' => 'dca', 'Dinv16926' => 'din', 'Dinv32963' => 'din', 'Dinv38382' => 'din', 'Dinv38383' => 'din', 'Duzib133G0974' => 'dzi', 'Duzib138G1867' => 'dzi', 'Duzib211G0420' => 'dzi', 'Duzib212G0930' => 'dzi', 'ECA234G1645' => 'eca', 'ECA247G3467' => 'eca', 'ECA248G1703' => 'eca', 'EL10Ac3g06327' => 'bvu', 'EL10Ac7g17204' => 'bvu', 'Eucgr.A00855' => 'egr', 'Eucgr.A00858' => 'egr', 'Eucgr.H01520' => 'egr', 'Eucgr.H03604' => 'egr', 'Eucgr.L03465' => 'egr', 'Eucgr.L03466' => 'egr', 'FAN01G0988' => 'fan', 'FAN02G3892' => 'fan', 'FAN05G3381' => 'fan', 'FAN07G0967' => 'fan', 'FAN07G1493' => 'fan', 'FAN08G3125' => 'fan', 'FAN09G0402' => 'fan', 'FAN12G2594' => 'fan', 'FAN12G3879' => 'fan', 'FAN14G1546' => 'fan', 'FAN15G3626' => 'fan', 'FAN17G0588' => 'fan', 'FAN17G0609' => 'fan', 'FAN18G2817' => 'fan', 'FAN19G1305' => 'fan', 'FAN20G1787' => 'fan', 'FAN22G0073' => 'fan', 'FAN22G0352' => 'fan', 'FAN22G0368' => 'fan', 'FAN22G2273' => 'fan', 'FAN24G1998' => 'fan', 'FAN27G1317' => 'fan', 'FvH4_2g23980' => 'fve', 'FvH4_4g14380' => 'fve', 'FvH4_4g14390' => 'fve', 'FvH4_6g09250' => 'fve', 'Glyma.03G151100' => 'gma', 'Glyma.04G122550' => 'gma', 'Glyma.05G001600' => 'gma', 'Glyma.09G270766' => 'gma', 'Glyma.09G270832' => 'gma', 'Glyma.13G209800' => 'gma', 'Glyma.15G102800' => 'gma', 'Glyma.18G218900' => 'gma', 'Glyma.19G001500' => 'gma', 'Glyma.19G153600' => 'gma', 'Gohir.A02G028600' => 'ghi', 'Gohir.A08G045000' => 'ghi', 'Gohir.A11G120500' => 'ghi', 'Gohir.A12G006200' => 'ghi', 'Gohir.A12G006250' => 'ghi', 'Gohir.D02G036300' => 'ghi', 'Gohir.D08G054700' => 'ghi', 'Gohir.D11G125600' => 'ghi', 'Gohir.D12G005700' => 'ghi', 'Gorai.004G055200' => 'gra', 'Gorai.005G040400' => 'gra', 'Gorai.007G134500' => 'gra', 'Gorai.008G005500' => 'gra', 'GSVIVG01011094001' => 'vvi', 'GSVIVG01017879001' => 'vvi', 'GSVIVG01025988001' => 'vvi', 'GSVIVG01029847001' => 'vvi', 'HanXRQChr10g0282901' => 'han', 'HanXRQChr10g0310371' => 'han', 'HanXRQChr10g0315041' => 'han', 'HanXRQChr11g0327651' => 'han', 'HanXRQChr12g0359391' => 'han', 'Haze_00972' => 'cav', 'Haze_00973' => 'cav', 'Haze_00974' => 'cav', 'Haze_04747' => 'cav', 'Haze_04749' => 'cav', 'Haze_04750' => 'cav', 'Haze_21217' => 'cav', 'Hma1.2p1_1037F.1_g250680' => 'hma', 'Hma1.2p1_1644F.1_g295320' => 'hma', 'HPP92_011322' => 'vpl', 'HPP92_011323' => 'vpl', 'HPP92_011324' => 'vpl', 'HPP92_011325' => 'vpl', 'HPP92_011326' => 'vpl', 'Hund12205' => 'sun', 'Hund17957' => 'sun', 'Lalb_Chr06g0176771' => 'lal', 'Lalb_Chr18g0056021' => 'lal', 'Lalb_Chr18g0056031' => 'lal', 'Lalb_Chr18g0056041' => 'lal', 'Lalb_Chr20g0107751' => 'lal', 'Lalb_Chr20g0118371' => 'lal', 'Lj1g0010239' => 'lja', 'Lj1g0017101' => 'lja', 'Lj2A1178G40' => 'lonja', 'Lj2A54G84' => 'lonja', 'Lj2g0015248' => 'lja', 'Lj3A761T51' => 'lonja', 'Lj6g0018116' => 'lja', 'Lsat_1_v5_gn_4_136040' => 'lsa', 'Lsat_1_v5_gn_5_187461' => 'lsa', 'Lsat_1_v5_gn_5_77001' => 'lsa', 'Lsat_1_v5_gn_9_4461' => 'lsa', 'Manes.01G210100' => 'mes', 'Manes.03G185600' => 'mes', 'Manes.05G073300' => 'mes', 'Manes.09G120300' => 'mes', 'Manes.15G022100' => 'mes', 'Mapoly0096s0053' => 'mpo', 'MBI03_g14058_MAGBIO' => 'mbi', 'MBI03_g33876_MAGBIO' => 'mbi', 'MBI03_g36854_MAGBIO' => 'mbi', 'MBI17_g11997_MAGBIO' => 'mbi', 'MD03G1269000' => 'mdo', 'MD04G1179600' => 'mdo', 'MD11G1289800' => 'mdo', 'MD12G1194700' => 'mdo', 'MD13G1182100' => 'mdo', 'MD13G1182200' => 'mdo', 'MD16G1182600' => 'mdo', 'Medtr2g021400' => 'mtr', 'Medtr2g021470' => 'mtr', 'Medtr2g105810' => 'mtr', 'Medtr3g033580' => 'mtr', 'Medtr6g007970' => 'mtr', 'Medtr7g056330' => 'mtr', 'Medtr7g074290' => 'mtr', 'Medtr7g074380' => 'mtr', 'Medtr7g094550' => 'mtr', 'Medtr8g069995' => 'mtr', 'MELO3C014345.2' => 'cme', 'MELO3C021395.2' => 'cme', 'Migut.D00262' => 'egut', 'Migut.G00257' => 'egut', 'MSTRG.21575' => 'ama', 'MSTRG.3985' => 'ama', 'Nitab4.5_0000295g0140' => 'nta', 'Nitab4.5_0000732g0140' => 'nta', 'Nitab4.5_0003162g0020' => 'nta', 'Nitab4.5_0006180g0090' => 'nta', 'Nitab4.5_0006390g0010' => 'nta', 'Nitab4.5_0007392g0040' => 'nta', 'Nn1g02140' => 'nnu', 'Nn4g26168' => 'nnu', 'Nn5g26754' => 'nnu', 'Oeu001433.1' => 'oeu', 'Oeu010299.2' => 'oeu', 'Oeu011171.1' => 'oeu', 'Oeu037675.1' => 'oeu', 'Oeu038359.1' => 'oeu', 'Oeu063834.1' => 'oeu', 'Oeu063835.1' => 'oeu', 'Os05g0312000' => 'osa', 'Os07g0211101' => 'osa', 'Os07g0211200' => 'osa', 'Os07g0681500' => 'osa', 'Peaxi162Scf00095g01015' => 'pax', 'Peaxi162Scf00104g00329' => 'pax', 'Peaxi162Scf00161g00137' => 'pax', 'PGR004G1665' => 'pgr', 'PGR031G2937' => 'pgr', 'PGR119G2145' => 'pgr', 'PGSC0003DMG400004351' => 'stu', 'PGSC0003DMG400014625' => 'stu', 'PGSC0003DMG401000943' => 'stu', 'Phvul.001G148600' => 'pvu', 'Phvul.004G001700' => 'pvu', 'Phvul.006G154900' => 'pvu', 'Phvul.008G078200' => 'pvu', 'Phvul.011G136500' => 'pvu', 'Potri.002G215600' => 'ptr', 'Potri.008G201600' => 'ptr', 'Potri.014G138400' => 'ptr', 'Potri.016G142500' => 'ptr', 'Pp3c16_10580' => 'ppa', 'Pp3c5_25280' => 'ppa', 'Prupe.1G150000' => 'ppe', 'Prupe.1G150100' => 'ppe', 'Prupe.6G299600' => 'ppe', 'Prupe.8G245000' => 'ppe', 'Psat0s4927g0040' => 'psa', 'Psat1g052080' => 'psa', 'Psat1g183800' => 'psa', 'Psat3g113840' => 'psa', 'Psat3g126120' => 'psa', 'Psat3g126160' => 'psa', 'Psat3g158760' => 'psa', 'Psat3g158840' => 'psa', 'PSO170G2858' => 'pso', 'PSO339G0606' => 'pso', 'PSO384G4709' => 'pso', 'PSO407G0334' => 'pso', 'QL04p040276' => 'qlo', 'QL06p005458' => 'qlo', 'QL06p005472' => 'qlo', 'QL07p030546' => 'qlo', 'QL07p031519' => 'qlo', 'QL09p050949' => 'qlo', 'QL09p050966' => 'qlo', 'QL09p051067' => 'qlo', 'QL12p022706' => 'qlo', 'RcHm_v2.0_Chr2g0119601' => 'rch', 'RcHm_v2.0_Chr3g0459591' => 'rch', 'RcHm_v2.0_Chr4g0418521' => 'rch', 'RcHm_v2.0_Chr4g0418531' => 'rch', 'RcHm_v2.0_Chr4g0418541' => 'rch', 'RcHm_v2.0_Chr6g0291641' => 'rch', 'Rhsim01G0086300' => 'rsi', 'Rhsim01G0276300' => 'rsi', 'Rhsim01G0276500' => 'rsi', 'Rhsim04G0207700' => 'rsi', 'Rhsim05G0234500' => 'rsi', 'Rhsim13G0022400' => 'rsi', 'Sabra02G0167900' => 'sbr', 'Sabra04G0158500' => 'sbr', 'Sabra08G0159800' => 'sbr', 'Sabra10G0011500' => 'sbr', 'Sabra14G0104400' => 'sbr', 'SalBow2G2440' => 'sbo', 'SalBow4G2265' => 'sbo', 'Sc02g0000060' => 'sci', 'Sc05g0005020' => 'sci', 'Sc13g0003890' => 'sci', 'Sed0014865' => 'sed', 'Sed0017224' => 'sed', 'Sed0026391' => 'sed', 'SEGI_00063' => 'sgi', 'SEGI_10967' => 'sgi', 'SEGI_17510' => 'sgi', 'SEGI_24396' => 'sgi', 'SEGI_39719' => 'sgi', 'SEGI_41392' => 'sgi', 'SGA_v2.0_scaffold11G05794' => 'sas', 'SGA_v2.0_scaffold142G35607' => 'sas', 'SGA_v2.0_scaffold1G00447' => 'sas', 'SHI15388' => 'shi', 'SHI15394' => 'shi', 'SHI15396' => 'shi', 'SHI15399' => 'shi', 'SMO343G0151' => 'smo', 'SMO367G1118' => 'smo', 'Solyc01g080200.3' => 'sly', 'Solyc06g008960.3' => 'sly', 'Solyc09g064780.3' => 'sly', 'Sopen01g031980' => 'spe', 'Sopen06g003710' => 'spe', 'Sopen09g026460' => 'spe', 'Sp3g21240' => 'spa', 'Sp4g30030' => 'spa', 'TAR365G0022' => 'tar', 'TAR365G1023' => 'tar', 'TAR365G1253' => 'tar', 'TAR623G0078' => 'tar', 'TAR623G1721' => 'tar', 'TAR633G0959' => 'tar', 'THA.LOC104802225' => 'tha', 'THA.LOC104804769' => 'tha', 'THA.LOC104808660' => 'tha', 'THA.LOC104812792' => 'tha', 'Thecc.01G284000' => 'tca', 'Thecc.04G220600' => 'tca', 'Thecc.05G268900' => 'tca', 'Thecc.08G171100' => 'tca', 'Thhalv10001284m.g' => 'esa', 'Thhalv10019912m.g' => 'esa', 'TPR.G14189' => 'tpr', 'TPR.G18110' => 'tpr', 'TPR.G18130' => 'tpr', 'TPR.G18131' => 'tpr', 'TPR.G18140' => 'tpr', 'TPR.G24282' => 'tpr', 'TPR.G25221' => 'tpr', 'TPR.G29267' => 'tpr', 'TPR.G35315' => 'tpr', 'TPR.G36173' => 'tpr', 'TWI09G0794' => 'twi', 'TWI59G1348' => 'twi', 'TWI74G0430' => 'twi', 'unitig_26.g8940' => 'ugi', 'unitig_749.g13744' => 'ugi', 'unitig_749.g13745' => 'ugi', 'vmacro08269' => 'vma', 'vmacro14937' => 'vma', 'vmacro20401' => 'vma', 'VMungo0464G1349' => 'vmu', 'VMungo0540G0289' => 'vmu', 'VMungo1215G1590' => 'vmu', 'VMungo1309G0221' => 'vmu', 'VMungo1309G2815' => 'vmu', 'VMungo1383G0239' => 'vmu', 'VMungo1383G2910' => 'vmu', 'Zm00001eb095270' => 'zma', 'Zm00001eb095280' => 'zma', 'Zm00001eb111630' => 'zma', 'Zm00001eb237080' => 'zma', 'Zm00001eb273740' => 'zma', 'Zm00001eb285040' => 'zma', 'Zm00001eb330790' => 'zma', 'Zm00001eb337380' => 'zma' ) $gf_id = 'HOM05D001484' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001484' ) $data_identifier = 'HOM05D001484' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 2, 'aly' => (int) 2, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 22, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 7, 'hma' => (int) 2, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 7, 'mtr' => (int) 10, 'cme' => (int) 2, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 4, 'ppa' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 4, 'qlo' => (int) 9, 'rch' => (int) 6, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 10, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 7, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb337380' $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' => 'HOM05D001484', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p31500' => 'bna', 'A05p00020' => 'bna', 'A07p08820' => 'bna', 'Aa31LG4G3300' => 'aar', 'Aa31LG8G10030' => 'aar', 'Actinidia00731' => 'ach', 'Actinidia11473' => 'ach', 'Actinidia23469' => 'ach', 'Actinidia24318' => 'ach', 'Actinidia40196' => 'ach', 'Actinidia40197' => 'ach', 'Actinidia40198' => 'ach', 'Ah.08g212990' => 'amhyb', 'Ah.15g091720' => 'amhyb', 'AL3G38260' => 'aly', 'AL4G47710' => 'aly', 'Aqoxy2G00671' => 'aox', 'Aqoxy2G03236' => 'aox', 'arahy.Tifrunner.gnm1.ann1.05IDCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KR684' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATY3SJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK6QJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6APGL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IDT7Z9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM073U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ0R87' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LE7RV4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT4QRX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V5ENPK' => 'arhy', 'AT2G48110' => 'ath', 'AT3G23590' => 'ath', 'ATR0626G186' => 'atr', 'ATR1127G141' => 'atr', 'Atru.chr4.2583' => 'acertr', 'Atru.chr5.1358' => 'acertr', 'Atru.chr5.1359' => 'acertr', 'Atru.chr8.46' => 'acertr', 'AUR62002640' => 'cqu', 'AUR62030055' => 'cqu', 'AUR62033713' => 'cqu', 'AUR62033714' => 'cqu', 'AUR62036795' => 'cqu', 'AUR62039891' => 'cqu', 'BcaB02g08737' => 'bca', 'BcaB04g20441' => 'bca', 'BcaB06g26509' => 'bca', 'BcaB06g26510' => 'bca', 'BcaB06g26511' => 'bca', 'BcaB06g26512' => 'bca', 'BcaB06g26513' => 'bca', 'BcaC02g12564' => 'bca', 'BcaC02g12565' => 'bca', 'BcaC02g12794' => 'bca', 'BcaC02g12795' => 'bca', 'BcaC02g12796' => 'bca', 'BcaC06g35541' => 'bca', 'BNapus_Darmor_BZH_scaffold_188p00080' => 'bna', 'BNapus_Darmor_BZH_scaffold_188p00090' => 'bna', 'BolC1t03972H' => 'bol', 'BolC1t03973H' => 'bol', 'BolC4t21680H' => 'bol', 'BolC7t41863H' => 'bol', 'BolSC55t61227H' => 'bol', 'BolSC55t61228H' => 'bol', 'BraA01t03278Z' => 'bra', 'BraA05t18998Z' => 'bra', 'BraA07t28673Z' => 'bra', 'C01p40150' => 'bna', 'C05p12370' => 'bna', 'C07p13680' => 'bna', 'CAN.G1006.16' => 'can', 'CAN.G1006.17' => 'can', 'CAN.G1170.2' => 'can', 'CAN.G962.7' => 'can', 'CANSAT25G2179' => 'cansat', 'CANSAT78G1573' => 'cansat', 'CARHR099510' => 'chi', 'CARHR143510' => 'chi', 'Carub.0003s2380' => 'cru', 'Carub.0004s3082' => 'cru', 'Ca_00614_v3' => 'car', 'Ca_07801_v3' => 'car', 'Ca_08567_v3' => 'car', 'Ca_09571_v3' => 'car', 'CBR_g19290' => 'cbr', 'Cc01_g19770' => 'ccan', 'Cc03_g03030' => 'ccan', 'CDE07G0968' => 'cde', 'CDE09G1441' => 'cde', 'Cfa006103' => 'cfa', 'Cfa015573' => 'cfa', 'Cfa016988' => 'cfa', 'Ciclev10006738m.g' => 'ccl', 'Ciclev10010920m.g' => 'ccl', 'Ciclev10018517m.g' => 'ccl', 'CiPaw.01G159200' => 'cil', 'CiPaw.02G091000' => 'cil', 'CiPaw.02G091100' => 'cil', 'CiPaw.08G103100' => 'cil', 'CiPaw.09G224900' => 'cil', 'ClCG06G005740' => 'cla', 'ClCG07G000090' => 'cla', 'ClCG07G000100' => 'cla', 'COL.COLO4_09143' => 'col', 'COL.COLO4_25124' => 'col', 'Cpa.g.sc16.34' => 'cpa', 'Cpa.g.sc3504.1' => 'cpa', 'Cpa.g.sc60.37' => 'cpa', 'CsaV3_6G018520' => 'csa', 'CsaV3_6G036860' => 'csa', 'CSS0001072' => 'camsi', 'CSS0020208' => 'camsi', 'CSS0021253' => 'camsi', 'CSS0022190' => 'camsi', 'CSS0036150' => 'camsi', 'CSS0040442' => 'camsi', 'CSS0042300' => 'camsi', 'CSS0045298' => 'camsi', 'DCAR_012449' => 'dca', 'DCAR_018405' => 'dca', 'DCAR_024573' => 'dca', 'DCAR_030591' => 'dca', 'Dinv16926' => 'din', 'Dinv32963' => 'din', 'Dinv38382' => 'din', 'Dinv38383' => 'din', 'Duzib133G0974' => 'dzi', 'Duzib138G1867' => 'dzi', 'Duzib211G0420' => 'dzi', 'Duzib212G0930' => 'dzi', 'ECA234G1645' => 'eca', 'ECA247G3467' => 'eca', 'ECA248G1703' => 'eca', 'EL10Ac3g06327' => 'bvu', 'EL10Ac7g17204' => 'bvu', 'Eucgr.A00855' => 'egr', 'Eucgr.A00858' => 'egr', 'Eucgr.H01520' => 'egr', 'Eucgr.H03604' => 'egr', 'Eucgr.L03465' => 'egr', 'Eucgr.L03466' => 'egr', 'FAN01G0988' => 'fan', 'FAN02G3892' => 'fan', 'FAN05G3381' => 'fan', 'FAN07G0967' => 'fan', 'FAN07G1493' => 'fan', 'FAN08G3125' => 'fan', 'FAN09G0402' => 'fan', 'FAN12G2594' => 'fan', 'FAN12G3879' => 'fan', 'FAN14G1546' => 'fan', 'FAN15G3626' => 'fan', 'FAN17G0588' => 'fan', 'FAN17G0609' => 'fan', 'FAN18G2817' => 'fan', 'FAN19G1305' => 'fan', 'FAN20G1787' => 'fan', 'FAN22G0073' => 'fan', 'FAN22G0352' => 'fan', 'FAN22G0368' => 'fan', 'FAN22G2273' => 'fan', 'FAN24G1998' => 'fan', 'FAN27G1317' => 'fan', 'FvH4_2g23980' => 'fve', 'FvH4_4g14380' => 'fve', 'FvH4_4g14390' => 'fve', 'FvH4_6g09250' => 'fve', 'Glyma.03G151100' => 'gma', 'Glyma.04G122550' => 'gma', 'Glyma.05G001600' => 'gma', 'Glyma.09G270766' => 'gma', 'Glyma.09G270832' => 'gma', 'Glyma.13G209800' => 'gma', 'Glyma.15G102800' => 'gma', 'Glyma.18G218900' => 'gma', 'Glyma.19G001500' => 'gma', 'Glyma.19G153600' => 'gma', 'Gohir.A02G028600' => 'ghi', 'Gohir.A08G045000' => 'ghi', 'Gohir.A11G120500' => 'ghi', 'Gohir.A12G006200' => 'ghi', 'Gohir.A12G006250' => 'ghi', 'Gohir.D02G036300' => 'ghi', 'Gohir.D08G054700' => 'ghi', 'Gohir.D11G125600' => 'ghi', 'Gohir.D12G005700' => 'ghi', 'Gorai.004G055200' => 'gra', 'Gorai.005G040400' => 'gra', 'Gorai.007G134500' => 'gra', 'Gorai.008G005500' => 'gra', 'GSVIVG01011094001' => 'vvi', 'GSVIVG01017879001' => 'vvi', 'GSVIVG01025988001' => 'vvi', 'GSVIVG01029847001' => 'vvi', 'HanXRQChr10g0282901' => 'han', 'HanXRQChr10g0310371' => 'han', 'HanXRQChr10g0315041' => 'han', 'HanXRQChr11g0327651' => 'han', 'HanXRQChr12g0359391' => 'han', 'Haze_00972' => 'cav', 'Haze_00973' => 'cav', 'Haze_00974' => 'cav', 'Haze_04747' => 'cav', 'Haze_04749' => 'cav', 'Haze_04750' => 'cav', 'Haze_21217' => 'cav', 'Hma1.2p1_1037F.1_g250680' => 'hma', 'Hma1.2p1_1644F.1_g295320' => 'hma', 'HPP92_011322' => 'vpl', 'HPP92_011323' => 'vpl', 'HPP92_011324' => 'vpl', 'HPP92_011325' => 'vpl', 'HPP92_011326' => 'vpl', 'Hund12205' => 'sun', 'Hund17957' => 'sun', 'Lalb_Chr06g0176771' => 'lal', 'Lalb_Chr18g0056021' => 'lal', 'Lalb_Chr18g0056031' => 'lal', 'Lalb_Chr18g0056041' => 'lal', 'Lalb_Chr20g0107751' => 'lal', 'Lalb_Chr20g0118371' => 'lal', 'Lj1g0010239' => 'lja', 'Lj1g0017101' => 'lja', 'Lj2A1178G40' => 'lonja', 'Lj2A54G84' => 'lonja', 'Lj2g0015248' => 'lja', 'Lj3A761T51' => 'lonja', 'Lj6g0018116' => 'lja', 'Lsat_1_v5_gn_4_136040' => 'lsa', 'Lsat_1_v5_gn_5_187461' => 'lsa', 'Lsat_1_v5_gn_5_77001' => 'lsa', 'Lsat_1_v5_gn_9_4461' => 'lsa', 'Manes.01G210100' => 'mes', 'Manes.03G185600' => 'mes', 'Manes.05G073300' => 'mes', 'Manes.09G120300' => 'mes', 'Manes.15G022100' => 'mes', 'Mapoly0096s0053' => 'mpo', 'MBI03_g14058_MAGBIO' => 'mbi', 'MBI03_g33876_MAGBIO' => 'mbi', 'MBI03_g36854_MAGBIO' => 'mbi', 'MBI17_g11997_MAGBIO' => 'mbi', 'MD03G1269000' => 'mdo', 'MD04G1179600' => 'mdo', 'MD11G1289800' => 'mdo', 'MD12G1194700' => 'mdo', 'MD13G1182100' => 'mdo', 'MD13G1182200' => 'mdo', 'MD16G1182600' => 'mdo', 'Medtr2g021400' => 'mtr', 'Medtr2g021470' => 'mtr', 'Medtr2g105810' => 'mtr', 'Medtr3g033580' => 'mtr', 'Medtr6g007970' => 'mtr', 'Medtr7g056330' => 'mtr', 'Medtr7g074290' => 'mtr', 'Medtr7g074380' => 'mtr', 'Medtr7g094550' => 'mtr', 'Medtr8g069995' => 'mtr', 'MELO3C014345.2' => 'cme', 'MELO3C021395.2' => 'cme', 'Migut.D00262' => 'egut', 'Migut.G00257' => 'egut', 'MSTRG.21575' => 'ama', 'MSTRG.3985' => 'ama', 'Nitab4.5_0000295g0140' => 'nta', 'Nitab4.5_0000732g0140' => 'nta', 'Nitab4.5_0003162g0020' => 'nta', 'Nitab4.5_0006180g0090' => 'nta', 'Nitab4.5_0006390g0010' => 'nta', 'Nitab4.5_0007392g0040' => 'nta', 'Nn1g02140' => 'nnu', 'Nn4g26168' => 'nnu', 'Nn5g26754' => 'nnu', 'Oeu001433.1' => 'oeu', 'Oeu010299.2' => 'oeu', 'Oeu011171.1' => 'oeu', 'Oeu037675.1' => 'oeu', 'Oeu038359.1' => 'oeu', 'Oeu063834.1' => 'oeu', 'Oeu063835.1' => 'oeu', 'Os05g0312000' => 'osa', 'Os07g0211101' => 'osa', 'Os07g0211200' => 'osa', 'Os07g0681500' => 'osa', 'Peaxi162Scf00095g01015' => 'pax', 'Peaxi162Scf00104g00329' => 'pax', 'Peaxi162Scf00161g00137' => 'pax', 'PGR004G1665' => 'pgr', 'PGR031G2937' => 'pgr', 'PGR119G2145' => 'pgr', 'PGSC0003DMG400004351' => 'stu', 'PGSC0003DMG400014625' => 'stu', 'PGSC0003DMG401000943' => 'stu', 'Phvul.001G148600' => 'pvu', 'Phvul.004G001700' => 'pvu', 'Phvul.006G154900' => 'pvu', 'Phvul.008G078200' => 'pvu', 'Phvul.011G136500' => 'pvu', 'Potri.002G215600' => 'ptr', 'Potri.008G201600' => 'ptr', 'Potri.014G138400' => 'ptr', 'Potri.016G142500' => 'ptr', 'Pp3c16_10580' => 'ppa', 'Pp3c5_25280' => 'ppa', 'Prupe.1G150000' => 'ppe', 'Prupe.1G150100' => 'ppe', 'Prupe.6G299600' => 'ppe', 'Prupe.8G245000' => 'ppe', 'Psat0s4927g0040' => 'psa', 'Psat1g052080' => 'psa', 'Psat1g183800' => 'psa', 'Psat3g113840' => 'psa', 'Psat3g126120' => 'psa', 'Psat3g126160' => 'psa', 'Psat3g158760' => 'psa', 'Psat3g158840' => 'psa', 'PSO170G2858' => 'pso', 'PSO339G0606' => 'pso', 'PSO384G4709' => 'pso', 'PSO407G0334' => 'pso', 'QL04p040276' => 'qlo', 'QL06p005458' => 'qlo', 'QL06p005472' => 'qlo', 'QL07p030546' => 'qlo', 'QL07p031519' => 'qlo', 'QL09p050949' => 'qlo', 'QL09p050966' => 'qlo', 'QL09p051067' => 'qlo', 'QL12p022706' => 'qlo', 'RcHm_v2.0_Chr2g0119601' => 'rch', 'RcHm_v2.0_Chr3g0459591' => 'rch', 'RcHm_v2.0_Chr4g0418521' => 'rch', 'RcHm_v2.0_Chr4g0418531' => 'rch', 'RcHm_v2.0_Chr4g0418541' => 'rch', 'RcHm_v2.0_Chr6g0291641' => 'rch', 'Rhsim01G0086300' => 'rsi', 'Rhsim01G0276300' => 'rsi', 'Rhsim01G0276500' => 'rsi', 'Rhsim04G0207700' => 'rsi', 'Rhsim05G0234500' => 'rsi', 'Rhsim13G0022400' => 'rsi', 'Sabra02G0167900' => 'sbr', 'Sabra04G0158500' => 'sbr', 'Sabra08G0159800' => 'sbr', 'Sabra10G0011500' => 'sbr', 'Sabra14G0104400' => 'sbr', 'SalBow2G2440' => 'sbo', 'SalBow4G2265' => 'sbo', 'Sc02g0000060' => 'sci', 'Sc05g0005020' => 'sci', 'Sc13g0003890' => 'sci', 'Sed0014865' => 'sed', 'Sed0017224' => 'sed', 'Sed0026391' => 'sed', 'SEGI_00063' => 'sgi', 'SEGI_10967' => 'sgi', 'SEGI_17510' => 'sgi', 'SEGI_24396' => 'sgi', 'SEGI_39719' => 'sgi', 'SEGI_41392' => 'sgi', 'SGA_v2.0_scaffold11G05794' => 'sas', 'SGA_v2.0_scaffold142G35607' => 'sas', 'SGA_v2.0_scaffold1G00447' => 'sas', 'SHI15388' => 'shi', 'SHI15394' => 'shi', 'SHI15396' => 'shi', 'SHI15399' => 'shi', 'SMO343G0151' => 'smo', 'SMO367G1118' => 'smo', 'Solyc01g080200.3' => 'sly', 'Solyc06g008960.3' => 'sly', 'Solyc09g064780.3' => 'sly', 'Sopen01g031980' => 'spe', 'Sopen06g003710' => 'spe', 'Sopen09g026460' => 'spe', 'Sp3g21240' => 'spa', 'Sp4g30030' => 'spa', 'TAR365G0022' => 'tar', 'TAR365G1023' => 'tar', 'TAR365G1253' => 'tar', 'TAR623G0078' => 'tar', 'TAR623G1721' => 'tar', 'TAR633G0959' => 'tar', 'THA.LOC104802225' => 'tha', 'THA.LOC104804769' => 'tha', 'THA.LOC104808660' => 'tha', 'THA.LOC104812792' => 'tha', 'Thecc.01G284000' => 'tca', 'Thecc.04G220600' => 'tca', 'Thecc.05G268900' => 'tca', 'Thecc.08G171100' => 'tca', 'Thhalv10001284m.g' => 'esa', 'Thhalv10019912m.g' => 'esa', 'TPR.G14189' => 'tpr', 'TPR.G18110' => 'tpr', 'TPR.G18130' => 'tpr', 'TPR.G18131' => 'tpr', 'TPR.G18140' => 'tpr', 'TPR.G24282' => 'tpr', 'TPR.G25221' => 'tpr', 'TPR.G29267' => 'tpr', 'TPR.G35315' => 'tpr', 'TPR.G36173' => 'tpr', 'TWI09G0794' => 'twi', 'TWI59G1348' => 'twi', 'TWI74G0430' => 'twi', 'unitig_26.g8940' => 'ugi', 'unitig_749.g13744' => 'ugi', 'unitig_749.g13745' => 'ugi', 'vmacro08269' => 'vma', 'vmacro14937' => 'vma', 'vmacro20401' => 'vma', 'VMungo0464G1349' => 'vmu', 'VMungo0540G0289' => 'vmu', 'VMungo1215G1590' => 'vmu', 'VMungo1309G0221' => 'vmu', 'VMungo1309G2815' => 'vmu', 'VMungo1383G0239' => 'vmu', 'VMungo1383G2910' => 'vmu', 'Zm00001eb095270' => 'zma', 'Zm00001eb095280' => 'zma', 'Zm00001eb111630' => 'zma', 'Zm00001eb237080' => 'zma', 'Zm00001eb273740' => 'zma', 'Zm00001eb285040' => 'zma', 'Zm00001eb330790' => 'zma', 'Zm00001eb337380' => 'zma' ), 'gf_id' => 'HOM05D001484', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001484' ), 'data_identifier' => 'HOM05D001484', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001484', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p31500' => 'bna', 'A05p00020' => 'bna', 'A07p08820' => 'bna', 'Aa31LG4G3300' => 'aar', 'Aa31LG8G10030' => 'aar', 'Actinidia00731' => 'ach', 'Actinidia11473' => 'ach', 'Actinidia23469' => 'ach', 'Actinidia24318' => 'ach', 'Actinidia40196' => 'ach', 'Actinidia40197' => 'ach', 'Actinidia40198' => 'ach', 'Ah.08g212990' => 'amhyb', 'Ah.15g091720' => 'amhyb', 'AL3G38260' => 'aly', 'AL4G47710' => 'aly', 'Aqoxy2G00671' => 'aox', 'Aqoxy2G03236' => 'aox', 'arahy.Tifrunner.gnm1.ann1.05IDCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KR684' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATY3SJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK6QJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6APGL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IDT7Z9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM073U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ0R87' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LE7RV4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT4QRX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V5ENPK' => 'arhy', 'AT2G48110' => 'ath', 'AT3G23590' => 'ath', 'ATR0626G186' => 'atr', 'ATR1127G141' => 'atr', 'Atru.chr4.2583' => 'acertr', 'Atru.chr5.1358' => 'acertr', 'Atru.chr5.1359' => 'acertr', 'Atru.chr8.46' => 'acertr', 'AUR62002640' => 'cqu', 'AUR62030055' => 'cqu', 'AUR62033713' => 'cqu', 'AUR62033714' => 'cqu', 'AUR62036795' => 'cqu', 'AUR62039891' => 'cqu', 'BcaB02g08737' => 'bca', 'BcaB04g20441' => 'bca', 'BcaB06g26509' => 'bca', 'BcaB06g26510' => 'bca', 'BcaB06g26511' => 'bca', 'BcaB06g26512' => 'bca', 'BcaB06g26513' => 'bca', 'BcaC02g12564' => 'bca', 'BcaC02g12565' => 'bca', 'BcaC02g12794' => 'bca', 'BcaC02g12795' => 'bca', 'BcaC02g12796' => 'bca', 'BcaC06g35541' => 'bca', 'BNapus_Darmor_BZH_scaffold_188p00080' => 'bna', 'BNapus_Darmor_BZH_scaffold_188p00090' => 'bna', 'BolC1t03972H' => 'bol', 'BolC1t03973H' => 'bol', 'BolC4t21680H' => 'bol', 'BolC7t41863H' => 'bol', 'BolSC55t61227H' => 'bol', 'BolSC55t61228H' => 'bol', 'BraA01t03278Z' => 'bra', 'BraA05t18998Z' => 'bra', 'BraA07t28673Z' => 'bra', 'C01p40150' => 'bna', 'C05p12370' => 'bna', 'C07p13680' => 'bna', 'CAN.G1006.16' => 'can', 'CAN.G1006.17' => 'can', 'CAN.G1170.2' => 'can', 'CAN.G962.7' => 'can', 'CANSAT25G2179' => 'cansat', 'CANSAT78G1573' => 'cansat', 'CARHR099510' => 'chi', 'CARHR143510' => 'chi', 'Carub.0003s2380' => 'cru', 'Carub.0004s3082' => 'cru', 'Ca_00614_v3' => 'car', 'Ca_07801_v3' => 'car', 'Ca_08567_v3' => 'car', 'Ca_09571_v3' => 'car', 'CBR_g19290' => 'cbr', 'Cc01_g19770' => 'ccan', 'Cc03_g03030' => 'ccan', 'CDE07G0968' => 'cde', 'CDE09G1441' => 'cde', 'Cfa006103' => 'cfa', 'Cfa015573' => 'cfa', 'Cfa016988' => 'cfa', 'Ciclev10006738m.g' => 'ccl', 'Ciclev10010920m.g' => 'ccl', 'Ciclev10018517m.g' => 'ccl', 'CiPaw.01G159200' => 'cil', 'CiPaw.02G091000' => 'cil', 'CiPaw.02G091100' => 'cil', 'CiPaw.08G103100' => 'cil', 'CiPaw.09G224900' => 'cil', 'ClCG06G005740' => 'cla', 'ClCG07G000090' => 'cla', 'ClCG07G000100' => 'cla', 'COL.COLO4_09143' => 'col', 'COL.COLO4_25124' => 'col', 'Cpa.g.sc16.34' => 'cpa', 'Cpa.g.sc3504.1' => 'cpa', 'Cpa.g.sc60.37' => 'cpa', 'CsaV3_6G018520' => 'csa', 'CsaV3_6G036860' => 'csa', 'CSS0001072' => 'camsi', 'CSS0020208' => 'camsi', 'CSS0021253' => 'camsi', 'CSS0022190' => 'camsi', 'CSS0036150' => 'camsi', 'CSS0040442' => 'camsi', 'CSS0042300' => 'camsi', 'CSS0045298' => 'camsi', 'DCAR_012449' => 'dca', 'DCAR_018405' => 'dca', 'DCAR_024573' => 'dca', 'DCAR_030591' => 'dca', 'Dinv16926' => 'din', 'Dinv32963' => 'din', 'Dinv38382' => 'din', 'Dinv38383' => 'din', 'Duzib133G0974' => 'dzi', 'Duzib138G1867' => 'dzi', 'Duzib211G0420' => 'dzi', 'Duzib212G0930' => 'dzi', 'ECA234G1645' => 'eca', 'ECA247G3467' => 'eca', 'ECA248G1703' => 'eca', 'EL10Ac3g06327' => 'bvu', 'EL10Ac7g17204' => 'bvu', 'Eucgr.A00855' => 'egr', 'Eucgr.A00858' => 'egr', 'Eucgr.H01520' => 'egr', 'Eucgr.H03604' => 'egr', 'Eucgr.L03465' => 'egr', 'Eucgr.L03466' => 'egr', 'FAN01G0988' => 'fan', 'FAN02G3892' => 'fan', 'FAN05G3381' => 'fan', 'FAN07G0967' => 'fan', 'FAN07G1493' => 'fan', 'FAN08G3125' => 'fan', 'FAN09G0402' => 'fan', 'FAN12G2594' => 'fan', 'FAN12G3879' => 'fan', 'FAN14G1546' => 'fan', 'FAN15G3626' => 'fan', 'FAN17G0588' => 'fan', 'FAN17G0609' => 'fan', 'FAN18G2817' => 'fan', 'FAN19G1305' => 'fan', 'FAN20G1787' => 'fan', 'FAN22G0073' => 'fan', 'FAN22G0352' => 'fan', 'FAN22G0368' => 'fan', 'FAN22G2273' => 'fan', 'FAN24G1998' => 'fan', 'FAN27G1317' => 'fan', 'FvH4_2g23980' => 'fve', 'FvH4_4g14380' => 'fve', 'FvH4_4g14390' => 'fve', 'FvH4_6g09250' => 'fve', 'Glyma.03G151100' => 'gma', 'Glyma.04G122550' => 'gma', 'Glyma.05G001600' => 'gma', 'Glyma.09G270766' => 'gma', 'Glyma.09G270832' => 'gma', 'Glyma.13G209800' => 'gma', 'Glyma.15G102800' => 'gma', 'Glyma.18G218900' => 'gma', 'Glyma.19G001500' => 'gma', 'Glyma.19G153600' => 'gma', 'Gohir.A02G028600' => 'ghi', 'Gohir.A08G045000' => 'ghi', 'Gohir.A11G120500' => 'ghi', 'Gohir.A12G006200' => 'ghi', 'Gohir.A12G006250' => 'ghi', 'Gohir.D02G036300' => 'ghi', 'Gohir.D08G054700' => 'ghi', 'Gohir.D11G125600' => 'ghi', 'Gohir.D12G005700' => 'ghi', 'Gorai.004G055200' => 'gra', 'Gorai.005G040400' => 'gra', 'Gorai.007G134500' => 'gra', 'Gorai.008G005500' => 'gra', 'GSVIVG01011094001' => 'vvi', 'GSVIVG01017879001' => 'vvi', 'GSVIVG01025988001' => 'vvi', 'GSVIVG01029847001' => 'vvi', 'HanXRQChr10g0282901' => 'han', 'HanXRQChr10g0310371' => 'han', 'HanXRQChr10g0315041' => 'han', 'HanXRQChr11g0327651' => 'han', 'HanXRQChr12g0359391' => 'han', 'Haze_00972' => 'cav', 'Haze_00973' => 'cav', 'Haze_00974' => 'cav', 'Haze_04747' => 'cav', 'Haze_04749' => 'cav', 'Haze_04750' => 'cav', 'Haze_21217' => 'cav', 'Hma1.2p1_1037F.1_g250680' => 'hma', 'Hma1.2p1_1644F.1_g295320' => 'hma', 'HPP92_011322' => 'vpl', 'HPP92_011323' => 'vpl', 'HPP92_011324' => 'vpl', 'HPP92_011325' => 'vpl', 'HPP92_011326' => 'vpl', 'Hund12205' => 'sun', 'Hund17957' => 'sun', 'Lalb_Chr06g0176771' => 'lal', 'Lalb_Chr18g0056021' => 'lal', 'Lalb_Chr18g0056031' => 'lal', 'Lalb_Chr18g0056041' => 'lal', 'Lalb_Chr20g0107751' => 'lal', 'Lalb_Chr20g0118371' => 'lal', 'Lj1g0010239' => 'lja', 'Lj1g0017101' => 'lja', 'Lj2A1178G40' => 'lonja', 'Lj2A54G84' => 'lonja', 'Lj2g0015248' => 'lja', 'Lj3A761T51' => 'lonja', 'Lj6g0018116' => 'lja', 'Lsat_1_v5_gn_4_136040' => 'lsa', 'Lsat_1_v5_gn_5_187461' => 'lsa', 'Lsat_1_v5_gn_5_77001' => 'lsa', 'Lsat_1_v5_gn_9_4461' => 'lsa', 'Manes.01G210100' => 'mes', 'Manes.03G185600' => 'mes', 'Manes.05G073300' => 'mes', 'Manes.09G120300' => 'mes', 'Manes.15G022100' => 'mes', 'Mapoly0096s0053' => 'mpo', 'MBI03_g14058_MAGBIO' => 'mbi', 'MBI03_g33876_MAGBIO' => 'mbi', 'MBI03_g36854_MAGBIO' => 'mbi', 'MBI17_g11997_MAGBIO' => 'mbi', 'MD03G1269000' => 'mdo', 'MD04G1179600' => 'mdo', 'MD11G1289800' => 'mdo', 'MD12G1194700' => 'mdo', 'MD13G1182100' => 'mdo', 'MD13G1182200' => 'mdo', 'MD16G1182600' => 'mdo', 'Medtr2g021400' => 'mtr', 'Medtr2g021470' => 'mtr', 'Medtr2g105810' => 'mtr', 'Medtr3g033580' => 'mtr', 'Medtr6g007970' => 'mtr', 'Medtr7g056330' => 'mtr', 'Medtr7g074290' => 'mtr', 'Medtr7g074380' => 'mtr', 'Medtr7g094550' => 'mtr', 'Medtr8g069995' => 'mtr', 'MELO3C014345.2' => 'cme', 'MELO3C021395.2' => 'cme', 'Migut.D00262' => 'egut', 'Migut.G00257' => 'egut', 'MSTRG.21575' => 'ama', 'MSTRG.3985' => 'ama', 'Nitab4.5_0000295g0140' => 'nta', 'Nitab4.5_0000732g0140' => 'nta', 'Nitab4.5_0003162g0020' => 'nta', 'Nitab4.5_0006180g0090' => 'nta', 'Nitab4.5_0006390g0010' => 'nta', 'Nitab4.5_0007392g0040' => 'nta', 'Nn1g02140' => 'nnu', 'Nn4g26168' => 'nnu', 'Nn5g26754' => 'nnu', 'Oeu001433.1' => 'oeu', 'Oeu010299.2' => 'oeu', 'Oeu011171.1' => 'oeu', 'Oeu037675.1' => 'oeu', 'Oeu038359.1' => 'oeu', 'Oeu063834.1' => 'oeu', 'Oeu063835.1' => 'oeu', 'Os05g0312000' => 'osa', 'Os07g0211101' => 'osa', 'Os07g0211200' => 'osa', 'Os07g0681500' => 'osa', 'Peaxi162Scf00095g01015' => 'pax', 'Peaxi162Scf00104g00329' => 'pax', 'Peaxi162Scf00161g00137' => 'pax', 'PGR004G1665' => 'pgr', 'PGR031G2937' => 'pgr', 'PGR119G2145' => 'pgr', 'PGSC0003DMG400004351' => 'stu', 'PGSC0003DMG400014625' => 'stu', 'PGSC0003DMG401000943' => 'stu', 'Phvul.001G148600' => 'pvu', 'Phvul.004G001700' => 'pvu', 'Phvul.006G154900' => 'pvu', 'Phvul.008G078200' => 'pvu', 'Phvul.011G136500' => 'pvu', 'Potri.002G215600' => 'ptr', 'Potri.008G201600' => 'ptr', 'Potri.014G138400' => 'ptr', 'Potri.016G142500' => 'ptr', 'Pp3c16_10580' => 'ppa', 'Pp3c5_25280' => 'ppa', 'Prupe.1G150000' => 'ppe', 'Prupe.1G150100' => 'ppe', 'Prupe.6G299600' => 'ppe', 'Prupe.8G245000' => 'ppe', 'Psat0s4927g0040' => 'psa', 'Psat1g052080' => 'psa', 'Psat1g183800' => 'psa', 'Psat3g113840' => 'psa', 'Psat3g126120' => 'psa', 'Psat3g126160' => 'psa', 'Psat3g158760' => 'psa', 'Psat3g158840' => 'psa', 'PSO170G2858' => 'pso', 'PSO339G0606' => 'pso', 'PSO384G4709' => 'pso', 'PSO407G0334' => 'pso', 'QL04p040276' => 'qlo', 'QL06p005458' => 'qlo', 'QL06p005472' => 'qlo', 'QL07p030546' => 'qlo', 'QL07p031519' => 'qlo', 'QL09p050949' => 'qlo', 'QL09p050966' => 'qlo', 'QL09p051067' => 'qlo', 'QL12p022706' => 'qlo', 'RcHm_v2.0_Chr2g0119601' => 'rch', 'RcHm_v2.0_Chr3g0459591' => 'rch', 'RcHm_v2.0_Chr4g0418521' => 'rch', 'RcHm_v2.0_Chr4g0418531' => 'rch', 'RcHm_v2.0_Chr4g0418541' => 'rch', 'RcHm_v2.0_Chr6g0291641' => 'rch', 'Rhsim01G0086300' => 'rsi', 'Rhsim01G0276300' => 'rsi', 'Rhsim01G0276500' => 'rsi', 'Rhsim04G0207700' => 'rsi', 'Rhsim05G0234500' => 'rsi', 'Rhsim13G0022400' => 'rsi', 'Sabra02G0167900' => 'sbr', 'Sabra04G0158500' => 'sbr', 'Sabra08G0159800' => 'sbr', 'Sabra10G0011500' => 'sbr', 'Sabra14G0104400' => 'sbr', 'SalBow2G2440' => 'sbo', 'SalBow4G2265' => 'sbo', 'Sc02g0000060' => 'sci', 'Sc05g0005020' => 'sci', 'Sc13g0003890' => 'sci', 'Sed0014865' => 'sed', 'Sed0017224' => 'sed', 'Sed0026391' => 'sed', 'SEGI_00063' => 'sgi', 'SEGI_10967' => 'sgi', 'SEGI_17510' => 'sgi', 'SEGI_24396' => 'sgi', 'SEGI_39719' => 'sgi', 'SEGI_41392' => 'sgi', 'SGA_v2.0_scaffold11G05794' => 'sas', 'SGA_v2.0_scaffold142G35607' => 'sas', 'SGA_v2.0_scaffold1G00447' => 'sas', 'SHI15388' => 'shi', 'SHI15394' => 'shi', 'SHI15396' => 'shi', 'SHI15399' => 'shi', 'SMO343G0151' => 'smo', 'SMO367G1118' => 'smo', 'Solyc01g080200.3' => 'sly', 'Solyc06g008960.3' => 'sly', 'Solyc09g064780.3' => 'sly', 'Sopen01g031980' => 'spe', 'Sopen06g003710' => 'spe', 'Sopen09g026460' => 'spe', 'Sp3g21240' => 'spa', 'Sp4g30030' => 'spa', 'TAR365G0022' => 'tar', 'TAR365G1023' => 'tar', 'TAR365G1253' => 'tar', 'TAR623G0078' => 'tar', 'TAR623G1721' => 'tar', 'TAR633G0959' => 'tar', 'THA.LOC104802225' => 'tha', 'THA.LOC104804769' => 'tha', 'THA.LOC104808660' => 'tha', 'THA.LOC104812792' => 'tha', 'Thecc.01G284000' => 'tca', 'Thecc.04G220600' => 'tca', 'Thecc.05G268900' => 'tca', 'Thecc.08G171100' => 'tca', 'Thhalv10001284m.g' => 'esa', 'Thhalv10019912m.g' => 'esa', 'TPR.G14189' => 'tpr', 'TPR.G18110' => 'tpr', 'TPR.G18130' => 'tpr', 'TPR.G18131' => 'tpr', 'TPR.G18140' => 'tpr', 'TPR.G24282' => 'tpr', 'TPR.G25221' => 'tpr', 'TPR.G29267' => 'tpr', 'TPR.G35315' => 'tpr', 'TPR.G36173' => 'tpr', 'TWI09G0794' => 'twi', 'TWI59G1348' => 'twi', 'TWI74G0430' => 'twi', 'unitig_26.g8940' => 'ugi', 'unitig_749.g13744' => 'ugi', 'unitig_749.g13745' => 'ugi', 'vmacro08269' => 'vma', 'vmacro14937' => 'vma', 'vmacro20401' => 'vma', 'VMungo0464G1349' => 'vmu', 'VMungo0540G0289' => 'vmu', 'VMungo1215G1590' => 'vmu', 'VMungo1309G0221' => 'vmu', 'VMungo1309G2815' => 'vmu', 'VMungo1383G0239' => 'vmu', 'VMungo1383G2910' => 'vmu', 'Zm00001eb095270' => 'zma', 'Zm00001eb095280' => 'zma', 'Zm00001eb111630' => 'zma', 'Zm00001eb237080' => 'zma', 'Zm00001eb273740' => 'zma', 'Zm00001eb285040' => 'zma', 'Zm00001eb330790' => 'zma', 'Zm00001eb337380' => 'zma' ) $gf_id = 'HOM05D001484' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001484' ) $data_identifier = 'HOM05D001484' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 2, 'aly' => (int) 2, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 22, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 7, 'hma' => (int) 2, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 7, 'mtr' => (int) 10, 'cme' => (int) 2, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 4, 'ppa' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 4, 'qlo' => (int) 9, 'rch' => (int) 6, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 10, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 7, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb337380' $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' => 'HOM05D001484', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p31500' => 'bna', 'A05p00020' => 'bna', 'A07p08820' => 'bna', 'Aa31LG4G3300' => 'aar', 'Aa31LG8G10030' => 'aar', 'Actinidia00731' => 'ach', 'Actinidia11473' => 'ach', 'Actinidia23469' => 'ach', 'Actinidia24318' => 'ach', 'Actinidia40196' => 'ach', 'Actinidia40197' => 'ach', 'Actinidia40198' => 'ach', 'Ah.08g212990' => 'amhyb', 'Ah.15g091720' => 'amhyb', 'AL3G38260' => 'aly', 'AL4G47710' => 'aly', 'Aqoxy2G00671' => 'aox', 'Aqoxy2G03236' => 'aox', 'arahy.Tifrunner.gnm1.ann1.05IDCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KR684' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATY3SJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK6QJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6APGL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IDT7Z9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM073U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ0R87' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LE7RV4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT4QRX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V5ENPK' => 'arhy', 'AT2G48110' => 'ath', 'AT3G23590' => 'ath', 'ATR0626G186' => 'atr', 'ATR1127G141' => 'atr', 'Atru.chr4.2583' => 'acertr', 'Atru.chr5.1358' => 'acertr', 'Atru.chr5.1359' => 'acertr', 'Atru.chr8.46' => 'acertr', 'AUR62002640' => 'cqu', 'AUR62030055' => 'cqu', 'AUR62033713' => 'cqu', 'AUR62033714' => 'cqu', 'AUR62036795' => 'cqu', 'AUR62039891' => 'cqu', 'BcaB02g08737' => 'bca', 'BcaB04g20441' => 'bca', 'BcaB06g26509' => 'bca', 'BcaB06g26510' => 'bca', 'BcaB06g26511' => 'bca', 'BcaB06g26512' => 'bca', 'BcaB06g26513' => 'bca', 'BcaC02g12564' => 'bca', 'BcaC02g12565' => 'bca', 'BcaC02g12794' => 'bca', 'BcaC02g12795' => 'bca', 'BcaC02g12796' => 'bca', 'BcaC06g35541' => 'bca', 'BNapus_Darmor_BZH_scaffold_188p00080' => 'bna', 'BNapus_Darmor_BZH_scaffold_188p00090' => 'bna', 'BolC1t03972H' => 'bol', 'BolC1t03973H' => 'bol', 'BolC4t21680H' => 'bol', 'BolC7t41863H' => 'bol', 'BolSC55t61227H' => 'bol', 'BolSC55t61228H' => 'bol', 'BraA01t03278Z' => 'bra', 'BraA05t18998Z' => 'bra', 'BraA07t28673Z' => 'bra', 'C01p40150' => 'bna', 'C05p12370' => 'bna', 'C07p13680' => 'bna', 'CAN.G1006.16' => 'can', 'CAN.G1006.17' => 'can', 'CAN.G1170.2' => 'can', 'CAN.G962.7' => 'can', 'CANSAT25G2179' => 'cansat', 'CANSAT78G1573' => 'cansat', 'CARHR099510' => 'chi', 'CARHR143510' => 'chi', 'Carub.0003s2380' => 'cru', 'Carub.0004s3082' => 'cru', 'Ca_00614_v3' => 'car', 'Ca_07801_v3' => 'car', 'Ca_08567_v3' => 'car', 'Ca_09571_v3' => 'car', 'CBR_g19290' => 'cbr', 'Cc01_g19770' => 'ccan', 'Cc03_g03030' => 'ccan', 'CDE07G0968' => 'cde', 'CDE09G1441' => 'cde', 'Cfa006103' => 'cfa', 'Cfa015573' => 'cfa', 'Cfa016988' => 'cfa', 'Ciclev10006738m.g' => 'ccl', 'Ciclev10010920m.g' => 'ccl', 'Ciclev10018517m.g' => 'ccl', 'CiPaw.01G159200' => 'cil', 'CiPaw.02G091000' => 'cil', 'CiPaw.02G091100' => 'cil', 'CiPaw.08G103100' => 'cil', 'CiPaw.09G224900' => 'cil', 'ClCG06G005740' => 'cla', 'ClCG07G000090' => 'cla', 'ClCG07G000100' => 'cla', 'COL.COLO4_09143' => 'col', 'COL.COLO4_25124' => 'col', 'Cpa.g.sc16.34' => 'cpa', 'Cpa.g.sc3504.1' => 'cpa', 'Cpa.g.sc60.37' => 'cpa', 'CsaV3_6G018520' => 'csa', 'CsaV3_6G036860' => 'csa', 'CSS0001072' => 'camsi', 'CSS0020208' => 'camsi', 'CSS0021253' => 'camsi', 'CSS0022190' => 'camsi', 'CSS0036150' => 'camsi', 'CSS0040442' => 'camsi', 'CSS0042300' => 'camsi', 'CSS0045298' => 'camsi', 'DCAR_012449' => 'dca', 'DCAR_018405' => 'dca', 'DCAR_024573' => 'dca', 'DCAR_030591' => 'dca', 'Dinv16926' => 'din', 'Dinv32963' => 'din', 'Dinv38382' => 'din', 'Dinv38383' => 'din', 'Duzib133G0974' => 'dzi', 'Duzib138G1867' => 'dzi', 'Duzib211G0420' => 'dzi', 'Duzib212G0930' => 'dzi', 'ECA234G1645' => 'eca', 'ECA247G3467' => 'eca', 'ECA248G1703' => 'eca', 'EL10Ac3g06327' => 'bvu', 'EL10Ac7g17204' => 'bvu', 'Eucgr.A00855' => 'egr', 'Eucgr.A00858' => 'egr', 'Eucgr.H01520' => 'egr', 'Eucgr.H03604' => 'egr', 'Eucgr.L03465' => 'egr', 'Eucgr.L03466' => 'egr', 'FAN01G0988' => 'fan', 'FAN02G3892' => 'fan', 'FAN05G3381' => 'fan', 'FAN07G0967' => 'fan', 'FAN07G1493' => 'fan', 'FAN08G3125' => 'fan', 'FAN09G0402' => 'fan', 'FAN12G2594' => 'fan', 'FAN12G3879' => 'fan', 'FAN14G1546' => 'fan', 'FAN15G3626' => 'fan', 'FAN17G0588' => 'fan', 'FAN17G0609' => 'fan', 'FAN18G2817' => 'fan', 'FAN19G1305' => 'fan', 'FAN20G1787' => 'fan', 'FAN22G0073' => 'fan', 'FAN22G0352' => 'fan', 'FAN22G0368' => 'fan', 'FAN22G2273' => 'fan', 'FAN24G1998' => 'fan', 'FAN27G1317' => 'fan', 'FvH4_2g23980' => 'fve', 'FvH4_4g14380' => 'fve', 'FvH4_4g14390' => 'fve', 'FvH4_6g09250' => 'fve', 'Glyma.03G151100' => 'gma', 'Glyma.04G122550' => 'gma', 'Glyma.05G001600' => 'gma', 'Glyma.09G270766' => 'gma', 'Glyma.09G270832' => 'gma', 'Glyma.13G209800' => 'gma', 'Glyma.15G102800' => 'gma', 'Glyma.18G218900' => 'gma', 'Glyma.19G001500' => 'gma', 'Glyma.19G153600' => 'gma', 'Gohir.A02G028600' => 'ghi', 'Gohir.A08G045000' => 'ghi', 'Gohir.A11G120500' => 'ghi', 'Gohir.A12G006200' => 'ghi', 'Gohir.A12G006250' => 'ghi', 'Gohir.D02G036300' => 'ghi', 'Gohir.D08G054700' => 'ghi', 'Gohir.D11G125600' => 'ghi', 'Gohir.D12G005700' => 'ghi', 'Gorai.004G055200' => 'gra', 'Gorai.005G040400' => 'gra', 'Gorai.007G134500' => 'gra', 'Gorai.008G005500' => 'gra', 'GSVIVG01011094001' => 'vvi', 'GSVIVG01017879001' => 'vvi', 'GSVIVG01025988001' => 'vvi', 'GSVIVG01029847001' => 'vvi', 'HanXRQChr10g0282901' => 'han', 'HanXRQChr10g0310371' => 'han', 'HanXRQChr10g0315041' => 'han', 'HanXRQChr11g0327651' => 'han', 'HanXRQChr12g0359391' => 'han', 'Haze_00972' => 'cav', 'Haze_00973' => 'cav', 'Haze_00974' => 'cav', 'Haze_04747' => 'cav', 'Haze_04749' => 'cav', 'Haze_04750' => 'cav', 'Haze_21217' => 'cav', 'Hma1.2p1_1037F.1_g250680' => 'hma', 'Hma1.2p1_1644F.1_g295320' => 'hma', 'HPP92_011322' => 'vpl', 'HPP92_011323' => 'vpl', 'HPP92_011324' => 'vpl', 'HPP92_011325' => 'vpl', 'HPP92_011326' => 'vpl', 'Hund12205' => 'sun', 'Hund17957' => 'sun', 'Lalb_Chr06g0176771' => 'lal', 'Lalb_Chr18g0056021' => 'lal', 'Lalb_Chr18g0056031' => 'lal', 'Lalb_Chr18g0056041' => 'lal', 'Lalb_Chr20g0107751' => 'lal', 'Lalb_Chr20g0118371' => 'lal', 'Lj1g0010239' => 'lja', 'Lj1g0017101' => 'lja', 'Lj2A1178G40' => 'lonja', 'Lj2A54G84' => 'lonja', 'Lj2g0015248' => 'lja', 'Lj3A761T51' => 'lonja', 'Lj6g0018116' => 'lja', 'Lsat_1_v5_gn_4_136040' => 'lsa', 'Lsat_1_v5_gn_5_187461' => 'lsa', 'Lsat_1_v5_gn_5_77001' => 'lsa', 'Lsat_1_v5_gn_9_4461' => 'lsa', 'Manes.01G210100' => 'mes', 'Manes.03G185600' => 'mes', 'Manes.05G073300' => 'mes', 'Manes.09G120300' => 'mes', 'Manes.15G022100' => 'mes', 'Mapoly0096s0053' => 'mpo', 'MBI03_g14058_MAGBIO' => 'mbi', 'MBI03_g33876_MAGBIO' => 'mbi', 'MBI03_g36854_MAGBIO' => 'mbi', 'MBI17_g11997_MAGBIO' => 'mbi', 'MD03G1269000' => 'mdo', 'MD04G1179600' => 'mdo', 'MD11G1289800' => 'mdo', 'MD12G1194700' => 'mdo', 'MD13G1182100' => 'mdo', 'MD13G1182200' => 'mdo', 'MD16G1182600' => 'mdo', 'Medtr2g021400' => 'mtr', 'Medtr2g021470' => 'mtr', 'Medtr2g105810' => 'mtr', 'Medtr3g033580' => 'mtr', 'Medtr6g007970' => 'mtr', 'Medtr7g056330' => 'mtr', 'Medtr7g074290' => 'mtr', 'Medtr7g074380' => 'mtr', 'Medtr7g094550' => 'mtr', 'Medtr8g069995' => 'mtr', 'MELO3C014345.2' => 'cme', 'MELO3C021395.2' => 'cme', 'Migut.D00262' => 'egut', 'Migut.G00257' => 'egut', 'MSTRG.21575' => 'ama', 'MSTRG.3985' => 'ama', 'Nitab4.5_0000295g0140' => 'nta', 'Nitab4.5_0000732g0140' => 'nta', 'Nitab4.5_0003162g0020' => 'nta', 'Nitab4.5_0006180g0090' => 'nta', 'Nitab4.5_0006390g0010' => 'nta', 'Nitab4.5_0007392g0040' => 'nta', 'Nn1g02140' => 'nnu', 'Nn4g26168' => 'nnu', 'Nn5g26754' => 'nnu', 'Oeu001433.1' => 'oeu', 'Oeu010299.2' => 'oeu', 'Oeu011171.1' => 'oeu', 'Oeu037675.1' => 'oeu', 'Oeu038359.1' => 'oeu', 'Oeu063834.1' => 'oeu', 'Oeu063835.1' => 'oeu', 'Os05g0312000' => 'osa', 'Os07g0211101' => 'osa', 'Os07g0211200' => 'osa', 'Os07g0681500' => 'osa', 'Peaxi162Scf00095g01015' => 'pax', 'Peaxi162Scf00104g00329' => 'pax', 'Peaxi162Scf00161g00137' => 'pax', 'PGR004G1665' => 'pgr', 'PGR031G2937' => 'pgr', 'PGR119G2145' => 'pgr', 'PGSC0003DMG400004351' => 'stu', 'PGSC0003DMG400014625' => 'stu', 'PGSC0003DMG401000943' => 'stu', 'Phvul.001G148600' => 'pvu', 'Phvul.004G001700' => 'pvu', 'Phvul.006G154900' => 'pvu', 'Phvul.008G078200' => 'pvu', 'Phvul.011G136500' => 'pvu', 'Potri.002G215600' => 'ptr', 'Potri.008G201600' => 'ptr', 'Potri.014G138400' => 'ptr', 'Potri.016G142500' => 'ptr', 'Pp3c16_10580' => 'ppa', 'Pp3c5_25280' => 'ppa', 'Prupe.1G150000' => 'ppe', 'Prupe.1G150100' => 'ppe', 'Prupe.6G299600' => 'ppe', 'Prupe.8G245000' => 'ppe', 'Psat0s4927g0040' => 'psa', 'Psat1g052080' => 'psa', 'Psat1g183800' => 'psa', 'Psat3g113840' => 'psa', 'Psat3g126120' => 'psa', 'Psat3g126160' => 'psa', 'Psat3g158760' => 'psa', 'Psat3g158840' => 'psa', 'PSO170G2858' => 'pso', 'PSO339G0606' => 'pso', 'PSO384G4709' => 'pso', 'PSO407G0334' => 'pso', 'QL04p040276' => 'qlo', 'QL06p005458' => 'qlo', 'QL06p005472' => 'qlo', 'QL07p030546' => 'qlo', 'QL07p031519' => 'qlo', 'QL09p050949' => 'qlo', 'QL09p050966' => 'qlo', 'QL09p051067' => 'qlo', 'QL12p022706' => 'qlo', 'RcHm_v2.0_Chr2g0119601' => 'rch', 'RcHm_v2.0_Chr3g0459591' => 'rch', 'RcHm_v2.0_Chr4g0418521' => 'rch', 'RcHm_v2.0_Chr4g0418531' => 'rch', 'RcHm_v2.0_Chr4g0418541' => 'rch', 'RcHm_v2.0_Chr6g0291641' => 'rch', 'Rhsim01G0086300' => 'rsi', 'Rhsim01G0276300' => 'rsi', 'Rhsim01G0276500' => 'rsi', 'Rhsim04G0207700' => 'rsi', 'Rhsim05G0234500' => 'rsi', 'Rhsim13G0022400' => 'rsi', 'Sabra02G0167900' => 'sbr', 'Sabra04G0158500' => 'sbr', 'Sabra08G0159800' => 'sbr', 'Sabra10G0011500' => 'sbr', 'Sabra14G0104400' => 'sbr', 'SalBow2G2440' => 'sbo', 'SalBow4G2265' => 'sbo', 'Sc02g0000060' => 'sci', 'Sc05g0005020' => 'sci', 'Sc13g0003890' => 'sci', 'Sed0014865' => 'sed', 'Sed0017224' => 'sed', 'Sed0026391' => 'sed', 'SEGI_00063' => 'sgi', 'SEGI_10967' => 'sgi', 'SEGI_17510' => 'sgi', 'SEGI_24396' => 'sgi', 'SEGI_39719' => 'sgi', 'SEGI_41392' => 'sgi', 'SGA_v2.0_scaffold11G05794' => 'sas', 'SGA_v2.0_scaffold142G35607' => 'sas', 'SGA_v2.0_scaffold1G00447' => 'sas', 'SHI15388' => 'shi', 'SHI15394' => 'shi', 'SHI15396' => 'shi', 'SHI15399' => 'shi', 'SMO343G0151' => 'smo', 'SMO367G1118' => 'smo', 'Solyc01g080200.3' => 'sly', 'Solyc06g008960.3' => 'sly', 'Solyc09g064780.3' => 'sly', 'Sopen01g031980' => 'spe', 'Sopen06g003710' => 'spe', 'Sopen09g026460' => 'spe', 'Sp3g21240' => 'spa', 'Sp4g30030' => 'spa', 'TAR365G0022' => 'tar', 'TAR365G1023' => 'tar', 'TAR365G1253' => 'tar', 'TAR623G0078' => 'tar', 'TAR623G1721' => 'tar', 'TAR633G0959' => 'tar', 'THA.LOC104802225' => 'tha', 'THA.LOC104804769' => 'tha', 'THA.LOC104808660' => 'tha', 'THA.LOC104812792' => 'tha', 'Thecc.01G284000' => 'tca', 'Thecc.04G220600' => 'tca', 'Thecc.05G268900' => 'tca', 'Thecc.08G171100' => 'tca', 'Thhalv10001284m.g' => 'esa', 'Thhalv10019912m.g' => 'esa', 'TPR.G14189' => 'tpr', 'TPR.G18110' => 'tpr', 'TPR.G18130' => 'tpr', 'TPR.G18131' => 'tpr', 'TPR.G18140' => 'tpr', 'TPR.G24282' => 'tpr', 'TPR.G25221' => 'tpr', 'TPR.G29267' => 'tpr', 'TPR.G35315' => 'tpr', 'TPR.G36173' => 'tpr', 'TWI09G0794' => 'twi', 'TWI59G1348' => 'twi', 'TWI74G0430' => 'twi', 'unitig_26.g8940' => 'ugi', 'unitig_749.g13744' => 'ugi', 'unitig_749.g13745' => 'ugi', 'vmacro08269' => 'vma', 'vmacro14937' => 'vma', 'vmacro20401' => 'vma', 'VMungo0464G1349' => 'vmu', 'VMungo0540G0289' => 'vmu', 'VMungo1215G1590' => 'vmu', 'VMungo1309G0221' => 'vmu', 'VMungo1309G2815' => 'vmu', 'VMungo1383G0239' => 'vmu', 'VMungo1383G2910' => 'vmu', 'Zm00001eb095270' => 'zma', 'Zm00001eb095280' => 'zma', 'Zm00001eb111630' => 'zma', 'Zm00001eb237080' => 'zma', 'Zm00001eb273740' => 'zma', 'Zm00001eb285040' => 'zma', 'Zm00001eb330790' => 'zma', 'Zm00001eb337380' => 'zma' ), 'gf_id' => 'HOM05D001484', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001484' ), 'data_identifier' => 'HOM05D001484', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001484', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p31500' => 'bna', 'A05p00020' => 'bna', 'A07p08820' => 'bna', 'Aa31LG4G3300' => 'aar', 'Aa31LG8G10030' => 'aar', 'Actinidia00731' => 'ach', 'Actinidia11473' => 'ach', 'Actinidia23469' => 'ach', 'Actinidia24318' => 'ach', 'Actinidia40196' => 'ach', 'Actinidia40197' => 'ach', 'Actinidia40198' => 'ach', 'Ah.08g212990' => 'amhyb', 'Ah.15g091720' => 'amhyb', 'AL3G38260' => 'aly', 'AL4G47710' => 'aly', 'Aqoxy2G00671' => 'aox', 'Aqoxy2G03236' => 'aox', 'arahy.Tifrunner.gnm1.ann1.05IDCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KR684' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATY3SJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK6QJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6APGL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IDT7Z9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM073U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ0R87' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LE7RV4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT4QRX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V5ENPK' => 'arhy', 'AT2G48110' => 'ath', 'AT3G23590' => 'ath', 'ATR0626G186' => 'atr', 'ATR1127G141' => 'atr', 'Atru.chr4.2583' => 'acertr', 'Atru.chr5.1358' => 'acertr', 'Atru.chr5.1359' => 'acertr', 'Atru.chr8.46' => 'acertr', 'AUR62002640' => 'cqu', 'AUR62030055' => 'cqu', 'AUR62033713' => 'cqu', 'AUR62033714' => 'cqu', 'AUR62036795' => 'cqu', 'AUR62039891' => 'cqu', 'BcaB02g08737' => 'bca', 'BcaB04g20441' => 'bca', 'BcaB06g26509' => 'bca', 'BcaB06g26510' => 'bca', 'BcaB06g26511' => 'bca', 'BcaB06g26512' => 'bca', 'BcaB06g26513' => 'bca', 'BcaC02g12564' => 'bca', 'BcaC02g12565' => 'bca', 'BcaC02g12794' => 'bca', 'BcaC02g12795' => 'bca', 'BcaC02g12796' => 'bca', 'BcaC06g35541' => 'bca', 'BNapus_Darmor_BZH_scaffold_188p00080' => 'bna', 'BNapus_Darmor_BZH_scaffold_188p00090' => 'bna', 'BolC1t03972H' => 'bol', 'BolC1t03973H' => 'bol', 'BolC4t21680H' => 'bol', 'BolC7t41863H' => 'bol', 'BolSC55t61227H' => 'bol', 'BolSC55t61228H' => 'bol', 'BraA01t03278Z' => 'bra', 'BraA05t18998Z' => 'bra', 'BraA07t28673Z' => 'bra', 'C01p40150' => 'bna', 'C05p12370' => 'bna', 'C07p13680' => 'bna', 'CAN.G1006.16' => 'can', 'CAN.G1006.17' => 'can', 'CAN.G1170.2' => 'can', 'CAN.G962.7' => 'can', 'CANSAT25G2179' => 'cansat', 'CANSAT78G1573' => 'cansat', 'CARHR099510' => 'chi', 'CARHR143510' => 'chi', 'Carub.0003s2380' => 'cru', 'Carub.0004s3082' => 'cru', 'Ca_00614_v3' => 'car', 'Ca_07801_v3' => 'car', 'Ca_08567_v3' => 'car', 'Ca_09571_v3' => 'car', 'CBR_g19290' => 'cbr', 'Cc01_g19770' => 'ccan', 'Cc03_g03030' => 'ccan', 'CDE07G0968' => 'cde', 'CDE09G1441' => 'cde', 'Cfa006103' => 'cfa', 'Cfa015573' => 'cfa', 'Cfa016988' => 'cfa', 'Ciclev10006738m.g' => 'ccl', 'Ciclev10010920m.g' => 'ccl', 'Ciclev10018517m.g' => 'ccl', 'CiPaw.01G159200' => 'cil', 'CiPaw.02G091000' => 'cil', 'CiPaw.02G091100' => 'cil', 'CiPaw.08G103100' => 'cil', 'CiPaw.09G224900' => 'cil', 'ClCG06G005740' => 'cla', 'ClCG07G000090' => 'cla', 'ClCG07G000100' => 'cla', 'COL.COLO4_09143' => 'col', 'COL.COLO4_25124' => 'col', 'Cpa.g.sc16.34' => 'cpa', 'Cpa.g.sc3504.1' => 'cpa', 'Cpa.g.sc60.37' => 'cpa', 'CsaV3_6G018520' => 'csa', 'CsaV3_6G036860' => 'csa', 'CSS0001072' => 'camsi', 'CSS0020208' => 'camsi', 'CSS0021253' => 'camsi', 'CSS0022190' => 'camsi', 'CSS0036150' => 'camsi', 'CSS0040442' => 'camsi', 'CSS0042300' => 'camsi', 'CSS0045298' => 'camsi', 'DCAR_012449' => 'dca', 'DCAR_018405' => 'dca', 'DCAR_024573' => 'dca', 'DCAR_030591' => 'dca', 'Dinv16926' => 'din', 'Dinv32963' => 'din', 'Dinv38382' => 'din', 'Dinv38383' => 'din', 'Duzib133G0974' => 'dzi', 'Duzib138G1867' => 'dzi', 'Duzib211G0420' => 'dzi', 'Duzib212G0930' => 'dzi', 'ECA234G1645' => 'eca', 'ECA247G3467' => 'eca', 'ECA248G1703' => 'eca', 'EL10Ac3g06327' => 'bvu', 'EL10Ac7g17204' => 'bvu', 'Eucgr.A00855' => 'egr', 'Eucgr.A00858' => 'egr', 'Eucgr.H01520' => 'egr', 'Eucgr.H03604' => 'egr', 'Eucgr.L03465' => 'egr', 'Eucgr.L03466' => 'egr', 'FAN01G0988' => 'fan', 'FAN02G3892' => 'fan', 'FAN05G3381' => 'fan', 'FAN07G0967' => 'fan', 'FAN07G1493' => 'fan', 'FAN08G3125' => 'fan', 'FAN09G0402' => 'fan', 'FAN12G2594' => 'fan', 'FAN12G3879' => 'fan', 'FAN14G1546' => 'fan', 'FAN15G3626' => 'fan', 'FAN17G0588' => 'fan', 'FAN17G0609' => 'fan', 'FAN18G2817' => 'fan', 'FAN19G1305' => 'fan', 'FAN20G1787' => 'fan', 'FAN22G0073' => 'fan', 'FAN22G0352' => 'fan', 'FAN22G0368' => 'fan', 'FAN22G2273' => 'fan', 'FAN24G1998' => 'fan', 'FAN27G1317' => 'fan', 'FvH4_2g23980' => 'fve', 'FvH4_4g14380' => 'fve', 'FvH4_4g14390' => 'fve', 'FvH4_6g09250' => 'fve', 'Glyma.03G151100' => 'gma', 'Glyma.04G122550' => 'gma', 'Glyma.05G001600' => 'gma', 'Glyma.09G270766' => 'gma', 'Glyma.09G270832' => 'gma', 'Glyma.13G209800' => 'gma', 'Glyma.15G102800' => 'gma', 'Glyma.18G218900' => 'gma', 'Glyma.19G001500' => 'gma', 'Glyma.19G153600' => 'gma', 'Gohir.A02G028600' => 'ghi', 'Gohir.A08G045000' => 'ghi', 'Gohir.A11G120500' => 'ghi', 'Gohir.A12G006200' => 'ghi', 'Gohir.A12G006250' => 'ghi', 'Gohir.D02G036300' => 'ghi', 'Gohir.D08G054700' => 'ghi', 'Gohir.D11G125600' => 'ghi', 'Gohir.D12G005700' => 'ghi', 'Gorai.004G055200' => 'gra', 'Gorai.005G040400' => 'gra', 'Gorai.007G134500' => 'gra', 'Gorai.008G005500' => 'gra', 'GSVIVG01011094001' => 'vvi', 'GSVIVG01017879001' => 'vvi', 'GSVIVG01025988001' => 'vvi', 'GSVIVG01029847001' => 'vvi', 'HanXRQChr10g0282901' => 'han', 'HanXRQChr10g0310371' => 'han', 'HanXRQChr10g0315041' => 'han', 'HanXRQChr11g0327651' => 'han', 'HanXRQChr12g0359391' => 'han', 'Haze_00972' => 'cav', 'Haze_00973' => 'cav', 'Haze_00974' => 'cav', 'Haze_04747' => 'cav', 'Haze_04749' => 'cav', 'Haze_04750' => 'cav', 'Haze_21217' => 'cav', 'Hma1.2p1_1037F.1_g250680' => 'hma', 'Hma1.2p1_1644F.1_g295320' => 'hma', 'HPP92_011322' => 'vpl', 'HPP92_011323' => 'vpl', 'HPP92_011324' => 'vpl', 'HPP92_011325' => 'vpl', 'HPP92_011326' => 'vpl', 'Hund12205' => 'sun', 'Hund17957' => 'sun', 'Lalb_Chr06g0176771' => 'lal', 'Lalb_Chr18g0056021' => 'lal', 'Lalb_Chr18g0056031' => 'lal', 'Lalb_Chr18g0056041' => 'lal', 'Lalb_Chr20g0107751' => 'lal', 'Lalb_Chr20g0118371' => 'lal', 'Lj1g0010239' => 'lja', 'Lj1g0017101' => 'lja', 'Lj2A1178G40' => 'lonja', 'Lj2A54G84' => 'lonja', 'Lj2g0015248' => 'lja', 'Lj3A761T51' => 'lonja', 'Lj6g0018116' => 'lja', 'Lsat_1_v5_gn_4_136040' => 'lsa', 'Lsat_1_v5_gn_5_187461' => 'lsa', 'Lsat_1_v5_gn_5_77001' => 'lsa', 'Lsat_1_v5_gn_9_4461' => 'lsa', 'Manes.01G210100' => 'mes', 'Manes.03G185600' => 'mes', 'Manes.05G073300' => 'mes', 'Manes.09G120300' => 'mes', 'Manes.15G022100' => 'mes', 'Mapoly0096s0053' => 'mpo', 'MBI03_g14058_MAGBIO' => 'mbi', 'MBI03_g33876_MAGBIO' => 'mbi', 'MBI03_g36854_MAGBIO' => 'mbi', 'MBI17_g11997_MAGBIO' => 'mbi', 'MD03G1269000' => 'mdo', 'MD04G1179600' => 'mdo', 'MD11G1289800' => 'mdo', 'MD12G1194700' => 'mdo', 'MD13G1182100' => 'mdo', 'MD13G1182200' => 'mdo', 'MD16G1182600' => 'mdo', 'Medtr2g021400' => 'mtr', 'Medtr2g021470' => 'mtr', 'Medtr2g105810' => 'mtr', 'Medtr3g033580' => 'mtr', 'Medtr6g007970' => 'mtr', 'Medtr7g056330' => 'mtr', 'Medtr7g074290' => 'mtr', 'Medtr7g074380' => 'mtr', 'Medtr7g094550' => 'mtr', 'Medtr8g069995' => 'mtr', 'MELO3C014345.2' => 'cme', 'MELO3C021395.2' => 'cme', 'Migut.D00262' => 'egut', 'Migut.G00257' => 'egut', 'MSTRG.21575' => 'ama', 'MSTRG.3985' => 'ama', 'Nitab4.5_0000295g0140' => 'nta', 'Nitab4.5_0000732g0140' => 'nta', 'Nitab4.5_0003162g0020' => 'nta', 'Nitab4.5_0006180g0090' => 'nta', 'Nitab4.5_0006390g0010' => 'nta', 'Nitab4.5_0007392g0040' => 'nta', 'Nn1g02140' => 'nnu', 'Nn4g26168' => 'nnu', 'Nn5g26754' => 'nnu', 'Oeu001433.1' => 'oeu', 'Oeu010299.2' => 'oeu', 'Oeu011171.1' => 'oeu', 'Oeu037675.1' => 'oeu', 'Oeu038359.1' => 'oeu', 'Oeu063834.1' => 'oeu', 'Oeu063835.1' => 'oeu', 'Os05g0312000' => 'osa', 'Os07g0211101' => 'osa', 'Os07g0211200' => 'osa', 'Os07g0681500' => 'osa', 'Peaxi162Scf00095g01015' => 'pax', 'Peaxi162Scf00104g00329' => 'pax', 'Peaxi162Scf00161g00137' => 'pax', 'PGR004G1665' => 'pgr', 'PGR031G2937' => 'pgr', 'PGR119G2145' => 'pgr', 'PGSC0003DMG400004351' => 'stu', 'PGSC0003DMG400014625' => 'stu', 'PGSC0003DMG401000943' => 'stu', 'Phvul.001G148600' => 'pvu', 'Phvul.004G001700' => 'pvu', 'Phvul.006G154900' => 'pvu', 'Phvul.008G078200' => 'pvu', 'Phvul.011G136500' => 'pvu', 'Potri.002G215600' => 'ptr', 'Potri.008G201600' => 'ptr', 'Potri.014G138400' => 'ptr', 'Potri.016G142500' => 'ptr', 'Pp3c16_10580' => 'ppa', 'Pp3c5_25280' => 'ppa', 'Prupe.1G150000' => 'ppe', 'Prupe.1G150100' => 'ppe', 'Prupe.6G299600' => 'ppe', 'Prupe.8G245000' => 'ppe', 'Psat0s4927g0040' => 'psa', 'Psat1g052080' => 'psa', 'Psat1g183800' => 'psa', 'Psat3g113840' => 'psa', 'Psat3g126120' => 'psa', 'Psat3g126160' => 'psa', 'Psat3g158760' => 'psa', 'Psat3g158840' => 'psa', 'PSO170G2858' => 'pso', 'PSO339G0606' => 'pso', 'PSO384G4709' => 'pso', 'PSO407G0334' => 'pso', 'QL04p040276' => 'qlo', 'QL06p005458' => 'qlo', 'QL06p005472' => 'qlo', 'QL07p030546' => 'qlo', 'QL07p031519' => 'qlo', 'QL09p050949' => 'qlo', 'QL09p050966' => 'qlo', 'QL09p051067' => 'qlo', 'QL12p022706' => 'qlo', 'RcHm_v2.0_Chr2g0119601' => 'rch', 'RcHm_v2.0_Chr3g0459591' => 'rch', 'RcHm_v2.0_Chr4g0418521' => 'rch', 'RcHm_v2.0_Chr4g0418531' => 'rch', 'RcHm_v2.0_Chr4g0418541' => 'rch', 'RcHm_v2.0_Chr6g0291641' => 'rch', 'Rhsim01G0086300' => 'rsi', 'Rhsim01G0276300' => 'rsi', 'Rhsim01G0276500' => 'rsi', 'Rhsim04G0207700' => 'rsi', 'Rhsim05G0234500' => 'rsi', 'Rhsim13G0022400' => 'rsi', 'Sabra02G0167900' => 'sbr', 'Sabra04G0158500' => 'sbr', 'Sabra08G0159800' => 'sbr', 'Sabra10G0011500' => 'sbr', 'Sabra14G0104400' => 'sbr', 'SalBow2G2440' => 'sbo', 'SalBow4G2265' => 'sbo', 'Sc02g0000060' => 'sci', 'Sc05g0005020' => 'sci', 'Sc13g0003890' => 'sci', 'Sed0014865' => 'sed', 'Sed0017224' => 'sed', 'Sed0026391' => 'sed', 'SEGI_00063' => 'sgi', 'SEGI_10967' => 'sgi', 'SEGI_17510' => 'sgi', 'SEGI_24396' => 'sgi', 'SEGI_39719' => 'sgi', 'SEGI_41392' => 'sgi', 'SGA_v2.0_scaffold11G05794' => 'sas', 'SGA_v2.0_scaffold142G35607' => 'sas', 'SGA_v2.0_scaffold1G00447' => 'sas', 'SHI15388' => 'shi', 'SHI15394' => 'shi', 'SHI15396' => 'shi', 'SHI15399' => 'shi', 'SMO343G0151' => 'smo', 'SMO367G1118' => 'smo', 'Solyc01g080200.3' => 'sly', 'Solyc06g008960.3' => 'sly', 'Solyc09g064780.3' => 'sly', 'Sopen01g031980' => 'spe', 'Sopen06g003710' => 'spe', 'Sopen09g026460' => 'spe', 'Sp3g21240' => 'spa', 'Sp4g30030' => 'spa', 'TAR365G0022' => 'tar', 'TAR365G1023' => 'tar', 'TAR365G1253' => 'tar', 'TAR623G0078' => 'tar', 'TAR623G1721' => 'tar', 'TAR633G0959' => 'tar', 'THA.LOC104802225' => 'tha', 'THA.LOC104804769' => 'tha', 'THA.LOC104808660' => 'tha', 'THA.LOC104812792' => 'tha', 'Thecc.01G284000' => 'tca', 'Thecc.04G220600' => 'tca', 'Thecc.05G268900' => 'tca', 'Thecc.08G171100' => 'tca', 'Thhalv10001284m.g' => 'esa', 'Thhalv10019912m.g' => 'esa', 'TPR.G14189' => 'tpr', 'TPR.G18110' => 'tpr', 'TPR.G18130' => 'tpr', 'TPR.G18131' => 'tpr', 'TPR.G18140' => 'tpr', 'TPR.G24282' => 'tpr', 'TPR.G25221' => 'tpr', 'TPR.G29267' => 'tpr', 'TPR.G35315' => 'tpr', 'TPR.G36173' => 'tpr', 'TWI09G0794' => 'twi', 'TWI59G1348' => 'twi', 'TWI74G0430' => 'twi', 'unitig_26.g8940' => 'ugi', 'unitig_749.g13744' => 'ugi', 'unitig_749.g13745' => 'ugi', 'vmacro08269' => 'vma', 'vmacro14937' => 'vma', 'vmacro20401' => 'vma', 'VMungo0464G1349' => 'vmu', 'VMungo0540G0289' => 'vmu', 'VMungo1215G1590' => 'vmu', 'VMungo1309G0221' => 'vmu', 'VMungo1309G2815' => 'vmu', 'VMungo1383G0239' => 'vmu', 'VMungo1383G2910' => 'vmu', 'Zm00001eb095270' => 'zma', 'Zm00001eb095280' => 'zma', 'Zm00001eb111630' => 'zma', 'Zm00001eb237080' => 'zma', 'Zm00001eb273740' => 'zma', 'Zm00001eb285040' => 'zma', 'Zm00001eb330790' => 'zma', 'Zm00001eb337380' => 'zma' ) $gf_id = 'HOM05D001484' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001484' ) $data_identifier = 'HOM05D001484' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 2, 'aly' => (int) 2, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 22, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 7, 'hma' => (int) 2, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 7, 'mtr' => (int) 10, 'cme' => (int) 2, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 4, 'ppa' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 4, 'qlo' => (int) 9, 'rch' => (int) 6, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 10, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 7, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb337380' $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' => 'HOM05D001484', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p31500' => 'bna', 'A05p00020' => 'bna', 'A07p08820' => 'bna', 'Aa31LG4G3300' => 'aar', 'Aa31LG8G10030' => 'aar', 'Actinidia00731' => 'ach', 'Actinidia11473' => 'ach', 'Actinidia23469' => 'ach', 'Actinidia24318' => 'ach', 'Actinidia40196' => 'ach', 'Actinidia40197' => 'ach', 'Actinidia40198' => 'ach', 'Ah.08g212990' => 'amhyb', 'Ah.15g091720' => 'amhyb', 'AL3G38260' => 'aly', 'AL4G47710' => 'aly', 'Aqoxy2G00671' => 'aox', 'Aqoxy2G03236' => 'aox', 'arahy.Tifrunner.gnm1.ann1.05IDCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KR684' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATY3SJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK6QJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6APGL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IDT7Z9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM073U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ0R87' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LE7RV4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT4QRX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V5ENPK' => 'arhy', 'AT2G48110' => 'ath', 'AT3G23590' => 'ath', 'ATR0626G186' => 'atr', 'ATR1127G141' => 'atr', 'Atru.chr4.2583' => 'acertr', 'Atru.chr5.1358' => 'acertr', 'Atru.chr5.1359' => 'acertr', 'Atru.chr8.46' => 'acertr', 'AUR62002640' => 'cqu', 'AUR62030055' => 'cqu', 'AUR62033713' => 'cqu', 'AUR62033714' => 'cqu', 'AUR62036795' => 'cqu', 'AUR62039891' => 'cqu', 'BcaB02g08737' => 'bca', 'BcaB04g20441' => 'bca', 'BcaB06g26509' => 'bca', 'BcaB06g26510' => 'bca', 'BcaB06g26511' => 'bca', 'BcaB06g26512' => 'bca', 'BcaB06g26513' => 'bca', 'BcaC02g12564' => 'bca', 'BcaC02g12565' => 'bca', 'BcaC02g12794' => 'bca', 'BcaC02g12795' => 'bca', 'BcaC02g12796' => 'bca', 'BcaC06g35541' => 'bca', 'BNapus_Darmor_BZH_scaffold_188p00080' => 'bna', 'BNapus_Darmor_BZH_scaffold_188p00090' => 'bna', 'BolC1t03972H' => 'bol', 'BolC1t03973H' => 'bol', 'BolC4t21680H' => 'bol', 'BolC7t41863H' => 'bol', 'BolSC55t61227H' => 'bol', 'BolSC55t61228H' => 'bol', 'BraA01t03278Z' => 'bra', 'BraA05t18998Z' => 'bra', 'BraA07t28673Z' => 'bra', 'C01p40150' => 'bna', 'C05p12370' => 'bna', 'C07p13680' => 'bna', 'CAN.G1006.16' => 'can', 'CAN.G1006.17' => 'can', 'CAN.G1170.2' => 'can', 'CAN.G962.7' => 'can', 'CANSAT25G2179' => 'cansat', 'CANSAT78G1573' => 'cansat', 'CARHR099510' => 'chi', 'CARHR143510' => 'chi', 'Carub.0003s2380' => 'cru', 'Carub.0004s3082' => 'cru', 'Ca_00614_v3' => 'car', 'Ca_07801_v3' => 'car', 'Ca_08567_v3' => 'car', 'Ca_09571_v3' => 'car', 'CBR_g19290' => 'cbr', 'Cc01_g19770' => 'ccan', 'Cc03_g03030' => 'ccan', 'CDE07G0968' => 'cde', 'CDE09G1441' => 'cde', 'Cfa006103' => 'cfa', 'Cfa015573' => 'cfa', 'Cfa016988' => 'cfa', 'Ciclev10006738m.g' => 'ccl', 'Ciclev10010920m.g' => 'ccl', 'Ciclev10018517m.g' => 'ccl', 'CiPaw.01G159200' => 'cil', 'CiPaw.02G091000' => 'cil', 'CiPaw.02G091100' => 'cil', 'CiPaw.08G103100' => 'cil', 'CiPaw.09G224900' => 'cil', 'ClCG06G005740' => 'cla', 'ClCG07G000090' => 'cla', 'ClCG07G000100' => 'cla', 'COL.COLO4_09143' => 'col', 'COL.COLO4_25124' => 'col', 'Cpa.g.sc16.34' => 'cpa', 'Cpa.g.sc3504.1' => 'cpa', 'Cpa.g.sc60.37' => 'cpa', 'CsaV3_6G018520' => 'csa', 'CsaV3_6G036860' => 'csa', 'CSS0001072' => 'camsi', 'CSS0020208' => 'camsi', 'CSS0021253' => 'camsi', 'CSS0022190' => 'camsi', 'CSS0036150' => 'camsi', 'CSS0040442' => 'camsi', 'CSS0042300' => 'camsi', 'CSS0045298' => 'camsi', 'DCAR_012449' => 'dca', 'DCAR_018405' => 'dca', 'DCAR_024573' => 'dca', 'DCAR_030591' => 'dca', 'Dinv16926' => 'din', 'Dinv32963' => 'din', 'Dinv38382' => 'din', 'Dinv38383' => 'din', 'Duzib133G0974' => 'dzi', 'Duzib138G1867' => 'dzi', 'Duzib211G0420' => 'dzi', 'Duzib212G0930' => 'dzi', 'ECA234G1645' => 'eca', 'ECA247G3467' => 'eca', 'ECA248G1703' => 'eca', 'EL10Ac3g06327' => 'bvu', 'EL10Ac7g17204' => 'bvu', 'Eucgr.A00855' => 'egr', 'Eucgr.A00858' => 'egr', 'Eucgr.H01520' => 'egr', 'Eucgr.H03604' => 'egr', 'Eucgr.L03465' => 'egr', 'Eucgr.L03466' => 'egr', 'FAN01G0988' => 'fan', 'FAN02G3892' => 'fan', 'FAN05G3381' => 'fan', 'FAN07G0967' => 'fan', 'FAN07G1493' => 'fan', 'FAN08G3125' => 'fan', 'FAN09G0402' => 'fan', 'FAN12G2594' => 'fan', 'FAN12G3879' => 'fan', 'FAN14G1546' => 'fan', 'FAN15G3626' => 'fan', 'FAN17G0588' => 'fan', 'FAN17G0609' => 'fan', 'FAN18G2817' => 'fan', 'FAN19G1305' => 'fan', 'FAN20G1787' => 'fan', 'FAN22G0073' => 'fan', 'FAN22G0352' => 'fan', 'FAN22G0368' => 'fan', 'FAN22G2273' => 'fan', 'FAN24G1998' => 'fan', 'FAN27G1317' => 'fan', 'FvH4_2g23980' => 'fve', 'FvH4_4g14380' => 'fve', 'FvH4_4g14390' => 'fve', 'FvH4_6g09250' => 'fve', 'Glyma.03G151100' => 'gma', 'Glyma.04G122550' => 'gma', 'Glyma.05G001600' => 'gma', 'Glyma.09G270766' => 'gma', 'Glyma.09G270832' => 'gma', 'Glyma.13G209800' => 'gma', 'Glyma.15G102800' => 'gma', 'Glyma.18G218900' => 'gma', 'Glyma.19G001500' => 'gma', 'Glyma.19G153600' => 'gma', 'Gohir.A02G028600' => 'ghi', 'Gohir.A08G045000' => 'ghi', 'Gohir.A11G120500' => 'ghi', 'Gohir.A12G006200' => 'ghi', 'Gohir.A12G006250' => 'ghi', 'Gohir.D02G036300' => 'ghi', 'Gohir.D08G054700' => 'ghi', 'Gohir.D11G125600' => 'ghi', 'Gohir.D12G005700' => 'ghi', 'Gorai.004G055200' => 'gra', 'Gorai.005G040400' => 'gra', 'Gorai.007G134500' => 'gra', 'Gorai.008G005500' => 'gra', 'GSVIVG01011094001' => 'vvi', 'GSVIVG01017879001' => 'vvi', 'GSVIVG01025988001' => 'vvi', 'GSVIVG01029847001' => 'vvi', 'HanXRQChr10g0282901' => 'han', 'HanXRQChr10g0310371' => 'han', 'HanXRQChr10g0315041' => 'han', 'HanXRQChr11g0327651' => 'han', 'HanXRQChr12g0359391' => 'han', 'Haze_00972' => 'cav', 'Haze_00973' => 'cav', 'Haze_00974' => 'cav', 'Haze_04747' => 'cav', 'Haze_04749' => 'cav', 'Haze_04750' => 'cav', 'Haze_21217' => 'cav', 'Hma1.2p1_1037F.1_g250680' => 'hma', 'Hma1.2p1_1644F.1_g295320' => 'hma', 'HPP92_011322' => 'vpl', 'HPP92_011323' => 'vpl', 'HPP92_011324' => 'vpl', 'HPP92_011325' => 'vpl', 'HPP92_011326' => 'vpl', 'Hund12205' => 'sun', 'Hund17957' => 'sun', 'Lalb_Chr06g0176771' => 'lal', 'Lalb_Chr18g0056021' => 'lal', 'Lalb_Chr18g0056031' => 'lal', 'Lalb_Chr18g0056041' => 'lal', 'Lalb_Chr20g0107751' => 'lal', 'Lalb_Chr20g0118371' => 'lal', 'Lj1g0010239' => 'lja', 'Lj1g0017101' => 'lja', 'Lj2A1178G40' => 'lonja', 'Lj2A54G84' => 'lonja', 'Lj2g0015248' => 'lja', 'Lj3A761T51' => 'lonja', 'Lj6g0018116' => 'lja', 'Lsat_1_v5_gn_4_136040' => 'lsa', 'Lsat_1_v5_gn_5_187461' => 'lsa', 'Lsat_1_v5_gn_5_77001' => 'lsa', 'Lsat_1_v5_gn_9_4461' => 'lsa', 'Manes.01G210100' => 'mes', 'Manes.03G185600' => 'mes', 'Manes.05G073300' => 'mes', 'Manes.09G120300' => 'mes', 'Manes.15G022100' => 'mes', 'Mapoly0096s0053' => 'mpo', 'MBI03_g14058_MAGBIO' => 'mbi', 'MBI03_g33876_MAGBIO' => 'mbi', 'MBI03_g36854_MAGBIO' => 'mbi', 'MBI17_g11997_MAGBIO' => 'mbi', 'MD03G1269000' => 'mdo', 'MD04G1179600' => 'mdo', 'MD11G1289800' => 'mdo', 'MD12G1194700' => 'mdo', 'MD13G1182100' => 'mdo', 'MD13G1182200' => 'mdo', 'MD16G1182600' => 'mdo', 'Medtr2g021400' => 'mtr', 'Medtr2g021470' => 'mtr', 'Medtr2g105810' => 'mtr', 'Medtr3g033580' => 'mtr', 'Medtr6g007970' => 'mtr', 'Medtr7g056330' => 'mtr', 'Medtr7g074290' => 'mtr', 'Medtr7g074380' => 'mtr', 'Medtr7g094550' => 'mtr', 'Medtr8g069995' => 'mtr', 'MELO3C014345.2' => 'cme', 'MELO3C021395.2' => 'cme', 'Migut.D00262' => 'egut', 'Migut.G00257' => 'egut', 'MSTRG.21575' => 'ama', 'MSTRG.3985' => 'ama', 'Nitab4.5_0000295g0140' => 'nta', 'Nitab4.5_0000732g0140' => 'nta', 'Nitab4.5_0003162g0020' => 'nta', 'Nitab4.5_0006180g0090' => 'nta', 'Nitab4.5_0006390g0010' => 'nta', 'Nitab4.5_0007392g0040' => 'nta', 'Nn1g02140' => 'nnu', 'Nn4g26168' => 'nnu', 'Nn5g26754' => 'nnu', 'Oeu001433.1' => 'oeu', 'Oeu010299.2' => 'oeu', 'Oeu011171.1' => 'oeu', 'Oeu037675.1' => 'oeu', 'Oeu038359.1' => 'oeu', 'Oeu063834.1' => 'oeu', 'Oeu063835.1' => 'oeu', 'Os05g0312000' => 'osa', 'Os07g0211101' => 'osa', 'Os07g0211200' => 'osa', 'Os07g0681500' => 'osa', 'Peaxi162Scf00095g01015' => 'pax', 'Peaxi162Scf00104g00329' => 'pax', 'Peaxi162Scf00161g00137' => 'pax', 'PGR004G1665' => 'pgr', 'PGR031G2937' => 'pgr', 'PGR119G2145' => 'pgr', 'PGSC0003DMG400004351' => 'stu', 'PGSC0003DMG400014625' => 'stu', 'PGSC0003DMG401000943' => 'stu', 'Phvul.001G148600' => 'pvu', 'Phvul.004G001700' => 'pvu', 'Phvul.006G154900' => 'pvu', 'Phvul.008G078200' => 'pvu', 'Phvul.011G136500' => 'pvu', 'Potri.002G215600' => 'ptr', 'Potri.008G201600' => 'ptr', 'Potri.014G138400' => 'ptr', 'Potri.016G142500' => 'ptr', 'Pp3c16_10580' => 'ppa', 'Pp3c5_25280' => 'ppa', 'Prupe.1G150000' => 'ppe', 'Prupe.1G150100' => 'ppe', 'Prupe.6G299600' => 'ppe', 'Prupe.8G245000' => 'ppe', 'Psat0s4927g0040' => 'psa', 'Psat1g052080' => 'psa', 'Psat1g183800' => 'psa', 'Psat3g113840' => 'psa', 'Psat3g126120' => 'psa', 'Psat3g126160' => 'psa', 'Psat3g158760' => 'psa', 'Psat3g158840' => 'psa', 'PSO170G2858' => 'pso', 'PSO339G0606' => 'pso', 'PSO384G4709' => 'pso', 'PSO407G0334' => 'pso', 'QL04p040276' => 'qlo', 'QL06p005458' => 'qlo', 'QL06p005472' => 'qlo', 'QL07p030546' => 'qlo', 'QL07p031519' => 'qlo', 'QL09p050949' => 'qlo', 'QL09p050966' => 'qlo', 'QL09p051067' => 'qlo', 'QL12p022706' => 'qlo', 'RcHm_v2.0_Chr2g0119601' => 'rch', 'RcHm_v2.0_Chr3g0459591' => 'rch', 'RcHm_v2.0_Chr4g0418521' => 'rch', 'RcHm_v2.0_Chr4g0418531' => 'rch', 'RcHm_v2.0_Chr4g0418541' => 'rch', 'RcHm_v2.0_Chr6g0291641' => 'rch', 'Rhsim01G0086300' => 'rsi', 'Rhsim01G0276300' => 'rsi', 'Rhsim01G0276500' => 'rsi', 'Rhsim04G0207700' => 'rsi', 'Rhsim05G0234500' => 'rsi', 'Rhsim13G0022400' => 'rsi', 'Sabra02G0167900' => 'sbr', 'Sabra04G0158500' => 'sbr', 'Sabra08G0159800' => 'sbr', 'Sabra10G0011500' => 'sbr', 'Sabra14G0104400' => 'sbr', 'SalBow2G2440' => 'sbo', 'SalBow4G2265' => 'sbo', 'Sc02g0000060' => 'sci', 'Sc05g0005020' => 'sci', 'Sc13g0003890' => 'sci', 'Sed0014865' => 'sed', 'Sed0017224' => 'sed', 'Sed0026391' => 'sed', 'SEGI_00063' => 'sgi', 'SEGI_10967' => 'sgi', 'SEGI_17510' => 'sgi', 'SEGI_24396' => 'sgi', 'SEGI_39719' => 'sgi', 'SEGI_41392' => 'sgi', 'SGA_v2.0_scaffold11G05794' => 'sas', 'SGA_v2.0_scaffold142G35607' => 'sas', 'SGA_v2.0_scaffold1G00447' => 'sas', 'SHI15388' => 'shi', 'SHI15394' => 'shi', 'SHI15396' => 'shi', 'SHI15399' => 'shi', 'SMO343G0151' => 'smo', 'SMO367G1118' => 'smo', 'Solyc01g080200.3' => 'sly', 'Solyc06g008960.3' => 'sly', 'Solyc09g064780.3' => 'sly', 'Sopen01g031980' => 'spe', 'Sopen06g003710' => 'spe', 'Sopen09g026460' => 'spe', 'Sp3g21240' => 'spa', 'Sp4g30030' => 'spa', 'TAR365G0022' => 'tar', 'TAR365G1023' => 'tar', 'TAR365G1253' => 'tar', 'TAR623G0078' => 'tar', 'TAR623G1721' => 'tar', 'TAR633G0959' => 'tar', 'THA.LOC104802225' => 'tha', 'THA.LOC104804769' => 'tha', 'THA.LOC104808660' => 'tha', 'THA.LOC104812792' => 'tha', 'Thecc.01G284000' => 'tca', 'Thecc.04G220600' => 'tca', 'Thecc.05G268900' => 'tca', 'Thecc.08G171100' => 'tca', 'Thhalv10001284m.g' => 'esa', 'Thhalv10019912m.g' => 'esa', 'TPR.G14189' => 'tpr', 'TPR.G18110' => 'tpr', 'TPR.G18130' => 'tpr', 'TPR.G18131' => 'tpr', 'TPR.G18140' => 'tpr', 'TPR.G24282' => 'tpr', 'TPR.G25221' => 'tpr', 'TPR.G29267' => 'tpr', 'TPR.G35315' => 'tpr', 'TPR.G36173' => 'tpr', 'TWI09G0794' => 'twi', 'TWI59G1348' => 'twi', 'TWI74G0430' => 'twi', 'unitig_26.g8940' => 'ugi', 'unitig_749.g13744' => 'ugi', 'unitig_749.g13745' => 'ugi', 'vmacro08269' => 'vma', 'vmacro14937' => 'vma', 'vmacro20401' => 'vma', 'VMungo0464G1349' => 'vmu', 'VMungo0540G0289' => 'vmu', 'VMungo1215G1590' => 'vmu', 'VMungo1309G0221' => 'vmu', 'VMungo1309G2815' => 'vmu', 'VMungo1383G0239' => 'vmu', 'VMungo1383G2910' => 'vmu', 'Zm00001eb095270' => 'zma', 'Zm00001eb095280' => 'zma', 'Zm00001eb111630' => 'zma', 'Zm00001eb237080' => 'zma', 'Zm00001eb273740' => 'zma', 'Zm00001eb285040' => 'zma', 'Zm00001eb330790' => 'zma', 'Zm00001eb337380' => 'zma' ), 'gf_id' => 'HOM05D001484', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001484' ), 'data_identifier' => 'HOM05D001484', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001484', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p31500' => 'bna', 'A05p00020' => 'bna', 'A07p08820' => 'bna', 'Aa31LG4G3300' => 'aar', 'Aa31LG8G10030' => 'aar', 'Actinidia00731' => 'ach', 'Actinidia11473' => 'ach', 'Actinidia23469' => 'ach', 'Actinidia24318' => 'ach', 'Actinidia40196' => 'ach', 'Actinidia40197' => 'ach', 'Actinidia40198' => 'ach', 'Ah.08g212990' => 'amhyb', 'Ah.15g091720' => 'amhyb', 'AL3G38260' => 'aly', 'AL4G47710' => 'aly', 'Aqoxy2G00671' => 'aox', 'Aqoxy2G03236' => 'aox', 'arahy.Tifrunner.gnm1.ann1.05IDCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KR684' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATY3SJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK6QJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6APGL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IDT7Z9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM073U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ0R87' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LE7RV4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT4QRX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V5ENPK' => 'arhy', 'AT2G48110' => 'ath', 'AT3G23590' => 'ath', 'ATR0626G186' => 'atr', 'ATR1127G141' => 'atr', 'Atru.chr4.2583' => 'acertr', 'Atru.chr5.1358' => 'acertr', 'Atru.chr5.1359' => 'acertr', 'Atru.chr8.46' => 'acertr', 'AUR62002640' => 'cqu', 'AUR62030055' => 'cqu', 'AUR62033713' => 'cqu', 'AUR62033714' => 'cqu', 'AUR62036795' => 'cqu', 'AUR62039891' => 'cqu', 'BcaB02g08737' => 'bca', 'BcaB04g20441' => 'bca', 'BcaB06g26509' => 'bca', 'BcaB06g26510' => 'bca', 'BcaB06g26511' => 'bca', 'BcaB06g26512' => 'bca', 'BcaB06g26513' => 'bca', 'BcaC02g12564' => 'bca', 'BcaC02g12565' => 'bca', 'BcaC02g12794' => 'bca', 'BcaC02g12795' => 'bca', 'BcaC02g12796' => 'bca', 'BcaC06g35541' => 'bca', 'BNapus_Darmor_BZH_scaffold_188p00080' => 'bna', 'BNapus_Darmor_BZH_scaffold_188p00090' => 'bna', 'BolC1t03972H' => 'bol', 'BolC1t03973H' => 'bol', 'BolC4t21680H' => 'bol', 'BolC7t41863H' => 'bol', 'BolSC55t61227H' => 'bol', 'BolSC55t61228H' => 'bol', 'BraA01t03278Z' => 'bra', 'BraA05t18998Z' => 'bra', 'BraA07t28673Z' => 'bra', 'C01p40150' => 'bna', 'C05p12370' => 'bna', 'C07p13680' => 'bna', 'CAN.G1006.16' => 'can', 'CAN.G1006.17' => 'can', 'CAN.G1170.2' => 'can', 'CAN.G962.7' => 'can', 'CANSAT25G2179' => 'cansat', 'CANSAT78G1573' => 'cansat', 'CARHR099510' => 'chi', 'CARHR143510' => 'chi', 'Carub.0003s2380' => 'cru', 'Carub.0004s3082' => 'cru', 'Ca_00614_v3' => 'car', 'Ca_07801_v3' => 'car', 'Ca_08567_v3' => 'car', 'Ca_09571_v3' => 'car', 'CBR_g19290' => 'cbr', 'Cc01_g19770' => 'ccan', 'Cc03_g03030' => 'ccan', 'CDE07G0968' => 'cde', 'CDE09G1441' => 'cde', 'Cfa006103' => 'cfa', 'Cfa015573' => 'cfa', 'Cfa016988' => 'cfa', 'Ciclev10006738m.g' => 'ccl', 'Ciclev10010920m.g' => 'ccl', 'Ciclev10018517m.g' => 'ccl', 'CiPaw.01G159200' => 'cil', 'CiPaw.02G091000' => 'cil', 'CiPaw.02G091100' => 'cil', 'CiPaw.08G103100' => 'cil', 'CiPaw.09G224900' => 'cil', 'ClCG06G005740' => 'cla', 'ClCG07G000090' => 'cla', 'ClCG07G000100' => 'cla', 'COL.COLO4_09143' => 'col', 'COL.COLO4_25124' => 'col', 'Cpa.g.sc16.34' => 'cpa', 'Cpa.g.sc3504.1' => 'cpa', 'Cpa.g.sc60.37' => 'cpa', 'CsaV3_6G018520' => 'csa', 'CsaV3_6G036860' => 'csa', 'CSS0001072' => 'camsi', 'CSS0020208' => 'camsi', 'CSS0021253' => 'camsi', 'CSS0022190' => 'camsi', 'CSS0036150' => 'camsi', 'CSS0040442' => 'camsi', 'CSS0042300' => 'camsi', 'CSS0045298' => 'camsi', 'DCAR_012449' => 'dca', 'DCAR_018405' => 'dca', 'DCAR_024573' => 'dca', 'DCAR_030591' => 'dca', 'Dinv16926' => 'din', 'Dinv32963' => 'din', 'Dinv38382' => 'din', 'Dinv38383' => 'din', 'Duzib133G0974' => 'dzi', 'Duzib138G1867' => 'dzi', 'Duzib211G0420' => 'dzi', 'Duzib212G0930' => 'dzi', 'ECA234G1645' => 'eca', 'ECA247G3467' => 'eca', 'ECA248G1703' => 'eca', 'EL10Ac3g06327' => 'bvu', 'EL10Ac7g17204' => 'bvu', 'Eucgr.A00855' => 'egr', 'Eucgr.A00858' => 'egr', 'Eucgr.H01520' => 'egr', 'Eucgr.H03604' => 'egr', 'Eucgr.L03465' => 'egr', 'Eucgr.L03466' => 'egr', 'FAN01G0988' => 'fan', 'FAN02G3892' => 'fan', 'FAN05G3381' => 'fan', 'FAN07G0967' => 'fan', 'FAN07G1493' => 'fan', 'FAN08G3125' => 'fan', 'FAN09G0402' => 'fan', 'FAN12G2594' => 'fan', 'FAN12G3879' => 'fan', 'FAN14G1546' => 'fan', 'FAN15G3626' => 'fan', 'FAN17G0588' => 'fan', 'FAN17G0609' => 'fan', 'FAN18G2817' => 'fan', 'FAN19G1305' => 'fan', 'FAN20G1787' => 'fan', 'FAN22G0073' => 'fan', 'FAN22G0352' => 'fan', 'FAN22G0368' => 'fan', 'FAN22G2273' => 'fan', 'FAN24G1998' => 'fan', 'FAN27G1317' => 'fan', 'FvH4_2g23980' => 'fve', 'FvH4_4g14380' => 'fve', 'FvH4_4g14390' => 'fve', 'FvH4_6g09250' => 'fve', 'Glyma.03G151100' => 'gma', 'Glyma.04G122550' => 'gma', 'Glyma.05G001600' => 'gma', 'Glyma.09G270766' => 'gma', 'Glyma.09G270832' => 'gma', 'Glyma.13G209800' => 'gma', 'Glyma.15G102800' => 'gma', 'Glyma.18G218900' => 'gma', 'Glyma.19G001500' => 'gma', 'Glyma.19G153600' => 'gma', 'Gohir.A02G028600' => 'ghi', 'Gohir.A08G045000' => 'ghi', 'Gohir.A11G120500' => 'ghi', 'Gohir.A12G006200' => 'ghi', 'Gohir.A12G006250' => 'ghi', 'Gohir.D02G036300' => 'ghi', 'Gohir.D08G054700' => 'ghi', 'Gohir.D11G125600' => 'ghi', 'Gohir.D12G005700' => 'ghi', 'Gorai.004G055200' => 'gra', 'Gorai.005G040400' => 'gra', 'Gorai.007G134500' => 'gra', 'Gorai.008G005500' => 'gra', 'GSVIVG01011094001' => 'vvi', 'GSVIVG01017879001' => 'vvi', 'GSVIVG01025988001' => 'vvi', 'GSVIVG01029847001' => 'vvi', 'HanXRQChr10g0282901' => 'han', 'HanXRQChr10g0310371' => 'han', 'HanXRQChr10g0315041' => 'han', 'HanXRQChr11g0327651' => 'han', 'HanXRQChr12g0359391' => 'han', 'Haze_00972' => 'cav', 'Haze_00973' => 'cav', 'Haze_00974' => 'cav', 'Haze_04747' => 'cav', 'Haze_04749' => 'cav', 'Haze_04750' => 'cav', 'Haze_21217' => 'cav', 'Hma1.2p1_1037F.1_g250680' => 'hma', 'Hma1.2p1_1644F.1_g295320' => 'hma', 'HPP92_011322' => 'vpl', 'HPP92_011323' => 'vpl', 'HPP92_011324' => 'vpl', 'HPP92_011325' => 'vpl', 'HPP92_011326' => 'vpl', 'Hund12205' => 'sun', 'Hund17957' => 'sun', 'Lalb_Chr06g0176771' => 'lal', 'Lalb_Chr18g0056021' => 'lal', 'Lalb_Chr18g0056031' => 'lal', 'Lalb_Chr18g0056041' => 'lal', 'Lalb_Chr20g0107751' => 'lal', 'Lalb_Chr20g0118371' => 'lal', 'Lj1g0010239' => 'lja', 'Lj1g0017101' => 'lja', 'Lj2A1178G40' => 'lonja', 'Lj2A54G84' => 'lonja', 'Lj2g0015248' => 'lja', 'Lj3A761T51' => 'lonja', 'Lj6g0018116' => 'lja', 'Lsat_1_v5_gn_4_136040' => 'lsa', 'Lsat_1_v5_gn_5_187461' => 'lsa', 'Lsat_1_v5_gn_5_77001' => 'lsa', 'Lsat_1_v5_gn_9_4461' => 'lsa', 'Manes.01G210100' => 'mes', 'Manes.03G185600' => 'mes', 'Manes.05G073300' => 'mes', 'Manes.09G120300' => 'mes', 'Manes.15G022100' => 'mes', 'Mapoly0096s0053' => 'mpo', 'MBI03_g14058_MAGBIO' => 'mbi', 'MBI03_g33876_MAGBIO' => 'mbi', 'MBI03_g36854_MAGBIO' => 'mbi', 'MBI17_g11997_MAGBIO' => 'mbi', 'MD03G1269000' => 'mdo', 'MD04G1179600' => 'mdo', 'MD11G1289800' => 'mdo', 'MD12G1194700' => 'mdo', 'MD13G1182100' => 'mdo', 'MD13G1182200' => 'mdo', 'MD16G1182600' => 'mdo', 'Medtr2g021400' => 'mtr', 'Medtr2g021470' => 'mtr', 'Medtr2g105810' => 'mtr', 'Medtr3g033580' => 'mtr', 'Medtr6g007970' => 'mtr', 'Medtr7g056330' => 'mtr', 'Medtr7g074290' => 'mtr', 'Medtr7g074380' => 'mtr', 'Medtr7g094550' => 'mtr', 'Medtr8g069995' => 'mtr', 'MELO3C014345.2' => 'cme', 'MELO3C021395.2' => 'cme', 'Migut.D00262' => 'egut', 'Migut.G00257' => 'egut', 'MSTRG.21575' => 'ama', 'MSTRG.3985' => 'ama', 'Nitab4.5_0000295g0140' => 'nta', 'Nitab4.5_0000732g0140' => 'nta', 'Nitab4.5_0003162g0020' => 'nta', 'Nitab4.5_0006180g0090' => 'nta', 'Nitab4.5_0006390g0010' => 'nta', 'Nitab4.5_0007392g0040' => 'nta', 'Nn1g02140' => 'nnu', 'Nn4g26168' => 'nnu', 'Nn5g26754' => 'nnu', 'Oeu001433.1' => 'oeu', 'Oeu010299.2' => 'oeu', 'Oeu011171.1' => 'oeu', 'Oeu037675.1' => 'oeu', 'Oeu038359.1' => 'oeu', 'Oeu063834.1' => 'oeu', 'Oeu063835.1' => 'oeu', 'Os05g0312000' => 'osa', 'Os07g0211101' => 'osa', 'Os07g0211200' => 'osa', 'Os07g0681500' => 'osa', 'Peaxi162Scf00095g01015' => 'pax', 'Peaxi162Scf00104g00329' => 'pax', 'Peaxi162Scf00161g00137' => 'pax', 'PGR004G1665' => 'pgr', 'PGR031G2937' => 'pgr', 'PGR119G2145' => 'pgr', 'PGSC0003DMG400004351' => 'stu', 'PGSC0003DMG400014625' => 'stu', 'PGSC0003DMG401000943' => 'stu', 'Phvul.001G148600' => 'pvu', 'Phvul.004G001700' => 'pvu', 'Phvul.006G154900' => 'pvu', 'Phvul.008G078200' => 'pvu', 'Phvul.011G136500' => 'pvu', 'Potri.002G215600' => 'ptr', 'Potri.008G201600' => 'ptr', 'Potri.014G138400' => 'ptr', 'Potri.016G142500' => 'ptr', 'Pp3c16_10580' => 'ppa', 'Pp3c5_25280' => 'ppa', 'Prupe.1G150000' => 'ppe', 'Prupe.1G150100' => 'ppe', 'Prupe.6G299600' => 'ppe', 'Prupe.8G245000' => 'ppe', 'Psat0s4927g0040' => 'psa', 'Psat1g052080' => 'psa', 'Psat1g183800' => 'psa', 'Psat3g113840' => 'psa', 'Psat3g126120' => 'psa', 'Psat3g126160' => 'psa', 'Psat3g158760' => 'psa', 'Psat3g158840' => 'psa', 'PSO170G2858' => 'pso', 'PSO339G0606' => 'pso', 'PSO384G4709' => 'pso', 'PSO407G0334' => 'pso', 'QL04p040276' => 'qlo', 'QL06p005458' => 'qlo', 'QL06p005472' => 'qlo', 'QL07p030546' => 'qlo', 'QL07p031519' => 'qlo', 'QL09p050949' => 'qlo', 'QL09p050966' => 'qlo', 'QL09p051067' => 'qlo', 'QL12p022706' => 'qlo', 'RcHm_v2.0_Chr2g0119601' => 'rch', 'RcHm_v2.0_Chr3g0459591' => 'rch', 'RcHm_v2.0_Chr4g0418521' => 'rch', 'RcHm_v2.0_Chr4g0418531' => 'rch', 'RcHm_v2.0_Chr4g0418541' => 'rch', 'RcHm_v2.0_Chr6g0291641' => 'rch', 'Rhsim01G0086300' => 'rsi', 'Rhsim01G0276300' => 'rsi', 'Rhsim01G0276500' => 'rsi', 'Rhsim04G0207700' => 'rsi', 'Rhsim05G0234500' => 'rsi', 'Rhsim13G0022400' => 'rsi', 'Sabra02G0167900' => 'sbr', 'Sabra04G0158500' => 'sbr', 'Sabra08G0159800' => 'sbr', 'Sabra10G0011500' => 'sbr', 'Sabra14G0104400' => 'sbr', 'SalBow2G2440' => 'sbo', 'SalBow4G2265' => 'sbo', 'Sc02g0000060' => 'sci', 'Sc05g0005020' => 'sci', 'Sc13g0003890' => 'sci', 'Sed0014865' => 'sed', 'Sed0017224' => 'sed', 'Sed0026391' => 'sed', 'SEGI_00063' => 'sgi', 'SEGI_10967' => 'sgi', 'SEGI_17510' => 'sgi', 'SEGI_24396' => 'sgi', 'SEGI_39719' => 'sgi', 'SEGI_41392' => 'sgi', 'SGA_v2.0_scaffold11G05794' => 'sas', 'SGA_v2.0_scaffold142G35607' => 'sas', 'SGA_v2.0_scaffold1G00447' => 'sas', 'SHI15388' => 'shi', 'SHI15394' => 'shi', 'SHI15396' => 'shi', 'SHI15399' => 'shi', 'SMO343G0151' => 'smo', 'SMO367G1118' => 'smo', 'Solyc01g080200.3' => 'sly', 'Solyc06g008960.3' => 'sly', 'Solyc09g064780.3' => 'sly', 'Sopen01g031980' => 'spe', 'Sopen06g003710' => 'spe', 'Sopen09g026460' => 'spe', 'Sp3g21240' => 'spa', 'Sp4g30030' => 'spa', 'TAR365G0022' => 'tar', 'TAR365G1023' => 'tar', 'TAR365G1253' => 'tar', 'TAR623G0078' => 'tar', 'TAR623G1721' => 'tar', 'TAR633G0959' => 'tar', 'THA.LOC104802225' => 'tha', 'THA.LOC104804769' => 'tha', 'THA.LOC104808660' => 'tha', 'THA.LOC104812792' => 'tha', 'Thecc.01G284000' => 'tca', 'Thecc.04G220600' => 'tca', 'Thecc.05G268900' => 'tca', 'Thecc.08G171100' => 'tca', 'Thhalv10001284m.g' => 'esa', 'Thhalv10019912m.g' => 'esa', 'TPR.G14189' => 'tpr', 'TPR.G18110' => 'tpr', 'TPR.G18130' => 'tpr', 'TPR.G18131' => 'tpr', 'TPR.G18140' => 'tpr', 'TPR.G24282' => 'tpr', 'TPR.G25221' => 'tpr', 'TPR.G29267' => 'tpr', 'TPR.G35315' => 'tpr', 'TPR.G36173' => 'tpr', 'TWI09G0794' => 'twi', 'TWI59G1348' => 'twi', 'TWI74G0430' => 'twi', 'unitig_26.g8940' => 'ugi', 'unitig_749.g13744' => 'ugi', 'unitig_749.g13745' => 'ugi', 'vmacro08269' => 'vma', 'vmacro14937' => 'vma', 'vmacro20401' => 'vma', 'VMungo0464G1349' => 'vmu', 'VMungo0540G0289' => 'vmu', 'VMungo1215G1590' => 'vmu', 'VMungo1309G0221' => 'vmu', 'VMungo1309G2815' => 'vmu', 'VMungo1383G0239' => 'vmu', 'VMungo1383G2910' => 'vmu', 'Zm00001eb095270' => 'zma', 'Zm00001eb095280' => 'zma', 'Zm00001eb111630' => 'zma', 'Zm00001eb237080' => 'zma', 'Zm00001eb273740' => 'zma', 'Zm00001eb285040' => 'zma', 'Zm00001eb330790' => 'zma', 'Zm00001eb337380' => 'zma' ) $gf_id = 'HOM05D001484' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001484' ) $data_identifier = 'HOM05D001484' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 2, 'aly' => (int) 2, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 22, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 7, 'hma' => (int) 2, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 7, 'mtr' => (int) 10, 'cme' => (int) 2, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 4, 'ppa' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 4, 'qlo' => (int) 9, 'rch' => (int) 6, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 10, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 7, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb337380' $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' => 'HOM05D001484', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p31500' => 'bna', 'A05p00020' => 'bna', 'A07p08820' => 'bna', 'Aa31LG4G3300' => 'aar', 'Aa31LG8G10030' => 'aar', 'Actinidia00731' => 'ach', 'Actinidia11473' => 'ach', 'Actinidia23469' => 'ach', 'Actinidia24318' => 'ach', 'Actinidia40196' => 'ach', 'Actinidia40197' => 'ach', 'Actinidia40198' => 'ach', 'Ah.08g212990' => 'amhyb', 'Ah.15g091720' => 'amhyb', 'AL3G38260' => 'aly', 'AL4G47710' => 'aly', 'Aqoxy2G00671' => 'aox', 'Aqoxy2G03236' => 'aox', 'arahy.Tifrunner.gnm1.ann1.05IDCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KR684' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATY3SJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK6QJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6APGL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IDT7Z9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM073U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ0R87' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LE7RV4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT4QRX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V5ENPK' => 'arhy', 'AT2G48110' => 'ath', 'AT3G23590' => 'ath', 'ATR0626G186' => 'atr', 'ATR1127G141' => 'atr', 'Atru.chr4.2583' => 'acertr', 'Atru.chr5.1358' => 'acertr', 'Atru.chr5.1359' => 'acertr', 'Atru.chr8.46' => 'acertr', 'AUR62002640' => 'cqu', 'AUR62030055' => 'cqu', 'AUR62033713' => 'cqu', 'AUR62033714' => 'cqu', 'AUR62036795' => 'cqu', 'AUR62039891' => 'cqu', 'BcaB02g08737' => 'bca', 'BcaB04g20441' => 'bca', 'BcaB06g26509' => 'bca', 'BcaB06g26510' => 'bca', 'BcaB06g26511' => 'bca', 'BcaB06g26512' => 'bca', 'BcaB06g26513' => 'bca', 'BcaC02g12564' => 'bca', 'BcaC02g12565' => 'bca', 'BcaC02g12794' => 'bca', 'BcaC02g12795' => 'bca', 'BcaC02g12796' => 'bca', 'BcaC06g35541' => 'bca', 'BNapus_Darmor_BZH_scaffold_188p00080' => 'bna', 'BNapus_Darmor_BZH_scaffold_188p00090' => 'bna', 'BolC1t03972H' => 'bol', 'BolC1t03973H' => 'bol', 'BolC4t21680H' => 'bol', 'BolC7t41863H' => 'bol', 'BolSC55t61227H' => 'bol', 'BolSC55t61228H' => 'bol', 'BraA01t03278Z' => 'bra', 'BraA05t18998Z' => 'bra', 'BraA07t28673Z' => 'bra', 'C01p40150' => 'bna', 'C05p12370' => 'bna', 'C07p13680' => 'bna', 'CAN.G1006.16' => 'can', 'CAN.G1006.17' => 'can', 'CAN.G1170.2' => 'can', 'CAN.G962.7' => 'can', 'CANSAT25G2179' => 'cansat', 'CANSAT78G1573' => 'cansat', 'CARHR099510' => 'chi', 'CARHR143510' => 'chi', 'Carub.0003s2380' => 'cru', 'Carub.0004s3082' => 'cru', 'Ca_00614_v3' => 'car', 'Ca_07801_v3' => 'car', 'Ca_08567_v3' => 'car', 'Ca_09571_v3' => 'car', 'CBR_g19290' => 'cbr', 'Cc01_g19770' => 'ccan', 'Cc03_g03030' => 'ccan', 'CDE07G0968' => 'cde', 'CDE09G1441' => 'cde', 'Cfa006103' => 'cfa', 'Cfa015573' => 'cfa', 'Cfa016988' => 'cfa', 'Ciclev10006738m.g' => 'ccl', 'Ciclev10010920m.g' => 'ccl', 'Ciclev10018517m.g' => 'ccl', 'CiPaw.01G159200' => 'cil', 'CiPaw.02G091000' => 'cil', 'CiPaw.02G091100' => 'cil', 'CiPaw.08G103100' => 'cil', 'CiPaw.09G224900' => 'cil', 'ClCG06G005740' => 'cla', 'ClCG07G000090' => 'cla', 'ClCG07G000100' => 'cla', 'COL.COLO4_09143' => 'col', 'COL.COLO4_25124' => 'col', 'Cpa.g.sc16.34' => 'cpa', 'Cpa.g.sc3504.1' => 'cpa', 'Cpa.g.sc60.37' => 'cpa', 'CsaV3_6G018520' => 'csa', 'CsaV3_6G036860' => 'csa', 'CSS0001072' => 'camsi', 'CSS0020208' => 'camsi', 'CSS0021253' => 'camsi', 'CSS0022190' => 'camsi', 'CSS0036150' => 'camsi', 'CSS0040442' => 'camsi', 'CSS0042300' => 'camsi', 'CSS0045298' => 'camsi', 'DCAR_012449' => 'dca', 'DCAR_018405' => 'dca', 'DCAR_024573' => 'dca', 'DCAR_030591' => 'dca', 'Dinv16926' => 'din', 'Dinv32963' => 'din', 'Dinv38382' => 'din', 'Dinv38383' => 'din', 'Duzib133G0974' => 'dzi', 'Duzib138G1867' => 'dzi', 'Duzib211G0420' => 'dzi', 'Duzib212G0930' => 'dzi', 'ECA234G1645' => 'eca', 'ECA247G3467' => 'eca', 'ECA248G1703' => 'eca', 'EL10Ac3g06327' => 'bvu', 'EL10Ac7g17204' => 'bvu', 'Eucgr.A00855' => 'egr', 'Eucgr.A00858' => 'egr', 'Eucgr.H01520' => 'egr', 'Eucgr.H03604' => 'egr', 'Eucgr.L03465' => 'egr', 'Eucgr.L03466' => 'egr', 'FAN01G0988' => 'fan', 'FAN02G3892' => 'fan', 'FAN05G3381' => 'fan', 'FAN07G0967' => 'fan', 'FAN07G1493' => 'fan', 'FAN08G3125' => 'fan', 'FAN09G0402' => 'fan', 'FAN12G2594' => 'fan', 'FAN12G3879' => 'fan', 'FAN14G1546' => 'fan', 'FAN15G3626' => 'fan', 'FAN17G0588' => 'fan', 'FAN17G0609' => 'fan', 'FAN18G2817' => 'fan', 'FAN19G1305' => 'fan', 'FAN20G1787' => 'fan', 'FAN22G0073' => 'fan', 'FAN22G0352' => 'fan', 'FAN22G0368' => 'fan', 'FAN22G2273' => 'fan', 'FAN24G1998' => 'fan', 'FAN27G1317' => 'fan', 'FvH4_2g23980' => 'fve', 'FvH4_4g14380' => 'fve', 'FvH4_4g14390' => 'fve', 'FvH4_6g09250' => 'fve', 'Glyma.03G151100' => 'gma', 'Glyma.04G122550' => 'gma', 'Glyma.05G001600' => 'gma', 'Glyma.09G270766' => 'gma', 'Glyma.09G270832' => 'gma', 'Glyma.13G209800' => 'gma', 'Glyma.15G102800' => 'gma', 'Glyma.18G218900' => 'gma', 'Glyma.19G001500' => 'gma', 'Glyma.19G153600' => 'gma', 'Gohir.A02G028600' => 'ghi', 'Gohir.A08G045000' => 'ghi', 'Gohir.A11G120500' => 'ghi', 'Gohir.A12G006200' => 'ghi', 'Gohir.A12G006250' => 'ghi', 'Gohir.D02G036300' => 'ghi', 'Gohir.D08G054700' => 'ghi', 'Gohir.D11G125600' => 'ghi', 'Gohir.D12G005700' => 'ghi', 'Gorai.004G055200' => 'gra', 'Gorai.005G040400' => 'gra', 'Gorai.007G134500' => 'gra', 'Gorai.008G005500' => 'gra', 'GSVIVG01011094001' => 'vvi', 'GSVIVG01017879001' => 'vvi', 'GSVIVG01025988001' => 'vvi', 'GSVIVG01029847001' => 'vvi', 'HanXRQChr10g0282901' => 'han', 'HanXRQChr10g0310371' => 'han', 'HanXRQChr10g0315041' => 'han', 'HanXRQChr11g0327651' => 'han', 'HanXRQChr12g0359391' => 'han', 'Haze_00972' => 'cav', 'Haze_00973' => 'cav', 'Haze_00974' => 'cav', 'Haze_04747' => 'cav', 'Haze_04749' => 'cav', 'Haze_04750' => 'cav', 'Haze_21217' => 'cav', 'Hma1.2p1_1037F.1_g250680' => 'hma', 'Hma1.2p1_1644F.1_g295320' => 'hma', 'HPP92_011322' => 'vpl', 'HPP92_011323' => 'vpl', 'HPP92_011324' => 'vpl', 'HPP92_011325' => 'vpl', 'HPP92_011326' => 'vpl', 'Hund12205' => 'sun', 'Hund17957' => 'sun', 'Lalb_Chr06g0176771' => 'lal', 'Lalb_Chr18g0056021' => 'lal', 'Lalb_Chr18g0056031' => 'lal', 'Lalb_Chr18g0056041' => 'lal', 'Lalb_Chr20g0107751' => 'lal', 'Lalb_Chr20g0118371' => 'lal', 'Lj1g0010239' => 'lja', 'Lj1g0017101' => 'lja', 'Lj2A1178G40' => 'lonja', 'Lj2A54G84' => 'lonja', 'Lj2g0015248' => 'lja', 'Lj3A761T51' => 'lonja', 'Lj6g0018116' => 'lja', 'Lsat_1_v5_gn_4_136040' => 'lsa', 'Lsat_1_v5_gn_5_187461' => 'lsa', 'Lsat_1_v5_gn_5_77001' => 'lsa', 'Lsat_1_v5_gn_9_4461' => 'lsa', 'Manes.01G210100' => 'mes', 'Manes.03G185600' => 'mes', 'Manes.05G073300' => 'mes', 'Manes.09G120300' => 'mes', 'Manes.15G022100' => 'mes', 'Mapoly0096s0053' => 'mpo', 'MBI03_g14058_MAGBIO' => 'mbi', 'MBI03_g33876_MAGBIO' => 'mbi', 'MBI03_g36854_MAGBIO' => 'mbi', 'MBI17_g11997_MAGBIO' => 'mbi', 'MD03G1269000' => 'mdo', 'MD04G1179600' => 'mdo', 'MD11G1289800' => 'mdo', 'MD12G1194700' => 'mdo', 'MD13G1182100' => 'mdo', 'MD13G1182200' => 'mdo', 'MD16G1182600' => 'mdo', 'Medtr2g021400' => 'mtr', 'Medtr2g021470' => 'mtr', 'Medtr2g105810' => 'mtr', 'Medtr3g033580' => 'mtr', 'Medtr6g007970' => 'mtr', 'Medtr7g056330' => 'mtr', 'Medtr7g074290' => 'mtr', 'Medtr7g074380' => 'mtr', 'Medtr7g094550' => 'mtr', 'Medtr8g069995' => 'mtr', 'MELO3C014345.2' => 'cme', 'MELO3C021395.2' => 'cme', 'Migut.D00262' => 'egut', 'Migut.G00257' => 'egut', 'MSTRG.21575' => 'ama', 'MSTRG.3985' => 'ama', 'Nitab4.5_0000295g0140' => 'nta', 'Nitab4.5_0000732g0140' => 'nta', 'Nitab4.5_0003162g0020' => 'nta', 'Nitab4.5_0006180g0090' => 'nta', 'Nitab4.5_0006390g0010' => 'nta', 'Nitab4.5_0007392g0040' => 'nta', 'Nn1g02140' => 'nnu', 'Nn4g26168' => 'nnu', 'Nn5g26754' => 'nnu', 'Oeu001433.1' => 'oeu', 'Oeu010299.2' => 'oeu', 'Oeu011171.1' => 'oeu', 'Oeu037675.1' => 'oeu', 'Oeu038359.1' => 'oeu', 'Oeu063834.1' => 'oeu', 'Oeu063835.1' => 'oeu', 'Os05g0312000' => 'osa', 'Os07g0211101' => 'osa', 'Os07g0211200' => 'osa', 'Os07g0681500' => 'osa', 'Peaxi162Scf00095g01015' => 'pax', 'Peaxi162Scf00104g00329' => 'pax', 'Peaxi162Scf00161g00137' => 'pax', 'PGR004G1665' => 'pgr', 'PGR031G2937' => 'pgr', 'PGR119G2145' => 'pgr', 'PGSC0003DMG400004351' => 'stu', 'PGSC0003DMG400014625' => 'stu', 'PGSC0003DMG401000943' => 'stu', 'Phvul.001G148600' => 'pvu', 'Phvul.004G001700' => 'pvu', 'Phvul.006G154900' => 'pvu', 'Phvul.008G078200' => 'pvu', 'Phvul.011G136500' => 'pvu', 'Potri.002G215600' => 'ptr', 'Potri.008G201600' => 'ptr', 'Potri.014G138400' => 'ptr', 'Potri.016G142500' => 'ptr', 'Pp3c16_10580' => 'ppa', 'Pp3c5_25280' => 'ppa', 'Prupe.1G150000' => 'ppe', 'Prupe.1G150100' => 'ppe', 'Prupe.6G299600' => 'ppe', 'Prupe.8G245000' => 'ppe', 'Psat0s4927g0040' => 'psa', 'Psat1g052080' => 'psa', 'Psat1g183800' => 'psa', 'Psat3g113840' => 'psa', 'Psat3g126120' => 'psa', 'Psat3g126160' => 'psa', 'Psat3g158760' => 'psa', 'Psat3g158840' => 'psa', 'PSO170G2858' => 'pso', 'PSO339G0606' => 'pso', 'PSO384G4709' => 'pso', 'PSO407G0334' => 'pso', 'QL04p040276' => 'qlo', 'QL06p005458' => 'qlo', 'QL06p005472' => 'qlo', 'QL07p030546' => 'qlo', 'QL07p031519' => 'qlo', 'QL09p050949' => 'qlo', 'QL09p050966' => 'qlo', 'QL09p051067' => 'qlo', 'QL12p022706' => 'qlo', 'RcHm_v2.0_Chr2g0119601' => 'rch', 'RcHm_v2.0_Chr3g0459591' => 'rch', 'RcHm_v2.0_Chr4g0418521' => 'rch', 'RcHm_v2.0_Chr4g0418531' => 'rch', 'RcHm_v2.0_Chr4g0418541' => 'rch', 'RcHm_v2.0_Chr6g0291641' => 'rch', 'Rhsim01G0086300' => 'rsi', 'Rhsim01G0276300' => 'rsi', 'Rhsim01G0276500' => 'rsi', 'Rhsim04G0207700' => 'rsi', 'Rhsim05G0234500' => 'rsi', 'Rhsim13G0022400' => 'rsi', 'Sabra02G0167900' => 'sbr', 'Sabra04G0158500' => 'sbr', 'Sabra08G0159800' => 'sbr', 'Sabra10G0011500' => 'sbr', 'Sabra14G0104400' => 'sbr', 'SalBow2G2440' => 'sbo', 'SalBow4G2265' => 'sbo', 'Sc02g0000060' => 'sci', 'Sc05g0005020' => 'sci', 'Sc13g0003890' => 'sci', 'Sed0014865' => 'sed', 'Sed0017224' => 'sed', 'Sed0026391' => 'sed', 'SEGI_00063' => 'sgi', 'SEGI_10967' => 'sgi', 'SEGI_17510' => 'sgi', 'SEGI_24396' => 'sgi', 'SEGI_39719' => 'sgi', 'SEGI_41392' => 'sgi', 'SGA_v2.0_scaffold11G05794' => 'sas', 'SGA_v2.0_scaffold142G35607' => 'sas', 'SGA_v2.0_scaffold1G00447' => 'sas', 'SHI15388' => 'shi', 'SHI15394' => 'shi', 'SHI15396' => 'shi', 'SHI15399' => 'shi', 'SMO343G0151' => 'smo', 'SMO367G1118' => 'smo', 'Solyc01g080200.3' => 'sly', 'Solyc06g008960.3' => 'sly', 'Solyc09g064780.3' => 'sly', 'Sopen01g031980' => 'spe', 'Sopen06g003710' => 'spe', 'Sopen09g026460' => 'spe', 'Sp3g21240' => 'spa', 'Sp4g30030' => 'spa', 'TAR365G0022' => 'tar', 'TAR365G1023' => 'tar', 'TAR365G1253' => 'tar', 'TAR623G0078' => 'tar', 'TAR623G1721' => 'tar', 'TAR633G0959' => 'tar', 'THA.LOC104802225' => 'tha', 'THA.LOC104804769' => 'tha', 'THA.LOC104808660' => 'tha', 'THA.LOC104812792' => 'tha', 'Thecc.01G284000' => 'tca', 'Thecc.04G220600' => 'tca', 'Thecc.05G268900' => 'tca', 'Thecc.08G171100' => 'tca', 'Thhalv10001284m.g' => 'esa', 'Thhalv10019912m.g' => 'esa', 'TPR.G14189' => 'tpr', 'TPR.G18110' => 'tpr', 'TPR.G18130' => 'tpr', 'TPR.G18131' => 'tpr', 'TPR.G18140' => 'tpr', 'TPR.G24282' => 'tpr', 'TPR.G25221' => 'tpr', 'TPR.G29267' => 'tpr', 'TPR.G35315' => 'tpr', 'TPR.G36173' => 'tpr', 'TWI09G0794' => 'twi', 'TWI59G1348' => 'twi', 'TWI74G0430' => 'twi', 'unitig_26.g8940' => 'ugi', 'unitig_749.g13744' => 'ugi', 'unitig_749.g13745' => 'ugi', 'vmacro08269' => 'vma', 'vmacro14937' => 'vma', 'vmacro20401' => 'vma', 'VMungo0464G1349' => 'vmu', 'VMungo0540G0289' => 'vmu', 'VMungo1215G1590' => 'vmu', 'VMungo1309G0221' => 'vmu', 'VMungo1309G2815' => 'vmu', 'VMungo1383G0239' => 'vmu', 'VMungo1383G2910' => 'vmu', 'Zm00001eb095270' => 'zma', 'Zm00001eb095280' => 'zma', 'Zm00001eb111630' => 'zma', 'Zm00001eb237080' => 'zma', 'Zm00001eb273740' => 'zma', 'Zm00001eb285040' => 'zma', 'Zm00001eb330790' => 'zma', 'Zm00001eb337380' => 'zma' ), 'gf_id' => 'HOM05D001484', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001484' ), 'data_identifier' => 'HOM05D001484', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001484', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p31500' => 'bna', 'A05p00020' => 'bna', 'A07p08820' => 'bna', 'Aa31LG4G3300' => 'aar', 'Aa31LG8G10030' => 'aar', 'Actinidia00731' => 'ach', 'Actinidia11473' => 'ach', 'Actinidia23469' => 'ach', 'Actinidia24318' => 'ach', 'Actinidia40196' => 'ach', 'Actinidia40197' => 'ach', 'Actinidia40198' => 'ach', 'Ah.08g212990' => 'amhyb', 'Ah.15g091720' => 'amhyb', 'AL3G38260' => 'aly', 'AL4G47710' => 'aly', 'Aqoxy2G00671' => 'aox', 'Aqoxy2G03236' => 'aox', 'arahy.Tifrunner.gnm1.ann1.05IDCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KR684' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATY3SJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK6QJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6APGL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IDT7Z9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM073U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ0R87' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LE7RV4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT4QRX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V5ENPK' => 'arhy', 'AT2G48110' => 'ath', 'AT3G23590' => 'ath', 'ATR0626G186' => 'atr', 'ATR1127G141' => 'atr', 'Atru.chr4.2583' => 'acertr', 'Atru.chr5.1358' => 'acertr', 'Atru.chr5.1359' => 'acertr', 'Atru.chr8.46' => 'acertr', 'AUR62002640' => 'cqu', 'AUR62030055' => 'cqu', 'AUR62033713' => 'cqu', 'AUR62033714' => 'cqu', 'AUR62036795' => 'cqu', 'AUR62039891' => 'cqu', 'BcaB02g08737' => 'bca', 'BcaB04g20441' => 'bca', 'BcaB06g26509' => 'bca', 'BcaB06g26510' => 'bca', 'BcaB06g26511' => 'bca', 'BcaB06g26512' => 'bca', 'BcaB06g26513' => 'bca', 'BcaC02g12564' => 'bca', 'BcaC02g12565' => 'bca', 'BcaC02g12794' => 'bca', 'BcaC02g12795' => 'bca', 'BcaC02g12796' => 'bca', 'BcaC06g35541' => 'bca', 'BNapus_Darmor_BZH_scaffold_188p00080' => 'bna', 'BNapus_Darmor_BZH_scaffold_188p00090' => 'bna', 'BolC1t03972H' => 'bol', 'BolC1t03973H' => 'bol', 'BolC4t21680H' => 'bol', 'BolC7t41863H' => 'bol', 'BolSC55t61227H' => 'bol', 'BolSC55t61228H' => 'bol', 'BraA01t03278Z' => 'bra', 'BraA05t18998Z' => 'bra', 'BraA07t28673Z' => 'bra', 'C01p40150' => 'bna', 'C05p12370' => 'bna', 'C07p13680' => 'bna', 'CAN.G1006.16' => 'can', 'CAN.G1006.17' => 'can', 'CAN.G1170.2' => 'can', 'CAN.G962.7' => 'can', 'CANSAT25G2179' => 'cansat', 'CANSAT78G1573' => 'cansat', 'CARHR099510' => 'chi', 'CARHR143510' => 'chi', 'Carub.0003s2380' => 'cru', 'Carub.0004s3082' => 'cru', 'Ca_00614_v3' => 'car', 'Ca_07801_v3' => 'car', 'Ca_08567_v3' => 'car', 'Ca_09571_v3' => 'car', 'CBR_g19290' => 'cbr', 'Cc01_g19770' => 'ccan', 'Cc03_g03030' => 'ccan', 'CDE07G0968' => 'cde', 'CDE09G1441' => 'cde', 'Cfa006103' => 'cfa', 'Cfa015573' => 'cfa', 'Cfa016988' => 'cfa', 'Ciclev10006738m.g' => 'ccl', 'Ciclev10010920m.g' => 'ccl', 'Ciclev10018517m.g' => 'ccl', 'CiPaw.01G159200' => 'cil', 'CiPaw.02G091000' => 'cil', 'CiPaw.02G091100' => 'cil', 'CiPaw.08G103100' => 'cil', 'CiPaw.09G224900' => 'cil', 'ClCG06G005740' => 'cla', 'ClCG07G000090' => 'cla', 'ClCG07G000100' => 'cla', 'COL.COLO4_09143' => 'col', 'COL.COLO4_25124' => 'col', 'Cpa.g.sc16.34' => 'cpa', 'Cpa.g.sc3504.1' => 'cpa', 'Cpa.g.sc60.37' => 'cpa', 'CsaV3_6G018520' => 'csa', 'CsaV3_6G036860' => 'csa', 'CSS0001072' => 'camsi', 'CSS0020208' => 'camsi', 'CSS0021253' => 'camsi', 'CSS0022190' => 'camsi', 'CSS0036150' => 'camsi', 'CSS0040442' => 'camsi', 'CSS0042300' => 'camsi', 'CSS0045298' => 'camsi', 'DCAR_012449' => 'dca', 'DCAR_018405' => 'dca', 'DCAR_024573' => 'dca', 'DCAR_030591' => 'dca', 'Dinv16926' => 'din', 'Dinv32963' => 'din', 'Dinv38382' => 'din', 'Dinv38383' => 'din', 'Duzib133G0974' => 'dzi', 'Duzib138G1867' => 'dzi', 'Duzib211G0420' => 'dzi', 'Duzib212G0930' => 'dzi', 'ECA234G1645' => 'eca', 'ECA247G3467' => 'eca', 'ECA248G1703' => 'eca', 'EL10Ac3g06327' => 'bvu', 'EL10Ac7g17204' => 'bvu', 'Eucgr.A00855' => 'egr', 'Eucgr.A00858' => 'egr', 'Eucgr.H01520' => 'egr', 'Eucgr.H03604' => 'egr', 'Eucgr.L03465' => 'egr', 'Eucgr.L03466' => 'egr', 'FAN01G0988' => 'fan', 'FAN02G3892' => 'fan', 'FAN05G3381' => 'fan', 'FAN07G0967' => 'fan', 'FAN07G1493' => 'fan', 'FAN08G3125' => 'fan', 'FAN09G0402' => 'fan', 'FAN12G2594' => 'fan', 'FAN12G3879' => 'fan', 'FAN14G1546' => 'fan', 'FAN15G3626' => 'fan', 'FAN17G0588' => 'fan', 'FAN17G0609' => 'fan', 'FAN18G2817' => 'fan', 'FAN19G1305' => 'fan', 'FAN20G1787' => 'fan', 'FAN22G0073' => 'fan', 'FAN22G0352' => 'fan', 'FAN22G0368' => 'fan', 'FAN22G2273' => 'fan', 'FAN24G1998' => 'fan', 'FAN27G1317' => 'fan', 'FvH4_2g23980' => 'fve', 'FvH4_4g14380' => 'fve', 'FvH4_4g14390' => 'fve', 'FvH4_6g09250' => 'fve', 'Glyma.03G151100' => 'gma', 'Glyma.04G122550' => 'gma', 'Glyma.05G001600' => 'gma', 'Glyma.09G270766' => 'gma', 'Glyma.09G270832' => 'gma', 'Glyma.13G209800' => 'gma', 'Glyma.15G102800' => 'gma', 'Glyma.18G218900' => 'gma', 'Glyma.19G001500' => 'gma', 'Glyma.19G153600' => 'gma', 'Gohir.A02G028600' => 'ghi', 'Gohir.A08G045000' => 'ghi', 'Gohir.A11G120500' => 'ghi', 'Gohir.A12G006200' => 'ghi', 'Gohir.A12G006250' => 'ghi', 'Gohir.D02G036300' => 'ghi', 'Gohir.D08G054700' => 'ghi', 'Gohir.D11G125600' => 'ghi', 'Gohir.D12G005700' => 'ghi', 'Gorai.004G055200' => 'gra', 'Gorai.005G040400' => 'gra', 'Gorai.007G134500' => 'gra', 'Gorai.008G005500' => 'gra', 'GSVIVG01011094001' => 'vvi', 'GSVIVG01017879001' => 'vvi', 'GSVIVG01025988001' => 'vvi', 'GSVIVG01029847001' => 'vvi', 'HanXRQChr10g0282901' => 'han', 'HanXRQChr10g0310371' => 'han', 'HanXRQChr10g0315041' => 'han', 'HanXRQChr11g0327651' => 'han', 'HanXRQChr12g0359391' => 'han', 'Haze_00972' => 'cav', 'Haze_00973' => 'cav', 'Haze_00974' => 'cav', 'Haze_04747' => 'cav', 'Haze_04749' => 'cav', 'Haze_04750' => 'cav', 'Haze_21217' => 'cav', 'Hma1.2p1_1037F.1_g250680' => 'hma', 'Hma1.2p1_1644F.1_g295320' => 'hma', 'HPP92_011322' => 'vpl', 'HPP92_011323' => 'vpl', 'HPP92_011324' => 'vpl', 'HPP92_011325' => 'vpl', 'HPP92_011326' => 'vpl', 'Hund12205' => 'sun', 'Hund17957' => 'sun', 'Lalb_Chr06g0176771' => 'lal', 'Lalb_Chr18g0056021' => 'lal', 'Lalb_Chr18g0056031' => 'lal', 'Lalb_Chr18g0056041' => 'lal', 'Lalb_Chr20g0107751' => 'lal', 'Lalb_Chr20g0118371' => 'lal', 'Lj1g0010239' => 'lja', 'Lj1g0017101' => 'lja', 'Lj2A1178G40' => 'lonja', 'Lj2A54G84' => 'lonja', 'Lj2g0015248' => 'lja', 'Lj3A761T51' => 'lonja', 'Lj6g0018116' => 'lja', 'Lsat_1_v5_gn_4_136040' => 'lsa', 'Lsat_1_v5_gn_5_187461' => 'lsa', 'Lsat_1_v5_gn_5_77001' => 'lsa', 'Lsat_1_v5_gn_9_4461' => 'lsa', 'Manes.01G210100' => 'mes', 'Manes.03G185600' => 'mes', 'Manes.05G073300' => 'mes', 'Manes.09G120300' => 'mes', 'Manes.15G022100' => 'mes', 'Mapoly0096s0053' => 'mpo', 'MBI03_g14058_MAGBIO' => 'mbi', 'MBI03_g33876_MAGBIO' => 'mbi', 'MBI03_g36854_MAGBIO' => 'mbi', 'MBI17_g11997_MAGBIO' => 'mbi', 'MD03G1269000' => 'mdo', 'MD04G1179600' => 'mdo', 'MD11G1289800' => 'mdo', 'MD12G1194700' => 'mdo', 'MD13G1182100' => 'mdo', 'MD13G1182200' => 'mdo', 'MD16G1182600' => 'mdo', 'Medtr2g021400' => 'mtr', 'Medtr2g021470' => 'mtr', 'Medtr2g105810' => 'mtr', 'Medtr3g033580' => 'mtr', 'Medtr6g007970' => 'mtr', 'Medtr7g056330' => 'mtr', 'Medtr7g074290' => 'mtr', 'Medtr7g074380' => 'mtr', 'Medtr7g094550' => 'mtr', 'Medtr8g069995' => 'mtr', 'MELO3C014345.2' => 'cme', 'MELO3C021395.2' => 'cme', 'Migut.D00262' => 'egut', 'Migut.G00257' => 'egut', 'MSTRG.21575' => 'ama', 'MSTRG.3985' => 'ama', 'Nitab4.5_0000295g0140' => 'nta', 'Nitab4.5_0000732g0140' => 'nta', 'Nitab4.5_0003162g0020' => 'nta', 'Nitab4.5_0006180g0090' => 'nta', 'Nitab4.5_0006390g0010' => 'nta', 'Nitab4.5_0007392g0040' => 'nta', 'Nn1g02140' => 'nnu', 'Nn4g26168' => 'nnu', 'Nn5g26754' => 'nnu', 'Oeu001433.1' => 'oeu', 'Oeu010299.2' => 'oeu', 'Oeu011171.1' => 'oeu', 'Oeu037675.1' => 'oeu', 'Oeu038359.1' => 'oeu', 'Oeu063834.1' => 'oeu', 'Oeu063835.1' => 'oeu', 'Os05g0312000' => 'osa', 'Os07g0211101' => 'osa', 'Os07g0211200' => 'osa', 'Os07g0681500' => 'osa', 'Peaxi162Scf00095g01015' => 'pax', 'Peaxi162Scf00104g00329' => 'pax', 'Peaxi162Scf00161g00137' => 'pax', 'PGR004G1665' => 'pgr', 'PGR031G2937' => 'pgr', 'PGR119G2145' => 'pgr', 'PGSC0003DMG400004351' => 'stu', 'PGSC0003DMG400014625' => 'stu', 'PGSC0003DMG401000943' => 'stu', 'Phvul.001G148600' => 'pvu', 'Phvul.004G001700' => 'pvu', 'Phvul.006G154900' => 'pvu', 'Phvul.008G078200' => 'pvu', 'Phvul.011G136500' => 'pvu', 'Potri.002G215600' => 'ptr', 'Potri.008G201600' => 'ptr', 'Potri.014G138400' => 'ptr', 'Potri.016G142500' => 'ptr', 'Pp3c16_10580' => 'ppa', 'Pp3c5_25280' => 'ppa', 'Prupe.1G150000' => 'ppe', 'Prupe.1G150100' => 'ppe', 'Prupe.6G299600' => 'ppe', 'Prupe.8G245000' => 'ppe', 'Psat0s4927g0040' => 'psa', 'Psat1g052080' => 'psa', 'Psat1g183800' => 'psa', 'Psat3g113840' => 'psa', 'Psat3g126120' => 'psa', 'Psat3g126160' => 'psa', 'Psat3g158760' => 'psa', 'Psat3g158840' => 'psa', 'PSO170G2858' => 'pso', 'PSO339G0606' => 'pso', 'PSO384G4709' => 'pso', 'PSO407G0334' => 'pso', 'QL04p040276' => 'qlo', 'QL06p005458' => 'qlo', 'QL06p005472' => 'qlo', 'QL07p030546' => 'qlo', 'QL07p031519' => 'qlo', 'QL09p050949' => 'qlo', 'QL09p050966' => 'qlo', 'QL09p051067' => 'qlo', 'QL12p022706' => 'qlo', 'RcHm_v2.0_Chr2g0119601' => 'rch', 'RcHm_v2.0_Chr3g0459591' => 'rch', 'RcHm_v2.0_Chr4g0418521' => 'rch', 'RcHm_v2.0_Chr4g0418531' => 'rch', 'RcHm_v2.0_Chr4g0418541' => 'rch', 'RcHm_v2.0_Chr6g0291641' => 'rch', 'Rhsim01G0086300' => 'rsi', 'Rhsim01G0276300' => 'rsi', 'Rhsim01G0276500' => 'rsi', 'Rhsim04G0207700' => 'rsi', 'Rhsim05G0234500' => 'rsi', 'Rhsim13G0022400' => 'rsi', 'Sabra02G0167900' => 'sbr', 'Sabra04G0158500' => 'sbr', 'Sabra08G0159800' => 'sbr', 'Sabra10G0011500' => 'sbr', 'Sabra14G0104400' => 'sbr', 'SalBow2G2440' => 'sbo', 'SalBow4G2265' => 'sbo', 'Sc02g0000060' => 'sci', 'Sc05g0005020' => 'sci', 'Sc13g0003890' => 'sci', 'Sed0014865' => 'sed', 'Sed0017224' => 'sed', 'Sed0026391' => 'sed', 'SEGI_00063' => 'sgi', 'SEGI_10967' => 'sgi', 'SEGI_17510' => 'sgi', 'SEGI_24396' => 'sgi', 'SEGI_39719' => 'sgi', 'SEGI_41392' => 'sgi', 'SGA_v2.0_scaffold11G05794' => 'sas', 'SGA_v2.0_scaffold142G35607' => 'sas', 'SGA_v2.0_scaffold1G00447' => 'sas', 'SHI15388' => 'shi', 'SHI15394' => 'shi', 'SHI15396' => 'shi', 'SHI15399' => 'shi', 'SMO343G0151' => 'smo', 'SMO367G1118' => 'smo', 'Solyc01g080200.3' => 'sly', 'Solyc06g008960.3' => 'sly', 'Solyc09g064780.3' => 'sly', 'Sopen01g031980' => 'spe', 'Sopen06g003710' => 'spe', 'Sopen09g026460' => 'spe', 'Sp3g21240' => 'spa', 'Sp4g30030' => 'spa', 'TAR365G0022' => 'tar', 'TAR365G1023' => 'tar', 'TAR365G1253' => 'tar', 'TAR623G0078' => 'tar', 'TAR623G1721' => 'tar', 'TAR633G0959' => 'tar', 'THA.LOC104802225' => 'tha', 'THA.LOC104804769' => 'tha', 'THA.LOC104808660' => 'tha', 'THA.LOC104812792' => 'tha', 'Thecc.01G284000' => 'tca', 'Thecc.04G220600' => 'tca', 'Thecc.05G268900' => 'tca', 'Thecc.08G171100' => 'tca', 'Thhalv10001284m.g' => 'esa', 'Thhalv10019912m.g' => 'esa', 'TPR.G14189' => 'tpr', 'TPR.G18110' => 'tpr', 'TPR.G18130' => 'tpr', 'TPR.G18131' => 'tpr', 'TPR.G18140' => 'tpr', 'TPR.G24282' => 'tpr', 'TPR.G25221' => 'tpr', 'TPR.G29267' => 'tpr', 'TPR.G35315' => 'tpr', 'TPR.G36173' => 'tpr', 'TWI09G0794' => 'twi', 'TWI59G1348' => 'twi', 'TWI74G0430' => 'twi', 'unitig_26.g8940' => 'ugi', 'unitig_749.g13744' => 'ugi', 'unitig_749.g13745' => 'ugi', 'vmacro08269' => 'vma', 'vmacro14937' => 'vma', 'vmacro20401' => 'vma', 'VMungo0464G1349' => 'vmu', 'VMungo0540G0289' => 'vmu', 'VMungo1215G1590' => 'vmu', 'VMungo1309G0221' => 'vmu', 'VMungo1309G2815' => 'vmu', 'VMungo1383G0239' => 'vmu', 'VMungo1383G2910' => 'vmu', 'Zm00001eb095270' => 'zma', 'Zm00001eb095280' => 'zma', 'Zm00001eb111630' => 'zma', 'Zm00001eb237080' => 'zma', 'Zm00001eb273740' => 'zma', 'Zm00001eb285040' => 'zma', 'Zm00001eb330790' => 'zma', 'Zm00001eb337380' => 'zma' ) $gf_id = 'HOM05D001484' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001484' ) $data_identifier = 'HOM05D001484' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 2, 'aly' => (int) 2, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 22, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 7, 'hma' => (int) 2, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 7, 'mtr' => (int) 10, 'cme' => (int) 2, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 4, 'ppa' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 4, 'qlo' => (int) 9, 'rch' => (int) 6, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 10, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 7, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb337380' $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' => 'HOM05D001484', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p31500' => 'bna', 'A05p00020' => 'bna', 'A07p08820' => 'bna', 'Aa31LG4G3300' => 'aar', 'Aa31LG8G10030' => 'aar', 'Actinidia00731' => 'ach', 'Actinidia11473' => 'ach', 'Actinidia23469' => 'ach', 'Actinidia24318' => 'ach', 'Actinidia40196' => 'ach', 'Actinidia40197' => 'ach', 'Actinidia40198' => 'ach', 'Ah.08g212990' => 'amhyb', 'Ah.15g091720' => 'amhyb', 'AL3G38260' => 'aly', 'AL4G47710' => 'aly', 'Aqoxy2G00671' => 'aox', 'Aqoxy2G03236' => 'aox', 'arahy.Tifrunner.gnm1.ann1.05IDCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KR684' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATY3SJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK6QJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6APGL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IDT7Z9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM073U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ0R87' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LE7RV4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT4QRX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V5ENPK' => 'arhy', 'AT2G48110' => 'ath', 'AT3G23590' => 'ath', 'ATR0626G186' => 'atr', 'ATR1127G141' => 'atr', 'Atru.chr4.2583' => 'acertr', 'Atru.chr5.1358' => 'acertr', 'Atru.chr5.1359' => 'acertr', 'Atru.chr8.46' => 'acertr', 'AUR62002640' => 'cqu', 'AUR62030055' => 'cqu', 'AUR62033713' => 'cqu', 'AUR62033714' => 'cqu', 'AUR62036795' => 'cqu', 'AUR62039891' => 'cqu', 'BcaB02g08737' => 'bca', 'BcaB04g20441' => 'bca', 'BcaB06g26509' => 'bca', 'BcaB06g26510' => 'bca', 'BcaB06g26511' => 'bca', 'BcaB06g26512' => 'bca', 'BcaB06g26513' => 'bca', 'BcaC02g12564' => 'bca', 'BcaC02g12565' => 'bca', 'BcaC02g12794' => 'bca', 'BcaC02g12795' => 'bca', 'BcaC02g12796' => 'bca', 'BcaC06g35541' => 'bca', 'BNapus_Darmor_BZH_scaffold_188p00080' => 'bna', 'BNapus_Darmor_BZH_scaffold_188p00090' => 'bna', 'BolC1t03972H' => 'bol', 'BolC1t03973H' => 'bol', 'BolC4t21680H' => 'bol', 'BolC7t41863H' => 'bol', 'BolSC55t61227H' => 'bol', 'BolSC55t61228H' => 'bol', 'BraA01t03278Z' => 'bra', 'BraA05t18998Z' => 'bra', 'BraA07t28673Z' => 'bra', 'C01p40150' => 'bna', 'C05p12370' => 'bna', 'C07p13680' => 'bna', 'CAN.G1006.16' => 'can', 'CAN.G1006.17' => 'can', 'CAN.G1170.2' => 'can', 'CAN.G962.7' => 'can', 'CANSAT25G2179' => 'cansat', 'CANSAT78G1573' => 'cansat', 'CARHR099510' => 'chi', 'CARHR143510' => 'chi', 'Carub.0003s2380' => 'cru', 'Carub.0004s3082' => 'cru', 'Ca_00614_v3' => 'car', 'Ca_07801_v3' => 'car', 'Ca_08567_v3' => 'car', 'Ca_09571_v3' => 'car', 'CBR_g19290' => 'cbr', 'Cc01_g19770' => 'ccan', 'Cc03_g03030' => 'ccan', 'CDE07G0968' => 'cde', 'CDE09G1441' => 'cde', 'Cfa006103' => 'cfa', 'Cfa015573' => 'cfa', 'Cfa016988' => 'cfa', 'Ciclev10006738m.g' => 'ccl', 'Ciclev10010920m.g' => 'ccl', 'Ciclev10018517m.g' => 'ccl', 'CiPaw.01G159200' => 'cil', 'CiPaw.02G091000' => 'cil', 'CiPaw.02G091100' => 'cil', 'CiPaw.08G103100' => 'cil', 'CiPaw.09G224900' => 'cil', 'ClCG06G005740' => 'cla', 'ClCG07G000090' => 'cla', 'ClCG07G000100' => 'cla', 'COL.COLO4_09143' => 'col', 'COL.COLO4_25124' => 'col', 'Cpa.g.sc16.34' => 'cpa', 'Cpa.g.sc3504.1' => 'cpa', 'Cpa.g.sc60.37' => 'cpa', 'CsaV3_6G018520' => 'csa', 'CsaV3_6G036860' => 'csa', 'CSS0001072' => 'camsi', 'CSS0020208' => 'camsi', 'CSS0021253' => 'camsi', 'CSS0022190' => 'camsi', 'CSS0036150' => 'camsi', 'CSS0040442' => 'camsi', 'CSS0042300' => 'camsi', 'CSS0045298' => 'camsi', 'DCAR_012449' => 'dca', 'DCAR_018405' => 'dca', 'DCAR_024573' => 'dca', 'DCAR_030591' => 'dca', 'Dinv16926' => 'din', 'Dinv32963' => 'din', 'Dinv38382' => 'din', 'Dinv38383' => 'din', 'Duzib133G0974' => 'dzi', 'Duzib138G1867' => 'dzi', 'Duzib211G0420' => 'dzi', 'Duzib212G0930' => 'dzi', 'ECA234G1645' => 'eca', 'ECA247G3467' => 'eca', 'ECA248G1703' => 'eca', 'EL10Ac3g06327' => 'bvu', 'EL10Ac7g17204' => 'bvu', 'Eucgr.A00855' => 'egr', 'Eucgr.A00858' => 'egr', 'Eucgr.H01520' => 'egr', 'Eucgr.H03604' => 'egr', 'Eucgr.L03465' => 'egr', 'Eucgr.L03466' => 'egr', 'FAN01G0988' => 'fan', 'FAN02G3892' => 'fan', 'FAN05G3381' => 'fan', 'FAN07G0967' => 'fan', 'FAN07G1493' => 'fan', 'FAN08G3125' => 'fan', 'FAN09G0402' => 'fan', 'FAN12G2594' => 'fan', 'FAN12G3879' => 'fan', 'FAN14G1546' => 'fan', 'FAN15G3626' => 'fan', 'FAN17G0588' => 'fan', 'FAN17G0609' => 'fan', 'FAN18G2817' => 'fan', 'FAN19G1305' => 'fan', 'FAN20G1787' => 'fan', 'FAN22G0073' => 'fan', 'FAN22G0352' => 'fan', 'FAN22G0368' => 'fan', 'FAN22G2273' => 'fan', 'FAN24G1998' => 'fan', 'FAN27G1317' => 'fan', 'FvH4_2g23980' => 'fve', 'FvH4_4g14380' => 'fve', 'FvH4_4g14390' => 'fve', 'FvH4_6g09250' => 'fve', 'Glyma.03G151100' => 'gma', 'Glyma.04G122550' => 'gma', 'Glyma.05G001600' => 'gma', 'Glyma.09G270766' => 'gma', 'Glyma.09G270832' => 'gma', 'Glyma.13G209800' => 'gma', 'Glyma.15G102800' => 'gma', 'Glyma.18G218900' => 'gma', 'Glyma.19G001500' => 'gma', 'Glyma.19G153600' => 'gma', 'Gohir.A02G028600' => 'ghi', 'Gohir.A08G045000' => 'ghi', 'Gohir.A11G120500' => 'ghi', 'Gohir.A12G006200' => 'ghi', 'Gohir.A12G006250' => 'ghi', 'Gohir.D02G036300' => 'ghi', 'Gohir.D08G054700' => 'ghi', 'Gohir.D11G125600' => 'ghi', 'Gohir.D12G005700' => 'ghi', 'Gorai.004G055200' => 'gra', 'Gorai.005G040400' => 'gra', 'Gorai.007G134500' => 'gra', 'Gorai.008G005500' => 'gra', 'GSVIVG01011094001' => 'vvi', 'GSVIVG01017879001' => 'vvi', 'GSVIVG01025988001' => 'vvi', 'GSVIVG01029847001' => 'vvi', 'HanXRQChr10g0282901' => 'han', 'HanXRQChr10g0310371' => 'han', 'HanXRQChr10g0315041' => 'han', 'HanXRQChr11g0327651' => 'han', 'HanXRQChr12g0359391' => 'han', 'Haze_00972' => 'cav', 'Haze_00973' => 'cav', 'Haze_00974' => 'cav', 'Haze_04747' => 'cav', 'Haze_04749' => 'cav', 'Haze_04750' => 'cav', 'Haze_21217' => 'cav', 'Hma1.2p1_1037F.1_g250680' => 'hma', 'Hma1.2p1_1644F.1_g295320' => 'hma', 'HPP92_011322' => 'vpl', 'HPP92_011323' => 'vpl', 'HPP92_011324' => 'vpl', 'HPP92_011325' => 'vpl', 'HPP92_011326' => 'vpl', 'Hund12205' => 'sun', 'Hund17957' => 'sun', 'Lalb_Chr06g0176771' => 'lal', 'Lalb_Chr18g0056021' => 'lal', 'Lalb_Chr18g0056031' => 'lal', 'Lalb_Chr18g0056041' => 'lal', 'Lalb_Chr20g0107751' => 'lal', 'Lalb_Chr20g0118371' => 'lal', 'Lj1g0010239' => 'lja', 'Lj1g0017101' => 'lja', 'Lj2A1178G40' => 'lonja', 'Lj2A54G84' => 'lonja', 'Lj2g0015248' => 'lja', 'Lj3A761T51' => 'lonja', 'Lj6g0018116' => 'lja', 'Lsat_1_v5_gn_4_136040' => 'lsa', 'Lsat_1_v5_gn_5_187461' => 'lsa', 'Lsat_1_v5_gn_5_77001' => 'lsa', 'Lsat_1_v5_gn_9_4461' => 'lsa', 'Manes.01G210100' => 'mes', 'Manes.03G185600' => 'mes', 'Manes.05G073300' => 'mes', 'Manes.09G120300' => 'mes', 'Manes.15G022100' => 'mes', 'Mapoly0096s0053' => 'mpo', 'MBI03_g14058_MAGBIO' => 'mbi', 'MBI03_g33876_MAGBIO' => 'mbi', 'MBI03_g36854_MAGBIO' => 'mbi', 'MBI17_g11997_MAGBIO' => 'mbi', 'MD03G1269000' => 'mdo', 'MD04G1179600' => 'mdo', 'MD11G1289800' => 'mdo', 'MD12G1194700' => 'mdo', 'MD13G1182100' => 'mdo', 'MD13G1182200' => 'mdo', 'MD16G1182600' => 'mdo', 'Medtr2g021400' => 'mtr', 'Medtr2g021470' => 'mtr', 'Medtr2g105810' => 'mtr', 'Medtr3g033580' => 'mtr', 'Medtr6g007970' => 'mtr', 'Medtr7g056330' => 'mtr', 'Medtr7g074290' => 'mtr', 'Medtr7g074380' => 'mtr', 'Medtr7g094550' => 'mtr', 'Medtr8g069995' => 'mtr', 'MELO3C014345.2' => 'cme', 'MELO3C021395.2' => 'cme', 'Migut.D00262' => 'egut', 'Migut.G00257' => 'egut', 'MSTRG.21575' => 'ama', 'MSTRG.3985' => 'ama', 'Nitab4.5_0000295g0140' => 'nta', 'Nitab4.5_0000732g0140' => 'nta', 'Nitab4.5_0003162g0020' => 'nta', 'Nitab4.5_0006180g0090' => 'nta', 'Nitab4.5_0006390g0010' => 'nta', 'Nitab4.5_0007392g0040' => 'nta', 'Nn1g02140' => 'nnu', 'Nn4g26168' => 'nnu', 'Nn5g26754' => 'nnu', 'Oeu001433.1' => 'oeu', 'Oeu010299.2' => 'oeu', 'Oeu011171.1' => 'oeu', 'Oeu037675.1' => 'oeu', 'Oeu038359.1' => 'oeu', 'Oeu063834.1' => 'oeu', 'Oeu063835.1' => 'oeu', 'Os05g0312000' => 'osa', 'Os07g0211101' => 'osa', 'Os07g0211200' => 'osa', 'Os07g0681500' => 'osa', 'Peaxi162Scf00095g01015' => 'pax', 'Peaxi162Scf00104g00329' => 'pax', 'Peaxi162Scf00161g00137' => 'pax', 'PGR004G1665' => 'pgr', 'PGR031G2937' => 'pgr', 'PGR119G2145' => 'pgr', 'PGSC0003DMG400004351' => 'stu', 'PGSC0003DMG400014625' => 'stu', 'PGSC0003DMG401000943' => 'stu', 'Phvul.001G148600' => 'pvu', 'Phvul.004G001700' => 'pvu', 'Phvul.006G154900' => 'pvu', 'Phvul.008G078200' => 'pvu', 'Phvul.011G136500' => 'pvu', 'Potri.002G215600' => 'ptr', 'Potri.008G201600' => 'ptr', 'Potri.014G138400' => 'ptr', 'Potri.016G142500' => 'ptr', 'Pp3c16_10580' => 'ppa', 'Pp3c5_25280' => 'ppa', 'Prupe.1G150000' => 'ppe', 'Prupe.1G150100' => 'ppe', 'Prupe.6G299600' => 'ppe', 'Prupe.8G245000' => 'ppe', 'Psat0s4927g0040' => 'psa', 'Psat1g052080' => 'psa', 'Psat1g183800' => 'psa', 'Psat3g113840' => 'psa', 'Psat3g126120' => 'psa', 'Psat3g126160' => 'psa', 'Psat3g158760' => 'psa', 'Psat3g158840' => 'psa', 'PSO170G2858' => 'pso', 'PSO339G0606' => 'pso', 'PSO384G4709' => 'pso', 'PSO407G0334' => 'pso', 'QL04p040276' => 'qlo', 'QL06p005458' => 'qlo', 'QL06p005472' => 'qlo', 'QL07p030546' => 'qlo', 'QL07p031519' => 'qlo', 'QL09p050949' => 'qlo', 'QL09p050966' => 'qlo', 'QL09p051067' => 'qlo', 'QL12p022706' => 'qlo', 'RcHm_v2.0_Chr2g0119601' => 'rch', 'RcHm_v2.0_Chr3g0459591' => 'rch', 'RcHm_v2.0_Chr4g0418521' => 'rch', 'RcHm_v2.0_Chr4g0418531' => 'rch', 'RcHm_v2.0_Chr4g0418541' => 'rch', 'RcHm_v2.0_Chr6g0291641' => 'rch', 'Rhsim01G0086300' => 'rsi', 'Rhsim01G0276300' => 'rsi', 'Rhsim01G0276500' => 'rsi', 'Rhsim04G0207700' => 'rsi', 'Rhsim05G0234500' => 'rsi', 'Rhsim13G0022400' => 'rsi', 'Sabra02G0167900' => 'sbr', 'Sabra04G0158500' => 'sbr', 'Sabra08G0159800' => 'sbr', 'Sabra10G0011500' => 'sbr', 'Sabra14G0104400' => 'sbr', 'SalBow2G2440' => 'sbo', 'SalBow4G2265' => 'sbo', 'Sc02g0000060' => 'sci', 'Sc05g0005020' => 'sci', 'Sc13g0003890' => 'sci', 'Sed0014865' => 'sed', 'Sed0017224' => 'sed', 'Sed0026391' => 'sed', 'SEGI_00063' => 'sgi', 'SEGI_10967' => 'sgi', 'SEGI_17510' => 'sgi', 'SEGI_24396' => 'sgi', 'SEGI_39719' => 'sgi', 'SEGI_41392' => 'sgi', 'SGA_v2.0_scaffold11G05794' => 'sas', 'SGA_v2.0_scaffold142G35607' => 'sas', 'SGA_v2.0_scaffold1G00447' => 'sas', 'SHI15388' => 'shi', 'SHI15394' => 'shi', 'SHI15396' => 'shi', 'SHI15399' => 'shi', 'SMO343G0151' => 'smo', 'SMO367G1118' => 'smo', 'Solyc01g080200.3' => 'sly', 'Solyc06g008960.3' => 'sly', 'Solyc09g064780.3' => 'sly', 'Sopen01g031980' => 'spe', 'Sopen06g003710' => 'spe', 'Sopen09g026460' => 'spe', 'Sp3g21240' => 'spa', 'Sp4g30030' => 'spa', 'TAR365G0022' => 'tar', 'TAR365G1023' => 'tar', 'TAR365G1253' => 'tar', 'TAR623G0078' => 'tar', 'TAR623G1721' => 'tar', 'TAR633G0959' => 'tar', 'THA.LOC104802225' => 'tha', 'THA.LOC104804769' => 'tha', 'THA.LOC104808660' => 'tha', 'THA.LOC104812792' => 'tha', 'Thecc.01G284000' => 'tca', 'Thecc.04G220600' => 'tca', 'Thecc.05G268900' => 'tca', 'Thecc.08G171100' => 'tca', 'Thhalv10001284m.g' => 'esa', 'Thhalv10019912m.g' => 'esa', 'TPR.G14189' => 'tpr', 'TPR.G18110' => 'tpr', 'TPR.G18130' => 'tpr', 'TPR.G18131' => 'tpr', 'TPR.G18140' => 'tpr', 'TPR.G24282' => 'tpr', 'TPR.G25221' => 'tpr', 'TPR.G29267' => 'tpr', 'TPR.G35315' => 'tpr', 'TPR.G36173' => 'tpr', 'TWI09G0794' => 'twi', 'TWI59G1348' => 'twi', 'TWI74G0430' => 'twi', 'unitig_26.g8940' => 'ugi', 'unitig_749.g13744' => 'ugi', 'unitig_749.g13745' => 'ugi', 'vmacro08269' => 'vma', 'vmacro14937' => 'vma', 'vmacro20401' => 'vma', 'VMungo0464G1349' => 'vmu', 'VMungo0540G0289' => 'vmu', 'VMungo1215G1590' => 'vmu', 'VMungo1309G0221' => 'vmu', 'VMungo1309G2815' => 'vmu', 'VMungo1383G0239' => 'vmu', 'VMungo1383G2910' => 'vmu', 'Zm00001eb095270' => 'zma', 'Zm00001eb095280' => 'zma', 'Zm00001eb111630' => 'zma', 'Zm00001eb237080' => 'zma', 'Zm00001eb273740' => 'zma', 'Zm00001eb285040' => 'zma', 'Zm00001eb330790' => 'zma', 'Zm00001eb337380' => 'zma' ), 'gf_id' => 'HOM05D001484', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001484' ), 'data_identifier' => 'HOM05D001484', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001484', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p31500' => 'bna', 'A05p00020' => 'bna', 'A07p08820' => 'bna', 'Aa31LG4G3300' => 'aar', 'Aa31LG8G10030' => 'aar', 'Actinidia00731' => 'ach', 'Actinidia11473' => 'ach', 'Actinidia23469' => 'ach', 'Actinidia24318' => 'ach', 'Actinidia40196' => 'ach', 'Actinidia40197' => 'ach', 'Actinidia40198' => 'ach', 'Ah.08g212990' => 'amhyb', 'Ah.15g091720' => 'amhyb', 'AL3G38260' => 'aly', 'AL4G47710' => 'aly', 'Aqoxy2G00671' => 'aox', 'Aqoxy2G03236' => 'aox', 'arahy.Tifrunner.gnm1.ann1.05IDCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KR684' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATY3SJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK6QJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6APGL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IDT7Z9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM073U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ0R87' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LE7RV4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT4QRX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V5ENPK' => 'arhy', 'AT2G48110' => 'ath', 'AT3G23590' => 'ath', 'ATR0626G186' => 'atr', 'ATR1127G141' => 'atr', 'Atru.chr4.2583' => 'acertr', 'Atru.chr5.1358' => 'acertr', 'Atru.chr5.1359' => 'acertr', 'Atru.chr8.46' => 'acertr', 'AUR62002640' => 'cqu', 'AUR62030055' => 'cqu', 'AUR62033713' => 'cqu', 'AUR62033714' => 'cqu', 'AUR62036795' => 'cqu', 'AUR62039891' => 'cqu', 'BcaB02g08737' => 'bca', 'BcaB04g20441' => 'bca', 'BcaB06g26509' => 'bca', 'BcaB06g26510' => 'bca', 'BcaB06g26511' => 'bca', 'BcaB06g26512' => 'bca', 'BcaB06g26513' => 'bca', 'BcaC02g12564' => 'bca', 'BcaC02g12565' => 'bca', 'BcaC02g12794' => 'bca', 'BcaC02g12795' => 'bca', 'BcaC02g12796' => 'bca', 'BcaC06g35541' => 'bca', 'BNapus_Darmor_BZH_scaffold_188p00080' => 'bna', 'BNapus_Darmor_BZH_scaffold_188p00090' => 'bna', 'BolC1t03972H' => 'bol', 'BolC1t03973H' => 'bol', 'BolC4t21680H' => 'bol', 'BolC7t41863H' => 'bol', 'BolSC55t61227H' => 'bol', 'BolSC55t61228H' => 'bol', 'BraA01t03278Z' => 'bra', 'BraA05t18998Z' => 'bra', 'BraA07t28673Z' => 'bra', 'C01p40150' => 'bna', 'C05p12370' => 'bna', 'C07p13680' => 'bna', 'CAN.G1006.16' => 'can', 'CAN.G1006.17' => 'can', 'CAN.G1170.2' => 'can', 'CAN.G962.7' => 'can', 'CANSAT25G2179' => 'cansat', 'CANSAT78G1573' => 'cansat', 'CARHR099510' => 'chi', 'CARHR143510' => 'chi', 'Carub.0003s2380' => 'cru', 'Carub.0004s3082' => 'cru', 'Ca_00614_v3' => 'car', 'Ca_07801_v3' => 'car', 'Ca_08567_v3' => 'car', 'Ca_09571_v3' => 'car', 'CBR_g19290' => 'cbr', 'Cc01_g19770' => 'ccan', 'Cc03_g03030' => 'ccan', 'CDE07G0968' => 'cde', 'CDE09G1441' => 'cde', 'Cfa006103' => 'cfa', 'Cfa015573' => 'cfa', 'Cfa016988' => 'cfa', 'Ciclev10006738m.g' => 'ccl', 'Ciclev10010920m.g' => 'ccl', 'Ciclev10018517m.g' => 'ccl', 'CiPaw.01G159200' => 'cil', 'CiPaw.02G091000' => 'cil', 'CiPaw.02G091100' => 'cil', 'CiPaw.08G103100' => 'cil', 'CiPaw.09G224900' => 'cil', 'ClCG06G005740' => 'cla', 'ClCG07G000090' => 'cla', 'ClCG07G000100' => 'cla', 'COL.COLO4_09143' => 'col', 'COL.COLO4_25124' => 'col', 'Cpa.g.sc16.34' => 'cpa', 'Cpa.g.sc3504.1' => 'cpa', 'Cpa.g.sc60.37' => 'cpa', 'CsaV3_6G018520' => 'csa', 'CsaV3_6G036860' => 'csa', 'CSS0001072' => 'camsi', 'CSS0020208' => 'camsi', 'CSS0021253' => 'camsi', 'CSS0022190' => 'camsi', 'CSS0036150' => 'camsi', 'CSS0040442' => 'camsi', 'CSS0042300' => 'camsi', 'CSS0045298' => 'camsi', 'DCAR_012449' => 'dca', 'DCAR_018405' => 'dca', 'DCAR_024573' => 'dca', 'DCAR_030591' => 'dca', 'Dinv16926' => 'din', 'Dinv32963' => 'din', 'Dinv38382' => 'din', 'Dinv38383' => 'din', 'Duzib133G0974' => 'dzi', 'Duzib138G1867' => 'dzi', 'Duzib211G0420' => 'dzi', 'Duzib212G0930' => 'dzi', 'ECA234G1645' => 'eca', 'ECA247G3467' => 'eca', 'ECA248G1703' => 'eca', 'EL10Ac3g06327' => 'bvu', 'EL10Ac7g17204' => 'bvu', 'Eucgr.A00855' => 'egr', 'Eucgr.A00858' => 'egr', 'Eucgr.H01520' => 'egr', 'Eucgr.H03604' => 'egr', 'Eucgr.L03465' => 'egr', 'Eucgr.L03466' => 'egr', 'FAN01G0988' => 'fan', 'FAN02G3892' => 'fan', 'FAN05G3381' => 'fan', 'FAN07G0967' => 'fan', 'FAN07G1493' => 'fan', 'FAN08G3125' => 'fan', 'FAN09G0402' => 'fan', 'FAN12G2594' => 'fan', 'FAN12G3879' => 'fan', 'FAN14G1546' => 'fan', 'FAN15G3626' => 'fan', 'FAN17G0588' => 'fan', 'FAN17G0609' => 'fan', 'FAN18G2817' => 'fan', 'FAN19G1305' => 'fan', 'FAN20G1787' => 'fan', 'FAN22G0073' => 'fan', 'FAN22G0352' => 'fan', 'FAN22G0368' => 'fan', 'FAN22G2273' => 'fan', 'FAN24G1998' => 'fan', 'FAN27G1317' => 'fan', 'FvH4_2g23980' => 'fve', 'FvH4_4g14380' => 'fve', 'FvH4_4g14390' => 'fve', 'FvH4_6g09250' => 'fve', 'Glyma.03G151100' => 'gma', 'Glyma.04G122550' => 'gma', 'Glyma.05G001600' => 'gma', 'Glyma.09G270766' => 'gma', 'Glyma.09G270832' => 'gma', 'Glyma.13G209800' => 'gma', 'Glyma.15G102800' => 'gma', 'Glyma.18G218900' => 'gma', 'Glyma.19G001500' => 'gma', 'Glyma.19G153600' => 'gma', 'Gohir.A02G028600' => 'ghi', 'Gohir.A08G045000' => 'ghi', 'Gohir.A11G120500' => 'ghi', 'Gohir.A12G006200' => 'ghi', 'Gohir.A12G006250' => 'ghi', 'Gohir.D02G036300' => 'ghi', 'Gohir.D08G054700' => 'ghi', 'Gohir.D11G125600' => 'ghi', 'Gohir.D12G005700' => 'ghi', 'Gorai.004G055200' => 'gra', 'Gorai.005G040400' => 'gra', 'Gorai.007G134500' => 'gra', 'Gorai.008G005500' => 'gra', 'GSVIVG01011094001' => 'vvi', 'GSVIVG01017879001' => 'vvi', 'GSVIVG01025988001' => 'vvi', 'GSVIVG01029847001' => 'vvi', 'HanXRQChr10g0282901' => 'han', 'HanXRQChr10g0310371' => 'han', 'HanXRQChr10g0315041' => 'han', 'HanXRQChr11g0327651' => 'han', 'HanXRQChr12g0359391' => 'han', 'Haze_00972' => 'cav', 'Haze_00973' => 'cav', 'Haze_00974' => 'cav', 'Haze_04747' => 'cav', 'Haze_04749' => 'cav', 'Haze_04750' => 'cav', 'Haze_21217' => 'cav', 'Hma1.2p1_1037F.1_g250680' => 'hma', 'Hma1.2p1_1644F.1_g295320' => 'hma', 'HPP92_011322' => 'vpl', 'HPP92_011323' => 'vpl', 'HPP92_011324' => 'vpl', 'HPP92_011325' => 'vpl', 'HPP92_011326' => 'vpl', 'Hund12205' => 'sun', 'Hund17957' => 'sun', 'Lalb_Chr06g0176771' => 'lal', 'Lalb_Chr18g0056021' => 'lal', 'Lalb_Chr18g0056031' => 'lal', 'Lalb_Chr18g0056041' => 'lal', 'Lalb_Chr20g0107751' => 'lal', 'Lalb_Chr20g0118371' => 'lal', 'Lj1g0010239' => 'lja', 'Lj1g0017101' => 'lja', 'Lj2A1178G40' => 'lonja', 'Lj2A54G84' => 'lonja', 'Lj2g0015248' => 'lja', 'Lj3A761T51' => 'lonja', 'Lj6g0018116' => 'lja', 'Lsat_1_v5_gn_4_136040' => 'lsa', 'Lsat_1_v5_gn_5_187461' => 'lsa', 'Lsat_1_v5_gn_5_77001' => 'lsa', 'Lsat_1_v5_gn_9_4461' => 'lsa', 'Manes.01G210100' => 'mes', 'Manes.03G185600' => 'mes', 'Manes.05G073300' => 'mes', 'Manes.09G120300' => 'mes', 'Manes.15G022100' => 'mes', 'Mapoly0096s0053' => 'mpo', 'MBI03_g14058_MAGBIO' => 'mbi', 'MBI03_g33876_MAGBIO' => 'mbi', 'MBI03_g36854_MAGBIO' => 'mbi', 'MBI17_g11997_MAGBIO' => 'mbi', 'MD03G1269000' => 'mdo', 'MD04G1179600' => 'mdo', 'MD11G1289800' => 'mdo', 'MD12G1194700' => 'mdo', 'MD13G1182100' => 'mdo', 'MD13G1182200' => 'mdo', 'MD16G1182600' => 'mdo', 'Medtr2g021400' => 'mtr', 'Medtr2g021470' => 'mtr', 'Medtr2g105810' => 'mtr', 'Medtr3g033580' => 'mtr', 'Medtr6g007970' => 'mtr', 'Medtr7g056330' => 'mtr', 'Medtr7g074290' => 'mtr', 'Medtr7g074380' => 'mtr', 'Medtr7g094550' => 'mtr', 'Medtr8g069995' => 'mtr', 'MELO3C014345.2' => 'cme', 'MELO3C021395.2' => 'cme', 'Migut.D00262' => 'egut', 'Migut.G00257' => 'egut', 'MSTRG.21575' => 'ama', 'MSTRG.3985' => 'ama', 'Nitab4.5_0000295g0140' => 'nta', 'Nitab4.5_0000732g0140' => 'nta', 'Nitab4.5_0003162g0020' => 'nta', 'Nitab4.5_0006180g0090' => 'nta', 'Nitab4.5_0006390g0010' => 'nta', 'Nitab4.5_0007392g0040' => 'nta', 'Nn1g02140' => 'nnu', 'Nn4g26168' => 'nnu', 'Nn5g26754' => 'nnu', 'Oeu001433.1' => 'oeu', 'Oeu010299.2' => 'oeu', 'Oeu011171.1' => 'oeu', 'Oeu037675.1' => 'oeu', 'Oeu038359.1' => 'oeu', 'Oeu063834.1' => 'oeu', 'Oeu063835.1' => 'oeu', 'Os05g0312000' => 'osa', 'Os07g0211101' => 'osa', 'Os07g0211200' => 'osa', 'Os07g0681500' => 'osa', 'Peaxi162Scf00095g01015' => 'pax', 'Peaxi162Scf00104g00329' => 'pax', 'Peaxi162Scf00161g00137' => 'pax', 'PGR004G1665' => 'pgr', 'PGR031G2937' => 'pgr', 'PGR119G2145' => 'pgr', 'PGSC0003DMG400004351' => 'stu', 'PGSC0003DMG400014625' => 'stu', 'PGSC0003DMG401000943' => 'stu', 'Phvul.001G148600' => 'pvu', 'Phvul.004G001700' => 'pvu', 'Phvul.006G154900' => 'pvu', 'Phvul.008G078200' => 'pvu', 'Phvul.011G136500' => 'pvu', 'Potri.002G215600' => 'ptr', 'Potri.008G201600' => 'ptr', 'Potri.014G138400' => 'ptr', 'Potri.016G142500' => 'ptr', 'Pp3c16_10580' => 'ppa', 'Pp3c5_25280' => 'ppa', 'Prupe.1G150000' => 'ppe', 'Prupe.1G150100' => 'ppe', 'Prupe.6G299600' => 'ppe', 'Prupe.8G245000' => 'ppe', 'Psat0s4927g0040' => 'psa', 'Psat1g052080' => 'psa', 'Psat1g183800' => 'psa', 'Psat3g113840' => 'psa', 'Psat3g126120' => 'psa', 'Psat3g126160' => 'psa', 'Psat3g158760' => 'psa', 'Psat3g158840' => 'psa', 'PSO170G2858' => 'pso', 'PSO339G0606' => 'pso', 'PSO384G4709' => 'pso', 'PSO407G0334' => 'pso', 'QL04p040276' => 'qlo', 'QL06p005458' => 'qlo', 'QL06p005472' => 'qlo', 'QL07p030546' => 'qlo', 'QL07p031519' => 'qlo', 'QL09p050949' => 'qlo', 'QL09p050966' => 'qlo', 'QL09p051067' => 'qlo', 'QL12p022706' => 'qlo', 'RcHm_v2.0_Chr2g0119601' => 'rch', 'RcHm_v2.0_Chr3g0459591' => 'rch', 'RcHm_v2.0_Chr4g0418521' => 'rch', 'RcHm_v2.0_Chr4g0418531' => 'rch', 'RcHm_v2.0_Chr4g0418541' => 'rch', 'RcHm_v2.0_Chr6g0291641' => 'rch', 'Rhsim01G0086300' => 'rsi', 'Rhsim01G0276300' => 'rsi', 'Rhsim01G0276500' => 'rsi', 'Rhsim04G0207700' => 'rsi', 'Rhsim05G0234500' => 'rsi', 'Rhsim13G0022400' => 'rsi', 'Sabra02G0167900' => 'sbr', 'Sabra04G0158500' => 'sbr', 'Sabra08G0159800' => 'sbr', 'Sabra10G0011500' => 'sbr', 'Sabra14G0104400' => 'sbr', 'SalBow2G2440' => 'sbo', 'SalBow4G2265' => 'sbo', 'Sc02g0000060' => 'sci', 'Sc05g0005020' => 'sci', 'Sc13g0003890' => 'sci', 'Sed0014865' => 'sed', 'Sed0017224' => 'sed', 'Sed0026391' => 'sed', 'SEGI_00063' => 'sgi', 'SEGI_10967' => 'sgi', 'SEGI_17510' => 'sgi', 'SEGI_24396' => 'sgi', 'SEGI_39719' => 'sgi', 'SEGI_41392' => 'sgi', 'SGA_v2.0_scaffold11G05794' => 'sas', 'SGA_v2.0_scaffold142G35607' => 'sas', 'SGA_v2.0_scaffold1G00447' => 'sas', 'SHI15388' => 'shi', 'SHI15394' => 'shi', 'SHI15396' => 'shi', 'SHI15399' => 'shi', 'SMO343G0151' => 'smo', 'SMO367G1118' => 'smo', 'Solyc01g080200.3' => 'sly', 'Solyc06g008960.3' => 'sly', 'Solyc09g064780.3' => 'sly', 'Sopen01g031980' => 'spe', 'Sopen06g003710' => 'spe', 'Sopen09g026460' => 'spe', 'Sp3g21240' => 'spa', 'Sp4g30030' => 'spa', 'TAR365G0022' => 'tar', 'TAR365G1023' => 'tar', 'TAR365G1253' => 'tar', 'TAR623G0078' => 'tar', 'TAR623G1721' => 'tar', 'TAR633G0959' => 'tar', 'THA.LOC104802225' => 'tha', 'THA.LOC104804769' => 'tha', 'THA.LOC104808660' => 'tha', 'THA.LOC104812792' => 'tha', 'Thecc.01G284000' => 'tca', 'Thecc.04G220600' => 'tca', 'Thecc.05G268900' => 'tca', 'Thecc.08G171100' => 'tca', 'Thhalv10001284m.g' => 'esa', 'Thhalv10019912m.g' => 'esa', 'TPR.G14189' => 'tpr', 'TPR.G18110' => 'tpr', 'TPR.G18130' => 'tpr', 'TPR.G18131' => 'tpr', 'TPR.G18140' => 'tpr', 'TPR.G24282' => 'tpr', 'TPR.G25221' => 'tpr', 'TPR.G29267' => 'tpr', 'TPR.G35315' => 'tpr', 'TPR.G36173' => 'tpr', 'TWI09G0794' => 'twi', 'TWI59G1348' => 'twi', 'TWI74G0430' => 'twi', 'unitig_26.g8940' => 'ugi', 'unitig_749.g13744' => 'ugi', 'unitig_749.g13745' => 'ugi', 'vmacro08269' => 'vma', 'vmacro14937' => 'vma', 'vmacro20401' => 'vma', 'VMungo0464G1349' => 'vmu', 'VMungo0540G0289' => 'vmu', 'VMungo1215G1590' => 'vmu', 'VMungo1309G0221' => 'vmu', 'VMungo1309G2815' => 'vmu', 'VMungo1383G0239' => 'vmu', 'VMungo1383G2910' => 'vmu', 'Zm00001eb095270' => 'zma', 'Zm00001eb095280' => 'zma', 'Zm00001eb111630' => 'zma', 'Zm00001eb237080' => 'zma', 'Zm00001eb273740' => 'zma', 'Zm00001eb285040' => 'zma', 'Zm00001eb330790' => 'zma', 'Zm00001eb337380' => 'zma' ) $gf_id = 'HOM05D001484' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001484' ) $data_identifier = 'HOM05D001484' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 2, 'aly' => (int) 2, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 22, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 7, 'hma' => (int) 2, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 7, 'mtr' => (int) 10, 'cme' => (int) 2, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 4, 'ppa' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 4, 'qlo' => (int) 9, 'rch' => (int) 6, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 10, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 7, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb337380' $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' => 'HOM05D001484', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p31500' => 'bna', 'A05p00020' => 'bna', 'A07p08820' => 'bna', 'Aa31LG4G3300' => 'aar', 'Aa31LG8G10030' => 'aar', 'Actinidia00731' => 'ach', 'Actinidia11473' => 'ach', 'Actinidia23469' => 'ach', 'Actinidia24318' => 'ach', 'Actinidia40196' => 'ach', 'Actinidia40197' => 'ach', 'Actinidia40198' => 'ach', 'Ah.08g212990' => 'amhyb', 'Ah.15g091720' => 'amhyb', 'AL3G38260' => 'aly', 'AL4G47710' => 'aly', 'Aqoxy2G00671' => 'aox', 'Aqoxy2G03236' => 'aox', 'arahy.Tifrunner.gnm1.ann1.05IDCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KR684' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATY3SJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK6QJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6APGL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IDT7Z9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM073U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ0R87' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LE7RV4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT4QRX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V5ENPK' => 'arhy', 'AT2G48110' => 'ath', 'AT3G23590' => 'ath', 'ATR0626G186' => 'atr', 'ATR1127G141' => 'atr', 'Atru.chr4.2583' => 'acertr', 'Atru.chr5.1358' => 'acertr', 'Atru.chr5.1359' => 'acertr', 'Atru.chr8.46' => 'acertr', 'AUR62002640' => 'cqu', 'AUR62030055' => 'cqu', 'AUR62033713' => 'cqu', 'AUR62033714' => 'cqu', 'AUR62036795' => 'cqu', 'AUR62039891' => 'cqu', 'BcaB02g08737' => 'bca', 'BcaB04g20441' => 'bca', 'BcaB06g26509' => 'bca', 'BcaB06g26510' => 'bca', 'BcaB06g26511' => 'bca', 'BcaB06g26512' => 'bca', 'BcaB06g26513' => 'bca', 'BcaC02g12564' => 'bca', 'BcaC02g12565' => 'bca', 'BcaC02g12794' => 'bca', 'BcaC02g12795' => 'bca', 'BcaC02g12796' => 'bca', 'BcaC06g35541' => 'bca', 'BNapus_Darmor_BZH_scaffold_188p00080' => 'bna', 'BNapus_Darmor_BZH_scaffold_188p00090' => 'bna', 'BolC1t03972H' => 'bol', 'BolC1t03973H' => 'bol', 'BolC4t21680H' => 'bol', 'BolC7t41863H' => 'bol', 'BolSC55t61227H' => 'bol', 'BolSC55t61228H' => 'bol', 'BraA01t03278Z' => 'bra', 'BraA05t18998Z' => 'bra', 'BraA07t28673Z' => 'bra', 'C01p40150' => 'bna', 'C05p12370' => 'bna', 'C07p13680' => 'bna', 'CAN.G1006.16' => 'can', 'CAN.G1006.17' => 'can', 'CAN.G1170.2' => 'can', 'CAN.G962.7' => 'can', 'CANSAT25G2179' => 'cansat', 'CANSAT78G1573' => 'cansat', 'CARHR099510' => 'chi', 'CARHR143510' => 'chi', 'Carub.0003s2380' => 'cru', 'Carub.0004s3082' => 'cru', 'Ca_00614_v3' => 'car', 'Ca_07801_v3' => 'car', 'Ca_08567_v3' => 'car', 'Ca_09571_v3' => 'car', 'CBR_g19290' => 'cbr', 'Cc01_g19770' => 'ccan', 'Cc03_g03030' => 'ccan', 'CDE07G0968' => 'cde', 'CDE09G1441' => 'cde', 'Cfa006103' => 'cfa', 'Cfa015573' => 'cfa', 'Cfa016988' => 'cfa', 'Ciclev10006738m.g' => 'ccl', 'Ciclev10010920m.g' => 'ccl', 'Ciclev10018517m.g' => 'ccl', 'CiPaw.01G159200' => 'cil', 'CiPaw.02G091000' => 'cil', 'CiPaw.02G091100' => 'cil', 'CiPaw.08G103100' => 'cil', 'CiPaw.09G224900' => 'cil', 'ClCG06G005740' => 'cla', 'ClCG07G000090' => 'cla', 'ClCG07G000100' => 'cla', 'COL.COLO4_09143' => 'col', 'COL.COLO4_25124' => 'col', 'Cpa.g.sc16.34' => 'cpa', 'Cpa.g.sc3504.1' => 'cpa', 'Cpa.g.sc60.37' => 'cpa', 'CsaV3_6G018520' => 'csa', 'CsaV3_6G036860' => 'csa', 'CSS0001072' => 'camsi', 'CSS0020208' => 'camsi', 'CSS0021253' => 'camsi', 'CSS0022190' => 'camsi', 'CSS0036150' => 'camsi', 'CSS0040442' => 'camsi', 'CSS0042300' => 'camsi', 'CSS0045298' => 'camsi', 'DCAR_012449' => 'dca', 'DCAR_018405' => 'dca', 'DCAR_024573' => 'dca', 'DCAR_030591' => 'dca', 'Dinv16926' => 'din', 'Dinv32963' => 'din', 'Dinv38382' => 'din', 'Dinv38383' => 'din', 'Duzib133G0974' => 'dzi', 'Duzib138G1867' => 'dzi', 'Duzib211G0420' => 'dzi', 'Duzib212G0930' => 'dzi', 'ECA234G1645' => 'eca', 'ECA247G3467' => 'eca', 'ECA248G1703' => 'eca', 'EL10Ac3g06327' => 'bvu', 'EL10Ac7g17204' => 'bvu', 'Eucgr.A00855' => 'egr', 'Eucgr.A00858' => 'egr', 'Eucgr.H01520' => 'egr', 'Eucgr.H03604' => 'egr', 'Eucgr.L03465' => 'egr', 'Eucgr.L03466' => 'egr', 'FAN01G0988' => 'fan', 'FAN02G3892' => 'fan', 'FAN05G3381' => 'fan', 'FAN07G0967' => 'fan', 'FAN07G1493' => 'fan', 'FAN08G3125' => 'fan', 'FAN09G0402' => 'fan', 'FAN12G2594' => 'fan', 'FAN12G3879' => 'fan', 'FAN14G1546' => 'fan', 'FAN15G3626' => 'fan', 'FAN17G0588' => 'fan', 'FAN17G0609' => 'fan', 'FAN18G2817' => 'fan', 'FAN19G1305' => 'fan', 'FAN20G1787' => 'fan', 'FAN22G0073' => 'fan', 'FAN22G0352' => 'fan', 'FAN22G0368' => 'fan', 'FAN22G2273' => 'fan', 'FAN24G1998' => 'fan', 'FAN27G1317' => 'fan', 'FvH4_2g23980' => 'fve', 'FvH4_4g14380' => 'fve', 'FvH4_4g14390' => 'fve', 'FvH4_6g09250' => 'fve', 'Glyma.03G151100' => 'gma', 'Glyma.04G122550' => 'gma', 'Glyma.05G001600' => 'gma', 'Glyma.09G270766' => 'gma', 'Glyma.09G270832' => 'gma', 'Glyma.13G209800' => 'gma', 'Glyma.15G102800' => 'gma', 'Glyma.18G218900' => 'gma', 'Glyma.19G001500' => 'gma', 'Glyma.19G153600' => 'gma', 'Gohir.A02G028600' => 'ghi', 'Gohir.A08G045000' => 'ghi', 'Gohir.A11G120500' => 'ghi', 'Gohir.A12G006200' => 'ghi', 'Gohir.A12G006250' => 'ghi', 'Gohir.D02G036300' => 'ghi', 'Gohir.D08G054700' => 'ghi', 'Gohir.D11G125600' => 'ghi', 'Gohir.D12G005700' => 'ghi', 'Gorai.004G055200' => 'gra', 'Gorai.005G040400' => 'gra', 'Gorai.007G134500' => 'gra', 'Gorai.008G005500' => 'gra', 'GSVIVG01011094001' => 'vvi', 'GSVIVG01017879001' => 'vvi', 'GSVIVG01025988001' => 'vvi', 'GSVIVG01029847001' => 'vvi', 'HanXRQChr10g0282901' => 'han', 'HanXRQChr10g0310371' => 'han', 'HanXRQChr10g0315041' => 'han', 'HanXRQChr11g0327651' => 'han', 'HanXRQChr12g0359391' => 'han', 'Haze_00972' => 'cav', 'Haze_00973' => 'cav', 'Haze_00974' => 'cav', 'Haze_04747' => 'cav', 'Haze_04749' => 'cav', 'Haze_04750' => 'cav', 'Haze_21217' => 'cav', 'Hma1.2p1_1037F.1_g250680' => 'hma', 'Hma1.2p1_1644F.1_g295320' => 'hma', 'HPP92_011322' => 'vpl', 'HPP92_011323' => 'vpl', 'HPP92_011324' => 'vpl', 'HPP92_011325' => 'vpl', 'HPP92_011326' => 'vpl', 'Hund12205' => 'sun', 'Hund17957' => 'sun', 'Lalb_Chr06g0176771' => 'lal', 'Lalb_Chr18g0056021' => 'lal', 'Lalb_Chr18g0056031' => 'lal', 'Lalb_Chr18g0056041' => 'lal', 'Lalb_Chr20g0107751' => 'lal', 'Lalb_Chr20g0118371' => 'lal', 'Lj1g0010239' => 'lja', 'Lj1g0017101' => 'lja', 'Lj2A1178G40' => 'lonja', 'Lj2A54G84' => 'lonja', 'Lj2g0015248' => 'lja', 'Lj3A761T51' => 'lonja', 'Lj6g0018116' => 'lja', 'Lsat_1_v5_gn_4_136040' => 'lsa', 'Lsat_1_v5_gn_5_187461' => 'lsa', 'Lsat_1_v5_gn_5_77001' => 'lsa', 'Lsat_1_v5_gn_9_4461' => 'lsa', 'Manes.01G210100' => 'mes', 'Manes.03G185600' => 'mes', 'Manes.05G073300' => 'mes', 'Manes.09G120300' => 'mes', 'Manes.15G022100' => 'mes', 'Mapoly0096s0053' => 'mpo', 'MBI03_g14058_MAGBIO' => 'mbi', 'MBI03_g33876_MAGBIO' => 'mbi', 'MBI03_g36854_MAGBIO' => 'mbi', 'MBI17_g11997_MAGBIO' => 'mbi', 'MD03G1269000' => 'mdo', 'MD04G1179600' => 'mdo', 'MD11G1289800' => 'mdo', 'MD12G1194700' => 'mdo', 'MD13G1182100' => 'mdo', 'MD13G1182200' => 'mdo', 'MD16G1182600' => 'mdo', 'Medtr2g021400' => 'mtr', 'Medtr2g021470' => 'mtr', 'Medtr2g105810' => 'mtr', 'Medtr3g033580' => 'mtr', 'Medtr6g007970' => 'mtr', 'Medtr7g056330' => 'mtr', 'Medtr7g074290' => 'mtr', 'Medtr7g074380' => 'mtr', 'Medtr7g094550' => 'mtr', 'Medtr8g069995' => 'mtr', 'MELO3C014345.2' => 'cme', 'MELO3C021395.2' => 'cme', 'Migut.D00262' => 'egut', 'Migut.G00257' => 'egut', 'MSTRG.21575' => 'ama', 'MSTRG.3985' => 'ama', 'Nitab4.5_0000295g0140' => 'nta', 'Nitab4.5_0000732g0140' => 'nta', 'Nitab4.5_0003162g0020' => 'nta', 'Nitab4.5_0006180g0090' => 'nta', 'Nitab4.5_0006390g0010' => 'nta', 'Nitab4.5_0007392g0040' => 'nta', 'Nn1g02140' => 'nnu', 'Nn4g26168' => 'nnu', 'Nn5g26754' => 'nnu', 'Oeu001433.1' => 'oeu', 'Oeu010299.2' => 'oeu', 'Oeu011171.1' => 'oeu', 'Oeu037675.1' => 'oeu', 'Oeu038359.1' => 'oeu', 'Oeu063834.1' => 'oeu', 'Oeu063835.1' => 'oeu', 'Os05g0312000' => 'osa', 'Os07g0211101' => 'osa', 'Os07g0211200' => 'osa', 'Os07g0681500' => 'osa', 'Peaxi162Scf00095g01015' => 'pax', 'Peaxi162Scf00104g00329' => 'pax', 'Peaxi162Scf00161g00137' => 'pax', 'PGR004G1665' => 'pgr', 'PGR031G2937' => 'pgr', 'PGR119G2145' => 'pgr', 'PGSC0003DMG400004351' => 'stu', 'PGSC0003DMG400014625' => 'stu', 'PGSC0003DMG401000943' => 'stu', 'Phvul.001G148600' => 'pvu', 'Phvul.004G001700' => 'pvu', 'Phvul.006G154900' => 'pvu', 'Phvul.008G078200' => 'pvu', 'Phvul.011G136500' => 'pvu', 'Potri.002G215600' => 'ptr', 'Potri.008G201600' => 'ptr', 'Potri.014G138400' => 'ptr', 'Potri.016G142500' => 'ptr', 'Pp3c16_10580' => 'ppa', 'Pp3c5_25280' => 'ppa', 'Prupe.1G150000' => 'ppe', 'Prupe.1G150100' => 'ppe', 'Prupe.6G299600' => 'ppe', 'Prupe.8G245000' => 'ppe', 'Psat0s4927g0040' => 'psa', 'Psat1g052080' => 'psa', 'Psat1g183800' => 'psa', 'Psat3g113840' => 'psa', 'Psat3g126120' => 'psa', 'Psat3g126160' => 'psa', 'Psat3g158760' => 'psa', 'Psat3g158840' => 'psa', 'PSO170G2858' => 'pso', 'PSO339G0606' => 'pso', 'PSO384G4709' => 'pso', 'PSO407G0334' => 'pso', 'QL04p040276' => 'qlo', 'QL06p005458' => 'qlo', 'QL06p005472' => 'qlo', 'QL07p030546' => 'qlo', 'QL07p031519' => 'qlo', 'QL09p050949' => 'qlo', 'QL09p050966' => 'qlo', 'QL09p051067' => 'qlo', 'QL12p022706' => 'qlo', 'RcHm_v2.0_Chr2g0119601' => 'rch', 'RcHm_v2.0_Chr3g0459591' => 'rch', 'RcHm_v2.0_Chr4g0418521' => 'rch', 'RcHm_v2.0_Chr4g0418531' => 'rch', 'RcHm_v2.0_Chr4g0418541' => 'rch', 'RcHm_v2.0_Chr6g0291641' => 'rch', 'Rhsim01G0086300' => 'rsi', 'Rhsim01G0276300' => 'rsi', 'Rhsim01G0276500' => 'rsi', 'Rhsim04G0207700' => 'rsi', 'Rhsim05G0234500' => 'rsi', 'Rhsim13G0022400' => 'rsi', 'Sabra02G0167900' => 'sbr', 'Sabra04G0158500' => 'sbr', 'Sabra08G0159800' => 'sbr', 'Sabra10G0011500' => 'sbr', 'Sabra14G0104400' => 'sbr', 'SalBow2G2440' => 'sbo', 'SalBow4G2265' => 'sbo', 'Sc02g0000060' => 'sci', 'Sc05g0005020' => 'sci', 'Sc13g0003890' => 'sci', 'Sed0014865' => 'sed', 'Sed0017224' => 'sed', 'Sed0026391' => 'sed', 'SEGI_00063' => 'sgi', 'SEGI_10967' => 'sgi', 'SEGI_17510' => 'sgi', 'SEGI_24396' => 'sgi', 'SEGI_39719' => 'sgi', 'SEGI_41392' => 'sgi', 'SGA_v2.0_scaffold11G05794' => 'sas', 'SGA_v2.0_scaffold142G35607' => 'sas', 'SGA_v2.0_scaffold1G00447' => 'sas', 'SHI15388' => 'shi', 'SHI15394' => 'shi', 'SHI15396' => 'shi', 'SHI15399' => 'shi', 'SMO343G0151' => 'smo', 'SMO367G1118' => 'smo', 'Solyc01g080200.3' => 'sly', 'Solyc06g008960.3' => 'sly', 'Solyc09g064780.3' => 'sly', 'Sopen01g031980' => 'spe', 'Sopen06g003710' => 'spe', 'Sopen09g026460' => 'spe', 'Sp3g21240' => 'spa', 'Sp4g30030' => 'spa', 'TAR365G0022' => 'tar', 'TAR365G1023' => 'tar', 'TAR365G1253' => 'tar', 'TAR623G0078' => 'tar', 'TAR623G1721' => 'tar', 'TAR633G0959' => 'tar', 'THA.LOC104802225' => 'tha', 'THA.LOC104804769' => 'tha', 'THA.LOC104808660' => 'tha', 'THA.LOC104812792' => 'tha', 'Thecc.01G284000' => 'tca', 'Thecc.04G220600' => 'tca', 'Thecc.05G268900' => 'tca', 'Thecc.08G171100' => 'tca', 'Thhalv10001284m.g' => 'esa', 'Thhalv10019912m.g' => 'esa', 'TPR.G14189' => 'tpr', 'TPR.G18110' => 'tpr', 'TPR.G18130' => 'tpr', 'TPR.G18131' => 'tpr', 'TPR.G18140' => 'tpr', 'TPR.G24282' => 'tpr', 'TPR.G25221' => 'tpr', 'TPR.G29267' => 'tpr', 'TPR.G35315' => 'tpr', 'TPR.G36173' => 'tpr', 'TWI09G0794' => 'twi', 'TWI59G1348' => 'twi', 'TWI74G0430' => 'twi', 'unitig_26.g8940' => 'ugi', 'unitig_749.g13744' => 'ugi', 'unitig_749.g13745' => 'ugi', 'vmacro08269' => 'vma', 'vmacro14937' => 'vma', 'vmacro20401' => 'vma', 'VMungo0464G1349' => 'vmu', 'VMungo0540G0289' => 'vmu', 'VMungo1215G1590' => 'vmu', 'VMungo1309G0221' => 'vmu', 'VMungo1309G2815' => 'vmu', 'VMungo1383G0239' => 'vmu', 'VMungo1383G2910' => 'vmu', 'Zm00001eb095270' => 'zma', 'Zm00001eb095280' => 'zma', 'Zm00001eb111630' => 'zma', 'Zm00001eb237080' => 'zma', 'Zm00001eb273740' => 'zma', 'Zm00001eb285040' => 'zma', 'Zm00001eb330790' => 'zma', 'Zm00001eb337380' => 'zma' ), 'gf_id' => 'HOM05D001484', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001484' ), 'data_identifier' => 'HOM05D001484', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001484', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p31500' => 'bna', 'A05p00020' => 'bna', 'A07p08820' => 'bna', 'Aa31LG4G3300' => 'aar', 'Aa31LG8G10030' => 'aar', 'Actinidia00731' => 'ach', 'Actinidia11473' => 'ach', 'Actinidia23469' => 'ach', 'Actinidia24318' => 'ach', 'Actinidia40196' => 'ach', 'Actinidia40197' => 'ach', 'Actinidia40198' => 'ach', 'Ah.08g212990' => 'amhyb', 'Ah.15g091720' => 'amhyb', 'AL3G38260' => 'aly', 'AL4G47710' => 'aly', 'Aqoxy2G00671' => 'aox', 'Aqoxy2G03236' => 'aox', 'arahy.Tifrunner.gnm1.ann1.05IDCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KR684' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATY3SJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK6QJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6APGL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IDT7Z9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM073U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ0R87' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LE7RV4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT4QRX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V5ENPK' => 'arhy', 'AT2G48110' => 'ath', 'AT3G23590' => 'ath', 'ATR0626G186' => 'atr', 'ATR1127G141' => 'atr', 'Atru.chr4.2583' => 'acertr', 'Atru.chr5.1358' => 'acertr', 'Atru.chr5.1359' => 'acertr', 'Atru.chr8.46' => 'acertr', 'AUR62002640' => 'cqu', 'AUR62030055' => 'cqu', 'AUR62033713' => 'cqu', 'AUR62033714' => 'cqu', 'AUR62036795' => 'cqu', 'AUR62039891' => 'cqu', 'BcaB02g08737' => 'bca', 'BcaB04g20441' => 'bca', 'BcaB06g26509' => 'bca', 'BcaB06g26510' => 'bca', 'BcaB06g26511' => 'bca', 'BcaB06g26512' => 'bca', 'BcaB06g26513' => 'bca', 'BcaC02g12564' => 'bca', 'BcaC02g12565' => 'bca', 'BcaC02g12794' => 'bca', 'BcaC02g12795' => 'bca', 'BcaC02g12796' => 'bca', 'BcaC06g35541' => 'bca', 'BNapus_Darmor_BZH_scaffold_188p00080' => 'bna', 'BNapus_Darmor_BZH_scaffold_188p00090' => 'bna', 'BolC1t03972H' => 'bol', 'BolC1t03973H' => 'bol', 'BolC4t21680H' => 'bol', 'BolC7t41863H' => 'bol', 'BolSC55t61227H' => 'bol', 'BolSC55t61228H' => 'bol', 'BraA01t03278Z' => 'bra', 'BraA05t18998Z' => 'bra', 'BraA07t28673Z' => 'bra', 'C01p40150' => 'bna', 'C05p12370' => 'bna', 'C07p13680' => 'bna', 'CAN.G1006.16' => 'can', 'CAN.G1006.17' => 'can', 'CAN.G1170.2' => 'can', 'CAN.G962.7' => 'can', 'CANSAT25G2179' => 'cansat', 'CANSAT78G1573' => 'cansat', 'CARHR099510' => 'chi', 'CARHR143510' => 'chi', 'Carub.0003s2380' => 'cru', 'Carub.0004s3082' => 'cru', 'Ca_00614_v3' => 'car', 'Ca_07801_v3' => 'car', 'Ca_08567_v3' => 'car', 'Ca_09571_v3' => 'car', 'CBR_g19290' => 'cbr', 'Cc01_g19770' => 'ccan', 'Cc03_g03030' => 'ccan', 'CDE07G0968' => 'cde', 'CDE09G1441' => 'cde', 'Cfa006103' => 'cfa', 'Cfa015573' => 'cfa', 'Cfa016988' => 'cfa', 'Ciclev10006738m.g' => 'ccl', 'Ciclev10010920m.g' => 'ccl', 'Ciclev10018517m.g' => 'ccl', 'CiPaw.01G159200' => 'cil', 'CiPaw.02G091000' => 'cil', 'CiPaw.02G091100' => 'cil', 'CiPaw.08G103100' => 'cil', 'CiPaw.09G224900' => 'cil', 'ClCG06G005740' => 'cla', 'ClCG07G000090' => 'cla', 'ClCG07G000100' => 'cla', 'COL.COLO4_09143' => 'col', 'COL.COLO4_25124' => 'col', 'Cpa.g.sc16.34' => 'cpa', 'Cpa.g.sc3504.1' => 'cpa', 'Cpa.g.sc60.37' => 'cpa', 'CsaV3_6G018520' => 'csa', 'CsaV3_6G036860' => 'csa', 'CSS0001072' => 'camsi', 'CSS0020208' => 'camsi', 'CSS0021253' => 'camsi', 'CSS0022190' => 'camsi', 'CSS0036150' => 'camsi', 'CSS0040442' => 'camsi', 'CSS0042300' => 'camsi', 'CSS0045298' => 'camsi', 'DCAR_012449' => 'dca', 'DCAR_018405' => 'dca', 'DCAR_024573' => 'dca', 'DCAR_030591' => 'dca', 'Dinv16926' => 'din', 'Dinv32963' => 'din', 'Dinv38382' => 'din', 'Dinv38383' => 'din', 'Duzib133G0974' => 'dzi', 'Duzib138G1867' => 'dzi', 'Duzib211G0420' => 'dzi', 'Duzib212G0930' => 'dzi', 'ECA234G1645' => 'eca', 'ECA247G3467' => 'eca', 'ECA248G1703' => 'eca', 'EL10Ac3g06327' => 'bvu', 'EL10Ac7g17204' => 'bvu', 'Eucgr.A00855' => 'egr', 'Eucgr.A00858' => 'egr', 'Eucgr.H01520' => 'egr', 'Eucgr.H03604' => 'egr', 'Eucgr.L03465' => 'egr', 'Eucgr.L03466' => 'egr', 'FAN01G0988' => 'fan', 'FAN02G3892' => 'fan', 'FAN05G3381' => 'fan', 'FAN07G0967' => 'fan', 'FAN07G1493' => 'fan', 'FAN08G3125' => 'fan', 'FAN09G0402' => 'fan', 'FAN12G2594' => 'fan', 'FAN12G3879' => 'fan', 'FAN14G1546' => 'fan', 'FAN15G3626' => 'fan', 'FAN17G0588' => 'fan', 'FAN17G0609' => 'fan', 'FAN18G2817' => 'fan', 'FAN19G1305' => 'fan', 'FAN20G1787' => 'fan', 'FAN22G0073' => 'fan', 'FAN22G0352' => 'fan', 'FAN22G0368' => 'fan', 'FAN22G2273' => 'fan', 'FAN24G1998' => 'fan', 'FAN27G1317' => 'fan', 'FvH4_2g23980' => 'fve', 'FvH4_4g14380' => 'fve', 'FvH4_4g14390' => 'fve', 'FvH4_6g09250' => 'fve', 'Glyma.03G151100' => 'gma', 'Glyma.04G122550' => 'gma', 'Glyma.05G001600' => 'gma', 'Glyma.09G270766' => 'gma', 'Glyma.09G270832' => 'gma', 'Glyma.13G209800' => 'gma', 'Glyma.15G102800' => 'gma', 'Glyma.18G218900' => 'gma', 'Glyma.19G001500' => 'gma', 'Glyma.19G153600' => 'gma', 'Gohir.A02G028600' => 'ghi', 'Gohir.A08G045000' => 'ghi', 'Gohir.A11G120500' => 'ghi', 'Gohir.A12G006200' => 'ghi', 'Gohir.A12G006250' => 'ghi', 'Gohir.D02G036300' => 'ghi', 'Gohir.D08G054700' => 'ghi', 'Gohir.D11G125600' => 'ghi', 'Gohir.D12G005700' => 'ghi', 'Gorai.004G055200' => 'gra', 'Gorai.005G040400' => 'gra', 'Gorai.007G134500' => 'gra', 'Gorai.008G005500' => 'gra', 'GSVIVG01011094001' => 'vvi', 'GSVIVG01017879001' => 'vvi', 'GSVIVG01025988001' => 'vvi', 'GSVIVG01029847001' => 'vvi', 'HanXRQChr10g0282901' => 'han', 'HanXRQChr10g0310371' => 'han', 'HanXRQChr10g0315041' => 'han', 'HanXRQChr11g0327651' => 'han', 'HanXRQChr12g0359391' => 'han', 'Haze_00972' => 'cav', 'Haze_00973' => 'cav', 'Haze_00974' => 'cav', 'Haze_04747' => 'cav', 'Haze_04749' => 'cav', 'Haze_04750' => 'cav', 'Haze_21217' => 'cav', 'Hma1.2p1_1037F.1_g250680' => 'hma', 'Hma1.2p1_1644F.1_g295320' => 'hma', 'HPP92_011322' => 'vpl', 'HPP92_011323' => 'vpl', 'HPP92_011324' => 'vpl', 'HPP92_011325' => 'vpl', 'HPP92_011326' => 'vpl', 'Hund12205' => 'sun', 'Hund17957' => 'sun', 'Lalb_Chr06g0176771' => 'lal', 'Lalb_Chr18g0056021' => 'lal', 'Lalb_Chr18g0056031' => 'lal', 'Lalb_Chr18g0056041' => 'lal', 'Lalb_Chr20g0107751' => 'lal', 'Lalb_Chr20g0118371' => 'lal', 'Lj1g0010239' => 'lja', 'Lj1g0017101' => 'lja', 'Lj2A1178G40' => 'lonja', 'Lj2A54G84' => 'lonja', 'Lj2g0015248' => 'lja', 'Lj3A761T51' => 'lonja', 'Lj6g0018116' => 'lja', 'Lsat_1_v5_gn_4_136040' => 'lsa', 'Lsat_1_v5_gn_5_187461' => 'lsa', 'Lsat_1_v5_gn_5_77001' => 'lsa', 'Lsat_1_v5_gn_9_4461' => 'lsa', 'Manes.01G210100' => 'mes', 'Manes.03G185600' => 'mes', 'Manes.05G073300' => 'mes', 'Manes.09G120300' => 'mes', 'Manes.15G022100' => 'mes', 'Mapoly0096s0053' => 'mpo', 'MBI03_g14058_MAGBIO' => 'mbi', 'MBI03_g33876_MAGBIO' => 'mbi', 'MBI03_g36854_MAGBIO' => 'mbi', 'MBI17_g11997_MAGBIO' => 'mbi', 'MD03G1269000' => 'mdo', 'MD04G1179600' => 'mdo', 'MD11G1289800' => 'mdo', 'MD12G1194700' => 'mdo', 'MD13G1182100' => 'mdo', 'MD13G1182200' => 'mdo', 'MD16G1182600' => 'mdo', 'Medtr2g021400' => 'mtr', 'Medtr2g021470' => 'mtr', 'Medtr2g105810' => 'mtr', 'Medtr3g033580' => 'mtr', 'Medtr6g007970' => 'mtr', 'Medtr7g056330' => 'mtr', 'Medtr7g074290' => 'mtr', 'Medtr7g074380' => 'mtr', 'Medtr7g094550' => 'mtr', 'Medtr8g069995' => 'mtr', 'MELO3C014345.2' => 'cme', 'MELO3C021395.2' => 'cme', 'Migut.D00262' => 'egut', 'Migut.G00257' => 'egut', 'MSTRG.21575' => 'ama', 'MSTRG.3985' => 'ama', 'Nitab4.5_0000295g0140' => 'nta', 'Nitab4.5_0000732g0140' => 'nta', 'Nitab4.5_0003162g0020' => 'nta', 'Nitab4.5_0006180g0090' => 'nta', 'Nitab4.5_0006390g0010' => 'nta', 'Nitab4.5_0007392g0040' => 'nta', 'Nn1g02140' => 'nnu', 'Nn4g26168' => 'nnu', 'Nn5g26754' => 'nnu', 'Oeu001433.1' => 'oeu', 'Oeu010299.2' => 'oeu', 'Oeu011171.1' => 'oeu', 'Oeu037675.1' => 'oeu', 'Oeu038359.1' => 'oeu', 'Oeu063834.1' => 'oeu', 'Oeu063835.1' => 'oeu', 'Os05g0312000' => 'osa', 'Os07g0211101' => 'osa', 'Os07g0211200' => 'osa', 'Os07g0681500' => 'osa', 'Peaxi162Scf00095g01015' => 'pax', 'Peaxi162Scf00104g00329' => 'pax', 'Peaxi162Scf00161g00137' => 'pax', 'PGR004G1665' => 'pgr', 'PGR031G2937' => 'pgr', 'PGR119G2145' => 'pgr', 'PGSC0003DMG400004351' => 'stu', 'PGSC0003DMG400014625' => 'stu', 'PGSC0003DMG401000943' => 'stu', 'Phvul.001G148600' => 'pvu', 'Phvul.004G001700' => 'pvu', 'Phvul.006G154900' => 'pvu', 'Phvul.008G078200' => 'pvu', 'Phvul.011G136500' => 'pvu', 'Potri.002G215600' => 'ptr', 'Potri.008G201600' => 'ptr', 'Potri.014G138400' => 'ptr', 'Potri.016G142500' => 'ptr', 'Pp3c16_10580' => 'ppa', 'Pp3c5_25280' => 'ppa', 'Prupe.1G150000' => 'ppe', 'Prupe.1G150100' => 'ppe', 'Prupe.6G299600' => 'ppe', 'Prupe.8G245000' => 'ppe', 'Psat0s4927g0040' => 'psa', 'Psat1g052080' => 'psa', 'Psat1g183800' => 'psa', 'Psat3g113840' => 'psa', 'Psat3g126120' => 'psa', 'Psat3g126160' => 'psa', 'Psat3g158760' => 'psa', 'Psat3g158840' => 'psa', 'PSO170G2858' => 'pso', 'PSO339G0606' => 'pso', 'PSO384G4709' => 'pso', 'PSO407G0334' => 'pso', 'QL04p040276' => 'qlo', 'QL06p005458' => 'qlo', 'QL06p005472' => 'qlo', 'QL07p030546' => 'qlo', 'QL07p031519' => 'qlo', 'QL09p050949' => 'qlo', 'QL09p050966' => 'qlo', 'QL09p051067' => 'qlo', 'QL12p022706' => 'qlo', 'RcHm_v2.0_Chr2g0119601' => 'rch', 'RcHm_v2.0_Chr3g0459591' => 'rch', 'RcHm_v2.0_Chr4g0418521' => 'rch', 'RcHm_v2.0_Chr4g0418531' => 'rch', 'RcHm_v2.0_Chr4g0418541' => 'rch', 'RcHm_v2.0_Chr6g0291641' => 'rch', 'Rhsim01G0086300' => 'rsi', 'Rhsim01G0276300' => 'rsi', 'Rhsim01G0276500' => 'rsi', 'Rhsim04G0207700' => 'rsi', 'Rhsim05G0234500' => 'rsi', 'Rhsim13G0022400' => 'rsi', 'Sabra02G0167900' => 'sbr', 'Sabra04G0158500' => 'sbr', 'Sabra08G0159800' => 'sbr', 'Sabra10G0011500' => 'sbr', 'Sabra14G0104400' => 'sbr', 'SalBow2G2440' => 'sbo', 'SalBow4G2265' => 'sbo', 'Sc02g0000060' => 'sci', 'Sc05g0005020' => 'sci', 'Sc13g0003890' => 'sci', 'Sed0014865' => 'sed', 'Sed0017224' => 'sed', 'Sed0026391' => 'sed', 'SEGI_00063' => 'sgi', 'SEGI_10967' => 'sgi', 'SEGI_17510' => 'sgi', 'SEGI_24396' => 'sgi', 'SEGI_39719' => 'sgi', 'SEGI_41392' => 'sgi', 'SGA_v2.0_scaffold11G05794' => 'sas', 'SGA_v2.0_scaffold142G35607' => 'sas', 'SGA_v2.0_scaffold1G00447' => 'sas', 'SHI15388' => 'shi', 'SHI15394' => 'shi', 'SHI15396' => 'shi', 'SHI15399' => 'shi', 'SMO343G0151' => 'smo', 'SMO367G1118' => 'smo', 'Solyc01g080200.3' => 'sly', 'Solyc06g008960.3' => 'sly', 'Solyc09g064780.3' => 'sly', 'Sopen01g031980' => 'spe', 'Sopen06g003710' => 'spe', 'Sopen09g026460' => 'spe', 'Sp3g21240' => 'spa', 'Sp4g30030' => 'spa', 'TAR365G0022' => 'tar', 'TAR365G1023' => 'tar', 'TAR365G1253' => 'tar', 'TAR623G0078' => 'tar', 'TAR623G1721' => 'tar', 'TAR633G0959' => 'tar', 'THA.LOC104802225' => 'tha', 'THA.LOC104804769' => 'tha', 'THA.LOC104808660' => 'tha', 'THA.LOC104812792' => 'tha', 'Thecc.01G284000' => 'tca', 'Thecc.04G220600' => 'tca', 'Thecc.05G268900' => 'tca', 'Thecc.08G171100' => 'tca', 'Thhalv10001284m.g' => 'esa', 'Thhalv10019912m.g' => 'esa', 'TPR.G14189' => 'tpr', 'TPR.G18110' => 'tpr', 'TPR.G18130' => 'tpr', 'TPR.G18131' => 'tpr', 'TPR.G18140' => 'tpr', 'TPR.G24282' => 'tpr', 'TPR.G25221' => 'tpr', 'TPR.G29267' => 'tpr', 'TPR.G35315' => 'tpr', 'TPR.G36173' => 'tpr', 'TWI09G0794' => 'twi', 'TWI59G1348' => 'twi', 'TWI74G0430' => 'twi', 'unitig_26.g8940' => 'ugi', 'unitig_749.g13744' => 'ugi', 'unitig_749.g13745' => 'ugi', 'vmacro08269' => 'vma', 'vmacro14937' => 'vma', 'vmacro20401' => 'vma', 'VMungo0464G1349' => 'vmu', 'VMungo0540G0289' => 'vmu', 'VMungo1215G1590' => 'vmu', 'VMungo1309G0221' => 'vmu', 'VMungo1309G2815' => 'vmu', 'VMungo1383G0239' => 'vmu', 'VMungo1383G2910' => 'vmu', 'Zm00001eb095270' => 'zma', 'Zm00001eb095280' => 'zma', 'Zm00001eb111630' => 'zma', 'Zm00001eb237080' => 'zma', 'Zm00001eb273740' => 'zma', 'Zm00001eb285040' => 'zma', 'Zm00001eb330790' => 'zma', 'Zm00001eb337380' => 'zma' ) $gf_id = 'HOM05D001484' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001484' ) $data_identifier = 'HOM05D001484' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 2, 'aly' => (int) 2, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 22, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 7, 'hma' => (int) 2, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 7, 'mtr' => (int) 10, 'cme' => (int) 2, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 4, 'ppa' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 4, 'qlo' => (int) 9, 'rch' => (int) 6, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 10, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 7, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb337380' $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' => 'HOM05D001484', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p31500' => 'bna', 'A05p00020' => 'bna', 'A07p08820' => 'bna', 'Aa31LG4G3300' => 'aar', 'Aa31LG8G10030' => 'aar', 'Actinidia00731' => 'ach', 'Actinidia11473' => 'ach', 'Actinidia23469' => 'ach', 'Actinidia24318' => 'ach', 'Actinidia40196' => 'ach', 'Actinidia40197' => 'ach', 'Actinidia40198' => 'ach', 'Ah.08g212990' => 'amhyb', 'Ah.15g091720' => 'amhyb', 'AL3G38260' => 'aly', 'AL4G47710' => 'aly', 'Aqoxy2G00671' => 'aox', 'Aqoxy2G03236' => 'aox', 'arahy.Tifrunner.gnm1.ann1.05IDCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KR684' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATY3SJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK6QJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6APGL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IDT7Z9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM073U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ0R87' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LE7RV4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT4QRX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V5ENPK' => 'arhy', 'AT2G48110' => 'ath', 'AT3G23590' => 'ath', 'ATR0626G186' => 'atr', 'ATR1127G141' => 'atr', 'Atru.chr4.2583' => 'acertr', 'Atru.chr5.1358' => 'acertr', 'Atru.chr5.1359' => 'acertr', 'Atru.chr8.46' => 'acertr', 'AUR62002640' => 'cqu', 'AUR62030055' => 'cqu', 'AUR62033713' => 'cqu', 'AUR62033714' => 'cqu', 'AUR62036795' => 'cqu', 'AUR62039891' => 'cqu', 'BcaB02g08737' => 'bca', 'BcaB04g20441' => 'bca', 'BcaB06g26509' => 'bca', 'BcaB06g26510' => 'bca', 'BcaB06g26511' => 'bca', 'BcaB06g26512' => 'bca', 'BcaB06g26513' => 'bca', 'BcaC02g12564' => 'bca', 'BcaC02g12565' => 'bca', 'BcaC02g12794' => 'bca', 'BcaC02g12795' => 'bca', 'BcaC02g12796' => 'bca', 'BcaC06g35541' => 'bca', 'BNapus_Darmor_BZH_scaffold_188p00080' => 'bna', 'BNapus_Darmor_BZH_scaffold_188p00090' => 'bna', 'BolC1t03972H' => 'bol', 'BolC1t03973H' => 'bol', 'BolC4t21680H' => 'bol', 'BolC7t41863H' => 'bol', 'BolSC55t61227H' => 'bol', 'BolSC55t61228H' => 'bol', 'BraA01t03278Z' => 'bra', 'BraA05t18998Z' => 'bra', 'BraA07t28673Z' => 'bra', 'C01p40150' => 'bna', 'C05p12370' => 'bna', 'C07p13680' => 'bna', 'CAN.G1006.16' => 'can', 'CAN.G1006.17' => 'can', 'CAN.G1170.2' => 'can', 'CAN.G962.7' => 'can', 'CANSAT25G2179' => 'cansat', 'CANSAT78G1573' => 'cansat', 'CARHR099510' => 'chi', 'CARHR143510' => 'chi', 'Carub.0003s2380' => 'cru', 'Carub.0004s3082' => 'cru', 'Ca_00614_v3' => 'car', 'Ca_07801_v3' => 'car', 'Ca_08567_v3' => 'car', 'Ca_09571_v3' => 'car', 'CBR_g19290' => 'cbr', 'Cc01_g19770' => 'ccan', 'Cc03_g03030' => 'ccan', 'CDE07G0968' => 'cde', 'CDE09G1441' => 'cde', 'Cfa006103' => 'cfa', 'Cfa015573' => 'cfa', 'Cfa016988' => 'cfa', 'Ciclev10006738m.g' => 'ccl', 'Ciclev10010920m.g' => 'ccl', 'Ciclev10018517m.g' => 'ccl', 'CiPaw.01G159200' => 'cil', 'CiPaw.02G091000' => 'cil', 'CiPaw.02G091100' => 'cil', 'CiPaw.08G103100' => 'cil', 'CiPaw.09G224900' => 'cil', 'ClCG06G005740' => 'cla', 'ClCG07G000090' => 'cla', 'ClCG07G000100' => 'cla', 'COL.COLO4_09143' => 'col', 'COL.COLO4_25124' => 'col', 'Cpa.g.sc16.34' => 'cpa', 'Cpa.g.sc3504.1' => 'cpa', 'Cpa.g.sc60.37' => 'cpa', 'CsaV3_6G018520' => 'csa', 'CsaV3_6G036860' => 'csa', 'CSS0001072' => 'camsi', 'CSS0020208' => 'camsi', 'CSS0021253' => 'camsi', 'CSS0022190' => 'camsi', 'CSS0036150' => 'camsi', 'CSS0040442' => 'camsi', 'CSS0042300' => 'camsi', 'CSS0045298' => 'camsi', 'DCAR_012449' => 'dca', 'DCAR_018405' => 'dca', 'DCAR_024573' => 'dca', 'DCAR_030591' => 'dca', 'Dinv16926' => 'din', 'Dinv32963' => 'din', 'Dinv38382' => 'din', 'Dinv38383' => 'din', 'Duzib133G0974' => 'dzi', 'Duzib138G1867' => 'dzi', 'Duzib211G0420' => 'dzi', 'Duzib212G0930' => 'dzi', 'ECA234G1645' => 'eca', 'ECA247G3467' => 'eca', 'ECA248G1703' => 'eca', 'EL10Ac3g06327' => 'bvu', 'EL10Ac7g17204' => 'bvu', 'Eucgr.A00855' => 'egr', 'Eucgr.A00858' => 'egr', 'Eucgr.H01520' => 'egr', 'Eucgr.H03604' => 'egr', 'Eucgr.L03465' => 'egr', 'Eucgr.L03466' => 'egr', 'FAN01G0988' => 'fan', 'FAN02G3892' => 'fan', 'FAN05G3381' => 'fan', 'FAN07G0967' => 'fan', 'FAN07G1493' => 'fan', 'FAN08G3125' => 'fan', 'FAN09G0402' => 'fan', 'FAN12G2594' => 'fan', 'FAN12G3879' => 'fan', 'FAN14G1546' => 'fan', 'FAN15G3626' => 'fan', 'FAN17G0588' => 'fan', 'FAN17G0609' => 'fan', 'FAN18G2817' => 'fan', 'FAN19G1305' => 'fan', 'FAN20G1787' => 'fan', 'FAN22G0073' => 'fan', 'FAN22G0352' => 'fan', 'FAN22G0368' => 'fan', 'FAN22G2273' => 'fan', 'FAN24G1998' => 'fan', 'FAN27G1317' => 'fan', 'FvH4_2g23980' => 'fve', 'FvH4_4g14380' => 'fve', 'FvH4_4g14390' => 'fve', 'FvH4_6g09250' => 'fve', 'Glyma.03G151100' => 'gma', 'Glyma.04G122550' => 'gma', 'Glyma.05G001600' => 'gma', 'Glyma.09G270766' => 'gma', 'Glyma.09G270832' => 'gma', 'Glyma.13G209800' => 'gma', 'Glyma.15G102800' => 'gma', 'Glyma.18G218900' => 'gma', 'Glyma.19G001500' => 'gma', 'Glyma.19G153600' => 'gma', 'Gohir.A02G028600' => 'ghi', 'Gohir.A08G045000' => 'ghi', 'Gohir.A11G120500' => 'ghi', 'Gohir.A12G006200' => 'ghi', 'Gohir.A12G006250' => 'ghi', 'Gohir.D02G036300' => 'ghi', 'Gohir.D08G054700' => 'ghi', 'Gohir.D11G125600' => 'ghi', 'Gohir.D12G005700' => 'ghi', 'Gorai.004G055200' => 'gra', 'Gorai.005G040400' => 'gra', 'Gorai.007G134500' => 'gra', 'Gorai.008G005500' => 'gra', 'GSVIVG01011094001' => 'vvi', 'GSVIVG01017879001' => 'vvi', 'GSVIVG01025988001' => 'vvi', 'GSVIVG01029847001' => 'vvi', 'HanXRQChr10g0282901' => 'han', 'HanXRQChr10g0310371' => 'han', 'HanXRQChr10g0315041' => 'han', 'HanXRQChr11g0327651' => 'han', 'HanXRQChr12g0359391' => 'han', 'Haze_00972' => 'cav', 'Haze_00973' => 'cav', 'Haze_00974' => 'cav', 'Haze_04747' => 'cav', 'Haze_04749' => 'cav', 'Haze_04750' => 'cav', 'Haze_21217' => 'cav', 'Hma1.2p1_1037F.1_g250680' => 'hma', 'Hma1.2p1_1644F.1_g295320' => 'hma', 'HPP92_011322' => 'vpl', 'HPP92_011323' => 'vpl', 'HPP92_011324' => 'vpl', 'HPP92_011325' => 'vpl', 'HPP92_011326' => 'vpl', 'Hund12205' => 'sun', 'Hund17957' => 'sun', 'Lalb_Chr06g0176771' => 'lal', 'Lalb_Chr18g0056021' => 'lal', 'Lalb_Chr18g0056031' => 'lal', 'Lalb_Chr18g0056041' => 'lal', 'Lalb_Chr20g0107751' => 'lal', 'Lalb_Chr20g0118371' => 'lal', 'Lj1g0010239' => 'lja', 'Lj1g0017101' => 'lja', 'Lj2A1178G40' => 'lonja', 'Lj2A54G84' => 'lonja', 'Lj2g0015248' => 'lja', 'Lj3A761T51' => 'lonja', 'Lj6g0018116' => 'lja', 'Lsat_1_v5_gn_4_136040' => 'lsa', 'Lsat_1_v5_gn_5_187461' => 'lsa', 'Lsat_1_v5_gn_5_77001' => 'lsa', 'Lsat_1_v5_gn_9_4461' => 'lsa', 'Manes.01G210100' => 'mes', 'Manes.03G185600' => 'mes', 'Manes.05G073300' => 'mes', 'Manes.09G120300' => 'mes', 'Manes.15G022100' => 'mes', 'Mapoly0096s0053' => 'mpo', 'MBI03_g14058_MAGBIO' => 'mbi', 'MBI03_g33876_MAGBIO' => 'mbi', 'MBI03_g36854_MAGBIO' => 'mbi', 'MBI17_g11997_MAGBIO' => 'mbi', 'MD03G1269000' => 'mdo', 'MD04G1179600' => 'mdo', 'MD11G1289800' => 'mdo', 'MD12G1194700' => 'mdo', 'MD13G1182100' => 'mdo', 'MD13G1182200' => 'mdo', 'MD16G1182600' => 'mdo', 'Medtr2g021400' => 'mtr', 'Medtr2g021470' => 'mtr', 'Medtr2g105810' => 'mtr', 'Medtr3g033580' => 'mtr', 'Medtr6g007970' => 'mtr', 'Medtr7g056330' => 'mtr', 'Medtr7g074290' => 'mtr', 'Medtr7g074380' => 'mtr', 'Medtr7g094550' => 'mtr', 'Medtr8g069995' => 'mtr', 'MELO3C014345.2' => 'cme', 'MELO3C021395.2' => 'cme', 'Migut.D00262' => 'egut', 'Migut.G00257' => 'egut', 'MSTRG.21575' => 'ama', 'MSTRG.3985' => 'ama', 'Nitab4.5_0000295g0140' => 'nta', 'Nitab4.5_0000732g0140' => 'nta', 'Nitab4.5_0003162g0020' => 'nta', 'Nitab4.5_0006180g0090' => 'nta', 'Nitab4.5_0006390g0010' => 'nta', 'Nitab4.5_0007392g0040' => 'nta', 'Nn1g02140' => 'nnu', 'Nn4g26168' => 'nnu', 'Nn5g26754' => 'nnu', 'Oeu001433.1' => 'oeu', 'Oeu010299.2' => 'oeu', 'Oeu011171.1' => 'oeu', 'Oeu037675.1' => 'oeu', 'Oeu038359.1' => 'oeu', 'Oeu063834.1' => 'oeu', 'Oeu063835.1' => 'oeu', 'Os05g0312000' => 'osa', 'Os07g0211101' => 'osa', 'Os07g0211200' => 'osa', 'Os07g0681500' => 'osa', 'Peaxi162Scf00095g01015' => 'pax', 'Peaxi162Scf00104g00329' => 'pax', 'Peaxi162Scf00161g00137' => 'pax', 'PGR004G1665' => 'pgr', 'PGR031G2937' => 'pgr', 'PGR119G2145' => 'pgr', 'PGSC0003DMG400004351' => 'stu', 'PGSC0003DMG400014625' => 'stu', 'PGSC0003DMG401000943' => 'stu', 'Phvul.001G148600' => 'pvu', 'Phvul.004G001700' => 'pvu', 'Phvul.006G154900' => 'pvu', 'Phvul.008G078200' => 'pvu', 'Phvul.011G136500' => 'pvu', 'Potri.002G215600' => 'ptr', 'Potri.008G201600' => 'ptr', 'Potri.014G138400' => 'ptr', 'Potri.016G142500' => 'ptr', 'Pp3c16_10580' => 'ppa', 'Pp3c5_25280' => 'ppa', 'Prupe.1G150000' => 'ppe', 'Prupe.1G150100' => 'ppe', 'Prupe.6G299600' => 'ppe', 'Prupe.8G245000' => 'ppe', 'Psat0s4927g0040' => 'psa', 'Psat1g052080' => 'psa', 'Psat1g183800' => 'psa', 'Psat3g113840' => 'psa', 'Psat3g126120' => 'psa', 'Psat3g126160' => 'psa', 'Psat3g158760' => 'psa', 'Psat3g158840' => 'psa', 'PSO170G2858' => 'pso', 'PSO339G0606' => 'pso', 'PSO384G4709' => 'pso', 'PSO407G0334' => 'pso', 'QL04p040276' => 'qlo', 'QL06p005458' => 'qlo', 'QL06p005472' => 'qlo', 'QL07p030546' => 'qlo', 'QL07p031519' => 'qlo', 'QL09p050949' => 'qlo', 'QL09p050966' => 'qlo', 'QL09p051067' => 'qlo', 'QL12p022706' => 'qlo', 'RcHm_v2.0_Chr2g0119601' => 'rch', 'RcHm_v2.0_Chr3g0459591' => 'rch', 'RcHm_v2.0_Chr4g0418521' => 'rch', 'RcHm_v2.0_Chr4g0418531' => 'rch', 'RcHm_v2.0_Chr4g0418541' => 'rch', 'RcHm_v2.0_Chr6g0291641' => 'rch', 'Rhsim01G0086300' => 'rsi', 'Rhsim01G0276300' => 'rsi', 'Rhsim01G0276500' => 'rsi', 'Rhsim04G0207700' => 'rsi', 'Rhsim05G0234500' => 'rsi', 'Rhsim13G0022400' => 'rsi', 'Sabra02G0167900' => 'sbr', 'Sabra04G0158500' => 'sbr', 'Sabra08G0159800' => 'sbr', 'Sabra10G0011500' => 'sbr', 'Sabra14G0104400' => 'sbr', 'SalBow2G2440' => 'sbo', 'SalBow4G2265' => 'sbo', 'Sc02g0000060' => 'sci', 'Sc05g0005020' => 'sci', 'Sc13g0003890' => 'sci', 'Sed0014865' => 'sed', 'Sed0017224' => 'sed', 'Sed0026391' => 'sed', 'SEGI_00063' => 'sgi', 'SEGI_10967' => 'sgi', 'SEGI_17510' => 'sgi', 'SEGI_24396' => 'sgi', 'SEGI_39719' => 'sgi', 'SEGI_41392' => 'sgi', 'SGA_v2.0_scaffold11G05794' => 'sas', 'SGA_v2.0_scaffold142G35607' => 'sas', 'SGA_v2.0_scaffold1G00447' => 'sas', 'SHI15388' => 'shi', 'SHI15394' => 'shi', 'SHI15396' => 'shi', 'SHI15399' => 'shi', 'SMO343G0151' => 'smo', 'SMO367G1118' => 'smo', 'Solyc01g080200.3' => 'sly', 'Solyc06g008960.3' => 'sly', 'Solyc09g064780.3' => 'sly', 'Sopen01g031980' => 'spe', 'Sopen06g003710' => 'spe', 'Sopen09g026460' => 'spe', 'Sp3g21240' => 'spa', 'Sp4g30030' => 'spa', 'TAR365G0022' => 'tar', 'TAR365G1023' => 'tar', 'TAR365G1253' => 'tar', 'TAR623G0078' => 'tar', 'TAR623G1721' => 'tar', 'TAR633G0959' => 'tar', 'THA.LOC104802225' => 'tha', 'THA.LOC104804769' => 'tha', 'THA.LOC104808660' => 'tha', 'THA.LOC104812792' => 'tha', 'Thecc.01G284000' => 'tca', 'Thecc.04G220600' => 'tca', 'Thecc.05G268900' => 'tca', 'Thecc.08G171100' => 'tca', 'Thhalv10001284m.g' => 'esa', 'Thhalv10019912m.g' => 'esa', 'TPR.G14189' => 'tpr', 'TPR.G18110' => 'tpr', 'TPR.G18130' => 'tpr', 'TPR.G18131' => 'tpr', 'TPR.G18140' => 'tpr', 'TPR.G24282' => 'tpr', 'TPR.G25221' => 'tpr', 'TPR.G29267' => 'tpr', 'TPR.G35315' => 'tpr', 'TPR.G36173' => 'tpr', 'TWI09G0794' => 'twi', 'TWI59G1348' => 'twi', 'TWI74G0430' => 'twi', 'unitig_26.g8940' => 'ugi', 'unitig_749.g13744' => 'ugi', 'unitig_749.g13745' => 'ugi', 'vmacro08269' => 'vma', 'vmacro14937' => 'vma', 'vmacro20401' => 'vma', 'VMungo0464G1349' => 'vmu', 'VMungo0540G0289' => 'vmu', 'VMungo1215G1590' => 'vmu', 'VMungo1309G0221' => 'vmu', 'VMungo1309G2815' => 'vmu', 'VMungo1383G0239' => 'vmu', 'VMungo1383G2910' => 'vmu', 'Zm00001eb095270' => 'zma', 'Zm00001eb095280' => 'zma', 'Zm00001eb111630' => 'zma', 'Zm00001eb237080' => 'zma', 'Zm00001eb273740' => 'zma', 'Zm00001eb285040' => 'zma', 'Zm00001eb330790' => 'zma', 'Zm00001eb337380' => 'zma' ), 'gf_id' => 'HOM05D001484', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001484' ), 'data_identifier' => 'HOM05D001484', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001484', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p31500' => 'bna', 'A05p00020' => 'bna', 'A07p08820' => 'bna', 'Aa31LG4G3300' => 'aar', 'Aa31LG8G10030' => 'aar', 'Actinidia00731' => 'ach', 'Actinidia11473' => 'ach', 'Actinidia23469' => 'ach', 'Actinidia24318' => 'ach', 'Actinidia40196' => 'ach', 'Actinidia40197' => 'ach', 'Actinidia40198' => 'ach', 'Ah.08g212990' => 'amhyb', 'Ah.15g091720' => 'amhyb', 'AL3G38260' => 'aly', 'AL4G47710' => 'aly', 'Aqoxy2G00671' => 'aox', 'Aqoxy2G03236' => 'aox', 'arahy.Tifrunner.gnm1.ann1.05IDCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KR684' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATY3SJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK6QJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6APGL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IDT7Z9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM073U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ0R87' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LE7RV4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT4QRX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V5ENPK' => 'arhy', 'AT2G48110' => 'ath', 'AT3G23590' => 'ath', 'ATR0626G186' => 'atr', 'ATR1127G141' => 'atr', 'Atru.chr4.2583' => 'acertr', 'Atru.chr5.1358' => 'acertr', 'Atru.chr5.1359' => 'acertr', 'Atru.chr8.46' => 'acertr', 'AUR62002640' => 'cqu', 'AUR62030055' => 'cqu', 'AUR62033713' => 'cqu', 'AUR62033714' => 'cqu', 'AUR62036795' => 'cqu', 'AUR62039891' => 'cqu', 'BcaB02g08737' => 'bca', 'BcaB04g20441' => 'bca', 'BcaB06g26509' => 'bca', 'BcaB06g26510' => 'bca', 'BcaB06g26511' => 'bca', 'BcaB06g26512' => 'bca', 'BcaB06g26513' => 'bca', 'BcaC02g12564' => 'bca', 'BcaC02g12565' => 'bca', 'BcaC02g12794' => 'bca', 'BcaC02g12795' => 'bca', 'BcaC02g12796' => 'bca', 'BcaC06g35541' => 'bca', 'BNapus_Darmor_BZH_scaffold_188p00080' => 'bna', 'BNapus_Darmor_BZH_scaffold_188p00090' => 'bna', 'BolC1t03972H' => 'bol', 'BolC1t03973H' => 'bol', 'BolC4t21680H' => 'bol', 'BolC7t41863H' => 'bol', 'BolSC55t61227H' => 'bol', 'BolSC55t61228H' => 'bol', 'BraA01t03278Z' => 'bra', 'BraA05t18998Z' => 'bra', 'BraA07t28673Z' => 'bra', 'C01p40150' => 'bna', 'C05p12370' => 'bna', 'C07p13680' => 'bna', 'CAN.G1006.16' => 'can', 'CAN.G1006.17' => 'can', 'CAN.G1170.2' => 'can', 'CAN.G962.7' => 'can', 'CANSAT25G2179' => 'cansat', 'CANSAT78G1573' => 'cansat', 'CARHR099510' => 'chi', 'CARHR143510' => 'chi', 'Carub.0003s2380' => 'cru', 'Carub.0004s3082' => 'cru', 'Ca_00614_v3' => 'car', 'Ca_07801_v3' => 'car', 'Ca_08567_v3' => 'car', 'Ca_09571_v3' => 'car', 'CBR_g19290' => 'cbr', 'Cc01_g19770' => 'ccan', 'Cc03_g03030' => 'ccan', 'CDE07G0968' => 'cde', 'CDE09G1441' => 'cde', 'Cfa006103' => 'cfa', 'Cfa015573' => 'cfa', 'Cfa016988' => 'cfa', 'Ciclev10006738m.g' => 'ccl', 'Ciclev10010920m.g' => 'ccl', 'Ciclev10018517m.g' => 'ccl', 'CiPaw.01G159200' => 'cil', 'CiPaw.02G091000' => 'cil', 'CiPaw.02G091100' => 'cil', 'CiPaw.08G103100' => 'cil', 'CiPaw.09G224900' => 'cil', 'ClCG06G005740' => 'cla', 'ClCG07G000090' => 'cla', 'ClCG07G000100' => 'cla', 'COL.COLO4_09143' => 'col', 'COL.COLO4_25124' => 'col', 'Cpa.g.sc16.34' => 'cpa', 'Cpa.g.sc3504.1' => 'cpa', 'Cpa.g.sc60.37' => 'cpa', 'CsaV3_6G018520' => 'csa', 'CsaV3_6G036860' => 'csa', 'CSS0001072' => 'camsi', 'CSS0020208' => 'camsi', 'CSS0021253' => 'camsi', 'CSS0022190' => 'camsi', 'CSS0036150' => 'camsi', 'CSS0040442' => 'camsi', 'CSS0042300' => 'camsi', 'CSS0045298' => 'camsi', 'DCAR_012449' => 'dca', 'DCAR_018405' => 'dca', 'DCAR_024573' => 'dca', 'DCAR_030591' => 'dca', 'Dinv16926' => 'din', 'Dinv32963' => 'din', 'Dinv38382' => 'din', 'Dinv38383' => 'din', 'Duzib133G0974' => 'dzi', 'Duzib138G1867' => 'dzi', 'Duzib211G0420' => 'dzi', 'Duzib212G0930' => 'dzi', 'ECA234G1645' => 'eca', 'ECA247G3467' => 'eca', 'ECA248G1703' => 'eca', 'EL10Ac3g06327' => 'bvu', 'EL10Ac7g17204' => 'bvu', 'Eucgr.A00855' => 'egr', 'Eucgr.A00858' => 'egr', 'Eucgr.H01520' => 'egr', 'Eucgr.H03604' => 'egr', 'Eucgr.L03465' => 'egr', 'Eucgr.L03466' => 'egr', 'FAN01G0988' => 'fan', 'FAN02G3892' => 'fan', 'FAN05G3381' => 'fan', 'FAN07G0967' => 'fan', 'FAN07G1493' => 'fan', 'FAN08G3125' => 'fan', 'FAN09G0402' => 'fan', 'FAN12G2594' => 'fan', 'FAN12G3879' => 'fan', 'FAN14G1546' => 'fan', 'FAN15G3626' => 'fan', 'FAN17G0588' => 'fan', 'FAN17G0609' => 'fan', 'FAN18G2817' => 'fan', 'FAN19G1305' => 'fan', 'FAN20G1787' => 'fan', 'FAN22G0073' => 'fan', 'FAN22G0352' => 'fan', 'FAN22G0368' => 'fan', 'FAN22G2273' => 'fan', 'FAN24G1998' => 'fan', 'FAN27G1317' => 'fan', 'FvH4_2g23980' => 'fve', 'FvH4_4g14380' => 'fve', 'FvH4_4g14390' => 'fve', 'FvH4_6g09250' => 'fve', 'Glyma.03G151100' => 'gma', 'Glyma.04G122550' => 'gma', 'Glyma.05G001600' => 'gma', 'Glyma.09G270766' => 'gma', 'Glyma.09G270832' => 'gma', 'Glyma.13G209800' => 'gma', 'Glyma.15G102800' => 'gma', 'Glyma.18G218900' => 'gma', 'Glyma.19G001500' => 'gma', 'Glyma.19G153600' => 'gma', 'Gohir.A02G028600' => 'ghi', 'Gohir.A08G045000' => 'ghi', 'Gohir.A11G120500' => 'ghi', 'Gohir.A12G006200' => 'ghi', 'Gohir.A12G006250' => 'ghi', 'Gohir.D02G036300' => 'ghi', 'Gohir.D08G054700' => 'ghi', 'Gohir.D11G125600' => 'ghi', 'Gohir.D12G005700' => 'ghi', 'Gorai.004G055200' => 'gra', 'Gorai.005G040400' => 'gra', 'Gorai.007G134500' => 'gra', 'Gorai.008G005500' => 'gra', 'GSVIVG01011094001' => 'vvi', 'GSVIVG01017879001' => 'vvi', 'GSVIVG01025988001' => 'vvi', 'GSVIVG01029847001' => 'vvi', 'HanXRQChr10g0282901' => 'han', 'HanXRQChr10g0310371' => 'han', 'HanXRQChr10g0315041' => 'han', 'HanXRQChr11g0327651' => 'han', 'HanXRQChr12g0359391' => 'han', 'Haze_00972' => 'cav', 'Haze_00973' => 'cav', 'Haze_00974' => 'cav', 'Haze_04747' => 'cav', 'Haze_04749' => 'cav', 'Haze_04750' => 'cav', 'Haze_21217' => 'cav', 'Hma1.2p1_1037F.1_g250680' => 'hma', 'Hma1.2p1_1644F.1_g295320' => 'hma', 'HPP92_011322' => 'vpl', 'HPP92_011323' => 'vpl', 'HPP92_011324' => 'vpl', 'HPP92_011325' => 'vpl', 'HPP92_011326' => 'vpl', 'Hund12205' => 'sun', 'Hund17957' => 'sun', 'Lalb_Chr06g0176771' => 'lal', 'Lalb_Chr18g0056021' => 'lal', 'Lalb_Chr18g0056031' => 'lal', 'Lalb_Chr18g0056041' => 'lal', 'Lalb_Chr20g0107751' => 'lal', 'Lalb_Chr20g0118371' => 'lal', 'Lj1g0010239' => 'lja', 'Lj1g0017101' => 'lja', 'Lj2A1178G40' => 'lonja', 'Lj2A54G84' => 'lonja', 'Lj2g0015248' => 'lja', 'Lj3A761T51' => 'lonja', 'Lj6g0018116' => 'lja', 'Lsat_1_v5_gn_4_136040' => 'lsa', 'Lsat_1_v5_gn_5_187461' => 'lsa', 'Lsat_1_v5_gn_5_77001' => 'lsa', 'Lsat_1_v5_gn_9_4461' => 'lsa', 'Manes.01G210100' => 'mes', 'Manes.03G185600' => 'mes', 'Manes.05G073300' => 'mes', 'Manes.09G120300' => 'mes', 'Manes.15G022100' => 'mes', 'Mapoly0096s0053' => 'mpo', 'MBI03_g14058_MAGBIO' => 'mbi', 'MBI03_g33876_MAGBIO' => 'mbi', 'MBI03_g36854_MAGBIO' => 'mbi', 'MBI17_g11997_MAGBIO' => 'mbi', 'MD03G1269000' => 'mdo', 'MD04G1179600' => 'mdo', 'MD11G1289800' => 'mdo', 'MD12G1194700' => 'mdo', 'MD13G1182100' => 'mdo', 'MD13G1182200' => 'mdo', 'MD16G1182600' => 'mdo', 'Medtr2g021400' => 'mtr', 'Medtr2g021470' => 'mtr', 'Medtr2g105810' => 'mtr', 'Medtr3g033580' => 'mtr', 'Medtr6g007970' => 'mtr', 'Medtr7g056330' => 'mtr', 'Medtr7g074290' => 'mtr', 'Medtr7g074380' => 'mtr', 'Medtr7g094550' => 'mtr', 'Medtr8g069995' => 'mtr', 'MELO3C014345.2' => 'cme', 'MELO3C021395.2' => 'cme', 'Migut.D00262' => 'egut', 'Migut.G00257' => 'egut', 'MSTRG.21575' => 'ama', 'MSTRG.3985' => 'ama', 'Nitab4.5_0000295g0140' => 'nta', 'Nitab4.5_0000732g0140' => 'nta', 'Nitab4.5_0003162g0020' => 'nta', 'Nitab4.5_0006180g0090' => 'nta', 'Nitab4.5_0006390g0010' => 'nta', 'Nitab4.5_0007392g0040' => 'nta', 'Nn1g02140' => 'nnu', 'Nn4g26168' => 'nnu', 'Nn5g26754' => 'nnu', 'Oeu001433.1' => 'oeu', 'Oeu010299.2' => 'oeu', 'Oeu011171.1' => 'oeu', 'Oeu037675.1' => 'oeu', 'Oeu038359.1' => 'oeu', 'Oeu063834.1' => 'oeu', 'Oeu063835.1' => 'oeu', 'Os05g0312000' => 'osa', 'Os07g0211101' => 'osa', 'Os07g0211200' => 'osa', 'Os07g0681500' => 'osa', 'Peaxi162Scf00095g01015' => 'pax', 'Peaxi162Scf00104g00329' => 'pax', 'Peaxi162Scf00161g00137' => 'pax', 'PGR004G1665' => 'pgr', 'PGR031G2937' => 'pgr', 'PGR119G2145' => 'pgr', 'PGSC0003DMG400004351' => 'stu', 'PGSC0003DMG400014625' => 'stu', 'PGSC0003DMG401000943' => 'stu', 'Phvul.001G148600' => 'pvu', 'Phvul.004G001700' => 'pvu', 'Phvul.006G154900' => 'pvu', 'Phvul.008G078200' => 'pvu', 'Phvul.011G136500' => 'pvu', 'Potri.002G215600' => 'ptr', 'Potri.008G201600' => 'ptr', 'Potri.014G138400' => 'ptr', 'Potri.016G142500' => 'ptr', 'Pp3c16_10580' => 'ppa', 'Pp3c5_25280' => 'ppa', 'Prupe.1G150000' => 'ppe', 'Prupe.1G150100' => 'ppe', 'Prupe.6G299600' => 'ppe', 'Prupe.8G245000' => 'ppe', 'Psat0s4927g0040' => 'psa', 'Psat1g052080' => 'psa', 'Psat1g183800' => 'psa', 'Psat3g113840' => 'psa', 'Psat3g126120' => 'psa', 'Psat3g126160' => 'psa', 'Psat3g158760' => 'psa', 'Psat3g158840' => 'psa', 'PSO170G2858' => 'pso', 'PSO339G0606' => 'pso', 'PSO384G4709' => 'pso', 'PSO407G0334' => 'pso', 'QL04p040276' => 'qlo', 'QL06p005458' => 'qlo', 'QL06p005472' => 'qlo', 'QL07p030546' => 'qlo', 'QL07p031519' => 'qlo', 'QL09p050949' => 'qlo', 'QL09p050966' => 'qlo', 'QL09p051067' => 'qlo', 'QL12p022706' => 'qlo', 'RcHm_v2.0_Chr2g0119601' => 'rch', 'RcHm_v2.0_Chr3g0459591' => 'rch', 'RcHm_v2.0_Chr4g0418521' => 'rch', 'RcHm_v2.0_Chr4g0418531' => 'rch', 'RcHm_v2.0_Chr4g0418541' => 'rch', 'RcHm_v2.0_Chr6g0291641' => 'rch', 'Rhsim01G0086300' => 'rsi', 'Rhsim01G0276300' => 'rsi', 'Rhsim01G0276500' => 'rsi', 'Rhsim04G0207700' => 'rsi', 'Rhsim05G0234500' => 'rsi', 'Rhsim13G0022400' => 'rsi', 'Sabra02G0167900' => 'sbr', 'Sabra04G0158500' => 'sbr', 'Sabra08G0159800' => 'sbr', 'Sabra10G0011500' => 'sbr', 'Sabra14G0104400' => 'sbr', 'SalBow2G2440' => 'sbo', 'SalBow4G2265' => 'sbo', 'Sc02g0000060' => 'sci', 'Sc05g0005020' => 'sci', 'Sc13g0003890' => 'sci', 'Sed0014865' => 'sed', 'Sed0017224' => 'sed', 'Sed0026391' => 'sed', 'SEGI_00063' => 'sgi', 'SEGI_10967' => 'sgi', 'SEGI_17510' => 'sgi', 'SEGI_24396' => 'sgi', 'SEGI_39719' => 'sgi', 'SEGI_41392' => 'sgi', 'SGA_v2.0_scaffold11G05794' => 'sas', 'SGA_v2.0_scaffold142G35607' => 'sas', 'SGA_v2.0_scaffold1G00447' => 'sas', 'SHI15388' => 'shi', 'SHI15394' => 'shi', 'SHI15396' => 'shi', 'SHI15399' => 'shi', 'SMO343G0151' => 'smo', 'SMO367G1118' => 'smo', 'Solyc01g080200.3' => 'sly', 'Solyc06g008960.3' => 'sly', 'Solyc09g064780.3' => 'sly', 'Sopen01g031980' => 'spe', 'Sopen06g003710' => 'spe', 'Sopen09g026460' => 'spe', 'Sp3g21240' => 'spa', 'Sp4g30030' => 'spa', 'TAR365G0022' => 'tar', 'TAR365G1023' => 'tar', 'TAR365G1253' => 'tar', 'TAR623G0078' => 'tar', 'TAR623G1721' => 'tar', 'TAR633G0959' => 'tar', 'THA.LOC104802225' => 'tha', 'THA.LOC104804769' => 'tha', 'THA.LOC104808660' => 'tha', 'THA.LOC104812792' => 'tha', 'Thecc.01G284000' => 'tca', 'Thecc.04G220600' => 'tca', 'Thecc.05G268900' => 'tca', 'Thecc.08G171100' => 'tca', 'Thhalv10001284m.g' => 'esa', 'Thhalv10019912m.g' => 'esa', 'TPR.G14189' => 'tpr', 'TPR.G18110' => 'tpr', 'TPR.G18130' => 'tpr', 'TPR.G18131' => 'tpr', 'TPR.G18140' => 'tpr', 'TPR.G24282' => 'tpr', 'TPR.G25221' => 'tpr', 'TPR.G29267' => 'tpr', 'TPR.G35315' => 'tpr', 'TPR.G36173' => 'tpr', 'TWI09G0794' => 'twi', 'TWI59G1348' => 'twi', 'TWI74G0430' => 'twi', 'unitig_26.g8940' => 'ugi', 'unitig_749.g13744' => 'ugi', 'unitig_749.g13745' => 'ugi', 'vmacro08269' => 'vma', 'vmacro14937' => 'vma', 'vmacro20401' => 'vma', 'VMungo0464G1349' => 'vmu', 'VMungo0540G0289' => 'vmu', 'VMungo1215G1590' => 'vmu', 'VMungo1309G0221' => 'vmu', 'VMungo1309G2815' => 'vmu', 'VMungo1383G0239' => 'vmu', 'VMungo1383G2910' => 'vmu', 'Zm00001eb095270' => 'zma', 'Zm00001eb095280' => 'zma', 'Zm00001eb111630' => 'zma', 'Zm00001eb237080' => 'zma', 'Zm00001eb273740' => 'zma', 'Zm00001eb285040' => 'zma', 'Zm00001eb330790' => 'zma', 'Zm00001eb337380' => 'zma' ) $gf_id = 'HOM05D001484' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001484' ) $data_identifier = 'HOM05D001484' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 2, 'aly' => (int) 2, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 22, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 7, 'hma' => (int) 2, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 7, 'mtr' => (int) 10, 'cme' => (int) 2, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 4, 'ppa' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 4, 'qlo' => (int) 9, 'rch' => (int) 6, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 10, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 7, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb337380' $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' => 'HOM05D001484', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p31500' => 'bna', 'A05p00020' => 'bna', 'A07p08820' => 'bna', 'Aa31LG4G3300' => 'aar', 'Aa31LG8G10030' => 'aar', 'Actinidia00731' => 'ach', 'Actinidia11473' => 'ach', 'Actinidia23469' => 'ach', 'Actinidia24318' => 'ach', 'Actinidia40196' => 'ach', 'Actinidia40197' => 'ach', 'Actinidia40198' => 'ach', 'Ah.08g212990' => 'amhyb', 'Ah.15g091720' => 'amhyb', 'AL3G38260' => 'aly', 'AL4G47710' => 'aly', 'Aqoxy2G00671' => 'aox', 'Aqoxy2G03236' => 'aox', 'arahy.Tifrunner.gnm1.ann1.05IDCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KR684' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATY3SJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK6QJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6APGL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IDT7Z9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM073U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ0R87' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LE7RV4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT4QRX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V5ENPK' => 'arhy', 'AT2G48110' => 'ath', 'AT3G23590' => 'ath', 'ATR0626G186' => 'atr', 'ATR1127G141' => 'atr', 'Atru.chr4.2583' => 'acertr', 'Atru.chr5.1358' => 'acertr', 'Atru.chr5.1359' => 'acertr', 'Atru.chr8.46' => 'acertr', 'AUR62002640' => 'cqu', 'AUR62030055' => 'cqu', 'AUR62033713' => 'cqu', 'AUR62033714' => 'cqu', 'AUR62036795' => 'cqu', 'AUR62039891' => 'cqu', 'BcaB02g08737' => 'bca', 'BcaB04g20441' => 'bca', 'BcaB06g26509' => 'bca', 'BcaB06g26510' => 'bca', 'BcaB06g26511' => 'bca', 'BcaB06g26512' => 'bca', 'BcaB06g26513' => 'bca', 'BcaC02g12564' => 'bca', 'BcaC02g12565' => 'bca', 'BcaC02g12794' => 'bca', 'BcaC02g12795' => 'bca', 'BcaC02g12796' => 'bca', 'BcaC06g35541' => 'bca', 'BNapus_Darmor_BZH_scaffold_188p00080' => 'bna', 'BNapus_Darmor_BZH_scaffold_188p00090' => 'bna', 'BolC1t03972H' => 'bol', 'BolC1t03973H' => 'bol', 'BolC4t21680H' => 'bol', 'BolC7t41863H' => 'bol', 'BolSC55t61227H' => 'bol', 'BolSC55t61228H' => 'bol', 'BraA01t03278Z' => 'bra', 'BraA05t18998Z' => 'bra', 'BraA07t28673Z' => 'bra', 'C01p40150' => 'bna', 'C05p12370' => 'bna', 'C07p13680' => 'bna', 'CAN.G1006.16' => 'can', 'CAN.G1006.17' => 'can', 'CAN.G1170.2' => 'can', 'CAN.G962.7' => 'can', 'CANSAT25G2179' => 'cansat', 'CANSAT78G1573' => 'cansat', 'CARHR099510' => 'chi', 'CARHR143510' => 'chi', 'Carub.0003s2380' => 'cru', 'Carub.0004s3082' => 'cru', 'Ca_00614_v3' => 'car', 'Ca_07801_v3' => 'car', 'Ca_08567_v3' => 'car', 'Ca_09571_v3' => 'car', 'CBR_g19290' => 'cbr', 'Cc01_g19770' => 'ccan', 'Cc03_g03030' => 'ccan', 'CDE07G0968' => 'cde', 'CDE09G1441' => 'cde', 'Cfa006103' => 'cfa', 'Cfa015573' => 'cfa', 'Cfa016988' => 'cfa', 'Ciclev10006738m.g' => 'ccl', 'Ciclev10010920m.g' => 'ccl', 'Ciclev10018517m.g' => 'ccl', 'CiPaw.01G159200' => 'cil', 'CiPaw.02G091000' => 'cil', 'CiPaw.02G091100' => 'cil', 'CiPaw.08G103100' => 'cil', 'CiPaw.09G224900' => 'cil', 'ClCG06G005740' => 'cla', 'ClCG07G000090' => 'cla', 'ClCG07G000100' => 'cla', 'COL.COLO4_09143' => 'col', 'COL.COLO4_25124' => 'col', 'Cpa.g.sc16.34' => 'cpa', 'Cpa.g.sc3504.1' => 'cpa', 'Cpa.g.sc60.37' => 'cpa', 'CsaV3_6G018520' => 'csa', 'CsaV3_6G036860' => 'csa', 'CSS0001072' => 'camsi', 'CSS0020208' => 'camsi', 'CSS0021253' => 'camsi', 'CSS0022190' => 'camsi', 'CSS0036150' => 'camsi', 'CSS0040442' => 'camsi', 'CSS0042300' => 'camsi', 'CSS0045298' => 'camsi', 'DCAR_012449' => 'dca', 'DCAR_018405' => 'dca', 'DCAR_024573' => 'dca', 'DCAR_030591' => 'dca', 'Dinv16926' => 'din', 'Dinv32963' => 'din', 'Dinv38382' => 'din', 'Dinv38383' => 'din', 'Duzib133G0974' => 'dzi', 'Duzib138G1867' => 'dzi', 'Duzib211G0420' => 'dzi', 'Duzib212G0930' => 'dzi', 'ECA234G1645' => 'eca', 'ECA247G3467' => 'eca', 'ECA248G1703' => 'eca', 'EL10Ac3g06327' => 'bvu', 'EL10Ac7g17204' => 'bvu', 'Eucgr.A00855' => 'egr', 'Eucgr.A00858' => 'egr', 'Eucgr.H01520' => 'egr', 'Eucgr.H03604' => 'egr', 'Eucgr.L03465' => 'egr', 'Eucgr.L03466' => 'egr', 'FAN01G0988' => 'fan', 'FAN02G3892' => 'fan', 'FAN05G3381' => 'fan', 'FAN07G0967' => 'fan', 'FAN07G1493' => 'fan', 'FAN08G3125' => 'fan', 'FAN09G0402' => 'fan', 'FAN12G2594' => 'fan', 'FAN12G3879' => 'fan', 'FAN14G1546' => 'fan', 'FAN15G3626' => 'fan', 'FAN17G0588' => 'fan', 'FAN17G0609' => 'fan', 'FAN18G2817' => 'fan', 'FAN19G1305' => 'fan', 'FAN20G1787' => 'fan', 'FAN22G0073' => 'fan', 'FAN22G0352' => 'fan', 'FAN22G0368' => 'fan', 'FAN22G2273' => 'fan', 'FAN24G1998' => 'fan', 'FAN27G1317' => 'fan', 'FvH4_2g23980' => 'fve', 'FvH4_4g14380' => 'fve', 'FvH4_4g14390' => 'fve', 'FvH4_6g09250' => 'fve', 'Glyma.03G151100' => 'gma', 'Glyma.04G122550' => 'gma', 'Glyma.05G001600' => 'gma', 'Glyma.09G270766' => 'gma', 'Glyma.09G270832' => 'gma', 'Glyma.13G209800' => 'gma', 'Glyma.15G102800' => 'gma', 'Glyma.18G218900' => 'gma', 'Glyma.19G001500' => 'gma', 'Glyma.19G153600' => 'gma', 'Gohir.A02G028600' => 'ghi', 'Gohir.A08G045000' => 'ghi', 'Gohir.A11G120500' => 'ghi', 'Gohir.A12G006200' => 'ghi', 'Gohir.A12G006250' => 'ghi', 'Gohir.D02G036300' => 'ghi', 'Gohir.D08G054700' => 'ghi', 'Gohir.D11G125600' => 'ghi', 'Gohir.D12G005700' => 'ghi', 'Gorai.004G055200' => 'gra', 'Gorai.005G040400' => 'gra', 'Gorai.007G134500' => 'gra', 'Gorai.008G005500' => 'gra', 'GSVIVG01011094001' => 'vvi', 'GSVIVG01017879001' => 'vvi', 'GSVIVG01025988001' => 'vvi', 'GSVIVG01029847001' => 'vvi', 'HanXRQChr10g0282901' => 'han', 'HanXRQChr10g0310371' => 'han', 'HanXRQChr10g0315041' => 'han', 'HanXRQChr11g0327651' => 'han', 'HanXRQChr12g0359391' => 'han', 'Haze_00972' => 'cav', 'Haze_00973' => 'cav', 'Haze_00974' => 'cav', 'Haze_04747' => 'cav', 'Haze_04749' => 'cav', 'Haze_04750' => 'cav', 'Haze_21217' => 'cav', 'Hma1.2p1_1037F.1_g250680' => 'hma', 'Hma1.2p1_1644F.1_g295320' => 'hma', 'HPP92_011322' => 'vpl', 'HPP92_011323' => 'vpl', 'HPP92_011324' => 'vpl', 'HPP92_011325' => 'vpl', 'HPP92_011326' => 'vpl', 'Hund12205' => 'sun', 'Hund17957' => 'sun', 'Lalb_Chr06g0176771' => 'lal', 'Lalb_Chr18g0056021' => 'lal', 'Lalb_Chr18g0056031' => 'lal', 'Lalb_Chr18g0056041' => 'lal', 'Lalb_Chr20g0107751' => 'lal', 'Lalb_Chr20g0118371' => 'lal', 'Lj1g0010239' => 'lja', 'Lj1g0017101' => 'lja', 'Lj2A1178G40' => 'lonja', 'Lj2A54G84' => 'lonja', 'Lj2g0015248' => 'lja', 'Lj3A761T51' => 'lonja', 'Lj6g0018116' => 'lja', 'Lsat_1_v5_gn_4_136040' => 'lsa', 'Lsat_1_v5_gn_5_187461' => 'lsa', 'Lsat_1_v5_gn_5_77001' => 'lsa', 'Lsat_1_v5_gn_9_4461' => 'lsa', 'Manes.01G210100' => 'mes', 'Manes.03G185600' => 'mes', 'Manes.05G073300' => 'mes', 'Manes.09G120300' => 'mes', 'Manes.15G022100' => 'mes', 'Mapoly0096s0053' => 'mpo', 'MBI03_g14058_MAGBIO' => 'mbi', 'MBI03_g33876_MAGBIO' => 'mbi', 'MBI03_g36854_MAGBIO' => 'mbi', 'MBI17_g11997_MAGBIO' => 'mbi', 'MD03G1269000' => 'mdo', 'MD04G1179600' => 'mdo', 'MD11G1289800' => 'mdo', 'MD12G1194700' => 'mdo', 'MD13G1182100' => 'mdo', 'MD13G1182200' => 'mdo', 'MD16G1182600' => 'mdo', 'Medtr2g021400' => 'mtr', 'Medtr2g021470' => 'mtr', 'Medtr2g105810' => 'mtr', 'Medtr3g033580' => 'mtr', 'Medtr6g007970' => 'mtr', 'Medtr7g056330' => 'mtr', 'Medtr7g074290' => 'mtr', 'Medtr7g074380' => 'mtr', 'Medtr7g094550' => 'mtr', 'Medtr8g069995' => 'mtr', 'MELO3C014345.2' => 'cme', 'MELO3C021395.2' => 'cme', 'Migut.D00262' => 'egut', 'Migut.G00257' => 'egut', 'MSTRG.21575' => 'ama', 'MSTRG.3985' => 'ama', 'Nitab4.5_0000295g0140' => 'nta', 'Nitab4.5_0000732g0140' => 'nta', 'Nitab4.5_0003162g0020' => 'nta', 'Nitab4.5_0006180g0090' => 'nta', 'Nitab4.5_0006390g0010' => 'nta', 'Nitab4.5_0007392g0040' => 'nta', 'Nn1g02140' => 'nnu', 'Nn4g26168' => 'nnu', 'Nn5g26754' => 'nnu', 'Oeu001433.1' => 'oeu', 'Oeu010299.2' => 'oeu', 'Oeu011171.1' => 'oeu', 'Oeu037675.1' => 'oeu', 'Oeu038359.1' => 'oeu', 'Oeu063834.1' => 'oeu', 'Oeu063835.1' => 'oeu', 'Os05g0312000' => 'osa', 'Os07g0211101' => 'osa', 'Os07g0211200' => 'osa', 'Os07g0681500' => 'osa', 'Peaxi162Scf00095g01015' => 'pax', 'Peaxi162Scf00104g00329' => 'pax', 'Peaxi162Scf00161g00137' => 'pax', 'PGR004G1665' => 'pgr', 'PGR031G2937' => 'pgr', 'PGR119G2145' => 'pgr', 'PGSC0003DMG400004351' => 'stu', 'PGSC0003DMG400014625' => 'stu', 'PGSC0003DMG401000943' => 'stu', 'Phvul.001G148600' => 'pvu', 'Phvul.004G001700' => 'pvu', 'Phvul.006G154900' => 'pvu', 'Phvul.008G078200' => 'pvu', 'Phvul.011G136500' => 'pvu', 'Potri.002G215600' => 'ptr', 'Potri.008G201600' => 'ptr', 'Potri.014G138400' => 'ptr', 'Potri.016G142500' => 'ptr', 'Pp3c16_10580' => 'ppa', 'Pp3c5_25280' => 'ppa', 'Prupe.1G150000' => 'ppe', 'Prupe.1G150100' => 'ppe', 'Prupe.6G299600' => 'ppe', 'Prupe.8G245000' => 'ppe', 'Psat0s4927g0040' => 'psa', 'Psat1g052080' => 'psa', 'Psat1g183800' => 'psa', 'Psat3g113840' => 'psa', 'Psat3g126120' => 'psa', 'Psat3g126160' => 'psa', 'Psat3g158760' => 'psa', 'Psat3g158840' => 'psa', 'PSO170G2858' => 'pso', 'PSO339G0606' => 'pso', 'PSO384G4709' => 'pso', 'PSO407G0334' => 'pso', 'QL04p040276' => 'qlo', 'QL06p005458' => 'qlo', 'QL06p005472' => 'qlo', 'QL07p030546' => 'qlo', 'QL07p031519' => 'qlo', 'QL09p050949' => 'qlo', 'QL09p050966' => 'qlo', 'QL09p051067' => 'qlo', 'QL12p022706' => 'qlo', 'RcHm_v2.0_Chr2g0119601' => 'rch', 'RcHm_v2.0_Chr3g0459591' => 'rch', 'RcHm_v2.0_Chr4g0418521' => 'rch', 'RcHm_v2.0_Chr4g0418531' => 'rch', 'RcHm_v2.0_Chr4g0418541' => 'rch', 'RcHm_v2.0_Chr6g0291641' => 'rch', 'Rhsim01G0086300' => 'rsi', 'Rhsim01G0276300' => 'rsi', 'Rhsim01G0276500' => 'rsi', 'Rhsim04G0207700' => 'rsi', 'Rhsim05G0234500' => 'rsi', 'Rhsim13G0022400' => 'rsi', 'Sabra02G0167900' => 'sbr', 'Sabra04G0158500' => 'sbr', 'Sabra08G0159800' => 'sbr', 'Sabra10G0011500' => 'sbr', 'Sabra14G0104400' => 'sbr', 'SalBow2G2440' => 'sbo', 'SalBow4G2265' => 'sbo', 'Sc02g0000060' => 'sci', 'Sc05g0005020' => 'sci', 'Sc13g0003890' => 'sci', 'Sed0014865' => 'sed', 'Sed0017224' => 'sed', 'Sed0026391' => 'sed', 'SEGI_00063' => 'sgi', 'SEGI_10967' => 'sgi', 'SEGI_17510' => 'sgi', 'SEGI_24396' => 'sgi', 'SEGI_39719' => 'sgi', 'SEGI_41392' => 'sgi', 'SGA_v2.0_scaffold11G05794' => 'sas', 'SGA_v2.0_scaffold142G35607' => 'sas', 'SGA_v2.0_scaffold1G00447' => 'sas', 'SHI15388' => 'shi', 'SHI15394' => 'shi', 'SHI15396' => 'shi', 'SHI15399' => 'shi', 'SMO343G0151' => 'smo', 'SMO367G1118' => 'smo', 'Solyc01g080200.3' => 'sly', 'Solyc06g008960.3' => 'sly', 'Solyc09g064780.3' => 'sly', 'Sopen01g031980' => 'spe', 'Sopen06g003710' => 'spe', 'Sopen09g026460' => 'spe', 'Sp3g21240' => 'spa', 'Sp4g30030' => 'spa', 'TAR365G0022' => 'tar', 'TAR365G1023' => 'tar', 'TAR365G1253' => 'tar', 'TAR623G0078' => 'tar', 'TAR623G1721' => 'tar', 'TAR633G0959' => 'tar', 'THA.LOC104802225' => 'tha', 'THA.LOC104804769' => 'tha', 'THA.LOC104808660' => 'tha', 'THA.LOC104812792' => 'tha', 'Thecc.01G284000' => 'tca', 'Thecc.04G220600' => 'tca', 'Thecc.05G268900' => 'tca', 'Thecc.08G171100' => 'tca', 'Thhalv10001284m.g' => 'esa', 'Thhalv10019912m.g' => 'esa', 'TPR.G14189' => 'tpr', 'TPR.G18110' => 'tpr', 'TPR.G18130' => 'tpr', 'TPR.G18131' => 'tpr', 'TPR.G18140' => 'tpr', 'TPR.G24282' => 'tpr', 'TPR.G25221' => 'tpr', 'TPR.G29267' => 'tpr', 'TPR.G35315' => 'tpr', 'TPR.G36173' => 'tpr', 'TWI09G0794' => 'twi', 'TWI59G1348' => 'twi', 'TWI74G0430' => 'twi', 'unitig_26.g8940' => 'ugi', 'unitig_749.g13744' => 'ugi', 'unitig_749.g13745' => 'ugi', 'vmacro08269' => 'vma', 'vmacro14937' => 'vma', 'vmacro20401' => 'vma', 'VMungo0464G1349' => 'vmu', 'VMungo0540G0289' => 'vmu', 'VMungo1215G1590' => 'vmu', 'VMungo1309G0221' => 'vmu', 'VMungo1309G2815' => 'vmu', 'VMungo1383G0239' => 'vmu', 'VMungo1383G2910' => 'vmu', 'Zm00001eb095270' => 'zma', 'Zm00001eb095280' => 'zma', 'Zm00001eb111630' => 'zma', 'Zm00001eb237080' => 'zma', 'Zm00001eb273740' => 'zma', 'Zm00001eb285040' => 'zma', 'Zm00001eb330790' => 'zma', 'Zm00001eb337380' => 'zma' ), 'gf_id' => 'HOM05D001484', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001484' ), 'data_identifier' => 'HOM05D001484', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001484', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p31500' => 'bna', 'A05p00020' => 'bna', 'A07p08820' => 'bna', 'Aa31LG4G3300' => 'aar', 'Aa31LG8G10030' => 'aar', 'Actinidia00731' => 'ach', 'Actinidia11473' => 'ach', 'Actinidia23469' => 'ach', 'Actinidia24318' => 'ach', 'Actinidia40196' => 'ach', 'Actinidia40197' => 'ach', 'Actinidia40198' => 'ach', 'Ah.08g212990' => 'amhyb', 'Ah.15g091720' => 'amhyb', 'AL3G38260' => 'aly', 'AL4G47710' => 'aly', 'Aqoxy2G00671' => 'aox', 'Aqoxy2G03236' => 'aox', 'arahy.Tifrunner.gnm1.ann1.05IDCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KR684' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATY3SJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK6QJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6APGL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IDT7Z9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM073U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ0R87' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LE7RV4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT4QRX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V5ENPK' => 'arhy', 'AT2G48110' => 'ath', 'AT3G23590' => 'ath', 'ATR0626G186' => 'atr', 'ATR1127G141' => 'atr', 'Atru.chr4.2583' => 'acertr', 'Atru.chr5.1358' => 'acertr', 'Atru.chr5.1359' => 'acertr', 'Atru.chr8.46' => 'acertr', 'AUR62002640' => 'cqu', 'AUR62030055' => 'cqu', 'AUR62033713' => 'cqu', 'AUR62033714' => 'cqu', 'AUR62036795' => 'cqu', 'AUR62039891' => 'cqu', 'BcaB02g08737' => 'bca', 'BcaB04g20441' => 'bca', 'BcaB06g26509' => 'bca', 'BcaB06g26510' => 'bca', 'BcaB06g26511' => 'bca', 'BcaB06g26512' => 'bca', 'BcaB06g26513' => 'bca', 'BcaC02g12564' => 'bca', 'BcaC02g12565' => 'bca', 'BcaC02g12794' => 'bca', 'BcaC02g12795' => 'bca', 'BcaC02g12796' => 'bca', 'BcaC06g35541' => 'bca', 'BNapus_Darmor_BZH_scaffold_188p00080' => 'bna', 'BNapus_Darmor_BZH_scaffold_188p00090' => 'bna', 'BolC1t03972H' => 'bol', 'BolC1t03973H' => 'bol', 'BolC4t21680H' => 'bol', 'BolC7t41863H' => 'bol', 'BolSC55t61227H' => 'bol', 'BolSC55t61228H' => 'bol', 'BraA01t03278Z' => 'bra', 'BraA05t18998Z' => 'bra', 'BraA07t28673Z' => 'bra', 'C01p40150' => 'bna', 'C05p12370' => 'bna', 'C07p13680' => 'bna', 'CAN.G1006.16' => 'can', 'CAN.G1006.17' => 'can', 'CAN.G1170.2' => 'can', 'CAN.G962.7' => 'can', 'CANSAT25G2179' => 'cansat', 'CANSAT78G1573' => 'cansat', 'CARHR099510' => 'chi', 'CARHR143510' => 'chi', 'Carub.0003s2380' => 'cru', 'Carub.0004s3082' => 'cru', 'Ca_00614_v3' => 'car', 'Ca_07801_v3' => 'car', 'Ca_08567_v3' => 'car', 'Ca_09571_v3' => 'car', 'CBR_g19290' => 'cbr', 'Cc01_g19770' => 'ccan', 'Cc03_g03030' => 'ccan', 'CDE07G0968' => 'cde', 'CDE09G1441' => 'cde', 'Cfa006103' => 'cfa', 'Cfa015573' => 'cfa', 'Cfa016988' => 'cfa', 'Ciclev10006738m.g' => 'ccl', 'Ciclev10010920m.g' => 'ccl', 'Ciclev10018517m.g' => 'ccl', 'CiPaw.01G159200' => 'cil', 'CiPaw.02G091000' => 'cil', 'CiPaw.02G091100' => 'cil', 'CiPaw.08G103100' => 'cil', 'CiPaw.09G224900' => 'cil', 'ClCG06G005740' => 'cla', 'ClCG07G000090' => 'cla', 'ClCG07G000100' => 'cla', 'COL.COLO4_09143' => 'col', 'COL.COLO4_25124' => 'col', 'Cpa.g.sc16.34' => 'cpa', 'Cpa.g.sc3504.1' => 'cpa', 'Cpa.g.sc60.37' => 'cpa', 'CsaV3_6G018520' => 'csa', 'CsaV3_6G036860' => 'csa', 'CSS0001072' => 'camsi', 'CSS0020208' => 'camsi', 'CSS0021253' => 'camsi', 'CSS0022190' => 'camsi', 'CSS0036150' => 'camsi', 'CSS0040442' => 'camsi', 'CSS0042300' => 'camsi', 'CSS0045298' => 'camsi', 'DCAR_012449' => 'dca', 'DCAR_018405' => 'dca', 'DCAR_024573' => 'dca', 'DCAR_030591' => 'dca', 'Dinv16926' => 'din', 'Dinv32963' => 'din', 'Dinv38382' => 'din', 'Dinv38383' => 'din', 'Duzib133G0974' => 'dzi', 'Duzib138G1867' => 'dzi', 'Duzib211G0420' => 'dzi', 'Duzib212G0930' => 'dzi', 'ECA234G1645' => 'eca', 'ECA247G3467' => 'eca', 'ECA248G1703' => 'eca', 'EL10Ac3g06327' => 'bvu', 'EL10Ac7g17204' => 'bvu', 'Eucgr.A00855' => 'egr', 'Eucgr.A00858' => 'egr', 'Eucgr.H01520' => 'egr', 'Eucgr.H03604' => 'egr', 'Eucgr.L03465' => 'egr', 'Eucgr.L03466' => 'egr', 'FAN01G0988' => 'fan', 'FAN02G3892' => 'fan', 'FAN05G3381' => 'fan', 'FAN07G0967' => 'fan', 'FAN07G1493' => 'fan', 'FAN08G3125' => 'fan', 'FAN09G0402' => 'fan', 'FAN12G2594' => 'fan', 'FAN12G3879' => 'fan', 'FAN14G1546' => 'fan', 'FAN15G3626' => 'fan', 'FAN17G0588' => 'fan', 'FAN17G0609' => 'fan', 'FAN18G2817' => 'fan', 'FAN19G1305' => 'fan', 'FAN20G1787' => 'fan', 'FAN22G0073' => 'fan', 'FAN22G0352' => 'fan', 'FAN22G0368' => 'fan', 'FAN22G2273' => 'fan', 'FAN24G1998' => 'fan', 'FAN27G1317' => 'fan', 'FvH4_2g23980' => 'fve', 'FvH4_4g14380' => 'fve', 'FvH4_4g14390' => 'fve', 'FvH4_6g09250' => 'fve', 'Glyma.03G151100' => 'gma', 'Glyma.04G122550' => 'gma', 'Glyma.05G001600' => 'gma', 'Glyma.09G270766' => 'gma', 'Glyma.09G270832' => 'gma', 'Glyma.13G209800' => 'gma', 'Glyma.15G102800' => 'gma', 'Glyma.18G218900' => 'gma', 'Glyma.19G001500' => 'gma', 'Glyma.19G153600' => 'gma', 'Gohir.A02G028600' => 'ghi', 'Gohir.A08G045000' => 'ghi', 'Gohir.A11G120500' => 'ghi', 'Gohir.A12G006200' => 'ghi', 'Gohir.A12G006250' => 'ghi', 'Gohir.D02G036300' => 'ghi', 'Gohir.D08G054700' => 'ghi', 'Gohir.D11G125600' => 'ghi', 'Gohir.D12G005700' => 'ghi', 'Gorai.004G055200' => 'gra', 'Gorai.005G040400' => 'gra', 'Gorai.007G134500' => 'gra', 'Gorai.008G005500' => 'gra', 'GSVIVG01011094001' => 'vvi', 'GSVIVG01017879001' => 'vvi', 'GSVIVG01025988001' => 'vvi', 'GSVIVG01029847001' => 'vvi', 'HanXRQChr10g0282901' => 'han', 'HanXRQChr10g0310371' => 'han', 'HanXRQChr10g0315041' => 'han', 'HanXRQChr11g0327651' => 'han', 'HanXRQChr12g0359391' => 'han', 'Haze_00972' => 'cav', 'Haze_00973' => 'cav', 'Haze_00974' => 'cav', 'Haze_04747' => 'cav', 'Haze_04749' => 'cav', 'Haze_04750' => 'cav', 'Haze_21217' => 'cav', 'Hma1.2p1_1037F.1_g250680' => 'hma', 'Hma1.2p1_1644F.1_g295320' => 'hma', 'HPP92_011322' => 'vpl', 'HPP92_011323' => 'vpl', 'HPP92_011324' => 'vpl', 'HPP92_011325' => 'vpl', 'HPP92_011326' => 'vpl', 'Hund12205' => 'sun', 'Hund17957' => 'sun', 'Lalb_Chr06g0176771' => 'lal', 'Lalb_Chr18g0056021' => 'lal', 'Lalb_Chr18g0056031' => 'lal', 'Lalb_Chr18g0056041' => 'lal', 'Lalb_Chr20g0107751' => 'lal', 'Lalb_Chr20g0118371' => 'lal', 'Lj1g0010239' => 'lja', 'Lj1g0017101' => 'lja', 'Lj2A1178G40' => 'lonja', 'Lj2A54G84' => 'lonja', 'Lj2g0015248' => 'lja', 'Lj3A761T51' => 'lonja', 'Lj6g0018116' => 'lja', 'Lsat_1_v5_gn_4_136040' => 'lsa', 'Lsat_1_v5_gn_5_187461' => 'lsa', 'Lsat_1_v5_gn_5_77001' => 'lsa', 'Lsat_1_v5_gn_9_4461' => 'lsa', 'Manes.01G210100' => 'mes', 'Manes.03G185600' => 'mes', 'Manes.05G073300' => 'mes', 'Manes.09G120300' => 'mes', 'Manes.15G022100' => 'mes', 'Mapoly0096s0053' => 'mpo', 'MBI03_g14058_MAGBIO' => 'mbi', 'MBI03_g33876_MAGBIO' => 'mbi', 'MBI03_g36854_MAGBIO' => 'mbi', 'MBI17_g11997_MAGBIO' => 'mbi', 'MD03G1269000' => 'mdo', 'MD04G1179600' => 'mdo', 'MD11G1289800' => 'mdo', 'MD12G1194700' => 'mdo', 'MD13G1182100' => 'mdo', 'MD13G1182200' => 'mdo', 'MD16G1182600' => 'mdo', 'Medtr2g021400' => 'mtr', 'Medtr2g021470' => 'mtr', 'Medtr2g105810' => 'mtr', 'Medtr3g033580' => 'mtr', 'Medtr6g007970' => 'mtr', 'Medtr7g056330' => 'mtr', 'Medtr7g074290' => 'mtr', 'Medtr7g074380' => 'mtr', 'Medtr7g094550' => 'mtr', 'Medtr8g069995' => 'mtr', 'MELO3C014345.2' => 'cme', 'MELO3C021395.2' => 'cme', 'Migut.D00262' => 'egut', 'Migut.G00257' => 'egut', 'MSTRG.21575' => 'ama', 'MSTRG.3985' => 'ama', 'Nitab4.5_0000295g0140' => 'nta', 'Nitab4.5_0000732g0140' => 'nta', 'Nitab4.5_0003162g0020' => 'nta', 'Nitab4.5_0006180g0090' => 'nta', 'Nitab4.5_0006390g0010' => 'nta', 'Nitab4.5_0007392g0040' => 'nta', 'Nn1g02140' => 'nnu', 'Nn4g26168' => 'nnu', 'Nn5g26754' => 'nnu', 'Oeu001433.1' => 'oeu', 'Oeu010299.2' => 'oeu', 'Oeu011171.1' => 'oeu', 'Oeu037675.1' => 'oeu', 'Oeu038359.1' => 'oeu', 'Oeu063834.1' => 'oeu', 'Oeu063835.1' => 'oeu', 'Os05g0312000' => 'osa', 'Os07g0211101' => 'osa', 'Os07g0211200' => 'osa', 'Os07g0681500' => 'osa', 'Peaxi162Scf00095g01015' => 'pax', 'Peaxi162Scf00104g00329' => 'pax', 'Peaxi162Scf00161g00137' => 'pax', 'PGR004G1665' => 'pgr', 'PGR031G2937' => 'pgr', 'PGR119G2145' => 'pgr', 'PGSC0003DMG400004351' => 'stu', 'PGSC0003DMG400014625' => 'stu', 'PGSC0003DMG401000943' => 'stu', 'Phvul.001G148600' => 'pvu', 'Phvul.004G001700' => 'pvu', 'Phvul.006G154900' => 'pvu', 'Phvul.008G078200' => 'pvu', 'Phvul.011G136500' => 'pvu', 'Potri.002G215600' => 'ptr', 'Potri.008G201600' => 'ptr', 'Potri.014G138400' => 'ptr', 'Potri.016G142500' => 'ptr', 'Pp3c16_10580' => 'ppa', 'Pp3c5_25280' => 'ppa', 'Prupe.1G150000' => 'ppe', 'Prupe.1G150100' => 'ppe', 'Prupe.6G299600' => 'ppe', 'Prupe.8G245000' => 'ppe', 'Psat0s4927g0040' => 'psa', 'Psat1g052080' => 'psa', 'Psat1g183800' => 'psa', 'Psat3g113840' => 'psa', 'Psat3g126120' => 'psa', 'Psat3g126160' => 'psa', 'Psat3g158760' => 'psa', 'Psat3g158840' => 'psa', 'PSO170G2858' => 'pso', 'PSO339G0606' => 'pso', 'PSO384G4709' => 'pso', 'PSO407G0334' => 'pso', 'QL04p040276' => 'qlo', 'QL06p005458' => 'qlo', 'QL06p005472' => 'qlo', 'QL07p030546' => 'qlo', 'QL07p031519' => 'qlo', 'QL09p050949' => 'qlo', 'QL09p050966' => 'qlo', 'QL09p051067' => 'qlo', 'QL12p022706' => 'qlo', 'RcHm_v2.0_Chr2g0119601' => 'rch', 'RcHm_v2.0_Chr3g0459591' => 'rch', 'RcHm_v2.0_Chr4g0418521' => 'rch', 'RcHm_v2.0_Chr4g0418531' => 'rch', 'RcHm_v2.0_Chr4g0418541' => 'rch', 'RcHm_v2.0_Chr6g0291641' => 'rch', 'Rhsim01G0086300' => 'rsi', 'Rhsim01G0276300' => 'rsi', 'Rhsim01G0276500' => 'rsi', 'Rhsim04G0207700' => 'rsi', 'Rhsim05G0234500' => 'rsi', 'Rhsim13G0022400' => 'rsi', 'Sabra02G0167900' => 'sbr', 'Sabra04G0158500' => 'sbr', 'Sabra08G0159800' => 'sbr', 'Sabra10G0011500' => 'sbr', 'Sabra14G0104400' => 'sbr', 'SalBow2G2440' => 'sbo', 'SalBow4G2265' => 'sbo', 'Sc02g0000060' => 'sci', 'Sc05g0005020' => 'sci', 'Sc13g0003890' => 'sci', 'Sed0014865' => 'sed', 'Sed0017224' => 'sed', 'Sed0026391' => 'sed', 'SEGI_00063' => 'sgi', 'SEGI_10967' => 'sgi', 'SEGI_17510' => 'sgi', 'SEGI_24396' => 'sgi', 'SEGI_39719' => 'sgi', 'SEGI_41392' => 'sgi', 'SGA_v2.0_scaffold11G05794' => 'sas', 'SGA_v2.0_scaffold142G35607' => 'sas', 'SGA_v2.0_scaffold1G00447' => 'sas', 'SHI15388' => 'shi', 'SHI15394' => 'shi', 'SHI15396' => 'shi', 'SHI15399' => 'shi', 'SMO343G0151' => 'smo', 'SMO367G1118' => 'smo', 'Solyc01g080200.3' => 'sly', 'Solyc06g008960.3' => 'sly', 'Solyc09g064780.3' => 'sly', 'Sopen01g031980' => 'spe', 'Sopen06g003710' => 'spe', 'Sopen09g026460' => 'spe', 'Sp3g21240' => 'spa', 'Sp4g30030' => 'spa', 'TAR365G0022' => 'tar', 'TAR365G1023' => 'tar', 'TAR365G1253' => 'tar', 'TAR623G0078' => 'tar', 'TAR623G1721' => 'tar', 'TAR633G0959' => 'tar', 'THA.LOC104802225' => 'tha', 'THA.LOC104804769' => 'tha', 'THA.LOC104808660' => 'tha', 'THA.LOC104812792' => 'tha', 'Thecc.01G284000' => 'tca', 'Thecc.04G220600' => 'tca', 'Thecc.05G268900' => 'tca', 'Thecc.08G171100' => 'tca', 'Thhalv10001284m.g' => 'esa', 'Thhalv10019912m.g' => 'esa', 'TPR.G14189' => 'tpr', 'TPR.G18110' => 'tpr', 'TPR.G18130' => 'tpr', 'TPR.G18131' => 'tpr', 'TPR.G18140' => 'tpr', 'TPR.G24282' => 'tpr', 'TPR.G25221' => 'tpr', 'TPR.G29267' => 'tpr', 'TPR.G35315' => 'tpr', 'TPR.G36173' => 'tpr', 'TWI09G0794' => 'twi', 'TWI59G1348' => 'twi', 'TWI74G0430' => 'twi', 'unitig_26.g8940' => 'ugi', 'unitig_749.g13744' => 'ugi', 'unitig_749.g13745' => 'ugi', 'vmacro08269' => 'vma', 'vmacro14937' => 'vma', 'vmacro20401' => 'vma', 'VMungo0464G1349' => 'vmu', 'VMungo0540G0289' => 'vmu', 'VMungo1215G1590' => 'vmu', 'VMungo1309G0221' => 'vmu', 'VMungo1309G2815' => 'vmu', 'VMungo1383G0239' => 'vmu', 'VMungo1383G2910' => 'vmu', 'Zm00001eb095270' => 'zma', 'Zm00001eb095280' => 'zma', 'Zm00001eb111630' => 'zma', 'Zm00001eb237080' => 'zma', 'Zm00001eb273740' => 'zma', 'Zm00001eb285040' => 'zma', 'Zm00001eb330790' => 'zma', 'Zm00001eb337380' => 'zma' ) $gf_id = 'HOM05D001484' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001484' ) $data_identifier = 'HOM05D001484' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 2, 'aly' => (int) 2, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 22, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 7, 'hma' => (int) 2, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 7, 'mtr' => (int) 10, 'cme' => (int) 2, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 4, 'ppa' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 4, 'qlo' => (int) 9, 'rch' => (int) 6, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 10, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 7, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb337380' $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' => 'HOM05D001484', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p31500' => 'bna', 'A05p00020' => 'bna', 'A07p08820' => 'bna', 'Aa31LG4G3300' => 'aar', 'Aa31LG8G10030' => 'aar', 'Actinidia00731' => 'ach', 'Actinidia11473' => 'ach', 'Actinidia23469' => 'ach', 'Actinidia24318' => 'ach', 'Actinidia40196' => 'ach', 'Actinidia40197' => 'ach', 'Actinidia40198' => 'ach', 'Ah.08g212990' => 'amhyb', 'Ah.15g091720' => 'amhyb', 'AL3G38260' => 'aly', 'AL4G47710' => 'aly', 'Aqoxy2G00671' => 'aox', 'Aqoxy2G03236' => 'aox', 'arahy.Tifrunner.gnm1.ann1.05IDCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KR684' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATY3SJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK6QJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6APGL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IDT7Z9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM073U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ0R87' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LE7RV4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT4QRX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V5ENPK' => 'arhy', 'AT2G48110' => 'ath', 'AT3G23590' => 'ath', 'ATR0626G186' => 'atr', 'ATR1127G141' => 'atr', 'Atru.chr4.2583' => 'acertr', 'Atru.chr5.1358' => 'acertr', 'Atru.chr5.1359' => 'acertr', 'Atru.chr8.46' => 'acertr', 'AUR62002640' => 'cqu', 'AUR62030055' => 'cqu', 'AUR62033713' => 'cqu', 'AUR62033714' => 'cqu', 'AUR62036795' => 'cqu', 'AUR62039891' => 'cqu', 'BcaB02g08737' => 'bca', 'BcaB04g20441' => 'bca', 'BcaB06g26509' => 'bca', 'BcaB06g26510' => 'bca', 'BcaB06g26511' => 'bca', 'BcaB06g26512' => 'bca', 'BcaB06g26513' => 'bca', 'BcaC02g12564' => 'bca', 'BcaC02g12565' => 'bca', 'BcaC02g12794' => 'bca', 'BcaC02g12795' => 'bca', 'BcaC02g12796' => 'bca', 'BcaC06g35541' => 'bca', 'BNapus_Darmor_BZH_scaffold_188p00080' => 'bna', 'BNapus_Darmor_BZH_scaffold_188p00090' => 'bna', 'BolC1t03972H' => 'bol', 'BolC1t03973H' => 'bol', 'BolC4t21680H' => 'bol', 'BolC7t41863H' => 'bol', 'BolSC55t61227H' => 'bol', 'BolSC55t61228H' => 'bol', 'BraA01t03278Z' => 'bra', 'BraA05t18998Z' => 'bra', 'BraA07t28673Z' => 'bra', 'C01p40150' => 'bna', 'C05p12370' => 'bna', 'C07p13680' => 'bna', 'CAN.G1006.16' => 'can', 'CAN.G1006.17' => 'can', 'CAN.G1170.2' => 'can', 'CAN.G962.7' => 'can', 'CANSAT25G2179' => 'cansat', 'CANSAT78G1573' => 'cansat', 'CARHR099510' => 'chi', 'CARHR143510' => 'chi', 'Carub.0003s2380' => 'cru', 'Carub.0004s3082' => 'cru', 'Ca_00614_v3' => 'car', 'Ca_07801_v3' => 'car', 'Ca_08567_v3' => 'car', 'Ca_09571_v3' => 'car', 'CBR_g19290' => 'cbr', 'Cc01_g19770' => 'ccan', 'Cc03_g03030' => 'ccan', 'CDE07G0968' => 'cde', 'CDE09G1441' => 'cde', 'Cfa006103' => 'cfa', 'Cfa015573' => 'cfa', 'Cfa016988' => 'cfa', 'Ciclev10006738m.g' => 'ccl', 'Ciclev10010920m.g' => 'ccl', 'Ciclev10018517m.g' => 'ccl', 'CiPaw.01G159200' => 'cil', 'CiPaw.02G091000' => 'cil', 'CiPaw.02G091100' => 'cil', 'CiPaw.08G103100' => 'cil', 'CiPaw.09G224900' => 'cil', 'ClCG06G005740' => 'cla', 'ClCG07G000090' => 'cla', 'ClCG07G000100' => 'cla', 'COL.COLO4_09143' => 'col', 'COL.COLO4_25124' => 'col', 'Cpa.g.sc16.34' => 'cpa', 'Cpa.g.sc3504.1' => 'cpa', 'Cpa.g.sc60.37' => 'cpa', 'CsaV3_6G018520' => 'csa', 'CsaV3_6G036860' => 'csa', 'CSS0001072' => 'camsi', 'CSS0020208' => 'camsi', 'CSS0021253' => 'camsi', 'CSS0022190' => 'camsi', 'CSS0036150' => 'camsi', 'CSS0040442' => 'camsi', 'CSS0042300' => 'camsi', 'CSS0045298' => 'camsi', 'DCAR_012449' => 'dca', 'DCAR_018405' => 'dca', 'DCAR_024573' => 'dca', 'DCAR_030591' => 'dca', 'Dinv16926' => 'din', 'Dinv32963' => 'din', 'Dinv38382' => 'din', 'Dinv38383' => 'din', 'Duzib133G0974' => 'dzi', 'Duzib138G1867' => 'dzi', 'Duzib211G0420' => 'dzi', 'Duzib212G0930' => 'dzi', 'ECA234G1645' => 'eca', 'ECA247G3467' => 'eca', 'ECA248G1703' => 'eca', 'EL10Ac3g06327' => 'bvu', 'EL10Ac7g17204' => 'bvu', 'Eucgr.A00855' => 'egr', 'Eucgr.A00858' => 'egr', 'Eucgr.H01520' => 'egr', 'Eucgr.H03604' => 'egr', 'Eucgr.L03465' => 'egr', 'Eucgr.L03466' => 'egr', 'FAN01G0988' => 'fan', 'FAN02G3892' => 'fan', 'FAN05G3381' => 'fan', 'FAN07G0967' => 'fan', 'FAN07G1493' => 'fan', 'FAN08G3125' => 'fan', 'FAN09G0402' => 'fan', 'FAN12G2594' => 'fan', 'FAN12G3879' => 'fan', 'FAN14G1546' => 'fan', 'FAN15G3626' => 'fan', 'FAN17G0588' => 'fan', 'FAN17G0609' => 'fan', 'FAN18G2817' => 'fan', 'FAN19G1305' => 'fan', 'FAN20G1787' => 'fan', 'FAN22G0073' => 'fan', 'FAN22G0352' => 'fan', 'FAN22G0368' => 'fan', 'FAN22G2273' => 'fan', 'FAN24G1998' => 'fan', 'FAN27G1317' => 'fan', 'FvH4_2g23980' => 'fve', 'FvH4_4g14380' => 'fve', 'FvH4_4g14390' => 'fve', 'FvH4_6g09250' => 'fve', 'Glyma.03G151100' => 'gma', 'Glyma.04G122550' => 'gma', 'Glyma.05G001600' => 'gma', 'Glyma.09G270766' => 'gma', 'Glyma.09G270832' => 'gma', 'Glyma.13G209800' => 'gma', 'Glyma.15G102800' => 'gma', 'Glyma.18G218900' => 'gma', 'Glyma.19G001500' => 'gma', 'Glyma.19G153600' => 'gma', 'Gohir.A02G028600' => 'ghi', 'Gohir.A08G045000' => 'ghi', 'Gohir.A11G120500' => 'ghi', 'Gohir.A12G006200' => 'ghi', 'Gohir.A12G006250' => 'ghi', 'Gohir.D02G036300' => 'ghi', 'Gohir.D08G054700' => 'ghi', 'Gohir.D11G125600' => 'ghi', 'Gohir.D12G005700' => 'ghi', 'Gorai.004G055200' => 'gra', 'Gorai.005G040400' => 'gra', 'Gorai.007G134500' => 'gra', 'Gorai.008G005500' => 'gra', 'GSVIVG01011094001' => 'vvi', 'GSVIVG01017879001' => 'vvi', 'GSVIVG01025988001' => 'vvi', 'GSVIVG01029847001' => 'vvi', 'HanXRQChr10g0282901' => 'han', 'HanXRQChr10g0310371' => 'han', 'HanXRQChr10g0315041' => 'han', 'HanXRQChr11g0327651' => 'han', 'HanXRQChr12g0359391' => 'han', 'Haze_00972' => 'cav', 'Haze_00973' => 'cav', 'Haze_00974' => 'cav', 'Haze_04747' => 'cav', 'Haze_04749' => 'cav', 'Haze_04750' => 'cav', 'Haze_21217' => 'cav', 'Hma1.2p1_1037F.1_g250680' => 'hma', 'Hma1.2p1_1644F.1_g295320' => 'hma', 'HPP92_011322' => 'vpl', 'HPP92_011323' => 'vpl', 'HPP92_011324' => 'vpl', 'HPP92_011325' => 'vpl', 'HPP92_011326' => 'vpl', 'Hund12205' => 'sun', 'Hund17957' => 'sun', 'Lalb_Chr06g0176771' => 'lal', 'Lalb_Chr18g0056021' => 'lal', 'Lalb_Chr18g0056031' => 'lal', 'Lalb_Chr18g0056041' => 'lal', 'Lalb_Chr20g0107751' => 'lal', 'Lalb_Chr20g0118371' => 'lal', 'Lj1g0010239' => 'lja', 'Lj1g0017101' => 'lja', 'Lj2A1178G40' => 'lonja', 'Lj2A54G84' => 'lonja', 'Lj2g0015248' => 'lja', 'Lj3A761T51' => 'lonja', 'Lj6g0018116' => 'lja', 'Lsat_1_v5_gn_4_136040' => 'lsa', 'Lsat_1_v5_gn_5_187461' => 'lsa', 'Lsat_1_v5_gn_5_77001' => 'lsa', 'Lsat_1_v5_gn_9_4461' => 'lsa', 'Manes.01G210100' => 'mes', 'Manes.03G185600' => 'mes', 'Manes.05G073300' => 'mes', 'Manes.09G120300' => 'mes', 'Manes.15G022100' => 'mes', 'Mapoly0096s0053' => 'mpo', 'MBI03_g14058_MAGBIO' => 'mbi', 'MBI03_g33876_MAGBIO' => 'mbi', 'MBI03_g36854_MAGBIO' => 'mbi', 'MBI17_g11997_MAGBIO' => 'mbi', 'MD03G1269000' => 'mdo', 'MD04G1179600' => 'mdo', 'MD11G1289800' => 'mdo', 'MD12G1194700' => 'mdo', 'MD13G1182100' => 'mdo', 'MD13G1182200' => 'mdo', 'MD16G1182600' => 'mdo', 'Medtr2g021400' => 'mtr', 'Medtr2g021470' => 'mtr', 'Medtr2g105810' => 'mtr', 'Medtr3g033580' => 'mtr', 'Medtr6g007970' => 'mtr', 'Medtr7g056330' => 'mtr', 'Medtr7g074290' => 'mtr', 'Medtr7g074380' => 'mtr', 'Medtr7g094550' => 'mtr', 'Medtr8g069995' => 'mtr', 'MELO3C014345.2' => 'cme', 'MELO3C021395.2' => 'cme', 'Migut.D00262' => 'egut', 'Migut.G00257' => 'egut', 'MSTRG.21575' => 'ama', 'MSTRG.3985' => 'ama', 'Nitab4.5_0000295g0140' => 'nta', 'Nitab4.5_0000732g0140' => 'nta', 'Nitab4.5_0003162g0020' => 'nta', 'Nitab4.5_0006180g0090' => 'nta', 'Nitab4.5_0006390g0010' => 'nta', 'Nitab4.5_0007392g0040' => 'nta', 'Nn1g02140' => 'nnu', 'Nn4g26168' => 'nnu', 'Nn5g26754' => 'nnu', 'Oeu001433.1' => 'oeu', 'Oeu010299.2' => 'oeu', 'Oeu011171.1' => 'oeu', 'Oeu037675.1' => 'oeu', 'Oeu038359.1' => 'oeu', 'Oeu063834.1' => 'oeu', 'Oeu063835.1' => 'oeu', 'Os05g0312000' => 'osa', 'Os07g0211101' => 'osa', 'Os07g0211200' => 'osa', 'Os07g0681500' => 'osa', 'Peaxi162Scf00095g01015' => 'pax', 'Peaxi162Scf00104g00329' => 'pax', 'Peaxi162Scf00161g00137' => 'pax', 'PGR004G1665' => 'pgr', 'PGR031G2937' => 'pgr', 'PGR119G2145' => 'pgr', 'PGSC0003DMG400004351' => 'stu', 'PGSC0003DMG400014625' => 'stu', 'PGSC0003DMG401000943' => 'stu', 'Phvul.001G148600' => 'pvu', 'Phvul.004G001700' => 'pvu', 'Phvul.006G154900' => 'pvu', 'Phvul.008G078200' => 'pvu', 'Phvul.011G136500' => 'pvu', 'Potri.002G215600' => 'ptr', 'Potri.008G201600' => 'ptr', 'Potri.014G138400' => 'ptr', 'Potri.016G142500' => 'ptr', 'Pp3c16_10580' => 'ppa', 'Pp3c5_25280' => 'ppa', 'Prupe.1G150000' => 'ppe', 'Prupe.1G150100' => 'ppe', 'Prupe.6G299600' => 'ppe', 'Prupe.8G245000' => 'ppe', 'Psat0s4927g0040' => 'psa', 'Psat1g052080' => 'psa', 'Psat1g183800' => 'psa', 'Psat3g113840' => 'psa', 'Psat3g126120' => 'psa', 'Psat3g126160' => 'psa', 'Psat3g158760' => 'psa', 'Psat3g158840' => 'psa', 'PSO170G2858' => 'pso', 'PSO339G0606' => 'pso', 'PSO384G4709' => 'pso', 'PSO407G0334' => 'pso', 'QL04p040276' => 'qlo', 'QL06p005458' => 'qlo', 'QL06p005472' => 'qlo', 'QL07p030546' => 'qlo', 'QL07p031519' => 'qlo', 'QL09p050949' => 'qlo', 'QL09p050966' => 'qlo', 'QL09p051067' => 'qlo', 'QL12p022706' => 'qlo', 'RcHm_v2.0_Chr2g0119601' => 'rch', 'RcHm_v2.0_Chr3g0459591' => 'rch', 'RcHm_v2.0_Chr4g0418521' => 'rch', 'RcHm_v2.0_Chr4g0418531' => 'rch', 'RcHm_v2.0_Chr4g0418541' => 'rch', 'RcHm_v2.0_Chr6g0291641' => 'rch', 'Rhsim01G0086300' => 'rsi', 'Rhsim01G0276300' => 'rsi', 'Rhsim01G0276500' => 'rsi', 'Rhsim04G0207700' => 'rsi', 'Rhsim05G0234500' => 'rsi', 'Rhsim13G0022400' => 'rsi', 'Sabra02G0167900' => 'sbr', 'Sabra04G0158500' => 'sbr', 'Sabra08G0159800' => 'sbr', 'Sabra10G0011500' => 'sbr', 'Sabra14G0104400' => 'sbr', 'SalBow2G2440' => 'sbo', 'SalBow4G2265' => 'sbo', 'Sc02g0000060' => 'sci', 'Sc05g0005020' => 'sci', 'Sc13g0003890' => 'sci', 'Sed0014865' => 'sed', 'Sed0017224' => 'sed', 'Sed0026391' => 'sed', 'SEGI_00063' => 'sgi', 'SEGI_10967' => 'sgi', 'SEGI_17510' => 'sgi', 'SEGI_24396' => 'sgi', 'SEGI_39719' => 'sgi', 'SEGI_41392' => 'sgi', 'SGA_v2.0_scaffold11G05794' => 'sas', 'SGA_v2.0_scaffold142G35607' => 'sas', 'SGA_v2.0_scaffold1G00447' => 'sas', 'SHI15388' => 'shi', 'SHI15394' => 'shi', 'SHI15396' => 'shi', 'SHI15399' => 'shi', 'SMO343G0151' => 'smo', 'SMO367G1118' => 'smo', 'Solyc01g080200.3' => 'sly', 'Solyc06g008960.3' => 'sly', 'Solyc09g064780.3' => 'sly', 'Sopen01g031980' => 'spe', 'Sopen06g003710' => 'spe', 'Sopen09g026460' => 'spe', 'Sp3g21240' => 'spa', 'Sp4g30030' => 'spa', 'TAR365G0022' => 'tar', 'TAR365G1023' => 'tar', 'TAR365G1253' => 'tar', 'TAR623G0078' => 'tar', 'TAR623G1721' => 'tar', 'TAR633G0959' => 'tar', 'THA.LOC104802225' => 'tha', 'THA.LOC104804769' => 'tha', 'THA.LOC104808660' => 'tha', 'THA.LOC104812792' => 'tha', 'Thecc.01G284000' => 'tca', 'Thecc.04G220600' => 'tca', 'Thecc.05G268900' => 'tca', 'Thecc.08G171100' => 'tca', 'Thhalv10001284m.g' => 'esa', 'Thhalv10019912m.g' => 'esa', 'TPR.G14189' => 'tpr', 'TPR.G18110' => 'tpr', 'TPR.G18130' => 'tpr', 'TPR.G18131' => 'tpr', 'TPR.G18140' => 'tpr', 'TPR.G24282' => 'tpr', 'TPR.G25221' => 'tpr', 'TPR.G29267' => 'tpr', 'TPR.G35315' => 'tpr', 'TPR.G36173' => 'tpr', 'TWI09G0794' => 'twi', 'TWI59G1348' => 'twi', 'TWI74G0430' => 'twi', 'unitig_26.g8940' => 'ugi', 'unitig_749.g13744' => 'ugi', 'unitig_749.g13745' => 'ugi', 'vmacro08269' => 'vma', 'vmacro14937' => 'vma', 'vmacro20401' => 'vma', 'VMungo0464G1349' => 'vmu', 'VMungo0540G0289' => 'vmu', 'VMungo1215G1590' => 'vmu', 'VMungo1309G0221' => 'vmu', 'VMungo1309G2815' => 'vmu', 'VMungo1383G0239' => 'vmu', 'VMungo1383G2910' => 'vmu', 'Zm00001eb095270' => 'zma', 'Zm00001eb095280' => 'zma', 'Zm00001eb111630' => 'zma', 'Zm00001eb237080' => 'zma', 'Zm00001eb273740' => 'zma', 'Zm00001eb285040' => 'zma', 'Zm00001eb330790' => 'zma', 'Zm00001eb337380' => 'zma' ), 'gf_id' => 'HOM05D001484', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001484' ), 'data_identifier' => 'HOM05D001484', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001484', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p31500' => 'bna', 'A05p00020' => 'bna', 'A07p08820' => 'bna', 'Aa31LG4G3300' => 'aar', 'Aa31LG8G10030' => 'aar', 'Actinidia00731' => 'ach', 'Actinidia11473' => 'ach', 'Actinidia23469' => 'ach', 'Actinidia24318' => 'ach', 'Actinidia40196' => 'ach', 'Actinidia40197' => 'ach', 'Actinidia40198' => 'ach', 'Ah.08g212990' => 'amhyb', 'Ah.15g091720' => 'amhyb', 'AL3G38260' => 'aly', 'AL4G47710' => 'aly', 'Aqoxy2G00671' => 'aox', 'Aqoxy2G03236' => 'aox', 'arahy.Tifrunner.gnm1.ann1.05IDCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KR684' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATY3SJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK6QJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6APGL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IDT7Z9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM073U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ0R87' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LE7RV4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT4QRX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V5ENPK' => 'arhy', 'AT2G48110' => 'ath', 'AT3G23590' => 'ath', 'ATR0626G186' => 'atr', 'ATR1127G141' => 'atr', 'Atru.chr4.2583' => 'acertr', 'Atru.chr5.1358' => 'acertr', 'Atru.chr5.1359' => 'acertr', 'Atru.chr8.46' => 'acertr', 'AUR62002640' => 'cqu', 'AUR62030055' => 'cqu', 'AUR62033713' => 'cqu', 'AUR62033714' => 'cqu', 'AUR62036795' => 'cqu', 'AUR62039891' => 'cqu', 'BcaB02g08737' => 'bca', 'BcaB04g20441' => 'bca', 'BcaB06g26509' => 'bca', 'BcaB06g26510' => 'bca', 'BcaB06g26511' => 'bca', 'BcaB06g26512' => 'bca', 'BcaB06g26513' => 'bca', 'BcaC02g12564' => 'bca', 'BcaC02g12565' => 'bca', 'BcaC02g12794' => 'bca', 'BcaC02g12795' => 'bca', 'BcaC02g12796' => 'bca', 'BcaC06g35541' => 'bca', 'BNapus_Darmor_BZH_scaffold_188p00080' => 'bna', 'BNapus_Darmor_BZH_scaffold_188p00090' => 'bna', 'BolC1t03972H' => 'bol', 'BolC1t03973H' => 'bol', 'BolC4t21680H' => 'bol', 'BolC7t41863H' => 'bol', 'BolSC55t61227H' => 'bol', 'BolSC55t61228H' => 'bol', 'BraA01t03278Z' => 'bra', 'BraA05t18998Z' => 'bra', 'BraA07t28673Z' => 'bra', 'C01p40150' => 'bna', 'C05p12370' => 'bna', 'C07p13680' => 'bna', 'CAN.G1006.16' => 'can', 'CAN.G1006.17' => 'can', 'CAN.G1170.2' => 'can', 'CAN.G962.7' => 'can', 'CANSAT25G2179' => 'cansat', 'CANSAT78G1573' => 'cansat', 'CARHR099510' => 'chi', 'CARHR143510' => 'chi', 'Carub.0003s2380' => 'cru', 'Carub.0004s3082' => 'cru', 'Ca_00614_v3' => 'car', 'Ca_07801_v3' => 'car', 'Ca_08567_v3' => 'car', 'Ca_09571_v3' => 'car', 'CBR_g19290' => 'cbr', 'Cc01_g19770' => 'ccan', 'Cc03_g03030' => 'ccan', 'CDE07G0968' => 'cde', 'CDE09G1441' => 'cde', 'Cfa006103' => 'cfa', 'Cfa015573' => 'cfa', 'Cfa016988' => 'cfa', 'Ciclev10006738m.g' => 'ccl', 'Ciclev10010920m.g' => 'ccl', 'Ciclev10018517m.g' => 'ccl', 'CiPaw.01G159200' => 'cil', 'CiPaw.02G091000' => 'cil', 'CiPaw.02G091100' => 'cil', 'CiPaw.08G103100' => 'cil', 'CiPaw.09G224900' => 'cil', 'ClCG06G005740' => 'cla', 'ClCG07G000090' => 'cla', 'ClCG07G000100' => 'cla', 'COL.COLO4_09143' => 'col', 'COL.COLO4_25124' => 'col', 'Cpa.g.sc16.34' => 'cpa', 'Cpa.g.sc3504.1' => 'cpa', 'Cpa.g.sc60.37' => 'cpa', 'CsaV3_6G018520' => 'csa', 'CsaV3_6G036860' => 'csa', 'CSS0001072' => 'camsi', 'CSS0020208' => 'camsi', 'CSS0021253' => 'camsi', 'CSS0022190' => 'camsi', 'CSS0036150' => 'camsi', 'CSS0040442' => 'camsi', 'CSS0042300' => 'camsi', 'CSS0045298' => 'camsi', 'DCAR_012449' => 'dca', 'DCAR_018405' => 'dca', 'DCAR_024573' => 'dca', 'DCAR_030591' => 'dca', 'Dinv16926' => 'din', 'Dinv32963' => 'din', 'Dinv38382' => 'din', 'Dinv38383' => 'din', 'Duzib133G0974' => 'dzi', 'Duzib138G1867' => 'dzi', 'Duzib211G0420' => 'dzi', 'Duzib212G0930' => 'dzi', 'ECA234G1645' => 'eca', 'ECA247G3467' => 'eca', 'ECA248G1703' => 'eca', 'EL10Ac3g06327' => 'bvu', 'EL10Ac7g17204' => 'bvu', 'Eucgr.A00855' => 'egr', 'Eucgr.A00858' => 'egr', 'Eucgr.H01520' => 'egr', 'Eucgr.H03604' => 'egr', 'Eucgr.L03465' => 'egr', 'Eucgr.L03466' => 'egr', 'FAN01G0988' => 'fan', 'FAN02G3892' => 'fan', 'FAN05G3381' => 'fan', 'FAN07G0967' => 'fan', 'FAN07G1493' => 'fan', 'FAN08G3125' => 'fan', 'FAN09G0402' => 'fan', 'FAN12G2594' => 'fan', 'FAN12G3879' => 'fan', 'FAN14G1546' => 'fan', 'FAN15G3626' => 'fan', 'FAN17G0588' => 'fan', 'FAN17G0609' => 'fan', 'FAN18G2817' => 'fan', 'FAN19G1305' => 'fan', 'FAN20G1787' => 'fan', 'FAN22G0073' => 'fan', 'FAN22G0352' => 'fan', 'FAN22G0368' => 'fan', 'FAN22G2273' => 'fan', 'FAN24G1998' => 'fan', 'FAN27G1317' => 'fan', 'FvH4_2g23980' => 'fve', 'FvH4_4g14380' => 'fve', 'FvH4_4g14390' => 'fve', 'FvH4_6g09250' => 'fve', 'Glyma.03G151100' => 'gma', 'Glyma.04G122550' => 'gma', 'Glyma.05G001600' => 'gma', 'Glyma.09G270766' => 'gma', 'Glyma.09G270832' => 'gma', 'Glyma.13G209800' => 'gma', 'Glyma.15G102800' => 'gma', 'Glyma.18G218900' => 'gma', 'Glyma.19G001500' => 'gma', 'Glyma.19G153600' => 'gma', 'Gohir.A02G028600' => 'ghi', 'Gohir.A08G045000' => 'ghi', 'Gohir.A11G120500' => 'ghi', 'Gohir.A12G006200' => 'ghi', 'Gohir.A12G006250' => 'ghi', 'Gohir.D02G036300' => 'ghi', 'Gohir.D08G054700' => 'ghi', 'Gohir.D11G125600' => 'ghi', 'Gohir.D12G005700' => 'ghi', 'Gorai.004G055200' => 'gra', 'Gorai.005G040400' => 'gra', 'Gorai.007G134500' => 'gra', 'Gorai.008G005500' => 'gra', 'GSVIVG01011094001' => 'vvi', 'GSVIVG01017879001' => 'vvi', 'GSVIVG01025988001' => 'vvi', 'GSVIVG01029847001' => 'vvi', 'HanXRQChr10g0282901' => 'han', 'HanXRQChr10g0310371' => 'han', 'HanXRQChr10g0315041' => 'han', 'HanXRQChr11g0327651' => 'han', 'HanXRQChr12g0359391' => 'han', 'Haze_00972' => 'cav', 'Haze_00973' => 'cav', 'Haze_00974' => 'cav', 'Haze_04747' => 'cav', 'Haze_04749' => 'cav', 'Haze_04750' => 'cav', 'Haze_21217' => 'cav', 'Hma1.2p1_1037F.1_g250680' => 'hma', 'Hma1.2p1_1644F.1_g295320' => 'hma', 'HPP92_011322' => 'vpl', 'HPP92_011323' => 'vpl', 'HPP92_011324' => 'vpl', 'HPP92_011325' => 'vpl', 'HPP92_011326' => 'vpl', 'Hund12205' => 'sun', 'Hund17957' => 'sun', 'Lalb_Chr06g0176771' => 'lal', 'Lalb_Chr18g0056021' => 'lal', 'Lalb_Chr18g0056031' => 'lal', 'Lalb_Chr18g0056041' => 'lal', 'Lalb_Chr20g0107751' => 'lal', 'Lalb_Chr20g0118371' => 'lal', 'Lj1g0010239' => 'lja', 'Lj1g0017101' => 'lja', 'Lj2A1178G40' => 'lonja', 'Lj2A54G84' => 'lonja', 'Lj2g0015248' => 'lja', 'Lj3A761T51' => 'lonja', 'Lj6g0018116' => 'lja', 'Lsat_1_v5_gn_4_136040' => 'lsa', 'Lsat_1_v5_gn_5_187461' => 'lsa', 'Lsat_1_v5_gn_5_77001' => 'lsa', 'Lsat_1_v5_gn_9_4461' => 'lsa', 'Manes.01G210100' => 'mes', 'Manes.03G185600' => 'mes', 'Manes.05G073300' => 'mes', 'Manes.09G120300' => 'mes', 'Manes.15G022100' => 'mes', 'Mapoly0096s0053' => 'mpo', 'MBI03_g14058_MAGBIO' => 'mbi', 'MBI03_g33876_MAGBIO' => 'mbi', 'MBI03_g36854_MAGBIO' => 'mbi', 'MBI17_g11997_MAGBIO' => 'mbi', 'MD03G1269000' => 'mdo', 'MD04G1179600' => 'mdo', 'MD11G1289800' => 'mdo', 'MD12G1194700' => 'mdo', 'MD13G1182100' => 'mdo', 'MD13G1182200' => 'mdo', 'MD16G1182600' => 'mdo', 'Medtr2g021400' => 'mtr', 'Medtr2g021470' => 'mtr', 'Medtr2g105810' => 'mtr', 'Medtr3g033580' => 'mtr', 'Medtr6g007970' => 'mtr', 'Medtr7g056330' => 'mtr', 'Medtr7g074290' => 'mtr', 'Medtr7g074380' => 'mtr', 'Medtr7g094550' => 'mtr', 'Medtr8g069995' => 'mtr', 'MELO3C014345.2' => 'cme', 'MELO3C021395.2' => 'cme', 'Migut.D00262' => 'egut', 'Migut.G00257' => 'egut', 'MSTRG.21575' => 'ama', 'MSTRG.3985' => 'ama', 'Nitab4.5_0000295g0140' => 'nta', 'Nitab4.5_0000732g0140' => 'nta', 'Nitab4.5_0003162g0020' => 'nta', 'Nitab4.5_0006180g0090' => 'nta', 'Nitab4.5_0006390g0010' => 'nta', 'Nitab4.5_0007392g0040' => 'nta', 'Nn1g02140' => 'nnu', 'Nn4g26168' => 'nnu', 'Nn5g26754' => 'nnu', 'Oeu001433.1' => 'oeu', 'Oeu010299.2' => 'oeu', 'Oeu011171.1' => 'oeu', 'Oeu037675.1' => 'oeu', 'Oeu038359.1' => 'oeu', 'Oeu063834.1' => 'oeu', 'Oeu063835.1' => 'oeu', 'Os05g0312000' => 'osa', 'Os07g0211101' => 'osa', 'Os07g0211200' => 'osa', 'Os07g0681500' => 'osa', 'Peaxi162Scf00095g01015' => 'pax', 'Peaxi162Scf00104g00329' => 'pax', 'Peaxi162Scf00161g00137' => 'pax', 'PGR004G1665' => 'pgr', 'PGR031G2937' => 'pgr', 'PGR119G2145' => 'pgr', 'PGSC0003DMG400004351' => 'stu', 'PGSC0003DMG400014625' => 'stu', 'PGSC0003DMG401000943' => 'stu', 'Phvul.001G148600' => 'pvu', 'Phvul.004G001700' => 'pvu', 'Phvul.006G154900' => 'pvu', 'Phvul.008G078200' => 'pvu', 'Phvul.011G136500' => 'pvu', 'Potri.002G215600' => 'ptr', 'Potri.008G201600' => 'ptr', 'Potri.014G138400' => 'ptr', 'Potri.016G142500' => 'ptr', 'Pp3c16_10580' => 'ppa', 'Pp3c5_25280' => 'ppa', 'Prupe.1G150000' => 'ppe', 'Prupe.1G150100' => 'ppe', 'Prupe.6G299600' => 'ppe', 'Prupe.8G245000' => 'ppe', 'Psat0s4927g0040' => 'psa', 'Psat1g052080' => 'psa', 'Psat1g183800' => 'psa', 'Psat3g113840' => 'psa', 'Psat3g126120' => 'psa', 'Psat3g126160' => 'psa', 'Psat3g158760' => 'psa', 'Psat3g158840' => 'psa', 'PSO170G2858' => 'pso', 'PSO339G0606' => 'pso', 'PSO384G4709' => 'pso', 'PSO407G0334' => 'pso', 'QL04p040276' => 'qlo', 'QL06p005458' => 'qlo', 'QL06p005472' => 'qlo', 'QL07p030546' => 'qlo', 'QL07p031519' => 'qlo', 'QL09p050949' => 'qlo', 'QL09p050966' => 'qlo', 'QL09p051067' => 'qlo', 'QL12p022706' => 'qlo', 'RcHm_v2.0_Chr2g0119601' => 'rch', 'RcHm_v2.0_Chr3g0459591' => 'rch', 'RcHm_v2.0_Chr4g0418521' => 'rch', 'RcHm_v2.0_Chr4g0418531' => 'rch', 'RcHm_v2.0_Chr4g0418541' => 'rch', 'RcHm_v2.0_Chr6g0291641' => 'rch', 'Rhsim01G0086300' => 'rsi', 'Rhsim01G0276300' => 'rsi', 'Rhsim01G0276500' => 'rsi', 'Rhsim04G0207700' => 'rsi', 'Rhsim05G0234500' => 'rsi', 'Rhsim13G0022400' => 'rsi', 'Sabra02G0167900' => 'sbr', 'Sabra04G0158500' => 'sbr', 'Sabra08G0159800' => 'sbr', 'Sabra10G0011500' => 'sbr', 'Sabra14G0104400' => 'sbr', 'SalBow2G2440' => 'sbo', 'SalBow4G2265' => 'sbo', 'Sc02g0000060' => 'sci', 'Sc05g0005020' => 'sci', 'Sc13g0003890' => 'sci', 'Sed0014865' => 'sed', 'Sed0017224' => 'sed', 'Sed0026391' => 'sed', 'SEGI_00063' => 'sgi', 'SEGI_10967' => 'sgi', 'SEGI_17510' => 'sgi', 'SEGI_24396' => 'sgi', 'SEGI_39719' => 'sgi', 'SEGI_41392' => 'sgi', 'SGA_v2.0_scaffold11G05794' => 'sas', 'SGA_v2.0_scaffold142G35607' => 'sas', 'SGA_v2.0_scaffold1G00447' => 'sas', 'SHI15388' => 'shi', 'SHI15394' => 'shi', 'SHI15396' => 'shi', 'SHI15399' => 'shi', 'SMO343G0151' => 'smo', 'SMO367G1118' => 'smo', 'Solyc01g080200.3' => 'sly', 'Solyc06g008960.3' => 'sly', 'Solyc09g064780.3' => 'sly', 'Sopen01g031980' => 'spe', 'Sopen06g003710' => 'spe', 'Sopen09g026460' => 'spe', 'Sp3g21240' => 'spa', 'Sp4g30030' => 'spa', 'TAR365G0022' => 'tar', 'TAR365G1023' => 'tar', 'TAR365G1253' => 'tar', 'TAR623G0078' => 'tar', 'TAR623G1721' => 'tar', 'TAR633G0959' => 'tar', 'THA.LOC104802225' => 'tha', 'THA.LOC104804769' => 'tha', 'THA.LOC104808660' => 'tha', 'THA.LOC104812792' => 'tha', 'Thecc.01G284000' => 'tca', 'Thecc.04G220600' => 'tca', 'Thecc.05G268900' => 'tca', 'Thecc.08G171100' => 'tca', 'Thhalv10001284m.g' => 'esa', 'Thhalv10019912m.g' => 'esa', 'TPR.G14189' => 'tpr', 'TPR.G18110' => 'tpr', 'TPR.G18130' => 'tpr', 'TPR.G18131' => 'tpr', 'TPR.G18140' => 'tpr', 'TPR.G24282' => 'tpr', 'TPR.G25221' => 'tpr', 'TPR.G29267' => 'tpr', 'TPR.G35315' => 'tpr', 'TPR.G36173' => 'tpr', 'TWI09G0794' => 'twi', 'TWI59G1348' => 'twi', 'TWI74G0430' => 'twi', 'unitig_26.g8940' => 'ugi', 'unitig_749.g13744' => 'ugi', 'unitig_749.g13745' => 'ugi', 'vmacro08269' => 'vma', 'vmacro14937' => 'vma', 'vmacro20401' => 'vma', 'VMungo0464G1349' => 'vmu', 'VMungo0540G0289' => 'vmu', 'VMungo1215G1590' => 'vmu', 'VMungo1309G0221' => 'vmu', 'VMungo1309G2815' => 'vmu', 'VMungo1383G0239' => 'vmu', 'VMungo1383G2910' => 'vmu', 'Zm00001eb095270' => 'zma', 'Zm00001eb095280' => 'zma', 'Zm00001eb111630' => 'zma', 'Zm00001eb237080' => 'zma', 'Zm00001eb273740' => 'zma', 'Zm00001eb285040' => 'zma', 'Zm00001eb330790' => 'zma', 'Zm00001eb337380' => 'zma' ) $gf_id = 'HOM05D001484' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001484' ) $data_identifier = 'HOM05D001484' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 2, 'aly' => (int) 2, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 22, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 7, 'hma' => (int) 2, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 7, 'mtr' => (int) 10, 'cme' => (int) 2, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 4, 'ppa' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 4, 'qlo' => (int) 9, 'rch' => (int) 6, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 10, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 7, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb337380' $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' => 'HOM05D001484', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p31500' => 'bna', 'A05p00020' => 'bna', 'A07p08820' => 'bna', 'Aa31LG4G3300' => 'aar', 'Aa31LG8G10030' => 'aar', 'Actinidia00731' => 'ach', 'Actinidia11473' => 'ach', 'Actinidia23469' => 'ach', 'Actinidia24318' => 'ach', 'Actinidia40196' => 'ach', 'Actinidia40197' => 'ach', 'Actinidia40198' => 'ach', 'Ah.08g212990' => 'amhyb', 'Ah.15g091720' => 'amhyb', 'AL3G38260' => 'aly', 'AL4G47710' => 'aly', 'Aqoxy2G00671' => 'aox', 'Aqoxy2G03236' => 'aox', 'arahy.Tifrunner.gnm1.ann1.05IDCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KR684' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATY3SJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK6QJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6APGL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IDT7Z9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM073U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ0R87' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LE7RV4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT4QRX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V5ENPK' => 'arhy', 'AT2G48110' => 'ath', 'AT3G23590' => 'ath', 'ATR0626G186' => 'atr', 'ATR1127G141' => 'atr', 'Atru.chr4.2583' => 'acertr', 'Atru.chr5.1358' => 'acertr', 'Atru.chr5.1359' => 'acertr', 'Atru.chr8.46' => 'acertr', 'AUR62002640' => 'cqu', 'AUR62030055' => 'cqu', 'AUR62033713' => 'cqu', 'AUR62033714' => 'cqu', 'AUR62036795' => 'cqu', 'AUR62039891' => 'cqu', 'BcaB02g08737' => 'bca', 'BcaB04g20441' => 'bca', 'BcaB06g26509' => 'bca', 'BcaB06g26510' => 'bca', 'BcaB06g26511' => 'bca', 'BcaB06g26512' => 'bca', 'BcaB06g26513' => 'bca', 'BcaC02g12564' => 'bca', 'BcaC02g12565' => 'bca', 'BcaC02g12794' => 'bca', 'BcaC02g12795' => 'bca', 'BcaC02g12796' => 'bca', 'BcaC06g35541' => 'bca', 'BNapus_Darmor_BZH_scaffold_188p00080' => 'bna', 'BNapus_Darmor_BZH_scaffold_188p00090' => 'bna', 'BolC1t03972H' => 'bol', 'BolC1t03973H' => 'bol', 'BolC4t21680H' => 'bol', 'BolC7t41863H' => 'bol', 'BolSC55t61227H' => 'bol', 'BolSC55t61228H' => 'bol', 'BraA01t03278Z' => 'bra', 'BraA05t18998Z' => 'bra', 'BraA07t28673Z' => 'bra', 'C01p40150' => 'bna', 'C05p12370' => 'bna', 'C07p13680' => 'bna', 'CAN.G1006.16' => 'can', 'CAN.G1006.17' => 'can', 'CAN.G1170.2' => 'can', 'CAN.G962.7' => 'can', 'CANSAT25G2179' => 'cansat', 'CANSAT78G1573' => 'cansat', 'CARHR099510' => 'chi', 'CARHR143510' => 'chi', 'Carub.0003s2380' => 'cru', 'Carub.0004s3082' => 'cru', 'Ca_00614_v3' => 'car', 'Ca_07801_v3' => 'car', 'Ca_08567_v3' => 'car', 'Ca_09571_v3' => 'car', 'CBR_g19290' => 'cbr', 'Cc01_g19770' => 'ccan', 'Cc03_g03030' => 'ccan', 'CDE07G0968' => 'cde', 'CDE09G1441' => 'cde', 'Cfa006103' => 'cfa', 'Cfa015573' => 'cfa', 'Cfa016988' => 'cfa', 'Ciclev10006738m.g' => 'ccl', 'Ciclev10010920m.g' => 'ccl', 'Ciclev10018517m.g' => 'ccl', 'CiPaw.01G159200' => 'cil', 'CiPaw.02G091000' => 'cil', 'CiPaw.02G091100' => 'cil', 'CiPaw.08G103100' => 'cil', 'CiPaw.09G224900' => 'cil', 'ClCG06G005740' => 'cla', 'ClCG07G000090' => 'cla', 'ClCG07G000100' => 'cla', 'COL.COLO4_09143' => 'col', 'COL.COLO4_25124' => 'col', 'Cpa.g.sc16.34' => 'cpa', 'Cpa.g.sc3504.1' => 'cpa', 'Cpa.g.sc60.37' => 'cpa', 'CsaV3_6G018520' => 'csa', 'CsaV3_6G036860' => 'csa', 'CSS0001072' => 'camsi', 'CSS0020208' => 'camsi', 'CSS0021253' => 'camsi', 'CSS0022190' => 'camsi', 'CSS0036150' => 'camsi', 'CSS0040442' => 'camsi', 'CSS0042300' => 'camsi', 'CSS0045298' => 'camsi', 'DCAR_012449' => 'dca', 'DCAR_018405' => 'dca', 'DCAR_024573' => 'dca', 'DCAR_030591' => 'dca', 'Dinv16926' => 'din', 'Dinv32963' => 'din', 'Dinv38382' => 'din', 'Dinv38383' => 'din', 'Duzib133G0974' => 'dzi', 'Duzib138G1867' => 'dzi', 'Duzib211G0420' => 'dzi', 'Duzib212G0930' => 'dzi', 'ECA234G1645' => 'eca', 'ECA247G3467' => 'eca', 'ECA248G1703' => 'eca', 'EL10Ac3g06327' => 'bvu', 'EL10Ac7g17204' => 'bvu', 'Eucgr.A00855' => 'egr', 'Eucgr.A00858' => 'egr', 'Eucgr.H01520' => 'egr', 'Eucgr.H03604' => 'egr', 'Eucgr.L03465' => 'egr', 'Eucgr.L03466' => 'egr', 'FAN01G0988' => 'fan', 'FAN02G3892' => 'fan', 'FAN05G3381' => 'fan', 'FAN07G0967' => 'fan', 'FAN07G1493' => 'fan', 'FAN08G3125' => 'fan', 'FAN09G0402' => 'fan', 'FAN12G2594' => 'fan', 'FAN12G3879' => 'fan', 'FAN14G1546' => 'fan', 'FAN15G3626' => 'fan', 'FAN17G0588' => 'fan', 'FAN17G0609' => 'fan', 'FAN18G2817' => 'fan', 'FAN19G1305' => 'fan', 'FAN20G1787' => 'fan', 'FAN22G0073' => 'fan', 'FAN22G0352' => 'fan', 'FAN22G0368' => 'fan', 'FAN22G2273' => 'fan', 'FAN24G1998' => 'fan', 'FAN27G1317' => 'fan', 'FvH4_2g23980' => 'fve', 'FvH4_4g14380' => 'fve', 'FvH4_4g14390' => 'fve', 'FvH4_6g09250' => 'fve', 'Glyma.03G151100' => 'gma', 'Glyma.04G122550' => 'gma', 'Glyma.05G001600' => 'gma', 'Glyma.09G270766' => 'gma', 'Glyma.09G270832' => 'gma', 'Glyma.13G209800' => 'gma', 'Glyma.15G102800' => 'gma', 'Glyma.18G218900' => 'gma', 'Glyma.19G001500' => 'gma', 'Glyma.19G153600' => 'gma', 'Gohir.A02G028600' => 'ghi', 'Gohir.A08G045000' => 'ghi', 'Gohir.A11G120500' => 'ghi', 'Gohir.A12G006200' => 'ghi', 'Gohir.A12G006250' => 'ghi', 'Gohir.D02G036300' => 'ghi', 'Gohir.D08G054700' => 'ghi', 'Gohir.D11G125600' => 'ghi', 'Gohir.D12G005700' => 'ghi', 'Gorai.004G055200' => 'gra', 'Gorai.005G040400' => 'gra', 'Gorai.007G134500' => 'gra', 'Gorai.008G005500' => 'gra', 'GSVIVG01011094001' => 'vvi', 'GSVIVG01017879001' => 'vvi', 'GSVIVG01025988001' => 'vvi', 'GSVIVG01029847001' => 'vvi', 'HanXRQChr10g0282901' => 'han', 'HanXRQChr10g0310371' => 'han', 'HanXRQChr10g0315041' => 'han', 'HanXRQChr11g0327651' => 'han', 'HanXRQChr12g0359391' => 'han', 'Haze_00972' => 'cav', 'Haze_00973' => 'cav', 'Haze_00974' => 'cav', 'Haze_04747' => 'cav', 'Haze_04749' => 'cav', 'Haze_04750' => 'cav', 'Haze_21217' => 'cav', 'Hma1.2p1_1037F.1_g250680' => 'hma', 'Hma1.2p1_1644F.1_g295320' => 'hma', 'HPP92_011322' => 'vpl', 'HPP92_011323' => 'vpl', 'HPP92_011324' => 'vpl', 'HPP92_011325' => 'vpl', 'HPP92_011326' => 'vpl', 'Hund12205' => 'sun', 'Hund17957' => 'sun', 'Lalb_Chr06g0176771' => 'lal', 'Lalb_Chr18g0056021' => 'lal', 'Lalb_Chr18g0056031' => 'lal', 'Lalb_Chr18g0056041' => 'lal', 'Lalb_Chr20g0107751' => 'lal', 'Lalb_Chr20g0118371' => 'lal', 'Lj1g0010239' => 'lja', 'Lj1g0017101' => 'lja', 'Lj2A1178G40' => 'lonja', 'Lj2A54G84' => 'lonja', 'Lj2g0015248' => 'lja', 'Lj3A761T51' => 'lonja', 'Lj6g0018116' => 'lja', 'Lsat_1_v5_gn_4_136040' => 'lsa', 'Lsat_1_v5_gn_5_187461' => 'lsa', 'Lsat_1_v5_gn_5_77001' => 'lsa', 'Lsat_1_v5_gn_9_4461' => 'lsa', 'Manes.01G210100' => 'mes', 'Manes.03G185600' => 'mes', 'Manes.05G073300' => 'mes', 'Manes.09G120300' => 'mes', 'Manes.15G022100' => 'mes', 'Mapoly0096s0053' => 'mpo', 'MBI03_g14058_MAGBIO' => 'mbi', 'MBI03_g33876_MAGBIO' => 'mbi', 'MBI03_g36854_MAGBIO' => 'mbi', 'MBI17_g11997_MAGBIO' => 'mbi', 'MD03G1269000' => 'mdo', 'MD04G1179600' => 'mdo', 'MD11G1289800' => 'mdo', 'MD12G1194700' => 'mdo', 'MD13G1182100' => 'mdo', 'MD13G1182200' => 'mdo', 'MD16G1182600' => 'mdo', 'Medtr2g021400' => 'mtr', 'Medtr2g021470' => 'mtr', 'Medtr2g105810' => 'mtr', 'Medtr3g033580' => 'mtr', 'Medtr6g007970' => 'mtr', 'Medtr7g056330' => 'mtr', 'Medtr7g074290' => 'mtr', 'Medtr7g074380' => 'mtr', 'Medtr7g094550' => 'mtr', 'Medtr8g069995' => 'mtr', 'MELO3C014345.2' => 'cme', 'MELO3C021395.2' => 'cme', 'Migut.D00262' => 'egut', 'Migut.G00257' => 'egut', 'MSTRG.21575' => 'ama', 'MSTRG.3985' => 'ama', 'Nitab4.5_0000295g0140' => 'nta', 'Nitab4.5_0000732g0140' => 'nta', 'Nitab4.5_0003162g0020' => 'nta', 'Nitab4.5_0006180g0090' => 'nta', 'Nitab4.5_0006390g0010' => 'nta', 'Nitab4.5_0007392g0040' => 'nta', 'Nn1g02140' => 'nnu', 'Nn4g26168' => 'nnu', 'Nn5g26754' => 'nnu', 'Oeu001433.1' => 'oeu', 'Oeu010299.2' => 'oeu', 'Oeu011171.1' => 'oeu', 'Oeu037675.1' => 'oeu', 'Oeu038359.1' => 'oeu', 'Oeu063834.1' => 'oeu', 'Oeu063835.1' => 'oeu', 'Os05g0312000' => 'osa', 'Os07g0211101' => 'osa', 'Os07g0211200' => 'osa', 'Os07g0681500' => 'osa', 'Peaxi162Scf00095g01015' => 'pax', 'Peaxi162Scf00104g00329' => 'pax', 'Peaxi162Scf00161g00137' => 'pax', 'PGR004G1665' => 'pgr', 'PGR031G2937' => 'pgr', 'PGR119G2145' => 'pgr', 'PGSC0003DMG400004351' => 'stu', 'PGSC0003DMG400014625' => 'stu', 'PGSC0003DMG401000943' => 'stu', 'Phvul.001G148600' => 'pvu', 'Phvul.004G001700' => 'pvu', 'Phvul.006G154900' => 'pvu', 'Phvul.008G078200' => 'pvu', 'Phvul.011G136500' => 'pvu', 'Potri.002G215600' => 'ptr', 'Potri.008G201600' => 'ptr', 'Potri.014G138400' => 'ptr', 'Potri.016G142500' => 'ptr', 'Pp3c16_10580' => 'ppa', 'Pp3c5_25280' => 'ppa', 'Prupe.1G150000' => 'ppe', 'Prupe.1G150100' => 'ppe', 'Prupe.6G299600' => 'ppe', 'Prupe.8G245000' => 'ppe', 'Psat0s4927g0040' => 'psa', 'Psat1g052080' => 'psa', 'Psat1g183800' => 'psa', 'Psat3g113840' => 'psa', 'Psat3g126120' => 'psa', 'Psat3g126160' => 'psa', 'Psat3g158760' => 'psa', 'Psat3g158840' => 'psa', 'PSO170G2858' => 'pso', 'PSO339G0606' => 'pso', 'PSO384G4709' => 'pso', 'PSO407G0334' => 'pso', 'QL04p040276' => 'qlo', 'QL06p005458' => 'qlo', 'QL06p005472' => 'qlo', 'QL07p030546' => 'qlo', 'QL07p031519' => 'qlo', 'QL09p050949' => 'qlo', 'QL09p050966' => 'qlo', 'QL09p051067' => 'qlo', 'QL12p022706' => 'qlo', 'RcHm_v2.0_Chr2g0119601' => 'rch', 'RcHm_v2.0_Chr3g0459591' => 'rch', 'RcHm_v2.0_Chr4g0418521' => 'rch', 'RcHm_v2.0_Chr4g0418531' => 'rch', 'RcHm_v2.0_Chr4g0418541' => 'rch', 'RcHm_v2.0_Chr6g0291641' => 'rch', 'Rhsim01G0086300' => 'rsi', 'Rhsim01G0276300' => 'rsi', 'Rhsim01G0276500' => 'rsi', 'Rhsim04G0207700' => 'rsi', 'Rhsim05G0234500' => 'rsi', 'Rhsim13G0022400' => 'rsi', 'Sabra02G0167900' => 'sbr', 'Sabra04G0158500' => 'sbr', 'Sabra08G0159800' => 'sbr', 'Sabra10G0011500' => 'sbr', 'Sabra14G0104400' => 'sbr', 'SalBow2G2440' => 'sbo', 'SalBow4G2265' => 'sbo', 'Sc02g0000060' => 'sci', 'Sc05g0005020' => 'sci', 'Sc13g0003890' => 'sci', 'Sed0014865' => 'sed', 'Sed0017224' => 'sed', 'Sed0026391' => 'sed', 'SEGI_00063' => 'sgi', 'SEGI_10967' => 'sgi', 'SEGI_17510' => 'sgi', 'SEGI_24396' => 'sgi', 'SEGI_39719' => 'sgi', 'SEGI_41392' => 'sgi', 'SGA_v2.0_scaffold11G05794' => 'sas', 'SGA_v2.0_scaffold142G35607' => 'sas', 'SGA_v2.0_scaffold1G00447' => 'sas', 'SHI15388' => 'shi', 'SHI15394' => 'shi', 'SHI15396' => 'shi', 'SHI15399' => 'shi', 'SMO343G0151' => 'smo', 'SMO367G1118' => 'smo', 'Solyc01g080200.3' => 'sly', 'Solyc06g008960.3' => 'sly', 'Solyc09g064780.3' => 'sly', 'Sopen01g031980' => 'spe', 'Sopen06g003710' => 'spe', 'Sopen09g026460' => 'spe', 'Sp3g21240' => 'spa', 'Sp4g30030' => 'spa', 'TAR365G0022' => 'tar', 'TAR365G1023' => 'tar', 'TAR365G1253' => 'tar', 'TAR623G0078' => 'tar', 'TAR623G1721' => 'tar', 'TAR633G0959' => 'tar', 'THA.LOC104802225' => 'tha', 'THA.LOC104804769' => 'tha', 'THA.LOC104808660' => 'tha', 'THA.LOC104812792' => 'tha', 'Thecc.01G284000' => 'tca', 'Thecc.04G220600' => 'tca', 'Thecc.05G268900' => 'tca', 'Thecc.08G171100' => 'tca', 'Thhalv10001284m.g' => 'esa', 'Thhalv10019912m.g' => 'esa', 'TPR.G14189' => 'tpr', 'TPR.G18110' => 'tpr', 'TPR.G18130' => 'tpr', 'TPR.G18131' => 'tpr', 'TPR.G18140' => 'tpr', 'TPR.G24282' => 'tpr', 'TPR.G25221' => 'tpr', 'TPR.G29267' => 'tpr', 'TPR.G35315' => 'tpr', 'TPR.G36173' => 'tpr', 'TWI09G0794' => 'twi', 'TWI59G1348' => 'twi', 'TWI74G0430' => 'twi', 'unitig_26.g8940' => 'ugi', 'unitig_749.g13744' => 'ugi', 'unitig_749.g13745' => 'ugi', 'vmacro08269' => 'vma', 'vmacro14937' => 'vma', 'vmacro20401' => 'vma', 'VMungo0464G1349' => 'vmu', 'VMungo0540G0289' => 'vmu', 'VMungo1215G1590' => 'vmu', 'VMungo1309G0221' => 'vmu', 'VMungo1309G2815' => 'vmu', 'VMungo1383G0239' => 'vmu', 'VMungo1383G2910' => 'vmu', 'Zm00001eb095270' => 'zma', 'Zm00001eb095280' => 'zma', 'Zm00001eb111630' => 'zma', 'Zm00001eb237080' => 'zma', 'Zm00001eb273740' => 'zma', 'Zm00001eb285040' => 'zma', 'Zm00001eb330790' => 'zma', 'Zm00001eb337380' => 'zma' ), 'gf_id' => 'HOM05D001484', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001484' ), 'data_identifier' => 'HOM05D001484', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001484', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p31500' => 'bna', 'A05p00020' => 'bna', 'A07p08820' => 'bna', 'Aa31LG4G3300' => 'aar', 'Aa31LG8G10030' => 'aar', 'Actinidia00731' => 'ach', 'Actinidia11473' => 'ach', 'Actinidia23469' => 'ach', 'Actinidia24318' => 'ach', 'Actinidia40196' => 'ach', 'Actinidia40197' => 'ach', 'Actinidia40198' => 'ach', 'Ah.08g212990' => 'amhyb', 'Ah.15g091720' => 'amhyb', 'AL3G38260' => 'aly', 'AL4G47710' => 'aly', 'Aqoxy2G00671' => 'aox', 'Aqoxy2G03236' => 'aox', 'arahy.Tifrunner.gnm1.ann1.05IDCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KR684' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATY3SJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK6QJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6APGL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IDT7Z9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM073U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ0R87' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LE7RV4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT4QRX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V5ENPK' => 'arhy', 'AT2G48110' => 'ath', 'AT3G23590' => 'ath', 'ATR0626G186' => 'atr', 'ATR1127G141' => 'atr', 'Atru.chr4.2583' => 'acertr', 'Atru.chr5.1358' => 'acertr', 'Atru.chr5.1359' => 'acertr', 'Atru.chr8.46' => 'acertr', 'AUR62002640' => 'cqu', 'AUR62030055' => 'cqu', 'AUR62033713' => 'cqu', 'AUR62033714' => 'cqu', 'AUR62036795' => 'cqu', 'AUR62039891' => 'cqu', 'BcaB02g08737' => 'bca', 'BcaB04g20441' => 'bca', 'BcaB06g26509' => 'bca', 'BcaB06g26510' => 'bca', 'BcaB06g26511' => 'bca', 'BcaB06g26512' => 'bca', 'BcaB06g26513' => 'bca', 'BcaC02g12564' => 'bca', 'BcaC02g12565' => 'bca', 'BcaC02g12794' => 'bca', 'BcaC02g12795' => 'bca', 'BcaC02g12796' => 'bca', 'BcaC06g35541' => 'bca', 'BNapus_Darmor_BZH_scaffold_188p00080' => 'bna', 'BNapus_Darmor_BZH_scaffold_188p00090' => 'bna', 'BolC1t03972H' => 'bol', 'BolC1t03973H' => 'bol', 'BolC4t21680H' => 'bol', 'BolC7t41863H' => 'bol', 'BolSC55t61227H' => 'bol', 'BolSC55t61228H' => 'bol', 'BraA01t03278Z' => 'bra', 'BraA05t18998Z' => 'bra', 'BraA07t28673Z' => 'bra', 'C01p40150' => 'bna', 'C05p12370' => 'bna', 'C07p13680' => 'bna', 'CAN.G1006.16' => 'can', 'CAN.G1006.17' => 'can', 'CAN.G1170.2' => 'can', 'CAN.G962.7' => 'can', 'CANSAT25G2179' => 'cansat', 'CANSAT78G1573' => 'cansat', 'CARHR099510' => 'chi', 'CARHR143510' => 'chi', 'Carub.0003s2380' => 'cru', 'Carub.0004s3082' => 'cru', 'Ca_00614_v3' => 'car', 'Ca_07801_v3' => 'car', 'Ca_08567_v3' => 'car', 'Ca_09571_v3' => 'car', 'CBR_g19290' => 'cbr', 'Cc01_g19770' => 'ccan', 'Cc03_g03030' => 'ccan', 'CDE07G0968' => 'cde', 'CDE09G1441' => 'cde', 'Cfa006103' => 'cfa', 'Cfa015573' => 'cfa', 'Cfa016988' => 'cfa', 'Ciclev10006738m.g' => 'ccl', 'Ciclev10010920m.g' => 'ccl', 'Ciclev10018517m.g' => 'ccl', 'CiPaw.01G159200' => 'cil', 'CiPaw.02G091000' => 'cil', 'CiPaw.02G091100' => 'cil', 'CiPaw.08G103100' => 'cil', 'CiPaw.09G224900' => 'cil', 'ClCG06G005740' => 'cla', 'ClCG07G000090' => 'cla', 'ClCG07G000100' => 'cla', 'COL.COLO4_09143' => 'col', 'COL.COLO4_25124' => 'col', 'Cpa.g.sc16.34' => 'cpa', 'Cpa.g.sc3504.1' => 'cpa', 'Cpa.g.sc60.37' => 'cpa', 'CsaV3_6G018520' => 'csa', 'CsaV3_6G036860' => 'csa', 'CSS0001072' => 'camsi', 'CSS0020208' => 'camsi', 'CSS0021253' => 'camsi', 'CSS0022190' => 'camsi', 'CSS0036150' => 'camsi', 'CSS0040442' => 'camsi', 'CSS0042300' => 'camsi', 'CSS0045298' => 'camsi', 'DCAR_012449' => 'dca', 'DCAR_018405' => 'dca', 'DCAR_024573' => 'dca', 'DCAR_030591' => 'dca', 'Dinv16926' => 'din', 'Dinv32963' => 'din', 'Dinv38382' => 'din', 'Dinv38383' => 'din', 'Duzib133G0974' => 'dzi', 'Duzib138G1867' => 'dzi', 'Duzib211G0420' => 'dzi', 'Duzib212G0930' => 'dzi', 'ECA234G1645' => 'eca', 'ECA247G3467' => 'eca', 'ECA248G1703' => 'eca', 'EL10Ac3g06327' => 'bvu', 'EL10Ac7g17204' => 'bvu', 'Eucgr.A00855' => 'egr', 'Eucgr.A00858' => 'egr', 'Eucgr.H01520' => 'egr', 'Eucgr.H03604' => 'egr', 'Eucgr.L03465' => 'egr', 'Eucgr.L03466' => 'egr', 'FAN01G0988' => 'fan', 'FAN02G3892' => 'fan', 'FAN05G3381' => 'fan', 'FAN07G0967' => 'fan', 'FAN07G1493' => 'fan', 'FAN08G3125' => 'fan', 'FAN09G0402' => 'fan', 'FAN12G2594' => 'fan', 'FAN12G3879' => 'fan', 'FAN14G1546' => 'fan', 'FAN15G3626' => 'fan', 'FAN17G0588' => 'fan', 'FAN17G0609' => 'fan', 'FAN18G2817' => 'fan', 'FAN19G1305' => 'fan', 'FAN20G1787' => 'fan', 'FAN22G0073' => 'fan', 'FAN22G0352' => 'fan', 'FAN22G0368' => 'fan', 'FAN22G2273' => 'fan', 'FAN24G1998' => 'fan', 'FAN27G1317' => 'fan', 'FvH4_2g23980' => 'fve', 'FvH4_4g14380' => 'fve', 'FvH4_4g14390' => 'fve', 'FvH4_6g09250' => 'fve', 'Glyma.03G151100' => 'gma', 'Glyma.04G122550' => 'gma', 'Glyma.05G001600' => 'gma', 'Glyma.09G270766' => 'gma', 'Glyma.09G270832' => 'gma', 'Glyma.13G209800' => 'gma', 'Glyma.15G102800' => 'gma', 'Glyma.18G218900' => 'gma', 'Glyma.19G001500' => 'gma', 'Glyma.19G153600' => 'gma', 'Gohir.A02G028600' => 'ghi', 'Gohir.A08G045000' => 'ghi', 'Gohir.A11G120500' => 'ghi', 'Gohir.A12G006200' => 'ghi', 'Gohir.A12G006250' => 'ghi', 'Gohir.D02G036300' => 'ghi', 'Gohir.D08G054700' => 'ghi', 'Gohir.D11G125600' => 'ghi', 'Gohir.D12G005700' => 'ghi', 'Gorai.004G055200' => 'gra', 'Gorai.005G040400' => 'gra', 'Gorai.007G134500' => 'gra', 'Gorai.008G005500' => 'gra', 'GSVIVG01011094001' => 'vvi', 'GSVIVG01017879001' => 'vvi', 'GSVIVG01025988001' => 'vvi', 'GSVIVG01029847001' => 'vvi', 'HanXRQChr10g0282901' => 'han', 'HanXRQChr10g0310371' => 'han', 'HanXRQChr10g0315041' => 'han', 'HanXRQChr11g0327651' => 'han', 'HanXRQChr12g0359391' => 'han', 'Haze_00972' => 'cav', 'Haze_00973' => 'cav', 'Haze_00974' => 'cav', 'Haze_04747' => 'cav', 'Haze_04749' => 'cav', 'Haze_04750' => 'cav', 'Haze_21217' => 'cav', 'Hma1.2p1_1037F.1_g250680' => 'hma', 'Hma1.2p1_1644F.1_g295320' => 'hma', 'HPP92_011322' => 'vpl', 'HPP92_011323' => 'vpl', 'HPP92_011324' => 'vpl', 'HPP92_011325' => 'vpl', 'HPP92_011326' => 'vpl', 'Hund12205' => 'sun', 'Hund17957' => 'sun', 'Lalb_Chr06g0176771' => 'lal', 'Lalb_Chr18g0056021' => 'lal', 'Lalb_Chr18g0056031' => 'lal', 'Lalb_Chr18g0056041' => 'lal', 'Lalb_Chr20g0107751' => 'lal', 'Lalb_Chr20g0118371' => 'lal', 'Lj1g0010239' => 'lja', 'Lj1g0017101' => 'lja', 'Lj2A1178G40' => 'lonja', 'Lj2A54G84' => 'lonja', 'Lj2g0015248' => 'lja', 'Lj3A761T51' => 'lonja', 'Lj6g0018116' => 'lja', 'Lsat_1_v5_gn_4_136040' => 'lsa', 'Lsat_1_v5_gn_5_187461' => 'lsa', 'Lsat_1_v5_gn_5_77001' => 'lsa', 'Lsat_1_v5_gn_9_4461' => 'lsa', 'Manes.01G210100' => 'mes', 'Manes.03G185600' => 'mes', 'Manes.05G073300' => 'mes', 'Manes.09G120300' => 'mes', 'Manes.15G022100' => 'mes', 'Mapoly0096s0053' => 'mpo', 'MBI03_g14058_MAGBIO' => 'mbi', 'MBI03_g33876_MAGBIO' => 'mbi', 'MBI03_g36854_MAGBIO' => 'mbi', 'MBI17_g11997_MAGBIO' => 'mbi', 'MD03G1269000' => 'mdo', 'MD04G1179600' => 'mdo', 'MD11G1289800' => 'mdo', 'MD12G1194700' => 'mdo', 'MD13G1182100' => 'mdo', 'MD13G1182200' => 'mdo', 'MD16G1182600' => 'mdo', 'Medtr2g021400' => 'mtr', 'Medtr2g021470' => 'mtr', 'Medtr2g105810' => 'mtr', 'Medtr3g033580' => 'mtr', 'Medtr6g007970' => 'mtr', 'Medtr7g056330' => 'mtr', 'Medtr7g074290' => 'mtr', 'Medtr7g074380' => 'mtr', 'Medtr7g094550' => 'mtr', 'Medtr8g069995' => 'mtr', 'MELO3C014345.2' => 'cme', 'MELO3C021395.2' => 'cme', 'Migut.D00262' => 'egut', 'Migut.G00257' => 'egut', 'MSTRG.21575' => 'ama', 'MSTRG.3985' => 'ama', 'Nitab4.5_0000295g0140' => 'nta', 'Nitab4.5_0000732g0140' => 'nta', 'Nitab4.5_0003162g0020' => 'nta', 'Nitab4.5_0006180g0090' => 'nta', 'Nitab4.5_0006390g0010' => 'nta', 'Nitab4.5_0007392g0040' => 'nta', 'Nn1g02140' => 'nnu', 'Nn4g26168' => 'nnu', 'Nn5g26754' => 'nnu', 'Oeu001433.1' => 'oeu', 'Oeu010299.2' => 'oeu', 'Oeu011171.1' => 'oeu', 'Oeu037675.1' => 'oeu', 'Oeu038359.1' => 'oeu', 'Oeu063834.1' => 'oeu', 'Oeu063835.1' => 'oeu', 'Os05g0312000' => 'osa', 'Os07g0211101' => 'osa', 'Os07g0211200' => 'osa', 'Os07g0681500' => 'osa', 'Peaxi162Scf00095g01015' => 'pax', 'Peaxi162Scf00104g00329' => 'pax', 'Peaxi162Scf00161g00137' => 'pax', 'PGR004G1665' => 'pgr', 'PGR031G2937' => 'pgr', 'PGR119G2145' => 'pgr', 'PGSC0003DMG400004351' => 'stu', 'PGSC0003DMG400014625' => 'stu', 'PGSC0003DMG401000943' => 'stu', 'Phvul.001G148600' => 'pvu', 'Phvul.004G001700' => 'pvu', 'Phvul.006G154900' => 'pvu', 'Phvul.008G078200' => 'pvu', 'Phvul.011G136500' => 'pvu', 'Potri.002G215600' => 'ptr', 'Potri.008G201600' => 'ptr', 'Potri.014G138400' => 'ptr', 'Potri.016G142500' => 'ptr', 'Pp3c16_10580' => 'ppa', 'Pp3c5_25280' => 'ppa', 'Prupe.1G150000' => 'ppe', 'Prupe.1G150100' => 'ppe', 'Prupe.6G299600' => 'ppe', 'Prupe.8G245000' => 'ppe', 'Psat0s4927g0040' => 'psa', 'Psat1g052080' => 'psa', 'Psat1g183800' => 'psa', 'Psat3g113840' => 'psa', 'Psat3g126120' => 'psa', 'Psat3g126160' => 'psa', 'Psat3g158760' => 'psa', 'Psat3g158840' => 'psa', 'PSO170G2858' => 'pso', 'PSO339G0606' => 'pso', 'PSO384G4709' => 'pso', 'PSO407G0334' => 'pso', 'QL04p040276' => 'qlo', 'QL06p005458' => 'qlo', 'QL06p005472' => 'qlo', 'QL07p030546' => 'qlo', 'QL07p031519' => 'qlo', 'QL09p050949' => 'qlo', 'QL09p050966' => 'qlo', 'QL09p051067' => 'qlo', 'QL12p022706' => 'qlo', 'RcHm_v2.0_Chr2g0119601' => 'rch', 'RcHm_v2.0_Chr3g0459591' => 'rch', 'RcHm_v2.0_Chr4g0418521' => 'rch', 'RcHm_v2.0_Chr4g0418531' => 'rch', 'RcHm_v2.0_Chr4g0418541' => 'rch', 'RcHm_v2.0_Chr6g0291641' => 'rch', 'Rhsim01G0086300' => 'rsi', 'Rhsim01G0276300' => 'rsi', 'Rhsim01G0276500' => 'rsi', 'Rhsim04G0207700' => 'rsi', 'Rhsim05G0234500' => 'rsi', 'Rhsim13G0022400' => 'rsi', 'Sabra02G0167900' => 'sbr', 'Sabra04G0158500' => 'sbr', 'Sabra08G0159800' => 'sbr', 'Sabra10G0011500' => 'sbr', 'Sabra14G0104400' => 'sbr', 'SalBow2G2440' => 'sbo', 'SalBow4G2265' => 'sbo', 'Sc02g0000060' => 'sci', 'Sc05g0005020' => 'sci', 'Sc13g0003890' => 'sci', 'Sed0014865' => 'sed', 'Sed0017224' => 'sed', 'Sed0026391' => 'sed', 'SEGI_00063' => 'sgi', 'SEGI_10967' => 'sgi', 'SEGI_17510' => 'sgi', 'SEGI_24396' => 'sgi', 'SEGI_39719' => 'sgi', 'SEGI_41392' => 'sgi', 'SGA_v2.0_scaffold11G05794' => 'sas', 'SGA_v2.0_scaffold142G35607' => 'sas', 'SGA_v2.0_scaffold1G00447' => 'sas', 'SHI15388' => 'shi', 'SHI15394' => 'shi', 'SHI15396' => 'shi', 'SHI15399' => 'shi', 'SMO343G0151' => 'smo', 'SMO367G1118' => 'smo', 'Solyc01g080200.3' => 'sly', 'Solyc06g008960.3' => 'sly', 'Solyc09g064780.3' => 'sly', 'Sopen01g031980' => 'spe', 'Sopen06g003710' => 'spe', 'Sopen09g026460' => 'spe', 'Sp3g21240' => 'spa', 'Sp4g30030' => 'spa', 'TAR365G0022' => 'tar', 'TAR365G1023' => 'tar', 'TAR365G1253' => 'tar', 'TAR623G0078' => 'tar', 'TAR623G1721' => 'tar', 'TAR633G0959' => 'tar', 'THA.LOC104802225' => 'tha', 'THA.LOC104804769' => 'tha', 'THA.LOC104808660' => 'tha', 'THA.LOC104812792' => 'tha', 'Thecc.01G284000' => 'tca', 'Thecc.04G220600' => 'tca', 'Thecc.05G268900' => 'tca', 'Thecc.08G171100' => 'tca', 'Thhalv10001284m.g' => 'esa', 'Thhalv10019912m.g' => 'esa', 'TPR.G14189' => 'tpr', 'TPR.G18110' => 'tpr', 'TPR.G18130' => 'tpr', 'TPR.G18131' => 'tpr', 'TPR.G18140' => 'tpr', 'TPR.G24282' => 'tpr', 'TPR.G25221' => 'tpr', 'TPR.G29267' => 'tpr', 'TPR.G35315' => 'tpr', 'TPR.G36173' => 'tpr', 'TWI09G0794' => 'twi', 'TWI59G1348' => 'twi', 'TWI74G0430' => 'twi', 'unitig_26.g8940' => 'ugi', 'unitig_749.g13744' => 'ugi', 'unitig_749.g13745' => 'ugi', 'vmacro08269' => 'vma', 'vmacro14937' => 'vma', 'vmacro20401' => 'vma', 'VMungo0464G1349' => 'vmu', 'VMungo0540G0289' => 'vmu', 'VMungo1215G1590' => 'vmu', 'VMungo1309G0221' => 'vmu', 'VMungo1309G2815' => 'vmu', 'VMungo1383G0239' => 'vmu', 'VMungo1383G2910' => 'vmu', 'Zm00001eb095270' => 'zma', 'Zm00001eb095280' => 'zma', 'Zm00001eb111630' => 'zma', 'Zm00001eb237080' => 'zma', 'Zm00001eb273740' => 'zma', 'Zm00001eb285040' => 'zma', 'Zm00001eb330790' => 'zma', 'Zm00001eb337380' => 'zma' ) $gf_id = 'HOM05D001484' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001484' ) $data_identifier = 'HOM05D001484' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 2, 'aly' => (int) 2, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 22, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 7, 'hma' => (int) 2, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 7, 'mtr' => (int) 10, 'cme' => (int) 2, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 4, 'ppa' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 4, 'qlo' => (int) 9, 'rch' => (int) 6, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 10, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 7, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb337380' $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' => 'HOM05D001484', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p31500' => 'bna', 'A05p00020' => 'bna', 'A07p08820' => 'bna', 'Aa31LG4G3300' => 'aar', 'Aa31LG8G10030' => 'aar', 'Actinidia00731' => 'ach', 'Actinidia11473' => 'ach', 'Actinidia23469' => 'ach', 'Actinidia24318' => 'ach', 'Actinidia40196' => 'ach', 'Actinidia40197' => 'ach', 'Actinidia40198' => 'ach', 'Ah.08g212990' => 'amhyb', 'Ah.15g091720' => 'amhyb', 'AL3G38260' => 'aly', 'AL4G47710' => 'aly', 'Aqoxy2G00671' => 'aox', 'Aqoxy2G03236' => 'aox', 'arahy.Tifrunner.gnm1.ann1.05IDCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KR684' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATY3SJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK6QJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6APGL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IDT7Z9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM073U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ0R87' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LE7RV4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT4QRX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V5ENPK' => 'arhy', 'AT2G48110' => 'ath', 'AT3G23590' => 'ath', 'ATR0626G186' => 'atr', 'ATR1127G141' => 'atr', 'Atru.chr4.2583' => 'acertr', 'Atru.chr5.1358' => 'acertr', 'Atru.chr5.1359' => 'acertr', 'Atru.chr8.46' => 'acertr', 'AUR62002640' => 'cqu', 'AUR62030055' => 'cqu', 'AUR62033713' => 'cqu', 'AUR62033714' => 'cqu', 'AUR62036795' => 'cqu', 'AUR62039891' => 'cqu', 'BcaB02g08737' => 'bca', 'BcaB04g20441' => 'bca', 'BcaB06g26509' => 'bca', 'BcaB06g26510' => 'bca', 'BcaB06g26511' => 'bca', 'BcaB06g26512' => 'bca', 'BcaB06g26513' => 'bca', 'BcaC02g12564' => 'bca', 'BcaC02g12565' => 'bca', 'BcaC02g12794' => 'bca', 'BcaC02g12795' => 'bca', 'BcaC02g12796' => 'bca', 'BcaC06g35541' => 'bca', 'BNapus_Darmor_BZH_scaffold_188p00080' => 'bna', 'BNapus_Darmor_BZH_scaffold_188p00090' => 'bna', 'BolC1t03972H' => 'bol', 'BolC1t03973H' => 'bol', 'BolC4t21680H' => 'bol', 'BolC7t41863H' => 'bol', 'BolSC55t61227H' => 'bol', 'BolSC55t61228H' => 'bol', 'BraA01t03278Z' => 'bra', 'BraA05t18998Z' => 'bra', 'BraA07t28673Z' => 'bra', 'C01p40150' => 'bna', 'C05p12370' => 'bna', 'C07p13680' => 'bna', 'CAN.G1006.16' => 'can', 'CAN.G1006.17' => 'can', 'CAN.G1170.2' => 'can', 'CAN.G962.7' => 'can', 'CANSAT25G2179' => 'cansat', 'CANSAT78G1573' => 'cansat', 'CARHR099510' => 'chi', 'CARHR143510' => 'chi', 'Carub.0003s2380' => 'cru', 'Carub.0004s3082' => 'cru', 'Ca_00614_v3' => 'car', 'Ca_07801_v3' => 'car', 'Ca_08567_v3' => 'car', 'Ca_09571_v3' => 'car', 'CBR_g19290' => 'cbr', 'Cc01_g19770' => 'ccan', 'Cc03_g03030' => 'ccan', 'CDE07G0968' => 'cde', 'CDE09G1441' => 'cde', 'Cfa006103' => 'cfa', 'Cfa015573' => 'cfa', 'Cfa016988' => 'cfa', 'Ciclev10006738m.g' => 'ccl', 'Ciclev10010920m.g' => 'ccl', 'Ciclev10018517m.g' => 'ccl', 'CiPaw.01G159200' => 'cil', 'CiPaw.02G091000' => 'cil', 'CiPaw.02G091100' => 'cil', 'CiPaw.08G103100' => 'cil', 'CiPaw.09G224900' => 'cil', 'ClCG06G005740' => 'cla', 'ClCG07G000090' => 'cla', 'ClCG07G000100' => 'cla', 'COL.COLO4_09143' => 'col', 'COL.COLO4_25124' => 'col', 'Cpa.g.sc16.34' => 'cpa', 'Cpa.g.sc3504.1' => 'cpa', 'Cpa.g.sc60.37' => 'cpa', 'CsaV3_6G018520' => 'csa', 'CsaV3_6G036860' => 'csa', 'CSS0001072' => 'camsi', 'CSS0020208' => 'camsi', 'CSS0021253' => 'camsi', 'CSS0022190' => 'camsi', 'CSS0036150' => 'camsi', 'CSS0040442' => 'camsi', 'CSS0042300' => 'camsi', 'CSS0045298' => 'camsi', 'DCAR_012449' => 'dca', 'DCAR_018405' => 'dca', 'DCAR_024573' => 'dca', 'DCAR_030591' => 'dca', 'Dinv16926' => 'din', 'Dinv32963' => 'din', 'Dinv38382' => 'din', 'Dinv38383' => 'din', 'Duzib133G0974' => 'dzi', 'Duzib138G1867' => 'dzi', 'Duzib211G0420' => 'dzi', 'Duzib212G0930' => 'dzi', 'ECA234G1645' => 'eca', 'ECA247G3467' => 'eca', 'ECA248G1703' => 'eca', 'EL10Ac3g06327' => 'bvu', 'EL10Ac7g17204' => 'bvu', 'Eucgr.A00855' => 'egr', 'Eucgr.A00858' => 'egr', 'Eucgr.H01520' => 'egr', 'Eucgr.H03604' => 'egr', 'Eucgr.L03465' => 'egr', 'Eucgr.L03466' => 'egr', 'FAN01G0988' => 'fan', 'FAN02G3892' => 'fan', 'FAN05G3381' => 'fan', 'FAN07G0967' => 'fan', 'FAN07G1493' => 'fan', 'FAN08G3125' => 'fan', 'FAN09G0402' => 'fan', 'FAN12G2594' => 'fan', 'FAN12G3879' => 'fan', 'FAN14G1546' => 'fan', 'FAN15G3626' => 'fan', 'FAN17G0588' => 'fan', 'FAN17G0609' => 'fan', 'FAN18G2817' => 'fan', 'FAN19G1305' => 'fan', 'FAN20G1787' => 'fan', 'FAN22G0073' => 'fan', 'FAN22G0352' => 'fan', 'FAN22G0368' => 'fan', 'FAN22G2273' => 'fan', 'FAN24G1998' => 'fan', 'FAN27G1317' => 'fan', 'FvH4_2g23980' => 'fve', 'FvH4_4g14380' => 'fve', 'FvH4_4g14390' => 'fve', 'FvH4_6g09250' => 'fve', 'Glyma.03G151100' => 'gma', 'Glyma.04G122550' => 'gma', 'Glyma.05G001600' => 'gma', 'Glyma.09G270766' => 'gma', 'Glyma.09G270832' => 'gma', 'Glyma.13G209800' => 'gma', 'Glyma.15G102800' => 'gma', 'Glyma.18G218900' => 'gma', 'Glyma.19G001500' => 'gma', 'Glyma.19G153600' => 'gma', 'Gohir.A02G028600' => 'ghi', 'Gohir.A08G045000' => 'ghi', 'Gohir.A11G120500' => 'ghi', 'Gohir.A12G006200' => 'ghi', 'Gohir.A12G006250' => 'ghi', 'Gohir.D02G036300' => 'ghi', 'Gohir.D08G054700' => 'ghi', 'Gohir.D11G125600' => 'ghi', 'Gohir.D12G005700' => 'ghi', 'Gorai.004G055200' => 'gra', 'Gorai.005G040400' => 'gra', 'Gorai.007G134500' => 'gra', 'Gorai.008G005500' => 'gra', 'GSVIVG01011094001' => 'vvi', 'GSVIVG01017879001' => 'vvi', 'GSVIVG01025988001' => 'vvi', 'GSVIVG01029847001' => 'vvi', 'HanXRQChr10g0282901' => 'han', 'HanXRQChr10g0310371' => 'han', 'HanXRQChr10g0315041' => 'han', 'HanXRQChr11g0327651' => 'han', 'HanXRQChr12g0359391' => 'han', 'Haze_00972' => 'cav', 'Haze_00973' => 'cav', 'Haze_00974' => 'cav', 'Haze_04747' => 'cav', 'Haze_04749' => 'cav', 'Haze_04750' => 'cav', 'Haze_21217' => 'cav', 'Hma1.2p1_1037F.1_g250680' => 'hma', 'Hma1.2p1_1644F.1_g295320' => 'hma', 'HPP92_011322' => 'vpl', 'HPP92_011323' => 'vpl', 'HPP92_011324' => 'vpl', 'HPP92_011325' => 'vpl', 'HPP92_011326' => 'vpl', 'Hund12205' => 'sun', 'Hund17957' => 'sun', 'Lalb_Chr06g0176771' => 'lal', 'Lalb_Chr18g0056021' => 'lal', 'Lalb_Chr18g0056031' => 'lal', 'Lalb_Chr18g0056041' => 'lal', 'Lalb_Chr20g0107751' => 'lal', 'Lalb_Chr20g0118371' => 'lal', 'Lj1g0010239' => 'lja', 'Lj1g0017101' => 'lja', 'Lj2A1178G40' => 'lonja', 'Lj2A54G84' => 'lonja', 'Lj2g0015248' => 'lja', 'Lj3A761T51' => 'lonja', 'Lj6g0018116' => 'lja', 'Lsat_1_v5_gn_4_136040' => 'lsa', 'Lsat_1_v5_gn_5_187461' => 'lsa', 'Lsat_1_v5_gn_5_77001' => 'lsa', 'Lsat_1_v5_gn_9_4461' => 'lsa', 'Manes.01G210100' => 'mes', 'Manes.03G185600' => 'mes', 'Manes.05G073300' => 'mes', 'Manes.09G120300' => 'mes', 'Manes.15G022100' => 'mes', 'Mapoly0096s0053' => 'mpo', 'MBI03_g14058_MAGBIO' => 'mbi', 'MBI03_g33876_MAGBIO' => 'mbi', 'MBI03_g36854_MAGBIO' => 'mbi', 'MBI17_g11997_MAGBIO' => 'mbi', 'MD03G1269000' => 'mdo', 'MD04G1179600' => 'mdo', 'MD11G1289800' => 'mdo', 'MD12G1194700' => 'mdo', 'MD13G1182100' => 'mdo', 'MD13G1182200' => 'mdo', 'MD16G1182600' => 'mdo', 'Medtr2g021400' => 'mtr', 'Medtr2g021470' => 'mtr', 'Medtr2g105810' => 'mtr', 'Medtr3g033580' => 'mtr', 'Medtr6g007970' => 'mtr', 'Medtr7g056330' => 'mtr', 'Medtr7g074290' => 'mtr', 'Medtr7g074380' => 'mtr', 'Medtr7g094550' => 'mtr', 'Medtr8g069995' => 'mtr', 'MELO3C014345.2' => 'cme', 'MELO3C021395.2' => 'cme', 'Migut.D00262' => 'egut', 'Migut.G00257' => 'egut', 'MSTRG.21575' => 'ama', 'MSTRG.3985' => 'ama', 'Nitab4.5_0000295g0140' => 'nta', 'Nitab4.5_0000732g0140' => 'nta', 'Nitab4.5_0003162g0020' => 'nta', 'Nitab4.5_0006180g0090' => 'nta', 'Nitab4.5_0006390g0010' => 'nta', 'Nitab4.5_0007392g0040' => 'nta', 'Nn1g02140' => 'nnu', 'Nn4g26168' => 'nnu', 'Nn5g26754' => 'nnu', 'Oeu001433.1' => 'oeu', 'Oeu010299.2' => 'oeu', 'Oeu011171.1' => 'oeu', 'Oeu037675.1' => 'oeu', 'Oeu038359.1' => 'oeu', 'Oeu063834.1' => 'oeu', 'Oeu063835.1' => 'oeu', 'Os05g0312000' => 'osa', 'Os07g0211101' => 'osa', 'Os07g0211200' => 'osa', 'Os07g0681500' => 'osa', 'Peaxi162Scf00095g01015' => 'pax', 'Peaxi162Scf00104g00329' => 'pax', 'Peaxi162Scf00161g00137' => 'pax', 'PGR004G1665' => 'pgr', 'PGR031G2937' => 'pgr', 'PGR119G2145' => 'pgr', 'PGSC0003DMG400004351' => 'stu', 'PGSC0003DMG400014625' => 'stu', 'PGSC0003DMG401000943' => 'stu', 'Phvul.001G148600' => 'pvu', 'Phvul.004G001700' => 'pvu', 'Phvul.006G154900' => 'pvu', 'Phvul.008G078200' => 'pvu', 'Phvul.011G136500' => 'pvu', 'Potri.002G215600' => 'ptr', 'Potri.008G201600' => 'ptr', 'Potri.014G138400' => 'ptr', 'Potri.016G142500' => 'ptr', 'Pp3c16_10580' => 'ppa', 'Pp3c5_25280' => 'ppa', 'Prupe.1G150000' => 'ppe', 'Prupe.1G150100' => 'ppe', 'Prupe.6G299600' => 'ppe', 'Prupe.8G245000' => 'ppe', 'Psat0s4927g0040' => 'psa', 'Psat1g052080' => 'psa', 'Psat1g183800' => 'psa', 'Psat3g113840' => 'psa', 'Psat3g126120' => 'psa', 'Psat3g126160' => 'psa', 'Psat3g158760' => 'psa', 'Psat3g158840' => 'psa', 'PSO170G2858' => 'pso', 'PSO339G0606' => 'pso', 'PSO384G4709' => 'pso', 'PSO407G0334' => 'pso', 'QL04p040276' => 'qlo', 'QL06p005458' => 'qlo', 'QL06p005472' => 'qlo', 'QL07p030546' => 'qlo', 'QL07p031519' => 'qlo', 'QL09p050949' => 'qlo', 'QL09p050966' => 'qlo', 'QL09p051067' => 'qlo', 'QL12p022706' => 'qlo', 'RcHm_v2.0_Chr2g0119601' => 'rch', 'RcHm_v2.0_Chr3g0459591' => 'rch', 'RcHm_v2.0_Chr4g0418521' => 'rch', 'RcHm_v2.0_Chr4g0418531' => 'rch', 'RcHm_v2.0_Chr4g0418541' => 'rch', 'RcHm_v2.0_Chr6g0291641' => 'rch', 'Rhsim01G0086300' => 'rsi', 'Rhsim01G0276300' => 'rsi', 'Rhsim01G0276500' => 'rsi', 'Rhsim04G0207700' => 'rsi', 'Rhsim05G0234500' => 'rsi', 'Rhsim13G0022400' => 'rsi', 'Sabra02G0167900' => 'sbr', 'Sabra04G0158500' => 'sbr', 'Sabra08G0159800' => 'sbr', 'Sabra10G0011500' => 'sbr', 'Sabra14G0104400' => 'sbr', 'SalBow2G2440' => 'sbo', 'SalBow4G2265' => 'sbo', 'Sc02g0000060' => 'sci', 'Sc05g0005020' => 'sci', 'Sc13g0003890' => 'sci', 'Sed0014865' => 'sed', 'Sed0017224' => 'sed', 'Sed0026391' => 'sed', 'SEGI_00063' => 'sgi', 'SEGI_10967' => 'sgi', 'SEGI_17510' => 'sgi', 'SEGI_24396' => 'sgi', 'SEGI_39719' => 'sgi', 'SEGI_41392' => 'sgi', 'SGA_v2.0_scaffold11G05794' => 'sas', 'SGA_v2.0_scaffold142G35607' => 'sas', 'SGA_v2.0_scaffold1G00447' => 'sas', 'SHI15388' => 'shi', 'SHI15394' => 'shi', 'SHI15396' => 'shi', 'SHI15399' => 'shi', 'SMO343G0151' => 'smo', 'SMO367G1118' => 'smo', 'Solyc01g080200.3' => 'sly', 'Solyc06g008960.3' => 'sly', 'Solyc09g064780.3' => 'sly', 'Sopen01g031980' => 'spe', 'Sopen06g003710' => 'spe', 'Sopen09g026460' => 'spe', 'Sp3g21240' => 'spa', 'Sp4g30030' => 'spa', 'TAR365G0022' => 'tar', 'TAR365G1023' => 'tar', 'TAR365G1253' => 'tar', 'TAR623G0078' => 'tar', 'TAR623G1721' => 'tar', 'TAR633G0959' => 'tar', 'THA.LOC104802225' => 'tha', 'THA.LOC104804769' => 'tha', 'THA.LOC104808660' => 'tha', 'THA.LOC104812792' => 'tha', 'Thecc.01G284000' => 'tca', 'Thecc.04G220600' => 'tca', 'Thecc.05G268900' => 'tca', 'Thecc.08G171100' => 'tca', 'Thhalv10001284m.g' => 'esa', 'Thhalv10019912m.g' => 'esa', 'TPR.G14189' => 'tpr', 'TPR.G18110' => 'tpr', 'TPR.G18130' => 'tpr', 'TPR.G18131' => 'tpr', 'TPR.G18140' => 'tpr', 'TPR.G24282' => 'tpr', 'TPR.G25221' => 'tpr', 'TPR.G29267' => 'tpr', 'TPR.G35315' => 'tpr', 'TPR.G36173' => 'tpr', 'TWI09G0794' => 'twi', 'TWI59G1348' => 'twi', 'TWI74G0430' => 'twi', 'unitig_26.g8940' => 'ugi', 'unitig_749.g13744' => 'ugi', 'unitig_749.g13745' => 'ugi', 'vmacro08269' => 'vma', 'vmacro14937' => 'vma', 'vmacro20401' => 'vma', 'VMungo0464G1349' => 'vmu', 'VMungo0540G0289' => 'vmu', 'VMungo1215G1590' => 'vmu', 'VMungo1309G0221' => 'vmu', 'VMungo1309G2815' => 'vmu', 'VMungo1383G0239' => 'vmu', 'VMungo1383G2910' => 'vmu', 'Zm00001eb095270' => 'zma', 'Zm00001eb095280' => 'zma', 'Zm00001eb111630' => 'zma', 'Zm00001eb237080' => 'zma', 'Zm00001eb273740' => 'zma', 'Zm00001eb285040' => 'zma', 'Zm00001eb330790' => 'zma', 'Zm00001eb337380' => 'zma' ), 'gf_id' => 'HOM05D001484', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001484' ), 'data_identifier' => 'HOM05D001484', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001484', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p31500' => 'bna', 'A05p00020' => 'bna', 'A07p08820' => 'bna', 'Aa31LG4G3300' => 'aar', 'Aa31LG8G10030' => 'aar', 'Actinidia00731' => 'ach', 'Actinidia11473' => 'ach', 'Actinidia23469' => 'ach', 'Actinidia24318' => 'ach', 'Actinidia40196' => 'ach', 'Actinidia40197' => 'ach', 'Actinidia40198' => 'ach', 'Ah.08g212990' => 'amhyb', 'Ah.15g091720' => 'amhyb', 'AL3G38260' => 'aly', 'AL4G47710' => 'aly', 'Aqoxy2G00671' => 'aox', 'Aqoxy2G03236' => 'aox', 'arahy.Tifrunner.gnm1.ann1.05IDCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KR684' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATY3SJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK6QJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6APGL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IDT7Z9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM073U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ0R87' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LE7RV4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT4QRX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V5ENPK' => 'arhy', 'AT2G48110' => 'ath', 'AT3G23590' => 'ath', 'ATR0626G186' => 'atr', 'ATR1127G141' => 'atr', 'Atru.chr4.2583' => 'acertr', 'Atru.chr5.1358' => 'acertr', 'Atru.chr5.1359' => 'acertr', 'Atru.chr8.46' => 'acertr', 'AUR62002640' => 'cqu', 'AUR62030055' => 'cqu', 'AUR62033713' => 'cqu', 'AUR62033714' => 'cqu', 'AUR62036795' => 'cqu', 'AUR62039891' => 'cqu', 'BcaB02g08737' => 'bca', 'BcaB04g20441' => 'bca', 'BcaB06g26509' => 'bca', 'BcaB06g26510' => 'bca', 'BcaB06g26511' => 'bca', 'BcaB06g26512' => 'bca', 'BcaB06g26513' => 'bca', 'BcaC02g12564' => 'bca', 'BcaC02g12565' => 'bca', 'BcaC02g12794' => 'bca', 'BcaC02g12795' => 'bca', 'BcaC02g12796' => 'bca', 'BcaC06g35541' => 'bca', 'BNapus_Darmor_BZH_scaffold_188p00080' => 'bna', 'BNapus_Darmor_BZH_scaffold_188p00090' => 'bna', 'BolC1t03972H' => 'bol', 'BolC1t03973H' => 'bol', 'BolC4t21680H' => 'bol', 'BolC7t41863H' => 'bol', 'BolSC55t61227H' => 'bol', 'BolSC55t61228H' => 'bol', 'BraA01t03278Z' => 'bra', 'BraA05t18998Z' => 'bra', 'BraA07t28673Z' => 'bra', 'C01p40150' => 'bna', 'C05p12370' => 'bna', 'C07p13680' => 'bna', 'CAN.G1006.16' => 'can', 'CAN.G1006.17' => 'can', 'CAN.G1170.2' => 'can', 'CAN.G962.7' => 'can', 'CANSAT25G2179' => 'cansat', 'CANSAT78G1573' => 'cansat', 'CARHR099510' => 'chi', 'CARHR143510' => 'chi', 'Carub.0003s2380' => 'cru', 'Carub.0004s3082' => 'cru', 'Ca_00614_v3' => 'car', 'Ca_07801_v3' => 'car', 'Ca_08567_v3' => 'car', 'Ca_09571_v3' => 'car', 'CBR_g19290' => 'cbr', 'Cc01_g19770' => 'ccan', 'Cc03_g03030' => 'ccan', 'CDE07G0968' => 'cde', 'CDE09G1441' => 'cde', 'Cfa006103' => 'cfa', 'Cfa015573' => 'cfa', 'Cfa016988' => 'cfa', 'Ciclev10006738m.g' => 'ccl', 'Ciclev10010920m.g' => 'ccl', 'Ciclev10018517m.g' => 'ccl', 'CiPaw.01G159200' => 'cil', 'CiPaw.02G091000' => 'cil', 'CiPaw.02G091100' => 'cil', 'CiPaw.08G103100' => 'cil', 'CiPaw.09G224900' => 'cil', 'ClCG06G005740' => 'cla', 'ClCG07G000090' => 'cla', 'ClCG07G000100' => 'cla', 'COL.COLO4_09143' => 'col', 'COL.COLO4_25124' => 'col', 'Cpa.g.sc16.34' => 'cpa', 'Cpa.g.sc3504.1' => 'cpa', 'Cpa.g.sc60.37' => 'cpa', 'CsaV3_6G018520' => 'csa', 'CsaV3_6G036860' => 'csa', 'CSS0001072' => 'camsi', 'CSS0020208' => 'camsi', 'CSS0021253' => 'camsi', 'CSS0022190' => 'camsi', 'CSS0036150' => 'camsi', 'CSS0040442' => 'camsi', 'CSS0042300' => 'camsi', 'CSS0045298' => 'camsi', 'DCAR_012449' => 'dca', 'DCAR_018405' => 'dca', 'DCAR_024573' => 'dca', 'DCAR_030591' => 'dca', 'Dinv16926' => 'din', 'Dinv32963' => 'din', 'Dinv38382' => 'din', 'Dinv38383' => 'din', 'Duzib133G0974' => 'dzi', 'Duzib138G1867' => 'dzi', 'Duzib211G0420' => 'dzi', 'Duzib212G0930' => 'dzi', 'ECA234G1645' => 'eca', 'ECA247G3467' => 'eca', 'ECA248G1703' => 'eca', 'EL10Ac3g06327' => 'bvu', 'EL10Ac7g17204' => 'bvu', 'Eucgr.A00855' => 'egr', 'Eucgr.A00858' => 'egr', 'Eucgr.H01520' => 'egr', 'Eucgr.H03604' => 'egr', 'Eucgr.L03465' => 'egr', 'Eucgr.L03466' => 'egr', 'FAN01G0988' => 'fan', 'FAN02G3892' => 'fan', 'FAN05G3381' => 'fan', 'FAN07G0967' => 'fan', 'FAN07G1493' => 'fan', 'FAN08G3125' => 'fan', 'FAN09G0402' => 'fan', 'FAN12G2594' => 'fan', 'FAN12G3879' => 'fan', 'FAN14G1546' => 'fan', 'FAN15G3626' => 'fan', 'FAN17G0588' => 'fan', 'FAN17G0609' => 'fan', 'FAN18G2817' => 'fan', 'FAN19G1305' => 'fan', 'FAN20G1787' => 'fan', 'FAN22G0073' => 'fan', 'FAN22G0352' => 'fan', 'FAN22G0368' => 'fan', 'FAN22G2273' => 'fan', 'FAN24G1998' => 'fan', 'FAN27G1317' => 'fan', 'FvH4_2g23980' => 'fve', 'FvH4_4g14380' => 'fve', 'FvH4_4g14390' => 'fve', 'FvH4_6g09250' => 'fve', 'Glyma.03G151100' => 'gma', 'Glyma.04G122550' => 'gma', 'Glyma.05G001600' => 'gma', 'Glyma.09G270766' => 'gma', 'Glyma.09G270832' => 'gma', 'Glyma.13G209800' => 'gma', 'Glyma.15G102800' => 'gma', 'Glyma.18G218900' => 'gma', 'Glyma.19G001500' => 'gma', 'Glyma.19G153600' => 'gma', 'Gohir.A02G028600' => 'ghi', 'Gohir.A08G045000' => 'ghi', 'Gohir.A11G120500' => 'ghi', 'Gohir.A12G006200' => 'ghi', 'Gohir.A12G006250' => 'ghi', 'Gohir.D02G036300' => 'ghi', 'Gohir.D08G054700' => 'ghi', 'Gohir.D11G125600' => 'ghi', 'Gohir.D12G005700' => 'ghi', 'Gorai.004G055200' => 'gra', 'Gorai.005G040400' => 'gra', 'Gorai.007G134500' => 'gra', 'Gorai.008G005500' => 'gra', 'GSVIVG01011094001' => 'vvi', 'GSVIVG01017879001' => 'vvi', 'GSVIVG01025988001' => 'vvi', 'GSVIVG01029847001' => 'vvi', 'HanXRQChr10g0282901' => 'han', 'HanXRQChr10g0310371' => 'han', 'HanXRQChr10g0315041' => 'han', 'HanXRQChr11g0327651' => 'han', 'HanXRQChr12g0359391' => 'han', 'Haze_00972' => 'cav', 'Haze_00973' => 'cav', 'Haze_00974' => 'cav', 'Haze_04747' => 'cav', 'Haze_04749' => 'cav', 'Haze_04750' => 'cav', 'Haze_21217' => 'cav', 'Hma1.2p1_1037F.1_g250680' => 'hma', 'Hma1.2p1_1644F.1_g295320' => 'hma', 'HPP92_011322' => 'vpl', 'HPP92_011323' => 'vpl', 'HPP92_011324' => 'vpl', 'HPP92_011325' => 'vpl', 'HPP92_011326' => 'vpl', 'Hund12205' => 'sun', 'Hund17957' => 'sun', 'Lalb_Chr06g0176771' => 'lal', 'Lalb_Chr18g0056021' => 'lal', 'Lalb_Chr18g0056031' => 'lal', 'Lalb_Chr18g0056041' => 'lal', 'Lalb_Chr20g0107751' => 'lal', 'Lalb_Chr20g0118371' => 'lal', 'Lj1g0010239' => 'lja', 'Lj1g0017101' => 'lja', 'Lj2A1178G40' => 'lonja', 'Lj2A54G84' => 'lonja', 'Lj2g0015248' => 'lja', 'Lj3A761T51' => 'lonja', 'Lj6g0018116' => 'lja', 'Lsat_1_v5_gn_4_136040' => 'lsa', 'Lsat_1_v5_gn_5_187461' => 'lsa', 'Lsat_1_v5_gn_5_77001' => 'lsa', 'Lsat_1_v5_gn_9_4461' => 'lsa', 'Manes.01G210100' => 'mes', 'Manes.03G185600' => 'mes', 'Manes.05G073300' => 'mes', 'Manes.09G120300' => 'mes', 'Manes.15G022100' => 'mes', 'Mapoly0096s0053' => 'mpo', 'MBI03_g14058_MAGBIO' => 'mbi', 'MBI03_g33876_MAGBIO' => 'mbi', 'MBI03_g36854_MAGBIO' => 'mbi', 'MBI17_g11997_MAGBIO' => 'mbi', 'MD03G1269000' => 'mdo', 'MD04G1179600' => 'mdo', 'MD11G1289800' => 'mdo', 'MD12G1194700' => 'mdo', 'MD13G1182100' => 'mdo', 'MD13G1182200' => 'mdo', 'MD16G1182600' => 'mdo', 'Medtr2g021400' => 'mtr', 'Medtr2g021470' => 'mtr', 'Medtr2g105810' => 'mtr', 'Medtr3g033580' => 'mtr', 'Medtr6g007970' => 'mtr', 'Medtr7g056330' => 'mtr', 'Medtr7g074290' => 'mtr', 'Medtr7g074380' => 'mtr', 'Medtr7g094550' => 'mtr', 'Medtr8g069995' => 'mtr', 'MELO3C014345.2' => 'cme', 'MELO3C021395.2' => 'cme', 'Migut.D00262' => 'egut', 'Migut.G00257' => 'egut', 'MSTRG.21575' => 'ama', 'MSTRG.3985' => 'ama', 'Nitab4.5_0000295g0140' => 'nta', 'Nitab4.5_0000732g0140' => 'nta', 'Nitab4.5_0003162g0020' => 'nta', 'Nitab4.5_0006180g0090' => 'nta', 'Nitab4.5_0006390g0010' => 'nta', 'Nitab4.5_0007392g0040' => 'nta', 'Nn1g02140' => 'nnu', 'Nn4g26168' => 'nnu', 'Nn5g26754' => 'nnu', 'Oeu001433.1' => 'oeu', 'Oeu010299.2' => 'oeu', 'Oeu011171.1' => 'oeu', 'Oeu037675.1' => 'oeu', 'Oeu038359.1' => 'oeu', 'Oeu063834.1' => 'oeu', 'Oeu063835.1' => 'oeu', 'Os05g0312000' => 'osa', 'Os07g0211101' => 'osa', 'Os07g0211200' => 'osa', 'Os07g0681500' => 'osa', 'Peaxi162Scf00095g01015' => 'pax', 'Peaxi162Scf00104g00329' => 'pax', 'Peaxi162Scf00161g00137' => 'pax', 'PGR004G1665' => 'pgr', 'PGR031G2937' => 'pgr', 'PGR119G2145' => 'pgr', 'PGSC0003DMG400004351' => 'stu', 'PGSC0003DMG400014625' => 'stu', 'PGSC0003DMG401000943' => 'stu', 'Phvul.001G148600' => 'pvu', 'Phvul.004G001700' => 'pvu', 'Phvul.006G154900' => 'pvu', 'Phvul.008G078200' => 'pvu', 'Phvul.011G136500' => 'pvu', 'Potri.002G215600' => 'ptr', 'Potri.008G201600' => 'ptr', 'Potri.014G138400' => 'ptr', 'Potri.016G142500' => 'ptr', 'Pp3c16_10580' => 'ppa', 'Pp3c5_25280' => 'ppa', 'Prupe.1G150000' => 'ppe', 'Prupe.1G150100' => 'ppe', 'Prupe.6G299600' => 'ppe', 'Prupe.8G245000' => 'ppe', 'Psat0s4927g0040' => 'psa', 'Psat1g052080' => 'psa', 'Psat1g183800' => 'psa', 'Psat3g113840' => 'psa', 'Psat3g126120' => 'psa', 'Psat3g126160' => 'psa', 'Psat3g158760' => 'psa', 'Psat3g158840' => 'psa', 'PSO170G2858' => 'pso', 'PSO339G0606' => 'pso', 'PSO384G4709' => 'pso', 'PSO407G0334' => 'pso', 'QL04p040276' => 'qlo', 'QL06p005458' => 'qlo', 'QL06p005472' => 'qlo', 'QL07p030546' => 'qlo', 'QL07p031519' => 'qlo', 'QL09p050949' => 'qlo', 'QL09p050966' => 'qlo', 'QL09p051067' => 'qlo', 'QL12p022706' => 'qlo', 'RcHm_v2.0_Chr2g0119601' => 'rch', 'RcHm_v2.0_Chr3g0459591' => 'rch', 'RcHm_v2.0_Chr4g0418521' => 'rch', 'RcHm_v2.0_Chr4g0418531' => 'rch', 'RcHm_v2.0_Chr4g0418541' => 'rch', 'RcHm_v2.0_Chr6g0291641' => 'rch', 'Rhsim01G0086300' => 'rsi', 'Rhsim01G0276300' => 'rsi', 'Rhsim01G0276500' => 'rsi', 'Rhsim04G0207700' => 'rsi', 'Rhsim05G0234500' => 'rsi', 'Rhsim13G0022400' => 'rsi', 'Sabra02G0167900' => 'sbr', 'Sabra04G0158500' => 'sbr', 'Sabra08G0159800' => 'sbr', 'Sabra10G0011500' => 'sbr', 'Sabra14G0104400' => 'sbr', 'SalBow2G2440' => 'sbo', 'SalBow4G2265' => 'sbo', 'Sc02g0000060' => 'sci', 'Sc05g0005020' => 'sci', 'Sc13g0003890' => 'sci', 'Sed0014865' => 'sed', 'Sed0017224' => 'sed', 'Sed0026391' => 'sed', 'SEGI_00063' => 'sgi', 'SEGI_10967' => 'sgi', 'SEGI_17510' => 'sgi', 'SEGI_24396' => 'sgi', 'SEGI_39719' => 'sgi', 'SEGI_41392' => 'sgi', 'SGA_v2.0_scaffold11G05794' => 'sas', 'SGA_v2.0_scaffold142G35607' => 'sas', 'SGA_v2.0_scaffold1G00447' => 'sas', 'SHI15388' => 'shi', 'SHI15394' => 'shi', 'SHI15396' => 'shi', 'SHI15399' => 'shi', 'SMO343G0151' => 'smo', 'SMO367G1118' => 'smo', 'Solyc01g080200.3' => 'sly', 'Solyc06g008960.3' => 'sly', 'Solyc09g064780.3' => 'sly', 'Sopen01g031980' => 'spe', 'Sopen06g003710' => 'spe', 'Sopen09g026460' => 'spe', 'Sp3g21240' => 'spa', 'Sp4g30030' => 'spa', 'TAR365G0022' => 'tar', 'TAR365G1023' => 'tar', 'TAR365G1253' => 'tar', 'TAR623G0078' => 'tar', 'TAR623G1721' => 'tar', 'TAR633G0959' => 'tar', 'THA.LOC104802225' => 'tha', 'THA.LOC104804769' => 'tha', 'THA.LOC104808660' => 'tha', 'THA.LOC104812792' => 'tha', 'Thecc.01G284000' => 'tca', 'Thecc.04G220600' => 'tca', 'Thecc.05G268900' => 'tca', 'Thecc.08G171100' => 'tca', 'Thhalv10001284m.g' => 'esa', 'Thhalv10019912m.g' => 'esa', 'TPR.G14189' => 'tpr', 'TPR.G18110' => 'tpr', 'TPR.G18130' => 'tpr', 'TPR.G18131' => 'tpr', 'TPR.G18140' => 'tpr', 'TPR.G24282' => 'tpr', 'TPR.G25221' => 'tpr', 'TPR.G29267' => 'tpr', 'TPR.G35315' => 'tpr', 'TPR.G36173' => 'tpr', 'TWI09G0794' => 'twi', 'TWI59G1348' => 'twi', 'TWI74G0430' => 'twi', 'unitig_26.g8940' => 'ugi', 'unitig_749.g13744' => 'ugi', 'unitig_749.g13745' => 'ugi', 'vmacro08269' => 'vma', 'vmacro14937' => 'vma', 'vmacro20401' => 'vma', 'VMungo0464G1349' => 'vmu', 'VMungo0540G0289' => 'vmu', 'VMungo1215G1590' => 'vmu', 'VMungo1309G0221' => 'vmu', 'VMungo1309G2815' => 'vmu', 'VMungo1383G0239' => 'vmu', 'VMungo1383G2910' => 'vmu', 'Zm00001eb095270' => 'zma', 'Zm00001eb095280' => 'zma', 'Zm00001eb111630' => 'zma', 'Zm00001eb237080' => 'zma', 'Zm00001eb273740' => 'zma', 'Zm00001eb285040' => 'zma', 'Zm00001eb330790' => 'zma', 'Zm00001eb337380' => 'zma' ) $gf_id = 'HOM05D001484' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001484' ) $data_identifier = 'HOM05D001484' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 2, 'aly' => (int) 2, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 22, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 7, 'hma' => (int) 2, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 7, 'mtr' => (int) 10, 'cme' => (int) 2, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 4, 'ppa' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 4, 'qlo' => (int) 9, 'rch' => (int) 6, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 10, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 7, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb337380' $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' => 'HOM05D001484', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p31500' => 'bna', 'A05p00020' => 'bna', 'A07p08820' => 'bna', 'Aa31LG4G3300' => 'aar', 'Aa31LG8G10030' => 'aar', 'Actinidia00731' => 'ach', 'Actinidia11473' => 'ach', 'Actinidia23469' => 'ach', 'Actinidia24318' => 'ach', 'Actinidia40196' => 'ach', 'Actinidia40197' => 'ach', 'Actinidia40198' => 'ach', 'Ah.08g212990' => 'amhyb', 'Ah.15g091720' => 'amhyb', 'AL3G38260' => 'aly', 'AL4G47710' => 'aly', 'Aqoxy2G00671' => 'aox', 'Aqoxy2G03236' => 'aox', 'arahy.Tifrunner.gnm1.ann1.05IDCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KR684' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATY3SJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK6QJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6APGL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IDT7Z9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM073U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ0R87' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LE7RV4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT4QRX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V5ENPK' => 'arhy', 'AT2G48110' => 'ath', 'AT3G23590' => 'ath', 'ATR0626G186' => 'atr', 'ATR1127G141' => 'atr', 'Atru.chr4.2583' => 'acertr', 'Atru.chr5.1358' => 'acertr', 'Atru.chr5.1359' => 'acertr', 'Atru.chr8.46' => 'acertr', 'AUR62002640' => 'cqu', 'AUR62030055' => 'cqu', 'AUR62033713' => 'cqu', 'AUR62033714' => 'cqu', 'AUR62036795' => 'cqu', 'AUR62039891' => 'cqu', 'BcaB02g08737' => 'bca', 'BcaB04g20441' => 'bca', 'BcaB06g26509' => 'bca', 'BcaB06g26510' => 'bca', 'BcaB06g26511' => 'bca', 'BcaB06g26512' => 'bca', 'BcaB06g26513' => 'bca', 'BcaC02g12564' => 'bca', 'BcaC02g12565' => 'bca', 'BcaC02g12794' => 'bca', 'BcaC02g12795' => 'bca', 'BcaC02g12796' => 'bca', 'BcaC06g35541' => 'bca', 'BNapus_Darmor_BZH_scaffold_188p00080' => 'bna', 'BNapus_Darmor_BZH_scaffold_188p00090' => 'bna', 'BolC1t03972H' => 'bol', 'BolC1t03973H' => 'bol', 'BolC4t21680H' => 'bol', 'BolC7t41863H' => 'bol', 'BolSC55t61227H' => 'bol', 'BolSC55t61228H' => 'bol', 'BraA01t03278Z' => 'bra', 'BraA05t18998Z' => 'bra', 'BraA07t28673Z' => 'bra', 'C01p40150' => 'bna', 'C05p12370' => 'bna', 'C07p13680' => 'bna', 'CAN.G1006.16' => 'can', 'CAN.G1006.17' => 'can', 'CAN.G1170.2' => 'can', 'CAN.G962.7' => 'can', 'CANSAT25G2179' => 'cansat', 'CANSAT78G1573' => 'cansat', 'CARHR099510' => 'chi', 'CARHR143510' => 'chi', 'Carub.0003s2380' => 'cru', 'Carub.0004s3082' => 'cru', 'Ca_00614_v3' => 'car', 'Ca_07801_v3' => 'car', 'Ca_08567_v3' => 'car', 'Ca_09571_v3' => 'car', 'CBR_g19290' => 'cbr', 'Cc01_g19770' => 'ccan', 'Cc03_g03030' => 'ccan', 'CDE07G0968' => 'cde', 'CDE09G1441' => 'cde', 'Cfa006103' => 'cfa', 'Cfa015573' => 'cfa', 'Cfa016988' => 'cfa', 'Ciclev10006738m.g' => 'ccl', 'Ciclev10010920m.g' => 'ccl', 'Ciclev10018517m.g' => 'ccl', 'CiPaw.01G159200' => 'cil', 'CiPaw.02G091000' => 'cil', 'CiPaw.02G091100' => 'cil', 'CiPaw.08G103100' => 'cil', 'CiPaw.09G224900' => 'cil', 'ClCG06G005740' => 'cla', 'ClCG07G000090' => 'cla', 'ClCG07G000100' => 'cla', 'COL.COLO4_09143' => 'col', 'COL.COLO4_25124' => 'col', 'Cpa.g.sc16.34' => 'cpa', 'Cpa.g.sc3504.1' => 'cpa', 'Cpa.g.sc60.37' => 'cpa', 'CsaV3_6G018520' => 'csa', 'CsaV3_6G036860' => 'csa', 'CSS0001072' => 'camsi', 'CSS0020208' => 'camsi', 'CSS0021253' => 'camsi', 'CSS0022190' => 'camsi', 'CSS0036150' => 'camsi', 'CSS0040442' => 'camsi', 'CSS0042300' => 'camsi', 'CSS0045298' => 'camsi', 'DCAR_012449' => 'dca', 'DCAR_018405' => 'dca', 'DCAR_024573' => 'dca', 'DCAR_030591' => 'dca', 'Dinv16926' => 'din', 'Dinv32963' => 'din', 'Dinv38382' => 'din', 'Dinv38383' => 'din', 'Duzib133G0974' => 'dzi', 'Duzib138G1867' => 'dzi', 'Duzib211G0420' => 'dzi', 'Duzib212G0930' => 'dzi', 'ECA234G1645' => 'eca', 'ECA247G3467' => 'eca', 'ECA248G1703' => 'eca', 'EL10Ac3g06327' => 'bvu', 'EL10Ac7g17204' => 'bvu', 'Eucgr.A00855' => 'egr', 'Eucgr.A00858' => 'egr', 'Eucgr.H01520' => 'egr', 'Eucgr.H03604' => 'egr', 'Eucgr.L03465' => 'egr', 'Eucgr.L03466' => 'egr', 'FAN01G0988' => 'fan', 'FAN02G3892' => 'fan', 'FAN05G3381' => 'fan', 'FAN07G0967' => 'fan', 'FAN07G1493' => 'fan', 'FAN08G3125' => 'fan', 'FAN09G0402' => 'fan', 'FAN12G2594' => 'fan', 'FAN12G3879' => 'fan', 'FAN14G1546' => 'fan', 'FAN15G3626' => 'fan', 'FAN17G0588' => 'fan', 'FAN17G0609' => 'fan', 'FAN18G2817' => 'fan', 'FAN19G1305' => 'fan', 'FAN20G1787' => 'fan', 'FAN22G0073' => 'fan', 'FAN22G0352' => 'fan', 'FAN22G0368' => 'fan', 'FAN22G2273' => 'fan', 'FAN24G1998' => 'fan', 'FAN27G1317' => 'fan', 'FvH4_2g23980' => 'fve', 'FvH4_4g14380' => 'fve', 'FvH4_4g14390' => 'fve', 'FvH4_6g09250' => 'fve', 'Glyma.03G151100' => 'gma', 'Glyma.04G122550' => 'gma', 'Glyma.05G001600' => 'gma', 'Glyma.09G270766' => 'gma', 'Glyma.09G270832' => 'gma', 'Glyma.13G209800' => 'gma', 'Glyma.15G102800' => 'gma', 'Glyma.18G218900' => 'gma', 'Glyma.19G001500' => 'gma', 'Glyma.19G153600' => 'gma', 'Gohir.A02G028600' => 'ghi', 'Gohir.A08G045000' => 'ghi', 'Gohir.A11G120500' => 'ghi', 'Gohir.A12G006200' => 'ghi', 'Gohir.A12G006250' => 'ghi', 'Gohir.D02G036300' => 'ghi', 'Gohir.D08G054700' => 'ghi', 'Gohir.D11G125600' => 'ghi', 'Gohir.D12G005700' => 'ghi', 'Gorai.004G055200' => 'gra', 'Gorai.005G040400' => 'gra', 'Gorai.007G134500' => 'gra', 'Gorai.008G005500' => 'gra', 'GSVIVG01011094001' => 'vvi', 'GSVIVG01017879001' => 'vvi', 'GSVIVG01025988001' => 'vvi', 'GSVIVG01029847001' => 'vvi', 'HanXRQChr10g0282901' => 'han', 'HanXRQChr10g0310371' => 'han', 'HanXRQChr10g0315041' => 'han', 'HanXRQChr11g0327651' => 'han', 'HanXRQChr12g0359391' => 'han', 'Haze_00972' => 'cav', 'Haze_00973' => 'cav', 'Haze_00974' => 'cav', 'Haze_04747' => 'cav', 'Haze_04749' => 'cav', 'Haze_04750' => 'cav', 'Haze_21217' => 'cav', 'Hma1.2p1_1037F.1_g250680' => 'hma', 'Hma1.2p1_1644F.1_g295320' => 'hma', 'HPP92_011322' => 'vpl', 'HPP92_011323' => 'vpl', 'HPP92_011324' => 'vpl', 'HPP92_011325' => 'vpl', 'HPP92_011326' => 'vpl', 'Hund12205' => 'sun', 'Hund17957' => 'sun', 'Lalb_Chr06g0176771' => 'lal', 'Lalb_Chr18g0056021' => 'lal', 'Lalb_Chr18g0056031' => 'lal', 'Lalb_Chr18g0056041' => 'lal', 'Lalb_Chr20g0107751' => 'lal', 'Lalb_Chr20g0118371' => 'lal', 'Lj1g0010239' => 'lja', 'Lj1g0017101' => 'lja', 'Lj2A1178G40' => 'lonja', 'Lj2A54G84' => 'lonja', 'Lj2g0015248' => 'lja', 'Lj3A761T51' => 'lonja', 'Lj6g0018116' => 'lja', 'Lsat_1_v5_gn_4_136040' => 'lsa', 'Lsat_1_v5_gn_5_187461' => 'lsa', 'Lsat_1_v5_gn_5_77001' => 'lsa', 'Lsat_1_v5_gn_9_4461' => 'lsa', 'Manes.01G210100' => 'mes', 'Manes.03G185600' => 'mes', 'Manes.05G073300' => 'mes', 'Manes.09G120300' => 'mes', 'Manes.15G022100' => 'mes', 'Mapoly0096s0053' => 'mpo', 'MBI03_g14058_MAGBIO' => 'mbi', 'MBI03_g33876_MAGBIO' => 'mbi', 'MBI03_g36854_MAGBIO' => 'mbi', 'MBI17_g11997_MAGBIO' => 'mbi', 'MD03G1269000' => 'mdo', 'MD04G1179600' => 'mdo', 'MD11G1289800' => 'mdo', 'MD12G1194700' => 'mdo', 'MD13G1182100' => 'mdo', 'MD13G1182200' => 'mdo', 'MD16G1182600' => 'mdo', 'Medtr2g021400' => 'mtr', 'Medtr2g021470' => 'mtr', 'Medtr2g105810' => 'mtr', 'Medtr3g033580' => 'mtr', 'Medtr6g007970' => 'mtr', 'Medtr7g056330' => 'mtr', 'Medtr7g074290' => 'mtr', 'Medtr7g074380' => 'mtr', 'Medtr7g094550' => 'mtr', 'Medtr8g069995' => 'mtr', 'MELO3C014345.2' => 'cme', 'MELO3C021395.2' => 'cme', 'Migut.D00262' => 'egut', 'Migut.G00257' => 'egut', 'MSTRG.21575' => 'ama', 'MSTRG.3985' => 'ama', 'Nitab4.5_0000295g0140' => 'nta', 'Nitab4.5_0000732g0140' => 'nta', 'Nitab4.5_0003162g0020' => 'nta', 'Nitab4.5_0006180g0090' => 'nta', 'Nitab4.5_0006390g0010' => 'nta', 'Nitab4.5_0007392g0040' => 'nta', 'Nn1g02140' => 'nnu', 'Nn4g26168' => 'nnu', 'Nn5g26754' => 'nnu', 'Oeu001433.1' => 'oeu', 'Oeu010299.2' => 'oeu', 'Oeu011171.1' => 'oeu', 'Oeu037675.1' => 'oeu', 'Oeu038359.1' => 'oeu', 'Oeu063834.1' => 'oeu', 'Oeu063835.1' => 'oeu', 'Os05g0312000' => 'osa', 'Os07g0211101' => 'osa', 'Os07g0211200' => 'osa', 'Os07g0681500' => 'osa', 'Peaxi162Scf00095g01015' => 'pax', 'Peaxi162Scf00104g00329' => 'pax', 'Peaxi162Scf00161g00137' => 'pax', 'PGR004G1665' => 'pgr', 'PGR031G2937' => 'pgr', 'PGR119G2145' => 'pgr', 'PGSC0003DMG400004351' => 'stu', 'PGSC0003DMG400014625' => 'stu', 'PGSC0003DMG401000943' => 'stu', 'Phvul.001G148600' => 'pvu', 'Phvul.004G001700' => 'pvu', 'Phvul.006G154900' => 'pvu', 'Phvul.008G078200' => 'pvu', 'Phvul.011G136500' => 'pvu', 'Potri.002G215600' => 'ptr', 'Potri.008G201600' => 'ptr', 'Potri.014G138400' => 'ptr', 'Potri.016G142500' => 'ptr', 'Pp3c16_10580' => 'ppa', 'Pp3c5_25280' => 'ppa', 'Prupe.1G150000' => 'ppe', 'Prupe.1G150100' => 'ppe', 'Prupe.6G299600' => 'ppe', 'Prupe.8G245000' => 'ppe', 'Psat0s4927g0040' => 'psa', 'Psat1g052080' => 'psa', 'Psat1g183800' => 'psa', 'Psat3g113840' => 'psa', 'Psat3g126120' => 'psa', 'Psat3g126160' => 'psa', 'Psat3g158760' => 'psa', 'Psat3g158840' => 'psa', 'PSO170G2858' => 'pso', 'PSO339G0606' => 'pso', 'PSO384G4709' => 'pso', 'PSO407G0334' => 'pso', 'QL04p040276' => 'qlo', 'QL06p005458' => 'qlo', 'QL06p005472' => 'qlo', 'QL07p030546' => 'qlo', 'QL07p031519' => 'qlo', 'QL09p050949' => 'qlo', 'QL09p050966' => 'qlo', 'QL09p051067' => 'qlo', 'QL12p022706' => 'qlo', 'RcHm_v2.0_Chr2g0119601' => 'rch', 'RcHm_v2.0_Chr3g0459591' => 'rch', 'RcHm_v2.0_Chr4g0418521' => 'rch', 'RcHm_v2.0_Chr4g0418531' => 'rch', 'RcHm_v2.0_Chr4g0418541' => 'rch', 'RcHm_v2.0_Chr6g0291641' => 'rch', 'Rhsim01G0086300' => 'rsi', 'Rhsim01G0276300' => 'rsi', 'Rhsim01G0276500' => 'rsi', 'Rhsim04G0207700' => 'rsi', 'Rhsim05G0234500' => 'rsi', 'Rhsim13G0022400' => 'rsi', 'Sabra02G0167900' => 'sbr', 'Sabra04G0158500' => 'sbr', 'Sabra08G0159800' => 'sbr', 'Sabra10G0011500' => 'sbr', 'Sabra14G0104400' => 'sbr', 'SalBow2G2440' => 'sbo', 'SalBow4G2265' => 'sbo', 'Sc02g0000060' => 'sci', 'Sc05g0005020' => 'sci', 'Sc13g0003890' => 'sci', 'Sed0014865' => 'sed', 'Sed0017224' => 'sed', 'Sed0026391' => 'sed', 'SEGI_00063' => 'sgi', 'SEGI_10967' => 'sgi', 'SEGI_17510' => 'sgi', 'SEGI_24396' => 'sgi', 'SEGI_39719' => 'sgi', 'SEGI_41392' => 'sgi', 'SGA_v2.0_scaffold11G05794' => 'sas', 'SGA_v2.0_scaffold142G35607' => 'sas', 'SGA_v2.0_scaffold1G00447' => 'sas', 'SHI15388' => 'shi', 'SHI15394' => 'shi', 'SHI15396' => 'shi', 'SHI15399' => 'shi', 'SMO343G0151' => 'smo', 'SMO367G1118' => 'smo', 'Solyc01g080200.3' => 'sly', 'Solyc06g008960.3' => 'sly', 'Solyc09g064780.3' => 'sly', 'Sopen01g031980' => 'spe', 'Sopen06g003710' => 'spe', 'Sopen09g026460' => 'spe', 'Sp3g21240' => 'spa', 'Sp4g30030' => 'spa', 'TAR365G0022' => 'tar', 'TAR365G1023' => 'tar', 'TAR365G1253' => 'tar', 'TAR623G0078' => 'tar', 'TAR623G1721' => 'tar', 'TAR633G0959' => 'tar', 'THA.LOC104802225' => 'tha', 'THA.LOC104804769' => 'tha', 'THA.LOC104808660' => 'tha', 'THA.LOC104812792' => 'tha', 'Thecc.01G284000' => 'tca', 'Thecc.04G220600' => 'tca', 'Thecc.05G268900' => 'tca', 'Thecc.08G171100' => 'tca', 'Thhalv10001284m.g' => 'esa', 'Thhalv10019912m.g' => 'esa', 'TPR.G14189' => 'tpr', 'TPR.G18110' => 'tpr', 'TPR.G18130' => 'tpr', 'TPR.G18131' => 'tpr', 'TPR.G18140' => 'tpr', 'TPR.G24282' => 'tpr', 'TPR.G25221' => 'tpr', 'TPR.G29267' => 'tpr', 'TPR.G35315' => 'tpr', 'TPR.G36173' => 'tpr', 'TWI09G0794' => 'twi', 'TWI59G1348' => 'twi', 'TWI74G0430' => 'twi', 'unitig_26.g8940' => 'ugi', 'unitig_749.g13744' => 'ugi', 'unitig_749.g13745' => 'ugi', 'vmacro08269' => 'vma', 'vmacro14937' => 'vma', 'vmacro20401' => 'vma', 'VMungo0464G1349' => 'vmu', 'VMungo0540G0289' => 'vmu', 'VMungo1215G1590' => 'vmu', 'VMungo1309G0221' => 'vmu', 'VMungo1309G2815' => 'vmu', 'VMungo1383G0239' => 'vmu', 'VMungo1383G2910' => 'vmu', 'Zm00001eb095270' => 'zma', 'Zm00001eb095280' => 'zma', 'Zm00001eb111630' => 'zma', 'Zm00001eb237080' => 'zma', 'Zm00001eb273740' => 'zma', 'Zm00001eb285040' => 'zma', 'Zm00001eb330790' => 'zma', 'Zm00001eb337380' => 'zma' ), 'gf_id' => 'HOM05D001484', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001484' ), 'data_identifier' => 'HOM05D001484', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001484', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p31500' => 'bna', 'A05p00020' => 'bna', 'A07p08820' => 'bna', 'Aa31LG4G3300' => 'aar', 'Aa31LG8G10030' => 'aar', 'Actinidia00731' => 'ach', 'Actinidia11473' => 'ach', 'Actinidia23469' => 'ach', 'Actinidia24318' => 'ach', 'Actinidia40196' => 'ach', 'Actinidia40197' => 'ach', 'Actinidia40198' => 'ach', 'Ah.08g212990' => 'amhyb', 'Ah.15g091720' => 'amhyb', 'AL3G38260' => 'aly', 'AL4G47710' => 'aly', 'Aqoxy2G00671' => 'aox', 'Aqoxy2G03236' => 'aox', 'arahy.Tifrunner.gnm1.ann1.05IDCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KR684' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATY3SJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK6QJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6APGL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IDT7Z9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM073U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ0R87' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LE7RV4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT4QRX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V5ENPK' => 'arhy', 'AT2G48110' => 'ath', 'AT3G23590' => 'ath', 'ATR0626G186' => 'atr', 'ATR1127G141' => 'atr', 'Atru.chr4.2583' => 'acertr', 'Atru.chr5.1358' => 'acertr', 'Atru.chr5.1359' => 'acertr', 'Atru.chr8.46' => 'acertr', 'AUR62002640' => 'cqu', 'AUR62030055' => 'cqu', 'AUR62033713' => 'cqu', 'AUR62033714' => 'cqu', 'AUR62036795' => 'cqu', 'AUR62039891' => 'cqu', 'BcaB02g08737' => 'bca', 'BcaB04g20441' => 'bca', 'BcaB06g26509' => 'bca', 'BcaB06g26510' => 'bca', 'BcaB06g26511' => 'bca', 'BcaB06g26512' => 'bca', 'BcaB06g26513' => 'bca', 'BcaC02g12564' => 'bca', 'BcaC02g12565' => 'bca', 'BcaC02g12794' => 'bca', 'BcaC02g12795' => 'bca', 'BcaC02g12796' => 'bca', 'BcaC06g35541' => 'bca', 'BNapus_Darmor_BZH_scaffold_188p00080' => 'bna', 'BNapus_Darmor_BZH_scaffold_188p00090' => 'bna', 'BolC1t03972H' => 'bol', 'BolC1t03973H' => 'bol', 'BolC4t21680H' => 'bol', 'BolC7t41863H' => 'bol', 'BolSC55t61227H' => 'bol', 'BolSC55t61228H' => 'bol', 'BraA01t03278Z' => 'bra', 'BraA05t18998Z' => 'bra', 'BraA07t28673Z' => 'bra', 'C01p40150' => 'bna', 'C05p12370' => 'bna', 'C07p13680' => 'bna', 'CAN.G1006.16' => 'can', 'CAN.G1006.17' => 'can', 'CAN.G1170.2' => 'can', 'CAN.G962.7' => 'can', 'CANSAT25G2179' => 'cansat', 'CANSAT78G1573' => 'cansat', 'CARHR099510' => 'chi', 'CARHR143510' => 'chi', 'Carub.0003s2380' => 'cru', 'Carub.0004s3082' => 'cru', 'Ca_00614_v3' => 'car', 'Ca_07801_v3' => 'car', 'Ca_08567_v3' => 'car', 'Ca_09571_v3' => 'car', 'CBR_g19290' => 'cbr', 'Cc01_g19770' => 'ccan', 'Cc03_g03030' => 'ccan', 'CDE07G0968' => 'cde', 'CDE09G1441' => 'cde', 'Cfa006103' => 'cfa', 'Cfa015573' => 'cfa', 'Cfa016988' => 'cfa', 'Ciclev10006738m.g' => 'ccl', 'Ciclev10010920m.g' => 'ccl', 'Ciclev10018517m.g' => 'ccl', 'CiPaw.01G159200' => 'cil', 'CiPaw.02G091000' => 'cil', 'CiPaw.02G091100' => 'cil', 'CiPaw.08G103100' => 'cil', 'CiPaw.09G224900' => 'cil', 'ClCG06G005740' => 'cla', 'ClCG07G000090' => 'cla', 'ClCG07G000100' => 'cla', 'COL.COLO4_09143' => 'col', 'COL.COLO4_25124' => 'col', 'Cpa.g.sc16.34' => 'cpa', 'Cpa.g.sc3504.1' => 'cpa', 'Cpa.g.sc60.37' => 'cpa', 'CsaV3_6G018520' => 'csa', 'CsaV3_6G036860' => 'csa', 'CSS0001072' => 'camsi', 'CSS0020208' => 'camsi', 'CSS0021253' => 'camsi', 'CSS0022190' => 'camsi', 'CSS0036150' => 'camsi', 'CSS0040442' => 'camsi', 'CSS0042300' => 'camsi', 'CSS0045298' => 'camsi', 'DCAR_012449' => 'dca', 'DCAR_018405' => 'dca', 'DCAR_024573' => 'dca', 'DCAR_030591' => 'dca', 'Dinv16926' => 'din', 'Dinv32963' => 'din', 'Dinv38382' => 'din', 'Dinv38383' => 'din', 'Duzib133G0974' => 'dzi', 'Duzib138G1867' => 'dzi', 'Duzib211G0420' => 'dzi', 'Duzib212G0930' => 'dzi', 'ECA234G1645' => 'eca', 'ECA247G3467' => 'eca', 'ECA248G1703' => 'eca', 'EL10Ac3g06327' => 'bvu', 'EL10Ac7g17204' => 'bvu', 'Eucgr.A00855' => 'egr', 'Eucgr.A00858' => 'egr', 'Eucgr.H01520' => 'egr', 'Eucgr.H03604' => 'egr', 'Eucgr.L03465' => 'egr', 'Eucgr.L03466' => 'egr', 'FAN01G0988' => 'fan', 'FAN02G3892' => 'fan', 'FAN05G3381' => 'fan', 'FAN07G0967' => 'fan', 'FAN07G1493' => 'fan', 'FAN08G3125' => 'fan', 'FAN09G0402' => 'fan', 'FAN12G2594' => 'fan', 'FAN12G3879' => 'fan', 'FAN14G1546' => 'fan', 'FAN15G3626' => 'fan', 'FAN17G0588' => 'fan', 'FAN17G0609' => 'fan', 'FAN18G2817' => 'fan', 'FAN19G1305' => 'fan', 'FAN20G1787' => 'fan', 'FAN22G0073' => 'fan', 'FAN22G0352' => 'fan', 'FAN22G0368' => 'fan', 'FAN22G2273' => 'fan', 'FAN24G1998' => 'fan', 'FAN27G1317' => 'fan', 'FvH4_2g23980' => 'fve', 'FvH4_4g14380' => 'fve', 'FvH4_4g14390' => 'fve', 'FvH4_6g09250' => 'fve', 'Glyma.03G151100' => 'gma', 'Glyma.04G122550' => 'gma', 'Glyma.05G001600' => 'gma', 'Glyma.09G270766' => 'gma', 'Glyma.09G270832' => 'gma', 'Glyma.13G209800' => 'gma', 'Glyma.15G102800' => 'gma', 'Glyma.18G218900' => 'gma', 'Glyma.19G001500' => 'gma', 'Glyma.19G153600' => 'gma', 'Gohir.A02G028600' => 'ghi', 'Gohir.A08G045000' => 'ghi', 'Gohir.A11G120500' => 'ghi', 'Gohir.A12G006200' => 'ghi', 'Gohir.A12G006250' => 'ghi', 'Gohir.D02G036300' => 'ghi', 'Gohir.D08G054700' => 'ghi', 'Gohir.D11G125600' => 'ghi', 'Gohir.D12G005700' => 'ghi', 'Gorai.004G055200' => 'gra', 'Gorai.005G040400' => 'gra', 'Gorai.007G134500' => 'gra', 'Gorai.008G005500' => 'gra', 'GSVIVG01011094001' => 'vvi', 'GSVIVG01017879001' => 'vvi', 'GSVIVG01025988001' => 'vvi', 'GSVIVG01029847001' => 'vvi', 'HanXRQChr10g0282901' => 'han', 'HanXRQChr10g0310371' => 'han', 'HanXRQChr10g0315041' => 'han', 'HanXRQChr11g0327651' => 'han', 'HanXRQChr12g0359391' => 'han', 'Haze_00972' => 'cav', 'Haze_00973' => 'cav', 'Haze_00974' => 'cav', 'Haze_04747' => 'cav', 'Haze_04749' => 'cav', 'Haze_04750' => 'cav', 'Haze_21217' => 'cav', 'Hma1.2p1_1037F.1_g250680' => 'hma', 'Hma1.2p1_1644F.1_g295320' => 'hma', 'HPP92_011322' => 'vpl', 'HPP92_011323' => 'vpl', 'HPP92_011324' => 'vpl', 'HPP92_011325' => 'vpl', 'HPP92_011326' => 'vpl', 'Hund12205' => 'sun', 'Hund17957' => 'sun', 'Lalb_Chr06g0176771' => 'lal', 'Lalb_Chr18g0056021' => 'lal', 'Lalb_Chr18g0056031' => 'lal', 'Lalb_Chr18g0056041' => 'lal', 'Lalb_Chr20g0107751' => 'lal', 'Lalb_Chr20g0118371' => 'lal', 'Lj1g0010239' => 'lja', 'Lj1g0017101' => 'lja', 'Lj2A1178G40' => 'lonja', 'Lj2A54G84' => 'lonja', 'Lj2g0015248' => 'lja', 'Lj3A761T51' => 'lonja', 'Lj6g0018116' => 'lja', 'Lsat_1_v5_gn_4_136040' => 'lsa', 'Lsat_1_v5_gn_5_187461' => 'lsa', 'Lsat_1_v5_gn_5_77001' => 'lsa', 'Lsat_1_v5_gn_9_4461' => 'lsa', 'Manes.01G210100' => 'mes', 'Manes.03G185600' => 'mes', 'Manes.05G073300' => 'mes', 'Manes.09G120300' => 'mes', 'Manes.15G022100' => 'mes', 'Mapoly0096s0053' => 'mpo', 'MBI03_g14058_MAGBIO' => 'mbi', 'MBI03_g33876_MAGBIO' => 'mbi', 'MBI03_g36854_MAGBIO' => 'mbi', 'MBI17_g11997_MAGBIO' => 'mbi', 'MD03G1269000' => 'mdo', 'MD04G1179600' => 'mdo', 'MD11G1289800' => 'mdo', 'MD12G1194700' => 'mdo', 'MD13G1182100' => 'mdo', 'MD13G1182200' => 'mdo', 'MD16G1182600' => 'mdo', 'Medtr2g021400' => 'mtr', 'Medtr2g021470' => 'mtr', 'Medtr2g105810' => 'mtr', 'Medtr3g033580' => 'mtr', 'Medtr6g007970' => 'mtr', 'Medtr7g056330' => 'mtr', 'Medtr7g074290' => 'mtr', 'Medtr7g074380' => 'mtr', 'Medtr7g094550' => 'mtr', 'Medtr8g069995' => 'mtr', 'MELO3C014345.2' => 'cme', 'MELO3C021395.2' => 'cme', 'Migut.D00262' => 'egut', 'Migut.G00257' => 'egut', 'MSTRG.21575' => 'ama', 'MSTRG.3985' => 'ama', 'Nitab4.5_0000295g0140' => 'nta', 'Nitab4.5_0000732g0140' => 'nta', 'Nitab4.5_0003162g0020' => 'nta', 'Nitab4.5_0006180g0090' => 'nta', 'Nitab4.5_0006390g0010' => 'nta', 'Nitab4.5_0007392g0040' => 'nta', 'Nn1g02140' => 'nnu', 'Nn4g26168' => 'nnu', 'Nn5g26754' => 'nnu', 'Oeu001433.1' => 'oeu', 'Oeu010299.2' => 'oeu', 'Oeu011171.1' => 'oeu', 'Oeu037675.1' => 'oeu', 'Oeu038359.1' => 'oeu', 'Oeu063834.1' => 'oeu', 'Oeu063835.1' => 'oeu', 'Os05g0312000' => 'osa', 'Os07g0211101' => 'osa', 'Os07g0211200' => 'osa', 'Os07g0681500' => 'osa', 'Peaxi162Scf00095g01015' => 'pax', 'Peaxi162Scf00104g00329' => 'pax', 'Peaxi162Scf00161g00137' => 'pax', 'PGR004G1665' => 'pgr', 'PGR031G2937' => 'pgr', 'PGR119G2145' => 'pgr', 'PGSC0003DMG400004351' => 'stu', 'PGSC0003DMG400014625' => 'stu', 'PGSC0003DMG401000943' => 'stu', 'Phvul.001G148600' => 'pvu', 'Phvul.004G001700' => 'pvu', 'Phvul.006G154900' => 'pvu', 'Phvul.008G078200' => 'pvu', 'Phvul.011G136500' => 'pvu', 'Potri.002G215600' => 'ptr', 'Potri.008G201600' => 'ptr', 'Potri.014G138400' => 'ptr', 'Potri.016G142500' => 'ptr', 'Pp3c16_10580' => 'ppa', 'Pp3c5_25280' => 'ppa', 'Prupe.1G150000' => 'ppe', 'Prupe.1G150100' => 'ppe', 'Prupe.6G299600' => 'ppe', 'Prupe.8G245000' => 'ppe', 'Psat0s4927g0040' => 'psa', 'Psat1g052080' => 'psa', 'Psat1g183800' => 'psa', 'Psat3g113840' => 'psa', 'Psat3g126120' => 'psa', 'Psat3g126160' => 'psa', 'Psat3g158760' => 'psa', 'Psat3g158840' => 'psa', 'PSO170G2858' => 'pso', 'PSO339G0606' => 'pso', 'PSO384G4709' => 'pso', 'PSO407G0334' => 'pso', 'QL04p040276' => 'qlo', 'QL06p005458' => 'qlo', 'QL06p005472' => 'qlo', 'QL07p030546' => 'qlo', 'QL07p031519' => 'qlo', 'QL09p050949' => 'qlo', 'QL09p050966' => 'qlo', 'QL09p051067' => 'qlo', 'QL12p022706' => 'qlo', 'RcHm_v2.0_Chr2g0119601' => 'rch', 'RcHm_v2.0_Chr3g0459591' => 'rch', 'RcHm_v2.0_Chr4g0418521' => 'rch', 'RcHm_v2.0_Chr4g0418531' => 'rch', 'RcHm_v2.0_Chr4g0418541' => 'rch', 'RcHm_v2.0_Chr6g0291641' => 'rch', 'Rhsim01G0086300' => 'rsi', 'Rhsim01G0276300' => 'rsi', 'Rhsim01G0276500' => 'rsi', 'Rhsim04G0207700' => 'rsi', 'Rhsim05G0234500' => 'rsi', 'Rhsim13G0022400' => 'rsi', 'Sabra02G0167900' => 'sbr', 'Sabra04G0158500' => 'sbr', 'Sabra08G0159800' => 'sbr', 'Sabra10G0011500' => 'sbr', 'Sabra14G0104400' => 'sbr', 'SalBow2G2440' => 'sbo', 'SalBow4G2265' => 'sbo', 'Sc02g0000060' => 'sci', 'Sc05g0005020' => 'sci', 'Sc13g0003890' => 'sci', 'Sed0014865' => 'sed', 'Sed0017224' => 'sed', 'Sed0026391' => 'sed', 'SEGI_00063' => 'sgi', 'SEGI_10967' => 'sgi', 'SEGI_17510' => 'sgi', 'SEGI_24396' => 'sgi', 'SEGI_39719' => 'sgi', 'SEGI_41392' => 'sgi', 'SGA_v2.0_scaffold11G05794' => 'sas', 'SGA_v2.0_scaffold142G35607' => 'sas', 'SGA_v2.0_scaffold1G00447' => 'sas', 'SHI15388' => 'shi', 'SHI15394' => 'shi', 'SHI15396' => 'shi', 'SHI15399' => 'shi', 'SMO343G0151' => 'smo', 'SMO367G1118' => 'smo', 'Solyc01g080200.3' => 'sly', 'Solyc06g008960.3' => 'sly', 'Solyc09g064780.3' => 'sly', 'Sopen01g031980' => 'spe', 'Sopen06g003710' => 'spe', 'Sopen09g026460' => 'spe', 'Sp3g21240' => 'spa', 'Sp4g30030' => 'spa', 'TAR365G0022' => 'tar', 'TAR365G1023' => 'tar', 'TAR365G1253' => 'tar', 'TAR623G0078' => 'tar', 'TAR623G1721' => 'tar', 'TAR633G0959' => 'tar', 'THA.LOC104802225' => 'tha', 'THA.LOC104804769' => 'tha', 'THA.LOC104808660' => 'tha', 'THA.LOC104812792' => 'tha', 'Thecc.01G284000' => 'tca', 'Thecc.04G220600' => 'tca', 'Thecc.05G268900' => 'tca', 'Thecc.08G171100' => 'tca', 'Thhalv10001284m.g' => 'esa', 'Thhalv10019912m.g' => 'esa', 'TPR.G14189' => 'tpr', 'TPR.G18110' => 'tpr', 'TPR.G18130' => 'tpr', 'TPR.G18131' => 'tpr', 'TPR.G18140' => 'tpr', 'TPR.G24282' => 'tpr', 'TPR.G25221' => 'tpr', 'TPR.G29267' => 'tpr', 'TPR.G35315' => 'tpr', 'TPR.G36173' => 'tpr', 'TWI09G0794' => 'twi', 'TWI59G1348' => 'twi', 'TWI74G0430' => 'twi', 'unitig_26.g8940' => 'ugi', 'unitig_749.g13744' => 'ugi', 'unitig_749.g13745' => 'ugi', 'vmacro08269' => 'vma', 'vmacro14937' => 'vma', 'vmacro20401' => 'vma', 'VMungo0464G1349' => 'vmu', 'VMungo0540G0289' => 'vmu', 'VMungo1215G1590' => 'vmu', 'VMungo1309G0221' => 'vmu', 'VMungo1309G2815' => 'vmu', 'VMungo1383G0239' => 'vmu', 'VMungo1383G2910' => 'vmu', 'Zm00001eb095270' => 'zma', 'Zm00001eb095280' => 'zma', 'Zm00001eb111630' => 'zma', 'Zm00001eb237080' => 'zma', 'Zm00001eb273740' => 'zma', 'Zm00001eb285040' => 'zma', 'Zm00001eb330790' => 'zma', 'Zm00001eb337380' => 'zma' ) $gf_id = 'HOM05D001484' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001484' ) $data_identifier = 'HOM05D001484' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 2, 'aly' => (int) 2, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 22, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 7, 'hma' => (int) 2, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 7, 'mtr' => (int) 10, 'cme' => (int) 2, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 4, 'ppa' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 4, 'qlo' => (int) 9, 'rch' => (int) 6, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 10, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 7, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb337380' $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' => 'HOM05D001484', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p31500' => 'bna', 'A05p00020' => 'bna', 'A07p08820' => 'bna', 'Aa31LG4G3300' => 'aar', 'Aa31LG8G10030' => 'aar', 'Actinidia00731' => 'ach', 'Actinidia11473' => 'ach', 'Actinidia23469' => 'ach', 'Actinidia24318' => 'ach', 'Actinidia40196' => 'ach', 'Actinidia40197' => 'ach', 'Actinidia40198' => 'ach', 'Ah.08g212990' => 'amhyb', 'Ah.15g091720' => 'amhyb', 'AL3G38260' => 'aly', 'AL4G47710' => 'aly', 'Aqoxy2G00671' => 'aox', 'Aqoxy2G03236' => 'aox', 'arahy.Tifrunner.gnm1.ann1.05IDCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KR684' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATY3SJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK6QJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6APGL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IDT7Z9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM073U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ0R87' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LE7RV4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT4QRX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V5ENPK' => 'arhy', 'AT2G48110' => 'ath', 'AT3G23590' => 'ath', 'ATR0626G186' => 'atr', 'ATR1127G141' => 'atr', 'Atru.chr4.2583' => 'acertr', 'Atru.chr5.1358' => 'acertr', 'Atru.chr5.1359' => 'acertr', 'Atru.chr8.46' => 'acertr', 'AUR62002640' => 'cqu', 'AUR62030055' => 'cqu', 'AUR62033713' => 'cqu', 'AUR62033714' => 'cqu', 'AUR62036795' => 'cqu', 'AUR62039891' => 'cqu', 'BcaB02g08737' => 'bca', 'BcaB04g20441' => 'bca', 'BcaB06g26509' => 'bca', 'BcaB06g26510' => 'bca', 'BcaB06g26511' => 'bca', 'BcaB06g26512' => 'bca', 'BcaB06g26513' => 'bca', 'BcaC02g12564' => 'bca', 'BcaC02g12565' => 'bca', 'BcaC02g12794' => 'bca', 'BcaC02g12795' => 'bca', 'BcaC02g12796' => 'bca', 'BcaC06g35541' => 'bca', 'BNapus_Darmor_BZH_scaffold_188p00080' => 'bna', 'BNapus_Darmor_BZH_scaffold_188p00090' => 'bna', 'BolC1t03972H' => 'bol', 'BolC1t03973H' => 'bol', 'BolC4t21680H' => 'bol', 'BolC7t41863H' => 'bol', 'BolSC55t61227H' => 'bol', 'BolSC55t61228H' => 'bol', 'BraA01t03278Z' => 'bra', 'BraA05t18998Z' => 'bra', 'BraA07t28673Z' => 'bra', 'C01p40150' => 'bna', 'C05p12370' => 'bna', 'C07p13680' => 'bna', 'CAN.G1006.16' => 'can', 'CAN.G1006.17' => 'can', 'CAN.G1170.2' => 'can', 'CAN.G962.7' => 'can', 'CANSAT25G2179' => 'cansat', 'CANSAT78G1573' => 'cansat', 'CARHR099510' => 'chi', 'CARHR143510' => 'chi', 'Carub.0003s2380' => 'cru', 'Carub.0004s3082' => 'cru', 'Ca_00614_v3' => 'car', 'Ca_07801_v3' => 'car', 'Ca_08567_v3' => 'car', 'Ca_09571_v3' => 'car', 'CBR_g19290' => 'cbr', 'Cc01_g19770' => 'ccan', 'Cc03_g03030' => 'ccan', 'CDE07G0968' => 'cde', 'CDE09G1441' => 'cde', 'Cfa006103' => 'cfa', 'Cfa015573' => 'cfa', 'Cfa016988' => 'cfa', 'Ciclev10006738m.g' => 'ccl', 'Ciclev10010920m.g' => 'ccl', 'Ciclev10018517m.g' => 'ccl', 'CiPaw.01G159200' => 'cil', 'CiPaw.02G091000' => 'cil', 'CiPaw.02G091100' => 'cil', 'CiPaw.08G103100' => 'cil', 'CiPaw.09G224900' => 'cil', 'ClCG06G005740' => 'cla', 'ClCG07G000090' => 'cla', 'ClCG07G000100' => 'cla', 'COL.COLO4_09143' => 'col', 'COL.COLO4_25124' => 'col', 'Cpa.g.sc16.34' => 'cpa', 'Cpa.g.sc3504.1' => 'cpa', 'Cpa.g.sc60.37' => 'cpa', 'CsaV3_6G018520' => 'csa', 'CsaV3_6G036860' => 'csa', 'CSS0001072' => 'camsi', 'CSS0020208' => 'camsi', 'CSS0021253' => 'camsi', 'CSS0022190' => 'camsi', 'CSS0036150' => 'camsi', 'CSS0040442' => 'camsi', 'CSS0042300' => 'camsi', 'CSS0045298' => 'camsi', 'DCAR_012449' => 'dca', 'DCAR_018405' => 'dca', 'DCAR_024573' => 'dca', 'DCAR_030591' => 'dca', 'Dinv16926' => 'din', 'Dinv32963' => 'din', 'Dinv38382' => 'din', 'Dinv38383' => 'din', 'Duzib133G0974' => 'dzi', 'Duzib138G1867' => 'dzi', 'Duzib211G0420' => 'dzi', 'Duzib212G0930' => 'dzi', 'ECA234G1645' => 'eca', 'ECA247G3467' => 'eca', 'ECA248G1703' => 'eca', 'EL10Ac3g06327' => 'bvu', 'EL10Ac7g17204' => 'bvu', 'Eucgr.A00855' => 'egr', 'Eucgr.A00858' => 'egr', 'Eucgr.H01520' => 'egr', 'Eucgr.H03604' => 'egr', 'Eucgr.L03465' => 'egr', 'Eucgr.L03466' => 'egr', 'FAN01G0988' => 'fan', 'FAN02G3892' => 'fan', 'FAN05G3381' => 'fan', 'FAN07G0967' => 'fan', 'FAN07G1493' => 'fan', 'FAN08G3125' => 'fan', 'FAN09G0402' => 'fan', 'FAN12G2594' => 'fan', 'FAN12G3879' => 'fan', 'FAN14G1546' => 'fan', 'FAN15G3626' => 'fan', 'FAN17G0588' => 'fan', 'FAN17G0609' => 'fan', 'FAN18G2817' => 'fan', 'FAN19G1305' => 'fan', 'FAN20G1787' => 'fan', 'FAN22G0073' => 'fan', 'FAN22G0352' => 'fan', 'FAN22G0368' => 'fan', 'FAN22G2273' => 'fan', 'FAN24G1998' => 'fan', 'FAN27G1317' => 'fan', 'FvH4_2g23980' => 'fve', 'FvH4_4g14380' => 'fve', 'FvH4_4g14390' => 'fve', 'FvH4_6g09250' => 'fve', 'Glyma.03G151100' => 'gma', 'Glyma.04G122550' => 'gma', 'Glyma.05G001600' => 'gma', 'Glyma.09G270766' => 'gma', 'Glyma.09G270832' => 'gma', 'Glyma.13G209800' => 'gma', 'Glyma.15G102800' => 'gma', 'Glyma.18G218900' => 'gma', 'Glyma.19G001500' => 'gma', 'Glyma.19G153600' => 'gma', 'Gohir.A02G028600' => 'ghi', 'Gohir.A08G045000' => 'ghi', 'Gohir.A11G120500' => 'ghi', 'Gohir.A12G006200' => 'ghi', 'Gohir.A12G006250' => 'ghi', 'Gohir.D02G036300' => 'ghi', 'Gohir.D08G054700' => 'ghi', 'Gohir.D11G125600' => 'ghi', 'Gohir.D12G005700' => 'ghi', 'Gorai.004G055200' => 'gra', 'Gorai.005G040400' => 'gra', 'Gorai.007G134500' => 'gra', 'Gorai.008G005500' => 'gra', 'GSVIVG01011094001' => 'vvi', 'GSVIVG01017879001' => 'vvi', 'GSVIVG01025988001' => 'vvi', 'GSVIVG01029847001' => 'vvi', 'HanXRQChr10g0282901' => 'han', 'HanXRQChr10g0310371' => 'han', 'HanXRQChr10g0315041' => 'han', 'HanXRQChr11g0327651' => 'han', 'HanXRQChr12g0359391' => 'han', 'Haze_00972' => 'cav', 'Haze_00973' => 'cav', 'Haze_00974' => 'cav', 'Haze_04747' => 'cav', 'Haze_04749' => 'cav', 'Haze_04750' => 'cav', 'Haze_21217' => 'cav', 'Hma1.2p1_1037F.1_g250680' => 'hma', 'Hma1.2p1_1644F.1_g295320' => 'hma', 'HPP92_011322' => 'vpl', 'HPP92_011323' => 'vpl', 'HPP92_011324' => 'vpl', 'HPP92_011325' => 'vpl', 'HPP92_011326' => 'vpl', 'Hund12205' => 'sun', 'Hund17957' => 'sun', 'Lalb_Chr06g0176771' => 'lal', 'Lalb_Chr18g0056021' => 'lal', 'Lalb_Chr18g0056031' => 'lal', 'Lalb_Chr18g0056041' => 'lal', 'Lalb_Chr20g0107751' => 'lal', 'Lalb_Chr20g0118371' => 'lal', 'Lj1g0010239' => 'lja', 'Lj1g0017101' => 'lja', 'Lj2A1178G40' => 'lonja', 'Lj2A54G84' => 'lonja', 'Lj2g0015248' => 'lja', 'Lj3A761T51' => 'lonja', 'Lj6g0018116' => 'lja', 'Lsat_1_v5_gn_4_136040' => 'lsa', 'Lsat_1_v5_gn_5_187461' => 'lsa', 'Lsat_1_v5_gn_5_77001' => 'lsa', 'Lsat_1_v5_gn_9_4461' => 'lsa', 'Manes.01G210100' => 'mes', 'Manes.03G185600' => 'mes', 'Manes.05G073300' => 'mes', 'Manes.09G120300' => 'mes', 'Manes.15G022100' => 'mes', 'Mapoly0096s0053' => 'mpo', 'MBI03_g14058_MAGBIO' => 'mbi', 'MBI03_g33876_MAGBIO' => 'mbi', 'MBI03_g36854_MAGBIO' => 'mbi', 'MBI17_g11997_MAGBIO' => 'mbi', 'MD03G1269000' => 'mdo', 'MD04G1179600' => 'mdo', 'MD11G1289800' => 'mdo', 'MD12G1194700' => 'mdo', 'MD13G1182100' => 'mdo', 'MD13G1182200' => 'mdo', 'MD16G1182600' => 'mdo', 'Medtr2g021400' => 'mtr', 'Medtr2g021470' => 'mtr', 'Medtr2g105810' => 'mtr', 'Medtr3g033580' => 'mtr', 'Medtr6g007970' => 'mtr', 'Medtr7g056330' => 'mtr', 'Medtr7g074290' => 'mtr', 'Medtr7g074380' => 'mtr', 'Medtr7g094550' => 'mtr', 'Medtr8g069995' => 'mtr', 'MELO3C014345.2' => 'cme', 'MELO3C021395.2' => 'cme', 'Migut.D00262' => 'egut', 'Migut.G00257' => 'egut', 'MSTRG.21575' => 'ama', 'MSTRG.3985' => 'ama', 'Nitab4.5_0000295g0140' => 'nta', 'Nitab4.5_0000732g0140' => 'nta', 'Nitab4.5_0003162g0020' => 'nta', 'Nitab4.5_0006180g0090' => 'nta', 'Nitab4.5_0006390g0010' => 'nta', 'Nitab4.5_0007392g0040' => 'nta', 'Nn1g02140' => 'nnu', 'Nn4g26168' => 'nnu', 'Nn5g26754' => 'nnu', 'Oeu001433.1' => 'oeu', 'Oeu010299.2' => 'oeu', 'Oeu011171.1' => 'oeu', 'Oeu037675.1' => 'oeu', 'Oeu038359.1' => 'oeu', 'Oeu063834.1' => 'oeu', 'Oeu063835.1' => 'oeu', 'Os05g0312000' => 'osa', 'Os07g0211101' => 'osa', 'Os07g0211200' => 'osa', 'Os07g0681500' => 'osa', 'Peaxi162Scf00095g01015' => 'pax', 'Peaxi162Scf00104g00329' => 'pax', 'Peaxi162Scf00161g00137' => 'pax', 'PGR004G1665' => 'pgr', 'PGR031G2937' => 'pgr', 'PGR119G2145' => 'pgr', 'PGSC0003DMG400004351' => 'stu', 'PGSC0003DMG400014625' => 'stu', 'PGSC0003DMG401000943' => 'stu', 'Phvul.001G148600' => 'pvu', 'Phvul.004G001700' => 'pvu', 'Phvul.006G154900' => 'pvu', 'Phvul.008G078200' => 'pvu', 'Phvul.011G136500' => 'pvu', 'Potri.002G215600' => 'ptr', 'Potri.008G201600' => 'ptr', 'Potri.014G138400' => 'ptr', 'Potri.016G142500' => 'ptr', 'Pp3c16_10580' => 'ppa', 'Pp3c5_25280' => 'ppa', 'Prupe.1G150000' => 'ppe', 'Prupe.1G150100' => 'ppe', 'Prupe.6G299600' => 'ppe', 'Prupe.8G245000' => 'ppe', 'Psat0s4927g0040' => 'psa', 'Psat1g052080' => 'psa', 'Psat1g183800' => 'psa', 'Psat3g113840' => 'psa', 'Psat3g126120' => 'psa', 'Psat3g126160' => 'psa', 'Psat3g158760' => 'psa', 'Psat3g158840' => 'psa', 'PSO170G2858' => 'pso', 'PSO339G0606' => 'pso', 'PSO384G4709' => 'pso', 'PSO407G0334' => 'pso', 'QL04p040276' => 'qlo', 'QL06p005458' => 'qlo', 'QL06p005472' => 'qlo', 'QL07p030546' => 'qlo', 'QL07p031519' => 'qlo', 'QL09p050949' => 'qlo', 'QL09p050966' => 'qlo', 'QL09p051067' => 'qlo', 'QL12p022706' => 'qlo', 'RcHm_v2.0_Chr2g0119601' => 'rch', 'RcHm_v2.0_Chr3g0459591' => 'rch', 'RcHm_v2.0_Chr4g0418521' => 'rch', 'RcHm_v2.0_Chr4g0418531' => 'rch', 'RcHm_v2.0_Chr4g0418541' => 'rch', 'RcHm_v2.0_Chr6g0291641' => 'rch', 'Rhsim01G0086300' => 'rsi', 'Rhsim01G0276300' => 'rsi', 'Rhsim01G0276500' => 'rsi', 'Rhsim04G0207700' => 'rsi', 'Rhsim05G0234500' => 'rsi', 'Rhsim13G0022400' => 'rsi', 'Sabra02G0167900' => 'sbr', 'Sabra04G0158500' => 'sbr', 'Sabra08G0159800' => 'sbr', 'Sabra10G0011500' => 'sbr', 'Sabra14G0104400' => 'sbr', 'SalBow2G2440' => 'sbo', 'SalBow4G2265' => 'sbo', 'Sc02g0000060' => 'sci', 'Sc05g0005020' => 'sci', 'Sc13g0003890' => 'sci', 'Sed0014865' => 'sed', 'Sed0017224' => 'sed', 'Sed0026391' => 'sed', 'SEGI_00063' => 'sgi', 'SEGI_10967' => 'sgi', 'SEGI_17510' => 'sgi', 'SEGI_24396' => 'sgi', 'SEGI_39719' => 'sgi', 'SEGI_41392' => 'sgi', 'SGA_v2.0_scaffold11G05794' => 'sas', 'SGA_v2.0_scaffold142G35607' => 'sas', 'SGA_v2.0_scaffold1G00447' => 'sas', 'SHI15388' => 'shi', 'SHI15394' => 'shi', 'SHI15396' => 'shi', 'SHI15399' => 'shi', 'SMO343G0151' => 'smo', 'SMO367G1118' => 'smo', 'Solyc01g080200.3' => 'sly', 'Solyc06g008960.3' => 'sly', 'Solyc09g064780.3' => 'sly', 'Sopen01g031980' => 'spe', 'Sopen06g003710' => 'spe', 'Sopen09g026460' => 'spe', 'Sp3g21240' => 'spa', 'Sp4g30030' => 'spa', 'TAR365G0022' => 'tar', 'TAR365G1023' => 'tar', 'TAR365G1253' => 'tar', 'TAR623G0078' => 'tar', 'TAR623G1721' => 'tar', 'TAR633G0959' => 'tar', 'THA.LOC104802225' => 'tha', 'THA.LOC104804769' => 'tha', 'THA.LOC104808660' => 'tha', 'THA.LOC104812792' => 'tha', 'Thecc.01G284000' => 'tca', 'Thecc.04G220600' => 'tca', 'Thecc.05G268900' => 'tca', 'Thecc.08G171100' => 'tca', 'Thhalv10001284m.g' => 'esa', 'Thhalv10019912m.g' => 'esa', 'TPR.G14189' => 'tpr', 'TPR.G18110' => 'tpr', 'TPR.G18130' => 'tpr', 'TPR.G18131' => 'tpr', 'TPR.G18140' => 'tpr', 'TPR.G24282' => 'tpr', 'TPR.G25221' => 'tpr', 'TPR.G29267' => 'tpr', 'TPR.G35315' => 'tpr', 'TPR.G36173' => 'tpr', 'TWI09G0794' => 'twi', 'TWI59G1348' => 'twi', 'TWI74G0430' => 'twi', 'unitig_26.g8940' => 'ugi', 'unitig_749.g13744' => 'ugi', 'unitig_749.g13745' => 'ugi', 'vmacro08269' => 'vma', 'vmacro14937' => 'vma', 'vmacro20401' => 'vma', 'VMungo0464G1349' => 'vmu', 'VMungo0540G0289' => 'vmu', 'VMungo1215G1590' => 'vmu', 'VMungo1309G0221' => 'vmu', 'VMungo1309G2815' => 'vmu', 'VMungo1383G0239' => 'vmu', 'VMungo1383G2910' => 'vmu', 'Zm00001eb095270' => 'zma', 'Zm00001eb095280' => 'zma', 'Zm00001eb111630' => 'zma', 'Zm00001eb237080' => 'zma', 'Zm00001eb273740' => 'zma', 'Zm00001eb285040' => 'zma', 'Zm00001eb330790' => 'zma', 'Zm00001eb337380' => 'zma' ), 'gf_id' => 'HOM05D001484', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001484' ), 'data_identifier' => 'HOM05D001484', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001484', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p31500' => 'bna', 'A05p00020' => 'bna', 'A07p08820' => 'bna', 'Aa31LG4G3300' => 'aar', 'Aa31LG8G10030' => 'aar', 'Actinidia00731' => 'ach', 'Actinidia11473' => 'ach', 'Actinidia23469' => 'ach', 'Actinidia24318' => 'ach', 'Actinidia40196' => 'ach', 'Actinidia40197' => 'ach', 'Actinidia40198' => 'ach', 'Ah.08g212990' => 'amhyb', 'Ah.15g091720' => 'amhyb', 'AL3G38260' => 'aly', 'AL4G47710' => 'aly', 'Aqoxy2G00671' => 'aox', 'Aqoxy2G03236' => 'aox', 'arahy.Tifrunner.gnm1.ann1.05IDCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KR684' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATY3SJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK6QJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6APGL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IDT7Z9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM073U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ0R87' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LE7RV4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT4QRX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V5ENPK' => 'arhy', 'AT2G48110' => 'ath', 'AT3G23590' => 'ath', 'ATR0626G186' => 'atr', 'ATR1127G141' => 'atr', 'Atru.chr4.2583' => 'acertr', 'Atru.chr5.1358' => 'acertr', 'Atru.chr5.1359' => 'acertr', 'Atru.chr8.46' => 'acertr', 'AUR62002640' => 'cqu', 'AUR62030055' => 'cqu', 'AUR62033713' => 'cqu', 'AUR62033714' => 'cqu', 'AUR62036795' => 'cqu', 'AUR62039891' => 'cqu', 'BcaB02g08737' => 'bca', 'BcaB04g20441' => 'bca', 'BcaB06g26509' => 'bca', 'BcaB06g26510' => 'bca', 'BcaB06g26511' => 'bca', 'BcaB06g26512' => 'bca', 'BcaB06g26513' => 'bca', 'BcaC02g12564' => 'bca', 'BcaC02g12565' => 'bca', 'BcaC02g12794' => 'bca', 'BcaC02g12795' => 'bca', 'BcaC02g12796' => 'bca', 'BcaC06g35541' => 'bca', 'BNapus_Darmor_BZH_scaffold_188p00080' => 'bna', 'BNapus_Darmor_BZH_scaffold_188p00090' => 'bna', 'BolC1t03972H' => 'bol', 'BolC1t03973H' => 'bol', 'BolC4t21680H' => 'bol', 'BolC7t41863H' => 'bol', 'BolSC55t61227H' => 'bol', 'BolSC55t61228H' => 'bol', 'BraA01t03278Z' => 'bra', 'BraA05t18998Z' => 'bra', 'BraA07t28673Z' => 'bra', 'C01p40150' => 'bna', 'C05p12370' => 'bna', 'C07p13680' => 'bna', 'CAN.G1006.16' => 'can', 'CAN.G1006.17' => 'can', 'CAN.G1170.2' => 'can', 'CAN.G962.7' => 'can', 'CANSAT25G2179' => 'cansat', 'CANSAT78G1573' => 'cansat', 'CARHR099510' => 'chi', 'CARHR143510' => 'chi', 'Carub.0003s2380' => 'cru', 'Carub.0004s3082' => 'cru', 'Ca_00614_v3' => 'car', 'Ca_07801_v3' => 'car', 'Ca_08567_v3' => 'car', 'Ca_09571_v3' => 'car', 'CBR_g19290' => 'cbr', 'Cc01_g19770' => 'ccan', 'Cc03_g03030' => 'ccan', 'CDE07G0968' => 'cde', 'CDE09G1441' => 'cde', 'Cfa006103' => 'cfa', 'Cfa015573' => 'cfa', 'Cfa016988' => 'cfa', 'Ciclev10006738m.g' => 'ccl', 'Ciclev10010920m.g' => 'ccl', 'Ciclev10018517m.g' => 'ccl', 'CiPaw.01G159200' => 'cil', 'CiPaw.02G091000' => 'cil', 'CiPaw.02G091100' => 'cil', 'CiPaw.08G103100' => 'cil', 'CiPaw.09G224900' => 'cil', 'ClCG06G005740' => 'cla', 'ClCG07G000090' => 'cla', 'ClCG07G000100' => 'cla', 'COL.COLO4_09143' => 'col', 'COL.COLO4_25124' => 'col', 'Cpa.g.sc16.34' => 'cpa', 'Cpa.g.sc3504.1' => 'cpa', 'Cpa.g.sc60.37' => 'cpa', 'CsaV3_6G018520' => 'csa', 'CsaV3_6G036860' => 'csa', 'CSS0001072' => 'camsi', 'CSS0020208' => 'camsi', 'CSS0021253' => 'camsi', 'CSS0022190' => 'camsi', 'CSS0036150' => 'camsi', 'CSS0040442' => 'camsi', 'CSS0042300' => 'camsi', 'CSS0045298' => 'camsi', 'DCAR_012449' => 'dca', 'DCAR_018405' => 'dca', 'DCAR_024573' => 'dca', 'DCAR_030591' => 'dca', 'Dinv16926' => 'din', 'Dinv32963' => 'din', 'Dinv38382' => 'din', 'Dinv38383' => 'din', 'Duzib133G0974' => 'dzi', 'Duzib138G1867' => 'dzi', 'Duzib211G0420' => 'dzi', 'Duzib212G0930' => 'dzi', 'ECA234G1645' => 'eca', 'ECA247G3467' => 'eca', 'ECA248G1703' => 'eca', 'EL10Ac3g06327' => 'bvu', 'EL10Ac7g17204' => 'bvu', 'Eucgr.A00855' => 'egr', 'Eucgr.A00858' => 'egr', 'Eucgr.H01520' => 'egr', 'Eucgr.H03604' => 'egr', 'Eucgr.L03465' => 'egr', 'Eucgr.L03466' => 'egr', 'FAN01G0988' => 'fan', 'FAN02G3892' => 'fan', 'FAN05G3381' => 'fan', 'FAN07G0967' => 'fan', 'FAN07G1493' => 'fan', 'FAN08G3125' => 'fan', 'FAN09G0402' => 'fan', 'FAN12G2594' => 'fan', 'FAN12G3879' => 'fan', 'FAN14G1546' => 'fan', 'FAN15G3626' => 'fan', 'FAN17G0588' => 'fan', 'FAN17G0609' => 'fan', 'FAN18G2817' => 'fan', 'FAN19G1305' => 'fan', 'FAN20G1787' => 'fan', 'FAN22G0073' => 'fan', 'FAN22G0352' => 'fan', 'FAN22G0368' => 'fan', 'FAN22G2273' => 'fan', 'FAN24G1998' => 'fan', 'FAN27G1317' => 'fan', 'FvH4_2g23980' => 'fve', 'FvH4_4g14380' => 'fve', 'FvH4_4g14390' => 'fve', 'FvH4_6g09250' => 'fve', 'Glyma.03G151100' => 'gma', 'Glyma.04G122550' => 'gma', 'Glyma.05G001600' => 'gma', 'Glyma.09G270766' => 'gma', 'Glyma.09G270832' => 'gma', 'Glyma.13G209800' => 'gma', 'Glyma.15G102800' => 'gma', 'Glyma.18G218900' => 'gma', 'Glyma.19G001500' => 'gma', 'Glyma.19G153600' => 'gma', 'Gohir.A02G028600' => 'ghi', 'Gohir.A08G045000' => 'ghi', 'Gohir.A11G120500' => 'ghi', 'Gohir.A12G006200' => 'ghi', 'Gohir.A12G006250' => 'ghi', 'Gohir.D02G036300' => 'ghi', 'Gohir.D08G054700' => 'ghi', 'Gohir.D11G125600' => 'ghi', 'Gohir.D12G005700' => 'ghi', 'Gorai.004G055200' => 'gra', 'Gorai.005G040400' => 'gra', 'Gorai.007G134500' => 'gra', 'Gorai.008G005500' => 'gra', 'GSVIVG01011094001' => 'vvi', 'GSVIVG01017879001' => 'vvi', 'GSVIVG01025988001' => 'vvi', 'GSVIVG01029847001' => 'vvi', 'HanXRQChr10g0282901' => 'han', 'HanXRQChr10g0310371' => 'han', 'HanXRQChr10g0315041' => 'han', 'HanXRQChr11g0327651' => 'han', 'HanXRQChr12g0359391' => 'han', 'Haze_00972' => 'cav', 'Haze_00973' => 'cav', 'Haze_00974' => 'cav', 'Haze_04747' => 'cav', 'Haze_04749' => 'cav', 'Haze_04750' => 'cav', 'Haze_21217' => 'cav', 'Hma1.2p1_1037F.1_g250680' => 'hma', 'Hma1.2p1_1644F.1_g295320' => 'hma', 'HPP92_011322' => 'vpl', 'HPP92_011323' => 'vpl', 'HPP92_011324' => 'vpl', 'HPP92_011325' => 'vpl', 'HPP92_011326' => 'vpl', 'Hund12205' => 'sun', 'Hund17957' => 'sun', 'Lalb_Chr06g0176771' => 'lal', 'Lalb_Chr18g0056021' => 'lal', 'Lalb_Chr18g0056031' => 'lal', 'Lalb_Chr18g0056041' => 'lal', 'Lalb_Chr20g0107751' => 'lal', 'Lalb_Chr20g0118371' => 'lal', 'Lj1g0010239' => 'lja', 'Lj1g0017101' => 'lja', 'Lj2A1178G40' => 'lonja', 'Lj2A54G84' => 'lonja', 'Lj2g0015248' => 'lja', 'Lj3A761T51' => 'lonja', 'Lj6g0018116' => 'lja', 'Lsat_1_v5_gn_4_136040' => 'lsa', 'Lsat_1_v5_gn_5_187461' => 'lsa', 'Lsat_1_v5_gn_5_77001' => 'lsa', 'Lsat_1_v5_gn_9_4461' => 'lsa', 'Manes.01G210100' => 'mes', 'Manes.03G185600' => 'mes', 'Manes.05G073300' => 'mes', 'Manes.09G120300' => 'mes', 'Manes.15G022100' => 'mes', 'Mapoly0096s0053' => 'mpo', 'MBI03_g14058_MAGBIO' => 'mbi', 'MBI03_g33876_MAGBIO' => 'mbi', 'MBI03_g36854_MAGBIO' => 'mbi', 'MBI17_g11997_MAGBIO' => 'mbi', 'MD03G1269000' => 'mdo', 'MD04G1179600' => 'mdo', 'MD11G1289800' => 'mdo', 'MD12G1194700' => 'mdo', 'MD13G1182100' => 'mdo', 'MD13G1182200' => 'mdo', 'MD16G1182600' => 'mdo', 'Medtr2g021400' => 'mtr', 'Medtr2g021470' => 'mtr', 'Medtr2g105810' => 'mtr', 'Medtr3g033580' => 'mtr', 'Medtr6g007970' => 'mtr', 'Medtr7g056330' => 'mtr', 'Medtr7g074290' => 'mtr', 'Medtr7g074380' => 'mtr', 'Medtr7g094550' => 'mtr', 'Medtr8g069995' => 'mtr', 'MELO3C014345.2' => 'cme', 'MELO3C021395.2' => 'cme', 'Migut.D00262' => 'egut', 'Migut.G00257' => 'egut', 'MSTRG.21575' => 'ama', 'MSTRG.3985' => 'ama', 'Nitab4.5_0000295g0140' => 'nta', 'Nitab4.5_0000732g0140' => 'nta', 'Nitab4.5_0003162g0020' => 'nta', 'Nitab4.5_0006180g0090' => 'nta', 'Nitab4.5_0006390g0010' => 'nta', 'Nitab4.5_0007392g0040' => 'nta', 'Nn1g02140' => 'nnu', 'Nn4g26168' => 'nnu', 'Nn5g26754' => 'nnu', 'Oeu001433.1' => 'oeu', 'Oeu010299.2' => 'oeu', 'Oeu011171.1' => 'oeu', 'Oeu037675.1' => 'oeu', 'Oeu038359.1' => 'oeu', 'Oeu063834.1' => 'oeu', 'Oeu063835.1' => 'oeu', 'Os05g0312000' => 'osa', 'Os07g0211101' => 'osa', 'Os07g0211200' => 'osa', 'Os07g0681500' => 'osa', 'Peaxi162Scf00095g01015' => 'pax', 'Peaxi162Scf00104g00329' => 'pax', 'Peaxi162Scf00161g00137' => 'pax', 'PGR004G1665' => 'pgr', 'PGR031G2937' => 'pgr', 'PGR119G2145' => 'pgr', 'PGSC0003DMG400004351' => 'stu', 'PGSC0003DMG400014625' => 'stu', 'PGSC0003DMG401000943' => 'stu', 'Phvul.001G148600' => 'pvu', 'Phvul.004G001700' => 'pvu', 'Phvul.006G154900' => 'pvu', 'Phvul.008G078200' => 'pvu', 'Phvul.011G136500' => 'pvu', 'Potri.002G215600' => 'ptr', 'Potri.008G201600' => 'ptr', 'Potri.014G138400' => 'ptr', 'Potri.016G142500' => 'ptr', 'Pp3c16_10580' => 'ppa', 'Pp3c5_25280' => 'ppa', 'Prupe.1G150000' => 'ppe', 'Prupe.1G150100' => 'ppe', 'Prupe.6G299600' => 'ppe', 'Prupe.8G245000' => 'ppe', 'Psat0s4927g0040' => 'psa', 'Psat1g052080' => 'psa', 'Psat1g183800' => 'psa', 'Psat3g113840' => 'psa', 'Psat3g126120' => 'psa', 'Psat3g126160' => 'psa', 'Psat3g158760' => 'psa', 'Psat3g158840' => 'psa', 'PSO170G2858' => 'pso', 'PSO339G0606' => 'pso', 'PSO384G4709' => 'pso', 'PSO407G0334' => 'pso', 'QL04p040276' => 'qlo', 'QL06p005458' => 'qlo', 'QL06p005472' => 'qlo', 'QL07p030546' => 'qlo', 'QL07p031519' => 'qlo', 'QL09p050949' => 'qlo', 'QL09p050966' => 'qlo', 'QL09p051067' => 'qlo', 'QL12p022706' => 'qlo', 'RcHm_v2.0_Chr2g0119601' => 'rch', 'RcHm_v2.0_Chr3g0459591' => 'rch', 'RcHm_v2.0_Chr4g0418521' => 'rch', 'RcHm_v2.0_Chr4g0418531' => 'rch', 'RcHm_v2.0_Chr4g0418541' => 'rch', 'RcHm_v2.0_Chr6g0291641' => 'rch', 'Rhsim01G0086300' => 'rsi', 'Rhsim01G0276300' => 'rsi', 'Rhsim01G0276500' => 'rsi', 'Rhsim04G0207700' => 'rsi', 'Rhsim05G0234500' => 'rsi', 'Rhsim13G0022400' => 'rsi', 'Sabra02G0167900' => 'sbr', 'Sabra04G0158500' => 'sbr', 'Sabra08G0159800' => 'sbr', 'Sabra10G0011500' => 'sbr', 'Sabra14G0104400' => 'sbr', 'SalBow2G2440' => 'sbo', 'SalBow4G2265' => 'sbo', 'Sc02g0000060' => 'sci', 'Sc05g0005020' => 'sci', 'Sc13g0003890' => 'sci', 'Sed0014865' => 'sed', 'Sed0017224' => 'sed', 'Sed0026391' => 'sed', 'SEGI_00063' => 'sgi', 'SEGI_10967' => 'sgi', 'SEGI_17510' => 'sgi', 'SEGI_24396' => 'sgi', 'SEGI_39719' => 'sgi', 'SEGI_41392' => 'sgi', 'SGA_v2.0_scaffold11G05794' => 'sas', 'SGA_v2.0_scaffold142G35607' => 'sas', 'SGA_v2.0_scaffold1G00447' => 'sas', 'SHI15388' => 'shi', 'SHI15394' => 'shi', 'SHI15396' => 'shi', 'SHI15399' => 'shi', 'SMO343G0151' => 'smo', 'SMO367G1118' => 'smo', 'Solyc01g080200.3' => 'sly', 'Solyc06g008960.3' => 'sly', 'Solyc09g064780.3' => 'sly', 'Sopen01g031980' => 'spe', 'Sopen06g003710' => 'spe', 'Sopen09g026460' => 'spe', 'Sp3g21240' => 'spa', 'Sp4g30030' => 'spa', 'TAR365G0022' => 'tar', 'TAR365G1023' => 'tar', 'TAR365G1253' => 'tar', 'TAR623G0078' => 'tar', 'TAR623G1721' => 'tar', 'TAR633G0959' => 'tar', 'THA.LOC104802225' => 'tha', 'THA.LOC104804769' => 'tha', 'THA.LOC104808660' => 'tha', 'THA.LOC104812792' => 'tha', 'Thecc.01G284000' => 'tca', 'Thecc.04G220600' => 'tca', 'Thecc.05G268900' => 'tca', 'Thecc.08G171100' => 'tca', 'Thhalv10001284m.g' => 'esa', 'Thhalv10019912m.g' => 'esa', 'TPR.G14189' => 'tpr', 'TPR.G18110' => 'tpr', 'TPR.G18130' => 'tpr', 'TPR.G18131' => 'tpr', 'TPR.G18140' => 'tpr', 'TPR.G24282' => 'tpr', 'TPR.G25221' => 'tpr', 'TPR.G29267' => 'tpr', 'TPR.G35315' => 'tpr', 'TPR.G36173' => 'tpr', 'TWI09G0794' => 'twi', 'TWI59G1348' => 'twi', 'TWI74G0430' => 'twi', 'unitig_26.g8940' => 'ugi', 'unitig_749.g13744' => 'ugi', 'unitig_749.g13745' => 'ugi', 'vmacro08269' => 'vma', 'vmacro14937' => 'vma', 'vmacro20401' => 'vma', 'VMungo0464G1349' => 'vmu', 'VMungo0540G0289' => 'vmu', 'VMungo1215G1590' => 'vmu', 'VMungo1309G0221' => 'vmu', 'VMungo1309G2815' => 'vmu', 'VMungo1383G0239' => 'vmu', 'VMungo1383G2910' => 'vmu', 'Zm00001eb095270' => 'zma', 'Zm00001eb095280' => 'zma', 'Zm00001eb111630' => 'zma', 'Zm00001eb237080' => 'zma', 'Zm00001eb273740' => 'zma', 'Zm00001eb285040' => 'zma', 'Zm00001eb330790' => 'zma', 'Zm00001eb337380' => 'zma' ) $gf_id = 'HOM05D001484' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001484' ) $data_identifier = 'HOM05D001484' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 2, 'aly' => (int) 2, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 22, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 7, 'hma' => (int) 2, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 7, 'mtr' => (int) 10, 'cme' => (int) 2, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 4, 'ppa' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 4, 'qlo' => (int) 9, 'rch' => (int) 6, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 10, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 7, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb337380' $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' => 'HOM05D001484', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p31500' => 'bna', 'A05p00020' => 'bna', 'A07p08820' => 'bna', 'Aa31LG4G3300' => 'aar', 'Aa31LG8G10030' => 'aar', 'Actinidia00731' => 'ach', 'Actinidia11473' => 'ach', 'Actinidia23469' => 'ach', 'Actinidia24318' => 'ach', 'Actinidia40196' => 'ach', 'Actinidia40197' => 'ach', 'Actinidia40198' => 'ach', 'Ah.08g212990' => 'amhyb', 'Ah.15g091720' => 'amhyb', 'AL3G38260' => 'aly', 'AL4G47710' => 'aly', 'Aqoxy2G00671' => 'aox', 'Aqoxy2G03236' => 'aox', 'arahy.Tifrunner.gnm1.ann1.05IDCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KR684' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATY3SJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK6QJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6APGL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IDT7Z9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM073U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ0R87' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LE7RV4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT4QRX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V5ENPK' => 'arhy', 'AT2G48110' => 'ath', 'AT3G23590' => 'ath', 'ATR0626G186' => 'atr', 'ATR1127G141' => 'atr', 'Atru.chr4.2583' => 'acertr', 'Atru.chr5.1358' => 'acertr', 'Atru.chr5.1359' => 'acertr', 'Atru.chr8.46' => 'acertr', 'AUR62002640' => 'cqu', 'AUR62030055' => 'cqu', 'AUR62033713' => 'cqu', 'AUR62033714' => 'cqu', 'AUR62036795' => 'cqu', 'AUR62039891' => 'cqu', 'BcaB02g08737' => 'bca', 'BcaB04g20441' => 'bca', 'BcaB06g26509' => 'bca', 'BcaB06g26510' => 'bca', 'BcaB06g26511' => 'bca', 'BcaB06g26512' => 'bca', 'BcaB06g26513' => 'bca', 'BcaC02g12564' => 'bca', 'BcaC02g12565' => 'bca', 'BcaC02g12794' => 'bca', 'BcaC02g12795' => 'bca', 'BcaC02g12796' => 'bca', 'BcaC06g35541' => 'bca', 'BNapus_Darmor_BZH_scaffold_188p00080' => 'bna', 'BNapus_Darmor_BZH_scaffold_188p00090' => 'bna', 'BolC1t03972H' => 'bol', 'BolC1t03973H' => 'bol', 'BolC4t21680H' => 'bol', 'BolC7t41863H' => 'bol', 'BolSC55t61227H' => 'bol', 'BolSC55t61228H' => 'bol', 'BraA01t03278Z' => 'bra', 'BraA05t18998Z' => 'bra', 'BraA07t28673Z' => 'bra', 'C01p40150' => 'bna', 'C05p12370' => 'bna', 'C07p13680' => 'bna', 'CAN.G1006.16' => 'can', 'CAN.G1006.17' => 'can', 'CAN.G1170.2' => 'can', 'CAN.G962.7' => 'can', 'CANSAT25G2179' => 'cansat', 'CANSAT78G1573' => 'cansat', 'CARHR099510' => 'chi', 'CARHR143510' => 'chi', 'Carub.0003s2380' => 'cru', 'Carub.0004s3082' => 'cru', 'Ca_00614_v3' => 'car', 'Ca_07801_v3' => 'car', 'Ca_08567_v3' => 'car', 'Ca_09571_v3' => 'car', 'CBR_g19290' => 'cbr', 'Cc01_g19770' => 'ccan', 'Cc03_g03030' => 'ccan', 'CDE07G0968' => 'cde', 'CDE09G1441' => 'cde', 'Cfa006103' => 'cfa', 'Cfa015573' => 'cfa', 'Cfa016988' => 'cfa', 'Ciclev10006738m.g' => 'ccl', 'Ciclev10010920m.g' => 'ccl', 'Ciclev10018517m.g' => 'ccl', 'CiPaw.01G159200' => 'cil', 'CiPaw.02G091000' => 'cil', 'CiPaw.02G091100' => 'cil', 'CiPaw.08G103100' => 'cil', 'CiPaw.09G224900' => 'cil', 'ClCG06G005740' => 'cla', 'ClCG07G000090' => 'cla', 'ClCG07G000100' => 'cla', 'COL.COLO4_09143' => 'col', 'COL.COLO4_25124' => 'col', 'Cpa.g.sc16.34' => 'cpa', 'Cpa.g.sc3504.1' => 'cpa', 'Cpa.g.sc60.37' => 'cpa', 'CsaV3_6G018520' => 'csa', 'CsaV3_6G036860' => 'csa', 'CSS0001072' => 'camsi', 'CSS0020208' => 'camsi', 'CSS0021253' => 'camsi', 'CSS0022190' => 'camsi', 'CSS0036150' => 'camsi', 'CSS0040442' => 'camsi', 'CSS0042300' => 'camsi', 'CSS0045298' => 'camsi', 'DCAR_012449' => 'dca', 'DCAR_018405' => 'dca', 'DCAR_024573' => 'dca', 'DCAR_030591' => 'dca', 'Dinv16926' => 'din', 'Dinv32963' => 'din', 'Dinv38382' => 'din', 'Dinv38383' => 'din', 'Duzib133G0974' => 'dzi', 'Duzib138G1867' => 'dzi', 'Duzib211G0420' => 'dzi', 'Duzib212G0930' => 'dzi', 'ECA234G1645' => 'eca', 'ECA247G3467' => 'eca', 'ECA248G1703' => 'eca', 'EL10Ac3g06327' => 'bvu', 'EL10Ac7g17204' => 'bvu', 'Eucgr.A00855' => 'egr', 'Eucgr.A00858' => 'egr', 'Eucgr.H01520' => 'egr', 'Eucgr.H03604' => 'egr', 'Eucgr.L03465' => 'egr', 'Eucgr.L03466' => 'egr', 'FAN01G0988' => 'fan', 'FAN02G3892' => 'fan', 'FAN05G3381' => 'fan', 'FAN07G0967' => 'fan', 'FAN07G1493' => 'fan', 'FAN08G3125' => 'fan', 'FAN09G0402' => 'fan', 'FAN12G2594' => 'fan', 'FAN12G3879' => 'fan', 'FAN14G1546' => 'fan', 'FAN15G3626' => 'fan', 'FAN17G0588' => 'fan', 'FAN17G0609' => 'fan', 'FAN18G2817' => 'fan', 'FAN19G1305' => 'fan', 'FAN20G1787' => 'fan', 'FAN22G0073' => 'fan', 'FAN22G0352' => 'fan', 'FAN22G0368' => 'fan', 'FAN22G2273' => 'fan', 'FAN24G1998' => 'fan', 'FAN27G1317' => 'fan', 'FvH4_2g23980' => 'fve', 'FvH4_4g14380' => 'fve', 'FvH4_4g14390' => 'fve', 'FvH4_6g09250' => 'fve', 'Glyma.03G151100' => 'gma', 'Glyma.04G122550' => 'gma', 'Glyma.05G001600' => 'gma', 'Glyma.09G270766' => 'gma', 'Glyma.09G270832' => 'gma', 'Glyma.13G209800' => 'gma', 'Glyma.15G102800' => 'gma', 'Glyma.18G218900' => 'gma', 'Glyma.19G001500' => 'gma', 'Glyma.19G153600' => 'gma', 'Gohir.A02G028600' => 'ghi', 'Gohir.A08G045000' => 'ghi', 'Gohir.A11G120500' => 'ghi', 'Gohir.A12G006200' => 'ghi', 'Gohir.A12G006250' => 'ghi', 'Gohir.D02G036300' => 'ghi', 'Gohir.D08G054700' => 'ghi', 'Gohir.D11G125600' => 'ghi', 'Gohir.D12G005700' => 'ghi', 'Gorai.004G055200' => 'gra', 'Gorai.005G040400' => 'gra', 'Gorai.007G134500' => 'gra', 'Gorai.008G005500' => 'gra', 'GSVIVG01011094001' => 'vvi', 'GSVIVG01017879001' => 'vvi', 'GSVIVG01025988001' => 'vvi', 'GSVIVG01029847001' => 'vvi', 'HanXRQChr10g0282901' => 'han', 'HanXRQChr10g0310371' => 'han', 'HanXRQChr10g0315041' => 'han', 'HanXRQChr11g0327651' => 'han', 'HanXRQChr12g0359391' => 'han', 'Haze_00972' => 'cav', 'Haze_00973' => 'cav', 'Haze_00974' => 'cav', 'Haze_04747' => 'cav', 'Haze_04749' => 'cav', 'Haze_04750' => 'cav', 'Haze_21217' => 'cav', 'Hma1.2p1_1037F.1_g250680' => 'hma', 'Hma1.2p1_1644F.1_g295320' => 'hma', 'HPP92_011322' => 'vpl', 'HPP92_011323' => 'vpl', 'HPP92_011324' => 'vpl', 'HPP92_011325' => 'vpl', 'HPP92_011326' => 'vpl', 'Hund12205' => 'sun', 'Hund17957' => 'sun', 'Lalb_Chr06g0176771' => 'lal', 'Lalb_Chr18g0056021' => 'lal', 'Lalb_Chr18g0056031' => 'lal', 'Lalb_Chr18g0056041' => 'lal', 'Lalb_Chr20g0107751' => 'lal', 'Lalb_Chr20g0118371' => 'lal', 'Lj1g0010239' => 'lja', 'Lj1g0017101' => 'lja', 'Lj2A1178G40' => 'lonja', 'Lj2A54G84' => 'lonja', 'Lj2g0015248' => 'lja', 'Lj3A761T51' => 'lonja', 'Lj6g0018116' => 'lja', 'Lsat_1_v5_gn_4_136040' => 'lsa', 'Lsat_1_v5_gn_5_187461' => 'lsa', 'Lsat_1_v5_gn_5_77001' => 'lsa', 'Lsat_1_v5_gn_9_4461' => 'lsa', 'Manes.01G210100' => 'mes', 'Manes.03G185600' => 'mes', 'Manes.05G073300' => 'mes', 'Manes.09G120300' => 'mes', 'Manes.15G022100' => 'mes', 'Mapoly0096s0053' => 'mpo', 'MBI03_g14058_MAGBIO' => 'mbi', 'MBI03_g33876_MAGBIO' => 'mbi', 'MBI03_g36854_MAGBIO' => 'mbi', 'MBI17_g11997_MAGBIO' => 'mbi', 'MD03G1269000' => 'mdo', 'MD04G1179600' => 'mdo', 'MD11G1289800' => 'mdo', 'MD12G1194700' => 'mdo', 'MD13G1182100' => 'mdo', 'MD13G1182200' => 'mdo', 'MD16G1182600' => 'mdo', 'Medtr2g021400' => 'mtr', 'Medtr2g021470' => 'mtr', 'Medtr2g105810' => 'mtr', 'Medtr3g033580' => 'mtr', 'Medtr6g007970' => 'mtr', 'Medtr7g056330' => 'mtr', 'Medtr7g074290' => 'mtr', 'Medtr7g074380' => 'mtr', 'Medtr7g094550' => 'mtr', 'Medtr8g069995' => 'mtr', 'MELO3C014345.2' => 'cme', 'MELO3C021395.2' => 'cme', 'Migut.D00262' => 'egut', 'Migut.G00257' => 'egut', 'MSTRG.21575' => 'ama', 'MSTRG.3985' => 'ama', 'Nitab4.5_0000295g0140' => 'nta', 'Nitab4.5_0000732g0140' => 'nta', 'Nitab4.5_0003162g0020' => 'nta', 'Nitab4.5_0006180g0090' => 'nta', 'Nitab4.5_0006390g0010' => 'nta', 'Nitab4.5_0007392g0040' => 'nta', 'Nn1g02140' => 'nnu', 'Nn4g26168' => 'nnu', 'Nn5g26754' => 'nnu', 'Oeu001433.1' => 'oeu', 'Oeu010299.2' => 'oeu', 'Oeu011171.1' => 'oeu', 'Oeu037675.1' => 'oeu', 'Oeu038359.1' => 'oeu', 'Oeu063834.1' => 'oeu', 'Oeu063835.1' => 'oeu', 'Os05g0312000' => 'osa', 'Os07g0211101' => 'osa', 'Os07g0211200' => 'osa', 'Os07g0681500' => 'osa', 'Peaxi162Scf00095g01015' => 'pax', 'Peaxi162Scf00104g00329' => 'pax', 'Peaxi162Scf00161g00137' => 'pax', 'PGR004G1665' => 'pgr', 'PGR031G2937' => 'pgr', 'PGR119G2145' => 'pgr', 'PGSC0003DMG400004351' => 'stu', 'PGSC0003DMG400014625' => 'stu', 'PGSC0003DMG401000943' => 'stu', 'Phvul.001G148600' => 'pvu', 'Phvul.004G001700' => 'pvu', 'Phvul.006G154900' => 'pvu', 'Phvul.008G078200' => 'pvu', 'Phvul.011G136500' => 'pvu', 'Potri.002G215600' => 'ptr', 'Potri.008G201600' => 'ptr', 'Potri.014G138400' => 'ptr', 'Potri.016G142500' => 'ptr', 'Pp3c16_10580' => 'ppa', 'Pp3c5_25280' => 'ppa', 'Prupe.1G150000' => 'ppe', 'Prupe.1G150100' => 'ppe', 'Prupe.6G299600' => 'ppe', 'Prupe.8G245000' => 'ppe', 'Psat0s4927g0040' => 'psa', 'Psat1g052080' => 'psa', 'Psat1g183800' => 'psa', 'Psat3g113840' => 'psa', 'Psat3g126120' => 'psa', 'Psat3g126160' => 'psa', 'Psat3g158760' => 'psa', 'Psat3g158840' => 'psa', 'PSO170G2858' => 'pso', 'PSO339G0606' => 'pso', 'PSO384G4709' => 'pso', 'PSO407G0334' => 'pso', 'QL04p040276' => 'qlo', 'QL06p005458' => 'qlo', 'QL06p005472' => 'qlo', 'QL07p030546' => 'qlo', 'QL07p031519' => 'qlo', 'QL09p050949' => 'qlo', 'QL09p050966' => 'qlo', 'QL09p051067' => 'qlo', 'QL12p022706' => 'qlo', 'RcHm_v2.0_Chr2g0119601' => 'rch', 'RcHm_v2.0_Chr3g0459591' => 'rch', 'RcHm_v2.0_Chr4g0418521' => 'rch', 'RcHm_v2.0_Chr4g0418531' => 'rch', 'RcHm_v2.0_Chr4g0418541' => 'rch', 'RcHm_v2.0_Chr6g0291641' => 'rch', 'Rhsim01G0086300' => 'rsi', 'Rhsim01G0276300' => 'rsi', 'Rhsim01G0276500' => 'rsi', 'Rhsim04G0207700' => 'rsi', 'Rhsim05G0234500' => 'rsi', 'Rhsim13G0022400' => 'rsi', 'Sabra02G0167900' => 'sbr', 'Sabra04G0158500' => 'sbr', 'Sabra08G0159800' => 'sbr', 'Sabra10G0011500' => 'sbr', 'Sabra14G0104400' => 'sbr', 'SalBow2G2440' => 'sbo', 'SalBow4G2265' => 'sbo', 'Sc02g0000060' => 'sci', 'Sc05g0005020' => 'sci', 'Sc13g0003890' => 'sci', 'Sed0014865' => 'sed', 'Sed0017224' => 'sed', 'Sed0026391' => 'sed', 'SEGI_00063' => 'sgi', 'SEGI_10967' => 'sgi', 'SEGI_17510' => 'sgi', 'SEGI_24396' => 'sgi', 'SEGI_39719' => 'sgi', 'SEGI_41392' => 'sgi', 'SGA_v2.0_scaffold11G05794' => 'sas', 'SGA_v2.0_scaffold142G35607' => 'sas', 'SGA_v2.0_scaffold1G00447' => 'sas', 'SHI15388' => 'shi', 'SHI15394' => 'shi', 'SHI15396' => 'shi', 'SHI15399' => 'shi', 'SMO343G0151' => 'smo', 'SMO367G1118' => 'smo', 'Solyc01g080200.3' => 'sly', 'Solyc06g008960.3' => 'sly', 'Solyc09g064780.3' => 'sly', 'Sopen01g031980' => 'spe', 'Sopen06g003710' => 'spe', 'Sopen09g026460' => 'spe', 'Sp3g21240' => 'spa', 'Sp4g30030' => 'spa', 'TAR365G0022' => 'tar', 'TAR365G1023' => 'tar', 'TAR365G1253' => 'tar', 'TAR623G0078' => 'tar', 'TAR623G1721' => 'tar', 'TAR633G0959' => 'tar', 'THA.LOC104802225' => 'tha', 'THA.LOC104804769' => 'tha', 'THA.LOC104808660' => 'tha', 'THA.LOC104812792' => 'tha', 'Thecc.01G284000' => 'tca', 'Thecc.04G220600' => 'tca', 'Thecc.05G268900' => 'tca', 'Thecc.08G171100' => 'tca', 'Thhalv10001284m.g' => 'esa', 'Thhalv10019912m.g' => 'esa', 'TPR.G14189' => 'tpr', 'TPR.G18110' => 'tpr', 'TPR.G18130' => 'tpr', 'TPR.G18131' => 'tpr', 'TPR.G18140' => 'tpr', 'TPR.G24282' => 'tpr', 'TPR.G25221' => 'tpr', 'TPR.G29267' => 'tpr', 'TPR.G35315' => 'tpr', 'TPR.G36173' => 'tpr', 'TWI09G0794' => 'twi', 'TWI59G1348' => 'twi', 'TWI74G0430' => 'twi', 'unitig_26.g8940' => 'ugi', 'unitig_749.g13744' => 'ugi', 'unitig_749.g13745' => 'ugi', 'vmacro08269' => 'vma', 'vmacro14937' => 'vma', 'vmacro20401' => 'vma', 'VMungo0464G1349' => 'vmu', 'VMungo0540G0289' => 'vmu', 'VMungo1215G1590' => 'vmu', 'VMungo1309G0221' => 'vmu', 'VMungo1309G2815' => 'vmu', 'VMungo1383G0239' => 'vmu', 'VMungo1383G2910' => 'vmu', 'Zm00001eb095270' => 'zma', 'Zm00001eb095280' => 'zma', 'Zm00001eb111630' => 'zma', 'Zm00001eb237080' => 'zma', 'Zm00001eb273740' => 'zma', 'Zm00001eb285040' => 'zma', 'Zm00001eb330790' => 'zma', 'Zm00001eb337380' => 'zma' ), 'gf_id' => 'HOM05D001484', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001484' ), 'data_identifier' => 'HOM05D001484', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001484', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p31500' => 'bna', 'A05p00020' => 'bna', 'A07p08820' => 'bna', 'Aa31LG4G3300' => 'aar', 'Aa31LG8G10030' => 'aar', 'Actinidia00731' => 'ach', 'Actinidia11473' => 'ach', 'Actinidia23469' => 'ach', 'Actinidia24318' => 'ach', 'Actinidia40196' => 'ach', 'Actinidia40197' => 'ach', 'Actinidia40198' => 'ach', 'Ah.08g212990' => 'amhyb', 'Ah.15g091720' => 'amhyb', 'AL3G38260' => 'aly', 'AL4G47710' => 'aly', 'Aqoxy2G00671' => 'aox', 'Aqoxy2G03236' => 'aox', 'arahy.Tifrunner.gnm1.ann1.05IDCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KR684' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATY3SJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK6QJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6APGL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IDT7Z9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM073U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ0R87' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LE7RV4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT4QRX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V5ENPK' => 'arhy', 'AT2G48110' => 'ath', 'AT3G23590' => 'ath', 'ATR0626G186' => 'atr', 'ATR1127G141' => 'atr', 'Atru.chr4.2583' => 'acertr', 'Atru.chr5.1358' => 'acertr', 'Atru.chr5.1359' => 'acertr', 'Atru.chr8.46' => 'acertr', 'AUR62002640' => 'cqu', 'AUR62030055' => 'cqu', 'AUR62033713' => 'cqu', 'AUR62033714' => 'cqu', 'AUR62036795' => 'cqu', 'AUR62039891' => 'cqu', 'BcaB02g08737' => 'bca', 'BcaB04g20441' => 'bca', 'BcaB06g26509' => 'bca', 'BcaB06g26510' => 'bca', 'BcaB06g26511' => 'bca', 'BcaB06g26512' => 'bca', 'BcaB06g26513' => 'bca', 'BcaC02g12564' => 'bca', 'BcaC02g12565' => 'bca', 'BcaC02g12794' => 'bca', 'BcaC02g12795' => 'bca', 'BcaC02g12796' => 'bca', 'BcaC06g35541' => 'bca', 'BNapus_Darmor_BZH_scaffold_188p00080' => 'bna', 'BNapus_Darmor_BZH_scaffold_188p00090' => 'bna', 'BolC1t03972H' => 'bol', 'BolC1t03973H' => 'bol', 'BolC4t21680H' => 'bol', 'BolC7t41863H' => 'bol', 'BolSC55t61227H' => 'bol', 'BolSC55t61228H' => 'bol', 'BraA01t03278Z' => 'bra', 'BraA05t18998Z' => 'bra', 'BraA07t28673Z' => 'bra', 'C01p40150' => 'bna', 'C05p12370' => 'bna', 'C07p13680' => 'bna', 'CAN.G1006.16' => 'can', 'CAN.G1006.17' => 'can', 'CAN.G1170.2' => 'can', 'CAN.G962.7' => 'can', 'CANSAT25G2179' => 'cansat', 'CANSAT78G1573' => 'cansat', 'CARHR099510' => 'chi', 'CARHR143510' => 'chi', 'Carub.0003s2380' => 'cru', 'Carub.0004s3082' => 'cru', 'Ca_00614_v3' => 'car', 'Ca_07801_v3' => 'car', 'Ca_08567_v3' => 'car', 'Ca_09571_v3' => 'car', 'CBR_g19290' => 'cbr', 'Cc01_g19770' => 'ccan', 'Cc03_g03030' => 'ccan', 'CDE07G0968' => 'cde', 'CDE09G1441' => 'cde', 'Cfa006103' => 'cfa', 'Cfa015573' => 'cfa', 'Cfa016988' => 'cfa', 'Ciclev10006738m.g' => 'ccl', 'Ciclev10010920m.g' => 'ccl', 'Ciclev10018517m.g' => 'ccl', 'CiPaw.01G159200' => 'cil', 'CiPaw.02G091000' => 'cil', 'CiPaw.02G091100' => 'cil', 'CiPaw.08G103100' => 'cil', 'CiPaw.09G224900' => 'cil', 'ClCG06G005740' => 'cla', 'ClCG07G000090' => 'cla', 'ClCG07G000100' => 'cla', 'COL.COLO4_09143' => 'col', 'COL.COLO4_25124' => 'col', 'Cpa.g.sc16.34' => 'cpa', 'Cpa.g.sc3504.1' => 'cpa', 'Cpa.g.sc60.37' => 'cpa', 'CsaV3_6G018520' => 'csa', 'CsaV3_6G036860' => 'csa', 'CSS0001072' => 'camsi', 'CSS0020208' => 'camsi', 'CSS0021253' => 'camsi', 'CSS0022190' => 'camsi', 'CSS0036150' => 'camsi', 'CSS0040442' => 'camsi', 'CSS0042300' => 'camsi', 'CSS0045298' => 'camsi', 'DCAR_012449' => 'dca', 'DCAR_018405' => 'dca', 'DCAR_024573' => 'dca', 'DCAR_030591' => 'dca', 'Dinv16926' => 'din', 'Dinv32963' => 'din', 'Dinv38382' => 'din', 'Dinv38383' => 'din', 'Duzib133G0974' => 'dzi', 'Duzib138G1867' => 'dzi', 'Duzib211G0420' => 'dzi', 'Duzib212G0930' => 'dzi', 'ECA234G1645' => 'eca', 'ECA247G3467' => 'eca', 'ECA248G1703' => 'eca', 'EL10Ac3g06327' => 'bvu', 'EL10Ac7g17204' => 'bvu', 'Eucgr.A00855' => 'egr', 'Eucgr.A00858' => 'egr', 'Eucgr.H01520' => 'egr', 'Eucgr.H03604' => 'egr', 'Eucgr.L03465' => 'egr', 'Eucgr.L03466' => 'egr', 'FAN01G0988' => 'fan', 'FAN02G3892' => 'fan', 'FAN05G3381' => 'fan', 'FAN07G0967' => 'fan', 'FAN07G1493' => 'fan', 'FAN08G3125' => 'fan', 'FAN09G0402' => 'fan', 'FAN12G2594' => 'fan', 'FAN12G3879' => 'fan', 'FAN14G1546' => 'fan', 'FAN15G3626' => 'fan', 'FAN17G0588' => 'fan', 'FAN17G0609' => 'fan', 'FAN18G2817' => 'fan', 'FAN19G1305' => 'fan', 'FAN20G1787' => 'fan', 'FAN22G0073' => 'fan', 'FAN22G0352' => 'fan', 'FAN22G0368' => 'fan', 'FAN22G2273' => 'fan', 'FAN24G1998' => 'fan', 'FAN27G1317' => 'fan', 'FvH4_2g23980' => 'fve', 'FvH4_4g14380' => 'fve', 'FvH4_4g14390' => 'fve', 'FvH4_6g09250' => 'fve', 'Glyma.03G151100' => 'gma', 'Glyma.04G122550' => 'gma', 'Glyma.05G001600' => 'gma', 'Glyma.09G270766' => 'gma', 'Glyma.09G270832' => 'gma', 'Glyma.13G209800' => 'gma', 'Glyma.15G102800' => 'gma', 'Glyma.18G218900' => 'gma', 'Glyma.19G001500' => 'gma', 'Glyma.19G153600' => 'gma', 'Gohir.A02G028600' => 'ghi', 'Gohir.A08G045000' => 'ghi', 'Gohir.A11G120500' => 'ghi', 'Gohir.A12G006200' => 'ghi', 'Gohir.A12G006250' => 'ghi', 'Gohir.D02G036300' => 'ghi', 'Gohir.D08G054700' => 'ghi', 'Gohir.D11G125600' => 'ghi', 'Gohir.D12G005700' => 'ghi', 'Gorai.004G055200' => 'gra', 'Gorai.005G040400' => 'gra', 'Gorai.007G134500' => 'gra', 'Gorai.008G005500' => 'gra', 'GSVIVG01011094001' => 'vvi', 'GSVIVG01017879001' => 'vvi', 'GSVIVG01025988001' => 'vvi', 'GSVIVG01029847001' => 'vvi', 'HanXRQChr10g0282901' => 'han', 'HanXRQChr10g0310371' => 'han', 'HanXRQChr10g0315041' => 'han', 'HanXRQChr11g0327651' => 'han', 'HanXRQChr12g0359391' => 'han', 'Haze_00972' => 'cav', 'Haze_00973' => 'cav', 'Haze_00974' => 'cav', 'Haze_04747' => 'cav', 'Haze_04749' => 'cav', 'Haze_04750' => 'cav', 'Haze_21217' => 'cav', 'Hma1.2p1_1037F.1_g250680' => 'hma', 'Hma1.2p1_1644F.1_g295320' => 'hma', 'HPP92_011322' => 'vpl', 'HPP92_011323' => 'vpl', 'HPP92_011324' => 'vpl', 'HPP92_011325' => 'vpl', 'HPP92_011326' => 'vpl', 'Hund12205' => 'sun', 'Hund17957' => 'sun', 'Lalb_Chr06g0176771' => 'lal', 'Lalb_Chr18g0056021' => 'lal', 'Lalb_Chr18g0056031' => 'lal', 'Lalb_Chr18g0056041' => 'lal', 'Lalb_Chr20g0107751' => 'lal', 'Lalb_Chr20g0118371' => 'lal', 'Lj1g0010239' => 'lja', 'Lj1g0017101' => 'lja', 'Lj2A1178G40' => 'lonja', 'Lj2A54G84' => 'lonja', 'Lj2g0015248' => 'lja', 'Lj3A761T51' => 'lonja', 'Lj6g0018116' => 'lja', 'Lsat_1_v5_gn_4_136040' => 'lsa', 'Lsat_1_v5_gn_5_187461' => 'lsa', 'Lsat_1_v5_gn_5_77001' => 'lsa', 'Lsat_1_v5_gn_9_4461' => 'lsa', 'Manes.01G210100' => 'mes', 'Manes.03G185600' => 'mes', 'Manes.05G073300' => 'mes', 'Manes.09G120300' => 'mes', 'Manes.15G022100' => 'mes', 'Mapoly0096s0053' => 'mpo', 'MBI03_g14058_MAGBIO' => 'mbi', 'MBI03_g33876_MAGBIO' => 'mbi', 'MBI03_g36854_MAGBIO' => 'mbi', 'MBI17_g11997_MAGBIO' => 'mbi', 'MD03G1269000' => 'mdo', 'MD04G1179600' => 'mdo', 'MD11G1289800' => 'mdo', 'MD12G1194700' => 'mdo', 'MD13G1182100' => 'mdo', 'MD13G1182200' => 'mdo', 'MD16G1182600' => 'mdo', 'Medtr2g021400' => 'mtr', 'Medtr2g021470' => 'mtr', 'Medtr2g105810' => 'mtr', 'Medtr3g033580' => 'mtr', 'Medtr6g007970' => 'mtr', 'Medtr7g056330' => 'mtr', 'Medtr7g074290' => 'mtr', 'Medtr7g074380' => 'mtr', 'Medtr7g094550' => 'mtr', 'Medtr8g069995' => 'mtr', 'MELO3C014345.2' => 'cme', 'MELO3C021395.2' => 'cme', 'Migut.D00262' => 'egut', 'Migut.G00257' => 'egut', 'MSTRG.21575' => 'ama', 'MSTRG.3985' => 'ama', 'Nitab4.5_0000295g0140' => 'nta', 'Nitab4.5_0000732g0140' => 'nta', 'Nitab4.5_0003162g0020' => 'nta', 'Nitab4.5_0006180g0090' => 'nta', 'Nitab4.5_0006390g0010' => 'nta', 'Nitab4.5_0007392g0040' => 'nta', 'Nn1g02140' => 'nnu', 'Nn4g26168' => 'nnu', 'Nn5g26754' => 'nnu', 'Oeu001433.1' => 'oeu', 'Oeu010299.2' => 'oeu', 'Oeu011171.1' => 'oeu', 'Oeu037675.1' => 'oeu', 'Oeu038359.1' => 'oeu', 'Oeu063834.1' => 'oeu', 'Oeu063835.1' => 'oeu', 'Os05g0312000' => 'osa', 'Os07g0211101' => 'osa', 'Os07g0211200' => 'osa', 'Os07g0681500' => 'osa', 'Peaxi162Scf00095g01015' => 'pax', 'Peaxi162Scf00104g00329' => 'pax', 'Peaxi162Scf00161g00137' => 'pax', 'PGR004G1665' => 'pgr', 'PGR031G2937' => 'pgr', 'PGR119G2145' => 'pgr', 'PGSC0003DMG400004351' => 'stu', 'PGSC0003DMG400014625' => 'stu', 'PGSC0003DMG401000943' => 'stu', 'Phvul.001G148600' => 'pvu', 'Phvul.004G001700' => 'pvu', 'Phvul.006G154900' => 'pvu', 'Phvul.008G078200' => 'pvu', 'Phvul.011G136500' => 'pvu', 'Potri.002G215600' => 'ptr', 'Potri.008G201600' => 'ptr', 'Potri.014G138400' => 'ptr', 'Potri.016G142500' => 'ptr', 'Pp3c16_10580' => 'ppa', 'Pp3c5_25280' => 'ppa', 'Prupe.1G150000' => 'ppe', 'Prupe.1G150100' => 'ppe', 'Prupe.6G299600' => 'ppe', 'Prupe.8G245000' => 'ppe', 'Psat0s4927g0040' => 'psa', 'Psat1g052080' => 'psa', 'Psat1g183800' => 'psa', 'Psat3g113840' => 'psa', 'Psat3g126120' => 'psa', 'Psat3g126160' => 'psa', 'Psat3g158760' => 'psa', 'Psat3g158840' => 'psa', 'PSO170G2858' => 'pso', 'PSO339G0606' => 'pso', 'PSO384G4709' => 'pso', 'PSO407G0334' => 'pso', 'QL04p040276' => 'qlo', 'QL06p005458' => 'qlo', 'QL06p005472' => 'qlo', 'QL07p030546' => 'qlo', 'QL07p031519' => 'qlo', 'QL09p050949' => 'qlo', 'QL09p050966' => 'qlo', 'QL09p051067' => 'qlo', 'QL12p022706' => 'qlo', 'RcHm_v2.0_Chr2g0119601' => 'rch', 'RcHm_v2.0_Chr3g0459591' => 'rch', 'RcHm_v2.0_Chr4g0418521' => 'rch', 'RcHm_v2.0_Chr4g0418531' => 'rch', 'RcHm_v2.0_Chr4g0418541' => 'rch', 'RcHm_v2.0_Chr6g0291641' => 'rch', 'Rhsim01G0086300' => 'rsi', 'Rhsim01G0276300' => 'rsi', 'Rhsim01G0276500' => 'rsi', 'Rhsim04G0207700' => 'rsi', 'Rhsim05G0234500' => 'rsi', 'Rhsim13G0022400' => 'rsi', 'Sabra02G0167900' => 'sbr', 'Sabra04G0158500' => 'sbr', 'Sabra08G0159800' => 'sbr', 'Sabra10G0011500' => 'sbr', 'Sabra14G0104400' => 'sbr', 'SalBow2G2440' => 'sbo', 'SalBow4G2265' => 'sbo', 'Sc02g0000060' => 'sci', 'Sc05g0005020' => 'sci', 'Sc13g0003890' => 'sci', 'Sed0014865' => 'sed', 'Sed0017224' => 'sed', 'Sed0026391' => 'sed', 'SEGI_00063' => 'sgi', 'SEGI_10967' => 'sgi', 'SEGI_17510' => 'sgi', 'SEGI_24396' => 'sgi', 'SEGI_39719' => 'sgi', 'SEGI_41392' => 'sgi', 'SGA_v2.0_scaffold11G05794' => 'sas', 'SGA_v2.0_scaffold142G35607' => 'sas', 'SGA_v2.0_scaffold1G00447' => 'sas', 'SHI15388' => 'shi', 'SHI15394' => 'shi', 'SHI15396' => 'shi', 'SHI15399' => 'shi', 'SMO343G0151' => 'smo', 'SMO367G1118' => 'smo', 'Solyc01g080200.3' => 'sly', 'Solyc06g008960.3' => 'sly', 'Solyc09g064780.3' => 'sly', 'Sopen01g031980' => 'spe', 'Sopen06g003710' => 'spe', 'Sopen09g026460' => 'spe', 'Sp3g21240' => 'spa', 'Sp4g30030' => 'spa', 'TAR365G0022' => 'tar', 'TAR365G1023' => 'tar', 'TAR365G1253' => 'tar', 'TAR623G0078' => 'tar', 'TAR623G1721' => 'tar', 'TAR633G0959' => 'tar', 'THA.LOC104802225' => 'tha', 'THA.LOC104804769' => 'tha', 'THA.LOC104808660' => 'tha', 'THA.LOC104812792' => 'tha', 'Thecc.01G284000' => 'tca', 'Thecc.04G220600' => 'tca', 'Thecc.05G268900' => 'tca', 'Thecc.08G171100' => 'tca', 'Thhalv10001284m.g' => 'esa', 'Thhalv10019912m.g' => 'esa', 'TPR.G14189' => 'tpr', 'TPR.G18110' => 'tpr', 'TPR.G18130' => 'tpr', 'TPR.G18131' => 'tpr', 'TPR.G18140' => 'tpr', 'TPR.G24282' => 'tpr', 'TPR.G25221' => 'tpr', 'TPR.G29267' => 'tpr', 'TPR.G35315' => 'tpr', 'TPR.G36173' => 'tpr', 'TWI09G0794' => 'twi', 'TWI59G1348' => 'twi', 'TWI74G0430' => 'twi', 'unitig_26.g8940' => 'ugi', 'unitig_749.g13744' => 'ugi', 'unitig_749.g13745' => 'ugi', 'vmacro08269' => 'vma', 'vmacro14937' => 'vma', 'vmacro20401' => 'vma', 'VMungo0464G1349' => 'vmu', 'VMungo0540G0289' => 'vmu', 'VMungo1215G1590' => 'vmu', 'VMungo1309G0221' => 'vmu', 'VMungo1309G2815' => 'vmu', 'VMungo1383G0239' => 'vmu', 'VMungo1383G2910' => 'vmu', 'Zm00001eb095270' => 'zma', 'Zm00001eb095280' => 'zma', 'Zm00001eb111630' => 'zma', 'Zm00001eb237080' => 'zma', 'Zm00001eb273740' => 'zma', 'Zm00001eb285040' => 'zma', 'Zm00001eb330790' => 'zma', 'Zm00001eb337380' => 'zma' ) $gf_id = 'HOM05D001484' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001484' ) $data_identifier = 'HOM05D001484' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 2, 'aly' => (int) 2, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 22, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 7, 'hma' => (int) 2, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 7, 'mtr' => (int) 10, 'cme' => (int) 2, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 4, 'ppa' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 4, 'qlo' => (int) 9, 'rch' => (int) 6, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 10, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 7, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb337380' $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' => 'HOM05D001484', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p31500' => 'bna', 'A05p00020' => 'bna', 'A07p08820' => 'bna', 'Aa31LG4G3300' => 'aar', 'Aa31LG8G10030' => 'aar', 'Actinidia00731' => 'ach', 'Actinidia11473' => 'ach', 'Actinidia23469' => 'ach', 'Actinidia24318' => 'ach', 'Actinidia40196' => 'ach', 'Actinidia40197' => 'ach', 'Actinidia40198' => 'ach', 'Ah.08g212990' => 'amhyb', 'Ah.15g091720' => 'amhyb', 'AL3G38260' => 'aly', 'AL4G47710' => 'aly', 'Aqoxy2G00671' => 'aox', 'Aqoxy2G03236' => 'aox', 'arahy.Tifrunner.gnm1.ann1.05IDCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KR684' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATY3SJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK6QJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6APGL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IDT7Z9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM073U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ0R87' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LE7RV4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT4QRX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V5ENPK' => 'arhy', 'AT2G48110' => 'ath', 'AT3G23590' => 'ath', 'ATR0626G186' => 'atr', 'ATR1127G141' => 'atr', 'Atru.chr4.2583' => 'acertr', 'Atru.chr5.1358' => 'acertr', 'Atru.chr5.1359' => 'acertr', 'Atru.chr8.46' => 'acertr', 'AUR62002640' => 'cqu', 'AUR62030055' => 'cqu', 'AUR62033713' => 'cqu', 'AUR62033714' => 'cqu', 'AUR62036795' => 'cqu', 'AUR62039891' => 'cqu', 'BcaB02g08737' => 'bca', 'BcaB04g20441' => 'bca', 'BcaB06g26509' => 'bca', 'BcaB06g26510' => 'bca', 'BcaB06g26511' => 'bca', 'BcaB06g26512' => 'bca', 'BcaB06g26513' => 'bca', 'BcaC02g12564' => 'bca', 'BcaC02g12565' => 'bca', 'BcaC02g12794' => 'bca', 'BcaC02g12795' => 'bca', 'BcaC02g12796' => 'bca', 'BcaC06g35541' => 'bca', 'BNapus_Darmor_BZH_scaffold_188p00080' => 'bna', 'BNapus_Darmor_BZH_scaffold_188p00090' => 'bna', 'BolC1t03972H' => 'bol', 'BolC1t03973H' => 'bol', 'BolC4t21680H' => 'bol', 'BolC7t41863H' => 'bol', 'BolSC55t61227H' => 'bol', 'BolSC55t61228H' => 'bol', 'BraA01t03278Z' => 'bra', 'BraA05t18998Z' => 'bra', 'BraA07t28673Z' => 'bra', 'C01p40150' => 'bna', 'C05p12370' => 'bna', 'C07p13680' => 'bna', 'CAN.G1006.16' => 'can', 'CAN.G1006.17' => 'can', 'CAN.G1170.2' => 'can', 'CAN.G962.7' => 'can', 'CANSAT25G2179' => 'cansat', 'CANSAT78G1573' => 'cansat', 'CARHR099510' => 'chi', 'CARHR143510' => 'chi', 'Carub.0003s2380' => 'cru', 'Carub.0004s3082' => 'cru', 'Ca_00614_v3' => 'car', 'Ca_07801_v3' => 'car', 'Ca_08567_v3' => 'car', 'Ca_09571_v3' => 'car', 'CBR_g19290' => 'cbr', 'Cc01_g19770' => 'ccan', 'Cc03_g03030' => 'ccan', 'CDE07G0968' => 'cde', 'CDE09G1441' => 'cde', 'Cfa006103' => 'cfa', 'Cfa015573' => 'cfa', 'Cfa016988' => 'cfa', 'Ciclev10006738m.g' => 'ccl', 'Ciclev10010920m.g' => 'ccl', 'Ciclev10018517m.g' => 'ccl', 'CiPaw.01G159200' => 'cil', 'CiPaw.02G091000' => 'cil', 'CiPaw.02G091100' => 'cil', 'CiPaw.08G103100' => 'cil', 'CiPaw.09G224900' => 'cil', 'ClCG06G005740' => 'cla', 'ClCG07G000090' => 'cla', 'ClCG07G000100' => 'cla', 'COL.COLO4_09143' => 'col', 'COL.COLO4_25124' => 'col', 'Cpa.g.sc16.34' => 'cpa', 'Cpa.g.sc3504.1' => 'cpa', 'Cpa.g.sc60.37' => 'cpa', 'CsaV3_6G018520' => 'csa', 'CsaV3_6G036860' => 'csa', 'CSS0001072' => 'camsi', 'CSS0020208' => 'camsi', 'CSS0021253' => 'camsi', 'CSS0022190' => 'camsi', 'CSS0036150' => 'camsi', 'CSS0040442' => 'camsi', 'CSS0042300' => 'camsi', 'CSS0045298' => 'camsi', 'DCAR_012449' => 'dca', 'DCAR_018405' => 'dca', 'DCAR_024573' => 'dca', 'DCAR_030591' => 'dca', 'Dinv16926' => 'din', 'Dinv32963' => 'din', 'Dinv38382' => 'din', 'Dinv38383' => 'din', 'Duzib133G0974' => 'dzi', 'Duzib138G1867' => 'dzi', 'Duzib211G0420' => 'dzi', 'Duzib212G0930' => 'dzi', 'ECA234G1645' => 'eca', 'ECA247G3467' => 'eca', 'ECA248G1703' => 'eca', 'EL10Ac3g06327' => 'bvu', 'EL10Ac7g17204' => 'bvu', 'Eucgr.A00855' => 'egr', 'Eucgr.A00858' => 'egr', 'Eucgr.H01520' => 'egr', 'Eucgr.H03604' => 'egr', 'Eucgr.L03465' => 'egr', 'Eucgr.L03466' => 'egr', 'FAN01G0988' => 'fan', 'FAN02G3892' => 'fan', 'FAN05G3381' => 'fan', 'FAN07G0967' => 'fan', 'FAN07G1493' => 'fan', 'FAN08G3125' => 'fan', 'FAN09G0402' => 'fan', 'FAN12G2594' => 'fan', 'FAN12G3879' => 'fan', 'FAN14G1546' => 'fan', 'FAN15G3626' => 'fan', 'FAN17G0588' => 'fan', 'FAN17G0609' => 'fan', 'FAN18G2817' => 'fan', 'FAN19G1305' => 'fan', 'FAN20G1787' => 'fan', 'FAN22G0073' => 'fan', 'FAN22G0352' => 'fan', 'FAN22G0368' => 'fan', 'FAN22G2273' => 'fan', 'FAN24G1998' => 'fan', 'FAN27G1317' => 'fan', 'FvH4_2g23980' => 'fve', 'FvH4_4g14380' => 'fve', 'FvH4_4g14390' => 'fve', 'FvH4_6g09250' => 'fve', 'Glyma.03G151100' => 'gma', 'Glyma.04G122550' => 'gma', 'Glyma.05G001600' => 'gma', 'Glyma.09G270766' => 'gma', 'Glyma.09G270832' => 'gma', 'Glyma.13G209800' => 'gma', 'Glyma.15G102800' => 'gma', 'Glyma.18G218900' => 'gma', 'Glyma.19G001500' => 'gma', 'Glyma.19G153600' => 'gma', 'Gohir.A02G028600' => 'ghi', 'Gohir.A08G045000' => 'ghi', 'Gohir.A11G120500' => 'ghi', 'Gohir.A12G006200' => 'ghi', 'Gohir.A12G006250' => 'ghi', 'Gohir.D02G036300' => 'ghi', 'Gohir.D08G054700' => 'ghi', 'Gohir.D11G125600' => 'ghi', 'Gohir.D12G005700' => 'ghi', 'Gorai.004G055200' => 'gra', 'Gorai.005G040400' => 'gra', 'Gorai.007G134500' => 'gra', 'Gorai.008G005500' => 'gra', 'GSVIVG01011094001' => 'vvi', 'GSVIVG01017879001' => 'vvi', 'GSVIVG01025988001' => 'vvi', 'GSVIVG01029847001' => 'vvi', 'HanXRQChr10g0282901' => 'han', 'HanXRQChr10g0310371' => 'han', 'HanXRQChr10g0315041' => 'han', 'HanXRQChr11g0327651' => 'han', 'HanXRQChr12g0359391' => 'han', 'Haze_00972' => 'cav', 'Haze_00973' => 'cav', 'Haze_00974' => 'cav', 'Haze_04747' => 'cav', 'Haze_04749' => 'cav', 'Haze_04750' => 'cav', 'Haze_21217' => 'cav', 'Hma1.2p1_1037F.1_g250680' => 'hma', 'Hma1.2p1_1644F.1_g295320' => 'hma', 'HPP92_011322' => 'vpl', 'HPP92_011323' => 'vpl', 'HPP92_011324' => 'vpl', 'HPP92_011325' => 'vpl', 'HPP92_011326' => 'vpl', 'Hund12205' => 'sun', 'Hund17957' => 'sun', 'Lalb_Chr06g0176771' => 'lal', 'Lalb_Chr18g0056021' => 'lal', 'Lalb_Chr18g0056031' => 'lal', 'Lalb_Chr18g0056041' => 'lal', 'Lalb_Chr20g0107751' => 'lal', 'Lalb_Chr20g0118371' => 'lal', 'Lj1g0010239' => 'lja', 'Lj1g0017101' => 'lja', 'Lj2A1178G40' => 'lonja', 'Lj2A54G84' => 'lonja', 'Lj2g0015248' => 'lja', 'Lj3A761T51' => 'lonja', 'Lj6g0018116' => 'lja', 'Lsat_1_v5_gn_4_136040' => 'lsa', 'Lsat_1_v5_gn_5_187461' => 'lsa', 'Lsat_1_v5_gn_5_77001' => 'lsa', 'Lsat_1_v5_gn_9_4461' => 'lsa', 'Manes.01G210100' => 'mes', 'Manes.03G185600' => 'mes', 'Manes.05G073300' => 'mes', 'Manes.09G120300' => 'mes', 'Manes.15G022100' => 'mes', 'Mapoly0096s0053' => 'mpo', 'MBI03_g14058_MAGBIO' => 'mbi', 'MBI03_g33876_MAGBIO' => 'mbi', 'MBI03_g36854_MAGBIO' => 'mbi', 'MBI17_g11997_MAGBIO' => 'mbi', 'MD03G1269000' => 'mdo', 'MD04G1179600' => 'mdo', 'MD11G1289800' => 'mdo', 'MD12G1194700' => 'mdo', 'MD13G1182100' => 'mdo', 'MD13G1182200' => 'mdo', 'MD16G1182600' => 'mdo', 'Medtr2g021400' => 'mtr', 'Medtr2g021470' => 'mtr', 'Medtr2g105810' => 'mtr', 'Medtr3g033580' => 'mtr', 'Medtr6g007970' => 'mtr', 'Medtr7g056330' => 'mtr', 'Medtr7g074290' => 'mtr', 'Medtr7g074380' => 'mtr', 'Medtr7g094550' => 'mtr', 'Medtr8g069995' => 'mtr', 'MELO3C014345.2' => 'cme', 'MELO3C021395.2' => 'cme', 'Migut.D00262' => 'egut', 'Migut.G00257' => 'egut', 'MSTRG.21575' => 'ama', 'MSTRG.3985' => 'ama', 'Nitab4.5_0000295g0140' => 'nta', 'Nitab4.5_0000732g0140' => 'nta', 'Nitab4.5_0003162g0020' => 'nta', 'Nitab4.5_0006180g0090' => 'nta', 'Nitab4.5_0006390g0010' => 'nta', 'Nitab4.5_0007392g0040' => 'nta', 'Nn1g02140' => 'nnu', 'Nn4g26168' => 'nnu', 'Nn5g26754' => 'nnu', 'Oeu001433.1' => 'oeu', 'Oeu010299.2' => 'oeu', 'Oeu011171.1' => 'oeu', 'Oeu037675.1' => 'oeu', 'Oeu038359.1' => 'oeu', 'Oeu063834.1' => 'oeu', 'Oeu063835.1' => 'oeu', 'Os05g0312000' => 'osa', 'Os07g0211101' => 'osa', 'Os07g0211200' => 'osa', 'Os07g0681500' => 'osa', 'Peaxi162Scf00095g01015' => 'pax', 'Peaxi162Scf00104g00329' => 'pax', 'Peaxi162Scf00161g00137' => 'pax', 'PGR004G1665' => 'pgr', 'PGR031G2937' => 'pgr', 'PGR119G2145' => 'pgr', 'PGSC0003DMG400004351' => 'stu', 'PGSC0003DMG400014625' => 'stu', 'PGSC0003DMG401000943' => 'stu', 'Phvul.001G148600' => 'pvu', 'Phvul.004G001700' => 'pvu', 'Phvul.006G154900' => 'pvu', 'Phvul.008G078200' => 'pvu', 'Phvul.011G136500' => 'pvu', 'Potri.002G215600' => 'ptr', 'Potri.008G201600' => 'ptr', 'Potri.014G138400' => 'ptr', 'Potri.016G142500' => 'ptr', 'Pp3c16_10580' => 'ppa', 'Pp3c5_25280' => 'ppa', 'Prupe.1G150000' => 'ppe', 'Prupe.1G150100' => 'ppe', 'Prupe.6G299600' => 'ppe', 'Prupe.8G245000' => 'ppe', 'Psat0s4927g0040' => 'psa', 'Psat1g052080' => 'psa', 'Psat1g183800' => 'psa', 'Psat3g113840' => 'psa', 'Psat3g126120' => 'psa', 'Psat3g126160' => 'psa', 'Psat3g158760' => 'psa', 'Psat3g158840' => 'psa', 'PSO170G2858' => 'pso', 'PSO339G0606' => 'pso', 'PSO384G4709' => 'pso', 'PSO407G0334' => 'pso', 'QL04p040276' => 'qlo', 'QL06p005458' => 'qlo', 'QL06p005472' => 'qlo', 'QL07p030546' => 'qlo', 'QL07p031519' => 'qlo', 'QL09p050949' => 'qlo', 'QL09p050966' => 'qlo', 'QL09p051067' => 'qlo', 'QL12p022706' => 'qlo', 'RcHm_v2.0_Chr2g0119601' => 'rch', 'RcHm_v2.0_Chr3g0459591' => 'rch', 'RcHm_v2.0_Chr4g0418521' => 'rch', 'RcHm_v2.0_Chr4g0418531' => 'rch', 'RcHm_v2.0_Chr4g0418541' => 'rch', 'RcHm_v2.0_Chr6g0291641' => 'rch', 'Rhsim01G0086300' => 'rsi', 'Rhsim01G0276300' => 'rsi', 'Rhsim01G0276500' => 'rsi', 'Rhsim04G0207700' => 'rsi', 'Rhsim05G0234500' => 'rsi', 'Rhsim13G0022400' => 'rsi', 'Sabra02G0167900' => 'sbr', 'Sabra04G0158500' => 'sbr', 'Sabra08G0159800' => 'sbr', 'Sabra10G0011500' => 'sbr', 'Sabra14G0104400' => 'sbr', 'SalBow2G2440' => 'sbo', 'SalBow4G2265' => 'sbo', 'Sc02g0000060' => 'sci', 'Sc05g0005020' => 'sci', 'Sc13g0003890' => 'sci', 'Sed0014865' => 'sed', 'Sed0017224' => 'sed', 'Sed0026391' => 'sed', 'SEGI_00063' => 'sgi', 'SEGI_10967' => 'sgi', 'SEGI_17510' => 'sgi', 'SEGI_24396' => 'sgi', 'SEGI_39719' => 'sgi', 'SEGI_41392' => 'sgi', 'SGA_v2.0_scaffold11G05794' => 'sas', 'SGA_v2.0_scaffold142G35607' => 'sas', 'SGA_v2.0_scaffold1G00447' => 'sas', 'SHI15388' => 'shi', 'SHI15394' => 'shi', 'SHI15396' => 'shi', 'SHI15399' => 'shi', 'SMO343G0151' => 'smo', 'SMO367G1118' => 'smo', 'Solyc01g080200.3' => 'sly', 'Solyc06g008960.3' => 'sly', 'Solyc09g064780.3' => 'sly', 'Sopen01g031980' => 'spe', 'Sopen06g003710' => 'spe', 'Sopen09g026460' => 'spe', 'Sp3g21240' => 'spa', 'Sp4g30030' => 'spa', 'TAR365G0022' => 'tar', 'TAR365G1023' => 'tar', 'TAR365G1253' => 'tar', 'TAR623G0078' => 'tar', 'TAR623G1721' => 'tar', 'TAR633G0959' => 'tar', 'THA.LOC104802225' => 'tha', 'THA.LOC104804769' => 'tha', 'THA.LOC104808660' => 'tha', 'THA.LOC104812792' => 'tha', 'Thecc.01G284000' => 'tca', 'Thecc.04G220600' => 'tca', 'Thecc.05G268900' => 'tca', 'Thecc.08G171100' => 'tca', 'Thhalv10001284m.g' => 'esa', 'Thhalv10019912m.g' => 'esa', 'TPR.G14189' => 'tpr', 'TPR.G18110' => 'tpr', 'TPR.G18130' => 'tpr', 'TPR.G18131' => 'tpr', 'TPR.G18140' => 'tpr', 'TPR.G24282' => 'tpr', 'TPR.G25221' => 'tpr', 'TPR.G29267' => 'tpr', 'TPR.G35315' => 'tpr', 'TPR.G36173' => 'tpr', 'TWI09G0794' => 'twi', 'TWI59G1348' => 'twi', 'TWI74G0430' => 'twi', 'unitig_26.g8940' => 'ugi', 'unitig_749.g13744' => 'ugi', 'unitig_749.g13745' => 'ugi', 'vmacro08269' => 'vma', 'vmacro14937' => 'vma', 'vmacro20401' => 'vma', 'VMungo0464G1349' => 'vmu', 'VMungo0540G0289' => 'vmu', 'VMungo1215G1590' => 'vmu', 'VMungo1309G0221' => 'vmu', 'VMungo1309G2815' => 'vmu', 'VMungo1383G0239' => 'vmu', 'VMungo1383G2910' => 'vmu', 'Zm00001eb095270' => 'zma', 'Zm00001eb095280' => 'zma', 'Zm00001eb111630' => 'zma', 'Zm00001eb237080' => 'zma', 'Zm00001eb273740' => 'zma', 'Zm00001eb285040' => 'zma', 'Zm00001eb330790' => 'zma', 'Zm00001eb337380' => 'zma' ), 'gf_id' => 'HOM05D001484', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001484' ), 'data_identifier' => 'HOM05D001484', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001484', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p31500' => 'bna', 'A05p00020' => 'bna', 'A07p08820' => 'bna', 'Aa31LG4G3300' => 'aar', 'Aa31LG8G10030' => 'aar', 'Actinidia00731' => 'ach', 'Actinidia11473' => 'ach', 'Actinidia23469' => 'ach', 'Actinidia24318' => 'ach', 'Actinidia40196' => 'ach', 'Actinidia40197' => 'ach', 'Actinidia40198' => 'ach', 'Ah.08g212990' => 'amhyb', 'Ah.15g091720' => 'amhyb', 'AL3G38260' => 'aly', 'AL4G47710' => 'aly', 'Aqoxy2G00671' => 'aox', 'Aqoxy2G03236' => 'aox', 'arahy.Tifrunner.gnm1.ann1.05IDCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KR684' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATY3SJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK6QJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6APGL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IDT7Z9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM073U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ0R87' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LE7RV4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT4QRX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V5ENPK' => 'arhy', 'AT2G48110' => 'ath', 'AT3G23590' => 'ath', 'ATR0626G186' => 'atr', 'ATR1127G141' => 'atr', 'Atru.chr4.2583' => 'acertr', 'Atru.chr5.1358' => 'acertr', 'Atru.chr5.1359' => 'acertr', 'Atru.chr8.46' => 'acertr', 'AUR62002640' => 'cqu', 'AUR62030055' => 'cqu', 'AUR62033713' => 'cqu', 'AUR62033714' => 'cqu', 'AUR62036795' => 'cqu', 'AUR62039891' => 'cqu', 'BcaB02g08737' => 'bca', 'BcaB04g20441' => 'bca', 'BcaB06g26509' => 'bca', 'BcaB06g26510' => 'bca', 'BcaB06g26511' => 'bca', 'BcaB06g26512' => 'bca', 'BcaB06g26513' => 'bca', 'BcaC02g12564' => 'bca', 'BcaC02g12565' => 'bca', 'BcaC02g12794' => 'bca', 'BcaC02g12795' => 'bca', 'BcaC02g12796' => 'bca', 'BcaC06g35541' => 'bca', 'BNapus_Darmor_BZH_scaffold_188p00080' => 'bna', 'BNapus_Darmor_BZH_scaffold_188p00090' => 'bna', 'BolC1t03972H' => 'bol', 'BolC1t03973H' => 'bol', 'BolC4t21680H' => 'bol', 'BolC7t41863H' => 'bol', 'BolSC55t61227H' => 'bol', 'BolSC55t61228H' => 'bol', 'BraA01t03278Z' => 'bra', 'BraA05t18998Z' => 'bra', 'BraA07t28673Z' => 'bra', 'C01p40150' => 'bna', 'C05p12370' => 'bna', 'C07p13680' => 'bna', 'CAN.G1006.16' => 'can', 'CAN.G1006.17' => 'can', 'CAN.G1170.2' => 'can', 'CAN.G962.7' => 'can', 'CANSAT25G2179' => 'cansat', 'CANSAT78G1573' => 'cansat', 'CARHR099510' => 'chi', 'CARHR143510' => 'chi', 'Carub.0003s2380' => 'cru', 'Carub.0004s3082' => 'cru', 'Ca_00614_v3' => 'car', 'Ca_07801_v3' => 'car', 'Ca_08567_v3' => 'car', 'Ca_09571_v3' => 'car', 'CBR_g19290' => 'cbr', 'Cc01_g19770' => 'ccan', 'Cc03_g03030' => 'ccan', 'CDE07G0968' => 'cde', 'CDE09G1441' => 'cde', 'Cfa006103' => 'cfa', 'Cfa015573' => 'cfa', 'Cfa016988' => 'cfa', 'Ciclev10006738m.g' => 'ccl', 'Ciclev10010920m.g' => 'ccl', 'Ciclev10018517m.g' => 'ccl', 'CiPaw.01G159200' => 'cil', 'CiPaw.02G091000' => 'cil', 'CiPaw.02G091100' => 'cil', 'CiPaw.08G103100' => 'cil', 'CiPaw.09G224900' => 'cil', 'ClCG06G005740' => 'cla', 'ClCG07G000090' => 'cla', 'ClCG07G000100' => 'cla', 'COL.COLO4_09143' => 'col', 'COL.COLO4_25124' => 'col', 'Cpa.g.sc16.34' => 'cpa', 'Cpa.g.sc3504.1' => 'cpa', 'Cpa.g.sc60.37' => 'cpa', 'CsaV3_6G018520' => 'csa', 'CsaV3_6G036860' => 'csa', 'CSS0001072' => 'camsi', 'CSS0020208' => 'camsi', 'CSS0021253' => 'camsi', 'CSS0022190' => 'camsi', 'CSS0036150' => 'camsi', 'CSS0040442' => 'camsi', 'CSS0042300' => 'camsi', 'CSS0045298' => 'camsi', 'DCAR_012449' => 'dca', 'DCAR_018405' => 'dca', 'DCAR_024573' => 'dca', 'DCAR_030591' => 'dca', 'Dinv16926' => 'din', 'Dinv32963' => 'din', 'Dinv38382' => 'din', 'Dinv38383' => 'din', 'Duzib133G0974' => 'dzi', 'Duzib138G1867' => 'dzi', 'Duzib211G0420' => 'dzi', 'Duzib212G0930' => 'dzi', 'ECA234G1645' => 'eca', 'ECA247G3467' => 'eca', 'ECA248G1703' => 'eca', 'EL10Ac3g06327' => 'bvu', 'EL10Ac7g17204' => 'bvu', 'Eucgr.A00855' => 'egr', 'Eucgr.A00858' => 'egr', 'Eucgr.H01520' => 'egr', 'Eucgr.H03604' => 'egr', 'Eucgr.L03465' => 'egr', 'Eucgr.L03466' => 'egr', 'FAN01G0988' => 'fan', 'FAN02G3892' => 'fan', 'FAN05G3381' => 'fan', 'FAN07G0967' => 'fan', 'FAN07G1493' => 'fan', 'FAN08G3125' => 'fan', 'FAN09G0402' => 'fan', 'FAN12G2594' => 'fan', 'FAN12G3879' => 'fan', 'FAN14G1546' => 'fan', 'FAN15G3626' => 'fan', 'FAN17G0588' => 'fan', 'FAN17G0609' => 'fan', 'FAN18G2817' => 'fan', 'FAN19G1305' => 'fan', 'FAN20G1787' => 'fan', 'FAN22G0073' => 'fan', 'FAN22G0352' => 'fan', 'FAN22G0368' => 'fan', 'FAN22G2273' => 'fan', 'FAN24G1998' => 'fan', 'FAN27G1317' => 'fan', 'FvH4_2g23980' => 'fve', 'FvH4_4g14380' => 'fve', 'FvH4_4g14390' => 'fve', 'FvH4_6g09250' => 'fve', 'Glyma.03G151100' => 'gma', 'Glyma.04G122550' => 'gma', 'Glyma.05G001600' => 'gma', 'Glyma.09G270766' => 'gma', 'Glyma.09G270832' => 'gma', 'Glyma.13G209800' => 'gma', 'Glyma.15G102800' => 'gma', 'Glyma.18G218900' => 'gma', 'Glyma.19G001500' => 'gma', 'Glyma.19G153600' => 'gma', 'Gohir.A02G028600' => 'ghi', 'Gohir.A08G045000' => 'ghi', 'Gohir.A11G120500' => 'ghi', 'Gohir.A12G006200' => 'ghi', 'Gohir.A12G006250' => 'ghi', 'Gohir.D02G036300' => 'ghi', 'Gohir.D08G054700' => 'ghi', 'Gohir.D11G125600' => 'ghi', 'Gohir.D12G005700' => 'ghi', 'Gorai.004G055200' => 'gra', 'Gorai.005G040400' => 'gra', 'Gorai.007G134500' => 'gra', 'Gorai.008G005500' => 'gra', 'GSVIVG01011094001' => 'vvi', 'GSVIVG01017879001' => 'vvi', 'GSVIVG01025988001' => 'vvi', 'GSVIVG01029847001' => 'vvi', 'HanXRQChr10g0282901' => 'han', 'HanXRQChr10g0310371' => 'han', 'HanXRQChr10g0315041' => 'han', 'HanXRQChr11g0327651' => 'han', 'HanXRQChr12g0359391' => 'han', 'Haze_00972' => 'cav', 'Haze_00973' => 'cav', 'Haze_00974' => 'cav', 'Haze_04747' => 'cav', 'Haze_04749' => 'cav', 'Haze_04750' => 'cav', 'Haze_21217' => 'cav', 'Hma1.2p1_1037F.1_g250680' => 'hma', 'Hma1.2p1_1644F.1_g295320' => 'hma', 'HPP92_011322' => 'vpl', 'HPP92_011323' => 'vpl', 'HPP92_011324' => 'vpl', 'HPP92_011325' => 'vpl', 'HPP92_011326' => 'vpl', 'Hund12205' => 'sun', 'Hund17957' => 'sun', 'Lalb_Chr06g0176771' => 'lal', 'Lalb_Chr18g0056021' => 'lal', 'Lalb_Chr18g0056031' => 'lal', 'Lalb_Chr18g0056041' => 'lal', 'Lalb_Chr20g0107751' => 'lal', 'Lalb_Chr20g0118371' => 'lal', 'Lj1g0010239' => 'lja', 'Lj1g0017101' => 'lja', 'Lj2A1178G40' => 'lonja', 'Lj2A54G84' => 'lonja', 'Lj2g0015248' => 'lja', 'Lj3A761T51' => 'lonja', 'Lj6g0018116' => 'lja', 'Lsat_1_v5_gn_4_136040' => 'lsa', 'Lsat_1_v5_gn_5_187461' => 'lsa', 'Lsat_1_v5_gn_5_77001' => 'lsa', 'Lsat_1_v5_gn_9_4461' => 'lsa', 'Manes.01G210100' => 'mes', 'Manes.03G185600' => 'mes', 'Manes.05G073300' => 'mes', 'Manes.09G120300' => 'mes', 'Manes.15G022100' => 'mes', 'Mapoly0096s0053' => 'mpo', 'MBI03_g14058_MAGBIO' => 'mbi', 'MBI03_g33876_MAGBIO' => 'mbi', 'MBI03_g36854_MAGBIO' => 'mbi', 'MBI17_g11997_MAGBIO' => 'mbi', 'MD03G1269000' => 'mdo', 'MD04G1179600' => 'mdo', 'MD11G1289800' => 'mdo', 'MD12G1194700' => 'mdo', 'MD13G1182100' => 'mdo', 'MD13G1182200' => 'mdo', 'MD16G1182600' => 'mdo', 'Medtr2g021400' => 'mtr', 'Medtr2g021470' => 'mtr', 'Medtr2g105810' => 'mtr', 'Medtr3g033580' => 'mtr', 'Medtr6g007970' => 'mtr', 'Medtr7g056330' => 'mtr', 'Medtr7g074290' => 'mtr', 'Medtr7g074380' => 'mtr', 'Medtr7g094550' => 'mtr', 'Medtr8g069995' => 'mtr', 'MELO3C014345.2' => 'cme', 'MELO3C021395.2' => 'cme', 'Migut.D00262' => 'egut', 'Migut.G00257' => 'egut', 'MSTRG.21575' => 'ama', 'MSTRG.3985' => 'ama', 'Nitab4.5_0000295g0140' => 'nta', 'Nitab4.5_0000732g0140' => 'nta', 'Nitab4.5_0003162g0020' => 'nta', 'Nitab4.5_0006180g0090' => 'nta', 'Nitab4.5_0006390g0010' => 'nta', 'Nitab4.5_0007392g0040' => 'nta', 'Nn1g02140' => 'nnu', 'Nn4g26168' => 'nnu', 'Nn5g26754' => 'nnu', 'Oeu001433.1' => 'oeu', 'Oeu010299.2' => 'oeu', 'Oeu011171.1' => 'oeu', 'Oeu037675.1' => 'oeu', 'Oeu038359.1' => 'oeu', 'Oeu063834.1' => 'oeu', 'Oeu063835.1' => 'oeu', 'Os05g0312000' => 'osa', 'Os07g0211101' => 'osa', 'Os07g0211200' => 'osa', 'Os07g0681500' => 'osa', 'Peaxi162Scf00095g01015' => 'pax', 'Peaxi162Scf00104g00329' => 'pax', 'Peaxi162Scf00161g00137' => 'pax', 'PGR004G1665' => 'pgr', 'PGR031G2937' => 'pgr', 'PGR119G2145' => 'pgr', 'PGSC0003DMG400004351' => 'stu', 'PGSC0003DMG400014625' => 'stu', 'PGSC0003DMG401000943' => 'stu', 'Phvul.001G148600' => 'pvu', 'Phvul.004G001700' => 'pvu', 'Phvul.006G154900' => 'pvu', 'Phvul.008G078200' => 'pvu', 'Phvul.011G136500' => 'pvu', 'Potri.002G215600' => 'ptr', 'Potri.008G201600' => 'ptr', 'Potri.014G138400' => 'ptr', 'Potri.016G142500' => 'ptr', 'Pp3c16_10580' => 'ppa', 'Pp3c5_25280' => 'ppa', 'Prupe.1G150000' => 'ppe', 'Prupe.1G150100' => 'ppe', 'Prupe.6G299600' => 'ppe', 'Prupe.8G245000' => 'ppe', 'Psat0s4927g0040' => 'psa', 'Psat1g052080' => 'psa', 'Psat1g183800' => 'psa', 'Psat3g113840' => 'psa', 'Psat3g126120' => 'psa', 'Psat3g126160' => 'psa', 'Psat3g158760' => 'psa', 'Psat3g158840' => 'psa', 'PSO170G2858' => 'pso', 'PSO339G0606' => 'pso', 'PSO384G4709' => 'pso', 'PSO407G0334' => 'pso', 'QL04p040276' => 'qlo', 'QL06p005458' => 'qlo', 'QL06p005472' => 'qlo', 'QL07p030546' => 'qlo', 'QL07p031519' => 'qlo', 'QL09p050949' => 'qlo', 'QL09p050966' => 'qlo', 'QL09p051067' => 'qlo', 'QL12p022706' => 'qlo', 'RcHm_v2.0_Chr2g0119601' => 'rch', 'RcHm_v2.0_Chr3g0459591' => 'rch', 'RcHm_v2.0_Chr4g0418521' => 'rch', 'RcHm_v2.0_Chr4g0418531' => 'rch', 'RcHm_v2.0_Chr4g0418541' => 'rch', 'RcHm_v2.0_Chr6g0291641' => 'rch', 'Rhsim01G0086300' => 'rsi', 'Rhsim01G0276300' => 'rsi', 'Rhsim01G0276500' => 'rsi', 'Rhsim04G0207700' => 'rsi', 'Rhsim05G0234500' => 'rsi', 'Rhsim13G0022400' => 'rsi', 'Sabra02G0167900' => 'sbr', 'Sabra04G0158500' => 'sbr', 'Sabra08G0159800' => 'sbr', 'Sabra10G0011500' => 'sbr', 'Sabra14G0104400' => 'sbr', 'SalBow2G2440' => 'sbo', 'SalBow4G2265' => 'sbo', 'Sc02g0000060' => 'sci', 'Sc05g0005020' => 'sci', 'Sc13g0003890' => 'sci', 'Sed0014865' => 'sed', 'Sed0017224' => 'sed', 'Sed0026391' => 'sed', 'SEGI_00063' => 'sgi', 'SEGI_10967' => 'sgi', 'SEGI_17510' => 'sgi', 'SEGI_24396' => 'sgi', 'SEGI_39719' => 'sgi', 'SEGI_41392' => 'sgi', 'SGA_v2.0_scaffold11G05794' => 'sas', 'SGA_v2.0_scaffold142G35607' => 'sas', 'SGA_v2.0_scaffold1G00447' => 'sas', 'SHI15388' => 'shi', 'SHI15394' => 'shi', 'SHI15396' => 'shi', 'SHI15399' => 'shi', 'SMO343G0151' => 'smo', 'SMO367G1118' => 'smo', 'Solyc01g080200.3' => 'sly', 'Solyc06g008960.3' => 'sly', 'Solyc09g064780.3' => 'sly', 'Sopen01g031980' => 'spe', 'Sopen06g003710' => 'spe', 'Sopen09g026460' => 'spe', 'Sp3g21240' => 'spa', 'Sp4g30030' => 'spa', 'TAR365G0022' => 'tar', 'TAR365G1023' => 'tar', 'TAR365G1253' => 'tar', 'TAR623G0078' => 'tar', 'TAR623G1721' => 'tar', 'TAR633G0959' => 'tar', 'THA.LOC104802225' => 'tha', 'THA.LOC104804769' => 'tha', 'THA.LOC104808660' => 'tha', 'THA.LOC104812792' => 'tha', 'Thecc.01G284000' => 'tca', 'Thecc.04G220600' => 'tca', 'Thecc.05G268900' => 'tca', 'Thecc.08G171100' => 'tca', 'Thhalv10001284m.g' => 'esa', 'Thhalv10019912m.g' => 'esa', 'TPR.G14189' => 'tpr', 'TPR.G18110' => 'tpr', 'TPR.G18130' => 'tpr', 'TPR.G18131' => 'tpr', 'TPR.G18140' => 'tpr', 'TPR.G24282' => 'tpr', 'TPR.G25221' => 'tpr', 'TPR.G29267' => 'tpr', 'TPR.G35315' => 'tpr', 'TPR.G36173' => 'tpr', 'TWI09G0794' => 'twi', 'TWI59G1348' => 'twi', 'TWI74G0430' => 'twi', 'unitig_26.g8940' => 'ugi', 'unitig_749.g13744' => 'ugi', 'unitig_749.g13745' => 'ugi', 'vmacro08269' => 'vma', 'vmacro14937' => 'vma', 'vmacro20401' => 'vma', 'VMungo0464G1349' => 'vmu', 'VMungo0540G0289' => 'vmu', 'VMungo1215G1590' => 'vmu', 'VMungo1309G0221' => 'vmu', 'VMungo1309G2815' => 'vmu', 'VMungo1383G0239' => 'vmu', 'VMungo1383G2910' => 'vmu', 'Zm00001eb095270' => 'zma', 'Zm00001eb095280' => 'zma', 'Zm00001eb111630' => 'zma', 'Zm00001eb237080' => 'zma', 'Zm00001eb273740' => 'zma', 'Zm00001eb285040' => 'zma', 'Zm00001eb330790' => 'zma', 'Zm00001eb337380' => 'zma' ) $gf_id = 'HOM05D001484' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001484' ) $data_identifier = 'HOM05D001484' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 2, 'aly' => (int) 2, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 22, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 7, 'hma' => (int) 2, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 7, 'mtr' => (int) 10, 'cme' => (int) 2, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 4, 'ppa' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 4, 'qlo' => (int) 9, 'rch' => (int) 6, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 10, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 7, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb337380' $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' => 'HOM05D001484', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p31500' => 'bna', 'A05p00020' => 'bna', 'A07p08820' => 'bna', 'Aa31LG4G3300' => 'aar', 'Aa31LG8G10030' => 'aar', 'Actinidia00731' => 'ach', 'Actinidia11473' => 'ach', 'Actinidia23469' => 'ach', 'Actinidia24318' => 'ach', 'Actinidia40196' => 'ach', 'Actinidia40197' => 'ach', 'Actinidia40198' => 'ach', 'Ah.08g212990' => 'amhyb', 'Ah.15g091720' => 'amhyb', 'AL3G38260' => 'aly', 'AL4G47710' => 'aly', 'Aqoxy2G00671' => 'aox', 'Aqoxy2G03236' => 'aox', 'arahy.Tifrunner.gnm1.ann1.05IDCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KR684' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATY3SJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK6QJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6APGL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IDT7Z9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM073U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ0R87' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LE7RV4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT4QRX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V5ENPK' => 'arhy', 'AT2G48110' => 'ath', 'AT3G23590' => 'ath', 'ATR0626G186' => 'atr', 'ATR1127G141' => 'atr', 'Atru.chr4.2583' => 'acertr', 'Atru.chr5.1358' => 'acertr', 'Atru.chr5.1359' => 'acertr', 'Atru.chr8.46' => 'acertr', 'AUR62002640' => 'cqu', 'AUR62030055' => 'cqu', 'AUR62033713' => 'cqu', 'AUR62033714' => 'cqu', 'AUR62036795' => 'cqu', 'AUR62039891' => 'cqu', 'BcaB02g08737' => 'bca', 'BcaB04g20441' => 'bca', 'BcaB06g26509' => 'bca', 'BcaB06g26510' => 'bca', 'BcaB06g26511' => 'bca', 'BcaB06g26512' => 'bca', 'BcaB06g26513' => 'bca', 'BcaC02g12564' => 'bca', 'BcaC02g12565' => 'bca', 'BcaC02g12794' => 'bca', 'BcaC02g12795' => 'bca', 'BcaC02g12796' => 'bca', 'BcaC06g35541' => 'bca', 'BNapus_Darmor_BZH_scaffold_188p00080' => 'bna', 'BNapus_Darmor_BZH_scaffold_188p00090' => 'bna', 'BolC1t03972H' => 'bol', 'BolC1t03973H' => 'bol', 'BolC4t21680H' => 'bol', 'BolC7t41863H' => 'bol', 'BolSC55t61227H' => 'bol', 'BolSC55t61228H' => 'bol', 'BraA01t03278Z' => 'bra', 'BraA05t18998Z' => 'bra', 'BraA07t28673Z' => 'bra', 'C01p40150' => 'bna', 'C05p12370' => 'bna', 'C07p13680' => 'bna', 'CAN.G1006.16' => 'can', 'CAN.G1006.17' => 'can', 'CAN.G1170.2' => 'can', 'CAN.G962.7' => 'can', 'CANSAT25G2179' => 'cansat', 'CANSAT78G1573' => 'cansat', 'CARHR099510' => 'chi', 'CARHR143510' => 'chi', 'Carub.0003s2380' => 'cru', 'Carub.0004s3082' => 'cru', 'Ca_00614_v3' => 'car', 'Ca_07801_v3' => 'car', 'Ca_08567_v3' => 'car', 'Ca_09571_v3' => 'car', 'CBR_g19290' => 'cbr', 'Cc01_g19770' => 'ccan', 'Cc03_g03030' => 'ccan', 'CDE07G0968' => 'cde', 'CDE09G1441' => 'cde', 'Cfa006103' => 'cfa', 'Cfa015573' => 'cfa', 'Cfa016988' => 'cfa', 'Ciclev10006738m.g' => 'ccl', 'Ciclev10010920m.g' => 'ccl', 'Ciclev10018517m.g' => 'ccl', 'CiPaw.01G159200' => 'cil', 'CiPaw.02G091000' => 'cil', 'CiPaw.02G091100' => 'cil', 'CiPaw.08G103100' => 'cil', 'CiPaw.09G224900' => 'cil', 'ClCG06G005740' => 'cla', 'ClCG07G000090' => 'cla', 'ClCG07G000100' => 'cla', 'COL.COLO4_09143' => 'col', 'COL.COLO4_25124' => 'col', 'Cpa.g.sc16.34' => 'cpa', 'Cpa.g.sc3504.1' => 'cpa', 'Cpa.g.sc60.37' => 'cpa', 'CsaV3_6G018520' => 'csa', 'CsaV3_6G036860' => 'csa', 'CSS0001072' => 'camsi', 'CSS0020208' => 'camsi', 'CSS0021253' => 'camsi', 'CSS0022190' => 'camsi', 'CSS0036150' => 'camsi', 'CSS0040442' => 'camsi', 'CSS0042300' => 'camsi', 'CSS0045298' => 'camsi', 'DCAR_012449' => 'dca', 'DCAR_018405' => 'dca', 'DCAR_024573' => 'dca', 'DCAR_030591' => 'dca', 'Dinv16926' => 'din', 'Dinv32963' => 'din', 'Dinv38382' => 'din', 'Dinv38383' => 'din', 'Duzib133G0974' => 'dzi', 'Duzib138G1867' => 'dzi', 'Duzib211G0420' => 'dzi', 'Duzib212G0930' => 'dzi', 'ECA234G1645' => 'eca', 'ECA247G3467' => 'eca', 'ECA248G1703' => 'eca', 'EL10Ac3g06327' => 'bvu', 'EL10Ac7g17204' => 'bvu', 'Eucgr.A00855' => 'egr', 'Eucgr.A00858' => 'egr', 'Eucgr.H01520' => 'egr', 'Eucgr.H03604' => 'egr', 'Eucgr.L03465' => 'egr', 'Eucgr.L03466' => 'egr', 'FAN01G0988' => 'fan', 'FAN02G3892' => 'fan', 'FAN05G3381' => 'fan', 'FAN07G0967' => 'fan', 'FAN07G1493' => 'fan', 'FAN08G3125' => 'fan', 'FAN09G0402' => 'fan', 'FAN12G2594' => 'fan', 'FAN12G3879' => 'fan', 'FAN14G1546' => 'fan', 'FAN15G3626' => 'fan', 'FAN17G0588' => 'fan', 'FAN17G0609' => 'fan', 'FAN18G2817' => 'fan', 'FAN19G1305' => 'fan', 'FAN20G1787' => 'fan', 'FAN22G0073' => 'fan', 'FAN22G0352' => 'fan', 'FAN22G0368' => 'fan', 'FAN22G2273' => 'fan', 'FAN24G1998' => 'fan', 'FAN27G1317' => 'fan', 'FvH4_2g23980' => 'fve', 'FvH4_4g14380' => 'fve', 'FvH4_4g14390' => 'fve', 'FvH4_6g09250' => 'fve', 'Glyma.03G151100' => 'gma', 'Glyma.04G122550' => 'gma', 'Glyma.05G001600' => 'gma', 'Glyma.09G270766' => 'gma', 'Glyma.09G270832' => 'gma', 'Glyma.13G209800' => 'gma', 'Glyma.15G102800' => 'gma', 'Glyma.18G218900' => 'gma', 'Glyma.19G001500' => 'gma', 'Glyma.19G153600' => 'gma', 'Gohir.A02G028600' => 'ghi', 'Gohir.A08G045000' => 'ghi', 'Gohir.A11G120500' => 'ghi', 'Gohir.A12G006200' => 'ghi', 'Gohir.A12G006250' => 'ghi', 'Gohir.D02G036300' => 'ghi', 'Gohir.D08G054700' => 'ghi', 'Gohir.D11G125600' => 'ghi', 'Gohir.D12G005700' => 'ghi', 'Gorai.004G055200' => 'gra', 'Gorai.005G040400' => 'gra', 'Gorai.007G134500' => 'gra', 'Gorai.008G005500' => 'gra', 'GSVIVG01011094001' => 'vvi', 'GSVIVG01017879001' => 'vvi', 'GSVIVG01025988001' => 'vvi', 'GSVIVG01029847001' => 'vvi', 'HanXRQChr10g0282901' => 'han', 'HanXRQChr10g0310371' => 'han', 'HanXRQChr10g0315041' => 'han', 'HanXRQChr11g0327651' => 'han', 'HanXRQChr12g0359391' => 'han', 'Haze_00972' => 'cav', 'Haze_00973' => 'cav', 'Haze_00974' => 'cav', 'Haze_04747' => 'cav', 'Haze_04749' => 'cav', 'Haze_04750' => 'cav', 'Haze_21217' => 'cav', 'Hma1.2p1_1037F.1_g250680' => 'hma', 'Hma1.2p1_1644F.1_g295320' => 'hma', 'HPP92_011322' => 'vpl', 'HPP92_011323' => 'vpl', 'HPP92_011324' => 'vpl', 'HPP92_011325' => 'vpl', 'HPP92_011326' => 'vpl', 'Hund12205' => 'sun', 'Hund17957' => 'sun', 'Lalb_Chr06g0176771' => 'lal', 'Lalb_Chr18g0056021' => 'lal', 'Lalb_Chr18g0056031' => 'lal', 'Lalb_Chr18g0056041' => 'lal', 'Lalb_Chr20g0107751' => 'lal', 'Lalb_Chr20g0118371' => 'lal', 'Lj1g0010239' => 'lja', 'Lj1g0017101' => 'lja', 'Lj2A1178G40' => 'lonja', 'Lj2A54G84' => 'lonja', 'Lj2g0015248' => 'lja', 'Lj3A761T51' => 'lonja', 'Lj6g0018116' => 'lja', 'Lsat_1_v5_gn_4_136040' => 'lsa', 'Lsat_1_v5_gn_5_187461' => 'lsa', 'Lsat_1_v5_gn_5_77001' => 'lsa', 'Lsat_1_v5_gn_9_4461' => 'lsa', 'Manes.01G210100' => 'mes', 'Manes.03G185600' => 'mes', 'Manes.05G073300' => 'mes', 'Manes.09G120300' => 'mes', 'Manes.15G022100' => 'mes', 'Mapoly0096s0053' => 'mpo', 'MBI03_g14058_MAGBIO' => 'mbi', 'MBI03_g33876_MAGBIO' => 'mbi', 'MBI03_g36854_MAGBIO' => 'mbi', 'MBI17_g11997_MAGBIO' => 'mbi', 'MD03G1269000' => 'mdo', 'MD04G1179600' => 'mdo', 'MD11G1289800' => 'mdo', 'MD12G1194700' => 'mdo', 'MD13G1182100' => 'mdo', 'MD13G1182200' => 'mdo', 'MD16G1182600' => 'mdo', 'Medtr2g021400' => 'mtr', 'Medtr2g021470' => 'mtr', 'Medtr2g105810' => 'mtr', 'Medtr3g033580' => 'mtr', 'Medtr6g007970' => 'mtr', 'Medtr7g056330' => 'mtr', 'Medtr7g074290' => 'mtr', 'Medtr7g074380' => 'mtr', 'Medtr7g094550' => 'mtr', 'Medtr8g069995' => 'mtr', 'MELO3C014345.2' => 'cme', 'MELO3C021395.2' => 'cme', 'Migut.D00262' => 'egut', 'Migut.G00257' => 'egut', 'MSTRG.21575' => 'ama', 'MSTRG.3985' => 'ama', 'Nitab4.5_0000295g0140' => 'nta', 'Nitab4.5_0000732g0140' => 'nta', 'Nitab4.5_0003162g0020' => 'nta', 'Nitab4.5_0006180g0090' => 'nta', 'Nitab4.5_0006390g0010' => 'nta', 'Nitab4.5_0007392g0040' => 'nta', 'Nn1g02140' => 'nnu', 'Nn4g26168' => 'nnu', 'Nn5g26754' => 'nnu', 'Oeu001433.1' => 'oeu', 'Oeu010299.2' => 'oeu', 'Oeu011171.1' => 'oeu', 'Oeu037675.1' => 'oeu', 'Oeu038359.1' => 'oeu', 'Oeu063834.1' => 'oeu', 'Oeu063835.1' => 'oeu', 'Os05g0312000' => 'osa', 'Os07g0211101' => 'osa', 'Os07g0211200' => 'osa', 'Os07g0681500' => 'osa', 'Peaxi162Scf00095g01015' => 'pax', 'Peaxi162Scf00104g00329' => 'pax', 'Peaxi162Scf00161g00137' => 'pax', 'PGR004G1665' => 'pgr', 'PGR031G2937' => 'pgr', 'PGR119G2145' => 'pgr', 'PGSC0003DMG400004351' => 'stu', 'PGSC0003DMG400014625' => 'stu', 'PGSC0003DMG401000943' => 'stu', 'Phvul.001G148600' => 'pvu', 'Phvul.004G001700' => 'pvu', 'Phvul.006G154900' => 'pvu', 'Phvul.008G078200' => 'pvu', 'Phvul.011G136500' => 'pvu', 'Potri.002G215600' => 'ptr', 'Potri.008G201600' => 'ptr', 'Potri.014G138400' => 'ptr', 'Potri.016G142500' => 'ptr', 'Pp3c16_10580' => 'ppa', 'Pp3c5_25280' => 'ppa', 'Prupe.1G150000' => 'ppe', 'Prupe.1G150100' => 'ppe', 'Prupe.6G299600' => 'ppe', 'Prupe.8G245000' => 'ppe', 'Psat0s4927g0040' => 'psa', 'Psat1g052080' => 'psa', 'Psat1g183800' => 'psa', 'Psat3g113840' => 'psa', 'Psat3g126120' => 'psa', 'Psat3g126160' => 'psa', 'Psat3g158760' => 'psa', 'Psat3g158840' => 'psa', 'PSO170G2858' => 'pso', 'PSO339G0606' => 'pso', 'PSO384G4709' => 'pso', 'PSO407G0334' => 'pso', 'QL04p040276' => 'qlo', 'QL06p005458' => 'qlo', 'QL06p005472' => 'qlo', 'QL07p030546' => 'qlo', 'QL07p031519' => 'qlo', 'QL09p050949' => 'qlo', 'QL09p050966' => 'qlo', 'QL09p051067' => 'qlo', 'QL12p022706' => 'qlo', 'RcHm_v2.0_Chr2g0119601' => 'rch', 'RcHm_v2.0_Chr3g0459591' => 'rch', 'RcHm_v2.0_Chr4g0418521' => 'rch', 'RcHm_v2.0_Chr4g0418531' => 'rch', 'RcHm_v2.0_Chr4g0418541' => 'rch', 'RcHm_v2.0_Chr6g0291641' => 'rch', 'Rhsim01G0086300' => 'rsi', 'Rhsim01G0276300' => 'rsi', 'Rhsim01G0276500' => 'rsi', 'Rhsim04G0207700' => 'rsi', 'Rhsim05G0234500' => 'rsi', 'Rhsim13G0022400' => 'rsi', 'Sabra02G0167900' => 'sbr', 'Sabra04G0158500' => 'sbr', 'Sabra08G0159800' => 'sbr', 'Sabra10G0011500' => 'sbr', 'Sabra14G0104400' => 'sbr', 'SalBow2G2440' => 'sbo', 'SalBow4G2265' => 'sbo', 'Sc02g0000060' => 'sci', 'Sc05g0005020' => 'sci', 'Sc13g0003890' => 'sci', 'Sed0014865' => 'sed', 'Sed0017224' => 'sed', 'Sed0026391' => 'sed', 'SEGI_00063' => 'sgi', 'SEGI_10967' => 'sgi', 'SEGI_17510' => 'sgi', 'SEGI_24396' => 'sgi', 'SEGI_39719' => 'sgi', 'SEGI_41392' => 'sgi', 'SGA_v2.0_scaffold11G05794' => 'sas', 'SGA_v2.0_scaffold142G35607' => 'sas', 'SGA_v2.0_scaffold1G00447' => 'sas', 'SHI15388' => 'shi', 'SHI15394' => 'shi', 'SHI15396' => 'shi', 'SHI15399' => 'shi', 'SMO343G0151' => 'smo', 'SMO367G1118' => 'smo', 'Solyc01g080200.3' => 'sly', 'Solyc06g008960.3' => 'sly', 'Solyc09g064780.3' => 'sly', 'Sopen01g031980' => 'spe', 'Sopen06g003710' => 'spe', 'Sopen09g026460' => 'spe', 'Sp3g21240' => 'spa', 'Sp4g30030' => 'spa', 'TAR365G0022' => 'tar', 'TAR365G1023' => 'tar', 'TAR365G1253' => 'tar', 'TAR623G0078' => 'tar', 'TAR623G1721' => 'tar', 'TAR633G0959' => 'tar', 'THA.LOC104802225' => 'tha', 'THA.LOC104804769' => 'tha', 'THA.LOC104808660' => 'tha', 'THA.LOC104812792' => 'tha', 'Thecc.01G284000' => 'tca', 'Thecc.04G220600' => 'tca', 'Thecc.05G268900' => 'tca', 'Thecc.08G171100' => 'tca', 'Thhalv10001284m.g' => 'esa', 'Thhalv10019912m.g' => 'esa', 'TPR.G14189' => 'tpr', 'TPR.G18110' => 'tpr', 'TPR.G18130' => 'tpr', 'TPR.G18131' => 'tpr', 'TPR.G18140' => 'tpr', 'TPR.G24282' => 'tpr', 'TPR.G25221' => 'tpr', 'TPR.G29267' => 'tpr', 'TPR.G35315' => 'tpr', 'TPR.G36173' => 'tpr', 'TWI09G0794' => 'twi', 'TWI59G1348' => 'twi', 'TWI74G0430' => 'twi', 'unitig_26.g8940' => 'ugi', 'unitig_749.g13744' => 'ugi', 'unitig_749.g13745' => 'ugi', 'vmacro08269' => 'vma', 'vmacro14937' => 'vma', 'vmacro20401' => 'vma', 'VMungo0464G1349' => 'vmu', 'VMungo0540G0289' => 'vmu', 'VMungo1215G1590' => 'vmu', 'VMungo1309G0221' => 'vmu', 'VMungo1309G2815' => 'vmu', 'VMungo1383G0239' => 'vmu', 'VMungo1383G2910' => 'vmu', 'Zm00001eb095270' => 'zma', 'Zm00001eb095280' => 'zma', 'Zm00001eb111630' => 'zma', 'Zm00001eb237080' => 'zma', 'Zm00001eb273740' => 'zma', 'Zm00001eb285040' => 'zma', 'Zm00001eb330790' => 'zma', 'Zm00001eb337380' => 'zma' ), 'gf_id' => 'HOM05D001484', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001484' ), 'data_identifier' => 'HOM05D001484', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001484', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p31500' => 'bna', 'A05p00020' => 'bna', 'A07p08820' => 'bna', 'Aa31LG4G3300' => 'aar', 'Aa31LG8G10030' => 'aar', 'Actinidia00731' => 'ach', 'Actinidia11473' => 'ach', 'Actinidia23469' => 'ach', 'Actinidia24318' => 'ach', 'Actinidia40196' => 'ach', 'Actinidia40197' => 'ach', 'Actinidia40198' => 'ach', 'Ah.08g212990' => 'amhyb', 'Ah.15g091720' => 'amhyb', 'AL3G38260' => 'aly', 'AL4G47710' => 'aly', 'Aqoxy2G00671' => 'aox', 'Aqoxy2G03236' => 'aox', 'arahy.Tifrunner.gnm1.ann1.05IDCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KR684' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATY3SJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK6QJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6APGL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IDT7Z9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM073U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ0R87' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LE7RV4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT4QRX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V5ENPK' => 'arhy', 'AT2G48110' => 'ath', 'AT3G23590' => 'ath', 'ATR0626G186' => 'atr', 'ATR1127G141' => 'atr', 'Atru.chr4.2583' => 'acertr', 'Atru.chr5.1358' => 'acertr', 'Atru.chr5.1359' => 'acertr', 'Atru.chr8.46' => 'acertr', 'AUR62002640' => 'cqu', 'AUR62030055' => 'cqu', 'AUR62033713' => 'cqu', 'AUR62033714' => 'cqu', 'AUR62036795' => 'cqu', 'AUR62039891' => 'cqu', 'BcaB02g08737' => 'bca', 'BcaB04g20441' => 'bca', 'BcaB06g26509' => 'bca', 'BcaB06g26510' => 'bca', 'BcaB06g26511' => 'bca', 'BcaB06g26512' => 'bca', 'BcaB06g26513' => 'bca', 'BcaC02g12564' => 'bca', 'BcaC02g12565' => 'bca', 'BcaC02g12794' => 'bca', 'BcaC02g12795' => 'bca', 'BcaC02g12796' => 'bca', 'BcaC06g35541' => 'bca', 'BNapus_Darmor_BZH_scaffold_188p00080' => 'bna', 'BNapus_Darmor_BZH_scaffold_188p00090' => 'bna', 'BolC1t03972H' => 'bol', 'BolC1t03973H' => 'bol', 'BolC4t21680H' => 'bol', 'BolC7t41863H' => 'bol', 'BolSC55t61227H' => 'bol', 'BolSC55t61228H' => 'bol', 'BraA01t03278Z' => 'bra', 'BraA05t18998Z' => 'bra', 'BraA07t28673Z' => 'bra', 'C01p40150' => 'bna', 'C05p12370' => 'bna', 'C07p13680' => 'bna', 'CAN.G1006.16' => 'can', 'CAN.G1006.17' => 'can', 'CAN.G1170.2' => 'can', 'CAN.G962.7' => 'can', 'CANSAT25G2179' => 'cansat', 'CANSAT78G1573' => 'cansat', 'CARHR099510' => 'chi', 'CARHR143510' => 'chi', 'Carub.0003s2380' => 'cru', 'Carub.0004s3082' => 'cru', 'Ca_00614_v3' => 'car', 'Ca_07801_v3' => 'car', 'Ca_08567_v3' => 'car', 'Ca_09571_v3' => 'car', 'CBR_g19290' => 'cbr', 'Cc01_g19770' => 'ccan', 'Cc03_g03030' => 'ccan', 'CDE07G0968' => 'cde', 'CDE09G1441' => 'cde', 'Cfa006103' => 'cfa', 'Cfa015573' => 'cfa', 'Cfa016988' => 'cfa', 'Ciclev10006738m.g' => 'ccl', 'Ciclev10010920m.g' => 'ccl', 'Ciclev10018517m.g' => 'ccl', 'CiPaw.01G159200' => 'cil', 'CiPaw.02G091000' => 'cil', 'CiPaw.02G091100' => 'cil', 'CiPaw.08G103100' => 'cil', 'CiPaw.09G224900' => 'cil', 'ClCG06G005740' => 'cla', 'ClCG07G000090' => 'cla', 'ClCG07G000100' => 'cla', 'COL.COLO4_09143' => 'col', 'COL.COLO4_25124' => 'col', 'Cpa.g.sc16.34' => 'cpa', 'Cpa.g.sc3504.1' => 'cpa', 'Cpa.g.sc60.37' => 'cpa', 'CsaV3_6G018520' => 'csa', 'CsaV3_6G036860' => 'csa', 'CSS0001072' => 'camsi', 'CSS0020208' => 'camsi', 'CSS0021253' => 'camsi', 'CSS0022190' => 'camsi', 'CSS0036150' => 'camsi', 'CSS0040442' => 'camsi', 'CSS0042300' => 'camsi', 'CSS0045298' => 'camsi', 'DCAR_012449' => 'dca', 'DCAR_018405' => 'dca', 'DCAR_024573' => 'dca', 'DCAR_030591' => 'dca', 'Dinv16926' => 'din', 'Dinv32963' => 'din', 'Dinv38382' => 'din', 'Dinv38383' => 'din', 'Duzib133G0974' => 'dzi', 'Duzib138G1867' => 'dzi', 'Duzib211G0420' => 'dzi', 'Duzib212G0930' => 'dzi', 'ECA234G1645' => 'eca', 'ECA247G3467' => 'eca', 'ECA248G1703' => 'eca', 'EL10Ac3g06327' => 'bvu', 'EL10Ac7g17204' => 'bvu', 'Eucgr.A00855' => 'egr', 'Eucgr.A00858' => 'egr', 'Eucgr.H01520' => 'egr', 'Eucgr.H03604' => 'egr', 'Eucgr.L03465' => 'egr', 'Eucgr.L03466' => 'egr', 'FAN01G0988' => 'fan', 'FAN02G3892' => 'fan', 'FAN05G3381' => 'fan', 'FAN07G0967' => 'fan', 'FAN07G1493' => 'fan', 'FAN08G3125' => 'fan', 'FAN09G0402' => 'fan', 'FAN12G2594' => 'fan', 'FAN12G3879' => 'fan', 'FAN14G1546' => 'fan', 'FAN15G3626' => 'fan', 'FAN17G0588' => 'fan', 'FAN17G0609' => 'fan', 'FAN18G2817' => 'fan', 'FAN19G1305' => 'fan', 'FAN20G1787' => 'fan', 'FAN22G0073' => 'fan', 'FAN22G0352' => 'fan', 'FAN22G0368' => 'fan', 'FAN22G2273' => 'fan', 'FAN24G1998' => 'fan', 'FAN27G1317' => 'fan', 'FvH4_2g23980' => 'fve', 'FvH4_4g14380' => 'fve', 'FvH4_4g14390' => 'fve', 'FvH4_6g09250' => 'fve', 'Glyma.03G151100' => 'gma', 'Glyma.04G122550' => 'gma', 'Glyma.05G001600' => 'gma', 'Glyma.09G270766' => 'gma', 'Glyma.09G270832' => 'gma', 'Glyma.13G209800' => 'gma', 'Glyma.15G102800' => 'gma', 'Glyma.18G218900' => 'gma', 'Glyma.19G001500' => 'gma', 'Glyma.19G153600' => 'gma', 'Gohir.A02G028600' => 'ghi', 'Gohir.A08G045000' => 'ghi', 'Gohir.A11G120500' => 'ghi', 'Gohir.A12G006200' => 'ghi', 'Gohir.A12G006250' => 'ghi', 'Gohir.D02G036300' => 'ghi', 'Gohir.D08G054700' => 'ghi', 'Gohir.D11G125600' => 'ghi', 'Gohir.D12G005700' => 'ghi', 'Gorai.004G055200' => 'gra', 'Gorai.005G040400' => 'gra', 'Gorai.007G134500' => 'gra', 'Gorai.008G005500' => 'gra', 'GSVIVG01011094001' => 'vvi', 'GSVIVG01017879001' => 'vvi', 'GSVIVG01025988001' => 'vvi', 'GSVIVG01029847001' => 'vvi', 'HanXRQChr10g0282901' => 'han', 'HanXRQChr10g0310371' => 'han', 'HanXRQChr10g0315041' => 'han', 'HanXRQChr11g0327651' => 'han', 'HanXRQChr12g0359391' => 'han', 'Haze_00972' => 'cav', 'Haze_00973' => 'cav', 'Haze_00974' => 'cav', 'Haze_04747' => 'cav', 'Haze_04749' => 'cav', 'Haze_04750' => 'cav', 'Haze_21217' => 'cav', 'Hma1.2p1_1037F.1_g250680' => 'hma', 'Hma1.2p1_1644F.1_g295320' => 'hma', 'HPP92_011322' => 'vpl', 'HPP92_011323' => 'vpl', 'HPP92_011324' => 'vpl', 'HPP92_011325' => 'vpl', 'HPP92_011326' => 'vpl', 'Hund12205' => 'sun', 'Hund17957' => 'sun', 'Lalb_Chr06g0176771' => 'lal', 'Lalb_Chr18g0056021' => 'lal', 'Lalb_Chr18g0056031' => 'lal', 'Lalb_Chr18g0056041' => 'lal', 'Lalb_Chr20g0107751' => 'lal', 'Lalb_Chr20g0118371' => 'lal', 'Lj1g0010239' => 'lja', 'Lj1g0017101' => 'lja', 'Lj2A1178G40' => 'lonja', 'Lj2A54G84' => 'lonja', 'Lj2g0015248' => 'lja', 'Lj3A761T51' => 'lonja', 'Lj6g0018116' => 'lja', 'Lsat_1_v5_gn_4_136040' => 'lsa', 'Lsat_1_v5_gn_5_187461' => 'lsa', 'Lsat_1_v5_gn_5_77001' => 'lsa', 'Lsat_1_v5_gn_9_4461' => 'lsa', 'Manes.01G210100' => 'mes', 'Manes.03G185600' => 'mes', 'Manes.05G073300' => 'mes', 'Manes.09G120300' => 'mes', 'Manes.15G022100' => 'mes', 'Mapoly0096s0053' => 'mpo', 'MBI03_g14058_MAGBIO' => 'mbi', 'MBI03_g33876_MAGBIO' => 'mbi', 'MBI03_g36854_MAGBIO' => 'mbi', 'MBI17_g11997_MAGBIO' => 'mbi', 'MD03G1269000' => 'mdo', 'MD04G1179600' => 'mdo', 'MD11G1289800' => 'mdo', 'MD12G1194700' => 'mdo', 'MD13G1182100' => 'mdo', 'MD13G1182200' => 'mdo', 'MD16G1182600' => 'mdo', 'Medtr2g021400' => 'mtr', 'Medtr2g021470' => 'mtr', 'Medtr2g105810' => 'mtr', 'Medtr3g033580' => 'mtr', 'Medtr6g007970' => 'mtr', 'Medtr7g056330' => 'mtr', 'Medtr7g074290' => 'mtr', 'Medtr7g074380' => 'mtr', 'Medtr7g094550' => 'mtr', 'Medtr8g069995' => 'mtr', 'MELO3C014345.2' => 'cme', 'MELO3C021395.2' => 'cme', 'Migut.D00262' => 'egut', 'Migut.G00257' => 'egut', 'MSTRG.21575' => 'ama', 'MSTRG.3985' => 'ama', 'Nitab4.5_0000295g0140' => 'nta', 'Nitab4.5_0000732g0140' => 'nta', 'Nitab4.5_0003162g0020' => 'nta', 'Nitab4.5_0006180g0090' => 'nta', 'Nitab4.5_0006390g0010' => 'nta', 'Nitab4.5_0007392g0040' => 'nta', 'Nn1g02140' => 'nnu', 'Nn4g26168' => 'nnu', 'Nn5g26754' => 'nnu', 'Oeu001433.1' => 'oeu', 'Oeu010299.2' => 'oeu', 'Oeu011171.1' => 'oeu', 'Oeu037675.1' => 'oeu', 'Oeu038359.1' => 'oeu', 'Oeu063834.1' => 'oeu', 'Oeu063835.1' => 'oeu', 'Os05g0312000' => 'osa', 'Os07g0211101' => 'osa', 'Os07g0211200' => 'osa', 'Os07g0681500' => 'osa', 'Peaxi162Scf00095g01015' => 'pax', 'Peaxi162Scf00104g00329' => 'pax', 'Peaxi162Scf00161g00137' => 'pax', 'PGR004G1665' => 'pgr', 'PGR031G2937' => 'pgr', 'PGR119G2145' => 'pgr', 'PGSC0003DMG400004351' => 'stu', 'PGSC0003DMG400014625' => 'stu', 'PGSC0003DMG401000943' => 'stu', 'Phvul.001G148600' => 'pvu', 'Phvul.004G001700' => 'pvu', 'Phvul.006G154900' => 'pvu', 'Phvul.008G078200' => 'pvu', 'Phvul.011G136500' => 'pvu', 'Potri.002G215600' => 'ptr', 'Potri.008G201600' => 'ptr', 'Potri.014G138400' => 'ptr', 'Potri.016G142500' => 'ptr', 'Pp3c16_10580' => 'ppa', 'Pp3c5_25280' => 'ppa', 'Prupe.1G150000' => 'ppe', 'Prupe.1G150100' => 'ppe', 'Prupe.6G299600' => 'ppe', 'Prupe.8G245000' => 'ppe', 'Psat0s4927g0040' => 'psa', 'Psat1g052080' => 'psa', 'Psat1g183800' => 'psa', 'Psat3g113840' => 'psa', 'Psat3g126120' => 'psa', 'Psat3g126160' => 'psa', 'Psat3g158760' => 'psa', 'Psat3g158840' => 'psa', 'PSO170G2858' => 'pso', 'PSO339G0606' => 'pso', 'PSO384G4709' => 'pso', 'PSO407G0334' => 'pso', 'QL04p040276' => 'qlo', 'QL06p005458' => 'qlo', 'QL06p005472' => 'qlo', 'QL07p030546' => 'qlo', 'QL07p031519' => 'qlo', 'QL09p050949' => 'qlo', 'QL09p050966' => 'qlo', 'QL09p051067' => 'qlo', 'QL12p022706' => 'qlo', 'RcHm_v2.0_Chr2g0119601' => 'rch', 'RcHm_v2.0_Chr3g0459591' => 'rch', 'RcHm_v2.0_Chr4g0418521' => 'rch', 'RcHm_v2.0_Chr4g0418531' => 'rch', 'RcHm_v2.0_Chr4g0418541' => 'rch', 'RcHm_v2.0_Chr6g0291641' => 'rch', 'Rhsim01G0086300' => 'rsi', 'Rhsim01G0276300' => 'rsi', 'Rhsim01G0276500' => 'rsi', 'Rhsim04G0207700' => 'rsi', 'Rhsim05G0234500' => 'rsi', 'Rhsim13G0022400' => 'rsi', 'Sabra02G0167900' => 'sbr', 'Sabra04G0158500' => 'sbr', 'Sabra08G0159800' => 'sbr', 'Sabra10G0011500' => 'sbr', 'Sabra14G0104400' => 'sbr', 'SalBow2G2440' => 'sbo', 'SalBow4G2265' => 'sbo', 'Sc02g0000060' => 'sci', 'Sc05g0005020' => 'sci', 'Sc13g0003890' => 'sci', 'Sed0014865' => 'sed', 'Sed0017224' => 'sed', 'Sed0026391' => 'sed', 'SEGI_00063' => 'sgi', 'SEGI_10967' => 'sgi', 'SEGI_17510' => 'sgi', 'SEGI_24396' => 'sgi', 'SEGI_39719' => 'sgi', 'SEGI_41392' => 'sgi', 'SGA_v2.0_scaffold11G05794' => 'sas', 'SGA_v2.0_scaffold142G35607' => 'sas', 'SGA_v2.0_scaffold1G00447' => 'sas', 'SHI15388' => 'shi', 'SHI15394' => 'shi', 'SHI15396' => 'shi', 'SHI15399' => 'shi', 'SMO343G0151' => 'smo', 'SMO367G1118' => 'smo', 'Solyc01g080200.3' => 'sly', 'Solyc06g008960.3' => 'sly', 'Solyc09g064780.3' => 'sly', 'Sopen01g031980' => 'spe', 'Sopen06g003710' => 'spe', 'Sopen09g026460' => 'spe', 'Sp3g21240' => 'spa', 'Sp4g30030' => 'spa', 'TAR365G0022' => 'tar', 'TAR365G1023' => 'tar', 'TAR365G1253' => 'tar', 'TAR623G0078' => 'tar', 'TAR623G1721' => 'tar', 'TAR633G0959' => 'tar', 'THA.LOC104802225' => 'tha', 'THA.LOC104804769' => 'tha', 'THA.LOC104808660' => 'tha', 'THA.LOC104812792' => 'tha', 'Thecc.01G284000' => 'tca', 'Thecc.04G220600' => 'tca', 'Thecc.05G268900' => 'tca', 'Thecc.08G171100' => 'tca', 'Thhalv10001284m.g' => 'esa', 'Thhalv10019912m.g' => 'esa', 'TPR.G14189' => 'tpr', 'TPR.G18110' => 'tpr', 'TPR.G18130' => 'tpr', 'TPR.G18131' => 'tpr', 'TPR.G18140' => 'tpr', 'TPR.G24282' => 'tpr', 'TPR.G25221' => 'tpr', 'TPR.G29267' => 'tpr', 'TPR.G35315' => 'tpr', 'TPR.G36173' => 'tpr', 'TWI09G0794' => 'twi', 'TWI59G1348' => 'twi', 'TWI74G0430' => 'twi', 'unitig_26.g8940' => 'ugi', 'unitig_749.g13744' => 'ugi', 'unitig_749.g13745' => 'ugi', 'vmacro08269' => 'vma', 'vmacro14937' => 'vma', 'vmacro20401' => 'vma', 'VMungo0464G1349' => 'vmu', 'VMungo0540G0289' => 'vmu', 'VMungo1215G1590' => 'vmu', 'VMungo1309G0221' => 'vmu', 'VMungo1309G2815' => 'vmu', 'VMungo1383G0239' => 'vmu', 'VMungo1383G2910' => 'vmu', 'Zm00001eb095270' => 'zma', 'Zm00001eb095280' => 'zma', 'Zm00001eb111630' => 'zma', 'Zm00001eb237080' => 'zma', 'Zm00001eb273740' => 'zma', 'Zm00001eb285040' => 'zma', 'Zm00001eb330790' => 'zma', 'Zm00001eb337380' => 'zma' ) $gf_id = 'HOM05D001484' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001484' ) $data_identifier = 'HOM05D001484' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 2, 'aly' => (int) 2, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 22, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 7, 'hma' => (int) 2, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 7, 'mtr' => (int) 10, 'cme' => (int) 2, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 4, 'ppa' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 4, 'qlo' => (int) 9, 'rch' => (int) 6, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 10, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 7, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb337380' $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' => 'HOM05D001484', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p31500' => 'bna', 'A05p00020' => 'bna', 'A07p08820' => 'bna', 'Aa31LG4G3300' => 'aar', 'Aa31LG8G10030' => 'aar', 'Actinidia00731' => 'ach', 'Actinidia11473' => 'ach', 'Actinidia23469' => 'ach', 'Actinidia24318' => 'ach', 'Actinidia40196' => 'ach', 'Actinidia40197' => 'ach', 'Actinidia40198' => 'ach', 'Ah.08g212990' => 'amhyb', 'Ah.15g091720' => 'amhyb', 'AL3G38260' => 'aly', 'AL4G47710' => 'aly', 'Aqoxy2G00671' => 'aox', 'Aqoxy2G03236' => 'aox', 'arahy.Tifrunner.gnm1.ann1.05IDCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KR684' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATY3SJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK6QJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6APGL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IDT7Z9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM073U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ0R87' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LE7RV4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT4QRX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V5ENPK' => 'arhy', 'AT2G48110' => 'ath', 'AT3G23590' => 'ath', 'ATR0626G186' => 'atr', 'ATR1127G141' => 'atr', 'Atru.chr4.2583' => 'acertr', 'Atru.chr5.1358' => 'acertr', 'Atru.chr5.1359' => 'acertr', 'Atru.chr8.46' => 'acertr', 'AUR62002640' => 'cqu', 'AUR62030055' => 'cqu', 'AUR62033713' => 'cqu', 'AUR62033714' => 'cqu', 'AUR62036795' => 'cqu', 'AUR62039891' => 'cqu', 'BcaB02g08737' => 'bca', 'BcaB04g20441' => 'bca', 'BcaB06g26509' => 'bca', 'BcaB06g26510' => 'bca', 'BcaB06g26511' => 'bca', 'BcaB06g26512' => 'bca', 'BcaB06g26513' => 'bca', 'BcaC02g12564' => 'bca', 'BcaC02g12565' => 'bca', 'BcaC02g12794' => 'bca', 'BcaC02g12795' => 'bca', 'BcaC02g12796' => 'bca', 'BcaC06g35541' => 'bca', 'BNapus_Darmor_BZH_scaffold_188p00080' => 'bna', 'BNapus_Darmor_BZH_scaffold_188p00090' => 'bna', 'BolC1t03972H' => 'bol', 'BolC1t03973H' => 'bol', 'BolC4t21680H' => 'bol', 'BolC7t41863H' => 'bol', 'BolSC55t61227H' => 'bol', 'BolSC55t61228H' => 'bol', 'BraA01t03278Z' => 'bra', 'BraA05t18998Z' => 'bra', 'BraA07t28673Z' => 'bra', 'C01p40150' => 'bna', 'C05p12370' => 'bna', 'C07p13680' => 'bna', 'CAN.G1006.16' => 'can', 'CAN.G1006.17' => 'can', 'CAN.G1170.2' => 'can', 'CAN.G962.7' => 'can', 'CANSAT25G2179' => 'cansat', 'CANSAT78G1573' => 'cansat', 'CARHR099510' => 'chi', 'CARHR143510' => 'chi', 'Carub.0003s2380' => 'cru', 'Carub.0004s3082' => 'cru', 'Ca_00614_v3' => 'car', 'Ca_07801_v3' => 'car', 'Ca_08567_v3' => 'car', 'Ca_09571_v3' => 'car', 'CBR_g19290' => 'cbr', 'Cc01_g19770' => 'ccan', 'Cc03_g03030' => 'ccan', 'CDE07G0968' => 'cde', 'CDE09G1441' => 'cde', 'Cfa006103' => 'cfa', 'Cfa015573' => 'cfa', 'Cfa016988' => 'cfa', 'Ciclev10006738m.g' => 'ccl', 'Ciclev10010920m.g' => 'ccl', 'Ciclev10018517m.g' => 'ccl', 'CiPaw.01G159200' => 'cil', 'CiPaw.02G091000' => 'cil', 'CiPaw.02G091100' => 'cil', 'CiPaw.08G103100' => 'cil', 'CiPaw.09G224900' => 'cil', 'ClCG06G005740' => 'cla', 'ClCG07G000090' => 'cla', 'ClCG07G000100' => 'cla', 'COL.COLO4_09143' => 'col', 'COL.COLO4_25124' => 'col', 'Cpa.g.sc16.34' => 'cpa', 'Cpa.g.sc3504.1' => 'cpa', 'Cpa.g.sc60.37' => 'cpa', 'CsaV3_6G018520' => 'csa', 'CsaV3_6G036860' => 'csa', 'CSS0001072' => 'camsi', 'CSS0020208' => 'camsi', 'CSS0021253' => 'camsi', 'CSS0022190' => 'camsi', 'CSS0036150' => 'camsi', 'CSS0040442' => 'camsi', 'CSS0042300' => 'camsi', 'CSS0045298' => 'camsi', 'DCAR_012449' => 'dca', 'DCAR_018405' => 'dca', 'DCAR_024573' => 'dca', 'DCAR_030591' => 'dca', 'Dinv16926' => 'din', 'Dinv32963' => 'din', 'Dinv38382' => 'din', 'Dinv38383' => 'din', 'Duzib133G0974' => 'dzi', 'Duzib138G1867' => 'dzi', 'Duzib211G0420' => 'dzi', 'Duzib212G0930' => 'dzi', 'ECA234G1645' => 'eca', 'ECA247G3467' => 'eca', 'ECA248G1703' => 'eca', 'EL10Ac3g06327' => 'bvu', 'EL10Ac7g17204' => 'bvu', 'Eucgr.A00855' => 'egr', 'Eucgr.A00858' => 'egr', 'Eucgr.H01520' => 'egr', 'Eucgr.H03604' => 'egr', 'Eucgr.L03465' => 'egr', 'Eucgr.L03466' => 'egr', 'FAN01G0988' => 'fan', 'FAN02G3892' => 'fan', 'FAN05G3381' => 'fan', 'FAN07G0967' => 'fan', 'FAN07G1493' => 'fan', 'FAN08G3125' => 'fan', 'FAN09G0402' => 'fan', 'FAN12G2594' => 'fan', 'FAN12G3879' => 'fan', 'FAN14G1546' => 'fan', 'FAN15G3626' => 'fan', 'FAN17G0588' => 'fan', 'FAN17G0609' => 'fan', 'FAN18G2817' => 'fan', 'FAN19G1305' => 'fan', 'FAN20G1787' => 'fan', 'FAN22G0073' => 'fan', 'FAN22G0352' => 'fan', 'FAN22G0368' => 'fan', 'FAN22G2273' => 'fan', 'FAN24G1998' => 'fan', 'FAN27G1317' => 'fan', 'FvH4_2g23980' => 'fve', 'FvH4_4g14380' => 'fve', 'FvH4_4g14390' => 'fve', 'FvH4_6g09250' => 'fve', 'Glyma.03G151100' => 'gma', 'Glyma.04G122550' => 'gma', 'Glyma.05G001600' => 'gma', 'Glyma.09G270766' => 'gma', 'Glyma.09G270832' => 'gma', 'Glyma.13G209800' => 'gma', 'Glyma.15G102800' => 'gma', 'Glyma.18G218900' => 'gma', 'Glyma.19G001500' => 'gma', 'Glyma.19G153600' => 'gma', 'Gohir.A02G028600' => 'ghi', 'Gohir.A08G045000' => 'ghi', 'Gohir.A11G120500' => 'ghi', 'Gohir.A12G006200' => 'ghi', 'Gohir.A12G006250' => 'ghi', 'Gohir.D02G036300' => 'ghi', 'Gohir.D08G054700' => 'ghi', 'Gohir.D11G125600' => 'ghi', 'Gohir.D12G005700' => 'ghi', 'Gorai.004G055200' => 'gra', 'Gorai.005G040400' => 'gra', 'Gorai.007G134500' => 'gra', 'Gorai.008G005500' => 'gra', 'GSVIVG01011094001' => 'vvi', 'GSVIVG01017879001' => 'vvi', 'GSVIVG01025988001' => 'vvi', 'GSVIVG01029847001' => 'vvi', 'HanXRQChr10g0282901' => 'han', 'HanXRQChr10g0310371' => 'han', 'HanXRQChr10g0315041' => 'han', 'HanXRQChr11g0327651' => 'han', 'HanXRQChr12g0359391' => 'han', 'Haze_00972' => 'cav', 'Haze_00973' => 'cav', 'Haze_00974' => 'cav', 'Haze_04747' => 'cav', 'Haze_04749' => 'cav', 'Haze_04750' => 'cav', 'Haze_21217' => 'cav', 'Hma1.2p1_1037F.1_g250680' => 'hma', 'Hma1.2p1_1644F.1_g295320' => 'hma', 'HPP92_011322' => 'vpl', 'HPP92_011323' => 'vpl', 'HPP92_011324' => 'vpl', 'HPP92_011325' => 'vpl', 'HPP92_011326' => 'vpl', 'Hund12205' => 'sun', 'Hund17957' => 'sun', 'Lalb_Chr06g0176771' => 'lal', 'Lalb_Chr18g0056021' => 'lal', 'Lalb_Chr18g0056031' => 'lal', 'Lalb_Chr18g0056041' => 'lal', 'Lalb_Chr20g0107751' => 'lal', 'Lalb_Chr20g0118371' => 'lal', 'Lj1g0010239' => 'lja', 'Lj1g0017101' => 'lja', 'Lj2A1178G40' => 'lonja', 'Lj2A54G84' => 'lonja', 'Lj2g0015248' => 'lja', 'Lj3A761T51' => 'lonja', 'Lj6g0018116' => 'lja', 'Lsat_1_v5_gn_4_136040' => 'lsa', 'Lsat_1_v5_gn_5_187461' => 'lsa', 'Lsat_1_v5_gn_5_77001' => 'lsa', 'Lsat_1_v5_gn_9_4461' => 'lsa', 'Manes.01G210100' => 'mes', 'Manes.03G185600' => 'mes', 'Manes.05G073300' => 'mes', 'Manes.09G120300' => 'mes', 'Manes.15G022100' => 'mes', 'Mapoly0096s0053' => 'mpo', 'MBI03_g14058_MAGBIO' => 'mbi', 'MBI03_g33876_MAGBIO' => 'mbi', 'MBI03_g36854_MAGBIO' => 'mbi', 'MBI17_g11997_MAGBIO' => 'mbi', 'MD03G1269000' => 'mdo', 'MD04G1179600' => 'mdo', 'MD11G1289800' => 'mdo', 'MD12G1194700' => 'mdo', 'MD13G1182100' => 'mdo', 'MD13G1182200' => 'mdo', 'MD16G1182600' => 'mdo', 'Medtr2g021400' => 'mtr', 'Medtr2g021470' => 'mtr', 'Medtr2g105810' => 'mtr', 'Medtr3g033580' => 'mtr', 'Medtr6g007970' => 'mtr', 'Medtr7g056330' => 'mtr', 'Medtr7g074290' => 'mtr', 'Medtr7g074380' => 'mtr', 'Medtr7g094550' => 'mtr', 'Medtr8g069995' => 'mtr', 'MELO3C014345.2' => 'cme', 'MELO3C021395.2' => 'cme', 'Migut.D00262' => 'egut', 'Migut.G00257' => 'egut', 'MSTRG.21575' => 'ama', 'MSTRG.3985' => 'ama', 'Nitab4.5_0000295g0140' => 'nta', 'Nitab4.5_0000732g0140' => 'nta', 'Nitab4.5_0003162g0020' => 'nta', 'Nitab4.5_0006180g0090' => 'nta', 'Nitab4.5_0006390g0010' => 'nta', 'Nitab4.5_0007392g0040' => 'nta', 'Nn1g02140' => 'nnu', 'Nn4g26168' => 'nnu', 'Nn5g26754' => 'nnu', 'Oeu001433.1' => 'oeu', 'Oeu010299.2' => 'oeu', 'Oeu011171.1' => 'oeu', 'Oeu037675.1' => 'oeu', 'Oeu038359.1' => 'oeu', 'Oeu063834.1' => 'oeu', 'Oeu063835.1' => 'oeu', 'Os05g0312000' => 'osa', 'Os07g0211101' => 'osa', 'Os07g0211200' => 'osa', 'Os07g0681500' => 'osa', 'Peaxi162Scf00095g01015' => 'pax', 'Peaxi162Scf00104g00329' => 'pax', 'Peaxi162Scf00161g00137' => 'pax', 'PGR004G1665' => 'pgr', 'PGR031G2937' => 'pgr', 'PGR119G2145' => 'pgr', 'PGSC0003DMG400004351' => 'stu', 'PGSC0003DMG400014625' => 'stu', 'PGSC0003DMG401000943' => 'stu', 'Phvul.001G148600' => 'pvu', 'Phvul.004G001700' => 'pvu', 'Phvul.006G154900' => 'pvu', 'Phvul.008G078200' => 'pvu', 'Phvul.011G136500' => 'pvu', 'Potri.002G215600' => 'ptr', 'Potri.008G201600' => 'ptr', 'Potri.014G138400' => 'ptr', 'Potri.016G142500' => 'ptr', 'Pp3c16_10580' => 'ppa', 'Pp3c5_25280' => 'ppa', 'Prupe.1G150000' => 'ppe', 'Prupe.1G150100' => 'ppe', 'Prupe.6G299600' => 'ppe', 'Prupe.8G245000' => 'ppe', 'Psat0s4927g0040' => 'psa', 'Psat1g052080' => 'psa', 'Psat1g183800' => 'psa', 'Psat3g113840' => 'psa', 'Psat3g126120' => 'psa', 'Psat3g126160' => 'psa', 'Psat3g158760' => 'psa', 'Psat3g158840' => 'psa', 'PSO170G2858' => 'pso', 'PSO339G0606' => 'pso', 'PSO384G4709' => 'pso', 'PSO407G0334' => 'pso', 'QL04p040276' => 'qlo', 'QL06p005458' => 'qlo', 'QL06p005472' => 'qlo', 'QL07p030546' => 'qlo', 'QL07p031519' => 'qlo', 'QL09p050949' => 'qlo', 'QL09p050966' => 'qlo', 'QL09p051067' => 'qlo', 'QL12p022706' => 'qlo', 'RcHm_v2.0_Chr2g0119601' => 'rch', 'RcHm_v2.0_Chr3g0459591' => 'rch', 'RcHm_v2.0_Chr4g0418521' => 'rch', 'RcHm_v2.0_Chr4g0418531' => 'rch', 'RcHm_v2.0_Chr4g0418541' => 'rch', 'RcHm_v2.0_Chr6g0291641' => 'rch', 'Rhsim01G0086300' => 'rsi', 'Rhsim01G0276300' => 'rsi', 'Rhsim01G0276500' => 'rsi', 'Rhsim04G0207700' => 'rsi', 'Rhsim05G0234500' => 'rsi', 'Rhsim13G0022400' => 'rsi', 'Sabra02G0167900' => 'sbr', 'Sabra04G0158500' => 'sbr', 'Sabra08G0159800' => 'sbr', 'Sabra10G0011500' => 'sbr', 'Sabra14G0104400' => 'sbr', 'SalBow2G2440' => 'sbo', 'SalBow4G2265' => 'sbo', 'Sc02g0000060' => 'sci', 'Sc05g0005020' => 'sci', 'Sc13g0003890' => 'sci', 'Sed0014865' => 'sed', 'Sed0017224' => 'sed', 'Sed0026391' => 'sed', 'SEGI_00063' => 'sgi', 'SEGI_10967' => 'sgi', 'SEGI_17510' => 'sgi', 'SEGI_24396' => 'sgi', 'SEGI_39719' => 'sgi', 'SEGI_41392' => 'sgi', 'SGA_v2.0_scaffold11G05794' => 'sas', 'SGA_v2.0_scaffold142G35607' => 'sas', 'SGA_v2.0_scaffold1G00447' => 'sas', 'SHI15388' => 'shi', 'SHI15394' => 'shi', 'SHI15396' => 'shi', 'SHI15399' => 'shi', 'SMO343G0151' => 'smo', 'SMO367G1118' => 'smo', 'Solyc01g080200.3' => 'sly', 'Solyc06g008960.3' => 'sly', 'Solyc09g064780.3' => 'sly', 'Sopen01g031980' => 'spe', 'Sopen06g003710' => 'spe', 'Sopen09g026460' => 'spe', 'Sp3g21240' => 'spa', 'Sp4g30030' => 'spa', 'TAR365G0022' => 'tar', 'TAR365G1023' => 'tar', 'TAR365G1253' => 'tar', 'TAR623G0078' => 'tar', 'TAR623G1721' => 'tar', 'TAR633G0959' => 'tar', 'THA.LOC104802225' => 'tha', 'THA.LOC104804769' => 'tha', 'THA.LOC104808660' => 'tha', 'THA.LOC104812792' => 'tha', 'Thecc.01G284000' => 'tca', 'Thecc.04G220600' => 'tca', 'Thecc.05G268900' => 'tca', 'Thecc.08G171100' => 'tca', 'Thhalv10001284m.g' => 'esa', 'Thhalv10019912m.g' => 'esa', 'TPR.G14189' => 'tpr', 'TPR.G18110' => 'tpr', 'TPR.G18130' => 'tpr', 'TPR.G18131' => 'tpr', 'TPR.G18140' => 'tpr', 'TPR.G24282' => 'tpr', 'TPR.G25221' => 'tpr', 'TPR.G29267' => 'tpr', 'TPR.G35315' => 'tpr', 'TPR.G36173' => 'tpr', 'TWI09G0794' => 'twi', 'TWI59G1348' => 'twi', 'TWI74G0430' => 'twi', 'unitig_26.g8940' => 'ugi', 'unitig_749.g13744' => 'ugi', 'unitig_749.g13745' => 'ugi', 'vmacro08269' => 'vma', 'vmacro14937' => 'vma', 'vmacro20401' => 'vma', 'VMungo0464G1349' => 'vmu', 'VMungo0540G0289' => 'vmu', 'VMungo1215G1590' => 'vmu', 'VMungo1309G0221' => 'vmu', 'VMungo1309G2815' => 'vmu', 'VMungo1383G0239' => 'vmu', 'VMungo1383G2910' => 'vmu', 'Zm00001eb095270' => 'zma', 'Zm00001eb095280' => 'zma', 'Zm00001eb111630' => 'zma', 'Zm00001eb237080' => 'zma', 'Zm00001eb273740' => 'zma', 'Zm00001eb285040' => 'zma', 'Zm00001eb330790' => 'zma', 'Zm00001eb337380' => 'zma' ), 'gf_id' => 'HOM05D001484', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001484' ), 'data_identifier' => 'HOM05D001484', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001484', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p31500' => 'bna', 'A05p00020' => 'bna', 'A07p08820' => 'bna', 'Aa31LG4G3300' => 'aar', 'Aa31LG8G10030' => 'aar', 'Actinidia00731' => 'ach', 'Actinidia11473' => 'ach', 'Actinidia23469' => 'ach', 'Actinidia24318' => 'ach', 'Actinidia40196' => 'ach', 'Actinidia40197' => 'ach', 'Actinidia40198' => 'ach', 'Ah.08g212990' => 'amhyb', 'Ah.15g091720' => 'amhyb', 'AL3G38260' => 'aly', 'AL4G47710' => 'aly', 'Aqoxy2G00671' => 'aox', 'Aqoxy2G03236' => 'aox', 'arahy.Tifrunner.gnm1.ann1.05IDCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KR684' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATY3SJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK6QJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6APGL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IDT7Z9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM073U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ0R87' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LE7RV4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT4QRX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V5ENPK' => 'arhy', 'AT2G48110' => 'ath', 'AT3G23590' => 'ath', 'ATR0626G186' => 'atr', 'ATR1127G141' => 'atr', 'Atru.chr4.2583' => 'acertr', 'Atru.chr5.1358' => 'acertr', 'Atru.chr5.1359' => 'acertr', 'Atru.chr8.46' => 'acertr', 'AUR62002640' => 'cqu', 'AUR62030055' => 'cqu', 'AUR62033713' => 'cqu', 'AUR62033714' => 'cqu', 'AUR62036795' => 'cqu', 'AUR62039891' => 'cqu', 'BcaB02g08737' => 'bca', 'BcaB04g20441' => 'bca', 'BcaB06g26509' => 'bca', 'BcaB06g26510' => 'bca', 'BcaB06g26511' => 'bca', 'BcaB06g26512' => 'bca', 'BcaB06g26513' => 'bca', 'BcaC02g12564' => 'bca', 'BcaC02g12565' => 'bca', 'BcaC02g12794' => 'bca', 'BcaC02g12795' => 'bca', 'BcaC02g12796' => 'bca', 'BcaC06g35541' => 'bca', 'BNapus_Darmor_BZH_scaffold_188p00080' => 'bna', 'BNapus_Darmor_BZH_scaffold_188p00090' => 'bna', 'BolC1t03972H' => 'bol', 'BolC1t03973H' => 'bol', 'BolC4t21680H' => 'bol', 'BolC7t41863H' => 'bol', 'BolSC55t61227H' => 'bol', 'BolSC55t61228H' => 'bol', 'BraA01t03278Z' => 'bra', 'BraA05t18998Z' => 'bra', 'BraA07t28673Z' => 'bra', 'C01p40150' => 'bna', 'C05p12370' => 'bna', 'C07p13680' => 'bna', 'CAN.G1006.16' => 'can', 'CAN.G1006.17' => 'can', 'CAN.G1170.2' => 'can', 'CAN.G962.7' => 'can', 'CANSAT25G2179' => 'cansat', 'CANSAT78G1573' => 'cansat', 'CARHR099510' => 'chi', 'CARHR143510' => 'chi', 'Carub.0003s2380' => 'cru', 'Carub.0004s3082' => 'cru', 'Ca_00614_v3' => 'car', 'Ca_07801_v3' => 'car', 'Ca_08567_v3' => 'car', 'Ca_09571_v3' => 'car', 'CBR_g19290' => 'cbr', 'Cc01_g19770' => 'ccan', 'Cc03_g03030' => 'ccan', 'CDE07G0968' => 'cde', 'CDE09G1441' => 'cde', 'Cfa006103' => 'cfa', 'Cfa015573' => 'cfa', 'Cfa016988' => 'cfa', 'Ciclev10006738m.g' => 'ccl', 'Ciclev10010920m.g' => 'ccl', 'Ciclev10018517m.g' => 'ccl', 'CiPaw.01G159200' => 'cil', 'CiPaw.02G091000' => 'cil', 'CiPaw.02G091100' => 'cil', 'CiPaw.08G103100' => 'cil', 'CiPaw.09G224900' => 'cil', 'ClCG06G005740' => 'cla', 'ClCG07G000090' => 'cla', 'ClCG07G000100' => 'cla', 'COL.COLO4_09143' => 'col', 'COL.COLO4_25124' => 'col', 'Cpa.g.sc16.34' => 'cpa', 'Cpa.g.sc3504.1' => 'cpa', 'Cpa.g.sc60.37' => 'cpa', 'CsaV3_6G018520' => 'csa', 'CsaV3_6G036860' => 'csa', 'CSS0001072' => 'camsi', 'CSS0020208' => 'camsi', 'CSS0021253' => 'camsi', 'CSS0022190' => 'camsi', 'CSS0036150' => 'camsi', 'CSS0040442' => 'camsi', 'CSS0042300' => 'camsi', 'CSS0045298' => 'camsi', 'DCAR_012449' => 'dca', 'DCAR_018405' => 'dca', 'DCAR_024573' => 'dca', 'DCAR_030591' => 'dca', 'Dinv16926' => 'din', 'Dinv32963' => 'din', 'Dinv38382' => 'din', 'Dinv38383' => 'din', 'Duzib133G0974' => 'dzi', 'Duzib138G1867' => 'dzi', 'Duzib211G0420' => 'dzi', 'Duzib212G0930' => 'dzi', 'ECA234G1645' => 'eca', 'ECA247G3467' => 'eca', 'ECA248G1703' => 'eca', 'EL10Ac3g06327' => 'bvu', 'EL10Ac7g17204' => 'bvu', 'Eucgr.A00855' => 'egr', 'Eucgr.A00858' => 'egr', 'Eucgr.H01520' => 'egr', 'Eucgr.H03604' => 'egr', 'Eucgr.L03465' => 'egr', 'Eucgr.L03466' => 'egr', 'FAN01G0988' => 'fan', 'FAN02G3892' => 'fan', 'FAN05G3381' => 'fan', 'FAN07G0967' => 'fan', 'FAN07G1493' => 'fan', 'FAN08G3125' => 'fan', 'FAN09G0402' => 'fan', 'FAN12G2594' => 'fan', 'FAN12G3879' => 'fan', 'FAN14G1546' => 'fan', 'FAN15G3626' => 'fan', 'FAN17G0588' => 'fan', 'FAN17G0609' => 'fan', 'FAN18G2817' => 'fan', 'FAN19G1305' => 'fan', 'FAN20G1787' => 'fan', 'FAN22G0073' => 'fan', 'FAN22G0352' => 'fan', 'FAN22G0368' => 'fan', 'FAN22G2273' => 'fan', 'FAN24G1998' => 'fan', 'FAN27G1317' => 'fan', 'FvH4_2g23980' => 'fve', 'FvH4_4g14380' => 'fve', 'FvH4_4g14390' => 'fve', 'FvH4_6g09250' => 'fve', 'Glyma.03G151100' => 'gma', 'Glyma.04G122550' => 'gma', 'Glyma.05G001600' => 'gma', 'Glyma.09G270766' => 'gma', 'Glyma.09G270832' => 'gma', 'Glyma.13G209800' => 'gma', 'Glyma.15G102800' => 'gma', 'Glyma.18G218900' => 'gma', 'Glyma.19G001500' => 'gma', 'Glyma.19G153600' => 'gma', 'Gohir.A02G028600' => 'ghi', 'Gohir.A08G045000' => 'ghi', 'Gohir.A11G120500' => 'ghi', 'Gohir.A12G006200' => 'ghi', 'Gohir.A12G006250' => 'ghi', 'Gohir.D02G036300' => 'ghi', 'Gohir.D08G054700' => 'ghi', 'Gohir.D11G125600' => 'ghi', 'Gohir.D12G005700' => 'ghi', 'Gorai.004G055200' => 'gra', 'Gorai.005G040400' => 'gra', 'Gorai.007G134500' => 'gra', 'Gorai.008G005500' => 'gra', 'GSVIVG01011094001' => 'vvi', 'GSVIVG01017879001' => 'vvi', 'GSVIVG01025988001' => 'vvi', 'GSVIVG01029847001' => 'vvi', 'HanXRQChr10g0282901' => 'han', 'HanXRQChr10g0310371' => 'han', 'HanXRQChr10g0315041' => 'han', 'HanXRQChr11g0327651' => 'han', 'HanXRQChr12g0359391' => 'han', 'Haze_00972' => 'cav', 'Haze_00973' => 'cav', 'Haze_00974' => 'cav', 'Haze_04747' => 'cav', 'Haze_04749' => 'cav', 'Haze_04750' => 'cav', 'Haze_21217' => 'cav', 'Hma1.2p1_1037F.1_g250680' => 'hma', 'Hma1.2p1_1644F.1_g295320' => 'hma', 'HPP92_011322' => 'vpl', 'HPP92_011323' => 'vpl', 'HPP92_011324' => 'vpl', 'HPP92_011325' => 'vpl', 'HPP92_011326' => 'vpl', 'Hund12205' => 'sun', 'Hund17957' => 'sun', 'Lalb_Chr06g0176771' => 'lal', 'Lalb_Chr18g0056021' => 'lal', 'Lalb_Chr18g0056031' => 'lal', 'Lalb_Chr18g0056041' => 'lal', 'Lalb_Chr20g0107751' => 'lal', 'Lalb_Chr20g0118371' => 'lal', 'Lj1g0010239' => 'lja', 'Lj1g0017101' => 'lja', 'Lj2A1178G40' => 'lonja', 'Lj2A54G84' => 'lonja', 'Lj2g0015248' => 'lja', 'Lj3A761T51' => 'lonja', 'Lj6g0018116' => 'lja', 'Lsat_1_v5_gn_4_136040' => 'lsa', 'Lsat_1_v5_gn_5_187461' => 'lsa', 'Lsat_1_v5_gn_5_77001' => 'lsa', 'Lsat_1_v5_gn_9_4461' => 'lsa', 'Manes.01G210100' => 'mes', 'Manes.03G185600' => 'mes', 'Manes.05G073300' => 'mes', 'Manes.09G120300' => 'mes', 'Manes.15G022100' => 'mes', 'Mapoly0096s0053' => 'mpo', 'MBI03_g14058_MAGBIO' => 'mbi', 'MBI03_g33876_MAGBIO' => 'mbi', 'MBI03_g36854_MAGBIO' => 'mbi', 'MBI17_g11997_MAGBIO' => 'mbi', 'MD03G1269000' => 'mdo', 'MD04G1179600' => 'mdo', 'MD11G1289800' => 'mdo', 'MD12G1194700' => 'mdo', 'MD13G1182100' => 'mdo', 'MD13G1182200' => 'mdo', 'MD16G1182600' => 'mdo', 'Medtr2g021400' => 'mtr', 'Medtr2g021470' => 'mtr', 'Medtr2g105810' => 'mtr', 'Medtr3g033580' => 'mtr', 'Medtr6g007970' => 'mtr', 'Medtr7g056330' => 'mtr', 'Medtr7g074290' => 'mtr', 'Medtr7g074380' => 'mtr', 'Medtr7g094550' => 'mtr', 'Medtr8g069995' => 'mtr', 'MELO3C014345.2' => 'cme', 'MELO3C021395.2' => 'cme', 'Migut.D00262' => 'egut', 'Migut.G00257' => 'egut', 'MSTRG.21575' => 'ama', 'MSTRG.3985' => 'ama', 'Nitab4.5_0000295g0140' => 'nta', 'Nitab4.5_0000732g0140' => 'nta', 'Nitab4.5_0003162g0020' => 'nta', 'Nitab4.5_0006180g0090' => 'nta', 'Nitab4.5_0006390g0010' => 'nta', 'Nitab4.5_0007392g0040' => 'nta', 'Nn1g02140' => 'nnu', 'Nn4g26168' => 'nnu', 'Nn5g26754' => 'nnu', 'Oeu001433.1' => 'oeu', 'Oeu010299.2' => 'oeu', 'Oeu011171.1' => 'oeu', 'Oeu037675.1' => 'oeu', 'Oeu038359.1' => 'oeu', 'Oeu063834.1' => 'oeu', 'Oeu063835.1' => 'oeu', 'Os05g0312000' => 'osa', 'Os07g0211101' => 'osa', 'Os07g0211200' => 'osa', 'Os07g0681500' => 'osa', 'Peaxi162Scf00095g01015' => 'pax', 'Peaxi162Scf00104g00329' => 'pax', 'Peaxi162Scf00161g00137' => 'pax', 'PGR004G1665' => 'pgr', 'PGR031G2937' => 'pgr', 'PGR119G2145' => 'pgr', 'PGSC0003DMG400004351' => 'stu', 'PGSC0003DMG400014625' => 'stu', 'PGSC0003DMG401000943' => 'stu', 'Phvul.001G148600' => 'pvu', 'Phvul.004G001700' => 'pvu', 'Phvul.006G154900' => 'pvu', 'Phvul.008G078200' => 'pvu', 'Phvul.011G136500' => 'pvu', 'Potri.002G215600' => 'ptr', 'Potri.008G201600' => 'ptr', 'Potri.014G138400' => 'ptr', 'Potri.016G142500' => 'ptr', 'Pp3c16_10580' => 'ppa', 'Pp3c5_25280' => 'ppa', 'Prupe.1G150000' => 'ppe', 'Prupe.1G150100' => 'ppe', 'Prupe.6G299600' => 'ppe', 'Prupe.8G245000' => 'ppe', 'Psat0s4927g0040' => 'psa', 'Psat1g052080' => 'psa', 'Psat1g183800' => 'psa', 'Psat3g113840' => 'psa', 'Psat3g126120' => 'psa', 'Psat3g126160' => 'psa', 'Psat3g158760' => 'psa', 'Psat3g158840' => 'psa', 'PSO170G2858' => 'pso', 'PSO339G0606' => 'pso', 'PSO384G4709' => 'pso', 'PSO407G0334' => 'pso', 'QL04p040276' => 'qlo', 'QL06p005458' => 'qlo', 'QL06p005472' => 'qlo', 'QL07p030546' => 'qlo', 'QL07p031519' => 'qlo', 'QL09p050949' => 'qlo', 'QL09p050966' => 'qlo', 'QL09p051067' => 'qlo', 'QL12p022706' => 'qlo', 'RcHm_v2.0_Chr2g0119601' => 'rch', 'RcHm_v2.0_Chr3g0459591' => 'rch', 'RcHm_v2.0_Chr4g0418521' => 'rch', 'RcHm_v2.0_Chr4g0418531' => 'rch', 'RcHm_v2.0_Chr4g0418541' => 'rch', 'RcHm_v2.0_Chr6g0291641' => 'rch', 'Rhsim01G0086300' => 'rsi', 'Rhsim01G0276300' => 'rsi', 'Rhsim01G0276500' => 'rsi', 'Rhsim04G0207700' => 'rsi', 'Rhsim05G0234500' => 'rsi', 'Rhsim13G0022400' => 'rsi', 'Sabra02G0167900' => 'sbr', 'Sabra04G0158500' => 'sbr', 'Sabra08G0159800' => 'sbr', 'Sabra10G0011500' => 'sbr', 'Sabra14G0104400' => 'sbr', 'SalBow2G2440' => 'sbo', 'SalBow4G2265' => 'sbo', 'Sc02g0000060' => 'sci', 'Sc05g0005020' => 'sci', 'Sc13g0003890' => 'sci', 'Sed0014865' => 'sed', 'Sed0017224' => 'sed', 'Sed0026391' => 'sed', 'SEGI_00063' => 'sgi', 'SEGI_10967' => 'sgi', 'SEGI_17510' => 'sgi', 'SEGI_24396' => 'sgi', 'SEGI_39719' => 'sgi', 'SEGI_41392' => 'sgi', 'SGA_v2.0_scaffold11G05794' => 'sas', 'SGA_v2.0_scaffold142G35607' => 'sas', 'SGA_v2.0_scaffold1G00447' => 'sas', 'SHI15388' => 'shi', 'SHI15394' => 'shi', 'SHI15396' => 'shi', 'SHI15399' => 'shi', 'SMO343G0151' => 'smo', 'SMO367G1118' => 'smo', 'Solyc01g080200.3' => 'sly', 'Solyc06g008960.3' => 'sly', 'Solyc09g064780.3' => 'sly', 'Sopen01g031980' => 'spe', 'Sopen06g003710' => 'spe', 'Sopen09g026460' => 'spe', 'Sp3g21240' => 'spa', 'Sp4g30030' => 'spa', 'TAR365G0022' => 'tar', 'TAR365G1023' => 'tar', 'TAR365G1253' => 'tar', 'TAR623G0078' => 'tar', 'TAR623G1721' => 'tar', 'TAR633G0959' => 'tar', 'THA.LOC104802225' => 'tha', 'THA.LOC104804769' => 'tha', 'THA.LOC104808660' => 'tha', 'THA.LOC104812792' => 'tha', 'Thecc.01G284000' => 'tca', 'Thecc.04G220600' => 'tca', 'Thecc.05G268900' => 'tca', 'Thecc.08G171100' => 'tca', 'Thhalv10001284m.g' => 'esa', 'Thhalv10019912m.g' => 'esa', 'TPR.G14189' => 'tpr', 'TPR.G18110' => 'tpr', 'TPR.G18130' => 'tpr', 'TPR.G18131' => 'tpr', 'TPR.G18140' => 'tpr', 'TPR.G24282' => 'tpr', 'TPR.G25221' => 'tpr', 'TPR.G29267' => 'tpr', 'TPR.G35315' => 'tpr', 'TPR.G36173' => 'tpr', 'TWI09G0794' => 'twi', 'TWI59G1348' => 'twi', 'TWI74G0430' => 'twi', 'unitig_26.g8940' => 'ugi', 'unitig_749.g13744' => 'ugi', 'unitig_749.g13745' => 'ugi', 'vmacro08269' => 'vma', 'vmacro14937' => 'vma', 'vmacro20401' => 'vma', 'VMungo0464G1349' => 'vmu', 'VMungo0540G0289' => 'vmu', 'VMungo1215G1590' => 'vmu', 'VMungo1309G0221' => 'vmu', 'VMungo1309G2815' => 'vmu', 'VMungo1383G0239' => 'vmu', 'VMungo1383G2910' => 'vmu', 'Zm00001eb095270' => 'zma', 'Zm00001eb095280' => 'zma', 'Zm00001eb111630' => 'zma', 'Zm00001eb237080' => 'zma', 'Zm00001eb273740' => 'zma', 'Zm00001eb285040' => 'zma', 'Zm00001eb330790' => 'zma', 'Zm00001eb337380' => 'zma' ) $gf_id = 'HOM05D001484' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001484' ) $data_identifier = 'HOM05D001484' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 2, 'aly' => (int) 2, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 22, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 7, 'hma' => (int) 2, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 7, 'mtr' => (int) 10, 'cme' => (int) 2, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 4, 'ppa' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 4, 'qlo' => (int) 9, 'rch' => (int) 6, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 10, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 7, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb337380' $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' => 'HOM05D001484', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p31500' => 'bna', 'A05p00020' => 'bna', 'A07p08820' => 'bna', 'Aa31LG4G3300' => 'aar', 'Aa31LG8G10030' => 'aar', 'Actinidia00731' => 'ach', 'Actinidia11473' => 'ach', 'Actinidia23469' => 'ach', 'Actinidia24318' => 'ach', 'Actinidia40196' => 'ach', 'Actinidia40197' => 'ach', 'Actinidia40198' => 'ach', 'Ah.08g212990' => 'amhyb', 'Ah.15g091720' => 'amhyb', 'AL3G38260' => 'aly', 'AL4G47710' => 'aly', 'Aqoxy2G00671' => 'aox', 'Aqoxy2G03236' => 'aox', 'arahy.Tifrunner.gnm1.ann1.05IDCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KR684' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATY3SJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK6QJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6APGL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IDT7Z9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM073U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ0R87' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LE7RV4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT4QRX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V5ENPK' => 'arhy', 'AT2G48110' => 'ath', 'AT3G23590' => 'ath', 'ATR0626G186' => 'atr', 'ATR1127G141' => 'atr', 'Atru.chr4.2583' => 'acertr', 'Atru.chr5.1358' => 'acertr', 'Atru.chr5.1359' => 'acertr', 'Atru.chr8.46' => 'acertr', 'AUR62002640' => 'cqu', 'AUR62030055' => 'cqu', 'AUR62033713' => 'cqu', 'AUR62033714' => 'cqu', 'AUR62036795' => 'cqu', 'AUR62039891' => 'cqu', 'BcaB02g08737' => 'bca', 'BcaB04g20441' => 'bca', 'BcaB06g26509' => 'bca', 'BcaB06g26510' => 'bca', 'BcaB06g26511' => 'bca', 'BcaB06g26512' => 'bca', 'BcaB06g26513' => 'bca', 'BcaC02g12564' => 'bca', 'BcaC02g12565' => 'bca', 'BcaC02g12794' => 'bca', 'BcaC02g12795' => 'bca', 'BcaC02g12796' => 'bca', 'BcaC06g35541' => 'bca', 'BNapus_Darmor_BZH_scaffold_188p00080' => 'bna', 'BNapus_Darmor_BZH_scaffold_188p00090' => 'bna', 'BolC1t03972H' => 'bol', 'BolC1t03973H' => 'bol', 'BolC4t21680H' => 'bol', 'BolC7t41863H' => 'bol', 'BolSC55t61227H' => 'bol', 'BolSC55t61228H' => 'bol', 'BraA01t03278Z' => 'bra', 'BraA05t18998Z' => 'bra', 'BraA07t28673Z' => 'bra', 'C01p40150' => 'bna', 'C05p12370' => 'bna', 'C07p13680' => 'bna', 'CAN.G1006.16' => 'can', 'CAN.G1006.17' => 'can', 'CAN.G1170.2' => 'can', 'CAN.G962.7' => 'can', 'CANSAT25G2179' => 'cansat', 'CANSAT78G1573' => 'cansat', 'CARHR099510' => 'chi', 'CARHR143510' => 'chi', 'Carub.0003s2380' => 'cru', 'Carub.0004s3082' => 'cru', 'Ca_00614_v3' => 'car', 'Ca_07801_v3' => 'car', 'Ca_08567_v3' => 'car', 'Ca_09571_v3' => 'car', 'CBR_g19290' => 'cbr', 'Cc01_g19770' => 'ccan', 'Cc03_g03030' => 'ccan', 'CDE07G0968' => 'cde', 'CDE09G1441' => 'cde', 'Cfa006103' => 'cfa', 'Cfa015573' => 'cfa', 'Cfa016988' => 'cfa', 'Ciclev10006738m.g' => 'ccl', 'Ciclev10010920m.g' => 'ccl', 'Ciclev10018517m.g' => 'ccl', 'CiPaw.01G159200' => 'cil', 'CiPaw.02G091000' => 'cil', 'CiPaw.02G091100' => 'cil', 'CiPaw.08G103100' => 'cil', 'CiPaw.09G224900' => 'cil', 'ClCG06G005740' => 'cla', 'ClCG07G000090' => 'cla', 'ClCG07G000100' => 'cla', 'COL.COLO4_09143' => 'col', 'COL.COLO4_25124' => 'col', 'Cpa.g.sc16.34' => 'cpa', 'Cpa.g.sc3504.1' => 'cpa', 'Cpa.g.sc60.37' => 'cpa', 'CsaV3_6G018520' => 'csa', 'CsaV3_6G036860' => 'csa', 'CSS0001072' => 'camsi', 'CSS0020208' => 'camsi', 'CSS0021253' => 'camsi', 'CSS0022190' => 'camsi', 'CSS0036150' => 'camsi', 'CSS0040442' => 'camsi', 'CSS0042300' => 'camsi', 'CSS0045298' => 'camsi', 'DCAR_012449' => 'dca', 'DCAR_018405' => 'dca', 'DCAR_024573' => 'dca', 'DCAR_030591' => 'dca', 'Dinv16926' => 'din', 'Dinv32963' => 'din', 'Dinv38382' => 'din', 'Dinv38383' => 'din', 'Duzib133G0974' => 'dzi', 'Duzib138G1867' => 'dzi', 'Duzib211G0420' => 'dzi', 'Duzib212G0930' => 'dzi', 'ECA234G1645' => 'eca', 'ECA247G3467' => 'eca', 'ECA248G1703' => 'eca', 'EL10Ac3g06327' => 'bvu', 'EL10Ac7g17204' => 'bvu', 'Eucgr.A00855' => 'egr', 'Eucgr.A00858' => 'egr', 'Eucgr.H01520' => 'egr', 'Eucgr.H03604' => 'egr', 'Eucgr.L03465' => 'egr', 'Eucgr.L03466' => 'egr', 'FAN01G0988' => 'fan', 'FAN02G3892' => 'fan', 'FAN05G3381' => 'fan', 'FAN07G0967' => 'fan', 'FAN07G1493' => 'fan', 'FAN08G3125' => 'fan', 'FAN09G0402' => 'fan', 'FAN12G2594' => 'fan', 'FAN12G3879' => 'fan', 'FAN14G1546' => 'fan', 'FAN15G3626' => 'fan', 'FAN17G0588' => 'fan', 'FAN17G0609' => 'fan', 'FAN18G2817' => 'fan', 'FAN19G1305' => 'fan', 'FAN20G1787' => 'fan', 'FAN22G0073' => 'fan', 'FAN22G0352' => 'fan', 'FAN22G0368' => 'fan', 'FAN22G2273' => 'fan', 'FAN24G1998' => 'fan', 'FAN27G1317' => 'fan', 'FvH4_2g23980' => 'fve', 'FvH4_4g14380' => 'fve', 'FvH4_4g14390' => 'fve', 'FvH4_6g09250' => 'fve', 'Glyma.03G151100' => 'gma', 'Glyma.04G122550' => 'gma', 'Glyma.05G001600' => 'gma', 'Glyma.09G270766' => 'gma', 'Glyma.09G270832' => 'gma', 'Glyma.13G209800' => 'gma', 'Glyma.15G102800' => 'gma', 'Glyma.18G218900' => 'gma', 'Glyma.19G001500' => 'gma', 'Glyma.19G153600' => 'gma', 'Gohir.A02G028600' => 'ghi', 'Gohir.A08G045000' => 'ghi', 'Gohir.A11G120500' => 'ghi', 'Gohir.A12G006200' => 'ghi', 'Gohir.A12G006250' => 'ghi', 'Gohir.D02G036300' => 'ghi', 'Gohir.D08G054700' => 'ghi', 'Gohir.D11G125600' => 'ghi', 'Gohir.D12G005700' => 'ghi', 'Gorai.004G055200' => 'gra', 'Gorai.005G040400' => 'gra', 'Gorai.007G134500' => 'gra', 'Gorai.008G005500' => 'gra', 'GSVIVG01011094001' => 'vvi', 'GSVIVG01017879001' => 'vvi', 'GSVIVG01025988001' => 'vvi', 'GSVIVG01029847001' => 'vvi', 'HanXRQChr10g0282901' => 'han', 'HanXRQChr10g0310371' => 'han', 'HanXRQChr10g0315041' => 'han', 'HanXRQChr11g0327651' => 'han', 'HanXRQChr12g0359391' => 'han', 'Haze_00972' => 'cav', 'Haze_00973' => 'cav', 'Haze_00974' => 'cav', 'Haze_04747' => 'cav', 'Haze_04749' => 'cav', 'Haze_04750' => 'cav', 'Haze_21217' => 'cav', 'Hma1.2p1_1037F.1_g250680' => 'hma', 'Hma1.2p1_1644F.1_g295320' => 'hma', 'HPP92_011322' => 'vpl', 'HPP92_011323' => 'vpl', 'HPP92_011324' => 'vpl', 'HPP92_011325' => 'vpl', 'HPP92_011326' => 'vpl', 'Hund12205' => 'sun', 'Hund17957' => 'sun', 'Lalb_Chr06g0176771' => 'lal', 'Lalb_Chr18g0056021' => 'lal', 'Lalb_Chr18g0056031' => 'lal', 'Lalb_Chr18g0056041' => 'lal', 'Lalb_Chr20g0107751' => 'lal', 'Lalb_Chr20g0118371' => 'lal', 'Lj1g0010239' => 'lja', 'Lj1g0017101' => 'lja', 'Lj2A1178G40' => 'lonja', 'Lj2A54G84' => 'lonja', 'Lj2g0015248' => 'lja', 'Lj3A761T51' => 'lonja', 'Lj6g0018116' => 'lja', 'Lsat_1_v5_gn_4_136040' => 'lsa', 'Lsat_1_v5_gn_5_187461' => 'lsa', 'Lsat_1_v5_gn_5_77001' => 'lsa', 'Lsat_1_v5_gn_9_4461' => 'lsa', 'Manes.01G210100' => 'mes', 'Manes.03G185600' => 'mes', 'Manes.05G073300' => 'mes', 'Manes.09G120300' => 'mes', 'Manes.15G022100' => 'mes', 'Mapoly0096s0053' => 'mpo', 'MBI03_g14058_MAGBIO' => 'mbi', 'MBI03_g33876_MAGBIO' => 'mbi', 'MBI03_g36854_MAGBIO' => 'mbi', 'MBI17_g11997_MAGBIO' => 'mbi', 'MD03G1269000' => 'mdo', 'MD04G1179600' => 'mdo', 'MD11G1289800' => 'mdo', 'MD12G1194700' => 'mdo', 'MD13G1182100' => 'mdo', 'MD13G1182200' => 'mdo', 'MD16G1182600' => 'mdo', 'Medtr2g021400' => 'mtr', 'Medtr2g021470' => 'mtr', 'Medtr2g105810' => 'mtr', 'Medtr3g033580' => 'mtr', 'Medtr6g007970' => 'mtr', 'Medtr7g056330' => 'mtr', 'Medtr7g074290' => 'mtr', 'Medtr7g074380' => 'mtr', 'Medtr7g094550' => 'mtr', 'Medtr8g069995' => 'mtr', 'MELO3C014345.2' => 'cme', 'MELO3C021395.2' => 'cme', 'Migut.D00262' => 'egut', 'Migut.G00257' => 'egut', 'MSTRG.21575' => 'ama', 'MSTRG.3985' => 'ama', 'Nitab4.5_0000295g0140' => 'nta', 'Nitab4.5_0000732g0140' => 'nta', 'Nitab4.5_0003162g0020' => 'nta', 'Nitab4.5_0006180g0090' => 'nta', 'Nitab4.5_0006390g0010' => 'nta', 'Nitab4.5_0007392g0040' => 'nta', 'Nn1g02140' => 'nnu', 'Nn4g26168' => 'nnu', 'Nn5g26754' => 'nnu', 'Oeu001433.1' => 'oeu', 'Oeu010299.2' => 'oeu', 'Oeu011171.1' => 'oeu', 'Oeu037675.1' => 'oeu', 'Oeu038359.1' => 'oeu', 'Oeu063834.1' => 'oeu', 'Oeu063835.1' => 'oeu', 'Os05g0312000' => 'osa', 'Os07g0211101' => 'osa', 'Os07g0211200' => 'osa', 'Os07g0681500' => 'osa', 'Peaxi162Scf00095g01015' => 'pax', 'Peaxi162Scf00104g00329' => 'pax', 'Peaxi162Scf00161g00137' => 'pax', 'PGR004G1665' => 'pgr', 'PGR031G2937' => 'pgr', 'PGR119G2145' => 'pgr', 'PGSC0003DMG400004351' => 'stu', 'PGSC0003DMG400014625' => 'stu', 'PGSC0003DMG401000943' => 'stu', 'Phvul.001G148600' => 'pvu', 'Phvul.004G001700' => 'pvu', 'Phvul.006G154900' => 'pvu', 'Phvul.008G078200' => 'pvu', 'Phvul.011G136500' => 'pvu', 'Potri.002G215600' => 'ptr', 'Potri.008G201600' => 'ptr', 'Potri.014G138400' => 'ptr', 'Potri.016G142500' => 'ptr', 'Pp3c16_10580' => 'ppa', 'Pp3c5_25280' => 'ppa', 'Prupe.1G150000' => 'ppe', 'Prupe.1G150100' => 'ppe', 'Prupe.6G299600' => 'ppe', 'Prupe.8G245000' => 'ppe', 'Psat0s4927g0040' => 'psa', 'Psat1g052080' => 'psa', 'Psat1g183800' => 'psa', 'Psat3g113840' => 'psa', 'Psat3g126120' => 'psa', 'Psat3g126160' => 'psa', 'Psat3g158760' => 'psa', 'Psat3g158840' => 'psa', 'PSO170G2858' => 'pso', 'PSO339G0606' => 'pso', 'PSO384G4709' => 'pso', 'PSO407G0334' => 'pso', 'QL04p040276' => 'qlo', 'QL06p005458' => 'qlo', 'QL06p005472' => 'qlo', 'QL07p030546' => 'qlo', 'QL07p031519' => 'qlo', 'QL09p050949' => 'qlo', 'QL09p050966' => 'qlo', 'QL09p051067' => 'qlo', 'QL12p022706' => 'qlo', 'RcHm_v2.0_Chr2g0119601' => 'rch', 'RcHm_v2.0_Chr3g0459591' => 'rch', 'RcHm_v2.0_Chr4g0418521' => 'rch', 'RcHm_v2.0_Chr4g0418531' => 'rch', 'RcHm_v2.0_Chr4g0418541' => 'rch', 'RcHm_v2.0_Chr6g0291641' => 'rch', 'Rhsim01G0086300' => 'rsi', 'Rhsim01G0276300' => 'rsi', 'Rhsim01G0276500' => 'rsi', 'Rhsim04G0207700' => 'rsi', 'Rhsim05G0234500' => 'rsi', 'Rhsim13G0022400' => 'rsi', 'Sabra02G0167900' => 'sbr', 'Sabra04G0158500' => 'sbr', 'Sabra08G0159800' => 'sbr', 'Sabra10G0011500' => 'sbr', 'Sabra14G0104400' => 'sbr', 'SalBow2G2440' => 'sbo', 'SalBow4G2265' => 'sbo', 'Sc02g0000060' => 'sci', 'Sc05g0005020' => 'sci', 'Sc13g0003890' => 'sci', 'Sed0014865' => 'sed', 'Sed0017224' => 'sed', 'Sed0026391' => 'sed', 'SEGI_00063' => 'sgi', 'SEGI_10967' => 'sgi', 'SEGI_17510' => 'sgi', 'SEGI_24396' => 'sgi', 'SEGI_39719' => 'sgi', 'SEGI_41392' => 'sgi', 'SGA_v2.0_scaffold11G05794' => 'sas', 'SGA_v2.0_scaffold142G35607' => 'sas', 'SGA_v2.0_scaffold1G00447' => 'sas', 'SHI15388' => 'shi', 'SHI15394' => 'shi', 'SHI15396' => 'shi', 'SHI15399' => 'shi', 'SMO343G0151' => 'smo', 'SMO367G1118' => 'smo', 'Solyc01g080200.3' => 'sly', 'Solyc06g008960.3' => 'sly', 'Solyc09g064780.3' => 'sly', 'Sopen01g031980' => 'spe', 'Sopen06g003710' => 'spe', 'Sopen09g026460' => 'spe', 'Sp3g21240' => 'spa', 'Sp4g30030' => 'spa', 'TAR365G0022' => 'tar', 'TAR365G1023' => 'tar', 'TAR365G1253' => 'tar', 'TAR623G0078' => 'tar', 'TAR623G1721' => 'tar', 'TAR633G0959' => 'tar', 'THA.LOC104802225' => 'tha', 'THA.LOC104804769' => 'tha', 'THA.LOC104808660' => 'tha', 'THA.LOC104812792' => 'tha', 'Thecc.01G284000' => 'tca', 'Thecc.04G220600' => 'tca', 'Thecc.05G268900' => 'tca', 'Thecc.08G171100' => 'tca', 'Thhalv10001284m.g' => 'esa', 'Thhalv10019912m.g' => 'esa', 'TPR.G14189' => 'tpr', 'TPR.G18110' => 'tpr', 'TPR.G18130' => 'tpr', 'TPR.G18131' => 'tpr', 'TPR.G18140' => 'tpr', 'TPR.G24282' => 'tpr', 'TPR.G25221' => 'tpr', 'TPR.G29267' => 'tpr', 'TPR.G35315' => 'tpr', 'TPR.G36173' => 'tpr', 'TWI09G0794' => 'twi', 'TWI59G1348' => 'twi', 'TWI74G0430' => 'twi', 'unitig_26.g8940' => 'ugi', 'unitig_749.g13744' => 'ugi', 'unitig_749.g13745' => 'ugi', 'vmacro08269' => 'vma', 'vmacro14937' => 'vma', 'vmacro20401' => 'vma', 'VMungo0464G1349' => 'vmu', 'VMungo0540G0289' => 'vmu', 'VMungo1215G1590' => 'vmu', 'VMungo1309G0221' => 'vmu', 'VMungo1309G2815' => 'vmu', 'VMungo1383G0239' => 'vmu', 'VMungo1383G2910' => 'vmu', 'Zm00001eb095270' => 'zma', 'Zm00001eb095280' => 'zma', 'Zm00001eb111630' => 'zma', 'Zm00001eb237080' => 'zma', 'Zm00001eb273740' => 'zma', 'Zm00001eb285040' => 'zma', 'Zm00001eb330790' => 'zma', 'Zm00001eb337380' => 'zma' ), 'gf_id' => 'HOM05D001484', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001484' ), 'data_identifier' => 'HOM05D001484', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001484', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p31500' => 'bna', 'A05p00020' => 'bna', 'A07p08820' => 'bna', 'Aa31LG4G3300' => 'aar', 'Aa31LG8G10030' => 'aar', 'Actinidia00731' => 'ach', 'Actinidia11473' => 'ach', 'Actinidia23469' => 'ach', 'Actinidia24318' => 'ach', 'Actinidia40196' => 'ach', 'Actinidia40197' => 'ach', 'Actinidia40198' => 'ach', 'Ah.08g212990' => 'amhyb', 'Ah.15g091720' => 'amhyb', 'AL3G38260' => 'aly', 'AL4G47710' => 'aly', 'Aqoxy2G00671' => 'aox', 'Aqoxy2G03236' => 'aox', 'arahy.Tifrunner.gnm1.ann1.05IDCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KR684' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATY3SJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK6QJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6APGL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IDT7Z9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM073U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ0R87' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LE7RV4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT4QRX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V5ENPK' => 'arhy', 'AT2G48110' => 'ath', 'AT3G23590' => 'ath', 'ATR0626G186' => 'atr', 'ATR1127G141' => 'atr', 'Atru.chr4.2583' => 'acertr', 'Atru.chr5.1358' => 'acertr', 'Atru.chr5.1359' => 'acertr', 'Atru.chr8.46' => 'acertr', 'AUR62002640' => 'cqu', 'AUR62030055' => 'cqu', 'AUR62033713' => 'cqu', 'AUR62033714' => 'cqu', 'AUR62036795' => 'cqu', 'AUR62039891' => 'cqu', 'BcaB02g08737' => 'bca', 'BcaB04g20441' => 'bca', 'BcaB06g26509' => 'bca', 'BcaB06g26510' => 'bca', 'BcaB06g26511' => 'bca', 'BcaB06g26512' => 'bca', 'BcaB06g26513' => 'bca', 'BcaC02g12564' => 'bca', 'BcaC02g12565' => 'bca', 'BcaC02g12794' => 'bca', 'BcaC02g12795' => 'bca', 'BcaC02g12796' => 'bca', 'BcaC06g35541' => 'bca', 'BNapus_Darmor_BZH_scaffold_188p00080' => 'bna', 'BNapus_Darmor_BZH_scaffold_188p00090' => 'bna', 'BolC1t03972H' => 'bol', 'BolC1t03973H' => 'bol', 'BolC4t21680H' => 'bol', 'BolC7t41863H' => 'bol', 'BolSC55t61227H' => 'bol', 'BolSC55t61228H' => 'bol', 'BraA01t03278Z' => 'bra', 'BraA05t18998Z' => 'bra', 'BraA07t28673Z' => 'bra', 'C01p40150' => 'bna', 'C05p12370' => 'bna', 'C07p13680' => 'bna', 'CAN.G1006.16' => 'can', 'CAN.G1006.17' => 'can', 'CAN.G1170.2' => 'can', 'CAN.G962.7' => 'can', 'CANSAT25G2179' => 'cansat', 'CANSAT78G1573' => 'cansat', 'CARHR099510' => 'chi', 'CARHR143510' => 'chi', 'Carub.0003s2380' => 'cru', 'Carub.0004s3082' => 'cru', 'Ca_00614_v3' => 'car', 'Ca_07801_v3' => 'car', 'Ca_08567_v3' => 'car', 'Ca_09571_v3' => 'car', 'CBR_g19290' => 'cbr', 'Cc01_g19770' => 'ccan', 'Cc03_g03030' => 'ccan', 'CDE07G0968' => 'cde', 'CDE09G1441' => 'cde', 'Cfa006103' => 'cfa', 'Cfa015573' => 'cfa', 'Cfa016988' => 'cfa', 'Ciclev10006738m.g' => 'ccl', 'Ciclev10010920m.g' => 'ccl', 'Ciclev10018517m.g' => 'ccl', 'CiPaw.01G159200' => 'cil', 'CiPaw.02G091000' => 'cil', 'CiPaw.02G091100' => 'cil', 'CiPaw.08G103100' => 'cil', 'CiPaw.09G224900' => 'cil', 'ClCG06G005740' => 'cla', 'ClCG07G000090' => 'cla', 'ClCG07G000100' => 'cla', 'COL.COLO4_09143' => 'col', 'COL.COLO4_25124' => 'col', 'Cpa.g.sc16.34' => 'cpa', 'Cpa.g.sc3504.1' => 'cpa', 'Cpa.g.sc60.37' => 'cpa', 'CsaV3_6G018520' => 'csa', 'CsaV3_6G036860' => 'csa', 'CSS0001072' => 'camsi', 'CSS0020208' => 'camsi', 'CSS0021253' => 'camsi', 'CSS0022190' => 'camsi', 'CSS0036150' => 'camsi', 'CSS0040442' => 'camsi', 'CSS0042300' => 'camsi', 'CSS0045298' => 'camsi', 'DCAR_012449' => 'dca', 'DCAR_018405' => 'dca', 'DCAR_024573' => 'dca', 'DCAR_030591' => 'dca', 'Dinv16926' => 'din', 'Dinv32963' => 'din', 'Dinv38382' => 'din', 'Dinv38383' => 'din', 'Duzib133G0974' => 'dzi', 'Duzib138G1867' => 'dzi', 'Duzib211G0420' => 'dzi', 'Duzib212G0930' => 'dzi', 'ECA234G1645' => 'eca', 'ECA247G3467' => 'eca', 'ECA248G1703' => 'eca', 'EL10Ac3g06327' => 'bvu', 'EL10Ac7g17204' => 'bvu', 'Eucgr.A00855' => 'egr', 'Eucgr.A00858' => 'egr', 'Eucgr.H01520' => 'egr', 'Eucgr.H03604' => 'egr', 'Eucgr.L03465' => 'egr', 'Eucgr.L03466' => 'egr', 'FAN01G0988' => 'fan', 'FAN02G3892' => 'fan', 'FAN05G3381' => 'fan', 'FAN07G0967' => 'fan', 'FAN07G1493' => 'fan', 'FAN08G3125' => 'fan', 'FAN09G0402' => 'fan', 'FAN12G2594' => 'fan', 'FAN12G3879' => 'fan', 'FAN14G1546' => 'fan', 'FAN15G3626' => 'fan', 'FAN17G0588' => 'fan', 'FAN17G0609' => 'fan', 'FAN18G2817' => 'fan', 'FAN19G1305' => 'fan', 'FAN20G1787' => 'fan', 'FAN22G0073' => 'fan', 'FAN22G0352' => 'fan', 'FAN22G0368' => 'fan', 'FAN22G2273' => 'fan', 'FAN24G1998' => 'fan', 'FAN27G1317' => 'fan', 'FvH4_2g23980' => 'fve', 'FvH4_4g14380' => 'fve', 'FvH4_4g14390' => 'fve', 'FvH4_6g09250' => 'fve', 'Glyma.03G151100' => 'gma', 'Glyma.04G122550' => 'gma', 'Glyma.05G001600' => 'gma', 'Glyma.09G270766' => 'gma', 'Glyma.09G270832' => 'gma', 'Glyma.13G209800' => 'gma', 'Glyma.15G102800' => 'gma', 'Glyma.18G218900' => 'gma', 'Glyma.19G001500' => 'gma', 'Glyma.19G153600' => 'gma', 'Gohir.A02G028600' => 'ghi', 'Gohir.A08G045000' => 'ghi', 'Gohir.A11G120500' => 'ghi', 'Gohir.A12G006200' => 'ghi', 'Gohir.A12G006250' => 'ghi', 'Gohir.D02G036300' => 'ghi', 'Gohir.D08G054700' => 'ghi', 'Gohir.D11G125600' => 'ghi', 'Gohir.D12G005700' => 'ghi', 'Gorai.004G055200' => 'gra', 'Gorai.005G040400' => 'gra', 'Gorai.007G134500' => 'gra', 'Gorai.008G005500' => 'gra', 'GSVIVG01011094001' => 'vvi', 'GSVIVG01017879001' => 'vvi', 'GSVIVG01025988001' => 'vvi', 'GSVIVG01029847001' => 'vvi', 'HanXRQChr10g0282901' => 'han', 'HanXRQChr10g0310371' => 'han', 'HanXRQChr10g0315041' => 'han', 'HanXRQChr11g0327651' => 'han', 'HanXRQChr12g0359391' => 'han', 'Haze_00972' => 'cav', 'Haze_00973' => 'cav', 'Haze_00974' => 'cav', 'Haze_04747' => 'cav', 'Haze_04749' => 'cav', 'Haze_04750' => 'cav', 'Haze_21217' => 'cav', 'Hma1.2p1_1037F.1_g250680' => 'hma', 'Hma1.2p1_1644F.1_g295320' => 'hma', 'HPP92_011322' => 'vpl', 'HPP92_011323' => 'vpl', 'HPP92_011324' => 'vpl', 'HPP92_011325' => 'vpl', 'HPP92_011326' => 'vpl', 'Hund12205' => 'sun', 'Hund17957' => 'sun', 'Lalb_Chr06g0176771' => 'lal', 'Lalb_Chr18g0056021' => 'lal', 'Lalb_Chr18g0056031' => 'lal', 'Lalb_Chr18g0056041' => 'lal', 'Lalb_Chr20g0107751' => 'lal', 'Lalb_Chr20g0118371' => 'lal', 'Lj1g0010239' => 'lja', 'Lj1g0017101' => 'lja', 'Lj2A1178G40' => 'lonja', 'Lj2A54G84' => 'lonja', 'Lj2g0015248' => 'lja', 'Lj3A761T51' => 'lonja', 'Lj6g0018116' => 'lja', 'Lsat_1_v5_gn_4_136040' => 'lsa', 'Lsat_1_v5_gn_5_187461' => 'lsa', 'Lsat_1_v5_gn_5_77001' => 'lsa', 'Lsat_1_v5_gn_9_4461' => 'lsa', 'Manes.01G210100' => 'mes', 'Manes.03G185600' => 'mes', 'Manes.05G073300' => 'mes', 'Manes.09G120300' => 'mes', 'Manes.15G022100' => 'mes', 'Mapoly0096s0053' => 'mpo', 'MBI03_g14058_MAGBIO' => 'mbi', 'MBI03_g33876_MAGBIO' => 'mbi', 'MBI03_g36854_MAGBIO' => 'mbi', 'MBI17_g11997_MAGBIO' => 'mbi', 'MD03G1269000' => 'mdo', 'MD04G1179600' => 'mdo', 'MD11G1289800' => 'mdo', 'MD12G1194700' => 'mdo', 'MD13G1182100' => 'mdo', 'MD13G1182200' => 'mdo', 'MD16G1182600' => 'mdo', 'Medtr2g021400' => 'mtr', 'Medtr2g021470' => 'mtr', 'Medtr2g105810' => 'mtr', 'Medtr3g033580' => 'mtr', 'Medtr6g007970' => 'mtr', 'Medtr7g056330' => 'mtr', 'Medtr7g074290' => 'mtr', 'Medtr7g074380' => 'mtr', 'Medtr7g094550' => 'mtr', 'Medtr8g069995' => 'mtr', 'MELO3C014345.2' => 'cme', 'MELO3C021395.2' => 'cme', 'Migut.D00262' => 'egut', 'Migut.G00257' => 'egut', 'MSTRG.21575' => 'ama', 'MSTRG.3985' => 'ama', 'Nitab4.5_0000295g0140' => 'nta', 'Nitab4.5_0000732g0140' => 'nta', 'Nitab4.5_0003162g0020' => 'nta', 'Nitab4.5_0006180g0090' => 'nta', 'Nitab4.5_0006390g0010' => 'nta', 'Nitab4.5_0007392g0040' => 'nta', 'Nn1g02140' => 'nnu', 'Nn4g26168' => 'nnu', 'Nn5g26754' => 'nnu', 'Oeu001433.1' => 'oeu', 'Oeu010299.2' => 'oeu', 'Oeu011171.1' => 'oeu', 'Oeu037675.1' => 'oeu', 'Oeu038359.1' => 'oeu', 'Oeu063834.1' => 'oeu', 'Oeu063835.1' => 'oeu', 'Os05g0312000' => 'osa', 'Os07g0211101' => 'osa', 'Os07g0211200' => 'osa', 'Os07g0681500' => 'osa', 'Peaxi162Scf00095g01015' => 'pax', 'Peaxi162Scf00104g00329' => 'pax', 'Peaxi162Scf00161g00137' => 'pax', 'PGR004G1665' => 'pgr', 'PGR031G2937' => 'pgr', 'PGR119G2145' => 'pgr', 'PGSC0003DMG400004351' => 'stu', 'PGSC0003DMG400014625' => 'stu', 'PGSC0003DMG401000943' => 'stu', 'Phvul.001G148600' => 'pvu', 'Phvul.004G001700' => 'pvu', 'Phvul.006G154900' => 'pvu', 'Phvul.008G078200' => 'pvu', 'Phvul.011G136500' => 'pvu', 'Potri.002G215600' => 'ptr', 'Potri.008G201600' => 'ptr', 'Potri.014G138400' => 'ptr', 'Potri.016G142500' => 'ptr', 'Pp3c16_10580' => 'ppa', 'Pp3c5_25280' => 'ppa', 'Prupe.1G150000' => 'ppe', 'Prupe.1G150100' => 'ppe', 'Prupe.6G299600' => 'ppe', 'Prupe.8G245000' => 'ppe', 'Psat0s4927g0040' => 'psa', 'Psat1g052080' => 'psa', 'Psat1g183800' => 'psa', 'Psat3g113840' => 'psa', 'Psat3g126120' => 'psa', 'Psat3g126160' => 'psa', 'Psat3g158760' => 'psa', 'Psat3g158840' => 'psa', 'PSO170G2858' => 'pso', 'PSO339G0606' => 'pso', 'PSO384G4709' => 'pso', 'PSO407G0334' => 'pso', 'QL04p040276' => 'qlo', 'QL06p005458' => 'qlo', 'QL06p005472' => 'qlo', 'QL07p030546' => 'qlo', 'QL07p031519' => 'qlo', 'QL09p050949' => 'qlo', 'QL09p050966' => 'qlo', 'QL09p051067' => 'qlo', 'QL12p022706' => 'qlo', 'RcHm_v2.0_Chr2g0119601' => 'rch', 'RcHm_v2.0_Chr3g0459591' => 'rch', 'RcHm_v2.0_Chr4g0418521' => 'rch', 'RcHm_v2.0_Chr4g0418531' => 'rch', 'RcHm_v2.0_Chr4g0418541' => 'rch', 'RcHm_v2.0_Chr6g0291641' => 'rch', 'Rhsim01G0086300' => 'rsi', 'Rhsim01G0276300' => 'rsi', 'Rhsim01G0276500' => 'rsi', 'Rhsim04G0207700' => 'rsi', 'Rhsim05G0234500' => 'rsi', 'Rhsim13G0022400' => 'rsi', 'Sabra02G0167900' => 'sbr', 'Sabra04G0158500' => 'sbr', 'Sabra08G0159800' => 'sbr', 'Sabra10G0011500' => 'sbr', 'Sabra14G0104400' => 'sbr', 'SalBow2G2440' => 'sbo', 'SalBow4G2265' => 'sbo', 'Sc02g0000060' => 'sci', 'Sc05g0005020' => 'sci', 'Sc13g0003890' => 'sci', 'Sed0014865' => 'sed', 'Sed0017224' => 'sed', 'Sed0026391' => 'sed', 'SEGI_00063' => 'sgi', 'SEGI_10967' => 'sgi', 'SEGI_17510' => 'sgi', 'SEGI_24396' => 'sgi', 'SEGI_39719' => 'sgi', 'SEGI_41392' => 'sgi', 'SGA_v2.0_scaffold11G05794' => 'sas', 'SGA_v2.0_scaffold142G35607' => 'sas', 'SGA_v2.0_scaffold1G00447' => 'sas', 'SHI15388' => 'shi', 'SHI15394' => 'shi', 'SHI15396' => 'shi', 'SHI15399' => 'shi', 'SMO343G0151' => 'smo', 'SMO367G1118' => 'smo', 'Solyc01g080200.3' => 'sly', 'Solyc06g008960.3' => 'sly', 'Solyc09g064780.3' => 'sly', 'Sopen01g031980' => 'spe', 'Sopen06g003710' => 'spe', 'Sopen09g026460' => 'spe', 'Sp3g21240' => 'spa', 'Sp4g30030' => 'spa', 'TAR365G0022' => 'tar', 'TAR365G1023' => 'tar', 'TAR365G1253' => 'tar', 'TAR623G0078' => 'tar', 'TAR623G1721' => 'tar', 'TAR633G0959' => 'tar', 'THA.LOC104802225' => 'tha', 'THA.LOC104804769' => 'tha', 'THA.LOC104808660' => 'tha', 'THA.LOC104812792' => 'tha', 'Thecc.01G284000' => 'tca', 'Thecc.04G220600' => 'tca', 'Thecc.05G268900' => 'tca', 'Thecc.08G171100' => 'tca', 'Thhalv10001284m.g' => 'esa', 'Thhalv10019912m.g' => 'esa', 'TPR.G14189' => 'tpr', 'TPR.G18110' => 'tpr', 'TPR.G18130' => 'tpr', 'TPR.G18131' => 'tpr', 'TPR.G18140' => 'tpr', 'TPR.G24282' => 'tpr', 'TPR.G25221' => 'tpr', 'TPR.G29267' => 'tpr', 'TPR.G35315' => 'tpr', 'TPR.G36173' => 'tpr', 'TWI09G0794' => 'twi', 'TWI59G1348' => 'twi', 'TWI74G0430' => 'twi', 'unitig_26.g8940' => 'ugi', 'unitig_749.g13744' => 'ugi', 'unitig_749.g13745' => 'ugi', 'vmacro08269' => 'vma', 'vmacro14937' => 'vma', 'vmacro20401' => 'vma', 'VMungo0464G1349' => 'vmu', 'VMungo0540G0289' => 'vmu', 'VMungo1215G1590' => 'vmu', 'VMungo1309G0221' => 'vmu', 'VMungo1309G2815' => 'vmu', 'VMungo1383G0239' => 'vmu', 'VMungo1383G2910' => 'vmu', 'Zm00001eb095270' => 'zma', 'Zm00001eb095280' => 'zma', 'Zm00001eb111630' => 'zma', 'Zm00001eb237080' => 'zma', 'Zm00001eb273740' => 'zma', 'Zm00001eb285040' => 'zma', 'Zm00001eb330790' => 'zma', 'Zm00001eb337380' => 'zma' ) $gf_id = 'HOM05D001484' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001484' ) $data_identifier = 'HOM05D001484' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 2, 'aly' => (int) 2, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 22, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 7, 'hma' => (int) 2, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 7, 'mtr' => (int) 10, 'cme' => (int) 2, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 4, 'ppa' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 4, 'qlo' => (int) 9, 'rch' => (int) 6, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 10, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 7, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb337380' $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' => 'HOM05D001484', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p31500' => 'bna', 'A05p00020' => 'bna', 'A07p08820' => 'bna', 'Aa31LG4G3300' => 'aar', 'Aa31LG8G10030' => 'aar', 'Actinidia00731' => 'ach', 'Actinidia11473' => 'ach', 'Actinidia23469' => 'ach', 'Actinidia24318' => 'ach', 'Actinidia40196' => 'ach', 'Actinidia40197' => 'ach', 'Actinidia40198' => 'ach', 'Ah.08g212990' => 'amhyb', 'Ah.15g091720' => 'amhyb', 'AL3G38260' => 'aly', 'AL4G47710' => 'aly', 'Aqoxy2G00671' => 'aox', 'Aqoxy2G03236' => 'aox', 'arahy.Tifrunner.gnm1.ann1.05IDCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KR684' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATY3SJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK6QJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6APGL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IDT7Z9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM073U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ0R87' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LE7RV4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT4QRX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V5ENPK' => 'arhy', 'AT2G48110' => 'ath', 'AT3G23590' => 'ath', 'ATR0626G186' => 'atr', 'ATR1127G141' => 'atr', 'Atru.chr4.2583' => 'acertr', 'Atru.chr5.1358' => 'acertr', 'Atru.chr5.1359' => 'acertr', 'Atru.chr8.46' => 'acertr', 'AUR62002640' => 'cqu', 'AUR62030055' => 'cqu', 'AUR62033713' => 'cqu', 'AUR62033714' => 'cqu', 'AUR62036795' => 'cqu', 'AUR62039891' => 'cqu', 'BcaB02g08737' => 'bca', 'BcaB04g20441' => 'bca', 'BcaB06g26509' => 'bca', 'BcaB06g26510' => 'bca', 'BcaB06g26511' => 'bca', 'BcaB06g26512' => 'bca', 'BcaB06g26513' => 'bca', 'BcaC02g12564' => 'bca', 'BcaC02g12565' => 'bca', 'BcaC02g12794' => 'bca', 'BcaC02g12795' => 'bca', 'BcaC02g12796' => 'bca', 'BcaC06g35541' => 'bca', 'BNapus_Darmor_BZH_scaffold_188p00080' => 'bna', 'BNapus_Darmor_BZH_scaffold_188p00090' => 'bna', 'BolC1t03972H' => 'bol', 'BolC1t03973H' => 'bol', 'BolC4t21680H' => 'bol', 'BolC7t41863H' => 'bol', 'BolSC55t61227H' => 'bol', 'BolSC55t61228H' => 'bol', 'BraA01t03278Z' => 'bra', 'BraA05t18998Z' => 'bra', 'BraA07t28673Z' => 'bra', 'C01p40150' => 'bna', 'C05p12370' => 'bna', 'C07p13680' => 'bna', 'CAN.G1006.16' => 'can', 'CAN.G1006.17' => 'can', 'CAN.G1170.2' => 'can', 'CAN.G962.7' => 'can', 'CANSAT25G2179' => 'cansat', 'CANSAT78G1573' => 'cansat', 'CARHR099510' => 'chi', 'CARHR143510' => 'chi', 'Carub.0003s2380' => 'cru', 'Carub.0004s3082' => 'cru', 'Ca_00614_v3' => 'car', 'Ca_07801_v3' => 'car', 'Ca_08567_v3' => 'car', 'Ca_09571_v3' => 'car', 'CBR_g19290' => 'cbr', 'Cc01_g19770' => 'ccan', 'Cc03_g03030' => 'ccan', 'CDE07G0968' => 'cde', 'CDE09G1441' => 'cde', 'Cfa006103' => 'cfa', 'Cfa015573' => 'cfa', 'Cfa016988' => 'cfa', 'Ciclev10006738m.g' => 'ccl', 'Ciclev10010920m.g' => 'ccl', 'Ciclev10018517m.g' => 'ccl', 'CiPaw.01G159200' => 'cil', 'CiPaw.02G091000' => 'cil', 'CiPaw.02G091100' => 'cil', 'CiPaw.08G103100' => 'cil', 'CiPaw.09G224900' => 'cil', 'ClCG06G005740' => 'cla', 'ClCG07G000090' => 'cla', 'ClCG07G000100' => 'cla', 'COL.COLO4_09143' => 'col', 'COL.COLO4_25124' => 'col', 'Cpa.g.sc16.34' => 'cpa', 'Cpa.g.sc3504.1' => 'cpa', 'Cpa.g.sc60.37' => 'cpa', 'CsaV3_6G018520' => 'csa', 'CsaV3_6G036860' => 'csa', 'CSS0001072' => 'camsi', 'CSS0020208' => 'camsi', 'CSS0021253' => 'camsi', 'CSS0022190' => 'camsi', 'CSS0036150' => 'camsi', 'CSS0040442' => 'camsi', 'CSS0042300' => 'camsi', 'CSS0045298' => 'camsi', 'DCAR_012449' => 'dca', 'DCAR_018405' => 'dca', 'DCAR_024573' => 'dca', 'DCAR_030591' => 'dca', 'Dinv16926' => 'din', 'Dinv32963' => 'din', 'Dinv38382' => 'din', 'Dinv38383' => 'din', 'Duzib133G0974' => 'dzi', 'Duzib138G1867' => 'dzi', 'Duzib211G0420' => 'dzi', 'Duzib212G0930' => 'dzi', 'ECA234G1645' => 'eca', 'ECA247G3467' => 'eca', 'ECA248G1703' => 'eca', 'EL10Ac3g06327' => 'bvu', 'EL10Ac7g17204' => 'bvu', 'Eucgr.A00855' => 'egr', 'Eucgr.A00858' => 'egr', 'Eucgr.H01520' => 'egr', 'Eucgr.H03604' => 'egr', 'Eucgr.L03465' => 'egr', 'Eucgr.L03466' => 'egr', 'FAN01G0988' => 'fan', 'FAN02G3892' => 'fan', 'FAN05G3381' => 'fan', 'FAN07G0967' => 'fan', 'FAN07G1493' => 'fan', 'FAN08G3125' => 'fan', 'FAN09G0402' => 'fan', 'FAN12G2594' => 'fan', 'FAN12G3879' => 'fan', 'FAN14G1546' => 'fan', 'FAN15G3626' => 'fan', 'FAN17G0588' => 'fan', 'FAN17G0609' => 'fan', 'FAN18G2817' => 'fan', 'FAN19G1305' => 'fan', 'FAN20G1787' => 'fan', 'FAN22G0073' => 'fan', 'FAN22G0352' => 'fan', 'FAN22G0368' => 'fan', 'FAN22G2273' => 'fan', 'FAN24G1998' => 'fan', 'FAN27G1317' => 'fan', 'FvH4_2g23980' => 'fve', 'FvH4_4g14380' => 'fve', 'FvH4_4g14390' => 'fve', 'FvH4_6g09250' => 'fve', 'Glyma.03G151100' => 'gma', 'Glyma.04G122550' => 'gma', 'Glyma.05G001600' => 'gma', 'Glyma.09G270766' => 'gma', 'Glyma.09G270832' => 'gma', 'Glyma.13G209800' => 'gma', 'Glyma.15G102800' => 'gma', 'Glyma.18G218900' => 'gma', 'Glyma.19G001500' => 'gma', 'Glyma.19G153600' => 'gma', 'Gohir.A02G028600' => 'ghi', 'Gohir.A08G045000' => 'ghi', 'Gohir.A11G120500' => 'ghi', 'Gohir.A12G006200' => 'ghi', 'Gohir.A12G006250' => 'ghi', 'Gohir.D02G036300' => 'ghi', 'Gohir.D08G054700' => 'ghi', 'Gohir.D11G125600' => 'ghi', 'Gohir.D12G005700' => 'ghi', 'Gorai.004G055200' => 'gra', 'Gorai.005G040400' => 'gra', 'Gorai.007G134500' => 'gra', 'Gorai.008G005500' => 'gra', 'GSVIVG01011094001' => 'vvi', 'GSVIVG01017879001' => 'vvi', 'GSVIVG01025988001' => 'vvi', 'GSVIVG01029847001' => 'vvi', 'HanXRQChr10g0282901' => 'han', 'HanXRQChr10g0310371' => 'han', 'HanXRQChr10g0315041' => 'han', 'HanXRQChr11g0327651' => 'han', 'HanXRQChr12g0359391' => 'han', 'Haze_00972' => 'cav', 'Haze_00973' => 'cav', 'Haze_00974' => 'cav', 'Haze_04747' => 'cav', 'Haze_04749' => 'cav', 'Haze_04750' => 'cav', 'Haze_21217' => 'cav', 'Hma1.2p1_1037F.1_g250680' => 'hma', 'Hma1.2p1_1644F.1_g295320' => 'hma', 'HPP92_011322' => 'vpl', 'HPP92_011323' => 'vpl', 'HPP92_011324' => 'vpl', 'HPP92_011325' => 'vpl', 'HPP92_011326' => 'vpl', 'Hund12205' => 'sun', 'Hund17957' => 'sun', 'Lalb_Chr06g0176771' => 'lal', 'Lalb_Chr18g0056021' => 'lal', 'Lalb_Chr18g0056031' => 'lal', 'Lalb_Chr18g0056041' => 'lal', 'Lalb_Chr20g0107751' => 'lal', 'Lalb_Chr20g0118371' => 'lal', 'Lj1g0010239' => 'lja', 'Lj1g0017101' => 'lja', 'Lj2A1178G40' => 'lonja', 'Lj2A54G84' => 'lonja', 'Lj2g0015248' => 'lja', 'Lj3A761T51' => 'lonja', 'Lj6g0018116' => 'lja', 'Lsat_1_v5_gn_4_136040' => 'lsa', 'Lsat_1_v5_gn_5_187461' => 'lsa', 'Lsat_1_v5_gn_5_77001' => 'lsa', 'Lsat_1_v5_gn_9_4461' => 'lsa', 'Manes.01G210100' => 'mes', 'Manes.03G185600' => 'mes', 'Manes.05G073300' => 'mes', 'Manes.09G120300' => 'mes', 'Manes.15G022100' => 'mes', 'Mapoly0096s0053' => 'mpo', 'MBI03_g14058_MAGBIO' => 'mbi', 'MBI03_g33876_MAGBIO' => 'mbi', 'MBI03_g36854_MAGBIO' => 'mbi', 'MBI17_g11997_MAGBIO' => 'mbi', 'MD03G1269000' => 'mdo', 'MD04G1179600' => 'mdo', 'MD11G1289800' => 'mdo', 'MD12G1194700' => 'mdo', 'MD13G1182100' => 'mdo', 'MD13G1182200' => 'mdo', 'MD16G1182600' => 'mdo', 'Medtr2g021400' => 'mtr', 'Medtr2g021470' => 'mtr', 'Medtr2g105810' => 'mtr', 'Medtr3g033580' => 'mtr', 'Medtr6g007970' => 'mtr', 'Medtr7g056330' => 'mtr', 'Medtr7g074290' => 'mtr', 'Medtr7g074380' => 'mtr', 'Medtr7g094550' => 'mtr', 'Medtr8g069995' => 'mtr', 'MELO3C014345.2' => 'cme', 'MELO3C021395.2' => 'cme', 'Migut.D00262' => 'egut', 'Migut.G00257' => 'egut', 'MSTRG.21575' => 'ama', 'MSTRG.3985' => 'ama', 'Nitab4.5_0000295g0140' => 'nta', 'Nitab4.5_0000732g0140' => 'nta', 'Nitab4.5_0003162g0020' => 'nta', 'Nitab4.5_0006180g0090' => 'nta', 'Nitab4.5_0006390g0010' => 'nta', 'Nitab4.5_0007392g0040' => 'nta', 'Nn1g02140' => 'nnu', 'Nn4g26168' => 'nnu', 'Nn5g26754' => 'nnu', 'Oeu001433.1' => 'oeu', 'Oeu010299.2' => 'oeu', 'Oeu011171.1' => 'oeu', 'Oeu037675.1' => 'oeu', 'Oeu038359.1' => 'oeu', 'Oeu063834.1' => 'oeu', 'Oeu063835.1' => 'oeu', 'Os05g0312000' => 'osa', 'Os07g0211101' => 'osa', 'Os07g0211200' => 'osa', 'Os07g0681500' => 'osa', 'Peaxi162Scf00095g01015' => 'pax', 'Peaxi162Scf00104g00329' => 'pax', 'Peaxi162Scf00161g00137' => 'pax', 'PGR004G1665' => 'pgr', 'PGR031G2937' => 'pgr', 'PGR119G2145' => 'pgr', 'PGSC0003DMG400004351' => 'stu', 'PGSC0003DMG400014625' => 'stu', 'PGSC0003DMG401000943' => 'stu', 'Phvul.001G148600' => 'pvu', 'Phvul.004G001700' => 'pvu', 'Phvul.006G154900' => 'pvu', 'Phvul.008G078200' => 'pvu', 'Phvul.011G136500' => 'pvu', 'Potri.002G215600' => 'ptr', 'Potri.008G201600' => 'ptr', 'Potri.014G138400' => 'ptr', 'Potri.016G142500' => 'ptr', 'Pp3c16_10580' => 'ppa', 'Pp3c5_25280' => 'ppa', 'Prupe.1G150000' => 'ppe', 'Prupe.1G150100' => 'ppe', 'Prupe.6G299600' => 'ppe', 'Prupe.8G245000' => 'ppe', 'Psat0s4927g0040' => 'psa', 'Psat1g052080' => 'psa', 'Psat1g183800' => 'psa', 'Psat3g113840' => 'psa', 'Psat3g126120' => 'psa', 'Psat3g126160' => 'psa', 'Psat3g158760' => 'psa', 'Psat3g158840' => 'psa', 'PSO170G2858' => 'pso', 'PSO339G0606' => 'pso', 'PSO384G4709' => 'pso', 'PSO407G0334' => 'pso', 'QL04p040276' => 'qlo', 'QL06p005458' => 'qlo', 'QL06p005472' => 'qlo', 'QL07p030546' => 'qlo', 'QL07p031519' => 'qlo', 'QL09p050949' => 'qlo', 'QL09p050966' => 'qlo', 'QL09p051067' => 'qlo', 'QL12p022706' => 'qlo', 'RcHm_v2.0_Chr2g0119601' => 'rch', 'RcHm_v2.0_Chr3g0459591' => 'rch', 'RcHm_v2.0_Chr4g0418521' => 'rch', 'RcHm_v2.0_Chr4g0418531' => 'rch', 'RcHm_v2.0_Chr4g0418541' => 'rch', 'RcHm_v2.0_Chr6g0291641' => 'rch', 'Rhsim01G0086300' => 'rsi', 'Rhsim01G0276300' => 'rsi', 'Rhsim01G0276500' => 'rsi', 'Rhsim04G0207700' => 'rsi', 'Rhsim05G0234500' => 'rsi', 'Rhsim13G0022400' => 'rsi', 'Sabra02G0167900' => 'sbr', 'Sabra04G0158500' => 'sbr', 'Sabra08G0159800' => 'sbr', 'Sabra10G0011500' => 'sbr', 'Sabra14G0104400' => 'sbr', 'SalBow2G2440' => 'sbo', 'SalBow4G2265' => 'sbo', 'Sc02g0000060' => 'sci', 'Sc05g0005020' => 'sci', 'Sc13g0003890' => 'sci', 'Sed0014865' => 'sed', 'Sed0017224' => 'sed', 'Sed0026391' => 'sed', 'SEGI_00063' => 'sgi', 'SEGI_10967' => 'sgi', 'SEGI_17510' => 'sgi', 'SEGI_24396' => 'sgi', 'SEGI_39719' => 'sgi', 'SEGI_41392' => 'sgi', 'SGA_v2.0_scaffold11G05794' => 'sas', 'SGA_v2.0_scaffold142G35607' => 'sas', 'SGA_v2.0_scaffold1G00447' => 'sas', 'SHI15388' => 'shi', 'SHI15394' => 'shi', 'SHI15396' => 'shi', 'SHI15399' => 'shi', 'SMO343G0151' => 'smo', 'SMO367G1118' => 'smo', 'Solyc01g080200.3' => 'sly', 'Solyc06g008960.3' => 'sly', 'Solyc09g064780.3' => 'sly', 'Sopen01g031980' => 'spe', 'Sopen06g003710' => 'spe', 'Sopen09g026460' => 'spe', 'Sp3g21240' => 'spa', 'Sp4g30030' => 'spa', 'TAR365G0022' => 'tar', 'TAR365G1023' => 'tar', 'TAR365G1253' => 'tar', 'TAR623G0078' => 'tar', 'TAR623G1721' => 'tar', 'TAR633G0959' => 'tar', 'THA.LOC104802225' => 'tha', 'THA.LOC104804769' => 'tha', 'THA.LOC104808660' => 'tha', 'THA.LOC104812792' => 'tha', 'Thecc.01G284000' => 'tca', 'Thecc.04G220600' => 'tca', 'Thecc.05G268900' => 'tca', 'Thecc.08G171100' => 'tca', 'Thhalv10001284m.g' => 'esa', 'Thhalv10019912m.g' => 'esa', 'TPR.G14189' => 'tpr', 'TPR.G18110' => 'tpr', 'TPR.G18130' => 'tpr', 'TPR.G18131' => 'tpr', 'TPR.G18140' => 'tpr', 'TPR.G24282' => 'tpr', 'TPR.G25221' => 'tpr', 'TPR.G29267' => 'tpr', 'TPR.G35315' => 'tpr', 'TPR.G36173' => 'tpr', 'TWI09G0794' => 'twi', 'TWI59G1348' => 'twi', 'TWI74G0430' => 'twi', 'unitig_26.g8940' => 'ugi', 'unitig_749.g13744' => 'ugi', 'unitig_749.g13745' => 'ugi', 'vmacro08269' => 'vma', 'vmacro14937' => 'vma', 'vmacro20401' => 'vma', 'VMungo0464G1349' => 'vmu', 'VMungo0540G0289' => 'vmu', 'VMungo1215G1590' => 'vmu', 'VMungo1309G0221' => 'vmu', 'VMungo1309G2815' => 'vmu', 'VMungo1383G0239' => 'vmu', 'VMungo1383G2910' => 'vmu', 'Zm00001eb095270' => 'zma', 'Zm00001eb095280' => 'zma', 'Zm00001eb111630' => 'zma', 'Zm00001eb237080' => 'zma', 'Zm00001eb273740' => 'zma', 'Zm00001eb285040' => 'zma', 'Zm00001eb330790' => 'zma', 'Zm00001eb337380' => 'zma' ), 'gf_id' => 'HOM05D001484', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001484' ), 'data_identifier' => 'HOM05D001484', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001484', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p31500' => 'bna', 'A05p00020' => 'bna', 'A07p08820' => 'bna', 'Aa31LG4G3300' => 'aar', 'Aa31LG8G10030' => 'aar', 'Actinidia00731' => 'ach', 'Actinidia11473' => 'ach', 'Actinidia23469' => 'ach', 'Actinidia24318' => 'ach', 'Actinidia40196' => 'ach', 'Actinidia40197' => 'ach', 'Actinidia40198' => 'ach', 'Ah.08g212990' => 'amhyb', 'Ah.15g091720' => 'amhyb', 'AL3G38260' => 'aly', 'AL4G47710' => 'aly', 'Aqoxy2G00671' => 'aox', 'Aqoxy2G03236' => 'aox', 'arahy.Tifrunner.gnm1.ann1.05IDCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KR684' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATY3SJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK6QJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6APGL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IDT7Z9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM073U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ0R87' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LE7RV4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT4QRX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V5ENPK' => 'arhy', 'AT2G48110' => 'ath', 'AT3G23590' => 'ath', 'ATR0626G186' => 'atr', 'ATR1127G141' => 'atr', 'Atru.chr4.2583' => 'acertr', 'Atru.chr5.1358' => 'acertr', 'Atru.chr5.1359' => 'acertr', 'Atru.chr8.46' => 'acertr', 'AUR62002640' => 'cqu', 'AUR62030055' => 'cqu', 'AUR62033713' => 'cqu', 'AUR62033714' => 'cqu', 'AUR62036795' => 'cqu', 'AUR62039891' => 'cqu', 'BcaB02g08737' => 'bca', 'BcaB04g20441' => 'bca', 'BcaB06g26509' => 'bca', 'BcaB06g26510' => 'bca', 'BcaB06g26511' => 'bca', 'BcaB06g26512' => 'bca', 'BcaB06g26513' => 'bca', 'BcaC02g12564' => 'bca', 'BcaC02g12565' => 'bca', 'BcaC02g12794' => 'bca', 'BcaC02g12795' => 'bca', 'BcaC02g12796' => 'bca', 'BcaC06g35541' => 'bca', 'BNapus_Darmor_BZH_scaffold_188p00080' => 'bna', 'BNapus_Darmor_BZH_scaffold_188p00090' => 'bna', 'BolC1t03972H' => 'bol', 'BolC1t03973H' => 'bol', 'BolC4t21680H' => 'bol', 'BolC7t41863H' => 'bol', 'BolSC55t61227H' => 'bol', 'BolSC55t61228H' => 'bol', 'BraA01t03278Z' => 'bra', 'BraA05t18998Z' => 'bra', 'BraA07t28673Z' => 'bra', 'C01p40150' => 'bna', 'C05p12370' => 'bna', 'C07p13680' => 'bna', 'CAN.G1006.16' => 'can', 'CAN.G1006.17' => 'can', 'CAN.G1170.2' => 'can', 'CAN.G962.7' => 'can', 'CANSAT25G2179' => 'cansat', 'CANSAT78G1573' => 'cansat', 'CARHR099510' => 'chi', 'CARHR143510' => 'chi', 'Carub.0003s2380' => 'cru', 'Carub.0004s3082' => 'cru', 'Ca_00614_v3' => 'car', 'Ca_07801_v3' => 'car', 'Ca_08567_v3' => 'car', 'Ca_09571_v3' => 'car', 'CBR_g19290' => 'cbr', 'Cc01_g19770' => 'ccan', 'Cc03_g03030' => 'ccan', 'CDE07G0968' => 'cde', 'CDE09G1441' => 'cde', 'Cfa006103' => 'cfa', 'Cfa015573' => 'cfa', 'Cfa016988' => 'cfa', 'Ciclev10006738m.g' => 'ccl', 'Ciclev10010920m.g' => 'ccl', 'Ciclev10018517m.g' => 'ccl', 'CiPaw.01G159200' => 'cil', 'CiPaw.02G091000' => 'cil', 'CiPaw.02G091100' => 'cil', 'CiPaw.08G103100' => 'cil', 'CiPaw.09G224900' => 'cil', 'ClCG06G005740' => 'cla', 'ClCG07G000090' => 'cla', 'ClCG07G000100' => 'cla', 'COL.COLO4_09143' => 'col', 'COL.COLO4_25124' => 'col', 'Cpa.g.sc16.34' => 'cpa', 'Cpa.g.sc3504.1' => 'cpa', 'Cpa.g.sc60.37' => 'cpa', 'CsaV3_6G018520' => 'csa', 'CsaV3_6G036860' => 'csa', 'CSS0001072' => 'camsi', 'CSS0020208' => 'camsi', 'CSS0021253' => 'camsi', 'CSS0022190' => 'camsi', 'CSS0036150' => 'camsi', 'CSS0040442' => 'camsi', 'CSS0042300' => 'camsi', 'CSS0045298' => 'camsi', 'DCAR_012449' => 'dca', 'DCAR_018405' => 'dca', 'DCAR_024573' => 'dca', 'DCAR_030591' => 'dca', 'Dinv16926' => 'din', 'Dinv32963' => 'din', 'Dinv38382' => 'din', 'Dinv38383' => 'din', 'Duzib133G0974' => 'dzi', 'Duzib138G1867' => 'dzi', 'Duzib211G0420' => 'dzi', 'Duzib212G0930' => 'dzi', 'ECA234G1645' => 'eca', 'ECA247G3467' => 'eca', 'ECA248G1703' => 'eca', 'EL10Ac3g06327' => 'bvu', 'EL10Ac7g17204' => 'bvu', 'Eucgr.A00855' => 'egr', 'Eucgr.A00858' => 'egr', 'Eucgr.H01520' => 'egr', 'Eucgr.H03604' => 'egr', 'Eucgr.L03465' => 'egr', 'Eucgr.L03466' => 'egr', 'FAN01G0988' => 'fan', 'FAN02G3892' => 'fan', 'FAN05G3381' => 'fan', 'FAN07G0967' => 'fan', 'FAN07G1493' => 'fan', 'FAN08G3125' => 'fan', 'FAN09G0402' => 'fan', 'FAN12G2594' => 'fan', 'FAN12G3879' => 'fan', 'FAN14G1546' => 'fan', 'FAN15G3626' => 'fan', 'FAN17G0588' => 'fan', 'FAN17G0609' => 'fan', 'FAN18G2817' => 'fan', 'FAN19G1305' => 'fan', 'FAN20G1787' => 'fan', 'FAN22G0073' => 'fan', 'FAN22G0352' => 'fan', 'FAN22G0368' => 'fan', 'FAN22G2273' => 'fan', 'FAN24G1998' => 'fan', 'FAN27G1317' => 'fan', 'FvH4_2g23980' => 'fve', 'FvH4_4g14380' => 'fve', 'FvH4_4g14390' => 'fve', 'FvH4_6g09250' => 'fve', 'Glyma.03G151100' => 'gma', 'Glyma.04G122550' => 'gma', 'Glyma.05G001600' => 'gma', 'Glyma.09G270766' => 'gma', 'Glyma.09G270832' => 'gma', 'Glyma.13G209800' => 'gma', 'Glyma.15G102800' => 'gma', 'Glyma.18G218900' => 'gma', 'Glyma.19G001500' => 'gma', 'Glyma.19G153600' => 'gma', 'Gohir.A02G028600' => 'ghi', 'Gohir.A08G045000' => 'ghi', 'Gohir.A11G120500' => 'ghi', 'Gohir.A12G006200' => 'ghi', 'Gohir.A12G006250' => 'ghi', 'Gohir.D02G036300' => 'ghi', 'Gohir.D08G054700' => 'ghi', 'Gohir.D11G125600' => 'ghi', 'Gohir.D12G005700' => 'ghi', 'Gorai.004G055200' => 'gra', 'Gorai.005G040400' => 'gra', 'Gorai.007G134500' => 'gra', 'Gorai.008G005500' => 'gra', 'GSVIVG01011094001' => 'vvi', 'GSVIVG01017879001' => 'vvi', 'GSVIVG01025988001' => 'vvi', 'GSVIVG01029847001' => 'vvi', 'HanXRQChr10g0282901' => 'han', 'HanXRQChr10g0310371' => 'han', 'HanXRQChr10g0315041' => 'han', 'HanXRQChr11g0327651' => 'han', 'HanXRQChr12g0359391' => 'han', 'Haze_00972' => 'cav', 'Haze_00973' => 'cav', 'Haze_00974' => 'cav', 'Haze_04747' => 'cav', 'Haze_04749' => 'cav', 'Haze_04750' => 'cav', 'Haze_21217' => 'cav', 'Hma1.2p1_1037F.1_g250680' => 'hma', 'Hma1.2p1_1644F.1_g295320' => 'hma', 'HPP92_011322' => 'vpl', 'HPP92_011323' => 'vpl', 'HPP92_011324' => 'vpl', 'HPP92_011325' => 'vpl', 'HPP92_011326' => 'vpl', 'Hund12205' => 'sun', 'Hund17957' => 'sun', 'Lalb_Chr06g0176771' => 'lal', 'Lalb_Chr18g0056021' => 'lal', 'Lalb_Chr18g0056031' => 'lal', 'Lalb_Chr18g0056041' => 'lal', 'Lalb_Chr20g0107751' => 'lal', 'Lalb_Chr20g0118371' => 'lal', 'Lj1g0010239' => 'lja', 'Lj1g0017101' => 'lja', 'Lj2A1178G40' => 'lonja', 'Lj2A54G84' => 'lonja', 'Lj2g0015248' => 'lja', 'Lj3A761T51' => 'lonja', 'Lj6g0018116' => 'lja', 'Lsat_1_v5_gn_4_136040' => 'lsa', 'Lsat_1_v5_gn_5_187461' => 'lsa', 'Lsat_1_v5_gn_5_77001' => 'lsa', 'Lsat_1_v5_gn_9_4461' => 'lsa', 'Manes.01G210100' => 'mes', 'Manes.03G185600' => 'mes', 'Manes.05G073300' => 'mes', 'Manes.09G120300' => 'mes', 'Manes.15G022100' => 'mes', 'Mapoly0096s0053' => 'mpo', 'MBI03_g14058_MAGBIO' => 'mbi', 'MBI03_g33876_MAGBIO' => 'mbi', 'MBI03_g36854_MAGBIO' => 'mbi', 'MBI17_g11997_MAGBIO' => 'mbi', 'MD03G1269000' => 'mdo', 'MD04G1179600' => 'mdo', 'MD11G1289800' => 'mdo', 'MD12G1194700' => 'mdo', 'MD13G1182100' => 'mdo', 'MD13G1182200' => 'mdo', 'MD16G1182600' => 'mdo', 'Medtr2g021400' => 'mtr', 'Medtr2g021470' => 'mtr', 'Medtr2g105810' => 'mtr', 'Medtr3g033580' => 'mtr', 'Medtr6g007970' => 'mtr', 'Medtr7g056330' => 'mtr', 'Medtr7g074290' => 'mtr', 'Medtr7g074380' => 'mtr', 'Medtr7g094550' => 'mtr', 'Medtr8g069995' => 'mtr', 'MELO3C014345.2' => 'cme', 'MELO3C021395.2' => 'cme', 'Migut.D00262' => 'egut', 'Migut.G00257' => 'egut', 'MSTRG.21575' => 'ama', 'MSTRG.3985' => 'ama', 'Nitab4.5_0000295g0140' => 'nta', 'Nitab4.5_0000732g0140' => 'nta', 'Nitab4.5_0003162g0020' => 'nta', 'Nitab4.5_0006180g0090' => 'nta', 'Nitab4.5_0006390g0010' => 'nta', 'Nitab4.5_0007392g0040' => 'nta', 'Nn1g02140' => 'nnu', 'Nn4g26168' => 'nnu', 'Nn5g26754' => 'nnu', 'Oeu001433.1' => 'oeu', 'Oeu010299.2' => 'oeu', 'Oeu011171.1' => 'oeu', 'Oeu037675.1' => 'oeu', 'Oeu038359.1' => 'oeu', 'Oeu063834.1' => 'oeu', 'Oeu063835.1' => 'oeu', 'Os05g0312000' => 'osa', 'Os07g0211101' => 'osa', 'Os07g0211200' => 'osa', 'Os07g0681500' => 'osa', 'Peaxi162Scf00095g01015' => 'pax', 'Peaxi162Scf00104g00329' => 'pax', 'Peaxi162Scf00161g00137' => 'pax', 'PGR004G1665' => 'pgr', 'PGR031G2937' => 'pgr', 'PGR119G2145' => 'pgr', 'PGSC0003DMG400004351' => 'stu', 'PGSC0003DMG400014625' => 'stu', 'PGSC0003DMG401000943' => 'stu', 'Phvul.001G148600' => 'pvu', 'Phvul.004G001700' => 'pvu', 'Phvul.006G154900' => 'pvu', 'Phvul.008G078200' => 'pvu', 'Phvul.011G136500' => 'pvu', 'Potri.002G215600' => 'ptr', 'Potri.008G201600' => 'ptr', 'Potri.014G138400' => 'ptr', 'Potri.016G142500' => 'ptr', 'Pp3c16_10580' => 'ppa', 'Pp3c5_25280' => 'ppa', 'Prupe.1G150000' => 'ppe', 'Prupe.1G150100' => 'ppe', 'Prupe.6G299600' => 'ppe', 'Prupe.8G245000' => 'ppe', 'Psat0s4927g0040' => 'psa', 'Psat1g052080' => 'psa', 'Psat1g183800' => 'psa', 'Psat3g113840' => 'psa', 'Psat3g126120' => 'psa', 'Psat3g126160' => 'psa', 'Psat3g158760' => 'psa', 'Psat3g158840' => 'psa', 'PSO170G2858' => 'pso', 'PSO339G0606' => 'pso', 'PSO384G4709' => 'pso', 'PSO407G0334' => 'pso', 'QL04p040276' => 'qlo', 'QL06p005458' => 'qlo', 'QL06p005472' => 'qlo', 'QL07p030546' => 'qlo', 'QL07p031519' => 'qlo', 'QL09p050949' => 'qlo', 'QL09p050966' => 'qlo', 'QL09p051067' => 'qlo', 'QL12p022706' => 'qlo', 'RcHm_v2.0_Chr2g0119601' => 'rch', 'RcHm_v2.0_Chr3g0459591' => 'rch', 'RcHm_v2.0_Chr4g0418521' => 'rch', 'RcHm_v2.0_Chr4g0418531' => 'rch', 'RcHm_v2.0_Chr4g0418541' => 'rch', 'RcHm_v2.0_Chr6g0291641' => 'rch', 'Rhsim01G0086300' => 'rsi', 'Rhsim01G0276300' => 'rsi', 'Rhsim01G0276500' => 'rsi', 'Rhsim04G0207700' => 'rsi', 'Rhsim05G0234500' => 'rsi', 'Rhsim13G0022400' => 'rsi', 'Sabra02G0167900' => 'sbr', 'Sabra04G0158500' => 'sbr', 'Sabra08G0159800' => 'sbr', 'Sabra10G0011500' => 'sbr', 'Sabra14G0104400' => 'sbr', 'SalBow2G2440' => 'sbo', 'SalBow4G2265' => 'sbo', 'Sc02g0000060' => 'sci', 'Sc05g0005020' => 'sci', 'Sc13g0003890' => 'sci', 'Sed0014865' => 'sed', 'Sed0017224' => 'sed', 'Sed0026391' => 'sed', 'SEGI_00063' => 'sgi', 'SEGI_10967' => 'sgi', 'SEGI_17510' => 'sgi', 'SEGI_24396' => 'sgi', 'SEGI_39719' => 'sgi', 'SEGI_41392' => 'sgi', 'SGA_v2.0_scaffold11G05794' => 'sas', 'SGA_v2.0_scaffold142G35607' => 'sas', 'SGA_v2.0_scaffold1G00447' => 'sas', 'SHI15388' => 'shi', 'SHI15394' => 'shi', 'SHI15396' => 'shi', 'SHI15399' => 'shi', 'SMO343G0151' => 'smo', 'SMO367G1118' => 'smo', 'Solyc01g080200.3' => 'sly', 'Solyc06g008960.3' => 'sly', 'Solyc09g064780.3' => 'sly', 'Sopen01g031980' => 'spe', 'Sopen06g003710' => 'spe', 'Sopen09g026460' => 'spe', 'Sp3g21240' => 'spa', 'Sp4g30030' => 'spa', 'TAR365G0022' => 'tar', 'TAR365G1023' => 'tar', 'TAR365G1253' => 'tar', 'TAR623G0078' => 'tar', 'TAR623G1721' => 'tar', 'TAR633G0959' => 'tar', 'THA.LOC104802225' => 'tha', 'THA.LOC104804769' => 'tha', 'THA.LOC104808660' => 'tha', 'THA.LOC104812792' => 'tha', 'Thecc.01G284000' => 'tca', 'Thecc.04G220600' => 'tca', 'Thecc.05G268900' => 'tca', 'Thecc.08G171100' => 'tca', 'Thhalv10001284m.g' => 'esa', 'Thhalv10019912m.g' => 'esa', 'TPR.G14189' => 'tpr', 'TPR.G18110' => 'tpr', 'TPR.G18130' => 'tpr', 'TPR.G18131' => 'tpr', 'TPR.G18140' => 'tpr', 'TPR.G24282' => 'tpr', 'TPR.G25221' => 'tpr', 'TPR.G29267' => 'tpr', 'TPR.G35315' => 'tpr', 'TPR.G36173' => 'tpr', 'TWI09G0794' => 'twi', 'TWI59G1348' => 'twi', 'TWI74G0430' => 'twi', 'unitig_26.g8940' => 'ugi', 'unitig_749.g13744' => 'ugi', 'unitig_749.g13745' => 'ugi', 'vmacro08269' => 'vma', 'vmacro14937' => 'vma', 'vmacro20401' => 'vma', 'VMungo0464G1349' => 'vmu', 'VMungo0540G0289' => 'vmu', 'VMungo1215G1590' => 'vmu', 'VMungo1309G0221' => 'vmu', 'VMungo1309G2815' => 'vmu', 'VMungo1383G0239' => 'vmu', 'VMungo1383G2910' => 'vmu', 'Zm00001eb095270' => 'zma', 'Zm00001eb095280' => 'zma', 'Zm00001eb111630' => 'zma', 'Zm00001eb237080' => 'zma', 'Zm00001eb273740' => 'zma', 'Zm00001eb285040' => 'zma', 'Zm00001eb330790' => 'zma', 'Zm00001eb337380' => 'zma' ) $gf_id = 'HOM05D001484' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001484' ) $data_identifier = 'HOM05D001484' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 2, 'aly' => (int) 2, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 22, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 7, 'hma' => (int) 2, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 7, 'mtr' => (int) 10, 'cme' => (int) 2, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 4, 'ppa' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 4, 'qlo' => (int) 9, 'rch' => (int) 6, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 10, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 7, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb337380' $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' => 'HOM05D001484', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p31500' => 'bna', 'A05p00020' => 'bna', 'A07p08820' => 'bna', 'Aa31LG4G3300' => 'aar', 'Aa31LG8G10030' => 'aar', 'Actinidia00731' => 'ach', 'Actinidia11473' => 'ach', 'Actinidia23469' => 'ach', 'Actinidia24318' => 'ach', 'Actinidia40196' => 'ach', 'Actinidia40197' => 'ach', 'Actinidia40198' => 'ach', 'Ah.08g212990' => 'amhyb', 'Ah.15g091720' => 'amhyb', 'AL3G38260' => 'aly', 'AL4G47710' => 'aly', 'Aqoxy2G00671' => 'aox', 'Aqoxy2G03236' => 'aox', 'arahy.Tifrunner.gnm1.ann1.05IDCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KR684' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATY3SJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK6QJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6APGL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IDT7Z9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM073U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ0R87' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LE7RV4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT4QRX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V5ENPK' => 'arhy', 'AT2G48110' => 'ath', 'AT3G23590' => 'ath', 'ATR0626G186' => 'atr', 'ATR1127G141' => 'atr', 'Atru.chr4.2583' => 'acertr', 'Atru.chr5.1358' => 'acertr', 'Atru.chr5.1359' => 'acertr', 'Atru.chr8.46' => 'acertr', 'AUR62002640' => 'cqu', 'AUR62030055' => 'cqu', 'AUR62033713' => 'cqu', 'AUR62033714' => 'cqu', 'AUR62036795' => 'cqu', 'AUR62039891' => 'cqu', 'BcaB02g08737' => 'bca', 'BcaB04g20441' => 'bca', 'BcaB06g26509' => 'bca', 'BcaB06g26510' => 'bca', 'BcaB06g26511' => 'bca', 'BcaB06g26512' => 'bca', 'BcaB06g26513' => 'bca', 'BcaC02g12564' => 'bca', 'BcaC02g12565' => 'bca', 'BcaC02g12794' => 'bca', 'BcaC02g12795' => 'bca', 'BcaC02g12796' => 'bca', 'BcaC06g35541' => 'bca', 'BNapus_Darmor_BZH_scaffold_188p00080' => 'bna', 'BNapus_Darmor_BZH_scaffold_188p00090' => 'bna', 'BolC1t03972H' => 'bol', 'BolC1t03973H' => 'bol', 'BolC4t21680H' => 'bol', 'BolC7t41863H' => 'bol', 'BolSC55t61227H' => 'bol', 'BolSC55t61228H' => 'bol', 'BraA01t03278Z' => 'bra', 'BraA05t18998Z' => 'bra', 'BraA07t28673Z' => 'bra', 'C01p40150' => 'bna', 'C05p12370' => 'bna', 'C07p13680' => 'bna', 'CAN.G1006.16' => 'can', 'CAN.G1006.17' => 'can', 'CAN.G1170.2' => 'can', 'CAN.G962.7' => 'can', 'CANSAT25G2179' => 'cansat', 'CANSAT78G1573' => 'cansat', 'CARHR099510' => 'chi', 'CARHR143510' => 'chi', 'Carub.0003s2380' => 'cru', 'Carub.0004s3082' => 'cru', 'Ca_00614_v3' => 'car', 'Ca_07801_v3' => 'car', 'Ca_08567_v3' => 'car', 'Ca_09571_v3' => 'car', 'CBR_g19290' => 'cbr', 'Cc01_g19770' => 'ccan', 'Cc03_g03030' => 'ccan', 'CDE07G0968' => 'cde', 'CDE09G1441' => 'cde', 'Cfa006103' => 'cfa', 'Cfa015573' => 'cfa', 'Cfa016988' => 'cfa', 'Ciclev10006738m.g' => 'ccl', 'Ciclev10010920m.g' => 'ccl', 'Ciclev10018517m.g' => 'ccl', 'CiPaw.01G159200' => 'cil', 'CiPaw.02G091000' => 'cil', 'CiPaw.02G091100' => 'cil', 'CiPaw.08G103100' => 'cil', 'CiPaw.09G224900' => 'cil', 'ClCG06G005740' => 'cla', 'ClCG07G000090' => 'cla', 'ClCG07G000100' => 'cla', 'COL.COLO4_09143' => 'col', 'COL.COLO4_25124' => 'col', 'Cpa.g.sc16.34' => 'cpa', 'Cpa.g.sc3504.1' => 'cpa', 'Cpa.g.sc60.37' => 'cpa', 'CsaV3_6G018520' => 'csa', 'CsaV3_6G036860' => 'csa', 'CSS0001072' => 'camsi', 'CSS0020208' => 'camsi', 'CSS0021253' => 'camsi', 'CSS0022190' => 'camsi', 'CSS0036150' => 'camsi', 'CSS0040442' => 'camsi', 'CSS0042300' => 'camsi', 'CSS0045298' => 'camsi', 'DCAR_012449' => 'dca', 'DCAR_018405' => 'dca', 'DCAR_024573' => 'dca', 'DCAR_030591' => 'dca', 'Dinv16926' => 'din', 'Dinv32963' => 'din', 'Dinv38382' => 'din', 'Dinv38383' => 'din', 'Duzib133G0974' => 'dzi', 'Duzib138G1867' => 'dzi', 'Duzib211G0420' => 'dzi', 'Duzib212G0930' => 'dzi', 'ECA234G1645' => 'eca', 'ECA247G3467' => 'eca', 'ECA248G1703' => 'eca', 'EL10Ac3g06327' => 'bvu', 'EL10Ac7g17204' => 'bvu', 'Eucgr.A00855' => 'egr', 'Eucgr.A00858' => 'egr', 'Eucgr.H01520' => 'egr', 'Eucgr.H03604' => 'egr', 'Eucgr.L03465' => 'egr', 'Eucgr.L03466' => 'egr', 'FAN01G0988' => 'fan', 'FAN02G3892' => 'fan', 'FAN05G3381' => 'fan', 'FAN07G0967' => 'fan', 'FAN07G1493' => 'fan', 'FAN08G3125' => 'fan', 'FAN09G0402' => 'fan', 'FAN12G2594' => 'fan', 'FAN12G3879' => 'fan', 'FAN14G1546' => 'fan', 'FAN15G3626' => 'fan', 'FAN17G0588' => 'fan', 'FAN17G0609' => 'fan', 'FAN18G2817' => 'fan', 'FAN19G1305' => 'fan', 'FAN20G1787' => 'fan', 'FAN22G0073' => 'fan', 'FAN22G0352' => 'fan', 'FAN22G0368' => 'fan', 'FAN22G2273' => 'fan', 'FAN24G1998' => 'fan', 'FAN27G1317' => 'fan', 'FvH4_2g23980' => 'fve', 'FvH4_4g14380' => 'fve', 'FvH4_4g14390' => 'fve', 'FvH4_6g09250' => 'fve', 'Glyma.03G151100' => 'gma', 'Glyma.04G122550' => 'gma', 'Glyma.05G001600' => 'gma', 'Glyma.09G270766' => 'gma', 'Glyma.09G270832' => 'gma', 'Glyma.13G209800' => 'gma', 'Glyma.15G102800' => 'gma', 'Glyma.18G218900' => 'gma', 'Glyma.19G001500' => 'gma', 'Glyma.19G153600' => 'gma', 'Gohir.A02G028600' => 'ghi', 'Gohir.A08G045000' => 'ghi', 'Gohir.A11G120500' => 'ghi', 'Gohir.A12G006200' => 'ghi', 'Gohir.A12G006250' => 'ghi', 'Gohir.D02G036300' => 'ghi', 'Gohir.D08G054700' => 'ghi', 'Gohir.D11G125600' => 'ghi', 'Gohir.D12G005700' => 'ghi', 'Gorai.004G055200' => 'gra', 'Gorai.005G040400' => 'gra', 'Gorai.007G134500' => 'gra', 'Gorai.008G005500' => 'gra', 'GSVIVG01011094001' => 'vvi', 'GSVIVG01017879001' => 'vvi', 'GSVIVG01025988001' => 'vvi', 'GSVIVG01029847001' => 'vvi', 'HanXRQChr10g0282901' => 'han', 'HanXRQChr10g0310371' => 'han', 'HanXRQChr10g0315041' => 'han', 'HanXRQChr11g0327651' => 'han', 'HanXRQChr12g0359391' => 'han', 'Haze_00972' => 'cav', 'Haze_00973' => 'cav', 'Haze_00974' => 'cav', 'Haze_04747' => 'cav', 'Haze_04749' => 'cav', 'Haze_04750' => 'cav', 'Haze_21217' => 'cav', 'Hma1.2p1_1037F.1_g250680' => 'hma', 'Hma1.2p1_1644F.1_g295320' => 'hma', 'HPP92_011322' => 'vpl', 'HPP92_011323' => 'vpl', 'HPP92_011324' => 'vpl', 'HPP92_011325' => 'vpl', 'HPP92_011326' => 'vpl', 'Hund12205' => 'sun', 'Hund17957' => 'sun', 'Lalb_Chr06g0176771' => 'lal', 'Lalb_Chr18g0056021' => 'lal', 'Lalb_Chr18g0056031' => 'lal', 'Lalb_Chr18g0056041' => 'lal', 'Lalb_Chr20g0107751' => 'lal', 'Lalb_Chr20g0118371' => 'lal', 'Lj1g0010239' => 'lja', 'Lj1g0017101' => 'lja', 'Lj2A1178G40' => 'lonja', 'Lj2A54G84' => 'lonja', 'Lj2g0015248' => 'lja', 'Lj3A761T51' => 'lonja', 'Lj6g0018116' => 'lja', 'Lsat_1_v5_gn_4_136040' => 'lsa', 'Lsat_1_v5_gn_5_187461' => 'lsa', 'Lsat_1_v5_gn_5_77001' => 'lsa', 'Lsat_1_v5_gn_9_4461' => 'lsa', 'Manes.01G210100' => 'mes', 'Manes.03G185600' => 'mes', 'Manes.05G073300' => 'mes', 'Manes.09G120300' => 'mes', 'Manes.15G022100' => 'mes', 'Mapoly0096s0053' => 'mpo', 'MBI03_g14058_MAGBIO' => 'mbi', 'MBI03_g33876_MAGBIO' => 'mbi', 'MBI03_g36854_MAGBIO' => 'mbi', 'MBI17_g11997_MAGBIO' => 'mbi', 'MD03G1269000' => 'mdo', 'MD04G1179600' => 'mdo', 'MD11G1289800' => 'mdo', 'MD12G1194700' => 'mdo', 'MD13G1182100' => 'mdo', 'MD13G1182200' => 'mdo', 'MD16G1182600' => 'mdo', 'Medtr2g021400' => 'mtr', 'Medtr2g021470' => 'mtr', 'Medtr2g105810' => 'mtr', 'Medtr3g033580' => 'mtr', 'Medtr6g007970' => 'mtr', 'Medtr7g056330' => 'mtr', 'Medtr7g074290' => 'mtr', 'Medtr7g074380' => 'mtr', 'Medtr7g094550' => 'mtr', 'Medtr8g069995' => 'mtr', 'MELO3C014345.2' => 'cme', 'MELO3C021395.2' => 'cme', 'Migut.D00262' => 'egut', 'Migut.G00257' => 'egut', 'MSTRG.21575' => 'ama', 'MSTRG.3985' => 'ama', 'Nitab4.5_0000295g0140' => 'nta', 'Nitab4.5_0000732g0140' => 'nta', 'Nitab4.5_0003162g0020' => 'nta', 'Nitab4.5_0006180g0090' => 'nta', 'Nitab4.5_0006390g0010' => 'nta', 'Nitab4.5_0007392g0040' => 'nta', 'Nn1g02140' => 'nnu', 'Nn4g26168' => 'nnu', 'Nn5g26754' => 'nnu', 'Oeu001433.1' => 'oeu', 'Oeu010299.2' => 'oeu', 'Oeu011171.1' => 'oeu', 'Oeu037675.1' => 'oeu', 'Oeu038359.1' => 'oeu', 'Oeu063834.1' => 'oeu', 'Oeu063835.1' => 'oeu', 'Os05g0312000' => 'osa', 'Os07g0211101' => 'osa', 'Os07g0211200' => 'osa', 'Os07g0681500' => 'osa', 'Peaxi162Scf00095g01015' => 'pax', 'Peaxi162Scf00104g00329' => 'pax', 'Peaxi162Scf00161g00137' => 'pax', 'PGR004G1665' => 'pgr', 'PGR031G2937' => 'pgr', 'PGR119G2145' => 'pgr', 'PGSC0003DMG400004351' => 'stu', 'PGSC0003DMG400014625' => 'stu', 'PGSC0003DMG401000943' => 'stu', 'Phvul.001G148600' => 'pvu', 'Phvul.004G001700' => 'pvu', 'Phvul.006G154900' => 'pvu', 'Phvul.008G078200' => 'pvu', 'Phvul.011G136500' => 'pvu', 'Potri.002G215600' => 'ptr', 'Potri.008G201600' => 'ptr', 'Potri.014G138400' => 'ptr', 'Potri.016G142500' => 'ptr', 'Pp3c16_10580' => 'ppa', 'Pp3c5_25280' => 'ppa', 'Prupe.1G150000' => 'ppe', 'Prupe.1G150100' => 'ppe', 'Prupe.6G299600' => 'ppe', 'Prupe.8G245000' => 'ppe', 'Psat0s4927g0040' => 'psa', 'Psat1g052080' => 'psa', 'Psat1g183800' => 'psa', 'Psat3g113840' => 'psa', 'Psat3g126120' => 'psa', 'Psat3g126160' => 'psa', 'Psat3g158760' => 'psa', 'Psat3g158840' => 'psa', 'PSO170G2858' => 'pso', 'PSO339G0606' => 'pso', 'PSO384G4709' => 'pso', 'PSO407G0334' => 'pso', 'QL04p040276' => 'qlo', 'QL06p005458' => 'qlo', 'QL06p005472' => 'qlo', 'QL07p030546' => 'qlo', 'QL07p031519' => 'qlo', 'QL09p050949' => 'qlo', 'QL09p050966' => 'qlo', 'QL09p051067' => 'qlo', 'QL12p022706' => 'qlo', 'RcHm_v2.0_Chr2g0119601' => 'rch', 'RcHm_v2.0_Chr3g0459591' => 'rch', 'RcHm_v2.0_Chr4g0418521' => 'rch', 'RcHm_v2.0_Chr4g0418531' => 'rch', 'RcHm_v2.0_Chr4g0418541' => 'rch', 'RcHm_v2.0_Chr6g0291641' => 'rch', 'Rhsim01G0086300' => 'rsi', 'Rhsim01G0276300' => 'rsi', 'Rhsim01G0276500' => 'rsi', 'Rhsim04G0207700' => 'rsi', 'Rhsim05G0234500' => 'rsi', 'Rhsim13G0022400' => 'rsi', 'Sabra02G0167900' => 'sbr', 'Sabra04G0158500' => 'sbr', 'Sabra08G0159800' => 'sbr', 'Sabra10G0011500' => 'sbr', 'Sabra14G0104400' => 'sbr', 'SalBow2G2440' => 'sbo', 'SalBow4G2265' => 'sbo', 'Sc02g0000060' => 'sci', 'Sc05g0005020' => 'sci', 'Sc13g0003890' => 'sci', 'Sed0014865' => 'sed', 'Sed0017224' => 'sed', 'Sed0026391' => 'sed', 'SEGI_00063' => 'sgi', 'SEGI_10967' => 'sgi', 'SEGI_17510' => 'sgi', 'SEGI_24396' => 'sgi', 'SEGI_39719' => 'sgi', 'SEGI_41392' => 'sgi', 'SGA_v2.0_scaffold11G05794' => 'sas', 'SGA_v2.0_scaffold142G35607' => 'sas', 'SGA_v2.0_scaffold1G00447' => 'sas', 'SHI15388' => 'shi', 'SHI15394' => 'shi', 'SHI15396' => 'shi', 'SHI15399' => 'shi', 'SMO343G0151' => 'smo', 'SMO367G1118' => 'smo', 'Solyc01g080200.3' => 'sly', 'Solyc06g008960.3' => 'sly', 'Solyc09g064780.3' => 'sly', 'Sopen01g031980' => 'spe', 'Sopen06g003710' => 'spe', 'Sopen09g026460' => 'spe', 'Sp3g21240' => 'spa', 'Sp4g30030' => 'spa', 'TAR365G0022' => 'tar', 'TAR365G1023' => 'tar', 'TAR365G1253' => 'tar', 'TAR623G0078' => 'tar', 'TAR623G1721' => 'tar', 'TAR633G0959' => 'tar', 'THA.LOC104802225' => 'tha', 'THA.LOC104804769' => 'tha', 'THA.LOC104808660' => 'tha', 'THA.LOC104812792' => 'tha', 'Thecc.01G284000' => 'tca', 'Thecc.04G220600' => 'tca', 'Thecc.05G268900' => 'tca', 'Thecc.08G171100' => 'tca', 'Thhalv10001284m.g' => 'esa', 'Thhalv10019912m.g' => 'esa', 'TPR.G14189' => 'tpr', 'TPR.G18110' => 'tpr', 'TPR.G18130' => 'tpr', 'TPR.G18131' => 'tpr', 'TPR.G18140' => 'tpr', 'TPR.G24282' => 'tpr', 'TPR.G25221' => 'tpr', 'TPR.G29267' => 'tpr', 'TPR.G35315' => 'tpr', 'TPR.G36173' => 'tpr', 'TWI09G0794' => 'twi', 'TWI59G1348' => 'twi', 'TWI74G0430' => 'twi', 'unitig_26.g8940' => 'ugi', 'unitig_749.g13744' => 'ugi', 'unitig_749.g13745' => 'ugi', 'vmacro08269' => 'vma', 'vmacro14937' => 'vma', 'vmacro20401' => 'vma', 'VMungo0464G1349' => 'vmu', 'VMungo0540G0289' => 'vmu', 'VMungo1215G1590' => 'vmu', 'VMungo1309G0221' => 'vmu', 'VMungo1309G2815' => 'vmu', 'VMungo1383G0239' => 'vmu', 'VMungo1383G2910' => 'vmu', 'Zm00001eb095270' => 'zma', 'Zm00001eb095280' => 'zma', 'Zm00001eb111630' => 'zma', 'Zm00001eb237080' => 'zma', 'Zm00001eb273740' => 'zma', 'Zm00001eb285040' => 'zma', 'Zm00001eb330790' => 'zma', 'Zm00001eb337380' => 'zma' ), 'gf_id' => 'HOM05D001484', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001484' ), 'data_identifier' => 'HOM05D001484', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001484', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p31500' => 'bna', 'A05p00020' => 'bna', 'A07p08820' => 'bna', 'Aa31LG4G3300' => 'aar', 'Aa31LG8G10030' => 'aar', 'Actinidia00731' => 'ach', 'Actinidia11473' => 'ach', 'Actinidia23469' => 'ach', 'Actinidia24318' => 'ach', 'Actinidia40196' => 'ach', 'Actinidia40197' => 'ach', 'Actinidia40198' => 'ach', 'Ah.08g212990' => 'amhyb', 'Ah.15g091720' => 'amhyb', 'AL3G38260' => 'aly', 'AL4G47710' => 'aly', 'Aqoxy2G00671' => 'aox', 'Aqoxy2G03236' => 'aox', 'arahy.Tifrunner.gnm1.ann1.05IDCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KR684' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATY3SJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK6QJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6APGL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IDT7Z9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM073U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ0R87' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LE7RV4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT4QRX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V5ENPK' => 'arhy', 'AT2G48110' => 'ath', 'AT3G23590' => 'ath', 'ATR0626G186' => 'atr', 'ATR1127G141' => 'atr', 'Atru.chr4.2583' => 'acertr', 'Atru.chr5.1358' => 'acertr', 'Atru.chr5.1359' => 'acertr', 'Atru.chr8.46' => 'acertr', 'AUR62002640' => 'cqu', 'AUR62030055' => 'cqu', 'AUR62033713' => 'cqu', 'AUR62033714' => 'cqu', 'AUR62036795' => 'cqu', 'AUR62039891' => 'cqu', 'BcaB02g08737' => 'bca', 'BcaB04g20441' => 'bca', 'BcaB06g26509' => 'bca', 'BcaB06g26510' => 'bca', 'BcaB06g26511' => 'bca', 'BcaB06g26512' => 'bca', 'BcaB06g26513' => 'bca', 'BcaC02g12564' => 'bca', 'BcaC02g12565' => 'bca', 'BcaC02g12794' => 'bca', 'BcaC02g12795' => 'bca', 'BcaC02g12796' => 'bca', 'BcaC06g35541' => 'bca', 'BNapus_Darmor_BZH_scaffold_188p00080' => 'bna', 'BNapus_Darmor_BZH_scaffold_188p00090' => 'bna', 'BolC1t03972H' => 'bol', 'BolC1t03973H' => 'bol', 'BolC4t21680H' => 'bol', 'BolC7t41863H' => 'bol', 'BolSC55t61227H' => 'bol', 'BolSC55t61228H' => 'bol', 'BraA01t03278Z' => 'bra', 'BraA05t18998Z' => 'bra', 'BraA07t28673Z' => 'bra', 'C01p40150' => 'bna', 'C05p12370' => 'bna', 'C07p13680' => 'bna', 'CAN.G1006.16' => 'can', 'CAN.G1006.17' => 'can', 'CAN.G1170.2' => 'can', 'CAN.G962.7' => 'can', 'CANSAT25G2179' => 'cansat', 'CANSAT78G1573' => 'cansat', 'CARHR099510' => 'chi', 'CARHR143510' => 'chi', 'Carub.0003s2380' => 'cru', 'Carub.0004s3082' => 'cru', 'Ca_00614_v3' => 'car', 'Ca_07801_v3' => 'car', 'Ca_08567_v3' => 'car', 'Ca_09571_v3' => 'car', 'CBR_g19290' => 'cbr', 'Cc01_g19770' => 'ccan', 'Cc03_g03030' => 'ccan', 'CDE07G0968' => 'cde', 'CDE09G1441' => 'cde', 'Cfa006103' => 'cfa', 'Cfa015573' => 'cfa', 'Cfa016988' => 'cfa', 'Ciclev10006738m.g' => 'ccl', 'Ciclev10010920m.g' => 'ccl', 'Ciclev10018517m.g' => 'ccl', 'CiPaw.01G159200' => 'cil', 'CiPaw.02G091000' => 'cil', 'CiPaw.02G091100' => 'cil', 'CiPaw.08G103100' => 'cil', 'CiPaw.09G224900' => 'cil', 'ClCG06G005740' => 'cla', 'ClCG07G000090' => 'cla', 'ClCG07G000100' => 'cla', 'COL.COLO4_09143' => 'col', 'COL.COLO4_25124' => 'col', 'Cpa.g.sc16.34' => 'cpa', 'Cpa.g.sc3504.1' => 'cpa', 'Cpa.g.sc60.37' => 'cpa', 'CsaV3_6G018520' => 'csa', 'CsaV3_6G036860' => 'csa', 'CSS0001072' => 'camsi', 'CSS0020208' => 'camsi', 'CSS0021253' => 'camsi', 'CSS0022190' => 'camsi', 'CSS0036150' => 'camsi', 'CSS0040442' => 'camsi', 'CSS0042300' => 'camsi', 'CSS0045298' => 'camsi', 'DCAR_012449' => 'dca', 'DCAR_018405' => 'dca', 'DCAR_024573' => 'dca', 'DCAR_030591' => 'dca', 'Dinv16926' => 'din', 'Dinv32963' => 'din', 'Dinv38382' => 'din', 'Dinv38383' => 'din', 'Duzib133G0974' => 'dzi', 'Duzib138G1867' => 'dzi', 'Duzib211G0420' => 'dzi', 'Duzib212G0930' => 'dzi', 'ECA234G1645' => 'eca', 'ECA247G3467' => 'eca', 'ECA248G1703' => 'eca', 'EL10Ac3g06327' => 'bvu', 'EL10Ac7g17204' => 'bvu', 'Eucgr.A00855' => 'egr', 'Eucgr.A00858' => 'egr', 'Eucgr.H01520' => 'egr', 'Eucgr.H03604' => 'egr', 'Eucgr.L03465' => 'egr', 'Eucgr.L03466' => 'egr', 'FAN01G0988' => 'fan', 'FAN02G3892' => 'fan', 'FAN05G3381' => 'fan', 'FAN07G0967' => 'fan', 'FAN07G1493' => 'fan', 'FAN08G3125' => 'fan', 'FAN09G0402' => 'fan', 'FAN12G2594' => 'fan', 'FAN12G3879' => 'fan', 'FAN14G1546' => 'fan', 'FAN15G3626' => 'fan', 'FAN17G0588' => 'fan', 'FAN17G0609' => 'fan', 'FAN18G2817' => 'fan', 'FAN19G1305' => 'fan', 'FAN20G1787' => 'fan', 'FAN22G0073' => 'fan', 'FAN22G0352' => 'fan', 'FAN22G0368' => 'fan', 'FAN22G2273' => 'fan', 'FAN24G1998' => 'fan', 'FAN27G1317' => 'fan', 'FvH4_2g23980' => 'fve', 'FvH4_4g14380' => 'fve', 'FvH4_4g14390' => 'fve', 'FvH4_6g09250' => 'fve', 'Glyma.03G151100' => 'gma', 'Glyma.04G122550' => 'gma', 'Glyma.05G001600' => 'gma', 'Glyma.09G270766' => 'gma', 'Glyma.09G270832' => 'gma', 'Glyma.13G209800' => 'gma', 'Glyma.15G102800' => 'gma', 'Glyma.18G218900' => 'gma', 'Glyma.19G001500' => 'gma', 'Glyma.19G153600' => 'gma', 'Gohir.A02G028600' => 'ghi', 'Gohir.A08G045000' => 'ghi', 'Gohir.A11G120500' => 'ghi', 'Gohir.A12G006200' => 'ghi', 'Gohir.A12G006250' => 'ghi', 'Gohir.D02G036300' => 'ghi', 'Gohir.D08G054700' => 'ghi', 'Gohir.D11G125600' => 'ghi', 'Gohir.D12G005700' => 'ghi', 'Gorai.004G055200' => 'gra', 'Gorai.005G040400' => 'gra', 'Gorai.007G134500' => 'gra', 'Gorai.008G005500' => 'gra', 'GSVIVG01011094001' => 'vvi', 'GSVIVG01017879001' => 'vvi', 'GSVIVG01025988001' => 'vvi', 'GSVIVG01029847001' => 'vvi', 'HanXRQChr10g0282901' => 'han', 'HanXRQChr10g0310371' => 'han', 'HanXRQChr10g0315041' => 'han', 'HanXRQChr11g0327651' => 'han', 'HanXRQChr12g0359391' => 'han', 'Haze_00972' => 'cav', 'Haze_00973' => 'cav', 'Haze_00974' => 'cav', 'Haze_04747' => 'cav', 'Haze_04749' => 'cav', 'Haze_04750' => 'cav', 'Haze_21217' => 'cav', 'Hma1.2p1_1037F.1_g250680' => 'hma', 'Hma1.2p1_1644F.1_g295320' => 'hma', 'HPP92_011322' => 'vpl', 'HPP92_011323' => 'vpl', 'HPP92_011324' => 'vpl', 'HPP92_011325' => 'vpl', 'HPP92_011326' => 'vpl', 'Hund12205' => 'sun', 'Hund17957' => 'sun', 'Lalb_Chr06g0176771' => 'lal', 'Lalb_Chr18g0056021' => 'lal', 'Lalb_Chr18g0056031' => 'lal', 'Lalb_Chr18g0056041' => 'lal', 'Lalb_Chr20g0107751' => 'lal', 'Lalb_Chr20g0118371' => 'lal', 'Lj1g0010239' => 'lja', 'Lj1g0017101' => 'lja', 'Lj2A1178G40' => 'lonja', 'Lj2A54G84' => 'lonja', 'Lj2g0015248' => 'lja', 'Lj3A761T51' => 'lonja', 'Lj6g0018116' => 'lja', 'Lsat_1_v5_gn_4_136040' => 'lsa', 'Lsat_1_v5_gn_5_187461' => 'lsa', 'Lsat_1_v5_gn_5_77001' => 'lsa', 'Lsat_1_v5_gn_9_4461' => 'lsa', 'Manes.01G210100' => 'mes', 'Manes.03G185600' => 'mes', 'Manes.05G073300' => 'mes', 'Manes.09G120300' => 'mes', 'Manes.15G022100' => 'mes', 'Mapoly0096s0053' => 'mpo', 'MBI03_g14058_MAGBIO' => 'mbi', 'MBI03_g33876_MAGBIO' => 'mbi', 'MBI03_g36854_MAGBIO' => 'mbi', 'MBI17_g11997_MAGBIO' => 'mbi', 'MD03G1269000' => 'mdo', 'MD04G1179600' => 'mdo', 'MD11G1289800' => 'mdo', 'MD12G1194700' => 'mdo', 'MD13G1182100' => 'mdo', 'MD13G1182200' => 'mdo', 'MD16G1182600' => 'mdo', 'Medtr2g021400' => 'mtr', 'Medtr2g021470' => 'mtr', 'Medtr2g105810' => 'mtr', 'Medtr3g033580' => 'mtr', 'Medtr6g007970' => 'mtr', 'Medtr7g056330' => 'mtr', 'Medtr7g074290' => 'mtr', 'Medtr7g074380' => 'mtr', 'Medtr7g094550' => 'mtr', 'Medtr8g069995' => 'mtr', 'MELO3C014345.2' => 'cme', 'MELO3C021395.2' => 'cme', 'Migut.D00262' => 'egut', 'Migut.G00257' => 'egut', 'MSTRG.21575' => 'ama', 'MSTRG.3985' => 'ama', 'Nitab4.5_0000295g0140' => 'nta', 'Nitab4.5_0000732g0140' => 'nta', 'Nitab4.5_0003162g0020' => 'nta', 'Nitab4.5_0006180g0090' => 'nta', 'Nitab4.5_0006390g0010' => 'nta', 'Nitab4.5_0007392g0040' => 'nta', 'Nn1g02140' => 'nnu', 'Nn4g26168' => 'nnu', 'Nn5g26754' => 'nnu', 'Oeu001433.1' => 'oeu', 'Oeu010299.2' => 'oeu', 'Oeu011171.1' => 'oeu', 'Oeu037675.1' => 'oeu', 'Oeu038359.1' => 'oeu', 'Oeu063834.1' => 'oeu', 'Oeu063835.1' => 'oeu', 'Os05g0312000' => 'osa', 'Os07g0211101' => 'osa', 'Os07g0211200' => 'osa', 'Os07g0681500' => 'osa', 'Peaxi162Scf00095g01015' => 'pax', 'Peaxi162Scf00104g00329' => 'pax', 'Peaxi162Scf00161g00137' => 'pax', 'PGR004G1665' => 'pgr', 'PGR031G2937' => 'pgr', 'PGR119G2145' => 'pgr', 'PGSC0003DMG400004351' => 'stu', 'PGSC0003DMG400014625' => 'stu', 'PGSC0003DMG401000943' => 'stu', 'Phvul.001G148600' => 'pvu', 'Phvul.004G001700' => 'pvu', 'Phvul.006G154900' => 'pvu', 'Phvul.008G078200' => 'pvu', 'Phvul.011G136500' => 'pvu', 'Potri.002G215600' => 'ptr', 'Potri.008G201600' => 'ptr', 'Potri.014G138400' => 'ptr', 'Potri.016G142500' => 'ptr', 'Pp3c16_10580' => 'ppa', 'Pp3c5_25280' => 'ppa', 'Prupe.1G150000' => 'ppe', 'Prupe.1G150100' => 'ppe', 'Prupe.6G299600' => 'ppe', 'Prupe.8G245000' => 'ppe', 'Psat0s4927g0040' => 'psa', 'Psat1g052080' => 'psa', 'Psat1g183800' => 'psa', 'Psat3g113840' => 'psa', 'Psat3g126120' => 'psa', 'Psat3g126160' => 'psa', 'Psat3g158760' => 'psa', 'Psat3g158840' => 'psa', 'PSO170G2858' => 'pso', 'PSO339G0606' => 'pso', 'PSO384G4709' => 'pso', 'PSO407G0334' => 'pso', 'QL04p040276' => 'qlo', 'QL06p005458' => 'qlo', 'QL06p005472' => 'qlo', 'QL07p030546' => 'qlo', 'QL07p031519' => 'qlo', 'QL09p050949' => 'qlo', 'QL09p050966' => 'qlo', 'QL09p051067' => 'qlo', 'QL12p022706' => 'qlo', 'RcHm_v2.0_Chr2g0119601' => 'rch', 'RcHm_v2.0_Chr3g0459591' => 'rch', 'RcHm_v2.0_Chr4g0418521' => 'rch', 'RcHm_v2.0_Chr4g0418531' => 'rch', 'RcHm_v2.0_Chr4g0418541' => 'rch', 'RcHm_v2.0_Chr6g0291641' => 'rch', 'Rhsim01G0086300' => 'rsi', 'Rhsim01G0276300' => 'rsi', 'Rhsim01G0276500' => 'rsi', 'Rhsim04G0207700' => 'rsi', 'Rhsim05G0234500' => 'rsi', 'Rhsim13G0022400' => 'rsi', 'Sabra02G0167900' => 'sbr', 'Sabra04G0158500' => 'sbr', 'Sabra08G0159800' => 'sbr', 'Sabra10G0011500' => 'sbr', 'Sabra14G0104400' => 'sbr', 'SalBow2G2440' => 'sbo', 'SalBow4G2265' => 'sbo', 'Sc02g0000060' => 'sci', 'Sc05g0005020' => 'sci', 'Sc13g0003890' => 'sci', 'Sed0014865' => 'sed', 'Sed0017224' => 'sed', 'Sed0026391' => 'sed', 'SEGI_00063' => 'sgi', 'SEGI_10967' => 'sgi', 'SEGI_17510' => 'sgi', 'SEGI_24396' => 'sgi', 'SEGI_39719' => 'sgi', 'SEGI_41392' => 'sgi', 'SGA_v2.0_scaffold11G05794' => 'sas', 'SGA_v2.0_scaffold142G35607' => 'sas', 'SGA_v2.0_scaffold1G00447' => 'sas', 'SHI15388' => 'shi', 'SHI15394' => 'shi', 'SHI15396' => 'shi', 'SHI15399' => 'shi', 'SMO343G0151' => 'smo', 'SMO367G1118' => 'smo', 'Solyc01g080200.3' => 'sly', 'Solyc06g008960.3' => 'sly', 'Solyc09g064780.3' => 'sly', 'Sopen01g031980' => 'spe', 'Sopen06g003710' => 'spe', 'Sopen09g026460' => 'spe', 'Sp3g21240' => 'spa', 'Sp4g30030' => 'spa', 'TAR365G0022' => 'tar', 'TAR365G1023' => 'tar', 'TAR365G1253' => 'tar', 'TAR623G0078' => 'tar', 'TAR623G1721' => 'tar', 'TAR633G0959' => 'tar', 'THA.LOC104802225' => 'tha', 'THA.LOC104804769' => 'tha', 'THA.LOC104808660' => 'tha', 'THA.LOC104812792' => 'tha', 'Thecc.01G284000' => 'tca', 'Thecc.04G220600' => 'tca', 'Thecc.05G268900' => 'tca', 'Thecc.08G171100' => 'tca', 'Thhalv10001284m.g' => 'esa', 'Thhalv10019912m.g' => 'esa', 'TPR.G14189' => 'tpr', 'TPR.G18110' => 'tpr', 'TPR.G18130' => 'tpr', 'TPR.G18131' => 'tpr', 'TPR.G18140' => 'tpr', 'TPR.G24282' => 'tpr', 'TPR.G25221' => 'tpr', 'TPR.G29267' => 'tpr', 'TPR.G35315' => 'tpr', 'TPR.G36173' => 'tpr', 'TWI09G0794' => 'twi', 'TWI59G1348' => 'twi', 'TWI74G0430' => 'twi', 'unitig_26.g8940' => 'ugi', 'unitig_749.g13744' => 'ugi', 'unitig_749.g13745' => 'ugi', 'vmacro08269' => 'vma', 'vmacro14937' => 'vma', 'vmacro20401' => 'vma', 'VMungo0464G1349' => 'vmu', 'VMungo0540G0289' => 'vmu', 'VMungo1215G1590' => 'vmu', 'VMungo1309G0221' => 'vmu', 'VMungo1309G2815' => 'vmu', 'VMungo1383G0239' => 'vmu', 'VMungo1383G2910' => 'vmu', 'Zm00001eb095270' => 'zma', 'Zm00001eb095280' => 'zma', 'Zm00001eb111630' => 'zma', 'Zm00001eb237080' => 'zma', 'Zm00001eb273740' => 'zma', 'Zm00001eb285040' => 'zma', 'Zm00001eb330790' => 'zma', 'Zm00001eb337380' => 'zma' ) $gf_id = 'HOM05D001484' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001484' ) $data_identifier = 'HOM05D001484' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 2, 'aly' => (int) 2, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 22, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 7, 'hma' => (int) 2, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 7, 'mtr' => (int) 10, 'cme' => (int) 2, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 4, 'ppa' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 4, 'qlo' => (int) 9, 'rch' => (int) 6, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 10, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 7, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb337380' $species_info = array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ) $local_species = 'cbr' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001484', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p31500' => 'bna', 'A05p00020' => 'bna', 'A07p08820' => 'bna', 'Aa31LG4G3300' => 'aar', 'Aa31LG8G10030' => 'aar', 'Actinidia00731' => 'ach', 'Actinidia11473' => 'ach', 'Actinidia23469' => 'ach', 'Actinidia24318' => 'ach', 'Actinidia40196' => 'ach', 'Actinidia40197' => 'ach', 'Actinidia40198' => 'ach', 'Ah.08g212990' => 'amhyb', 'Ah.15g091720' => 'amhyb', 'AL3G38260' => 'aly', 'AL4G47710' => 'aly', 'Aqoxy2G00671' => 'aox', 'Aqoxy2G03236' => 'aox', 'arahy.Tifrunner.gnm1.ann1.05IDCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KR684' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATY3SJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK6QJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6APGL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IDT7Z9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM073U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ0R87' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LE7RV4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT4QRX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V5ENPK' => 'arhy', 'AT2G48110' => 'ath', 'AT3G23590' => 'ath', 'ATR0626G186' => 'atr', 'ATR1127G141' => 'atr', 'Atru.chr4.2583' => 'acertr', 'Atru.chr5.1358' => 'acertr', 'Atru.chr5.1359' => 'acertr', 'Atru.chr8.46' => 'acertr', 'AUR62002640' => 'cqu', 'AUR62030055' => 'cqu', 'AUR62033713' => 'cqu', 'AUR62033714' => 'cqu', 'AUR62036795' => 'cqu', 'AUR62039891' => 'cqu', 'BcaB02g08737' => 'bca', 'BcaB04g20441' => 'bca', 'BcaB06g26509' => 'bca', 'BcaB06g26510' => 'bca', 'BcaB06g26511' => 'bca', 'BcaB06g26512' => 'bca', 'BcaB06g26513' => 'bca', 'BcaC02g12564' => 'bca', 'BcaC02g12565' => 'bca', 'BcaC02g12794' => 'bca', 'BcaC02g12795' => 'bca', 'BcaC02g12796' => 'bca', 'BcaC06g35541' => 'bca', 'BNapus_Darmor_BZH_scaffold_188p00080' => 'bna', 'BNapus_Darmor_BZH_scaffold_188p00090' => 'bna', 'BolC1t03972H' => 'bol', 'BolC1t03973H' => 'bol', 'BolC4t21680H' => 'bol', 'BolC7t41863H' => 'bol', 'BolSC55t61227H' => 'bol', 'BolSC55t61228H' => 'bol', 'BraA01t03278Z' => 'bra', 'BraA05t18998Z' => 'bra', 'BraA07t28673Z' => 'bra', 'C01p40150' => 'bna', 'C05p12370' => 'bna', 'C07p13680' => 'bna', 'CAN.G1006.16' => 'can', 'CAN.G1006.17' => 'can', 'CAN.G1170.2' => 'can', 'CAN.G962.7' => 'can', 'CANSAT25G2179' => 'cansat', 'CANSAT78G1573' => 'cansat', 'CARHR099510' => 'chi', 'CARHR143510' => 'chi', 'Carub.0003s2380' => 'cru', 'Carub.0004s3082' => 'cru', 'Ca_00614_v3' => 'car', 'Ca_07801_v3' => 'car', 'Ca_08567_v3' => 'car', 'Ca_09571_v3' => 'car', 'CBR_g19290' => 'cbr', 'Cc01_g19770' => 'ccan', 'Cc03_g03030' => 'ccan', 'CDE07G0968' => 'cde', 'CDE09G1441' => 'cde', 'Cfa006103' => 'cfa', 'Cfa015573' => 'cfa', 'Cfa016988' => 'cfa', 'Ciclev10006738m.g' => 'ccl', 'Ciclev10010920m.g' => 'ccl', 'Ciclev10018517m.g' => 'ccl', 'CiPaw.01G159200' => 'cil', 'CiPaw.02G091000' => 'cil', 'CiPaw.02G091100' => 'cil', 'CiPaw.08G103100' => 'cil', 'CiPaw.09G224900' => 'cil', 'ClCG06G005740' => 'cla', 'ClCG07G000090' => 'cla', 'ClCG07G000100' => 'cla', 'COL.COLO4_09143' => 'col', 'COL.COLO4_25124' => 'col', 'Cpa.g.sc16.34' => 'cpa', 'Cpa.g.sc3504.1' => 'cpa', 'Cpa.g.sc60.37' => 'cpa', 'CsaV3_6G018520' => 'csa', 'CsaV3_6G036860' => 'csa', 'CSS0001072' => 'camsi', 'CSS0020208' => 'camsi', 'CSS0021253' => 'camsi', 'CSS0022190' => 'camsi', 'CSS0036150' => 'camsi', 'CSS0040442' => 'camsi', 'CSS0042300' => 'camsi', 'CSS0045298' => 'camsi', 'DCAR_012449' => 'dca', 'DCAR_018405' => 'dca', 'DCAR_024573' => 'dca', 'DCAR_030591' => 'dca', 'Dinv16926' => 'din', 'Dinv32963' => 'din', 'Dinv38382' => 'din', 'Dinv38383' => 'din', 'Duzib133G0974' => 'dzi', 'Duzib138G1867' => 'dzi', 'Duzib211G0420' => 'dzi', 'Duzib212G0930' => 'dzi', 'ECA234G1645' => 'eca', 'ECA247G3467' => 'eca', 'ECA248G1703' => 'eca', 'EL10Ac3g06327' => 'bvu', 'EL10Ac7g17204' => 'bvu', 'Eucgr.A00855' => 'egr', 'Eucgr.A00858' => 'egr', 'Eucgr.H01520' => 'egr', 'Eucgr.H03604' => 'egr', 'Eucgr.L03465' => 'egr', 'Eucgr.L03466' => 'egr', 'FAN01G0988' => 'fan', 'FAN02G3892' => 'fan', 'FAN05G3381' => 'fan', 'FAN07G0967' => 'fan', 'FAN07G1493' => 'fan', 'FAN08G3125' => 'fan', 'FAN09G0402' => 'fan', 'FAN12G2594' => 'fan', 'FAN12G3879' => 'fan', 'FAN14G1546' => 'fan', 'FAN15G3626' => 'fan', 'FAN17G0588' => 'fan', 'FAN17G0609' => 'fan', 'FAN18G2817' => 'fan', 'FAN19G1305' => 'fan', 'FAN20G1787' => 'fan', 'FAN22G0073' => 'fan', 'FAN22G0352' => 'fan', 'FAN22G0368' => 'fan', 'FAN22G2273' => 'fan', 'FAN24G1998' => 'fan', 'FAN27G1317' => 'fan', 'FvH4_2g23980' => 'fve', 'FvH4_4g14380' => 'fve', 'FvH4_4g14390' => 'fve', 'FvH4_6g09250' => 'fve', 'Glyma.03G151100' => 'gma', 'Glyma.04G122550' => 'gma', 'Glyma.05G001600' => 'gma', 'Glyma.09G270766' => 'gma', 'Glyma.09G270832' => 'gma', 'Glyma.13G209800' => 'gma', 'Glyma.15G102800' => 'gma', 'Glyma.18G218900' => 'gma', 'Glyma.19G001500' => 'gma', 'Glyma.19G153600' => 'gma', 'Gohir.A02G028600' => 'ghi', 'Gohir.A08G045000' => 'ghi', 'Gohir.A11G120500' => 'ghi', 'Gohir.A12G006200' => 'ghi', 'Gohir.A12G006250' => 'ghi', 'Gohir.D02G036300' => 'ghi', 'Gohir.D08G054700' => 'ghi', 'Gohir.D11G125600' => 'ghi', 'Gohir.D12G005700' => 'ghi', 'Gorai.004G055200' => 'gra', 'Gorai.005G040400' => 'gra', 'Gorai.007G134500' => 'gra', 'Gorai.008G005500' => 'gra', 'GSVIVG01011094001' => 'vvi', 'GSVIVG01017879001' => 'vvi', 'GSVIVG01025988001' => 'vvi', 'GSVIVG01029847001' => 'vvi', 'HanXRQChr10g0282901' => 'han', 'HanXRQChr10g0310371' => 'han', 'HanXRQChr10g0315041' => 'han', 'HanXRQChr11g0327651' => 'han', 'HanXRQChr12g0359391' => 'han', 'Haze_00972' => 'cav', 'Haze_00973' => 'cav', 'Haze_00974' => 'cav', 'Haze_04747' => 'cav', 'Haze_04749' => 'cav', 'Haze_04750' => 'cav', 'Haze_21217' => 'cav', 'Hma1.2p1_1037F.1_g250680' => 'hma', 'Hma1.2p1_1644F.1_g295320' => 'hma', 'HPP92_011322' => 'vpl', 'HPP92_011323' => 'vpl', 'HPP92_011324' => 'vpl', 'HPP92_011325' => 'vpl', 'HPP92_011326' => 'vpl', 'Hund12205' => 'sun', 'Hund17957' => 'sun', 'Lalb_Chr06g0176771' => 'lal', 'Lalb_Chr18g0056021' => 'lal', 'Lalb_Chr18g0056031' => 'lal', 'Lalb_Chr18g0056041' => 'lal', 'Lalb_Chr20g0107751' => 'lal', 'Lalb_Chr20g0118371' => 'lal', 'Lj1g0010239' => 'lja', 'Lj1g0017101' => 'lja', 'Lj2A1178G40' => 'lonja', 'Lj2A54G84' => 'lonja', 'Lj2g0015248' => 'lja', 'Lj3A761T51' => 'lonja', 'Lj6g0018116' => 'lja', 'Lsat_1_v5_gn_4_136040' => 'lsa', 'Lsat_1_v5_gn_5_187461' => 'lsa', 'Lsat_1_v5_gn_5_77001' => 'lsa', 'Lsat_1_v5_gn_9_4461' => 'lsa', 'Manes.01G210100' => 'mes', 'Manes.03G185600' => 'mes', 'Manes.05G073300' => 'mes', 'Manes.09G120300' => 'mes', 'Manes.15G022100' => 'mes', 'Mapoly0096s0053' => 'mpo', 'MBI03_g14058_MAGBIO' => 'mbi', 'MBI03_g33876_MAGBIO' => 'mbi', 'MBI03_g36854_MAGBIO' => 'mbi', 'MBI17_g11997_MAGBIO' => 'mbi', 'MD03G1269000' => 'mdo', 'MD04G1179600' => 'mdo', 'MD11G1289800' => 'mdo', 'MD12G1194700' => 'mdo', 'MD13G1182100' => 'mdo', 'MD13G1182200' => 'mdo', 'MD16G1182600' => 'mdo', 'Medtr2g021400' => 'mtr', 'Medtr2g021470' => 'mtr', 'Medtr2g105810' => 'mtr', 'Medtr3g033580' => 'mtr', 'Medtr6g007970' => 'mtr', 'Medtr7g056330' => 'mtr', 'Medtr7g074290' => 'mtr', 'Medtr7g074380' => 'mtr', 'Medtr7g094550' => 'mtr', 'Medtr8g069995' => 'mtr', 'MELO3C014345.2' => 'cme', 'MELO3C021395.2' => 'cme', 'Migut.D00262' => 'egut', 'Migut.G00257' => 'egut', 'MSTRG.21575' => 'ama', 'MSTRG.3985' => 'ama', 'Nitab4.5_0000295g0140' => 'nta', 'Nitab4.5_0000732g0140' => 'nta', 'Nitab4.5_0003162g0020' => 'nta', 'Nitab4.5_0006180g0090' => 'nta', 'Nitab4.5_0006390g0010' => 'nta', 'Nitab4.5_0007392g0040' => 'nta', 'Nn1g02140' => 'nnu', 'Nn4g26168' => 'nnu', 'Nn5g26754' => 'nnu', 'Oeu001433.1' => 'oeu', 'Oeu010299.2' => 'oeu', 'Oeu011171.1' => 'oeu', 'Oeu037675.1' => 'oeu', 'Oeu038359.1' => 'oeu', 'Oeu063834.1' => 'oeu', 'Oeu063835.1' => 'oeu', 'Os05g0312000' => 'osa', 'Os07g0211101' => 'osa', 'Os07g0211200' => 'osa', 'Os07g0681500' => 'osa', 'Peaxi162Scf00095g01015' => 'pax', 'Peaxi162Scf00104g00329' => 'pax', 'Peaxi162Scf00161g00137' => 'pax', 'PGR004G1665' => 'pgr', 'PGR031G2937' => 'pgr', 'PGR119G2145' => 'pgr', 'PGSC0003DMG400004351' => 'stu', 'PGSC0003DMG400014625' => 'stu', 'PGSC0003DMG401000943' => 'stu', 'Phvul.001G148600' => 'pvu', 'Phvul.004G001700' => 'pvu', 'Phvul.006G154900' => 'pvu', 'Phvul.008G078200' => 'pvu', 'Phvul.011G136500' => 'pvu', 'Potri.002G215600' => 'ptr', 'Potri.008G201600' => 'ptr', 'Potri.014G138400' => 'ptr', 'Potri.016G142500' => 'ptr', 'Pp3c16_10580' => 'ppa', 'Pp3c5_25280' => 'ppa', 'Prupe.1G150000' => 'ppe', 'Prupe.1G150100' => 'ppe', 'Prupe.6G299600' => 'ppe', 'Prupe.8G245000' => 'ppe', 'Psat0s4927g0040' => 'psa', 'Psat1g052080' => 'psa', 'Psat1g183800' => 'psa', 'Psat3g113840' => 'psa', 'Psat3g126120' => 'psa', 'Psat3g126160' => 'psa', 'Psat3g158760' => 'psa', 'Psat3g158840' => 'psa', 'PSO170G2858' => 'pso', 'PSO339G0606' => 'pso', 'PSO384G4709' => 'pso', 'PSO407G0334' => 'pso', 'QL04p040276' => 'qlo', 'QL06p005458' => 'qlo', 'QL06p005472' => 'qlo', 'QL07p030546' => 'qlo', 'QL07p031519' => 'qlo', 'QL09p050949' => 'qlo', 'QL09p050966' => 'qlo', 'QL09p051067' => 'qlo', 'QL12p022706' => 'qlo', 'RcHm_v2.0_Chr2g0119601' => 'rch', 'RcHm_v2.0_Chr3g0459591' => 'rch', 'RcHm_v2.0_Chr4g0418521' => 'rch', 'RcHm_v2.0_Chr4g0418531' => 'rch', 'RcHm_v2.0_Chr4g0418541' => 'rch', 'RcHm_v2.0_Chr6g0291641' => 'rch', 'Rhsim01G0086300' => 'rsi', 'Rhsim01G0276300' => 'rsi', 'Rhsim01G0276500' => 'rsi', 'Rhsim04G0207700' => 'rsi', 'Rhsim05G0234500' => 'rsi', 'Rhsim13G0022400' => 'rsi', 'Sabra02G0167900' => 'sbr', 'Sabra04G0158500' => 'sbr', 'Sabra08G0159800' => 'sbr', 'Sabra10G0011500' => 'sbr', 'Sabra14G0104400' => 'sbr', 'SalBow2G2440' => 'sbo', 'SalBow4G2265' => 'sbo', 'Sc02g0000060' => 'sci', 'Sc05g0005020' => 'sci', 'Sc13g0003890' => 'sci', 'Sed0014865' => 'sed', 'Sed0017224' => 'sed', 'Sed0026391' => 'sed', 'SEGI_00063' => 'sgi', 'SEGI_10967' => 'sgi', 'SEGI_17510' => 'sgi', 'SEGI_24396' => 'sgi', 'SEGI_39719' => 'sgi', 'SEGI_41392' => 'sgi', 'SGA_v2.0_scaffold11G05794' => 'sas', 'SGA_v2.0_scaffold142G35607' => 'sas', 'SGA_v2.0_scaffold1G00447' => 'sas', 'SHI15388' => 'shi', 'SHI15394' => 'shi', 'SHI15396' => 'shi', 'SHI15399' => 'shi', 'SMO343G0151' => 'smo', 'SMO367G1118' => 'smo', 'Solyc01g080200.3' => 'sly', 'Solyc06g008960.3' => 'sly', 'Solyc09g064780.3' => 'sly', 'Sopen01g031980' => 'spe', 'Sopen06g003710' => 'spe', 'Sopen09g026460' => 'spe', 'Sp3g21240' => 'spa', 'Sp4g30030' => 'spa', 'TAR365G0022' => 'tar', 'TAR365G1023' => 'tar', 'TAR365G1253' => 'tar', 'TAR623G0078' => 'tar', 'TAR623G1721' => 'tar', 'TAR633G0959' => 'tar', 'THA.LOC104802225' => 'tha', 'THA.LOC104804769' => 'tha', 'THA.LOC104808660' => 'tha', 'THA.LOC104812792' => 'tha', 'Thecc.01G284000' => 'tca', 'Thecc.04G220600' => 'tca', 'Thecc.05G268900' => 'tca', 'Thecc.08G171100' => 'tca', 'Thhalv10001284m.g' => 'esa', 'Thhalv10019912m.g' => 'esa', 'TPR.G14189' => 'tpr', 'TPR.G18110' => 'tpr', 'TPR.G18130' => 'tpr', 'TPR.G18131' => 'tpr', 'TPR.G18140' => 'tpr', 'TPR.G24282' => 'tpr', 'TPR.G25221' => 'tpr', 'TPR.G29267' => 'tpr', 'TPR.G35315' => 'tpr', 'TPR.G36173' => 'tpr', 'TWI09G0794' => 'twi', 'TWI59G1348' => 'twi', 'TWI74G0430' => 'twi', 'unitig_26.g8940' => 'ugi', 'unitig_749.g13744' => 'ugi', 'unitig_749.g13745' => 'ugi', 'vmacro08269' => 'vma', 'vmacro14937' => 'vma', 'vmacro20401' => 'vma', 'VMungo0464G1349' => 'vmu', 'VMungo0540G0289' => 'vmu', 'VMungo1215G1590' => 'vmu', 'VMungo1309G0221' => 'vmu', 'VMungo1309G2815' => 'vmu', 'VMungo1383G0239' => 'vmu', 'VMungo1383G2910' => 'vmu', 'Zm00001eb095270' => 'zma', 'Zm00001eb095280' => 'zma', 'Zm00001eb111630' => 'zma', 'Zm00001eb237080' => 'zma', 'Zm00001eb273740' => 'zma', 'Zm00001eb285040' => 'zma', 'Zm00001eb330790' => 'zma', 'Zm00001eb337380' => 'zma' ), 'gf_id' => 'HOM05D001484', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001484' ), 'data_identifier' => 'HOM05D001484', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001484', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p31500' => 'bna', 'A05p00020' => 'bna', 'A07p08820' => 'bna', 'Aa31LG4G3300' => 'aar', 'Aa31LG8G10030' => 'aar', 'Actinidia00731' => 'ach', 'Actinidia11473' => 'ach', 'Actinidia23469' => 'ach', 'Actinidia24318' => 'ach', 'Actinidia40196' => 'ach', 'Actinidia40197' => 'ach', 'Actinidia40198' => 'ach', 'Ah.08g212990' => 'amhyb', 'Ah.15g091720' => 'amhyb', 'AL3G38260' => 'aly', 'AL4G47710' => 'aly', 'Aqoxy2G00671' => 'aox', 'Aqoxy2G03236' => 'aox', 'arahy.Tifrunner.gnm1.ann1.05IDCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KR684' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATY3SJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK6QJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6APGL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IDT7Z9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM073U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ0R87' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LE7RV4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT4QRX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V5ENPK' => 'arhy', 'AT2G48110' => 'ath', 'AT3G23590' => 'ath', 'ATR0626G186' => 'atr', 'ATR1127G141' => 'atr', 'Atru.chr4.2583' => 'acertr', 'Atru.chr5.1358' => 'acertr', 'Atru.chr5.1359' => 'acertr', 'Atru.chr8.46' => 'acertr', 'AUR62002640' => 'cqu', 'AUR62030055' => 'cqu', 'AUR62033713' => 'cqu', 'AUR62033714' => 'cqu', 'AUR62036795' => 'cqu', 'AUR62039891' => 'cqu', 'BcaB02g08737' => 'bca', 'BcaB04g20441' => 'bca', 'BcaB06g26509' => 'bca', 'BcaB06g26510' => 'bca', 'BcaB06g26511' => 'bca', 'BcaB06g26512' => 'bca', 'BcaB06g26513' => 'bca', 'BcaC02g12564' => 'bca', 'BcaC02g12565' => 'bca', 'BcaC02g12794' => 'bca', 'BcaC02g12795' => 'bca', 'BcaC02g12796' => 'bca', 'BcaC06g35541' => 'bca', 'BNapus_Darmor_BZH_scaffold_188p00080' => 'bna', 'BNapus_Darmor_BZH_scaffold_188p00090' => 'bna', 'BolC1t03972H' => 'bol', 'BolC1t03973H' => 'bol', 'BolC4t21680H' => 'bol', 'BolC7t41863H' => 'bol', 'BolSC55t61227H' => 'bol', 'BolSC55t61228H' => 'bol', 'BraA01t03278Z' => 'bra', 'BraA05t18998Z' => 'bra', 'BraA07t28673Z' => 'bra', 'C01p40150' => 'bna', 'C05p12370' => 'bna', 'C07p13680' => 'bna', 'CAN.G1006.16' => 'can', 'CAN.G1006.17' => 'can', 'CAN.G1170.2' => 'can', 'CAN.G962.7' => 'can', 'CANSAT25G2179' => 'cansat', 'CANSAT78G1573' => 'cansat', 'CARHR099510' => 'chi', 'CARHR143510' => 'chi', 'Carub.0003s2380' => 'cru', 'Carub.0004s3082' => 'cru', 'Ca_00614_v3' => 'car', 'Ca_07801_v3' => 'car', 'Ca_08567_v3' => 'car', 'Ca_09571_v3' => 'car', 'CBR_g19290' => 'cbr', 'Cc01_g19770' => 'ccan', 'Cc03_g03030' => 'ccan', 'CDE07G0968' => 'cde', 'CDE09G1441' => 'cde', 'Cfa006103' => 'cfa', 'Cfa015573' => 'cfa', 'Cfa016988' => 'cfa', 'Ciclev10006738m.g' => 'ccl', 'Ciclev10010920m.g' => 'ccl', 'Ciclev10018517m.g' => 'ccl', 'CiPaw.01G159200' => 'cil', 'CiPaw.02G091000' => 'cil', 'CiPaw.02G091100' => 'cil', 'CiPaw.08G103100' => 'cil', 'CiPaw.09G224900' => 'cil', 'ClCG06G005740' => 'cla', 'ClCG07G000090' => 'cla', 'ClCG07G000100' => 'cla', 'COL.COLO4_09143' => 'col', 'COL.COLO4_25124' => 'col', 'Cpa.g.sc16.34' => 'cpa', 'Cpa.g.sc3504.1' => 'cpa', 'Cpa.g.sc60.37' => 'cpa', 'CsaV3_6G018520' => 'csa', 'CsaV3_6G036860' => 'csa', 'CSS0001072' => 'camsi', 'CSS0020208' => 'camsi', 'CSS0021253' => 'camsi', 'CSS0022190' => 'camsi', 'CSS0036150' => 'camsi', 'CSS0040442' => 'camsi', 'CSS0042300' => 'camsi', 'CSS0045298' => 'camsi', 'DCAR_012449' => 'dca', 'DCAR_018405' => 'dca', 'DCAR_024573' => 'dca', 'DCAR_030591' => 'dca', 'Dinv16926' => 'din', 'Dinv32963' => 'din', 'Dinv38382' => 'din', 'Dinv38383' => 'din', 'Duzib133G0974' => 'dzi', 'Duzib138G1867' => 'dzi', 'Duzib211G0420' => 'dzi', 'Duzib212G0930' => 'dzi', 'ECA234G1645' => 'eca', 'ECA247G3467' => 'eca', 'ECA248G1703' => 'eca', 'EL10Ac3g06327' => 'bvu', 'EL10Ac7g17204' => 'bvu', 'Eucgr.A00855' => 'egr', 'Eucgr.A00858' => 'egr', 'Eucgr.H01520' => 'egr', 'Eucgr.H03604' => 'egr', 'Eucgr.L03465' => 'egr', 'Eucgr.L03466' => 'egr', 'FAN01G0988' => 'fan', 'FAN02G3892' => 'fan', 'FAN05G3381' => 'fan', 'FAN07G0967' => 'fan', 'FAN07G1493' => 'fan', 'FAN08G3125' => 'fan', 'FAN09G0402' => 'fan', 'FAN12G2594' => 'fan', 'FAN12G3879' => 'fan', 'FAN14G1546' => 'fan', 'FAN15G3626' => 'fan', 'FAN17G0588' => 'fan', 'FAN17G0609' => 'fan', 'FAN18G2817' => 'fan', 'FAN19G1305' => 'fan', 'FAN20G1787' => 'fan', 'FAN22G0073' => 'fan', 'FAN22G0352' => 'fan', 'FAN22G0368' => 'fan', 'FAN22G2273' => 'fan', 'FAN24G1998' => 'fan', 'FAN27G1317' => 'fan', 'FvH4_2g23980' => 'fve', 'FvH4_4g14380' => 'fve', 'FvH4_4g14390' => 'fve', 'FvH4_6g09250' => 'fve', 'Glyma.03G151100' => 'gma', 'Glyma.04G122550' => 'gma', 'Glyma.05G001600' => 'gma', 'Glyma.09G270766' => 'gma', 'Glyma.09G270832' => 'gma', 'Glyma.13G209800' => 'gma', 'Glyma.15G102800' => 'gma', 'Glyma.18G218900' => 'gma', 'Glyma.19G001500' => 'gma', 'Glyma.19G153600' => 'gma', 'Gohir.A02G028600' => 'ghi', 'Gohir.A08G045000' => 'ghi', 'Gohir.A11G120500' => 'ghi', 'Gohir.A12G006200' => 'ghi', 'Gohir.A12G006250' => 'ghi', 'Gohir.D02G036300' => 'ghi', 'Gohir.D08G054700' => 'ghi', 'Gohir.D11G125600' => 'ghi', 'Gohir.D12G005700' => 'ghi', 'Gorai.004G055200' => 'gra', 'Gorai.005G040400' => 'gra', 'Gorai.007G134500' => 'gra', 'Gorai.008G005500' => 'gra', 'GSVIVG01011094001' => 'vvi', 'GSVIVG01017879001' => 'vvi', 'GSVIVG01025988001' => 'vvi', 'GSVIVG01029847001' => 'vvi', 'HanXRQChr10g0282901' => 'han', 'HanXRQChr10g0310371' => 'han', 'HanXRQChr10g0315041' => 'han', 'HanXRQChr11g0327651' => 'han', 'HanXRQChr12g0359391' => 'han', 'Haze_00972' => 'cav', 'Haze_00973' => 'cav', 'Haze_00974' => 'cav', 'Haze_04747' => 'cav', 'Haze_04749' => 'cav', 'Haze_04750' => 'cav', 'Haze_21217' => 'cav', 'Hma1.2p1_1037F.1_g250680' => 'hma', 'Hma1.2p1_1644F.1_g295320' => 'hma', 'HPP92_011322' => 'vpl', 'HPP92_011323' => 'vpl', 'HPP92_011324' => 'vpl', 'HPP92_011325' => 'vpl', 'HPP92_011326' => 'vpl', 'Hund12205' => 'sun', 'Hund17957' => 'sun', 'Lalb_Chr06g0176771' => 'lal', 'Lalb_Chr18g0056021' => 'lal', 'Lalb_Chr18g0056031' => 'lal', 'Lalb_Chr18g0056041' => 'lal', 'Lalb_Chr20g0107751' => 'lal', 'Lalb_Chr20g0118371' => 'lal', 'Lj1g0010239' => 'lja', 'Lj1g0017101' => 'lja', 'Lj2A1178G40' => 'lonja', 'Lj2A54G84' => 'lonja', 'Lj2g0015248' => 'lja', 'Lj3A761T51' => 'lonja', 'Lj6g0018116' => 'lja', 'Lsat_1_v5_gn_4_136040' => 'lsa', 'Lsat_1_v5_gn_5_187461' => 'lsa', 'Lsat_1_v5_gn_5_77001' => 'lsa', 'Lsat_1_v5_gn_9_4461' => 'lsa', 'Manes.01G210100' => 'mes', 'Manes.03G185600' => 'mes', 'Manes.05G073300' => 'mes', 'Manes.09G120300' => 'mes', 'Manes.15G022100' => 'mes', 'Mapoly0096s0053' => 'mpo', 'MBI03_g14058_MAGBIO' => 'mbi', 'MBI03_g33876_MAGBIO' => 'mbi', 'MBI03_g36854_MAGBIO' => 'mbi', 'MBI17_g11997_MAGBIO' => 'mbi', 'MD03G1269000' => 'mdo', 'MD04G1179600' => 'mdo', 'MD11G1289800' => 'mdo', 'MD12G1194700' => 'mdo', 'MD13G1182100' => 'mdo', 'MD13G1182200' => 'mdo', 'MD16G1182600' => 'mdo', 'Medtr2g021400' => 'mtr', 'Medtr2g021470' => 'mtr', 'Medtr2g105810' => 'mtr', 'Medtr3g033580' => 'mtr', 'Medtr6g007970' => 'mtr', 'Medtr7g056330' => 'mtr', 'Medtr7g074290' => 'mtr', 'Medtr7g074380' => 'mtr', 'Medtr7g094550' => 'mtr', 'Medtr8g069995' => 'mtr', 'MELO3C014345.2' => 'cme', 'MELO3C021395.2' => 'cme', 'Migut.D00262' => 'egut', 'Migut.G00257' => 'egut', 'MSTRG.21575' => 'ama', 'MSTRG.3985' => 'ama', 'Nitab4.5_0000295g0140' => 'nta', 'Nitab4.5_0000732g0140' => 'nta', 'Nitab4.5_0003162g0020' => 'nta', 'Nitab4.5_0006180g0090' => 'nta', 'Nitab4.5_0006390g0010' => 'nta', 'Nitab4.5_0007392g0040' => 'nta', 'Nn1g02140' => 'nnu', 'Nn4g26168' => 'nnu', 'Nn5g26754' => 'nnu', 'Oeu001433.1' => 'oeu', 'Oeu010299.2' => 'oeu', 'Oeu011171.1' => 'oeu', 'Oeu037675.1' => 'oeu', 'Oeu038359.1' => 'oeu', 'Oeu063834.1' => 'oeu', 'Oeu063835.1' => 'oeu', 'Os05g0312000' => 'osa', 'Os07g0211101' => 'osa', 'Os07g0211200' => 'osa', 'Os07g0681500' => 'osa', 'Peaxi162Scf00095g01015' => 'pax', 'Peaxi162Scf00104g00329' => 'pax', 'Peaxi162Scf00161g00137' => 'pax', 'PGR004G1665' => 'pgr', 'PGR031G2937' => 'pgr', 'PGR119G2145' => 'pgr', 'PGSC0003DMG400004351' => 'stu', 'PGSC0003DMG400014625' => 'stu', 'PGSC0003DMG401000943' => 'stu', 'Phvul.001G148600' => 'pvu', 'Phvul.004G001700' => 'pvu', 'Phvul.006G154900' => 'pvu', 'Phvul.008G078200' => 'pvu', 'Phvul.011G136500' => 'pvu', 'Potri.002G215600' => 'ptr', 'Potri.008G201600' => 'ptr', 'Potri.014G138400' => 'ptr', 'Potri.016G142500' => 'ptr', 'Pp3c16_10580' => 'ppa', 'Pp3c5_25280' => 'ppa', 'Prupe.1G150000' => 'ppe', 'Prupe.1G150100' => 'ppe', 'Prupe.6G299600' => 'ppe', 'Prupe.8G245000' => 'ppe', 'Psat0s4927g0040' => 'psa', 'Psat1g052080' => 'psa', 'Psat1g183800' => 'psa', 'Psat3g113840' => 'psa', 'Psat3g126120' => 'psa', 'Psat3g126160' => 'psa', 'Psat3g158760' => 'psa', 'Psat3g158840' => 'psa', 'PSO170G2858' => 'pso', 'PSO339G0606' => 'pso', 'PSO384G4709' => 'pso', 'PSO407G0334' => 'pso', 'QL04p040276' => 'qlo', 'QL06p005458' => 'qlo', 'QL06p005472' => 'qlo', 'QL07p030546' => 'qlo', 'QL07p031519' => 'qlo', 'QL09p050949' => 'qlo', 'QL09p050966' => 'qlo', 'QL09p051067' => 'qlo', 'QL12p022706' => 'qlo', 'RcHm_v2.0_Chr2g0119601' => 'rch', 'RcHm_v2.0_Chr3g0459591' => 'rch', 'RcHm_v2.0_Chr4g0418521' => 'rch', 'RcHm_v2.0_Chr4g0418531' => 'rch', 'RcHm_v2.0_Chr4g0418541' => 'rch', 'RcHm_v2.0_Chr6g0291641' => 'rch', 'Rhsim01G0086300' => 'rsi', 'Rhsim01G0276300' => 'rsi', 'Rhsim01G0276500' => 'rsi', 'Rhsim04G0207700' => 'rsi', 'Rhsim05G0234500' => 'rsi', 'Rhsim13G0022400' => 'rsi', 'Sabra02G0167900' => 'sbr', 'Sabra04G0158500' => 'sbr', 'Sabra08G0159800' => 'sbr', 'Sabra10G0011500' => 'sbr', 'Sabra14G0104400' => 'sbr', 'SalBow2G2440' => 'sbo', 'SalBow4G2265' => 'sbo', 'Sc02g0000060' => 'sci', 'Sc05g0005020' => 'sci', 'Sc13g0003890' => 'sci', 'Sed0014865' => 'sed', 'Sed0017224' => 'sed', 'Sed0026391' => 'sed', 'SEGI_00063' => 'sgi', 'SEGI_10967' => 'sgi', 'SEGI_17510' => 'sgi', 'SEGI_24396' => 'sgi', 'SEGI_39719' => 'sgi', 'SEGI_41392' => 'sgi', 'SGA_v2.0_scaffold11G05794' => 'sas', 'SGA_v2.0_scaffold142G35607' => 'sas', 'SGA_v2.0_scaffold1G00447' => 'sas', 'SHI15388' => 'shi', 'SHI15394' => 'shi', 'SHI15396' => 'shi', 'SHI15399' => 'shi', 'SMO343G0151' => 'smo', 'SMO367G1118' => 'smo', 'Solyc01g080200.3' => 'sly', 'Solyc06g008960.3' => 'sly', 'Solyc09g064780.3' => 'sly', 'Sopen01g031980' => 'spe', 'Sopen06g003710' => 'spe', 'Sopen09g026460' => 'spe', 'Sp3g21240' => 'spa', 'Sp4g30030' => 'spa', 'TAR365G0022' => 'tar', 'TAR365G1023' => 'tar', 'TAR365G1253' => 'tar', 'TAR623G0078' => 'tar', 'TAR623G1721' => 'tar', 'TAR633G0959' => 'tar', 'THA.LOC104802225' => 'tha', 'THA.LOC104804769' => 'tha', 'THA.LOC104808660' => 'tha', 'THA.LOC104812792' => 'tha', 'Thecc.01G284000' => 'tca', 'Thecc.04G220600' => 'tca', 'Thecc.05G268900' => 'tca', 'Thecc.08G171100' => 'tca', 'Thhalv10001284m.g' => 'esa', 'Thhalv10019912m.g' => 'esa', 'TPR.G14189' => 'tpr', 'TPR.G18110' => 'tpr', 'TPR.G18130' => 'tpr', 'TPR.G18131' => 'tpr', 'TPR.G18140' => 'tpr', 'TPR.G24282' => 'tpr', 'TPR.G25221' => 'tpr', 'TPR.G29267' => 'tpr', 'TPR.G35315' => 'tpr', 'TPR.G36173' => 'tpr', 'TWI09G0794' => 'twi', 'TWI59G1348' => 'twi', 'TWI74G0430' => 'twi', 'unitig_26.g8940' => 'ugi', 'unitig_749.g13744' => 'ugi', 'unitig_749.g13745' => 'ugi', 'vmacro08269' => 'vma', 'vmacro14937' => 'vma', 'vmacro20401' => 'vma', 'VMungo0464G1349' => 'vmu', 'VMungo0540G0289' => 'vmu', 'VMungo1215G1590' => 'vmu', 'VMungo1309G0221' => 'vmu', 'VMungo1309G2815' => 'vmu', 'VMungo1383G0239' => 'vmu', 'VMungo1383G2910' => 'vmu', 'Zm00001eb095270' => 'zma', 'Zm00001eb095280' => 'zma', 'Zm00001eb111630' => 'zma', 'Zm00001eb237080' => 'zma', 'Zm00001eb273740' => 'zma', 'Zm00001eb285040' => 'zma', 'Zm00001eb330790' => 'zma', 'Zm00001eb337380' => 'zma' ) $gf_id = 'HOM05D001484' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001484' ) $data_identifier = 'HOM05D001484' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 2, 'aly' => (int) 2, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 22, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 7, 'hma' => (int) 2, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 7, 'mtr' => (int) 10, 'cme' => (int) 2, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 4, 'ppa' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 4, 'qlo' => (int) 9, 'rch' => (int) 6, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 10, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 7, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb337380' $species_info = array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ) $local_species = 'cbr' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001484', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p31500' => 'bna', 'A05p00020' => 'bna', 'A07p08820' => 'bna', 'Aa31LG4G3300' => 'aar', 'Aa31LG8G10030' => 'aar', 'Actinidia00731' => 'ach', 'Actinidia11473' => 'ach', 'Actinidia23469' => 'ach', 'Actinidia24318' => 'ach', 'Actinidia40196' => 'ach', 'Actinidia40197' => 'ach', 'Actinidia40198' => 'ach', 'Ah.08g212990' => 'amhyb', 'Ah.15g091720' => 'amhyb', 'AL3G38260' => 'aly', 'AL4G47710' => 'aly', 'Aqoxy2G00671' => 'aox', 'Aqoxy2G03236' => 'aox', 'arahy.Tifrunner.gnm1.ann1.05IDCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KR684' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATY3SJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK6QJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6APGL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IDT7Z9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM073U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ0R87' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LE7RV4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT4QRX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V5ENPK' => 'arhy', 'AT2G48110' => 'ath', 'AT3G23590' => 'ath', 'ATR0626G186' => 'atr', 'ATR1127G141' => 'atr', 'Atru.chr4.2583' => 'acertr', 'Atru.chr5.1358' => 'acertr', 'Atru.chr5.1359' => 'acertr', 'Atru.chr8.46' => 'acertr', 'AUR62002640' => 'cqu', 'AUR62030055' => 'cqu', 'AUR62033713' => 'cqu', 'AUR62033714' => 'cqu', 'AUR62036795' => 'cqu', 'AUR62039891' => 'cqu', 'BcaB02g08737' => 'bca', 'BcaB04g20441' => 'bca', 'BcaB06g26509' => 'bca', 'BcaB06g26510' => 'bca', 'BcaB06g26511' => 'bca', 'BcaB06g26512' => 'bca', 'BcaB06g26513' => 'bca', 'BcaC02g12564' => 'bca', 'BcaC02g12565' => 'bca', 'BcaC02g12794' => 'bca', 'BcaC02g12795' => 'bca', 'BcaC02g12796' => 'bca', 'BcaC06g35541' => 'bca', 'BNapus_Darmor_BZH_scaffold_188p00080' => 'bna', 'BNapus_Darmor_BZH_scaffold_188p00090' => 'bna', 'BolC1t03972H' => 'bol', 'BolC1t03973H' => 'bol', 'BolC4t21680H' => 'bol', 'BolC7t41863H' => 'bol', 'BolSC55t61227H' => 'bol', 'BolSC55t61228H' => 'bol', 'BraA01t03278Z' => 'bra', 'BraA05t18998Z' => 'bra', 'BraA07t28673Z' => 'bra', 'C01p40150' => 'bna', 'C05p12370' => 'bna', 'C07p13680' => 'bna', 'CAN.G1006.16' => 'can', 'CAN.G1006.17' => 'can', 'CAN.G1170.2' => 'can', 'CAN.G962.7' => 'can', 'CANSAT25G2179' => 'cansat', 'CANSAT78G1573' => 'cansat', 'CARHR099510' => 'chi', 'CARHR143510' => 'chi', 'Carub.0003s2380' => 'cru', 'Carub.0004s3082' => 'cru', 'Ca_00614_v3' => 'car', 'Ca_07801_v3' => 'car', 'Ca_08567_v3' => 'car', 'Ca_09571_v3' => 'car', 'CBR_g19290' => 'cbr', 'Cc01_g19770' => 'ccan', 'Cc03_g03030' => 'ccan', 'CDE07G0968' => 'cde', 'CDE09G1441' => 'cde', 'Cfa006103' => 'cfa', 'Cfa015573' => 'cfa', 'Cfa016988' => 'cfa', 'Ciclev10006738m.g' => 'ccl', 'Ciclev10010920m.g' => 'ccl', 'Ciclev10018517m.g' => 'ccl', 'CiPaw.01G159200' => 'cil', 'CiPaw.02G091000' => 'cil', 'CiPaw.02G091100' => 'cil', 'CiPaw.08G103100' => 'cil', 'CiPaw.09G224900' => 'cil', 'ClCG06G005740' => 'cla', 'ClCG07G000090' => 'cla', 'ClCG07G000100' => 'cla', 'COL.COLO4_09143' => 'col', 'COL.COLO4_25124' => 'col', 'Cpa.g.sc16.34' => 'cpa', 'Cpa.g.sc3504.1' => 'cpa', 'Cpa.g.sc60.37' => 'cpa', 'CsaV3_6G018520' => 'csa', 'CsaV3_6G036860' => 'csa', 'CSS0001072' => 'camsi', 'CSS0020208' => 'camsi', 'CSS0021253' => 'camsi', 'CSS0022190' => 'camsi', 'CSS0036150' => 'camsi', 'CSS0040442' => 'camsi', 'CSS0042300' => 'camsi', 'CSS0045298' => 'camsi', 'DCAR_012449' => 'dca', 'DCAR_018405' => 'dca', 'DCAR_024573' => 'dca', 'DCAR_030591' => 'dca', 'Dinv16926' => 'din', 'Dinv32963' => 'din', 'Dinv38382' => 'din', 'Dinv38383' => 'din', 'Duzib133G0974' => 'dzi', 'Duzib138G1867' => 'dzi', 'Duzib211G0420' => 'dzi', 'Duzib212G0930' => 'dzi', 'ECA234G1645' => 'eca', 'ECA247G3467' => 'eca', 'ECA248G1703' => 'eca', 'EL10Ac3g06327' => 'bvu', 'EL10Ac7g17204' => 'bvu', 'Eucgr.A00855' => 'egr', 'Eucgr.A00858' => 'egr', 'Eucgr.H01520' => 'egr', 'Eucgr.H03604' => 'egr', 'Eucgr.L03465' => 'egr', 'Eucgr.L03466' => 'egr', 'FAN01G0988' => 'fan', 'FAN02G3892' => 'fan', 'FAN05G3381' => 'fan', 'FAN07G0967' => 'fan', 'FAN07G1493' => 'fan', 'FAN08G3125' => 'fan', 'FAN09G0402' => 'fan', 'FAN12G2594' => 'fan', 'FAN12G3879' => 'fan', 'FAN14G1546' => 'fan', 'FAN15G3626' => 'fan', 'FAN17G0588' => 'fan', 'FAN17G0609' => 'fan', 'FAN18G2817' => 'fan', 'FAN19G1305' => 'fan', 'FAN20G1787' => 'fan', 'FAN22G0073' => 'fan', 'FAN22G0352' => 'fan', 'FAN22G0368' => 'fan', 'FAN22G2273' => 'fan', 'FAN24G1998' => 'fan', 'FAN27G1317' => 'fan', 'FvH4_2g23980' => 'fve', 'FvH4_4g14380' => 'fve', 'FvH4_4g14390' => 'fve', 'FvH4_6g09250' => 'fve', 'Glyma.03G151100' => 'gma', 'Glyma.04G122550' => 'gma', 'Glyma.05G001600' => 'gma', 'Glyma.09G270766' => 'gma', 'Glyma.09G270832' => 'gma', 'Glyma.13G209800' => 'gma', 'Glyma.15G102800' => 'gma', 'Glyma.18G218900' => 'gma', 'Glyma.19G001500' => 'gma', 'Glyma.19G153600' => 'gma', 'Gohir.A02G028600' => 'ghi', 'Gohir.A08G045000' => 'ghi', 'Gohir.A11G120500' => 'ghi', 'Gohir.A12G006200' => 'ghi', 'Gohir.A12G006250' => 'ghi', 'Gohir.D02G036300' => 'ghi', 'Gohir.D08G054700' => 'ghi', 'Gohir.D11G125600' => 'ghi', 'Gohir.D12G005700' => 'ghi', 'Gorai.004G055200' => 'gra', 'Gorai.005G040400' => 'gra', 'Gorai.007G134500' => 'gra', 'Gorai.008G005500' => 'gra', 'GSVIVG01011094001' => 'vvi', 'GSVIVG01017879001' => 'vvi', 'GSVIVG01025988001' => 'vvi', 'GSVIVG01029847001' => 'vvi', 'HanXRQChr10g0282901' => 'han', 'HanXRQChr10g0310371' => 'han', 'HanXRQChr10g0315041' => 'han', 'HanXRQChr11g0327651' => 'han', 'HanXRQChr12g0359391' => 'han', 'Haze_00972' => 'cav', 'Haze_00973' => 'cav', 'Haze_00974' => 'cav', 'Haze_04747' => 'cav', 'Haze_04749' => 'cav', 'Haze_04750' => 'cav', 'Haze_21217' => 'cav', 'Hma1.2p1_1037F.1_g250680' => 'hma', 'Hma1.2p1_1644F.1_g295320' => 'hma', 'HPP92_011322' => 'vpl', 'HPP92_011323' => 'vpl', 'HPP92_011324' => 'vpl', 'HPP92_011325' => 'vpl', 'HPP92_011326' => 'vpl', 'Hund12205' => 'sun', 'Hund17957' => 'sun', 'Lalb_Chr06g0176771' => 'lal', 'Lalb_Chr18g0056021' => 'lal', 'Lalb_Chr18g0056031' => 'lal', 'Lalb_Chr18g0056041' => 'lal', 'Lalb_Chr20g0107751' => 'lal', 'Lalb_Chr20g0118371' => 'lal', 'Lj1g0010239' => 'lja', 'Lj1g0017101' => 'lja', 'Lj2A1178G40' => 'lonja', 'Lj2A54G84' => 'lonja', 'Lj2g0015248' => 'lja', 'Lj3A761T51' => 'lonja', 'Lj6g0018116' => 'lja', 'Lsat_1_v5_gn_4_136040' => 'lsa', 'Lsat_1_v5_gn_5_187461' => 'lsa', 'Lsat_1_v5_gn_5_77001' => 'lsa', 'Lsat_1_v5_gn_9_4461' => 'lsa', 'Manes.01G210100' => 'mes', 'Manes.03G185600' => 'mes', 'Manes.05G073300' => 'mes', 'Manes.09G120300' => 'mes', 'Manes.15G022100' => 'mes', 'Mapoly0096s0053' => 'mpo', 'MBI03_g14058_MAGBIO' => 'mbi', 'MBI03_g33876_MAGBIO' => 'mbi', 'MBI03_g36854_MAGBIO' => 'mbi', 'MBI17_g11997_MAGBIO' => 'mbi', 'MD03G1269000' => 'mdo', 'MD04G1179600' => 'mdo', 'MD11G1289800' => 'mdo', 'MD12G1194700' => 'mdo', 'MD13G1182100' => 'mdo', 'MD13G1182200' => 'mdo', 'MD16G1182600' => 'mdo', 'Medtr2g021400' => 'mtr', 'Medtr2g021470' => 'mtr', 'Medtr2g105810' => 'mtr', 'Medtr3g033580' => 'mtr', 'Medtr6g007970' => 'mtr', 'Medtr7g056330' => 'mtr', 'Medtr7g074290' => 'mtr', 'Medtr7g074380' => 'mtr', 'Medtr7g094550' => 'mtr', 'Medtr8g069995' => 'mtr', 'MELO3C014345.2' => 'cme', 'MELO3C021395.2' => 'cme', 'Migut.D00262' => 'egut', 'Migut.G00257' => 'egut', 'MSTRG.21575' => 'ama', 'MSTRG.3985' => 'ama', 'Nitab4.5_0000295g0140' => 'nta', 'Nitab4.5_0000732g0140' => 'nta', 'Nitab4.5_0003162g0020' => 'nta', 'Nitab4.5_0006180g0090' => 'nta', 'Nitab4.5_0006390g0010' => 'nta', 'Nitab4.5_0007392g0040' => 'nta', 'Nn1g02140' => 'nnu', 'Nn4g26168' => 'nnu', 'Nn5g26754' => 'nnu', 'Oeu001433.1' => 'oeu', 'Oeu010299.2' => 'oeu', 'Oeu011171.1' => 'oeu', 'Oeu037675.1' => 'oeu', 'Oeu038359.1' => 'oeu', 'Oeu063834.1' => 'oeu', 'Oeu063835.1' => 'oeu', 'Os05g0312000' => 'osa', 'Os07g0211101' => 'osa', 'Os07g0211200' => 'osa', 'Os07g0681500' => 'osa', 'Peaxi162Scf00095g01015' => 'pax', 'Peaxi162Scf00104g00329' => 'pax', 'Peaxi162Scf00161g00137' => 'pax', 'PGR004G1665' => 'pgr', 'PGR031G2937' => 'pgr', 'PGR119G2145' => 'pgr', 'PGSC0003DMG400004351' => 'stu', 'PGSC0003DMG400014625' => 'stu', 'PGSC0003DMG401000943' => 'stu', 'Phvul.001G148600' => 'pvu', 'Phvul.004G001700' => 'pvu', 'Phvul.006G154900' => 'pvu', 'Phvul.008G078200' => 'pvu', 'Phvul.011G136500' => 'pvu', 'Potri.002G215600' => 'ptr', 'Potri.008G201600' => 'ptr', 'Potri.014G138400' => 'ptr', 'Potri.016G142500' => 'ptr', 'Pp3c16_10580' => 'ppa', 'Pp3c5_25280' => 'ppa', 'Prupe.1G150000' => 'ppe', 'Prupe.1G150100' => 'ppe', 'Prupe.6G299600' => 'ppe', 'Prupe.8G245000' => 'ppe', 'Psat0s4927g0040' => 'psa', 'Psat1g052080' => 'psa', 'Psat1g183800' => 'psa', 'Psat3g113840' => 'psa', 'Psat3g126120' => 'psa', 'Psat3g126160' => 'psa', 'Psat3g158760' => 'psa', 'Psat3g158840' => 'psa', 'PSO170G2858' => 'pso', 'PSO339G0606' => 'pso', 'PSO384G4709' => 'pso', 'PSO407G0334' => 'pso', 'QL04p040276' => 'qlo', 'QL06p005458' => 'qlo', 'QL06p005472' => 'qlo', 'QL07p030546' => 'qlo', 'QL07p031519' => 'qlo', 'QL09p050949' => 'qlo', 'QL09p050966' => 'qlo', 'QL09p051067' => 'qlo', 'QL12p022706' => 'qlo', 'RcHm_v2.0_Chr2g0119601' => 'rch', 'RcHm_v2.0_Chr3g0459591' => 'rch', 'RcHm_v2.0_Chr4g0418521' => 'rch', 'RcHm_v2.0_Chr4g0418531' => 'rch', 'RcHm_v2.0_Chr4g0418541' => 'rch', 'RcHm_v2.0_Chr6g0291641' => 'rch', 'Rhsim01G0086300' => 'rsi', 'Rhsim01G0276300' => 'rsi', 'Rhsim01G0276500' => 'rsi', 'Rhsim04G0207700' => 'rsi', 'Rhsim05G0234500' => 'rsi', 'Rhsim13G0022400' => 'rsi', 'Sabra02G0167900' => 'sbr', 'Sabra04G0158500' => 'sbr', 'Sabra08G0159800' => 'sbr', 'Sabra10G0011500' => 'sbr', 'Sabra14G0104400' => 'sbr', 'SalBow2G2440' => 'sbo', 'SalBow4G2265' => 'sbo', 'Sc02g0000060' => 'sci', 'Sc05g0005020' => 'sci', 'Sc13g0003890' => 'sci', 'Sed0014865' => 'sed', 'Sed0017224' => 'sed', 'Sed0026391' => 'sed', 'SEGI_00063' => 'sgi', 'SEGI_10967' => 'sgi', 'SEGI_17510' => 'sgi', 'SEGI_24396' => 'sgi', 'SEGI_39719' => 'sgi', 'SEGI_41392' => 'sgi', 'SGA_v2.0_scaffold11G05794' => 'sas', 'SGA_v2.0_scaffold142G35607' => 'sas', 'SGA_v2.0_scaffold1G00447' => 'sas', 'SHI15388' => 'shi', 'SHI15394' => 'shi', 'SHI15396' => 'shi', 'SHI15399' => 'shi', 'SMO343G0151' => 'smo', 'SMO367G1118' => 'smo', 'Solyc01g080200.3' => 'sly', 'Solyc06g008960.3' => 'sly', 'Solyc09g064780.3' => 'sly', 'Sopen01g031980' => 'spe', 'Sopen06g003710' => 'spe', 'Sopen09g026460' => 'spe', 'Sp3g21240' => 'spa', 'Sp4g30030' => 'spa', 'TAR365G0022' => 'tar', 'TAR365G1023' => 'tar', 'TAR365G1253' => 'tar', 'TAR623G0078' => 'tar', 'TAR623G1721' => 'tar', 'TAR633G0959' => 'tar', 'THA.LOC104802225' => 'tha', 'THA.LOC104804769' => 'tha', 'THA.LOC104808660' => 'tha', 'THA.LOC104812792' => 'tha', 'Thecc.01G284000' => 'tca', 'Thecc.04G220600' => 'tca', 'Thecc.05G268900' => 'tca', 'Thecc.08G171100' => 'tca', 'Thhalv10001284m.g' => 'esa', 'Thhalv10019912m.g' => 'esa', 'TPR.G14189' => 'tpr', 'TPR.G18110' => 'tpr', 'TPR.G18130' => 'tpr', 'TPR.G18131' => 'tpr', 'TPR.G18140' => 'tpr', 'TPR.G24282' => 'tpr', 'TPR.G25221' => 'tpr', 'TPR.G29267' => 'tpr', 'TPR.G35315' => 'tpr', 'TPR.G36173' => 'tpr', 'TWI09G0794' => 'twi', 'TWI59G1348' => 'twi', 'TWI74G0430' => 'twi', 'unitig_26.g8940' => 'ugi', 'unitig_749.g13744' => 'ugi', 'unitig_749.g13745' => 'ugi', 'vmacro08269' => 'vma', 'vmacro14937' => 'vma', 'vmacro20401' => 'vma', 'VMungo0464G1349' => 'vmu', 'VMungo0540G0289' => 'vmu', 'VMungo1215G1590' => 'vmu', 'VMungo1309G0221' => 'vmu', 'VMungo1309G2815' => 'vmu', 'VMungo1383G0239' => 'vmu', 'VMungo1383G2910' => 'vmu', 'Zm00001eb095270' => 'zma', 'Zm00001eb095280' => 'zma', 'Zm00001eb111630' => 'zma', 'Zm00001eb237080' => 'zma', 'Zm00001eb273740' => 'zma', 'Zm00001eb285040' => 'zma', 'Zm00001eb330790' => 'zma', 'Zm00001eb337380' => 'zma' ), 'gf_id' => 'HOM05D001484', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001484' ), 'data_identifier' => 'HOM05D001484', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001484', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p31500' => 'bna', 'A05p00020' => 'bna', 'A07p08820' => 'bna', 'Aa31LG4G3300' => 'aar', 'Aa31LG8G10030' => 'aar', 'Actinidia00731' => 'ach', 'Actinidia11473' => 'ach', 'Actinidia23469' => 'ach', 'Actinidia24318' => 'ach', 'Actinidia40196' => 'ach', 'Actinidia40197' => 'ach', 'Actinidia40198' => 'ach', 'Ah.08g212990' => 'amhyb', 'Ah.15g091720' => 'amhyb', 'AL3G38260' => 'aly', 'AL4G47710' => 'aly', 'Aqoxy2G00671' => 'aox', 'Aqoxy2G03236' => 'aox', 'arahy.Tifrunner.gnm1.ann1.05IDCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KR684' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATY3SJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK6QJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6APGL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IDT7Z9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM073U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ0R87' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LE7RV4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT4QRX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V5ENPK' => 'arhy', 'AT2G48110' => 'ath', 'AT3G23590' => 'ath', 'ATR0626G186' => 'atr', 'ATR1127G141' => 'atr', 'Atru.chr4.2583' => 'acertr', 'Atru.chr5.1358' => 'acertr', 'Atru.chr5.1359' => 'acertr', 'Atru.chr8.46' => 'acertr', 'AUR62002640' => 'cqu', 'AUR62030055' => 'cqu', 'AUR62033713' => 'cqu', 'AUR62033714' => 'cqu', 'AUR62036795' => 'cqu', 'AUR62039891' => 'cqu', 'BcaB02g08737' => 'bca', 'BcaB04g20441' => 'bca', 'BcaB06g26509' => 'bca', 'BcaB06g26510' => 'bca', 'BcaB06g26511' => 'bca', 'BcaB06g26512' => 'bca', 'BcaB06g26513' => 'bca', 'BcaC02g12564' => 'bca', 'BcaC02g12565' => 'bca', 'BcaC02g12794' => 'bca', 'BcaC02g12795' => 'bca', 'BcaC02g12796' => 'bca', 'BcaC06g35541' => 'bca', 'BNapus_Darmor_BZH_scaffold_188p00080' => 'bna', 'BNapus_Darmor_BZH_scaffold_188p00090' => 'bna', 'BolC1t03972H' => 'bol', 'BolC1t03973H' => 'bol', 'BolC4t21680H' => 'bol', 'BolC7t41863H' => 'bol', 'BolSC55t61227H' => 'bol', 'BolSC55t61228H' => 'bol', 'BraA01t03278Z' => 'bra', 'BraA05t18998Z' => 'bra', 'BraA07t28673Z' => 'bra', 'C01p40150' => 'bna', 'C05p12370' => 'bna', 'C07p13680' => 'bna', 'CAN.G1006.16' => 'can', 'CAN.G1006.17' => 'can', 'CAN.G1170.2' => 'can', 'CAN.G962.7' => 'can', 'CANSAT25G2179' => 'cansat', 'CANSAT78G1573' => 'cansat', 'CARHR099510' => 'chi', 'CARHR143510' => 'chi', 'Carub.0003s2380' => 'cru', 'Carub.0004s3082' => 'cru', 'Ca_00614_v3' => 'car', 'Ca_07801_v3' => 'car', 'Ca_08567_v3' => 'car', 'Ca_09571_v3' => 'car', 'CBR_g19290' => 'cbr', 'Cc01_g19770' => 'ccan', 'Cc03_g03030' => 'ccan', 'CDE07G0968' => 'cde', 'CDE09G1441' => 'cde', 'Cfa006103' => 'cfa', 'Cfa015573' => 'cfa', 'Cfa016988' => 'cfa', 'Ciclev10006738m.g' => 'ccl', 'Ciclev10010920m.g' => 'ccl', 'Ciclev10018517m.g' => 'ccl', 'CiPaw.01G159200' => 'cil', 'CiPaw.02G091000' => 'cil', 'CiPaw.02G091100' => 'cil', 'CiPaw.08G103100' => 'cil', 'CiPaw.09G224900' => 'cil', 'ClCG06G005740' => 'cla', 'ClCG07G000090' => 'cla', 'ClCG07G000100' => 'cla', 'COL.COLO4_09143' => 'col', 'COL.COLO4_25124' => 'col', 'Cpa.g.sc16.34' => 'cpa', 'Cpa.g.sc3504.1' => 'cpa', 'Cpa.g.sc60.37' => 'cpa', 'CsaV3_6G018520' => 'csa', 'CsaV3_6G036860' => 'csa', 'CSS0001072' => 'camsi', 'CSS0020208' => 'camsi', 'CSS0021253' => 'camsi', 'CSS0022190' => 'camsi', 'CSS0036150' => 'camsi', 'CSS0040442' => 'camsi', 'CSS0042300' => 'camsi', 'CSS0045298' => 'camsi', 'DCAR_012449' => 'dca', 'DCAR_018405' => 'dca', 'DCAR_024573' => 'dca', 'DCAR_030591' => 'dca', 'Dinv16926' => 'din', 'Dinv32963' => 'din', 'Dinv38382' => 'din', 'Dinv38383' => 'din', 'Duzib133G0974' => 'dzi', 'Duzib138G1867' => 'dzi', 'Duzib211G0420' => 'dzi', 'Duzib212G0930' => 'dzi', 'ECA234G1645' => 'eca', 'ECA247G3467' => 'eca', 'ECA248G1703' => 'eca', 'EL10Ac3g06327' => 'bvu', 'EL10Ac7g17204' => 'bvu', 'Eucgr.A00855' => 'egr', 'Eucgr.A00858' => 'egr', 'Eucgr.H01520' => 'egr', 'Eucgr.H03604' => 'egr', 'Eucgr.L03465' => 'egr', 'Eucgr.L03466' => 'egr', 'FAN01G0988' => 'fan', 'FAN02G3892' => 'fan', 'FAN05G3381' => 'fan', 'FAN07G0967' => 'fan', 'FAN07G1493' => 'fan', 'FAN08G3125' => 'fan', 'FAN09G0402' => 'fan', 'FAN12G2594' => 'fan', 'FAN12G3879' => 'fan', 'FAN14G1546' => 'fan', 'FAN15G3626' => 'fan', 'FAN17G0588' => 'fan', 'FAN17G0609' => 'fan', 'FAN18G2817' => 'fan', 'FAN19G1305' => 'fan', 'FAN20G1787' => 'fan', 'FAN22G0073' => 'fan', 'FAN22G0352' => 'fan', 'FAN22G0368' => 'fan', 'FAN22G2273' => 'fan', 'FAN24G1998' => 'fan', 'FAN27G1317' => 'fan', 'FvH4_2g23980' => 'fve', 'FvH4_4g14380' => 'fve', 'FvH4_4g14390' => 'fve', 'FvH4_6g09250' => 'fve', 'Glyma.03G151100' => 'gma', 'Glyma.04G122550' => 'gma', 'Glyma.05G001600' => 'gma', 'Glyma.09G270766' => 'gma', 'Glyma.09G270832' => 'gma', 'Glyma.13G209800' => 'gma', 'Glyma.15G102800' => 'gma', 'Glyma.18G218900' => 'gma', 'Glyma.19G001500' => 'gma', 'Glyma.19G153600' => 'gma', 'Gohir.A02G028600' => 'ghi', 'Gohir.A08G045000' => 'ghi', 'Gohir.A11G120500' => 'ghi', 'Gohir.A12G006200' => 'ghi', 'Gohir.A12G006250' => 'ghi', 'Gohir.D02G036300' => 'ghi', 'Gohir.D08G054700' => 'ghi', 'Gohir.D11G125600' => 'ghi', 'Gohir.D12G005700' => 'ghi', 'Gorai.004G055200' => 'gra', 'Gorai.005G040400' => 'gra', 'Gorai.007G134500' => 'gra', 'Gorai.008G005500' => 'gra', 'GSVIVG01011094001' => 'vvi', 'GSVIVG01017879001' => 'vvi', 'GSVIVG01025988001' => 'vvi', 'GSVIVG01029847001' => 'vvi', 'HanXRQChr10g0282901' => 'han', 'HanXRQChr10g0310371' => 'han', 'HanXRQChr10g0315041' => 'han', 'HanXRQChr11g0327651' => 'han', 'HanXRQChr12g0359391' => 'han', 'Haze_00972' => 'cav', 'Haze_00973' => 'cav', 'Haze_00974' => 'cav', 'Haze_04747' => 'cav', 'Haze_04749' => 'cav', 'Haze_04750' => 'cav', 'Haze_21217' => 'cav', 'Hma1.2p1_1037F.1_g250680' => 'hma', 'Hma1.2p1_1644F.1_g295320' => 'hma', 'HPP92_011322' => 'vpl', 'HPP92_011323' => 'vpl', 'HPP92_011324' => 'vpl', 'HPP92_011325' => 'vpl', 'HPP92_011326' => 'vpl', 'Hund12205' => 'sun', 'Hund17957' => 'sun', 'Lalb_Chr06g0176771' => 'lal', 'Lalb_Chr18g0056021' => 'lal', 'Lalb_Chr18g0056031' => 'lal', 'Lalb_Chr18g0056041' => 'lal', 'Lalb_Chr20g0107751' => 'lal', 'Lalb_Chr20g0118371' => 'lal', 'Lj1g0010239' => 'lja', 'Lj1g0017101' => 'lja', 'Lj2A1178G40' => 'lonja', 'Lj2A54G84' => 'lonja', 'Lj2g0015248' => 'lja', 'Lj3A761T51' => 'lonja', 'Lj6g0018116' => 'lja', 'Lsat_1_v5_gn_4_136040' => 'lsa', 'Lsat_1_v5_gn_5_187461' => 'lsa', 'Lsat_1_v5_gn_5_77001' => 'lsa', 'Lsat_1_v5_gn_9_4461' => 'lsa', 'Manes.01G210100' => 'mes', 'Manes.03G185600' => 'mes', 'Manes.05G073300' => 'mes', 'Manes.09G120300' => 'mes', 'Manes.15G022100' => 'mes', 'Mapoly0096s0053' => 'mpo', 'MBI03_g14058_MAGBIO' => 'mbi', 'MBI03_g33876_MAGBIO' => 'mbi', 'MBI03_g36854_MAGBIO' => 'mbi', 'MBI17_g11997_MAGBIO' => 'mbi', 'MD03G1269000' => 'mdo', 'MD04G1179600' => 'mdo', 'MD11G1289800' => 'mdo', 'MD12G1194700' => 'mdo', 'MD13G1182100' => 'mdo', 'MD13G1182200' => 'mdo', 'MD16G1182600' => 'mdo', 'Medtr2g021400' => 'mtr', 'Medtr2g021470' => 'mtr', 'Medtr2g105810' => 'mtr', 'Medtr3g033580' => 'mtr', 'Medtr6g007970' => 'mtr', 'Medtr7g056330' => 'mtr', 'Medtr7g074290' => 'mtr', 'Medtr7g074380' => 'mtr', 'Medtr7g094550' => 'mtr', 'Medtr8g069995' => 'mtr', 'MELO3C014345.2' => 'cme', 'MELO3C021395.2' => 'cme', 'Migut.D00262' => 'egut', 'Migut.G00257' => 'egut', 'MSTRG.21575' => 'ama', 'MSTRG.3985' => 'ama', 'Nitab4.5_0000295g0140' => 'nta', 'Nitab4.5_0000732g0140' => 'nta', 'Nitab4.5_0003162g0020' => 'nta', 'Nitab4.5_0006180g0090' => 'nta', 'Nitab4.5_0006390g0010' => 'nta', 'Nitab4.5_0007392g0040' => 'nta', 'Nn1g02140' => 'nnu', 'Nn4g26168' => 'nnu', 'Nn5g26754' => 'nnu', 'Oeu001433.1' => 'oeu', 'Oeu010299.2' => 'oeu', 'Oeu011171.1' => 'oeu', 'Oeu037675.1' => 'oeu', 'Oeu038359.1' => 'oeu', 'Oeu063834.1' => 'oeu', 'Oeu063835.1' => 'oeu', 'Os05g0312000' => 'osa', 'Os07g0211101' => 'osa', 'Os07g0211200' => 'osa', 'Os07g0681500' => 'osa', 'Peaxi162Scf00095g01015' => 'pax', 'Peaxi162Scf00104g00329' => 'pax', 'Peaxi162Scf00161g00137' => 'pax', 'PGR004G1665' => 'pgr', 'PGR031G2937' => 'pgr', 'PGR119G2145' => 'pgr', 'PGSC0003DMG400004351' => 'stu', 'PGSC0003DMG400014625' => 'stu', 'PGSC0003DMG401000943' => 'stu', 'Phvul.001G148600' => 'pvu', 'Phvul.004G001700' => 'pvu', 'Phvul.006G154900' => 'pvu', 'Phvul.008G078200' => 'pvu', 'Phvul.011G136500' => 'pvu', 'Potri.002G215600' => 'ptr', 'Potri.008G201600' => 'ptr', 'Potri.014G138400' => 'ptr', 'Potri.016G142500' => 'ptr', 'Pp3c16_10580' => 'ppa', 'Pp3c5_25280' => 'ppa', 'Prupe.1G150000' => 'ppe', 'Prupe.1G150100' => 'ppe', 'Prupe.6G299600' => 'ppe', 'Prupe.8G245000' => 'ppe', 'Psat0s4927g0040' => 'psa', 'Psat1g052080' => 'psa', 'Psat1g183800' => 'psa', 'Psat3g113840' => 'psa', 'Psat3g126120' => 'psa', 'Psat3g126160' => 'psa', 'Psat3g158760' => 'psa', 'Psat3g158840' => 'psa', 'PSO170G2858' => 'pso', 'PSO339G0606' => 'pso', 'PSO384G4709' => 'pso', 'PSO407G0334' => 'pso', 'QL04p040276' => 'qlo', 'QL06p005458' => 'qlo', 'QL06p005472' => 'qlo', 'QL07p030546' => 'qlo', 'QL07p031519' => 'qlo', 'QL09p050949' => 'qlo', 'QL09p050966' => 'qlo', 'QL09p051067' => 'qlo', 'QL12p022706' => 'qlo', 'RcHm_v2.0_Chr2g0119601' => 'rch', 'RcHm_v2.0_Chr3g0459591' => 'rch', 'RcHm_v2.0_Chr4g0418521' => 'rch', 'RcHm_v2.0_Chr4g0418531' => 'rch', 'RcHm_v2.0_Chr4g0418541' => 'rch', 'RcHm_v2.0_Chr6g0291641' => 'rch', 'Rhsim01G0086300' => 'rsi', 'Rhsim01G0276300' => 'rsi', 'Rhsim01G0276500' => 'rsi', 'Rhsim04G0207700' => 'rsi', 'Rhsim05G0234500' => 'rsi', 'Rhsim13G0022400' => 'rsi', 'Sabra02G0167900' => 'sbr', 'Sabra04G0158500' => 'sbr', 'Sabra08G0159800' => 'sbr', 'Sabra10G0011500' => 'sbr', 'Sabra14G0104400' => 'sbr', 'SalBow2G2440' => 'sbo', 'SalBow4G2265' => 'sbo', 'Sc02g0000060' => 'sci', 'Sc05g0005020' => 'sci', 'Sc13g0003890' => 'sci', 'Sed0014865' => 'sed', 'Sed0017224' => 'sed', 'Sed0026391' => 'sed', 'SEGI_00063' => 'sgi', 'SEGI_10967' => 'sgi', 'SEGI_17510' => 'sgi', 'SEGI_24396' => 'sgi', 'SEGI_39719' => 'sgi', 'SEGI_41392' => 'sgi', 'SGA_v2.0_scaffold11G05794' => 'sas', 'SGA_v2.0_scaffold142G35607' => 'sas', 'SGA_v2.0_scaffold1G00447' => 'sas', 'SHI15388' => 'shi', 'SHI15394' => 'shi', 'SHI15396' => 'shi', 'SHI15399' => 'shi', 'SMO343G0151' => 'smo', 'SMO367G1118' => 'smo', 'Solyc01g080200.3' => 'sly', 'Solyc06g008960.3' => 'sly', 'Solyc09g064780.3' => 'sly', 'Sopen01g031980' => 'spe', 'Sopen06g003710' => 'spe', 'Sopen09g026460' => 'spe', 'Sp3g21240' => 'spa', 'Sp4g30030' => 'spa', 'TAR365G0022' => 'tar', 'TAR365G1023' => 'tar', 'TAR365G1253' => 'tar', 'TAR623G0078' => 'tar', 'TAR623G1721' => 'tar', 'TAR633G0959' => 'tar', 'THA.LOC104802225' => 'tha', 'THA.LOC104804769' => 'tha', 'THA.LOC104808660' => 'tha', 'THA.LOC104812792' => 'tha', 'Thecc.01G284000' => 'tca', 'Thecc.04G220600' => 'tca', 'Thecc.05G268900' => 'tca', 'Thecc.08G171100' => 'tca', 'Thhalv10001284m.g' => 'esa', 'Thhalv10019912m.g' => 'esa', 'TPR.G14189' => 'tpr', 'TPR.G18110' => 'tpr', 'TPR.G18130' => 'tpr', 'TPR.G18131' => 'tpr', 'TPR.G18140' => 'tpr', 'TPR.G24282' => 'tpr', 'TPR.G25221' => 'tpr', 'TPR.G29267' => 'tpr', 'TPR.G35315' => 'tpr', 'TPR.G36173' => 'tpr', 'TWI09G0794' => 'twi', 'TWI59G1348' => 'twi', 'TWI74G0430' => 'twi', 'unitig_26.g8940' => 'ugi', 'unitig_749.g13744' => 'ugi', 'unitig_749.g13745' => 'ugi', 'vmacro08269' => 'vma', 'vmacro14937' => 'vma', 'vmacro20401' => 'vma', 'VMungo0464G1349' => 'vmu', 'VMungo0540G0289' => 'vmu', 'VMungo1215G1590' => 'vmu', 'VMungo1309G0221' => 'vmu', 'VMungo1309G2815' => 'vmu', 'VMungo1383G0239' => 'vmu', 'VMungo1383G2910' => 'vmu', 'Zm00001eb095270' => 'zma', 'Zm00001eb095280' => 'zma', 'Zm00001eb111630' => 'zma', 'Zm00001eb237080' => 'zma', 'Zm00001eb273740' => 'zma', 'Zm00001eb285040' => 'zma', 'Zm00001eb330790' => 'zma', 'Zm00001eb337380' => 'zma' ) $gf_id = 'HOM05D001484' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001484' ) $data_identifier = 'HOM05D001484' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 2, 'aly' => (int) 2, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 22, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 7, 'hma' => (int) 2, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 7, 'mtr' => (int) 10, 'cme' => (int) 2, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 4, 'ppa' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 4, 'qlo' => (int) 9, 'rch' => (int) 6, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 10, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 7, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb337380' $species_info = array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ) $local_species = 'cqu' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001484', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p31500' => 'bna', 'A05p00020' => 'bna', 'A07p08820' => 'bna', 'Aa31LG4G3300' => 'aar', 'Aa31LG8G10030' => 'aar', 'Actinidia00731' => 'ach', 'Actinidia11473' => 'ach', 'Actinidia23469' => 'ach', 'Actinidia24318' => 'ach', 'Actinidia40196' => 'ach', 'Actinidia40197' => 'ach', 'Actinidia40198' => 'ach', 'Ah.08g212990' => 'amhyb', 'Ah.15g091720' => 'amhyb', 'AL3G38260' => 'aly', 'AL4G47710' => 'aly', 'Aqoxy2G00671' => 'aox', 'Aqoxy2G03236' => 'aox', 'arahy.Tifrunner.gnm1.ann1.05IDCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KR684' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATY3SJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK6QJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6APGL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IDT7Z9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM073U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ0R87' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LE7RV4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT4QRX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V5ENPK' => 'arhy', 'AT2G48110' => 'ath', 'AT3G23590' => 'ath', 'ATR0626G186' => 'atr', 'ATR1127G141' => 'atr', 'Atru.chr4.2583' => 'acertr', 'Atru.chr5.1358' => 'acertr', 'Atru.chr5.1359' => 'acertr', 'Atru.chr8.46' => 'acertr', 'AUR62002640' => 'cqu', 'AUR62030055' => 'cqu', 'AUR62033713' => 'cqu', 'AUR62033714' => 'cqu', 'AUR62036795' => 'cqu', 'AUR62039891' => 'cqu', 'BcaB02g08737' => 'bca', 'BcaB04g20441' => 'bca', 'BcaB06g26509' => 'bca', 'BcaB06g26510' => 'bca', 'BcaB06g26511' => 'bca', 'BcaB06g26512' => 'bca', 'BcaB06g26513' => 'bca', 'BcaC02g12564' => 'bca', 'BcaC02g12565' => 'bca', 'BcaC02g12794' => 'bca', 'BcaC02g12795' => 'bca', 'BcaC02g12796' => 'bca', 'BcaC06g35541' => 'bca', 'BNapus_Darmor_BZH_scaffold_188p00080' => 'bna', 'BNapus_Darmor_BZH_scaffold_188p00090' => 'bna', 'BolC1t03972H' => 'bol', 'BolC1t03973H' => 'bol', 'BolC4t21680H' => 'bol', 'BolC7t41863H' => 'bol', 'BolSC55t61227H' => 'bol', 'BolSC55t61228H' => 'bol', 'BraA01t03278Z' => 'bra', 'BraA05t18998Z' => 'bra', 'BraA07t28673Z' => 'bra', 'C01p40150' => 'bna', 'C05p12370' => 'bna', 'C07p13680' => 'bna', 'CAN.G1006.16' => 'can', 'CAN.G1006.17' => 'can', 'CAN.G1170.2' => 'can', 'CAN.G962.7' => 'can', 'CANSAT25G2179' => 'cansat', 'CANSAT78G1573' => 'cansat', 'CARHR099510' => 'chi', 'CARHR143510' => 'chi', 'Carub.0003s2380' => 'cru', 'Carub.0004s3082' => 'cru', 'Ca_00614_v3' => 'car', 'Ca_07801_v3' => 'car', 'Ca_08567_v3' => 'car', 'Ca_09571_v3' => 'car', 'CBR_g19290' => 'cbr', 'Cc01_g19770' => 'ccan', 'Cc03_g03030' => 'ccan', 'CDE07G0968' => 'cde', 'CDE09G1441' => 'cde', 'Cfa006103' => 'cfa', 'Cfa015573' => 'cfa', 'Cfa016988' => 'cfa', 'Ciclev10006738m.g' => 'ccl', 'Ciclev10010920m.g' => 'ccl', 'Ciclev10018517m.g' => 'ccl', 'CiPaw.01G159200' => 'cil', 'CiPaw.02G091000' => 'cil', 'CiPaw.02G091100' => 'cil', 'CiPaw.08G103100' => 'cil', 'CiPaw.09G224900' => 'cil', 'ClCG06G005740' => 'cla', 'ClCG07G000090' => 'cla', 'ClCG07G000100' => 'cla', 'COL.COLO4_09143' => 'col', 'COL.COLO4_25124' => 'col', 'Cpa.g.sc16.34' => 'cpa', 'Cpa.g.sc3504.1' => 'cpa', 'Cpa.g.sc60.37' => 'cpa', 'CsaV3_6G018520' => 'csa', 'CsaV3_6G036860' => 'csa', 'CSS0001072' => 'camsi', 'CSS0020208' => 'camsi', 'CSS0021253' => 'camsi', 'CSS0022190' => 'camsi', 'CSS0036150' => 'camsi', 'CSS0040442' => 'camsi', 'CSS0042300' => 'camsi', 'CSS0045298' => 'camsi', 'DCAR_012449' => 'dca', 'DCAR_018405' => 'dca', 'DCAR_024573' => 'dca', 'DCAR_030591' => 'dca', 'Dinv16926' => 'din', 'Dinv32963' => 'din', 'Dinv38382' => 'din', 'Dinv38383' => 'din', 'Duzib133G0974' => 'dzi', 'Duzib138G1867' => 'dzi', 'Duzib211G0420' => 'dzi', 'Duzib212G0930' => 'dzi', 'ECA234G1645' => 'eca', 'ECA247G3467' => 'eca', 'ECA248G1703' => 'eca', 'EL10Ac3g06327' => 'bvu', 'EL10Ac7g17204' => 'bvu', 'Eucgr.A00855' => 'egr', 'Eucgr.A00858' => 'egr', 'Eucgr.H01520' => 'egr', 'Eucgr.H03604' => 'egr', 'Eucgr.L03465' => 'egr', 'Eucgr.L03466' => 'egr', 'FAN01G0988' => 'fan', 'FAN02G3892' => 'fan', 'FAN05G3381' => 'fan', 'FAN07G0967' => 'fan', 'FAN07G1493' => 'fan', 'FAN08G3125' => 'fan', 'FAN09G0402' => 'fan', 'FAN12G2594' => 'fan', 'FAN12G3879' => 'fan', 'FAN14G1546' => 'fan', 'FAN15G3626' => 'fan', 'FAN17G0588' => 'fan', 'FAN17G0609' => 'fan', 'FAN18G2817' => 'fan', 'FAN19G1305' => 'fan', 'FAN20G1787' => 'fan', 'FAN22G0073' => 'fan', 'FAN22G0352' => 'fan', 'FAN22G0368' => 'fan', 'FAN22G2273' => 'fan', 'FAN24G1998' => 'fan', 'FAN27G1317' => 'fan', 'FvH4_2g23980' => 'fve', 'FvH4_4g14380' => 'fve', 'FvH4_4g14390' => 'fve', 'FvH4_6g09250' => 'fve', 'Glyma.03G151100' => 'gma', 'Glyma.04G122550' => 'gma', 'Glyma.05G001600' => 'gma', 'Glyma.09G270766' => 'gma', 'Glyma.09G270832' => 'gma', 'Glyma.13G209800' => 'gma', 'Glyma.15G102800' => 'gma', 'Glyma.18G218900' => 'gma', 'Glyma.19G001500' => 'gma', 'Glyma.19G153600' => 'gma', 'Gohir.A02G028600' => 'ghi', 'Gohir.A08G045000' => 'ghi', 'Gohir.A11G120500' => 'ghi', 'Gohir.A12G006200' => 'ghi', 'Gohir.A12G006250' => 'ghi', 'Gohir.D02G036300' => 'ghi', 'Gohir.D08G054700' => 'ghi', 'Gohir.D11G125600' => 'ghi', 'Gohir.D12G005700' => 'ghi', 'Gorai.004G055200' => 'gra', 'Gorai.005G040400' => 'gra', 'Gorai.007G134500' => 'gra', 'Gorai.008G005500' => 'gra', 'GSVIVG01011094001' => 'vvi', 'GSVIVG01017879001' => 'vvi', 'GSVIVG01025988001' => 'vvi', 'GSVIVG01029847001' => 'vvi', 'HanXRQChr10g0282901' => 'han', 'HanXRQChr10g0310371' => 'han', 'HanXRQChr10g0315041' => 'han', 'HanXRQChr11g0327651' => 'han', 'HanXRQChr12g0359391' => 'han', 'Haze_00972' => 'cav', 'Haze_00973' => 'cav', 'Haze_00974' => 'cav', 'Haze_04747' => 'cav', 'Haze_04749' => 'cav', 'Haze_04750' => 'cav', 'Haze_21217' => 'cav', 'Hma1.2p1_1037F.1_g250680' => 'hma', 'Hma1.2p1_1644F.1_g295320' => 'hma', 'HPP92_011322' => 'vpl', 'HPP92_011323' => 'vpl', 'HPP92_011324' => 'vpl', 'HPP92_011325' => 'vpl', 'HPP92_011326' => 'vpl', 'Hund12205' => 'sun', 'Hund17957' => 'sun', 'Lalb_Chr06g0176771' => 'lal', 'Lalb_Chr18g0056021' => 'lal', 'Lalb_Chr18g0056031' => 'lal', 'Lalb_Chr18g0056041' => 'lal', 'Lalb_Chr20g0107751' => 'lal', 'Lalb_Chr20g0118371' => 'lal', 'Lj1g0010239' => 'lja', 'Lj1g0017101' => 'lja', 'Lj2A1178G40' => 'lonja', 'Lj2A54G84' => 'lonja', 'Lj2g0015248' => 'lja', 'Lj3A761T51' => 'lonja', 'Lj6g0018116' => 'lja', 'Lsat_1_v5_gn_4_136040' => 'lsa', 'Lsat_1_v5_gn_5_187461' => 'lsa', 'Lsat_1_v5_gn_5_77001' => 'lsa', 'Lsat_1_v5_gn_9_4461' => 'lsa', 'Manes.01G210100' => 'mes', 'Manes.03G185600' => 'mes', 'Manes.05G073300' => 'mes', 'Manes.09G120300' => 'mes', 'Manes.15G022100' => 'mes', 'Mapoly0096s0053' => 'mpo', 'MBI03_g14058_MAGBIO' => 'mbi', 'MBI03_g33876_MAGBIO' => 'mbi', 'MBI03_g36854_MAGBIO' => 'mbi', 'MBI17_g11997_MAGBIO' => 'mbi', 'MD03G1269000' => 'mdo', 'MD04G1179600' => 'mdo', 'MD11G1289800' => 'mdo', 'MD12G1194700' => 'mdo', 'MD13G1182100' => 'mdo', 'MD13G1182200' => 'mdo', 'MD16G1182600' => 'mdo', 'Medtr2g021400' => 'mtr', 'Medtr2g021470' => 'mtr', 'Medtr2g105810' => 'mtr', 'Medtr3g033580' => 'mtr', 'Medtr6g007970' => 'mtr', 'Medtr7g056330' => 'mtr', 'Medtr7g074290' => 'mtr', 'Medtr7g074380' => 'mtr', 'Medtr7g094550' => 'mtr', 'Medtr8g069995' => 'mtr', 'MELO3C014345.2' => 'cme', 'MELO3C021395.2' => 'cme', 'Migut.D00262' => 'egut', 'Migut.G00257' => 'egut', 'MSTRG.21575' => 'ama', 'MSTRG.3985' => 'ama', 'Nitab4.5_0000295g0140' => 'nta', 'Nitab4.5_0000732g0140' => 'nta', 'Nitab4.5_0003162g0020' => 'nta', 'Nitab4.5_0006180g0090' => 'nta', 'Nitab4.5_0006390g0010' => 'nta', 'Nitab4.5_0007392g0040' => 'nta', 'Nn1g02140' => 'nnu', 'Nn4g26168' => 'nnu', 'Nn5g26754' => 'nnu', 'Oeu001433.1' => 'oeu', 'Oeu010299.2' => 'oeu', 'Oeu011171.1' => 'oeu', 'Oeu037675.1' => 'oeu', 'Oeu038359.1' => 'oeu', 'Oeu063834.1' => 'oeu', 'Oeu063835.1' => 'oeu', 'Os05g0312000' => 'osa', 'Os07g0211101' => 'osa', 'Os07g0211200' => 'osa', 'Os07g0681500' => 'osa', 'Peaxi162Scf00095g01015' => 'pax', 'Peaxi162Scf00104g00329' => 'pax', 'Peaxi162Scf00161g00137' => 'pax', 'PGR004G1665' => 'pgr', 'PGR031G2937' => 'pgr', 'PGR119G2145' => 'pgr', 'PGSC0003DMG400004351' => 'stu', 'PGSC0003DMG400014625' => 'stu', 'PGSC0003DMG401000943' => 'stu', 'Phvul.001G148600' => 'pvu', 'Phvul.004G001700' => 'pvu', 'Phvul.006G154900' => 'pvu', 'Phvul.008G078200' => 'pvu', 'Phvul.011G136500' => 'pvu', 'Potri.002G215600' => 'ptr', 'Potri.008G201600' => 'ptr', 'Potri.014G138400' => 'ptr', 'Potri.016G142500' => 'ptr', 'Pp3c16_10580' => 'ppa', 'Pp3c5_25280' => 'ppa', 'Prupe.1G150000' => 'ppe', 'Prupe.1G150100' => 'ppe', 'Prupe.6G299600' => 'ppe', 'Prupe.8G245000' => 'ppe', 'Psat0s4927g0040' => 'psa', 'Psat1g052080' => 'psa', 'Psat1g183800' => 'psa', 'Psat3g113840' => 'psa', 'Psat3g126120' => 'psa', 'Psat3g126160' => 'psa', 'Psat3g158760' => 'psa', 'Psat3g158840' => 'psa', 'PSO170G2858' => 'pso', 'PSO339G0606' => 'pso', 'PSO384G4709' => 'pso', 'PSO407G0334' => 'pso', 'QL04p040276' => 'qlo', 'QL06p005458' => 'qlo', 'QL06p005472' => 'qlo', 'QL07p030546' => 'qlo', 'QL07p031519' => 'qlo', 'QL09p050949' => 'qlo', 'QL09p050966' => 'qlo', 'QL09p051067' => 'qlo', 'QL12p022706' => 'qlo', 'RcHm_v2.0_Chr2g0119601' => 'rch', 'RcHm_v2.0_Chr3g0459591' => 'rch', 'RcHm_v2.0_Chr4g0418521' => 'rch', 'RcHm_v2.0_Chr4g0418531' => 'rch', 'RcHm_v2.0_Chr4g0418541' => 'rch', 'RcHm_v2.0_Chr6g0291641' => 'rch', 'Rhsim01G0086300' => 'rsi', 'Rhsim01G0276300' => 'rsi', 'Rhsim01G0276500' => 'rsi', 'Rhsim04G0207700' => 'rsi', 'Rhsim05G0234500' => 'rsi', 'Rhsim13G0022400' => 'rsi', 'Sabra02G0167900' => 'sbr', 'Sabra04G0158500' => 'sbr', 'Sabra08G0159800' => 'sbr', 'Sabra10G0011500' => 'sbr', 'Sabra14G0104400' => 'sbr', 'SalBow2G2440' => 'sbo', 'SalBow4G2265' => 'sbo', 'Sc02g0000060' => 'sci', 'Sc05g0005020' => 'sci', 'Sc13g0003890' => 'sci', 'Sed0014865' => 'sed', 'Sed0017224' => 'sed', 'Sed0026391' => 'sed', 'SEGI_00063' => 'sgi', 'SEGI_10967' => 'sgi', 'SEGI_17510' => 'sgi', 'SEGI_24396' => 'sgi', 'SEGI_39719' => 'sgi', 'SEGI_41392' => 'sgi', 'SGA_v2.0_scaffold11G05794' => 'sas', 'SGA_v2.0_scaffold142G35607' => 'sas', 'SGA_v2.0_scaffold1G00447' => 'sas', 'SHI15388' => 'shi', 'SHI15394' => 'shi', 'SHI15396' => 'shi', 'SHI15399' => 'shi', 'SMO343G0151' => 'smo', 'SMO367G1118' => 'smo', 'Solyc01g080200.3' => 'sly', 'Solyc06g008960.3' => 'sly', 'Solyc09g064780.3' => 'sly', 'Sopen01g031980' => 'spe', 'Sopen06g003710' => 'spe', 'Sopen09g026460' => 'spe', 'Sp3g21240' => 'spa', 'Sp4g30030' => 'spa', 'TAR365G0022' => 'tar', 'TAR365G1023' => 'tar', 'TAR365G1253' => 'tar', 'TAR623G0078' => 'tar', 'TAR623G1721' => 'tar', 'TAR633G0959' => 'tar', 'THA.LOC104802225' => 'tha', 'THA.LOC104804769' => 'tha', 'THA.LOC104808660' => 'tha', 'THA.LOC104812792' => 'tha', 'Thecc.01G284000' => 'tca', 'Thecc.04G220600' => 'tca', 'Thecc.05G268900' => 'tca', 'Thecc.08G171100' => 'tca', 'Thhalv10001284m.g' => 'esa', 'Thhalv10019912m.g' => 'esa', 'TPR.G14189' => 'tpr', 'TPR.G18110' => 'tpr', 'TPR.G18130' => 'tpr', 'TPR.G18131' => 'tpr', 'TPR.G18140' => 'tpr', 'TPR.G24282' => 'tpr', 'TPR.G25221' => 'tpr', 'TPR.G29267' => 'tpr', 'TPR.G35315' => 'tpr', 'TPR.G36173' => 'tpr', 'TWI09G0794' => 'twi', 'TWI59G1348' => 'twi', 'TWI74G0430' => 'twi', 'unitig_26.g8940' => 'ugi', 'unitig_749.g13744' => 'ugi', 'unitig_749.g13745' => 'ugi', 'vmacro08269' => 'vma', 'vmacro14937' => 'vma', 'vmacro20401' => 'vma', 'VMungo0464G1349' => 'vmu', 'VMungo0540G0289' => 'vmu', 'VMungo1215G1590' => 'vmu', 'VMungo1309G0221' => 'vmu', 'VMungo1309G2815' => 'vmu', 'VMungo1383G0239' => 'vmu', 'VMungo1383G2910' => 'vmu', 'Zm00001eb095270' => 'zma', 'Zm00001eb095280' => 'zma', 'Zm00001eb111630' => 'zma', 'Zm00001eb237080' => 'zma', 'Zm00001eb273740' => 'zma', 'Zm00001eb285040' => 'zma', 'Zm00001eb330790' => 'zma', 'Zm00001eb337380' => 'zma' ), 'gf_id' => 'HOM05D001484', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001484' ), 'data_identifier' => 'HOM05D001484', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001484', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p31500' => 'bna', 'A05p00020' => 'bna', 'A07p08820' => 'bna', 'Aa31LG4G3300' => 'aar', 'Aa31LG8G10030' => 'aar', 'Actinidia00731' => 'ach', 'Actinidia11473' => 'ach', 'Actinidia23469' => 'ach', 'Actinidia24318' => 'ach', 'Actinidia40196' => 'ach', 'Actinidia40197' => 'ach', 'Actinidia40198' => 'ach', 'Ah.08g212990' => 'amhyb', 'Ah.15g091720' => 'amhyb', 'AL3G38260' => 'aly', 'AL4G47710' => 'aly', 'Aqoxy2G00671' => 'aox', 'Aqoxy2G03236' => 'aox', 'arahy.Tifrunner.gnm1.ann1.05IDCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KR684' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATY3SJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK6QJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6APGL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IDT7Z9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM073U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ0R87' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LE7RV4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT4QRX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V5ENPK' => 'arhy', 'AT2G48110' => 'ath', 'AT3G23590' => 'ath', 'ATR0626G186' => 'atr', 'ATR1127G141' => 'atr', 'Atru.chr4.2583' => 'acertr', 'Atru.chr5.1358' => 'acertr', 'Atru.chr5.1359' => 'acertr', 'Atru.chr8.46' => 'acertr', 'AUR62002640' => 'cqu', 'AUR62030055' => 'cqu', 'AUR62033713' => 'cqu', 'AUR62033714' => 'cqu', 'AUR62036795' => 'cqu', 'AUR62039891' => 'cqu', 'BcaB02g08737' => 'bca', 'BcaB04g20441' => 'bca', 'BcaB06g26509' => 'bca', 'BcaB06g26510' => 'bca', 'BcaB06g26511' => 'bca', 'BcaB06g26512' => 'bca', 'BcaB06g26513' => 'bca', 'BcaC02g12564' => 'bca', 'BcaC02g12565' => 'bca', 'BcaC02g12794' => 'bca', 'BcaC02g12795' => 'bca', 'BcaC02g12796' => 'bca', 'BcaC06g35541' => 'bca', 'BNapus_Darmor_BZH_scaffold_188p00080' => 'bna', 'BNapus_Darmor_BZH_scaffold_188p00090' => 'bna', 'BolC1t03972H' => 'bol', 'BolC1t03973H' => 'bol', 'BolC4t21680H' => 'bol', 'BolC7t41863H' => 'bol', 'BolSC55t61227H' => 'bol', 'BolSC55t61228H' => 'bol', 'BraA01t03278Z' => 'bra', 'BraA05t18998Z' => 'bra', 'BraA07t28673Z' => 'bra', 'C01p40150' => 'bna', 'C05p12370' => 'bna', 'C07p13680' => 'bna', 'CAN.G1006.16' => 'can', 'CAN.G1006.17' => 'can', 'CAN.G1170.2' => 'can', 'CAN.G962.7' => 'can', 'CANSAT25G2179' => 'cansat', 'CANSAT78G1573' => 'cansat', 'CARHR099510' => 'chi', 'CARHR143510' => 'chi', 'Carub.0003s2380' => 'cru', 'Carub.0004s3082' => 'cru', 'Ca_00614_v3' => 'car', 'Ca_07801_v3' => 'car', 'Ca_08567_v3' => 'car', 'Ca_09571_v3' => 'car', 'CBR_g19290' => 'cbr', 'Cc01_g19770' => 'ccan', 'Cc03_g03030' => 'ccan', 'CDE07G0968' => 'cde', 'CDE09G1441' => 'cde', 'Cfa006103' => 'cfa', 'Cfa015573' => 'cfa', 'Cfa016988' => 'cfa', 'Ciclev10006738m.g' => 'ccl', 'Ciclev10010920m.g' => 'ccl', 'Ciclev10018517m.g' => 'ccl', 'CiPaw.01G159200' => 'cil', 'CiPaw.02G091000' => 'cil', 'CiPaw.02G091100' => 'cil', 'CiPaw.08G103100' => 'cil', 'CiPaw.09G224900' => 'cil', 'ClCG06G005740' => 'cla', 'ClCG07G000090' => 'cla', 'ClCG07G000100' => 'cla', 'COL.COLO4_09143' => 'col', 'COL.COLO4_25124' => 'col', 'Cpa.g.sc16.34' => 'cpa', 'Cpa.g.sc3504.1' => 'cpa', 'Cpa.g.sc60.37' => 'cpa', 'CsaV3_6G018520' => 'csa', 'CsaV3_6G036860' => 'csa', 'CSS0001072' => 'camsi', 'CSS0020208' => 'camsi', 'CSS0021253' => 'camsi', 'CSS0022190' => 'camsi', 'CSS0036150' => 'camsi', 'CSS0040442' => 'camsi', 'CSS0042300' => 'camsi', 'CSS0045298' => 'camsi', 'DCAR_012449' => 'dca', 'DCAR_018405' => 'dca', 'DCAR_024573' => 'dca', 'DCAR_030591' => 'dca', 'Dinv16926' => 'din', 'Dinv32963' => 'din', 'Dinv38382' => 'din', 'Dinv38383' => 'din', 'Duzib133G0974' => 'dzi', 'Duzib138G1867' => 'dzi', 'Duzib211G0420' => 'dzi', 'Duzib212G0930' => 'dzi', 'ECA234G1645' => 'eca', 'ECA247G3467' => 'eca', 'ECA248G1703' => 'eca', 'EL10Ac3g06327' => 'bvu', 'EL10Ac7g17204' => 'bvu', 'Eucgr.A00855' => 'egr', 'Eucgr.A00858' => 'egr', 'Eucgr.H01520' => 'egr', 'Eucgr.H03604' => 'egr', 'Eucgr.L03465' => 'egr', 'Eucgr.L03466' => 'egr', 'FAN01G0988' => 'fan', 'FAN02G3892' => 'fan', 'FAN05G3381' => 'fan', 'FAN07G0967' => 'fan', 'FAN07G1493' => 'fan', 'FAN08G3125' => 'fan', 'FAN09G0402' => 'fan', 'FAN12G2594' => 'fan', 'FAN12G3879' => 'fan', 'FAN14G1546' => 'fan', 'FAN15G3626' => 'fan', 'FAN17G0588' => 'fan', 'FAN17G0609' => 'fan', 'FAN18G2817' => 'fan', 'FAN19G1305' => 'fan', 'FAN20G1787' => 'fan', 'FAN22G0073' => 'fan', 'FAN22G0352' => 'fan', 'FAN22G0368' => 'fan', 'FAN22G2273' => 'fan', 'FAN24G1998' => 'fan', 'FAN27G1317' => 'fan', 'FvH4_2g23980' => 'fve', 'FvH4_4g14380' => 'fve', 'FvH4_4g14390' => 'fve', 'FvH4_6g09250' => 'fve', 'Glyma.03G151100' => 'gma', 'Glyma.04G122550' => 'gma', 'Glyma.05G001600' => 'gma', 'Glyma.09G270766' => 'gma', 'Glyma.09G270832' => 'gma', 'Glyma.13G209800' => 'gma', 'Glyma.15G102800' => 'gma', 'Glyma.18G218900' => 'gma', 'Glyma.19G001500' => 'gma', 'Glyma.19G153600' => 'gma', 'Gohir.A02G028600' => 'ghi', 'Gohir.A08G045000' => 'ghi', 'Gohir.A11G120500' => 'ghi', 'Gohir.A12G006200' => 'ghi', 'Gohir.A12G006250' => 'ghi', 'Gohir.D02G036300' => 'ghi', 'Gohir.D08G054700' => 'ghi', 'Gohir.D11G125600' => 'ghi', 'Gohir.D12G005700' => 'ghi', 'Gorai.004G055200' => 'gra', 'Gorai.005G040400' => 'gra', 'Gorai.007G134500' => 'gra', 'Gorai.008G005500' => 'gra', 'GSVIVG01011094001' => 'vvi', 'GSVIVG01017879001' => 'vvi', 'GSVIVG01025988001' => 'vvi', 'GSVIVG01029847001' => 'vvi', 'HanXRQChr10g0282901' => 'han', 'HanXRQChr10g0310371' => 'han', 'HanXRQChr10g0315041' => 'han', 'HanXRQChr11g0327651' => 'han', 'HanXRQChr12g0359391' => 'han', 'Haze_00972' => 'cav', 'Haze_00973' => 'cav', 'Haze_00974' => 'cav', 'Haze_04747' => 'cav', 'Haze_04749' => 'cav', 'Haze_04750' => 'cav', 'Haze_21217' => 'cav', 'Hma1.2p1_1037F.1_g250680' => 'hma', 'Hma1.2p1_1644F.1_g295320' => 'hma', 'HPP92_011322' => 'vpl', 'HPP92_011323' => 'vpl', 'HPP92_011324' => 'vpl', 'HPP92_011325' => 'vpl', 'HPP92_011326' => 'vpl', 'Hund12205' => 'sun', 'Hund17957' => 'sun', 'Lalb_Chr06g0176771' => 'lal', 'Lalb_Chr18g0056021' => 'lal', 'Lalb_Chr18g0056031' => 'lal', 'Lalb_Chr18g0056041' => 'lal', 'Lalb_Chr20g0107751' => 'lal', 'Lalb_Chr20g0118371' => 'lal', 'Lj1g0010239' => 'lja', 'Lj1g0017101' => 'lja', 'Lj2A1178G40' => 'lonja', 'Lj2A54G84' => 'lonja', 'Lj2g0015248' => 'lja', 'Lj3A761T51' => 'lonja', 'Lj6g0018116' => 'lja', 'Lsat_1_v5_gn_4_136040' => 'lsa', 'Lsat_1_v5_gn_5_187461' => 'lsa', 'Lsat_1_v5_gn_5_77001' => 'lsa', 'Lsat_1_v5_gn_9_4461' => 'lsa', 'Manes.01G210100' => 'mes', 'Manes.03G185600' => 'mes', 'Manes.05G073300' => 'mes', 'Manes.09G120300' => 'mes', 'Manes.15G022100' => 'mes', 'Mapoly0096s0053' => 'mpo', 'MBI03_g14058_MAGBIO' => 'mbi', 'MBI03_g33876_MAGBIO' => 'mbi', 'MBI03_g36854_MAGBIO' => 'mbi', 'MBI17_g11997_MAGBIO' => 'mbi', 'MD03G1269000' => 'mdo', 'MD04G1179600' => 'mdo', 'MD11G1289800' => 'mdo', 'MD12G1194700' => 'mdo', 'MD13G1182100' => 'mdo', 'MD13G1182200' => 'mdo', 'MD16G1182600' => 'mdo', 'Medtr2g021400' => 'mtr', 'Medtr2g021470' => 'mtr', 'Medtr2g105810' => 'mtr', 'Medtr3g033580' => 'mtr', 'Medtr6g007970' => 'mtr', 'Medtr7g056330' => 'mtr', 'Medtr7g074290' => 'mtr', 'Medtr7g074380' => 'mtr', 'Medtr7g094550' => 'mtr', 'Medtr8g069995' => 'mtr', 'MELO3C014345.2' => 'cme', 'MELO3C021395.2' => 'cme', 'Migut.D00262' => 'egut', 'Migut.G00257' => 'egut', 'MSTRG.21575' => 'ama', 'MSTRG.3985' => 'ama', 'Nitab4.5_0000295g0140' => 'nta', 'Nitab4.5_0000732g0140' => 'nta', 'Nitab4.5_0003162g0020' => 'nta', 'Nitab4.5_0006180g0090' => 'nta', 'Nitab4.5_0006390g0010' => 'nta', 'Nitab4.5_0007392g0040' => 'nta', 'Nn1g02140' => 'nnu', 'Nn4g26168' => 'nnu', 'Nn5g26754' => 'nnu', 'Oeu001433.1' => 'oeu', 'Oeu010299.2' => 'oeu', 'Oeu011171.1' => 'oeu', 'Oeu037675.1' => 'oeu', 'Oeu038359.1' => 'oeu', 'Oeu063834.1' => 'oeu', 'Oeu063835.1' => 'oeu', 'Os05g0312000' => 'osa', 'Os07g0211101' => 'osa', 'Os07g0211200' => 'osa', 'Os07g0681500' => 'osa', 'Peaxi162Scf00095g01015' => 'pax', 'Peaxi162Scf00104g00329' => 'pax', 'Peaxi162Scf00161g00137' => 'pax', 'PGR004G1665' => 'pgr', 'PGR031G2937' => 'pgr', 'PGR119G2145' => 'pgr', 'PGSC0003DMG400004351' => 'stu', 'PGSC0003DMG400014625' => 'stu', 'PGSC0003DMG401000943' => 'stu', 'Phvul.001G148600' => 'pvu', 'Phvul.004G001700' => 'pvu', 'Phvul.006G154900' => 'pvu', 'Phvul.008G078200' => 'pvu', 'Phvul.011G136500' => 'pvu', 'Potri.002G215600' => 'ptr', 'Potri.008G201600' => 'ptr', 'Potri.014G138400' => 'ptr', 'Potri.016G142500' => 'ptr', 'Pp3c16_10580' => 'ppa', 'Pp3c5_25280' => 'ppa', 'Prupe.1G150000' => 'ppe', 'Prupe.1G150100' => 'ppe', 'Prupe.6G299600' => 'ppe', 'Prupe.8G245000' => 'ppe', 'Psat0s4927g0040' => 'psa', 'Psat1g052080' => 'psa', 'Psat1g183800' => 'psa', 'Psat3g113840' => 'psa', 'Psat3g126120' => 'psa', 'Psat3g126160' => 'psa', 'Psat3g158760' => 'psa', 'Psat3g158840' => 'psa', 'PSO170G2858' => 'pso', 'PSO339G0606' => 'pso', 'PSO384G4709' => 'pso', 'PSO407G0334' => 'pso', 'QL04p040276' => 'qlo', 'QL06p005458' => 'qlo', 'QL06p005472' => 'qlo', 'QL07p030546' => 'qlo', 'QL07p031519' => 'qlo', 'QL09p050949' => 'qlo', 'QL09p050966' => 'qlo', 'QL09p051067' => 'qlo', 'QL12p022706' => 'qlo', 'RcHm_v2.0_Chr2g0119601' => 'rch', 'RcHm_v2.0_Chr3g0459591' => 'rch', 'RcHm_v2.0_Chr4g0418521' => 'rch', 'RcHm_v2.0_Chr4g0418531' => 'rch', 'RcHm_v2.0_Chr4g0418541' => 'rch', 'RcHm_v2.0_Chr6g0291641' => 'rch', 'Rhsim01G0086300' => 'rsi', 'Rhsim01G0276300' => 'rsi', 'Rhsim01G0276500' => 'rsi', 'Rhsim04G0207700' => 'rsi', 'Rhsim05G0234500' => 'rsi', 'Rhsim13G0022400' => 'rsi', 'Sabra02G0167900' => 'sbr', 'Sabra04G0158500' => 'sbr', 'Sabra08G0159800' => 'sbr', 'Sabra10G0011500' => 'sbr', 'Sabra14G0104400' => 'sbr', 'SalBow2G2440' => 'sbo', 'SalBow4G2265' => 'sbo', 'Sc02g0000060' => 'sci', 'Sc05g0005020' => 'sci', 'Sc13g0003890' => 'sci', 'Sed0014865' => 'sed', 'Sed0017224' => 'sed', 'Sed0026391' => 'sed', 'SEGI_00063' => 'sgi', 'SEGI_10967' => 'sgi', 'SEGI_17510' => 'sgi', 'SEGI_24396' => 'sgi', 'SEGI_39719' => 'sgi', 'SEGI_41392' => 'sgi', 'SGA_v2.0_scaffold11G05794' => 'sas', 'SGA_v2.0_scaffold142G35607' => 'sas', 'SGA_v2.0_scaffold1G00447' => 'sas', 'SHI15388' => 'shi', 'SHI15394' => 'shi', 'SHI15396' => 'shi', 'SHI15399' => 'shi', 'SMO343G0151' => 'smo', 'SMO367G1118' => 'smo', 'Solyc01g080200.3' => 'sly', 'Solyc06g008960.3' => 'sly', 'Solyc09g064780.3' => 'sly', 'Sopen01g031980' => 'spe', 'Sopen06g003710' => 'spe', 'Sopen09g026460' => 'spe', 'Sp3g21240' => 'spa', 'Sp4g30030' => 'spa', 'TAR365G0022' => 'tar', 'TAR365G1023' => 'tar', 'TAR365G1253' => 'tar', 'TAR623G0078' => 'tar', 'TAR623G1721' => 'tar', 'TAR633G0959' => 'tar', 'THA.LOC104802225' => 'tha', 'THA.LOC104804769' => 'tha', 'THA.LOC104808660' => 'tha', 'THA.LOC104812792' => 'tha', 'Thecc.01G284000' => 'tca', 'Thecc.04G220600' => 'tca', 'Thecc.05G268900' => 'tca', 'Thecc.08G171100' => 'tca', 'Thhalv10001284m.g' => 'esa', 'Thhalv10019912m.g' => 'esa', 'TPR.G14189' => 'tpr', 'TPR.G18110' => 'tpr', 'TPR.G18130' => 'tpr', 'TPR.G18131' => 'tpr', 'TPR.G18140' => 'tpr', 'TPR.G24282' => 'tpr', 'TPR.G25221' => 'tpr', 'TPR.G29267' => 'tpr', 'TPR.G35315' => 'tpr', 'TPR.G36173' => 'tpr', 'TWI09G0794' => 'twi', 'TWI59G1348' => 'twi', 'TWI74G0430' => 'twi', 'unitig_26.g8940' => 'ugi', 'unitig_749.g13744' => 'ugi', 'unitig_749.g13745' => 'ugi', 'vmacro08269' => 'vma', 'vmacro14937' => 'vma', 'vmacro20401' => 'vma', 'VMungo0464G1349' => 'vmu', 'VMungo0540G0289' => 'vmu', 'VMungo1215G1590' => 'vmu', 'VMungo1309G0221' => 'vmu', 'VMungo1309G2815' => 'vmu', 'VMungo1383G0239' => 'vmu', 'VMungo1383G2910' => 'vmu', 'Zm00001eb095270' => 'zma', 'Zm00001eb095280' => 'zma', 'Zm00001eb111630' => 'zma', 'Zm00001eb237080' => 'zma', 'Zm00001eb273740' => 'zma', 'Zm00001eb285040' => 'zma', 'Zm00001eb330790' => 'zma', 'Zm00001eb337380' => 'zma' ) $gf_id = 'HOM05D001484' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001484' ) $data_identifier = 'HOM05D001484' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 2, 'aly' => (int) 2, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 22, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 7, 'hma' => (int) 2, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 7, 'mtr' => (int) 10, 'cme' => (int) 2, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 4, 'ppa' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 4, 'qlo' => (int) 9, 'rch' => (int) 6, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 10, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 7, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb337380' $species_info = array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ) $local_species = 'cqu' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001484', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p31500' => 'bna', 'A05p00020' => 'bna', 'A07p08820' => 'bna', 'Aa31LG4G3300' => 'aar', 'Aa31LG8G10030' => 'aar', 'Actinidia00731' => 'ach', 'Actinidia11473' => 'ach', 'Actinidia23469' => 'ach', 'Actinidia24318' => 'ach', 'Actinidia40196' => 'ach', 'Actinidia40197' => 'ach', 'Actinidia40198' => 'ach', 'Ah.08g212990' => 'amhyb', 'Ah.15g091720' => 'amhyb', 'AL3G38260' => 'aly', 'AL4G47710' => 'aly', 'Aqoxy2G00671' => 'aox', 'Aqoxy2G03236' => 'aox', 'arahy.Tifrunner.gnm1.ann1.05IDCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KR684' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATY3SJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK6QJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6APGL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IDT7Z9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM073U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ0R87' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LE7RV4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT4QRX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V5ENPK' => 'arhy', 'AT2G48110' => 'ath', 'AT3G23590' => 'ath', 'ATR0626G186' => 'atr', 'ATR1127G141' => 'atr', 'Atru.chr4.2583' => 'acertr', 'Atru.chr5.1358' => 'acertr', 'Atru.chr5.1359' => 'acertr', 'Atru.chr8.46' => 'acertr', 'AUR62002640' => 'cqu', 'AUR62030055' => 'cqu', 'AUR62033713' => 'cqu', 'AUR62033714' => 'cqu', 'AUR62036795' => 'cqu', 'AUR62039891' => 'cqu', 'BcaB02g08737' => 'bca', 'BcaB04g20441' => 'bca', 'BcaB06g26509' => 'bca', 'BcaB06g26510' => 'bca', 'BcaB06g26511' => 'bca', 'BcaB06g26512' => 'bca', 'BcaB06g26513' => 'bca', 'BcaC02g12564' => 'bca', 'BcaC02g12565' => 'bca', 'BcaC02g12794' => 'bca', 'BcaC02g12795' => 'bca', 'BcaC02g12796' => 'bca', 'BcaC06g35541' => 'bca', 'BNapus_Darmor_BZH_scaffold_188p00080' => 'bna', 'BNapus_Darmor_BZH_scaffold_188p00090' => 'bna', 'BolC1t03972H' => 'bol', 'BolC1t03973H' => 'bol', 'BolC4t21680H' => 'bol', 'BolC7t41863H' => 'bol', 'BolSC55t61227H' => 'bol', 'BolSC55t61228H' => 'bol', 'BraA01t03278Z' => 'bra', 'BraA05t18998Z' => 'bra', 'BraA07t28673Z' => 'bra', 'C01p40150' => 'bna', 'C05p12370' => 'bna', 'C07p13680' => 'bna', 'CAN.G1006.16' => 'can', 'CAN.G1006.17' => 'can', 'CAN.G1170.2' => 'can', 'CAN.G962.7' => 'can', 'CANSAT25G2179' => 'cansat', 'CANSAT78G1573' => 'cansat', 'CARHR099510' => 'chi', 'CARHR143510' => 'chi', 'Carub.0003s2380' => 'cru', 'Carub.0004s3082' => 'cru', 'Ca_00614_v3' => 'car', 'Ca_07801_v3' => 'car', 'Ca_08567_v3' => 'car', 'Ca_09571_v3' => 'car', 'CBR_g19290' => 'cbr', 'Cc01_g19770' => 'ccan', 'Cc03_g03030' => 'ccan', 'CDE07G0968' => 'cde', 'CDE09G1441' => 'cde', 'Cfa006103' => 'cfa', 'Cfa015573' => 'cfa', 'Cfa016988' => 'cfa', 'Ciclev10006738m.g' => 'ccl', 'Ciclev10010920m.g' => 'ccl', 'Ciclev10018517m.g' => 'ccl', 'CiPaw.01G159200' => 'cil', 'CiPaw.02G091000' => 'cil', 'CiPaw.02G091100' => 'cil', 'CiPaw.08G103100' => 'cil', 'CiPaw.09G224900' => 'cil', 'ClCG06G005740' => 'cla', 'ClCG07G000090' => 'cla', 'ClCG07G000100' => 'cla', 'COL.COLO4_09143' => 'col', 'COL.COLO4_25124' => 'col', 'Cpa.g.sc16.34' => 'cpa', 'Cpa.g.sc3504.1' => 'cpa', 'Cpa.g.sc60.37' => 'cpa', 'CsaV3_6G018520' => 'csa', 'CsaV3_6G036860' => 'csa', 'CSS0001072' => 'camsi', 'CSS0020208' => 'camsi', 'CSS0021253' => 'camsi', 'CSS0022190' => 'camsi', 'CSS0036150' => 'camsi', 'CSS0040442' => 'camsi', 'CSS0042300' => 'camsi', 'CSS0045298' => 'camsi', 'DCAR_012449' => 'dca', 'DCAR_018405' => 'dca', 'DCAR_024573' => 'dca', 'DCAR_030591' => 'dca', 'Dinv16926' => 'din', 'Dinv32963' => 'din', 'Dinv38382' => 'din', 'Dinv38383' => 'din', 'Duzib133G0974' => 'dzi', 'Duzib138G1867' => 'dzi', 'Duzib211G0420' => 'dzi', 'Duzib212G0930' => 'dzi', 'ECA234G1645' => 'eca', 'ECA247G3467' => 'eca', 'ECA248G1703' => 'eca', 'EL10Ac3g06327' => 'bvu', 'EL10Ac7g17204' => 'bvu', 'Eucgr.A00855' => 'egr', 'Eucgr.A00858' => 'egr', 'Eucgr.H01520' => 'egr', 'Eucgr.H03604' => 'egr', 'Eucgr.L03465' => 'egr', 'Eucgr.L03466' => 'egr', 'FAN01G0988' => 'fan', 'FAN02G3892' => 'fan', 'FAN05G3381' => 'fan', 'FAN07G0967' => 'fan', 'FAN07G1493' => 'fan', 'FAN08G3125' => 'fan', 'FAN09G0402' => 'fan', 'FAN12G2594' => 'fan', 'FAN12G3879' => 'fan', 'FAN14G1546' => 'fan', 'FAN15G3626' => 'fan', 'FAN17G0588' => 'fan', 'FAN17G0609' => 'fan', 'FAN18G2817' => 'fan', 'FAN19G1305' => 'fan', 'FAN20G1787' => 'fan', 'FAN22G0073' => 'fan', 'FAN22G0352' => 'fan', 'FAN22G0368' => 'fan', 'FAN22G2273' => 'fan', 'FAN24G1998' => 'fan', 'FAN27G1317' => 'fan', 'FvH4_2g23980' => 'fve', 'FvH4_4g14380' => 'fve', 'FvH4_4g14390' => 'fve', 'FvH4_6g09250' => 'fve', 'Glyma.03G151100' => 'gma', 'Glyma.04G122550' => 'gma', 'Glyma.05G001600' => 'gma', 'Glyma.09G270766' => 'gma', 'Glyma.09G270832' => 'gma', 'Glyma.13G209800' => 'gma', 'Glyma.15G102800' => 'gma', 'Glyma.18G218900' => 'gma', 'Glyma.19G001500' => 'gma', 'Glyma.19G153600' => 'gma', 'Gohir.A02G028600' => 'ghi', 'Gohir.A08G045000' => 'ghi', 'Gohir.A11G120500' => 'ghi', 'Gohir.A12G006200' => 'ghi', 'Gohir.A12G006250' => 'ghi', 'Gohir.D02G036300' => 'ghi', 'Gohir.D08G054700' => 'ghi', 'Gohir.D11G125600' => 'ghi', 'Gohir.D12G005700' => 'ghi', 'Gorai.004G055200' => 'gra', 'Gorai.005G040400' => 'gra', 'Gorai.007G134500' => 'gra', 'Gorai.008G005500' => 'gra', 'GSVIVG01011094001' => 'vvi', 'GSVIVG01017879001' => 'vvi', 'GSVIVG01025988001' => 'vvi', 'GSVIVG01029847001' => 'vvi', 'HanXRQChr10g0282901' => 'han', 'HanXRQChr10g0310371' => 'han', 'HanXRQChr10g0315041' => 'han', 'HanXRQChr11g0327651' => 'han', 'HanXRQChr12g0359391' => 'han', 'Haze_00972' => 'cav', 'Haze_00973' => 'cav', 'Haze_00974' => 'cav', 'Haze_04747' => 'cav', 'Haze_04749' => 'cav', 'Haze_04750' => 'cav', 'Haze_21217' => 'cav', 'Hma1.2p1_1037F.1_g250680' => 'hma', 'Hma1.2p1_1644F.1_g295320' => 'hma', 'HPP92_011322' => 'vpl', 'HPP92_011323' => 'vpl', 'HPP92_011324' => 'vpl', 'HPP92_011325' => 'vpl', 'HPP92_011326' => 'vpl', 'Hund12205' => 'sun', 'Hund17957' => 'sun', 'Lalb_Chr06g0176771' => 'lal', 'Lalb_Chr18g0056021' => 'lal', 'Lalb_Chr18g0056031' => 'lal', 'Lalb_Chr18g0056041' => 'lal', 'Lalb_Chr20g0107751' => 'lal', 'Lalb_Chr20g0118371' => 'lal', 'Lj1g0010239' => 'lja', 'Lj1g0017101' => 'lja', 'Lj2A1178G40' => 'lonja', 'Lj2A54G84' => 'lonja', 'Lj2g0015248' => 'lja', 'Lj3A761T51' => 'lonja', 'Lj6g0018116' => 'lja', 'Lsat_1_v5_gn_4_136040' => 'lsa', 'Lsat_1_v5_gn_5_187461' => 'lsa', 'Lsat_1_v5_gn_5_77001' => 'lsa', 'Lsat_1_v5_gn_9_4461' => 'lsa', 'Manes.01G210100' => 'mes', 'Manes.03G185600' => 'mes', 'Manes.05G073300' => 'mes', 'Manes.09G120300' => 'mes', 'Manes.15G022100' => 'mes', 'Mapoly0096s0053' => 'mpo', 'MBI03_g14058_MAGBIO' => 'mbi', 'MBI03_g33876_MAGBIO' => 'mbi', 'MBI03_g36854_MAGBIO' => 'mbi', 'MBI17_g11997_MAGBIO' => 'mbi', 'MD03G1269000' => 'mdo', 'MD04G1179600' => 'mdo', 'MD11G1289800' => 'mdo', 'MD12G1194700' => 'mdo', 'MD13G1182100' => 'mdo', 'MD13G1182200' => 'mdo', 'MD16G1182600' => 'mdo', 'Medtr2g021400' => 'mtr', 'Medtr2g021470' => 'mtr', 'Medtr2g105810' => 'mtr', 'Medtr3g033580' => 'mtr', 'Medtr6g007970' => 'mtr', 'Medtr7g056330' => 'mtr', 'Medtr7g074290' => 'mtr', 'Medtr7g074380' => 'mtr', 'Medtr7g094550' => 'mtr', 'Medtr8g069995' => 'mtr', 'MELO3C014345.2' => 'cme', 'MELO3C021395.2' => 'cme', 'Migut.D00262' => 'egut', 'Migut.G00257' => 'egut', 'MSTRG.21575' => 'ama', 'MSTRG.3985' => 'ama', 'Nitab4.5_0000295g0140' => 'nta', 'Nitab4.5_0000732g0140' => 'nta', 'Nitab4.5_0003162g0020' => 'nta', 'Nitab4.5_0006180g0090' => 'nta', 'Nitab4.5_0006390g0010' => 'nta', 'Nitab4.5_0007392g0040' => 'nta', 'Nn1g02140' => 'nnu', 'Nn4g26168' => 'nnu', 'Nn5g26754' => 'nnu', 'Oeu001433.1' => 'oeu', 'Oeu010299.2' => 'oeu', 'Oeu011171.1' => 'oeu', 'Oeu037675.1' => 'oeu', 'Oeu038359.1' => 'oeu', 'Oeu063834.1' => 'oeu', 'Oeu063835.1' => 'oeu', 'Os05g0312000' => 'osa', 'Os07g0211101' => 'osa', 'Os07g0211200' => 'osa', 'Os07g0681500' => 'osa', 'Peaxi162Scf00095g01015' => 'pax', 'Peaxi162Scf00104g00329' => 'pax', 'Peaxi162Scf00161g00137' => 'pax', 'PGR004G1665' => 'pgr', 'PGR031G2937' => 'pgr', 'PGR119G2145' => 'pgr', 'PGSC0003DMG400004351' => 'stu', 'PGSC0003DMG400014625' => 'stu', 'PGSC0003DMG401000943' => 'stu', 'Phvul.001G148600' => 'pvu', 'Phvul.004G001700' => 'pvu', 'Phvul.006G154900' => 'pvu', 'Phvul.008G078200' => 'pvu', 'Phvul.011G136500' => 'pvu', 'Potri.002G215600' => 'ptr', 'Potri.008G201600' => 'ptr', 'Potri.014G138400' => 'ptr', 'Potri.016G142500' => 'ptr', 'Pp3c16_10580' => 'ppa', 'Pp3c5_25280' => 'ppa', 'Prupe.1G150000' => 'ppe', 'Prupe.1G150100' => 'ppe', 'Prupe.6G299600' => 'ppe', 'Prupe.8G245000' => 'ppe', 'Psat0s4927g0040' => 'psa', 'Psat1g052080' => 'psa', 'Psat1g183800' => 'psa', 'Psat3g113840' => 'psa', 'Psat3g126120' => 'psa', 'Psat3g126160' => 'psa', 'Psat3g158760' => 'psa', 'Psat3g158840' => 'psa', 'PSO170G2858' => 'pso', 'PSO339G0606' => 'pso', 'PSO384G4709' => 'pso', 'PSO407G0334' => 'pso', 'QL04p040276' => 'qlo', 'QL06p005458' => 'qlo', 'QL06p005472' => 'qlo', 'QL07p030546' => 'qlo', 'QL07p031519' => 'qlo', 'QL09p050949' => 'qlo', 'QL09p050966' => 'qlo', 'QL09p051067' => 'qlo', 'QL12p022706' => 'qlo', 'RcHm_v2.0_Chr2g0119601' => 'rch', 'RcHm_v2.0_Chr3g0459591' => 'rch', 'RcHm_v2.0_Chr4g0418521' => 'rch', 'RcHm_v2.0_Chr4g0418531' => 'rch', 'RcHm_v2.0_Chr4g0418541' => 'rch', 'RcHm_v2.0_Chr6g0291641' => 'rch', 'Rhsim01G0086300' => 'rsi', 'Rhsim01G0276300' => 'rsi', 'Rhsim01G0276500' => 'rsi', 'Rhsim04G0207700' => 'rsi', 'Rhsim05G0234500' => 'rsi', 'Rhsim13G0022400' => 'rsi', 'Sabra02G0167900' => 'sbr', 'Sabra04G0158500' => 'sbr', 'Sabra08G0159800' => 'sbr', 'Sabra10G0011500' => 'sbr', 'Sabra14G0104400' => 'sbr', 'SalBow2G2440' => 'sbo', 'SalBow4G2265' => 'sbo', 'Sc02g0000060' => 'sci', 'Sc05g0005020' => 'sci', 'Sc13g0003890' => 'sci', 'Sed0014865' => 'sed', 'Sed0017224' => 'sed', 'Sed0026391' => 'sed', 'SEGI_00063' => 'sgi', 'SEGI_10967' => 'sgi', 'SEGI_17510' => 'sgi', 'SEGI_24396' => 'sgi', 'SEGI_39719' => 'sgi', 'SEGI_41392' => 'sgi', 'SGA_v2.0_scaffold11G05794' => 'sas', 'SGA_v2.0_scaffold142G35607' => 'sas', 'SGA_v2.0_scaffold1G00447' => 'sas', 'SHI15388' => 'shi', 'SHI15394' => 'shi', 'SHI15396' => 'shi', 'SHI15399' => 'shi', 'SMO343G0151' => 'smo', 'SMO367G1118' => 'smo', 'Solyc01g080200.3' => 'sly', 'Solyc06g008960.3' => 'sly', 'Solyc09g064780.3' => 'sly', 'Sopen01g031980' => 'spe', 'Sopen06g003710' => 'spe', 'Sopen09g026460' => 'spe', 'Sp3g21240' => 'spa', 'Sp4g30030' => 'spa', 'TAR365G0022' => 'tar', 'TAR365G1023' => 'tar', 'TAR365G1253' => 'tar', 'TAR623G0078' => 'tar', 'TAR623G1721' => 'tar', 'TAR633G0959' => 'tar', 'THA.LOC104802225' => 'tha', 'THA.LOC104804769' => 'tha', 'THA.LOC104808660' => 'tha', 'THA.LOC104812792' => 'tha', 'Thecc.01G284000' => 'tca', 'Thecc.04G220600' => 'tca', 'Thecc.05G268900' => 'tca', 'Thecc.08G171100' => 'tca', 'Thhalv10001284m.g' => 'esa', 'Thhalv10019912m.g' => 'esa', 'TPR.G14189' => 'tpr', 'TPR.G18110' => 'tpr', 'TPR.G18130' => 'tpr', 'TPR.G18131' => 'tpr', 'TPR.G18140' => 'tpr', 'TPR.G24282' => 'tpr', 'TPR.G25221' => 'tpr', 'TPR.G29267' => 'tpr', 'TPR.G35315' => 'tpr', 'TPR.G36173' => 'tpr', 'TWI09G0794' => 'twi', 'TWI59G1348' => 'twi', 'TWI74G0430' => 'twi', 'unitig_26.g8940' => 'ugi', 'unitig_749.g13744' => 'ugi', 'unitig_749.g13745' => 'ugi', 'vmacro08269' => 'vma', 'vmacro14937' => 'vma', 'vmacro20401' => 'vma', 'VMungo0464G1349' => 'vmu', 'VMungo0540G0289' => 'vmu', 'VMungo1215G1590' => 'vmu', 'VMungo1309G0221' => 'vmu', 'VMungo1309G2815' => 'vmu', 'VMungo1383G0239' => 'vmu', 'VMungo1383G2910' => 'vmu', 'Zm00001eb095270' => 'zma', 'Zm00001eb095280' => 'zma', 'Zm00001eb111630' => 'zma', 'Zm00001eb237080' => 'zma', 'Zm00001eb273740' => 'zma', 'Zm00001eb285040' => 'zma', 'Zm00001eb330790' => 'zma', 'Zm00001eb337380' => 'zma' ), 'gf_id' => 'HOM05D001484', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001484' ), 'data_identifier' => 'HOM05D001484', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001484', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p31500' => 'bna', 'A05p00020' => 'bna', 'A07p08820' => 'bna', 'Aa31LG4G3300' => 'aar', 'Aa31LG8G10030' => 'aar', 'Actinidia00731' => 'ach', 'Actinidia11473' => 'ach', 'Actinidia23469' => 'ach', 'Actinidia24318' => 'ach', 'Actinidia40196' => 'ach', 'Actinidia40197' => 'ach', 'Actinidia40198' => 'ach', 'Ah.08g212990' => 'amhyb', 'Ah.15g091720' => 'amhyb', 'AL3G38260' => 'aly', 'AL4G47710' => 'aly', 'Aqoxy2G00671' => 'aox', 'Aqoxy2G03236' => 'aox', 'arahy.Tifrunner.gnm1.ann1.05IDCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KR684' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATY3SJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK6QJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6APGL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IDT7Z9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM073U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ0R87' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LE7RV4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT4QRX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V5ENPK' => 'arhy', 'AT2G48110' => 'ath', 'AT3G23590' => 'ath', 'ATR0626G186' => 'atr', 'ATR1127G141' => 'atr', 'Atru.chr4.2583' => 'acertr', 'Atru.chr5.1358' => 'acertr', 'Atru.chr5.1359' => 'acertr', 'Atru.chr8.46' => 'acertr', 'AUR62002640' => 'cqu', 'AUR62030055' => 'cqu', 'AUR62033713' => 'cqu', 'AUR62033714' => 'cqu', 'AUR62036795' => 'cqu', 'AUR62039891' => 'cqu', 'BcaB02g08737' => 'bca', 'BcaB04g20441' => 'bca', 'BcaB06g26509' => 'bca', 'BcaB06g26510' => 'bca', 'BcaB06g26511' => 'bca', 'BcaB06g26512' => 'bca', 'BcaB06g26513' => 'bca', 'BcaC02g12564' => 'bca', 'BcaC02g12565' => 'bca', 'BcaC02g12794' => 'bca', 'BcaC02g12795' => 'bca', 'BcaC02g12796' => 'bca', 'BcaC06g35541' => 'bca', 'BNapus_Darmor_BZH_scaffold_188p00080' => 'bna', 'BNapus_Darmor_BZH_scaffold_188p00090' => 'bna', 'BolC1t03972H' => 'bol', 'BolC1t03973H' => 'bol', 'BolC4t21680H' => 'bol', 'BolC7t41863H' => 'bol', 'BolSC55t61227H' => 'bol', 'BolSC55t61228H' => 'bol', 'BraA01t03278Z' => 'bra', 'BraA05t18998Z' => 'bra', 'BraA07t28673Z' => 'bra', 'C01p40150' => 'bna', 'C05p12370' => 'bna', 'C07p13680' => 'bna', 'CAN.G1006.16' => 'can', 'CAN.G1006.17' => 'can', 'CAN.G1170.2' => 'can', 'CAN.G962.7' => 'can', 'CANSAT25G2179' => 'cansat', 'CANSAT78G1573' => 'cansat', 'CARHR099510' => 'chi', 'CARHR143510' => 'chi', 'Carub.0003s2380' => 'cru', 'Carub.0004s3082' => 'cru', 'Ca_00614_v3' => 'car', 'Ca_07801_v3' => 'car', 'Ca_08567_v3' => 'car', 'Ca_09571_v3' => 'car', 'CBR_g19290' => 'cbr', 'Cc01_g19770' => 'ccan', 'Cc03_g03030' => 'ccan', 'CDE07G0968' => 'cde', 'CDE09G1441' => 'cde', 'Cfa006103' => 'cfa', 'Cfa015573' => 'cfa', 'Cfa016988' => 'cfa', 'Ciclev10006738m.g' => 'ccl', 'Ciclev10010920m.g' => 'ccl', 'Ciclev10018517m.g' => 'ccl', 'CiPaw.01G159200' => 'cil', 'CiPaw.02G091000' => 'cil', 'CiPaw.02G091100' => 'cil', 'CiPaw.08G103100' => 'cil', 'CiPaw.09G224900' => 'cil', 'ClCG06G005740' => 'cla', 'ClCG07G000090' => 'cla', 'ClCG07G000100' => 'cla', 'COL.COLO4_09143' => 'col', 'COL.COLO4_25124' => 'col', 'Cpa.g.sc16.34' => 'cpa', 'Cpa.g.sc3504.1' => 'cpa', 'Cpa.g.sc60.37' => 'cpa', 'CsaV3_6G018520' => 'csa', 'CsaV3_6G036860' => 'csa', 'CSS0001072' => 'camsi', 'CSS0020208' => 'camsi', 'CSS0021253' => 'camsi', 'CSS0022190' => 'camsi', 'CSS0036150' => 'camsi', 'CSS0040442' => 'camsi', 'CSS0042300' => 'camsi', 'CSS0045298' => 'camsi', 'DCAR_012449' => 'dca', 'DCAR_018405' => 'dca', 'DCAR_024573' => 'dca', 'DCAR_030591' => 'dca', 'Dinv16926' => 'din', 'Dinv32963' => 'din', 'Dinv38382' => 'din', 'Dinv38383' => 'din', 'Duzib133G0974' => 'dzi', 'Duzib138G1867' => 'dzi', 'Duzib211G0420' => 'dzi', 'Duzib212G0930' => 'dzi', 'ECA234G1645' => 'eca', 'ECA247G3467' => 'eca', 'ECA248G1703' => 'eca', 'EL10Ac3g06327' => 'bvu', 'EL10Ac7g17204' => 'bvu', 'Eucgr.A00855' => 'egr', 'Eucgr.A00858' => 'egr', 'Eucgr.H01520' => 'egr', 'Eucgr.H03604' => 'egr', 'Eucgr.L03465' => 'egr', 'Eucgr.L03466' => 'egr', 'FAN01G0988' => 'fan', 'FAN02G3892' => 'fan', 'FAN05G3381' => 'fan', 'FAN07G0967' => 'fan', 'FAN07G1493' => 'fan', 'FAN08G3125' => 'fan', 'FAN09G0402' => 'fan', 'FAN12G2594' => 'fan', 'FAN12G3879' => 'fan', 'FAN14G1546' => 'fan', 'FAN15G3626' => 'fan', 'FAN17G0588' => 'fan', 'FAN17G0609' => 'fan', 'FAN18G2817' => 'fan', 'FAN19G1305' => 'fan', 'FAN20G1787' => 'fan', 'FAN22G0073' => 'fan', 'FAN22G0352' => 'fan', 'FAN22G0368' => 'fan', 'FAN22G2273' => 'fan', 'FAN24G1998' => 'fan', 'FAN27G1317' => 'fan', 'FvH4_2g23980' => 'fve', 'FvH4_4g14380' => 'fve', 'FvH4_4g14390' => 'fve', 'FvH4_6g09250' => 'fve', 'Glyma.03G151100' => 'gma', 'Glyma.04G122550' => 'gma', 'Glyma.05G001600' => 'gma', 'Glyma.09G270766' => 'gma', 'Glyma.09G270832' => 'gma', 'Glyma.13G209800' => 'gma', 'Glyma.15G102800' => 'gma', 'Glyma.18G218900' => 'gma', 'Glyma.19G001500' => 'gma', 'Glyma.19G153600' => 'gma', 'Gohir.A02G028600' => 'ghi', 'Gohir.A08G045000' => 'ghi', 'Gohir.A11G120500' => 'ghi', 'Gohir.A12G006200' => 'ghi', 'Gohir.A12G006250' => 'ghi', 'Gohir.D02G036300' => 'ghi', 'Gohir.D08G054700' => 'ghi', 'Gohir.D11G125600' => 'ghi', 'Gohir.D12G005700' => 'ghi', 'Gorai.004G055200' => 'gra', 'Gorai.005G040400' => 'gra', 'Gorai.007G134500' => 'gra', 'Gorai.008G005500' => 'gra', 'GSVIVG01011094001' => 'vvi', 'GSVIVG01017879001' => 'vvi', 'GSVIVG01025988001' => 'vvi', 'GSVIVG01029847001' => 'vvi', 'HanXRQChr10g0282901' => 'han', 'HanXRQChr10g0310371' => 'han', 'HanXRQChr10g0315041' => 'han', 'HanXRQChr11g0327651' => 'han', 'HanXRQChr12g0359391' => 'han', 'Haze_00972' => 'cav', 'Haze_00973' => 'cav', 'Haze_00974' => 'cav', 'Haze_04747' => 'cav', 'Haze_04749' => 'cav', 'Haze_04750' => 'cav', 'Haze_21217' => 'cav', 'Hma1.2p1_1037F.1_g250680' => 'hma', 'Hma1.2p1_1644F.1_g295320' => 'hma', 'HPP92_011322' => 'vpl', 'HPP92_011323' => 'vpl', 'HPP92_011324' => 'vpl', 'HPP92_011325' => 'vpl', 'HPP92_011326' => 'vpl', 'Hund12205' => 'sun', 'Hund17957' => 'sun', 'Lalb_Chr06g0176771' => 'lal', 'Lalb_Chr18g0056021' => 'lal', 'Lalb_Chr18g0056031' => 'lal', 'Lalb_Chr18g0056041' => 'lal', 'Lalb_Chr20g0107751' => 'lal', 'Lalb_Chr20g0118371' => 'lal', 'Lj1g0010239' => 'lja', 'Lj1g0017101' => 'lja', 'Lj2A1178G40' => 'lonja', 'Lj2A54G84' => 'lonja', 'Lj2g0015248' => 'lja', 'Lj3A761T51' => 'lonja', 'Lj6g0018116' => 'lja', 'Lsat_1_v5_gn_4_136040' => 'lsa', 'Lsat_1_v5_gn_5_187461' => 'lsa', 'Lsat_1_v5_gn_5_77001' => 'lsa', 'Lsat_1_v5_gn_9_4461' => 'lsa', 'Manes.01G210100' => 'mes', 'Manes.03G185600' => 'mes', 'Manes.05G073300' => 'mes', 'Manes.09G120300' => 'mes', 'Manes.15G022100' => 'mes', 'Mapoly0096s0053' => 'mpo', 'MBI03_g14058_MAGBIO' => 'mbi', 'MBI03_g33876_MAGBIO' => 'mbi', 'MBI03_g36854_MAGBIO' => 'mbi', 'MBI17_g11997_MAGBIO' => 'mbi', 'MD03G1269000' => 'mdo', 'MD04G1179600' => 'mdo', 'MD11G1289800' => 'mdo', 'MD12G1194700' => 'mdo', 'MD13G1182100' => 'mdo', 'MD13G1182200' => 'mdo', 'MD16G1182600' => 'mdo', 'Medtr2g021400' => 'mtr', 'Medtr2g021470' => 'mtr', 'Medtr2g105810' => 'mtr', 'Medtr3g033580' => 'mtr', 'Medtr6g007970' => 'mtr', 'Medtr7g056330' => 'mtr', 'Medtr7g074290' => 'mtr', 'Medtr7g074380' => 'mtr', 'Medtr7g094550' => 'mtr', 'Medtr8g069995' => 'mtr', 'MELO3C014345.2' => 'cme', 'MELO3C021395.2' => 'cme', 'Migut.D00262' => 'egut', 'Migut.G00257' => 'egut', 'MSTRG.21575' => 'ama', 'MSTRG.3985' => 'ama', 'Nitab4.5_0000295g0140' => 'nta', 'Nitab4.5_0000732g0140' => 'nta', 'Nitab4.5_0003162g0020' => 'nta', 'Nitab4.5_0006180g0090' => 'nta', 'Nitab4.5_0006390g0010' => 'nta', 'Nitab4.5_0007392g0040' => 'nta', 'Nn1g02140' => 'nnu', 'Nn4g26168' => 'nnu', 'Nn5g26754' => 'nnu', 'Oeu001433.1' => 'oeu', 'Oeu010299.2' => 'oeu', 'Oeu011171.1' => 'oeu', 'Oeu037675.1' => 'oeu', 'Oeu038359.1' => 'oeu', 'Oeu063834.1' => 'oeu', 'Oeu063835.1' => 'oeu', 'Os05g0312000' => 'osa', 'Os07g0211101' => 'osa', 'Os07g0211200' => 'osa', 'Os07g0681500' => 'osa', 'Peaxi162Scf00095g01015' => 'pax', 'Peaxi162Scf00104g00329' => 'pax', 'Peaxi162Scf00161g00137' => 'pax', 'PGR004G1665' => 'pgr', 'PGR031G2937' => 'pgr', 'PGR119G2145' => 'pgr', 'PGSC0003DMG400004351' => 'stu', 'PGSC0003DMG400014625' => 'stu', 'PGSC0003DMG401000943' => 'stu', 'Phvul.001G148600' => 'pvu', 'Phvul.004G001700' => 'pvu', 'Phvul.006G154900' => 'pvu', 'Phvul.008G078200' => 'pvu', 'Phvul.011G136500' => 'pvu', 'Potri.002G215600' => 'ptr', 'Potri.008G201600' => 'ptr', 'Potri.014G138400' => 'ptr', 'Potri.016G142500' => 'ptr', 'Pp3c16_10580' => 'ppa', 'Pp3c5_25280' => 'ppa', 'Prupe.1G150000' => 'ppe', 'Prupe.1G150100' => 'ppe', 'Prupe.6G299600' => 'ppe', 'Prupe.8G245000' => 'ppe', 'Psat0s4927g0040' => 'psa', 'Psat1g052080' => 'psa', 'Psat1g183800' => 'psa', 'Psat3g113840' => 'psa', 'Psat3g126120' => 'psa', 'Psat3g126160' => 'psa', 'Psat3g158760' => 'psa', 'Psat3g158840' => 'psa', 'PSO170G2858' => 'pso', 'PSO339G0606' => 'pso', 'PSO384G4709' => 'pso', 'PSO407G0334' => 'pso', 'QL04p040276' => 'qlo', 'QL06p005458' => 'qlo', 'QL06p005472' => 'qlo', 'QL07p030546' => 'qlo', 'QL07p031519' => 'qlo', 'QL09p050949' => 'qlo', 'QL09p050966' => 'qlo', 'QL09p051067' => 'qlo', 'QL12p022706' => 'qlo', 'RcHm_v2.0_Chr2g0119601' => 'rch', 'RcHm_v2.0_Chr3g0459591' => 'rch', 'RcHm_v2.0_Chr4g0418521' => 'rch', 'RcHm_v2.0_Chr4g0418531' => 'rch', 'RcHm_v2.0_Chr4g0418541' => 'rch', 'RcHm_v2.0_Chr6g0291641' => 'rch', 'Rhsim01G0086300' => 'rsi', 'Rhsim01G0276300' => 'rsi', 'Rhsim01G0276500' => 'rsi', 'Rhsim04G0207700' => 'rsi', 'Rhsim05G0234500' => 'rsi', 'Rhsim13G0022400' => 'rsi', 'Sabra02G0167900' => 'sbr', 'Sabra04G0158500' => 'sbr', 'Sabra08G0159800' => 'sbr', 'Sabra10G0011500' => 'sbr', 'Sabra14G0104400' => 'sbr', 'SalBow2G2440' => 'sbo', 'SalBow4G2265' => 'sbo', 'Sc02g0000060' => 'sci', 'Sc05g0005020' => 'sci', 'Sc13g0003890' => 'sci', 'Sed0014865' => 'sed', 'Sed0017224' => 'sed', 'Sed0026391' => 'sed', 'SEGI_00063' => 'sgi', 'SEGI_10967' => 'sgi', 'SEGI_17510' => 'sgi', 'SEGI_24396' => 'sgi', 'SEGI_39719' => 'sgi', 'SEGI_41392' => 'sgi', 'SGA_v2.0_scaffold11G05794' => 'sas', 'SGA_v2.0_scaffold142G35607' => 'sas', 'SGA_v2.0_scaffold1G00447' => 'sas', 'SHI15388' => 'shi', 'SHI15394' => 'shi', 'SHI15396' => 'shi', 'SHI15399' => 'shi', 'SMO343G0151' => 'smo', 'SMO367G1118' => 'smo', 'Solyc01g080200.3' => 'sly', 'Solyc06g008960.3' => 'sly', 'Solyc09g064780.3' => 'sly', 'Sopen01g031980' => 'spe', 'Sopen06g003710' => 'spe', 'Sopen09g026460' => 'spe', 'Sp3g21240' => 'spa', 'Sp4g30030' => 'spa', 'TAR365G0022' => 'tar', 'TAR365G1023' => 'tar', 'TAR365G1253' => 'tar', 'TAR623G0078' => 'tar', 'TAR623G1721' => 'tar', 'TAR633G0959' => 'tar', 'THA.LOC104802225' => 'tha', 'THA.LOC104804769' => 'tha', 'THA.LOC104808660' => 'tha', 'THA.LOC104812792' => 'tha', 'Thecc.01G284000' => 'tca', 'Thecc.04G220600' => 'tca', 'Thecc.05G268900' => 'tca', 'Thecc.08G171100' => 'tca', 'Thhalv10001284m.g' => 'esa', 'Thhalv10019912m.g' => 'esa', 'TPR.G14189' => 'tpr', 'TPR.G18110' => 'tpr', 'TPR.G18130' => 'tpr', 'TPR.G18131' => 'tpr', 'TPR.G18140' => 'tpr', 'TPR.G24282' => 'tpr', 'TPR.G25221' => 'tpr', 'TPR.G29267' => 'tpr', 'TPR.G35315' => 'tpr', 'TPR.G36173' => 'tpr', 'TWI09G0794' => 'twi', 'TWI59G1348' => 'twi', 'TWI74G0430' => 'twi', 'unitig_26.g8940' => 'ugi', 'unitig_749.g13744' => 'ugi', 'unitig_749.g13745' => 'ugi', 'vmacro08269' => 'vma', 'vmacro14937' => 'vma', 'vmacro20401' => 'vma', 'VMungo0464G1349' => 'vmu', 'VMungo0540G0289' => 'vmu', 'VMungo1215G1590' => 'vmu', 'VMungo1309G0221' => 'vmu', 'VMungo1309G2815' => 'vmu', 'VMungo1383G0239' => 'vmu', 'VMungo1383G2910' => 'vmu', 'Zm00001eb095270' => 'zma', 'Zm00001eb095280' => 'zma', 'Zm00001eb111630' => 'zma', 'Zm00001eb237080' => 'zma', 'Zm00001eb273740' => 'zma', 'Zm00001eb285040' => 'zma', 'Zm00001eb330790' => 'zma', 'Zm00001eb337380' => 'zma' ) $gf_id = 'HOM05D001484' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001484' ) $data_identifier = 'HOM05D001484' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 2, 'aly' => (int) 2, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 22, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 7, 'hma' => (int) 2, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 7, 'mtr' => (int) 10, 'cme' => (int) 2, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 4, 'ppa' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 4, 'qlo' => (int) 9, 'rch' => (int) 6, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 10, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 7, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb337380' $species_info = array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ) $local_species = 'car' $disabled = '' $selected = '' $num_hits = (int) 0include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001484', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p31500' => 'bna', 'A05p00020' => 'bna', 'A07p08820' => 'bna', 'Aa31LG4G3300' => 'aar', 'Aa31LG8G10030' => 'aar', 'Actinidia00731' => 'ach', 'Actinidia11473' => 'ach', 'Actinidia23469' => 'ach', 'Actinidia24318' => 'ach', 'Actinidia40196' => 'ach', 'Actinidia40197' => 'ach', 'Actinidia40198' => 'ach', 'Ah.08g212990' => 'amhyb', 'Ah.15g091720' => 'amhyb', 'AL3G38260' => 'aly', 'AL4G47710' => 'aly', 'Aqoxy2G00671' => 'aox', 'Aqoxy2G03236' => 'aox', 'arahy.Tifrunner.gnm1.ann1.05IDCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KR684' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATY3SJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK6QJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6APGL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IDT7Z9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM073U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ0R87' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LE7RV4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT4QRX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V5ENPK' => 'arhy', 'AT2G48110' => 'ath', 'AT3G23590' => 'ath', 'ATR0626G186' => 'atr', 'ATR1127G141' => 'atr', 'Atru.chr4.2583' => 'acertr', 'Atru.chr5.1358' => 'acertr', 'Atru.chr5.1359' => 'acertr', 'Atru.chr8.46' => 'acertr', 'AUR62002640' => 'cqu', 'AUR62030055' => 'cqu', 'AUR62033713' => 'cqu', 'AUR62033714' => 'cqu', 'AUR62036795' => 'cqu', 'AUR62039891' => 'cqu', 'BcaB02g08737' => 'bca', 'BcaB04g20441' => 'bca', 'BcaB06g26509' => 'bca', 'BcaB06g26510' => 'bca', 'BcaB06g26511' => 'bca', 'BcaB06g26512' => 'bca', 'BcaB06g26513' => 'bca', 'BcaC02g12564' => 'bca', 'BcaC02g12565' => 'bca', 'BcaC02g12794' => 'bca', 'BcaC02g12795' => 'bca', 'BcaC02g12796' => 'bca', 'BcaC06g35541' => 'bca', 'BNapus_Darmor_BZH_scaffold_188p00080' => 'bna', 'BNapus_Darmor_BZH_scaffold_188p00090' => 'bna', 'BolC1t03972H' => 'bol', 'BolC1t03973H' => 'bol', 'BolC4t21680H' => 'bol', 'BolC7t41863H' => 'bol', 'BolSC55t61227H' => 'bol', 'BolSC55t61228H' => 'bol', 'BraA01t03278Z' => 'bra', 'BraA05t18998Z' => 'bra', 'BraA07t28673Z' => 'bra', 'C01p40150' => 'bna', 'C05p12370' => 'bna', 'C07p13680' => 'bna', 'CAN.G1006.16' => 'can', 'CAN.G1006.17' => 'can', 'CAN.G1170.2' => 'can', 'CAN.G962.7' => 'can', 'CANSAT25G2179' => 'cansat', 'CANSAT78G1573' => 'cansat', 'CARHR099510' => 'chi', 'CARHR143510' => 'chi', 'Carub.0003s2380' => 'cru', 'Carub.0004s3082' => 'cru', 'Ca_00614_v3' => 'car', 'Ca_07801_v3' => 'car', 'Ca_08567_v3' => 'car', 'Ca_09571_v3' => 'car', 'CBR_g19290' => 'cbr', 'Cc01_g19770' => 'ccan', 'Cc03_g03030' => 'ccan', 'CDE07G0968' => 'cde', 'CDE09G1441' => 'cde', 'Cfa006103' => 'cfa', 'Cfa015573' => 'cfa', 'Cfa016988' => 'cfa', 'Ciclev10006738m.g' => 'ccl', 'Ciclev10010920m.g' => 'ccl', 'Ciclev10018517m.g' => 'ccl', 'CiPaw.01G159200' => 'cil', 'CiPaw.02G091000' => 'cil', 'CiPaw.02G091100' => 'cil', 'CiPaw.08G103100' => 'cil', 'CiPaw.09G224900' => 'cil', 'ClCG06G005740' => 'cla', 'ClCG07G000090' => 'cla', 'ClCG07G000100' => 'cla', 'COL.COLO4_09143' => 'col', 'COL.COLO4_25124' => 'col', 'Cpa.g.sc16.34' => 'cpa', 'Cpa.g.sc3504.1' => 'cpa', 'Cpa.g.sc60.37' => 'cpa', 'CsaV3_6G018520' => 'csa', 'CsaV3_6G036860' => 'csa', 'CSS0001072' => 'camsi', 'CSS0020208' => 'camsi', 'CSS0021253' => 'camsi', 'CSS0022190' => 'camsi', 'CSS0036150' => 'camsi', 'CSS0040442' => 'camsi', 'CSS0042300' => 'camsi', 'CSS0045298' => 'camsi', 'DCAR_012449' => 'dca', 'DCAR_018405' => 'dca', 'DCAR_024573' => 'dca', 'DCAR_030591' => 'dca', 'Dinv16926' => 'din', 'Dinv32963' => 'din', 'Dinv38382' => 'din', 'Dinv38383' => 'din', 'Duzib133G0974' => 'dzi', 'Duzib138G1867' => 'dzi', 'Duzib211G0420' => 'dzi', 'Duzib212G0930' => 'dzi', 'ECA234G1645' => 'eca', 'ECA247G3467' => 'eca', 'ECA248G1703' => 'eca', 'EL10Ac3g06327' => 'bvu', 'EL10Ac7g17204' => 'bvu', 'Eucgr.A00855' => 'egr', 'Eucgr.A00858' => 'egr', 'Eucgr.H01520' => 'egr', 'Eucgr.H03604' => 'egr', 'Eucgr.L03465' => 'egr', 'Eucgr.L03466' => 'egr', 'FAN01G0988' => 'fan', 'FAN02G3892' => 'fan', 'FAN05G3381' => 'fan', 'FAN07G0967' => 'fan', 'FAN07G1493' => 'fan', 'FAN08G3125' => 'fan', 'FAN09G0402' => 'fan', 'FAN12G2594' => 'fan', 'FAN12G3879' => 'fan', 'FAN14G1546' => 'fan', 'FAN15G3626' => 'fan', 'FAN17G0588' => 'fan', 'FAN17G0609' => 'fan', 'FAN18G2817' => 'fan', 'FAN19G1305' => 'fan', 'FAN20G1787' => 'fan', 'FAN22G0073' => 'fan', 'FAN22G0352' => 'fan', 'FAN22G0368' => 'fan', 'FAN22G2273' => 'fan', 'FAN24G1998' => 'fan', 'FAN27G1317' => 'fan', 'FvH4_2g23980' => 'fve', 'FvH4_4g14380' => 'fve', 'FvH4_4g14390' => 'fve', 'FvH4_6g09250' => 'fve', 'Glyma.03G151100' => 'gma', 'Glyma.04G122550' => 'gma', 'Glyma.05G001600' => 'gma', 'Glyma.09G270766' => 'gma', 'Glyma.09G270832' => 'gma', 'Glyma.13G209800' => 'gma', 'Glyma.15G102800' => 'gma', 'Glyma.18G218900' => 'gma', 'Glyma.19G001500' => 'gma', 'Glyma.19G153600' => 'gma', 'Gohir.A02G028600' => 'ghi', 'Gohir.A08G045000' => 'ghi', 'Gohir.A11G120500' => 'ghi', 'Gohir.A12G006200' => 'ghi', 'Gohir.A12G006250' => 'ghi', 'Gohir.D02G036300' => 'ghi', 'Gohir.D08G054700' => 'ghi', 'Gohir.D11G125600' => 'ghi', 'Gohir.D12G005700' => 'ghi', 'Gorai.004G055200' => 'gra', 'Gorai.005G040400' => 'gra', 'Gorai.007G134500' => 'gra', 'Gorai.008G005500' => 'gra', 'GSVIVG01011094001' => 'vvi', 'GSVIVG01017879001' => 'vvi', 'GSVIVG01025988001' => 'vvi', 'GSVIVG01029847001' => 'vvi', 'HanXRQChr10g0282901' => 'han', 'HanXRQChr10g0310371' => 'han', 'HanXRQChr10g0315041' => 'han', 'HanXRQChr11g0327651' => 'han', 'HanXRQChr12g0359391' => 'han', 'Haze_00972' => 'cav', 'Haze_00973' => 'cav', 'Haze_00974' => 'cav', 'Haze_04747' => 'cav', 'Haze_04749' => 'cav', 'Haze_04750' => 'cav', 'Haze_21217' => 'cav', 'Hma1.2p1_1037F.1_g250680' => 'hma', 'Hma1.2p1_1644F.1_g295320' => 'hma', 'HPP92_011322' => 'vpl', 'HPP92_011323' => 'vpl', 'HPP92_011324' => 'vpl', 'HPP92_011325' => 'vpl', 'HPP92_011326' => 'vpl', 'Hund12205' => 'sun', 'Hund17957' => 'sun', 'Lalb_Chr06g0176771' => 'lal', 'Lalb_Chr18g0056021' => 'lal', 'Lalb_Chr18g0056031' => 'lal', 'Lalb_Chr18g0056041' => 'lal', 'Lalb_Chr20g0107751' => 'lal', 'Lalb_Chr20g0118371' => 'lal', 'Lj1g0010239' => 'lja', 'Lj1g0017101' => 'lja', 'Lj2A1178G40' => 'lonja', 'Lj2A54G84' => 'lonja', 'Lj2g0015248' => 'lja', 'Lj3A761T51' => 'lonja', 'Lj6g0018116' => 'lja', 'Lsat_1_v5_gn_4_136040' => 'lsa', 'Lsat_1_v5_gn_5_187461' => 'lsa', 'Lsat_1_v5_gn_5_77001' => 'lsa', 'Lsat_1_v5_gn_9_4461' => 'lsa', 'Manes.01G210100' => 'mes', 'Manes.03G185600' => 'mes', 'Manes.05G073300' => 'mes', 'Manes.09G120300' => 'mes', 'Manes.15G022100' => 'mes', 'Mapoly0096s0053' => 'mpo', 'MBI03_g14058_MAGBIO' => 'mbi', 'MBI03_g33876_MAGBIO' => 'mbi', 'MBI03_g36854_MAGBIO' => 'mbi', 'MBI17_g11997_MAGBIO' => 'mbi', 'MD03G1269000' => 'mdo', 'MD04G1179600' => 'mdo', 'MD11G1289800' => 'mdo', 'MD12G1194700' => 'mdo', 'MD13G1182100' => 'mdo', 'MD13G1182200' => 'mdo', 'MD16G1182600' => 'mdo', 'Medtr2g021400' => 'mtr', 'Medtr2g021470' => 'mtr', 'Medtr2g105810' => 'mtr', 'Medtr3g033580' => 'mtr', 'Medtr6g007970' => 'mtr', 'Medtr7g056330' => 'mtr', 'Medtr7g074290' => 'mtr', 'Medtr7g074380' => 'mtr', 'Medtr7g094550' => 'mtr', 'Medtr8g069995' => 'mtr', 'MELO3C014345.2' => 'cme', 'MELO3C021395.2' => 'cme', 'Migut.D00262' => 'egut', 'Migut.G00257' => 'egut', 'MSTRG.21575' => 'ama', 'MSTRG.3985' => 'ama', 'Nitab4.5_0000295g0140' => 'nta', 'Nitab4.5_0000732g0140' => 'nta', 'Nitab4.5_0003162g0020' => 'nta', 'Nitab4.5_0006180g0090' => 'nta', 'Nitab4.5_0006390g0010' => 'nta', 'Nitab4.5_0007392g0040' => 'nta', 'Nn1g02140' => 'nnu', 'Nn4g26168' => 'nnu', 'Nn5g26754' => 'nnu', 'Oeu001433.1' => 'oeu', 'Oeu010299.2' => 'oeu', 'Oeu011171.1' => 'oeu', 'Oeu037675.1' => 'oeu', 'Oeu038359.1' => 'oeu', 'Oeu063834.1' => 'oeu', 'Oeu063835.1' => 'oeu', 'Os05g0312000' => 'osa', 'Os07g0211101' => 'osa', 'Os07g0211200' => 'osa', 'Os07g0681500' => 'osa', 'Peaxi162Scf00095g01015' => 'pax', 'Peaxi162Scf00104g00329' => 'pax', 'Peaxi162Scf00161g00137' => 'pax', 'PGR004G1665' => 'pgr', 'PGR031G2937' => 'pgr', 'PGR119G2145' => 'pgr', 'PGSC0003DMG400004351' => 'stu', 'PGSC0003DMG400014625' => 'stu', 'PGSC0003DMG401000943' => 'stu', 'Phvul.001G148600' => 'pvu', 'Phvul.004G001700' => 'pvu', 'Phvul.006G154900' => 'pvu', 'Phvul.008G078200' => 'pvu', 'Phvul.011G136500' => 'pvu', 'Potri.002G215600' => 'ptr', 'Potri.008G201600' => 'ptr', 'Potri.014G138400' => 'ptr', 'Potri.016G142500' => 'ptr', 'Pp3c16_10580' => 'ppa', 'Pp3c5_25280' => 'ppa', 'Prupe.1G150000' => 'ppe', 'Prupe.1G150100' => 'ppe', 'Prupe.6G299600' => 'ppe', 'Prupe.8G245000' => 'ppe', 'Psat0s4927g0040' => 'psa', 'Psat1g052080' => 'psa', 'Psat1g183800' => 'psa', 'Psat3g113840' => 'psa', 'Psat3g126120' => 'psa', 'Psat3g126160' => 'psa', 'Psat3g158760' => 'psa', 'Psat3g158840' => 'psa', 'PSO170G2858' => 'pso', 'PSO339G0606' => 'pso', 'PSO384G4709' => 'pso', 'PSO407G0334' => 'pso', 'QL04p040276' => 'qlo', 'QL06p005458' => 'qlo', 'QL06p005472' => 'qlo', 'QL07p030546' => 'qlo', 'QL07p031519' => 'qlo', 'QL09p050949' => 'qlo', 'QL09p050966' => 'qlo', 'QL09p051067' => 'qlo', 'QL12p022706' => 'qlo', 'RcHm_v2.0_Chr2g0119601' => 'rch', 'RcHm_v2.0_Chr3g0459591' => 'rch', 'RcHm_v2.0_Chr4g0418521' => 'rch', 'RcHm_v2.0_Chr4g0418531' => 'rch', 'RcHm_v2.0_Chr4g0418541' => 'rch', 'RcHm_v2.0_Chr6g0291641' => 'rch', 'Rhsim01G0086300' => 'rsi', 'Rhsim01G0276300' => 'rsi', 'Rhsim01G0276500' => 'rsi', 'Rhsim04G0207700' => 'rsi', 'Rhsim05G0234500' => 'rsi', 'Rhsim13G0022400' => 'rsi', 'Sabra02G0167900' => 'sbr', 'Sabra04G0158500' => 'sbr', 'Sabra08G0159800' => 'sbr', 'Sabra10G0011500' => 'sbr', 'Sabra14G0104400' => 'sbr', 'SalBow2G2440' => 'sbo', 'SalBow4G2265' => 'sbo', 'Sc02g0000060' => 'sci', 'Sc05g0005020' => 'sci', 'Sc13g0003890' => 'sci', 'Sed0014865' => 'sed', 'Sed0017224' => 'sed', 'Sed0026391' => 'sed', 'SEGI_00063' => 'sgi', 'SEGI_10967' => 'sgi', 'SEGI_17510' => 'sgi', 'SEGI_24396' => 'sgi', 'SEGI_39719' => 'sgi', 'SEGI_41392' => 'sgi', 'SGA_v2.0_scaffold11G05794' => 'sas', 'SGA_v2.0_scaffold142G35607' => 'sas', 'SGA_v2.0_scaffold1G00447' => 'sas', 'SHI15388' => 'shi', 'SHI15394' => 'shi', 'SHI15396' => 'shi', 'SHI15399' => 'shi', 'SMO343G0151' => 'smo', 'SMO367G1118' => 'smo', 'Solyc01g080200.3' => 'sly', 'Solyc06g008960.3' => 'sly', 'Solyc09g064780.3' => 'sly', 'Sopen01g031980' => 'spe', 'Sopen06g003710' => 'spe', 'Sopen09g026460' => 'spe', 'Sp3g21240' => 'spa', 'Sp4g30030' => 'spa', 'TAR365G0022' => 'tar', 'TAR365G1023' => 'tar', 'TAR365G1253' => 'tar', 'TAR623G0078' => 'tar', 'TAR623G1721' => 'tar', 'TAR633G0959' => 'tar', 'THA.LOC104802225' => 'tha', 'THA.LOC104804769' => 'tha', 'THA.LOC104808660' => 'tha', 'THA.LOC104812792' => 'tha', 'Thecc.01G284000' => 'tca', 'Thecc.04G220600' => 'tca', 'Thecc.05G268900' => 'tca', 'Thecc.08G171100' => 'tca', 'Thhalv10001284m.g' => 'esa', 'Thhalv10019912m.g' => 'esa', 'TPR.G14189' => 'tpr', 'TPR.G18110' => 'tpr', 'TPR.G18130' => 'tpr', 'TPR.G18131' => 'tpr', 'TPR.G18140' => 'tpr', 'TPR.G24282' => 'tpr', 'TPR.G25221' => 'tpr', 'TPR.G29267' => 'tpr', 'TPR.G35315' => 'tpr', 'TPR.G36173' => 'tpr', 'TWI09G0794' => 'twi', 'TWI59G1348' => 'twi', 'TWI74G0430' => 'twi', 'unitig_26.g8940' => 'ugi', 'unitig_749.g13744' => 'ugi', 'unitig_749.g13745' => 'ugi', 'vmacro08269' => 'vma', 'vmacro14937' => 'vma', 'vmacro20401' => 'vma', 'VMungo0464G1349' => 'vmu', 'VMungo0540G0289' => 'vmu', 'VMungo1215G1590' => 'vmu', 'VMungo1309G0221' => 'vmu', 'VMungo1309G2815' => 'vmu', 'VMungo1383G0239' => 'vmu', 'VMungo1383G2910' => 'vmu', 'Zm00001eb095270' => 'zma', 'Zm00001eb095280' => 'zma', 'Zm00001eb111630' => 'zma', 'Zm00001eb237080' => 'zma', 'Zm00001eb273740' => 'zma', 'Zm00001eb285040' => 'zma', 'Zm00001eb330790' => 'zma', 'Zm00001eb337380' => 'zma' ), 'gf_id' => 'HOM05D001484', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001484' ), 'data_identifier' => 'HOM05D001484', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001484', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p31500' => 'bna', 'A05p00020' => 'bna', 'A07p08820' => 'bna', 'Aa31LG4G3300' => 'aar', 'Aa31LG8G10030' => 'aar', 'Actinidia00731' => 'ach', 'Actinidia11473' => 'ach', 'Actinidia23469' => 'ach', 'Actinidia24318' => 'ach', 'Actinidia40196' => 'ach', 'Actinidia40197' => 'ach', 'Actinidia40198' => 'ach', 'Ah.08g212990' => 'amhyb', 'Ah.15g091720' => 'amhyb', 'AL3G38260' => 'aly', 'AL4G47710' => 'aly', 'Aqoxy2G00671' => 'aox', 'Aqoxy2G03236' => 'aox', 'arahy.Tifrunner.gnm1.ann1.05IDCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KR684' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATY3SJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK6QJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6APGL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IDT7Z9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM073U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ0R87' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LE7RV4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT4QRX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V5ENPK' => 'arhy', 'AT2G48110' => 'ath', 'AT3G23590' => 'ath', 'ATR0626G186' => 'atr', 'ATR1127G141' => 'atr', 'Atru.chr4.2583' => 'acertr', 'Atru.chr5.1358' => 'acertr', 'Atru.chr5.1359' => 'acertr', 'Atru.chr8.46' => 'acertr', 'AUR62002640' => 'cqu', 'AUR62030055' => 'cqu', 'AUR62033713' => 'cqu', 'AUR62033714' => 'cqu', 'AUR62036795' => 'cqu', 'AUR62039891' => 'cqu', 'BcaB02g08737' => 'bca', 'BcaB04g20441' => 'bca', 'BcaB06g26509' => 'bca', 'BcaB06g26510' => 'bca', 'BcaB06g26511' => 'bca', 'BcaB06g26512' => 'bca', 'BcaB06g26513' => 'bca', 'BcaC02g12564' => 'bca', 'BcaC02g12565' => 'bca', 'BcaC02g12794' => 'bca', 'BcaC02g12795' => 'bca', 'BcaC02g12796' => 'bca', 'BcaC06g35541' => 'bca', 'BNapus_Darmor_BZH_scaffold_188p00080' => 'bna', 'BNapus_Darmor_BZH_scaffold_188p00090' => 'bna', 'BolC1t03972H' => 'bol', 'BolC1t03973H' => 'bol', 'BolC4t21680H' => 'bol', 'BolC7t41863H' => 'bol', 'BolSC55t61227H' => 'bol', 'BolSC55t61228H' => 'bol', 'BraA01t03278Z' => 'bra', 'BraA05t18998Z' => 'bra', 'BraA07t28673Z' => 'bra', 'C01p40150' => 'bna', 'C05p12370' => 'bna', 'C07p13680' => 'bna', 'CAN.G1006.16' => 'can', 'CAN.G1006.17' => 'can', 'CAN.G1170.2' => 'can', 'CAN.G962.7' => 'can', 'CANSAT25G2179' => 'cansat', 'CANSAT78G1573' => 'cansat', 'CARHR099510' => 'chi', 'CARHR143510' => 'chi', 'Carub.0003s2380' => 'cru', 'Carub.0004s3082' => 'cru', 'Ca_00614_v3' => 'car', 'Ca_07801_v3' => 'car', 'Ca_08567_v3' => 'car', 'Ca_09571_v3' => 'car', 'CBR_g19290' => 'cbr', 'Cc01_g19770' => 'ccan', 'Cc03_g03030' => 'ccan', 'CDE07G0968' => 'cde', 'CDE09G1441' => 'cde', 'Cfa006103' => 'cfa', 'Cfa015573' => 'cfa', 'Cfa016988' => 'cfa', 'Ciclev10006738m.g' => 'ccl', 'Ciclev10010920m.g' => 'ccl', 'Ciclev10018517m.g' => 'ccl', 'CiPaw.01G159200' => 'cil', 'CiPaw.02G091000' => 'cil', 'CiPaw.02G091100' => 'cil', 'CiPaw.08G103100' => 'cil', 'CiPaw.09G224900' => 'cil', 'ClCG06G005740' => 'cla', 'ClCG07G000090' => 'cla', 'ClCG07G000100' => 'cla', 'COL.COLO4_09143' => 'col', 'COL.COLO4_25124' => 'col', 'Cpa.g.sc16.34' => 'cpa', 'Cpa.g.sc3504.1' => 'cpa', 'Cpa.g.sc60.37' => 'cpa', 'CsaV3_6G018520' => 'csa', 'CsaV3_6G036860' => 'csa', 'CSS0001072' => 'camsi', 'CSS0020208' => 'camsi', 'CSS0021253' => 'camsi', 'CSS0022190' => 'camsi', 'CSS0036150' => 'camsi', 'CSS0040442' => 'camsi', 'CSS0042300' => 'camsi', 'CSS0045298' => 'camsi', 'DCAR_012449' => 'dca', 'DCAR_018405' => 'dca', 'DCAR_024573' => 'dca', 'DCAR_030591' => 'dca', 'Dinv16926' => 'din', 'Dinv32963' => 'din', 'Dinv38382' => 'din', 'Dinv38383' => 'din', 'Duzib133G0974' => 'dzi', 'Duzib138G1867' => 'dzi', 'Duzib211G0420' => 'dzi', 'Duzib212G0930' => 'dzi', 'ECA234G1645' => 'eca', 'ECA247G3467' => 'eca', 'ECA248G1703' => 'eca', 'EL10Ac3g06327' => 'bvu', 'EL10Ac7g17204' => 'bvu', 'Eucgr.A00855' => 'egr', 'Eucgr.A00858' => 'egr', 'Eucgr.H01520' => 'egr', 'Eucgr.H03604' => 'egr', 'Eucgr.L03465' => 'egr', 'Eucgr.L03466' => 'egr', 'FAN01G0988' => 'fan', 'FAN02G3892' => 'fan', 'FAN05G3381' => 'fan', 'FAN07G0967' => 'fan', 'FAN07G1493' => 'fan', 'FAN08G3125' => 'fan', 'FAN09G0402' => 'fan', 'FAN12G2594' => 'fan', 'FAN12G3879' => 'fan', 'FAN14G1546' => 'fan', 'FAN15G3626' => 'fan', 'FAN17G0588' => 'fan', 'FAN17G0609' => 'fan', 'FAN18G2817' => 'fan', 'FAN19G1305' => 'fan', 'FAN20G1787' => 'fan', 'FAN22G0073' => 'fan', 'FAN22G0352' => 'fan', 'FAN22G0368' => 'fan', 'FAN22G2273' => 'fan', 'FAN24G1998' => 'fan', 'FAN27G1317' => 'fan', 'FvH4_2g23980' => 'fve', 'FvH4_4g14380' => 'fve', 'FvH4_4g14390' => 'fve', 'FvH4_6g09250' => 'fve', 'Glyma.03G151100' => 'gma', 'Glyma.04G122550' => 'gma', 'Glyma.05G001600' => 'gma', 'Glyma.09G270766' => 'gma', 'Glyma.09G270832' => 'gma', 'Glyma.13G209800' => 'gma', 'Glyma.15G102800' => 'gma', 'Glyma.18G218900' => 'gma', 'Glyma.19G001500' => 'gma', 'Glyma.19G153600' => 'gma', 'Gohir.A02G028600' => 'ghi', 'Gohir.A08G045000' => 'ghi', 'Gohir.A11G120500' => 'ghi', 'Gohir.A12G006200' => 'ghi', 'Gohir.A12G006250' => 'ghi', 'Gohir.D02G036300' => 'ghi', 'Gohir.D08G054700' => 'ghi', 'Gohir.D11G125600' => 'ghi', 'Gohir.D12G005700' => 'ghi', 'Gorai.004G055200' => 'gra', 'Gorai.005G040400' => 'gra', 'Gorai.007G134500' => 'gra', 'Gorai.008G005500' => 'gra', 'GSVIVG01011094001' => 'vvi', 'GSVIVG01017879001' => 'vvi', 'GSVIVG01025988001' => 'vvi', 'GSVIVG01029847001' => 'vvi', 'HanXRQChr10g0282901' => 'han', 'HanXRQChr10g0310371' => 'han', 'HanXRQChr10g0315041' => 'han', 'HanXRQChr11g0327651' => 'han', 'HanXRQChr12g0359391' => 'han', 'Haze_00972' => 'cav', 'Haze_00973' => 'cav', 'Haze_00974' => 'cav', 'Haze_04747' => 'cav', 'Haze_04749' => 'cav', 'Haze_04750' => 'cav', 'Haze_21217' => 'cav', 'Hma1.2p1_1037F.1_g250680' => 'hma', 'Hma1.2p1_1644F.1_g295320' => 'hma', 'HPP92_011322' => 'vpl', 'HPP92_011323' => 'vpl', 'HPP92_011324' => 'vpl', 'HPP92_011325' => 'vpl', 'HPP92_011326' => 'vpl', 'Hund12205' => 'sun', 'Hund17957' => 'sun', 'Lalb_Chr06g0176771' => 'lal', 'Lalb_Chr18g0056021' => 'lal', 'Lalb_Chr18g0056031' => 'lal', 'Lalb_Chr18g0056041' => 'lal', 'Lalb_Chr20g0107751' => 'lal', 'Lalb_Chr20g0118371' => 'lal', 'Lj1g0010239' => 'lja', 'Lj1g0017101' => 'lja', 'Lj2A1178G40' => 'lonja', 'Lj2A54G84' => 'lonja', 'Lj2g0015248' => 'lja', 'Lj3A761T51' => 'lonja', 'Lj6g0018116' => 'lja', 'Lsat_1_v5_gn_4_136040' => 'lsa', 'Lsat_1_v5_gn_5_187461' => 'lsa', 'Lsat_1_v5_gn_5_77001' => 'lsa', 'Lsat_1_v5_gn_9_4461' => 'lsa', 'Manes.01G210100' => 'mes', 'Manes.03G185600' => 'mes', 'Manes.05G073300' => 'mes', 'Manes.09G120300' => 'mes', 'Manes.15G022100' => 'mes', 'Mapoly0096s0053' => 'mpo', 'MBI03_g14058_MAGBIO' => 'mbi', 'MBI03_g33876_MAGBIO' => 'mbi', 'MBI03_g36854_MAGBIO' => 'mbi', 'MBI17_g11997_MAGBIO' => 'mbi', 'MD03G1269000' => 'mdo', 'MD04G1179600' => 'mdo', 'MD11G1289800' => 'mdo', 'MD12G1194700' => 'mdo', 'MD13G1182100' => 'mdo', 'MD13G1182200' => 'mdo', 'MD16G1182600' => 'mdo', 'Medtr2g021400' => 'mtr', 'Medtr2g021470' => 'mtr', 'Medtr2g105810' => 'mtr', 'Medtr3g033580' => 'mtr', 'Medtr6g007970' => 'mtr', 'Medtr7g056330' => 'mtr', 'Medtr7g074290' => 'mtr', 'Medtr7g074380' => 'mtr', 'Medtr7g094550' => 'mtr', 'Medtr8g069995' => 'mtr', 'MELO3C014345.2' => 'cme', 'MELO3C021395.2' => 'cme', 'Migut.D00262' => 'egut', 'Migut.G00257' => 'egut', 'MSTRG.21575' => 'ama', 'MSTRG.3985' => 'ama', 'Nitab4.5_0000295g0140' => 'nta', 'Nitab4.5_0000732g0140' => 'nta', 'Nitab4.5_0003162g0020' => 'nta', 'Nitab4.5_0006180g0090' => 'nta', 'Nitab4.5_0006390g0010' => 'nta', 'Nitab4.5_0007392g0040' => 'nta', 'Nn1g02140' => 'nnu', 'Nn4g26168' => 'nnu', 'Nn5g26754' => 'nnu', 'Oeu001433.1' => 'oeu', 'Oeu010299.2' => 'oeu', 'Oeu011171.1' => 'oeu', 'Oeu037675.1' => 'oeu', 'Oeu038359.1' => 'oeu', 'Oeu063834.1' => 'oeu', 'Oeu063835.1' => 'oeu', 'Os05g0312000' => 'osa', 'Os07g0211101' => 'osa', 'Os07g0211200' => 'osa', 'Os07g0681500' => 'osa', 'Peaxi162Scf00095g01015' => 'pax', 'Peaxi162Scf00104g00329' => 'pax', 'Peaxi162Scf00161g00137' => 'pax', 'PGR004G1665' => 'pgr', 'PGR031G2937' => 'pgr', 'PGR119G2145' => 'pgr', 'PGSC0003DMG400004351' => 'stu', 'PGSC0003DMG400014625' => 'stu', 'PGSC0003DMG401000943' => 'stu', 'Phvul.001G148600' => 'pvu', 'Phvul.004G001700' => 'pvu', 'Phvul.006G154900' => 'pvu', 'Phvul.008G078200' => 'pvu', 'Phvul.011G136500' => 'pvu', 'Potri.002G215600' => 'ptr', 'Potri.008G201600' => 'ptr', 'Potri.014G138400' => 'ptr', 'Potri.016G142500' => 'ptr', 'Pp3c16_10580' => 'ppa', 'Pp3c5_25280' => 'ppa', 'Prupe.1G150000' => 'ppe', 'Prupe.1G150100' => 'ppe', 'Prupe.6G299600' => 'ppe', 'Prupe.8G245000' => 'ppe', 'Psat0s4927g0040' => 'psa', 'Psat1g052080' => 'psa', 'Psat1g183800' => 'psa', 'Psat3g113840' => 'psa', 'Psat3g126120' => 'psa', 'Psat3g126160' => 'psa', 'Psat3g158760' => 'psa', 'Psat3g158840' => 'psa', 'PSO170G2858' => 'pso', 'PSO339G0606' => 'pso', 'PSO384G4709' => 'pso', 'PSO407G0334' => 'pso', 'QL04p040276' => 'qlo', 'QL06p005458' => 'qlo', 'QL06p005472' => 'qlo', 'QL07p030546' => 'qlo', 'QL07p031519' => 'qlo', 'QL09p050949' => 'qlo', 'QL09p050966' => 'qlo', 'QL09p051067' => 'qlo', 'QL12p022706' => 'qlo', 'RcHm_v2.0_Chr2g0119601' => 'rch', 'RcHm_v2.0_Chr3g0459591' => 'rch', 'RcHm_v2.0_Chr4g0418521' => 'rch', 'RcHm_v2.0_Chr4g0418531' => 'rch', 'RcHm_v2.0_Chr4g0418541' => 'rch', 'RcHm_v2.0_Chr6g0291641' => 'rch', 'Rhsim01G0086300' => 'rsi', 'Rhsim01G0276300' => 'rsi', 'Rhsim01G0276500' => 'rsi', 'Rhsim04G0207700' => 'rsi', 'Rhsim05G0234500' => 'rsi', 'Rhsim13G0022400' => 'rsi', 'Sabra02G0167900' => 'sbr', 'Sabra04G0158500' => 'sbr', 'Sabra08G0159800' => 'sbr', 'Sabra10G0011500' => 'sbr', 'Sabra14G0104400' => 'sbr', 'SalBow2G2440' => 'sbo', 'SalBow4G2265' => 'sbo', 'Sc02g0000060' => 'sci', 'Sc05g0005020' => 'sci', 'Sc13g0003890' => 'sci', 'Sed0014865' => 'sed', 'Sed0017224' => 'sed', 'Sed0026391' => 'sed', 'SEGI_00063' => 'sgi', 'SEGI_10967' => 'sgi', 'SEGI_17510' => 'sgi', 'SEGI_24396' => 'sgi', 'SEGI_39719' => 'sgi', 'SEGI_41392' => 'sgi', 'SGA_v2.0_scaffold11G05794' => 'sas', 'SGA_v2.0_scaffold142G35607' => 'sas', 'SGA_v2.0_scaffold1G00447' => 'sas', 'SHI15388' => 'shi', 'SHI15394' => 'shi', 'SHI15396' => 'shi', 'SHI15399' => 'shi', 'SMO343G0151' => 'smo', 'SMO367G1118' => 'smo', 'Solyc01g080200.3' => 'sly', 'Solyc06g008960.3' => 'sly', 'Solyc09g064780.3' => 'sly', 'Sopen01g031980' => 'spe', 'Sopen06g003710' => 'spe', 'Sopen09g026460' => 'spe', 'Sp3g21240' => 'spa', 'Sp4g30030' => 'spa', 'TAR365G0022' => 'tar', 'TAR365G1023' => 'tar', 'TAR365G1253' => 'tar', 'TAR623G0078' => 'tar', 'TAR623G1721' => 'tar', 'TAR633G0959' => 'tar', 'THA.LOC104802225' => 'tha', 'THA.LOC104804769' => 'tha', 'THA.LOC104808660' => 'tha', 'THA.LOC104812792' => 'tha', 'Thecc.01G284000' => 'tca', 'Thecc.04G220600' => 'tca', 'Thecc.05G268900' => 'tca', 'Thecc.08G171100' => 'tca', 'Thhalv10001284m.g' => 'esa', 'Thhalv10019912m.g' => 'esa', 'TPR.G14189' => 'tpr', 'TPR.G18110' => 'tpr', 'TPR.G18130' => 'tpr', 'TPR.G18131' => 'tpr', 'TPR.G18140' => 'tpr', 'TPR.G24282' => 'tpr', 'TPR.G25221' => 'tpr', 'TPR.G29267' => 'tpr', 'TPR.G35315' => 'tpr', 'TPR.G36173' => 'tpr', 'TWI09G0794' => 'twi', 'TWI59G1348' => 'twi', 'TWI74G0430' => 'twi', 'unitig_26.g8940' => 'ugi', 'unitig_749.g13744' => 'ugi', 'unitig_749.g13745' => 'ugi', 'vmacro08269' => 'vma', 'vmacro14937' => 'vma', 'vmacro20401' => 'vma', 'VMungo0464G1349' => 'vmu', 'VMungo0540G0289' => 'vmu', 'VMungo1215G1590' => 'vmu', 'VMungo1309G0221' => 'vmu', 'VMungo1309G2815' => 'vmu', 'VMungo1383G0239' => 'vmu', 'VMungo1383G2910' => 'vmu', 'Zm00001eb095270' => 'zma', 'Zm00001eb095280' => 'zma', 'Zm00001eb111630' => 'zma', 'Zm00001eb237080' => 'zma', 'Zm00001eb273740' => 'zma', 'Zm00001eb285040' => 'zma', 'Zm00001eb330790' => 'zma', 'Zm00001eb337380' => 'zma' ) $gf_id = 'HOM05D001484' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001484' ) $data_identifier = 'HOM05D001484' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 2, 'aly' => (int) 2, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 22, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 7, 'hma' => (int) 2, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 7, 'mtr' => (int) 10, 'cme' => (int) 2, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 4, 'ppa' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 4, 'qlo' => (int) 9, 'rch' => (int) 6, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 10, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 7, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb337380' $species_info = array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ) $local_species = 'car' $disabled = '' $selected = '' $num_hits = (int) 0
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001484', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p31500' => 'bna', 'A05p00020' => 'bna', 'A07p08820' => 'bna', 'Aa31LG4G3300' => 'aar', 'Aa31LG8G10030' => 'aar', 'Actinidia00731' => 'ach', 'Actinidia11473' => 'ach', 'Actinidia23469' => 'ach', 'Actinidia24318' => 'ach', 'Actinidia40196' => 'ach', 'Actinidia40197' => 'ach', 'Actinidia40198' => 'ach', 'Ah.08g212990' => 'amhyb', 'Ah.15g091720' => 'amhyb', 'AL3G38260' => 'aly', 'AL4G47710' => 'aly', 'Aqoxy2G00671' => 'aox', 'Aqoxy2G03236' => 'aox', 'arahy.Tifrunner.gnm1.ann1.05IDCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KR684' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATY3SJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK6QJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6APGL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IDT7Z9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM073U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ0R87' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LE7RV4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT4QRX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V5ENPK' => 'arhy', 'AT2G48110' => 'ath', 'AT3G23590' => 'ath', 'ATR0626G186' => 'atr', 'ATR1127G141' => 'atr', 'Atru.chr4.2583' => 'acertr', 'Atru.chr5.1358' => 'acertr', 'Atru.chr5.1359' => 'acertr', 'Atru.chr8.46' => 'acertr', 'AUR62002640' => 'cqu', 'AUR62030055' => 'cqu', 'AUR62033713' => 'cqu', 'AUR62033714' => 'cqu', 'AUR62036795' => 'cqu', 'AUR62039891' => 'cqu', 'BcaB02g08737' => 'bca', 'BcaB04g20441' => 'bca', 'BcaB06g26509' => 'bca', 'BcaB06g26510' => 'bca', 'BcaB06g26511' => 'bca', 'BcaB06g26512' => 'bca', 'BcaB06g26513' => 'bca', 'BcaC02g12564' => 'bca', 'BcaC02g12565' => 'bca', 'BcaC02g12794' => 'bca', 'BcaC02g12795' => 'bca', 'BcaC02g12796' => 'bca', 'BcaC06g35541' => 'bca', 'BNapus_Darmor_BZH_scaffold_188p00080' => 'bna', 'BNapus_Darmor_BZH_scaffold_188p00090' => 'bna', 'BolC1t03972H' => 'bol', 'BolC1t03973H' => 'bol', 'BolC4t21680H' => 'bol', 'BolC7t41863H' => 'bol', 'BolSC55t61227H' => 'bol', 'BolSC55t61228H' => 'bol', 'BraA01t03278Z' => 'bra', 'BraA05t18998Z' => 'bra', 'BraA07t28673Z' => 'bra', 'C01p40150' => 'bna', 'C05p12370' => 'bna', 'C07p13680' => 'bna', 'CAN.G1006.16' => 'can', 'CAN.G1006.17' => 'can', 'CAN.G1170.2' => 'can', 'CAN.G962.7' => 'can', 'CANSAT25G2179' => 'cansat', 'CANSAT78G1573' => 'cansat', 'CARHR099510' => 'chi', 'CARHR143510' => 'chi', 'Carub.0003s2380' => 'cru', 'Carub.0004s3082' => 'cru', 'Ca_00614_v3' => 'car', 'Ca_07801_v3' => 'car', 'Ca_08567_v3' => 'car', 'Ca_09571_v3' => 'car', 'CBR_g19290' => 'cbr', 'Cc01_g19770' => 'ccan', 'Cc03_g03030' => 'ccan', 'CDE07G0968' => 'cde', 'CDE09G1441' => 'cde', 'Cfa006103' => 'cfa', 'Cfa015573' => 'cfa', 'Cfa016988' => 'cfa', 'Ciclev10006738m.g' => 'ccl', 'Ciclev10010920m.g' => 'ccl', 'Ciclev10018517m.g' => 'ccl', 'CiPaw.01G159200' => 'cil', 'CiPaw.02G091000' => 'cil', 'CiPaw.02G091100' => 'cil', 'CiPaw.08G103100' => 'cil', 'CiPaw.09G224900' => 'cil', 'ClCG06G005740' => 'cla', 'ClCG07G000090' => 'cla', 'ClCG07G000100' => 'cla', 'COL.COLO4_09143' => 'col', 'COL.COLO4_25124' => 'col', 'Cpa.g.sc16.34' => 'cpa', 'Cpa.g.sc3504.1' => 'cpa', 'Cpa.g.sc60.37' => 'cpa', 'CsaV3_6G018520' => 'csa', 'CsaV3_6G036860' => 'csa', 'CSS0001072' => 'camsi', 'CSS0020208' => 'camsi', 'CSS0021253' => 'camsi', 'CSS0022190' => 'camsi', 'CSS0036150' => 'camsi', 'CSS0040442' => 'camsi', 'CSS0042300' => 'camsi', 'CSS0045298' => 'camsi', 'DCAR_012449' => 'dca', 'DCAR_018405' => 'dca', 'DCAR_024573' => 'dca', 'DCAR_030591' => 'dca', 'Dinv16926' => 'din', 'Dinv32963' => 'din', 'Dinv38382' => 'din', 'Dinv38383' => 'din', 'Duzib133G0974' => 'dzi', 'Duzib138G1867' => 'dzi', 'Duzib211G0420' => 'dzi', 'Duzib212G0930' => 'dzi', 'ECA234G1645' => 'eca', 'ECA247G3467' => 'eca', 'ECA248G1703' => 'eca', 'EL10Ac3g06327' => 'bvu', 'EL10Ac7g17204' => 'bvu', 'Eucgr.A00855' => 'egr', 'Eucgr.A00858' => 'egr', 'Eucgr.H01520' => 'egr', 'Eucgr.H03604' => 'egr', 'Eucgr.L03465' => 'egr', 'Eucgr.L03466' => 'egr', 'FAN01G0988' => 'fan', 'FAN02G3892' => 'fan', 'FAN05G3381' => 'fan', 'FAN07G0967' => 'fan', 'FAN07G1493' => 'fan', 'FAN08G3125' => 'fan', 'FAN09G0402' => 'fan', 'FAN12G2594' => 'fan', 'FAN12G3879' => 'fan', 'FAN14G1546' => 'fan', 'FAN15G3626' => 'fan', 'FAN17G0588' => 'fan', 'FAN17G0609' => 'fan', 'FAN18G2817' => 'fan', 'FAN19G1305' => 'fan', 'FAN20G1787' => 'fan', 'FAN22G0073' => 'fan', 'FAN22G0352' => 'fan', 'FAN22G0368' => 'fan', 'FAN22G2273' => 'fan', 'FAN24G1998' => 'fan', 'FAN27G1317' => 'fan', 'FvH4_2g23980' => 'fve', 'FvH4_4g14380' => 'fve', 'FvH4_4g14390' => 'fve', 'FvH4_6g09250' => 'fve', 'Glyma.03G151100' => 'gma', 'Glyma.04G122550' => 'gma', 'Glyma.05G001600' => 'gma', 'Glyma.09G270766' => 'gma', 'Glyma.09G270832' => 'gma', 'Glyma.13G209800' => 'gma', 'Glyma.15G102800' => 'gma', 'Glyma.18G218900' => 'gma', 'Glyma.19G001500' => 'gma', 'Glyma.19G153600' => 'gma', 'Gohir.A02G028600' => 'ghi', 'Gohir.A08G045000' => 'ghi', 'Gohir.A11G120500' => 'ghi', 'Gohir.A12G006200' => 'ghi', 'Gohir.A12G006250' => 'ghi', 'Gohir.D02G036300' => 'ghi', 'Gohir.D08G054700' => 'ghi', 'Gohir.D11G125600' => 'ghi', 'Gohir.D12G005700' => 'ghi', 'Gorai.004G055200' => 'gra', 'Gorai.005G040400' => 'gra', 'Gorai.007G134500' => 'gra', 'Gorai.008G005500' => 'gra', 'GSVIVG01011094001' => 'vvi', 'GSVIVG01017879001' => 'vvi', 'GSVIVG01025988001' => 'vvi', 'GSVIVG01029847001' => 'vvi', 'HanXRQChr10g0282901' => 'han', 'HanXRQChr10g0310371' => 'han', 'HanXRQChr10g0315041' => 'han', 'HanXRQChr11g0327651' => 'han', 'HanXRQChr12g0359391' => 'han', 'Haze_00972' => 'cav', 'Haze_00973' => 'cav', 'Haze_00974' => 'cav', 'Haze_04747' => 'cav', 'Haze_04749' => 'cav', 'Haze_04750' => 'cav', 'Haze_21217' => 'cav', 'Hma1.2p1_1037F.1_g250680' => 'hma', 'Hma1.2p1_1644F.1_g295320' => 'hma', 'HPP92_011322' => 'vpl', 'HPP92_011323' => 'vpl', 'HPP92_011324' => 'vpl', 'HPP92_011325' => 'vpl', 'HPP92_011326' => 'vpl', 'Hund12205' => 'sun', 'Hund17957' => 'sun', 'Lalb_Chr06g0176771' => 'lal', 'Lalb_Chr18g0056021' => 'lal', 'Lalb_Chr18g0056031' => 'lal', 'Lalb_Chr18g0056041' => 'lal', 'Lalb_Chr20g0107751' => 'lal', 'Lalb_Chr20g0118371' => 'lal', 'Lj1g0010239' => 'lja', 'Lj1g0017101' => 'lja', 'Lj2A1178G40' => 'lonja', 'Lj2A54G84' => 'lonja', 'Lj2g0015248' => 'lja', 'Lj3A761T51' => 'lonja', 'Lj6g0018116' => 'lja', 'Lsat_1_v5_gn_4_136040' => 'lsa', 'Lsat_1_v5_gn_5_187461' => 'lsa', 'Lsat_1_v5_gn_5_77001' => 'lsa', 'Lsat_1_v5_gn_9_4461' => 'lsa', 'Manes.01G210100' => 'mes', 'Manes.03G185600' => 'mes', 'Manes.05G073300' => 'mes', 'Manes.09G120300' => 'mes', 'Manes.15G022100' => 'mes', 'Mapoly0096s0053' => 'mpo', 'MBI03_g14058_MAGBIO' => 'mbi', 'MBI03_g33876_MAGBIO' => 'mbi', 'MBI03_g36854_MAGBIO' => 'mbi', 'MBI17_g11997_MAGBIO' => 'mbi', 'MD03G1269000' => 'mdo', 'MD04G1179600' => 'mdo', 'MD11G1289800' => 'mdo', 'MD12G1194700' => 'mdo', 'MD13G1182100' => 'mdo', 'MD13G1182200' => 'mdo', 'MD16G1182600' => 'mdo', 'Medtr2g021400' => 'mtr', 'Medtr2g021470' => 'mtr', 'Medtr2g105810' => 'mtr', 'Medtr3g033580' => 'mtr', 'Medtr6g007970' => 'mtr', 'Medtr7g056330' => 'mtr', 'Medtr7g074290' => 'mtr', 'Medtr7g074380' => 'mtr', 'Medtr7g094550' => 'mtr', 'Medtr8g069995' => 'mtr', 'MELO3C014345.2' => 'cme', 'MELO3C021395.2' => 'cme', 'Migut.D00262' => 'egut', 'Migut.G00257' => 'egut', 'MSTRG.21575' => 'ama', 'MSTRG.3985' => 'ama', 'Nitab4.5_0000295g0140' => 'nta', 'Nitab4.5_0000732g0140' => 'nta', 'Nitab4.5_0003162g0020' => 'nta', 'Nitab4.5_0006180g0090' => 'nta', 'Nitab4.5_0006390g0010' => 'nta', 'Nitab4.5_0007392g0040' => 'nta', 'Nn1g02140' => 'nnu', 'Nn4g26168' => 'nnu', 'Nn5g26754' => 'nnu', 'Oeu001433.1' => 'oeu', 'Oeu010299.2' => 'oeu', 'Oeu011171.1' => 'oeu', 'Oeu037675.1' => 'oeu', 'Oeu038359.1' => 'oeu', 'Oeu063834.1' => 'oeu', 'Oeu063835.1' => 'oeu', 'Os05g0312000' => 'osa', 'Os07g0211101' => 'osa', 'Os07g0211200' => 'osa', 'Os07g0681500' => 'osa', 'Peaxi162Scf00095g01015' => 'pax', 'Peaxi162Scf00104g00329' => 'pax', 'Peaxi162Scf00161g00137' => 'pax', 'PGR004G1665' => 'pgr', 'PGR031G2937' => 'pgr', 'PGR119G2145' => 'pgr', 'PGSC0003DMG400004351' => 'stu', 'PGSC0003DMG400014625' => 'stu', 'PGSC0003DMG401000943' => 'stu', 'Phvul.001G148600' => 'pvu', 'Phvul.004G001700' => 'pvu', 'Phvul.006G154900' => 'pvu', 'Phvul.008G078200' => 'pvu', 'Phvul.011G136500' => 'pvu', 'Potri.002G215600' => 'ptr', 'Potri.008G201600' => 'ptr', 'Potri.014G138400' => 'ptr', 'Potri.016G142500' => 'ptr', 'Pp3c16_10580' => 'ppa', 'Pp3c5_25280' => 'ppa', 'Prupe.1G150000' => 'ppe', 'Prupe.1G150100' => 'ppe', 'Prupe.6G299600' => 'ppe', 'Prupe.8G245000' => 'ppe', 'Psat0s4927g0040' => 'psa', 'Psat1g052080' => 'psa', 'Psat1g183800' => 'psa', 'Psat3g113840' => 'psa', 'Psat3g126120' => 'psa', 'Psat3g126160' => 'psa', 'Psat3g158760' => 'psa', 'Psat3g158840' => 'psa', 'PSO170G2858' => 'pso', 'PSO339G0606' => 'pso', 'PSO384G4709' => 'pso', 'PSO407G0334' => 'pso', 'QL04p040276' => 'qlo', 'QL06p005458' => 'qlo', 'QL06p005472' => 'qlo', 'QL07p030546' => 'qlo', 'QL07p031519' => 'qlo', 'QL09p050949' => 'qlo', 'QL09p050966' => 'qlo', 'QL09p051067' => 'qlo', 'QL12p022706' => 'qlo', 'RcHm_v2.0_Chr2g0119601' => 'rch', 'RcHm_v2.0_Chr3g0459591' => 'rch', 'RcHm_v2.0_Chr4g0418521' => 'rch', 'RcHm_v2.0_Chr4g0418531' => 'rch', 'RcHm_v2.0_Chr4g0418541' => 'rch', 'RcHm_v2.0_Chr6g0291641' => 'rch', 'Rhsim01G0086300' => 'rsi', 'Rhsim01G0276300' => 'rsi', 'Rhsim01G0276500' => 'rsi', 'Rhsim04G0207700' => 'rsi', 'Rhsim05G0234500' => 'rsi', 'Rhsim13G0022400' => 'rsi', 'Sabra02G0167900' => 'sbr', 'Sabra04G0158500' => 'sbr', 'Sabra08G0159800' => 'sbr', 'Sabra10G0011500' => 'sbr', 'Sabra14G0104400' => 'sbr', 'SalBow2G2440' => 'sbo', 'SalBow4G2265' => 'sbo', 'Sc02g0000060' => 'sci', 'Sc05g0005020' => 'sci', 'Sc13g0003890' => 'sci', 'Sed0014865' => 'sed', 'Sed0017224' => 'sed', 'Sed0026391' => 'sed', 'SEGI_00063' => 'sgi', 'SEGI_10967' => 'sgi', 'SEGI_17510' => 'sgi', 'SEGI_24396' => 'sgi', 'SEGI_39719' => 'sgi', 'SEGI_41392' => 'sgi', 'SGA_v2.0_scaffold11G05794' => 'sas', 'SGA_v2.0_scaffold142G35607' => 'sas', 'SGA_v2.0_scaffold1G00447' => 'sas', 'SHI15388' => 'shi', 'SHI15394' => 'shi', 'SHI15396' => 'shi', 'SHI15399' => 'shi', 'SMO343G0151' => 'smo', 'SMO367G1118' => 'smo', 'Solyc01g080200.3' => 'sly', 'Solyc06g008960.3' => 'sly', 'Solyc09g064780.3' => 'sly', 'Sopen01g031980' => 'spe', 'Sopen06g003710' => 'spe', 'Sopen09g026460' => 'spe', 'Sp3g21240' => 'spa', 'Sp4g30030' => 'spa', 'TAR365G0022' => 'tar', 'TAR365G1023' => 'tar', 'TAR365G1253' => 'tar', 'TAR623G0078' => 'tar', 'TAR623G1721' => 'tar', 'TAR633G0959' => 'tar', 'THA.LOC104802225' => 'tha', 'THA.LOC104804769' => 'tha', 'THA.LOC104808660' => 'tha', 'THA.LOC104812792' => 'tha', 'Thecc.01G284000' => 'tca', 'Thecc.04G220600' => 'tca', 'Thecc.05G268900' => 'tca', 'Thecc.08G171100' => 'tca', 'Thhalv10001284m.g' => 'esa', 'Thhalv10019912m.g' => 'esa', 'TPR.G14189' => 'tpr', 'TPR.G18110' => 'tpr', 'TPR.G18130' => 'tpr', 'TPR.G18131' => 'tpr', 'TPR.G18140' => 'tpr', 'TPR.G24282' => 'tpr', 'TPR.G25221' => 'tpr', 'TPR.G29267' => 'tpr', 'TPR.G35315' => 'tpr', 'TPR.G36173' => 'tpr', 'TWI09G0794' => 'twi', 'TWI59G1348' => 'twi', 'TWI74G0430' => 'twi', 'unitig_26.g8940' => 'ugi', 'unitig_749.g13744' => 'ugi', 'unitig_749.g13745' => 'ugi', 'vmacro08269' => 'vma', 'vmacro14937' => 'vma', 'vmacro20401' => 'vma', 'VMungo0464G1349' => 'vmu', 'VMungo0540G0289' => 'vmu', 'VMungo1215G1590' => 'vmu', 'VMungo1309G0221' => 'vmu', 'VMungo1309G2815' => 'vmu', 'VMungo1383G0239' => 'vmu', 'VMungo1383G2910' => 'vmu', 'Zm00001eb095270' => 'zma', 'Zm00001eb095280' => 'zma', 'Zm00001eb111630' => 'zma', 'Zm00001eb237080' => 'zma', 'Zm00001eb273740' => 'zma', 'Zm00001eb285040' => 'zma', 'Zm00001eb330790' => 'zma', 'Zm00001eb337380' => 'zma' ), 'gf_id' => 'HOM05D001484', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001484' ), 'data_identifier' => 'HOM05D001484', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001484', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p31500' => 'bna', 'A05p00020' => 'bna', 'A07p08820' => 'bna', 'Aa31LG4G3300' => 'aar', 'Aa31LG8G10030' => 'aar', 'Actinidia00731' => 'ach', 'Actinidia11473' => 'ach', 'Actinidia23469' => 'ach', 'Actinidia24318' => 'ach', 'Actinidia40196' => 'ach', 'Actinidia40197' => 'ach', 'Actinidia40198' => 'ach', 'Ah.08g212990' => 'amhyb', 'Ah.15g091720' => 'amhyb', 'AL3G38260' => 'aly', 'AL4G47710' => 'aly', 'Aqoxy2G00671' => 'aox', 'Aqoxy2G03236' => 'aox', 'arahy.Tifrunner.gnm1.ann1.05IDCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KR684' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATY3SJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK6QJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6APGL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IDT7Z9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM073U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ0R87' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LE7RV4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT4QRX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V5ENPK' => 'arhy', 'AT2G48110' => 'ath', 'AT3G23590' => 'ath', 'ATR0626G186' => 'atr', 'ATR1127G141' => 'atr', 'Atru.chr4.2583' => 'acertr', 'Atru.chr5.1358' => 'acertr', 'Atru.chr5.1359' => 'acertr', 'Atru.chr8.46' => 'acertr', 'AUR62002640' => 'cqu', 'AUR62030055' => 'cqu', 'AUR62033713' => 'cqu', 'AUR62033714' => 'cqu', 'AUR62036795' => 'cqu', 'AUR62039891' => 'cqu', 'BcaB02g08737' => 'bca', 'BcaB04g20441' => 'bca', 'BcaB06g26509' => 'bca', 'BcaB06g26510' => 'bca', 'BcaB06g26511' => 'bca', 'BcaB06g26512' => 'bca', 'BcaB06g26513' => 'bca', 'BcaC02g12564' => 'bca', 'BcaC02g12565' => 'bca', 'BcaC02g12794' => 'bca', 'BcaC02g12795' => 'bca', 'BcaC02g12796' => 'bca', 'BcaC06g35541' => 'bca', 'BNapus_Darmor_BZH_scaffold_188p00080' => 'bna', 'BNapus_Darmor_BZH_scaffold_188p00090' => 'bna', 'BolC1t03972H' => 'bol', 'BolC1t03973H' => 'bol', 'BolC4t21680H' => 'bol', 'BolC7t41863H' => 'bol', 'BolSC55t61227H' => 'bol', 'BolSC55t61228H' => 'bol', 'BraA01t03278Z' => 'bra', 'BraA05t18998Z' => 'bra', 'BraA07t28673Z' => 'bra', 'C01p40150' => 'bna', 'C05p12370' => 'bna', 'C07p13680' => 'bna', 'CAN.G1006.16' => 'can', 'CAN.G1006.17' => 'can', 'CAN.G1170.2' => 'can', 'CAN.G962.7' => 'can', 'CANSAT25G2179' => 'cansat', 'CANSAT78G1573' => 'cansat', 'CARHR099510' => 'chi', 'CARHR143510' => 'chi', 'Carub.0003s2380' => 'cru', 'Carub.0004s3082' => 'cru', 'Ca_00614_v3' => 'car', 'Ca_07801_v3' => 'car', 'Ca_08567_v3' => 'car', 'Ca_09571_v3' => 'car', 'CBR_g19290' => 'cbr', 'Cc01_g19770' => 'ccan', 'Cc03_g03030' => 'ccan', 'CDE07G0968' => 'cde', 'CDE09G1441' => 'cde', 'Cfa006103' => 'cfa', 'Cfa015573' => 'cfa', 'Cfa016988' => 'cfa', 'Ciclev10006738m.g' => 'ccl', 'Ciclev10010920m.g' => 'ccl', 'Ciclev10018517m.g' => 'ccl', 'CiPaw.01G159200' => 'cil', 'CiPaw.02G091000' => 'cil', 'CiPaw.02G091100' => 'cil', 'CiPaw.08G103100' => 'cil', 'CiPaw.09G224900' => 'cil', 'ClCG06G005740' => 'cla', 'ClCG07G000090' => 'cla', 'ClCG07G000100' => 'cla', 'COL.COLO4_09143' => 'col', 'COL.COLO4_25124' => 'col', 'Cpa.g.sc16.34' => 'cpa', 'Cpa.g.sc3504.1' => 'cpa', 'Cpa.g.sc60.37' => 'cpa', 'CsaV3_6G018520' => 'csa', 'CsaV3_6G036860' => 'csa', 'CSS0001072' => 'camsi', 'CSS0020208' => 'camsi', 'CSS0021253' => 'camsi', 'CSS0022190' => 'camsi', 'CSS0036150' => 'camsi', 'CSS0040442' => 'camsi', 'CSS0042300' => 'camsi', 'CSS0045298' => 'camsi', 'DCAR_012449' => 'dca', 'DCAR_018405' => 'dca', 'DCAR_024573' => 'dca', 'DCAR_030591' => 'dca', 'Dinv16926' => 'din', 'Dinv32963' => 'din', 'Dinv38382' => 'din', 'Dinv38383' => 'din', 'Duzib133G0974' => 'dzi', 'Duzib138G1867' => 'dzi', 'Duzib211G0420' => 'dzi', 'Duzib212G0930' => 'dzi', 'ECA234G1645' => 'eca', 'ECA247G3467' => 'eca', 'ECA248G1703' => 'eca', 'EL10Ac3g06327' => 'bvu', 'EL10Ac7g17204' => 'bvu', 'Eucgr.A00855' => 'egr', 'Eucgr.A00858' => 'egr', 'Eucgr.H01520' => 'egr', 'Eucgr.H03604' => 'egr', 'Eucgr.L03465' => 'egr', 'Eucgr.L03466' => 'egr', 'FAN01G0988' => 'fan', 'FAN02G3892' => 'fan', 'FAN05G3381' => 'fan', 'FAN07G0967' => 'fan', 'FAN07G1493' => 'fan', 'FAN08G3125' => 'fan', 'FAN09G0402' => 'fan', 'FAN12G2594' => 'fan', 'FAN12G3879' => 'fan', 'FAN14G1546' => 'fan', 'FAN15G3626' => 'fan', 'FAN17G0588' => 'fan', 'FAN17G0609' => 'fan', 'FAN18G2817' => 'fan', 'FAN19G1305' => 'fan', 'FAN20G1787' => 'fan', 'FAN22G0073' => 'fan', 'FAN22G0352' => 'fan', 'FAN22G0368' => 'fan', 'FAN22G2273' => 'fan', 'FAN24G1998' => 'fan', 'FAN27G1317' => 'fan', 'FvH4_2g23980' => 'fve', 'FvH4_4g14380' => 'fve', 'FvH4_4g14390' => 'fve', 'FvH4_6g09250' => 'fve', 'Glyma.03G151100' => 'gma', 'Glyma.04G122550' => 'gma', 'Glyma.05G001600' => 'gma', 'Glyma.09G270766' => 'gma', 'Glyma.09G270832' => 'gma', 'Glyma.13G209800' => 'gma', 'Glyma.15G102800' => 'gma', 'Glyma.18G218900' => 'gma', 'Glyma.19G001500' => 'gma', 'Glyma.19G153600' => 'gma', 'Gohir.A02G028600' => 'ghi', 'Gohir.A08G045000' => 'ghi', 'Gohir.A11G120500' => 'ghi', 'Gohir.A12G006200' => 'ghi', 'Gohir.A12G006250' => 'ghi', 'Gohir.D02G036300' => 'ghi', 'Gohir.D08G054700' => 'ghi', 'Gohir.D11G125600' => 'ghi', 'Gohir.D12G005700' => 'ghi', 'Gorai.004G055200' => 'gra', 'Gorai.005G040400' => 'gra', 'Gorai.007G134500' => 'gra', 'Gorai.008G005500' => 'gra', 'GSVIVG01011094001' => 'vvi', 'GSVIVG01017879001' => 'vvi', 'GSVIVG01025988001' => 'vvi', 'GSVIVG01029847001' => 'vvi', 'HanXRQChr10g0282901' => 'han', 'HanXRQChr10g0310371' => 'han', 'HanXRQChr10g0315041' => 'han', 'HanXRQChr11g0327651' => 'han', 'HanXRQChr12g0359391' => 'han', 'Haze_00972' => 'cav', 'Haze_00973' => 'cav', 'Haze_00974' => 'cav', 'Haze_04747' => 'cav', 'Haze_04749' => 'cav', 'Haze_04750' => 'cav', 'Haze_21217' => 'cav', 'Hma1.2p1_1037F.1_g250680' => 'hma', 'Hma1.2p1_1644F.1_g295320' => 'hma', 'HPP92_011322' => 'vpl', 'HPP92_011323' => 'vpl', 'HPP92_011324' => 'vpl', 'HPP92_011325' => 'vpl', 'HPP92_011326' => 'vpl', 'Hund12205' => 'sun', 'Hund17957' => 'sun', 'Lalb_Chr06g0176771' => 'lal', 'Lalb_Chr18g0056021' => 'lal', 'Lalb_Chr18g0056031' => 'lal', 'Lalb_Chr18g0056041' => 'lal', 'Lalb_Chr20g0107751' => 'lal', 'Lalb_Chr20g0118371' => 'lal', 'Lj1g0010239' => 'lja', 'Lj1g0017101' => 'lja', 'Lj2A1178G40' => 'lonja', 'Lj2A54G84' => 'lonja', 'Lj2g0015248' => 'lja', 'Lj3A761T51' => 'lonja', 'Lj6g0018116' => 'lja', 'Lsat_1_v5_gn_4_136040' => 'lsa', 'Lsat_1_v5_gn_5_187461' => 'lsa', 'Lsat_1_v5_gn_5_77001' => 'lsa', 'Lsat_1_v5_gn_9_4461' => 'lsa', 'Manes.01G210100' => 'mes', 'Manes.03G185600' => 'mes', 'Manes.05G073300' => 'mes', 'Manes.09G120300' => 'mes', 'Manes.15G022100' => 'mes', 'Mapoly0096s0053' => 'mpo', 'MBI03_g14058_MAGBIO' => 'mbi', 'MBI03_g33876_MAGBIO' => 'mbi', 'MBI03_g36854_MAGBIO' => 'mbi', 'MBI17_g11997_MAGBIO' => 'mbi', 'MD03G1269000' => 'mdo', 'MD04G1179600' => 'mdo', 'MD11G1289800' => 'mdo', 'MD12G1194700' => 'mdo', 'MD13G1182100' => 'mdo', 'MD13G1182200' => 'mdo', 'MD16G1182600' => 'mdo', 'Medtr2g021400' => 'mtr', 'Medtr2g021470' => 'mtr', 'Medtr2g105810' => 'mtr', 'Medtr3g033580' => 'mtr', 'Medtr6g007970' => 'mtr', 'Medtr7g056330' => 'mtr', 'Medtr7g074290' => 'mtr', 'Medtr7g074380' => 'mtr', 'Medtr7g094550' => 'mtr', 'Medtr8g069995' => 'mtr', 'MELO3C014345.2' => 'cme', 'MELO3C021395.2' => 'cme', 'Migut.D00262' => 'egut', 'Migut.G00257' => 'egut', 'MSTRG.21575' => 'ama', 'MSTRG.3985' => 'ama', 'Nitab4.5_0000295g0140' => 'nta', 'Nitab4.5_0000732g0140' => 'nta', 'Nitab4.5_0003162g0020' => 'nta', 'Nitab4.5_0006180g0090' => 'nta', 'Nitab4.5_0006390g0010' => 'nta', 'Nitab4.5_0007392g0040' => 'nta', 'Nn1g02140' => 'nnu', 'Nn4g26168' => 'nnu', 'Nn5g26754' => 'nnu', 'Oeu001433.1' => 'oeu', 'Oeu010299.2' => 'oeu', 'Oeu011171.1' => 'oeu', 'Oeu037675.1' => 'oeu', 'Oeu038359.1' => 'oeu', 'Oeu063834.1' => 'oeu', 'Oeu063835.1' => 'oeu', 'Os05g0312000' => 'osa', 'Os07g0211101' => 'osa', 'Os07g0211200' => 'osa', 'Os07g0681500' => 'osa', 'Peaxi162Scf00095g01015' => 'pax', 'Peaxi162Scf00104g00329' => 'pax', 'Peaxi162Scf00161g00137' => 'pax', 'PGR004G1665' => 'pgr', 'PGR031G2937' => 'pgr', 'PGR119G2145' => 'pgr', 'PGSC0003DMG400004351' => 'stu', 'PGSC0003DMG400014625' => 'stu', 'PGSC0003DMG401000943' => 'stu', 'Phvul.001G148600' => 'pvu', 'Phvul.004G001700' => 'pvu', 'Phvul.006G154900' => 'pvu', 'Phvul.008G078200' => 'pvu', 'Phvul.011G136500' => 'pvu', 'Potri.002G215600' => 'ptr', 'Potri.008G201600' => 'ptr', 'Potri.014G138400' => 'ptr', 'Potri.016G142500' => 'ptr', 'Pp3c16_10580' => 'ppa', 'Pp3c5_25280' => 'ppa', 'Prupe.1G150000' => 'ppe', 'Prupe.1G150100' => 'ppe', 'Prupe.6G299600' => 'ppe', 'Prupe.8G245000' => 'ppe', 'Psat0s4927g0040' => 'psa', 'Psat1g052080' => 'psa', 'Psat1g183800' => 'psa', 'Psat3g113840' => 'psa', 'Psat3g126120' => 'psa', 'Psat3g126160' => 'psa', 'Psat3g158760' => 'psa', 'Psat3g158840' => 'psa', 'PSO170G2858' => 'pso', 'PSO339G0606' => 'pso', 'PSO384G4709' => 'pso', 'PSO407G0334' => 'pso', 'QL04p040276' => 'qlo', 'QL06p005458' => 'qlo', 'QL06p005472' => 'qlo', 'QL07p030546' => 'qlo', 'QL07p031519' => 'qlo', 'QL09p050949' => 'qlo', 'QL09p050966' => 'qlo', 'QL09p051067' => 'qlo', 'QL12p022706' => 'qlo', 'RcHm_v2.0_Chr2g0119601' => 'rch', 'RcHm_v2.0_Chr3g0459591' => 'rch', 'RcHm_v2.0_Chr4g0418521' => 'rch', 'RcHm_v2.0_Chr4g0418531' => 'rch', 'RcHm_v2.0_Chr4g0418541' => 'rch', 'RcHm_v2.0_Chr6g0291641' => 'rch', 'Rhsim01G0086300' => 'rsi', 'Rhsim01G0276300' => 'rsi', 'Rhsim01G0276500' => 'rsi', 'Rhsim04G0207700' => 'rsi', 'Rhsim05G0234500' => 'rsi', 'Rhsim13G0022400' => 'rsi', 'Sabra02G0167900' => 'sbr', 'Sabra04G0158500' => 'sbr', 'Sabra08G0159800' => 'sbr', 'Sabra10G0011500' => 'sbr', 'Sabra14G0104400' => 'sbr', 'SalBow2G2440' => 'sbo', 'SalBow4G2265' => 'sbo', 'Sc02g0000060' => 'sci', 'Sc05g0005020' => 'sci', 'Sc13g0003890' => 'sci', 'Sed0014865' => 'sed', 'Sed0017224' => 'sed', 'Sed0026391' => 'sed', 'SEGI_00063' => 'sgi', 'SEGI_10967' => 'sgi', 'SEGI_17510' => 'sgi', 'SEGI_24396' => 'sgi', 'SEGI_39719' => 'sgi', 'SEGI_41392' => 'sgi', 'SGA_v2.0_scaffold11G05794' => 'sas', 'SGA_v2.0_scaffold142G35607' => 'sas', 'SGA_v2.0_scaffold1G00447' => 'sas', 'SHI15388' => 'shi', 'SHI15394' => 'shi', 'SHI15396' => 'shi', 'SHI15399' => 'shi', 'SMO343G0151' => 'smo', 'SMO367G1118' => 'smo', 'Solyc01g080200.3' => 'sly', 'Solyc06g008960.3' => 'sly', 'Solyc09g064780.3' => 'sly', 'Sopen01g031980' => 'spe', 'Sopen06g003710' => 'spe', 'Sopen09g026460' => 'spe', 'Sp3g21240' => 'spa', 'Sp4g30030' => 'spa', 'TAR365G0022' => 'tar', 'TAR365G1023' => 'tar', 'TAR365G1253' => 'tar', 'TAR623G0078' => 'tar', 'TAR623G1721' => 'tar', 'TAR633G0959' => 'tar', 'THA.LOC104802225' => 'tha', 'THA.LOC104804769' => 'tha', 'THA.LOC104808660' => 'tha', 'THA.LOC104812792' => 'tha', 'Thecc.01G284000' => 'tca', 'Thecc.04G220600' => 'tca', 'Thecc.05G268900' => 'tca', 'Thecc.08G171100' => 'tca', 'Thhalv10001284m.g' => 'esa', 'Thhalv10019912m.g' => 'esa', 'TPR.G14189' => 'tpr', 'TPR.G18110' => 'tpr', 'TPR.G18130' => 'tpr', 'TPR.G18131' => 'tpr', 'TPR.G18140' => 'tpr', 'TPR.G24282' => 'tpr', 'TPR.G25221' => 'tpr', 'TPR.G29267' => 'tpr', 'TPR.G35315' => 'tpr', 'TPR.G36173' => 'tpr', 'TWI09G0794' => 'twi', 'TWI59G1348' => 'twi', 'TWI74G0430' => 'twi', 'unitig_26.g8940' => 'ugi', 'unitig_749.g13744' => 'ugi', 'unitig_749.g13745' => 'ugi', 'vmacro08269' => 'vma', 'vmacro14937' => 'vma', 'vmacro20401' => 'vma', 'VMungo0464G1349' => 'vmu', 'VMungo0540G0289' => 'vmu', 'VMungo1215G1590' => 'vmu', 'VMungo1309G0221' => 'vmu', 'VMungo1309G2815' => 'vmu', 'VMungo1383G0239' => 'vmu', 'VMungo1383G2910' => 'vmu', 'Zm00001eb095270' => 'zma', 'Zm00001eb095280' => 'zma', 'Zm00001eb111630' => 'zma', 'Zm00001eb237080' => 'zma', 'Zm00001eb273740' => 'zma', 'Zm00001eb285040' => 'zma', 'Zm00001eb330790' => 'zma', 'Zm00001eb337380' => 'zma' ) $gf_id = 'HOM05D001484' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001484' ) $data_identifier = 'HOM05D001484' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 2, 'aly' => (int) 2, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 22, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 7, 'hma' => (int) 2, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 7, 'mtr' => (int) 10, 'cme' => (int) 2, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 4, 'ppa' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 4, 'qlo' => (int) 9, 'rch' => (int) 6, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 10, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 7, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb337380' $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' => 'HOM05D001484', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p31500' => 'bna', 'A05p00020' => 'bna', 'A07p08820' => 'bna', 'Aa31LG4G3300' => 'aar', 'Aa31LG8G10030' => 'aar', 'Actinidia00731' => 'ach', 'Actinidia11473' => 'ach', 'Actinidia23469' => 'ach', 'Actinidia24318' => 'ach', 'Actinidia40196' => 'ach', 'Actinidia40197' => 'ach', 'Actinidia40198' => 'ach', 'Ah.08g212990' => 'amhyb', 'Ah.15g091720' => 'amhyb', 'AL3G38260' => 'aly', 'AL4G47710' => 'aly', 'Aqoxy2G00671' => 'aox', 'Aqoxy2G03236' => 'aox', 'arahy.Tifrunner.gnm1.ann1.05IDCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KR684' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATY3SJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK6QJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6APGL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IDT7Z9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM073U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ0R87' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LE7RV4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT4QRX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V5ENPK' => 'arhy', 'AT2G48110' => 'ath', 'AT3G23590' => 'ath', 'ATR0626G186' => 'atr', 'ATR1127G141' => 'atr', 'Atru.chr4.2583' => 'acertr', 'Atru.chr5.1358' => 'acertr', 'Atru.chr5.1359' => 'acertr', 'Atru.chr8.46' => 'acertr', 'AUR62002640' => 'cqu', 'AUR62030055' => 'cqu', 'AUR62033713' => 'cqu', 'AUR62033714' => 'cqu', 'AUR62036795' => 'cqu', 'AUR62039891' => 'cqu', 'BcaB02g08737' => 'bca', 'BcaB04g20441' => 'bca', 'BcaB06g26509' => 'bca', 'BcaB06g26510' => 'bca', 'BcaB06g26511' => 'bca', 'BcaB06g26512' => 'bca', 'BcaB06g26513' => 'bca', 'BcaC02g12564' => 'bca', 'BcaC02g12565' => 'bca', 'BcaC02g12794' => 'bca', 'BcaC02g12795' => 'bca', 'BcaC02g12796' => 'bca', 'BcaC06g35541' => 'bca', 'BNapus_Darmor_BZH_scaffold_188p00080' => 'bna', 'BNapus_Darmor_BZH_scaffold_188p00090' => 'bna', 'BolC1t03972H' => 'bol', 'BolC1t03973H' => 'bol', 'BolC4t21680H' => 'bol', 'BolC7t41863H' => 'bol', 'BolSC55t61227H' => 'bol', 'BolSC55t61228H' => 'bol', 'BraA01t03278Z' => 'bra', 'BraA05t18998Z' => 'bra', 'BraA07t28673Z' => 'bra', 'C01p40150' => 'bna', 'C05p12370' => 'bna', 'C07p13680' => 'bna', 'CAN.G1006.16' => 'can', 'CAN.G1006.17' => 'can', 'CAN.G1170.2' => 'can', 'CAN.G962.7' => 'can', 'CANSAT25G2179' => 'cansat', 'CANSAT78G1573' => 'cansat', 'CARHR099510' => 'chi', 'CARHR143510' => 'chi', 'Carub.0003s2380' => 'cru', 'Carub.0004s3082' => 'cru', 'Ca_00614_v3' => 'car', 'Ca_07801_v3' => 'car', 'Ca_08567_v3' => 'car', 'Ca_09571_v3' => 'car', 'CBR_g19290' => 'cbr', 'Cc01_g19770' => 'ccan', 'Cc03_g03030' => 'ccan', 'CDE07G0968' => 'cde', 'CDE09G1441' => 'cde', 'Cfa006103' => 'cfa', 'Cfa015573' => 'cfa', 'Cfa016988' => 'cfa', 'Ciclev10006738m.g' => 'ccl', 'Ciclev10010920m.g' => 'ccl', 'Ciclev10018517m.g' => 'ccl', 'CiPaw.01G159200' => 'cil', 'CiPaw.02G091000' => 'cil', 'CiPaw.02G091100' => 'cil', 'CiPaw.08G103100' => 'cil', 'CiPaw.09G224900' => 'cil', 'ClCG06G005740' => 'cla', 'ClCG07G000090' => 'cla', 'ClCG07G000100' => 'cla', 'COL.COLO4_09143' => 'col', 'COL.COLO4_25124' => 'col', 'Cpa.g.sc16.34' => 'cpa', 'Cpa.g.sc3504.1' => 'cpa', 'Cpa.g.sc60.37' => 'cpa', 'CsaV3_6G018520' => 'csa', 'CsaV3_6G036860' => 'csa', 'CSS0001072' => 'camsi', 'CSS0020208' => 'camsi', 'CSS0021253' => 'camsi', 'CSS0022190' => 'camsi', 'CSS0036150' => 'camsi', 'CSS0040442' => 'camsi', 'CSS0042300' => 'camsi', 'CSS0045298' => 'camsi', 'DCAR_012449' => 'dca', 'DCAR_018405' => 'dca', 'DCAR_024573' => 'dca', 'DCAR_030591' => 'dca', 'Dinv16926' => 'din', 'Dinv32963' => 'din', 'Dinv38382' => 'din', 'Dinv38383' => 'din', 'Duzib133G0974' => 'dzi', 'Duzib138G1867' => 'dzi', 'Duzib211G0420' => 'dzi', 'Duzib212G0930' => 'dzi', 'ECA234G1645' => 'eca', 'ECA247G3467' => 'eca', 'ECA248G1703' => 'eca', 'EL10Ac3g06327' => 'bvu', 'EL10Ac7g17204' => 'bvu', 'Eucgr.A00855' => 'egr', 'Eucgr.A00858' => 'egr', 'Eucgr.H01520' => 'egr', 'Eucgr.H03604' => 'egr', 'Eucgr.L03465' => 'egr', 'Eucgr.L03466' => 'egr', 'FAN01G0988' => 'fan', 'FAN02G3892' => 'fan', 'FAN05G3381' => 'fan', 'FAN07G0967' => 'fan', 'FAN07G1493' => 'fan', 'FAN08G3125' => 'fan', 'FAN09G0402' => 'fan', 'FAN12G2594' => 'fan', 'FAN12G3879' => 'fan', 'FAN14G1546' => 'fan', 'FAN15G3626' => 'fan', 'FAN17G0588' => 'fan', 'FAN17G0609' => 'fan', 'FAN18G2817' => 'fan', 'FAN19G1305' => 'fan', 'FAN20G1787' => 'fan', 'FAN22G0073' => 'fan', 'FAN22G0352' => 'fan', 'FAN22G0368' => 'fan', 'FAN22G2273' => 'fan', 'FAN24G1998' => 'fan', 'FAN27G1317' => 'fan', 'FvH4_2g23980' => 'fve', 'FvH4_4g14380' => 'fve', 'FvH4_4g14390' => 'fve', 'FvH4_6g09250' => 'fve', 'Glyma.03G151100' => 'gma', 'Glyma.04G122550' => 'gma', 'Glyma.05G001600' => 'gma', 'Glyma.09G270766' => 'gma', 'Glyma.09G270832' => 'gma', 'Glyma.13G209800' => 'gma', 'Glyma.15G102800' => 'gma', 'Glyma.18G218900' => 'gma', 'Glyma.19G001500' => 'gma', 'Glyma.19G153600' => 'gma', 'Gohir.A02G028600' => 'ghi', 'Gohir.A08G045000' => 'ghi', 'Gohir.A11G120500' => 'ghi', 'Gohir.A12G006200' => 'ghi', 'Gohir.A12G006250' => 'ghi', 'Gohir.D02G036300' => 'ghi', 'Gohir.D08G054700' => 'ghi', 'Gohir.D11G125600' => 'ghi', 'Gohir.D12G005700' => 'ghi', 'Gorai.004G055200' => 'gra', 'Gorai.005G040400' => 'gra', 'Gorai.007G134500' => 'gra', 'Gorai.008G005500' => 'gra', 'GSVIVG01011094001' => 'vvi', 'GSVIVG01017879001' => 'vvi', 'GSVIVG01025988001' => 'vvi', 'GSVIVG01029847001' => 'vvi', 'HanXRQChr10g0282901' => 'han', 'HanXRQChr10g0310371' => 'han', 'HanXRQChr10g0315041' => 'han', 'HanXRQChr11g0327651' => 'han', 'HanXRQChr12g0359391' => 'han', 'Haze_00972' => 'cav', 'Haze_00973' => 'cav', 'Haze_00974' => 'cav', 'Haze_04747' => 'cav', 'Haze_04749' => 'cav', 'Haze_04750' => 'cav', 'Haze_21217' => 'cav', 'Hma1.2p1_1037F.1_g250680' => 'hma', 'Hma1.2p1_1644F.1_g295320' => 'hma', 'HPP92_011322' => 'vpl', 'HPP92_011323' => 'vpl', 'HPP92_011324' => 'vpl', 'HPP92_011325' => 'vpl', 'HPP92_011326' => 'vpl', 'Hund12205' => 'sun', 'Hund17957' => 'sun', 'Lalb_Chr06g0176771' => 'lal', 'Lalb_Chr18g0056021' => 'lal', 'Lalb_Chr18g0056031' => 'lal', 'Lalb_Chr18g0056041' => 'lal', 'Lalb_Chr20g0107751' => 'lal', 'Lalb_Chr20g0118371' => 'lal', 'Lj1g0010239' => 'lja', 'Lj1g0017101' => 'lja', 'Lj2A1178G40' => 'lonja', 'Lj2A54G84' => 'lonja', 'Lj2g0015248' => 'lja', 'Lj3A761T51' => 'lonja', 'Lj6g0018116' => 'lja', 'Lsat_1_v5_gn_4_136040' => 'lsa', 'Lsat_1_v5_gn_5_187461' => 'lsa', 'Lsat_1_v5_gn_5_77001' => 'lsa', 'Lsat_1_v5_gn_9_4461' => 'lsa', 'Manes.01G210100' => 'mes', 'Manes.03G185600' => 'mes', 'Manes.05G073300' => 'mes', 'Manes.09G120300' => 'mes', 'Manes.15G022100' => 'mes', 'Mapoly0096s0053' => 'mpo', 'MBI03_g14058_MAGBIO' => 'mbi', 'MBI03_g33876_MAGBIO' => 'mbi', 'MBI03_g36854_MAGBIO' => 'mbi', 'MBI17_g11997_MAGBIO' => 'mbi', 'MD03G1269000' => 'mdo', 'MD04G1179600' => 'mdo', 'MD11G1289800' => 'mdo', 'MD12G1194700' => 'mdo', 'MD13G1182100' => 'mdo', 'MD13G1182200' => 'mdo', 'MD16G1182600' => 'mdo', 'Medtr2g021400' => 'mtr', 'Medtr2g021470' => 'mtr', 'Medtr2g105810' => 'mtr', 'Medtr3g033580' => 'mtr', 'Medtr6g007970' => 'mtr', 'Medtr7g056330' => 'mtr', 'Medtr7g074290' => 'mtr', 'Medtr7g074380' => 'mtr', 'Medtr7g094550' => 'mtr', 'Medtr8g069995' => 'mtr', 'MELO3C014345.2' => 'cme', 'MELO3C021395.2' => 'cme', 'Migut.D00262' => 'egut', 'Migut.G00257' => 'egut', 'MSTRG.21575' => 'ama', 'MSTRG.3985' => 'ama', 'Nitab4.5_0000295g0140' => 'nta', 'Nitab4.5_0000732g0140' => 'nta', 'Nitab4.5_0003162g0020' => 'nta', 'Nitab4.5_0006180g0090' => 'nta', 'Nitab4.5_0006390g0010' => 'nta', 'Nitab4.5_0007392g0040' => 'nta', 'Nn1g02140' => 'nnu', 'Nn4g26168' => 'nnu', 'Nn5g26754' => 'nnu', 'Oeu001433.1' => 'oeu', 'Oeu010299.2' => 'oeu', 'Oeu011171.1' => 'oeu', 'Oeu037675.1' => 'oeu', 'Oeu038359.1' => 'oeu', 'Oeu063834.1' => 'oeu', 'Oeu063835.1' => 'oeu', 'Os05g0312000' => 'osa', 'Os07g0211101' => 'osa', 'Os07g0211200' => 'osa', 'Os07g0681500' => 'osa', 'Peaxi162Scf00095g01015' => 'pax', 'Peaxi162Scf00104g00329' => 'pax', 'Peaxi162Scf00161g00137' => 'pax', 'PGR004G1665' => 'pgr', 'PGR031G2937' => 'pgr', 'PGR119G2145' => 'pgr', 'PGSC0003DMG400004351' => 'stu', 'PGSC0003DMG400014625' => 'stu', 'PGSC0003DMG401000943' => 'stu', 'Phvul.001G148600' => 'pvu', 'Phvul.004G001700' => 'pvu', 'Phvul.006G154900' => 'pvu', 'Phvul.008G078200' => 'pvu', 'Phvul.011G136500' => 'pvu', 'Potri.002G215600' => 'ptr', 'Potri.008G201600' => 'ptr', 'Potri.014G138400' => 'ptr', 'Potri.016G142500' => 'ptr', 'Pp3c16_10580' => 'ppa', 'Pp3c5_25280' => 'ppa', 'Prupe.1G150000' => 'ppe', 'Prupe.1G150100' => 'ppe', 'Prupe.6G299600' => 'ppe', 'Prupe.8G245000' => 'ppe', 'Psat0s4927g0040' => 'psa', 'Psat1g052080' => 'psa', 'Psat1g183800' => 'psa', 'Psat3g113840' => 'psa', 'Psat3g126120' => 'psa', 'Psat3g126160' => 'psa', 'Psat3g158760' => 'psa', 'Psat3g158840' => 'psa', 'PSO170G2858' => 'pso', 'PSO339G0606' => 'pso', 'PSO384G4709' => 'pso', 'PSO407G0334' => 'pso', 'QL04p040276' => 'qlo', 'QL06p005458' => 'qlo', 'QL06p005472' => 'qlo', 'QL07p030546' => 'qlo', 'QL07p031519' => 'qlo', 'QL09p050949' => 'qlo', 'QL09p050966' => 'qlo', 'QL09p051067' => 'qlo', 'QL12p022706' => 'qlo', 'RcHm_v2.0_Chr2g0119601' => 'rch', 'RcHm_v2.0_Chr3g0459591' => 'rch', 'RcHm_v2.0_Chr4g0418521' => 'rch', 'RcHm_v2.0_Chr4g0418531' => 'rch', 'RcHm_v2.0_Chr4g0418541' => 'rch', 'RcHm_v2.0_Chr6g0291641' => 'rch', 'Rhsim01G0086300' => 'rsi', 'Rhsim01G0276300' => 'rsi', 'Rhsim01G0276500' => 'rsi', 'Rhsim04G0207700' => 'rsi', 'Rhsim05G0234500' => 'rsi', 'Rhsim13G0022400' => 'rsi', 'Sabra02G0167900' => 'sbr', 'Sabra04G0158500' => 'sbr', 'Sabra08G0159800' => 'sbr', 'Sabra10G0011500' => 'sbr', 'Sabra14G0104400' => 'sbr', 'SalBow2G2440' => 'sbo', 'SalBow4G2265' => 'sbo', 'Sc02g0000060' => 'sci', 'Sc05g0005020' => 'sci', 'Sc13g0003890' => 'sci', 'Sed0014865' => 'sed', 'Sed0017224' => 'sed', 'Sed0026391' => 'sed', 'SEGI_00063' => 'sgi', 'SEGI_10967' => 'sgi', 'SEGI_17510' => 'sgi', 'SEGI_24396' => 'sgi', 'SEGI_39719' => 'sgi', 'SEGI_41392' => 'sgi', 'SGA_v2.0_scaffold11G05794' => 'sas', 'SGA_v2.0_scaffold142G35607' => 'sas', 'SGA_v2.0_scaffold1G00447' => 'sas', 'SHI15388' => 'shi', 'SHI15394' => 'shi', 'SHI15396' => 'shi', 'SHI15399' => 'shi', 'SMO343G0151' => 'smo', 'SMO367G1118' => 'smo', 'Solyc01g080200.3' => 'sly', 'Solyc06g008960.3' => 'sly', 'Solyc09g064780.3' => 'sly', 'Sopen01g031980' => 'spe', 'Sopen06g003710' => 'spe', 'Sopen09g026460' => 'spe', 'Sp3g21240' => 'spa', 'Sp4g30030' => 'spa', 'TAR365G0022' => 'tar', 'TAR365G1023' => 'tar', 'TAR365G1253' => 'tar', 'TAR623G0078' => 'tar', 'TAR623G1721' => 'tar', 'TAR633G0959' => 'tar', 'THA.LOC104802225' => 'tha', 'THA.LOC104804769' => 'tha', 'THA.LOC104808660' => 'tha', 'THA.LOC104812792' => 'tha', 'Thecc.01G284000' => 'tca', 'Thecc.04G220600' => 'tca', 'Thecc.05G268900' => 'tca', 'Thecc.08G171100' => 'tca', 'Thhalv10001284m.g' => 'esa', 'Thhalv10019912m.g' => 'esa', 'TPR.G14189' => 'tpr', 'TPR.G18110' => 'tpr', 'TPR.G18130' => 'tpr', 'TPR.G18131' => 'tpr', 'TPR.G18140' => 'tpr', 'TPR.G24282' => 'tpr', 'TPR.G25221' => 'tpr', 'TPR.G29267' => 'tpr', 'TPR.G35315' => 'tpr', 'TPR.G36173' => 'tpr', 'TWI09G0794' => 'twi', 'TWI59G1348' => 'twi', 'TWI74G0430' => 'twi', 'unitig_26.g8940' => 'ugi', 'unitig_749.g13744' => 'ugi', 'unitig_749.g13745' => 'ugi', 'vmacro08269' => 'vma', 'vmacro14937' => 'vma', 'vmacro20401' => 'vma', 'VMungo0464G1349' => 'vmu', 'VMungo0540G0289' => 'vmu', 'VMungo1215G1590' => 'vmu', 'VMungo1309G0221' => 'vmu', 'VMungo1309G2815' => 'vmu', 'VMungo1383G0239' => 'vmu', 'VMungo1383G2910' => 'vmu', 'Zm00001eb095270' => 'zma', 'Zm00001eb095280' => 'zma', 'Zm00001eb111630' => 'zma', 'Zm00001eb237080' => 'zma', 'Zm00001eb273740' => 'zma', 'Zm00001eb285040' => 'zma', 'Zm00001eb330790' => 'zma', 'Zm00001eb337380' => 'zma' ), 'gf_id' => 'HOM05D001484', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001484' ), 'data_identifier' => 'HOM05D001484', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001484', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p31500' => 'bna', 'A05p00020' => 'bna', 'A07p08820' => 'bna', 'Aa31LG4G3300' => 'aar', 'Aa31LG8G10030' => 'aar', 'Actinidia00731' => 'ach', 'Actinidia11473' => 'ach', 'Actinidia23469' => 'ach', 'Actinidia24318' => 'ach', 'Actinidia40196' => 'ach', 'Actinidia40197' => 'ach', 'Actinidia40198' => 'ach', 'Ah.08g212990' => 'amhyb', 'Ah.15g091720' => 'amhyb', 'AL3G38260' => 'aly', 'AL4G47710' => 'aly', 'Aqoxy2G00671' => 'aox', 'Aqoxy2G03236' => 'aox', 'arahy.Tifrunner.gnm1.ann1.05IDCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KR684' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATY3SJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK6QJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6APGL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IDT7Z9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM073U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ0R87' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LE7RV4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT4QRX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V5ENPK' => 'arhy', 'AT2G48110' => 'ath', 'AT3G23590' => 'ath', 'ATR0626G186' => 'atr', 'ATR1127G141' => 'atr', 'Atru.chr4.2583' => 'acertr', 'Atru.chr5.1358' => 'acertr', 'Atru.chr5.1359' => 'acertr', 'Atru.chr8.46' => 'acertr', 'AUR62002640' => 'cqu', 'AUR62030055' => 'cqu', 'AUR62033713' => 'cqu', 'AUR62033714' => 'cqu', 'AUR62036795' => 'cqu', 'AUR62039891' => 'cqu', 'BcaB02g08737' => 'bca', 'BcaB04g20441' => 'bca', 'BcaB06g26509' => 'bca', 'BcaB06g26510' => 'bca', 'BcaB06g26511' => 'bca', 'BcaB06g26512' => 'bca', 'BcaB06g26513' => 'bca', 'BcaC02g12564' => 'bca', 'BcaC02g12565' => 'bca', 'BcaC02g12794' => 'bca', 'BcaC02g12795' => 'bca', 'BcaC02g12796' => 'bca', 'BcaC06g35541' => 'bca', 'BNapus_Darmor_BZH_scaffold_188p00080' => 'bna', 'BNapus_Darmor_BZH_scaffold_188p00090' => 'bna', 'BolC1t03972H' => 'bol', 'BolC1t03973H' => 'bol', 'BolC4t21680H' => 'bol', 'BolC7t41863H' => 'bol', 'BolSC55t61227H' => 'bol', 'BolSC55t61228H' => 'bol', 'BraA01t03278Z' => 'bra', 'BraA05t18998Z' => 'bra', 'BraA07t28673Z' => 'bra', 'C01p40150' => 'bna', 'C05p12370' => 'bna', 'C07p13680' => 'bna', 'CAN.G1006.16' => 'can', 'CAN.G1006.17' => 'can', 'CAN.G1170.2' => 'can', 'CAN.G962.7' => 'can', 'CANSAT25G2179' => 'cansat', 'CANSAT78G1573' => 'cansat', 'CARHR099510' => 'chi', 'CARHR143510' => 'chi', 'Carub.0003s2380' => 'cru', 'Carub.0004s3082' => 'cru', 'Ca_00614_v3' => 'car', 'Ca_07801_v3' => 'car', 'Ca_08567_v3' => 'car', 'Ca_09571_v3' => 'car', 'CBR_g19290' => 'cbr', 'Cc01_g19770' => 'ccan', 'Cc03_g03030' => 'ccan', 'CDE07G0968' => 'cde', 'CDE09G1441' => 'cde', 'Cfa006103' => 'cfa', 'Cfa015573' => 'cfa', 'Cfa016988' => 'cfa', 'Ciclev10006738m.g' => 'ccl', 'Ciclev10010920m.g' => 'ccl', 'Ciclev10018517m.g' => 'ccl', 'CiPaw.01G159200' => 'cil', 'CiPaw.02G091000' => 'cil', 'CiPaw.02G091100' => 'cil', 'CiPaw.08G103100' => 'cil', 'CiPaw.09G224900' => 'cil', 'ClCG06G005740' => 'cla', 'ClCG07G000090' => 'cla', 'ClCG07G000100' => 'cla', 'COL.COLO4_09143' => 'col', 'COL.COLO4_25124' => 'col', 'Cpa.g.sc16.34' => 'cpa', 'Cpa.g.sc3504.1' => 'cpa', 'Cpa.g.sc60.37' => 'cpa', 'CsaV3_6G018520' => 'csa', 'CsaV3_6G036860' => 'csa', 'CSS0001072' => 'camsi', 'CSS0020208' => 'camsi', 'CSS0021253' => 'camsi', 'CSS0022190' => 'camsi', 'CSS0036150' => 'camsi', 'CSS0040442' => 'camsi', 'CSS0042300' => 'camsi', 'CSS0045298' => 'camsi', 'DCAR_012449' => 'dca', 'DCAR_018405' => 'dca', 'DCAR_024573' => 'dca', 'DCAR_030591' => 'dca', 'Dinv16926' => 'din', 'Dinv32963' => 'din', 'Dinv38382' => 'din', 'Dinv38383' => 'din', 'Duzib133G0974' => 'dzi', 'Duzib138G1867' => 'dzi', 'Duzib211G0420' => 'dzi', 'Duzib212G0930' => 'dzi', 'ECA234G1645' => 'eca', 'ECA247G3467' => 'eca', 'ECA248G1703' => 'eca', 'EL10Ac3g06327' => 'bvu', 'EL10Ac7g17204' => 'bvu', 'Eucgr.A00855' => 'egr', 'Eucgr.A00858' => 'egr', 'Eucgr.H01520' => 'egr', 'Eucgr.H03604' => 'egr', 'Eucgr.L03465' => 'egr', 'Eucgr.L03466' => 'egr', 'FAN01G0988' => 'fan', 'FAN02G3892' => 'fan', 'FAN05G3381' => 'fan', 'FAN07G0967' => 'fan', 'FAN07G1493' => 'fan', 'FAN08G3125' => 'fan', 'FAN09G0402' => 'fan', 'FAN12G2594' => 'fan', 'FAN12G3879' => 'fan', 'FAN14G1546' => 'fan', 'FAN15G3626' => 'fan', 'FAN17G0588' => 'fan', 'FAN17G0609' => 'fan', 'FAN18G2817' => 'fan', 'FAN19G1305' => 'fan', 'FAN20G1787' => 'fan', 'FAN22G0073' => 'fan', 'FAN22G0352' => 'fan', 'FAN22G0368' => 'fan', 'FAN22G2273' => 'fan', 'FAN24G1998' => 'fan', 'FAN27G1317' => 'fan', 'FvH4_2g23980' => 'fve', 'FvH4_4g14380' => 'fve', 'FvH4_4g14390' => 'fve', 'FvH4_6g09250' => 'fve', 'Glyma.03G151100' => 'gma', 'Glyma.04G122550' => 'gma', 'Glyma.05G001600' => 'gma', 'Glyma.09G270766' => 'gma', 'Glyma.09G270832' => 'gma', 'Glyma.13G209800' => 'gma', 'Glyma.15G102800' => 'gma', 'Glyma.18G218900' => 'gma', 'Glyma.19G001500' => 'gma', 'Glyma.19G153600' => 'gma', 'Gohir.A02G028600' => 'ghi', 'Gohir.A08G045000' => 'ghi', 'Gohir.A11G120500' => 'ghi', 'Gohir.A12G006200' => 'ghi', 'Gohir.A12G006250' => 'ghi', 'Gohir.D02G036300' => 'ghi', 'Gohir.D08G054700' => 'ghi', 'Gohir.D11G125600' => 'ghi', 'Gohir.D12G005700' => 'ghi', 'Gorai.004G055200' => 'gra', 'Gorai.005G040400' => 'gra', 'Gorai.007G134500' => 'gra', 'Gorai.008G005500' => 'gra', 'GSVIVG01011094001' => 'vvi', 'GSVIVG01017879001' => 'vvi', 'GSVIVG01025988001' => 'vvi', 'GSVIVG01029847001' => 'vvi', 'HanXRQChr10g0282901' => 'han', 'HanXRQChr10g0310371' => 'han', 'HanXRQChr10g0315041' => 'han', 'HanXRQChr11g0327651' => 'han', 'HanXRQChr12g0359391' => 'han', 'Haze_00972' => 'cav', 'Haze_00973' => 'cav', 'Haze_00974' => 'cav', 'Haze_04747' => 'cav', 'Haze_04749' => 'cav', 'Haze_04750' => 'cav', 'Haze_21217' => 'cav', 'Hma1.2p1_1037F.1_g250680' => 'hma', 'Hma1.2p1_1644F.1_g295320' => 'hma', 'HPP92_011322' => 'vpl', 'HPP92_011323' => 'vpl', 'HPP92_011324' => 'vpl', 'HPP92_011325' => 'vpl', 'HPP92_011326' => 'vpl', 'Hund12205' => 'sun', 'Hund17957' => 'sun', 'Lalb_Chr06g0176771' => 'lal', 'Lalb_Chr18g0056021' => 'lal', 'Lalb_Chr18g0056031' => 'lal', 'Lalb_Chr18g0056041' => 'lal', 'Lalb_Chr20g0107751' => 'lal', 'Lalb_Chr20g0118371' => 'lal', 'Lj1g0010239' => 'lja', 'Lj1g0017101' => 'lja', 'Lj2A1178G40' => 'lonja', 'Lj2A54G84' => 'lonja', 'Lj2g0015248' => 'lja', 'Lj3A761T51' => 'lonja', 'Lj6g0018116' => 'lja', 'Lsat_1_v5_gn_4_136040' => 'lsa', 'Lsat_1_v5_gn_5_187461' => 'lsa', 'Lsat_1_v5_gn_5_77001' => 'lsa', 'Lsat_1_v5_gn_9_4461' => 'lsa', 'Manes.01G210100' => 'mes', 'Manes.03G185600' => 'mes', 'Manes.05G073300' => 'mes', 'Manes.09G120300' => 'mes', 'Manes.15G022100' => 'mes', 'Mapoly0096s0053' => 'mpo', 'MBI03_g14058_MAGBIO' => 'mbi', 'MBI03_g33876_MAGBIO' => 'mbi', 'MBI03_g36854_MAGBIO' => 'mbi', 'MBI17_g11997_MAGBIO' => 'mbi', 'MD03G1269000' => 'mdo', 'MD04G1179600' => 'mdo', 'MD11G1289800' => 'mdo', 'MD12G1194700' => 'mdo', 'MD13G1182100' => 'mdo', 'MD13G1182200' => 'mdo', 'MD16G1182600' => 'mdo', 'Medtr2g021400' => 'mtr', 'Medtr2g021470' => 'mtr', 'Medtr2g105810' => 'mtr', 'Medtr3g033580' => 'mtr', 'Medtr6g007970' => 'mtr', 'Medtr7g056330' => 'mtr', 'Medtr7g074290' => 'mtr', 'Medtr7g074380' => 'mtr', 'Medtr7g094550' => 'mtr', 'Medtr8g069995' => 'mtr', 'MELO3C014345.2' => 'cme', 'MELO3C021395.2' => 'cme', 'Migut.D00262' => 'egut', 'Migut.G00257' => 'egut', 'MSTRG.21575' => 'ama', 'MSTRG.3985' => 'ama', 'Nitab4.5_0000295g0140' => 'nta', 'Nitab4.5_0000732g0140' => 'nta', 'Nitab4.5_0003162g0020' => 'nta', 'Nitab4.5_0006180g0090' => 'nta', 'Nitab4.5_0006390g0010' => 'nta', 'Nitab4.5_0007392g0040' => 'nta', 'Nn1g02140' => 'nnu', 'Nn4g26168' => 'nnu', 'Nn5g26754' => 'nnu', 'Oeu001433.1' => 'oeu', 'Oeu010299.2' => 'oeu', 'Oeu011171.1' => 'oeu', 'Oeu037675.1' => 'oeu', 'Oeu038359.1' => 'oeu', 'Oeu063834.1' => 'oeu', 'Oeu063835.1' => 'oeu', 'Os05g0312000' => 'osa', 'Os07g0211101' => 'osa', 'Os07g0211200' => 'osa', 'Os07g0681500' => 'osa', 'Peaxi162Scf00095g01015' => 'pax', 'Peaxi162Scf00104g00329' => 'pax', 'Peaxi162Scf00161g00137' => 'pax', 'PGR004G1665' => 'pgr', 'PGR031G2937' => 'pgr', 'PGR119G2145' => 'pgr', 'PGSC0003DMG400004351' => 'stu', 'PGSC0003DMG400014625' => 'stu', 'PGSC0003DMG401000943' => 'stu', 'Phvul.001G148600' => 'pvu', 'Phvul.004G001700' => 'pvu', 'Phvul.006G154900' => 'pvu', 'Phvul.008G078200' => 'pvu', 'Phvul.011G136500' => 'pvu', 'Potri.002G215600' => 'ptr', 'Potri.008G201600' => 'ptr', 'Potri.014G138400' => 'ptr', 'Potri.016G142500' => 'ptr', 'Pp3c16_10580' => 'ppa', 'Pp3c5_25280' => 'ppa', 'Prupe.1G150000' => 'ppe', 'Prupe.1G150100' => 'ppe', 'Prupe.6G299600' => 'ppe', 'Prupe.8G245000' => 'ppe', 'Psat0s4927g0040' => 'psa', 'Psat1g052080' => 'psa', 'Psat1g183800' => 'psa', 'Psat3g113840' => 'psa', 'Psat3g126120' => 'psa', 'Psat3g126160' => 'psa', 'Psat3g158760' => 'psa', 'Psat3g158840' => 'psa', 'PSO170G2858' => 'pso', 'PSO339G0606' => 'pso', 'PSO384G4709' => 'pso', 'PSO407G0334' => 'pso', 'QL04p040276' => 'qlo', 'QL06p005458' => 'qlo', 'QL06p005472' => 'qlo', 'QL07p030546' => 'qlo', 'QL07p031519' => 'qlo', 'QL09p050949' => 'qlo', 'QL09p050966' => 'qlo', 'QL09p051067' => 'qlo', 'QL12p022706' => 'qlo', 'RcHm_v2.0_Chr2g0119601' => 'rch', 'RcHm_v2.0_Chr3g0459591' => 'rch', 'RcHm_v2.0_Chr4g0418521' => 'rch', 'RcHm_v2.0_Chr4g0418531' => 'rch', 'RcHm_v2.0_Chr4g0418541' => 'rch', 'RcHm_v2.0_Chr6g0291641' => 'rch', 'Rhsim01G0086300' => 'rsi', 'Rhsim01G0276300' => 'rsi', 'Rhsim01G0276500' => 'rsi', 'Rhsim04G0207700' => 'rsi', 'Rhsim05G0234500' => 'rsi', 'Rhsim13G0022400' => 'rsi', 'Sabra02G0167900' => 'sbr', 'Sabra04G0158500' => 'sbr', 'Sabra08G0159800' => 'sbr', 'Sabra10G0011500' => 'sbr', 'Sabra14G0104400' => 'sbr', 'SalBow2G2440' => 'sbo', 'SalBow4G2265' => 'sbo', 'Sc02g0000060' => 'sci', 'Sc05g0005020' => 'sci', 'Sc13g0003890' => 'sci', 'Sed0014865' => 'sed', 'Sed0017224' => 'sed', 'Sed0026391' => 'sed', 'SEGI_00063' => 'sgi', 'SEGI_10967' => 'sgi', 'SEGI_17510' => 'sgi', 'SEGI_24396' => 'sgi', 'SEGI_39719' => 'sgi', 'SEGI_41392' => 'sgi', 'SGA_v2.0_scaffold11G05794' => 'sas', 'SGA_v2.0_scaffold142G35607' => 'sas', 'SGA_v2.0_scaffold1G00447' => 'sas', 'SHI15388' => 'shi', 'SHI15394' => 'shi', 'SHI15396' => 'shi', 'SHI15399' => 'shi', 'SMO343G0151' => 'smo', 'SMO367G1118' => 'smo', 'Solyc01g080200.3' => 'sly', 'Solyc06g008960.3' => 'sly', 'Solyc09g064780.3' => 'sly', 'Sopen01g031980' => 'spe', 'Sopen06g003710' => 'spe', 'Sopen09g026460' => 'spe', 'Sp3g21240' => 'spa', 'Sp4g30030' => 'spa', 'TAR365G0022' => 'tar', 'TAR365G1023' => 'tar', 'TAR365G1253' => 'tar', 'TAR623G0078' => 'tar', 'TAR623G1721' => 'tar', 'TAR633G0959' => 'tar', 'THA.LOC104802225' => 'tha', 'THA.LOC104804769' => 'tha', 'THA.LOC104808660' => 'tha', 'THA.LOC104812792' => 'tha', 'Thecc.01G284000' => 'tca', 'Thecc.04G220600' => 'tca', 'Thecc.05G268900' => 'tca', 'Thecc.08G171100' => 'tca', 'Thhalv10001284m.g' => 'esa', 'Thhalv10019912m.g' => 'esa', 'TPR.G14189' => 'tpr', 'TPR.G18110' => 'tpr', 'TPR.G18130' => 'tpr', 'TPR.G18131' => 'tpr', 'TPR.G18140' => 'tpr', 'TPR.G24282' => 'tpr', 'TPR.G25221' => 'tpr', 'TPR.G29267' => 'tpr', 'TPR.G35315' => 'tpr', 'TPR.G36173' => 'tpr', 'TWI09G0794' => 'twi', 'TWI59G1348' => 'twi', 'TWI74G0430' => 'twi', 'unitig_26.g8940' => 'ugi', 'unitig_749.g13744' => 'ugi', 'unitig_749.g13745' => 'ugi', 'vmacro08269' => 'vma', 'vmacro14937' => 'vma', 'vmacro20401' => 'vma', 'VMungo0464G1349' => 'vmu', 'VMungo0540G0289' => 'vmu', 'VMungo1215G1590' => 'vmu', 'VMungo1309G0221' => 'vmu', 'VMungo1309G2815' => 'vmu', 'VMungo1383G0239' => 'vmu', 'VMungo1383G2910' => 'vmu', 'Zm00001eb095270' => 'zma', 'Zm00001eb095280' => 'zma', 'Zm00001eb111630' => 'zma', 'Zm00001eb237080' => 'zma', 'Zm00001eb273740' => 'zma', 'Zm00001eb285040' => 'zma', 'Zm00001eb330790' => 'zma', 'Zm00001eb337380' => 'zma' ) $gf_id = 'HOM05D001484' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001484' ) $data_identifier = 'HOM05D001484' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 2, 'aly' => (int) 2, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 22, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 7, 'hma' => (int) 2, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 7, 'mtr' => (int) 10, 'cme' => (int) 2, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 4, 'ppa' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 4, 'qlo' => (int) 9, 'rch' => (int) 6, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 10, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 7, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb337380' $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' => 'HOM05D001484', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p31500' => 'bna', 'A05p00020' => 'bna', 'A07p08820' => 'bna', 'Aa31LG4G3300' => 'aar', 'Aa31LG8G10030' => 'aar', 'Actinidia00731' => 'ach', 'Actinidia11473' => 'ach', 'Actinidia23469' => 'ach', 'Actinidia24318' => 'ach', 'Actinidia40196' => 'ach', 'Actinidia40197' => 'ach', 'Actinidia40198' => 'ach', 'Ah.08g212990' => 'amhyb', 'Ah.15g091720' => 'amhyb', 'AL3G38260' => 'aly', 'AL4G47710' => 'aly', 'Aqoxy2G00671' => 'aox', 'Aqoxy2G03236' => 'aox', 'arahy.Tifrunner.gnm1.ann1.05IDCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KR684' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATY3SJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK6QJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6APGL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IDT7Z9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM073U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ0R87' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LE7RV4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT4QRX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V5ENPK' => 'arhy', 'AT2G48110' => 'ath', 'AT3G23590' => 'ath', 'ATR0626G186' => 'atr', 'ATR1127G141' => 'atr', 'Atru.chr4.2583' => 'acertr', 'Atru.chr5.1358' => 'acertr', 'Atru.chr5.1359' => 'acertr', 'Atru.chr8.46' => 'acertr', 'AUR62002640' => 'cqu', 'AUR62030055' => 'cqu', 'AUR62033713' => 'cqu', 'AUR62033714' => 'cqu', 'AUR62036795' => 'cqu', 'AUR62039891' => 'cqu', 'BcaB02g08737' => 'bca', 'BcaB04g20441' => 'bca', 'BcaB06g26509' => 'bca', 'BcaB06g26510' => 'bca', 'BcaB06g26511' => 'bca', 'BcaB06g26512' => 'bca', 'BcaB06g26513' => 'bca', 'BcaC02g12564' => 'bca', 'BcaC02g12565' => 'bca', 'BcaC02g12794' => 'bca', 'BcaC02g12795' => 'bca', 'BcaC02g12796' => 'bca', 'BcaC06g35541' => 'bca', 'BNapus_Darmor_BZH_scaffold_188p00080' => 'bna', 'BNapus_Darmor_BZH_scaffold_188p00090' => 'bna', 'BolC1t03972H' => 'bol', 'BolC1t03973H' => 'bol', 'BolC4t21680H' => 'bol', 'BolC7t41863H' => 'bol', 'BolSC55t61227H' => 'bol', 'BolSC55t61228H' => 'bol', 'BraA01t03278Z' => 'bra', 'BraA05t18998Z' => 'bra', 'BraA07t28673Z' => 'bra', 'C01p40150' => 'bna', 'C05p12370' => 'bna', 'C07p13680' => 'bna', 'CAN.G1006.16' => 'can', 'CAN.G1006.17' => 'can', 'CAN.G1170.2' => 'can', 'CAN.G962.7' => 'can', 'CANSAT25G2179' => 'cansat', 'CANSAT78G1573' => 'cansat', 'CARHR099510' => 'chi', 'CARHR143510' => 'chi', 'Carub.0003s2380' => 'cru', 'Carub.0004s3082' => 'cru', 'Ca_00614_v3' => 'car', 'Ca_07801_v3' => 'car', 'Ca_08567_v3' => 'car', 'Ca_09571_v3' => 'car', 'CBR_g19290' => 'cbr', 'Cc01_g19770' => 'ccan', 'Cc03_g03030' => 'ccan', 'CDE07G0968' => 'cde', 'CDE09G1441' => 'cde', 'Cfa006103' => 'cfa', 'Cfa015573' => 'cfa', 'Cfa016988' => 'cfa', 'Ciclev10006738m.g' => 'ccl', 'Ciclev10010920m.g' => 'ccl', 'Ciclev10018517m.g' => 'ccl', 'CiPaw.01G159200' => 'cil', 'CiPaw.02G091000' => 'cil', 'CiPaw.02G091100' => 'cil', 'CiPaw.08G103100' => 'cil', 'CiPaw.09G224900' => 'cil', 'ClCG06G005740' => 'cla', 'ClCG07G000090' => 'cla', 'ClCG07G000100' => 'cla', 'COL.COLO4_09143' => 'col', 'COL.COLO4_25124' => 'col', 'Cpa.g.sc16.34' => 'cpa', 'Cpa.g.sc3504.1' => 'cpa', 'Cpa.g.sc60.37' => 'cpa', 'CsaV3_6G018520' => 'csa', 'CsaV3_6G036860' => 'csa', 'CSS0001072' => 'camsi', 'CSS0020208' => 'camsi', 'CSS0021253' => 'camsi', 'CSS0022190' => 'camsi', 'CSS0036150' => 'camsi', 'CSS0040442' => 'camsi', 'CSS0042300' => 'camsi', 'CSS0045298' => 'camsi', 'DCAR_012449' => 'dca', 'DCAR_018405' => 'dca', 'DCAR_024573' => 'dca', 'DCAR_030591' => 'dca', 'Dinv16926' => 'din', 'Dinv32963' => 'din', 'Dinv38382' => 'din', 'Dinv38383' => 'din', 'Duzib133G0974' => 'dzi', 'Duzib138G1867' => 'dzi', 'Duzib211G0420' => 'dzi', 'Duzib212G0930' => 'dzi', 'ECA234G1645' => 'eca', 'ECA247G3467' => 'eca', 'ECA248G1703' => 'eca', 'EL10Ac3g06327' => 'bvu', 'EL10Ac7g17204' => 'bvu', 'Eucgr.A00855' => 'egr', 'Eucgr.A00858' => 'egr', 'Eucgr.H01520' => 'egr', 'Eucgr.H03604' => 'egr', 'Eucgr.L03465' => 'egr', 'Eucgr.L03466' => 'egr', 'FAN01G0988' => 'fan', 'FAN02G3892' => 'fan', 'FAN05G3381' => 'fan', 'FAN07G0967' => 'fan', 'FAN07G1493' => 'fan', 'FAN08G3125' => 'fan', 'FAN09G0402' => 'fan', 'FAN12G2594' => 'fan', 'FAN12G3879' => 'fan', 'FAN14G1546' => 'fan', 'FAN15G3626' => 'fan', 'FAN17G0588' => 'fan', 'FAN17G0609' => 'fan', 'FAN18G2817' => 'fan', 'FAN19G1305' => 'fan', 'FAN20G1787' => 'fan', 'FAN22G0073' => 'fan', 'FAN22G0352' => 'fan', 'FAN22G0368' => 'fan', 'FAN22G2273' => 'fan', 'FAN24G1998' => 'fan', 'FAN27G1317' => 'fan', 'FvH4_2g23980' => 'fve', 'FvH4_4g14380' => 'fve', 'FvH4_4g14390' => 'fve', 'FvH4_6g09250' => 'fve', 'Glyma.03G151100' => 'gma', 'Glyma.04G122550' => 'gma', 'Glyma.05G001600' => 'gma', 'Glyma.09G270766' => 'gma', 'Glyma.09G270832' => 'gma', 'Glyma.13G209800' => 'gma', 'Glyma.15G102800' => 'gma', 'Glyma.18G218900' => 'gma', 'Glyma.19G001500' => 'gma', 'Glyma.19G153600' => 'gma', 'Gohir.A02G028600' => 'ghi', 'Gohir.A08G045000' => 'ghi', 'Gohir.A11G120500' => 'ghi', 'Gohir.A12G006200' => 'ghi', 'Gohir.A12G006250' => 'ghi', 'Gohir.D02G036300' => 'ghi', 'Gohir.D08G054700' => 'ghi', 'Gohir.D11G125600' => 'ghi', 'Gohir.D12G005700' => 'ghi', 'Gorai.004G055200' => 'gra', 'Gorai.005G040400' => 'gra', 'Gorai.007G134500' => 'gra', 'Gorai.008G005500' => 'gra', 'GSVIVG01011094001' => 'vvi', 'GSVIVG01017879001' => 'vvi', 'GSVIVG01025988001' => 'vvi', 'GSVIVG01029847001' => 'vvi', 'HanXRQChr10g0282901' => 'han', 'HanXRQChr10g0310371' => 'han', 'HanXRQChr10g0315041' => 'han', 'HanXRQChr11g0327651' => 'han', 'HanXRQChr12g0359391' => 'han', 'Haze_00972' => 'cav', 'Haze_00973' => 'cav', 'Haze_00974' => 'cav', 'Haze_04747' => 'cav', 'Haze_04749' => 'cav', 'Haze_04750' => 'cav', 'Haze_21217' => 'cav', 'Hma1.2p1_1037F.1_g250680' => 'hma', 'Hma1.2p1_1644F.1_g295320' => 'hma', 'HPP92_011322' => 'vpl', 'HPP92_011323' => 'vpl', 'HPP92_011324' => 'vpl', 'HPP92_011325' => 'vpl', 'HPP92_011326' => 'vpl', 'Hund12205' => 'sun', 'Hund17957' => 'sun', 'Lalb_Chr06g0176771' => 'lal', 'Lalb_Chr18g0056021' => 'lal', 'Lalb_Chr18g0056031' => 'lal', 'Lalb_Chr18g0056041' => 'lal', 'Lalb_Chr20g0107751' => 'lal', 'Lalb_Chr20g0118371' => 'lal', 'Lj1g0010239' => 'lja', 'Lj1g0017101' => 'lja', 'Lj2A1178G40' => 'lonja', 'Lj2A54G84' => 'lonja', 'Lj2g0015248' => 'lja', 'Lj3A761T51' => 'lonja', 'Lj6g0018116' => 'lja', 'Lsat_1_v5_gn_4_136040' => 'lsa', 'Lsat_1_v5_gn_5_187461' => 'lsa', 'Lsat_1_v5_gn_5_77001' => 'lsa', 'Lsat_1_v5_gn_9_4461' => 'lsa', 'Manes.01G210100' => 'mes', 'Manes.03G185600' => 'mes', 'Manes.05G073300' => 'mes', 'Manes.09G120300' => 'mes', 'Manes.15G022100' => 'mes', 'Mapoly0096s0053' => 'mpo', 'MBI03_g14058_MAGBIO' => 'mbi', 'MBI03_g33876_MAGBIO' => 'mbi', 'MBI03_g36854_MAGBIO' => 'mbi', 'MBI17_g11997_MAGBIO' => 'mbi', 'MD03G1269000' => 'mdo', 'MD04G1179600' => 'mdo', 'MD11G1289800' => 'mdo', 'MD12G1194700' => 'mdo', 'MD13G1182100' => 'mdo', 'MD13G1182200' => 'mdo', 'MD16G1182600' => 'mdo', 'Medtr2g021400' => 'mtr', 'Medtr2g021470' => 'mtr', 'Medtr2g105810' => 'mtr', 'Medtr3g033580' => 'mtr', 'Medtr6g007970' => 'mtr', 'Medtr7g056330' => 'mtr', 'Medtr7g074290' => 'mtr', 'Medtr7g074380' => 'mtr', 'Medtr7g094550' => 'mtr', 'Medtr8g069995' => 'mtr', 'MELO3C014345.2' => 'cme', 'MELO3C021395.2' => 'cme', 'Migut.D00262' => 'egut', 'Migut.G00257' => 'egut', 'MSTRG.21575' => 'ama', 'MSTRG.3985' => 'ama', 'Nitab4.5_0000295g0140' => 'nta', 'Nitab4.5_0000732g0140' => 'nta', 'Nitab4.5_0003162g0020' => 'nta', 'Nitab4.5_0006180g0090' => 'nta', 'Nitab4.5_0006390g0010' => 'nta', 'Nitab4.5_0007392g0040' => 'nta', 'Nn1g02140' => 'nnu', 'Nn4g26168' => 'nnu', 'Nn5g26754' => 'nnu', 'Oeu001433.1' => 'oeu', 'Oeu010299.2' => 'oeu', 'Oeu011171.1' => 'oeu', 'Oeu037675.1' => 'oeu', 'Oeu038359.1' => 'oeu', 'Oeu063834.1' => 'oeu', 'Oeu063835.1' => 'oeu', 'Os05g0312000' => 'osa', 'Os07g0211101' => 'osa', 'Os07g0211200' => 'osa', 'Os07g0681500' => 'osa', 'Peaxi162Scf00095g01015' => 'pax', 'Peaxi162Scf00104g00329' => 'pax', 'Peaxi162Scf00161g00137' => 'pax', 'PGR004G1665' => 'pgr', 'PGR031G2937' => 'pgr', 'PGR119G2145' => 'pgr', 'PGSC0003DMG400004351' => 'stu', 'PGSC0003DMG400014625' => 'stu', 'PGSC0003DMG401000943' => 'stu', 'Phvul.001G148600' => 'pvu', 'Phvul.004G001700' => 'pvu', 'Phvul.006G154900' => 'pvu', 'Phvul.008G078200' => 'pvu', 'Phvul.011G136500' => 'pvu', 'Potri.002G215600' => 'ptr', 'Potri.008G201600' => 'ptr', 'Potri.014G138400' => 'ptr', 'Potri.016G142500' => 'ptr', 'Pp3c16_10580' => 'ppa', 'Pp3c5_25280' => 'ppa', 'Prupe.1G150000' => 'ppe', 'Prupe.1G150100' => 'ppe', 'Prupe.6G299600' => 'ppe', 'Prupe.8G245000' => 'ppe', 'Psat0s4927g0040' => 'psa', 'Psat1g052080' => 'psa', 'Psat1g183800' => 'psa', 'Psat3g113840' => 'psa', 'Psat3g126120' => 'psa', 'Psat3g126160' => 'psa', 'Psat3g158760' => 'psa', 'Psat3g158840' => 'psa', 'PSO170G2858' => 'pso', 'PSO339G0606' => 'pso', 'PSO384G4709' => 'pso', 'PSO407G0334' => 'pso', 'QL04p040276' => 'qlo', 'QL06p005458' => 'qlo', 'QL06p005472' => 'qlo', 'QL07p030546' => 'qlo', 'QL07p031519' => 'qlo', 'QL09p050949' => 'qlo', 'QL09p050966' => 'qlo', 'QL09p051067' => 'qlo', 'QL12p022706' => 'qlo', 'RcHm_v2.0_Chr2g0119601' => 'rch', 'RcHm_v2.0_Chr3g0459591' => 'rch', 'RcHm_v2.0_Chr4g0418521' => 'rch', 'RcHm_v2.0_Chr4g0418531' => 'rch', 'RcHm_v2.0_Chr4g0418541' => 'rch', 'RcHm_v2.0_Chr6g0291641' => 'rch', 'Rhsim01G0086300' => 'rsi', 'Rhsim01G0276300' => 'rsi', 'Rhsim01G0276500' => 'rsi', 'Rhsim04G0207700' => 'rsi', 'Rhsim05G0234500' => 'rsi', 'Rhsim13G0022400' => 'rsi', 'Sabra02G0167900' => 'sbr', 'Sabra04G0158500' => 'sbr', 'Sabra08G0159800' => 'sbr', 'Sabra10G0011500' => 'sbr', 'Sabra14G0104400' => 'sbr', 'SalBow2G2440' => 'sbo', 'SalBow4G2265' => 'sbo', 'Sc02g0000060' => 'sci', 'Sc05g0005020' => 'sci', 'Sc13g0003890' => 'sci', 'Sed0014865' => 'sed', 'Sed0017224' => 'sed', 'Sed0026391' => 'sed', 'SEGI_00063' => 'sgi', 'SEGI_10967' => 'sgi', 'SEGI_17510' => 'sgi', 'SEGI_24396' => 'sgi', 'SEGI_39719' => 'sgi', 'SEGI_41392' => 'sgi', 'SGA_v2.0_scaffold11G05794' => 'sas', 'SGA_v2.0_scaffold142G35607' => 'sas', 'SGA_v2.0_scaffold1G00447' => 'sas', 'SHI15388' => 'shi', 'SHI15394' => 'shi', 'SHI15396' => 'shi', 'SHI15399' => 'shi', 'SMO343G0151' => 'smo', 'SMO367G1118' => 'smo', 'Solyc01g080200.3' => 'sly', 'Solyc06g008960.3' => 'sly', 'Solyc09g064780.3' => 'sly', 'Sopen01g031980' => 'spe', 'Sopen06g003710' => 'spe', 'Sopen09g026460' => 'spe', 'Sp3g21240' => 'spa', 'Sp4g30030' => 'spa', 'TAR365G0022' => 'tar', 'TAR365G1023' => 'tar', 'TAR365G1253' => 'tar', 'TAR623G0078' => 'tar', 'TAR623G1721' => 'tar', 'TAR633G0959' => 'tar', 'THA.LOC104802225' => 'tha', 'THA.LOC104804769' => 'tha', 'THA.LOC104808660' => 'tha', 'THA.LOC104812792' => 'tha', 'Thecc.01G284000' => 'tca', 'Thecc.04G220600' => 'tca', 'Thecc.05G268900' => 'tca', 'Thecc.08G171100' => 'tca', 'Thhalv10001284m.g' => 'esa', 'Thhalv10019912m.g' => 'esa', 'TPR.G14189' => 'tpr', 'TPR.G18110' => 'tpr', 'TPR.G18130' => 'tpr', 'TPR.G18131' => 'tpr', 'TPR.G18140' => 'tpr', 'TPR.G24282' => 'tpr', 'TPR.G25221' => 'tpr', 'TPR.G29267' => 'tpr', 'TPR.G35315' => 'tpr', 'TPR.G36173' => 'tpr', 'TWI09G0794' => 'twi', 'TWI59G1348' => 'twi', 'TWI74G0430' => 'twi', 'unitig_26.g8940' => 'ugi', 'unitig_749.g13744' => 'ugi', 'unitig_749.g13745' => 'ugi', 'vmacro08269' => 'vma', 'vmacro14937' => 'vma', 'vmacro20401' => 'vma', 'VMungo0464G1349' => 'vmu', 'VMungo0540G0289' => 'vmu', 'VMungo1215G1590' => 'vmu', 'VMungo1309G0221' => 'vmu', 'VMungo1309G2815' => 'vmu', 'VMungo1383G0239' => 'vmu', 'VMungo1383G2910' => 'vmu', 'Zm00001eb095270' => 'zma', 'Zm00001eb095280' => 'zma', 'Zm00001eb111630' => 'zma', 'Zm00001eb237080' => 'zma', 'Zm00001eb273740' => 'zma', 'Zm00001eb285040' => 'zma', 'Zm00001eb330790' => 'zma', 'Zm00001eb337380' => 'zma' ), 'gf_id' => 'HOM05D001484', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001484' ), 'data_identifier' => 'HOM05D001484', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001484', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p31500' => 'bna', 'A05p00020' => 'bna', 'A07p08820' => 'bna', 'Aa31LG4G3300' => 'aar', 'Aa31LG8G10030' => 'aar', 'Actinidia00731' => 'ach', 'Actinidia11473' => 'ach', 'Actinidia23469' => 'ach', 'Actinidia24318' => 'ach', 'Actinidia40196' => 'ach', 'Actinidia40197' => 'ach', 'Actinidia40198' => 'ach', 'Ah.08g212990' => 'amhyb', 'Ah.15g091720' => 'amhyb', 'AL3G38260' => 'aly', 'AL4G47710' => 'aly', 'Aqoxy2G00671' => 'aox', 'Aqoxy2G03236' => 'aox', 'arahy.Tifrunner.gnm1.ann1.05IDCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KR684' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATY3SJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK6QJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6APGL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IDT7Z9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM073U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ0R87' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LE7RV4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT4QRX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V5ENPK' => 'arhy', 'AT2G48110' => 'ath', 'AT3G23590' => 'ath', 'ATR0626G186' => 'atr', 'ATR1127G141' => 'atr', 'Atru.chr4.2583' => 'acertr', 'Atru.chr5.1358' => 'acertr', 'Atru.chr5.1359' => 'acertr', 'Atru.chr8.46' => 'acertr', 'AUR62002640' => 'cqu', 'AUR62030055' => 'cqu', 'AUR62033713' => 'cqu', 'AUR62033714' => 'cqu', 'AUR62036795' => 'cqu', 'AUR62039891' => 'cqu', 'BcaB02g08737' => 'bca', 'BcaB04g20441' => 'bca', 'BcaB06g26509' => 'bca', 'BcaB06g26510' => 'bca', 'BcaB06g26511' => 'bca', 'BcaB06g26512' => 'bca', 'BcaB06g26513' => 'bca', 'BcaC02g12564' => 'bca', 'BcaC02g12565' => 'bca', 'BcaC02g12794' => 'bca', 'BcaC02g12795' => 'bca', 'BcaC02g12796' => 'bca', 'BcaC06g35541' => 'bca', 'BNapus_Darmor_BZH_scaffold_188p00080' => 'bna', 'BNapus_Darmor_BZH_scaffold_188p00090' => 'bna', 'BolC1t03972H' => 'bol', 'BolC1t03973H' => 'bol', 'BolC4t21680H' => 'bol', 'BolC7t41863H' => 'bol', 'BolSC55t61227H' => 'bol', 'BolSC55t61228H' => 'bol', 'BraA01t03278Z' => 'bra', 'BraA05t18998Z' => 'bra', 'BraA07t28673Z' => 'bra', 'C01p40150' => 'bna', 'C05p12370' => 'bna', 'C07p13680' => 'bna', 'CAN.G1006.16' => 'can', 'CAN.G1006.17' => 'can', 'CAN.G1170.2' => 'can', 'CAN.G962.7' => 'can', 'CANSAT25G2179' => 'cansat', 'CANSAT78G1573' => 'cansat', 'CARHR099510' => 'chi', 'CARHR143510' => 'chi', 'Carub.0003s2380' => 'cru', 'Carub.0004s3082' => 'cru', 'Ca_00614_v3' => 'car', 'Ca_07801_v3' => 'car', 'Ca_08567_v3' => 'car', 'Ca_09571_v3' => 'car', 'CBR_g19290' => 'cbr', 'Cc01_g19770' => 'ccan', 'Cc03_g03030' => 'ccan', 'CDE07G0968' => 'cde', 'CDE09G1441' => 'cde', 'Cfa006103' => 'cfa', 'Cfa015573' => 'cfa', 'Cfa016988' => 'cfa', 'Ciclev10006738m.g' => 'ccl', 'Ciclev10010920m.g' => 'ccl', 'Ciclev10018517m.g' => 'ccl', 'CiPaw.01G159200' => 'cil', 'CiPaw.02G091000' => 'cil', 'CiPaw.02G091100' => 'cil', 'CiPaw.08G103100' => 'cil', 'CiPaw.09G224900' => 'cil', 'ClCG06G005740' => 'cla', 'ClCG07G000090' => 'cla', 'ClCG07G000100' => 'cla', 'COL.COLO4_09143' => 'col', 'COL.COLO4_25124' => 'col', 'Cpa.g.sc16.34' => 'cpa', 'Cpa.g.sc3504.1' => 'cpa', 'Cpa.g.sc60.37' => 'cpa', 'CsaV3_6G018520' => 'csa', 'CsaV3_6G036860' => 'csa', 'CSS0001072' => 'camsi', 'CSS0020208' => 'camsi', 'CSS0021253' => 'camsi', 'CSS0022190' => 'camsi', 'CSS0036150' => 'camsi', 'CSS0040442' => 'camsi', 'CSS0042300' => 'camsi', 'CSS0045298' => 'camsi', 'DCAR_012449' => 'dca', 'DCAR_018405' => 'dca', 'DCAR_024573' => 'dca', 'DCAR_030591' => 'dca', 'Dinv16926' => 'din', 'Dinv32963' => 'din', 'Dinv38382' => 'din', 'Dinv38383' => 'din', 'Duzib133G0974' => 'dzi', 'Duzib138G1867' => 'dzi', 'Duzib211G0420' => 'dzi', 'Duzib212G0930' => 'dzi', 'ECA234G1645' => 'eca', 'ECA247G3467' => 'eca', 'ECA248G1703' => 'eca', 'EL10Ac3g06327' => 'bvu', 'EL10Ac7g17204' => 'bvu', 'Eucgr.A00855' => 'egr', 'Eucgr.A00858' => 'egr', 'Eucgr.H01520' => 'egr', 'Eucgr.H03604' => 'egr', 'Eucgr.L03465' => 'egr', 'Eucgr.L03466' => 'egr', 'FAN01G0988' => 'fan', 'FAN02G3892' => 'fan', 'FAN05G3381' => 'fan', 'FAN07G0967' => 'fan', 'FAN07G1493' => 'fan', 'FAN08G3125' => 'fan', 'FAN09G0402' => 'fan', 'FAN12G2594' => 'fan', 'FAN12G3879' => 'fan', 'FAN14G1546' => 'fan', 'FAN15G3626' => 'fan', 'FAN17G0588' => 'fan', 'FAN17G0609' => 'fan', 'FAN18G2817' => 'fan', 'FAN19G1305' => 'fan', 'FAN20G1787' => 'fan', 'FAN22G0073' => 'fan', 'FAN22G0352' => 'fan', 'FAN22G0368' => 'fan', 'FAN22G2273' => 'fan', 'FAN24G1998' => 'fan', 'FAN27G1317' => 'fan', 'FvH4_2g23980' => 'fve', 'FvH4_4g14380' => 'fve', 'FvH4_4g14390' => 'fve', 'FvH4_6g09250' => 'fve', 'Glyma.03G151100' => 'gma', 'Glyma.04G122550' => 'gma', 'Glyma.05G001600' => 'gma', 'Glyma.09G270766' => 'gma', 'Glyma.09G270832' => 'gma', 'Glyma.13G209800' => 'gma', 'Glyma.15G102800' => 'gma', 'Glyma.18G218900' => 'gma', 'Glyma.19G001500' => 'gma', 'Glyma.19G153600' => 'gma', 'Gohir.A02G028600' => 'ghi', 'Gohir.A08G045000' => 'ghi', 'Gohir.A11G120500' => 'ghi', 'Gohir.A12G006200' => 'ghi', 'Gohir.A12G006250' => 'ghi', 'Gohir.D02G036300' => 'ghi', 'Gohir.D08G054700' => 'ghi', 'Gohir.D11G125600' => 'ghi', 'Gohir.D12G005700' => 'ghi', 'Gorai.004G055200' => 'gra', 'Gorai.005G040400' => 'gra', 'Gorai.007G134500' => 'gra', 'Gorai.008G005500' => 'gra', 'GSVIVG01011094001' => 'vvi', 'GSVIVG01017879001' => 'vvi', 'GSVIVG01025988001' => 'vvi', 'GSVIVG01029847001' => 'vvi', 'HanXRQChr10g0282901' => 'han', 'HanXRQChr10g0310371' => 'han', 'HanXRQChr10g0315041' => 'han', 'HanXRQChr11g0327651' => 'han', 'HanXRQChr12g0359391' => 'han', 'Haze_00972' => 'cav', 'Haze_00973' => 'cav', 'Haze_00974' => 'cav', 'Haze_04747' => 'cav', 'Haze_04749' => 'cav', 'Haze_04750' => 'cav', 'Haze_21217' => 'cav', 'Hma1.2p1_1037F.1_g250680' => 'hma', 'Hma1.2p1_1644F.1_g295320' => 'hma', 'HPP92_011322' => 'vpl', 'HPP92_011323' => 'vpl', 'HPP92_011324' => 'vpl', 'HPP92_011325' => 'vpl', 'HPP92_011326' => 'vpl', 'Hund12205' => 'sun', 'Hund17957' => 'sun', 'Lalb_Chr06g0176771' => 'lal', 'Lalb_Chr18g0056021' => 'lal', 'Lalb_Chr18g0056031' => 'lal', 'Lalb_Chr18g0056041' => 'lal', 'Lalb_Chr20g0107751' => 'lal', 'Lalb_Chr20g0118371' => 'lal', 'Lj1g0010239' => 'lja', 'Lj1g0017101' => 'lja', 'Lj2A1178G40' => 'lonja', 'Lj2A54G84' => 'lonja', 'Lj2g0015248' => 'lja', 'Lj3A761T51' => 'lonja', 'Lj6g0018116' => 'lja', 'Lsat_1_v5_gn_4_136040' => 'lsa', 'Lsat_1_v5_gn_5_187461' => 'lsa', 'Lsat_1_v5_gn_5_77001' => 'lsa', 'Lsat_1_v5_gn_9_4461' => 'lsa', 'Manes.01G210100' => 'mes', 'Manes.03G185600' => 'mes', 'Manes.05G073300' => 'mes', 'Manes.09G120300' => 'mes', 'Manes.15G022100' => 'mes', 'Mapoly0096s0053' => 'mpo', 'MBI03_g14058_MAGBIO' => 'mbi', 'MBI03_g33876_MAGBIO' => 'mbi', 'MBI03_g36854_MAGBIO' => 'mbi', 'MBI17_g11997_MAGBIO' => 'mbi', 'MD03G1269000' => 'mdo', 'MD04G1179600' => 'mdo', 'MD11G1289800' => 'mdo', 'MD12G1194700' => 'mdo', 'MD13G1182100' => 'mdo', 'MD13G1182200' => 'mdo', 'MD16G1182600' => 'mdo', 'Medtr2g021400' => 'mtr', 'Medtr2g021470' => 'mtr', 'Medtr2g105810' => 'mtr', 'Medtr3g033580' => 'mtr', 'Medtr6g007970' => 'mtr', 'Medtr7g056330' => 'mtr', 'Medtr7g074290' => 'mtr', 'Medtr7g074380' => 'mtr', 'Medtr7g094550' => 'mtr', 'Medtr8g069995' => 'mtr', 'MELO3C014345.2' => 'cme', 'MELO3C021395.2' => 'cme', 'Migut.D00262' => 'egut', 'Migut.G00257' => 'egut', 'MSTRG.21575' => 'ama', 'MSTRG.3985' => 'ama', 'Nitab4.5_0000295g0140' => 'nta', 'Nitab4.5_0000732g0140' => 'nta', 'Nitab4.5_0003162g0020' => 'nta', 'Nitab4.5_0006180g0090' => 'nta', 'Nitab4.5_0006390g0010' => 'nta', 'Nitab4.5_0007392g0040' => 'nta', 'Nn1g02140' => 'nnu', 'Nn4g26168' => 'nnu', 'Nn5g26754' => 'nnu', 'Oeu001433.1' => 'oeu', 'Oeu010299.2' => 'oeu', 'Oeu011171.1' => 'oeu', 'Oeu037675.1' => 'oeu', 'Oeu038359.1' => 'oeu', 'Oeu063834.1' => 'oeu', 'Oeu063835.1' => 'oeu', 'Os05g0312000' => 'osa', 'Os07g0211101' => 'osa', 'Os07g0211200' => 'osa', 'Os07g0681500' => 'osa', 'Peaxi162Scf00095g01015' => 'pax', 'Peaxi162Scf00104g00329' => 'pax', 'Peaxi162Scf00161g00137' => 'pax', 'PGR004G1665' => 'pgr', 'PGR031G2937' => 'pgr', 'PGR119G2145' => 'pgr', 'PGSC0003DMG400004351' => 'stu', 'PGSC0003DMG400014625' => 'stu', 'PGSC0003DMG401000943' => 'stu', 'Phvul.001G148600' => 'pvu', 'Phvul.004G001700' => 'pvu', 'Phvul.006G154900' => 'pvu', 'Phvul.008G078200' => 'pvu', 'Phvul.011G136500' => 'pvu', 'Potri.002G215600' => 'ptr', 'Potri.008G201600' => 'ptr', 'Potri.014G138400' => 'ptr', 'Potri.016G142500' => 'ptr', 'Pp3c16_10580' => 'ppa', 'Pp3c5_25280' => 'ppa', 'Prupe.1G150000' => 'ppe', 'Prupe.1G150100' => 'ppe', 'Prupe.6G299600' => 'ppe', 'Prupe.8G245000' => 'ppe', 'Psat0s4927g0040' => 'psa', 'Psat1g052080' => 'psa', 'Psat1g183800' => 'psa', 'Psat3g113840' => 'psa', 'Psat3g126120' => 'psa', 'Psat3g126160' => 'psa', 'Psat3g158760' => 'psa', 'Psat3g158840' => 'psa', 'PSO170G2858' => 'pso', 'PSO339G0606' => 'pso', 'PSO384G4709' => 'pso', 'PSO407G0334' => 'pso', 'QL04p040276' => 'qlo', 'QL06p005458' => 'qlo', 'QL06p005472' => 'qlo', 'QL07p030546' => 'qlo', 'QL07p031519' => 'qlo', 'QL09p050949' => 'qlo', 'QL09p050966' => 'qlo', 'QL09p051067' => 'qlo', 'QL12p022706' => 'qlo', 'RcHm_v2.0_Chr2g0119601' => 'rch', 'RcHm_v2.0_Chr3g0459591' => 'rch', 'RcHm_v2.0_Chr4g0418521' => 'rch', 'RcHm_v2.0_Chr4g0418531' => 'rch', 'RcHm_v2.0_Chr4g0418541' => 'rch', 'RcHm_v2.0_Chr6g0291641' => 'rch', 'Rhsim01G0086300' => 'rsi', 'Rhsim01G0276300' => 'rsi', 'Rhsim01G0276500' => 'rsi', 'Rhsim04G0207700' => 'rsi', 'Rhsim05G0234500' => 'rsi', 'Rhsim13G0022400' => 'rsi', 'Sabra02G0167900' => 'sbr', 'Sabra04G0158500' => 'sbr', 'Sabra08G0159800' => 'sbr', 'Sabra10G0011500' => 'sbr', 'Sabra14G0104400' => 'sbr', 'SalBow2G2440' => 'sbo', 'SalBow4G2265' => 'sbo', 'Sc02g0000060' => 'sci', 'Sc05g0005020' => 'sci', 'Sc13g0003890' => 'sci', 'Sed0014865' => 'sed', 'Sed0017224' => 'sed', 'Sed0026391' => 'sed', 'SEGI_00063' => 'sgi', 'SEGI_10967' => 'sgi', 'SEGI_17510' => 'sgi', 'SEGI_24396' => 'sgi', 'SEGI_39719' => 'sgi', 'SEGI_41392' => 'sgi', 'SGA_v2.0_scaffold11G05794' => 'sas', 'SGA_v2.0_scaffold142G35607' => 'sas', 'SGA_v2.0_scaffold1G00447' => 'sas', 'SHI15388' => 'shi', 'SHI15394' => 'shi', 'SHI15396' => 'shi', 'SHI15399' => 'shi', 'SMO343G0151' => 'smo', 'SMO367G1118' => 'smo', 'Solyc01g080200.3' => 'sly', 'Solyc06g008960.3' => 'sly', 'Solyc09g064780.3' => 'sly', 'Sopen01g031980' => 'spe', 'Sopen06g003710' => 'spe', 'Sopen09g026460' => 'spe', 'Sp3g21240' => 'spa', 'Sp4g30030' => 'spa', 'TAR365G0022' => 'tar', 'TAR365G1023' => 'tar', 'TAR365G1253' => 'tar', 'TAR623G0078' => 'tar', 'TAR623G1721' => 'tar', 'TAR633G0959' => 'tar', 'THA.LOC104802225' => 'tha', 'THA.LOC104804769' => 'tha', 'THA.LOC104808660' => 'tha', 'THA.LOC104812792' => 'tha', 'Thecc.01G284000' => 'tca', 'Thecc.04G220600' => 'tca', 'Thecc.05G268900' => 'tca', 'Thecc.08G171100' => 'tca', 'Thhalv10001284m.g' => 'esa', 'Thhalv10019912m.g' => 'esa', 'TPR.G14189' => 'tpr', 'TPR.G18110' => 'tpr', 'TPR.G18130' => 'tpr', 'TPR.G18131' => 'tpr', 'TPR.G18140' => 'tpr', 'TPR.G24282' => 'tpr', 'TPR.G25221' => 'tpr', 'TPR.G29267' => 'tpr', 'TPR.G35315' => 'tpr', 'TPR.G36173' => 'tpr', 'TWI09G0794' => 'twi', 'TWI59G1348' => 'twi', 'TWI74G0430' => 'twi', 'unitig_26.g8940' => 'ugi', 'unitig_749.g13744' => 'ugi', 'unitig_749.g13745' => 'ugi', 'vmacro08269' => 'vma', 'vmacro14937' => 'vma', 'vmacro20401' => 'vma', 'VMungo0464G1349' => 'vmu', 'VMungo0540G0289' => 'vmu', 'VMungo1215G1590' => 'vmu', 'VMungo1309G0221' => 'vmu', 'VMungo1309G2815' => 'vmu', 'VMungo1383G0239' => 'vmu', 'VMungo1383G2910' => 'vmu', 'Zm00001eb095270' => 'zma', 'Zm00001eb095280' => 'zma', 'Zm00001eb111630' => 'zma', 'Zm00001eb237080' => 'zma', 'Zm00001eb273740' => 'zma', 'Zm00001eb285040' => 'zma', 'Zm00001eb330790' => 'zma', 'Zm00001eb337380' => 'zma' ) $gf_id = 'HOM05D001484' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001484' ) $data_identifier = 'HOM05D001484' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 2, 'aly' => (int) 2, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 22, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 7, 'hma' => (int) 2, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 7, 'mtr' => (int) 10, 'cme' => (int) 2, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 4, 'ppa' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 4, 'qlo' => (int) 9, 'rch' => (int) 6, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 10, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 7, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb337380' $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' => 'HOM05D001484', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p31500' => 'bna', 'A05p00020' => 'bna', 'A07p08820' => 'bna', 'Aa31LG4G3300' => 'aar', 'Aa31LG8G10030' => 'aar', 'Actinidia00731' => 'ach', 'Actinidia11473' => 'ach', 'Actinidia23469' => 'ach', 'Actinidia24318' => 'ach', 'Actinidia40196' => 'ach', 'Actinidia40197' => 'ach', 'Actinidia40198' => 'ach', 'Ah.08g212990' => 'amhyb', 'Ah.15g091720' => 'amhyb', 'AL3G38260' => 'aly', 'AL4G47710' => 'aly', 'Aqoxy2G00671' => 'aox', 'Aqoxy2G03236' => 'aox', 'arahy.Tifrunner.gnm1.ann1.05IDCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KR684' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATY3SJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK6QJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6APGL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IDT7Z9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM073U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ0R87' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LE7RV4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT4QRX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V5ENPK' => 'arhy', 'AT2G48110' => 'ath', 'AT3G23590' => 'ath', 'ATR0626G186' => 'atr', 'ATR1127G141' => 'atr', 'Atru.chr4.2583' => 'acertr', 'Atru.chr5.1358' => 'acertr', 'Atru.chr5.1359' => 'acertr', 'Atru.chr8.46' => 'acertr', 'AUR62002640' => 'cqu', 'AUR62030055' => 'cqu', 'AUR62033713' => 'cqu', 'AUR62033714' => 'cqu', 'AUR62036795' => 'cqu', 'AUR62039891' => 'cqu', 'BcaB02g08737' => 'bca', 'BcaB04g20441' => 'bca', 'BcaB06g26509' => 'bca', 'BcaB06g26510' => 'bca', 'BcaB06g26511' => 'bca', 'BcaB06g26512' => 'bca', 'BcaB06g26513' => 'bca', 'BcaC02g12564' => 'bca', 'BcaC02g12565' => 'bca', 'BcaC02g12794' => 'bca', 'BcaC02g12795' => 'bca', 'BcaC02g12796' => 'bca', 'BcaC06g35541' => 'bca', 'BNapus_Darmor_BZH_scaffold_188p00080' => 'bna', 'BNapus_Darmor_BZH_scaffold_188p00090' => 'bna', 'BolC1t03972H' => 'bol', 'BolC1t03973H' => 'bol', 'BolC4t21680H' => 'bol', 'BolC7t41863H' => 'bol', 'BolSC55t61227H' => 'bol', 'BolSC55t61228H' => 'bol', 'BraA01t03278Z' => 'bra', 'BraA05t18998Z' => 'bra', 'BraA07t28673Z' => 'bra', 'C01p40150' => 'bna', 'C05p12370' => 'bna', 'C07p13680' => 'bna', 'CAN.G1006.16' => 'can', 'CAN.G1006.17' => 'can', 'CAN.G1170.2' => 'can', 'CAN.G962.7' => 'can', 'CANSAT25G2179' => 'cansat', 'CANSAT78G1573' => 'cansat', 'CARHR099510' => 'chi', 'CARHR143510' => 'chi', 'Carub.0003s2380' => 'cru', 'Carub.0004s3082' => 'cru', 'Ca_00614_v3' => 'car', 'Ca_07801_v3' => 'car', 'Ca_08567_v3' => 'car', 'Ca_09571_v3' => 'car', 'CBR_g19290' => 'cbr', 'Cc01_g19770' => 'ccan', 'Cc03_g03030' => 'ccan', 'CDE07G0968' => 'cde', 'CDE09G1441' => 'cde', 'Cfa006103' => 'cfa', 'Cfa015573' => 'cfa', 'Cfa016988' => 'cfa', 'Ciclev10006738m.g' => 'ccl', 'Ciclev10010920m.g' => 'ccl', 'Ciclev10018517m.g' => 'ccl', 'CiPaw.01G159200' => 'cil', 'CiPaw.02G091000' => 'cil', 'CiPaw.02G091100' => 'cil', 'CiPaw.08G103100' => 'cil', 'CiPaw.09G224900' => 'cil', 'ClCG06G005740' => 'cla', 'ClCG07G000090' => 'cla', 'ClCG07G000100' => 'cla', 'COL.COLO4_09143' => 'col', 'COL.COLO4_25124' => 'col', 'Cpa.g.sc16.34' => 'cpa', 'Cpa.g.sc3504.1' => 'cpa', 'Cpa.g.sc60.37' => 'cpa', 'CsaV3_6G018520' => 'csa', 'CsaV3_6G036860' => 'csa', 'CSS0001072' => 'camsi', 'CSS0020208' => 'camsi', 'CSS0021253' => 'camsi', 'CSS0022190' => 'camsi', 'CSS0036150' => 'camsi', 'CSS0040442' => 'camsi', 'CSS0042300' => 'camsi', 'CSS0045298' => 'camsi', 'DCAR_012449' => 'dca', 'DCAR_018405' => 'dca', 'DCAR_024573' => 'dca', 'DCAR_030591' => 'dca', 'Dinv16926' => 'din', 'Dinv32963' => 'din', 'Dinv38382' => 'din', 'Dinv38383' => 'din', 'Duzib133G0974' => 'dzi', 'Duzib138G1867' => 'dzi', 'Duzib211G0420' => 'dzi', 'Duzib212G0930' => 'dzi', 'ECA234G1645' => 'eca', 'ECA247G3467' => 'eca', 'ECA248G1703' => 'eca', 'EL10Ac3g06327' => 'bvu', 'EL10Ac7g17204' => 'bvu', 'Eucgr.A00855' => 'egr', 'Eucgr.A00858' => 'egr', 'Eucgr.H01520' => 'egr', 'Eucgr.H03604' => 'egr', 'Eucgr.L03465' => 'egr', 'Eucgr.L03466' => 'egr', 'FAN01G0988' => 'fan', 'FAN02G3892' => 'fan', 'FAN05G3381' => 'fan', 'FAN07G0967' => 'fan', 'FAN07G1493' => 'fan', 'FAN08G3125' => 'fan', 'FAN09G0402' => 'fan', 'FAN12G2594' => 'fan', 'FAN12G3879' => 'fan', 'FAN14G1546' => 'fan', 'FAN15G3626' => 'fan', 'FAN17G0588' => 'fan', 'FAN17G0609' => 'fan', 'FAN18G2817' => 'fan', 'FAN19G1305' => 'fan', 'FAN20G1787' => 'fan', 'FAN22G0073' => 'fan', 'FAN22G0352' => 'fan', 'FAN22G0368' => 'fan', 'FAN22G2273' => 'fan', 'FAN24G1998' => 'fan', 'FAN27G1317' => 'fan', 'FvH4_2g23980' => 'fve', 'FvH4_4g14380' => 'fve', 'FvH4_4g14390' => 'fve', 'FvH4_6g09250' => 'fve', 'Glyma.03G151100' => 'gma', 'Glyma.04G122550' => 'gma', 'Glyma.05G001600' => 'gma', 'Glyma.09G270766' => 'gma', 'Glyma.09G270832' => 'gma', 'Glyma.13G209800' => 'gma', 'Glyma.15G102800' => 'gma', 'Glyma.18G218900' => 'gma', 'Glyma.19G001500' => 'gma', 'Glyma.19G153600' => 'gma', 'Gohir.A02G028600' => 'ghi', 'Gohir.A08G045000' => 'ghi', 'Gohir.A11G120500' => 'ghi', 'Gohir.A12G006200' => 'ghi', 'Gohir.A12G006250' => 'ghi', 'Gohir.D02G036300' => 'ghi', 'Gohir.D08G054700' => 'ghi', 'Gohir.D11G125600' => 'ghi', 'Gohir.D12G005700' => 'ghi', 'Gorai.004G055200' => 'gra', 'Gorai.005G040400' => 'gra', 'Gorai.007G134500' => 'gra', 'Gorai.008G005500' => 'gra', 'GSVIVG01011094001' => 'vvi', 'GSVIVG01017879001' => 'vvi', 'GSVIVG01025988001' => 'vvi', 'GSVIVG01029847001' => 'vvi', 'HanXRQChr10g0282901' => 'han', 'HanXRQChr10g0310371' => 'han', 'HanXRQChr10g0315041' => 'han', 'HanXRQChr11g0327651' => 'han', 'HanXRQChr12g0359391' => 'han', 'Haze_00972' => 'cav', 'Haze_00973' => 'cav', 'Haze_00974' => 'cav', 'Haze_04747' => 'cav', 'Haze_04749' => 'cav', 'Haze_04750' => 'cav', 'Haze_21217' => 'cav', 'Hma1.2p1_1037F.1_g250680' => 'hma', 'Hma1.2p1_1644F.1_g295320' => 'hma', 'HPP92_011322' => 'vpl', 'HPP92_011323' => 'vpl', 'HPP92_011324' => 'vpl', 'HPP92_011325' => 'vpl', 'HPP92_011326' => 'vpl', 'Hund12205' => 'sun', 'Hund17957' => 'sun', 'Lalb_Chr06g0176771' => 'lal', 'Lalb_Chr18g0056021' => 'lal', 'Lalb_Chr18g0056031' => 'lal', 'Lalb_Chr18g0056041' => 'lal', 'Lalb_Chr20g0107751' => 'lal', 'Lalb_Chr20g0118371' => 'lal', 'Lj1g0010239' => 'lja', 'Lj1g0017101' => 'lja', 'Lj2A1178G40' => 'lonja', 'Lj2A54G84' => 'lonja', 'Lj2g0015248' => 'lja', 'Lj3A761T51' => 'lonja', 'Lj6g0018116' => 'lja', 'Lsat_1_v5_gn_4_136040' => 'lsa', 'Lsat_1_v5_gn_5_187461' => 'lsa', 'Lsat_1_v5_gn_5_77001' => 'lsa', 'Lsat_1_v5_gn_9_4461' => 'lsa', 'Manes.01G210100' => 'mes', 'Manes.03G185600' => 'mes', 'Manes.05G073300' => 'mes', 'Manes.09G120300' => 'mes', 'Manes.15G022100' => 'mes', 'Mapoly0096s0053' => 'mpo', 'MBI03_g14058_MAGBIO' => 'mbi', 'MBI03_g33876_MAGBIO' => 'mbi', 'MBI03_g36854_MAGBIO' => 'mbi', 'MBI17_g11997_MAGBIO' => 'mbi', 'MD03G1269000' => 'mdo', 'MD04G1179600' => 'mdo', 'MD11G1289800' => 'mdo', 'MD12G1194700' => 'mdo', 'MD13G1182100' => 'mdo', 'MD13G1182200' => 'mdo', 'MD16G1182600' => 'mdo', 'Medtr2g021400' => 'mtr', 'Medtr2g021470' => 'mtr', 'Medtr2g105810' => 'mtr', 'Medtr3g033580' => 'mtr', 'Medtr6g007970' => 'mtr', 'Medtr7g056330' => 'mtr', 'Medtr7g074290' => 'mtr', 'Medtr7g074380' => 'mtr', 'Medtr7g094550' => 'mtr', 'Medtr8g069995' => 'mtr', 'MELO3C014345.2' => 'cme', 'MELO3C021395.2' => 'cme', 'Migut.D00262' => 'egut', 'Migut.G00257' => 'egut', 'MSTRG.21575' => 'ama', 'MSTRG.3985' => 'ama', 'Nitab4.5_0000295g0140' => 'nta', 'Nitab4.5_0000732g0140' => 'nta', 'Nitab4.5_0003162g0020' => 'nta', 'Nitab4.5_0006180g0090' => 'nta', 'Nitab4.5_0006390g0010' => 'nta', 'Nitab4.5_0007392g0040' => 'nta', 'Nn1g02140' => 'nnu', 'Nn4g26168' => 'nnu', 'Nn5g26754' => 'nnu', 'Oeu001433.1' => 'oeu', 'Oeu010299.2' => 'oeu', 'Oeu011171.1' => 'oeu', 'Oeu037675.1' => 'oeu', 'Oeu038359.1' => 'oeu', 'Oeu063834.1' => 'oeu', 'Oeu063835.1' => 'oeu', 'Os05g0312000' => 'osa', 'Os07g0211101' => 'osa', 'Os07g0211200' => 'osa', 'Os07g0681500' => 'osa', 'Peaxi162Scf00095g01015' => 'pax', 'Peaxi162Scf00104g00329' => 'pax', 'Peaxi162Scf00161g00137' => 'pax', 'PGR004G1665' => 'pgr', 'PGR031G2937' => 'pgr', 'PGR119G2145' => 'pgr', 'PGSC0003DMG400004351' => 'stu', 'PGSC0003DMG400014625' => 'stu', 'PGSC0003DMG401000943' => 'stu', 'Phvul.001G148600' => 'pvu', 'Phvul.004G001700' => 'pvu', 'Phvul.006G154900' => 'pvu', 'Phvul.008G078200' => 'pvu', 'Phvul.011G136500' => 'pvu', 'Potri.002G215600' => 'ptr', 'Potri.008G201600' => 'ptr', 'Potri.014G138400' => 'ptr', 'Potri.016G142500' => 'ptr', 'Pp3c16_10580' => 'ppa', 'Pp3c5_25280' => 'ppa', 'Prupe.1G150000' => 'ppe', 'Prupe.1G150100' => 'ppe', 'Prupe.6G299600' => 'ppe', 'Prupe.8G245000' => 'ppe', 'Psat0s4927g0040' => 'psa', 'Psat1g052080' => 'psa', 'Psat1g183800' => 'psa', 'Psat3g113840' => 'psa', 'Psat3g126120' => 'psa', 'Psat3g126160' => 'psa', 'Psat3g158760' => 'psa', 'Psat3g158840' => 'psa', 'PSO170G2858' => 'pso', 'PSO339G0606' => 'pso', 'PSO384G4709' => 'pso', 'PSO407G0334' => 'pso', 'QL04p040276' => 'qlo', 'QL06p005458' => 'qlo', 'QL06p005472' => 'qlo', 'QL07p030546' => 'qlo', 'QL07p031519' => 'qlo', 'QL09p050949' => 'qlo', 'QL09p050966' => 'qlo', 'QL09p051067' => 'qlo', 'QL12p022706' => 'qlo', 'RcHm_v2.0_Chr2g0119601' => 'rch', 'RcHm_v2.0_Chr3g0459591' => 'rch', 'RcHm_v2.0_Chr4g0418521' => 'rch', 'RcHm_v2.0_Chr4g0418531' => 'rch', 'RcHm_v2.0_Chr4g0418541' => 'rch', 'RcHm_v2.0_Chr6g0291641' => 'rch', 'Rhsim01G0086300' => 'rsi', 'Rhsim01G0276300' => 'rsi', 'Rhsim01G0276500' => 'rsi', 'Rhsim04G0207700' => 'rsi', 'Rhsim05G0234500' => 'rsi', 'Rhsim13G0022400' => 'rsi', 'Sabra02G0167900' => 'sbr', 'Sabra04G0158500' => 'sbr', 'Sabra08G0159800' => 'sbr', 'Sabra10G0011500' => 'sbr', 'Sabra14G0104400' => 'sbr', 'SalBow2G2440' => 'sbo', 'SalBow4G2265' => 'sbo', 'Sc02g0000060' => 'sci', 'Sc05g0005020' => 'sci', 'Sc13g0003890' => 'sci', 'Sed0014865' => 'sed', 'Sed0017224' => 'sed', 'Sed0026391' => 'sed', 'SEGI_00063' => 'sgi', 'SEGI_10967' => 'sgi', 'SEGI_17510' => 'sgi', 'SEGI_24396' => 'sgi', 'SEGI_39719' => 'sgi', 'SEGI_41392' => 'sgi', 'SGA_v2.0_scaffold11G05794' => 'sas', 'SGA_v2.0_scaffold142G35607' => 'sas', 'SGA_v2.0_scaffold1G00447' => 'sas', 'SHI15388' => 'shi', 'SHI15394' => 'shi', 'SHI15396' => 'shi', 'SHI15399' => 'shi', 'SMO343G0151' => 'smo', 'SMO367G1118' => 'smo', 'Solyc01g080200.3' => 'sly', 'Solyc06g008960.3' => 'sly', 'Solyc09g064780.3' => 'sly', 'Sopen01g031980' => 'spe', 'Sopen06g003710' => 'spe', 'Sopen09g026460' => 'spe', 'Sp3g21240' => 'spa', 'Sp4g30030' => 'spa', 'TAR365G0022' => 'tar', 'TAR365G1023' => 'tar', 'TAR365G1253' => 'tar', 'TAR623G0078' => 'tar', 'TAR623G1721' => 'tar', 'TAR633G0959' => 'tar', 'THA.LOC104802225' => 'tha', 'THA.LOC104804769' => 'tha', 'THA.LOC104808660' => 'tha', 'THA.LOC104812792' => 'tha', 'Thecc.01G284000' => 'tca', 'Thecc.04G220600' => 'tca', 'Thecc.05G268900' => 'tca', 'Thecc.08G171100' => 'tca', 'Thhalv10001284m.g' => 'esa', 'Thhalv10019912m.g' => 'esa', 'TPR.G14189' => 'tpr', 'TPR.G18110' => 'tpr', 'TPR.G18130' => 'tpr', 'TPR.G18131' => 'tpr', 'TPR.G18140' => 'tpr', 'TPR.G24282' => 'tpr', 'TPR.G25221' => 'tpr', 'TPR.G29267' => 'tpr', 'TPR.G35315' => 'tpr', 'TPR.G36173' => 'tpr', 'TWI09G0794' => 'twi', 'TWI59G1348' => 'twi', 'TWI74G0430' => 'twi', 'unitig_26.g8940' => 'ugi', 'unitig_749.g13744' => 'ugi', 'unitig_749.g13745' => 'ugi', 'vmacro08269' => 'vma', 'vmacro14937' => 'vma', 'vmacro20401' => 'vma', 'VMungo0464G1349' => 'vmu', 'VMungo0540G0289' => 'vmu', 'VMungo1215G1590' => 'vmu', 'VMungo1309G0221' => 'vmu', 'VMungo1309G2815' => 'vmu', 'VMungo1383G0239' => 'vmu', 'VMungo1383G2910' => 'vmu', 'Zm00001eb095270' => 'zma', 'Zm00001eb095280' => 'zma', 'Zm00001eb111630' => 'zma', 'Zm00001eb237080' => 'zma', 'Zm00001eb273740' => 'zma', 'Zm00001eb285040' => 'zma', 'Zm00001eb330790' => 'zma', 'Zm00001eb337380' => 'zma' ), 'gf_id' => 'HOM05D001484', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001484' ), 'data_identifier' => 'HOM05D001484', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001484', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p31500' => 'bna', 'A05p00020' => 'bna', 'A07p08820' => 'bna', 'Aa31LG4G3300' => 'aar', 'Aa31LG8G10030' => 'aar', 'Actinidia00731' => 'ach', 'Actinidia11473' => 'ach', 'Actinidia23469' => 'ach', 'Actinidia24318' => 'ach', 'Actinidia40196' => 'ach', 'Actinidia40197' => 'ach', 'Actinidia40198' => 'ach', 'Ah.08g212990' => 'amhyb', 'Ah.15g091720' => 'amhyb', 'AL3G38260' => 'aly', 'AL4G47710' => 'aly', 'Aqoxy2G00671' => 'aox', 'Aqoxy2G03236' => 'aox', 'arahy.Tifrunner.gnm1.ann1.05IDCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KR684' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATY3SJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK6QJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6APGL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IDT7Z9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM073U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ0R87' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LE7RV4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT4QRX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V5ENPK' => 'arhy', 'AT2G48110' => 'ath', 'AT3G23590' => 'ath', 'ATR0626G186' => 'atr', 'ATR1127G141' => 'atr', 'Atru.chr4.2583' => 'acertr', 'Atru.chr5.1358' => 'acertr', 'Atru.chr5.1359' => 'acertr', 'Atru.chr8.46' => 'acertr', 'AUR62002640' => 'cqu', 'AUR62030055' => 'cqu', 'AUR62033713' => 'cqu', 'AUR62033714' => 'cqu', 'AUR62036795' => 'cqu', 'AUR62039891' => 'cqu', 'BcaB02g08737' => 'bca', 'BcaB04g20441' => 'bca', 'BcaB06g26509' => 'bca', 'BcaB06g26510' => 'bca', 'BcaB06g26511' => 'bca', 'BcaB06g26512' => 'bca', 'BcaB06g26513' => 'bca', 'BcaC02g12564' => 'bca', 'BcaC02g12565' => 'bca', 'BcaC02g12794' => 'bca', 'BcaC02g12795' => 'bca', 'BcaC02g12796' => 'bca', 'BcaC06g35541' => 'bca', 'BNapus_Darmor_BZH_scaffold_188p00080' => 'bna', 'BNapus_Darmor_BZH_scaffold_188p00090' => 'bna', 'BolC1t03972H' => 'bol', 'BolC1t03973H' => 'bol', 'BolC4t21680H' => 'bol', 'BolC7t41863H' => 'bol', 'BolSC55t61227H' => 'bol', 'BolSC55t61228H' => 'bol', 'BraA01t03278Z' => 'bra', 'BraA05t18998Z' => 'bra', 'BraA07t28673Z' => 'bra', 'C01p40150' => 'bna', 'C05p12370' => 'bna', 'C07p13680' => 'bna', 'CAN.G1006.16' => 'can', 'CAN.G1006.17' => 'can', 'CAN.G1170.2' => 'can', 'CAN.G962.7' => 'can', 'CANSAT25G2179' => 'cansat', 'CANSAT78G1573' => 'cansat', 'CARHR099510' => 'chi', 'CARHR143510' => 'chi', 'Carub.0003s2380' => 'cru', 'Carub.0004s3082' => 'cru', 'Ca_00614_v3' => 'car', 'Ca_07801_v3' => 'car', 'Ca_08567_v3' => 'car', 'Ca_09571_v3' => 'car', 'CBR_g19290' => 'cbr', 'Cc01_g19770' => 'ccan', 'Cc03_g03030' => 'ccan', 'CDE07G0968' => 'cde', 'CDE09G1441' => 'cde', 'Cfa006103' => 'cfa', 'Cfa015573' => 'cfa', 'Cfa016988' => 'cfa', 'Ciclev10006738m.g' => 'ccl', 'Ciclev10010920m.g' => 'ccl', 'Ciclev10018517m.g' => 'ccl', 'CiPaw.01G159200' => 'cil', 'CiPaw.02G091000' => 'cil', 'CiPaw.02G091100' => 'cil', 'CiPaw.08G103100' => 'cil', 'CiPaw.09G224900' => 'cil', 'ClCG06G005740' => 'cla', 'ClCG07G000090' => 'cla', 'ClCG07G000100' => 'cla', 'COL.COLO4_09143' => 'col', 'COL.COLO4_25124' => 'col', 'Cpa.g.sc16.34' => 'cpa', 'Cpa.g.sc3504.1' => 'cpa', 'Cpa.g.sc60.37' => 'cpa', 'CsaV3_6G018520' => 'csa', 'CsaV3_6G036860' => 'csa', 'CSS0001072' => 'camsi', 'CSS0020208' => 'camsi', 'CSS0021253' => 'camsi', 'CSS0022190' => 'camsi', 'CSS0036150' => 'camsi', 'CSS0040442' => 'camsi', 'CSS0042300' => 'camsi', 'CSS0045298' => 'camsi', 'DCAR_012449' => 'dca', 'DCAR_018405' => 'dca', 'DCAR_024573' => 'dca', 'DCAR_030591' => 'dca', 'Dinv16926' => 'din', 'Dinv32963' => 'din', 'Dinv38382' => 'din', 'Dinv38383' => 'din', 'Duzib133G0974' => 'dzi', 'Duzib138G1867' => 'dzi', 'Duzib211G0420' => 'dzi', 'Duzib212G0930' => 'dzi', 'ECA234G1645' => 'eca', 'ECA247G3467' => 'eca', 'ECA248G1703' => 'eca', 'EL10Ac3g06327' => 'bvu', 'EL10Ac7g17204' => 'bvu', 'Eucgr.A00855' => 'egr', 'Eucgr.A00858' => 'egr', 'Eucgr.H01520' => 'egr', 'Eucgr.H03604' => 'egr', 'Eucgr.L03465' => 'egr', 'Eucgr.L03466' => 'egr', 'FAN01G0988' => 'fan', 'FAN02G3892' => 'fan', 'FAN05G3381' => 'fan', 'FAN07G0967' => 'fan', 'FAN07G1493' => 'fan', 'FAN08G3125' => 'fan', 'FAN09G0402' => 'fan', 'FAN12G2594' => 'fan', 'FAN12G3879' => 'fan', 'FAN14G1546' => 'fan', 'FAN15G3626' => 'fan', 'FAN17G0588' => 'fan', 'FAN17G0609' => 'fan', 'FAN18G2817' => 'fan', 'FAN19G1305' => 'fan', 'FAN20G1787' => 'fan', 'FAN22G0073' => 'fan', 'FAN22G0352' => 'fan', 'FAN22G0368' => 'fan', 'FAN22G2273' => 'fan', 'FAN24G1998' => 'fan', 'FAN27G1317' => 'fan', 'FvH4_2g23980' => 'fve', 'FvH4_4g14380' => 'fve', 'FvH4_4g14390' => 'fve', 'FvH4_6g09250' => 'fve', 'Glyma.03G151100' => 'gma', 'Glyma.04G122550' => 'gma', 'Glyma.05G001600' => 'gma', 'Glyma.09G270766' => 'gma', 'Glyma.09G270832' => 'gma', 'Glyma.13G209800' => 'gma', 'Glyma.15G102800' => 'gma', 'Glyma.18G218900' => 'gma', 'Glyma.19G001500' => 'gma', 'Glyma.19G153600' => 'gma', 'Gohir.A02G028600' => 'ghi', 'Gohir.A08G045000' => 'ghi', 'Gohir.A11G120500' => 'ghi', 'Gohir.A12G006200' => 'ghi', 'Gohir.A12G006250' => 'ghi', 'Gohir.D02G036300' => 'ghi', 'Gohir.D08G054700' => 'ghi', 'Gohir.D11G125600' => 'ghi', 'Gohir.D12G005700' => 'ghi', 'Gorai.004G055200' => 'gra', 'Gorai.005G040400' => 'gra', 'Gorai.007G134500' => 'gra', 'Gorai.008G005500' => 'gra', 'GSVIVG01011094001' => 'vvi', 'GSVIVG01017879001' => 'vvi', 'GSVIVG01025988001' => 'vvi', 'GSVIVG01029847001' => 'vvi', 'HanXRQChr10g0282901' => 'han', 'HanXRQChr10g0310371' => 'han', 'HanXRQChr10g0315041' => 'han', 'HanXRQChr11g0327651' => 'han', 'HanXRQChr12g0359391' => 'han', 'Haze_00972' => 'cav', 'Haze_00973' => 'cav', 'Haze_00974' => 'cav', 'Haze_04747' => 'cav', 'Haze_04749' => 'cav', 'Haze_04750' => 'cav', 'Haze_21217' => 'cav', 'Hma1.2p1_1037F.1_g250680' => 'hma', 'Hma1.2p1_1644F.1_g295320' => 'hma', 'HPP92_011322' => 'vpl', 'HPP92_011323' => 'vpl', 'HPP92_011324' => 'vpl', 'HPP92_011325' => 'vpl', 'HPP92_011326' => 'vpl', 'Hund12205' => 'sun', 'Hund17957' => 'sun', 'Lalb_Chr06g0176771' => 'lal', 'Lalb_Chr18g0056021' => 'lal', 'Lalb_Chr18g0056031' => 'lal', 'Lalb_Chr18g0056041' => 'lal', 'Lalb_Chr20g0107751' => 'lal', 'Lalb_Chr20g0118371' => 'lal', 'Lj1g0010239' => 'lja', 'Lj1g0017101' => 'lja', 'Lj2A1178G40' => 'lonja', 'Lj2A54G84' => 'lonja', 'Lj2g0015248' => 'lja', 'Lj3A761T51' => 'lonja', 'Lj6g0018116' => 'lja', 'Lsat_1_v5_gn_4_136040' => 'lsa', 'Lsat_1_v5_gn_5_187461' => 'lsa', 'Lsat_1_v5_gn_5_77001' => 'lsa', 'Lsat_1_v5_gn_9_4461' => 'lsa', 'Manes.01G210100' => 'mes', 'Manes.03G185600' => 'mes', 'Manes.05G073300' => 'mes', 'Manes.09G120300' => 'mes', 'Manes.15G022100' => 'mes', 'Mapoly0096s0053' => 'mpo', 'MBI03_g14058_MAGBIO' => 'mbi', 'MBI03_g33876_MAGBIO' => 'mbi', 'MBI03_g36854_MAGBIO' => 'mbi', 'MBI17_g11997_MAGBIO' => 'mbi', 'MD03G1269000' => 'mdo', 'MD04G1179600' => 'mdo', 'MD11G1289800' => 'mdo', 'MD12G1194700' => 'mdo', 'MD13G1182100' => 'mdo', 'MD13G1182200' => 'mdo', 'MD16G1182600' => 'mdo', 'Medtr2g021400' => 'mtr', 'Medtr2g021470' => 'mtr', 'Medtr2g105810' => 'mtr', 'Medtr3g033580' => 'mtr', 'Medtr6g007970' => 'mtr', 'Medtr7g056330' => 'mtr', 'Medtr7g074290' => 'mtr', 'Medtr7g074380' => 'mtr', 'Medtr7g094550' => 'mtr', 'Medtr8g069995' => 'mtr', 'MELO3C014345.2' => 'cme', 'MELO3C021395.2' => 'cme', 'Migut.D00262' => 'egut', 'Migut.G00257' => 'egut', 'MSTRG.21575' => 'ama', 'MSTRG.3985' => 'ama', 'Nitab4.5_0000295g0140' => 'nta', 'Nitab4.5_0000732g0140' => 'nta', 'Nitab4.5_0003162g0020' => 'nta', 'Nitab4.5_0006180g0090' => 'nta', 'Nitab4.5_0006390g0010' => 'nta', 'Nitab4.5_0007392g0040' => 'nta', 'Nn1g02140' => 'nnu', 'Nn4g26168' => 'nnu', 'Nn5g26754' => 'nnu', 'Oeu001433.1' => 'oeu', 'Oeu010299.2' => 'oeu', 'Oeu011171.1' => 'oeu', 'Oeu037675.1' => 'oeu', 'Oeu038359.1' => 'oeu', 'Oeu063834.1' => 'oeu', 'Oeu063835.1' => 'oeu', 'Os05g0312000' => 'osa', 'Os07g0211101' => 'osa', 'Os07g0211200' => 'osa', 'Os07g0681500' => 'osa', 'Peaxi162Scf00095g01015' => 'pax', 'Peaxi162Scf00104g00329' => 'pax', 'Peaxi162Scf00161g00137' => 'pax', 'PGR004G1665' => 'pgr', 'PGR031G2937' => 'pgr', 'PGR119G2145' => 'pgr', 'PGSC0003DMG400004351' => 'stu', 'PGSC0003DMG400014625' => 'stu', 'PGSC0003DMG401000943' => 'stu', 'Phvul.001G148600' => 'pvu', 'Phvul.004G001700' => 'pvu', 'Phvul.006G154900' => 'pvu', 'Phvul.008G078200' => 'pvu', 'Phvul.011G136500' => 'pvu', 'Potri.002G215600' => 'ptr', 'Potri.008G201600' => 'ptr', 'Potri.014G138400' => 'ptr', 'Potri.016G142500' => 'ptr', 'Pp3c16_10580' => 'ppa', 'Pp3c5_25280' => 'ppa', 'Prupe.1G150000' => 'ppe', 'Prupe.1G150100' => 'ppe', 'Prupe.6G299600' => 'ppe', 'Prupe.8G245000' => 'ppe', 'Psat0s4927g0040' => 'psa', 'Psat1g052080' => 'psa', 'Psat1g183800' => 'psa', 'Psat3g113840' => 'psa', 'Psat3g126120' => 'psa', 'Psat3g126160' => 'psa', 'Psat3g158760' => 'psa', 'Psat3g158840' => 'psa', 'PSO170G2858' => 'pso', 'PSO339G0606' => 'pso', 'PSO384G4709' => 'pso', 'PSO407G0334' => 'pso', 'QL04p040276' => 'qlo', 'QL06p005458' => 'qlo', 'QL06p005472' => 'qlo', 'QL07p030546' => 'qlo', 'QL07p031519' => 'qlo', 'QL09p050949' => 'qlo', 'QL09p050966' => 'qlo', 'QL09p051067' => 'qlo', 'QL12p022706' => 'qlo', 'RcHm_v2.0_Chr2g0119601' => 'rch', 'RcHm_v2.0_Chr3g0459591' => 'rch', 'RcHm_v2.0_Chr4g0418521' => 'rch', 'RcHm_v2.0_Chr4g0418531' => 'rch', 'RcHm_v2.0_Chr4g0418541' => 'rch', 'RcHm_v2.0_Chr6g0291641' => 'rch', 'Rhsim01G0086300' => 'rsi', 'Rhsim01G0276300' => 'rsi', 'Rhsim01G0276500' => 'rsi', 'Rhsim04G0207700' => 'rsi', 'Rhsim05G0234500' => 'rsi', 'Rhsim13G0022400' => 'rsi', 'Sabra02G0167900' => 'sbr', 'Sabra04G0158500' => 'sbr', 'Sabra08G0159800' => 'sbr', 'Sabra10G0011500' => 'sbr', 'Sabra14G0104400' => 'sbr', 'SalBow2G2440' => 'sbo', 'SalBow4G2265' => 'sbo', 'Sc02g0000060' => 'sci', 'Sc05g0005020' => 'sci', 'Sc13g0003890' => 'sci', 'Sed0014865' => 'sed', 'Sed0017224' => 'sed', 'Sed0026391' => 'sed', 'SEGI_00063' => 'sgi', 'SEGI_10967' => 'sgi', 'SEGI_17510' => 'sgi', 'SEGI_24396' => 'sgi', 'SEGI_39719' => 'sgi', 'SEGI_41392' => 'sgi', 'SGA_v2.0_scaffold11G05794' => 'sas', 'SGA_v2.0_scaffold142G35607' => 'sas', 'SGA_v2.0_scaffold1G00447' => 'sas', 'SHI15388' => 'shi', 'SHI15394' => 'shi', 'SHI15396' => 'shi', 'SHI15399' => 'shi', 'SMO343G0151' => 'smo', 'SMO367G1118' => 'smo', 'Solyc01g080200.3' => 'sly', 'Solyc06g008960.3' => 'sly', 'Solyc09g064780.3' => 'sly', 'Sopen01g031980' => 'spe', 'Sopen06g003710' => 'spe', 'Sopen09g026460' => 'spe', 'Sp3g21240' => 'spa', 'Sp4g30030' => 'spa', 'TAR365G0022' => 'tar', 'TAR365G1023' => 'tar', 'TAR365G1253' => 'tar', 'TAR623G0078' => 'tar', 'TAR623G1721' => 'tar', 'TAR633G0959' => 'tar', 'THA.LOC104802225' => 'tha', 'THA.LOC104804769' => 'tha', 'THA.LOC104808660' => 'tha', 'THA.LOC104812792' => 'tha', 'Thecc.01G284000' => 'tca', 'Thecc.04G220600' => 'tca', 'Thecc.05G268900' => 'tca', 'Thecc.08G171100' => 'tca', 'Thhalv10001284m.g' => 'esa', 'Thhalv10019912m.g' => 'esa', 'TPR.G14189' => 'tpr', 'TPR.G18110' => 'tpr', 'TPR.G18130' => 'tpr', 'TPR.G18131' => 'tpr', 'TPR.G18140' => 'tpr', 'TPR.G24282' => 'tpr', 'TPR.G25221' => 'tpr', 'TPR.G29267' => 'tpr', 'TPR.G35315' => 'tpr', 'TPR.G36173' => 'tpr', 'TWI09G0794' => 'twi', 'TWI59G1348' => 'twi', 'TWI74G0430' => 'twi', 'unitig_26.g8940' => 'ugi', 'unitig_749.g13744' => 'ugi', 'unitig_749.g13745' => 'ugi', 'vmacro08269' => 'vma', 'vmacro14937' => 'vma', 'vmacro20401' => 'vma', 'VMungo0464G1349' => 'vmu', 'VMungo0540G0289' => 'vmu', 'VMungo1215G1590' => 'vmu', 'VMungo1309G0221' => 'vmu', 'VMungo1309G2815' => 'vmu', 'VMungo1383G0239' => 'vmu', 'VMungo1383G2910' => 'vmu', 'Zm00001eb095270' => 'zma', 'Zm00001eb095280' => 'zma', 'Zm00001eb111630' => 'zma', 'Zm00001eb237080' => 'zma', 'Zm00001eb273740' => 'zma', 'Zm00001eb285040' => 'zma', 'Zm00001eb330790' => 'zma', 'Zm00001eb337380' => 'zma' ) $gf_id = 'HOM05D001484' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001484' ) $data_identifier = 'HOM05D001484' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 2, 'aly' => (int) 2, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 22, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 7, 'hma' => (int) 2, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 7, 'mtr' => (int) 10, 'cme' => (int) 2, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 4, 'ppa' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 4, 'qlo' => (int) 9, 'rch' => (int) 6, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 10, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 7, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb337380' $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' => 'HOM05D001484', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p31500' => 'bna', 'A05p00020' => 'bna', 'A07p08820' => 'bna', 'Aa31LG4G3300' => 'aar', 'Aa31LG8G10030' => 'aar', 'Actinidia00731' => 'ach', 'Actinidia11473' => 'ach', 'Actinidia23469' => 'ach', 'Actinidia24318' => 'ach', 'Actinidia40196' => 'ach', 'Actinidia40197' => 'ach', 'Actinidia40198' => 'ach', 'Ah.08g212990' => 'amhyb', 'Ah.15g091720' => 'amhyb', 'AL3G38260' => 'aly', 'AL4G47710' => 'aly', 'Aqoxy2G00671' => 'aox', 'Aqoxy2G03236' => 'aox', 'arahy.Tifrunner.gnm1.ann1.05IDCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KR684' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATY3SJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK6QJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6APGL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IDT7Z9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM073U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ0R87' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LE7RV4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT4QRX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V5ENPK' => 'arhy', 'AT2G48110' => 'ath', 'AT3G23590' => 'ath', 'ATR0626G186' => 'atr', 'ATR1127G141' => 'atr', 'Atru.chr4.2583' => 'acertr', 'Atru.chr5.1358' => 'acertr', 'Atru.chr5.1359' => 'acertr', 'Atru.chr8.46' => 'acertr', 'AUR62002640' => 'cqu', 'AUR62030055' => 'cqu', 'AUR62033713' => 'cqu', 'AUR62033714' => 'cqu', 'AUR62036795' => 'cqu', 'AUR62039891' => 'cqu', 'BcaB02g08737' => 'bca', 'BcaB04g20441' => 'bca', 'BcaB06g26509' => 'bca', 'BcaB06g26510' => 'bca', 'BcaB06g26511' => 'bca', 'BcaB06g26512' => 'bca', 'BcaB06g26513' => 'bca', 'BcaC02g12564' => 'bca', 'BcaC02g12565' => 'bca', 'BcaC02g12794' => 'bca', 'BcaC02g12795' => 'bca', 'BcaC02g12796' => 'bca', 'BcaC06g35541' => 'bca', 'BNapus_Darmor_BZH_scaffold_188p00080' => 'bna', 'BNapus_Darmor_BZH_scaffold_188p00090' => 'bna', 'BolC1t03972H' => 'bol', 'BolC1t03973H' => 'bol', 'BolC4t21680H' => 'bol', 'BolC7t41863H' => 'bol', 'BolSC55t61227H' => 'bol', 'BolSC55t61228H' => 'bol', 'BraA01t03278Z' => 'bra', 'BraA05t18998Z' => 'bra', 'BraA07t28673Z' => 'bra', 'C01p40150' => 'bna', 'C05p12370' => 'bna', 'C07p13680' => 'bna', 'CAN.G1006.16' => 'can', 'CAN.G1006.17' => 'can', 'CAN.G1170.2' => 'can', 'CAN.G962.7' => 'can', 'CANSAT25G2179' => 'cansat', 'CANSAT78G1573' => 'cansat', 'CARHR099510' => 'chi', 'CARHR143510' => 'chi', 'Carub.0003s2380' => 'cru', 'Carub.0004s3082' => 'cru', 'Ca_00614_v3' => 'car', 'Ca_07801_v3' => 'car', 'Ca_08567_v3' => 'car', 'Ca_09571_v3' => 'car', 'CBR_g19290' => 'cbr', 'Cc01_g19770' => 'ccan', 'Cc03_g03030' => 'ccan', 'CDE07G0968' => 'cde', 'CDE09G1441' => 'cde', 'Cfa006103' => 'cfa', 'Cfa015573' => 'cfa', 'Cfa016988' => 'cfa', 'Ciclev10006738m.g' => 'ccl', 'Ciclev10010920m.g' => 'ccl', 'Ciclev10018517m.g' => 'ccl', 'CiPaw.01G159200' => 'cil', 'CiPaw.02G091000' => 'cil', 'CiPaw.02G091100' => 'cil', 'CiPaw.08G103100' => 'cil', 'CiPaw.09G224900' => 'cil', 'ClCG06G005740' => 'cla', 'ClCG07G000090' => 'cla', 'ClCG07G000100' => 'cla', 'COL.COLO4_09143' => 'col', 'COL.COLO4_25124' => 'col', 'Cpa.g.sc16.34' => 'cpa', 'Cpa.g.sc3504.1' => 'cpa', 'Cpa.g.sc60.37' => 'cpa', 'CsaV3_6G018520' => 'csa', 'CsaV3_6G036860' => 'csa', 'CSS0001072' => 'camsi', 'CSS0020208' => 'camsi', 'CSS0021253' => 'camsi', 'CSS0022190' => 'camsi', 'CSS0036150' => 'camsi', 'CSS0040442' => 'camsi', 'CSS0042300' => 'camsi', 'CSS0045298' => 'camsi', 'DCAR_012449' => 'dca', 'DCAR_018405' => 'dca', 'DCAR_024573' => 'dca', 'DCAR_030591' => 'dca', 'Dinv16926' => 'din', 'Dinv32963' => 'din', 'Dinv38382' => 'din', 'Dinv38383' => 'din', 'Duzib133G0974' => 'dzi', 'Duzib138G1867' => 'dzi', 'Duzib211G0420' => 'dzi', 'Duzib212G0930' => 'dzi', 'ECA234G1645' => 'eca', 'ECA247G3467' => 'eca', 'ECA248G1703' => 'eca', 'EL10Ac3g06327' => 'bvu', 'EL10Ac7g17204' => 'bvu', 'Eucgr.A00855' => 'egr', 'Eucgr.A00858' => 'egr', 'Eucgr.H01520' => 'egr', 'Eucgr.H03604' => 'egr', 'Eucgr.L03465' => 'egr', 'Eucgr.L03466' => 'egr', 'FAN01G0988' => 'fan', 'FAN02G3892' => 'fan', 'FAN05G3381' => 'fan', 'FAN07G0967' => 'fan', 'FAN07G1493' => 'fan', 'FAN08G3125' => 'fan', 'FAN09G0402' => 'fan', 'FAN12G2594' => 'fan', 'FAN12G3879' => 'fan', 'FAN14G1546' => 'fan', 'FAN15G3626' => 'fan', 'FAN17G0588' => 'fan', 'FAN17G0609' => 'fan', 'FAN18G2817' => 'fan', 'FAN19G1305' => 'fan', 'FAN20G1787' => 'fan', 'FAN22G0073' => 'fan', 'FAN22G0352' => 'fan', 'FAN22G0368' => 'fan', 'FAN22G2273' => 'fan', 'FAN24G1998' => 'fan', 'FAN27G1317' => 'fan', 'FvH4_2g23980' => 'fve', 'FvH4_4g14380' => 'fve', 'FvH4_4g14390' => 'fve', 'FvH4_6g09250' => 'fve', 'Glyma.03G151100' => 'gma', 'Glyma.04G122550' => 'gma', 'Glyma.05G001600' => 'gma', 'Glyma.09G270766' => 'gma', 'Glyma.09G270832' => 'gma', 'Glyma.13G209800' => 'gma', 'Glyma.15G102800' => 'gma', 'Glyma.18G218900' => 'gma', 'Glyma.19G001500' => 'gma', 'Glyma.19G153600' => 'gma', 'Gohir.A02G028600' => 'ghi', 'Gohir.A08G045000' => 'ghi', 'Gohir.A11G120500' => 'ghi', 'Gohir.A12G006200' => 'ghi', 'Gohir.A12G006250' => 'ghi', 'Gohir.D02G036300' => 'ghi', 'Gohir.D08G054700' => 'ghi', 'Gohir.D11G125600' => 'ghi', 'Gohir.D12G005700' => 'ghi', 'Gorai.004G055200' => 'gra', 'Gorai.005G040400' => 'gra', 'Gorai.007G134500' => 'gra', 'Gorai.008G005500' => 'gra', 'GSVIVG01011094001' => 'vvi', 'GSVIVG01017879001' => 'vvi', 'GSVIVG01025988001' => 'vvi', 'GSVIVG01029847001' => 'vvi', 'HanXRQChr10g0282901' => 'han', 'HanXRQChr10g0310371' => 'han', 'HanXRQChr10g0315041' => 'han', 'HanXRQChr11g0327651' => 'han', 'HanXRQChr12g0359391' => 'han', 'Haze_00972' => 'cav', 'Haze_00973' => 'cav', 'Haze_00974' => 'cav', 'Haze_04747' => 'cav', 'Haze_04749' => 'cav', 'Haze_04750' => 'cav', 'Haze_21217' => 'cav', 'Hma1.2p1_1037F.1_g250680' => 'hma', 'Hma1.2p1_1644F.1_g295320' => 'hma', 'HPP92_011322' => 'vpl', 'HPP92_011323' => 'vpl', 'HPP92_011324' => 'vpl', 'HPP92_011325' => 'vpl', 'HPP92_011326' => 'vpl', 'Hund12205' => 'sun', 'Hund17957' => 'sun', 'Lalb_Chr06g0176771' => 'lal', 'Lalb_Chr18g0056021' => 'lal', 'Lalb_Chr18g0056031' => 'lal', 'Lalb_Chr18g0056041' => 'lal', 'Lalb_Chr20g0107751' => 'lal', 'Lalb_Chr20g0118371' => 'lal', 'Lj1g0010239' => 'lja', 'Lj1g0017101' => 'lja', 'Lj2A1178G40' => 'lonja', 'Lj2A54G84' => 'lonja', 'Lj2g0015248' => 'lja', 'Lj3A761T51' => 'lonja', 'Lj6g0018116' => 'lja', 'Lsat_1_v5_gn_4_136040' => 'lsa', 'Lsat_1_v5_gn_5_187461' => 'lsa', 'Lsat_1_v5_gn_5_77001' => 'lsa', 'Lsat_1_v5_gn_9_4461' => 'lsa', 'Manes.01G210100' => 'mes', 'Manes.03G185600' => 'mes', 'Manes.05G073300' => 'mes', 'Manes.09G120300' => 'mes', 'Manes.15G022100' => 'mes', 'Mapoly0096s0053' => 'mpo', 'MBI03_g14058_MAGBIO' => 'mbi', 'MBI03_g33876_MAGBIO' => 'mbi', 'MBI03_g36854_MAGBIO' => 'mbi', 'MBI17_g11997_MAGBIO' => 'mbi', 'MD03G1269000' => 'mdo', 'MD04G1179600' => 'mdo', 'MD11G1289800' => 'mdo', 'MD12G1194700' => 'mdo', 'MD13G1182100' => 'mdo', 'MD13G1182200' => 'mdo', 'MD16G1182600' => 'mdo', 'Medtr2g021400' => 'mtr', 'Medtr2g021470' => 'mtr', 'Medtr2g105810' => 'mtr', 'Medtr3g033580' => 'mtr', 'Medtr6g007970' => 'mtr', 'Medtr7g056330' => 'mtr', 'Medtr7g074290' => 'mtr', 'Medtr7g074380' => 'mtr', 'Medtr7g094550' => 'mtr', 'Medtr8g069995' => 'mtr', 'MELO3C014345.2' => 'cme', 'MELO3C021395.2' => 'cme', 'Migut.D00262' => 'egut', 'Migut.G00257' => 'egut', 'MSTRG.21575' => 'ama', 'MSTRG.3985' => 'ama', 'Nitab4.5_0000295g0140' => 'nta', 'Nitab4.5_0000732g0140' => 'nta', 'Nitab4.5_0003162g0020' => 'nta', 'Nitab4.5_0006180g0090' => 'nta', 'Nitab4.5_0006390g0010' => 'nta', 'Nitab4.5_0007392g0040' => 'nta', 'Nn1g02140' => 'nnu', 'Nn4g26168' => 'nnu', 'Nn5g26754' => 'nnu', 'Oeu001433.1' => 'oeu', 'Oeu010299.2' => 'oeu', 'Oeu011171.1' => 'oeu', 'Oeu037675.1' => 'oeu', 'Oeu038359.1' => 'oeu', 'Oeu063834.1' => 'oeu', 'Oeu063835.1' => 'oeu', 'Os05g0312000' => 'osa', 'Os07g0211101' => 'osa', 'Os07g0211200' => 'osa', 'Os07g0681500' => 'osa', 'Peaxi162Scf00095g01015' => 'pax', 'Peaxi162Scf00104g00329' => 'pax', 'Peaxi162Scf00161g00137' => 'pax', 'PGR004G1665' => 'pgr', 'PGR031G2937' => 'pgr', 'PGR119G2145' => 'pgr', 'PGSC0003DMG400004351' => 'stu', 'PGSC0003DMG400014625' => 'stu', 'PGSC0003DMG401000943' => 'stu', 'Phvul.001G148600' => 'pvu', 'Phvul.004G001700' => 'pvu', 'Phvul.006G154900' => 'pvu', 'Phvul.008G078200' => 'pvu', 'Phvul.011G136500' => 'pvu', 'Potri.002G215600' => 'ptr', 'Potri.008G201600' => 'ptr', 'Potri.014G138400' => 'ptr', 'Potri.016G142500' => 'ptr', 'Pp3c16_10580' => 'ppa', 'Pp3c5_25280' => 'ppa', 'Prupe.1G150000' => 'ppe', 'Prupe.1G150100' => 'ppe', 'Prupe.6G299600' => 'ppe', 'Prupe.8G245000' => 'ppe', 'Psat0s4927g0040' => 'psa', 'Psat1g052080' => 'psa', 'Psat1g183800' => 'psa', 'Psat3g113840' => 'psa', 'Psat3g126120' => 'psa', 'Psat3g126160' => 'psa', 'Psat3g158760' => 'psa', 'Psat3g158840' => 'psa', 'PSO170G2858' => 'pso', 'PSO339G0606' => 'pso', 'PSO384G4709' => 'pso', 'PSO407G0334' => 'pso', 'QL04p040276' => 'qlo', 'QL06p005458' => 'qlo', 'QL06p005472' => 'qlo', 'QL07p030546' => 'qlo', 'QL07p031519' => 'qlo', 'QL09p050949' => 'qlo', 'QL09p050966' => 'qlo', 'QL09p051067' => 'qlo', 'QL12p022706' => 'qlo', 'RcHm_v2.0_Chr2g0119601' => 'rch', 'RcHm_v2.0_Chr3g0459591' => 'rch', 'RcHm_v2.0_Chr4g0418521' => 'rch', 'RcHm_v2.0_Chr4g0418531' => 'rch', 'RcHm_v2.0_Chr4g0418541' => 'rch', 'RcHm_v2.0_Chr6g0291641' => 'rch', 'Rhsim01G0086300' => 'rsi', 'Rhsim01G0276300' => 'rsi', 'Rhsim01G0276500' => 'rsi', 'Rhsim04G0207700' => 'rsi', 'Rhsim05G0234500' => 'rsi', 'Rhsim13G0022400' => 'rsi', 'Sabra02G0167900' => 'sbr', 'Sabra04G0158500' => 'sbr', 'Sabra08G0159800' => 'sbr', 'Sabra10G0011500' => 'sbr', 'Sabra14G0104400' => 'sbr', 'SalBow2G2440' => 'sbo', 'SalBow4G2265' => 'sbo', 'Sc02g0000060' => 'sci', 'Sc05g0005020' => 'sci', 'Sc13g0003890' => 'sci', 'Sed0014865' => 'sed', 'Sed0017224' => 'sed', 'Sed0026391' => 'sed', 'SEGI_00063' => 'sgi', 'SEGI_10967' => 'sgi', 'SEGI_17510' => 'sgi', 'SEGI_24396' => 'sgi', 'SEGI_39719' => 'sgi', 'SEGI_41392' => 'sgi', 'SGA_v2.0_scaffold11G05794' => 'sas', 'SGA_v2.0_scaffold142G35607' => 'sas', 'SGA_v2.0_scaffold1G00447' => 'sas', 'SHI15388' => 'shi', 'SHI15394' => 'shi', 'SHI15396' => 'shi', 'SHI15399' => 'shi', 'SMO343G0151' => 'smo', 'SMO367G1118' => 'smo', 'Solyc01g080200.3' => 'sly', 'Solyc06g008960.3' => 'sly', 'Solyc09g064780.3' => 'sly', 'Sopen01g031980' => 'spe', 'Sopen06g003710' => 'spe', 'Sopen09g026460' => 'spe', 'Sp3g21240' => 'spa', 'Sp4g30030' => 'spa', 'TAR365G0022' => 'tar', 'TAR365G1023' => 'tar', 'TAR365G1253' => 'tar', 'TAR623G0078' => 'tar', 'TAR623G1721' => 'tar', 'TAR633G0959' => 'tar', 'THA.LOC104802225' => 'tha', 'THA.LOC104804769' => 'tha', 'THA.LOC104808660' => 'tha', 'THA.LOC104812792' => 'tha', 'Thecc.01G284000' => 'tca', 'Thecc.04G220600' => 'tca', 'Thecc.05G268900' => 'tca', 'Thecc.08G171100' => 'tca', 'Thhalv10001284m.g' => 'esa', 'Thhalv10019912m.g' => 'esa', 'TPR.G14189' => 'tpr', 'TPR.G18110' => 'tpr', 'TPR.G18130' => 'tpr', 'TPR.G18131' => 'tpr', 'TPR.G18140' => 'tpr', 'TPR.G24282' => 'tpr', 'TPR.G25221' => 'tpr', 'TPR.G29267' => 'tpr', 'TPR.G35315' => 'tpr', 'TPR.G36173' => 'tpr', 'TWI09G0794' => 'twi', 'TWI59G1348' => 'twi', 'TWI74G0430' => 'twi', 'unitig_26.g8940' => 'ugi', 'unitig_749.g13744' => 'ugi', 'unitig_749.g13745' => 'ugi', 'vmacro08269' => 'vma', 'vmacro14937' => 'vma', 'vmacro20401' => 'vma', 'VMungo0464G1349' => 'vmu', 'VMungo0540G0289' => 'vmu', 'VMungo1215G1590' => 'vmu', 'VMungo1309G0221' => 'vmu', 'VMungo1309G2815' => 'vmu', 'VMungo1383G0239' => 'vmu', 'VMungo1383G2910' => 'vmu', 'Zm00001eb095270' => 'zma', 'Zm00001eb095280' => 'zma', 'Zm00001eb111630' => 'zma', 'Zm00001eb237080' => 'zma', 'Zm00001eb273740' => 'zma', 'Zm00001eb285040' => 'zma', 'Zm00001eb330790' => 'zma', 'Zm00001eb337380' => 'zma' ), 'gf_id' => 'HOM05D001484', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001484' ), 'data_identifier' => 'HOM05D001484', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001484', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p31500' => 'bna', 'A05p00020' => 'bna', 'A07p08820' => 'bna', 'Aa31LG4G3300' => 'aar', 'Aa31LG8G10030' => 'aar', 'Actinidia00731' => 'ach', 'Actinidia11473' => 'ach', 'Actinidia23469' => 'ach', 'Actinidia24318' => 'ach', 'Actinidia40196' => 'ach', 'Actinidia40197' => 'ach', 'Actinidia40198' => 'ach', 'Ah.08g212990' => 'amhyb', 'Ah.15g091720' => 'amhyb', 'AL3G38260' => 'aly', 'AL4G47710' => 'aly', 'Aqoxy2G00671' => 'aox', 'Aqoxy2G03236' => 'aox', 'arahy.Tifrunner.gnm1.ann1.05IDCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KR684' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATY3SJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK6QJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6APGL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IDT7Z9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM073U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ0R87' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LE7RV4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT4QRX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V5ENPK' => 'arhy', 'AT2G48110' => 'ath', 'AT3G23590' => 'ath', 'ATR0626G186' => 'atr', 'ATR1127G141' => 'atr', 'Atru.chr4.2583' => 'acertr', 'Atru.chr5.1358' => 'acertr', 'Atru.chr5.1359' => 'acertr', 'Atru.chr8.46' => 'acertr', 'AUR62002640' => 'cqu', 'AUR62030055' => 'cqu', 'AUR62033713' => 'cqu', 'AUR62033714' => 'cqu', 'AUR62036795' => 'cqu', 'AUR62039891' => 'cqu', 'BcaB02g08737' => 'bca', 'BcaB04g20441' => 'bca', 'BcaB06g26509' => 'bca', 'BcaB06g26510' => 'bca', 'BcaB06g26511' => 'bca', 'BcaB06g26512' => 'bca', 'BcaB06g26513' => 'bca', 'BcaC02g12564' => 'bca', 'BcaC02g12565' => 'bca', 'BcaC02g12794' => 'bca', 'BcaC02g12795' => 'bca', 'BcaC02g12796' => 'bca', 'BcaC06g35541' => 'bca', 'BNapus_Darmor_BZH_scaffold_188p00080' => 'bna', 'BNapus_Darmor_BZH_scaffold_188p00090' => 'bna', 'BolC1t03972H' => 'bol', 'BolC1t03973H' => 'bol', 'BolC4t21680H' => 'bol', 'BolC7t41863H' => 'bol', 'BolSC55t61227H' => 'bol', 'BolSC55t61228H' => 'bol', 'BraA01t03278Z' => 'bra', 'BraA05t18998Z' => 'bra', 'BraA07t28673Z' => 'bra', 'C01p40150' => 'bna', 'C05p12370' => 'bna', 'C07p13680' => 'bna', 'CAN.G1006.16' => 'can', 'CAN.G1006.17' => 'can', 'CAN.G1170.2' => 'can', 'CAN.G962.7' => 'can', 'CANSAT25G2179' => 'cansat', 'CANSAT78G1573' => 'cansat', 'CARHR099510' => 'chi', 'CARHR143510' => 'chi', 'Carub.0003s2380' => 'cru', 'Carub.0004s3082' => 'cru', 'Ca_00614_v3' => 'car', 'Ca_07801_v3' => 'car', 'Ca_08567_v3' => 'car', 'Ca_09571_v3' => 'car', 'CBR_g19290' => 'cbr', 'Cc01_g19770' => 'ccan', 'Cc03_g03030' => 'ccan', 'CDE07G0968' => 'cde', 'CDE09G1441' => 'cde', 'Cfa006103' => 'cfa', 'Cfa015573' => 'cfa', 'Cfa016988' => 'cfa', 'Ciclev10006738m.g' => 'ccl', 'Ciclev10010920m.g' => 'ccl', 'Ciclev10018517m.g' => 'ccl', 'CiPaw.01G159200' => 'cil', 'CiPaw.02G091000' => 'cil', 'CiPaw.02G091100' => 'cil', 'CiPaw.08G103100' => 'cil', 'CiPaw.09G224900' => 'cil', 'ClCG06G005740' => 'cla', 'ClCG07G000090' => 'cla', 'ClCG07G000100' => 'cla', 'COL.COLO4_09143' => 'col', 'COL.COLO4_25124' => 'col', 'Cpa.g.sc16.34' => 'cpa', 'Cpa.g.sc3504.1' => 'cpa', 'Cpa.g.sc60.37' => 'cpa', 'CsaV3_6G018520' => 'csa', 'CsaV3_6G036860' => 'csa', 'CSS0001072' => 'camsi', 'CSS0020208' => 'camsi', 'CSS0021253' => 'camsi', 'CSS0022190' => 'camsi', 'CSS0036150' => 'camsi', 'CSS0040442' => 'camsi', 'CSS0042300' => 'camsi', 'CSS0045298' => 'camsi', 'DCAR_012449' => 'dca', 'DCAR_018405' => 'dca', 'DCAR_024573' => 'dca', 'DCAR_030591' => 'dca', 'Dinv16926' => 'din', 'Dinv32963' => 'din', 'Dinv38382' => 'din', 'Dinv38383' => 'din', 'Duzib133G0974' => 'dzi', 'Duzib138G1867' => 'dzi', 'Duzib211G0420' => 'dzi', 'Duzib212G0930' => 'dzi', 'ECA234G1645' => 'eca', 'ECA247G3467' => 'eca', 'ECA248G1703' => 'eca', 'EL10Ac3g06327' => 'bvu', 'EL10Ac7g17204' => 'bvu', 'Eucgr.A00855' => 'egr', 'Eucgr.A00858' => 'egr', 'Eucgr.H01520' => 'egr', 'Eucgr.H03604' => 'egr', 'Eucgr.L03465' => 'egr', 'Eucgr.L03466' => 'egr', 'FAN01G0988' => 'fan', 'FAN02G3892' => 'fan', 'FAN05G3381' => 'fan', 'FAN07G0967' => 'fan', 'FAN07G1493' => 'fan', 'FAN08G3125' => 'fan', 'FAN09G0402' => 'fan', 'FAN12G2594' => 'fan', 'FAN12G3879' => 'fan', 'FAN14G1546' => 'fan', 'FAN15G3626' => 'fan', 'FAN17G0588' => 'fan', 'FAN17G0609' => 'fan', 'FAN18G2817' => 'fan', 'FAN19G1305' => 'fan', 'FAN20G1787' => 'fan', 'FAN22G0073' => 'fan', 'FAN22G0352' => 'fan', 'FAN22G0368' => 'fan', 'FAN22G2273' => 'fan', 'FAN24G1998' => 'fan', 'FAN27G1317' => 'fan', 'FvH4_2g23980' => 'fve', 'FvH4_4g14380' => 'fve', 'FvH4_4g14390' => 'fve', 'FvH4_6g09250' => 'fve', 'Glyma.03G151100' => 'gma', 'Glyma.04G122550' => 'gma', 'Glyma.05G001600' => 'gma', 'Glyma.09G270766' => 'gma', 'Glyma.09G270832' => 'gma', 'Glyma.13G209800' => 'gma', 'Glyma.15G102800' => 'gma', 'Glyma.18G218900' => 'gma', 'Glyma.19G001500' => 'gma', 'Glyma.19G153600' => 'gma', 'Gohir.A02G028600' => 'ghi', 'Gohir.A08G045000' => 'ghi', 'Gohir.A11G120500' => 'ghi', 'Gohir.A12G006200' => 'ghi', 'Gohir.A12G006250' => 'ghi', 'Gohir.D02G036300' => 'ghi', 'Gohir.D08G054700' => 'ghi', 'Gohir.D11G125600' => 'ghi', 'Gohir.D12G005700' => 'ghi', 'Gorai.004G055200' => 'gra', 'Gorai.005G040400' => 'gra', 'Gorai.007G134500' => 'gra', 'Gorai.008G005500' => 'gra', 'GSVIVG01011094001' => 'vvi', 'GSVIVG01017879001' => 'vvi', 'GSVIVG01025988001' => 'vvi', 'GSVIVG01029847001' => 'vvi', 'HanXRQChr10g0282901' => 'han', 'HanXRQChr10g0310371' => 'han', 'HanXRQChr10g0315041' => 'han', 'HanXRQChr11g0327651' => 'han', 'HanXRQChr12g0359391' => 'han', 'Haze_00972' => 'cav', 'Haze_00973' => 'cav', 'Haze_00974' => 'cav', 'Haze_04747' => 'cav', 'Haze_04749' => 'cav', 'Haze_04750' => 'cav', 'Haze_21217' => 'cav', 'Hma1.2p1_1037F.1_g250680' => 'hma', 'Hma1.2p1_1644F.1_g295320' => 'hma', 'HPP92_011322' => 'vpl', 'HPP92_011323' => 'vpl', 'HPP92_011324' => 'vpl', 'HPP92_011325' => 'vpl', 'HPP92_011326' => 'vpl', 'Hund12205' => 'sun', 'Hund17957' => 'sun', 'Lalb_Chr06g0176771' => 'lal', 'Lalb_Chr18g0056021' => 'lal', 'Lalb_Chr18g0056031' => 'lal', 'Lalb_Chr18g0056041' => 'lal', 'Lalb_Chr20g0107751' => 'lal', 'Lalb_Chr20g0118371' => 'lal', 'Lj1g0010239' => 'lja', 'Lj1g0017101' => 'lja', 'Lj2A1178G40' => 'lonja', 'Lj2A54G84' => 'lonja', 'Lj2g0015248' => 'lja', 'Lj3A761T51' => 'lonja', 'Lj6g0018116' => 'lja', 'Lsat_1_v5_gn_4_136040' => 'lsa', 'Lsat_1_v5_gn_5_187461' => 'lsa', 'Lsat_1_v5_gn_5_77001' => 'lsa', 'Lsat_1_v5_gn_9_4461' => 'lsa', 'Manes.01G210100' => 'mes', 'Manes.03G185600' => 'mes', 'Manes.05G073300' => 'mes', 'Manes.09G120300' => 'mes', 'Manes.15G022100' => 'mes', 'Mapoly0096s0053' => 'mpo', 'MBI03_g14058_MAGBIO' => 'mbi', 'MBI03_g33876_MAGBIO' => 'mbi', 'MBI03_g36854_MAGBIO' => 'mbi', 'MBI17_g11997_MAGBIO' => 'mbi', 'MD03G1269000' => 'mdo', 'MD04G1179600' => 'mdo', 'MD11G1289800' => 'mdo', 'MD12G1194700' => 'mdo', 'MD13G1182100' => 'mdo', 'MD13G1182200' => 'mdo', 'MD16G1182600' => 'mdo', 'Medtr2g021400' => 'mtr', 'Medtr2g021470' => 'mtr', 'Medtr2g105810' => 'mtr', 'Medtr3g033580' => 'mtr', 'Medtr6g007970' => 'mtr', 'Medtr7g056330' => 'mtr', 'Medtr7g074290' => 'mtr', 'Medtr7g074380' => 'mtr', 'Medtr7g094550' => 'mtr', 'Medtr8g069995' => 'mtr', 'MELO3C014345.2' => 'cme', 'MELO3C021395.2' => 'cme', 'Migut.D00262' => 'egut', 'Migut.G00257' => 'egut', 'MSTRG.21575' => 'ama', 'MSTRG.3985' => 'ama', 'Nitab4.5_0000295g0140' => 'nta', 'Nitab4.5_0000732g0140' => 'nta', 'Nitab4.5_0003162g0020' => 'nta', 'Nitab4.5_0006180g0090' => 'nta', 'Nitab4.5_0006390g0010' => 'nta', 'Nitab4.5_0007392g0040' => 'nta', 'Nn1g02140' => 'nnu', 'Nn4g26168' => 'nnu', 'Nn5g26754' => 'nnu', 'Oeu001433.1' => 'oeu', 'Oeu010299.2' => 'oeu', 'Oeu011171.1' => 'oeu', 'Oeu037675.1' => 'oeu', 'Oeu038359.1' => 'oeu', 'Oeu063834.1' => 'oeu', 'Oeu063835.1' => 'oeu', 'Os05g0312000' => 'osa', 'Os07g0211101' => 'osa', 'Os07g0211200' => 'osa', 'Os07g0681500' => 'osa', 'Peaxi162Scf00095g01015' => 'pax', 'Peaxi162Scf00104g00329' => 'pax', 'Peaxi162Scf00161g00137' => 'pax', 'PGR004G1665' => 'pgr', 'PGR031G2937' => 'pgr', 'PGR119G2145' => 'pgr', 'PGSC0003DMG400004351' => 'stu', 'PGSC0003DMG400014625' => 'stu', 'PGSC0003DMG401000943' => 'stu', 'Phvul.001G148600' => 'pvu', 'Phvul.004G001700' => 'pvu', 'Phvul.006G154900' => 'pvu', 'Phvul.008G078200' => 'pvu', 'Phvul.011G136500' => 'pvu', 'Potri.002G215600' => 'ptr', 'Potri.008G201600' => 'ptr', 'Potri.014G138400' => 'ptr', 'Potri.016G142500' => 'ptr', 'Pp3c16_10580' => 'ppa', 'Pp3c5_25280' => 'ppa', 'Prupe.1G150000' => 'ppe', 'Prupe.1G150100' => 'ppe', 'Prupe.6G299600' => 'ppe', 'Prupe.8G245000' => 'ppe', 'Psat0s4927g0040' => 'psa', 'Psat1g052080' => 'psa', 'Psat1g183800' => 'psa', 'Psat3g113840' => 'psa', 'Psat3g126120' => 'psa', 'Psat3g126160' => 'psa', 'Psat3g158760' => 'psa', 'Psat3g158840' => 'psa', 'PSO170G2858' => 'pso', 'PSO339G0606' => 'pso', 'PSO384G4709' => 'pso', 'PSO407G0334' => 'pso', 'QL04p040276' => 'qlo', 'QL06p005458' => 'qlo', 'QL06p005472' => 'qlo', 'QL07p030546' => 'qlo', 'QL07p031519' => 'qlo', 'QL09p050949' => 'qlo', 'QL09p050966' => 'qlo', 'QL09p051067' => 'qlo', 'QL12p022706' => 'qlo', 'RcHm_v2.0_Chr2g0119601' => 'rch', 'RcHm_v2.0_Chr3g0459591' => 'rch', 'RcHm_v2.0_Chr4g0418521' => 'rch', 'RcHm_v2.0_Chr4g0418531' => 'rch', 'RcHm_v2.0_Chr4g0418541' => 'rch', 'RcHm_v2.0_Chr6g0291641' => 'rch', 'Rhsim01G0086300' => 'rsi', 'Rhsim01G0276300' => 'rsi', 'Rhsim01G0276500' => 'rsi', 'Rhsim04G0207700' => 'rsi', 'Rhsim05G0234500' => 'rsi', 'Rhsim13G0022400' => 'rsi', 'Sabra02G0167900' => 'sbr', 'Sabra04G0158500' => 'sbr', 'Sabra08G0159800' => 'sbr', 'Sabra10G0011500' => 'sbr', 'Sabra14G0104400' => 'sbr', 'SalBow2G2440' => 'sbo', 'SalBow4G2265' => 'sbo', 'Sc02g0000060' => 'sci', 'Sc05g0005020' => 'sci', 'Sc13g0003890' => 'sci', 'Sed0014865' => 'sed', 'Sed0017224' => 'sed', 'Sed0026391' => 'sed', 'SEGI_00063' => 'sgi', 'SEGI_10967' => 'sgi', 'SEGI_17510' => 'sgi', 'SEGI_24396' => 'sgi', 'SEGI_39719' => 'sgi', 'SEGI_41392' => 'sgi', 'SGA_v2.0_scaffold11G05794' => 'sas', 'SGA_v2.0_scaffold142G35607' => 'sas', 'SGA_v2.0_scaffold1G00447' => 'sas', 'SHI15388' => 'shi', 'SHI15394' => 'shi', 'SHI15396' => 'shi', 'SHI15399' => 'shi', 'SMO343G0151' => 'smo', 'SMO367G1118' => 'smo', 'Solyc01g080200.3' => 'sly', 'Solyc06g008960.3' => 'sly', 'Solyc09g064780.3' => 'sly', 'Sopen01g031980' => 'spe', 'Sopen06g003710' => 'spe', 'Sopen09g026460' => 'spe', 'Sp3g21240' => 'spa', 'Sp4g30030' => 'spa', 'TAR365G0022' => 'tar', 'TAR365G1023' => 'tar', 'TAR365G1253' => 'tar', 'TAR623G0078' => 'tar', 'TAR623G1721' => 'tar', 'TAR633G0959' => 'tar', 'THA.LOC104802225' => 'tha', 'THA.LOC104804769' => 'tha', 'THA.LOC104808660' => 'tha', 'THA.LOC104812792' => 'tha', 'Thecc.01G284000' => 'tca', 'Thecc.04G220600' => 'tca', 'Thecc.05G268900' => 'tca', 'Thecc.08G171100' => 'tca', 'Thhalv10001284m.g' => 'esa', 'Thhalv10019912m.g' => 'esa', 'TPR.G14189' => 'tpr', 'TPR.G18110' => 'tpr', 'TPR.G18130' => 'tpr', 'TPR.G18131' => 'tpr', 'TPR.G18140' => 'tpr', 'TPR.G24282' => 'tpr', 'TPR.G25221' => 'tpr', 'TPR.G29267' => 'tpr', 'TPR.G35315' => 'tpr', 'TPR.G36173' => 'tpr', 'TWI09G0794' => 'twi', 'TWI59G1348' => 'twi', 'TWI74G0430' => 'twi', 'unitig_26.g8940' => 'ugi', 'unitig_749.g13744' => 'ugi', 'unitig_749.g13745' => 'ugi', 'vmacro08269' => 'vma', 'vmacro14937' => 'vma', 'vmacro20401' => 'vma', 'VMungo0464G1349' => 'vmu', 'VMungo0540G0289' => 'vmu', 'VMungo1215G1590' => 'vmu', 'VMungo1309G0221' => 'vmu', 'VMungo1309G2815' => 'vmu', 'VMungo1383G0239' => 'vmu', 'VMungo1383G2910' => 'vmu', 'Zm00001eb095270' => 'zma', 'Zm00001eb095280' => 'zma', 'Zm00001eb111630' => 'zma', 'Zm00001eb237080' => 'zma', 'Zm00001eb273740' => 'zma', 'Zm00001eb285040' => 'zma', 'Zm00001eb330790' => 'zma', 'Zm00001eb337380' => 'zma' ) $gf_id = 'HOM05D001484' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001484' ) $data_identifier = 'HOM05D001484' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 2, 'aly' => (int) 2, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 22, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 7, 'hma' => (int) 2, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 7, 'mtr' => (int) 10, 'cme' => (int) 2, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 4, 'ppa' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 4, 'qlo' => (int) 9, 'rch' => (int) 6, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 10, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 7, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb337380' $species_info = array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ) $local_species = 'ccan' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001484', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p31500' => 'bna', 'A05p00020' => 'bna', 'A07p08820' => 'bna', 'Aa31LG4G3300' => 'aar', 'Aa31LG8G10030' => 'aar', 'Actinidia00731' => 'ach', 'Actinidia11473' => 'ach', 'Actinidia23469' => 'ach', 'Actinidia24318' => 'ach', 'Actinidia40196' => 'ach', 'Actinidia40197' => 'ach', 'Actinidia40198' => 'ach', 'Ah.08g212990' => 'amhyb', 'Ah.15g091720' => 'amhyb', 'AL3G38260' => 'aly', 'AL4G47710' => 'aly', 'Aqoxy2G00671' => 'aox', 'Aqoxy2G03236' => 'aox', 'arahy.Tifrunner.gnm1.ann1.05IDCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KR684' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATY3SJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK6QJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6APGL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IDT7Z9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM073U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ0R87' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LE7RV4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT4QRX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V5ENPK' => 'arhy', 'AT2G48110' => 'ath', 'AT3G23590' => 'ath', 'ATR0626G186' => 'atr', 'ATR1127G141' => 'atr', 'Atru.chr4.2583' => 'acertr', 'Atru.chr5.1358' => 'acertr', 'Atru.chr5.1359' => 'acertr', 'Atru.chr8.46' => 'acertr', 'AUR62002640' => 'cqu', 'AUR62030055' => 'cqu', 'AUR62033713' => 'cqu', 'AUR62033714' => 'cqu', 'AUR62036795' => 'cqu', 'AUR62039891' => 'cqu', 'BcaB02g08737' => 'bca', 'BcaB04g20441' => 'bca', 'BcaB06g26509' => 'bca', 'BcaB06g26510' => 'bca', 'BcaB06g26511' => 'bca', 'BcaB06g26512' => 'bca', 'BcaB06g26513' => 'bca', 'BcaC02g12564' => 'bca', 'BcaC02g12565' => 'bca', 'BcaC02g12794' => 'bca', 'BcaC02g12795' => 'bca', 'BcaC02g12796' => 'bca', 'BcaC06g35541' => 'bca', 'BNapus_Darmor_BZH_scaffold_188p00080' => 'bna', 'BNapus_Darmor_BZH_scaffold_188p00090' => 'bna', 'BolC1t03972H' => 'bol', 'BolC1t03973H' => 'bol', 'BolC4t21680H' => 'bol', 'BolC7t41863H' => 'bol', 'BolSC55t61227H' => 'bol', 'BolSC55t61228H' => 'bol', 'BraA01t03278Z' => 'bra', 'BraA05t18998Z' => 'bra', 'BraA07t28673Z' => 'bra', 'C01p40150' => 'bna', 'C05p12370' => 'bna', 'C07p13680' => 'bna', 'CAN.G1006.16' => 'can', 'CAN.G1006.17' => 'can', 'CAN.G1170.2' => 'can', 'CAN.G962.7' => 'can', 'CANSAT25G2179' => 'cansat', 'CANSAT78G1573' => 'cansat', 'CARHR099510' => 'chi', 'CARHR143510' => 'chi', 'Carub.0003s2380' => 'cru', 'Carub.0004s3082' => 'cru', 'Ca_00614_v3' => 'car', 'Ca_07801_v3' => 'car', 'Ca_08567_v3' => 'car', 'Ca_09571_v3' => 'car', 'CBR_g19290' => 'cbr', 'Cc01_g19770' => 'ccan', 'Cc03_g03030' => 'ccan', 'CDE07G0968' => 'cde', 'CDE09G1441' => 'cde', 'Cfa006103' => 'cfa', 'Cfa015573' => 'cfa', 'Cfa016988' => 'cfa', 'Ciclev10006738m.g' => 'ccl', 'Ciclev10010920m.g' => 'ccl', 'Ciclev10018517m.g' => 'ccl', 'CiPaw.01G159200' => 'cil', 'CiPaw.02G091000' => 'cil', 'CiPaw.02G091100' => 'cil', 'CiPaw.08G103100' => 'cil', 'CiPaw.09G224900' => 'cil', 'ClCG06G005740' => 'cla', 'ClCG07G000090' => 'cla', 'ClCG07G000100' => 'cla', 'COL.COLO4_09143' => 'col', 'COL.COLO4_25124' => 'col', 'Cpa.g.sc16.34' => 'cpa', 'Cpa.g.sc3504.1' => 'cpa', 'Cpa.g.sc60.37' => 'cpa', 'CsaV3_6G018520' => 'csa', 'CsaV3_6G036860' => 'csa', 'CSS0001072' => 'camsi', 'CSS0020208' => 'camsi', 'CSS0021253' => 'camsi', 'CSS0022190' => 'camsi', 'CSS0036150' => 'camsi', 'CSS0040442' => 'camsi', 'CSS0042300' => 'camsi', 'CSS0045298' => 'camsi', 'DCAR_012449' => 'dca', 'DCAR_018405' => 'dca', 'DCAR_024573' => 'dca', 'DCAR_030591' => 'dca', 'Dinv16926' => 'din', 'Dinv32963' => 'din', 'Dinv38382' => 'din', 'Dinv38383' => 'din', 'Duzib133G0974' => 'dzi', 'Duzib138G1867' => 'dzi', 'Duzib211G0420' => 'dzi', 'Duzib212G0930' => 'dzi', 'ECA234G1645' => 'eca', 'ECA247G3467' => 'eca', 'ECA248G1703' => 'eca', 'EL10Ac3g06327' => 'bvu', 'EL10Ac7g17204' => 'bvu', 'Eucgr.A00855' => 'egr', 'Eucgr.A00858' => 'egr', 'Eucgr.H01520' => 'egr', 'Eucgr.H03604' => 'egr', 'Eucgr.L03465' => 'egr', 'Eucgr.L03466' => 'egr', 'FAN01G0988' => 'fan', 'FAN02G3892' => 'fan', 'FAN05G3381' => 'fan', 'FAN07G0967' => 'fan', 'FAN07G1493' => 'fan', 'FAN08G3125' => 'fan', 'FAN09G0402' => 'fan', 'FAN12G2594' => 'fan', 'FAN12G3879' => 'fan', 'FAN14G1546' => 'fan', 'FAN15G3626' => 'fan', 'FAN17G0588' => 'fan', 'FAN17G0609' => 'fan', 'FAN18G2817' => 'fan', 'FAN19G1305' => 'fan', 'FAN20G1787' => 'fan', 'FAN22G0073' => 'fan', 'FAN22G0352' => 'fan', 'FAN22G0368' => 'fan', 'FAN22G2273' => 'fan', 'FAN24G1998' => 'fan', 'FAN27G1317' => 'fan', 'FvH4_2g23980' => 'fve', 'FvH4_4g14380' => 'fve', 'FvH4_4g14390' => 'fve', 'FvH4_6g09250' => 'fve', 'Glyma.03G151100' => 'gma', 'Glyma.04G122550' => 'gma', 'Glyma.05G001600' => 'gma', 'Glyma.09G270766' => 'gma', 'Glyma.09G270832' => 'gma', 'Glyma.13G209800' => 'gma', 'Glyma.15G102800' => 'gma', 'Glyma.18G218900' => 'gma', 'Glyma.19G001500' => 'gma', 'Glyma.19G153600' => 'gma', 'Gohir.A02G028600' => 'ghi', 'Gohir.A08G045000' => 'ghi', 'Gohir.A11G120500' => 'ghi', 'Gohir.A12G006200' => 'ghi', 'Gohir.A12G006250' => 'ghi', 'Gohir.D02G036300' => 'ghi', 'Gohir.D08G054700' => 'ghi', 'Gohir.D11G125600' => 'ghi', 'Gohir.D12G005700' => 'ghi', 'Gorai.004G055200' => 'gra', 'Gorai.005G040400' => 'gra', 'Gorai.007G134500' => 'gra', 'Gorai.008G005500' => 'gra', 'GSVIVG01011094001' => 'vvi', 'GSVIVG01017879001' => 'vvi', 'GSVIVG01025988001' => 'vvi', 'GSVIVG01029847001' => 'vvi', 'HanXRQChr10g0282901' => 'han', 'HanXRQChr10g0310371' => 'han', 'HanXRQChr10g0315041' => 'han', 'HanXRQChr11g0327651' => 'han', 'HanXRQChr12g0359391' => 'han', 'Haze_00972' => 'cav', 'Haze_00973' => 'cav', 'Haze_00974' => 'cav', 'Haze_04747' => 'cav', 'Haze_04749' => 'cav', 'Haze_04750' => 'cav', 'Haze_21217' => 'cav', 'Hma1.2p1_1037F.1_g250680' => 'hma', 'Hma1.2p1_1644F.1_g295320' => 'hma', 'HPP92_011322' => 'vpl', 'HPP92_011323' => 'vpl', 'HPP92_011324' => 'vpl', 'HPP92_011325' => 'vpl', 'HPP92_011326' => 'vpl', 'Hund12205' => 'sun', 'Hund17957' => 'sun', 'Lalb_Chr06g0176771' => 'lal', 'Lalb_Chr18g0056021' => 'lal', 'Lalb_Chr18g0056031' => 'lal', 'Lalb_Chr18g0056041' => 'lal', 'Lalb_Chr20g0107751' => 'lal', 'Lalb_Chr20g0118371' => 'lal', 'Lj1g0010239' => 'lja', 'Lj1g0017101' => 'lja', 'Lj2A1178G40' => 'lonja', 'Lj2A54G84' => 'lonja', 'Lj2g0015248' => 'lja', 'Lj3A761T51' => 'lonja', 'Lj6g0018116' => 'lja', 'Lsat_1_v5_gn_4_136040' => 'lsa', 'Lsat_1_v5_gn_5_187461' => 'lsa', 'Lsat_1_v5_gn_5_77001' => 'lsa', 'Lsat_1_v5_gn_9_4461' => 'lsa', 'Manes.01G210100' => 'mes', 'Manes.03G185600' => 'mes', 'Manes.05G073300' => 'mes', 'Manes.09G120300' => 'mes', 'Manes.15G022100' => 'mes', 'Mapoly0096s0053' => 'mpo', 'MBI03_g14058_MAGBIO' => 'mbi', 'MBI03_g33876_MAGBIO' => 'mbi', 'MBI03_g36854_MAGBIO' => 'mbi', 'MBI17_g11997_MAGBIO' => 'mbi', 'MD03G1269000' => 'mdo', 'MD04G1179600' => 'mdo', 'MD11G1289800' => 'mdo', 'MD12G1194700' => 'mdo', 'MD13G1182100' => 'mdo', 'MD13G1182200' => 'mdo', 'MD16G1182600' => 'mdo', 'Medtr2g021400' => 'mtr', 'Medtr2g021470' => 'mtr', 'Medtr2g105810' => 'mtr', 'Medtr3g033580' => 'mtr', 'Medtr6g007970' => 'mtr', 'Medtr7g056330' => 'mtr', 'Medtr7g074290' => 'mtr', 'Medtr7g074380' => 'mtr', 'Medtr7g094550' => 'mtr', 'Medtr8g069995' => 'mtr', 'MELO3C014345.2' => 'cme', 'MELO3C021395.2' => 'cme', 'Migut.D00262' => 'egut', 'Migut.G00257' => 'egut', 'MSTRG.21575' => 'ama', 'MSTRG.3985' => 'ama', 'Nitab4.5_0000295g0140' => 'nta', 'Nitab4.5_0000732g0140' => 'nta', 'Nitab4.5_0003162g0020' => 'nta', 'Nitab4.5_0006180g0090' => 'nta', 'Nitab4.5_0006390g0010' => 'nta', 'Nitab4.5_0007392g0040' => 'nta', 'Nn1g02140' => 'nnu', 'Nn4g26168' => 'nnu', 'Nn5g26754' => 'nnu', 'Oeu001433.1' => 'oeu', 'Oeu010299.2' => 'oeu', 'Oeu011171.1' => 'oeu', 'Oeu037675.1' => 'oeu', 'Oeu038359.1' => 'oeu', 'Oeu063834.1' => 'oeu', 'Oeu063835.1' => 'oeu', 'Os05g0312000' => 'osa', 'Os07g0211101' => 'osa', 'Os07g0211200' => 'osa', 'Os07g0681500' => 'osa', 'Peaxi162Scf00095g01015' => 'pax', 'Peaxi162Scf00104g00329' => 'pax', 'Peaxi162Scf00161g00137' => 'pax', 'PGR004G1665' => 'pgr', 'PGR031G2937' => 'pgr', 'PGR119G2145' => 'pgr', 'PGSC0003DMG400004351' => 'stu', 'PGSC0003DMG400014625' => 'stu', 'PGSC0003DMG401000943' => 'stu', 'Phvul.001G148600' => 'pvu', 'Phvul.004G001700' => 'pvu', 'Phvul.006G154900' => 'pvu', 'Phvul.008G078200' => 'pvu', 'Phvul.011G136500' => 'pvu', 'Potri.002G215600' => 'ptr', 'Potri.008G201600' => 'ptr', 'Potri.014G138400' => 'ptr', 'Potri.016G142500' => 'ptr', 'Pp3c16_10580' => 'ppa', 'Pp3c5_25280' => 'ppa', 'Prupe.1G150000' => 'ppe', 'Prupe.1G150100' => 'ppe', 'Prupe.6G299600' => 'ppe', 'Prupe.8G245000' => 'ppe', 'Psat0s4927g0040' => 'psa', 'Psat1g052080' => 'psa', 'Psat1g183800' => 'psa', 'Psat3g113840' => 'psa', 'Psat3g126120' => 'psa', 'Psat3g126160' => 'psa', 'Psat3g158760' => 'psa', 'Psat3g158840' => 'psa', 'PSO170G2858' => 'pso', 'PSO339G0606' => 'pso', 'PSO384G4709' => 'pso', 'PSO407G0334' => 'pso', 'QL04p040276' => 'qlo', 'QL06p005458' => 'qlo', 'QL06p005472' => 'qlo', 'QL07p030546' => 'qlo', 'QL07p031519' => 'qlo', 'QL09p050949' => 'qlo', 'QL09p050966' => 'qlo', 'QL09p051067' => 'qlo', 'QL12p022706' => 'qlo', 'RcHm_v2.0_Chr2g0119601' => 'rch', 'RcHm_v2.0_Chr3g0459591' => 'rch', 'RcHm_v2.0_Chr4g0418521' => 'rch', 'RcHm_v2.0_Chr4g0418531' => 'rch', 'RcHm_v2.0_Chr4g0418541' => 'rch', 'RcHm_v2.0_Chr6g0291641' => 'rch', 'Rhsim01G0086300' => 'rsi', 'Rhsim01G0276300' => 'rsi', 'Rhsim01G0276500' => 'rsi', 'Rhsim04G0207700' => 'rsi', 'Rhsim05G0234500' => 'rsi', 'Rhsim13G0022400' => 'rsi', 'Sabra02G0167900' => 'sbr', 'Sabra04G0158500' => 'sbr', 'Sabra08G0159800' => 'sbr', 'Sabra10G0011500' => 'sbr', 'Sabra14G0104400' => 'sbr', 'SalBow2G2440' => 'sbo', 'SalBow4G2265' => 'sbo', 'Sc02g0000060' => 'sci', 'Sc05g0005020' => 'sci', 'Sc13g0003890' => 'sci', 'Sed0014865' => 'sed', 'Sed0017224' => 'sed', 'Sed0026391' => 'sed', 'SEGI_00063' => 'sgi', 'SEGI_10967' => 'sgi', 'SEGI_17510' => 'sgi', 'SEGI_24396' => 'sgi', 'SEGI_39719' => 'sgi', 'SEGI_41392' => 'sgi', 'SGA_v2.0_scaffold11G05794' => 'sas', 'SGA_v2.0_scaffold142G35607' => 'sas', 'SGA_v2.0_scaffold1G00447' => 'sas', 'SHI15388' => 'shi', 'SHI15394' => 'shi', 'SHI15396' => 'shi', 'SHI15399' => 'shi', 'SMO343G0151' => 'smo', 'SMO367G1118' => 'smo', 'Solyc01g080200.3' => 'sly', 'Solyc06g008960.3' => 'sly', 'Solyc09g064780.3' => 'sly', 'Sopen01g031980' => 'spe', 'Sopen06g003710' => 'spe', 'Sopen09g026460' => 'spe', 'Sp3g21240' => 'spa', 'Sp4g30030' => 'spa', 'TAR365G0022' => 'tar', 'TAR365G1023' => 'tar', 'TAR365G1253' => 'tar', 'TAR623G0078' => 'tar', 'TAR623G1721' => 'tar', 'TAR633G0959' => 'tar', 'THA.LOC104802225' => 'tha', 'THA.LOC104804769' => 'tha', 'THA.LOC104808660' => 'tha', 'THA.LOC104812792' => 'tha', 'Thecc.01G284000' => 'tca', 'Thecc.04G220600' => 'tca', 'Thecc.05G268900' => 'tca', 'Thecc.08G171100' => 'tca', 'Thhalv10001284m.g' => 'esa', 'Thhalv10019912m.g' => 'esa', 'TPR.G14189' => 'tpr', 'TPR.G18110' => 'tpr', 'TPR.G18130' => 'tpr', 'TPR.G18131' => 'tpr', 'TPR.G18140' => 'tpr', 'TPR.G24282' => 'tpr', 'TPR.G25221' => 'tpr', 'TPR.G29267' => 'tpr', 'TPR.G35315' => 'tpr', 'TPR.G36173' => 'tpr', 'TWI09G0794' => 'twi', 'TWI59G1348' => 'twi', 'TWI74G0430' => 'twi', 'unitig_26.g8940' => 'ugi', 'unitig_749.g13744' => 'ugi', 'unitig_749.g13745' => 'ugi', 'vmacro08269' => 'vma', 'vmacro14937' => 'vma', 'vmacro20401' => 'vma', 'VMungo0464G1349' => 'vmu', 'VMungo0540G0289' => 'vmu', 'VMungo1215G1590' => 'vmu', 'VMungo1309G0221' => 'vmu', 'VMungo1309G2815' => 'vmu', 'VMungo1383G0239' => 'vmu', 'VMungo1383G2910' => 'vmu', 'Zm00001eb095270' => 'zma', 'Zm00001eb095280' => 'zma', 'Zm00001eb111630' => 'zma', 'Zm00001eb237080' => 'zma', 'Zm00001eb273740' => 'zma', 'Zm00001eb285040' => 'zma', 'Zm00001eb330790' => 'zma', 'Zm00001eb337380' => 'zma' ), 'gf_id' => 'HOM05D001484', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001484' ), 'data_identifier' => 'HOM05D001484', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001484', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p31500' => 'bna', 'A05p00020' => 'bna', 'A07p08820' => 'bna', 'Aa31LG4G3300' => 'aar', 'Aa31LG8G10030' => 'aar', 'Actinidia00731' => 'ach', 'Actinidia11473' => 'ach', 'Actinidia23469' => 'ach', 'Actinidia24318' => 'ach', 'Actinidia40196' => 'ach', 'Actinidia40197' => 'ach', 'Actinidia40198' => 'ach', 'Ah.08g212990' => 'amhyb', 'Ah.15g091720' => 'amhyb', 'AL3G38260' => 'aly', 'AL4G47710' => 'aly', 'Aqoxy2G00671' => 'aox', 'Aqoxy2G03236' => 'aox', 'arahy.Tifrunner.gnm1.ann1.05IDCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KR684' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATY3SJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK6QJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6APGL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IDT7Z9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM073U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ0R87' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LE7RV4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT4QRX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V5ENPK' => 'arhy', 'AT2G48110' => 'ath', 'AT3G23590' => 'ath', 'ATR0626G186' => 'atr', 'ATR1127G141' => 'atr', 'Atru.chr4.2583' => 'acertr', 'Atru.chr5.1358' => 'acertr', 'Atru.chr5.1359' => 'acertr', 'Atru.chr8.46' => 'acertr', 'AUR62002640' => 'cqu', 'AUR62030055' => 'cqu', 'AUR62033713' => 'cqu', 'AUR62033714' => 'cqu', 'AUR62036795' => 'cqu', 'AUR62039891' => 'cqu', 'BcaB02g08737' => 'bca', 'BcaB04g20441' => 'bca', 'BcaB06g26509' => 'bca', 'BcaB06g26510' => 'bca', 'BcaB06g26511' => 'bca', 'BcaB06g26512' => 'bca', 'BcaB06g26513' => 'bca', 'BcaC02g12564' => 'bca', 'BcaC02g12565' => 'bca', 'BcaC02g12794' => 'bca', 'BcaC02g12795' => 'bca', 'BcaC02g12796' => 'bca', 'BcaC06g35541' => 'bca', 'BNapus_Darmor_BZH_scaffold_188p00080' => 'bna', 'BNapus_Darmor_BZH_scaffold_188p00090' => 'bna', 'BolC1t03972H' => 'bol', 'BolC1t03973H' => 'bol', 'BolC4t21680H' => 'bol', 'BolC7t41863H' => 'bol', 'BolSC55t61227H' => 'bol', 'BolSC55t61228H' => 'bol', 'BraA01t03278Z' => 'bra', 'BraA05t18998Z' => 'bra', 'BraA07t28673Z' => 'bra', 'C01p40150' => 'bna', 'C05p12370' => 'bna', 'C07p13680' => 'bna', 'CAN.G1006.16' => 'can', 'CAN.G1006.17' => 'can', 'CAN.G1170.2' => 'can', 'CAN.G962.7' => 'can', 'CANSAT25G2179' => 'cansat', 'CANSAT78G1573' => 'cansat', 'CARHR099510' => 'chi', 'CARHR143510' => 'chi', 'Carub.0003s2380' => 'cru', 'Carub.0004s3082' => 'cru', 'Ca_00614_v3' => 'car', 'Ca_07801_v3' => 'car', 'Ca_08567_v3' => 'car', 'Ca_09571_v3' => 'car', 'CBR_g19290' => 'cbr', 'Cc01_g19770' => 'ccan', 'Cc03_g03030' => 'ccan', 'CDE07G0968' => 'cde', 'CDE09G1441' => 'cde', 'Cfa006103' => 'cfa', 'Cfa015573' => 'cfa', 'Cfa016988' => 'cfa', 'Ciclev10006738m.g' => 'ccl', 'Ciclev10010920m.g' => 'ccl', 'Ciclev10018517m.g' => 'ccl', 'CiPaw.01G159200' => 'cil', 'CiPaw.02G091000' => 'cil', 'CiPaw.02G091100' => 'cil', 'CiPaw.08G103100' => 'cil', 'CiPaw.09G224900' => 'cil', 'ClCG06G005740' => 'cla', 'ClCG07G000090' => 'cla', 'ClCG07G000100' => 'cla', 'COL.COLO4_09143' => 'col', 'COL.COLO4_25124' => 'col', 'Cpa.g.sc16.34' => 'cpa', 'Cpa.g.sc3504.1' => 'cpa', 'Cpa.g.sc60.37' => 'cpa', 'CsaV3_6G018520' => 'csa', 'CsaV3_6G036860' => 'csa', 'CSS0001072' => 'camsi', 'CSS0020208' => 'camsi', 'CSS0021253' => 'camsi', 'CSS0022190' => 'camsi', 'CSS0036150' => 'camsi', 'CSS0040442' => 'camsi', 'CSS0042300' => 'camsi', 'CSS0045298' => 'camsi', 'DCAR_012449' => 'dca', 'DCAR_018405' => 'dca', 'DCAR_024573' => 'dca', 'DCAR_030591' => 'dca', 'Dinv16926' => 'din', 'Dinv32963' => 'din', 'Dinv38382' => 'din', 'Dinv38383' => 'din', 'Duzib133G0974' => 'dzi', 'Duzib138G1867' => 'dzi', 'Duzib211G0420' => 'dzi', 'Duzib212G0930' => 'dzi', 'ECA234G1645' => 'eca', 'ECA247G3467' => 'eca', 'ECA248G1703' => 'eca', 'EL10Ac3g06327' => 'bvu', 'EL10Ac7g17204' => 'bvu', 'Eucgr.A00855' => 'egr', 'Eucgr.A00858' => 'egr', 'Eucgr.H01520' => 'egr', 'Eucgr.H03604' => 'egr', 'Eucgr.L03465' => 'egr', 'Eucgr.L03466' => 'egr', 'FAN01G0988' => 'fan', 'FAN02G3892' => 'fan', 'FAN05G3381' => 'fan', 'FAN07G0967' => 'fan', 'FAN07G1493' => 'fan', 'FAN08G3125' => 'fan', 'FAN09G0402' => 'fan', 'FAN12G2594' => 'fan', 'FAN12G3879' => 'fan', 'FAN14G1546' => 'fan', 'FAN15G3626' => 'fan', 'FAN17G0588' => 'fan', 'FAN17G0609' => 'fan', 'FAN18G2817' => 'fan', 'FAN19G1305' => 'fan', 'FAN20G1787' => 'fan', 'FAN22G0073' => 'fan', 'FAN22G0352' => 'fan', 'FAN22G0368' => 'fan', 'FAN22G2273' => 'fan', 'FAN24G1998' => 'fan', 'FAN27G1317' => 'fan', 'FvH4_2g23980' => 'fve', 'FvH4_4g14380' => 'fve', 'FvH4_4g14390' => 'fve', 'FvH4_6g09250' => 'fve', 'Glyma.03G151100' => 'gma', 'Glyma.04G122550' => 'gma', 'Glyma.05G001600' => 'gma', 'Glyma.09G270766' => 'gma', 'Glyma.09G270832' => 'gma', 'Glyma.13G209800' => 'gma', 'Glyma.15G102800' => 'gma', 'Glyma.18G218900' => 'gma', 'Glyma.19G001500' => 'gma', 'Glyma.19G153600' => 'gma', 'Gohir.A02G028600' => 'ghi', 'Gohir.A08G045000' => 'ghi', 'Gohir.A11G120500' => 'ghi', 'Gohir.A12G006200' => 'ghi', 'Gohir.A12G006250' => 'ghi', 'Gohir.D02G036300' => 'ghi', 'Gohir.D08G054700' => 'ghi', 'Gohir.D11G125600' => 'ghi', 'Gohir.D12G005700' => 'ghi', 'Gorai.004G055200' => 'gra', 'Gorai.005G040400' => 'gra', 'Gorai.007G134500' => 'gra', 'Gorai.008G005500' => 'gra', 'GSVIVG01011094001' => 'vvi', 'GSVIVG01017879001' => 'vvi', 'GSVIVG01025988001' => 'vvi', 'GSVIVG01029847001' => 'vvi', 'HanXRQChr10g0282901' => 'han', 'HanXRQChr10g0310371' => 'han', 'HanXRQChr10g0315041' => 'han', 'HanXRQChr11g0327651' => 'han', 'HanXRQChr12g0359391' => 'han', 'Haze_00972' => 'cav', 'Haze_00973' => 'cav', 'Haze_00974' => 'cav', 'Haze_04747' => 'cav', 'Haze_04749' => 'cav', 'Haze_04750' => 'cav', 'Haze_21217' => 'cav', 'Hma1.2p1_1037F.1_g250680' => 'hma', 'Hma1.2p1_1644F.1_g295320' => 'hma', 'HPP92_011322' => 'vpl', 'HPP92_011323' => 'vpl', 'HPP92_011324' => 'vpl', 'HPP92_011325' => 'vpl', 'HPP92_011326' => 'vpl', 'Hund12205' => 'sun', 'Hund17957' => 'sun', 'Lalb_Chr06g0176771' => 'lal', 'Lalb_Chr18g0056021' => 'lal', 'Lalb_Chr18g0056031' => 'lal', 'Lalb_Chr18g0056041' => 'lal', 'Lalb_Chr20g0107751' => 'lal', 'Lalb_Chr20g0118371' => 'lal', 'Lj1g0010239' => 'lja', 'Lj1g0017101' => 'lja', 'Lj2A1178G40' => 'lonja', 'Lj2A54G84' => 'lonja', 'Lj2g0015248' => 'lja', 'Lj3A761T51' => 'lonja', 'Lj6g0018116' => 'lja', 'Lsat_1_v5_gn_4_136040' => 'lsa', 'Lsat_1_v5_gn_5_187461' => 'lsa', 'Lsat_1_v5_gn_5_77001' => 'lsa', 'Lsat_1_v5_gn_9_4461' => 'lsa', 'Manes.01G210100' => 'mes', 'Manes.03G185600' => 'mes', 'Manes.05G073300' => 'mes', 'Manes.09G120300' => 'mes', 'Manes.15G022100' => 'mes', 'Mapoly0096s0053' => 'mpo', 'MBI03_g14058_MAGBIO' => 'mbi', 'MBI03_g33876_MAGBIO' => 'mbi', 'MBI03_g36854_MAGBIO' => 'mbi', 'MBI17_g11997_MAGBIO' => 'mbi', 'MD03G1269000' => 'mdo', 'MD04G1179600' => 'mdo', 'MD11G1289800' => 'mdo', 'MD12G1194700' => 'mdo', 'MD13G1182100' => 'mdo', 'MD13G1182200' => 'mdo', 'MD16G1182600' => 'mdo', 'Medtr2g021400' => 'mtr', 'Medtr2g021470' => 'mtr', 'Medtr2g105810' => 'mtr', 'Medtr3g033580' => 'mtr', 'Medtr6g007970' => 'mtr', 'Medtr7g056330' => 'mtr', 'Medtr7g074290' => 'mtr', 'Medtr7g074380' => 'mtr', 'Medtr7g094550' => 'mtr', 'Medtr8g069995' => 'mtr', 'MELO3C014345.2' => 'cme', 'MELO3C021395.2' => 'cme', 'Migut.D00262' => 'egut', 'Migut.G00257' => 'egut', 'MSTRG.21575' => 'ama', 'MSTRG.3985' => 'ama', 'Nitab4.5_0000295g0140' => 'nta', 'Nitab4.5_0000732g0140' => 'nta', 'Nitab4.5_0003162g0020' => 'nta', 'Nitab4.5_0006180g0090' => 'nta', 'Nitab4.5_0006390g0010' => 'nta', 'Nitab4.5_0007392g0040' => 'nta', 'Nn1g02140' => 'nnu', 'Nn4g26168' => 'nnu', 'Nn5g26754' => 'nnu', 'Oeu001433.1' => 'oeu', 'Oeu010299.2' => 'oeu', 'Oeu011171.1' => 'oeu', 'Oeu037675.1' => 'oeu', 'Oeu038359.1' => 'oeu', 'Oeu063834.1' => 'oeu', 'Oeu063835.1' => 'oeu', 'Os05g0312000' => 'osa', 'Os07g0211101' => 'osa', 'Os07g0211200' => 'osa', 'Os07g0681500' => 'osa', 'Peaxi162Scf00095g01015' => 'pax', 'Peaxi162Scf00104g00329' => 'pax', 'Peaxi162Scf00161g00137' => 'pax', 'PGR004G1665' => 'pgr', 'PGR031G2937' => 'pgr', 'PGR119G2145' => 'pgr', 'PGSC0003DMG400004351' => 'stu', 'PGSC0003DMG400014625' => 'stu', 'PGSC0003DMG401000943' => 'stu', 'Phvul.001G148600' => 'pvu', 'Phvul.004G001700' => 'pvu', 'Phvul.006G154900' => 'pvu', 'Phvul.008G078200' => 'pvu', 'Phvul.011G136500' => 'pvu', 'Potri.002G215600' => 'ptr', 'Potri.008G201600' => 'ptr', 'Potri.014G138400' => 'ptr', 'Potri.016G142500' => 'ptr', 'Pp3c16_10580' => 'ppa', 'Pp3c5_25280' => 'ppa', 'Prupe.1G150000' => 'ppe', 'Prupe.1G150100' => 'ppe', 'Prupe.6G299600' => 'ppe', 'Prupe.8G245000' => 'ppe', 'Psat0s4927g0040' => 'psa', 'Psat1g052080' => 'psa', 'Psat1g183800' => 'psa', 'Psat3g113840' => 'psa', 'Psat3g126120' => 'psa', 'Psat3g126160' => 'psa', 'Psat3g158760' => 'psa', 'Psat3g158840' => 'psa', 'PSO170G2858' => 'pso', 'PSO339G0606' => 'pso', 'PSO384G4709' => 'pso', 'PSO407G0334' => 'pso', 'QL04p040276' => 'qlo', 'QL06p005458' => 'qlo', 'QL06p005472' => 'qlo', 'QL07p030546' => 'qlo', 'QL07p031519' => 'qlo', 'QL09p050949' => 'qlo', 'QL09p050966' => 'qlo', 'QL09p051067' => 'qlo', 'QL12p022706' => 'qlo', 'RcHm_v2.0_Chr2g0119601' => 'rch', 'RcHm_v2.0_Chr3g0459591' => 'rch', 'RcHm_v2.0_Chr4g0418521' => 'rch', 'RcHm_v2.0_Chr4g0418531' => 'rch', 'RcHm_v2.0_Chr4g0418541' => 'rch', 'RcHm_v2.0_Chr6g0291641' => 'rch', 'Rhsim01G0086300' => 'rsi', 'Rhsim01G0276300' => 'rsi', 'Rhsim01G0276500' => 'rsi', 'Rhsim04G0207700' => 'rsi', 'Rhsim05G0234500' => 'rsi', 'Rhsim13G0022400' => 'rsi', 'Sabra02G0167900' => 'sbr', 'Sabra04G0158500' => 'sbr', 'Sabra08G0159800' => 'sbr', 'Sabra10G0011500' => 'sbr', 'Sabra14G0104400' => 'sbr', 'SalBow2G2440' => 'sbo', 'SalBow4G2265' => 'sbo', 'Sc02g0000060' => 'sci', 'Sc05g0005020' => 'sci', 'Sc13g0003890' => 'sci', 'Sed0014865' => 'sed', 'Sed0017224' => 'sed', 'Sed0026391' => 'sed', 'SEGI_00063' => 'sgi', 'SEGI_10967' => 'sgi', 'SEGI_17510' => 'sgi', 'SEGI_24396' => 'sgi', 'SEGI_39719' => 'sgi', 'SEGI_41392' => 'sgi', 'SGA_v2.0_scaffold11G05794' => 'sas', 'SGA_v2.0_scaffold142G35607' => 'sas', 'SGA_v2.0_scaffold1G00447' => 'sas', 'SHI15388' => 'shi', 'SHI15394' => 'shi', 'SHI15396' => 'shi', 'SHI15399' => 'shi', 'SMO343G0151' => 'smo', 'SMO367G1118' => 'smo', 'Solyc01g080200.3' => 'sly', 'Solyc06g008960.3' => 'sly', 'Solyc09g064780.3' => 'sly', 'Sopen01g031980' => 'spe', 'Sopen06g003710' => 'spe', 'Sopen09g026460' => 'spe', 'Sp3g21240' => 'spa', 'Sp4g30030' => 'spa', 'TAR365G0022' => 'tar', 'TAR365G1023' => 'tar', 'TAR365G1253' => 'tar', 'TAR623G0078' => 'tar', 'TAR623G1721' => 'tar', 'TAR633G0959' => 'tar', 'THA.LOC104802225' => 'tha', 'THA.LOC104804769' => 'tha', 'THA.LOC104808660' => 'tha', 'THA.LOC104812792' => 'tha', 'Thecc.01G284000' => 'tca', 'Thecc.04G220600' => 'tca', 'Thecc.05G268900' => 'tca', 'Thecc.08G171100' => 'tca', 'Thhalv10001284m.g' => 'esa', 'Thhalv10019912m.g' => 'esa', 'TPR.G14189' => 'tpr', 'TPR.G18110' => 'tpr', 'TPR.G18130' => 'tpr', 'TPR.G18131' => 'tpr', 'TPR.G18140' => 'tpr', 'TPR.G24282' => 'tpr', 'TPR.G25221' => 'tpr', 'TPR.G29267' => 'tpr', 'TPR.G35315' => 'tpr', 'TPR.G36173' => 'tpr', 'TWI09G0794' => 'twi', 'TWI59G1348' => 'twi', 'TWI74G0430' => 'twi', 'unitig_26.g8940' => 'ugi', 'unitig_749.g13744' => 'ugi', 'unitig_749.g13745' => 'ugi', 'vmacro08269' => 'vma', 'vmacro14937' => 'vma', 'vmacro20401' => 'vma', 'VMungo0464G1349' => 'vmu', 'VMungo0540G0289' => 'vmu', 'VMungo1215G1590' => 'vmu', 'VMungo1309G0221' => 'vmu', 'VMungo1309G2815' => 'vmu', 'VMungo1383G0239' => 'vmu', 'VMungo1383G2910' => 'vmu', 'Zm00001eb095270' => 'zma', 'Zm00001eb095280' => 'zma', 'Zm00001eb111630' => 'zma', 'Zm00001eb237080' => 'zma', 'Zm00001eb273740' => 'zma', 'Zm00001eb285040' => 'zma', 'Zm00001eb330790' => 'zma', 'Zm00001eb337380' => 'zma' ) $gf_id = 'HOM05D001484' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001484' ) $data_identifier = 'HOM05D001484' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 2, 'aly' => (int) 2, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 22, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 7, 'hma' => (int) 2, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 7, 'mtr' => (int) 10, 'cme' => (int) 2, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 4, 'ppa' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 4, 'qlo' => (int) 9, 'rch' => (int) 6, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 10, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 7, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb337380' $species_info = array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ) $local_species = 'ccan' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001484', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p31500' => 'bna', 'A05p00020' => 'bna', 'A07p08820' => 'bna', 'Aa31LG4G3300' => 'aar', 'Aa31LG8G10030' => 'aar', 'Actinidia00731' => 'ach', 'Actinidia11473' => 'ach', 'Actinidia23469' => 'ach', 'Actinidia24318' => 'ach', 'Actinidia40196' => 'ach', 'Actinidia40197' => 'ach', 'Actinidia40198' => 'ach', 'Ah.08g212990' => 'amhyb', 'Ah.15g091720' => 'amhyb', 'AL3G38260' => 'aly', 'AL4G47710' => 'aly', 'Aqoxy2G00671' => 'aox', 'Aqoxy2G03236' => 'aox', 'arahy.Tifrunner.gnm1.ann1.05IDCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KR684' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATY3SJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK6QJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6APGL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IDT7Z9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM073U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ0R87' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LE7RV4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT4QRX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V5ENPK' => 'arhy', 'AT2G48110' => 'ath', 'AT3G23590' => 'ath', 'ATR0626G186' => 'atr', 'ATR1127G141' => 'atr', 'Atru.chr4.2583' => 'acertr', 'Atru.chr5.1358' => 'acertr', 'Atru.chr5.1359' => 'acertr', 'Atru.chr8.46' => 'acertr', 'AUR62002640' => 'cqu', 'AUR62030055' => 'cqu', 'AUR62033713' => 'cqu', 'AUR62033714' => 'cqu', 'AUR62036795' => 'cqu', 'AUR62039891' => 'cqu', 'BcaB02g08737' => 'bca', 'BcaB04g20441' => 'bca', 'BcaB06g26509' => 'bca', 'BcaB06g26510' => 'bca', 'BcaB06g26511' => 'bca', 'BcaB06g26512' => 'bca', 'BcaB06g26513' => 'bca', 'BcaC02g12564' => 'bca', 'BcaC02g12565' => 'bca', 'BcaC02g12794' => 'bca', 'BcaC02g12795' => 'bca', 'BcaC02g12796' => 'bca', 'BcaC06g35541' => 'bca', 'BNapus_Darmor_BZH_scaffold_188p00080' => 'bna', 'BNapus_Darmor_BZH_scaffold_188p00090' => 'bna', 'BolC1t03972H' => 'bol', 'BolC1t03973H' => 'bol', 'BolC4t21680H' => 'bol', 'BolC7t41863H' => 'bol', 'BolSC55t61227H' => 'bol', 'BolSC55t61228H' => 'bol', 'BraA01t03278Z' => 'bra', 'BraA05t18998Z' => 'bra', 'BraA07t28673Z' => 'bra', 'C01p40150' => 'bna', 'C05p12370' => 'bna', 'C07p13680' => 'bna', 'CAN.G1006.16' => 'can', 'CAN.G1006.17' => 'can', 'CAN.G1170.2' => 'can', 'CAN.G962.7' => 'can', 'CANSAT25G2179' => 'cansat', 'CANSAT78G1573' => 'cansat', 'CARHR099510' => 'chi', 'CARHR143510' => 'chi', 'Carub.0003s2380' => 'cru', 'Carub.0004s3082' => 'cru', 'Ca_00614_v3' => 'car', 'Ca_07801_v3' => 'car', 'Ca_08567_v3' => 'car', 'Ca_09571_v3' => 'car', 'CBR_g19290' => 'cbr', 'Cc01_g19770' => 'ccan', 'Cc03_g03030' => 'ccan', 'CDE07G0968' => 'cde', 'CDE09G1441' => 'cde', 'Cfa006103' => 'cfa', 'Cfa015573' => 'cfa', 'Cfa016988' => 'cfa', 'Ciclev10006738m.g' => 'ccl', 'Ciclev10010920m.g' => 'ccl', 'Ciclev10018517m.g' => 'ccl', 'CiPaw.01G159200' => 'cil', 'CiPaw.02G091000' => 'cil', 'CiPaw.02G091100' => 'cil', 'CiPaw.08G103100' => 'cil', 'CiPaw.09G224900' => 'cil', 'ClCG06G005740' => 'cla', 'ClCG07G000090' => 'cla', 'ClCG07G000100' => 'cla', 'COL.COLO4_09143' => 'col', 'COL.COLO4_25124' => 'col', 'Cpa.g.sc16.34' => 'cpa', 'Cpa.g.sc3504.1' => 'cpa', 'Cpa.g.sc60.37' => 'cpa', 'CsaV3_6G018520' => 'csa', 'CsaV3_6G036860' => 'csa', 'CSS0001072' => 'camsi', 'CSS0020208' => 'camsi', 'CSS0021253' => 'camsi', 'CSS0022190' => 'camsi', 'CSS0036150' => 'camsi', 'CSS0040442' => 'camsi', 'CSS0042300' => 'camsi', 'CSS0045298' => 'camsi', 'DCAR_012449' => 'dca', 'DCAR_018405' => 'dca', 'DCAR_024573' => 'dca', 'DCAR_030591' => 'dca', 'Dinv16926' => 'din', 'Dinv32963' => 'din', 'Dinv38382' => 'din', 'Dinv38383' => 'din', 'Duzib133G0974' => 'dzi', 'Duzib138G1867' => 'dzi', 'Duzib211G0420' => 'dzi', 'Duzib212G0930' => 'dzi', 'ECA234G1645' => 'eca', 'ECA247G3467' => 'eca', 'ECA248G1703' => 'eca', 'EL10Ac3g06327' => 'bvu', 'EL10Ac7g17204' => 'bvu', 'Eucgr.A00855' => 'egr', 'Eucgr.A00858' => 'egr', 'Eucgr.H01520' => 'egr', 'Eucgr.H03604' => 'egr', 'Eucgr.L03465' => 'egr', 'Eucgr.L03466' => 'egr', 'FAN01G0988' => 'fan', 'FAN02G3892' => 'fan', 'FAN05G3381' => 'fan', 'FAN07G0967' => 'fan', 'FAN07G1493' => 'fan', 'FAN08G3125' => 'fan', 'FAN09G0402' => 'fan', 'FAN12G2594' => 'fan', 'FAN12G3879' => 'fan', 'FAN14G1546' => 'fan', 'FAN15G3626' => 'fan', 'FAN17G0588' => 'fan', 'FAN17G0609' => 'fan', 'FAN18G2817' => 'fan', 'FAN19G1305' => 'fan', 'FAN20G1787' => 'fan', 'FAN22G0073' => 'fan', 'FAN22G0352' => 'fan', 'FAN22G0368' => 'fan', 'FAN22G2273' => 'fan', 'FAN24G1998' => 'fan', 'FAN27G1317' => 'fan', 'FvH4_2g23980' => 'fve', 'FvH4_4g14380' => 'fve', 'FvH4_4g14390' => 'fve', 'FvH4_6g09250' => 'fve', 'Glyma.03G151100' => 'gma', 'Glyma.04G122550' => 'gma', 'Glyma.05G001600' => 'gma', 'Glyma.09G270766' => 'gma', 'Glyma.09G270832' => 'gma', 'Glyma.13G209800' => 'gma', 'Glyma.15G102800' => 'gma', 'Glyma.18G218900' => 'gma', 'Glyma.19G001500' => 'gma', 'Glyma.19G153600' => 'gma', 'Gohir.A02G028600' => 'ghi', 'Gohir.A08G045000' => 'ghi', 'Gohir.A11G120500' => 'ghi', 'Gohir.A12G006200' => 'ghi', 'Gohir.A12G006250' => 'ghi', 'Gohir.D02G036300' => 'ghi', 'Gohir.D08G054700' => 'ghi', 'Gohir.D11G125600' => 'ghi', 'Gohir.D12G005700' => 'ghi', 'Gorai.004G055200' => 'gra', 'Gorai.005G040400' => 'gra', 'Gorai.007G134500' => 'gra', 'Gorai.008G005500' => 'gra', 'GSVIVG01011094001' => 'vvi', 'GSVIVG01017879001' => 'vvi', 'GSVIVG01025988001' => 'vvi', 'GSVIVG01029847001' => 'vvi', 'HanXRQChr10g0282901' => 'han', 'HanXRQChr10g0310371' => 'han', 'HanXRQChr10g0315041' => 'han', 'HanXRQChr11g0327651' => 'han', 'HanXRQChr12g0359391' => 'han', 'Haze_00972' => 'cav', 'Haze_00973' => 'cav', 'Haze_00974' => 'cav', 'Haze_04747' => 'cav', 'Haze_04749' => 'cav', 'Haze_04750' => 'cav', 'Haze_21217' => 'cav', 'Hma1.2p1_1037F.1_g250680' => 'hma', 'Hma1.2p1_1644F.1_g295320' => 'hma', 'HPP92_011322' => 'vpl', 'HPP92_011323' => 'vpl', 'HPP92_011324' => 'vpl', 'HPP92_011325' => 'vpl', 'HPP92_011326' => 'vpl', 'Hund12205' => 'sun', 'Hund17957' => 'sun', 'Lalb_Chr06g0176771' => 'lal', 'Lalb_Chr18g0056021' => 'lal', 'Lalb_Chr18g0056031' => 'lal', 'Lalb_Chr18g0056041' => 'lal', 'Lalb_Chr20g0107751' => 'lal', 'Lalb_Chr20g0118371' => 'lal', 'Lj1g0010239' => 'lja', 'Lj1g0017101' => 'lja', 'Lj2A1178G40' => 'lonja', 'Lj2A54G84' => 'lonja', 'Lj2g0015248' => 'lja', 'Lj3A761T51' => 'lonja', 'Lj6g0018116' => 'lja', 'Lsat_1_v5_gn_4_136040' => 'lsa', 'Lsat_1_v5_gn_5_187461' => 'lsa', 'Lsat_1_v5_gn_5_77001' => 'lsa', 'Lsat_1_v5_gn_9_4461' => 'lsa', 'Manes.01G210100' => 'mes', 'Manes.03G185600' => 'mes', 'Manes.05G073300' => 'mes', 'Manes.09G120300' => 'mes', 'Manes.15G022100' => 'mes', 'Mapoly0096s0053' => 'mpo', 'MBI03_g14058_MAGBIO' => 'mbi', 'MBI03_g33876_MAGBIO' => 'mbi', 'MBI03_g36854_MAGBIO' => 'mbi', 'MBI17_g11997_MAGBIO' => 'mbi', 'MD03G1269000' => 'mdo', 'MD04G1179600' => 'mdo', 'MD11G1289800' => 'mdo', 'MD12G1194700' => 'mdo', 'MD13G1182100' => 'mdo', 'MD13G1182200' => 'mdo', 'MD16G1182600' => 'mdo', 'Medtr2g021400' => 'mtr', 'Medtr2g021470' => 'mtr', 'Medtr2g105810' => 'mtr', 'Medtr3g033580' => 'mtr', 'Medtr6g007970' => 'mtr', 'Medtr7g056330' => 'mtr', 'Medtr7g074290' => 'mtr', 'Medtr7g074380' => 'mtr', 'Medtr7g094550' => 'mtr', 'Medtr8g069995' => 'mtr', 'MELO3C014345.2' => 'cme', 'MELO3C021395.2' => 'cme', 'Migut.D00262' => 'egut', 'Migut.G00257' => 'egut', 'MSTRG.21575' => 'ama', 'MSTRG.3985' => 'ama', 'Nitab4.5_0000295g0140' => 'nta', 'Nitab4.5_0000732g0140' => 'nta', 'Nitab4.5_0003162g0020' => 'nta', 'Nitab4.5_0006180g0090' => 'nta', 'Nitab4.5_0006390g0010' => 'nta', 'Nitab4.5_0007392g0040' => 'nta', 'Nn1g02140' => 'nnu', 'Nn4g26168' => 'nnu', 'Nn5g26754' => 'nnu', 'Oeu001433.1' => 'oeu', 'Oeu010299.2' => 'oeu', 'Oeu011171.1' => 'oeu', 'Oeu037675.1' => 'oeu', 'Oeu038359.1' => 'oeu', 'Oeu063834.1' => 'oeu', 'Oeu063835.1' => 'oeu', 'Os05g0312000' => 'osa', 'Os07g0211101' => 'osa', 'Os07g0211200' => 'osa', 'Os07g0681500' => 'osa', 'Peaxi162Scf00095g01015' => 'pax', 'Peaxi162Scf00104g00329' => 'pax', 'Peaxi162Scf00161g00137' => 'pax', 'PGR004G1665' => 'pgr', 'PGR031G2937' => 'pgr', 'PGR119G2145' => 'pgr', 'PGSC0003DMG400004351' => 'stu', 'PGSC0003DMG400014625' => 'stu', 'PGSC0003DMG401000943' => 'stu', 'Phvul.001G148600' => 'pvu', 'Phvul.004G001700' => 'pvu', 'Phvul.006G154900' => 'pvu', 'Phvul.008G078200' => 'pvu', 'Phvul.011G136500' => 'pvu', 'Potri.002G215600' => 'ptr', 'Potri.008G201600' => 'ptr', 'Potri.014G138400' => 'ptr', 'Potri.016G142500' => 'ptr', 'Pp3c16_10580' => 'ppa', 'Pp3c5_25280' => 'ppa', 'Prupe.1G150000' => 'ppe', 'Prupe.1G150100' => 'ppe', 'Prupe.6G299600' => 'ppe', 'Prupe.8G245000' => 'ppe', 'Psat0s4927g0040' => 'psa', 'Psat1g052080' => 'psa', 'Psat1g183800' => 'psa', 'Psat3g113840' => 'psa', 'Psat3g126120' => 'psa', 'Psat3g126160' => 'psa', 'Psat3g158760' => 'psa', 'Psat3g158840' => 'psa', 'PSO170G2858' => 'pso', 'PSO339G0606' => 'pso', 'PSO384G4709' => 'pso', 'PSO407G0334' => 'pso', 'QL04p040276' => 'qlo', 'QL06p005458' => 'qlo', 'QL06p005472' => 'qlo', 'QL07p030546' => 'qlo', 'QL07p031519' => 'qlo', 'QL09p050949' => 'qlo', 'QL09p050966' => 'qlo', 'QL09p051067' => 'qlo', 'QL12p022706' => 'qlo', 'RcHm_v2.0_Chr2g0119601' => 'rch', 'RcHm_v2.0_Chr3g0459591' => 'rch', 'RcHm_v2.0_Chr4g0418521' => 'rch', 'RcHm_v2.0_Chr4g0418531' => 'rch', 'RcHm_v2.0_Chr4g0418541' => 'rch', 'RcHm_v2.0_Chr6g0291641' => 'rch', 'Rhsim01G0086300' => 'rsi', 'Rhsim01G0276300' => 'rsi', 'Rhsim01G0276500' => 'rsi', 'Rhsim04G0207700' => 'rsi', 'Rhsim05G0234500' => 'rsi', 'Rhsim13G0022400' => 'rsi', 'Sabra02G0167900' => 'sbr', 'Sabra04G0158500' => 'sbr', 'Sabra08G0159800' => 'sbr', 'Sabra10G0011500' => 'sbr', 'Sabra14G0104400' => 'sbr', 'SalBow2G2440' => 'sbo', 'SalBow4G2265' => 'sbo', 'Sc02g0000060' => 'sci', 'Sc05g0005020' => 'sci', 'Sc13g0003890' => 'sci', 'Sed0014865' => 'sed', 'Sed0017224' => 'sed', 'Sed0026391' => 'sed', 'SEGI_00063' => 'sgi', 'SEGI_10967' => 'sgi', 'SEGI_17510' => 'sgi', 'SEGI_24396' => 'sgi', 'SEGI_39719' => 'sgi', 'SEGI_41392' => 'sgi', 'SGA_v2.0_scaffold11G05794' => 'sas', 'SGA_v2.0_scaffold142G35607' => 'sas', 'SGA_v2.0_scaffold1G00447' => 'sas', 'SHI15388' => 'shi', 'SHI15394' => 'shi', 'SHI15396' => 'shi', 'SHI15399' => 'shi', 'SMO343G0151' => 'smo', 'SMO367G1118' => 'smo', 'Solyc01g080200.3' => 'sly', 'Solyc06g008960.3' => 'sly', 'Solyc09g064780.3' => 'sly', 'Sopen01g031980' => 'spe', 'Sopen06g003710' => 'spe', 'Sopen09g026460' => 'spe', 'Sp3g21240' => 'spa', 'Sp4g30030' => 'spa', 'TAR365G0022' => 'tar', 'TAR365G1023' => 'tar', 'TAR365G1253' => 'tar', 'TAR623G0078' => 'tar', 'TAR623G1721' => 'tar', 'TAR633G0959' => 'tar', 'THA.LOC104802225' => 'tha', 'THA.LOC104804769' => 'tha', 'THA.LOC104808660' => 'tha', 'THA.LOC104812792' => 'tha', 'Thecc.01G284000' => 'tca', 'Thecc.04G220600' => 'tca', 'Thecc.05G268900' => 'tca', 'Thecc.08G171100' => 'tca', 'Thhalv10001284m.g' => 'esa', 'Thhalv10019912m.g' => 'esa', 'TPR.G14189' => 'tpr', 'TPR.G18110' => 'tpr', 'TPR.G18130' => 'tpr', 'TPR.G18131' => 'tpr', 'TPR.G18140' => 'tpr', 'TPR.G24282' => 'tpr', 'TPR.G25221' => 'tpr', 'TPR.G29267' => 'tpr', 'TPR.G35315' => 'tpr', 'TPR.G36173' => 'tpr', 'TWI09G0794' => 'twi', 'TWI59G1348' => 'twi', 'TWI74G0430' => 'twi', 'unitig_26.g8940' => 'ugi', 'unitig_749.g13744' => 'ugi', 'unitig_749.g13745' => 'ugi', 'vmacro08269' => 'vma', 'vmacro14937' => 'vma', 'vmacro20401' => 'vma', 'VMungo0464G1349' => 'vmu', 'VMungo0540G0289' => 'vmu', 'VMungo1215G1590' => 'vmu', 'VMungo1309G0221' => 'vmu', 'VMungo1309G2815' => 'vmu', 'VMungo1383G0239' => 'vmu', 'VMungo1383G2910' => 'vmu', 'Zm00001eb095270' => 'zma', 'Zm00001eb095280' => 'zma', 'Zm00001eb111630' => 'zma', 'Zm00001eb237080' => 'zma', 'Zm00001eb273740' => 'zma', 'Zm00001eb285040' => 'zma', 'Zm00001eb330790' => 'zma', 'Zm00001eb337380' => 'zma' ), 'gf_id' => 'HOM05D001484', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001484' ), 'data_identifier' => 'HOM05D001484', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001484', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p31500' => 'bna', 'A05p00020' => 'bna', 'A07p08820' => 'bna', 'Aa31LG4G3300' => 'aar', 'Aa31LG8G10030' => 'aar', 'Actinidia00731' => 'ach', 'Actinidia11473' => 'ach', 'Actinidia23469' => 'ach', 'Actinidia24318' => 'ach', 'Actinidia40196' => 'ach', 'Actinidia40197' => 'ach', 'Actinidia40198' => 'ach', 'Ah.08g212990' => 'amhyb', 'Ah.15g091720' => 'amhyb', 'AL3G38260' => 'aly', 'AL4G47710' => 'aly', 'Aqoxy2G00671' => 'aox', 'Aqoxy2G03236' => 'aox', 'arahy.Tifrunner.gnm1.ann1.05IDCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KR684' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATY3SJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK6QJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6APGL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IDT7Z9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM073U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ0R87' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LE7RV4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT4QRX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V5ENPK' => 'arhy', 'AT2G48110' => 'ath', 'AT3G23590' => 'ath', 'ATR0626G186' => 'atr', 'ATR1127G141' => 'atr', 'Atru.chr4.2583' => 'acertr', 'Atru.chr5.1358' => 'acertr', 'Atru.chr5.1359' => 'acertr', 'Atru.chr8.46' => 'acertr', 'AUR62002640' => 'cqu', 'AUR62030055' => 'cqu', 'AUR62033713' => 'cqu', 'AUR62033714' => 'cqu', 'AUR62036795' => 'cqu', 'AUR62039891' => 'cqu', 'BcaB02g08737' => 'bca', 'BcaB04g20441' => 'bca', 'BcaB06g26509' => 'bca', 'BcaB06g26510' => 'bca', 'BcaB06g26511' => 'bca', 'BcaB06g26512' => 'bca', 'BcaB06g26513' => 'bca', 'BcaC02g12564' => 'bca', 'BcaC02g12565' => 'bca', 'BcaC02g12794' => 'bca', 'BcaC02g12795' => 'bca', 'BcaC02g12796' => 'bca', 'BcaC06g35541' => 'bca', 'BNapus_Darmor_BZH_scaffold_188p00080' => 'bna', 'BNapus_Darmor_BZH_scaffold_188p00090' => 'bna', 'BolC1t03972H' => 'bol', 'BolC1t03973H' => 'bol', 'BolC4t21680H' => 'bol', 'BolC7t41863H' => 'bol', 'BolSC55t61227H' => 'bol', 'BolSC55t61228H' => 'bol', 'BraA01t03278Z' => 'bra', 'BraA05t18998Z' => 'bra', 'BraA07t28673Z' => 'bra', 'C01p40150' => 'bna', 'C05p12370' => 'bna', 'C07p13680' => 'bna', 'CAN.G1006.16' => 'can', 'CAN.G1006.17' => 'can', 'CAN.G1170.2' => 'can', 'CAN.G962.7' => 'can', 'CANSAT25G2179' => 'cansat', 'CANSAT78G1573' => 'cansat', 'CARHR099510' => 'chi', 'CARHR143510' => 'chi', 'Carub.0003s2380' => 'cru', 'Carub.0004s3082' => 'cru', 'Ca_00614_v3' => 'car', 'Ca_07801_v3' => 'car', 'Ca_08567_v3' => 'car', 'Ca_09571_v3' => 'car', 'CBR_g19290' => 'cbr', 'Cc01_g19770' => 'ccan', 'Cc03_g03030' => 'ccan', 'CDE07G0968' => 'cde', 'CDE09G1441' => 'cde', 'Cfa006103' => 'cfa', 'Cfa015573' => 'cfa', 'Cfa016988' => 'cfa', 'Ciclev10006738m.g' => 'ccl', 'Ciclev10010920m.g' => 'ccl', 'Ciclev10018517m.g' => 'ccl', 'CiPaw.01G159200' => 'cil', 'CiPaw.02G091000' => 'cil', 'CiPaw.02G091100' => 'cil', 'CiPaw.08G103100' => 'cil', 'CiPaw.09G224900' => 'cil', 'ClCG06G005740' => 'cla', 'ClCG07G000090' => 'cla', 'ClCG07G000100' => 'cla', 'COL.COLO4_09143' => 'col', 'COL.COLO4_25124' => 'col', 'Cpa.g.sc16.34' => 'cpa', 'Cpa.g.sc3504.1' => 'cpa', 'Cpa.g.sc60.37' => 'cpa', 'CsaV3_6G018520' => 'csa', 'CsaV3_6G036860' => 'csa', 'CSS0001072' => 'camsi', 'CSS0020208' => 'camsi', 'CSS0021253' => 'camsi', 'CSS0022190' => 'camsi', 'CSS0036150' => 'camsi', 'CSS0040442' => 'camsi', 'CSS0042300' => 'camsi', 'CSS0045298' => 'camsi', 'DCAR_012449' => 'dca', 'DCAR_018405' => 'dca', 'DCAR_024573' => 'dca', 'DCAR_030591' => 'dca', 'Dinv16926' => 'din', 'Dinv32963' => 'din', 'Dinv38382' => 'din', 'Dinv38383' => 'din', 'Duzib133G0974' => 'dzi', 'Duzib138G1867' => 'dzi', 'Duzib211G0420' => 'dzi', 'Duzib212G0930' => 'dzi', 'ECA234G1645' => 'eca', 'ECA247G3467' => 'eca', 'ECA248G1703' => 'eca', 'EL10Ac3g06327' => 'bvu', 'EL10Ac7g17204' => 'bvu', 'Eucgr.A00855' => 'egr', 'Eucgr.A00858' => 'egr', 'Eucgr.H01520' => 'egr', 'Eucgr.H03604' => 'egr', 'Eucgr.L03465' => 'egr', 'Eucgr.L03466' => 'egr', 'FAN01G0988' => 'fan', 'FAN02G3892' => 'fan', 'FAN05G3381' => 'fan', 'FAN07G0967' => 'fan', 'FAN07G1493' => 'fan', 'FAN08G3125' => 'fan', 'FAN09G0402' => 'fan', 'FAN12G2594' => 'fan', 'FAN12G3879' => 'fan', 'FAN14G1546' => 'fan', 'FAN15G3626' => 'fan', 'FAN17G0588' => 'fan', 'FAN17G0609' => 'fan', 'FAN18G2817' => 'fan', 'FAN19G1305' => 'fan', 'FAN20G1787' => 'fan', 'FAN22G0073' => 'fan', 'FAN22G0352' => 'fan', 'FAN22G0368' => 'fan', 'FAN22G2273' => 'fan', 'FAN24G1998' => 'fan', 'FAN27G1317' => 'fan', 'FvH4_2g23980' => 'fve', 'FvH4_4g14380' => 'fve', 'FvH4_4g14390' => 'fve', 'FvH4_6g09250' => 'fve', 'Glyma.03G151100' => 'gma', 'Glyma.04G122550' => 'gma', 'Glyma.05G001600' => 'gma', 'Glyma.09G270766' => 'gma', 'Glyma.09G270832' => 'gma', 'Glyma.13G209800' => 'gma', 'Glyma.15G102800' => 'gma', 'Glyma.18G218900' => 'gma', 'Glyma.19G001500' => 'gma', 'Glyma.19G153600' => 'gma', 'Gohir.A02G028600' => 'ghi', 'Gohir.A08G045000' => 'ghi', 'Gohir.A11G120500' => 'ghi', 'Gohir.A12G006200' => 'ghi', 'Gohir.A12G006250' => 'ghi', 'Gohir.D02G036300' => 'ghi', 'Gohir.D08G054700' => 'ghi', 'Gohir.D11G125600' => 'ghi', 'Gohir.D12G005700' => 'ghi', 'Gorai.004G055200' => 'gra', 'Gorai.005G040400' => 'gra', 'Gorai.007G134500' => 'gra', 'Gorai.008G005500' => 'gra', 'GSVIVG01011094001' => 'vvi', 'GSVIVG01017879001' => 'vvi', 'GSVIVG01025988001' => 'vvi', 'GSVIVG01029847001' => 'vvi', 'HanXRQChr10g0282901' => 'han', 'HanXRQChr10g0310371' => 'han', 'HanXRQChr10g0315041' => 'han', 'HanXRQChr11g0327651' => 'han', 'HanXRQChr12g0359391' => 'han', 'Haze_00972' => 'cav', 'Haze_00973' => 'cav', 'Haze_00974' => 'cav', 'Haze_04747' => 'cav', 'Haze_04749' => 'cav', 'Haze_04750' => 'cav', 'Haze_21217' => 'cav', 'Hma1.2p1_1037F.1_g250680' => 'hma', 'Hma1.2p1_1644F.1_g295320' => 'hma', 'HPP92_011322' => 'vpl', 'HPP92_011323' => 'vpl', 'HPP92_011324' => 'vpl', 'HPP92_011325' => 'vpl', 'HPP92_011326' => 'vpl', 'Hund12205' => 'sun', 'Hund17957' => 'sun', 'Lalb_Chr06g0176771' => 'lal', 'Lalb_Chr18g0056021' => 'lal', 'Lalb_Chr18g0056031' => 'lal', 'Lalb_Chr18g0056041' => 'lal', 'Lalb_Chr20g0107751' => 'lal', 'Lalb_Chr20g0118371' => 'lal', 'Lj1g0010239' => 'lja', 'Lj1g0017101' => 'lja', 'Lj2A1178G40' => 'lonja', 'Lj2A54G84' => 'lonja', 'Lj2g0015248' => 'lja', 'Lj3A761T51' => 'lonja', 'Lj6g0018116' => 'lja', 'Lsat_1_v5_gn_4_136040' => 'lsa', 'Lsat_1_v5_gn_5_187461' => 'lsa', 'Lsat_1_v5_gn_5_77001' => 'lsa', 'Lsat_1_v5_gn_9_4461' => 'lsa', 'Manes.01G210100' => 'mes', 'Manes.03G185600' => 'mes', 'Manes.05G073300' => 'mes', 'Manes.09G120300' => 'mes', 'Manes.15G022100' => 'mes', 'Mapoly0096s0053' => 'mpo', 'MBI03_g14058_MAGBIO' => 'mbi', 'MBI03_g33876_MAGBIO' => 'mbi', 'MBI03_g36854_MAGBIO' => 'mbi', 'MBI17_g11997_MAGBIO' => 'mbi', 'MD03G1269000' => 'mdo', 'MD04G1179600' => 'mdo', 'MD11G1289800' => 'mdo', 'MD12G1194700' => 'mdo', 'MD13G1182100' => 'mdo', 'MD13G1182200' => 'mdo', 'MD16G1182600' => 'mdo', 'Medtr2g021400' => 'mtr', 'Medtr2g021470' => 'mtr', 'Medtr2g105810' => 'mtr', 'Medtr3g033580' => 'mtr', 'Medtr6g007970' => 'mtr', 'Medtr7g056330' => 'mtr', 'Medtr7g074290' => 'mtr', 'Medtr7g074380' => 'mtr', 'Medtr7g094550' => 'mtr', 'Medtr8g069995' => 'mtr', 'MELO3C014345.2' => 'cme', 'MELO3C021395.2' => 'cme', 'Migut.D00262' => 'egut', 'Migut.G00257' => 'egut', 'MSTRG.21575' => 'ama', 'MSTRG.3985' => 'ama', 'Nitab4.5_0000295g0140' => 'nta', 'Nitab4.5_0000732g0140' => 'nta', 'Nitab4.5_0003162g0020' => 'nta', 'Nitab4.5_0006180g0090' => 'nta', 'Nitab4.5_0006390g0010' => 'nta', 'Nitab4.5_0007392g0040' => 'nta', 'Nn1g02140' => 'nnu', 'Nn4g26168' => 'nnu', 'Nn5g26754' => 'nnu', 'Oeu001433.1' => 'oeu', 'Oeu010299.2' => 'oeu', 'Oeu011171.1' => 'oeu', 'Oeu037675.1' => 'oeu', 'Oeu038359.1' => 'oeu', 'Oeu063834.1' => 'oeu', 'Oeu063835.1' => 'oeu', 'Os05g0312000' => 'osa', 'Os07g0211101' => 'osa', 'Os07g0211200' => 'osa', 'Os07g0681500' => 'osa', 'Peaxi162Scf00095g01015' => 'pax', 'Peaxi162Scf00104g00329' => 'pax', 'Peaxi162Scf00161g00137' => 'pax', 'PGR004G1665' => 'pgr', 'PGR031G2937' => 'pgr', 'PGR119G2145' => 'pgr', 'PGSC0003DMG400004351' => 'stu', 'PGSC0003DMG400014625' => 'stu', 'PGSC0003DMG401000943' => 'stu', 'Phvul.001G148600' => 'pvu', 'Phvul.004G001700' => 'pvu', 'Phvul.006G154900' => 'pvu', 'Phvul.008G078200' => 'pvu', 'Phvul.011G136500' => 'pvu', 'Potri.002G215600' => 'ptr', 'Potri.008G201600' => 'ptr', 'Potri.014G138400' => 'ptr', 'Potri.016G142500' => 'ptr', 'Pp3c16_10580' => 'ppa', 'Pp3c5_25280' => 'ppa', 'Prupe.1G150000' => 'ppe', 'Prupe.1G150100' => 'ppe', 'Prupe.6G299600' => 'ppe', 'Prupe.8G245000' => 'ppe', 'Psat0s4927g0040' => 'psa', 'Psat1g052080' => 'psa', 'Psat1g183800' => 'psa', 'Psat3g113840' => 'psa', 'Psat3g126120' => 'psa', 'Psat3g126160' => 'psa', 'Psat3g158760' => 'psa', 'Psat3g158840' => 'psa', 'PSO170G2858' => 'pso', 'PSO339G0606' => 'pso', 'PSO384G4709' => 'pso', 'PSO407G0334' => 'pso', 'QL04p040276' => 'qlo', 'QL06p005458' => 'qlo', 'QL06p005472' => 'qlo', 'QL07p030546' => 'qlo', 'QL07p031519' => 'qlo', 'QL09p050949' => 'qlo', 'QL09p050966' => 'qlo', 'QL09p051067' => 'qlo', 'QL12p022706' => 'qlo', 'RcHm_v2.0_Chr2g0119601' => 'rch', 'RcHm_v2.0_Chr3g0459591' => 'rch', 'RcHm_v2.0_Chr4g0418521' => 'rch', 'RcHm_v2.0_Chr4g0418531' => 'rch', 'RcHm_v2.0_Chr4g0418541' => 'rch', 'RcHm_v2.0_Chr6g0291641' => 'rch', 'Rhsim01G0086300' => 'rsi', 'Rhsim01G0276300' => 'rsi', 'Rhsim01G0276500' => 'rsi', 'Rhsim04G0207700' => 'rsi', 'Rhsim05G0234500' => 'rsi', 'Rhsim13G0022400' => 'rsi', 'Sabra02G0167900' => 'sbr', 'Sabra04G0158500' => 'sbr', 'Sabra08G0159800' => 'sbr', 'Sabra10G0011500' => 'sbr', 'Sabra14G0104400' => 'sbr', 'SalBow2G2440' => 'sbo', 'SalBow4G2265' => 'sbo', 'Sc02g0000060' => 'sci', 'Sc05g0005020' => 'sci', 'Sc13g0003890' => 'sci', 'Sed0014865' => 'sed', 'Sed0017224' => 'sed', 'Sed0026391' => 'sed', 'SEGI_00063' => 'sgi', 'SEGI_10967' => 'sgi', 'SEGI_17510' => 'sgi', 'SEGI_24396' => 'sgi', 'SEGI_39719' => 'sgi', 'SEGI_41392' => 'sgi', 'SGA_v2.0_scaffold11G05794' => 'sas', 'SGA_v2.0_scaffold142G35607' => 'sas', 'SGA_v2.0_scaffold1G00447' => 'sas', 'SHI15388' => 'shi', 'SHI15394' => 'shi', 'SHI15396' => 'shi', 'SHI15399' => 'shi', 'SMO343G0151' => 'smo', 'SMO367G1118' => 'smo', 'Solyc01g080200.3' => 'sly', 'Solyc06g008960.3' => 'sly', 'Solyc09g064780.3' => 'sly', 'Sopen01g031980' => 'spe', 'Sopen06g003710' => 'spe', 'Sopen09g026460' => 'spe', 'Sp3g21240' => 'spa', 'Sp4g30030' => 'spa', 'TAR365G0022' => 'tar', 'TAR365G1023' => 'tar', 'TAR365G1253' => 'tar', 'TAR623G0078' => 'tar', 'TAR623G1721' => 'tar', 'TAR633G0959' => 'tar', 'THA.LOC104802225' => 'tha', 'THA.LOC104804769' => 'tha', 'THA.LOC104808660' => 'tha', 'THA.LOC104812792' => 'tha', 'Thecc.01G284000' => 'tca', 'Thecc.04G220600' => 'tca', 'Thecc.05G268900' => 'tca', 'Thecc.08G171100' => 'tca', 'Thhalv10001284m.g' => 'esa', 'Thhalv10019912m.g' => 'esa', 'TPR.G14189' => 'tpr', 'TPR.G18110' => 'tpr', 'TPR.G18130' => 'tpr', 'TPR.G18131' => 'tpr', 'TPR.G18140' => 'tpr', 'TPR.G24282' => 'tpr', 'TPR.G25221' => 'tpr', 'TPR.G29267' => 'tpr', 'TPR.G35315' => 'tpr', 'TPR.G36173' => 'tpr', 'TWI09G0794' => 'twi', 'TWI59G1348' => 'twi', 'TWI74G0430' => 'twi', 'unitig_26.g8940' => 'ugi', 'unitig_749.g13744' => 'ugi', 'unitig_749.g13745' => 'ugi', 'vmacro08269' => 'vma', 'vmacro14937' => 'vma', 'vmacro20401' => 'vma', 'VMungo0464G1349' => 'vmu', 'VMungo0540G0289' => 'vmu', 'VMungo1215G1590' => 'vmu', 'VMungo1309G0221' => 'vmu', 'VMungo1309G2815' => 'vmu', 'VMungo1383G0239' => 'vmu', 'VMungo1383G2910' => 'vmu', 'Zm00001eb095270' => 'zma', 'Zm00001eb095280' => 'zma', 'Zm00001eb111630' => 'zma', 'Zm00001eb237080' => 'zma', 'Zm00001eb273740' => 'zma', 'Zm00001eb285040' => 'zma', 'Zm00001eb330790' => 'zma', 'Zm00001eb337380' => 'zma' ) $gf_id = 'HOM05D001484' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001484' ) $data_identifier = 'HOM05D001484' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 2, 'aly' => (int) 2, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 22, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 7, 'hma' => (int) 2, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 7, 'mtr' => (int) 10, 'cme' => (int) 2, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 4, 'ppa' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 4, 'qlo' => (int) 9, 'rch' => (int) 6, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 10, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 7, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb337380' $species_info = array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ) $local_species = 'col' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001484', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p31500' => 'bna', 'A05p00020' => 'bna', 'A07p08820' => 'bna', 'Aa31LG4G3300' => 'aar', 'Aa31LG8G10030' => 'aar', 'Actinidia00731' => 'ach', 'Actinidia11473' => 'ach', 'Actinidia23469' => 'ach', 'Actinidia24318' => 'ach', 'Actinidia40196' => 'ach', 'Actinidia40197' => 'ach', 'Actinidia40198' => 'ach', 'Ah.08g212990' => 'amhyb', 'Ah.15g091720' => 'amhyb', 'AL3G38260' => 'aly', 'AL4G47710' => 'aly', 'Aqoxy2G00671' => 'aox', 'Aqoxy2G03236' => 'aox', 'arahy.Tifrunner.gnm1.ann1.05IDCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KR684' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATY3SJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK6QJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6APGL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IDT7Z9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM073U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ0R87' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LE7RV4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT4QRX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V5ENPK' => 'arhy', 'AT2G48110' => 'ath', 'AT3G23590' => 'ath', 'ATR0626G186' => 'atr', 'ATR1127G141' => 'atr', 'Atru.chr4.2583' => 'acertr', 'Atru.chr5.1358' => 'acertr', 'Atru.chr5.1359' => 'acertr', 'Atru.chr8.46' => 'acertr', 'AUR62002640' => 'cqu', 'AUR62030055' => 'cqu', 'AUR62033713' => 'cqu', 'AUR62033714' => 'cqu', 'AUR62036795' => 'cqu', 'AUR62039891' => 'cqu', 'BcaB02g08737' => 'bca', 'BcaB04g20441' => 'bca', 'BcaB06g26509' => 'bca', 'BcaB06g26510' => 'bca', 'BcaB06g26511' => 'bca', 'BcaB06g26512' => 'bca', 'BcaB06g26513' => 'bca', 'BcaC02g12564' => 'bca', 'BcaC02g12565' => 'bca', 'BcaC02g12794' => 'bca', 'BcaC02g12795' => 'bca', 'BcaC02g12796' => 'bca', 'BcaC06g35541' => 'bca', 'BNapus_Darmor_BZH_scaffold_188p00080' => 'bna', 'BNapus_Darmor_BZH_scaffold_188p00090' => 'bna', 'BolC1t03972H' => 'bol', 'BolC1t03973H' => 'bol', 'BolC4t21680H' => 'bol', 'BolC7t41863H' => 'bol', 'BolSC55t61227H' => 'bol', 'BolSC55t61228H' => 'bol', 'BraA01t03278Z' => 'bra', 'BraA05t18998Z' => 'bra', 'BraA07t28673Z' => 'bra', 'C01p40150' => 'bna', 'C05p12370' => 'bna', 'C07p13680' => 'bna', 'CAN.G1006.16' => 'can', 'CAN.G1006.17' => 'can', 'CAN.G1170.2' => 'can', 'CAN.G962.7' => 'can', 'CANSAT25G2179' => 'cansat', 'CANSAT78G1573' => 'cansat', 'CARHR099510' => 'chi', 'CARHR143510' => 'chi', 'Carub.0003s2380' => 'cru', 'Carub.0004s3082' => 'cru', 'Ca_00614_v3' => 'car', 'Ca_07801_v3' => 'car', 'Ca_08567_v3' => 'car', 'Ca_09571_v3' => 'car', 'CBR_g19290' => 'cbr', 'Cc01_g19770' => 'ccan', 'Cc03_g03030' => 'ccan', 'CDE07G0968' => 'cde', 'CDE09G1441' => 'cde', 'Cfa006103' => 'cfa', 'Cfa015573' => 'cfa', 'Cfa016988' => 'cfa', 'Ciclev10006738m.g' => 'ccl', 'Ciclev10010920m.g' => 'ccl', 'Ciclev10018517m.g' => 'ccl', 'CiPaw.01G159200' => 'cil', 'CiPaw.02G091000' => 'cil', 'CiPaw.02G091100' => 'cil', 'CiPaw.08G103100' => 'cil', 'CiPaw.09G224900' => 'cil', 'ClCG06G005740' => 'cla', 'ClCG07G000090' => 'cla', 'ClCG07G000100' => 'cla', 'COL.COLO4_09143' => 'col', 'COL.COLO4_25124' => 'col', 'Cpa.g.sc16.34' => 'cpa', 'Cpa.g.sc3504.1' => 'cpa', 'Cpa.g.sc60.37' => 'cpa', 'CsaV3_6G018520' => 'csa', 'CsaV3_6G036860' => 'csa', 'CSS0001072' => 'camsi', 'CSS0020208' => 'camsi', 'CSS0021253' => 'camsi', 'CSS0022190' => 'camsi', 'CSS0036150' => 'camsi', 'CSS0040442' => 'camsi', 'CSS0042300' => 'camsi', 'CSS0045298' => 'camsi', 'DCAR_012449' => 'dca', 'DCAR_018405' => 'dca', 'DCAR_024573' => 'dca', 'DCAR_030591' => 'dca', 'Dinv16926' => 'din', 'Dinv32963' => 'din', 'Dinv38382' => 'din', 'Dinv38383' => 'din', 'Duzib133G0974' => 'dzi', 'Duzib138G1867' => 'dzi', 'Duzib211G0420' => 'dzi', 'Duzib212G0930' => 'dzi', 'ECA234G1645' => 'eca', 'ECA247G3467' => 'eca', 'ECA248G1703' => 'eca', 'EL10Ac3g06327' => 'bvu', 'EL10Ac7g17204' => 'bvu', 'Eucgr.A00855' => 'egr', 'Eucgr.A00858' => 'egr', 'Eucgr.H01520' => 'egr', 'Eucgr.H03604' => 'egr', 'Eucgr.L03465' => 'egr', 'Eucgr.L03466' => 'egr', 'FAN01G0988' => 'fan', 'FAN02G3892' => 'fan', 'FAN05G3381' => 'fan', 'FAN07G0967' => 'fan', 'FAN07G1493' => 'fan', 'FAN08G3125' => 'fan', 'FAN09G0402' => 'fan', 'FAN12G2594' => 'fan', 'FAN12G3879' => 'fan', 'FAN14G1546' => 'fan', 'FAN15G3626' => 'fan', 'FAN17G0588' => 'fan', 'FAN17G0609' => 'fan', 'FAN18G2817' => 'fan', 'FAN19G1305' => 'fan', 'FAN20G1787' => 'fan', 'FAN22G0073' => 'fan', 'FAN22G0352' => 'fan', 'FAN22G0368' => 'fan', 'FAN22G2273' => 'fan', 'FAN24G1998' => 'fan', 'FAN27G1317' => 'fan', 'FvH4_2g23980' => 'fve', 'FvH4_4g14380' => 'fve', 'FvH4_4g14390' => 'fve', 'FvH4_6g09250' => 'fve', 'Glyma.03G151100' => 'gma', 'Glyma.04G122550' => 'gma', 'Glyma.05G001600' => 'gma', 'Glyma.09G270766' => 'gma', 'Glyma.09G270832' => 'gma', 'Glyma.13G209800' => 'gma', 'Glyma.15G102800' => 'gma', 'Glyma.18G218900' => 'gma', 'Glyma.19G001500' => 'gma', 'Glyma.19G153600' => 'gma', 'Gohir.A02G028600' => 'ghi', 'Gohir.A08G045000' => 'ghi', 'Gohir.A11G120500' => 'ghi', 'Gohir.A12G006200' => 'ghi', 'Gohir.A12G006250' => 'ghi', 'Gohir.D02G036300' => 'ghi', 'Gohir.D08G054700' => 'ghi', 'Gohir.D11G125600' => 'ghi', 'Gohir.D12G005700' => 'ghi', 'Gorai.004G055200' => 'gra', 'Gorai.005G040400' => 'gra', 'Gorai.007G134500' => 'gra', 'Gorai.008G005500' => 'gra', 'GSVIVG01011094001' => 'vvi', 'GSVIVG01017879001' => 'vvi', 'GSVIVG01025988001' => 'vvi', 'GSVIVG01029847001' => 'vvi', 'HanXRQChr10g0282901' => 'han', 'HanXRQChr10g0310371' => 'han', 'HanXRQChr10g0315041' => 'han', 'HanXRQChr11g0327651' => 'han', 'HanXRQChr12g0359391' => 'han', 'Haze_00972' => 'cav', 'Haze_00973' => 'cav', 'Haze_00974' => 'cav', 'Haze_04747' => 'cav', 'Haze_04749' => 'cav', 'Haze_04750' => 'cav', 'Haze_21217' => 'cav', 'Hma1.2p1_1037F.1_g250680' => 'hma', 'Hma1.2p1_1644F.1_g295320' => 'hma', 'HPP92_011322' => 'vpl', 'HPP92_011323' => 'vpl', 'HPP92_011324' => 'vpl', 'HPP92_011325' => 'vpl', 'HPP92_011326' => 'vpl', 'Hund12205' => 'sun', 'Hund17957' => 'sun', 'Lalb_Chr06g0176771' => 'lal', 'Lalb_Chr18g0056021' => 'lal', 'Lalb_Chr18g0056031' => 'lal', 'Lalb_Chr18g0056041' => 'lal', 'Lalb_Chr20g0107751' => 'lal', 'Lalb_Chr20g0118371' => 'lal', 'Lj1g0010239' => 'lja', 'Lj1g0017101' => 'lja', 'Lj2A1178G40' => 'lonja', 'Lj2A54G84' => 'lonja', 'Lj2g0015248' => 'lja', 'Lj3A761T51' => 'lonja', 'Lj6g0018116' => 'lja', 'Lsat_1_v5_gn_4_136040' => 'lsa', 'Lsat_1_v5_gn_5_187461' => 'lsa', 'Lsat_1_v5_gn_5_77001' => 'lsa', 'Lsat_1_v5_gn_9_4461' => 'lsa', 'Manes.01G210100' => 'mes', 'Manes.03G185600' => 'mes', 'Manes.05G073300' => 'mes', 'Manes.09G120300' => 'mes', 'Manes.15G022100' => 'mes', 'Mapoly0096s0053' => 'mpo', 'MBI03_g14058_MAGBIO' => 'mbi', 'MBI03_g33876_MAGBIO' => 'mbi', 'MBI03_g36854_MAGBIO' => 'mbi', 'MBI17_g11997_MAGBIO' => 'mbi', 'MD03G1269000' => 'mdo', 'MD04G1179600' => 'mdo', 'MD11G1289800' => 'mdo', 'MD12G1194700' => 'mdo', 'MD13G1182100' => 'mdo', 'MD13G1182200' => 'mdo', 'MD16G1182600' => 'mdo', 'Medtr2g021400' => 'mtr', 'Medtr2g021470' => 'mtr', 'Medtr2g105810' => 'mtr', 'Medtr3g033580' => 'mtr', 'Medtr6g007970' => 'mtr', 'Medtr7g056330' => 'mtr', 'Medtr7g074290' => 'mtr', 'Medtr7g074380' => 'mtr', 'Medtr7g094550' => 'mtr', 'Medtr8g069995' => 'mtr', 'MELO3C014345.2' => 'cme', 'MELO3C021395.2' => 'cme', 'Migut.D00262' => 'egut', 'Migut.G00257' => 'egut', 'MSTRG.21575' => 'ama', 'MSTRG.3985' => 'ama', 'Nitab4.5_0000295g0140' => 'nta', 'Nitab4.5_0000732g0140' => 'nta', 'Nitab4.5_0003162g0020' => 'nta', 'Nitab4.5_0006180g0090' => 'nta', 'Nitab4.5_0006390g0010' => 'nta', 'Nitab4.5_0007392g0040' => 'nta', 'Nn1g02140' => 'nnu', 'Nn4g26168' => 'nnu', 'Nn5g26754' => 'nnu', 'Oeu001433.1' => 'oeu', 'Oeu010299.2' => 'oeu', 'Oeu011171.1' => 'oeu', 'Oeu037675.1' => 'oeu', 'Oeu038359.1' => 'oeu', 'Oeu063834.1' => 'oeu', 'Oeu063835.1' => 'oeu', 'Os05g0312000' => 'osa', 'Os07g0211101' => 'osa', 'Os07g0211200' => 'osa', 'Os07g0681500' => 'osa', 'Peaxi162Scf00095g01015' => 'pax', 'Peaxi162Scf00104g00329' => 'pax', 'Peaxi162Scf00161g00137' => 'pax', 'PGR004G1665' => 'pgr', 'PGR031G2937' => 'pgr', 'PGR119G2145' => 'pgr', 'PGSC0003DMG400004351' => 'stu', 'PGSC0003DMG400014625' => 'stu', 'PGSC0003DMG401000943' => 'stu', 'Phvul.001G148600' => 'pvu', 'Phvul.004G001700' => 'pvu', 'Phvul.006G154900' => 'pvu', 'Phvul.008G078200' => 'pvu', 'Phvul.011G136500' => 'pvu', 'Potri.002G215600' => 'ptr', 'Potri.008G201600' => 'ptr', 'Potri.014G138400' => 'ptr', 'Potri.016G142500' => 'ptr', 'Pp3c16_10580' => 'ppa', 'Pp3c5_25280' => 'ppa', 'Prupe.1G150000' => 'ppe', 'Prupe.1G150100' => 'ppe', 'Prupe.6G299600' => 'ppe', 'Prupe.8G245000' => 'ppe', 'Psat0s4927g0040' => 'psa', 'Psat1g052080' => 'psa', 'Psat1g183800' => 'psa', 'Psat3g113840' => 'psa', 'Psat3g126120' => 'psa', 'Psat3g126160' => 'psa', 'Psat3g158760' => 'psa', 'Psat3g158840' => 'psa', 'PSO170G2858' => 'pso', 'PSO339G0606' => 'pso', 'PSO384G4709' => 'pso', 'PSO407G0334' => 'pso', 'QL04p040276' => 'qlo', 'QL06p005458' => 'qlo', 'QL06p005472' => 'qlo', 'QL07p030546' => 'qlo', 'QL07p031519' => 'qlo', 'QL09p050949' => 'qlo', 'QL09p050966' => 'qlo', 'QL09p051067' => 'qlo', 'QL12p022706' => 'qlo', 'RcHm_v2.0_Chr2g0119601' => 'rch', 'RcHm_v2.0_Chr3g0459591' => 'rch', 'RcHm_v2.0_Chr4g0418521' => 'rch', 'RcHm_v2.0_Chr4g0418531' => 'rch', 'RcHm_v2.0_Chr4g0418541' => 'rch', 'RcHm_v2.0_Chr6g0291641' => 'rch', 'Rhsim01G0086300' => 'rsi', 'Rhsim01G0276300' => 'rsi', 'Rhsim01G0276500' => 'rsi', 'Rhsim04G0207700' => 'rsi', 'Rhsim05G0234500' => 'rsi', 'Rhsim13G0022400' => 'rsi', 'Sabra02G0167900' => 'sbr', 'Sabra04G0158500' => 'sbr', 'Sabra08G0159800' => 'sbr', 'Sabra10G0011500' => 'sbr', 'Sabra14G0104400' => 'sbr', 'SalBow2G2440' => 'sbo', 'SalBow4G2265' => 'sbo', 'Sc02g0000060' => 'sci', 'Sc05g0005020' => 'sci', 'Sc13g0003890' => 'sci', 'Sed0014865' => 'sed', 'Sed0017224' => 'sed', 'Sed0026391' => 'sed', 'SEGI_00063' => 'sgi', 'SEGI_10967' => 'sgi', 'SEGI_17510' => 'sgi', 'SEGI_24396' => 'sgi', 'SEGI_39719' => 'sgi', 'SEGI_41392' => 'sgi', 'SGA_v2.0_scaffold11G05794' => 'sas', 'SGA_v2.0_scaffold142G35607' => 'sas', 'SGA_v2.0_scaffold1G00447' => 'sas', 'SHI15388' => 'shi', 'SHI15394' => 'shi', 'SHI15396' => 'shi', 'SHI15399' => 'shi', 'SMO343G0151' => 'smo', 'SMO367G1118' => 'smo', 'Solyc01g080200.3' => 'sly', 'Solyc06g008960.3' => 'sly', 'Solyc09g064780.3' => 'sly', 'Sopen01g031980' => 'spe', 'Sopen06g003710' => 'spe', 'Sopen09g026460' => 'spe', 'Sp3g21240' => 'spa', 'Sp4g30030' => 'spa', 'TAR365G0022' => 'tar', 'TAR365G1023' => 'tar', 'TAR365G1253' => 'tar', 'TAR623G0078' => 'tar', 'TAR623G1721' => 'tar', 'TAR633G0959' => 'tar', 'THA.LOC104802225' => 'tha', 'THA.LOC104804769' => 'tha', 'THA.LOC104808660' => 'tha', 'THA.LOC104812792' => 'tha', 'Thecc.01G284000' => 'tca', 'Thecc.04G220600' => 'tca', 'Thecc.05G268900' => 'tca', 'Thecc.08G171100' => 'tca', 'Thhalv10001284m.g' => 'esa', 'Thhalv10019912m.g' => 'esa', 'TPR.G14189' => 'tpr', 'TPR.G18110' => 'tpr', 'TPR.G18130' => 'tpr', 'TPR.G18131' => 'tpr', 'TPR.G18140' => 'tpr', 'TPR.G24282' => 'tpr', 'TPR.G25221' => 'tpr', 'TPR.G29267' => 'tpr', 'TPR.G35315' => 'tpr', 'TPR.G36173' => 'tpr', 'TWI09G0794' => 'twi', 'TWI59G1348' => 'twi', 'TWI74G0430' => 'twi', 'unitig_26.g8940' => 'ugi', 'unitig_749.g13744' => 'ugi', 'unitig_749.g13745' => 'ugi', 'vmacro08269' => 'vma', 'vmacro14937' => 'vma', 'vmacro20401' => 'vma', 'VMungo0464G1349' => 'vmu', 'VMungo0540G0289' => 'vmu', 'VMungo1215G1590' => 'vmu', 'VMungo1309G0221' => 'vmu', 'VMungo1309G2815' => 'vmu', 'VMungo1383G0239' => 'vmu', 'VMungo1383G2910' => 'vmu', 'Zm00001eb095270' => 'zma', 'Zm00001eb095280' => 'zma', 'Zm00001eb111630' => 'zma', 'Zm00001eb237080' => 'zma', 'Zm00001eb273740' => 'zma', 'Zm00001eb285040' => 'zma', 'Zm00001eb330790' => 'zma', 'Zm00001eb337380' => 'zma' ), 'gf_id' => 'HOM05D001484', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001484' ), 'data_identifier' => 'HOM05D001484', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001484', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p31500' => 'bna', 'A05p00020' => 'bna', 'A07p08820' => 'bna', 'Aa31LG4G3300' => 'aar', 'Aa31LG8G10030' => 'aar', 'Actinidia00731' => 'ach', 'Actinidia11473' => 'ach', 'Actinidia23469' => 'ach', 'Actinidia24318' => 'ach', 'Actinidia40196' => 'ach', 'Actinidia40197' => 'ach', 'Actinidia40198' => 'ach', 'Ah.08g212990' => 'amhyb', 'Ah.15g091720' => 'amhyb', 'AL3G38260' => 'aly', 'AL4G47710' => 'aly', 'Aqoxy2G00671' => 'aox', 'Aqoxy2G03236' => 'aox', 'arahy.Tifrunner.gnm1.ann1.05IDCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KR684' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATY3SJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK6QJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6APGL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IDT7Z9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM073U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ0R87' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LE7RV4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT4QRX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V5ENPK' => 'arhy', 'AT2G48110' => 'ath', 'AT3G23590' => 'ath', 'ATR0626G186' => 'atr', 'ATR1127G141' => 'atr', 'Atru.chr4.2583' => 'acertr', 'Atru.chr5.1358' => 'acertr', 'Atru.chr5.1359' => 'acertr', 'Atru.chr8.46' => 'acertr', 'AUR62002640' => 'cqu', 'AUR62030055' => 'cqu', 'AUR62033713' => 'cqu', 'AUR62033714' => 'cqu', 'AUR62036795' => 'cqu', 'AUR62039891' => 'cqu', 'BcaB02g08737' => 'bca', 'BcaB04g20441' => 'bca', 'BcaB06g26509' => 'bca', 'BcaB06g26510' => 'bca', 'BcaB06g26511' => 'bca', 'BcaB06g26512' => 'bca', 'BcaB06g26513' => 'bca', 'BcaC02g12564' => 'bca', 'BcaC02g12565' => 'bca', 'BcaC02g12794' => 'bca', 'BcaC02g12795' => 'bca', 'BcaC02g12796' => 'bca', 'BcaC06g35541' => 'bca', 'BNapus_Darmor_BZH_scaffold_188p00080' => 'bna', 'BNapus_Darmor_BZH_scaffold_188p00090' => 'bna', 'BolC1t03972H' => 'bol', 'BolC1t03973H' => 'bol', 'BolC4t21680H' => 'bol', 'BolC7t41863H' => 'bol', 'BolSC55t61227H' => 'bol', 'BolSC55t61228H' => 'bol', 'BraA01t03278Z' => 'bra', 'BraA05t18998Z' => 'bra', 'BraA07t28673Z' => 'bra', 'C01p40150' => 'bna', 'C05p12370' => 'bna', 'C07p13680' => 'bna', 'CAN.G1006.16' => 'can', 'CAN.G1006.17' => 'can', 'CAN.G1170.2' => 'can', 'CAN.G962.7' => 'can', 'CANSAT25G2179' => 'cansat', 'CANSAT78G1573' => 'cansat', 'CARHR099510' => 'chi', 'CARHR143510' => 'chi', 'Carub.0003s2380' => 'cru', 'Carub.0004s3082' => 'cru', 'Ca_00614_v3' => 'car', 'Ca_07801_v3' => 'car', 'Ca_08567_v3' => 'car', 'Ca_09571_v3' => 'car', 'CBR_g19290' => 'cbr', 'Cc01_g19770' => 'ccan', 'Cc03_g03030' => 'ccan', 'CDE07G0968' => 'cde', 'CDE09G1441' => 'cde', 'Cfa006103' => 'cfa', 'Cfa015573' => 'cfa', 'Cfa016988' => 'cfa', 'Ciclev10006738m.g' => 'ccl', 'Ciclev10010920m.g' => 'ccl', 'Ciclev10018517m.g' => 'ccl', 'CiPaw.01G159200' => 'cil', 'CiPaw.02G091000' => 'cil', 'CiPaw.02G091100' => 'cil', 'CiPaw.08G103100' => 'cil', 'CiPaw.09G224900' => 'cil', 'ClCG06G005740' => 'cla', 'ClCG07G000090' => 'cla', 'ClCG07G000100' => 'cla', 'COL.COLO4_09143' => 'col', 'COL.COLO4_25124' => 'col', 'Cpa.g.sc16.34' => 'cpa', 'Cpa.g.sc3504.1' => 'cpa', 'Cpa.g.sc60.37' => 'cpa', 'CsaV3_6G018520' => 'csa', 'CsaV3_6G036860' => 'csa', 'CSS0001072' => 'camsi', 'CSS0020208' => 'camsi', 'CSS0021253' => 'camsi', 'CSS0022190' => 'camsi', 'CSS0036150' => 'camsi', 'CSS0040442' => 'camsi', 'CSS0042300' => 'camsi', 'CSS0045298' => 'camsi', 'DCAR_012449' => 'dca', 'DCAR_018405' => 'dca', 'DCAR_024573' => 'dca', 'DCAR_030591' => 'dca', 'Dinv16926' => 'din', 'Dinv32963' => 'din', 'Dinv38382' => 'din', 'Dinv38383' => 'din', 'Duzib133G0974' => 'dzi', 'Duzib138G1867' => 'dzi', 'Duzib211G0420' => 'dzi', 'Duzib212G0930' => 'dzi', 'ECA234G1645' => 'eca', 'ECA247G3467' => 'eca', 'ECA248G1703' => 'eca', 'EL10Ac3g06327' => 'bvu', 'EL10Ac7g17204' => 'bvu', 'Eucgr.A00855' => 'egr', 'Eucgr.A00858' => 'egr', 'Eucgr.H01520' => 'egr', 'Eucgr.H03604' => 'egr', 'Eucgr.L03465' => 'egr', 'Eucgr.L03466' => 'egr', 'FAN01G0988' => 'fan', 'FAN02G3892' => 'fan', 'FAN05G3381' => 'fan', 'FAN07G0967' => 'fan', 'FAN07G1493' => 'fan', 'FAN08G3125' => 'fan', 'FAN09G0402' => 'fan', 'FAN12G2594' => 'fan', 'FAN12G3879' => 'fan', 'FAN14G1546' => 'fan', 'FAN15G3626' => 'fan', 'FAN17G0588' => 'fan', 'FAN17G0609' => 'fan', 'FAN18G2817' => 'fan', 'FAN19G1305' => 'fan', 'FAN20G1787' => 'fan', 'FAN22G0073' => 'fan', 'FAN22G0352' => 'fan', 'FAN22G0368' => 'fan', 'FAN22G2273' => 'fan', 'FAN24G1998' => 'fan', 'FAN27G1317' => 'fan', 'FvH4_2g23980' => 'fve', 'FvH4_4g14380' => 'fve', 'FvH4_4g14390' => 'fve', 'FvH4_6g09250' => 'fve', 'Glyma.03G151100' => 'gma', 'Glyma.04G122550' => 'gma', 'Glyma.05G001600' => 'gma', 'Glyma.09G270766' => 'gma', 'Glyma.09G270832' => 'gma', 'Glyma.13G209800' => 'gma', 'Glyma.15G102800' => 'gma', 'Glyma.18G218900' => 'gma', 'Glyma.19G001500' => 'gma', 'Glyma.19G153600' => 'gma', 'Gohir.A02G028600' => 'ghi', 'Gohir.A08G045000' => 'ghi', 'Gohir.A11G120500' => 'ghi', 'Gohir.A12G006200' => 'ghi', 'Gohir.A12G006250' => 'ghi', 'Gohir.D02G036300' => 'ghi', 'Gohir.D08G054700' => 'ghi', 'Gohir.D11G125600' => 'ghi', 'Gohir.D12G005700' => 'ghi', 'Gorai.004G055200' => 'gra', 'Gorai.005G040400' => 'gra', 'Gorai.007G134500' => 'gra', 'Gorai.008G005500' => 'gra', 'GSVIVG01011094001' => 'vvi', 'GSVIVG01017879001' => 'vvi', 'GSVIVG01025988001' => 'vvi', 'GSVIVG01029847001' => 'vvi', 'HanXRQChr10g0282901' => 'han', 'HanXRQChr10g0310371' => 'han', 'HanXRQChr10g0315041' => 'han', 'HanXRQChr11g0327651' => 'han', 'HanXRQChr12g0359391' => 'han', 'Haze_00972' => 'cav', 'Haze_00973' => 'cav', 'Haze_00974' => 'cav', 'Haze_04747' => 'cav', 'Haze_04749' => 'cav', 'Haze_04750' => 'cav', 'Haze_21217' => 'cav', 'Hma1.2p1_1037F.1_g250680' => 'hma', 'Hma1.2p1_1644F.1_g295320' => 'hma', 'HPP92_011322' => 'vpl', 'HPP92_011323' => 'vpl', 'HPP92_011324' => 'vpl', 'HPP92_011325' => 'vpl', 'HPP92_011326' => 'vpl', 'Hund12205' => 'sun', 'Hund17957' => 'sun', 'Lalb_Chr06g0176771' => 'lal', 'Lalb_Chr18g0056021' => 'lal', 'Lalb_Chr18g0056031' => 'lal', 'Lalb_Chr18g0056041' => 'lal', 'Lalb_Chr20g0107751' => 'lal', 'Lalb_Chr20g0118371' => 'lal', 'Lj1g0010239' => 'lja', 'Lj1g0017101' => 'lja', 'Lj2A1178G40' => 'lonja', 'Lj2A54G84' => 'lonja', 'Lj2g0015248' => 'lja', 'Lj3A761T51' => 'lonja', 'Lj6g0018116' => 'lja', 'Lsat_1_v5_gn_4_136040' => 'lsa', 'Lsat_1_v5_gn_5_187461' => 'lsa', 'Lsat_1_v5_gn_5_77001' => 'lsa', 'Lsat_1_v5_gn_9_4461' => 'lsa', 'Manes.01G210100' => 'mes', 'Manes.03G185600' => 'mes', 'Manes.05G073300' => 'mes', 'Manes.09G120300' => 'mes', 'Manes.15G022100' => 'mes', 'Mapoly0096s0053' => 'mpo', 'MBI03_g14058_MAGBIO' => 'mbi', 'MBI03_g33876_MAGBIO' => 'mbi', 'MBI03_g36854_MAGBIO' => 'mbi', 'MBI17_g11997_MAGBIO' => 'mbi', 'MD03G1269000' => 'mdo', 'MD04G1179600' => 'mdo', 'MD11G1289800' => 'mdo', 'MD12G1194700' => 'mdo', 'MD13G1182100' => 'mdo', 'MD13G1182200' => 'mdo', 'MD16G1182600' => 'mdo', 'Medtr2g021400' => 'mtr', 'Medtr2g021470' => 'mtr', 'Medtr2g105810' => 'mtr', 'Medtr3g033580' => 'mtr', 'Medtr6g007970' => 'mtr', 'Medtr7g056330' => 'mtr', 'Medtr7g074290' => 'mtr', 'Medtr7g074380' => 'mtr', 'Medtr7g094550' => 'mtr', 'Medtr8g069995' => 'mtr', 'MELO3C014345.2' => 'cme', 'MELO3C021395.2' => 'cme', 'Migut.D00262' => 'egut', 'Migut.G00257' => 'egut', 'MSTRG.21575' => 'ama', 'MSTRG.3985' => 'ama', 'Nitab4.5_0000295g0140' => 'nta', 'Nitab4.5_0000732g0140' => 'nta', 'Nitab4.5_0003162g0020' => 'nta', 'Nitab4.5_0006180g0090' => 'nta', 'Nitab4.5_0006390g0010' => 'nta', 'Nitab4.5_0007392g0040' => 'nta', 'Nn1g02140' => 'nnu', 'Nn4g26168' => 'nnu', 'Nn5g26754' => 'nnu', 'Oeu001433.1' => 'oeu', 'Oeu010299.2' => 'oeu', 'Oeu011171.1' => 'oeu', 'Oeu037675.1' => 'oeu', 'Oeu038359.1' => 'oeu', 'Oeu063834.1' => 'oeu', 'Oeu063835.1' => 'oeu', 'Os05g0312000' => 'osa', 'Os07g0211101' => 'osa', 'Os07g0211200' => 'osa', 'Os07g0681500' => 'osa', 'Peaxi162Scf00095g01015' => 'pax', 'Peaxi162Scf00104g00329' => 'pax', 'Peaxi162Scf00161g00137' => 'pax', 'PGR004G1665' => 'pgr', 'PGR031G2937' => 'pgr', 'PGR119G2145' => 'pgr', 'PGSC0003DMG400004351' => 'stu', 'PGSC0003DMG400014625' => 'stu', 'PGSC0003DMG401000943' => 'stu', 'Phvul.001G148600' => 'pvu', 'Phvul.004G001700' => 'pvu', 'Phvul.006G154900' => 'pvu', 'Phvul.008G078200' => 'pvu', 'Phvul.011G136500' => 'pvu', 'Potri.002G215600' => 'ptr', 'Potri.008G201600' => 'ptr', 'Potri.014G138400' => 'ptr', 'Potri.016G142500' => 'ptr', 'Pp3c16_10580' => 'ppa', 'Pp3c5_25280' => 'ppa', 'Prupe.1G150000' => 'ppe', 'Prupe.1G150100' => 'ppe', 'Prupe.6G299600' => 'ppe', 'Prupe.8G245000' => 'ppe', 'Psat0s4927g0040' => 'psa', 'Psat1g052080' => 'psa', 'Psat1g183800' => 'psa', 'Psat3g113840' => 'psa', 'Psat3g126120' => 'psa', 'Psat3g126160' => 'psa', 'Psat3g158760' => 'psa', 'Psat3g158840' => 'psa', 'PSO170G2858' => 'pso', 'PSO339G0606' => 'pso', 'PSO384G4709' => 'pso', 'PSO407G0334' => 'pso', 'QL04p040276' => 'qlo', 'QL06p005458' => 'qlo', 'QL06p005472' => 'qlo', 'QL07p030546' => 'qlo', 'QL07p031519' => 'qlo', 'QL09p050949' => 'qlo', 'QL09p050966' => 'qlo', 'QL09p051067' => 'qlo', 'QL12p022706' => 'qlo', 'RcHm_v2.0_Chr2g0119601' => 'rch', 'RcHm_v2.0_Chr3g0459591' => 'rch', 'RcHm_v2.0_Chr4g0418521' => 'rch', 'RcHm_v2.0_Chr4g0418531' => 'rch', 'RcHm_v2.0_Chr4g0418541' => 'rch', 'RcHm_v2.0_Chr6g0291641' => 'rch', 'Rhsim01G0086300' => 'rsi', 'Rhsim01G0276300' => 'rsi', 'Rhsim01G0276500' => 'rsi', 'Rhsim04G0207700' => 'rsi', 'Rhsim05G0234500' => 'rsi', 'Rhsim13G0022400' => 'rsi', 'Sabra02G0167900' => 'sbr', 'Sabra04G0158500' => 'sbr', 'Sabra08G0159800' => 'sbr', 'Sabra10G0011500' => 'sbr', 'Sabra14G0104400' => 'sbr', 'SalBow2G2440' => 'sbo', 'SalBow4G2265' => 'sbo', 'Sc02g0000060' => 'sci', 'Sc05g0005020' => 'sci', 'Sc13g0003890' => 'sci', 'Sed0014865' => 'sed', 'Sed0017224' => 'sed', 'Sed0026391' => 'sed', 'SEGI_00063' => 'sgi', 'SEGI_10967' => 'sgi', 'SEGI_17510' => 'sgi', 'SEGI_24396' => 'sgi', 'SEGI_39719' => 'sgi', 'SEGI_41392' => 'sgi', 'SGA_v2.0_scaffold11G05794' => 'sas', 'SGA_v2.0_scaffold142G35607' => 'sas', 'SGA_v2.0_scaffold1G00447' => 'sas', 'SHI15388' => 'shi', 'SHI15394' => 'shi', 'SHI15396' => 'shi', 'SHI15399' => 'shi', 'SMO343G0151' => 'smo', 'SMO367G1118' => 'smo', 'Solyc01g080200.3' => 'sly', 'Solyc06g008960.3' => 'sly', 'Solyc09g064780.3' => 'sly', 'Sopen01g031980' => 'spe', 'Sopen06g003710' => 'spe', 'Sopen09g026460' => 'spe', 'Sp3g21240' => 'spa', 'Sp4g30030' => 'spa', 'TAR365G0022' => 'tar', 'TAR365G1023' => 'tar', 'TAR365G1253' => 'tar', 'TAR623G0078' => 'tar', 'TAR623G1721' => 'tar', 'TAR633G0959' => 'tar', 'THA.LOC104802225' => 'tha', 'THA.LOC104804769' => 'tha', 'THA.LOC104808660' => 'tha', 'THA.LOC104812792' => 'tha', 'Thecc.01G284000' => 'tca', 'Thecc.04G220600' => 'tca', 'Thecc.05G268900' => 'tca', 'Thecc.08G171100' => 'tca', 'Thhalv10001284m.g' => 'esa', 'Thhalv10019912m.g' => 'esa', 'TPR.G14189' => 'tpr', 'TPR.G18110' => 'tpr', 'TPR.G18130' => 'tpr', 'TPR.G18131' => 'tpr', 'TPR.G18140' => 'tpr', 'TPR.G24282' => 'tpr', 'TPR.G25221' => 'tpr', 'TPR.G29267' => 'tpr', 'TPR.G35315' => 'tpr', 'TPR.G36173' => 'tpr', 'TWI09G0794' => 'twi', 'TWI59G1348' => 'twi', 'TWI74G0430' => 'twi', 'unitig_26.g8940' => 'ugi', 'unitig_749.g13744' => 'ugi', 'unitig_749.g13745' => 'ugi', 'vmacro08269' => 'vma', 'vmacro14937' => 'vma', 'vmacro20401' => 'vma', 'VMungo0464G1349' => 'vmu', 'VMungo0540G0289' => 'vmu', 'VMungo1215G1590' => 'vmu', 'VMungo1309G0221' => 'vmu', 'VMungo1309G2815' => 'vmu', 'VMungo1383G0239' => 'vmu', 'VMungo1383G2910' => 'vmu', 'Zm00001eb095270' => 'zma', 'Zm00001eb095280' => 'zma', 'Zm00001eb111630' => 'zma', 'Zm00001eb237080' => 'zma', 'Zm00001eb273740' => 'zma', 'Zm00001eb285040' => 'zma', 'Zm00001eb330790' => 'zma', 'Zm00001eb337380' => 'zma' ) $gf_id = 'HOM05D001484' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001484' ) $data_identifier = 'HOM05D001484' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 2, 'aly' => (int) 2, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 22, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 7, 'hma' => (int) 2, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 7, 'mtr' => (int) 10, 'cme' => (int) 2, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 4, 'ppa' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 4, 'qlo' => (int) 9, 'rch' => (int) 6, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 10, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 7, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb337380' $species_info = array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ) $local_species = 'col' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001484', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p31500' => 'bna', 'A05p00020' => 'bna', 'A07p08820' => 'bna', 'Aa31LG4G3300' => 'aar', 'Aa31LG8G10030' => 'aar', 'Actinidia00731' => 'ach', 'Actinidia11473' => 'ach', 'Actinidia23469' => 'ach', 'Actinidia24318' => 'ach', 'Actinidia40196' => 'ach', 'Actinidia40197' => 'ach', 'Actinidia40198' => 'ach', 'Ah.08g212990' => 'amhyb', 'Ah.15g091720' => 'amhyb', 'AL3G38260' => 'aly', 'AL4G47710' => 'aly', 'Aqoxy2G00671' => 'aox', 'Aqoxy2G03236' => 'aox', 'arahy.Tifrunner.gnm1.ann1.05IDCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KR684' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATY3SJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK6QJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6APGL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IDT7Z9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM073U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ0R87' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LE7RV4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT4QRX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V5ENPK' => 'arhy', 'AT2G48110' => 'ath', 'AT3G23590' => 'ath', 'ATR0626G186' => 'atr', 'ATR1127G141' => 'atr', 'Atru.chr4.2583' => 'acertr', 'Atru.chr5.1358' => 'acertr', 'Atru.chr5.1359' => 'acertr', 'Atru.chr8.46' => 'acertr', 'AUR62002640' => 'cqu', 'AUR62030055' => 'cqu', 'AUR62033713' => 'cqu', 'AUR62033714' => 'cqu', 'AUR62036795' => 'cqu', 'AUR62039891' => 'cqu', 'BcaB02g08737' => 'bca', 'BcaB04g20441' => 'bca', 'BcaB06g26509' => 'bca', 'BcaB06g26510' => 'bca', 'BcaB06g26511' => 'bca', 'BcaB06g26512' => 'bca', 'BcaB06g26513' => 'bca', 'BcaC02g12564' => 'bca', 'BcaC02g12565' => 'bca', 'BcaC02g12794' => 'bca', 'BcaC02g12795' => 'bca', 'BcaC02g12796' => 'bca', 'BcaC06g35541' => 'bca', 'BNapus_Darmor_BZH_scaffold_188p00080' => 'bna', 'BNapus_Darmor_BZH_scaffold_188p00090' => 'bna', 'BolC1t03972H' => 'bol', 'BolC1t03973H' => 'bol', 'BolC4t21680H' => 'bol', 'BolC7t41863H' => 'bol', 'BolSC55t61227H' => 'bol', 'BolSC55t61228H' => 'bol', 'BraA01t03278Z' => 'bra', 'BraA05t18998Z' => 'bra', 'BraA07t28673Z' => 'bra', 'C01p40150' => 'bna', 'C05p12370' => 'bna', 'C07p13680' => 'bna', 'CAN.G1006.16' => 'can', 'CAN.G1006.17' => 'can', 'CAN.G1170.2' => 'can', 'CAN.G962.7' => 'can', 'CANSAT25G2179' => 'cansat', 'CANSAT78G1573' => 'cansat', 'CARHR099510' => 'chi', 'CARHR143510' => 'chi', 'Carub.0003s2380' => 'cru', 'Carub.0004s3082' => 'cru', 'Ca_00614_v3' => 'car', 'Ca_07801_v3' => 'car', 'Ca_08567_v3' => 'car', 'Ca_09571_v3' => 'car', 'CBR_g19290' => 'cbr', 'Cc01_g19770' => 'ccan', 'Cc03_g03030' => 'ccan', 'CDE07G0968' => 'cde', 'CDE09G1441' => 'cde', 'Cfa006103' => 'cfa', 'Cfa015573' => 'cfa', 'Cfa016988' => 'cfa', 'Ciclev10006738m.g' => 'ccl', 'Ciclev10010920m.g' => 'ccl', 'Ciclev10018517m.g' => 'ccl', 'CiPaw.01G159200' => 'cil', 'CiPaw.02G091000' => 'cil', 'CiPaw.02G091100' => 'cil', 'CiPaw.08G103100' => 'cil', 'CiPaw.09G224900' => 'cil', 'ClCG06G005740' => 'cla', 'ClCG07G000090' => 'cla', 'ClCG07G000100' => 'cla', 'COL.COLO4_09143' => 'col', 'COL.COLO4_25124' => 'col', 'Cpa.g.sc16.34' => 'cpa', 'Cpa.g.sc3504.1' => 'cpa', 'Cpa.g.sc60.37' => 'cpa', 'CsaV3_6G018520' => 'csa', 'CsaV3_6G036860' => 'csa', 'CSS0001072' => 'camsi', 'CSS0020208' => 'camsi', 'CSS0021253' => 'camsi', 'CSS0022190' => 'camsi', 'CSS0036150' => 'camsi', 'CSS0040442' => 'camsi', 'CSS0042300' => 'camsi', 'CSS0045298' => 'camsi', 'DCAR_012449' => 'dca', 'DCAR_018405' => 'dca', 'DCAR_024573' => 'dca', 'DCAR_030591' => 'dca', 'Dinv16926' => 'din', 'Dinv32963' => 'din', 'Dinv38382' => 'din', 'Dinv38383' => 'din', 'Duzib133G0974' => 'dzi', 'Duzib138G1867' => 'dzi', 'Duzib211G0420' => 'dzi', 'Duzib212G0930' => 'dzi', 'ECA234G1645' => 'eca', 'ECA247G3467' => 'eca', 'ECA248G1703' => 'eca', 'EL10Ac3g06327' => 'bvu', 'EL10Ac7g17204' => 'bvu', 'Eucgr.A00855' => 'egr', 'Eucgr.A00858' => 'egr', 'Eucgr.H01520' => 'egr', 'Eucgr.H03604' => 'egr', 'Eucgr.L03465' => 'egr', 'Eucgr.L03466' => 'egr', 'FAN01G0988' => 'fan', 'FAN02G3892' => 'fan', 'FAN05G3381' => 'fan', 'FAN07G0967' => 'fan', 'FAN07G1493' => 'fan', 'FAN08G3125' => 'fan', 'FAN09G0402' => 'fan', 'FAN12G2594' => 'fan', 'FAN12G3879' => 'fan', 'FAN14G1546' => 'fan', 'FAN15G3626' => 'fan', 'FAN17G0588' => 'fan', 'FAN17G0609' => 'fan', 'FAN18G2817' => 'fan', 'FAN19G1305' => 'fan', 'FAN20G1787' => 'fan', 'FAN22G0073' => 'fan', 'FAN22G0352' => 'fan', 'FAN22G0368' => 'fan', 'FAN22G2273' => 'fan', 'FAN24G1998' => 'fan', 'FAN27G1317' => 'fan', 'FvH4_2g23980' => 'fve', 'FvH4_4g14380' => 'fve', 'FvH4_4g14390' => 'fve', 'FvH4_6g09250' => 'fve', 'Glyma.03G151100' => 'gma', 'Glyma.04G122550' => 'gma', 'Glyma.05G001600' => 'gma', 'Glyma.09G270766' => 'gma', 'Glyma.09G270832' => 'gma', 'Glyma.13G209800' => 'gma', 'Glyma.15G102800' => 'gma', 'Glyma.18G218900' => 'gma', 'Glyma.19G001500' => 'gma', 'Glyma.19G153600' => 'gma', 'Gohir.A02G028600' => 'ghi', 'Gohir.A08G045000' => 'ghi', 'Gohir.A11G120500' => 'ghi', 'Gohir.A12G006200' => 'ghi', 'Gohir.A12G006250' => 'ghi', 'Gohir.D02G036300' => 'ghi', 'Gohir.D08G054700' => 'ghi', 'Gohir.D11G125600' => 'ghi', 'Gohir.D12G005700' => 'ghi', 'Gorai.004G055200' => 'gra', 'Gorai.005G040400' => 'gra', 'Gorai.007G134500' => 'gra', 'Gorai.008G005500' => 'gra', 'GSVIVG01011094001' => 'vvi', 'GSVIVG01017879001' => 'vvi', 'GSVIVG01025988001' => 'vvi', 'GSVIVG01029847001' => 'vvi', 'HanXRQChr10g0282901' => 'han', 'HanXRQChr10g0310371' => 'han', 'HanXRQChr10g0315041' => 'han', 'HanXRQChr11g0327651' => 'han', 'HanXRQChr12g0359391' => 'han', 'Haze_00972' => 'cav', 'Haze_00973' => 'cav', 'Haze_00974' => 'cav', 'Haze_04747' => 'cav', 'Haze_04749' => 'cav', 'Haze_04750' => 'cav', 'Haze_21217' => 'cav', 'Hma1.2p1_1037F.1_g250680' => 'hma', 'Hma1.2p1_1644F.1_g295320' => 'hma', 'HPP92_011322' => 'vpl', 'HPP92_011323' => 'vpl', 'HPP92_011324' => 'vpl', 'HPP92_011325' => 'vpl', 'HPP92_011326' => 'vpl', 'Hund12205' => 'sun', 'Hund17957' => 'sun', 'Lalb_Chr06g0176771' => 'lal', 'Lalb_Chr18g0056021' => 'lal', 'Lalb_Chr18g0056031' => 'lal', 'Lalb_Chr18g0056041' => 'lal', 'Lalb_Chr20g0107751' => 'lal', 'Lalb_Chr20g0118371' => 'lal', 'Lj1g0010239' => 'lja', 'Lj1g0017101' => 'lja', 'Lj2A1178G40' => 'lonja', 'Lj2A54G84' => 'lonja', 'Lj2g0015248' => 'lja', 'Lj3A761T51' => 'lonja', 'Lj6g0018116' => 'lja', 'Lsat_1_v5_gn_4_136040' => 'lsa', 'Lsat_1_v5_gn_5_187461' => 'lsa', 'Lsat_1_v5_gn_5_77001' => 'lsa', 'Lsat_1_v5_gn_9_4461' => 'lsa', 'Manes.01G210100' => 'mes', 'Manes.03G185600' => 'mes', 'Manes.05G073300' => 'mes', 'Manes.09G120300' => 'mes', 'Manes.15G022100' => 'mes', 'Mapoly0096s0053' => 'mpo', 'MBI03_g14058_MAGBIO' => 'mbi', 'MBI03_g33876_MAGBIO' => 'mbi', 'MBI03_g36854_MAGBIO' => 'mbi', 'MBI17_g11997_MAGBIO' => 'mbi', 'MD03G1269000' => 'mdo', 'MD04G1179600' => 'mdo', 'MD11G1289800' => 'mdo', 'MD12G1194700' => 'mdo', 'MD13G1182100' => 'mdo', 'MD13G1182200' => 'mdo', 'MD16G1182600' => 'mdo', 'Medtr2g021400' => 'mtr', 'Medtr2g021470' => 'mtr', 'Medtr2g105810' => 'mtr', 'Medtr3g033580' => 'mtr', 'Medtr6g007970' => 'mtr', 'Medtr7g056330' => 'mtr', 'Medtr7g074290' => 'mtr', 'Medtr7g074380' => 'mtr', 'Medtr7g094550' => 'mtr', 'Medtr8g069995' => 'mtr', 'MELO3C014345.2' => 'cme', 'MELO3C021395.2' => 'cme', 'Migut.D00262' => 'egut', 'Migut.G00257' => 'egut', 'MSTRG.21575' => 'ama', 'MSTRG.3985' => 'ama', 'Nitab4.5_0000295g0140' => 'nta', 'Nitab4.5_0000732g0140' => 'nta', 'Nitab4.5_0003162g0020' => 'nta', 'Nitab4.5_0006180g0090' => 'nta', 'Nitab4.5_0006390g0010' => 'nta', 'Nitab4.5_0007392g0040' => 'nta', 'Nn1g02140' => 'nnu', 'Nn4g26168' => 'nnu', 'Nn5g26754' => 'nnu', 'Oeu001433.1' => 'oeu', 'Oeu010299.2' => 'oeu', 'Oeu011171.1' => 'oeu', 'Oeu037675.1' => 'oeu', 'Oeu038359.1' => 'oeu', 'Oeu063834.1' => 'oeu', 'Oeu063835.1' => 'oeu', 'Os05g0312000' => 'osa', 'Os07g0211101' => 'osa', 'Os07g0211200' => 'osa', 'Os07g0681500' => 'osa', 'Peaxi162Scf00095g01015' => 'pax', 'Peaxi162Scf00104g00329' => 'pax', 'Peaxi162Scf00161g00137' => 'pax', 'PGR004G1665' => 'pgr', 'PGR031G2937' => 'pgr', 'PGR119G2145' => 'pgr', 'PGSC0003DMG400004351' => 'stu', 'PGSC0003DMG400014625' => 'stu', 'PGSC0003DMG401000943' => 'stu', 'Phvul.001G148600' => 'pvu', 'Phvul.004G001700' => 'pvu', 'Phvul.006G154900' => 'pvu', 'Phvul.008G078200' => 'pvu', 'Phvul.011G136500' => 'pvu', 'Potri.002G215600' => 'ptr', 'Potri.008G201600' => 'ptr', 'Potri.014G138400' => 'ptr', 'Potri.016G142500' => 'ptr', 'Pp3c16_10580' => 'ppa', 'Pp3c5_25280' => 'ppa', 'Prupe.1G150000' => 'ppe', 'Prupe.1G150100' => 'ppe', 'Prupe.6G299600' => 'ppe', 'Prupe.8G245000' => 'ppe', 'Psat0s4927g0040' => 'psa', 'Psat1g052080' => 'psa', 'Psat1g183800' => 'psa', 'Psat3g113840' => 'psa', 'Psat3g126120' => 'psa', 'Psat3g126160' => 'psa', 'Psat3g158760' => 'psa', 'Psat3g158840' => 'psa', 'PSO170G2858' => 'pso', 'PSO339G0606' => 'pso', 'PSO384G4709' => 'pso', 'PSO407G0334' => 'pso', 'QL04p040276' => 'qlo', 'QL06p005458' => 'qlo', 'QL06p005472' => 'qlo', 'QL07p030546' => 'qlo', 'QL07p031519' => 'qlo', 'QL09p050949' => 'qlo', 'QL09p050966' => 'qlo', 'QL09p051067' => 'qlo', 'QL12p022706' => 'qlo', 'RcHm_v2.0_Chr2g0119601' => 'rch', 'RcHm_v2.0_Chr3g0459591' => 'rch', 'RcHm_v2.0_Chr4g0418521' => 'rch', 'RcHm_v2.0_Chr4g0418531' => 'rch', 'RcHm_v2.0_Chr4g0418541' => 'rch', 'RcHm_v2.0_Chr6g0291641' => 'rch', 'Rhsim01G0086300' => 'rsi', 'Rhsim01G0276300' => 'rsi', 'Rhsim01G0276500' => 'rsi', 'Rhsim04G0207700' => 'rsi', 'Rhsim05G0234500' => 'rsi', 'Rhsim13G0022400' => 'rsi', 'Sabra02G0167900' => 'sbr', 'Sabra04G0158500' => 'sbr', 'Sabra08G0159800' => 'sbr', 'Sabra10G0011500' => 'sbr', 'Sabra14G0104400' => 'sbr', 'SalBow2G2440' => 'sbo', 'SalBow4G2265' => 'sbo', 'Sc02g0000060' => 'sci', 'Sc05g0005020' => 'sci', 'Sc13g0003890' => 'sci', 'Sed0014865' => 'sed', 'Sed0017224' => 'sed', 'Sed0026391' => 'sed', 'SEGI_00063' => 'sgi', 'SEGI_10967' => 'sgi', 'SEGI_17510' => 'sgi', 'SEGI_24396' => 'sgi', 'SEGI_39719' => 'sgi', 'SEGI_41392' => 'sgi', 'SGA_v2.0_scaffold11G05794' => 'sas', 'SGA_v2.0_scaffold142G35607' => 'sas', 'SGA_v2.0_scaffold1G00447' => 'sas', 'SHI15388' => 'shi', 'SHI15394' => 'shi', 'SHI15396' => 'shi', 'SHI15399' => 'shi', 'SMO343G0151' => 'smo', 'SMO367G1118' => 'smo', 'Solyc01g080200.3' => 'sly', 'Solyc06g008960.3' => 'sly', 'Solyc09g064780.3' => 'sly', 'Sopen01g031980' => 'spe', 'Sopen06g003710' => 'spe', 'Sopen09g026460' => 'spe', 'Sp3g21240' => 'spa', 'Sp4g30030' => 'spa', 'TAR365G0022' => 'tar', 'TAR365G1023' => 'tar', 'TAR365G1253' => 'tar', 'TAR623G0078' => 'tar', 'TAR623G1721' => 'tar', 'TAR633G0959' => 'tar', 'THA.LOC104802225' => 'tha', 'THA.LOC104804769' => 'tha', 'THA.LOC104808660' => 'tha', 'THA.LOC104812792' => 'tha', 'Thecc.01G284000' => 'tca', 'Thecc.04G220600' => 'tca', 'Thecc.05G268900' => 'tca', 'Thecc.08G171100' => 'tca', 'Thhalv10001284m.g' => 'esa', 'Thhalv10019912m.g' => 'esa', 'TPR.G14189' => 'tpr', 'TPR.G18110' => 'tpr', 'TPR.G18130' => 'tpr', 'TPR.G18131' => 'tpr', 'TPR.G18140' => 'tpr', 'TPR.G24282' => 'tpr', 'TPR.G25221' => 'tpr', 'TPR.G29267' => 'tpr', 'TPR.G35315' => 'tpr', 'TPR.G36173' => 'tpr', 'TWI09G0794' => 'twi', 'TWI59G1348' => 'twi', 'TWI74G0430' => 'twi', 'unitig_26.g8940' => 'ugi', 'unitig_749.g13744' => 'ugi', 'unitig_749.g13745' => 'ugi', 'vmacro08269' => 'vma', 'vmacro14937' => 'vma', 'vmacro20401' => 'vma', 'VMungo0464G1349' => 'vmu', 'VMungo0540G0289' => 'vmu', 'VMungo1215G1590' => 'vmu', 'VMungo1309G0221' => 'vmu', 'VMungo1309G2815' => 'vmu', 'VMungo1383G0239' => 'vmu', 'VMungo1383G2910' => 'vmu', 'Zm00001eb095270' => 'zma', 'Zm00001eb095280' => 'zma', 'Zm00001eb111630' => 'zma', 'Zm00001eb237080' => 'zma', 'Zm00001eb273740' => 'zma', 'Zm00001eb285040' => 'zma', 'Zm00001eb330790' => 'zma', 'Zm00001eb337380' => 'zma' ), 'gf_id' => 'HOM05D001484', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001484' ), 'data_identifier' => 'HOM05D001484', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001484', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p31500' => 'bna', 'A05p00020' => 'bna', 'A07p08820' => 'bna', 'Aa31LG4G3300' => 'aar', 'Aa31LG8G10030' => 'aar', 'Actinidia00731' => 'ach', 'Actinidia11473' => 'ach', 'Actinidia23469' => 'ach', 'Actinidia24318' => 'ach', 'Actinidia40196' => 'ach', 'Actinidia40197' => 'ach', 'Actinidia40198' => 'ach', 'Ah.08g212990' => 'amhyb', 'Ah.15g091720' => 'amhyb', 'AL3G38260' => 'aly', 'AL4G47710' => 'aly', 'Aqoxy2G00671' => 'aox', 'Aqoxy2G03236' => 'aox', 'arahy.Tifrunner.gnm1.ann1.05IDCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KR684' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATY3SJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK6QJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6APGL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IDT7Z9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM073U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ0R87' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LE7RV4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT4QRX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V5ENPK' => 'arhy', 'AT2G48110' => 'ath', 'AT3G23590' => 'ath', 'ATR0626G186' => 'atr', 'ATR1127G141' => 'atr', 'Atru.chr4.2583' => 'acertr', 'Atru.chr5.1358' => 'acertr', 'Atru.chr5.1359' => 'acertr', 'Atru.chr8.46' => 'acertr', 'AUR62002640' => 'cqu', 'AUR62030055' => 'cqu', 'AUR62033713' => 'cqu', 'AUR62033714' => 'cqu', 'AUR62036795' => 'cqu', 'AUR62039891' => 'cqu', 'BcaB02g08737' => 'bca', 'BcaB04g20441' => 'bca', 'BcaB06g26509' => 'bca', 'BcaB06g26510' => 'bca', 'BcaB06g26511' => 'bca', 'BcaB06g26512' => 'bca', 'BcaB06g26513' => 'bca', 'BcaC02g12564' => 'bca', 'BcaC02g12565' => 'bca', 'BcaC02g12794' => 'bca', 'BcaC02g12795' => 'bca', 'BcaC02g12796' => 'bca', 'BcaC06g35541' => 'bca', 'BNapus_Darmor_BZH_scaffold_188p00080' => 'bna', 'BNapus_Darmor_BZH_scaffold_188p00090' => 'bna', 'BolC1t03972H' => 'bol', 'BolC1t03973H' => 'bol', 'BolC4t21680H' => 'bol', 'BolC7t41863H' => 'bol', 'BolSC55t61227H' => 'bol', 'BolSC55t61228H' => 'bol', 'BraA01t03278Z' => 'bra', 'BraA05t18998Z' => 'bra', 'BraA07t28673Z' => 'bra', 'C01p40150' => 'bna', 'C05p12370' => 'bna', 'C07p13680' => 'bna', 'CAN.G1006.16' => 'can', 'CAN.G1006.17' => 'can', 'CAN.G1170.2' => 'can', 'CAN.G962.7' => 'can', 'CANSAT25G2179' => 'cansat', 'CANSAT78G1573' => 'cansat', 'CARHR099510' => 'chi', 'CARHR143510' => 'chi', 'Carub.0003s2380' => 'cru', 'Carub.0004s3082' => 'cru', 'Ca_00614_v3' => 'car', 'Ca_07801_v3' => 'car', 'Ca_08567_v3' => 'car', 'Ca_09571_v3' => 'car', 'CBR_g19290' => 'cbr', 'Cc01_g19770' => 'ccan', 'Cc03_g03030' => 'ccan', 'CDE07G0968' => 'cde', 'CDE09G1441' => 'cde', 'Cfa006103' => 'cfa', 'Cfa015573' => 'cfa', 'Cfa016988' => 'cfa', 'Ciclev10006738m.g' => 'ccl', 'Ciclev10010920m.g' => 'ccl', 'Ciclev10018517m.g' => 'ccl', 'CiPaw.01G159200' => 'cil', 'CiPaw.02G091000' => 'cil', 'CiPaw.02G091100' => 'cil', 'CiPaw.08G103100' => 'cil', 'CiPaw.09G224900' => 'cil', 'ClCG06G005740' => 'cla', 'ClCG07G000090' => 'cla', 'ClCG07G000100' => 'cla', 'COL.COLO4_09143' => 'col', 'COL.COLO4_25124' => 'col', 'Cpa.g.sc16.34' => 'cpa', 'Cpa.g.sc3504.1' => 'cpa', 'Cpa.g.sc60.37' => 'cpa', 'CsaV3_6G018520' => 'csa', 'CsaV3_6G036860' => 'csa', 'CSS0001072' => 'camsi', 'CSS0020208' => 'camsi', 'CSS0021253' => 'camsi', 'CSS0022190' => 'camsi', 'CSS0036150' => 'camsi', 'CSS0040442' => 'camsi', 'CSS0042300' => 'camsi', 'CSS0045298' => 'camsi', 'DCAR_012449' => 'dca', 'DCAR_018405' => 'dca', 'DCAR_024573' => 'dca', 'DCAR_030591' => 'dca', 'Dinv16926' => 'din', 'Dinv32963' => 'din', 'Dinv38382' => 'din', 'Dinv38383' => 'din', 'Duzib133G0974' => 'dzi', 'Duzib138G1867' => 'dzi', 'Duzib211G0420' => 'dzi', 'Duzib212G0930' => 'dzi', 'ECA234G1645' => 'eca', 'ECA247G3467' => 'eca', 'ECA248G1703' => 'eca', 'EL10Ac3g06327' => 'bvu', 'EL10Ac7g17204' => 'bvu', 'Eucgr.A00855' => 'egr', 'Eucgr.A00858' => 'egr', 'Eucgr.H01520' => 'egr', 'Eucgr.H03604' => 'egr', 'Eucgr.L03465' => 'egr', 'Eucgr.L03466' => 'egr', 'FAN01G0988' => 'fan', 'FAN02G3892' => 'fan', 'FAN05G3381' => 'fan', 'FAN07G0967' => 'fan', 'FAN07G1493' => 'fan', 'FAN08G3125' => 'fan', 'FAN09G0402' => 'fan', 'FAN12G2594' => 'fan', 'FAN12G3879' => 'fan', 'FAN14G1546' => 'fan', 'FAN15G3626' => 'fan', 'FAN17G0588' => 'fan', 'FAN17G0609' => 'fan', 'FAN18G2817' => 'fan', 'FAN19G1305' => 'fan', 'FAN20G1787' => 'fan', 'FAN22G0073' => 'fan', 'FAN22G0352' => 'fan', 'FAN22G0368' => 'fan', 'FAN22G2273' => 'fan', 'FAN24G1998' => 'fan', 'FAN27G1317' => 'fan', 'FvH4_2g23980' => 'fve', 'FvH4_4g14380' => 'fve', 'FvH4_4g14390' => 'fve', 'FvH4_6g09250' => 'fve', 'Glyma.03G151100' => 'gma', 'Glyma.04G122550' => 'gma', 'Glyma.05G001600' => 'gma', 'Glyma.09G270766' => 'gma', 'Glyma.09G270832' => 'gma', 'Glyma.13G209800' => 'gma', 'Glyma.15G102800' => 'gma', 'Glyma.18G218900' => 'gma', 'Glyma.19G001500' => 'gma', 'Glyma.19G153600' => 'gma', 'Gohir.A02G028600' => 'ghi', 'Gohir.A08G045000' => 'ghi', 'Gohir.A11G120500' => 'ghi', 'Gohir.A12G006200' => 'ghi', 'Gohir.A12G006250' => 'ghi', 'Gohir.D02G036300' => 'ghi', 'Gohir.D08G054700' => 'ghi', 'Gohir.D11G125600' => 'ghi', 'Gohir.D12G005700' => 'ghi', 'Gorai.004G055200' => 'gra', 'Gorai.005G040400' => 'gra', 'Gorai.007G134500' => 'gra', 'Gorai.008G005500' => 'gra', 'GSVIVG01011094001' => 'vvi', 'GSVIVG01017879001' => 'vvi', 'GSVIVG01025988001' => 'vvi', 'GSVIVG01029847001' => 'vvi', 'HanXRQChr10g0282901' => 'han', 'HanXRQChr10g0310371' => 'han', 'HanXRQChr10g0315041' => 'han', 'HanXRQChr11g0327651' => 'han', 'HanXRQChr12g0359391' => 'han', 'Haze_00972' => 'cav', 'Haze_00973' => 'cav', 'Haze_00974' => 'cav', 'Haze_04747' => 'cav', 'Haze_04749' => 'cav', 'Haze_04750' => 'cav', 'Haze_21217' => 'cav', 'Hma1.2p1_1037F.1_g250680' => 'hma', 'Hma1.2p1_1644F.1_g295320' => 'hma', 'HPP92_011322' => 'vpl', 'HPP92_011323' => 'vpl', 'HPP92_011324' => 'vpl', 'HPP92_011325' => 'vpl', 'HPP92_011326' => 'vpl', 'Hund12205' => 'sun', 'Hund17957' => 'sun', 'Lalb_Chr06g0176771' => 'lal', 'Lalb_Chr18g0056021' => 'lal', 'Lalb_Chr18g0056031' => 'lal', 'Lalb_Chr18g0056041' => 'lal', 'Lalb_Chr20g0107751' => 'lal', 'Lalb_Chr20g0118371' => 'lal', 'Lj1g0010239' => 'lja', 'Lj1g0017101' => 'lja', 'Lj2A1178G40' => 'lonja', 'Lj2A54G84' => 'lonja', 'Lj2g0015248' => 'lja', 'Lj3A761T51' => 'lonja', 'Lj6g0018116' => 'lja', 'Lsat_1_v5_gn_4_136040' => 'lsa', 'Lsat_1_v5_gn_5_187461' => 'lsa', 'Lsat_1_v5_gn_5_77001' => 'lsa', 'Lsat_1_v5_gn_9_4461' => 'lsa', 'Manes.01G210100' => 'mes', 'Manes.03G185600' => 'mes', 'Manes.05G073300' => 'mes', 'Manes.09G120300' => 'mes', 'Manes.15G022100' => 'mes', 'Mapoly0096s0053' => 'mpo', 'MBI03_g14058_MAGBIO' => 'mbi', 'MBI03_g33876_MAGBIO' => 'mbi', 'MBI03_g36854_MAGBIO' => 'mbi', 'MBI17_g11997_MAGBIO' => 'mbi', 'MD03G1269000' => 'mdo', 'MD04G1179600' => 'mdo', 'MD11G1289800' => 'mdo', 'MD12G1194700' => 'mdo', 'MD13G1182100' => 'mdo', 'MD13G1182200' => 'mdo', 'MD16G1182600' => 'mdo', 'Medtr2g021400' => 'mtr', 'Medtr2g021470' => 'mtr', 'Medtr2g105810' => 'mtr', 'Medtr3g033580' => 'mtr', 'Medtr6g007970' => 'mtr', 'Medtr7g056330' => 'mtr', 'Medtr7g074290' => 'mtr', 'Medtr7g074380' => 'mtr', 'Medtr7g094550' => 'mtr', 'Medtr8g069995' => 'mtr', 'MELO3C014345.2' => 'cme', 'MELO3C021395.2' => 'cme', 'Migut.D00262' => 'egut', 'Migut.G00257' => 'egut', 'MSTRG.21575' => 'ama', 'MSTRG.3985' => 'ama', 'Nitab4.5_0000295g0140' => 'nta', 'Nitab4.5_0000732g0140' => 'nta', 'Nitab4.5_0003162g0020' => 'nta', 'Nitab4.5_0006180g0090' => 'nta', 'Nitab4.5_0006390g0010' => 'nta', 'Nitab4.5_0007392g0040' => 'nta', 'Nn1g02140' => 'nnu', 'Nn4g26168' => 'nnu', 'Nn5g26754' => 'nnu', 'Oeu001433.1' => 'oeu', 'Oeu010299.2' => 'oeu', 'Oeu011171.1' => 'oeu', 'Oeu037675.1' => 'oeu', 'Oeu038359.1' => 'oeu', 'Oeu063834.1' => 'oeu', 'Oeu063835.1' => 'oeu', 'Os05g0312000' => 'osa', 'Os07g0211101' => 'osa', 'Os07g0211200' => 'osa', 'Os07g0681500' => 'osa', 'Peaxi162Scf00095g01015' => 'pax', 'Peaxi162Scf00104g00329' => 'pax', 'Peaxi162Scf00161g00137' => 'pax', 'PGR004G1665' => 'pgr', 'PGR031G2937' => 'pgr', 'PGR119G2145' => 'pgr', 'PGSC0003DMG400004351' => 'stu', 'PGSC0003DMG400014625' => 'stu', 'PGSC0003DMG401000943' => 'stu', 'Phvul.001G148600' => 'pvu', 'Phvul.004G001700' => 'pvu', 'Phvul.006G154900' => 'pvu', 'Phvul.008G078200' => 'pvu', 'Phvul.011G136500' => 'pvu', 'Potri.002G215600' => 'ptr', 'Potri.008G201600' => 'ptr', 'Potri.014G138400' => 'ptr', 'Potri.016G142500' => 'ptr', 'Pp3c16_10580' => 'ppa', 'Pp3c5_25280' => 'ppa', 'Prupe.1G150000' => 'ppe', 'Prupe.1G150100' => 'ppe', 'Prupe.6G299600' => 'ppe', 'Prupe.8G245000' => 'ppe', 'Psat0s4927g0040' => 'psa', 'Psat1g052080' => 'psa', 'Psat1g183800' => 'psa', 'Psat3g113840' => 'psa', 'Psat3g126120' => 'psa', 'Psat3g126160' => 'psa', 'Psat3g158760' => 'psa', 'Psat3g158840' => 'psa', 'PSO170G2858' => 'pso', 'PSO339G0606' => 'pso', 'PSO384G4709' => 'pso', 'PSO407G0334' => 'pso', 'QL04p040276' => 'qlo', 'QL06p005458' => 'qlo', 'QL06p005472' => 'qlo', 'QL07p030546' => 'qlo', 'QL07p031519' => 'qlo', 'QL09p050949' => 'qlo', 'QL09p050966' => 'qlo', 'QL09p051067' => 'qlo', 'QL12p022706' => 'qlo', 'RcHm_v2.0_Chr2g0119601' => 'rch', 'RcHm_v2.0_Chr3g0459591' => 'rch', 'RcHm_v2.0_Chr4g0418521' => 'rch', 'RcHm_v2.0_Chr4g0418531' => 'rch', 'RcHm_v2.0_Chr4g0418541' => 'rch', 'RcHm_v2.0_Chr6g0291641' => 'rch', 'Rhsim01G0086300' => 'rsi', 'Rhsim01G0276300' => 'rsi', 'Rhsim01G0276500' => 'rsi', 'Rhsim04G0207700' => 'rsi', 'Rhsim05G0234500' => 'rsi', 'Rhsim13G0022400' => 'rsi', 'Sabra02G0167900' => 'sbr', 'Sabra04G0158500' => 'sbr', 'Sabra08G0159800' => 'sbr', 'Sabra10G0011500' => 'sbr', 'Sabra14G0104400' => 'sbr', 'SalBow2G2440' => 'sbo', 'SalBow4G2265' => 'sbo', 'Sc02g0000060' => 'sci', 'Sc05g0005020' => 'sci', 'Sc13g0003890' => 'sci', 'Sed0014865' => 'sed', 'Sed0017224' => 'sed', 'Sed0026391' => 'sed', 'SEGI_00063' => 'sgi', 'SEGI_10967' => 'sgi', 'SEGI_17510' => 'sgi', 'SEGI_24396' => 'sgi', 'SEGI_39719' => 'sgi', 'SEGI_41392' => 'sgi', 'SGA_v2.0_scaffold11G05794' => 'sas', 'SGA_v2.0_scaffold142G35607' => 'sas', 'SGA_v2.0_scaffold1G00447' => 'sas', 'SHI15388' => 'shi', 'SHI15394' => 'shi', 'SHI15396' => 'shi', 'SHI15399' => 'shi', 'SMO343G0151' => 'smo', 'SMO367G1118' => 'smo', 'Solyc01g080200.3' => 'sly', 'Solyc06g008960.3' => 'sly', 'Solyc09g064780.3' => 'sly', 'Sopen01g031980' => 'spe', 'Sopen06g003710' => 'spe', 'Sopen09g026460' => 'spe', 'Sp3g21240' => 'spa', 'Sp4g30030' => 'spa', 'TAR365G0022' => 'tar', 'TAR365G1023' => 'tar', 'TAR365G1253' => 'tar', 'TAR623G0078' => 'tar', 'TAR623G1721' => 'tar', 'TAR633G0959' => 'tar', 'THA.LOC104802225' => 'tha', 'THA.LOC104804769' => 'tha', 'THA.LOC104808660' => 'tha', 'THA.LOC104812792' => 'tha', 'Thecc.01G284000' => 'tca', 'Thecc.04G220600' => 'tca', 'Thecc.05G268900' => 'tca', 'Thecc.08G171100' => 'tca', 'Thhalv10001284m.g' => 'esa', 'Thhalv10019912m.g' => 'esa', 'TPR.G14189' => 'tpr', 'TPR.G18110' => 'tpr', 'TPR.G18130' => 'tpr', 'TPR.G18131' => 'tpr', 'TPR.G18140' => 'tpr', 'TPR.G24282' => 'tpr', 'TPR.G25221' => 'tpr', 'TPR.G29267' => 'tpr', 'TPR.G35315' => 'tpr', 'TPR.G36173' => 'tpr', 'TWI09G0794' => 'twi', 'TWI59G1348' => 'twi', 'TWI74G0430' => 'twi', 'unitig_26.g8940' => 'ugi', 'unitig_749.g13744' => 'ugi', 'unitig_749.g13745' => 'ugi', 'vmacro08269' => 'vma', 'vmacro14937' => 'vma', 'vmacro20401' => 'vma', 'VMungo0464G1349' => 'vmu', 'VMungo0540G0289' => 'vmu', 'VMungo1215G1590' => 'vmu', 'VMungo1309G0221' => 'vmu', 'VMungo1309G2815' => 'vmu', 'VMungo1383G0239' => 'vmu', 'VMungo1383G2910' => 'vmu', 'Zm00001eb095270' => 'zma', 'Zm00001eb095280' => 'zma', 'Zm00001eb111630' => 'zma', 'Zm00001eb237080' => 'zma', 'Zm00001eb273740' => 'zma', 'Zm00001eb285040' => 'zma', 'Zm00001eb330790' => 'zma', 'Zm00001eb337380' => 'zma' ) $gf_id = 'HOM05D001484' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001484' ) $data_identifier = 'HOM05D001484' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 2, 'aly' => (int) 2, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 22, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 7, 'hma' => (int) 2, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 7, 'mtr' => (int) 10, 'cme' => (int) 2, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 4, 'ppa' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 4, 'qlo' => (int) 9, 'rch' => (int) 6, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 10, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 7, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb337380' $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' => 'HOM05D001484', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p31500' => 'bna', 'A05p00020' => 'bna', 'A07p08820' => 'bna', 'Aa31LG4G3300' => 'aar', 'Aa31LG8G10030' => 'aar', 'Actinidia00731' => 'ach', 'Actinidia11473' => 'ach', 'Actinidia23469' => 'ach', 'Actinidia24318' => 'ach', 'Actinidia40196' => 'ach', 'Actinidia40197' => 'ach', 'Actinidia40198' => 'ach', 'Ah.08g212990' => 'amhyb', 'Ah.15g091720' => 'amhyb', 'AL3G38260' => 'aly', 'AL4G47710' => 'aly', 'Aqoxy2G00671' => 'aox', 'Aqoxy2G03236' => 'aox', 'arahy.Tifrunner.gnm1.ann1.05IDCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KR684' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATY3SJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK6QJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6APGL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IDT7Z9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM073U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ0R87' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LE7RV4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT4QRX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V5ENPK' => 'arhy', 'AT2G48110' => 'ath', 'AT3G23590' => 'ath', 'ATR0626G186' => 'atr', 'ATR1127G141' => 'atr', 'Atru.chr4.2583' => 'acertr', 'Atru.chr5.1358' => 'acertr', 'Atru.chr5.1359' => 'acertr', 'Atru.chr8.46' => 'acertr', 'AUR62002640' => 'cqu', 'AUR62030055' => 'cqu', 'AUR62033713' => 'cqu', 'AUR62033714' => 'cqu', 'AUR62036795' => 'cqu', 'AUR62039891' => 'cqu', 'BcaB02g08737' => 'bca', 'BcaB04g20441' => 'bca', 'BcaB06g26509' => 'bca', 'BcaB06g26510' => 'bca', 'BcaB06g26511' => 'bca', 'BcaB06g26512' => 'bca', 'BcaB06g26513' => 'bca', 'BcaC02g12564' => 'bca', 'BcaC02g12565' => 'bca', 'BcaC02g12794' => 'bca', 'BcaC02g12795' => 'bca', 'BcaC02g12796' => 'bca', 'BcaC06g35541' => 'bca', 'BNapus_Darmor_BZH_scaffold_188p00080' => 'bna', 'BNapus_Darmor_BZH_scaffold_188p00090' => 'bna', 'BolC1t03972H' => 'bol', 'BolC1t03973H' => 'bol', 'BolC4t21680H' => 'bol', 'BolC7t41863H' => 'bol', 'BolSC55t61227H' => 'bol', 'BolSC55t61228H' => 'bol', 'BraA01t03278Z' => 'bra', 'BraA05t18998Z' => 'bra', 'BraA07t28673Z' => 'bra', 'C01p40150' => 'bna', 'C05p12370' => 'bna', 'C07p13680' => 'bna', 'CAN.G1006.16' => 'can', 'CAN.G1006.17' => 'can', 'CAN.G1170.2' => 'can', 'CAN.G962.7' => 'can', 'CANSAT25G2179' => 'cansat', 'CANSAT78G1573' => 'cansat', 'CARHR099510' => 'chi', 'CARHR143510' => 'chi', 'Carub.0003s2380' => 'cru', 'Carub.0004s3082' => 'cru', 'Ca_00614_v3' => 'car', 'Ca_07801_v3' => 'car', 'Ca_08567_v3' => 'car', 'Ca_09571_v3' => 'car', 'CBR_g19290' => 'cbr', 'Cc01_g19770' => 'ccan', 'Cc03_g03030' => 'ccan', 'CDE07G0968' => 'cde', 'CDE09G1441' => 'cde', 'Cfa006103' => 'cfa', 'Cfa015573' => 'cfa', 'Cfa016988' => 'cfa', 'Ciclev10006738m.g' => 'ccl', 'Ciclev10010920m.g' => 'ccl', 'Ciclev10018517m.g' => 'ccl', 'CiPaw.01G159200' => 'cil', 'CiPaw.02G091000' => 'cil', 'CiPaw.02G091100' => 'cil', 'CiPaw.08G103100' => 'cil', 'CiPaw.09G224900' => 'cil', 'ClCG06G005740' => 'cla', 'ClCG07G000090' => 'cla', 'ClCG07G000100' => 'cla', 'COL.COLO4_09143' => 'col', 'COL.COLO4_25124' => 'col', 'Cpa.g.sc16.34' => 'cpa', 'Cpa.g.sc3504.1' => 'cpa', 'Cpa.g.sc60.37' => 'cpa', 'CsaV3_6G018520' => 'csa', 'CsaV3_6G036860' => 'csa', 'CSS0001072' => 'camsi', 'CSS0020208' => 'camsi', 'CSS0021253' => 'camsi', 'CSS0022190' => 'camsi', 'CSS0036150' => 'camsi', 'CSS0040442' => 'camsi', 'CSS0042300' => 'camsi', 'CSS0045298' => 'camsi', 'DCAR_012449' => 'dca', 'DCAR_018405' => 'dca', 'DCAR_024573' => 'dca', 'DCAR_030591' => 'dca', 'Dinv16926' => 'din', 'Dinv32963' => 'din', 'Dinv38382' => 'din', 'Dinv38383' => 'din', 'Duzib133G0974' => 'dzi', 'Duzib138G1867' => 'dzi', 'Duzib211G0420' => 'dzi', 'Duzib212G0930' => 'dzi', 'ECA234G1645' => 'eca', 'ECA247G3467' => 'eca', 'ECA248G1703' => 'eca', 'EL10Ac3g06327' => 'bvu', 'EL10Ac7g17204' => 'bvu', 'Eucgr.A00855' => 'egr', 'Eucgr.A00858' => 'egr', 'Eucgr.H01520' => 'egr', 'Eucgr.H03604' => 'egr', 'Eucgr.L03465' => 'egr', 'Eucgr.L03466' => 'egr', 'FAN01G0988' => 'fan', 'FAN02G3892' => 'fan', 'FAN05G3381' => 'fan', 'FAN07G0967' => 'fan', 'FAN07G1493' => 'fan', 'FAN08G3125' => 'fan', 'FAN09G0402' => 'fan', 'FAN12G2594' => 'fan', 'FAN12G3879' => 'fan', 'FAN14G1546' => 'fan', 'FAN15G3626' => 'fan', 'FAN17G0588' => 'fan', 'FAN17G0609' => 'fan', 'FAN18G2817' => 'fan', 'FAN19G1305' => 'fan', 'FAN20G1787' => 'fan', 'FAN22G0073' => 'fan', 'FAN22G0352' => 'fan', 'FAN22G0368' => 'fan', 'FAN22G2273' => 'fan', 'FAN24G1998' => 'fan', 'FAN27G1317' => 'fan', 'FvH4_2g23980' => 'fve', 'FvH4_4g14380' => 'fve', 'FvH4_4g14390' => 'fve', 'FvH4_6g09250' => 'fve', 'Glyma.03G151100' => 'gma', 'Glyma.04G122550' => 'gma', 'Glyma.05G001600' => 'gma', 'Glyma.09G270766' => 'gma', 'Glyma.09G270832' => 'gma', 'Glyma.13G209800' => 'gma', 'Glyma.15G102800' => 'gma', 'Glyma.18G218900' => 'gma', 'Glyma.19G001500' => 'gma', 'Glyma.19G153600' => 'gma', 'Gohir.A02G028600' => 'ghi', 'Gohir.A08G045000' => 'ghi', 'Gohir.A11G120500' => 'ghi', 'Gohir.A12G006200' => 'ghi', 'Gohir.A12G006250' => 'ghi', 'Gohir.D02G036300' => 'ghi', 'Gohir.D08G054700' => 'ghi', 'Gohir.D11G125600' => 'ghi', 'Gohir.D12G005700' => 'ghi', 'Gorai.004G055200' => 'gra', 'Gorai.005G040400' => 'gra', 'Gorai.007G134500' => 'gra', 'Gorai.008G005500' => 'gra', 'GSVIVG01011094001' => 'vvi', 'GSVIVG01017879001' => 'vvi', 'GSVIVG01025988001' => 'vvi', 'GSVIVG01029847001' => 'vvi', 'HanXRQChr10g0282901' => 'han', 'HanXRQChr10g0310371' => 'han', 'HanXRQChr10g0315041' => 'han', 'HanXRQChr11g0327651' => 'han', 'HanXRQChr12g0359391' => 'han', 'Haze_00972' => 'cav', 'Haze_00973' => 'cav', 'Haze_00974' => 'cav', 'Haze_04747' => 'cav', 'Haze_04749' => 'cav', 'Haze_04750' => 'cav', 'Haze_21217' => 'cav', 'Hma1.2p1_1037F.1_g250680' => 'hma', 'Hma1.2p1_1644F.1_g295320' => 'hma', 'HPP92_011322' => 'vpl', 'HPP92_011323' => 'vpl', 'HPP92_011324' => 'vpl', 'HPP92_011325' => 'vpl', 'HPP92_011326' => 'vpl', 'Hund12205' => 'sun', 'Hund17957' => 'sun', 'Lalb_Chr06g0176771' => 'lal', 'Lalb_Chr18g0056021' => 'lal', 'Lalb_Chr18g0056031' => 'lal', 'Lalb_Chr18g0056041' => 'lal', 'Lalb_Chr20g0107751' => 'lal', 'Lalb_Chr20g0118371' => 'lal', 'Lj1g0010239' => 'lja', 'Lj1g0017101' => 'lja', 'Lj2A1178G40' => 'lonja', 'Lj2A54G84' => 'lonja', 'Lj2g0015248' => 'lja', 'Lj3A761T51' => 'lonja', 'Lj6g0018116' => 'lja', 'Lsat_1_v5_gn_4_136040' => 'lsa', 'Lsat_1_v5_gn_5_187461' => 'lsa', 'Lsat_1_v5_gn_5_77001' => 'lsa', 'Lsat_1_v5_gn_9_4461' => 'lsa', 'Manes.01G210100' => 'mes', 'Manes.03G185600' => 'mes', 'Manes.05G073300' => 'mes', 'Manes.09G120300' => 'mes', 'Manes.15G022100' => 'mes', 'Mapoly0096s0053' => 'mpo', 'MBI03_g14058_MAGBIO' => 'mbi', 'MBI03_g33876_MAGBIO' => 'mbi', 'MBI03_g36854_MAGBIO' => 'mbi', 'MBI17_g11997_MAGBIO' => 'mbi', 'MD03G1269000' => 'mdo', 'MD04G1179600' => 'mdo', 'MD11G1289800' => 'mdo', 'MD12G1194700' => 'mdo', 'MD13G1182100' => 'mdo', 'MD13G1182200' => 'mdo', 'MD16G1182600' => 'mdo', 'Medtr2g021400' => 'mtr', 'Medtr2g021470' => 'mtr', 'Medtr2g105810' => 'mtr', 'Medtr3g033580' => 'mtr', 'Medtr6g007970' => 'mtr', 'Medtr7g056330' => 'mtr', 'Medtr7g074290' => 'mtr', 'Medtr7g074380' => 'mtr', 'Medtr7g094550' => 'mtr', 'Medtr8g069995' => 'mtr', 'MELO3C014345.2' => 'cme', 'MELO3C021395.2' => 'cme', 'Migut.D00262' => 'egut', 'Migut.G00257' => 'egut', 'MSTRG.21575' => 'ama', 'MSTRG.3985' => 'ama', 'Nitab4.5_0000295g0140' => 'nta', 'Nitab4.5_0000732g0140' => 'nta', 'Nitab4.5_0003162g0020' => 'nta', 'Nitab4.5_0006180g0090' => 'nta', 'Nitab4.5_0006390g0010' => 'nta', 'Nitab4.5_0007392g0040' => 'nta', 'Nn1g02140' => 'nnu', 'Nn4g26168' => 'nnu', 'Nn5g26754' => 'nnu', 'Oeu001433.1' => 'oeu', 'Oeu010299.2' => 'oeu', 'Oeu011171.1' => 'oeu', 'Oeu037675.1' => 'oeu', 'Oeu038359.1' => 'oeu', 'Oeu063834.1' => 'oeu', 'Oeu063835.1' => 'oeu', 'Os05g0312000' => 'osa', 'Os07g0211101' => 'osa', 'Os07g0211200' => 'osa', 'Os07g0681500' => 'osa', 'Peaxi162Scf00095g01015' => 'pax', 'Peaxi162Scf00104g00329' => 'pax', 'Peaxi162Scf00161g00137' => 'pax', 'PGR004G1665' => 'pgr', 'PGR031G2937' => 'pgr', 'PGR119G2145' => 'pgr', 'PGSC0003DMG400004351' => 'stu', 'PGSC0003DMG400014625' => 'stu', 'PGSC0003DMG401000943' => 'stu', 'Phvul.001G148600' => 'pvu', 'Phvul.004G001700' => 'pvu', 'Phvul.006G154900' => 'pvu', 'Phvul.008G078200' => 'pvu', 'Phvul.011G136500' => 'pvu', 'Potri.002G215600' => 'ptr', 'Potri.008G201600' => 'ptr', 'Potri.014G138400' => 'ptr', 'Potri.016G142500' => 'ptr', 'Pp3c16_10580' => 'ppa', 'Pp3c5_25280' => 'ppa', 'Prupe.1G150000' => 'ppe', 'Prupe.1G150100' => 'ppe', 'Prupe.6G299600' => 'ppe', 'Prupe.8G245000' => 'ppe', 'Psat0s4927g0040' => 'psa', 'Psat1g052080' => 'psa', 'Psat1g183800' => 'psa', 'Psat3g113840' => 'psa', 'Psat3g126120' => 'psa', 'Psat3g126160' => 'psa', 'Psat3g158760' => 'psa', 'Psat3g158840' => 'psa', 'PSO170G2858' => 'pso', 'PSO339G0606' => 'pso', 'PSO384G4709' => 'pso', 'PSO407G0334' => 'pso', 'QL04p040276' => 'qlo', 'QL06p005458' => 'qlo', 'QL06p005472' => 'qlo', 'QL07p030546' => 'qlo', 'QL07p031519' => 'qlo', 'QL09p050949' => 'qlo', 'QL09p050966' => 'qlo', 'QL09p051067' => 'qlo', 'QL12p022706' => 'qlo', 'RcHm_v2.0_Chr2g0119601' => 'rch', 'RcHm_v2.0_Chr3g0459591' => 'rch', 'RcHm_v2.0_Chr4g0418521' => 'rch', 'RcHm_v2.0_Chr4g0418531' => 'rch', 'RcHm_v2.0_Chr4g0418541' => 'rch', 'RcHm_v2.0_Chr6g0291641' => 'rch', 'Rhsim01G0086300' => 'rsi', 'Rhsim01G0276300' => 'rsi', 'Rhsim01G0276500' => 'rsi', 'Rhsim04G0207700' => 'rsi', 'Rhsim05G0234500' => 'rsi', 'Rhsim13G0022400' => 'rsi', 'Sabra02G0167900' => 'sbr', 'Sabra04G0158500' => 'sbr', 'Sabra08G0159800' => 'sbr', 'Sabra10G0011500' => 'sbr', 'Sabra14G0104400' => 'sbr', 'SalBow2G2440' => 'sbo', 'SalBow4G2265' => 'sbo', 'Sc02g0000060' => 'sci', 'Sc05g0005020' => 'sci', 'Sc13g0003890' => 'sci', 'Sed0014865' => 'sed', 'Sed0017224' => 'sed', 'Sed0026391' => 'sed', 'SEGI_00063' => 'sgi', 'SEGI_10967' => 'sgi', 'SEGI_17510' => 'sgi', 'SEGI_24396' => 'sgi', 'SEGI_39719' => 'sgi', 'SEGI_41392' => 'sgi', 'SGA_v2.0_scaffold11G05794' => 'sas', 'SGA_v2.0_scaffold142G35607' => 'sas', 'SGA_v2.0_scaffold1G00447' => 'sas', 'SHI15388' => 'shi', 'SHI15394' => 'shi', 'SHI15396' => 'shi', 'SHI15399' => 'shi', 'SMO343G0151' => 'smo', 'SMO367G1118' => 'smo', 'Solyc01g080200.3' => 'sly', 'Solyc06g008960.3' => 'sly', 'Solyc09g064780.3' => 'sly', 'Sopen01g031980' => 'spe', 'Sopen06g003710' => 'spe', 'Sopen09g026460' => 'spe', 'Sp3g21240' => 'spa', 'Sp4g30030' => 'spa', 'TAR365G0022' => 'tar', 'TAR365G1023' => 'tar', 'TAR365G1253' => 'tar', 'TAR623G0078' => 'tar', 'TAR623G1721' => 'tar', 'TAR633G0959' => 'tar', 'THA.LOC104802225' => 'tha', 'THA.LOC104804769' => 'tha', 'THA.LOC104808660' => 'tha', 'THA.LOC104812792' => 'tha', 'Thecc.01G284000' => 'tca', 'Thecc.04G220600' => 'tca', 'Thecc.05G268900' => 'tca', 'Thecc.08G171100' => 'tca', 'Thhalv10001284m.g' => 'esa', 'Thhalv10019912m.g' => 'esa', 'TPR.G14189' => 'tpr', 'TPR.G18110' => 'tpr', 'TPR.G18130' => 'tpr', 'TPR.G18131' => 'tpr', 'TPR.G18140' => 'tpr', 'TPR.G24282' => 'tpr', 'TPR.G25221' => 'tpr', 'TPR.G29267' => 'tpr', 'TPR.G35315' => 'tpr', 'TPR.G36173' => 'tpr', 'TWI09G0794' => 'twi', 'TWI59G1348' => 'twi', 'TWI74G0430' => 'twi', 'unitig_26.g8940' => 'ugi', 'unitig_749.g13744' => 'ugi', 'unitig_749.g13745' => 'ugi', 'vmacro08269' => 'vma', 'vmacro14937' => 'vma', 'vmacro20401' => 'vma', 'VMungo0464G1349' => 'vmu', 'VMungo0540G0289' => 'vmu', 'VMungo1215G1590' => 'vmu', 'VMungo1309G0221' => 'vmu', 'VMungo1309G2815' => 'vmu', 'VMungo1383G0239' => 'vmu', 'VMungo1383G2910' => 'vmu', 'Zm00001eb095270' => 'zma', 'Zm00001eb095280' => 'zma', 'Zm00001eb111630' => 'zma', 'Zm00001eb237080' => 'zma', 'Zm00001eb273740' => 'zma', 'Zm00001eb285040' => 'zma', 'Zm00001eb330790' => 'zma', 'Zm00001eb337380' => 'zma' ), 'gf_id' => 'HOM05D001484', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001484' ), 'data_identifier' => 'HOM05D001484', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001484', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p31500' => 'bna', 'A05p00020' => 'bna', 'A07p08820' => 'bna', 'Aa31LG4G3300' => 'aar', 'Aa31LG8G10030' => 'aar', 'Actinidia00731' => 'ach', 'Actinidia11473' => 'ach', 'Actinidia23469' => 'ach', 'Actinidia24318' => 'ach', 'Actinidia40196' => 'ach', 'Actinidia40197' => 'ach', 'Actinidia40198' => 'ach', 'Ah.08g212990' => 'amhyb', 'Ah.15g091720' => 'amhyb', 'AL3G38260' => 'aly', 'AL4G47710' => 'aly', 'Aqoxy2G00671' => 'aox', 'Aqoxy2G03236' => 'aox', 'arahy.Tifrunner.gnm1.ann1.05IDCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KR684' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATY3SJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK6QJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6APGL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IDT7Z9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM073U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ0R87' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LE7RV4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT4QRX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V5ENPK' => 'arhy', 'AT2G48110' => 'ath', 'AT3G23590' => 'ath', 'ATR0626G186' => 'atr', 'ATR1127G141' => 'atr', 'Atru.chr4.2583' => 'acertr', 'Atru.chr5.1358' => 'acertr', 'Atru.chr5.1359' => 'acertr', 'Atru.chr8.46' => 'acertr', 'AUR62002640' => 'cqu', 'AUR62030055' => 'cqu', 'AUR62033713' => 'cqu', 'AUR62033714' => 'cqu', 'AUR62036795' => 'cqu', 'AUR62039891' => 'cqu', 'BcaB02g08737' => 'bca', 'BcaB04g20441' => 'bca', 'BcaB06g26509' => 'bca', 'BcaB06g26510' => 'bca', 'BcaB06g26511' => 'bca', 'BcaB06g26512' => 'bca', 'BcaB06g26513' => 'bca', 'BcaC02g12564' => 'bca', 'BcaC02g12565' => 'bca', 'BcaC02g12794' => 'bca', 'BcaC02g12795' => 'bca', 'BcaC02g12796' => 'bca', 'BcaC06g35541' => 'bca', 'BNapus_Darmor_BZH_scaffold_188p00080' => 'bna', 'BNapus_Darmor_BZH_scaffold_188p00090' => 'bna', 'BolC1t03972H' => 'bol', 'BolC1t03973H' => 'bol', 'BolC4t21680H' => 'bol', 'BolC7t41863H' => 'bol', 'BolSC55t61227H' => 'bol', 'BolSC55t61228H' => 'bol', 'BraA01t03278Z' => 'bra', 'BraA05t18998Z' => 'bra', 'BraA07t28673Z' => 'bra', 'C01p40150' => 'bna', 'C05p12370' => 'bna', 'C07p13680' => 'bna', 'CAN.G1006.16' => 'can', 'CAN.G1006.17' => 'can', 'CAN.G1170.2' => 'can', 'CAN.G962.7' => 'can', 'CANSAT25G2179' => 'cansat', 'CANSAT78G1573' => 'cansat', 'CARHR099510' => 'chi', 'CARHR143510' => 'chi', 'Carub.0003s2380' => 'cru', 'Carub.0004s3082' => 'cru', 'Ca_00614_v3' => 'car', 'Ca_07801_v3' => 'car', 'Ca_08567_v3' => 'car', 'Ca_09571_v3' => 'car', 'CBR_g19290' => 'cbr', 'Cc01_g19770' => 'ccan', 'Cc03_g03030' => 'ccan', 'CDE07G0968' => 'cde', 'CDE09G1441' => 'cde', 'Cfa006103' => 'cfa', 'Cfa015573' => 'cfa', 'Cfa016988' => 'cfa', 'Ciclev10006738m.g' => 'ccl', 'Ciclev10010920m.g' => 'ccl', 'Ciclev10018517m.g' => 'ccl', 'CiPaw.01G159200' => 'cil', 'CiPaw.02G091000' => 'cil', 'CiPaw.02G091100' => 'cil', 'CiPaw.08G103100' => 'cil', 'CiPaw.09G224900' => 'cil', 'ClCG06G005740' => 'cla', 'ClCG07G000090' => 'cla', 'ClCG07G000100' => 'cla', 'COL.COLO4_09143' => 'col', 'COL.COLO4_25124' => 'col', 'Cpa.g.sc16.34' => 'cpa', 'Cpa.g.sc3504.1' => 'cpa', 'Cpa.g.sc60.37' => 'cpa', 'CsaV3_6G018520' => 'csa', 'CsaV3_6G036860' => 'csa', 'CSS0001072' => 'camsi', 'CSS0020208' => 'camsi', 'CSS0021253' => 'camsi', 'CSS0022190' => 'camsi', 'CSS0036150' => 'camsi', 'CSS0040442' => 'camsi', 'CSS0042300' => 'camsi', 'CSS0045298' => 'camsi', 'DCAR_012449' => 'dca', 'DCAR_018405' => 'dca', 'DCAR_024573' => 'dca', 'DCAR_030591' => 'dca', 'Dinv16926' => 'din', 'Dinv32963' => 'din', 'Dinv38382' => 'din', 'Dinv38383' => 'din', 'Duzib133G0974' => 'dzi', 'Duzib138G1867' => 'dzi', 'Duzib211G0420' => 'dzi', 'Duzib212G0930' => 'dzi', 'ECA234G1645' => 'eca', 'ECA247G3467' => 'eca', 'ECA248G1703' => 'eca', 'EL10Ac3g06327' => 'bvu', 'EL10Ac7g17204' => 'bvu', 'Eucgr.A00855' => 'egr', 'Eucgr.A00858' => 'egr', 'Eucgr.H01520' => 'egr', 'Eucgr.H03604' => 'egr', 'Eucgr.L03465' => 'egr', 'Eucgr.L03466' => 'egr', 'FAN01G0988' => 'fan', 'FAN02G3892' => 'fan', 'FAN05G3381' => 'fan', 'FAN07G0967' => 'fan', 'FAN07G1493' => 'fan', 'FAN08G3125' => 'fan', 'FAN09G0402' => 'fan', 'FAN12G2594' => 'fan', 'FAN12G3879' => 'fan', 'FAN14G1546' => 'fan', 'FAN15G3626' => 'fan', 'FAN17G0588' => 'fan', 'FAN17G0609' => 'fan', 'FAN18G2817' => 'fan', 'FAN19G1305' => 'fan', 'FAN20G1787' => 'fan', 'FAN22G0073' => 'fan', 'FAN22G0352' => 'fan', 'FAN22G0368' => 'fan', 'FAN22G2273' => 'fan', 'FAN24G1998' => 'fan', 'FAN27G1317' => 'fan', 'FvH4_2g23980' => 'fve', 'FvH4_4g14380' => 'fve', 'FvH4_4g14390' => 'fve', 'FvH4_6g09250' => 'fve', 'Glyma.03G151100' => 'gma', 'Glyma.04G122550' => 'gma', 'Glyma.05G001600' => 'gma', 'Glyma.09G270766' => 'gma', 'Glyma.09G270832' => 'gma', 'Glyma.13G209800' => 'gma', 'Glyma.15G102800' => 'gma', 'Glyma.18G218900' => 'gma', 'Glyma.19G001500' => 'gma', 'Glyma.19G153600' => 'gma', 'Gohir.A02G028600' => 'ghi', 'Gohir.A08G045000' => 'ghi', 'Gohir.A11G120500' => 'ghi', 'Gohir.A12G006200' => 'ghi', 'Gohir.A12G006250' => 'ghi', 'Gohir.D02G036300' => 'ghi', 'Gohir.D08G054700' => 'ghi', 'Gohir.D11G125600' => 'ghi', 'Gohir.D12G005700' => 'ghi', 'Gorai.004G055200' => 'gra', 'Gorai.005G040400' => 'gra', 'Gorai.007G134500' => 'gra', 'Gorai.008G005500' => 'gra', 'GSVIVG01011094001' => 'vvi', 'GSVIVG01017879001' => 'vvi', 'GSVIVG01025988001' => 'vvi', 'GSVIVG01029847001' => 'vvi', 'HanXRQChr10g0282901' => 'han', 'HanXRQChr10g0310371' => 'han', 'HanXRQChr10g0315041' => 'han', 'HanXRQChr11g0327651' => 'han', 'HanXRQChr12g0359391' => 'han', 'Haze_00972' => 'cav', 'Haze_00973' => 'cav', 'Haze_00974' => 'cav', 'Haze_04747' => 'cav', 'Haze_04749' => 'cav', 'Haze_04750' => 'cav', 'Haze_21217' => 'cav', 'Hma1.2p1_1037F.1_g250680' => 'hma', 'Hma1.2p1_1644F.1_g295320' => 'hma', 'HPP92_011322' => 'vpl', 'HPP92_011323' => 'vpl', 'HPP92_011324' => 'vpl', 'HPP92_011325' => 'vpl', 'HPP92_011326' => 'vpl', 'Hund12205' => 'sun', 'Hund17957' => 'sun', 'Lalb_Chr06g0176771' => 'lal', 'Lalb_Chr18g0056021' => 'lal', 'Lalb_Chr18g0056031' => 'lal', 'Lalb_Chr18g0056041' => 'lal', 'Lalb_Chr20g0107751' => 'lal', 'Lalb_Chr20g0118371' => 'lal', 'Lj1g0010239' => 'lja', 'Lj1g0017101' => 'lja', 'Lj2A1178G40' => 'lonja', 'Lj2A54G84' => 'lonja', 'Lj2g0015248' => 'lja', 'Lj3A761T51' => 'lonja', 'Lj6g0018116' => 'lja', 'Lsat_1_v5_gn_4_136040' => 'lsa', 'Lsat_1_v5_gn_5_187461' => 'lsa', 'Lsat_1_v5_gn_5_77001' => 'lsa', 'Lsat_1_v5_gn_9_4461' => 'lsa', 'Manes.01G210100' => 'mes', 'Manes.03G185600' => 'mes', 'Manes.05G073300' => 'mes', 'Manes.09G120300' => 'mes', 'Manes.15G022100' => 'mes', 'Mapoly0096s0053' => 'mpo', 'MBI03_g14058_MAGBIO' => 'mbi', 'MBI03_g33876_MAGBIO' => 'mbi', 'MBI03_g36854_MAGBIO' => 'mbi', 'MBI17_g11997_MAGBIO' => 'mbi', 'MD03G1269000' => 'mdo', 'MD04G1179600' => 'mdo', 'MD11G1289800' => 'mdo', 'MD12G1194700' => 'mdo', 'MD13G1182100' => 'mdo', 'MD13G1182200' => 'mdo', 'MD16G1182600' => 'mdo', 'Medtr2g021400' => 'mtr', 'Medtr2g021470' => 'mtr', 'Medtr2g105810' => 'mtr', 'Medtr3g033580' => 'mtr', 'Medtr6g007970' => 'mtr', 'Medtr7g056330' => 'mtr', 'Medtr7g074290' => 'mtr', 'Medtr7g074380' => 'mtr', 'Medtr7g094550' => 'mtr', 'Medtr8g069995' => 'mtr', 'MELO3C014345.2' => 'cme', 'MELO3C021395.2' => 'cme', 'Migut.D00262' => 'egut', 'Migut.G00257' => 'egut', 'MSTRG.21575' => 'ama', 'MSTRG.3985' => 'ama', 'Nitab4.5_0000295g0140' => 'nta', 'Nitab4.5_0000732g0140' => 'nta', 'Nitab4.5_0003162g0020' => 'nta', 'Nitab4.5_0006180g0090' => 'nta', 'Nitab4.5_0006390g0010' => 'nta', 'Nitab4.5_0007392g0040' => 'nta', 'Nn1g02140' => 'nnu', 'Nn4g26168' => 'nnu', 'Nn5g26754' => 'nnu', 'Oeu001433.1' => 'oeu', 'Oeu010299.2' => 'oeu', 'Oeu011171.1' => 'oeu', 'Oeu037675.1' => 'oeu', 'Oeu038359.1' => 'oeu', 'Oeu063834.1' => 'oeu', 'Oeu063835.1' => 'oeu', 'Os05g0312000' => 'osa', 'Os07g0211101' => 'osa', 'Os07g0211200' => 'osa', 'Os07g0681500' => 'osa', 'Peaxi162Scf00095g01015' => 'pax', 'Peaxi162Scf00104g00329' => 'pax', 'Peaxi162Scf00161g00137' => 'pax', 'PGR004G1665' => 'pgr', 'PGR031G2937' => 'pgr', 'PGR119G2145' => 'pgr', 'PGSC0003DMG400004351' => 'stu', 'PGSC0003DMG400014625' => 'stu', 'PGSC0003DMG401000943' => 'stu', 'Phvul.001G148600' => 'pvu', 'Phvul.004G001700' => 'pvu', 'Phvul.006G154900' => 'pvu', 'Phvul.008G078200' => 'pvu', 'Phvul.011G136500' => 'pvu', 'Potri.002G215600' => 'ptr', 'Potri.008G201600' => 'ptr', 'Potri.014G138400' => 'ptr', 'Potri.016G142500' => 'ptr', 'Pp3c16_10580' => 'ppa', 'Pp3c5_25280' => 'ppa', 'Prupe.1G150000' => 'ppe', 'Prupe.1G150100' => 'ppe', 'Prupe.6G299600' => 'ppe', 'Prupe.8G245000' => 'ppe', 'Psat0s4927g0040' => 'psa', 'Psat1g052080' => 'psa', 'Psat1g183800' => 'psa', 'Psat3g113840' => 'psa', 'Psat3g126120' => 'psa', 'Psat3g126160' => 'psa', 'Psat3g158760' => 'psa', 'Psat3g158840' => 'psa', 'PSO170G2858' => 'pso', 'PSO339G0606' => 'pso', 'PSO384G4709' => 'pso', 'PSO407G0334' => 'pso', 'QL04p040276' => 'qlo', 'QL06p005458' => 'qlo', 'QL06p005472' => 'qlo', 'QL07p030546' => 'qlo', 'QL07p031519' => 'qlo', 'QL09p050949' => 'qlo', 'QL09p050966' => 'qlo', 'QL09p051067' => 'qlo', 'QL12p022706' => 'qlo', 'RcHm_v2.0_Chr2g0119601' => 'rch', 'RcHm_v2.0_Chr3g0459591' => 'rch', 'RcHm_v2.0_Chr4g0418521' => 'rch', 'RcHm_v2.0_Chr4g0418531' => 'rch', 'RcHm_v2.0_Chr4g0418541' => 'rch', 'RcHm_v2.0_Chr6g0291641' => 'rch', 'Rhsim01G0086300' => 'rsi', 'Rhsim01G0276300' => 'rsi', 'Rhsim01G0276500' => 'rsi', 'Rhsim04G0207700' => 'rsi', 'Rhsim05G0234500' => 'rsi', 'Rhsim13G0022400' => 'rsi', 'Sabra02G0167900' => 'sbr', 'Sabra04G0158500' => 'sbr', 'Sabra08G0159800' => 'sbr', 'Sabra10G0011500' => 'sbr', 'Sabra14G0104400' => 'sbr', 'SalBow2G2440' => 'sbo', 'SalBow4G2265' => 'sbo', 'Sc02g0000060' => 'sci', 'Sc05g0005020' => 'sci', 'Sc13g0003890' => 'sci', 'Sed0014865' => 'sed', 'Sed0017224' => 'sed', 'Sed0026391' => 'sed', 'SEGI_00063' => 'sgi', 'SEGI_10967' => 'sgi', 'SEGI_17510' => 'sgi', 'SEGI_24396' => 'sgi', 'SEGI_39719' => 'sgi', 'SEGI_41392' => 'sgi', 'SGA_v2.0_scaffold11G05794' => 'sas', 'SGA_v2.0_scaffold142G35607' => 'sas', 'SGA_v2.0_scaffold1G00447' => 'sas', 'SHI15388' => 'shi', 'SHI15394' => 'shi', 'SHI15396' => 'shi', 'SHI15399' => 'shi', 'SMO343G0151' => 'smo', 'SMO367G1118' => 'smo', 'Solyc01g080200.3' => 'sly', 'Solyc06g008960.3' => 'sly', 'Solyc09g064780.3' => 'sly', 'Sopen01g031980' => 'spe', 'Sopen06g003710' => 'spe', 'Sopen09g026460' => 'spe', 'Sp3g21240' => 'spa', 'Sp4g30030' => 'spa', 'TAR365G0022' => 'tar', 'TAR365G1023' => 'tar', 'TAR365G1253' => 'tar', 'TAR623G0078' => 'tar', 'TAR623G1721' => 'tar', 'TAR633G0959' => 'tar', 'THA.LOC104802225' => 'tha', 'THA.LOC104804769' => 'tha', 'THA.LOC104808660' => 'tha', 'THA.LOC104812792' => 'tha', 'Thecc.01G284000' => 'tca', 'Thecc.04G220600' => 'tca', 'Thecc.05G268900' => 'tca', 'Thecc.08G171100' => 'tca', 'Thhalv10001284m.g' => 'esa', 'Thhalv10019912m.g' => 'esa', 'TPR.G14189' => 'tpr', 'TPR.G18110' => 'tpr', 'TPR.G18130' => 'tpr', 'TPR.G18131' => 'tpr', 'TPR.G18140' => 'tpr', 'TPR.G24282' => 'tpr', 'TPR.G25221' => 'tpr', 'TPR.G29267' => 'tpr', 'TPR.G35315' => 'tpr', 'TPR.G36173' => 'tpr', 'TWI09G0794' => 'twi', 'TWI59G1348' => 'twi', 'TWI74G0430' => 'twi', 'unitig_26.g8940' => 'ugi', 'unitig_749.g13744' => 'ugi', 'unitig_749.g13745' => 'ugi', 'vmacro08269' => 'vma', 'vmacro14937' => 'vma', 'vmacro20401' => 'vma', 'VMungo0464G1349' => 'vmu', 'VMungo0540G0289' => 'vmu', 'VMungo1215G1590' => 'vmu', 'VMungo1309G0221' => 'vmu', 'VMungo1309G2815' => 'vmu', 'VMungo1383G0239' => 'vmu', 'VMungo1383G2910' => 'vmu', 'Zm00001eb095270' => 'zma', 'Zm00001eb095280' => 'zma', 'Zm00001eb111630' => 'zma', 'Zm00001eb237080' => 'zma', 'Zm00001eb273740' => 'zma', 'Zm00001eb285040' => 'zma', 'Zm00001eb330790' => 'zma', 'Zm00001eb337380' => 'zma' ) $gf_id = 'HOM05D001484' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001484' ) $data_identifier = 'HOM05D001484' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 2, 'aly' => (int) 2, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 22, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 7, 'hma' => (int) 2, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 7, 'mtr' => (int) 10, 'cme' => (int) 2, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 4, 'ppa' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 4, 'qlo' => (int) 9, 'rch' => (int) 6, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 10, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 7, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb337380' $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' => 'HOM05D001484', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p31500' => 'bna', 'A05p00020' => 'bna', 'A07p08820' => 'bna', 'Aa31LG4G3300' => 'aar', 'Aa31LG8G10030' => 'aar', 'Actinidia00731' => 'ach', 'Actinidia11473' => 'ach', 'Actinidia23469' => 'ach', 'Actinidia24318' => 'ach', 'Actinidia40196' => 'ach', 'Actinidia40197' => 'ach', 'Actinidia40198' => 'ach', 'Ah.08g212990' => 'amhyb', 'Ah.15g091720' => 'amhyb', 'AL3G38260' => 'aly', 'AL4G47710' => 'aly', 'Aqoxy2G00671' => 'aox', 'Aqoxy2G03236' => 'aox', 'arahy.Tifrunner.gnm1.ann1.05IDCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KR684' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATY3SJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK6QJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6APGL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IDT7Z9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM073U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ0R87' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LE7RV4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT4QRX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V5ENPK' => 'arhy', 'AT2G48110' => 'ath', 'AT3G23590' => 'ath', 'ATR0626G186' => 'atr', 'ATR1127G141' => 'atr', 'Atru.chr4.2583' => 'acertr', 'Atru.chr5.1358' => 'acertr', 'Atru.chr5.1359' => 'acertr', 'Atru.chr8.46' => 'acertr', 'AUR62002640' => 'cqu', 'AUR62030055' => 'cqu', 'AUR62033713' => 'cqu', 'AUR62033714' => 'cqu', 'AUR62036795' => 'cqu', 'AUR62039891' => 'cqu', 'BcaB02g08737' => 'bca', 'BcaB04g20441' => 'bca', 'BcaB06g26509' => 'bca', 'BcaB06g26510' => 'bca', 'BcaB06g26511' => 'bca', 'BcaB06g26512' => 'bca', 'BcaB06g26513' => 'bca', 'BcaC02g12564' => 'bca', 'BcaC02g12565' => 'bca', 'BcaC02g12794' => 'bca', 'BcaC02g12795' => 'bca', 'BcaC02g12796' => 'bca', 'BcaC06g35541' => 'bca', 'BNapus_Darmor_BZH_scaffold_188p00080' => 'bna', 'BNapus_Darmor_BZH_scaffold_188p00090' => 'bna', 'BolC1t03972H' => 'bol', 'BolC1t03973H' => 'bol', 'BolC4t21680H' => 'bol', 'BolC7t41863H' => 'bol', 'BolSC55t61227H' => 'bol', 'BolSC55t61228H' => 'bol', 'BraA01t03278Z' => 'bra', 'BraA05t18998Z' => 'bra', 'BraA07t28673Z' => 'bra', 'C01p40150' => 'bna', 'C05p12370' => 'bna', 'C07p13680' => 'bna', 'CAN.G1006.16' => 'can', 'CAN.G1006.17' => 'can', 'CAN.G1170.2' => 'can', 'CAN.G962.7' => 'can', 'CANSAT25G2179' => 'cansat', 'CANSAT78G1573' => 'cansat', 'CARHR099510' => 'chi', 'CARHR143510' => 'chi', 'Carub.0003s2380' => 'cru', 'Carub.0004s3082' => 'cru', 'Ca_00614_v3' => 'car', 'Ca_07801_v3' => 'car', 'Ca_08567_v3' => 'car', 'Ca_09571_v3' => 'car', 'CBR_g19290' => 'cbr', 'Cc01_g19770' => 'ccan', 'Cc03_g03030' => 'ccan', 'CDE07G0968' => 'cde', 'CDE09G1441' => 'cde', 'Cfa006103' => 'cfa', 'Cfa015573' => 'cfa', 'Cfa016988' => 'cfa', 'Ciclev10006738m.g' => 'ccl', 'Ciclev10010920m.g' => 'ccl', 'Ciclev10018517m.g' => 'ccl', 'CiPaw.01G159200' => 'cil', 'CiPaw.02G091000' => 'cil', 'CiPaw.02G091100' => 'cil', 'CiPaw.08G103100' => 'cil', 'CiPaw.09G224900' => 'cil', 'ClCG06G005740' => 'cla', 'ClCG07G000090' => 'cla', 'ClCG07G000100' => 'cla', 'COL.COLO4_09143' => 'col', 'COL.COLO4_25124' => 'col', 'Cpa.g.sc16.34' => 'cpa', 'Cpa.g.sc3504.1' => 'cpa', 'Cpa.g.sc60.37' => 'cpa', 'CsaV3_6G018520' => 'csa', 'CsaV3_6G036860' => 'csa', 'CSS0001072' => 'camsi', 'CSS0020208' => 'camsi', 'CSS0021253' => 'camsi', 'CSS0022190' => 'camsi', 'CSS0036150' => 'camsi', 'CSS0040442' => 'camsi', 'CSS0042300' => 'camsi', 'CSS0045298' => 'camsi', 'DCAR_012449' => 'dca', 'DCAR_018405' => 'dca', 'DCAR_024573' => 'dca', 'DCAR_030591' => 'dca', 'Dinv16926' => 'din', 'Dinv32963' => 'din', 'Dinv38382' => 'din', 'Dinv38383' => 'din', 'Duzib133G0974' => 'dzi', 'Duzib138G1867' => 'dzi', 'Duzib211G0420' => 'dzi', 'Duzib212G0930' => 'dzi', 'ECA234G1645' => 'eca', 'ECA247G3467' => 'eca', 'ECA248G1703' => 'eca', 'EL10Ac3g06327' => 'bvu', 'EL10Ac7g17204' => 'bvu', 'Eucgr.A00855' => 'egr', 'Eucgr.A00858' => 'egr', 'Eucgr.H01520' => 'egr', 'Eucgr.H03604' => 'egr', 'Eucgr.L03465' => 'egr', 'Eucgr.L03466' => 'egr', 'FAN01G0988' => 'fan', 'FAN02G3892' => 'fan', 'FAN05G3381' => 'fan', 'FAN07G0967' => 'fan', 'FAN07G1493' => 'fan', 'FAN08G3125' => 'fan', 'FAN09G0402' => 'fan', 'FAN12G2594' => 'fan', 'FAN12G3879' => 'fan', 'FAN14G1546' => 'fan', 'FAN15G3626' => 'fan', 'FAN17G0588' => 'fan', 'FAN17G0609' => 'fan', 'FAN18G2817' => 'fan', 'FAN19G1305' => 'fan', 'FAN20G1787' => 'fan', 'FAN22G0073' => 'fan', 'FAN22G0352' => 'fan', 'FAN22G0368' => 'fan', 'FAN22G2273' => 'fan', 'FAN24G1998' => 'fan', 'FAN27G1317' => 'fan', 'FvH4_2g23980' => 'fve', 'FvH4_4g14380' => 'fve', 'FvH4_4g14390' => 'fve', 'FvH4_6g09250' => 'fve', 'Glyma.03G151100' => 'gma', 'Glyma.04G122550' => 'gma', 'Glyma.05G001600' => 'gma', 'Glyma.09G270766' => 'gma', 'Glyma.09G270832' => 'gma', 'Glyma.13G209800' => 'gma', 'Glyma.15G102800' => 'gma', 'Glyma.18G218900' => 'gma', 'Glyma.19G001500' => 'gma', 'Glyma.19G153600' => 'gma', 'Gohir.A02G028600' => 'ghi', 'Gohir.A08G045000' => 'ghi', 'Gohir.A11G120500' => 'ghi', 'Gohir.A12G006200' => 'ghi', 'Gohir.A12G006250' => 'ghi', 'Gohir.D02G036300' => 'ghi', 'Gohir.D08G054700' => 'ghi', 'Gohir.D11G125600' => 'ghi', 'Gohir.D12G005700' => 'ghi', 'Gorai.004G055200' => 'gra', 'Gorai.005G040400' => 'gra', 'Gorai.007G134500' => 'gra', 'Gorai.008G005500' => 'gra', 'GSVIVG01011094001' => 'vvi', 'GSVIVG01017879001' => 'vvi', 'GSVIVG01025988001' => 'vvi', 'GSVIVG01029847001' => 'vvi', 'HanXRQChr10g0282901' => 'han', 'HanXRQChr10g0310371' => 'han', 'HanXRQChr10g0315041' => 'han', 'HanXRQChr11g0327651' => 'han', 'HanXRQChr12g0359391' => 'han', 'Haze_00972' => 'cav', 'Haze_00973' => 'cav', 'Haze_00974' => 'cav', 'Haze_04747' => 'cav', 'Haze_04749' => 'cav', 'Haze_04750' => 'cav', 'Haze_21217' => 'cav', 'Hma1.2p1_1037F.1_g250680' => 'hma', 'Hma1.2p1_1644F.1_g295320' => 'hma', 'HPP92_011322' => 'vpl', 'HPP92_011323' => 'vpl', 'HPP92_011324' => 'vpl', 'HPP92_011325' => 'vpl', 'HPP92_011326' => 'vpl', 'Hund12205' => 'sun', 'Hund17957' => 'sun', 'Lalb_Chr06g0176771' => 'lal', 'Lalb_Chr18g0056021' => 'lal', 'Lalb_Chr18g0056031' => 'lal', 'Lalb_Chr18g0056041' => 'lal', 'Lalb_Chr20g0107751' => 'lal', 'Lalb_Chr20g0118371' => 'lal', 'Lj1g0010239' => 'lja', 'Lj1g0017101' => 'lja', 'Lj2A1178G40' => 'lonja', 'Lj2A54G84' => 'lonja', 'Lj2g0015248' => 'lja', 'Lj3A761T51' => 'lonja', 'Lj6g0018116' => 'lja', 'Lsat_1_v5_gn_4_136040' => 'lsa', 'Lsat_1_v5_gn_5_187461' => 'lsa', 'Lsat_1_v5_gn_5_77001' => 'lsa', 'Lsat_1_v5_gn_9_4461' => 'lsa', 'Manes.01G210100' => 'mes', 'Manes.03G185600' => 'mes', 'Manes.05G073300' => 'mes', 'Manes.09G120300' => 'mes', 'Manes.15G022100' => 'mes', 'Mapoly0096s0053' => 'mpo', 'MBI03_g14058_MAGBIO' => 'mbi', 'MBI03_g33876_MAGBIO' => 'mbi', 'MBI03_g36854_MAGBIO' => 'mbi', 'MBI17_g11997_MAGBIO' => 'mbi', 'MD03G1269000' => 'mdo', 'MD04G1179600' => 'mdo', 'MD11G1289800' => 'mdo', 'MD12G1194700' => 'mdo', 'MD13G1182100' => 'mdo', 'MD13G1182200' => 'mdo', 'MD16G1182600' => 'mdo', 'Medtr2g021400' => 'mtr', 'Medtr2g021470' => 'mtr', 'Medtr2g105810' => 'mtr', 'Medtr3g033580' => 'mtr', 'Medtr6g007970' => 'mtr', 'Medtr7g056330' => 'mtr', 'Medtr7g074290' => 'mtr', 'Medtr7g074380' => 'mtr', 'Medtr7g094550' => 'mtr', 'Medtr8g069995' => 'mtr', 'MELO3C014345.2' => 'cme', 'MELO3C021395.2' => 'cme', 'Migut.D00262' => 'egut', 'Migut.G00257' => 'egut', 'MSTRG.21575' => 'ama', 'MSTRG.3985' => 'ama', 'Nitab4.5_0000295g0140' => 'nta', 'Nitab4.5_0000732g0140' => 'nta', 'Nitab4.5_0003162g0020' => 'nta', 'Nitab4.5_0006180g0090' => 'nta', 'Nitab4.5_0006390g0010' => 'nta', 'Nitab4.5_0007392g0040' => 'nta', 'Nn1g02140' => 'nnu', 'Nn4g26168' => 'nnu', 'Nn5g26754' => 'nnu', 'Oeu001433.1' => 'oeu', 'Oeu010299.2' => 'oeu', 'Oeu011171.1' => 'oeu', 'Oeu037675.1' => 'oeu', 'Oeu038359.1' => 'oeu', 'Oeu063834.1' => 'oeu', 'Oeu063835.1' => 'oeu', 'Os05g0312000' => 'osa', 'Os07g0211101' => 'osa', 'Os07g0211200' => 'osa', 'Os07g0681500' => 'osa', 'Peaxi162Scf00095g01015' => 'pax', 'Peaxi162Scf00104g00329' => 'pax', 'Peaxi162Scf00161g00137' => 'pax', 'PGR004G1665' => 'pgr', 'PGR031G2937' => 'pgr', 'PGR119G2145' => 'pgr', 'PGSC0003DMG400004351' => 'stu', 'PGSC0003DMG400014625' => 'stu', 'PGSC0003DMG401000943' => 'stu', 'Phvul.001G148600' => 'pvu', 'Phvul.004G001700' => 'pvu', 'Phvul.006G154900' => 'pvu', 'Phvul.008G078200' => 'pvu', 'Phvul.011G136500' => 'pvu', 'Potri.002G215600' => 'ptr', 'Potri.008G201600' => 'ptr', 'Potri.014G138400' => 'ptr', 'Potri.016G142500' => 'ptr', 'Pp3c16_10580' => 'ppa', 'Pp3c5_25280' => 'ppa', 'Prupe.1G150000' => 'ppe', 'Prupe.1G150100' => 'ppe', 'Prupe.6G299600' => 'ppe', 'Prupe.8G245000' => 'ppe', 'Psat0s4927g0040' => 'psa', 'Psat1g052080' => 'psa', 'Psat1g183800' => 'psa', 'Psat3g113840' => 'psa', 'Psat3g126120' => 'psa', 'Psat3g126160' => 'psa', 'Psat3g158760' => 'psa', 'Psat3g158840' => 'psa', 'PSO170G2858' => 'pso', 'PSO339G0606' => 'pso', 'PSO384G4709' => 'pso', 'PSO407G0334' => 'pso', 'QL04p040276' => 'qlo', 'QL06p005458' => 'qlo', 'QL06p005472' => 'qlo', 'QL07p030546' => 'qlo', 'QL07p031519' => 'qlo', 'QL09p050949' => 'qlo', 'QL09p050966' => 'qlo', 'QL09p051067' => 'qlo', 'QL12p022706' => 'qlo', 'RcHm_v2.0_Chr2g0119601' => 'rch', 'RcHm_v2.0_Chr3g0459591' => 'rch', 'RcHm_v2.0_Chr4g0418521' => 'rch', 'RcHm_v2.0_Chr4g0418531' => 'rch', 'RcHm_v2.0_Chr4g0418541' => 'rch', 'RcHm_v2.0_Chr6g0291641' => 'rch', 'Rhsim01G0086300' => 'rsi', 'Rhsim01G0276300' => 'rsi', 'Rhsim01G0276500' => 'rsi', 'Rhsim04G0207700' => 'rsi', 'Rhsim05G0234500' => 'rsi', 'Rhsim13G0022400' => 'rsi', 'Sabra02G0167900' => 'sbr', 'Sabra04G0158500' => 'sbr', 'Sabra08G0159800' => 'sbr', 'Sabra10G0011500' => 'sbr', 'Sabra14G0104400' => 'sbr', 'SalBow2G2440' => 'sbo', 'SalBow4G2265' => 'sbo', 'Sc02g0000060' => 'sci', 'Sc05g0005020' => 'sci', 'Sc13g0003890' => 'sci', 'Sed0014865' => 'sed', 'Sed0017224' => 'sed', 'Sed0026391' => 'sed', 'SEGI_00063' => 'sgi', 'SEGI_10967' => 'sgi', 'SEGI_17510' => 'sgi', 'SEGI_24396' => 'sgi', 'SEGI_39719' => 'sgi', 'SEGI_41392' => 'sgi', 'SGA_v2.0_scaffold11G05794' => 'sas', 'SGA_v2.0_scaffold142G35607' => 'sas', 'SGA_v2.0_scaffold1G00447' => 'sas', 'SHI15388' => 'shi', 'SHI15394' => 'shi', 'SHI15396' => 'shi', 'SHI15399' => 'shi', 'SMO343G0151' => 'smo', 'SMO367G1118' => 'smo', 'Solyc01g080200.3' => 'sly', 'Solyc06g008960.3' => 'sly', 'Solyc09g064780.3' => 'sly', 'Sopen01g031980' => 'spe', 'Sopen06g003710' => 'spe', 'Sopen09g026460' => 'spe', 'Sp3g21240' => 'spa', 'Sp4g30030' => 'spa', 'TAR365G0022' => 'tar', 'TAR365G1023' => 'tar', 'TAR365G1253' => 'tar', 'TAR623G0078' => 'tar', 'TAR623G1721' => 'tar', 'TAR633G0959' => 'tar', 'THA.LOC104802225' => 'tha', 'THA.LOC104804769' => 'tha', 'THA.LOC104808660' => 'tha', 'THA.LOC104812792' => 'tha', 'Thecc.01G284000' => 'tca', 'Thecc.04G220600' => 'tca', 'Thecc.05G268900' => 'tca', 'Thecc.08G171100' => 'tca', 'Thhalv10001284m.g' => 'esa', 'Thhalv10019912m.g' => 'esa', 'TPR.G14189' => 'tpr', 'TPR.G18110' => 'tpr', 'TPR.G18130' => 'tpr', 'TPR.G18131' => 'tpr', 'TPR.G18140' => 'tpr', 'TPR.G24282' => 'tpr', 'TPR.G25221' => 'tpr', 'TPR.G29267' => 'tpr', 'TPR.G35315' => 'tpr', 'TPR.G36173' => 'tpr', 'TWI09G0794' => 'twi', 'TWI59G1348' => 'twi', 'TWI74G0430' => 'twi', 'unitig_26.g8940' => 'ugi', 'unitig_749.g13744' => 'ugi', 'unitig_749.g13745' => 'ugi', 'vmacro08269' => 'vma', 'vmacro14937' => 'vma', 'vmacro20401' => 'vma', 'VMungo0464G1349' => 'vmu', 'VMungo0540G0289' => 'vmu', 'VMungo1215G1590' => 'vmu', 'VMungo1309G0221' => 'vmu', 'VMungo1309G2815' => 'vmu', 'VMungo1383G0239' => 'vmu', 'VMungo1383G2910' => 'vmu', 'Zm00001eb095270' => 'zma', 'Zm00001eb095280' => 'zma', 'Zm00001eb111630' => 'zma', 'Zm00001eb237080' => 'zma', 'Zm00001eb273740' => 'zma', 'Zm00001eb285040' => 'zma', 'Zm00001eb330790' => 'zma', 'Zm00001eb337380' => 'zma' ), 'gf_id' => 'HOM05D001484', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001484' ), 'data_identifier' => 'HOM05D001484', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001484', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p31500' => 'bna', 'A05p00020' => 'bna', 'A07p08820' => 'bna', 'Aa31LG4G3300' => 'aar', 'Aa31LG8G10030' => 'aar', 'Actinidia00731' => 'ach', 'Actinidia11473' => 'ach', 'Actinidia23469' => 'ach', 'Actinidia24318' => 'ach', 'Actinidia40196' => 'ach', 'Actinidia40197' => 'ach', 'Actinidia40198' => 'ach', 'Ah.08g212990' => 'amhyb', 'Ah.15g091720' => 'amhyb', 'AL3G38260' => 'aly', 'AL4G47710' => 'aly', 'Aqoxy2G00671' => 'aox', 'Aqoxy2G03236' => 'aox', 'arahy.Tifrunner.gnm1.ann1.05IDCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KR684' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATY3SJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK6QJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6APGL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IDT7Z9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM073U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ0R87' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LE7RV4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT4QRX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V5ENPK' => 'arhy', 'AT2G48110' => 'ath', 'AT3G23590' => 'ath', 'ATR0626G186' => 'atr', 'ATR1127G141' => 'atr', 'Atru.chr4.2583' => 'acertr', 'Atru.chr5.1358' => 'acertr', 'Atru.chr5.1359' => 'acertr', 'Atru.chr8.46' => 'acertr', 'AUR62002640' => 'cqu', 'AUR62030055' => 'cqu', 'AUR62033713' => 'cqu', 'AUR62033714' => 'cqu', 'AUR62036795' => 'cqu', 'AUR62039891' => 'cqu', 'BcaB02g08737' => 'bca', 'BcaB04g20441' => 'bca', 'BcaB06g26509' => 'bca', 'BcaB06g26510' => 'bca', 'BcaB06g26511' => 'bca', 'BcaB06g26512' => 'bca', 'BcaB06g26513' => 'bca', 'BcaC02g12564' => 'bca', 'BcaC02g12565' => 'bca', 'BcaC02g12794' => 'bca', 'BcaC02g12795' => 'bca', 'BcaC02g12796' => 'bca', 'BcaC06g35541' => 'bca', 'BNapus_Darmor_BZH_scaffold_188p00080' => 'bna', 'BNapus_Darmor_BZH_scaffold_188p00090' => 'bna', 'BolC1t03972H' => 'bol', 'BolC1t03973H' => 'bol', 'BolC4t21680H' => 'bol', 'BolC7t41863H' => 'bol', 'BolSC55t61227H' => 'bol', 'BolSC55t61228H' => 'bol', 'BraA01t03278Z' => 'bra', 'BraA05t18998Z' => 'bra', 'BraA07t28673Z' => 'bra', 'C01p40150' => 'bna', 'C05p12370' => 'bna', 'C07p13680' => 'bna', 'CAN.G1006.16' => 'can', 'CAN.G1006.17' => 'can', 'CAN.G1170.2' => 'can', 'CAN.G962.7' => 'can', 'CANSAT25G2179' => 'cansat', 'CANSAT78G1573' => 'cansat', 'CARHR099510' => 'chi', 'CARHR143510' => 'chi', 'Carub.0003s2380' => 'cru', 'Carub.0004s3082' => 'cru', 'Ca_00614_v3' => 'car', 'Ca_07801_v3' => 'car', 'Ca_08567_v3' => 'car', 'Ca_09571_v3' => 'car', 'CBR_g19290' => 'cbr', 'Cc01_g19770' => 'ccan', 'Cc03_g03030' => 'ccan', 'CDE07G0968' => 'cde', 'CDE09G1441' => 'cde', 'Cfa006103' => 'cfa', 'Cfa015573' => 'cfa', 'Cfa016988' => 'cfa', 'Ciclev10006738m.g' => 'ccl', 'Ciclev10010920m.g' => 'ccl', 'Ciclev10018517m.g' => 'ccl', 'CiPaw.01G159200' => 'cil', 'CiPaw.02G091000' => 'cil', 'CiPaw.02G091100' => 'cil', 'CiPaw.08G103100' => 'cil', 'CiPaw.09G224900' => 'cil', 'ClCG06G005740' => 'cla', 'ClCG07G000090' => 'cla', 'ClCG07G000100' => 'cla', 'COL.COLO4_09143' => 'col', 'COL.COLO4_25124' => 'col', 'Cpa.g.sc16.34' => 'cpa', 'Cpa.g.sc3504.1' => 'cpa', 'Cpa.g.sc60.37' => 'cpa', 'CsaV3_6G018520' => 'csa', 'CsaV3_6G036860' => 'csa', 'CSS0001072' => 'camsi', 'CSS0020208' => 'camsi', 'CSS0021253' => 'camsi', 'CSS0022190' => 'camsi', 'CSS0036150' => 'camsi', 'CSS0040442' => 'camsi', 'CSS0042300' => 'camsi', 'CSS0045298' => 'camsi', 'DCAR_012449' => 'dca', 'DCAR_018405' => 'dca', 'DCAR_024573' => 'dca', 'DCAR_030591' => 'dca', 'Dinv16926' => 'din', 'Dinv32963' => 'din', 'Dinv38382' => 'din', 'Dinv38383' => 'din', 'Duzib133G0974' => 'dzi', 'Duzib138G1867' => 'dzi', 'Duzib211G0420' => 'dzi', 'Duzib212G0930' => 'dzi', 'ECA234G1645' => 'eca', 'ECA247G3467' => 'eca', 'ECA248G1703' => 'eca', 'EL10Ac3g06327' => 'bvu', 'EL10Ac7g17204' => 'bvu', 'Eucgr.A00855' => 'egr', 'Eucgr.A00858' => 'egr', 'Eucgr.H01520' => 'egr', 'Eucgr.H03604' => 'egr', 'Eucgr.L03465' => 'egr', 'Eucgr.L03466' => 'egr', 'FAN01G0988' => 'fan', 'FAN02G3892' => 'fan', 'FAN05G3381' => 'fan', 'FAN07G0967' => 'fan', 'FAN07G1493' => 'fan', 'FAN08G3125' => 'fan', 'FAN09G0402' => 'fan', 'FAN12G2594' => 'fan', 'FAN12G3879' => 'fan', 'FAN14G1546' => 'fan', 'FAN15G3626' => 'fan', 'FAN17G0588' => 'fan', 'FAN17G0609' => 'fan', 'FAN18G2817' => 'fan', 'FAN19G1305' => 'fan', 'FAN20G1787' => 'fan', 'FAN22G0073' => 'fan', 'FAN22G0352' => 'fan', 'FAN22G0368' => 'fan', 'FAN22G2273' => 'fan', 'FAN24G1998' => 'fan', 'FAN27G1317' => 'fan', 'FvH4_2g23980' => 'fve', 'FvH4_4g14380' => 'fve', 'FvH4_4g14390' => 'fve', 'FvH4_6g09250' => 'fve', 'Glyma.03G151100' => 'gma', 'Glyma.04G122550' => 'gma', 'Glyma.05G001600' => 'gma', 'Glyma.09G270766' => 'gma', 'Glyma.09G270832' => 'gma', 'Glyma.13G209800' => 'gma', 'Glyma.15G102800' => 'gma', 'Glyma.18G218900' => 'gma', 'Glyma.19G001500' => 'gma', 'Glyma.19G153600' => 'gma', 'Gohir.A02G028600' => 'ghi', 'Gohir.A08G045000' => 'ghi', 'Gohir.A11G120500' => 'ghi', 'Gohir.A12G006200' => 'ghi', 'Gohir.A12G006250' => 'ghi', 'Gohir.D02G036300' => 'ghi', 'Gohir.D08G054700' => 'ghi', 'Gohir.D11G125600' => 'ghi', 'Gohir.D12G005700' => 'ghi', 'Gorai.004G055200' => 'gra', 'Gorai.005G040400' => 'gra', 'Gorai.007G134500' => 'gra', 'Gorai.008G005500' => 'gra', 'GSVIVG01011094001' => 'vvi', 'GSVIVG01017879001' => 'vvi', 'GSVIVG01025988001' => 'vvi', 'GSVIVG01029847001' => 'vvi', 'HanXRQChr10g0282901' => 'han', 'HanXRQChr10g0310371' => 'han', 'HanXRQChr10g0315041' => 'han', 'HanXRQChr11g0327651' => 'han', 'HanXRQChr12g0359391' => 'han', 'Haze_00972' => 'cav', 'Haze_00973' => 'cav', 'Haze_00974' => 'cav', 'Haze_04747' => 'cav', 'Haze_04749' => 'cav', 'Haze_04750' => 'cav', 'Haze_21217' => 'cav', 'Hma1.2p1_1037F.1_g250680' => 'hma', 'Hma1.2p1_1644F.1_g295320' => 'hma', 'HPP92_011322' => 'vpl', 'HPP92_011323' => 'vpl', 'HPP92_011324' => 'vpl', 'HPP92_011325' => 'vpl', 'HPP92_011326' => 'vpl', 'Hund12205' => 'sun', 'Hund17957' => 'sun', 'Lalb_Chr06g0176771' => 'lal', 'Lalb_Chr18g0056021' => 'lal', 'Lalb_Chr18g0056031' => 'lal', 'Lalb_Chr18g0056041' => 'lal', 'Lalb_Chr20g0107751' => 'lal', 'Lalb_Chr20g0118371' => 'lal', 'Lj1g0010239' => 'lja', 'Lj1g0017101' => 'lja', 'Lj2A1178G40' => 'lonja', 'Lj2A54G84' => 'lonja', 'Lj2g0015248' => 'lja', 'Lj3A761T51' => 'lonja', 'Lj6g0018116' => 'lja', 'Lsat_1_v5_gn_4_136040' => 'lsa', 'Lsat_1_v5_gn_5_187461' => 'lsa', 'Lsat_1_v5_gn_5_77001' => 'lsa', 'Lsat_1_v5_gn_9_4461' => 'lsa', 'Manes.01G210100' => 'mes', 'Manes.03G185600' => 'mes', 'Manes.05G073300' => 'mes', 'Manes.09G120300' => 'mes', 'Manes.15G022100' => 'mes', 'Mapoly0096s0053' => 'mpo', 'MBI03_g14058_MAGBIO' => 'mbi', 'MBI03_g33876_MAGBIO' => 'mbi', 'MBI03_g36854_MAGBIO' => 'mbi', 'MBI17_g11997_MAGBIO' => 'mbi', 'MD03G1269000' => 'mdo', 'MD04G1179600' => 'mdo', 'MD11G1289800' => 'mdo', 'MD12G1194700' => 'mdo', 'MD13G1182100' => 'mdo', 'MD13G1182200' => 'mdo', 'MD16G1182600' => 'mdo', 'Medtr2g021400' => 'mtr', 'Medtr2g021470' => 'mtr', 'Medtr2g105810' => 'mtr', 'Medtr3g033580' => 'mtr', 'Medtr6g007970' => 'mtr', 'Medtr7g056330' => 'mtr', 'Medtr7g074290' => 'mtr', 'Medtr7g074380' => 'mtr', 'Medtr7g094550' => 'mtr', 'Medtr8g069995' => 'mtr', 'MELO3C014345.2' => 'cme', 'MELO3C021395.2' => 'cme', 'Migut.D00262' => 'egut', 'Migut.G00257' => 'egut', 'MSTRG.21575' => 'ama', 'MSTRG.3985' => 'ama', 'Nitab4.5_0000295g0140' => 'nta', 'Nitab4.5_0000732g0140' => 'nta', 'Nitab4.5_0003162g0020' => 'nta', 'Nitab4.5_0006180g0090' => 'nta', 'Nitab4.5_0006390g0010' => 'nta', 'Nitab4.5_0007392g0040' => 'nta', 'Nn1g02140' => 'nnu', 'Nn4g26168' => 'nnu', 'Nn5g26754' => 'nnu', 'Oeu001433.1' => 'oeu', 'Oeu010299.2' => 'oeu', 'Oeu011171.1' => 'oeu', 'Oeu037675.1' => 'oeu', 'Oeu038359.1' => 'oeu', 'Oeu063834.1' => 'oeu', 'Oeu063835.1' => 'oeu', 'Os05g0312000' => 'osa', 'Os07g0211101' => 'osa', 'Os07g0211200' => 'osa', 'Os07g0681500' => 'osa', 'Peaxi162Scf00095g01015' => 'pax', 'Peaxi162Scf00104g00329' => 'pax', 'Peaxi162Scf00161g00137' => 'pax', 'PGR004G1665' => 'pgr', 'PGR031G2937' => 'pgr', 'PGR119G2145' => 'pgr', 'PGSC0003DMG400004351' => 'stu', 'PGSC0003DMG400014625' => 'stu', 'PGSC0003DMG401000943' => 'stu', 'Phvul.001G148600' => 'pvu', 'Phvul.004G001700' => 'pvu', 'Phvul.006G154900' => 'pvu', 'Phvul.008G078200' => 'pvu', 'Phvul.011G136500' => 'pvu', 'Potri.002G215600' => 'ptr', 'Potri.008G201600' => 'ptr', 'Potri.014G138400' => 'ptr', 'Potri.016G142500' => 'ptr', 'Pp3c16_10580' => 'ppa', 'Pp3c5_25280' => 'ppa', 'Prupe.1G150000' => 'ppe', 'Prupe.1G150100' => 'ppe', 'Prupe.6G299600' => 'ppe', 'Prupe.8G245000' => 'ppe', 'Psat0s4927g0040' => 'psa', 'Psat1g052080' => 'psa', 'Psat1g183800' => 'psa', 'Psat3g113840' => 'psa', 'Psat3g126120' => 'psa', 'Psat3g126160' => 'psa', 'Psat3g158760' => 'psa', 'Psat3g158840' => 'psa', 'PSO170G2858' => 'pso', 'PSO339G0606' => 'pso', 'PSO384G4709' => 'pso', 'PSO407G0334' => 'pso', 'QL04p040276' => 'qlo', 'QL06p005458' => 'qlo', 'QL06p005472' => 'qlo', 'QL07p030546' => 'qlo', 'QL07p031519' => 'qlo', 'QL09p050949' => 'qlo', 'QL09p050966' => 'qlo', 'QL09p051067' => 'qlo', 'QL12p022706' => 'qlo', 'RcHm_v2.0_Chr2g0119601' => 'rch', 'RcHm_v2.0_Chr3g0459591' => 'rch', 'RcHm_v2.0_Chr4g0418521' => 'rch', 'RcHm_v2.0_Chr4g0418531' => 'rch', 'RcHm_v2.0_Chr4g0418541' => 'rch', 'RcHm_v2.0_Chr6g0291641' => 'rch', 'Rhsim01G0086300' => 'rsi', 'Rhsim01G0276300' => 'rsi', 'Rhsim01G0276500' => 'rsi', 'Rhsim04G0207700' => 'rsi', 'Rhsim05G0234500' => 'rsi', 'Rhsim13G0022400' => 'rsi', 'Sabra02G0167900' => 'sbr', 'Sabra04G0158500' => 'sbr', 'Sabra08G0159800' => 'sbr', 'Sabra10G0011500' => 'sbr', 'Sabra14G0104400' => 'sbr', 'SalBow2G2440' => 'sbo', 'SalBow4G2265' => 'sbo', 'Sc02g0000060' => 'sci', 'Sc05g0005020' => 'sci', 'Sc13g0003890' => 'sci', 'Sed0014865' => 'sed', 'Sed0017224' => 'sed', 'Sed0026391' => 'sed', 'SEGI_00063' => 'sgi', 'SEGI_10967' => 'sgi', 'SEGI_17510' => 'sgi', 'SEGI_24396' => 'sgi', 'SEGI_39719' => 'sgi', 'SEGI_41392' => 'sgi', 'SGA_v2.0_scaffold11G05794' => 'sas', 'SGA_v2.0_scaffold142G35607' => 'sas', 'SGA_v2.0_scaffold1G00447' => 'sas', 'SHI15388' => 'shi', 'SHI15394' => 'shi', 'SHI15396' => 'shi', 'SHI15399' => 'shi', 'SMO343G0151' => 'smo', 'SMO367G1118' => 'smo', 'Solyc01g080200.3' => 'sly', 'Solyc06g008960.3' => 'sly', 'Solyc09g064780.3' => 'sly', 'Sopen01g031980' => 'spe', 'Sopen06g003710' => 'spe', 'Sopen09g026460' => 'spe', 'Sp3g21240' => 'spa', 'Sp4g30030' => 'spa', 'TAR365G0022' => 'tar', 'TAR365G1023' => 'tar', 'TAR365G1253' => 'tar', 'TAR623G0078' => 'tar', 'TAR623G1721' => 'tar', 'TAR633G0959' => 'tar', 'THA.LOC104802225' => 'tha', 'THA.LOC104804769' => 'tha', 'THA.LOC104808660' => 'tha', 'THA.LOC104812792' => 'tha', 'Thecc.01G284000' => 'tca', 'Thecc.04G220600' => 'tca', 'Thecc.05G268900' => 'tca', 'Thecc.08G171100' => 'tca', 'Thhalv10001284m.g' => 'esa', 'Thhalv10019912m.g' => 'esa', 'TPR.G14189' => 'tpr', 'TPR.G18110' => 'tpr', 'TPR.G18130' => 'tpr', 'TPR.G18131' => 'tpr', 'TPR.G18140' => 'tpr', 'TPR.G24282' => 'tpr', 'TPR.G25221' => 'tpr', 'TPR.G29267' => 'tpr', 'TPR.G35315' => 'tpr', 'TPR.G36173' => 'tpr', 'TWI09G0794' => 'twi', 'TWI59G1348' => 'twi', 'TWI74G0430' => 'twi', 'unitig_26.g8940' => 'ugi', 'unitig_749.g13744' => 'ugi', 'unitig_749.g13745' => 'ugi', 'vmacro08269' => 'vma', 'vmacro14937' => 'vma', 'vmacro20401' => 'vma', 'VMungo0464G1349' => 'vmu', 'VMungo0540G0289' => 'vmu', 'VMungo1215G1590' => 'vmu', 'VMungo1309G0221' => 'vmu', 'VMungo1309G2815' => 'vmu', 'VMungo1383G0239' => 'vmu', 'VMungo1383G2910' => 'vmu', 'Zm00001eb095270' => 'zma', 'Zm00001eb095280' => 'zma', 'Zm00001eb111630' => 'zma', 'Zm00001eb237080' => 'zma', 'Zm00001eb273740' => 'zma', 'Zm00001eb285040' => 'zma', 'Zm00001eb330790' => 'zma', 'Zm00001eb337380' => 'zma' ) $gf_id = 'HOM05D001484' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001484' ) $data_identifier = 'HOM05D001484' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 2, 'aly' => (int) 2, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 22, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 7, 'hma' => (int) 2, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 7, 'mtr' => (int) 10, 'cme' => (int) 2, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 4, 'ppa' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 4, 'qlo' => (int) 9, 'rch' => (int) 6, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 10, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 7, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb337380' $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' => 'HOM05D001484', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p31500' => 'bna', 'A05p00020' => 'bna', 'A07p08820' => 'bna', 'Aa31LG4G3300' => 'aar', 'Aa31LG8G10030' => 'aar', 'Actinidia00731' => 'ach', 'Actinidia11473' => 'ach', 'Actinidia23469' => 'ach', 'Actinidia24318' => 'ach', 'Actinidia40196' => 'ach', 'Actinidia40197' => 'ach', 'Actinidia40198' => 'ach', 'Ah.08g212990' => 'amhyb', 'Ah.15g091720' => 'amhyb', 'AL3G38260' => 'aly', 'AL4G47710' => 'aly', 'Aqoxy2G00671' => 'aox', 'Aqoxy2G03236' => 'aox', 'arahy.Tifrunner.gnm1.ann1.05IDCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KR684' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATY3SJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK6QJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6APGL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IDT7Z9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM073U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ0R87' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LE7RV4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT4QRX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V5ENPK' => 'arhy', 'AT2G48110' => 'ath', 'AT3G23590' => 'ath', 'ATR0626G186' => 'atr', 'ATR1127G141' => 'atr', 'Atru.chr4.2583' => 'acertr', 'Atru.chr5.1358' => 'acertr', 'Atru.chr5.1359' => 'acertr', 'Atru.chr8.46' => 'acertr', 'AUR62002640' => 'cqu', 'AUR62030055' => 'cqu', 'AUR62033713' => 'cqu', 'AUR62033714' => 'cqu', 'AUR62036795' => 'cqu', 'AUR62039891' => 'cqu', 'BcaB02g08737' => 'bca', 'BcaB04g20441' => 'bca', 'BcaB06g26509' => 'bca', 'BcaB06g26510' => 'bca', 'BcaB06g26511' => 'bca', 'BcaB06g26512' => 'bca', 'BcaB06g26513' => 'bca', 'BcaC02g12564' => 'bca', 'BcaC02g12565' => 'bca', 'BcaC02g12794' => 'bca', 'BcaC02g12795' => 'bca', 'BcaC02g12796' => 'bca', 'BcaC06g35541' => 'bca', 'BNapus_Darmor_BZH_scaffold_188p00080' => 'bna', 'BNapus_Darmor_BZH_scaffold_188p00090' => 'bna', 'BolC1t03972H' => 'bol', 'BolC1t03973H' => 'bol', 'BolC4t21680H' => 'bol', 'BolC7t41863H' => 'bol', 'BolSC55t61227H' => 'bol', 'BolSC55t61228H' => 'bol', 'BraA01t03278Z' => 'bra', 'BraA05t18998Z' => 'bra', 'BraA07t28673Z' => 'bra', 'C01p40150' => 'bna', 'C05p12370' => 'bna', 'C07p13680' => 'bna', 'CAN.G1006.16' => 'can', 'CAN.G1006.17' => 'can', 'CAN.G1170.2' => 'can', 'CAN.G962.7' => 'can', 'CANSAT25G2179' => 'cansat', 'CANSAT78G1573' => 'cansat', 'CARHR099510' => 'chi', 'CARHR143510' => 'chi', 'Carub.0003s2380' => 'cru', 'Carub.0004s3082' => 'cru', 'Ca_00614_v3' => 'car', 'Ca_07801_v3' => 'car', 'Ca_08567_v3' => 'car', 'Ca_09571_v3' => 'car', 'CBR_g19290' => 'cbr', 'Cc01_g19770' => 'ccan', 'Cc03_g03030' => 'ccan', 'CDE07G0968' => 'cde', 'CDE09G1441' => 'cde', 'Cfa006103' => 'cfa', 'Cfa015573' => 'cfa', 'Cfa016988' => 'cfa', 'Ciclev10006738m.g' => 'ccl', 'Ciclev10010920m.g' => 'ccl', 'Ciclev10018517m.g' => 'ccl', 'CiPaw.01G159200' => 'cil', 'CiPaw.02G091000' => 'cil', 'CiPaw.02G091100' => 'cil', 'CiPaw.08G103100' => 'cil', 'CiPaw.09G224900' => 'cil', 'ClCG06G005740' => 'cla', 'ClCG07G000090' => 'cla', 'ClCG07G000100' => 'cla', 'COL.COLO4_09143' => 'col', 'COL.COLO4_25124' => 'col', 'Cpa.g.sc16.34' => 'cpa', 'Cpa.g.sc3504.1' => 'cpa', 'Cpa.g.sc60.37' => 'cpa', 'CsaV3_6G018520' => 'csa', 'CsaV3_6G036860' => 'csa', 'CSS0001072' => 'camsi', 'CSS0020208' => 'camsi', 'CSS0021253' => 'camsi', 'CSS0022190' => 'camsi', 'CSS0036150' => 'camsi', 'CSS0040442' => 'camsi', 'CSS0042300' => 'camsi', 'CSS0045298' => 'camsi', 'DCAR_012449' => 'dca', 'DCAR_018405' => 'dca', 'DCAR_024573' => 'dca', 'DCAR_030591' => 'dca', 'Dinv16926' => 'din', 'Dinv32963' => 'din', 'Dinv38382' => 'din', 'Dinv38383' => 'din', 'Duzib133G0974' => 'dzi', 'Duzib138G1867' => 'dzi', 'Duzib211G0420' => 'dzi', 'Duzib212G0930' => 'dzi', 'ECA234G1645' => 'eca', 'ECA247G3467' => 'eca', 'ECA248G1703' => 'eca', 'EL10Ac3g06327' => 'bvu', 'EL10Ac7g17204' => 'bvu', 'Eucgr.A00855' => 'egr', 'Eucgr.A00858' => 'egr', 'Eucgr.H01520' => 'egr', 'Eucgr.H03604' => 'egr', 'Eucgr.L03465' => 'egr', 'Eucgr.L03466' => 'egr', 'FAN01G0988' => 'fan', 'FAN02G3892' => 'fan', 'FAN05G3381' => 'fan', 'FAN07G0967' => 'fan', 'FAN07G1493' => 'fan', 'FAN08G3125' => 'fan', 'FAN09G0402' => 'fan', 'FAN12G2594' => 'fan', 'FAN12G3879' => 'fan', 'FAN14G1546' => 'fan', 'FAN15G3626' => 'fan', 'FAN17G0588' => 'fan', 'FAN17G0609' => 'fan', 'FAN18G2817' => 'fan', 'FAN19G1305' => 'fan', 'FAN20G1787' => 'fan', 'FAN22G0073' => 'fan', 'FAN22G0352' => 'fan', 'FAN22G0368' => 'fan', 'FAN22G2273' => 'fan', 'FAN24G1998' => 'fan', 'FAN27G1317' => 'fan', 'FvH4_2g23980' => 'fve', 'FvH4_4g14380' => 'fve', 'FvH4_4g14390' => 'fve', 'FvH4_6g09250' => 'fve', 'Glyma.03G151100' => 'gma', 'Glyma.04G122550' => 'gma', 'Glyma.05G001600' => 'gma', 'Glyma.09G270766' => 'gma', 'Glyma.09G270832' => 'gma', 'Glyma.13G209800' => 'gma', 'Glyma.15G102800' => 'gma', 'Glyma.18G218900' => 'gma', 'Glyma.19G001500' => 'gma', 'Glyma.19G153600' => 'gma', 'Gohir.A02G028600' => 'ghi', 'Gohir.A08G045000' => 'ghi', 'Gohir.A11G120500' => 'ghi', 'Gohir.A12G006200' => 'ghi', 'Gohir.A12G006250' => 'ghi', 'Gohir.D02G036300' => 'ghi', 'Gohir.D08G054700' => 'ghi', 'Gohir.D11G125600' => 'ghi', 'Gohir.D12G005700' => 'ghi', 'Gorai.004G055200' => 'gra', 'Gorai.005G040400' => 'gra', 'Gorai.007G134500' => 'gra', 'Gorai.008G005500' => 'gra', 'GSVIVG01011094001' => 'vvi', 'GSVIVG01017879001' => 'vvi', 'GSVIVG01025988001' => 'vvi', 'GSVIVG01029847001' => 'vvi', 'HanXRQChr10g0282901' => 'han', 'HanXRQChr10g0310371' => 'han', 'HanXRQChr10g0315041' => 'han', 'HanXRQChr11g0327651' => 'han', 'HanXRQChr12g0359391' => 'han', 'Haze_00972' => 'cav', 'Haze_00973' => 'cav', 'Haze_00974' => 'cav', 'Haze_04747' => 'cav', 'Haze_04749' => 'cav', 'Haze_04750' => 'cav', 'Haze_21217' => 'cav', 'Hma1.2p1_1037F.1_g250680' => 'hma', 'Hma1.2p1_1644F.1_g295320' => 'hma', 'HPP92_011322' => 'vpl', 'HPP92_011323' => 'vpl', 'HPP92_011324' => 'vpl', 'HPP92_011325' => 'vpl', 'HPP92_011326' => 'vpl', 'Hund12205' => 'sun', 'Hund17957' => 'sun', 'Lalb_Chr06g0176771' => 'lal', 'Lalb_Chr18g0056021' => 'lal', 'Lalb_Chr18g0056031' => 'lal', 'Lalb_Chr18g0056041' => 'lal', 'Lalb_Chr20g0107751' => 'lal', 'Lalb_Chr20g0118371' => 'lal', 'Lj1g0010239' => 'lja', 'Lj1g0017101' => 'lja', 'Lj2A1178G40' => 'lonja', 'Lj2A54G84' => 'lonja', 'Lj2g0015248' => 'lja', 'Lj3A761T51' => 'lonja', 'Lj6g0018116' => 'lja', 'Lsat_1_v5_gn_4_136040' => 'lsa', 'Lsat_1_v5_gn_5_187461' => 'lsa', 'Lsat_1_v5_gn_5_77001' => 'lsa', 'Lsat_1_v5_gn_9_4461' => 'lsa', 'Manes.01G210100' => 'mes', 'Manes.03G185600' => 'mes', 'Manes.05G073300' => 'mes', 'Manes.09G120300' => 'mes', 'Manes.15G022100' => 'mes', 'Mapoly0096s0053' => 'mpo', 'MBI03_g14058_MAGBIO' => 'mbi', 'MBI03_g33876_MAGBIO' => 'mbi', 'MBI03_g36854_MAGBIO' => 'mbi', 'MBI17_g11997_MAGBIO' => 'mbi', 'MD03G1269000' => 'mdo', 'MD04G1179600' => 'mdo', 'MD11G1289800' => 'mdo', 'MD12G1194700' => 'mdo', 'MD13G1182100' => 'mdo', 'MD13G1182200' => 'mdo', 'MD16G1182600' => 'mdo', 'Medtr2g021400' => 'mtr', 'Medtr2g021470' => 'mtr', 'Medtr2g105810' => 'mtr', 'Medtr3g033580' => 'mtr', 'Medtr6g007970' => 'mtr', 'Medtr7g056330' => 'mtr', 'Medtr7g074290' => 'mtr', 'Medtr7g074380' => 'mtr', 'Medtr7g094550' => 'mtr', 'Medtr8g069995' => 'mtr', 'MELO3C014345.2' => 'cme', 'MELO3C021395.2' => 'cme', 'Migut.D00262' => 'egut', 'Migut.G00257' => 'egut', 'MSTRG.21575' => 'ama', 'MSTRG.3985' => 'ama', 'Nitab4.5_0000295g0140' => 'nta', 'Nitab4.5_0000732g0140' => 'nta', 'Nitab4.5_0003162g0020' => 'nta', 'Nitab4.5_0006180g0090' => 'nta', 'Nitab4.5_0006390g0010' => 'nta', 'Nitab4.5_0007392g0040' => 'nta', 'Nn1g02140' => 'nnu', 'Nn4g26168' => 'nnu', 'Nn5g26754' => 'nnu', 'Oeu001433.1' => 'oeu', 'Oeu010299.2' => 'oeu', 'Oeu011171.1' => 'oeu', 'Oeu037675.1' => 'oeu', 'Oeu038359.1' => 'oeu', 'Oeu063834.1' => 'oeu', 'Oeu063835.1' => 'oeu', 'Os05g0312000' => 'osa', 'Os07g0211101' => 'osa', 'Os07g0211200' => 'osa', 'Os07g0681500' => 'osa', 'Peaxi162Scf00095g01015' => 'pax', 'Peaxi162Scf00104g00329' => 'pax', 'Peaxi162Scf00161g00137' => 'pax', 'PGR004G1665' => 'pgr', 'PGR031G2937' => 'pgr', 'PGR119G2145' => 'pgr', 'PGSC0003DMG400004351' => 'stu', 'PGSC0003DMG400014625' => 'stu', 'PGSC0003DMG401000943' => 'stu', 'Phvul.001G148600' => 'pvu', 'Phvul.004G001700' => 'pvu', 'Phvul.006G154900' => 'pvu', 'Phvul.008G078200' => 'pvu', 'Phvul.011G136500' => 'pvu', 'Potri.002G215600' => 'ptr', 'Potri.008G201600' => 'ptr', 'Potri.014G138400' => 'ptr', 'Potri.016G142500' => 'ptr', 'Pp3c16_10580' => 'ppa', 'Pp3c5_25280' => 'ppa', 'Prupe.1G150000' => 'ppe', 'Prupe.1G150100' => 'ppe', 'Prupe.6G299600' => 'ppe', 'Prupe.8G245000' => 'ppe', 'Psat0s4927g0040' => 'psa', 'Psat1g052080' => 'psa', 'Psat1g183800' => 'psa', 'Psat3g113840' => 'psa', 'Psat3g126120' => 'psa', 'Psat3g126160' => 'psa', 'Psat3g158760' => 'psa', 'Psat3g158840' => 'psa', 'PSO170G2858' => 'pso', 'PSO339G0606' => 'pso', 'PSO384G4709' => 'pso', 'PSO407G0334' => 'pso', 'QL04p040276' => 'qlo', 'QL06p005458' => 'qlo', 'QL06p005472' => 'qlo', 'QL07p030546' => 'qlo', 'QL07p031519' => 'qlo', 'QL09p050949' => 'qlo', 'QL09p050966' => 'qlo', 'QL09p051067' => 'qlo', 'QL12p022706' => 'qlo', 'RcHm_v2.0_Chr2g0119601' => 'rch', 'RcHm_v2.0_Chr3g0459591' => 'rch', 'RcHm_v2.0_Chr4g0418521' => 'rch', 'RcHm_v2.0_Chr4g0418531' => 'rch', 'RcHm_v2.0_Chr4g0418541' => 'rch', 'RcHm_v2.0_Chr6g0291641' => 'rch', 'Rhsim01G0086300' => 'rsi', 'Rhsim01G0276300' => 'rsi', 'Rhsim01G0276500' => 'rsi', 'Rhsim04G0207700' => 'rsi', 'Rhsim05G0234500' => 'rsi', 'Rhsim13G0022400' => 'rsi', 'Sabra02G0167900' => 'sbr', 'Sabra04G0158500' => 'sbr', 'Sabra08G0159800' => 'sbr', 'Sabra10G0011500' => 'sbr', 'Sabra14G0104400' => 'sbr', 'SalBow2G2440' => 'sbo', 'SalBow4G2265' => 'sbo', 'Sc02g0000060' => 'sci', 'Sc05g0005020' => 'sci', 'Sc13g0003890' => 'sci', 'Sed0014865' => 'sed', 'Sed0017224' => 'sed', 'Sed0026391' => 'sed', 'SEGI_00063' => 'sgi', 'SEGI_10967' => 'sgi', 'SEGI_17510' => 'sgi', 'SEGI_24396' => 'sgi', 'SEGI_39719' => 'sgi', 'SEGI_41392' => 'sgi', 'SGA_v2.0_scaffold11G05794' => 'sas', 'SGA_v2.0_scaffold142G35607' => 'sas', 'SGA_v2.0_scaffold1G00447' => 'sas', 'SHI15388' => 'shi', 'SHI15394' => 'shi', 'SHI15396' => 'shi', 'SHI15399' => 'shi', 'SMO343G0151' => 'smo', 'SMO367G1118' => 'smo', 'Solyc01g080200.3' => 'sly', 'Solyc06g008960.3' => 'sly', 'Solyc09g064780.3' => 'sly', 'Sopen01g031980' => 'spe', 'Sopen06g003710' => 'spe', 'Sopen09g026460' => 'spe', 'Sp3g21240' => 'spa', 'Sp4g30030' => 'spa', 'TAR365G0022' => 'tar', 'TAR365G1023' => 'tar', 'TAR365G1253' => 'tar', 'TAR623G0078' => 'tar', 'TAR623G1721' => 'tar', 'TAR633G0959' => 'tar', 'THA.LOC104802225' => 'tha', 'THA.LOC104804769' => 'tha', 'THA.LOC104808660' => 'tha', 'THA.LOC104812792' => 'tha', 'Thecc.01G284000' => 'tca', 'Thecc.04G220600' => 'tca', 'Thecc.05G268900' => 'tca', 'Thecc.08G171100' => 'tca', 'Thhalv10001284m.g' => 'esa', 'Thhalv10019912m.g' => 'esa', 'TPR.G14189' => 'tpr', 'TPR.G18110' => 'tpr', 'TPR.G18130' => 'tpr', 'TPR.G18131' => 'tpr', 'TPR.G18140' => 'tpr', 'TPR.G24282' => 'tpr', 'TPR.G25221' => 'tpr', 'TPR.G29267' => 'tpr', 'TPR.G35315' => 'tpr', 'TPR.G36173' => 'tpr', 'TWI09G0794' => 'twi', 'TWI59G1348' => 'twi', 'TWI74G0430' => 'twi', 'unitig_26.g8940' => 'ugi', 'unitig_749.g13744' => 'ugi', 'unitig_749.g13745' => 'ugi', 'vmacro08269' => 'vma', 'vmacro14937' => 'vma', 'vmacro20401' => 'vma', 'VMungo0464G1349' => 'vmu', 'VMungo0540G0289' => 'vmu', 'VMungo1215G1590' => 'vmu', 'VMungo1309G0221' => 'vmu', 'VMungo1309G2815' => 'vmu', 'VMungo1383G0239' => 'vmu', 'VMungo1383G2910' => 'vmu', 'Zm00001eb095270' => 'zma', 'Zm00001eb095280' => 'zma', 'Zm00001eb111630' => 'zma', 'Zm00001eb237080' => 'zma', 'Zm00001eb273740' => 'zma', 'Zm00001eb285040' => 'zma', 'Zm00001eb330790' => 'zma', 'Zm00001eb337380' => 'zma' ), 'gf_id' => 'HOM05D001484', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001484' ), 'data_identifier' => 'HOM05D001484', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001484', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p31500' => 'bna', 'A05p00020' => 'bna', 'A07p08820' => 'bna', 'Aa31LG4G3300' => 'aar', 'Aa31LG8G10030' => 'aar', 'Actinidia00731' => 'ach', 'Actinidia11473' => 'ach', 'Actinidia23469' => 'ach', 'Actinidia24318' => 'ach', 'Actinidia40196' => 'ach', 'Actinidia40197' => 'ach', 'Actinidia40198' => 'ach', 'Ah.08g212990' => 'amhyb', 'Ah.15g091720' => 'amhyb', 'AL3G38260' => 'aly', 'AL4G47710' => 'aly', 'Aqoxy2G00671' => 'aox', 'Aqoxy2G03236' => 'aox', 'arahy.Tifrunner.gnm1.ann1.05IDCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KR684' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATY3SJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK6QJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6APGL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IDT7Z9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM073U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ0R87' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LE7RV4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT4QRX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V5ENPK' => 'arhy', 'AT2G48110' => 'ath', 'AT3G23590' => 'ath', 'ATR0626G186' => 'atr', 'ATR1127G141' => 'atr', 'Atru.chr4.2583' => 'acertr', 'Atru.chr5.1358' => 'acertr', 'Atru.chr5.1359' => 'acertr', 'Atru.chr8.46' => 'acertr', 'AUR62002640' => 'cqu', 'AUR62030055' => 'cqu', 'AUR62033713' => 'cqu', 'AUR62033714' => 'cqu', 'AUR62036795' => 'cqu', 'AUR62039891' => 'cqu', 'BcaB02g08737' => 'bca', 'BcaB04g20441' => 'bca', 'BcaB06g26509' => 'bca', 'BcaB06g26510' => 'bca', 'BcaB06g26511' => 'bca', 'BcaB06g26512' => 'bca', 'BcaB06g26513' => 'bca', 'BcaC02g12564' => 'bca', 'BcaC02g12565' => 'bca', 'BcaC02g12794' => 'bca', 'BcaC02g12795' => 'bca', 'BcaC02g12796' => 'bca', 'BcaC06g35541' => 'bca', 'BNapus_Darmor_BZH_scaffold_188p00080' => 'bna', 'BNapus_Darmor_BZH_scaffold_188p00090' => 'bna', 'BolC1t03972H' => 'bol', 'BolC1t03973H' => 'bol', 'BolC4t21680H' => 'bol', 'BolC7t41863H' => 'bol', 'BolSC55t61227H' => 'bol', 'BolSC55t61228H' => 'bol', 'BraA01t03278Z' => 'bra', 'BraA05t18998Z' => 'bra', 'BraA07t28673Z' => 'bra', 'C01p40150' => 'bna', 'C05p12370' => 'bna', 'C07p13680' => 'bna', 'CAN.G1006.16' => 'can', 'CAN.G1006.17' => 'can', 'CAN.G1170.2' => 'can', 'CAN.G962.7' => 'can', 'CANSAT25G2179' => 'cansat', 'CANSAT78G1573' => 'cansat', 'CARHR099510' => 'chi', 'CARHR143510' => 'chi', 'Carub.0003s2380' => 'cru', 'Carub.0004s3082' => 'cru', 'Ca_00614_v3' => 'car', 'Ca_07801_v3' => 'car', 'Ca_08567_v3' => 'car', 'Ca_09571_v3' => 'car', 'CBR_g19290' => 'cbr', 'Cc01_g19770' => 'ccan', 'Cc03_g03030' => 'ccan', 'CDE07G0968' => 'cde', 'CDE09G1441' => 'cde', 'Cfa006103' => 'cfa', 'Cfa015573' => 'cfa', 'Cfa016988' => 'cfa', 'Ciclev10006738m.g' => 'ccl', 'Ciclev10010920m.g' => 'ccl', 'Ciclev10018517m.g' => 'ccl', 'CiPaw.01G159200' => 'cil', 'CiPaw.02G091000' => 'cil', 'CiPaw.02G091100' => 'cil', 'CiPaw.08G103100' => 'cil', 'CiPaw.09G224900' => 'cil', 'ClCG06G005740' => 'cla', 'ClCG07G000090' => 'cla', 'ClCG07G000100' => 'cla', 'COL.COLO4_09143' => 'col', 'COL.COLO4_25124' => 'col', 'Cpa.g.sc16.34' => 'cpa', 'Cpa.g.sc3504.1' => 'cpa', 'Cpa.g.sc60.37' => 'cpa', 'CsaV3_6G018520' => 'csa', 'CsaV3_6G036860' => 'csa', 'CSS0001072' => 'camsi', 'CSS0020208' => 'camsi', 'CSS0021253' => 'camsi', 'CSS0022190' => 'camsi', 'CSS0036150' => 'camsi', 'CSS0040442' => 'camsi', 'CSS0042300' => 'camsi', 'CSS0045298' => 'camsi', 'DCAR_012449' => 'dca', 'DCAR_018405' => 'dca', 'DCAR_024573' => 'dca', 'DCAR_030591' => 'dca', 'Dinv16926' => 'din', 'Dinv32963' => 'din', 'Dinv38382' => 'din', 'Dinv38383' => 'din', 'Duzib133G0974' => 'dzi', 'Duzib138G1867' => 'dzi', 'Duzib211G0420' => 'dzi', 'Duzib212G0930' => 'dzi', 'ECA234G1645' => 'eca', 'ECA247G3467' => 'eca', 'ECA248G1703' => 'eca', 'EL10Ac3g06327' => 'bvu', 'EL10Ac7g17204' => 'bvu', 'Eucgr.A00855' => 'egr', 'Eucgr.A00858' => 'egr', 'Eucgr.H01520' => 'egr', 'Eucgr.H03604' => 'egr', 'Eucgr.L03465' => 'egr', 'Eucgr.L03466' => 'egr', 'FAN01G0988' => 'fan', 'FAN02G3892' => 'fan', 'FAN05G3381' => 'fan', 'FAN07G0967' => 'fan', 'FAN07G1493' => 'fan', 'FAN08G3125' => 'fan', 'FAN09G0402' => 'fan', 'FAN12G2594' => 'fan', 'FAN12G3879' => 'fan', 'FAN14G1546' => 'fan', 'FAN15G3626' => 'fan', 'FAN17G0588' => 'fan', 'FAN17G0609' => 'fan', 'FAN18G2817' => 'fan', 'FAN19G1305' => 'fan', 'FAN20G1787' => 'fan', 'FAN22G0073' => 'fan', 'FAN22G0352' => 'fan', 'FAN22G0368' => 'fan', 'FAN22G2273' => 'fan', 'FAN24G1998' => 'fan', 'FAN27G1317' => 'fan', 'FvH4_2g23980' => 'fve', 'FvH4_4g14380' => 'fve', 'FvH4_4g14390' => 'fve', 'FvH4_6g09250' => 'fve', 'Glyma.03G151100' => 'gma', 'Glyma.04G122550' => 'gma', 'Glyma.05G001600' => 'gma', 'Glyma.09G270766' => 'gma', 'Glyma.09G270832' => 'gma', 'Glyma.13G209800' => 'gma', 'Glyma.15G102800' => 'gma', 'Glyma.18G218900' => 'gma', 'Glyma.19G001500' => 'gma', 'Glyma.19G153600' => 'gma', 'Gohir.A02G028600' => 'ghi', 'Gohir.A08G045000' => 'ghi', 'Gohir.A11G120500' => 'ghi', 'Gohir.A12G006200' => 'ghi', 'Gohir.A12G006250' => 'ghi', 'Gohir.D02G036300' => 'ghi', 'Gohir.D08G054700' => 'ghi', 'Gohir.D11G125600' => 'ghi', 'Gohir.D12G005700' => 'ghi', 'Gorai.004G055200' => 'gra', 'Gorai.005G040400' => 'gra', 'Gorai.007G134500' => 'gra', 'Gorai.008G005500' => 'gra', 'GSVIVG01011094001' => 'vvi', 'GSVIVG01017879001' => 'vvi', 'GSVIVG01025988001' => 'vvi', 'GSVIVG01029847001' => 'vvi', 'HanXRQChr10g0282901' => 'han', 'HanXRQChr10g0310371' => 'han', 'HanXRQChr10g0315041' => 'han', 'HanXRQChr11g0327651' => 'han', 'HanXRQChr12g0359391' => 'han', 'Haze_00972' => 'cav', 'Haze_00973' => 'cav', 'Haze_00974' => 'cav', 'Haze_04747' => 'cav', 'Haze_04749' => 'cav', 'Haze_04750' => 'cav', 'Haze_21217' => 'cav', 'Hma1.2p1_1037F.1_g250680' => 'hma', 'Hma1.2p1_1644F.1_g295320' => 'hma', 'HPP92_011322' => 'vpl', 'HPP92_011323' => 'vpl', 'HPP92_011324' => 'vpl', 'HPP92_011325' => 'vpl', 'HPP92_011326' => 'vpl', 'Hund12205' => 'sun', 'Hund17957' => 'sun', 'Lalb_Chr06g0176771' => 'lal', 'Lalb_Chr18g0056021' => 'lal', 'Lalb_Chr18g0056031' => 'lal', 'Lalb_Chr18g0056041' => 'lal', 'Lalb_Chr20g0107751' => 'lal', 'Lalb_Chr20g0118371' => 'lal', 'Lj1g0010239' => 'lja', 'Lj1g0017101' => 'lja', 'Lj2A1178G40' => 'lonja', 'Lj2A54G84' => 'lonja', 'Lj2g0015248' => 'lja', 'Lj3A761T51' => 'lonja', 'Lj6g0018116' => 'lja', 'Lsat_1_v5_gn_4_136040' => 'lsa', 'Lsat_1_v5_gn_5_187461' => 'lsa', 'Lsat_1_v5_gn_5_77001' => 'lsa', 'Lsat_1_v5_gn_9_4461' => 'lsa', 'Manes.01G210100' => 'mes', 'Manes.03G185600' => 'mes', 'Manes.05G073300' => 'mes', 'Manes.09G120300' => 'mes', 'Manes.15G022100' => 'mes', 'Mapoly0096s0053' => 'mpo', 'MBI03_g14058_MAGBIO' => 'mbi', 'MBI03_g33876_MAGBIO' => 'mbi', 'MBI03_g36854_MAGBIO' => 'mbi', 'MBI17_g11997_MAGBIO' => 'mbi', 'MD03G1269000' => 'mdo', 'MD04G1179600' => 'mdo', 'MD11G1289800' => 'mdo', 'MD12G1194700' => 'mdo', 'MD13G1182100' => 'mdo', 'MD13G1182200' => 'mdo', 'MD16G1182600' => 'mdo', 'Medtr2g021400' => 'mtr', 'Medtr2g021470' => 'mtr', 'Medtr2g105810' => 'mtr', 'Medtr3g033580' => 'mtr', 'Medtr6g007970' => 'mtr', 'Medtr7g056330' => 'mtr', 'Medtr7g074290' => 'mtr', 'Medtr7g074380' => 'mtr', 'Medtr7g094550' => 'mtr', 'Medtr8g069995' => 'mtr', 'MELO3C014345.2' => 'cme', 'MELO3C021395.2' => 'cme', 'Migut.D00262' => 'egut', 'Migut.G00257' => 'egut', 'MSTRG.21575' => 'ama', 'MSTRG.3985' => 'ama', 'Nitab4.5_0000295g0140' => 'nta', 'Nitab4.5_0000732g0140' => 'nta', 'Nitab4.5_0003162g0020' => 'nta', 'Nitab4.5_0006180g0090' => 'nta', 'Nitab4.5_0006390g0010' => 'nta', 'Nitab4.5_0007392g0040' => 'nta', 'Nn1g02140' => 'nnu', 'Nn4g26168' => 'nnu', 'Nn5g26754' => 'nnu', 'Oeu001433.1' => 'oeu', 'Oeu010299.2' => 'oeu', 'Oeu011171.1' => 'oeu', 'Oeu037675.1' => 'oeu', 'Oeu038359.1' => 'oeu', 'Oeu063834.1' => 'oeu', 'Oeu063835.1' => 'oeu', 'Os05g0312000' => 'osa', 'Os07g0211101' => 'osa', 'Os07g0211200' => 'osa', 'Os07g0681500' => 'osa', 'Peaxi162Scf00095g01015' => 'pax', 'Peaxi162Scf00104g00329' => 'pax', 'Peaxi162Scf00161g00137' => 'pax', 'PGR004G1665' => 'pgr', 'PGR031G2937' => 'pgr', 'PGR119G2145' => 'pgr', 'PGSC0003DMG400004351' => 'stu', 'PGSC0003DMG400014625' => 'stu', 'PGSC0003DMG401000943' => 'stu', 'Phvul.001G148600' => 'pvu', 'Phvul.004G001700' => 'pvu', 'Phvul.006G154900' => 'pvu', 'Phvul.008G078200' => 'pvu', 'Phvul.011G136500' => 'pvu', 'Potri.002G215600' => 'ptr', 'Potri.008G201600' => 'ptr', 'Potri.014G138400' => 'ptr', 'Potri.016G142500' => 'ptr', 'Pp3c16_10580' => 'ppa', 'Pp3c5_25280' => 'ppa', 'Prupe.1G150000' => 'ppe', 'Prupe.1G150100' => 'ppe', 'Prupe.6G299600' => 'ppe', 'Prupe.8G245000' => 'ppe', 'Psat0s4927g0040' => 'psa', 'Psat1g052080' => 'psa', 'Psat1g183800' => 'psa', 'Psat3g113840' => 'psa', 'Psat3g126120' => 'psa', 'Psat3g126160' => 'psa', 'Psat3g158760' => 'psa', 'Psat3g158840' => 'psa', 'PSO170G2858' => 'pso', 'PSO339G0606' => 'pso', 'PSO384G4709' => 'pso', 'PSO407G0334' => 'pso', 'QL04p040276' => 'qlo', 'QL06p005458' => 'qlo', 'QL06p005472' => 'qlo', 'QL07p030546' => 'qlo', 'QL07p031519' => 'qlo', 'QL09p050949' => 'qlo', 'QL09p050966' => 'qlo', 'QL09p051067' => 'qlo', 'QL12p022706' => 'qlo', 'RcHm_v2.0_Chr2g0119601' => 'rch', 'RcHm_v2.0_Chr3g0459591' => 'rch', 'RcHm_v2.0_Chr4g0418521' => 'rch', 'RcHm_v2.0_Chr4g0418531' => 'rch', 'RcHm_v2.0_Chr4g0418541' => 'rch', 'RcHm_v2.0_Chr6g0291641' => 'rch', 'Rhsim01G0086300' => 'rsi', 'Rhsim01G0276300' => 'rsi', 'Rhsim01G0276500' => 'rsi', 'Rhsim04G0207700' => 'rsi', 'Rhsim05G0234500' => 'rsi', 'Rhsim13G0022400' => 'rsi', 'Sabra02G0167900' => 'sbr', 'Sabra04G0158500' => 'sbr', 'Sabra08G0159800' => 'sbr', 'Sabra10G0011500' => 'sbr', 'Sabra14G0104400' => 'sbr', 'SalBow2G2440' => 'sbo', 'SalBow4G2265' => 'sbo', 'Sc02g0000060' => 'sci', 'Sc05g0005020' => 'sci', 'Sc13g0003890' => 'sci', 'Sed0014865' => 'sed', 'Sed0017224' => 'sed', 'Sed0026391' => 'sed', 'SEGI_00063' => 'sgi', 'SEGI_10967' => 'sgi', 'SEGI_17510' => 'sgi', 'SEGI_24396' => 'sgi', 'SEGI_39719' => 'sgi', 'SEGI_41392' => 'sgi', 'SGA_v2.0_scaffold11G05794' => 'sas', 'SGA_v2.0_scaffold142G35607' => 'sas', 'SGA_v2.0_scaffold1G00447' => 'sas', 'SHI15388' => 'shi', 'SHI15394' => 'shi', 'SHI15396' => 'shi', 'SHI15399' => 'shi', 'SMO343G0151' => 'smo', 'SMO367G1118' => 'smo', 'Solyc01g080200.3' => 'sly', 'Solyc06g008960.3' => 'sly', 'Solyc09g064780.3' => 'sly', 'Sopen01g031980' => 'spe', 'Sopen06g003710' => 'spe', 'Sopen09g026460' => 'spe', 'Sp3g21240' => 'spa', 'Sp4g30030' => 'spa', 'TAR365G0022' => 'tar', 'TAR365G1023' => 'tar', 'TAR365G1253' => 'tar', 'TAR623G0078' => 'tar', 'TAR623G1721' => 'tar', 'TAR633G0959' => 'tar', 'THA.LOC104802225' => 'tha', 'THA.LOC104804769' => 'tha', 'THA.LOC104808660' => 'tha', 'THA.LOC104812792' => 'tha', 'Thecc.01G284000' => 'tca', 'Thecc.04G220600' => 'tca', 'Thecc.05G268900' => 'tca', 'Thecc.08G171100' => 'tca', 'Thhalv10001284m.g' => 'esa', 'Thhalv10019912m.g' => 'esa', 'TPR.G14189' => 'tpr', 'TPR.G18110' => 'tpr', 'TPR.G18130' => 'tpr', 'TPR.G18131' => 'tpr', 'TPR.G18140' => 'tpr', 'TPR.G24282' => 'tpr', 'TPR.G25221' => 'tpr', 'TPR.G29267' => 'tpr', 'TPR.G35315' => 'tpr', 'TPR.G36173' => 'tpr', 'TWI09G0794' => 'twi', 'TWI59G1348' => 'twi', 'TWI74G0430' => 'twi', 'unitig_26.g8940' => 'ugi', 'unitig_749.g13744' => 'ugi', 'unitig_749.g13745' => 'ugi', 'vmacro08269' => 'vma', 'vmacro14937' => 'vma', 'vmacro20401' => 'vma', 'VMungo0464G1349' => 'vmu', 'VMungo0540G0289' => 'vmu', 'VMungo1215G1590' => 'vmu', 'VMungo1309G0221' => 'vmu', 'VMungo1309G2815' => 'vmu', 'VMungo1383G0239' => 'vmu', 'VMungo1383G2910' => 'vmu', 'Zm00001eb095270' => 'zma', 'Zm00001eb095280' => 'zma', 'Zm00001eb111630' => 'zma', 'Zm00001eb237080' => 'zma', 'Zm00001eb273740' => 'zma', 'Zm00001eb285040' => 'zma', 'Zm00001eb330790' => 'zma', 'Zm00001eb337380' => 'zma' ) $gf_id = 'HOM05D001484' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001484' ) $data_identifier = 'HOM05D001484' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 2, 'aly' => (int) 2, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 22, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 7, 'hma' => (int) 2, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 7, 'mtr' => (int) 10, 'cme' => (int) 2, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 4, 'ppa' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 4, 'qlo' => (int) 9, 'rch' => (int) 6, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 10, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 7, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb337380' $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' => 'HOM05D001484', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p31500' => 'bna', 'A05p00020' => 'bna', 'A07p08820' => 'bna', 'Aa31LG4G3300' => 'aar', 'Aa31LG8G10030' => 'aar', 'Actinidia00731' => 'ach', 'Actinidia11473' => 'ach', 'Actinidia23469' => 'ach', 'Actinidia24318' => 'ach', 'Actinidia40196' => 'ach', 'Actinidia40197' => 'ach', 'Actinidia40198' => 'ach', 'Ah.08g212990' => 'amhyb', 'Ah.15g091720' => 'amhyb', 'AL3G38260' => 'aly', 'AL4G47710' => 'aly', 'Aqoxy2G00671' => 'aox', 'Aqoxy2G03236' => 'aox', 'arahy.Tifrunner.gnm1.ann1.05IDCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KR684' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATY3SJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK6QJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6APGL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IDT7Z9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM073U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ0R87' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LE7RV4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT4QRX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V5ENPK' => 'arhy', 'AT2G48110' => 'ath', 'AT3G23590' => 'ath', 'ATR0626G186' => 'atr', 'ATR1127G141' => 'atr', 'Atru.chr4.2583' => 'acertr', 'Atru.chr5.1358' => 'acertr', 'Atru.chr5.1359' => 'acertr', 'Atru.chr8.46' => 'acertr', 'AUR62002640' => 'cqu', 'AUR62030055' => 'cqu', 'AUR62033713' => 'cqu', 'AUR62033714' => 'cqu', 'AUR62036795' => 'cqu', 'AUR62039891' => 'cqu', 'BcaB02g08737' => 'bca', 'BcaB04g20441' => 'bca', 'BcaB06g26509' => 'bca', 'BcaB06g26510' => 'bca', 'BcaB06g26511' => 'bca', 'BcaB06g26512' => 'bca', 'BcaB06g26513' => 'bca', 'BcaC02g12564' => 'bca', 'BcaC02g12565' => 'bca', 'BcaC02g12794' => 'bca', 'BcaC02g12795' => 'bca', 'BcaC02g12796' => 'bca', 'BcaC06g35541' => 'bca', 'BNapus_Darmor_BZH_scaffold_188p00080' => 'bna', 'BNapus_Darmor_BZH_scaffold_188p00090' => 'bna', 'BolC1t03972H' => 'bol', 'BolC1t03973H' => 'bol', 'BolC4t21680H' => 'bol', 'BolC7t41863H' => 'bol', 'BolSC55t61227H' => 'bol', 'BolSC55t61228H' => 'bol', 'BraA01t03278Z' => 'bra', 'BraA05t18998Z' => 'bra', 'BraA07t28673Z' => 'bra', 'C01p40150' => 'bna', 'C05p12370' => 'bna', 'C07p13680' => 'bna', 'CAN.G1006.16' => 'can', 'CAN.G1006.17' => 'can', 'CAN.G1170.2' => 'can', 'CAN.G962.7' => 'can', 'CANSAT25G2179' => 'cansat', 'CANSAT78G1573' => 'cansat', 'CARHR099510' => 'chi', 'CARHR143510' => 'chi', 'Carub.0003s2380' => 'cru', 'Carub.0004s3082' => 'cru', 'Ca_00614_v3' => 'car', 'Ca_07801_v3' => 'car', 'Ca_08567_v3' => 'car', 'Ca_09571_v3' => 'car', 'CBR_g19290' => 'cbr', 'Cc01_g19770' => 'ccan', 'Cc03_g03030' => 'ccan', 'CDE07G0968' => 'cde', 'CDE09G1441' => 'cde', 'Cfa006103' => 'cfa', 'Cfa015573' => 'cfa', 'Cfa016988' => 'cfa', 'Ciclev10006738m.g' => 'ccl', 'Ciclev10010920m.g' => 'ccl', 'Ciclev10018517m.g' => 'ccl', 'CiPaw.01G159200' => 'cil', 'CiPaw.02G091000' => 'cil', 'CiPaw.02G091100' => 'cil', 'CiPaw.08G103100' => 'cil', 'CiPaw.09G224900' => 'cil', 'ClCG06G005740' => 'cla', 'ClCG07G000090' => 'cla', 'ClCG07G000100' => 'cla', 'COL.COLO4_09143' => 'col', 'COL.COLO4_25124' => 'col', 'Cpa.g.sc16.34' => 'cpa', 'Cpa.g.sc3504.1' => 'cpa', 'Cpa.g.sc60.37' => 'cpa', 'CsaV3_6G018520' => 'csa', 'CsaV3_6G036860' => 'csa', 'CSS0001072' => 'camsi', 'CSS0020208' => 'camsi', 'CSS0021253' => 'camsi', 'CSS0022190' => 'camsi', 'CSS0036150' => 'camsi', 'CSS0040442' => 'camsi', 'CSS0042300' => 'camsi', 'CSS0045298' => 'camsi', 'DCAR_012449' => 'dca', 'DCAR_018405' => 'dca', 'DCAR_024573' => 'dca', 'DCAR_030591' => 'dca', 'Dinv16926' => 'din', 'Dinv32963' => 'din', 'Dinv38382' => 'din', 'Dinv38383' => 'din', 'Duzib133G0974' => 'dzi', 'Duzib138G1867' => 'dzi', 'Duzib211G0420' => 'dzi', 'Duzib212G0930' => 'dzi', 'ECA234G1645' => 'eca', 'ECA247G3467' => 'eca', 'ECA248G1703' => 'eca', 'EL10Ac3g06327' => 'bvu', 'EL10Ac7g17204' => 'bvu', 'Eucgr.A00855' => 'egr', 'Eucgr.A00858' => 'egr', 'Eucgr.H01520' => 'egr', 'Eucgr.H03604' => 'egr', 'Eucgr.L03465' => 'egr', 'Eucgr.L03466' => 'egr', 'FAN01G0988' => 'fan', 'FAN02G3892' => 'fan', 'FAN05G3381' => 'fan', 'FAN07G0967' => 'fan', 'FAN07G1493' => 'fan', 'FAN08G3125' => 'fan', 'FAN09G0402' => 'fan', 'FAN12G2594' => 'fan', 'FAN12G3879' => 'fan', 'FAN14G1546' => 'fan', 'FAN15G3626' => 'fan', 'FAN17G0588' => 'fan', 'FAN17G0609' => 'fan', 'FAN18G2817' => 'fan', 'FAN19G1305' => 'fan', 'FAN20G1787' => 'fan', 'FAN22G0073' => 'fan', 'FAN22G0352' => 'fan', 'FAN22G0368' => 'fan', 'FAN22G2273' => 'fan', 'FAN24G1998' => 'fan', 'FAN27G1317' => 'fan', 'FvH4_2g23980' => 'fve', 'FvH4_4g14380' => 'fve', 'FvH4_4g14390' => 'fve', 'FvH4_6g09250' => 'fve', 'Glyma.03G151100' => 'gma', 'Glyma.04G122550' => 'gma', 'Glyma.05G001600' => 'gma', 'Glyma.09G270766' => 'gma', 'Glyma.09G270832' => 'gma', 'Glyma.13G209800' => 'gma', 'Glyma.15G102800' => 'gma', 'Glyma.18G218900' => 'gma', 'Glyma.19G001500' => 'gma', 'Glyma.19G153600' => 'gma', 'Gohir.A02G028600' => 'ghi', 'Gohir.A08G045000' => 'ghi', 'Gohir.A11G120500' => 'ghi', 'Gohir.A12G006200' => 'ghi', 'Gohir.A12G006250' => 'ghi', 'Gohir.D02G036300' => 'ghi', 'Gohir.D08G054700' => 'ghi', 'Gohir.D11G125600' => 'ghi', 'Gohir.D12G005700' => 'ghi', 'Gorai.004G055200' => 'gra', 'Gorai.005G040400' => 'gra', 'Gorai.007G134500' => 'gra', 'Gorai.008G005500' => 'gra', 'GSVIVG01011094001' => 'vvi', 'GSVIVG01017879001' => 'vvi', 'GSVIVG01025988001' => 'vvi', 'GSVIVG01029847001' => 'vvi', 'HanXRQChr10g0282901' => 'han', 'HanXRQChr10g0310371' => 'han', 'HanXRQChr10g0315041' => 'han', 'HanXRQChr11g0327651' => 'han', 'HanXRQChr12g0359391' => 'han', 'Haze_00972' => 'cav', 'Haze_00973' => 'cav', 'Haze_00974' => 'cav', 'Haze_04747' => 'cav', 'Haze_04749' => 'cav', 'Haze_04750' => 'cav', 'Haze_21217' => 'cav', 'Hma1.2p1_1037F.1_g250680' => 'hma', 'Hma1.2p1_1644F.1_g295320' => 'hma', 'HPP92_011322' => 'vpl', 'HPP92_011323' => 'vpl', 'HPP92_011324' => 'vpl', 'HPP92_011325' => 'vpl', 'HPP92_011326' => 'vpl', 'Hund12205' => 'sun', 'Hund17957' => 'sun', 'Lalb_Chr06g0176771' => 'lal', 'Lalb_Chr18g0056021' => 'lal', 'Lalb_Chr18g0056031' => 'lal', 'Lalb_Chr18g0056041' => 'lal', 'Lalb_Chr20g0107751' => 'lal', 'Lalb_Chr20g0118371' => 'lal', 'Lj1g0010239' => 'lja', 'Lj1g0017101' => 'lja', 'Lj2A1178G40' => 'lonja', 'Lj2A54G84' => 'lonja', 'Lj2g0015248' => 'lja', 'Lj3A761T51' => 'lonja', 'Lj6g0018116' => 'lja', 'Lsat_1_v5_gn_4_136040' => 'lsa', 'Lsat_1_v5_gn_5_187461' => 'lsa', 'Lsat_1_v5_gn_5_77001' => 'lsa', 'Lsat_1_v5_gn_9_4461' => 'lsa', 'Manes.01G210100' => 'mes', 'Manes.03G185600' => 'mes', 'Manes.05G073300' => 'mes', 'Manes.09G120300' => 'mes', 'Manes.15G022100' => 'mes', 'Mapoly0096s0053' => 'mpo', 'MBI03_g14058_MAGBIO' => 'mbi', 'MBI03_g33876_MAGBIO' => 'mbi', 'MBI03_g36854_MAGBIO' => 'mbi', 'MBI17_g11997_MAGBIO' => 'mbi', 'MD03G1269000' => 'mdo', 'MD04G1179600' => 'mdo', 'MD11G1289800' => 'mdo', 'MD12G1194700' => 'mdo', 'MD13G1182100' => 'mdo', 'MD13G1182200' => 'mdo', 'MD16G1182600' => 'mdo', 'Medtr2g021400' => 'mtr', 'Medtr2g021470' => 'mtr', 'Medtr2g105810' => 'mtr', 'Medtr3g033580' => 'mtr', 'Medtr6g007970' => 'mtr', 'Medtr7g056330' => 'mtr', 'Medtr7g074290' => 'mtr', 'Medtr7g074380' => 'mtr', 'Medtr7g094550' => 'mtr', 'Medtr8g069995' => 'mtr', 'MELO3C014345.2' => 'cme', 'MELO3C021395.2' => 'cme', 'Migut.D00262' => 'egut', 'Migut.G00257' => 'egut', 'MSTRG.21575' => 'ama', 'MSTRG.3985' => 'ama', 'Nitab4.5_0000295g0140' => 'nta', 'Nitab4.5_0000732g0140' => 'nta', 'Nitab4.5_0003162g0020' => 'nta', 'Nitab4.5_0006180g0090' => 'nta', 'Nitab4.5_0006390g0010' => 'nta', 'Nitab4.5_0007392g0040' => 'nta', 'Nn1g02140' => 'nnu', 'Nn4g26168' => 'nnu', 'Nn5g26754' => 'nnu', 'Oeu001433.1' => 'oeu', 'Oeu010299.2' => 'oeu', 'Oeu011171.1' => 'oeu', 'Oeu037675.1' => 'oeu', 'Oeu038359.1' => 'oeu', 'Oeu063834.1' => 'oeu', 'Oeu063835.1' => 'oeu', 'Os05g0312000' => 'osa', 'Os07g0211101' => 'osa', 'Os07g0211200' => 'osa', 'Os07g0681500' => 'osa', 'Peaxi162Scf00095g01015' => 'pax', 'Peaxi162Scf00104g00329' => 'pax', 'Peaxi162Scf00161g00137' => 'pax', 'PGR004G1665' => 'pgr', 'PGR031G2937' => 'pgr', 'PGR119G2145' => 'pgr', 'PGSC0003DMG400004351' => 'stu', 'PGSC0003DMG400014625' => 'stu', 'PGSC0003DMG401000943' => 'stu', 'Phvul.001G148600' => 'pvu', 'Phvul.004G001700' => 'pvu', 'Phvul.006G154900' => 'pvu', 'Phvul.008G078200' => 'pvu', 'Phvul.011G136500' => 'pvu', 'Potri.002G215600' => 'ptr', 'Potri.008G201600' => 'ptr', 'Potri.014G138400' => 'ptr', 'Potri.016G142500' => 'ptr', 'Pp3c16_10580' => 'ppa', 'Pp3c5_25280' => 'ppa', 'Prupe.1G150000' => 'ppe', 'Prupe.1G150100' => 'ppe', 'Prupe.6G299600' => 'ppe', 'Prupe.8G245000' => 'ppe', 'Psat0s4927g0040' => 'psa', 'Psat1g052080' => 'psa', 'Psat1g183800' => 'psa', 'Psat3g113840' => 'psa', 'Psat3g126120' => 'psa', 'Psat3g126160' => 'psa', 'Psat3g158760' => 'psa', 'Psat3g158840' => 'psa', 'PSO170G2858' => 'pso', 'PSO339G0606' => 'pso', 'PSO384G4709' => 'pso', 'PSO407G0334' => 'pso', 'QL04p040276' => 'qlo', 'QL06p005458' => 'qlo', 'QL06p005472' => 'qlo', 'QL07p030546' => 'qlo', 'QL07p031519' => 'qlo', 'QL09p050949' => 'qlo', 'QL09p050966' => 'qlo', 'QL09p051067' => 'qlo', 'QL12p022706' => 'qlo', 'RcHm_v2.0_Chr2g0119601' => 'rch', 'RcHm_v2.0_Chr3g0459591' => 'rch', 'RcHm_v2.0_Chr4g0418521' => 'rch', 'RcHm_v2.0_Chr4g0418531' => 'rch', 'RcHm_v2.0_Chr4g0418541' => 'rch', 'RcHm_v2.0_Chr6g0291641' => 'rch', 'Rhsim01G0086300' => 'rsi', 'Rhsim01G0276300' => 'rsi', 'Rhsim01G0276500' => 'rsi', 'Rhsim04G0207700' => 'rsi', 'Rhsim05G0234500' => 'rsi', 'Rhsim13G0022400' => 'rsi', 'Sabra02G0167900' => 'sbr', 'Sabra04G0158500' => 'sbr', 'Sabra08G0159800' => 'sbr', 'Sabra10G0011500' => 'sbr', 'Sabra14G0104400' => 'sbr', 'SalBow2G2440' => 'sbo', 'SalBow4G2265' => 'sbo', 'Sc02g0000060' => 'sci', 'Sc05g0005020' => 'sci', 'Sc13g0003890' => 'sci', 'Sed0014865' => 'sed', 'Sed0017224' => 'sed', 'Sed0026391' => 'sed', 'SEGI_00063' => 'sgi', 'SEGI_10967' => 'sgi', 'SEGI_17510' => 'sgi', 'SEGI_24396' => 'sgi', 'SEGI_39719' => 'sgi', 'SEGI_41392' => 'sgi', 'SGA_v2.0_scaffold11G05794' => 'sas', 'SGA_v2.0_scaffold142G35607' => 'sas', 'SGA_v2.0_scaffold1G00447' => 'sas', 'SHI15388' => 'shi', 'SHI15394' => 'shi', 'SHI15396' => 'shi', 'SHI15399' => 'shi', 'SMO343G0151' => 'smo', 'SMO367G1118' => 'smo', 'Solyc01g080200.3' => 'sly', 'Solyc06g008960.3' => 'sly', 'Solyc09g064780.3' => 'sly', 'Sopen01g031980' => 'spe', 'Sopen06g003710' => 'spe', 'Sopen09g026460' => 'spe', 'Sp3g21240' => 'spa', 'Sp4g30030' => 'spa', 'TAR365G0022' => 'tar', 'TAR365G1023' => 'tar', 'TAR365G1253' => 'tar', 'TAR623G0078' => 'tar', 'TAR623G1721' => 'tar', 'TAR633G0959' => 'tar', 'THA.LOC104802225' => 'tha', 'THA.LOC104804769' => 'tha', 'THA.LOC104808660' => 'tha', 'THA.LOC104812792' => 'tha', 'Thecc.01G284000' => 'tca', 'Thecc.04G220600' => 'tca', 'Thecc.05G268900' => 'tca', 'Thecc.08G171100' => 'tca', 'Thhalv10001284m.g' => 'esa', 'Thhalv10019912m.g' => 'esa', 'TPR.G14189' => 'tpr', 'TPR.G18110' => 'tpr', 'TPR.G18130' => 'tpr', 'TPR.G18131' => 'tpr', 'TPR.G18140' => 'tpr', 'TPR.G24282' => 'tpr', 'TPR.G25221' => 'tpr', 'TPR.G29267' => 'tpr', 'TPR.G35315' => 'tpr', 'TPR.G36173' => 'tpr', 'TWI09G0794' => 'twi', 'TWI59G1348' => 'twi', 'TWI74G0430' => 'twi', 'unitig_26.g8940' => 'ugi', 'unitig_749.g13744' => 'ugi', 'unitig_749.g13745' => 'ugi', 'vmacro08269' => 'vma', 'vmacro14937' => 'vma', 'vmacro20401' => 'vma', 'VMungo0464G1349' => 'vmu', 'VMungo0540G0289' => 'vmu', 'VMungo1215G1590' => 'vmu', 'VMungo1309G0221' => 'vmu', 'VMungo1309G2815' => 'vmu', 'VMungo1383G0239' => 'vmu', 'VMungo1383G2910' => 'vmu', 'Zm00001eb095270' => 'zma', 'Zm00001eb095280' => 'zma', 'Zm00001eb111630' => 'zma', 'Zm00001eb237080' => 'zma', 'Zm00001eb273740' => 'zma', 'Zm00001eb285040' => 'zma', 'Zm00001eb330790' => 'zma', 'Zm00001eb337380' => 'zma' ), 'gf_id' => 'HOM05D001484', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001484' ), 'data_identifier' => 'HOM05D001484', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001484', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p31500' => 'bna', 'A05p00020' => 'bna', 'A07p08820' => 'bna', 'Aa31LG4G3300' => 'aar', 'Aa31LG8G10030' => 'aar', 'Actinidia00731' => 'ach', 'Actinidia11473' => 'ach', 'Actinidia23469' => 'ach', 'Actinidia24318' => 'ach', 'Actinidia40196' => 'ach', 'Actinidia40197' => 'ach', 'Actinidia40198' => 'ach', 'Ah.08g212990' => 'amhyb', 'Ah.15g091720' => 'amhyb', 'AL3G38260' => 'aly', 'AL4G47710' => 'aly', 'Aqoxy2G00671' => 'aox', 'Aqoxy2G03236' => 'aox', 'arahy.Tifrunner.gnm1.ann1.05IDCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KR684' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATY3SJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK6QJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6APGL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IDT7Z9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM073U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ0R87' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LE7RV4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT4QRX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V5ENPK' => 'arhy', 'AT2G48110' => 'ath', 'AT3G23590' => 'ath', 'ATR0626G186' => 'atr', 'ATR1127G141' => 'atr', 'Atru.chr4.2583' => 'acertr', 'Atru.chr5.1358' => 'acertr', 'Atru.chr5.1359' => 'acertr', 'Atru.chr8.46' => 'acertr', 'AUR62002640' => 'cqu', 'AUR62030055' => 'cqu', 'AUR62033713' => 'cqu', 'AUR62033714' => 'cqu', 'AUR62036795' => 'cqu', 'AUR62039891' => 'cqu', 'BcaB02g08737' => 'bca', 'BcaB04g20441' => 'bca', 'BcaB06g26509' => 'bca', 'BcaB06g26510' => 'bca', 'BcaB06g26511' => 'bca', 'BcaB06g26512' => 'bca', 'BcaB06g26513' => 'bca', 'BcaC02g12564' => 'bca', 'BcaC02g12565' => 'bca', 'BcaC02g12794' => 'bca', 'BcaC02g12795' => 'bca', 'BcaC02g12796' => 'bca', 'BcaC06g35541' => 'bca', 'BNapus_Darmor_BZH_scaffold_188p00080' => 'bna', 'BNapus_Darmor_BZH_scaffold_188p00090' => 'bna', 'BolC1t03972H' => 'bol', 'BolC1t03973H' => 'bol', 'BolC4t21680H' => 'bol', 'BolC7t41863H' => 'bol', 'BolSC55t61227H' => 'bol', 'BolSC55t61228H' => 'bol', 'BraA01t03278Z' => 'bra', 'BraA05t18998Z' => 'bra', 'BraA07t28673Z' => 'bra', 'C01p40150' => 'bna', 'C05p12370' => 'bna', 'C07p13680' => 'bna', 'CAN.G1006.16' => 'can', 'CAN.G1006.17' => 'can', 'CAN.G1170.2' => 'can', 'CAN.G962.7' => 'can', 'CANSAT25G2179' => 'cansat', 'CANSAT78G1573' => 'cansat', 'CARHR099510' => 'chi', 'CARHR143510' => 'chi', 'Carub.0003s2380' => 'cru', 'Carub.0004s3082' => 'cru', 'Ca_00614_v3' => 'car', 'Ca_07801_v3' => 'car', 'Ca_08567_v3' => 'car', 'Ca_09571_v3' => 'car', 'CBR_g19290' => 'cbr', 'Cc01_g19770' => 'ccan', 'Cc03_g03030' => 'ccan', 'CDE07G0968' => 'cde', 'CDE09G1441' => 'cde', 'Cfa006103' => 'cfa', 'Cfa015573' => 'cfa', 'Cfa016988' => 'cfa', 'Ciclev10006738m.g' => 'ccl', 'Ciclev10010920m.g' => 'ccl', 'Ciclev10018517m.g' => 'ccl', 'CiPaw.01G159200' => 'cil', 'CiPaw.02G091000' => 'cil', 'CiPaw.02G091100' => 'cil', 'CiPaw.08G103100' => 'cil', 'CiPaw.09G224900' => 'cil', 'ClCG06G005740' => 'cla', 'ClCG07G000090' => 'cla', 'ClCG07G000100' => 'cla', 'COL.COLO4_09143' => 'col', 'COL.COLO4_25124' => 'col', 'Cpa.g.sc16.34' => 'cpa', 'Cpa.g.sc3504.1' => 'cpa', 'Cpa.g.sc60.37' => 'cpa', 'CsaV3_6G018520' => 'csa', 'CsaV3_6G036860' => 'csa', 'CSS0001072' => 'camsi', 'CSS0020208' => 'camsi', 'CSS0021253' => 'camsi', 'CSS0022190' => 'camsi', 'CSS0036150' => 'camsi', 'CSS0040442' => 'camsi', 'CSS0042300' => 'camsi', 'CSS0045298' => 'camsi', 'DCAR_012449' => 'dca', 'DCAR_018405' => 'dca', 'DCAR_024573' => 'dca', 'DCAR_030591' => 'dca', 'Dinv16926' => 'din', 'Dinv32963' => 'din', 'Dinv38382' => 'din', 'Dinv38383' => 'din', 'Duzib133G0974' => 'dzi', 'Duzib138G1867' => 'dzi', 'Duzib211G0420' => 'dzi', 'Duzib212G0930' => 'dzi', 'ECA234G1645' => 'eca', 'ECA247G3467' => 'eca', 'ECA248G1703' => 'eca', 'EL10Ac3g06327' => 'bvu', 'EL10Ac7g17204' => 'bvu', 'Eucgr.A00855' => 'egr', 'Eucgr.A00858' => 'egr', 'Eucgr.H01520' => 'egr', 'Eucgr.H03604' => 'egr', 'Eucgr.L03465' => 'egr', 'Eucgr.L03466' => 'egr', 'FAN01G0988' => 'fan', 'FAN02G3892' => 'fan', 'FAN05G3381' => 'fan', 'FAN07G0967' => 'fan', 'FAN07G1493' => 'fan', 'FAN08G3125' => 'fan', 'FAN09G0402' => 'fan', 'FAN12G2594' => 'fan', 'FAN12G3879' => 'fan', 'FAN14G1546' => 'fan', 'FAN15G3626' => 'fan', 'FAN17G0588' => 'fan', 'FAN17G0609' => 'fan', 'FAN18G2817' => 'fan', 'FAN19G1305' => 'fan', 'FAN20G1787' => 'fan', 'FAN22G0073' => 'fan', 'FAN22G0352' => 'fan', 'FAN22G0368' => 'fan', 'FAN22G2273' => 'fan', 'FAN24G1998' => 'fan', 'FAN27G1317' => 'fan', 'FvH4_2g23980' => 'fve', 'FvH4_4g14380' => 'fve', 'FvH4_4g14390' => 'fve', 'FvH4_6g09250' => 'fve', 'Glyma.03G151100' => 'gma', 'Glyma.04G122550' => 'gma', 'Glyma.05G001600' => 'gma', 'Glyma.09G270766' => 'gma', 'Glyma.09G270832' => 'gma', 'Glyma.13G209800' => 'gma', 'Glyma.15G102800' => 'gma', 'Glyma.18G218900' => 'gma', 'Glyma.19G001500' => 'gma', 'Glyma.19G153600' => 'gma', 'Gohir.A02G028600' => 'ghi', 'Gohir.A08G045000' => 'ghi', 'Gohir.A11G120500' => 'ghi', 'Gohir.A12G006200' => 'ghi', 'Gohir.A12G006250' => 'ghi', 'Gohir.D02G036300' => 'ghi', 'Gohir.D08G054700' => 'ghi', 'Gohir.D11G125600' => 'ghi', 'Gohir.D12G005700' => 'ghi', 'Gorai.004G055200' => 'gra', 'Gorai.005G040400' => 'gra', 'Gorai.007G134500' => 'gra', 'Gorai.008G005500' => 'gra', 'GSVIVG01011094001' => 'vvi', 'GSVIVG01017879001' => 'vvi', 'GSVIVG01025988001' => 'vvi', 'GSVIVG01029847001' => 'vvi', 'HanXRQChr10g0282901' => 'han', 'HanXRQChr10g0310371' => 'han', 'HanXRQChr10g0315041' => 'han', 'HanXRQChr11g0327651' => 'han', 'HanXRQChr12g0359391' => 'han', 'Haze_00972' => 'cav', 'Haze_00973' => 'cav', 'Haze_00974' => 'cav', 'Haze_04747' => 'cav', 'Haze_04749' => 'cav', 'Haze_04750' => 'cav', 'Haze_21217' => 'cav', 'Hma1.2p1_1037F.1_g250680' => 'hma', 'Hma1.2p1_1644F.1_g295320' => 'hma', 'HPP92_011322' => 'vpl', 'HPP92_011323' => 'vpl', 'HPP92_011324' => 'vpl', 'HPP92_011325' => 'vpl', 'HPP92_011326' => 'vpl', 'Hund12205' => 'sun', 'Hund17957' => 'sun', 'Lalb_Chr06g0176771' => 'lal', 'Lalb_Chr18g0056021' => 'lal', 'Lalb_Chr18g0056031' => 'lal', 'Lalb_Chr18g0056041' => 'lal', 'Lalb_Chr20g0107751' => 'lal', 'Lalb_Chr20g0118371' => 'lal', 'Lj1g0010239' => 'lja', 'Lj1g0017101' => 'lja', 'Lj2A1178G40' => 'lonja', 'Lj2A54G84' => 'lonja', 'Lj2g0015248' => 'lja', 'Lj3A761T51' => 'lonja', 'Lj6g0018116' => 'lja', 'Lsat_1_v5_gn_4_136040' => 'lsa', 'Lsat_1_v5_gn_5_187461' => 'lsa', 'Lsat_1_v5_gn_5_77001' => 'lsa', 'Lsat_1_v5_gn_9_4461' => 'lsa', 'Manes.01G210100' => 'mes', 'Manes.03G185600' => 'mes', 'Manes.05G073300' => 'mes', 'Manes.09G120300' => 'mes', 'Manes.15G022100' => 'mes', 'Mapoly0096s0053' => 'mpo', 'MBI03_g14058_MAGBIO' => 'mbi', 'MBI03_g33876_MAGBIO' => 'mbi', 'MBI03_g36854_MAGBIO' => 'mbi', 'MBI17_g11997_MAGBIO' => 'mbi', 'MD03G1269000' => 'mdo', 'MD04G1179600' => 'mdo', 'MD11G1289800' => 'mdo', 'MD12G1194700' => 'mdo', 'MD13G1182100' => 'mdo', 'MD13G1182200' => 'mdo', 'MD16G1182600' => 'mdo', 'Medtr2g021400' => 'mtr', 'Medtr2g021470' => 'mtr', 'Medtr2g105810' => 'mtr', 'Medtr3g033580' => 'mtr', 'Medtr6g007970' => 'mtr', 'Medtr7g056330' => 'mtr', 'Medtr7g074290' => 'mtr', 'Medtr7g074380' => 'mtr', 'Medtr7g094550' => 'mtr', 'Medtr8g069995' => 'mtr', 'MELO3C014345.2' => 'cme', 'MELO3C021395.2' => 'cme', 'Migut.D00262' => 'egut', 'Migut.G00257' => 'egut', 'MSTRG.21575' => 'ama', 'MSTRG.3985' => 'ama', 'Nitab4.5_0000295g0140' => 'nta', 'Nitab4.5_0000732g0140' => 'nta', 'Nitab4.5_0003162g0020' => 'nta', 'Nitab4.5_0006180g0090' => 'nta', 'Nitab4.5_0006390g0010' => 'nta', 'Nitab4.5_0007392g0040' => 'nta', 'Nn1g02140' => 'nnu', 'Nn4g26168' => 'nnu', 'Nn5g26754' => 'nnu', 'Oeu001433.1' => 'oeu', 'Oeu010299.2' => 'oeu', 'Oeu011171.1' => 'oeu', 'Oeu037675.1' => 'oeu', 'Oeu038359.1' => 'oeu', 'Oeu063834.1' => 'oeu', 'Oeu063835.1' => 'oeu', 'Os05g0312000' => 'osa', 'Os07g0211101' => 'osa', 'Os07g0211200' => 'osa', 'Os07g0681500' => 'osa', 'Peaxi162Scf00095g01015' => 'pax', 'Peaxi162Scf00104g00329' => 'pax', 'Peaxi162Scf00161g00137' => 'pax', 'PGR004G1665' => 'pgr', 'PGR031G2937' => 'pgr', 'PGR119G2145' => 'pgr', 'PGSC0003DMG400004351' => 'stu', 'PGSC0003DMG400014625' => 'stu', 'PGSC0003DMG401000943' => 'stu', 'Phvul.001G148600' => 'pvu', 'Phvul.004G001700' => 'pvu', 'Phvul.006G154900' => 'pvu', 'Phvul.008G078200' => 'pvu', 'Phvul.011G136500' => 'pvu', 'Potri.002G215600' => 'ptr', 'Potri.008G201600' => 'ptr', 'Potri.014G138400' => 'ptr', 'Potri.016G142500' => 'ptr', 'Pp3c16_10580' => 'ppa', 'Pp3c5_25280' => 'ppa', 'Prupe.1G150000' => 'ppe', 'Prupe.1G150100' => 'ppe', 'Prupe.6G299600' => 'ppe', 'Prupe.8G245000' => 'ppe', 'Psat0s4927g0040' => 'psa', 'Psat1g052080' => 'psa', 'Psat1g183800' => 'psa', 'Psat3g113840' => 'psa', 'Psat3g126120' => 'psa', 'Psat3g126160' => 'psa', 'Psat3g158760' => 'psa', 'Psat3g158840' => 'psa', 'PSO170G2858' => 'pso', 'PSO339G0606' => 'pso', 'PSO384G4709' => 'pso', 'PSO407G0334' => 'pso', 'QL04p040276' => 'qlo', 'QL06p005458' => 'qlo', 'QL06p005472' => 'qlo', 'QL07p030546' => 'qlo', 'QL07p031519' => 'qlo', 'QL09p050949' => 'qlo', 'QL09p050966' => 'qlo', 'QL09p051067' => 'qlo', 'QL12p022706' => 'qlo', 'RcHm_v2.0_Chr2g0119601' => 'rch', 'RcHm_v2.0_Chr3g0459591' => 'rch', 'RcHm_v2.0_Chr4g0418521' => 'rch', 'RcHm_v2.0_Chr4g0418531' => 'rch', 'RcHm_v2.0_Chr4g0418541' => 'rch', 'RcHm_v2.0_Chr6g0291641' => 'rch', 'Rhsim01G0086300' => 'rsi', 'Rhsim01G0276300' => 'rsi', 'Rhsim01G0276500' => 'rsi', 'Rhsim04G0207700' => 'rsi', 'Rhsim05G0234500' => 'rsi', 'Rhsim13G0022400' => 'rsi', 'Sabra02G0167900' => 'sbr', 'Sabra04G0158500' => 'sbr', 'Sabra08G0159800' => 'sbr', 'Sabra10G0011500' => 'sbr', 'Sabra14G0104400' => 'sbr', 'SalBow2G2440' => 'sbo', 'SalBow4G2265' => 'sbo', 'Sc02g0000060' => 'sci', 'Sc05g0005020' => 'sci', 'Sc13g0003890' => 'sci', 'Sed0014865' => 'sed', 'Sed0017224' => 'sed', 'Sed0026391' => 'sed', 'SEGI_00063' => 'sgi', 'SEGI_10967' => 'sgi', 'SEGI_17510' => 'sgi', 'SEGI_24396' => 'sgi', 'SEGI_39719' => 'sgi', 'SEGI_41392' => 'sgi', 'SGA_v2.0_scaffold11G05794' => 'sas', 'SGA_v2.0_scaffold142G35607' => 'sas', 'SGA_v2.0_scaffold1G00447' => 'sas', 'SHI15388' => 'shi', 'SHI15394' => 'shi', 'SHI15396' => 'shi', 'SHI15399' => 'shi', 'SMO343G0151' => 'smo', 'SMO367G1118' => 'smo', 'Solyc01g080200.3' => 'sly', 'Solyc06g008960.3' => 'sly', 'Solyc09g064780.3' => 'sly', 'Sopen01g031980' => 'spe', 'Sopen06g003710' => 'spe', 'Sopen09g026460' => 'spe', 'Sp3g21240' => 'spa', 'Sp4g30030' => 'spa', 'TAR365G0022' => 'tar', 'TAR365G1023' => 'tar', 'TAR365G1253' => 'tar', 'TAR623G0078' => 'tar', 'TAR623G1721' => 'tar', 'TAR633G0959' => 'tar', 'THA.LOC104802225' => 'tha', 'THA.LOC104804769' => 'tha', 'THA.LOC104808660' => 'tha', 'THA.LOC104812792' => 'tha', 'Thecc.01G284000' => 'tca', 'Thecc.04G220600' => 'tca', 'Thecc.05G268900' => 'tca', 'Thecc.08G171100' => 'tca', 'Thhalv10001284m.g' => 'esa', 'Thhalv10019912m.g' => 'esa', 'TPR.G14189' => 'tpr', 'TPR.G18110' => 'tpr', 'TPR.G18130' => 'tpr', 'TPR.G18131' => 'tpr', 'TPR.G18140' => 'tpr', 'TPR.G24282' => 'tpr', 'TPR.G25221' => 'tpr', 'TPR.G29267' => 'tpr', 'TPR.G35315' => 'tpr', 'TPR.G36173' => 'tpr', 'TWI09G0794' => 'twi', 'TWI59G1348' => 'twi', 'TWI74G0430' => 'twi', 'unitig_26.g8940' => 'ugi', 'unitig_749.g13744' => 'ugi', 'unitig_749.g13745' => 'ugi', 'vmacro08269' => 'vma', 'vmacro14937' => 'vma', 'vmacro20401' => 'vma', 'VMungo0464G1349' => 'vmu', 'VMungo0540G0289' => 'vmu', 'VMungo1215G1590' => 'vmu', 'VMungo1309G0221' => 'vmu', 'VMungo1309G2815' => 'vmu', 'VMungo1383G0239' => 'vmu', 'VMungo1383G2910' => 'vmu', 'Zm00001eb095270' => 'zma', 'Zm00001eb095280' => 'zma', 'Zm00001eb111630' => 'zma', 'Zm00001eb237080' => 'zma', 'Zm00001eb273740' => 'zma', 'Zm00001eb285040' => 'zma', 'Zm00001eb330790' => 'zma', 'Zm00001eb337380' => 'zma' ) $gf_id = 'HOM05D001484' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001484' ) $data_identifier = 'HOM05D001484' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 2, 'aly' => (int) 2, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 22, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 7, 'hma' => (int) 2, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 7, 'mtr' => (int) 10, 'cme' => (int) 2, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 4, 'ppa' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 4, 'qlo' => (int) 9, 'rch' => (int) 6, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 10, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 7, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb337380' $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' => 'HOM05D001484', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p31500' => 'bna', 'A05p00020' => 'bna', 'A07p08820' => 'bna', 'Aa31LG4G3300' => 'aar', 'Aa31LG8G10030' => 'aar', 'Actinidia00731' => 'ach', 'Actinidia11473' => 'ach', 'Actinidia23469' => 'ach', 'Actinidia24318' => 'ach', 'Actinidia40196' => 'ach', 'Actinidia40197' => 'ach', 'Actinidia40198' => 'ach', 'Ah.08g212990' => 'amhyb', 'Ah.15g091720' => 'amhyb', 'AL3G38260' => 'aly', 'AL4G47710' => 'aly', 'Aqoxy2G00671' => 'aox', 'Aqoxy2G03236' => 'aox', 'arahy.Tifrunner.gnm1.ann1.05IDCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KR684' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATY3SJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK6QJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6APGL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IDT7Z9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM073U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ0R87' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LE7RV4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT4QRX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V5ENPK' => 'arhy', 'AT2G48110' => 'ath', 'AT3G23590' => 'ath', 'ATR0626G186' => 'atr', 'ATR1127G141' => 'atr', 'Atru.chr4.2583' => 'acertr', 'Atru.chr5.1358' => 'acertr', 'Atru.chr5.1359' => 'acertr', 'Atru.chr8.46' => 'acertr', 'AUR62002640' => 'cqu', 'AUR62030055' => 'cqu', 'AUR62033713' => 'cqu', 'AUR62033714' => 'cqu', 'AUR62036795' => 'cqu', 'AUR62039891' => 'cqu', 'BcaB02g08737' => 'bca', 'BcaB04g20441' => 'bca', 'BcaB06g26509' => 'bca', 'BcaB06g26510' => 'bca', 'BcaB06g26511' => 'bca', 'BcaB06g26512' => 'bca', 'BcaB06g26513' => 'bca', 'BcaC02g12564' => 'bca', 'BcaC02g12565' => 'bca', 'BcaC02g12794' => 'bca', 'BcaC02g12795' => 'bca', 'BcaC02g12796' => 'bca', 'BcaC06g35541' => 'bca', 'BNapus_Darmor_BZH_scaffold_188p00080' => 'bna', 'BNapus_Darmor_BZH_scaffold_188p00090' => 'bna', 'BolC1t03972H' => 'bol', 'BolC1t03973H' => 'bol', 'BolC4t21680H' => 'bol', 'BolC7t41863H' => 'bol', 'BolSC55t61227H' => 'bol', 'BolSC55t61228H' => 'bol', 'BraA01t03278Z' => 'bra', 'BraA05t18998Z' => 'bra', 'BraA07t28673Z' => 'bra', 'C01p40150' => 'bna', 'C05p12370' => 'bna', 'C07p13680' => 'bna', 'CAN.G1006.16' => 'can', 'CAN.G1006.17' => 'can', 'CAN.G1170.2' => 'can', 'CAN.G962.7' => 'can', 'CANSAT25G2179' => 'cansat', 'CANSAT78G1573' => 'cansat', 'CARHR099510' => 'chi', 'CARHR143510' => 'chi', 'Carub.0003s2380' => 'cru', 'Carub.0004s3082' => 'cru', 'Ca_00614_v3' => 'car', 'Ca_07801_v3' => 'car', 'Ca_08567_v3' => 'car', 'Ca_09571_v3' => 'car', 'CBR_g19290' => 'cbr', 'Cc01_g19770' => 'ccan', 'Cc03_g03030' => 'ccan', 'CDE07G0968' => 'cde', 'CDE09G1441' => 'cde', 'Cfa006103' => 'cfa', 'Cfa015573' => 'cfa', 'Cfa016988' => 'cfa', 'Ciclev10006738m.g' => 'ccl', 'Ciclev10010920m.g' => 'ccl', 'Ciclev10018517m.g' => 'ccl', 'CiPaw.01G159200' => 'cil', 'CiPaw.02G091000' => 'cil', 'CiPaw.02G091100' => 'cil', 'CiPaw.08G103100' => 'cil', 'CiPaw.09G224900' => 'cil', 'ClCG06G005740' => 'cla', 'ClCG07G000090' => 'cla', 'ClCG07G000100' => 'cla', 'COL.COLO4_09143' => 'col', 'COL.COLO4_25124' => 'col', 'Cpa.g.sc16.34' => 'cpa', 'Cpa.g.sc3504.1' => 'cpa', 'Cpa.g.sc60.37' => 'cpa', 'CsaV3_6G018520' => 'csa', 'CsaV3_6G036860' => 'csa', 'CSS0001072' => 'camsi', 'CSS0020208' => 'camsi', 'CSS0021253' => 'camsi', 'CSS0022190' => 'camsi', 'CSS0036150' => 'camsi', 'CSS0040442' => 'camsi', 'CSS0042300' => 'camsi', 'CSS0045298' => 'camsi', 'DCAR_012449' => 'dca', 'DCAR_018405' => 'dca', 'DCAR_024573' => 'dca', 'DCAR_030591' => 'dca', 'Dinv16926' => 'din', 'Dinv32963' => 'din', 'Dinv38382' => 'din', 'Dinv38383' => 'din', 'Duzib133G0974' => 'dzi', 'Duzib138G1867' => 'dzi', 'Duzib211G0420' => 'dzi', 'Duzib212G0930' => 'dzi', 'ECA234G1645' => 'eca', 'ECA247G3467' => 'eca', 'ECA248G1703' => 'eca', 'EL10Ac3g06327' => 'bvu', 'EL10Ac7g17204' => 'bvu', 'Eucgr.A00855' => 'egr', 'Eucgr.A00858' => 'egr', 'Eucgr.H01520' => 'egr', 'Eucgr.H03604' => 'egr', 'Eucgr.L03465' => 'egr', 'Eucgr.L03466' => 'egr', 'FAN01G0988' => 'fan', 'FAN02G3892' => 'fan', 'FAN05G3381' => 'fan', 'FAN07G0967' => 'fan', 'FAN07G1493' => 'fan', 'FAN08G3125' => 'fan', 'FAN09G0402' => 'fan', 'FAN12G2594' => 'fan', 'FAN12G3879' => 'fan', 'FAN14G1546' => 'fan', 'FAN15G3626' => 'fan', 'FAN17G0588' => 'fan', 'FAN17G0609' => 'fan', 'FAN18G2817' => 'fan', 'FAN19G1305' => 'fan', 'FAN20G1787' => 'fan', 'FAN22G0073' => 'fan', 'FAN22G0352' => 'fan', 'FAN22G0368' => 'fan', 'FAN22G2273' => 'fan', 'FAN24G1998' => 'fan', 'FAN27G1317' => 'fan', 'FvH4_2g23980' => 'fve', 'FvH4_4g14380' => 'fve', 'FvH4_4g14390' => 'fve', 'FvH4_6g09250' => 'fve', 'Glyma.03G151100' => 'gma', 'Glyma.04G122550' => 'gma', 'Glyma.05G001600' => 'gma', 'Glyma.09G270766' => 'gma', 'Glyma.09G270832' => 'gma', 'Glyma.13G209800' => 'gma', 'Glyma.15G102800' => 'gma', 'Glyma.18G218900' => 'gma', 'Glyma.19G001500' => 'gma', 'Glyma.19G153600' => 'gma', 'Gohir.A02G028600' => 'ghi', 'Gohir.A08G045000' => 'ghi', 'Gohir.A11G120500' => 'ghi', 'Gohir.A12G006200' => 'ghi', 'Gohir.A12G006250' => 'ghi', 'Gohir.D02G036300' => 'ghi', 'Gohir.D08G054700' => 'ghi', 'Gohir.D11G125600' => 'ghi', 'Gohir.D12G005700' => 'ghi', 'Gorai.004G055200' => 'gra', 'Gorai.005G040400' => 'gra', 'Gorai.007G134500' => 'gra', 'Gorai.008G005500' => 'gra', 'GSVIVG01011094001' => 'vvi', 'GSVIVG01017879001' => 'vvi', 'GSVIVG01025988001' => 'vvi', 'GSVIVG01029847001' => 'vvi', 'HanXRQChr10g0282901' => 'han', 'HanXRQChr10g0310371' => 'han', 'HanXRQChr10g0315041' => 'han', 'HanXRQChr11g0327651' => 'han', 'HanXRQChr12g0359391' => 'han', 'Haze_00972' => 'cav', 'Haze_00973' => 'cav', 'Haze_00974' => 'cav', 'Haze_04747' => 'cav', 'Haze_04749' => 'cav', 'Haze_04750' => 'cav', 'Haze_21217' => 'cav', 'Hma1.2p1_1037F.1_g250680' => 'hma', 'Hma1.2p1_1644F.1_g295320' => 'hma', 'HPP92_011322' => 'vpl', 'HPP92_011323' => 'vpl', 'HPP92_011324' => 'vpl', 'HPP92_011325' => 'vpl', 'HPP92_011326' => 'vpl', 'Hund12205' => 'sun', 'Hund17957' => 'sun', 'Lalb_Chr06g0176771' => 'lal', 'Lalb_Chr18g0056021' => 'lal', 'Lalb_Chr18g0056031' => 'lal', 'Lalb_Chr18g0056041' => 'lal', 'Lalb_Chr20g0107751' => 'lal', 'Lalb_Chr20g0118371' => 'lal', 'Lj1g0010239' => 'lja', 'Lj1g0017101' => 'lja', 'Lj2A1178G40' => 'lonja', 'Lj2A54G84' => 'lonja', 'Lj2g0015248' => 'lja', 'Lj3A761T51' => 'lonja', 'Lj6g0018116' => 'lja', 'Lsat_1_v5_gn_4_136040' => 'lsa', 'Lsat_1_v5_gn_5_187461' => 'lsa', 'Lsat_1_v5_gn_5_77001' => 'lsa', 'Lsat_1_v5_gn_9_4461' => 'lsa', 'Manes.01G210100' => 'mes', 'Manes.03G185600' => 'mes', 'Manes.05G073300' => 'mes', 'Manes.09G120300' => 'mes', 'Manes.15G022100' => 'mes', 'Mapoly0096s0053' => 'mpo', 'MBI03_g14058_MAGBIO' => 'mbi', 'MBI03_g33876_MAGBIO' => 'mbi', 'MBI03_g36854_MAGBIO' => 'mbi', 'MBI17_g11997_MAGBIO' => 'mbi', 'MD03G1269000' => 'mdo', 'MD04G1179600' => 'mdo', 'MD11G1289800' => 'mdo', 'MD12G1194700' => 'mdo', 'MD13G1182100' => 'mdo', 'MD13G1182200' => 'mdo', 'MD16G1182600' => 'mdo', 'Medtr2g021400' => 'mtr', 'Medtr2g021470' => 'mtr', 'Medtr2g105810' => 'mtr', 'Medtr3g033580' => 'mtr', 'Medtr6g007970' => 'mtr', 'Medtr7g056330' => 'mtr', 'Medtr7g074290' => 'mtr', 'Medtr7g074380' => 'mtr', 'Medtr7g094550' => 'mtr', 'Medtr8g069995' => 'mtr', 'MELO3C014345.2' => 'cme', 'MELO3C021395.2' => 'cme', 'Migut.D00262' => 'egut', 'Migut.G00257' => 'egut', 'MSTRG.21575' => 'ama', 'MSTRG.3985' => 'ama', 'Nitab4.5_0000295g0140' => 'nta', 'Nitab4.5_0000732g0140' => 'nta', 'Nitab4.5_0003162g0020' => 'nta', 'Nitab4.5_0006180g0090' => 'nta', 'Nitab4.5_0006390g0010' => 'nta', 'Nitab4.5_0007392g0040' => 'nta', 'Nn1g02140' => 'nnu', 'Nn4g26168' => 'nnu', 'Nn5g26754' => 'nnu', 'Oeu001433.1' => 'oeu', 'Oeu010299.2' => 'oeu', 'Oeu011171.1' => 'oeu', 'Oeu037675.1' => 'oeu', 'Oeu038359.1' => 'oeu', 'Oeu063834.1' => 'oeu', 'Oeu063835.1' => 'oeu', 'Os05g0312000' => 'osa', 'Os07g0211101' => 'osa', 'Os07g0211200' => 'osa', 'Os07g0681500' => 'osa', 'Peaxi162Scf00095g01015' => 'pax', 'Peaxi162Scf00104g00329' => 'pax', 'Peaxi162Scf00161g00137' => 'pax', 'PGR004G1665' => 'pgr', 'PGR031G2937' => 'pgr', 'PGR119G2145' => 'pgr', 'PGSC0003DMG400004351' => 'stu', 'PGSC0003DMG400014625' => 'stu', 'PGSC0003DMG401000943' => 'stu', 'Phvul.001G148600' => 'pvu', 'Phvul.004G001700' => 'pvu', 'Phvul.006G154900' => 'pvu', 'Phvul.008G078200' => 'pvu', 'Phvul.011G136500' => 'pvu', 'Potri.002G215600' => 'ptr', 'Potri.008G201600' => 'ptr', 'Potri.014G138400' => 'ptr', 'Potri.016G142500' => 'ptr', 'Pp3c16_10580' => 'ppa', 'Pp3c5_25280' => 'ppa', 'Prupe.1G150000' => 'ppe', 'Prupe.1G150100' => 'ppe', 'Prupe.6G299600' => 'ppe', 'Prupe.8G245000' => 'ppe', 'Psat0s4927g0040' => 'psa', 'Psat1g052080' => 'psa', 'Psat1g183800' => 'psa', 'Psat3g113840' => 'psa', 'Psat3g126120' => 'psa', 'Psat3g126160' => 'psa', 'Psat3g158760' => 'psa', 'Psat3g158840' => 'psa', 'PSO170G2858' => 'pso', 'PSO339G0606' => 'pso', 'PSO384G4709' => 'pso', 'PSO407G0334' => 'pso', 'QL04p040276' => 'qlo', 'QL06p005458' => 'qlo', 'QL06p005472' => 'qlo', 'QL07p030546' => 'qlo', 'QL07p031519' => 'qlo', 'QL09p050949' => 'qlo', 'QL09p050966' => 'qlo', 'QL09p051067' => 'qlo', 'QL12p022706' => 'qlo', 'RcHm_v2.0_Chr2g0119601' => 'rch', 'RcHm_v2.0_Chr3g0459591' => 'rch', 'RcHm_v2.0_Chr4g0418521' => 'rch', 'RcHm_v2.0_Chr4g0418531' => 'rch', 'RcHm_v2.0_Chr4g0418541' => 'rch', 'RcHm_v2.0_Chr6g0291641' => 'rch', 'Rhsim01G0086300' => 'rsi', 'Rhsim01G0276300' => 'rsi', 'Rhsim01G0276500' => 'rsi', 'Rhsim04G0207700' => 'rsi', 'Rhsim05G0234500' => 'rsi', 'Rhsim13G0022400' => 'rsi', 'Sabra02G0167900' => 'sbr', 'Sabra04G0158500' => 'sbr', 'Sabra08G0159800' => 'sbr', 'Sabra10G0011500' => 'sbr', 'Sabra14G0104400' => 'sbr', 'SalBow2G2440' => 'sbo', 'SalBow4G2265' => 'sbo', 'Sc02g0000060' => 'sci', 'Sc05g0005020' => 'sci', 'Sc13g0003890' => 'sci', 'Sed0014865' => 'sed', 'Sed0017224' => 'sed', 'Sed0026391' => 'sed', 'SEGI_00063' => 'sgi', 'SEGI_10967' => 'sgi', 'SEGI_17510' => 'sgi', 'SEGI_24396' => 'sgi', 'SEGI_39719' => 'sgi', 'SEGI_41392' => 'sgi', 'SGA_v2.0_scaffold11G05794' => 'sas', 'SGA_v2.0_scaffold142G35607' => 'sas', 'SGA_v2.0_scaffold1G00447' => 'sas', 'SHI15388' => 'shi', 'SHI15394' => 'shi', 'SHI15396' => 'shi', 'SHI15399' => 'shi', 'SMO343G0151' => 'smo', 'SMO367G1118' => 'smo', 'Solyc01g080200.3' => 'sly', 'Solyc06g008960.3' => 'sly', 'Solyc09g064780.3' => 'sly', 'Sopen01g031980' => 'spe', 'Sopen06g003710' => 'spe', 'Sopen09g026460' => 'spe', 'Sp3g21240' => 'spa', 'Sp4g30030' => 'spa', 'TAR365G0022' => 'tar', 'TAR365G1023' => 'tar', 'TAR365G1253' => 'tar', 'TAR623G0078' => 'tar', 'TAR623G1721' => 'tar', 'TAR633G0959' => 'tar', 'THA.LOC104802225' => 'tha', 'THA.LOC104804769' => 'tha', 'THA.LOC104808660' => 'tha', 'THA.LOC104812792' => 'tha', 'Thecc.01G284000' => 'tca', 'Thecc.04G220600' => 'tca', 'Thecc.05G268900' => 'tca', 'Thecc.08G171100' => 'tca', 'Thhalv10001284m.g' => 'esa', 'Thhalv10019912m.g' => 'esa', 'TPR.G14189' => 'tpr', 'TPR.G18110' => 'tpr', 'TPR.G18130' => 'tpr', 'TPR.G18131' => 'tpr', 'TPR.G18140' => 'tpr', 'TPR.G24282' => 'tpr', 'TPR.G25221' => 'tpr', 'TPR.G29267' => 'tpr', 'TPR.G35315' => 'tpr', 'TPR.G36173' => 'tpr', 'TWI09G0794' => 'twi', 'TWI59G1348' => 'twi', 'TWI74G0430' => 'twi', 'unitig_26.g8940' => 'ugi', 'unitig_749.g13744' => 'ugi', 'unitig_749.g13745' => 'ugi', 'vmacro08269' => 'vma', 'vmacro14937' => 'vma', 'vmacro20401' => 'vma', 'VMungo0464G1349' => 'vmu', 'VMungo0540G0289' => 'vmu', 'VMungo1215G1590' => 'vmu', 'VMungo1309G0221' => 'vmu', 'VMungo1309G2815' => 'vmu', 'VMungo1383G0239' => 'vmu', 'VMungo1383G2910' => 'vmu', 'Zm00001eb095270' => 'zma', 'Zm00001eb095280' => 'zma', 'Zm00001eb111630' => 'zma', 'Zm00001eb237080' => 'zma', 'Zm00001eb273740' => 'zma', 'Zm00001eb285040' => 'zma', 'Zm00001eb330790' => 'zma', 'Zm00001eb337380' => 'zma' ), 'gf_id' => 'HOM05D001484', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001484' ), 'data_identifier' => 'HOM05D001484', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001484', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p31500' => 'bna', 'A05p00020' => 'bna', 'A07p08820' => 'bna', 'Aa31LG4G3300' => 'aar', 'Aa31LG8G10030' => 'aar', 'Actinidia00731' => 'ach', 'Actinidia11473' => 'ach', 'Actinidia23469' => 'ach', 'Actinidia24318' => 'ach', 'Actinidia40196' => 'ach', 'Actinidia40197' => 'ach', 'Actinidia40198' => 'ach', 'Ah.08g212990' => 'amhyb', 'Ah.15g091720' => 'amhyb', 'AL3G38260' => 'aly', 'AL4G47710' => 'aly', 'Aqoxy2G00671' => 'aox', 'Aqoxy2G03236' => 'aox', 'arahy.Tifrunner.gnm1.ann1.05IDCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KR684' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATY3SJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK6QJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6APGL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IDT7Z9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM073U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ0R87' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LE7RV4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT4QRX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V5ENPK' => 'arhy', 'AT2G48110' => 'ath', 'AT3G23590' => 'ath', 'ATR0626G186' => 'atr', 'ATR1127G141' => 'atr', 'Atru.chr4.2583' => 'acertr', 'Atru.chr5.1358' => 'acertr', 'Atru.chr5.1359' => 'acertr', 'Atru.chr8.46' => 'acertr', 'AUR62002640' => 'cqu', 'AUR62030055' => 'cqu', 'AUR62033713' => 'cqu', 'AUR62033714' => 'cqu', 'AUR62036795' => 'cqu', 'AUR62039891' => 'cqu', 'BcaB02g08737' => 'bca', 'BcaB04g20441' => 'bca', 'BcaB06g26509' => 'bca', 'BcaB06g26510' => 'bca', 'BcaB06g26511' => 'bca', 'BcaB06g26512' => 'bca', 'BcaB06g26513' => 'bca', 'BcaC02g12564' => 'bca', 'BcaC02g12565' => 'bca', 'BcaC02g12794' => 'bca', 'BcaC02g12795' => 'bca', 'BcaC02g12796' => 'bca', 'BcaC06g35541' => 'bca', 'BNapus_Darmor_BZH_scaffold_188p00080' => 'bna', 'BNapus_Darmor_BZH_scaffold_188p00090' => 'bna', 'BolC1t03972H' => 'bol', 'BolC1t03973H' => 'bol', 'BolC4t21680H' => 'bol', 'BolC7t41863H' => 'bol', 'BolSC55t61227H' => 'bol', 'BolSC55t61228H' => 'bol', 'BraA01t03278Z' => 'bra', 'BraA05t18998Z' => 'bra', 'BraA07t28673Z' => 'bra', 'C01p40150' => 'bna', 'C05p12370' => 'bna', 'C07p13680' => 'bna', 'CAN.G1006.16' => 'can', 'CAN.G1006.17' => 'can', 'CAN.G1170.2' => 'can', 'CAN.G962.7' => 'can', 'CANSAT25G2179' => 'cansat', 'CANSAT78G1573' => 'cansat', 'CARHR099510' => 'chi', 'CARHR143510' => 'chi', 'Carub.0003s2380' => 'cru', 'Carub.0004s3082' => 'cru', 'Ca_00614_v3' => 'car', 'Ca_07801_v3' => 'car', 'Ca_08567_v3' => 'car', 'Ca_09571_v3' => 'car', 'CBR_g19290' => 'cbr', 'Cc01_g19770' => 'ccan', 'Cc03_g03030' => 'ccan', 'CDE07G0968' => 'cde', 'CDE09G1441' => 'cde', 'Cfa006103' => 'cfa', 'Cfa015573' => 'cfa', 'Cfa016988' => 'cfa', 'Ciclev10006738m.g' => 'ccl', 'Ciclev10010920m.g' => 'ccl', 'Ciclev10018517m.g' => 'ccl', 'CiPaw.01G159200' => 'cil', 'CiPaw.02G091000' => 'cil', 'CiPaw.02G091100' => 'cil', 'CiPaw.08G103100' => 'cil', 'CiPaw.09G224900' => 'cil', 'ClCG06G005740' => 'cla', 'ClCG07G000090' => 'cla', 'ClCG07G000100' => 'cla', 'COL.COLO4_09143' => 'col', 'COL.COLO4_25124' => 'col', 'Cpa.g.sc16.34' => 'cpa', 'Cpa.g.sc3504.1' => 'cpa', 'Cpa.g.sc60.37' => 'cpa', 'CsaV3_6G018520' => 'csa', 'CsaV3_6G036860' => 'csa', 'CSS0001072' => 'camsi', 'CSS0020208' => 'camsi', 'CSS0021253' => 'camsi', 'CSS0022190' => 'camsi', 'CSS0036150' => 'camsi', 'CSS0040442' => 'camsi', 'CSS0042300' => 'camsi', 'CSS0045298' => 'camsi', 'DCAR_012449' => 'dca', 'DCAR_018405' => 'dca', 'DCAR_024573' => 'dca', 'DCAR_030591' => 'dca', 'Dinv16926' => 'din', 'Dinv32963' => 'din', 'Dinv38382' => 'din', 'Dinv38383' => 'din', 'Duzib133G0974' => 'dzi', 'Duzib138G1867' => 'dzi', 'Duzib211G0420' => 'dzi', 'Duzib212G0930' => 'dzi', 'ECA234G1645' => 'eca', 'ECA247G3467' => 'eca', 'ECA248G1703' => 'eca', 'EL10Ac3g06327' => 'bvu', 'EL10Ac7g17204' => 'bvu', 'Eucgr.A00855' => 'egr', 'Eucgr.A00858' => 'egr', 'Eucgr.H01520' => 'egr', 'Eucgr.H03604' => 'egr', 'Eucgr.L03465' => 'egr', 'Eucgr.L03466' => 'egr', 'FAN01G0988' => 'fan', 'FAN02G3892' => 'fan', 'FAN05G3381' => 'fan', 'FAN07G0967' => 'fan', 'FAN07G1493' => 'fan', 'FAN08G3125' => 'fan', 'FAN09G0402' => 'fan', 'FAN12G2594' => 'fan', 'FAN12G3879' => 'fan', 'FAN14G1546' => 'fan', 'FAN15G3626' => 'fan', 'FAN17G0588' => 'fan', 'FAN17G0609' => 'fan', 'FAN18G2817' => 'fan', 'FAN19G1305' => 'fan', 'FAN20G1787' => 'fan', 'FAN22G0073' => 'fan', 'FAN22G0352' => 'fan', 'FAN22G0368' => 'fan', 'FAN22G2273' => 'fan', 'FAN24G1998' => 'fan', 'FAN27G1317' => 'fan', 'FvH4_2g23980' => 'fve', 'FvH4_4g14380' => 'fve', 'FvH4_4g14390' => 'fve', 'FvH4_6g09250' => 'fve', 'Glyma.03G151100' => 'gma', 'Glyma.04G122550' => 'gma', 'Glyma.05G001600' => 'gma', 'Glyma.09G270766' => 'gma', 'Glyma.09G270832' => 'gma', 'Glyma.13G209800' => 'gma', 'Glyma.15G102800' => 'gma', 'Glyma.18G218900' => 'gma', 'Glyma.19G001500' => 'gma', 'Glyma.19G153600' => 'gma', 'Gohir.A02G028600' => 'ghi', 'Gohir.A08G045000' => 'ghi', 'Gohir.A11G120500' => 'ghi', 'Gohir.A12G006200' => 'ghi', 'Gohir.A12G006250' => 'ghi', 'Gohir.D02G036300' => 'ghi', 'Gohir.D08G054700' => 'ghi', 'Gohir.D11G125600' => 'ghi', 'Gohir.D12G005700' => 'ghi', 'Gorai.004G055200' => 'gra', 'Gorai.005G040400' => 'gra', 'Gorai.007G134500' => 'gra', 'Gorai.008G005500' => 'gra', 'GSVIVG01011094001' => 'vvi', 'GSVIVG01017879001' => 'vvi', 'GSVIVG01025988001' => 'vvi', 'GSVIVG01029847001' => 'vvi', 'HanXRQChr10g0282901' => 'han', 'HanXRQChr10g0310371' => 'han', 'HanXRQChr10g0315041' => 'han', 'HanXRQChr11g0327651' => 'han', 'HanXRQChr12g0359391' => 'han', 'Haze_00972' => 'cav', 'Haze_00973' => 'cav', 'Haze_00974' => 'cav', 'Haze_04747' => 'cav', 'Haze_04749' => 'cav', 'Haze_04750' => 'cav', 'Haze_21217' => 'cav', 'Hma1.2p1_1037F.1_g250680' => 'hma', 'Hma1.2p1_1644F.1_g295320' => 'hma', 'HPP92_011322' => 'vpl', 'HPP92_011323' => 'vpl', 'HPP92_011324' => 'vpl', 'HPP92_011325' => 'vpl', 'HPP92_011326' => 'vpl', 'Hund12205' => 'sun', 'Hund17957' => 'sun', 'Lalb_Chr06g0176771' => 'lal', 'Lalb_Chr18g0056021' => 'lal', 'Lalb_Chr18g0056031' => 'lal', 'Lalb_Chr18g0056041' => 'lal', 'Lalb_Chr20g0107751' => 'lal', 'Lalb_Chr20g0118371' => 'lal', 'Lj1g0010239' => 'lja', 'Lj1g0017101' => 'lja', 'Lj2A1178G40' => 'lonja', 'Lj2A54G84' => 'lonja', 'Lj2g0015248' => 'lja', 'Lj3A761T51' => 'lonja', 'Lj6g0018116' => 'lja', 'Lsat_1_v5_gn_4_136040' => 'lsa', 'Lsat_1_v5_gn_5_187461' => 'lsa', 'Lsat_1_v5_gn_5_77001' => 'lsa', 'Lsat_1_v5_gn_9_4461' => 'lsa', 'Manes.01G210100' => 'mes', 'Manes.03G185600' => 'mes', 'Manes.05G073300' => 'mes', 'Manes.09G120300' => 'mes', 'Manes.15G022100' => 'mes', 'Mapoly0096s0053' => 'mpo', 'MBI03_g14058_MAGBIO' => 'mbi', 'MBI03_g33876_MAGBIO' => 'mbi', 'MBI03_g36854_MAGBIO' => 'mbi', 'MBI17_g11997_MAGBIO' => 'mbi', 'MD03G1269000' => 'mdo', 'MD04G1179600' => 'mdo', 'MD11G1289800' => 'mdo', 'MD12G1194700' => 'mdo', 'MD13G1182100' => 'mdo', 'MD13G1182200' => 'mdo', 'MD16G1182600' => 'mdo', 'Medtr2g021400' => 'mtr', 'Medtr2g021470' => 'mtr', 'Medtr2g105810' => 'mtr', 'Medtr3g033580' => 'mtr', 'Medtr6g007970' => 'mtr', 'Medtr7g056330' => 'mtr', 'Medtr7g074290' => 'mtr', 'Medtr7g074380' => 'mtr', 'Medtr7g094550' => 'mtr', 'Medtr8g069995' => 'mtr', 'MELO3C014345.2' => 'cme', 'MELO3C021395.2' => 'cme', 'Migut.D00262' => 'egut', 'Migut.G00257' => 'egut', 'MSTRG.21575' => 'ama', 'MSTRG.3985' => 'ama', 'Nitab4.5_0000295g0140' => 'nta', 'Nitab4.5_0000732g0140' => 'nta', 'Nitab4.5_0003162g0020' => 'nta', 'Nitab4.5_0006180g0090' => 'nta', 'Nitab4.5_0006390g0010' => 'nta', 'Nitab4.5_0007392g0040' => 'nta', 'Nn1g02140' => 'nnu', 'Nn4g26168' => 'nnu', 'Nn5g26754' => 'nnu', 'Oeu001433.1' => 'oeu', 'Oeu010299.2' => 'oeu', 'Oeu011171.1' => 'oeu', 'Oeu037675.1' => 'oeu', 'Oeu038359.1' => 'oeu', 'Oeu063834.1' => 'oeu', 'Oeu063835.1' => 'oeu', 'Os05g0312000' => 'osa', 'Os07g0211101' => 'osa', 'Os07g0211200' => 'osa', 'Os07g0681500' => 'osa', 'Peaxi162Scf00095g01015' => 'pax', 'Peaxi162Scf00104g00329' => 'pax', 'Peaxi162Scf00161g00137' => 'pax', 'PGR004G1665' => 'pgr', 'PGR031G2937' => 'pgr', 'PGR119G2145' => 'pgr', 'PGSC0003DMG400004351' => 'stu', 'PGSC0003DMG400014625' => 'stu', 'PGSC0003DMG401000943' => 'stu', 'Phvul.001G148600' => 'pvu', 'Phvul.004G001700' => 'pvu', 'Phvul.006G154900' => 'pvu', 'Phvul.008G078200' => 'pvu', 'Phvul.011G136500' => 'pvu', 'Potri.002G215600' => 'ptr', 'Potri.008G201600' => 'ptr', 'Potri.014G138400' => 'ptr', 'Potri.016G142500' => 'ptr', 'Pp3c16_10580' => 'ppa', 'Pp3c5_25280' => 'ppa', 'Prupe.1G150000' => 'ppe', 'Prupe.1G150100' => 'ppe', 'Prupe.6G299600' => 'ppe', 'Prupe.8G245000' => 'ppe', 'Psat0s4927g0040' => 'psa', 'Psat1g052080' => 'psa', 'Psat1g183800' => 'psa', 'Psat3g113840' => 'psa', 'Psat3g126120' => 'psa', 'Psat3g126160' => 'psa', 'Psat3g158760' => 'psa', 'Psat3g158840' => 'psa', 'PSO170G2858' => 'pso', 'PSO339G0606' => 'pso', 'PSO384G4709' => 'pso', 'PSO407G0334' => 'pso', 'QL04p040276' => 'qlo', 'QL06p005458' => 'qlo', 'QL06p005472' => 'qlo', 'QL07p030546' => 'qlo', 'QL07p031519' => 'qlo', 'QL09p050949' => 'qlo', 'QL09p050966' => 'qlo', 'QL09p051067' => 'qlo', 'QL12p022706' => 'qlo', 'RcHm_v2.0_Chr2g0119601' => 'rch', 'RcHm_v2.0_Chr3g0459591' => 'rch', 'RcHm_v2.0_Chr4g0418521' => 'rch', 'RcHm_v2.0_Chr4g0418531' => 'rch', 'RcHm_v2.0_Chr4g0418541' => 'rch', 'RcHm_v2.0_Chr6g0291641' => 'rch', 'Rhsim01G0086300' => 'rsi', 'Rhsim01G0276300' => 'rsi', 'Rhsim01G0276500' => 'rsi', 'Rhsim04G0207700' => 'rsi', 'Rhsim05G0234500' => 'rsi', 'Rhsim13G0022400' => 'rsi', 'Sabra02G0167900' => 'sbr', 'Sabra04G0158500' => 'sbr', 'Sabra08G0159800' => 'sbr', 'Sabra10G0011500' => 'sbr', 'Sabra14G0104400' => 'sbr', 'SalBow2G2440' => 'sbo', 'SalBow4G2265' => 'sbo', 'Sc02g0000060' => 'sci', 'Sc05g0005020' => 'sci', 'Sc13g0003890' => 'sci', 'Sed0014865' => 'sed', 'Sed0017224' => 'sed', 'Sed0026391' => 'sed', 'SEGI_00063' => 'sgi', 'SEGI_10967' => 'sgi', 'SEGI_17510' => 'sgi', 'SEGI_24396' => 'sgi', 'SEGI_39719' => 'sgi', 'SEGI_41392' => 'sgi', 'SGA_v2.0_scaffold11G05794' => 'sas', 'SGA_v2.0_scaffold142G35607' => 'sas', 'SGA_v2.0_scaffold1G00447' => 'sas', 'SHI15388' => 'shi', 'SHI15394' => 'shi', 'SHI15396' => 'shi', 'SHI15399' => 'shi', 'SMO343G0151' => 'smo', 'SMO367G1118' => 'smo', 'Solyc01g080200.3' => 'sly', 'Solyc06g008960.3' => 'sly', 'Solyc09g064780.3' => 'sly', 'Sopen01g031980' => 'spe', 'Sopen06g003710' => 'spe', 'Sopen09g026460' => 'spe', 'Sp3g21240' => 'spa', 'Sp4g30030' => 'spa', 'TAR365G0022' => 'tar', 'TAR365G1023' => 'tar', 'TAR365G1253' => 'tar', 'TAR623G0078' => 'tar', 'TAR623G1721' => 'tar', 'TAR633G0959' => 'tar', 'THA.LOC104802225' => 'tha', 'THA.LOC104804769' => 'tha', 'THA.LOC104808660' => 'tha', 'THA.LOC104812792' => 'tha', 'Thecc.01G284000' => 'tca', 'Thecc.04G220600' => 'tca', 'Thecc.05G268900' => 'tca', 'Thecc.08G171100' => 'tca', 'Thhalv10001284m.g' => 'esa', 'Thhalv10019912m.g' => 'esa', 'TPR.G14189' => 'tpr', 'TPR.G18110' => 'tpr', 'TPR.G18130' => 'tpr', 'TPR.G18131' => 'tpr', 'TPR.G18140' => 'tpr', 'TPR.G24282' => 'tpr', 'TPR.G25221' => 'tpr', 'TPR.G29267' => 'tpr', 'TPR.G35315' => 'tpr', 'TPR.G36173' => 'tpr', 'TWI09G0794' => 'twi', 'TWI59G1348' => 'twi', 'TWI74G0430' => 'twi', 'unitig_26.g8940' => 'ugi', 'unitig_749.g13744' => 'ugi', 'unitig_749.g13745' => 'ugi', 'vmacro08269' => 'vma', 'vmacro14937' => 'vma', 'vmacro20401' => 'vma', 'VMungo0464G1349' => 'vmu', 'VMungo0540G0289' => 'vmu', 'VMungo1215G1590' => 'vmu', 'VMungo1309G0221' => 'vmu', 'VMungo1309G2815' => 'vmu', 'VMungo1383G0239' => 'vmu', 'VMungo1383G2910' => 'vmu', 'Zm00001eb095270' => 'zma', 'Zm00001eb095280' => 'zma', 'Zm00001eb111630' => 'zma', 'Zm00001eb237080' => 'zma', 'Zm00001eb273740' => 'zma', 'Zm00001eb285040' => 'zma', 'Zm00001eb330790' => 'zma', 'Zm00001eb337380' => 'zma' ) $gf_id = 'HOM05D001484' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001484' ) $data_identifier = 'HOM05D001484' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 2, 'aly' => (int) 2, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 22, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 7, 'hma' => (int) 2, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 7, 'mtr' => (int) 10, 'cme' => (int) 2, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 4, 'ppa' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 4, 'qlo' => (int) 9, 'rch' => (int) 6, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 10, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 7, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb337380' $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' => 'HOM05D001484', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p31500' => 'bna', 'A05p00020' => 'bna', 'A07p08820' => 'bna', 'Aa31LG4G3300' => 'aar', 'Aa31LG8G10030' => 'aar', 'Actinidia00731' => 'ach', 'Actinidia11473' => 'ach', 'Actinidia23469' => 'ach', 'Actinidia24318' => 'ach', 'Actinidia40196' => 'ach', 'Actinidia40197' => 'ach', 'Actinidia40198' => 'ach', 'Ah.08g212990' => 'amhyb', 'Ah.15g091720' => 'amhyb', 'AL3G38260' => 'aly', 'AL4G47710' => 'aly', 'Aqoxy2G00671' => 'aox', 'Aqoxy2G03236' => 'aox', 'arahy.Tifrunner.gnm1.ann1.05IDCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KR684' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATY3SJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK6QJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6APGL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IDT7Z9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM073U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ0R87' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LE7RV4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT4QRX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V5ENPK' => 'arhy', 'AT2G48110' => 'ath', 'AT3G23590' => 'ath', 'ATR0626G186' => 'atr', 'ATR1127G141' => 'atr', 'Atru.chr4.2583' => 'acertr', 'Atru.chr5.1358' => 'acertr', 'Atru.chr5.1359' => 'acertr', 'Atru.chr8.46' => 'acertr', 'AUR62002640' => 'cqu', 'AUR62030055' => 'cqu', 'AUR62033713' => 'cqu', 'AUR62033714' => 'cqu', 'AUR62036795' => 'cqu', 'AUR62039891' => 'cqu', 'BcaB02g08737' => 'bca', 'BcaB04g20441' => 'bca', 'BcaB06g26509' => 'bca', 'BcaB06g26510' => 'bca', 'BcaB06g26511' => 'bca', 'BcaB06g26512' => 'bca', 'BcaB06g26513' => 'bca', 'BcaC02g12564' => 'bca', 'BcaC02g12565' => 'bca', 'BcaC02g12794' => 'bca', 'BcaC02g12795' => 'bca', 'BcaC02g12796' => 'bca', 'BcaC06g35541' => 'bca', 'BNapus_Darmor_BZH_scaffold_188p00080' => 'bna', 'BNapus_Darmor_BZH_scaffold_188p00090' => 'bna', 'BolC1t03972H' => 'bol', 'BolC1t03973H' => 'bol', 'BolC4t21680H' => 'bol', 'BolC7t41863H' => 'bol', 'BolSC55t61227H' => 'bol', 'BolSC55t61228H' => 'bol', 'BraA01t03278Z' => 'bra', 'BraA05t18998Z' => 'bra', 'BraA07t28673Z' => 'bra', 'C01p40150' => 'bna', 'C05p12370' => 'bna', 'C07p13680' => 'bna', 'CAN.G1006.16' => 'can', 'CAN.G1006.17' => 'can', 'CAN.G1170.2' => 'can', 'CAN.G962.7' => 'can', 'CANSAT25G2179' => 'cansat', 'CANSAT78G1573' => 'cansat', 'CARHR099510' => 'chi', 'CARHR143510' => 'chi', 'Carub.0003s2380' => 'cru', 'Carub.0004s3082' => 'cru', 'Ca_00614_v3' => 'car', 'Ca_07801_v3' => 'car', 'Ca_08567_v3' => 'car', 'Ca_09571_v3' => 'car', 'CBR_g19290' => 'cbr', 'Cc01_g19770' => 'ccan', 'Cc03_g03030' => 'ccan', 'CDE07G0968' => 'cde', 'CDE09G1441' => 'cde', 'Cfa006103' => 'cfa', 'Cfa015573' => 'cfa', 'Cfa016988' => 'cfa', 'Ciclev10006738m.g' => 'ccl', 'Ciclev10010920m.g' => 'ccl', 'Ciclev10018517m.g' => 'ccl', 'CiPaw.01G159200' => 'cil', 'CiPaw.02G091000' => 'cil', 'CiPaw.02G091100' => 'cil', 'CiPaw.08G103100' => 'cil', 'CiPaw.09G224900' => 'cil', 'ClCG06G005740' => 'cla', 'ClCG07G000090' => 'cla', 'ClCG07G000100' => 'cla', 'COL.COLO4_09143' => 'col', 'COL.COLO4_25124' => 'col', 'Cpa.g.sc16.34' => 'cpa', 'Cpa.g.sc3504.1' => 'cpa', 'Cpa.g.sc60.37' => 'cpa', 'CsaV3_6G018520' => 'csa', 'CsaV3_6G036860' => 'csa', 'CSS0001072' => 'camsi', 'CSS0020208' => 'camsi', 'CSS0021253' => 'camsi', 'CSS0022190' => 'camsi', 'CSS0036150' => 'camsi', 'CSS0040442' => 'camsi', 'CSS0042300' => 'camsi', 'CSS0045298' => 'camsi', 'DCAR_012449' => 'dca', 'DCAR_018405' => 'dca', 'DCAR_024573' => 'dca', 'DCAR_030591' => 'dca', 'Dinv16926' => 'din', 'Dinv32963' => 'din', 'Dinv38382' => 'din', 'Dinv38383' => 'din', 'Duzib133G0974' => 'dzi', 'Duzib138G1867' => 'dzi', 'Duzib211G0420' => 'dzi', 'Duzib212G0930' => 'dzi', 'ECA234G1645' => 'eca', 'ECA247G3467' => 'eca', 'ECA248G1703' => 'eca', 'EL10Ac3g06327' => 'bvu', 'EL10Ac7g17204' => 'bvu', 'Eucgr.A00855' => 'egr', 'Eucgr.A00858' => 'egr', 'Eucgr.H01520' => 'egr', 'Eucgr.H03604' => 'egr', 'Eucgr.L03465' => 'egr', 'Eucgr.L03466' => 'egr', 'FAN01G0988' => 'fan', 'FAN02G3892' => 'fan', 'FAN05G3381' => 'fan', 'FAN07G0967' => 'fan', 'FAN07G1493' => 'fan', 'FAN08G3125' => 'fan', 'FAN09G0402' => 'fan', 'FAN12G2594' => 'fan', 'FAN12G3879' => 'fan', 'FAN14G1546' => 'fan', 'FAN15G3626' => 'fan', 'FAN17G0588' => 'fan', 'FAN17G0609' => 'fan', 'FAN18G2817' => 'fan', 'FAN19G1305' => 'fan', 'FAN20G1787' => 'fan', 'FAN22G0073' => 'fan', 'FAN22G0352' => 'fan', 'FAN22G0368' => 'fan', 'FAN22G2273' => 'fan', 'FAN24G1998' => 'fan', 'FAN27G1317' => 'fan', 'FvH4_2g23980' => 'fve', 'FvH4_4g14380' => 'fve', 'FvH4_4g14390' => 'fve', 'FvH4_6g09250' => 'fve', 'Glyma.03G151100' => 'gma', 'Glyma.04G122550' => 'gma', 'Glyma.05G001600' => 'gma', 'Glyma.09G270766' => 'gma', 'Glyma.09G270832' => 'gma', 'Glyma.13G209800' => 'gma', 'Glyma.15G102800' => 'gma', 'Glyma.18G218900' => 'gma', 'Glyma.19G001500' => 'gma', 'Glyma.19G153600' => 'gma', 'Gohir.A02G028600' => 'ghi', 'Gohir.A08G045000' => 'ghi', 'Gohir.A11G120500' => 'ghi', 'Gohir.A12G006200' => 'ghi', 'Gohir.A12G006250' => 'ghi', 'Gohir.D02G036300' => 'ghi', 'Gohir.D08G054700' => 'ghi', 'Gohir.D11G125600' => 'ghi', 'Gohir.D12G005700' => 'ghi', 'Gorai.004G055200' => 'gra', 'Gorai.005G040400' => 'gra', 'Gorai.007G134500' => 'gra', 'Gorai.008G005500' => 'gra', 'GSVIVG01011094001' => 'vvi', 'GSVIVG01017879001' => 'vvi', 'GSVIVG01025988001' => 'vvi', 'GSVIVG01029847001' => 'vvi', 'HanXRQChr10g0282901' => 'han', 'HanXRQChr10g0310371' => 'han', 'HanXRQChr10g0315041' => 'han', 'HanXRQChr11g0327651' => 'han', 'HanXRQChr12g0359391' => 'han', 'Haze_00972' => 'cav', 'Haze_00973' => 'cav', 'Haze_00974' => 'cav', 'Haze_04747' => 'cav', 'Haze_04749' => 'cav', 'Haze_04750' => 'cav', 'Haze_21217' => 'cav', 'Hma1.2p1_1037F.1_g250680' => 'hma', 'Hma1.2p1_1644F.1_g295320' => 'hma', 'HPP92_011322' => 'vpl', 'HPP92_011323' => 'vpl', 'HPP92_011324' => 'vpl', 'HPP92_011325' => 'vpl', 'HPP92_011326' => 'vpl', 'Hund12205' => 'sun', 'Hund17957' => 'sun', 'Lalb_Chr06g0176771' => 'lal', 'Lalb_Chr18g0056021' => 'lal', 'Lalb_Chr18g0056031' => 'lal', 'Lalb_Chr18g0056041' => 'lal', 'Lalb_Chr20g0107751' => 'lal', 'Lalb_Chr20g0118371' => 'lal', 'Lj1g0010239' => 'lja', 'Lj1g0017101' => 'lja', 'Lj2A1178G40' => 'lonja', 'Lj2A54G84' => 'lonja', 'Lj2g0015248' => 'lja', 'Lj3A761T51' => 'lonja', 'Lj6g0018116' => 'lja', 'Lsat_1_v5_gn_4_136040' => 'lsa', 'Lsat_1_v5_gn_5_187461' => 'lsa', 'Lsat_1_v5_gn_5_77001' => 'lsa', 'Lsat_1_v5_gn_9_4461' => 'lsa', 'Manes.01G210100' => 'mes', 'Manes.03G185600' => 'mes', 'Manes.05G073300' => 'mes', 'Manes.09G120300' => 'mes', 'Manes.15G022100' => 'mes', 'Mapoly0096s0053' => 'mpo', 'MBI03_g14058_MAGBIO' => 'mbi', 'MBI03_g33876_MAGBIO' => 'mbi', 'MBI03_g36854_MAGBIO' => 'mbi', 'MBI17_g11997_MAGBIO' => 'mbi', 'MD03G1269000' => 'mdo', 'MD04G1179600' => 'mdo', 'MD11G1289800' => 'mdo', 'MD12G1194700' => 'mdo', 'MD13G1182100' => 'mdo', 'MD13G1182200' => 'mdo', 'MD16G1182600' => 'mdo', 'Medtr2g021400' => 'mtr', 'Medtr2g021470' => 'mtr', 'Medtr2g105810' => 'mtr', 'Medtr3g033580' => 'mtr', 'Medtr6g007970' => 'mtr', 'Medtr7g056330' => 'mtr', 'Medtr7g074290' => 'mtr', 'Medtr7g074380' => 'mtr', 'Medtr7g094550' => 'mtr', 'Medtr8g069995' => 'mtr', 'MELO3C014345.2' => 'cme', 'MELO3C021395.2' => 'cme', 'Migut.D00262' => 'egut', 'Migut.G00257' => 'egut', 'MSTRG.21575' => 'ama', 'MSTRG.3985' => 'ama', 'Nitab4.5_0000295g0140' => 'nta', 'Nitab4.5_0000732g0140' => 'nta', 'Nitab4.5_0003162g0020' => 'nta', 'Nitab4.5_0006180g0090' => 'nta', 'Nitab4.5_0006390g0010' => 'nta', 'Nitab4.5_0007392g0040' => 'nta', 'Nn1g02140' => 'nnu', 'Nn4g26168' => 'nnu', 'Nn5g26754' => 'nnu', 'Oeu001433.1' => 'oeu', 'Oeu010299.2' => 'oeu', 'Oeu011171.1' => 'oeu', 'Oeu037675.1' => 'oeu', 'Oeu038359.1' => 'oeu', 'Oeu063834.1' => 'oeu', 'Oeu063835.1' => 'oeu', 'Os05g0312000' => 'osa', 'Os07g0211101' => 'osa', 'Os07g0211200' => 'osa', 'Os07g0681500' => 'osa', 'Peaxi162Scf00095g01015' => 'pax', 'Peaxi162Scf00104g00329' => 'pax', 'Peaxi162Scf00161g00137' => 'pax', 'PGR004G1665' => 'pgr', 'PGR031G2937' => 'pgr', 'PGR119G2145' => 'pgr', 'PGSC0003DMG400004351' => 'stu', 'PGSC0003DMG400014625' => 'stu', 'PGSC0003DMG401000943' => 'stu', 'Phvul.001G148600' => 'pvu', 'Phvul.004G001700' => 'pvu', 'Phvul.006G154900' => 'pvu', 'Phvul.008G078200' => 'pvu', 'Phvul.011G136500' => 'pvu', 'Potri.002G215600' => 'ptr', 'Potri.008G201600' => 'ptr', 'Potri.014G138400' => 'ptr', 'Potri.016G142500' => 'ptr', 'Pp3c16_10580' => 'ppa', 'Pp3c5_25280' => 'ppa', 'Prupe.1G150000' => 'ppe', 'Prupe.1G150100' => 'ppe', 'Prupe.6G299600' => 'ppe', 'Prupe.8G245000' => 'ppe', 'Psat0s4927g0040' => 'psa', 'Psat1g052080' => 'psa', 'Psat1g183800' => 'psa', 'Psat3g113840' => 'psa', 'Psat3g126120' => 'psa', 'Psat3g126160' => 'psa', 'Psat3g158760' => 'psa', 'Psat3g158840' => 'psa', 'PSO170G2858' => 'pso', 'PSO339G0606' => 'pso', 'PSO384G4709' => 'pso', 'PSO407G0334' => 'pso', 'QL04p040276' => 'qlo', 'QL06p005458' => 'qlo', 'QL06p005472' => 'qlo', 'QL07p030546' => 'qlo', 'QL07p031519' => 'qlo', 'QL09p050949' => 'qlo', 'QL09p050966' => 'qlo', 'QL09p051067' => 'qlo', 'QL12p022706' => 'qlo', 'RcHm_v2.0_Chr2g0119601' => 'rch', 'RcHm_v2.0_Chr3g0459591' => 'rch', 'RcHm_v2.0_Chr4g0418521' => 'rch', 'RcHm_v2.0_Chr4g0418531' => 'rch', 'RcHm_v2.0_Chr4g0418541' => 'rch', 'RcHm_v2.0_Chr6g0291641' => 'rch', 'Rhsim01G0086300' => 'rsi', 'Rhsim01G0276300' => 'rsi', 'Rhsim01G0276500' => 'rsi', 'Rhsim04G0207700' => 'rsi', 'Rhsim05G0234500' => 'rsi', 'Rhsim13G0022400' => 'rsi', 'Sabra02G0167900' => 'sbr', 'Sabra04G0158500' => 'sbr', 'Sabra08G0159800' => 'sbr', 'Sabra10G0011500' => 'sbr', 'Sabra14G0104400' => 'sbr', 'SalBow2G2440' => 'sbo', 'SalBow4G2265' => 'sbo', 'Sc02g0000060' => 'sci', 'Sc05g0005020' => 'sci', 'Sc13g0003890' => 'sci', 'Sed0014865' => 'sed', 'Sed0017224' => 'sed', 'Sed0026391' => 'sed', 'SEGI_00063' => 'sgi', 'SEGI_10967' => 'sgi', 'SEGI_17510' => 'sgi', 'SEGI_24396' => 'sgi', 'SEGI_39719' => 'sgi', 'SEGI_41392' => 'sgi', 'SGA_v2.0_scaffold11G05794' => 'sas', 'SGA_v2.0_scaffold142G35607' => 'sas', 'SGA_v2.0_scaffold1G00447' => 'sas', 'SHI15388' => 'shi', 'SHI15394' => 'shi', 'SHI15396' => 'shi', 'SHI15399' => 'shi', 'SMO343G0151' => 'smo', 'SMO367G1118' => 'smo', 'Solyc01g080200.3' => 'sly', 'Solyc06g008960.3' => 'sly', 'Solyc09g064780.3' => 'sly', 'Sopen01g031980' => 'spe', 'Sopen06g003710' => 'spe', 'Sopen09g026460' => 'spe', 'Sp3g21240' => 'spa', 'Sp4g30030' => 'spa', 'TAR365G0022' => 'tar', 'TAR365G1023' => 'tar', 'TAR365G1253' => 'tar', 'TAR623G0078' => 'tar', 'TAR623G1721' => 'tar', 'TAR633G0959' => 'tar', 'THA.LOC104802225' => 'tha', 'THA.LOC104804769' => 'tha', 'THA.LOC104808660' => 'tha', 'THA.LOC104812792' => 'tha', 'Thecc.01G284000' => 'tca', 'Thecc.04G220600' => 'tca', 'Thecc.05G268900' => 'tca', 'Thecc.08G171100' => 'tca', 'Thhalv10001284m.g' => 'esa', 'Thhalv10019912m.g' => 'esa', 'TPR.G14189' => 'tpr', 'TPR.G18110' => 'tpr', 'TPR.G18130' => 'tpr', 'TPR.G18131' => 'tpr', 'TPR.G18140' => 'tpr', 'TPR.G24282' => 'tpr', 'TPR.G25221' => 'tpr', 'TPR.G29267' => 'tpr', 'TPR.G35315' => 'tpr', 'TPR.G36173' => 'tpr', 'TWI09G0794' => 'twi', 'TWI59G1348' => 'twi', 'TWI74G0430' => 'twi', 'unitig_26.g8940' => 'ugi', 'unitig_749.g13744' => 'ugi', 'unitig_749.g13745' => 'ugi', 'vmacro08269' => 'vma', 'vmacro14937' => 'vma', 'vmacro20401' => 'vma', 'VMungo0464G1349' => 'vmu', 'VMungo0540G0289' => 'vmu', 'VMungo1215G1590' => 'vmu', 'VMungo1309G0221' => 'vmu', 'VMungo1309G2815' => 'vmu', 'VMungo1383G0239' => 'vmu', 'VMungo1383G2910' => 'vmu', 'Zm00001eb095270' => 'zma', 'Zm00001eb095280' => 'zma', 'Zm00001eb111630' => 'zma', 'Zm00001eb237080' => 'zma', 'Zm00001eb273740' => 'zma', 'Zm00001eb285040' => 'zma', 'Zm00001eb330790' => 'zma', 'Zm00001eb337380' => 'zma' ), 'gf_id' => 'HOM05D001484', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001484' ), 'data_identifier' => 'HOM05D001484', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001484', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p31500' => 'bna', 'A05p00020' => 'bna', 'A07p08820' => 'bna', 'Aa31LG4G3300' => 'aar', 'Aa31LG8G10030' => 'aar', 'Actinidia00731' => 'ach', 'Actinidia11473' => 'ach', 'Actinidia23469' => 'ach', 'Actinidia24318' => 'ach', 'Actinidia40196' => 'ach', 'Actinidia40197' => 'ach', 'Actinidia40198' => 'ach', 'Ah.08g212990' => 'amhyb', 'Ah.15g091720' => 'amhyb', 'AL3G38260' => 'aly', 'AL4G47710' => 'aly', 'Aqoxy2G00671' => 'aox', 'Aqoxy2G03236' => 'aox', 'arahy.Tifrunner.gnm1.ann1.05IDCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KR684' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATY3SJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK6QJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6APGL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IDT7Z9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM073U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ0R87' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LE7RV4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT4QRX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V5ENPK' => 'arhy', 'AT2G48110' => 'ath', 'AT3G23590' => 'ath', 'ATR0626G186' => 'atr', 'ATR1127G141' => 'atr', 'Atru.chr4.2583' => 'acertr', 'Atru.chr5.1358' => 'acertr', 'Atru.chr5.1359' => 'acertr', 'Atru.chr8.46' => 'acertr', 'AUR62002640' => 'cqu', 'AUR62030055' => 'cqu', 'AUR62033713' => 'cqu', 'AUR62033714' => 'cqu', 'AUR62036795' => 'cqu', 'AUR62039891' => 'cqu', 'BcaB02g08737' => 'bca', 'BcaB04g20441' => 'bca', 'BcaB06g26509' => 'bca', 'BcaB06g26510' => 'bca', 'BcaB06g26511' => 'bca', 'BcaB06g26512' => 'bca', 'BcaB06g26513' => 'bca', 'BcaC02g12564' => 'bca', 'BcaC02g12565' => 'bca', 'BcaC02g12794' => 'bca', 'BcaC02g12795' => 'bca', 'BcaC02g12796' => 'bca', 'BcaC06g35541' => 'bca', 'BNapus_Darmor_BZH_scaffold_188p00080' => 'bna', 'BNapus_Darmor_BZH_scaffold_188p00090' => 'bna', 'BolC1t03972H' => 'bol', 'BolC1t03973H' => 'bol', 'BolC4t21680H' => 'bol', 'BolC7t41863H' => 'bol', 'BolSC55t61227H' => 'bol', 'BolSC55t61228H' => 'bol', 'BraA01t03278Z' => 'bra', 'BraA05t18998Z' => 'bra', 'BraA07t28673Z' => 'bra', 'C01p40150' => 'bna', 'C05p12370' => 'bna', 'C07p13680' => 'bna', 'CAN.G1006.16' => 'can', 'CAN.G1006.17' => 'can', 'CAN.G1170.2' => 'can', 'CAN.G962.7' => 'can', 'CANSAT25G2179' => 'cansat', 'CANSAT78G1573' => 'cansat', 'CARHR099510' => 'chi', 'CARHR143510' => 'chi', 'Carub.0003s2380' => 'cru', 'Carub.0004s3082' => 'cru', 'Ca_00614_v3' => 'car', 'Ca_07801_v3' => 'car', 'Ca_08567_v3' => 'car', 'Ca_09571_v3' => 'car', 'CBR_g19290' => 'cbr', 'Cc01_g19770' => 'ccan', 'Cc03_g03030' => 'ccan', 'CDE07G0968' => 'cde', 'CDE09G1441' => 'cde', 'Cfa006103' => 'cfa', 'Cfa015573' => 'cfa', 'Cfa016988' => 'cfa', 'Ciclev10006738m.g' => 'ccl', 'Ciclev10010920m.g' => 'ccl', 'Ciclev10018517m.g' => 'ccl', 'CiPaw.01G159200' => 'cil', 'CiPaw.02G091000' => 'cil', 'CiPaw.02G091100' => 'cil', 'CiPaw.08G103100' => 'cil', 'CiPaw.09G224900' => 'cil', 'ClCG06G005740' => 'cla', 'ClCG07G000090' => 'cla', 'ClCG07G000100' => 'cla', 'COL.COLO4_09143' => 'col', 'COL.COLO4_25124' => 'col', 'Cpa.g.sc16.34' => 'cpa', 'Cpa.g.sc3504.1' => 'cpa', 'Cpa.g.sc60.37' => 'cpa', 'CsaV3_6G018520' => 'csa', 'CsaV3_6G036860' => 'csa', 'CSS0001072' => 'camsi', 'CSS0020208' => 'camsi', 'CSS0021253' => 'camsi', 'CSS0022190' => 'camsi', 'CSS0036150' => 'camsi', 'CSS0040442' => 'camsi', 'CSS0042300' => 'camsi', 'CSS0045298' => 'camsi', 'DCAR_012449' => 'dca', 'DCAR_018405' => 'dca', 'DCAR_024573' => 'dca', 'DCAR_030591' => 'dca', 'Dinv16926' => 'din', 'Dinv32963' => 'din', 'Dinv38382' => 'din', 'Dinv38383' => 'din', 'Duzib133G0974' => 'dzi', 'Duzib138G1867' => 'dzi', 'Duzib211G0420' => 'dzi', 'Duzib212G0930' => 'dzi', 'ECA234G1645' => 'eca', 'ECA247G3467' => 'eca', 'ECA248G1703' => 'eca', 'EL10Ac3g06327' => 'bvu', 'EL10Ac7g17204' => 'bvu', 'Eucgr.A00855' => 'egr', 'Eucgr.A00858' => 'egr', 'Eucgr.H01520' => 'egr', 'Eucgr.H03604' => 'egr', 'Eucgr.L03465' => 'egr', 'Eucgr.L03466' => 'egr', 'FAN01G0988' => 'fan', 'FAN02G3892' => 'fan', 'FAN05G3381' => 'fan', 'FAN07G0967' => 'fan', 'FAN07G1493' => 'fan', 'FAN08G3125' => 'fan', 'FAN09G0402' => 'fan', 'FAN12G2594' => 'fan', 'FAN12G3879' => 'fan', 'FAN14G1546' => 'fan', 'FAN15G3626' => 'fan', 'FAN17G0588' => 'fan', 'FAN17G0609' => 'fan', 'FAN18G2817' => 'fan', 'FAN19G1305' => 'fan', 'FAN20G1787' => 'fan', 'FAN22G0073' => 'fan', 'FAN22G0352' => 'fan', 'FAN22G0368' => 'fan', 'FAN22G2273' => 'fan', 'FAN24G1998' => 'fan', 'FAN27G1317' => 'fan', 'FvH4_2g23980' => 'fve', 'FvH4_4g14380' => 'fve', 'FvH4_4g14390' => 'fve', 'FvH4_6g09250' => 'fve', 'Glyma.03G151100' => 'gma', 'Glyma.04G122550' => 'gma', 'Glyma.05G001600' => 'gma', 'Glyma.09G270766' => 'gma', 'Glyma.09G270832' => 'gma', 'Glyma.13G209800' => 'gma', 'Glyma.15G102800' => 'gma', 'Glyma.18G218900' => 'gma', 'Glyma.19G001500' => 'gma', 'Glyma.19G153600' => 'gma', 'Gohir.A02G028600' => 'ghi', 'Gohir.A08G045000' => 'ghi', 'Gohir.A11G120500' => 'ghi', 'Gohir.A12G006200' => 'ghi', 'Gohir.A12G006250' => 'ghi', 'Gohir.D02G036300' => 'ghi', 'Gohir.D08G054700' => 'ghi', 'Gohir.D11G125600' => 'ghi', 'Gohir.D12G005700' => 'ghi', 'Gorai.004G055200' => 'gra', 'Gorai.005G040400' => 'gra', 'Gorai.007G134500' => 'gra', 'Gorai.008G005500' => 'gra', 'GSVIVG01011094001' => 'vvi', 'GSVIVG01017879001' => 'vvi', 'GSVIVG01025988001' => 'vvi', 'GSVIVG01029847001' => 'vvi', 'HanXRQChr10g0282901' => 'han', 'HanXRQChr10g0310371' => 'han', 'HanXRQChr10g0315041' => 'han', 'HanXRQChr11g0327651' => 'han', 'HanXRQChr12g0359391' => 'han', 'Haze_00972' => 'cav', 'Haze_00973' => 'cav', 'Haze_00974' => 'cav', 'Haze_04747' => 'cav', 'Haze_04749' => 'cav', 'Haze_04750' => 'cav', 'Haze_21217' => 'cav', 'Hma1.2p1_1037F.1_g250680' => 'hma', 'Hma1.2p1_1644F.1_g295320' => 'hma', 'HPP92_011322' => 'vpl', 'HPP92_011323' => 'vpl', 'HPP92_011324' => 'vpl', 'HPP92_011325' => 'vpl', 'HPP92_011326' => 'vpl', 'Hund12205' => 'sun', 'Hund17957' => 'sun', 'Lalb_Chr06g0176771' => 'lal', 'Lalb_Chr18g0056021' => 'lal', 'Lalb_Chr18g0056031' => 'lal', 'Lalb_Chr18g0056041' => 'lal', 'Lalb_Chr20g0107751' => 'lal', 'Lalb_Chr20g0118371' => 'lal', 'Lj1g0010239' => 'lja', 'Lj1g0017101' => 'lja', 'Lj2A1178G40' => 'lonja', 'Lj2A54G84' => 'lonja', 'Lj2g0015248' => 'lja', 'Lj3A761T51' => 'lonja', 'Lj6g0018116' => 'lja', 'Lsat_1_v5_gn_4_136040' => 'lsa', 'Lsat_1_v5_gn_5_187461' => 'lsa', 'Lsat_1_v5_gn_5_77001' => 'lsa', 'Lsat_1_v5_gn_9_4461' => 'lsa', 'Manes.01G210100' => 'mes', 'Manes.03G185600' => 'mes', 'Manes.05G073300' => 'mes', 'Manes.09G120300' => 'mes', 'Manes.15G022100' => 'mes', 'Mapoly0096s0053' => 'mpo', 'MBI03_g14058_MAGBIO' => 'mbi', 'MBI03_g33876_MAGBIO' => 'mbi', 'MBI03_g36854_MAGBIO' => 'mbi', 'MBI17_g11997_MAGBIO' => 'mbi', 'MD03G1269000' => 'mdo', 'MD04G1179600' => 'mdo', 'MD11G1289800' => 'mdo', 'MD12G1194700' => 'mdo', 'MD13G1182100' => 'mdo', 'MD13G1182200' => 'mdo', 'MD16G1182600' => 'mdo', 'Medtr2g021400' => 'mtr', 'Medtr2g021470' => 'mtr', 'Medtr2g105810' => 'mtr', 'Medtr3g033580' => 'mtr', 'Medtr6g007970' => 'mtr', 'Medtr7g056330' => 'mtr', 'Medtr7g074290' => 'mtr', 'Medtr7g074380' => 'mtr', 'Medtr7g094550' => 'mtr', 'Medtr8g069995' => 'mtr', 'MELO3C014345.2' => 'cme', 'MELO3C021395.2' => 'cme', 'Migut.D00262' => 'egut', 'Migut.G00257' => 'egut', 'MSTRG.21575' => 'ama', 'MSTRG.3985' => 'ama', 'Nitab4.5_0000295g0140' => 'nta', 'Nitab4.5_0000732g0140' => 'nta', 'Nitab4.5_0003162g0020' => 'nta', 'Nitab4.5_0006180g0090' => 'nta', 'Nitab4.5_0006390g0010' => 'nta', 'Nitab4.5_0007392g0040' => 'nta', 'Nn1g02140' => 'nnu', 'Nn4g26168' => 'nnu', 'Nn5g26754' => 'nnu', 'Oeu001433.1' => 'oeu', 'Oeu010299.2' => 'oeu', 'Oeu011171.1' => 'oeu', 'Oeu037675.1' => 'oeu', 'Oeu038359.1' => 'oeu', 'Oeu063834.1' => 'oeu', 'Oeu063835.1' => 'oeu', 'Os05g0312000' => 'osa', 'Os07g0211101' => 'osa', 'Os07g0211200' => 'osa', 'Os07g0681500' => 'osa', 'Peaxi162Scf00095g01015' => 'pax', 'Peaxi162Scf00104g00329' => 'pax', 'Peaxi162Scf00161g00137' => 'pax', 'PGR004G1665' => 'pgr', 'PGR031G2937' => 'pgr', 'PGR119G2145' => 'pgr', 'PGSC0003DMG400004351' => 'stu', 'PGSC0003DMG400014625' => 'stu', 'PGSC0003DMG401000943' => 'stu', 'Phvul.001G148600' => 'pvu', 'Phvul.004G001700' => 'pvu', 'Phvul.006G154900' => 'pvu', 'Phvul.008G078200' => 'pvu', 'Phvul.011G136500' => 'pvu', 'Potri.002G215600' => 'ptr', 'Potri.008G201600' => 'ptr', 'Potri.014G138400' => 'ptr', 'Potri.016G142500' => 'ptr', 'Pp3c16_10580' => 'ppa', 'Pp3c5_25280' => 'ppa', 'Prupe.1G150000' => 'ppe', 'Prupe.1G150100' => 'ppe', 'Prupe.6G299600' => 'ppe', 'Prupe.8G245000' => 'ppe', 'Psat0s4927g0040' => 'psa', 'Psat1g052080' => 'psa', 'Psat1g183800' => 'psa', 'Psat3g113840' => 'psa', 'Psat3g126120' => 'psa', 'Psat3g126160' => 'psa', 'Psat3g158760' => 'psa', 'Psat3g158840' => 'psa', 'PSO170G2858' => 'pso', 'PSO339G0606' => 'pso', 'PSO384G4709' => 'pso', 'PSO407G0334' => 'pso', 'QL04p040276' => 'qlo', 'QL06p005458' => 'qlo', 'QL06p005472' => 'qlo', 'QL07p030546' => 'qlo', 'QL07p031519' => 'qlo', 'QL09p050949' => 'qlo', 'QL09p050966' => 'qlo', 'QL09p051067' => 'qlo', 'QL12p022706' => 'qlo', 'RcHm_v2.0_Chr2g0119601' => 'rch', 'RcHm_v2.0_Chr3g0459591' => 'rch', 'RcHm_v2.0_Chr4g0418521' => 'rch', 'RcHm_v2.0_Chr4g0418531' => 'rch', 'RcHm_v2.0_Chr4g0418541' => 'rch', 'RcHm_v2.0_Chr6g0291641' => 'rch', 'Rhsim01G0086300' => 'rsi', 'Rhsim01G0276300' => 'rsi', 'Rhsim01G0276500' => 'rsi', 'Rhsim04G0207700' => 'rsi', 'Rhsim05G0234500' => 'rsi', 'Rhsim13G0022400' => 'rsi', 'Sabra02G0167900' => 'sbr', 'Sabra04G0158500' => 'sbr', 'Sabra08G0159800' => 'sbr', 'Sabra10G0011500' => 'sbr', 'Sabra14G0104400' => 'sbr', 'SalBow2G2440' => 'sbo', 'SalBow4G2265' => 'sbo', 'Sc02g0000060' => 'sci', 'Sc05g0005020' => 'sci', 'Sc13g0003890' => 'sci', 'Sed0014865' => 'sed', 'Sed0017224' => 'sed', 'Sed0026391' => 'sed', 'SEGI_00063' => 'sgi', 'SEGI_10967' => 'sgi', 'SEGI_17510' => 'sgi', 'SEGI_24396' => 'sgi', 'SEGI_39719' => 'sgi', 'SEGI_41392' => 'sgi', 'SGA_v2.0_scaffold11G05794' => 'sas', 'SGA_v2.0_scaffold142G35607' => 'sas', 'SGA_v2.0_scaffold1G00447' => 'sas', 'SHI15388' => 'shi', 'SHI15394' => 'shi', 'SHI15396' => 'shi', 'SHI15399' => 'shi', 'SMO343G0151' => 'smo', 'SMO367G1118' => 'smo', 'Solyc01g080200.3' => 'sly', 'Solyc06g008960.3' => 'sly', 'Solyc09g064780.3' => 'sly', 'Sopen01g031980' => 'spe', 'Sopen06g003710' => 'spe', 'Sopen09g026460' => 'spe', 'Sp3g21240' => 'spa', 'Sp4g30030' => 'spa', 'TAR365G0022' => 'tar', 'TAR365G1023' => 'tar', 'TAR365G1253' => 'tar', 'TAR623G0078' => 'tar', 'TAR623G1721' => 'tar', 'TAR633G0959' => 'tar', 'THA.LOC104802225' => 'tha', 'THA.LOC104804769' => 'tha', 'THA.LOC104808660' => 'tha', 'THA.LOC104812792' => 'tha', 'Thecc.01G284000' => 'tca', 'Thecc.04G220600' => 'tca', 'Thecc.05G268900' => 'tca', 'Thecc.08G171100' => 'tca', 'Thhalv10001284m.g' => 'esa', 'Thhalv10019912m.g' => 'esa', 'TPR.G14189' => 'tpr', 'TPR.G18110' => 'tpr', 'TPR.G18130' => 'tpr', 'TPR.G18131' => 'tpr', 'TPR.G18140' => 'tpr', 'TPR.G24282' => 'tpr', 'TPR.G25221' => 'tpr', 'TPR.G29267' => 'tpr', 'TPR.G35315' => 'tpr', 'TPR.G36173' => 'tpr', 'TWI09G0794' => 'twi', 'TWI59G1348' => 'twi', 'TWI74G0430' => 'twi', 'unitig_26.g8940' => 'ugi', 'unitig_749.g13744' => 'ugi', 'unitig_749.g13745' => 'ugi', 'vmacro08269' => 'vma', 'vmacro14937' => 'vma', 'vmacro20401' => 'vma', 'VMungo0464G1349' => 'vmu', 'VMungo0540G0289' => 'vmu', 'VMungo1215G1590' => 'vmu', 'VMungo1309G0221' => 'vmu', 'VMungo1309G2815' => 'vmu', 'VMungo1383G0239' => 'vmu', 'VMungo1383G2910' => 'vmu', 'Zm00001eb095270' => 'zma', 'Zm00001eb095280' => 'zma', 'Zm00001eb111630' => 'zma', 'Zm00001eb237080' => 'zma', 'Zm00001eb273740' => 'zma', 'Zm00001eb285040' => 'zma', 'Zm00001eb330790' => 'zma', 'Zm00001eb337380' => 'zma' ) $gf_id = 'HOM05D001484' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001484' ) $data_identifier = 'HOM05D001484' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 2, 'aly' => (int) 2, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 22, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 7, 'hma' => (int) 2, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 7, 'mtr' => (int) 10, 'cme' => (int) 2, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 4, 'ppa' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 4, 'qlo' => (int) 9, 'rch' => (int) 6, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 10, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 7, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb337380' $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' => 'HOM05D001484', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p31500' => 'bna', 'A05p00020' => 'bna', 'A07p08820' => 'bna', 'Aa31LG4G3300' => 'aar', 'Aa31LG8G10030' => 'aar', 'Actinidia00731' => 'ach', 'Actinidia11473' => 'ach', 'Actinidia23469' => 'ach', 'Actinidia24318' => 'ach', 'Actinidia40196' => 'ach', 'Actinidia40197' => 'ach', 'Actinidia40198' => 'ach', 'Ah.08g212990' => 'amhyb', 'Ah.15g091720' => 'amhyb', 'AL3G38260' => 'aly', 'AL4G47710' => 'aly', 'Aqoxy2G00671' => 'aox', 'Aqoxy2G03236' => 'aox', 'arahy.Tifrunner.gnm1.ann1.05IDCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KR684' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATY3SJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK6QJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6APGL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IDT7Z9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM073U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ0R87' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LE7RV4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT4QRX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V5ENPK' => 'arhy', 'AT2G48110' => 'ath', 'AT3G23590' => 'ath', 'ATR0626G186' => 'atr', 'ATR1127G141' => 'atr', 'Atru.chr4.2583' => 'acertr', 'Atru.chr5.1358' => 'acertr', 'Atru.chr5.1359' => 'acertr', 'Atru.chr8.46' => 'acertr', 'AUR62002640' => 'cqu', 'AUR62030055' => 'cqu', 'AUR62033713' => 'cqu', 'AUR62033714' => 'cqu', 'AUR62036795' => 'cqu', 'AUR62039891' => 'cqu', 'BcaB02g08737' => 'bca', 'BcaB04g20441' => 'bca', 'BcaB06g26509' => 'bca', 'BcaB06g26510' => 'bca', 'BcaB06g26511' => 'bca', 'BcaB06g26512' => 'bca', 'BcaB06g26513' => 'bca', 'BcaC02g12564' => 'bca', 'BcaC02g12565' => 'bca', 'BcaC02g12794' => 'bca', 'BcaC02g12795' => 'bca', 'BcaC02g12796' => 'bca', 'BcaC06g35541' => 'bca', 'BNapus_Darmor_BZH_scaffold_188p00080' => 'bna', 'BNapus_Darmor_BZH_scaffold_188p00090' => 'bna', 'BolC1t03972H' => 'bol', 'BolC1t03973H' => 'bol', 'BolC4t21680H' => 'bol', 'BolC7t41863H' => 'bol', 'BolSC55t61227H' => 'bol', 'BolSC55t61228H' => 'bol', 'BraA01t03278Z' => 'bra', 'BraA05t18998Z' => 'bra', 'BraA07t28673Z' => 'bra', 'C01p40150' => 'bna', 'C05p12370' => 'bna', 'C07p13680' => 'bna', 'CAN.G1006.16' => 'can', 'CAN.G1006.17' => 'can', 'CAN.G1170.2' => 'can', 'CAN.G962.7' => 'can', 'CANSAT25G2179' => 'cansat', 'CANSAT78G1573' => 'cansat', 'CARHR099510' => 'chi', 'CARHR143510' => 'chi', 'Carub.0003s2380' => 'cru', 'Carub.0004s3082' => 'cru', 'Ca_00614_v3' => 'car', 'Ca_07801_v3' => 'car', 'Ca_08567_v3' => 'car', 'Ca_09571_v3' => 'car', 'CBR_g19290' => 'cbr', 'Cc01_g19770' => 'ccan', 'Cc03_g03030' => 'ccan', 'CDE07G0968' => 'cde', 'CDE09G1441' => 'cde', 'Cfa006103' => 'cfa', 'Cfa015573' => 'cfa', 'Cfa016988' => 'cfa', 'Ciclev10006738m.g' => 'ccl', 'Ciclev10010920m.g' => 'ccl', 'Ciclev10018517m.g' => 'ccl', 'CiPaw.01G159200' => 'cil', 'CiPaw.02G091000' => 'cil', 'CiPaw.02G091100' => 'cil', 'CiPaw.08G103100' => 'cil', 'CiPaw.09G224900' => 'cil', 'ClCG06G005740' => 'cla', 'ClCG07G000090' => 'cla', 'ClCG07G000100' => 'cla', 'COL.COLO4_09143' => 'col', 'COL.COLO4_25124' => 'col', 'Cpa.g.sc16.34' => 'cpa', 'Cpa.g.sc3504.1' => 'cpa', 'Cpa.g.sc60.37' => 'cpa', 'CsaV3_6G018520' => 'csa', 'CsaV3_6G036860' => 'csa', 'CSS0001072' => 'camsi', 'CSS0020208' => 'camsi', 'CSS0021253' => 'camsi', 'CSS0022190' => 'camsi', 'CSS0036150' => 'camsi', 'CSS0040442' => 'camsi', 'CSS0042300' => 'camsi', 'CSS0045298' => 'camsi', 'DCAR_012449' => 'dca', 'DCAR_018405' => 'dca', 'DCAR_024573' => 'dca', 'DCAR_030591' => 'dca', 'Dinv16926' => 'din', 'Dinv32963' => 'din', 'Dinv38382' => 'din', 'Dinv38383' => 'din', 'Duzib133G0974' => 'dzi', 'Duzib138G1867' => 'dzi', 'Duzib211G0420' => 'dzi', 'Duzib212G0930' => 'dzi', 'ECA234G1645' => 'eca', 'ECA247G3467' => 'eca', 'ECA248G1703' => 'eca', 'EL10Ac3g06327' => 'bvu', 'EL10Ac7g17204' => 'bvu', 'Eucgr.A00855' => 'egr', 'Eucgr.A00858' => 'egr', 'Eucgr.H01520' => 'egr', 'Eucgr.H03604' => 'egr', 'Eucgr.L03465' => 'egr', 'Eucgr.L03466' => 'egr', 'FAN01G0988' => 'fan', 'FAN02G3892' => 'fan', 'FAN05G3381' => 'fan', 'FAN07G0967' => 'fan', 'FAN07G1493' => 'fan', 'FAN08G3125' => 'fan', 'FAN09G0402' => 'fan', 'FAN12G2594' => 'fan', 'FAN12G3879' => 'fan', 'FAN14G1546' => 'fan', 'FAN15G3626' => 'fan', 'FAN17G0588' => 'fan', 'FAN17G0609' => 'fan', 'FAN18G2817' => 'fan', 'FAN19G1305' => 'fan', 'FAN20G1787' => 'fan', 'FAN22G0073' => 'fan', 'FAN22G0352' => 'fan', 'FAN22G0368' => 'fan', 'FAN22G2273' => 'fan', 'FAN24G1998' => 'fan', 'FAN27G1317' => 'fan', 'FvH4_2g23980' => 'fve', 'FvH4_4g14380' => 'fve', 'FvH4_4g14390' => 'fve', 'FvH4_6g09250' => 'fve', 'Glyma.03G151100' => 'gma', 'Glyma.04G122550' => 'gma', 'Glyma.05G001600' => 'gma', 'Glyma.09G270766' => 'gma', 'Glyma.09G270832' => 'gma', 'Glyma.13G209800' => 'gma', 'Glyma.15G102800' => 'gma', 'Glyma.18G218900' => 'gma', 'Glyma.19G001500' => 'gma', 'Glyma.19G153600' => 'gma', 'Gohir.A02G028600' => 'ghi', 'Gohir.A08G045000' => 'ghi', 'Gohir.A11G120500' => 'ghi', 'Gohir.A12G006200' => 'ghi', 'Gohir.A12G006250' => 'ghi', 'Gohir.D02G036300' => 'ghi', 'Gohir.D08G054700' => 'ghi', 'Gohir.D11G125600' => 'ghi', 'Gohir.D12G005700' => 'ghi', 'Gorai.004G055200' => 'gra', 'Gorai.005G040400' => 'gra', 'Gorai.007G134500' => 'gra', 'Gorai.008G005500' => 'gra', 'GSVIVG01011094001' => 'vvi', 'GSVIVG01017879001' => 'vvi', 'GSVIVG01025988001' => 'vvi', 'GSVIVG01029847001' => 'vvi', 'HanXRQChr10g0282901' => 'han', 'HanXRQChr10g0310371' => 'han', 'HanXRQChr10g0315041' => 'han', 'HanXRQChr11g0327651' => 'han', 'HanXRQChr12g0359391' => 'han', 'Haze_00972' => 'cav', 'Haze_00973' => 'cav', 'Haze_00974' => 'cav', 'Haze_04747' => 'cav', 'Haze_04749' => 'cav', 'Haze_04750' => 'cav', 'Haze_21217' => 'cav', 'Hma1.2p1_1037F.1_g250680' => 'hma', 'Hma1.2p1_1644F.1_g295320' => 'hma', 'HPP92_011322' => 'vpl', 'HPP92_011323' => 'vpl', 'HPP92_011324' => 'vpl', 'HPP92_011325' => 'vpl', 'HPP92_011326' => 'vpl', 'Hund12205' => 'sun', 'Hund17957' => 'sun', 'Lalb_Chr06g0176771' => 'lal', 'Lalb_Chr18g0056021' => 'lal', 'Lalb_Chr18g0056031' => 'lal', 'Lalb_Chr18g0056041' => 'lal', 'Lalb_Chr20g0107751' => 'lal', 'Lalb_Chr20g0118371' => 'lal', 'Lj1g0010239' => 'lja', 'Lj1g0017101' => 'lja', 'Lj2A1178G40' => 'lonja', 'Lj2A54G84' => 'lonja', 'Lj2g0015248' => 'lja', 'Lj3A761T51' => 'lonja', 'Lj6g0018116' => 'lja', 'Lsat_1_v5_gn_4_136040' => 'lsa', 'Lsat_1_v5_gn_5_187461' => 'lsa', 'Lsat_1_v5_gn_5_77001' => 'lsa', 'Lsat_1_v5_gn_9_4461' => 'lsa', 'Manes.01G210100' => 'mes', 'Manes.03G185600' => 'mes', 'Manes.05G073300' => 'mes', 'Manes.09G120300' => 'mes', 'Manes.15G022100' => 'mes', 'Mapoly0096s0053' => 'mpo', 'MBI03_g14058_MAGBIO' => 'mbi', 'MBI03_g33876_MAGBIO' => 'mbi', 'MBI03_g36854_MAGBIO' => 'mbi', 'MBI17_g11997_MAGBIO' => 'mbi', 'MD03G1269000' => 'mdo', 'MD04G1179600' => 'mdo', 'MD11G1289800' => 'mdo', 'MD12G1194700' => 'mdo', 'MD13G1182100' => 'mdo', 'MD13G1182200' => 'mdo', 'MD16G1182600' => 'mdo', 'Medtr2g021400' => 'mtr', 'Medtr2g021470' => 'mtr', 'Medtr2g105810' => 'mtr', 'Medtr3g033580' => 'mtr', 'Medtr6g007970' => 'mtr', 'Medtr7g056330' => 'mtr', 'Medtr7g074290' => 'mtr', 'Medtr7g074380' => 'mtr', 'Medtr7g094550' => 'mtr', 'Medtr8g069995' => 'mtr', 'MELO3C014345.2' => 'cme', 'MELO3C021395.2' => 'cme', 'Migut.D00262' => 'egut', 'Migut.G00257' => 'egut', 'MSTRG.21575' => 'ama', 'MSTRG.3985' => 'ama', 'Nitab4.5_0000295g0140' => 'nta', 'Nitab4.5_0000732g0140' => 'nta', 'Nitab4.5_0003162g0020' => 'nta', 'Nitab4.5_0006180g0090' => 'nta', 'Nitab4.5_0006390g0010' => 'nta', 'Nitab4.5_0007392g0040' => 'nta', 'Nn1g02140' => 'nnu', 'Nn4g26168' => 'nnu', 'Nn5g26754' => 'nnu', 'Oeu001433.1' => 'oeu', 'Oeu010299.2' => 'oeu', 'Oeu011171.1' => 'oeu', 'Oeu037675.1' => 'oeu', 'Oeu038359.1' => 'oeu', 'Oeu063834.1' => 'oeu', 'Oeu063835.1' => 'oeu', 'Os05g0312000' => 'osa', 'Os07g0211101' => 'osa', 'Os07g0211200' => 'osa', 'Os07g0681500' => 'osa', 'Peaxi162Scf00095g01015' => 'pax', 'Peaxi162Scf00104g00329' => 'pax', 'Peaxi162Scf00161g00137' => 'pax', 'PGR004G1665' => 'pgr', 'PGR031G2937' => 'pgr', 'PGR119G2145' => 'pgr', 'PGSC0003DMG400004351' => 'stu', 'PGSC0003DMG400014625' => 'stu', 'PGSC0003DMG401000943' => 'stu', 'Phvul.001G148600' => 'pvu', 'Phvul.004G001700' => 'pvu', 'Phvul.006G154900' => 'pvu', 'Phvul.008G078200' => 'pvu', 'Phvul.011G136500' => 'pvu', 'Potri.002G215600' => 'ptr', 'Potri.008G201600' => 'ptr', 'Potri.014G138400' => 'ptr', 'Potri.016G142500' => 'ptr', 'Pp3c16_10580' => 'ppa', 'Pp3c5_25280' => 'ppa', 'Prupe.1G150000' => 'ppe', 'Prupe.1G150100' => 'ppe', 'Prupe.6G299600' => 'ppe', 'Prupe.8G245000' => 'ppe', 'Psat0s4927g0040' => 'psa', 'Psat1g052080' => 'psa', 'Psat1g183800' => 'psa', 'Psat3g113840' => 'psa', 'Psat3g126120' => 'psa', 'Psat3g126160' => 'psa', 'Psat3g158760' => 'psa', 'Psat3g158840' => 'psa', 'PSO170G2858' => 'pso', 'PSO339G0606' => 'pso', 'PSO384G4709' => 'pso', 'PSO407G0334' => 'pso', 'QL04p040276' => 'qlo', 'QL06p005458' => 'qlo', 'QL06p005472' => 'qlo', 'QL07p030546' => 'qlo', 'QL07p031519' => 'qlo', 'QL09p050949' => 'qlo', 'QL09p050966' => 'qlo', 'QL09p051067' => 'qlo', 'QL12p022706' => 'qlo', 'RcHm_v2.0_Chr2g0119601' => 'rch', 'RcHm_v2.0_Chr3g0459591' => 'rch', 'RcHm_v2.0_Chr4g0418521' => 'rch', 'RcHm_v2.0_Chr4g0418531' => 'rch', 'RcHm_v2.0_Chr4g0418541' => 'rch', 'RcHm_v2.0_Chr6g0291641' => 'rch', 'Rhsim01G0086300' => 'rsi', 'Rhsim01G0276300' => 'rsi', 'Rhsim01G0276500' => 'rsi', 'Rhsim04G0207700' => 'rsi', 'Rhsim05G0234500' => 'rsi', 'Rhsim13G0022400' => 'rsi', 'Sabra02G0167900' => 'sbr', 'Sabra04G0158500' => 'sbr', 'Sabra08G0159800' => 'sbr', 'Sabra10G0011500' => 'sbr', 'Sabra14G0104400' => 'sbr', 'SalBow2G2440' => 'sbo', 'SalBow4G2265' => 'sbo', 'Sc02g0000060' => 'sci', 'Sc05g0005020' => 'sci', 'Sc13g0003890' => 'sci', 'Sed0014865' => 'sed', 'Sed0017224' => 'sed', 'Sed0026391' => 'sed', 'SEGI_00063' => 'sgi', 'SEGI_10967' => 'sgi', 'SEGI_17510' => 'sgi', 'SEGI_24396' => 'sgi', 'SEGI_39719' => 'sgi', 'SEGI_41392' => 'sgi', 'SGA_v2.0_scaffold11G05794' => 'sas', 'SGA_v2.0_scaffold142G35607' => 'sas', 'SGA_v2.0_scaffold1G00447' => 'sas', 'SHI15388' => 'shi', 'SHI15394' => 'shi', 'SHI15396' => 'shi', 'SHI15399' => 'shi', 'SMO343G0151' => 'smo', 'SMO367G1118' => 'smo', 'Solyc01g080200.3' => 'sly', 'Solyc06g008960.3' => 'sly', 'Solyc09g064780.3' => 'sly', 'Sopen01g031980' => 'spe', 'Sopen06g003710' => 'spe', 'Sopen09g026460' => 'spe', 'Sp3g21240' => 'spa', 'Sp4g30030' => 'spa', 'TAR365G0022' => 'tar', 'TAR365G1023' => 'tar', 'TAR365G1253' => 'tar', 'TAR623G0078' => 'tar', 'TAR623G1721' => 'tar', 'TAR633G0959' => 'tar', 'THA.LOC104802225' => 'tha', 'THA.LOC104804769' => 'tha', 'THA.LOC104808660' => 'tha', 'THA.LOC104812792' => 'tha', 'Thecc.01G284000' => 'tca', 'Thecc.04G220600' => 'tca', 'Thecc.05G268900' => 'tca', 'Thecc.08G171100' => 'tca', 'Thhalv10001284m.g' => 'esa', 'Thhalv10019912m.g' => 'esa', 'TPR.G14189' => 'tpr', 'TPR.G18110' => 'tpr', 'TPR.G18130' => 'tpr', 'TPR.G18131' => 'tpr', 'TPR.G18140' => 'tpr', 'TPR.G24282' => 'tpr', 'TPR.G25221' => 'tpr', 'TPR.G29267' => 'tpr', 'TPR.G35315' => 'tpr', 'TPR.G36173' => 'tpr', 'TWI09G0794' => 'twi', 'TWI59G1348' => 'twi', 'TWI74G0430' => 'twi', 'unitig_26.g8940' => 'ugi', 'unitig_749.g13744' => 'ugi', 'unitig_749.g13745' => 'ugi', 'vmacro08269' => 'vma', 'vmacro14937' => 'vma', 'vmacro20401' => 'vma', 'VMungo0464G1349' => 'vmu', 'VMungo0540G0289' => 'vmu', 'VMungo1215G1590' => 'vmu', 'VMungo1309G0221' => 'vmu', 'VMungo1309G2815' => 'vmu', 'VMungo1383G0239' => 'vmu', 'VMungo1383G2910' => 'vmu', 'Zm00001eb095270' => 'zma', 'Zm00001eb095280' => 'zma', 'Zm00001eb111630' => 'zma', 'Zm00001eb237080' => 'zma', 'Zm00001eb273740' => 'zma', 'Zm00001eb285040' => 'zma', 'Zm00001eb330790' => 'zma', 'Zm00001eb337380' => 'zma' ), 'gf_id' => 'HOM05D001484', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001484' ), 'data_identifier' => 'HOM05D001484', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001484', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p31500' => 'bna', 'A05p00020' => 'bna', 'A07p08820' => 'bna', 'Aa31LG4G3300' => 'aar', 'Aa31LG8G10030' => 'aar', 'Actinidia00731' => 'ach', 'Actinidia11473' => 'ach', 'Actinidia23469' => 'ach', 'Actinidia24318' => 'ach', 'Actinidia40196' => 'ach', 'Actinidia40197' => 'ach', 'Actinidia40198' => 'ach', 'Ah.08g212990' => 'amhyb', 'Ah.15g091720' => 'amhyb', 'AL3G38260' => 'aly', 'AL4G47710' => 'aly', 'Aqoxy2G00671' => 'aox', 'Aqoxy2G03236' => 'aox', 'arahy.Tifrunner.gnm1.ann1.05IDCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KR684' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATY3SJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK6QJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6APGL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IDT7Z9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM073U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ0R87' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LE7RV4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT4QRX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V5ENPK' => 'arhy', 'AT2G48110' => 'ath', 'AT3G23590' => 'ath', 'ATR0626G186' => 'atr', 'ATR1127G141' => 'atr', 'Atru.chr4.2583' => 'acertr', 'Atru.chr5.1358' => 'acertr', 'Atru.chr5.1359' => 'acertr', 'Atru.chr8.46' => 'acertr', 'AUR62002640' => 'cqu', 'AUR62030055' => 'cqu', 'AUR62033713' => 'cqu', 'AUR62033714' => 'cqu', 'AUR62036795' => 'cqu', 'AUR62039891' => 'cqu', 'BcaB02g08737' => 'bca', 'BcaB04g20441' => 'bca', 'BcaB06g26509' => 'bca', 'BcaB06g26510' => 'bca', 'BcaB06g26511' => 'bca', 'BcaB06g26512' => 'bca', 'BcaB06g26513' => 'bca', 'BcaC02g12564' => 'bca', 'BcaC02g12565' => 'bca', 'BcaC02g12794' => 'bca', 'BcaC02g12795' => 'bca', 'BcaC02g12796' => 'bca', 'BcaC06g35541' => 'bca', 'BNapus_Darmor_BZH_scaffold_188p00080' => 'bna', 'BNapus_Darmor_BZH_scaffold_188p00090' => 'bna', 'BolC1t03972H' => 'bol', 'BolC1t03973H' => 'bol', 'BolC4t21680H' => 'bol', 'BolC7t41863H' => 'bol', 'BolSC55t61227H' => 'bol', 'BolSC55t61228H' => 'bol', 'BraA01t03278Z' => 'bra', 'BraA05t18998Z' => 'bra', 'BraA07t28673Z' => 'bra', 'C01p40150' => 'bna', 'C05p12370' => 'bna', 'C07p13680' => 'bna', 'CAN.G1006.16' => 'can', 'CAN.G1006.17' => 'can', 'CAN.G1170.2' => 'can', 'CAN.G962.7' => 'can', 'CANSAT25G2179' => 'cansat', 'CANSAT78G1573' => 'cansat', 'CARHR099510' => 'chi', 'CARHR143510' => 'chi', 'Carub.0003s2380' => 'cru', 'Carub.0004s3082' => 'cru', 'Ca_00614_v3' => 'car', 'Ca_07801_v3' => 'car', 'Ca_08567_v3' => 'car', 'Ca_09571_v3' => 'car', 'CBR_g19290' => 'cbr', 'Cc01_g19770' => 'ccan', 'Cc03_g03030' => 'ccan', 'CDE07G0968' => 'cde', 'CDE09G1441' => 'cde', 'Cfa006103' => 'cfa', 'Cfa015573' => 'cfa', 'Cfa016988' => 'cfa', 'Ciclev10006738m.g' => 'ccl', 'Ciclev10010920m.g' => 'ccl', 'Ciclev10018517m.g' => 'ccl', 'CiPaw.01G159200' => 'cil', 'CiPaw.02G091000' => 'cil', 'CiPaw.02G091100' => 'cil', 'CiPaw.08G103100' => 'cil', 'CiPaw.09G224900' => 'cil', 'ClCG06G005740' => 'cla', 'ClCG07G000090' => 'cla', 'ClCG07G000100' => 'cla', 'COL.COLO4_09143' => 'col', 'COL.COLO4_25124' => 'col', 'Cpa.g.sc16.34' => 'cpa', 'Cpa.g.sc3504.1' => 'cpa', 'Cpa.g.sc60.37' => 'cpa', 'CsaV3_6G018520' => 'csa', 'CsaV3_6G036860' => 'csa', 'CSS0001072' => 'camsi', 'CSS0020208' => 'camsi', 'CSS0021253' => 'camsi', 'CSS0022190' => 'camsi', 'CSS0036150' => 'camsi', 'CSS0040442' => 'camsi', 'CSS0042300' => 'camsi', 'CSS0045298' => 'camsi', 'DCAR_012449' => 'dca', 'DCAR_018405' => 'dca', 'DCAR_024573' => 'dca', 'DCAR_030591' => 'dca', 'Dinv16926' => 'din', 'Dinv32963' => 'din', 'Dinv38382' => 'din', 'Dinv38383' => 'din', 'Duzib133G0974' => 'dzi', 'Duzib138G1867' => 'dzi', 'Duzib211G0420' => 'dzi', 'Duzib212G0930' => 'dzi', 'ECA234G1645' => 'eca', 'ECA247G3467' => 'eca', 'ECA248G1703' => 'eca', 'EL10Ac3g06327' => 'bvu', 'EL10Ac7g17204' => 'bvu', 'Eucgr.A00855' => 'egr', 'Eucgr.A00858' => 'egr', 'Eucgr.H01520' => 'egr', 'Eucgr.H03604' => 'egr', 'Eucgr.L03465' => 'egr', 'Eucgr.L03466' => 'egr', 'FAN01G0988' => 'fan', 'FAN02G3892' => 'fan', 'FAN05G3381' => 'fan', 'FAN07G0967' => 'fan', 'FAN07G1493' => 'fan', 'FAN08G3125' => 'fan', 'FAN09G0402' => 'fan', 'FAN12G2594' => 'fan', 'FAN12G3879' => 'fan', 'FAN14G1546' => 'fan', 'FAN15G3626' => 'fan', 'FAN17G0588' => 'fan', 'FAN17G0609' => 'fan', 'FAN18G2817' => 'fan', 'FAN19G1305' => 'fan', 'FAN20G1787' => 'fan', 'FAN22G0073' => 'fan', 'FAN22G0352' => 'fan', 'FAN22G0368' => 'fan', 'FAN22G2273' => 'fan', 'FAN24G1998' => 'fan', 'FAN27G1317' => 'fan', 'FvH4_2g23980' => 'fve', 'FvH4_4g14380' => 'fve', 'FvH4_4g14390' => 'fve', 'FvH4_6g09250' => 'fve', 'Glyma.03G151100' => 'gma', 'Glyma.04G122550' => 'gma', 'Glyma.05G001600' => 'gma', 'Glyma.09G270766' => 'gma', 'Glyma.09G270832' => 'gma', 'Glyma.13G209800' => 'gma', 'Glyma.15G102800' => 'gma', 'Glyma.18G218900' => 'gma', 'Glyma.19G001500' => 'gma', 'Glyma.19G153600' => 'gma', 'Gohir.A02G028600' => 'ghi', 'Gohir.A08G045000' => 'ghi', 'Gohir.A11G120500' => 'ghi', 'Gohir.A12G006200' => 'ghi', 'Gohir.A12G006250' => 'ghi', 'Gohir.D02G036300' => 'ghi', 'Gohir.D08G054700' => 'ghi', 'Gohir.D11G125600' => 'ghi', 'Gohir.D12G005700' => 'ghi', 'Gorai.004G055200' => 'gra', 'Gorai.005G040400' => 'gra', 'Gorai.007G134500' => 'gra', 'Gorai.008G005500' => 'gra', 'GSVIVG01011094001' => 'vvi', 'GSVIVG01017879001' => 'vvi', 'GSVIVG01025988001' => 'vvi', 'GSVIVG01029847001' => 'vvi', 'HanXRQChr10g0282901' => 'han', 'HanXRQChr10g0310371' => 'han', 'HanXRQChr10g0315041' => 'han', 'HanXRQChr11g0327651' => 'han', 'HanXRQChr12g0359391' => 'han', 'Haze_00972' => 'cav', 'Haze_00973' => 'cav', 'Haze_00974' => 'cav', 'Haze_04747' => 'cav', 'Haze_04749' => 'cav', 'Haze_04750' => 'cav', 'Haze_21217' => 'cav', 'Hma1.2p1_1037F.1_g250680' => 'hma', 'Hma1.2p1_1644F.1_g295320' => 'hma', 'HPP92_011322' => 'vpl', 'HPP92_011323' => 'vpl', 'HPP92_011324' => 'vpl', 'HPP92_011325' => 'vpl', 'HPP92_011326' => 'vpl', 'Hund12205' => 'sun', 'Hund17957' => 'sun', 'Lalb_Chr06g0176771' => 'lal', 'Lalb_Chr18g0056021' => 'lal', 'Lalb_Chr18g0056031' => 'lal', 'Lalb_Chr18g0056041' => 'lal', 'Lalb_Chr20g0107751' => 'lal', 'Lalb_Chr20g0118371' => 'lal', 'Lj1g0010239' => 'lja', 'Lj1g0017101' => 'lja', 'Lj2A1178G40' => 'lonja', 'Lj2A54G84' => 'lonja', 'Lj2g0015248' => 'lja', 'Lj3A761T51' => 'lonja', 'Lj6g0018116' => 'lja', 'Lsat_1_v5_gn_4_136040' => 'lsa', 'Lsat_1_v5_gn_5_187461' => 'lsa', 'Lsat_1_v5_gn_5_77001' => 'lsa', 'Lsat_1_v5_gn_9_4461' => 'lsa', 'Manes.01G210100' => 'mes', 'Manes.03G185600' => 'mes', 'Manes.05G073300' => 'mes', 'Manes.09G120300' => 'mes', 'Manes.15G022100' => 'mes', 'Mapoly0096s0053' => 'mpo', 'MBI03_g14058_MAGBIO' => 'mbi', 'MBI03_g33876_MAGBIO' => 'mbi', 'MBI03_g36854_MAGBIO' => 'mbi', 'MBI17_g11997_MAGBIO' => 'mbi', 'MD03G1269000' => 'mdo', 'MD04G1179600' => 'mdo', 'MD11G1289800' => 'mdo', 'MD12G1194700' => 'mdo', 'MD13G1182100' => 'mdo', 'MD13G1182200' => 'mdo', 'MD16G1182600' => 'mdo', 'Medtr2g021400' => 'mtr', 'Medtr2g021470' => 'mtr', 'Medtr2g105810' => 'mtr', 'Medtr3g033580' => 'mtr', 'Medtr6g007970' => 'mtr', 'Medtr7g056330' => 'mtr', 'Medtr7g074290' => 'mtr', 'Medtr7g074380' => 'mtr', 'Medtr7g094550' => 'mtr', 'Medtr8g069995' => 'mtr', 'MELO3C014345.2' => 'cme', 'MELO3C021395.2' => 'cme', 'Migut.D00262' => 'egut', 'Migut.G00257' => 'egut', 'MSTRG.21575' => 'ama', 'MSTRG.3985' => 'ama', 'Nitab4.5_0000295g0140' => 'nta', 'Nitab4.5_0000732g0140' => 'nta', 'Nitab4.5_0003162g0020' => 'nta', 'Nitab4.5_0006180g0090' => 'nta', 'Nitab4.5_0006390g0010' => 'nta', 'Nitab4.5_0007392g0040' => 'nta', 'Nn1g02140' => 'nnu', 'Nn4g26168' => 'nnu', 'Nn5g26754' => 'nnu', 'Oeu001433.1' => 'oeu', 'Oeu010299.2' => 'oeu', 'Oeu011171.1' => 'oeu', 'Oeu037675.1' => 'oeu', 'Oeu038359.1' => 'oeu', 'Oeu063834.1' => 'oeu', 'Oeu063835.1' => 'oeu', 'Os05g0312000' => 'osa', 'Os07g0211101' => 'osa', 'Os07g0211200' => 'osa', 'Os07g0681500' => 'osa', 'Peaxi162Scf00095g01015' => 'pax', 'Peaxi162Scf00104g00329' => 'pax', 'Peaxi162Scf00161g00137' => 'pax', 'PGR004G1665' => 'pgr', 'PGR031G2937' => 'pgr', 'PGR119G2145' => 'pgr', 'PGSC0003DMG400004351' => 'stu', 'PGSC0003DMG400014625' => 'stu', 'PGSC0003DMG401000943' => 'stu', 'Phvul.001G148600' => 'pvu', 'Phvul.004G001700' => 'pvu', 'Phvul.006G154900' => 'pvu', 'Phvul.008G078200' => 'pvu', 'Phvul.011G136500' => 'pvu', 'Potri.002G215600' => 'ptr', 'Potri.008G201600' => 'ptr', 'Potri.014G138400' => 'ptr', 'Potri.016G142500' => 'ptr', 'Pp3c16_10580' => 'ppa', 'Pp3c5_25280' => 'ppa', 'Prupe.1G150000' => 'ppe', 'Prupe.1G150100' => 'ppe', 'Prupe.6G299600' => 'ppe', 'Prupe.8G245000' => 'ppe', 'Psat0s4927g0040' => 'psa', 'Psat1g052080' => 'psa', 'Psat1g183800' => 'psa', 'Psat3g113840' => 'psa', 'Psat3g126120' => 'psa', 'Psat3g126160' => 'psa', 'Psat3g158760' => 'psa', 'Psat3g158840' => 'psa', 'PSO170G2858' => 'pso', 'PSO339G0606' => 'pso', 'PSO384G4709' => 'pso', 'PSO407G0334' => 'pso', 'QL04p040276' => 'qlo', 'QL06p005458' => 'qlo', 'QL06p005472' => 'qlo', 'QL07p030546' => 'qlo', 'QL07p031519' => 'qlo', 'QL09p050949' => 'qlo', 'QL09p050966' => 'qlo', 'QL09p051067' => 'qlo', 'QL12p022706' => 'qlo', 'RcHm_v2.0_Chr2g0119601' => 'rch', 'RcHm_v2.0_Chr3g0459591' => 'rch', 'RcHm_v2.0_Chr4g0418521' => 'rch', 'RcHm_v2.0_Chr4g0418531' => 'rch', 'RcHm_v2.0_Chr4g0418541' => 'rch', 'RcHm_v2.0_Chr6g0291641' => 'rch', 'Rhsim01G0086300' => 'rsi', 'Rhsim01G0276300' => 'rsi', 'Rhsim01G0276500' => 'rsi', 'Rhsim04G0207700' => 'rsi', 'Rhsim05G0234500' => 'rsi', 'Rhsim13G0022400' => 'rsi', 'Sabra02G0167900' => 'sbr', 'Sabra04G0158500' => 'sbr', 'Sabra08G0159800' => 'sbr', 'Sabra10G0011500' => 'sbr', 'Sabra14G0104400' => 'sbr', 'SalBow2G2440' => 'sbo', 'SalBow4G2265' => 'sbo', 'Sc02g0000060' => 'sci', 'Sc05g0005020' => 'sci', 'Sc13g0003890' => 'sci', 'Sed0014865' => 'sed', 'Sed0017224' => 'sed', 'Sed0026391' => 'sed', 'SEGI_00063' => 'sgi', 'SEGI_10967' => 'sgi', 'SEGI_17510' => 'sgi', 'SEGI_24396' => 'sgi', 'SEGI_39719' => 'sgi', 'SEGI_41392' => 'sgi', 'SGA_v2.0_scaffold11G05794' => 'sas', 'SGA_v2.0_scaffold142G35607' => 'sas', 'SGA_v2.0_scaffold1G00447' => 'sas', 'SHI15388' => 'shi', 'SHI15394' => 'shi', 'SHI15396' => 'shi', 'SHI15399' => 'shi', 'SMO343G0151' => 'smo', 'SMO367G1118' => 'smo', 'Solyc01g080200.3' => 'sly', 'Solyc06g008960.3' => 'sly', 'Solyc09g064780.3' => 'sly', 'Sopen01g031980' => 'spe', 'Sopen06g003710' => 'spe', 'Sopen09g026460' => 'spe', 'Sp3g21240' => 'spa', 'Sp4g30030' => 'spa', 'TAR365G0022' => 'tar', 'TAR365G1023' => 'tar', 'TAR365G1253' => 'tar', 'TAR623G0078' => 'tar', 'TAR623G1721' => 'tar', 'TAR633G0959' => 'tar', 'THA.LOC104802225' => 'tha', 'THA.LOC104804769' => 'tha', 'THA.LOC104808660' => 'tha', 'THA.LOC104812792' => 'tha', 'Thecc.01G284000' => 'tca', 'Thecc.04G220600' => 'tca', 'Thecc.05G268900' => 'tca', 'Thecc.08G171100' => 'tca', 'Thhalv10001284m.g' => 'esa', 'Thhalv10019912m.g' => 'esa', 'TPR.G14189' => 'tpr', 'TPR.G18110' => 'tpr', 'TPR.G18130' => 'tpr', 'TPR.G18131' => 'tpr', 'TPR.G18140' => 'tpr', 'TPR.G24282' => 'tpr', 'TPR.G25221' => 'tpr', 'TPR.G29267' => 'tpr', 'TPR.G35315' => 'tpr', 'TPR.G36173' => 'tpr', 'TWI09G0794' => 'twi', 'TWI59G1348' => 'twi', 'TWI74G0430' => 'twi', 'unitig_26.g8940' => 'ugi', 'unitig_749.g13744' => 'ugi', 'unitig_749.g13745' => 'ugi', 'vmacro08269' => 'vma', 'vmacro14937' => 'vma', 'vmacro20401' => 'vma', 'VMungo0464G1349' => 'vmu', 'VMungo0540G0289' => 'vmu', 'VMungo1215G1590' => 'vmu', 'VMungo1309G0221' => 'vmu', 'VMungo1309G2815' => 'vmu', 'VMungo1383G0239' => 'vmu', 'VMungo1383G2910' => 'vmu', 'Zm00001eb095270' => 'zma', 'Zm00001eb095280' => 'zma', 'Zm00001eb111630' => 'zma', 'Zm00001eb237080' => 'zma', 'Zm00001eb273740' => 'zma', 'Zm00001eb285040' => 'zma', 'Zm00001eb330790' => 'zma', 'Zm00001eb337380' => 'zma' ) $gf_id = 'HOM05D001484' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001484' ) $data_identifier = 'HOM05D001484' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 2, 'aly' => (int) 2, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 22, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 7, 'hma' => (int) 2, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 7, 'mtr' => (int) 10, 'cme' => (int) 2, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 4, 'ppa' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 4, 'qlo' => (int) 9, 'rch' => (int) 6, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 10, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 7, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb337380' $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' => 'HOM05D001484', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p31500' => 'bna', 'A05p00020' => 'bna', 'A07p08820' => 'bna', 'Aa31LG4G3300' => 'aar', 'Aa31LG8G10030' => 'aar', 'Actinidia00731' => 'ach', 'Actinidia11473' => 'ach', 'Actinidia23469' => 'ach', 'Actinidia24318' => 'ach', 'Actinidia40196' => 'ach', 'Actinidia40197' => 'ach', 'Actinidia40198' => 'ach', 'Ah.08g212990' => 'amhyb', 'Ah.15g091720' => 'amhyb', 'AL3G38260' => 'aly', 'AL4G47710' => 'aly', 'Aqoxy2G00671' => 'aox', 'Aqoxy2G03236' => 'aox', 'arahy.Tifrunner.gnm1.ann1.05IDCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KR684' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATY3SJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK6QJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6APGL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IDT7Z9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM073U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ0R87' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LE7RV4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT4QRX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V5ENPK' => 'arhy', 'AT2G48110' => 'ath', 'AT3G23590' => 'ath', 'ATR0626G186' => 'atr', 'ATR1127G141' => 'atr', 'Atru.chr4.2583' => 'acertr', 'Atru.chr5.1358' => 'acertr', 'Atru.chr5.1359' => 'acertr', 'Atru.chr8.46' => 'acertr', 'AUR62002640' => 'cqu', 'AUR62030055' => 'cqu', 'AUR62033713' => 'cqu', 'AUR62033714' => 'cqu', 'AUR62036795' => 'cqu', 'AUR62039891' => 'cqu', 'BcaB02g08737' => 'bca', 'BcaB04g20441' => 'bca', 'BcaB06g26509' => 'bca', 'BcaB06g26510' => 'bca', 'BcaB06g26511' => 'bca', 'BcaB06g26512' => 'bca', 'BcaB06g26513' => 'bca', 'BcaC02g12564' => 'bca', 'BcaC02g12565' => 'bca', 'BcaC02g12794' => 'bca', 'BcaC02g12795' => 'bca', 'BcaC02g12796' => 'bca', 'BcaC06g35541' => 'bca', 'BNapus_Darmor_BZH_scaffold_188p00080' => 'bna', 'BNapus_Darmor_BZH_scaffold_188p00090' => 'bna', 'BolC1t03972H' => 'bol', 'BolC1t03973H' => 'bol', 'BolC4t21680H' => 'bol', 'BolC7t41863H' => 'bol', 'BolSC55t61227H' => 'bol', 'BolSC55t61228H' => 'bol', 'BraA01t03278Z' => 'bra', 'BraA05t18998Z' => 'bra', 'BraA07t28673Z' => 'bra', 'C01p40150' => 'bna', 'C05p12370' => 'bna', 'C07p13680' => 'bna', 'CAN.G1006.16' => 'can', 'CAN.G1006.17' => 'can', 'CAN.G1170.2' => 'can', 'CAN.G962.7' => 'can', 'CANSAT25G2179' => 'cansat', 'CANSAT78G1573' => 'cansat', 'CARHR099510' => 'chi', 'CARHR143510' => 'chi', 'Carub.0003s2380' => 'cru', 'Carub.0004s3082' => 'cru', 'Ca_00614_v3' => 'car', 'Ca_07801_v3' => 'car', 'Ca_08567_v3' => 'car', 'Ca_09571_v3' => 'car', 'CBR_g19290' => 'cbr', 'Cc01_g19770' => 'ccan', 'Cc03_g03030' => 'ccan', 'CDE07G0968' => 'cde', 'CDE09G1441' => 'cde', 'Cfa006103' => 'cfa', 'Cfa015573' => 'cfa', 'Cfa016988' => 'cfa', 'Ciclev10006738m.g' => 'ccl', 'Ciclev10010920m.g' => 'ccl', 'Ciclev10018517m.g' => 'ccl', 'CiPaw.01G159200' => 'cil', 'CiPaw.02G091000' => 'cil', 'CiPaw.02G091100' => 'cil', 'CiPaw.08G103100' => 'cil', 'CiPaw.09G224900' => 'cil', 'ClCG06G005740' => 'cla', 'ClCG07G000090' => 'cla', 'ClCG07G000100' => 'cla', 'COL.COLO4_09143' => 'col', 'COL.COLO4_25124' => 'col', 'Cpa.g.sc16.34' => 'cpa', 'Cpa.g.sc3504.1' => 'cpa', 'Cpa.g.sc60.37' => 'cpa', 'CsaV3_6G018520' => 'csa', 'CsaV3_6G036860' => 'csa', 'CSS0001072' => 'camsi', 'CSS0020208' => 'camsi', 'CSS0021253' => 'camsi', 'CSS0022190' => 'camsi', 'CSS0036150' => 'camsi', 'CSS0040442' => 'camsi', 'CSS0042300' => 'camsi', 'CSS0045298' => 'camsi', 'DCAR_012449' => 'dca', 'DCAR_018405' => 'dca', 'DCAR_024573' => 'dca', 'DCAR_030591' => 'dca', 'Dinv16926' => 'din', 'Dinv32963' => 'din', 'Dinv38382' => 'din', 'Dinv38383' => 'din', 'Duzib133G0974' => 'dzi', 'Duzib138G1867' => 'dzi', 'Duzib211G0420' => 'dzi', 'Duzib212G0930' => 'dzi', 'ECA234G1645' => 'eca', 'ECA247G3467' => 'eca', 'ECA248G1703' => 'eca', 'EL10Ac3g06327' => 'bvu', 'EL10Ac7g17204' => 'bvu', 'Eucgr.A00855' => 'egr', 'Eucgr.A00858' => 'egr', 'Eucgr.H01520' => 'egr', 'Eucgr.H03604' => 'egr', 'Eucgr.L03465' => 'egr', 'Eucgr.L03466' => 'egr', 'FAN01G0988' => 'fan', 'FAN02G3892' => 'fan', 'FAN05G3381' => 'fan', 'FAN07G0967' => 'fan', 'FAN07G1493' => 'fan', 'FAN08G3125' => 'fan', 'FAN09G0402' => 'fan', 'FAN12G2594' => 'fan', 'FAN12G3879' => 'fan', 'FAN14G1546' => 'fan', 'FAN15G3626' => 'fan', 'FAN17G0588' => 'fan', 'FAN17G0609' => 'fan', 'FAN18G2817' => 'fan', 'FAN19G1305' => 'fan', 'FAN20G1787' => 'fan', 'FAN22G0073' => 'fan', 'FAN22G0352' => 'fan', 'FAN22G0368' => 'fan', 'FAN22G2273' => 'fan', 'FAN24G1998' => 'fan', 'FAN27G1317' => 'fan', 'FvH4_2g23980' => 'fve', 'FvH4_4g14380' => 'fve', 'FvH4_4g14390' => 'fve', 'FvH4_6g09250' => 'fve', 'Glyma.03G151100' => 'gma', 'Glyma.04G122550' => 'gma', 'Glyma.05G001600' => 'gma', 'Glyma.09G270766' => 'gma', 'Glyma.09G270832' => 'gma', 'Glyma.13G209800' => 'gma', 'Glyma.15G102800' => 'gma', 'Glyma.18G218900' => 'gma', 'Glyma.19G001500' => 'gma', 'Glyma.19G153600' => 'gma', 'Gohir.A02G028600' => 'ghi', 'Gohir.A08G045000' => 'ghi', 'Gohir.A11G120500' => 'ghi', 'Gohir.A12G006200' => 'ghi', 'Gohir.A12G006250' => 'ghi', 'Gohir.D02G036300' => 'ghi', 'Gohir.D08G054700' => 'ghi', 'Gohir.D11G125600' => 'ghi', 'Gohir.D12G005700' => 'ghi', 'Gorai.004G055200' => 'gra', 'Gorai.005G040400' => 'gra', 'Gorai.007G134500' => 'gra', 'Gorai.008G005500' => 'gra', 'GSVIVG01011094001' => 'vvi', 'GSVIVG01017879001' => 'vvi', 'GSVIVG01025988001' => 'vvi', 'GSVIVG01029847001' => 'vvi', 'HanXRQChr10g0282901' => 'han', 'HanXRQChr10g0310371' => 'han', 'HanXRQChr10g0315041' => 'han', 'HanXRQChr11g0327651' => 'han', 'HanXRQChr12g0359391' => 'han', 'Haze_00972' => 'cav', 'Haze_00973' => 'cav', 'Haze_00974' => 'cav', 'Haze_04747' => 'cav', 'Haze_04749' => 'cav', 'Haze_04750' => 'cav', 'Haze_21217' => 'cav', 'Hma1.2p1_1037F.1_g250680' => 'hma', 'Hma1.2p1_1644F.1_g295320' => 'hma', 'HPP92_011322' => 'vpl', 'HPP92_011323' => 'vpl', 'HPP92_011324' => 'vpl', 'HPP92_011325' => 'vpl', 'HPP92_011326' => 'vpl', 'Hund12205' => 'sun', 'Hund17957' => 'sun', 'Lalb_Chr06g0176771' => 'lal', 'Lalb_Chr18g0056021' => 'lal', 'Lalb_Chr18g0056031' => 'lal', 'Lalb_Chr18g0056041' => 'lal', 'Lalb_Chr20g0107751' => 'lal', 'Lalb_Chr20g0118371' => 'lal', 'Lj1g0010239' => 'lja', 'Lj1g0017101' => 'lja', 'Lj2A1178G40' => 'lonja', 'Lj2A54G84' => 'lonja', 'Lj2g0015248' => 'lja', 'Lj3A761T51' => 'lonja', 'Lj6g0018116' => 'lja', 'Lsat_1_v5_gn_4_136040' => 'lsa', 'Lsat_1_v5_gn_5_187461' => 'lsa', 'Lsat_1_v5_gn_5_77001' => 'lsa', 'Lsat_1_v5_gn_9_4461' => 'lsa', 'Manes.01G210100' => 'mes', 'Manes.03G185600' => 'mes', 'Manes.05G073300' => 'mes', 'Manes.09G120300' => 'mes', 'Manes.15G022100' => 'mes', 'Mapoly0096s0053' => 'mpo', 'MBI03_g14058_MAGBIO' => 'mbi', 'MBI03_g33876_MAGBIO' => 'mbi', 'MBI03_g36854_MAGBIO' => 'mbi', 'MBI17_g11997_MAGBIO' => 'mbi', 'MD03G1269000' => 'mdo', 'MD04G1179600' => 'mdo', 'MD11G1289800' => 'mdo', 'MD12G1194700' => 'mdo', 'MD13G1182100' => 'mdo', 'MD13G1182200' => 'mdo', 'MD16G1182600' => 'mdo', 'Medtr2g021400' => 'mtr', 'Medtr2g021470' => 'mtr', 'Medtr2g105810' => 'mtr', 'Medtr3g033580' => 'mtr', 'Medtr6g007970' => 'mtr', 'Medtr7g056330' => 'mtr', 'Medtr7g074290' => 'mtr', 'Medtr7g074380' => 'mtr', 'Medtr7g094550' => 'mtr', 'Medtr8g069995' => 'mtr', 'MELO3C014345.2' => 'cme', 'MELO3C021395.2' => 'cme', 'Migut.D00262' => 'egut', 'Migut.G00257' => 'egut', 'MSTRG.21575' => 'ama', 'MSTRG.3985' => 'ama', 'Nitab4.5_0000295g0140' => 'nta', 'Nitab4.5_0000732g0140' => 'nta', 'Nitab4.5_0003162g0020' => 'nta', 'Nitab4.5_0006180g0090' => 'nta', 'Nitab4.5_0006390g0010' => 'nta', 'Nitab4.5_0007392g0040' => 'nta', 'Nn1g02140' => 'nnu', 'Nn4g26168' => 'nnu', 'Nn5g26754' => 'nnu', 'Oeu001433.1' => 'oeu', 'Oeu010299.2' => 'oeu', 'Oeu011171.1' => 'oeu', 'Oeu037675.1' => 'oeu', 'Oeu038359.1' => 'oeu', 'Oeu063834.1' => 'oeu', 'Oeu063835.1' => 'oeu', 'Os05g0312000' => 'osa', 'Os07g0211101' => 'osa', 'Os07g0211200' => 'osa', 'Os07g0681500' => 'osa', 'Peaxi162Scf00095g01015' => 'pax', 'Peaxi162Scf00104g00329' => 'pax', 'Peaxi162Scf00161g00137' => 'pax', 'PGR004G1665' => 'pgr', 'PGR031G2937' => 'pgr', 'PGR119G2145' => 'pgr', 'PGSC0003DMG400004351' => 'stu', 'PGSC0003DMG400014625' => 'stu', 'PGSC0003DMG401000943' => 'stu', 'Phvul.001G148600' => 'pvu', 'Phvul.004G001700' => 'pvu', 'Phvul.006G154900' => 'pvu', 'Phvul.008G078200' => 'pvu', 'Phvul.011G136500' => 'pvu', 'Potri.002G215600' => 'ptr', 'Potri.008G201600' => 'ptr', 'Potri.014G138400' => 'ptr', 'Potri.016G142500' => 'ptr', 'Pp3c16_10580' => 'ppa', 'Pp3c5_25280' => 'ppa', 'Prupe.1G150000' => 'ppe', 'Prupe.1G150100' => 'ppe', 'Prupe.6G299600' => 'ppe', 'Prupe.8G245000' => 'ppe', 'Psat0s4927g0040' => 'psa', 'Psat1g052080' => 'psa', 'Psat1g183800' => 'psa', 'Psat3g113840' => 'psa', 'Psat3g126120' => 'psa', 'Psat3g126160' => 'psa', 'Psat3g158760' => 'psa', 'Psat3g158840' => 'psa', 'PSO170G2858' => 'pso', 'PSO339G0606' => 'pso', 'PSO384G4709' => 'pso', 'PSO407G0334' => 'pso', 'QL04p040276' => 'qlo', 'QL06p005458' => 'qlo', 'QL06p005472' => 'qlo', 'QL07p030546' => 'qlo', 'QL07p031519' => 'qlo', 'QL09p050949' => 'qlo', 'QL09p050966' => 'qlo', 'QL09p051067' => 'qlo', 'QL12p022706' => 'qlo', 'RcHm_v2.0_Chr2g0119601' => 'rch', 'RcHm_v2.0_Chr3g0459591' => 'rch', 'RcHm_v2.0_Chr4g0418521' => 'rch', 'RcHm_v2.0_Chr4g0418531' => 'rch', 'RcHm_v2.0_Chr4g0418541' => 'rch', 'RcHm_v2.0_Chr6g0291641' => 'rch', 'Rhsim01G0086300' => 'rsi', 'Rhsim01G0276300' => 'rsi', 'Rhsim01G0276500' => 'rsi', 'Rhsim04G0207700' => 'rsi', 'Rhsim05G0234500' => 'rsi', 'Rhsim13G0022400' => 'rsi', 'Sabra02G0167900' => 'sbr', 'Sabra04G0158500' => 'sbr', 'Sabra08G0159800' => 'sbr', 'Sabra10G0011500' => 'sbr', 'Sabra14G0104400' => 'sbr', 'SalBow2G2440' => 'sbo', 'SalBow4G2265' => 'sbo', 'Sc02g0000060' => 'sci', 'Sc05g0005020' => 'sci', 'Sc13g0003890' => 'sci', 'Sed0014865' => 'sed', 'Sed0017224' => 'sed', 'Sed0026391' => 'sed', 'SEGI_00063' => 'sgi', 'SEGI_10967' => 'sgi', 'SEGI_17510' => 'sgi', 'SEGI_24396' => 'sgi', 'SEGI_39719' => 'sgi', 'SEGI_41392' => 'sgi', 'SGA_v2.0_scaffold11G05794' => 'sas', 'SGA_v2.0_scaffold142G35607' => 'sas', 'SGA_v2.0_scaffold1G00447' => 'sas', 'SHI15388' => 'shi', 'SHI15394' => 'shi', 'SHI15396' => 'shi', 'SHI15399' => 'shi', 'SMO343G0151' => 'smo', 'SMO367G1118' => 'smo', 'Solyc01g080200.3' => 'sly', 'Solyc06g008960.3' => 'sly', 'Solyc09g064780.3' => 'sly', 'Sopen01g031980' => 'spe', 'Sopen06g003710' => 'spe', 'Sopen09g026460' => 'spe', 'Sp3g21240' => 'spa', 'Sp4g30030' => 'spa', 'TAR365G0022' => 'tar', 'TAR365G1023' => 'tar', 'TAR365G1253' => 'tar', 'TAR623G0078' => 'tar', 'TAR623G1721' => 'tar', 'TAR633G0959' => 'tar', 'THA.LOC104802225' => 'tha', 'THA.LOC104804769' => 'tha', 'THA.LOC104808660' => 'tha', 'THA.LOC104812792' => 'tha', 'Thecc.01G284000' => 'tca', 'Thecc.04G220600' => 'tca', 'Thecc.05G268900' => 'tca', 'Thecc.08G171100' => 'tca', 'Thhalv10001284m.g' => 'esa', 'Thhalv10019912m.g' => 'esa', 'TPR.G14189' => 'tpr', 'TPR.G18110' => 'tpr', 'TPR.G18130' => 'tpr', 'TPR.G18131' => 'tpr', 'TPR.G18140' => 'tpr', 'TPR.G24282' => 'tpr', 'TPR.G25221' => 'tpr', 'TPR.G29267' => 'tpr', 'TPR.G35315' => 'tpr', 'TPR.G36173' => 'tpr', 'TWI09G0794' => 'twi', 'TWI59G1348' => 'twi', 'TWI74G0430' => 'twi', 'unitig_26.g8940' => 'ugi', 'unitig_749.g13744' => 'ugi', 'unitig_749.g13745' => 'ugi', 'vmacro08269' => 'vma', 'vmacro14937' => 'vma', 'vmacro20401' => 'vma', 'VMungo0464G1349' => 'vmu', 'VMungo0540G0289' => 'vmu', 'VMungo1215G1590' => 'vmu', 'VMungo1309G0221' => 'vmu', 'VMungo1309G2815' => 'vmu', 'VMungo1383G0239' => 'vmu', 'VMungo1383G2910' => 'vmu', 'Zm00001eb095270' => 'zma', 'Zm00001eb095280' => 'zma', 'Zm00001eb111630' => 'zma', 'Zm00001eb237080' => 'zma', 'Zm00001eb273740' => 'zma', 'Zm00001eb285040' => 'zma', 'Zm00001eb330790' => 'zma', 'Zm00001eb337380' => 'zma' ), 'gf_id' => 'HOM05D001484', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001484' ), 'data_identifier' => 'HOM05D001484', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001484', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p31500' => 'bna', 'A05p00020' => 'bna', 'A07p08820' => 'bna', 'Aa31LG4G3300' => 'aar', 'Aa31LG8G10030' => 'aar', 'Actinidia00731' => 'ach', 'Actinidia11473' => 'ach', 'Actinidia23469' => 'ach', 'Actinidia24318' => 'ach', 'Actinidia40196' => 'ach', 'Actinidia40197' => 'ach', 'Actinidia40198' => 'ach', 'Ah.08g212990' => 'amhyb', 'Ah.15g091720' => 'amhyb', 'AL3G38260' => 'aly', 'AL4G47710' => 'aly', 'Aqoxy2G00671' => 'aox', 'Aqoxy2G03236' => 'aox', 'arahy.Tifrunner.gnm1.ann1.05IDCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KR684' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATY3SJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK6QJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6APGL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IDT7Z9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM073U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ0R87' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LE7RV4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT4QRX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V5ENPK' => 'arhy', 'AT2G48110' => 'ath', 'AT3G23590' => 'ath', 'ATR0626G186' => 'atr', 'ATR1127G141' => 'atr', 'Atru.chr4.2583' => 'acertr', 'Atru.chr5.1358' => 'acertr', 'Atru.chr5.1359' => 'acertr', 'Atru.chr8.46' => 'acertr', 'AUR62002640' => 'cqu', 'AUR62030055' => 'cqu', 'AUR62033713' => 'cqu', 'AUR62033714' => 'cqu', 'AUR62036795' => 'cqu', 'AUR62039891' => 'cqu', 'BcaB02g08737' => 'bca', 'BcaB04g20441' => 'bca', 'BcaB06g26509' => 'bca', 'BcaB06g26510' => 'bca', 'BcaB06g26511' => 'bca', 'BcaB06g26512' => 'bca', 'BcaB06g26513' => 'bca', 'BcaC02g12564' => 'bca', 'BcaC02g12565' => 'bca', 'BcaC02g12794' => 'bca', 'BcaC02g12795' => 'bca', 'BcaC02g12796' => 'bca', 'BcaC06g35541' => 'bca', 'BNapus_Darmor_BZH_scaffold_188p00080' => 'bna', 'BNapus_Darmor_BZH_scaffold_188p00090' => 'bna', 'BolC1t03972H' => 'bol', 'BolC1t03973H' => 'bol', 'BolC4t21680H' => 'bol', 'BolC7t41863H' => 'bol', 'BolSC55t61227H' => 'bol', 'BolSC55t61228H' => 'bol', 'BraA01t03278Z' => 'bra', 'BraA05t18998Z' => 'bra', 'BraA07t28673Z' => 'bra', 'C01p40150' => 'bna', 'C05p12370' => 'bna', 'C07p13680' => 'bna', 'CAN.G1006.16' => 'can', 'CAN.G1006.17' => 'can', 'CAN.G1170.2' => 'can', 'CAN.G962.7' => 'can', 'CANSAT25G2179' => 'cansat', 'CANSAT78G1573' => 'cansat', 'CARHR099510' => 'chi', 'CARHR143510' => 'chi', 'Carub.0003s2380' => 'cru', 'Carub.0004s3082' => 'cru', 'Ca_00614_v3' => 'car', 'Ca_07801_v3' => 'car', 'Ca_08567_v3' => 'car', 'Ca_09571_v3' => 'car', 'CBR_g19290' => 'cbr', 'Cc01_g19770' => 'ccan', 'Cc03_g03030' => 'ccan', 'CDE07G0968' => 'cde', 'CDE09G1441' => 'cde', 'Cfa006103' => 'cfa', 'Cfa015573' => 'cfa', 'Cfa016988' => 'cfa', 'Ciclev10006738m.g' => 'ccl', 'Ciclev10010920m.g' => 'ccl', 'Ciclev10018517m.g' => 'ccl', 'CiPaw.01G159200' => 'cil', 'CiPaw.02G091000' => 'cil', 'CiPaw.02G091100' => 'cil', 'CiPaw.08G103100' => 'cil', 'CiPaw.09G224900' => 'cil', 'ClCG06G005740' => 'cla', 'ClCG07G000090' => 'cla', 'ClCG07G000100' => 'cla', 'COL.COLO4_09143' => 'col', 'COL.COLO4_25124' => 'col', 'Cpa.g.sc16.34' => 'cpa', 'Cpa.g.sc3504.1' => 'cpa', 'Cpa.g.sc60.37' => 'cpa', 'CsaV3_6G018520' => 'csa', 'CsaV3_6G036860' => 'csa', 'CSS0001072' => 'camsi', 'CSS0020208' => 'camsi', 'CSS0021253' => 'camsi', 'CSS0022190' => 'camsi', 'CSS0036150' => 'camsi', 'CSS0040442' => 'camsi', 'CSS0042300' => 'camsi', 'CSS0045298' => 'camsi', 'DCAR_012449' => 'dca', 'DCAR_018405' => 'dca', 'DCAR_024573' => 'dca', 'DCAR_030591' => 'dca', 'Dinv16926' => 'din', 'Dinv32963' => 'din', 'Dinv38382' => 'din', 'Dinv38383' => 'din', 'Duzib133G0974' => 'dzi', 'Duzib138G1867' => 'dzi', 'Duzib211G0420' => 'dzi', 'Duzib212G0930' => 'dzi', 'ECA234G1645' => 'eca', 'ECA247G3467' => 'eca', 'ECA248G1703' => 'eca', 'EL10Ac3g06327' => 'bvu', 'EL10Ac7g17204' => 'bvu', 'Eucgr.A00855' => 'egr', 'Eucgr.A00858' => 'egr', 'Eucgr.H01520' => 'egr', 'Eucgr.H03604' => 'egr', 'Eucgr.L03465' => 'egr', 'Eucgr.L03466' => 'egr', 'FAN01G0988' => 'fan', 'FAN02G3892' => 'fan', 'FAN05G3381' => 'fan', 'FAN07G0967' => 'fan', 'FAN07G1493' => 'fan', 'FAN08G3125' => 'fan', 'FAN09G0402' => 'fan', 'FAN12G2594' => 'fan', 'FAN12G3879' => 'fan', 'FAN14G1546' => 'fan', 'FAN15G3626' => 'fan', 'FAN17G0588' => 'fan', 'FAN17G0609' => 'fan', 'FAN18G2817' => 'fan', 'FAN19G1305' => 'fan', 'FAN20G1787' => 'fan', 'FAN22G0073' => 'fan', 'FAN22G0352' => 'fan', 'FAN22G0368' => 'fan', 'FAN22G2273' => 'fan', 'FAN24G1998' => 'fan', 'FAN27G1317' => 'fan', 'FvH4_2g23980' => 'fve', 'FvH4_4g14380' => 'fve', 'FvH4_4g14390' => 'fve', 'FvH4_6g09250' => 'fve', 'Glyma.03G151100' => 'gma', 'Glyma.04G122550' => 'gma', 'Glyma.05G001600' => 'gma', 'Glyma.09G270766' => 'gma', 'Glyma.09G270832' => 'gma', 'Glyma.13G209800' => 'gma', 'Glyma.15G102800' => 'gma', 'Glyma.18G218900' => 'gma', 'Glyma.19G001500' => 'gma', 'Glyma.19G153600' => 'gma', 'Gohir.A02G028600' => 'ghi', 'Gohir.A08G045000' => 'ghi', 'Gohir.A11G120500' => 'ghi', 'Gohir.A12G006200' => 'ghi', 'Gohir.A12G006250' => 'ghi', 'Gohir.D02G036300' => 'ghi', 'Gohir.D08G054700' => 'ghi', 'Gohir.D11G125600' => 'ghi', 'Gohir.D12G005700' => 'ghi', 'Gorai.004G055200' => 'gra', 'Gorai.005G040400' => 'gra', 'Gorai.007G134500' => 'gra', 'Gorai.008G005500' => 'gra', 'GSVIVG01011094001' => 'vvi', 'GSVIVG01017879001' => 'vvi', 'GSVIVG01025988001' => 'vvi', 'GSVIVG01029847001' => 'vvi', 'HanXRQChr10g0282901' => 'han', 'HanXRQChr10g0310371' => 'han', 'HanXRQChr10g0315041' => 'han', 'HanXRQChr11g0327651' => 'han', 'HanXRQChr12g0359391' => 'han', 'Haze_00972' => 'cav', 'Haze_00973' => 'cav', 'Haze_00974' => 'cav', 'Haze_04747' => 'cav', 'Haze_04749' => 'cav', 'Haze_04750' => 'cav', 'Haze_21217' => 'cav', 'Hma1.2p1_1037F.1_g250680' => 'hma', 'Hma1.2p1_1644F.1_g295320' => 'hma', 'HPP92_011322' => 'vpl', 'HPP92_011323' => 'vpl', 'HPP92_011324' => 'vpl', 'HPP92_011325' => 'vpl', 'HPP92_011326' => 'vpl', 'Hund12205' => 'sun', 'Hund17957' => 'sun', 'Lalb_Chr06g0176771' => 'lal', 'Lalb_Chr18g0056021' => 'lal', 'Lalb_Chr18g0056031' => 'lal', 'Lalb_Chr18g0056041' => 'lal', 'Lalb_Chr20g0107751' => 'lal', 'Lalb_Chr20g0118371' => 'lal', 'Lj1g0010239' => 'lja', 'Lj1g0017101' => 'lja', 'Lj2A1178G40' => 'lonja', 'Lj2A54G84' => 'lonja', 'Lj2g0015248' => 'lja', 'Lj3A761T51' => 'lonja', 'Lj6g0018116' => 'lja', 'Lsat_1_v5_gn_4_136040' => 'lsa', 'Lsat_1_v5_gn_5_187461' => 'lsa', 'Lsat_1_v5_gn_5_77001' => 'lsa', 'Lsat_1_v5_gn_9_4461' => 'lsa', 'Manes.01G210100' => 'mes', 'Manes.03G185600' => 'mes', 'Manes.05G073300' => 'mes', 'Manes.09G120300' => 'mes', 'Manes.15G022100' => 'mes', 'Mapoly0096s0053' => 'mpo', 'MBI03_g14058_MAGBIO' => 'mbi', 'MBI03_g33876_MAGBIO' => 'mbi', 'MBI03_g36854_MAGBIO' => 'mbi', 'MBI17_g11997_MAGBIO' => 'mbi', 'MD03G1269000' => 'mdo', 'MD04G1179600' => 'mdo', 'MD11G1289800' => 'mdo', 'MD12G1194700' => 'mdo', 'MD13G1182100' => 'mdo', 'MD13G1182200' => 'mdo', 'MD16G1182600' => 'mdo', 'Medtr2g021400' => 'mtr', 'Medtr2g021470' => 'mtr', 'Medtr2g105810' => 'mtr', 'Medtr3g033580' => 'mtr', 'Medtr6g007970' => 'mtr', 'Medtr7g056330' => 'mtr', 'Medtr7g074290' => 'mtr', 'Medtr7g074380' => 'mtr', 'Medtr7g094550' => 'mtr', 'Medtr8g069995' => 'mtr', 'MELO3C014345.2' => 'cme', 'MELO3C021395.2' => 'cme', 'Migut.D00262' => 'egut', 'Migut.G00257' => 'egut', 'MSTRG.21575' => 'ama', 'MSTRG.3985' => 'ama', 'Nitab4.5_0000295g0140' => 'nta', 'Nitab4.5_0000732g0140' => 'nta', 'Nitab4.5_0003162g0020' => 'nta', 'Nitab4.5_0006180g0090' => 'nta', 'Nitab4.5_0006390g0010' => 'nta', 'Nitab4.5_0007392g0040' => 'nta', 'Nn1g02140' => 'nnu', 'Nn4g26168' => 'nnu', 'Nn5g26754' => 'nnu', 'Oeu001433.1' => 'oeu', 'Oeu010299.2' => 'oeu', 'Oeu011171.1' => 'oeu', 'Oeu037675.1' => 'oeu', 'Oeu038359.1' => 'oeu', 'Oeu063834.1' => 'oeu', 'Oeu063835.1' => 'oeu', 'Os05g0312000' => 'osa', 'Os07g0211101' => 'osa', 'Os07g0211200' => 'osa', 'Os07g0681500' => 'osa', 'Peaxi162Scf00095g01015' => 'pax', 'Peaxi162Scf00104g00329' => 'pax', 'Peaxi162Scf00161g00137' => 'pax', 'PGR004G1665' => 'pgr', 'PGR031G2937' => 'pgr', 'PGR119G2145' => 'pgr', 'PGSC0003DMG400004351' => 'stu', 'PGSC0003DMG400014625' => 'stu', 'PGSC0003DMG401000943' => 'stu', 'Phvul.001G148600' => 'pvu', 'Phvul.004G001700' => 'pvu', 'Phvul.006G154900' => 'pvu', 'Phvul.008G078200' => 'pvu', 'Phvul.011G136500' => 'pvu', 'Potri.002G215600' => 'ptr', 'Potri.008G201600' => 'ptr', 'Potri.014G138400' => 'ptr', 'Potri.016G142500' => 'ptr', 'Pp3c16_10580' => 'ppa', 'Pp3c5_25280' => 'ppa', 'Prupe.1G150000' => 'ppe', 'Prupe.1G150100' => 'ppe', 'Prupe.6G299600' => 'ppe', 'Prupe.8G245000' => 'ppe', 'Psat0s4927g0040' => 'psa', 'Psat1g052080' => 'psa', 'Psat1g183800' => 'psa', 'Psat3g113840' => 'psa', 'Psat3g126120' => 'psa', 'Psat3g126160' => 'psa', 'Psat3g158760' => 'psa', 'Psat3g158840' => 'psa', 'PSO170G2858' => 'pso', 'PSO339G0606' => 'pso', 'PSO384G4709' => 'pso', 'PSO407G0334' => 'pso', 'QL04p040276' => 'qlo', 'QL06p005458' => 'qlo', 'QL06p005472' => 'qlo', 'QL07p030546' => 'qlo', 'QL07p031519' => 'qlo', 'QL09p050949' => 'qlo', 'QL09p050966' => 'qlo', 'QL09p051067' => 'qlo', 'QL12p022706' => 'qlo', 'RcHm_v2.0_Chr2g0119601' => 'rch', 'RcHm_v2.0_Chr3g0459591' => 'rch', 'RcHm_v2.0_Chr4g0418521' => 'rch', 'RcHm_v2.0_Chr4g0418531' => 'rch', 'RcHm_v2.0_Chr4g0418541' => 'rch', 'RcHm_v2.0_Chr6g0291641' => 'rch', 'Rhsim01G0086300' => 'rsi', 'Rhsim01G0276300' => 'rsi', 'Rhsim01G0276500' => 'rsi', 'Rhsim04G0207700' => 'rsi', 'Rhsim05G0234500' => 'rsi', 'Rhsim13G0022400' => 'rsi', 'Sabra02G0167900' => 'sbr', 'Sabra04G0158500' => 'sbr', 'Sabra08G0159800' => 'sbr', 'Sabra10G0011500' => 'sbr', 'Sabra14G0104400' => 'sbr', 'SalBow2G2440' => 'sbo', 'SalBow4G2265' => 'sbo', 'Sc02g0000060' => 'sci', 'Sc05g0005020' => 'sci', 'Sc13g0003890' => 'sci', 'Sed0014865' => 'sed', 'Sed0017224' => 'sed', 'Sed0026391' => 'sed', 'SEGI_00063' => 'sgi', 'SEGI_10967' => 'sgi', 'SEGI_17510' => 'sgi', 'SEGI_24396' => 'sgi', 'SEGI_39719' => 'sgi', 'SEGI_41392' => 'sgi', 'SGA_v2.0_scaffold11G05794' => 'sas', 'SGA_v2.0_scaffold142G35607' => 'sas', 'SGA_v2.0_scaffold1G00447' => 'sas', 'SHI15388' => 'shi', 'SHI15394' => 'shi', 'SHI15396' => 'shi', 'SHI15399' => 'shi', 'SMO343G0151' => 'smo', 'SMO367G1118' => 'smo', 'Solyc01g080200.3' => 'sly', 'Solyc06g008960.3' => 'sly', 'Solyc09g064780.3' => 'sly', 'Sopen01g031980' => 'spe', 'Sopen06g003710' => 'spe', 'Sopen09g026460' => 'spe', 'Sp3g21240' => 'spa', 'Sp4g30030' => 'spa', 'TAR365G0022' => 'tar', 'TAR365G1023' => 'tar', 'TAR365G1253' => 'tar', 'TAR623G0078' => 'tar', 'TAR623G1721' => 'tar', 'TAR633G0959' => 'tar', 'THA.LOC104802225' => 'tha', 'THA.LOC104804769' => 'tha', 'THA.LOC104808660' => 'tha', 'THA.LOC104812792' => 'tha', 'Thecc.01G284000' => 'tca', 'Thecc.04G220600' => 'tca', 'Thecc.05G268900' => 'tca', 'Thecc.08G171100' => 'tca', 'Thhalv10001284m.g' => 'esa', 'Thhalv10019912m.g' => 'esa', 'TPR.G14189' => 'tpr', 'TPR.G18110' => 'tpr', 'TPR.G18130' => 'tpr', 'TPR.G18131' => 'tpr', 'TPR.G18140' => 'tpr', 'TPR.G24282' => 'tpr', 'TPR.G25221' => 'tpr', 'TPR.G29267' => 'tpr', 'TPR.G35315' => 'tpr', 'TPR.G36173' => 'tpr', 'TWI09G0794' => 'twi', 'TWI59G1348' => 'twi', 'TWI74G0430' => 'twi', 'unitig_26.g8940' => 'ugi', 'unitig_749.g13744' => 'ugi', 'unitig_749.g13745' => 'ugi', 'vmacro08269' => 'vma', 'vmacro14937' => 'vma', 'vmacro20401' => 'vma', 'VMungo0464G1349' => 'vmu', 'VMungo0540G0289' => 'vmu', 'VMungo1215G1590' => 'vmu', 'VMungo1309G0221' => 'vmu', 'VMungo1309G2815' => 'vmu', 'VMungo1383G0239' => 'vmu', 'VMungo1383G2910' => 'vmu', 'Zm00001eb095270' => 'zma', 'Zm00001eb095280' => 'zma', 'Zm00001eb111630' => 'zma', 'Zm00001eb237080' => 'zma', 'Zm00001eb273740' => 'zma', 'Zm00001eb285040' => 'zma', 'Zm00001eb330790' => 'zma', 'Zm00001eb337380' => 'zma' ) $gf_id = 'HOM05D001484' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001484' ) $data_identifier = 'HOM05D001484' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 2, 'aly' => (int) 2, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 22, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 7, 'hma' => (int) 2, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 7, 'mtr' => (int) 10, 'cme' => (int) 2, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 4, 'ppa' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 4, 'qlo' => (int) 9, 'rch' => (int) 6, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 10, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 7, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb337380' $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' => 'HOM05D001484', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p31500' => 'bna', 'A05p00020' => 'bna', 'A07p08820' => 'bna', 'Aa31LG4G3300' => 'aar', 'Aa31LG8G10030' => 'aar', 'Actinidia00731' => 'ach', 'Actinidia11473' => 'ach', 'Actinidia23469' => 'ach', 'Actinidia24318' => 'ach', 'Actinidia40196' => 'ach', 'Actinidia40197' => 'ach', 'Actinidia40198' => 'ach', 'Ah.08g212990' => 'amhyb', 'Ah.15g091720' => 'amhyb', 'AL3G38260' => 'aly', 'AL4G47710' => 'aly', 'Aqoxy2G00671' => 'aox', 'Aqoxy2G03236' => 'aox', 'arahy.Tifrunner.gnm1.ann1.05IDCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KR684' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATY3SJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK6QJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6APGL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IDT7Z9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM073U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ0R87' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LE7RV4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT4QRX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V5ENPK' => 'arhy', 'AT2G48110' => 'ath', 'AT3G23590' => 'ath', 'ATR0626G186' => 'atr', 'ATR1127G141' => 'atr', 'Atru.chr4.2583' => 'acertr', 'Atru.chr5.1358' => 'acertr', 'Atru.chr5.1359' => 'acertr', 'Atru.chr8.46' => 'acertr', 'AUR62002640' => 'cqu', 'AUR62030055' => 'cqu', 'AUR62033713' => 'cqu', 'AUR62033714' => 'cqu', 'AUR62036795' => 'cqu', 'AUR62039891' => 'cqu', 'BcaB02g08737' => 'bca', 'BcaB04g20441' => 'bca', 'BcaB06g26509' => 'bca', 'BcaB06g26510' => 'bca', 'BcaB06g26511' => 'bca', 'BcaB06g26512' => 'bca', 'BcaB06g26513' => 'bca', 'BcaC02g12564' => 'bca', 'BcaC02g12565' => 'bca', 'BcaC02g12794' => 'bca', 'BcaC02g12795' => 'bca', 'BcaC02g12796' => 'bca', 'BcaC06g35541' => 'bca', 'BNapus_Darmor_BZH_scaffold_188p00080' => 'bna', 'BNapus_Darmor_BZH_scaffold_188p00090' => 'bna', 'BolC1t03972H' => 'bol', 'BolC1t03973H' => 'bol', 'BolC4t21680H' => 'bol', 'BolC7t41863H' => 'bol', 'BolSC55t61227H' => 'bol', 'BolSC55t61228H' => 'bol', 'BraA01t03278Z' => 'bra', 'BraA05t18998Z' => 'bra', 'BraA07t28673Z' => 'bra', 'C01p40150' => 'bna', 'C05p12370' => 'bna', 'C07p13680' => 'bna', 'CAN.G1006.16' => 'can', 'CAN.G1006.17' => 'can', 'CAN.G1170.2' => 'can', 'CAN.G962.7' => 'can', 'CANSAT25G2179' => 'cansat', 'CANSAT78G1573' => 'cansat', 'CARHR099510' => 'chi', 'CARHR143510' => 'chi', 'Carub.0003s2380' => 'cru', 'Carub.0004s3082' => 'cru', 'Ca_00614_v3' => 'car', 'Ca_07801_v3' => 'car', 'Ca_08567_v3' => 'car', 'Ca_09571_v3' => 'car', 'CBR_g19290' => 'cbr', 'Cc01_g19770' => 'ccan', 'Cc03_g03030' => 'ccan', 'CDE07G0968' => 'cde', 'CDE09G1441' => 'cde', 'Cfa006103' => 'cfa', 'Cfa015573' => 'cfa', 'Cfa016988' => 'cfa', 'Ciclev10006738m.g' => 'ccl', 'Ciclev10010920m.g' => 'ccl', 'Ciclev10018517m.g' => 'ccl', 'CiPaw.01G159200' => 'cil', 'CiPaw.02G091000' => 'cil', 'CiPaw.02G091100' => 'cil', 'CiPaw.08G103100' => 'cil', 'CiPaw.09G224900' => 'cil', 'ClCG06G005740' => 'cla', 'ClCG07G000090' => 'cla', 'ClCG07G000100' => 'cla', 'COL.COLO4_09143' => 'col', 'COL.COLO4_25124' => 'col', 'Cpa.g.sc16.34' => 'cpa', 'Cpa.g.sc3504.1' => 'cpa', 'Cpa.g.sc60.37' => 'cpa', 'CsaV3_6G018520' => 'csa', 'CsaV3_6G036860' => 'csa', 'CSS0001072' => 'camsi', 'CSS0020208' => 'camsi', 'CSS0021253' => 'camsi', 'CSS0022190' => 'camsi', 'CSS0036150' => 'camsi', 'CSS0040442' => 'camsi', 'CSS0042300' => 'camsi', 'CSS0045298' => 'camsi', 'DCAR_012449' => 'dca', 'DCAR_018405' => 'dca', 'DCAR_024573' => 'dca', 'DCAR_030591' => 'dca', 'Dinv16926' => 'din', 'Dinv32963' => 'din', 'Dinv38382' => 'din', 'Dinv38383' => 'din', 'Duzib133G0974' => 'dzi', 'Duzib138G1867' => 'dzi', 'Duzib211G0420' => 'dzi', 'Duzib212G0930' => 'dzi', 'ECA234G1645' => 'eca', 'ECA247G3467' => 'eca', 'ECA248G1703' => 'eca', 'EL10Ac3g06327' => 'bvu', 'EL10Ac7g17204' => 'bvu', 'Eucgr.A00855' => 'egr', 'Eucgr.A00858' => 'egr', 'Eucgr.H01520' => 'egr', 'Eucgr.H03604' => 'egr', 'Eucgr.L03465' => 'egr', 'Eucgr.L03466' => 'egr', 'FAN01G0988' => 'fan', 'FAN02G3892' => 'fan', 'FAN05G3381' => 'fan', 'FAN07G0967' => 'fan', 'FAN07G1493' => 'fan', 'FAN08G3125' => 'fan', 'FAN09G0402' => 'fan', 'FAN12G2594' => 'fan', 'FAN12G3879' => 'fan', 'FAN14G1546' => 'fan', 'FAN15G3626' => 'fan', 'FAN17G0588' => 'fan', 'FAN17G0609' => 'fan', 'FAN18G2817' => 'fan', 'FAN19G1305' => 'fan', 'FAN20G1787' => 'fan', 'FAN22G0073' => 'fan', 'FAN22G0352' => 'fan', 'FAN22G0368' => 'fan', 'FAN22G2273' => 'fan', 'FAN24G1998' => 'fan', 'FAN27G1317' => 'fan', 'FvH4_2g23980' => 'fve', 'FvH4_4g14380' => 'fve', 'FvH4_4g14390' => 'fve', 'FvH4_6g09250' => 'fve', 'Glyma.03G151100' => 'gma', 'Glyma.04G122550' => 'gma', 'Glyma.05G001600' => 'gma', 'Glyma.09G270766' => 'gma', 'Glyma.09G270832' => 'gma', 'Glyma.13G209800' => 'gma', 'Glyma.15G102800' => 'gma', 'Glyma.18G218900' => 'gma', 'Glyma.19G001500' => 'gma', 'Glyma.19G153600' => 'gma', 'Gohir.A02G028600' => 'ghi', 'Gohir.A08G045000' => 'ghi', 'Gohir.A11G120500' => 'ghi', 'Gohir.A12G006200' => 'ghi', 'Gohir.A12G006250' => 'ghi', 'Gohir.D02G036300' => 'ghi', 'Gohir.D08G054700' => 'ghi', 'Gohir.D11G125600' => 'ghi', 'Gohir.D12G005700' => 'ghi', 'Gorai.004G055200' => 'gra', 'Gorai.005G040400' => 'gra', 'Gorai.007G134500' => 'gra', 'Gorai.008G005500' => 'gra', 'GSVIVG01011094001' => 'vvi', 'GSVIVG01017879001' => 'vvi', 'GSVIVG01025988001' => 'vvi', 'GSVIVG01029847001' => 'vvi', 'HanXRQChr10g0282901' => 'han', 'HanXRQChr10g0310371' => 'han', 'HanXRQChr10g0315041' => 'han', 'HanXRQChr11g0327651' => 'han', 'HanXRQChr12g0359391' => 'han', 'Haze_00972' => 'cav', 'Haze_00973' => 'cav', 'Haze_00974' => 'cav', 'Haze_04747' => 'cav', 'Haze_04749' => 'cav', 'Haze_04750' => 'cav', 'Haze_21217' => 'cav', 'Hma1.2p1_1037F.1_g250680' => 'hma', 'Hma1.2p1_1644F.1_g295320' => 'hma', 'HPP92_011322' => 'vpl', 'HPP92_011323' => 'vpl', 'HPP92_011324' => 'vpl', 'HPP92_011325' => 'vpl', 'HPP92_011326' => 'vpl', 'Hund12205' => 'sun', 'Hund17957' => 'sun', 'Lalb_Chr06g0176771' => 'lal', 'Lalb_Chr18g0056021' => 'lal', 'Lalb_Chr18g0056031' => 'lal', 'Lalb_Chr18g0056041' => 'lal', 'Lalb_Chr20g0107751' => 'lal', 'Lalb_Chr20g0118371' => 'lal', 'Lj1g0010239' => 'lja', 'Lj1g0017101' => 'lja', 'Lj2A1178G40' => 'lonja', 'Lj2A54G84' => 'lonja', 'Lj2g0015248' => 'lja', 'Lj3A761T51' => 'lonja', 'Lj6g0018116' => 'lja', 'Lsat_1_v5_gn_4_136040' => 'lsa', 'Lsat_1_v5_gn_5_187461' => 'lsa', 'Lsat_1_v5_gn_5_77001' => 'lsa', 'Lsat_1_v5_gn_9_4461' => 'lsa', 'Manes.01G210100' => 'mes', 'Manes.03G185600' => 'mes', 'Manes.05G073300' => 'mes', 'Manes.09G120300' => 'mes', 'Manes.15G022100' => 'mes', 'Mapoly0096s0053' => 'mpo', 'MBI03_g14058_MAGBIO' => 'mbi', 'MBI03_g33876_MAGBIO' => 'mbi', 'MBI03_g36854_MAGBIO' => 'mbi', 'MBI17_g11997_MAGBIO' => 'mbi', 'MD03G1269000' => 'mdo', 'MD04G1179600' => 'mdo', 'MD11G1289800' => 'mdo', 'MD12G1194700' => 'mdo', 'MD13G1182100' => 'mdo', 'MD13G1182200' => 'mdo', 'MD16G1182600' => 'mdo', 'Medtr2g021400' => 'mtr', 'Medtr2g021470' => 'mtr', 'Medtr2g105810' => 'mtr', 'Medtr3g033580' => 'mtr', 'Medtr6g007970' => 'mtr', 'Medtr7g056330' => 'mtr', 'Medtr7g074290' => 'mtr', 'Medtr7g074380' => 'mtr', 'Medtr7g094550' => 'mtr', 'Medtr8g069995' => 'mtr', 'MELO3C014345.2' => 'cme', 'MELO3C021395.2' => 'cme', 'Migut.D00262' => 'egut', 'Migut.G00257' => 'egut', 'MSTRG.21575' => 'ama', 'MSTRG.3985' => 'ama', 'Nitab4.5_0000295g0140' => 'nta', 'Nitab4.5_0000732g0140' => 'nta', 'Nitab4.5_0003162g0020' => 'nta', 'Nitab4.5_0006180g0090' => 'nta', 'Nitab4.5_0006390g0010' => 'nta', 'Nitab4.5_0007392g0040' => 'nta', 'Nn1g02140' => 'nnu', 'Nn4g26168' => 'nnu', 'Nn5g26754' => 'nnu', 'Oeu001433.1' => 'oeu', 'Oeu010299.2' => 'oeu', 'Oeu011171.1' => 'oeu', 'Oeu037675.1' => 'oeu', 'Oeu038359.1' => 'oeu', 'Oeu063834.1' => 'oeu', 'Oeu063835.1' => 'oeu', 'Os05g0312000' => 'osa', 'Os07g0211101' => 'osa', 'Os07g0211200' => 'osa', 'Os07g0681500' => 'osa', 'Peaxi162Scf00095g01015' => 'pax', 'Peaxi162Scf00104g00329' => 'pax', 'Peaxi162Scf00161g00137' => 'pax', 'PGR004G1665' => 'pgr', 'PGR031G2937' => 'pgr', 'PGR119G2145' => 'pgr', 'PGSC0003DMG400004351' => 'stu', 'PGSC0003DMG400014625' => 'stu', 'PGSC0003DMG401000943' => 'stu', 'Phvul.001G148600' => 'pvu', 'Phvul.004G001700' => 'pvu', 'Phvul.006G154900' => 'pvu', 'Phvul.008G078200' => 'pvu', 'Phvul.011G136500' => 'pvu', 'Potri.002G215600' => 'ptr', 'Potri.008G201600' => 'ptr', 'Potri.014G138400' => 'ptr', 'Potri.016G142500' => 'ptr', 'Pp3c16_10580' => 'ppa', 'Pp3c5_25280' => 'ppa', 'Prupe.1G150000' => 'ppe', 'Prupe.1G150100' => 'ppe', 'Prupe.6G299600' => 'ppe', 'Prupe.8G245000' => 'ppe', 'Psat0s4927g0040' => 'psa', 'Psat1g052080' => 'psa', 'Psat1g183800' => 'psa', 'Psat3g113840' => 'psa', 'Psat3g126120' => 'psa', 'Psat3g126160' => 'psa', 'Psat3g158760' => 'psa', 'Psat3g158840' => 'psa', 'PSO170G2858' => 'pso', 'PSO339G0606' => 'pso', 'PSO384G4709' => 'pso', 'PSO407G0334' => 'pso', 'QL04p040276' => 'qlo', 'QL06p005458' => 'qlo', 'QL06p005472' => 'qlo', 'QL07p030546' => 'qlo', 'QL07p031519' => 'qlo', 'QL09p050949' => 'qlo', 'QL09p050966' => 'qlo', 'QL09p051067' => 'qlo', 'QL12p022706' => 'qlo', 'RcHm_v2.0_Chr2g0119601' => 'rch', 'RcHm_v2.0_Chr3g0459591' => 'rch', 'RcHm_v2.0_Chr4g0418521' => 'rch', 'RcHm_v2.0_Chr4g0418531' => 'rch', 'RcHm_v2.0_Chr4g0418541' => 'rch', 'RcHm_v2.0_Chr6g0291641' => 'rch', 'Rhsim01G0086300' => 'rsi', 'Rhsim01G0276300' => 'rsi', 'Rhsim01G0276500' => 'rsi', 'Rhsim04G0207700' => 'rsi', 'Rhsim05G0234500' => 'rsi', 'Rhsim13G0022400' => 'rsi', 'Sabra02G0167900' => 'sbr', 'Sabra04G0158500' => 'sbr', 'Sabra08G0159800' => 'sbr', 'Sabra10G0011500' => 'sbr', 'Sabra14G0104400' => 'sbr', 'SalBow2G2440' => 'sbo', 'SalBow4G2265' => 'sbo', 'Sc02g0000060' => 'sci', 'Sc05g0005020' => 'sci', 'Sc13g0003890' => 'sci', 'Sed0014865' => 'sed', 'Sed0017224' => 'sed', 'Sed0026391' => 'sed', 'SEGI_00063' => 'sgi', 'SEGI_10967' => 'sgi', 'SEGI_17510' => 'sgi', 'SEGI_24396' => 'sgi', 'SEGI_39719' => 'sgi', 'SEGI_41392' => 'sgi', 'SGA_v2.0_scaffold11G05794' => 'sas', 'SGA_v2.0_scaffold142G35607' => 'sas', 'SGA_v2.0_scaffold1G00447' => 'sas', 'SHI15388' => 'shi', 'SHI15394' => 'shi', 'SHI15396' => 'shi', 'SHI15399' => 'shi', 'SMO343G0151' => 'smo', 'SMO367G1118' => 'smo', 'Solyc01g080200.3' => 'sly', 'Solyc06g008960.3' => 'sly', 'Solyc09g064780.3' => 'sly', 'Sopen01g031980' => 'spe', 'Sopen06g003710' => 'spe', 'Sopen09g026460' => 'spe', 'Sp3g21240' => 'spa', 'Sp4g30030' => 'spa', 'TAR365G0022' => 'tar', 'TAR365G1023' => 'tar', 'TAR365G1253' => 'tar', 'TAR623G0078' => 'tar', 'TAR623G1721' => 'tar', 'TAR633G0959' => 'tar', 'THA.LOC104802225' => 'tha', 'THA.LOC104804769' => 'tha', 'THA.LOC104808660' => 'tha', 'THA.LOC104812792' => 'tha', 'Thecc.01G284000' => 'tca', 'Thecc.04G220600' => 'tca', 'Thecc.05G268900' => 'tca', 'Thecc.08G171100' => 'tca', 'Thhalv10001284m.g' => 'esa', 'Thhalv10019912m.g' => 'esa', 'TPR.G14189' => 'tpr', 'TPR.G18110' => 'tpr', 'TPR.G18130' => 'tpr', 'TPR.G18131' => 'tpr', 'TPR.G18140' => 'tpr', 'TPR.G24282' => 'tpr', 'TPR.G25221' => 'tpr', 'TPR.G29267' => 'tpr', 'TPR.G35315' => 'tpr', 'TPR.G36173' => 'tpr', 'TWI09G0794' => 'twi', 'TWI59G1348' => 'twi', 'TWI74G0430' => 'twi', 'unitig_26.g8940' => 'ugi', 'unitig_749.g13744' => 'ugi', 'unitig_749.g13745' => 'ugi', 'vmacro08269' => 'vma', 'vmacro14937' => 'vma', 'vmacro20401' => 'vma', 'VMungo0464G1349' => 'vmu', 'VMungo0540G0289' => 'vmu', 'VMungo1215G1590' => 'vmu', 'VMungo1309G0221' => 'vmu', 'VMungo1309G2815' => 'vmu', 'VMungo1383G0239' => 'vmu', 'VMungo1383G2910' => 'vmu', 'Zm00001eb095270' => 'zma', 'Zm00001eb095280' => 'zma', 'Zm00001eb111630' => 'zma', 'Zm00001eb237080' => 'zma', 'Zm00001eb273740' => 'zma', 'Zm00001eb285040' => 'zma', 'Zm00001eb330790' => 'zma', 'Zm00001eb337380' => 'zma' ), 'gf_id' => 'HOM05D001484', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001484' ), 'data_identifier' => 'HOM05D001484', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001484', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p31500' => 'bna', 'A05p00020' => 'bna', 'A07p08820' => 'bna', 'Aa31LG4G3300' => 'aar', 'Aa31LG8G10030' => 'aar', 'Actinidia00731' => 'ach', 'Actinidia11473' => 'ach', 'Actinidia23469' => 'ach', 'Actinidia24318' => 'ach', 'Actinidia40196' => 'ach', 'Actinidia40197' => 'ach', 'Actinidia40198' => 'ach', 'Ah.08g212990' => 'amhyb', 'Ah.15g091720' => 'amhyb', 'AL3G38260' => 'aly', 'AL4G47710' => 'aly', 'Aqoxy2G00671' => 'aox', 'Aqoxy2G03236' => 'aox', 'arahy.Tifrunner.gnm1.ann1.05IDCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KR684' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATY3SJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK6QJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6APGL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IDT7Z9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM073U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ0R87' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LE7RV4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT4QRX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V5ENPK' => 'arhy', 'AT2G48110' => 'ath', 'AT3G23590' => 'ath', 'ATR0626G186' => 'atr', 'ATR1127G141' => 'atr', 'Atru.chr4.2583' => 'acertr', 'Atru.chr5.1358' => 'acertr', 'Atru.chr5.1359' => 'acertr', 'Atru.chr8.46' => 'acertr', 'AUR62002640' => 'cqu', 'AUR62030055' => 'cqu', 'AUR62033713' => 'cqu', 'AUR62033714' => 'cqu', 'AUR62036795' => 'cqu', 'AUR62039891' => 'cqu', 'BcaB02g08737' => 'bca', 'BcaB04g20441' => 'bca', 'BcaB06g26509' => 'bca', 'BcaB06g26510' => 'bca', 'BcaB06g26511' => 'bca', 'BcaB06g26512' => 'bca', 'BcaB06g26513' => 'bca', 'BcaC02g12564' => 'bca', 'BcaC02g12565' => 'bca', 'BcaC02g12794' => 'bca', 'BcaC02g12795' => 'bca', 'BcaC02g12796' => 'bca', 'BcaC06g35541' => 'bca', 'BNapus_Darmor_BZH_scaffold_188p00080' => 'bna', 'BNapus_Darmor_BZH_scaffold_188p00090' => 'bna', 'BolC1t03972H' => 'bol', 'BolC1t03973H' => 'bol', 'BolC4t21680H' => 'bol', 'BolC7t41863H' => 'bol', 'BolSC55t61227H' => 'bol', 'BolSC55t61228H' => 'bol', 'BraA01t03278Z' => 'bra', 'BraA05t18998Z' => 'bra', 'BraA07t28673Z' => 'bra', 'C01p40150' => 'bna', 'C05p12370' => 'bna', 'C07p13680' => 'bna', 'CAN.G1006.16' => 'can', 'CAN.G1006.17' => 'can', 'CAN.G1170.2' => 'can', 'CAN.G962.7' => 'can', 'CANSAT25G2179' => 'cansat', 'CANSAT78G1573' => 'cansat', 'CARHR099510' => 'chi', 'CARHR143510' => 'chi', 'Carub.0003s2380' => 'cru', 'Carub.0004s3082' => 'cru', 'Ca_00614_v3' => 'car', 'Ca_07801_v3' => 'car', 'Ca_08567_v3' => 'car', 'Ca_09571_v3' => 'car', 'CBR_g19290' => 'cbr', 'Cc01_g19770' => 'ccan', 'Cc03_g03030' => 'ccan', 'CDE07G0968' => 'cde', 'CDE09G1441' => 'cde', 'Cfa006103' => 'cfa', 'Cfa015573' => 'cfa', 'Cfa016988' => 'cfa', 'Ciclev10006738m.g' => 'ccl', 'Ciclev10010920m.g' => 'ccl', 'Ciclev10018517m.g' => 'ccl', 'CiPaw.01G159200' => 'cil', 'CiPaw.02G091000' => 'cil', 'CiPaw.02G091100' => 'cil', 'CiPaw.08G103100' => 'cil', 'CiPaw.09G224900' => 'cil', 'ClCG06G005740' => 'cla', 'ClCG07G000090' => 'cla', 'ClCG07G000100' => 'cla', 'COL.COLO4_09143' => 'col', 'COL.COLO4_25124' => 'col', 'Cpa.g.sc16.34' => 'cpa', 'Cpa.g.sc3504.1' => 'cpa', 'Cpa.g.sc60.37' => 'cpa', 'CsaV3_6G018520' => 'csa', 'CsaV3_6G036860' => 'csa', 'CSS0001072' => 'camsi', 'CSS0020208' => 'camsi', 'CSS0021253' => 'camsi', 'CSS0022190' => 'camsi', 'CSS0036150' => 'camsi', 'CSS0040442' => 'camsi', 'CSS0042300' => 'camsi', 'CSS0045298' => 'camsi', 'DCAR_012449' => 'dca', 'DCAR_018405' => 'dca', 'DCAR_024573' => 'dca', 'DCAR_030591' => 'dca', 'Dinv16926' => 'din', 'Dinv32963' => 'din', 'Dinv38382' => 'din', 'Dinv38383' => 'din', 'Duzib133G0974' => 'dzi', 'Duzib138G1867' => 'dzi', 'Duzib211G0420' => 'dzi', 'Duzib212G0930' => 'dzi', 'ECA234G1645' => 'eca', 'ECA247G3467' => 'eca', 'ECA248G1703' => 'eca', 'EL10Ac3g06327' => 'bvu', 'EL10Ac7g17204' => 'bvu', 'Eucgr.A00855' => 'egr', 'Eucgr.A00858' => 'egr', 'Eucgr.H01520' => 'egr', 'Eucgr.H03604' => 'egr', 'Eucgr.L03465' => 'egr', 'Eucgr.L03466' => 'egr', 'FAN01G0988' => 'fan', 'FAN02G3892' => 'fan', 'FAN05G3381' => 'fan', 'FAN07G0967' => 'fan', 'FAN07G1493' => 'fan', 'FAN08G3125' => 'fan', 'FAN09G0402' => 'fan', 'FAN12G2594' => 'fan', 'FAN12G3879' => 'fan', 'FAN14G1546' => 'fan', 'FAN15G3626' => 'fan', 'FAN17G0588' => 'fan', 'FAN17G0609' => 'fan', 'FAN18G2817' => 'fan', 'FAN19G1305' => 'fan', 'FAN20G1787' => 'fan', 'FAN22G0073' => 'fan', 'FAN22G0352' => 'fan', 'FAN22G0368' => 'fan', 'FAN22G2273' => 'fan', 'FAN24G1998' => 'fan', 'FAN27G1317' => 'fan', 'FvH4_2g23980' => 'fve', 'FvH4_4g14380' => 'fve', 'FvH4_4g14390' => 'fve', 'FvH4_6g09250' => 'fve', 'Glyma.03G151100' => 'gma', 'Glyma.04G122550' => 'gma', 'Glyma.05G001600' => 'gma', 'Glyma.09G270766' => 'gma', 'Glyma.09G270832' => 'gma', 'Glyma.13G209800' => 'gma', 'Glyma.15G102800' => 'gma', 'Glyma.18G218900' => 'gma', 'Glyma.19G001500' => 'gma', 'Glyma.19G153600' => 'gma', 'Gohir.A02G028600' => 'ghi', 'Gohir.A08G045000' => 'ghi', 'Gohir.A11G120500' => 'ghi', 'Gohir.A12G006200' => 'ghi', 'Gohir.A12G006250' => 'ghi', 'Gohir.D02G036300' => 'ghi', 'Gohir.D08G054700' => 'ghi', 'Gohir.D11G125600' => 'ghi', 'Gohir.D12G005700' => 'ghi', 'Gorai.004G055200' => 'gra', 'Gorai.005G040400' => 'gra', 'Gorai.007G134500' => 'gra', 'Gorai.008G005500' => 'gra', 'GSVIVG01011094001' => 'vvi', 'GSVIVG01017879001' => 'vvi', 'GSVIVG01025988001' => 'vvi', 'GSVIVG01029847001' => 'vvi', 'HanXRQChr10g0282901' => 'han', 'HanXRQChr10g0310371' => 'han', 'HanXRQChr10g0315041' => 'han', 'HanXRQChr11g0327651' => 'han', 'HanXRQChr12g0359391' => 'han', 'Haze_00972' => 'cav', 'Haze_00973' => 'cav', 'Haze_00974' => 'cav', 'Haze_04747' => 'cav', 'Haze_04749' => 'cav', 'Haze_04750' => 'cav', 'Haze_21217' => 'cav', 'Hma1.2p1_1037F.1_g250680' => 'hma', 'Hma1.2p1_1644F.1_g295320' => 'hma', 'HPP92_011322' => 'vpl', 'HPP92_011323' => 'vpl', 'HPP92_011324' => 'vpl', 'HPP92_011325' => 'vpl', 'HPP92_011326' => 'vpl', 'Hund12205' => 'sun', 'Hund17957' => 'sun', 'Lalb_Chr06g0176771' => 'lal', 'Lalb_Chr18g0056021' => 'lal', 'Lalb_Chr18g0056031' => 'lal', 'Lalb_Chr18g0056041' => 'lal', 'Lalb_Chr20g0107751' => 'lal', 'Lalb_Chr20g0118371' => 'lal', 'Lj1g0010239' => 'lja', 'Lj1g0017101' => 'lja', 'Lj2A1178G40' => 'lonja', 'Lj2A54G84' => 'lonja', 'Lj2g0015248' => 'lja', 'Lj3A761T51' => 'lonja', 'Lj6g0018116' => 'lja', 'Lsat_1_v5_gn_4_136040' => 'lsa', 'Lsat_1_v5_gn_5_187461' => 'lsa', 'Lsat_1_v5_gn_5_77001' => 'lsa', 'Lsat_1_v5_gn_9_4461' => 'lsa', 'Manes.01G210100' => 'mes', 'Manes.03G185600' => 'mes', 'Manes.05G073300' => 'mes', 'Manes.09G120300' => 'mes', 'Manes.15G022100' => 'mes', 'Mapoly0096s0053' => 'mpo', 'MBI03_g14058_MAGBIO' => 'mbi', 'MBI03_g33876_MAGBIO' => 'mbi', 'MBI03_g36854_MAGBIO' => 'mbi', 'MBI17_g11997_MAGBIO' => 'mbi', 'MD03G1269000' => 'mdo', 'MD04G1179600' => 'mdo', 'MD11G1289800' => 'mdo', 'MD12G1194700' => 'mdo', 'MD13G1182100' => 'mdo', 'MD13G1182200' => 'mdo', 'MD16G1182600' => 'mdo', 'Medtr2g021400' => 'mtr', 'Medtr2g021470' => 'mtr', 'Medtr2g105810' => 'mtr', 'Medtr3g033580' => 'mtr', 'Medtr6g007970' => 'mtr', 'Medtr7g056330' => 'mtr', 'Medtr7g074290' => 'mtr', 'Medtr7g074380' => 'mtr', 'Medtr7g094550' => 'mtr', 'Medtr8g069995' => 'mtr', 'MELO3C014345.2' => 'cme', 'MELO3C021395.2' => 'cme', 'Migut.D00262' => 'egut', 'Migut.G00257' => 'egut', 'MSTRG.21575' => 'ama', 'MSTRG.3985' => 'ama', 'Nitab4.5_0000295g0140' => 'nta', 'Nitab4.5_0000732g0140' => 'nta', 'Nitab4.5_0003162g0020' => 'nta', 'Nitab4.5_0006180g0090' => 'nta', 'Nitab4.5_0006390g0010' => 'nta', 'Nitab4.5_0007392g0040' => 'nta', 'Nn1g02140' => 'nnu', 'Nn4g26168' => 'nnu', 'Nn5g26754' => 'nnu', 'Oeu001433.1' => 'oeu', 'Oeu010299.2' => 'oeu', 'Oeu011171.1' => 'oeu', 'Oeu037675.1' => 'oeu', 'Oeu038359.1' => 'oeu', 'Oeu063834.1' => 'oeu', 'Oeu063835.1' => 'oeu', 'Os05g0312000' => 'osa', 'Os07g0211101' => 'osa', 'Os07g0211200' => 'osa', 'Os07g0681500' => 'osa', 'Peaxi162Scf00095g01015' => 'pax', 'Peaxi162Scf00104g00329' => 'pax', 'Peaxi162Scf00161g00137' => 'pax', 'PGR004G1665' => 'pgr', 'PGR031G2937' => 'pgr', 'PGR119G2145' => 'pgr', 'PGSC0003DMG400004351' => 'stu', 'PGSC0003DMG400014625' => 'stu', 'PGSC0003DMG401000943' => 'stu', 'Phvul.001G148600' => 'pvu', 'Phvul.004G001700' => 'pvu', 'Phvul.006G154900' => 'pvu', 'Phvul.008G078200' => 'pvu', 'Phvul.011G136500' => 'pvu', 'Potri.002G215600' => 'ptr', 'Potri.008G201600' => 'ptr', 'Potri.014G138400' => 'ptr', 'Potri.016G142500' => 'ptr', 'Pp3c16_10580' => 'ppa', 'Pp3c5_25280' => 'ppa', 'Prupe.1G150000' => 'ppe', 'Prupe.1G150100' => 'ppe', 'Prupe.6G299600' => 'ppe', 'Prupe.8G245000' => 'ppe', 'Psat0s4927g0040' => 'psa', 'Psat1g052080' => 'psa', 'Psat1g183800' => 'psa', 'Psat3g113840' => 'psa', 'Psat3g126120' => 'psa', 'Psat3g126160' => 'psa', 'Psat3g158760' => 'psa', 'Psat3g158840' => 'psa', 'PSO170G2858' => 'pso', 'PSO339G0606' => 'pso', 'PSO384G4709' => 'pso', 'PSO407G0334' => 'pso', 'QL04p040276' => 'qlo', 'QL06p005458' => 'qlo', 'QL06p005472' => 'qlo', 'QL07p030546' => 'qlo', 'QL07p031519' => 'qlo', 'QL09p050949' => 'qlo', 'QL09p050966' => 'qlo', 'QL09p051067' => 'qlo', 'QL12p022706' => 'qlo', 'RcHm_v2.0_Chr2g0119601' => 'rch', 'RcHm_v2.0_Chr3g0459591' => 'rch', 'RcHm_v2.0_Chr4g0418521' => 'rch', 'RcHm_v2.0_Chr4g0418531' => 'rch', 'RcHm_v2.0_Chr4g0418541' => 'rch', 'RcHm_v2.0_Chr6g0291641' => 'rch', 'Rhsim01G0086300' => 'rsi', 'Rhsim01G0276300' => 'rsi', 'Rhsim01G0276500' => 'rsi', 'Rhsim04G0207700' => 'rsi', 'Rhsim05G0234500' => 'rsi', 'Rhsim13G0022400' => 'rsi', 'Sabra02G0167900' => 'sbr', 'Sabra04G0158500' => 'sbr', 'Sabra08G0159800' => 'sbr', 'Sabra10G0011500' => 'sbr', 'Sabra14G0104400' => 'sbr', 'SalBow2G2440' => 'sbo', 'SalBow4G2265' => 'sbo', 'Sc02g0000060' => 'sci', 'Sc05g0005020' => 'sci', 'Sc13g0003890' => 'sci', 'Sed0014865' => 'sed', 'Sed0017224' => 'sed', 'Sed0026391' => 'sed', 'SEGI_00063' => 'sgi', 'SEGI_10967' => 'sgi', 'SEGI_17510' => 'sgi', 'SEGI_24396' => 'sgi', 'SEGI_39719' => 'sgi', 'SEGI_41392' => 'sgi', 'SGA_v2.0_scaffold11G05794' => 'sas', 'SGA_v2.0_scaffold142G35607' => 'sas', 'SGA_v2.0_scaffold1G00447' => 'sas', 'SHI15388' => 'shi', 'SHI15394' => 'shi', 'SHI15396' => 'shi', 'SHI15399' => 'shi', 'SMO343G0151' => 'smo', 'SMO367G1118' => 'smo', 'Solyc01g080200.3' => 'sly', 'Solyc06g008960.3' => 'sly', 'Solyc09g064780.3' => 'sly', 'Sopen01g031980' => 'spe', 'Sopen06g003710' => 'spe', 'Sopen09g026460' => 'spe', 'Sp3g21240' => 'spa', 'Sp4g30030' => 'spa', 'TAR365G0022' => 'tar', 'TAR365G1023' => 'tar', 'TAR365G1253' => 'tar', 'TAR623G0078' => 'tar', 'TAR623G1721' => 'tar', 'TAR633G0959' => 'tar', 'THA.LOC104802225' => 'tha', 'THA.LOC104804769' => 'tha', 'THA.LOC104808660' => 'tha', 'THA.LOC104812792' => 'tha', 'Thecc.01G284000' => 'tca', 'Thecc.04G220600' => 'tca', 'Thecc.05G268900' => 'tca', 'Thecc.08G171100' => 'tca', 'Thhalv10001284m.g' => 'esa', 'Thhalv10019912m.g' => 'esa', 'TPR.G14189' => 'tpr', 'TPR.G18110' => 'tpr', 'TPR.G18130' => 'tpr', 'TPR.G18131' => 'tpr', 'TPR.G18140' => 'tpr', 'TPR.G24282' => 'tpr', 'TPR.G25221' => 'tpr', 'TPR.G29267' => 'tpr', 'TPR.G35315' => 'tpr', 'TPR.G36173' => 'tpr', 'TWI09G0794' => 'twi', 'TWI59G1348' => 'twi', 'TWI74G0430' => 'twi', 'unitig_26.g8940' => 'ugi', 'unitig_749.g13744' => 'ugi', 'unitig_749.g13745' => 'ugi', 'vmacro08269' => 'vma', 'vmacro14937' => 'vma', 'vmacro20401' => 'vma', 'VMungo0464G1349' => 'vmu', 'VMungo0540G0289' => 'vmu', 'VMungo1215G1590' => 'vmu', 'VMungo1309G0221' => 'vmu', 'VMungo1309G2815' => 'vmu', 'VMungo1383G0239' => 'vmu', 'VMungo1383G2910' => 'vmu', 'Zm00001eb095270' => 'zma', 'Zm00001eb095280' => 'zma', 'Zm00001eb111630' => 'zma', 'Zm00001eb237080' => 'zma', 'Zm00001eb273740' => 'zma', 'Zm00001eb285040' => 'zma', 'Zm00001eb330790' => 'zma', 'Zm00001eb337380' => 'zma' ) $gf_id = 'HOM05D001484' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001484' ) $data_identifier = 'HOM05D001484' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 2, 'aly' => (int) 2, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 22, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 7, 'hma' => (int) 2, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 7, 'mtr' => (int) 10, 'cme' => (int) 2, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 4, 'ppa' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 4, 'qlo' => (int) 9, 'rch' => (int) 6, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 10, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 7, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb337380' $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' => 'HOM05D001484', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p31500' => 'bna', 'A05p00020' => 'bna', 'A07p08820' => 'bna', 'Aa31LG4G3300' => 'aar', 'Aa31LG8G10030' => 'aar', 'Actinidia00731' => 'ach', 'Actinidia11473' => 'ach', 'Actinidia23469' => 'ach', 'Actinidia24318' => 'ach', 'Actinidia40196' => 'ach', 'Actinidia40197' => 'ach', 'Actinidia40198' => 'ach', 'Ah.08g212990' => 'amhyb', 'Ah.15g091720' => 'amhyb', 'AL3G38260' => 'aly', 'AL4G47710' => 'aly', 'Aqoxy2G00671' => 'aox', 'Aqoxy2G03236' => 'aox', 'arahy.Tifrunner.gnm1.ann1.05IDCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KR684' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATY3SJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK6QJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6APGL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IDT7Z9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM073U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ0R87' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LE7RV4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT4QRX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V5ENPK' => 'arhy', 'AT2G48110' => 'ath', 'AT3G23590' => 'ath', 'ATR0626G186' => 'atr', 'ATR1127G141' => 'atr', 'Atru.chr4.2583' => 'acertr', 'Atru.chr5.1358' => 'acertr', 'Atru.chr5.1359' => 'acertr', 'Atru.chr8.46' => 'acertr', 'AUR62002640' => 'cqu', 'AUR62030055' => 'cqu', 'AUR62033713' => 'cqu', 'AUR62033714' => 'cqu', 'AUR62036795' => 'cqu', 'AUR62039891' => 'cqu', 'BcaB02g08737' => 'bca', 'BcaB04g20441' => 'bca', 'BcaB06g26509' => 'bca', 'BcaB06g26510' => 'bca', 'BcaB06g26511' => 'bca', 'BcaB06g26512' => 'bca', 'BcaB06g26513' => 'bca', 'BcaC02g12564' => 'bca', 'BcaC02g12565' => 'bca', 'BcaC02g12794' => 'bca', 'BcaC02g12795' => 'bca', 'BcaC02g12796' => 'bca', 'BcaC06g35541' => 'bca', 'BNapus_Darmor_BZH_scaffold_188p00080' => 'bna', 'BNapus_Darmor_BZH_scaffold_188p00090' => 'bna', 'BolC1t03972H' => 'bol', 'BolC1t03973H' => 'bol', 'BolC4t21680H' => 'bol', 'BolC7t41863H' => 'bol', 'BolSC55t61227H' => 'bol', 'BolSC55t61228H' => 'bol', 'BraA01t03278Z' => 'bra', 'BraA05t18998Z' => 'bra', 'BraA07t28673Z' => 'bra', 'C01p40150' => 'bna', 'C05p12370' => 'bna', 'C07p13680' => 'bna', 'CAN.G1006.16' => 'can', 'CAN.G1006.17' => 'can', 'CAN.G1170.2' => 'can', 'CAN.G962.7' => 'can', 'CANSAT25G2179' => 'cansat', 'CANSAT78G1573' => 'cansat', 'CARHR099510' => 'chi', 'CARHR143510' => 'chi', 'Carub.0003s2380' => 'cru', 'Carub.0004s3082' => 'cru', 'Ca_00614_v3' => 'car', 'Ca_07801_v3' => 'car', 'Ca_08567_v3' => 'car', 'Ca_09571_v3' => 'car', 'CBR_g19290' => 'cbr', 'Cc01_g19770' => 'ccan', 'Cc03_g03030' => 'ccan', 'CDE07G0968' => 'cde', 'CDE09G1441' => 'cde', 'Cfa006103' => 'cfa', 'Cfa015573' => 'cfa', 'Cfa016988' => 'cfa', 'Ciclev10006738m.g' => 'ccl', 'Ciclev10010920m.g' => 'ccl', 'Ciclev10018517m.g' => 'ccl', 'CiPaw.01G159200' => 'cil', 'CiPaw.02G091000' => 'cil', 'CiPaw.02G091100' => 'cil', 'CiPaw.08G103100' => 'cil', 'CiPaw.09G224900' => 'cil', 'ClCG06G005740' => 'cla', 'ClCG07G000090' => 'cla', 'ClCG07G000100' => 'cla', 'COL.COLO4_09143' => 'col', 'COL.COLO4_25124' => 'col', 'Cpa.g.sc16.34' => 'cpa', 'Cpa.g.sc3504.1' => 'cpa', 'Cpa.g.sc60.37' => 'cpa', 'CsaV3_6G018520' => 'csa', 'CsaV3_6G036860' => 'csa', 'CSS0001072' => 'camsi', 'CSS0020208' => 'camsi', 'CSS0021253' => 'camsi', 'CSS0022190' => 'camsi', 'CSS0036150' => 'camsi', 'CSS0040442' => 'camsi', 'CSS0042300' => 'camsi', 'CSS0045298' => 'camsi', 'DCAR_012449' => 'dca', 'DCAR_018405' => 'dca', 'DCAR_024573' => 'dca', 'DCAR_030591' => 'dca', 'Dinv16926' => 'din', 'Dinv32963' => 'din', 'Dinv38382' => 'din', 'Dinv38383' => 'din', 'Duzib133G0974' => 'dzi', 'Duzib138G1867' => 'dzi', 'Duzib211G0420' => 'dzi', 'Duzib212G0930' => 'dzi', 'ECA234G1645' => 'eca', 'ECA247G3467' => 'eca', 'ECA248G1703' => 'eca', 'EL10Ac3g06327' => 'bvu', 'EL10Ac7g17204' => 'bvu', 'Eucgr.A00855' => 'egr', 'Eucgr.A00858' => 'egr', 'Eucgr.H01520' => 'egr', 'Eucgr.H03604' => 'egr', 'Eucgr.L03465' => 'egr', 'Eucgr.L03466' => 'egr', 'FAN01G0988' => 'fan', 'FAN02G3892' => 'fan', 'FAN05G3381' => 'fan', 'FAN07G0967' => 'fan', 'FAN07G1493' => 'fan', 'FAN08G3125' => 'fan', 'FAN09G0402' => 'fan', 'FAN12G2594' => 'fan', 'FAN12G3879' => 'fan', 'FAN14G1546' => 'fan', 'FAN15G3626' => 'fan', 'FAN17G0588' => 'fan', 'FAN17G0609' => 'fan', 'FAN18G2817' => 'fan', 'FAN19G1305' => 'fan', 'FAN20G1787' => 'fan', 'FAN22G0073' => 'fan', 'FAN22G0352' => 'fan', 'FAN22G0368' => 'fan', 'FAN22G2273' => 'fan', 'FAN24G1998' => 'fan', 'FAN27G1317' => 'fan', 'FvH4_2g23980' => 'fve', 'FvH4_4g14380' => 'fve', 'FvH4_4g14390' => 'fve', 'FvH4_6g09250' => 'fve', 'Glyma.03G151100' => 'gma', 'Glyma.04G122550' => 'gma', 'Glyma.05G001600' => 'gma', 'Glyma.09G270766' => 'gma', 'Glyma.09G270832' => 'gma', 'Glyma.13G209800' => 'gma', 'Glyma.15G102800' => 'gma', 'Glyma.18G218900' => 'gma', 'Glyma.19G001500' => 'gma', 'Glyma.19G153600' => 'gma', 'Gohir.A02G028600' => 'ghi', 'Gohir.A08G045000' => 'ghi', 'Gohir.A11G120500' => 'ghi', 'Gohir.A12G006200' => 'ghi', 'Gohir.A12G006250' => 'ghi', 'Gohir.D02G036300' => 'ghi', 'Gohir.D08G054700' => 'ghi', 'Gohir.D11G125600' => 'ghi', 'Gohir.D12G005700' => 'ghi', 'Gorai.004G055200' => 'gra', 'Gorai.005G040400' => 'gra', 'Gorai.007G134500' => 'gra', 'Gorai.008G005500' => 'gra', 'GSVIVG01011094001' => 'vvi', 'GSVIVG01017879001' => 'vvi', 'GSVIVG01025988001' => 'vvi', 'GSVIVG01029847001' => 'vvi', 'HanXRQChr10g0282901' => 'han', 'HanXRQChr10g0310371' => 'han', 'HanXRQChr10g0315041' => 'han', 'HanXRQChr11g0327651' => 'han', 'HanXRQChr12g0359391' => 'han', 'Haze_00972' => 'cav', 'Haze_00973' => 'cav', 'Haze_00974' => 'cav', 'Haze_04747' => 'cav', 'Haze_04749' => 'cav', 'Haze_04750' => 'cav', 'Haze_21217' => 'cav', 'Hma1.2p1_1037F.1_g250680' => 'hma', 'Hma1.2p1_1644F.1_g295320' => 'hma', 'HPP92_011322' => 'vpl', 'HPP92_011323' => 'vpl', 'HPP92_011324' => 'vpl', 'HPP92_011325' => 'vpl', 'HPP92_011326' => 'vpl', 'Hund12205' => 'sun', 'Hund17957' => 'sun', 'Lalb_Chr06g0176771' => 'lal', 'Lalb_Chr18g0056021' => 'lal', 'Lalb_Chr18g0056031' => 'lal', 'Lalb_Chr18g0056041' => 'lal', 'Lalb_Chr20g0107751' => 'lal', 'Lalb_Chr20g0118371' => 'lal', 'Lj1g0010239' => 'lja', 'Lj1g0017101' => 'lja', 'Lj2A1178G40' => 'lonja', 'Lj2A54G84' => 'lonja', 'Lj2g0015248' => 'lja', 'Lj3A761T51' => 'lonja', 'Lj6g0018116' => 'lja', 'Lsat_1_v5_gn_4_136040' => 'lsa', 'Lsat_1_v5_gn_5_187461' => 'lsa', 'Lsat_1_v5_gn_5_77001' => 'lsa', 'Lsat_1_v5_gn_9_4461' => 'lsa', 'Manes.01G210100' => 'mes', 'Manes.03G185600' => 'mes', 'Manes.05G073300' => 'mes', 'Manes.09G120300' => 'mes', 'Manes.15G022100' => 'mes', 'Mapoly0096s0053' => 'mpo', 'MBI03_g14058_MAGBIO' => 'mbi', 'MBI03_g33876_MAGBIO' => 'mbi', 'MBI03_g36854_MAGBIO' => 'mbi', 'MBI17_g11997_MAGBIO' => 'mbi', 'MD03G1269000' => 'mdo', 'MD04G1179600' => 'mdo', 'MD11G1289800' => 'mdo', 'MD12G1194700' => 'mdo', 'MD13G1182100' => 'mdo', 'MD13G1182200' => 'mdo', 'MD16G1182600' => 'mdo', 'Medtr2g021400' => 'mtr', 'Medtr2g021470' => 'mtr', 'Medtr2g105810' => 'mtr', 'Medtr3g033580' => 'mtr', 'Medtr6g007970' => 'mtr', 'Medtr7g056330' => 'mtr', 'Medtr7g074290' => 'mtr', 'Medtr7g074380' => 'mtr', 'Medtr7g094550' => 'mtr', 'Medtr8g069995' => 'mtr', 'MELO3C014345.2' => 'cme', 'MELO3C021395.2' => 'cme', 'Migut.D00262' => 'egut', 'Migut.G00257' => 'egut', 'MSTRG.21575' => 'ama', 'MSTRG.3985' => 'ama', 'Nitab4.5_0000295g0140' => 'nta', 'Nitab4.5_0000732g0140' => 'nta', 'Nitab4.5_0003162g0020' => 'nta', 'Nitab4.5_0006180g0090' => 'nta', 'Nitab4.5_0006390g0010' => 'nta', 'Nitab4.5_0007392g0040' => 'nta', 'Nn1g02140' => 'nnu', 'Nn4g26168' => 'nnu', 'Nn5g26754' => 'nnu', 'Oeu001433.1' => 'oeu', 'Oeu010299.2' => 'oeu', 'Oeu011171.1' => 'oeu', 'Oeu037675.1' => 'oeu', 'Oeu038359.1' => 'oeu', 'Oeu063834.1' => 'oeu', 'Oeu063835.1' => 'oeu', 'Os05g0312000' => 'osa', 'Os07g0211101' => 'osa', 'Os07g0211200' => 'osa', 'Os07g0681500' => 'osa', 'Peaxi162Scf00095g01015' => 'pax', 'Peaxi162Scf00104g00329' => 'pax', 'Peaxi162Scf00161g00137' => 'pax', 'PGR004G1665' => 'pgr', 'PGR031G2937' => 'pgr', 'PGR119G2145' => 'pgr', 'PGSC0003DMG400004351' => 'stu', 'PGSC0003DMG400014625' => 'stu', 'PGSC0003DMG401000943' => 'stu', 'Phvul.001G148600' => 'pvu', 'Phvul.004G001700' => 'pvu', 'Phvul.006G154900' => 'pvu', 'Phvul.008G078200' => 'pvu', 'Phvul.011G136500' => 'pvu', 'Potri.002G215600' => 'ptr', 'Potri.008G201600' => 'ptr', 'Potri.014G138400' => 'ptr', 'Potri.016G142500' => 'ptr', 'Pp3c16_10580' => 'ppa', 'Pp3c5_25280' => 'ppa', 'Prupe.1G150000' => 'ppe', 'Prupe.1G150100' => 'ppe', 'Prupe.6G299600' => 'ppe', 'Prupe.8G245000' => 'ppe', 'Psat0s4927g0040' => 'psa', 'Psat1g052080' => 'psa', 'Psat1g183800' => 'psa', 'Psat3g113840' => 'psa', 'Psat3g126120' => 'psa', 'Psat3g126160' => 'psa', 'Psat3g158760' => 'psa', 'Psat3g158840' => 'psa', 'PSO170G2858' => 'pso', 'PSO339G0606' => 'pso', 'PSO384G4709' => 'pso', 'PSO407G0334' => 'pso', 'QL04p040276' => 'qlo', 'QL06p005458' => 'qlo', 'QL06p005472' => 'qlo', 'QL07p030546' => 'qlo', 'QL07p031519' => 'qlo', 'QL09p050949' => 'qlo', 'QL09p050966' => 'qlo', 'QL09p051067' => 'qlo', 'QL12p022706' => 'qlo', 'RcHm_v2.0_Chr2g0119601' => 'rch', 'RcHm_v2.0_Chr3g0459591' => 'rch', 'RcHm_v2.0_Chr4g0418521' => 'rch', 'RcHm_v2.0_Chr4g0418531' => 'rch', 'RcHm_v2.0_Chr4g0418541' => 'rch', 'RcHm_v2.0_Chr6g0291641' => 'rch', 'Rhsim01G0086300' => 'rsi', 'Rhsim01G0276300' => 'rsi', 'Rhsim01G0276500' => 'rsi', 'Rhsim04G0207700' => 'rsi', 'Rhsim05G0234500' => 'rsi', 'Rhsim13G0022400' => 'rsi', 'Sabra02G0167900' => 'sbr', 'Sabra04G0158500' => 'sbr', 'Sabra08G0159800' => 'sbr', 'Sabra10G0011500' => 'sbr', 'Sabra14G0104400' => 'sbr', 'SalBow2G2440' => 'sbo', 'SalBow4G2265' => 'sbo', 'Sc02g0000060' => 'sci', 'Sc05g0005020' => 'sci', 'Sc13g0003890' => 'sci', 'Sed0014865' => 'sed', 'Sed0017224' => 'sed', 'Sed0026391' => 'sed', 'SEGI_00063' => 'sgi', 'SEGI_10967' => 'sgi', 'SEGI_17510' => 'sgi', 'SEGI_24396' => 'sgi', 'SEGI_39719' => 'sgi', 'SEGI_41392' => 'sgi', 'SGA_v2.0_scaffold11G05794' => 'sas', 'SGA_v2.0_scaffold142G35607' => 'sas', 'SGA_v2.0_scaffold1G00447' => 'sas', 'SHI15388' => 'shi', 'SHI15394' => 'shi', 'SHI15396' => 'shi', 'SHI15399' => 'shi', 'SMO343G0151' => 'smo', 'SMO367G1118' => 'smo', 'Solyc01g080200.3' => 'sly', 'Solyc06g008960.3' => 'sly', 'Solyc09g064780.3' => 'sly', 'Sopen01g031980' => 'spe', 'Sopen06g003710' => 'spe', 'Sopen09g026460' => 'spe', 'Sp3g21240' => 'spa', 'Sp4g30030' => 'spa', 'TAR365G0022' => 'tar', 'TAR365G1023' => 'tar', 'TAR365G1253' => 'tar', 'TAR623G0078' => 'tar', 'TAR623G1721' => 'tar', 'TAR633G0959' => 'tar', 'THA.LOC104802225' => 'tha', 'THA.LOC104804769' => 'tha', 'THA.LOC104808660' => 'tha', 'THA.LOC104812792' => 'tha', 'Thecc.01G284000' => 'tca', 'Thecc.04G220600' => 'tca', 'Thecc.05G268900' => 'tca', 'Thecc.08G171100' => 'tca', 'Thhalv10001284m.g' => 'esa', 'Thhalv10019912m.g' => 'esa', 'TPR.G14189' => 'tpr', 'TPR.G18110' => 'tpr', 'TPR.G18130' => 'tpr', 'TPR.G18131' => 'tpr', 'TPR.G18140' => 'tpr', 'TPR.G24282' => 'tpr', 'TPR.G25221' => 'tpr', 'TPR.G29267' => 'tpr', 'TPR.G35315' => 'tpr', 'TPR.G36173' => 'tpr', 'TWI09G0794' => 'twi', 'TWI59G1348' => 'twi', 'TWI74G0430' => 'twi', 'unitig_26.g8940' => 'ugi', 'unitig_749.g13744' => 'ugi', 'unitig_749.g13745' => 'ugi', 'vmacro08269' => 'vma', 'vmacro14937' => 'vma', 'vmacro20401' => 'vma', 'VMungo0464G1349' => 'vmu', 'VMungo0540G0289' => 'vmu', 'VMungo1215G1590' => 'vmu', 'VMungo1309G0221' => 'vmu', 'VMungo1309G2815' => 'vmu', 'VMungo1383G0239' => 'vmu', 'VMungo1383G2910' => 'vmu', 'Zm00001eb095270' => 'zma', 'Zm00001eb095280' => 'zma', 'Zm00001eb111630' => 'zma', 'Zm00001eb237080' => 'zma', 'Zm00001eb273740' => 'zma', 'Zm00001eb285040' => 'zma', 'Zm00001eb330790' => 'zma', 'Zm00001eb337380' => 'zma' ), 'gf_id' => 'HOM05D001484', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001484' ), 'data_identifier' => 'HOM05D001484', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001484', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p31500' => 'bna', 'A05p00020' => 'bna', 'A07p08820' => 'bna', 'Aa31LG4G3300' => 'aar', 'Aa31LG8G10030' => 'aar', 'Actinidia00731' => 'ach', 'Actinidia11473' => 'ach', 'Actinidia23469' => 'ach', 'Actinidia24318' => 'ach', 'Actinidia40196' => 'ach', 'Actinidia40197' => 'ach', 'Actinidia40198' => 'ach', 'Ah.08g212990' => 'amhyb', 'Ah.15g091720' => 'amhyb', 'AL3G38260' => 'aly', 'AL4G47710' => 'aly', 'Aqoxy2G00671' => 'aox', 'Aqoxy2G03236' => 'aox', 'arahy.Tifrunner.gnm1.ann1.05IDCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KR684' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATY3SJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK6QJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6APGL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IDT7Z9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM073U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ0R87' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LE7RV4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT4QRX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V5ENPK' => 'arhy', 'AT2G48110' => 'ath', 'AT3G23590' => 'ath', 'ATR0626G186' => 'atr', 'ATR1127G141' => 'atr', 'Atru.chr4.2583' => 'acertr', 'Atru.chr5.1358' => 'acertr', 'Atru.chr5.1359' => 'acertr', 'Atru.chr8.46' => 'acertr', 'AUR62002640' => 'cqu', 'AUR62030055' => 'cqu', 'AUR62033713' => 'cqu', 'AUR62033714' => 'cqu', 'AUR62036795' => 'cqu', 'AUR62039891' => 'cqu', 'BcaB02g08737' => 'bca', 'BcaB04g20441' => 'bca', 'BcaB06g26509' => 'bca', 'BcaB06g26510' => 'bca', 'BcaB06g26511' => 'bca', 'BcaB06g26512' => 'bca', 'BcaB06g26513' => 'bca', 'BcaC02g12564' => 'bca', 'BcaC02g12565' => 'bca', 'BcaC02g12794' => 'bca', 'BcaC02g12795' => 'bca', 'BcaC02g12796' => 'bca', 'BcaC06g35541' => 'bca', 'BNapus_Darmor_BZH_scaffold_188p00080' => 'bna', 'BNapus_Darmor_BZH_scaffold_188p00090' => 'bna', 'BolC1t03972H' => 'bol', 'BolC1t03973H' => 'bol', 'BolC4t21680H' => 'bol', 'BolC7t41863H' => 'bol', 'BolSC55t61227H' => 'bol', 'BolSC55t61228H' => 'bol', 'BraA01t03278Z' => 'bra', 'BraA05t18998Z' => 'bra', 'BraA07t28673Z' => 'bra', 'C01p40150' => 'bna', 'C05p12370' => 'bna', 'C07p13680' => 'bna', 'CAN.G1006.16' => 'can', 'CAN.G1006.17' => 'can', 'CAN.G1170.2' => 'can', 'CAN.G962.7' => 'can', 'CANSAT25G2179' => 'cansat', 'CANSAT78G1573' => 'cansat', 'CARHR099510' => 'chi', 'CARHR143510' => 'chi', 'Carub.0003s2380' => 'cru', 'Carub.0004s3082' => 'cru', 'Ca_00614_v3' => 'car', 'Ca_07801_v3' => 'car', 'Ca_08567_v3' => 'car', 'Ca_09571_v3' => 'car', 'CBR_g19290' => 'cbr', 'Cc01_g19770' => 'ccan', 'Cc03_g03030' => 'ccan', 'CDE07G0968' => 'cde', 'CDE09G1441' => 'cde', 'Cfa006103' => 'cfa', 'Cfa015573' => 'cfa', 'Cfa016988' => 'cfa', 'Ciclev10006738m.g' => 'ccl', 'Ciclev10010920m.g' => 'ccl', 'Ciclev10018517m.g' => 'ccl', 'CiPaw.01G159200' => 'cil', 'CiPaw.02G091000' => 'cil', 'CiPaw.02G091100' => 'cil', 'CiPaw.08G103100' => 'cil', 'CiPaw.09G224900' => 'cil', 'ClCG06G005740' => 'cla', 'ClCG07G000090' => 'cla', 'ClCG07G000100' => 'cla', 'COL.COLO4_09143' => 'col', 'COL.COLO4_25124' => 'col', 'Cpa.g.sc16.34' => 'cpa', 'Cpa.g.sc3504.1' => 'cpa', 'Cpa.g.sc60.37' => 'cpa', 'CsaV3_6G018520' => 'csa', 'CsaV3_6G036860' => 'csa', 'CSS0001072' => 'camsi', 'CSS0020208' => 'camsi', 'CSS0021253' => 'camsi', 'CSS0022190' => 'camsi', 'CSS0036150' => 'camsi', 'CSS0040442' => 'camsi', 'CSS0042300' => 'camsi', 'CSS0045298' => 'camsi', 'DCAR_012449' => 'dca', 'DCAR_018405' => 'dca', 'DCAR_024573' => 'dca', 'DCAR_030591' => 'dca', 'Dinv16926' => 'din', 'Dinv32963' => 'din', 'Dinv38382' => 'din', 'Dinv38383' => 'din', 'Duzib133G0974' => 'dzi', 'Duzib138G1867' => 'dzi', 'Duzib211G0420' => 'dzi', 'Duzib212G0930' => 'dzi', 'ECA234G1645' => 'eca', 'ECA247G3467' => 'eca', 'ECA248G1703' => 'eca', 'EL10Ac3g06327' => 'bvu', 'EL10Ac7g17204' => 'bvu', 'Eucgr.A00855' => 'egr', 'Eucgr.A00858' => 'egr', 'Eucgr.H01520' => 'egr', 'Eucgr.H03604' => 'egr', 'Eucgr.L03465' => 'egr', 'Eucgr.L03466' => 'egr', 'FAN01G0988' => 'fan', 'FAN02G3892' => 'fan', 'FAN05G3381' => 'fan', 'FAN07G0967' => 'fan', 'FAN07G1493' => 'fan', 'FAN08G3125' => 'fan', 'FAN09G0402' => 'fan', 'FAN12G2594' => 'fan', 'FAN12G3879' => 'fan', 'FAN14G1546' => 'fan', 'FAN15G3626' => 'fan', 'FAN17G0588' => 'fan', 'FAN17G0609' => 'fan', 'FAN18G2817' => 'fan', 'FAN19G1305' => 'fan', 'FAN20G1787' => 'fan', 'FAN22G0073' => 'fan', 'FAN22G0352' => 'fan', 'FAN22G0368' => 'fan', 'FAN22G2273' => 'fan', 'FAN24G1998' => 'fan', 'FAN27G1317' => 'fan', 'FvH4_2g23980' => 'fve', 'FvH4_4g14380' => 'fve', 'FvH4_4g14390' => 'fve', 'FvH4_6g09250' => 'fve', 'Glyma.03G151100' => 'gma', 'Glyma.04G122550' => 'gma', 'Glyma.05G001600' => 'gma', 'Glyma.09G270766' => 'gma', 'Glyma.09G270832' => 'gma', 'Glyma.13G209800' => 'gma', 'Glyma.15G102800' => 'gma', 'Glyma.18G218900' => 'gma', 'Glyma.19G001500' => 'gma', 'Glyma.19G153600' => 'gma', 'Gohir.A02G028600' => 'ghi', 'Gohir.A08G045000' => 'ghi', 'Gohir.A11G120500' => 'ghi', 'Gohir.A12G006200' => 'ghi', 'Gohir.A12G006250' => 'ghi', 'Gohir.D02G036300' => 'ghi', 'Gohir.D08G054700' => 'ghi', 'Gohir.D11G125600' => 'ghi', 'Gohir.D12G005700' => 'ghi', 'Gorai.004G055200' => 'gra', 'Gorai.005G040400' => 'gra', 'Gorai.007G134500' => 'gra', 'Gorai.008G005500' => 'gra', 'GSVIVG01011094001' => 'vvi', 'GSVIVG01017879001' => 'vvi', 'GSVIVG01025988001' => 'vvi', 'GSVIVG01029847001' => 'vvi', 'HanXRQChr10g0282901' => 'han', 'HanXRQChr10g0310371' => 'han', 'HanXRQChr10g0315041' => 'han', 'HanXRQChr11g0327651' => 'han', 'HanXRQChr12g0359391' => 'han', 'Haze_00972' => 'cav', 'Haze_00973' => 'cav', 'Haze_00974' => 'cav', 'Haze_04747' => 'cav', 'Haze_04749' => 'cav', 'Haze_04750' => 'cav', 'Haze_21217' => 'cav', 'Hma1.2p1_1037F.1_g250680' => 'hma', 'Hma1.2p1_1644F.1_g295320' => 'hma', 'HPP92_011322' => 'vpl', 'HPP92_011323' => 'vpl', 'HPP92_011324' => 'vpl', 'HPP92_011325' => 'vpl', 'HPP92_011326' => 'vpl', 'Hund12205' => 'sun', 'Hund17957' => 'sun', 'Lalb_Chr06g0176771' => 'lal', 'Lalb_Chr18g0056021' => 'lal', 'Lalb_Chr18g0056031' => 'lal', 'Lalb_Chr18g0056041' => 'lal', 'Lalb_Chr20g0107751' => 'lal', 'Lalb_Chr20g0118371' => 'lal', 'Lj1g0010239' => 'lja', 'Lj1g0017101' => 'lja', 'Lj2A1178G40' => 'lonja', 'Lj2A54G84' => 'lonja', 'Lj2g0015248' => 'lja', 'Lj3A761T51' => 'lonja', 'Lj6g0018116' => 'lja', 'Lsat_1_v5_gn_4_136040' => 'lsa', 'Lsat_1_v5_gn_5_187461' => 'lsa', 'Lsat_1_v5_gn_5_77001' => 'lsa', 'Lsat_1_v5_gn_9_4461' => 'lsa', 'Manes.01G210100' => 'mes', 'Manes.03G185600' => 'mes', 'Manes.05G073300' => 'mes', 'Manes.09G120300' => 'mes', 'Manes.15G022100' => 'mes', 'Mapoly0096s0053' => 'mpo', 'MBI03_g14058_MAGBIO' => 'mbi', 'MBI03_g33876_MAGBIO' => 'mbi', 'MBI03_g36854_MAGBIO' => 'mbi', 'MBI17_g11997_MAGBIO' => 'mbi', 'MD03G1269000' => 'mdo', 'MD04G1179600' => 'mdo', 'MD11G1289800' => 'mdo', 'MD12G1194700' => 'mdo', 'MD13G1182100' => 'mdo', 'MD13G1182200' => 'mdo', 'MD16G1182600' => 'mdo', 'Medtr2g021400' => 'mtr', 'Medtr2g021470' => 'mtr', 'Medtr2g105810' => 'mtr', 'Medtr3g033580' => 'mtr', 'Medtr6g007970' => 'mtr', 'Medtr7g056330' => 'mtr', 'Medtr7g074290' => 'mtr', 'Medtr7g074380' => 'mtr', 'Medtr7g094550' => 'mtr', 'Medtr8g069995' => 'mtr', 'MELO3C014345.2' => 'cme', 'MELO3C021395.2' => 'cme', 'Migut.D00262' => 'egut', 'Migut.G00257' => 'egut', 'MSTRG.21575' => 'ama', 'MSTRG.3985' => 'ama', 'Nitab4.5_0000295g0140' => 'nta', 'Nitab4.5_0000732g0140' => 'nta', 'Nitab4.5_0003162g0020' => 'nta', 'Nitab4.5_0006180g0090' => 'nta', 'Nitab4.5_0006390g0010' => 'nta', 'Nitab4.5_0007392g0040' => 'nta', 'Nn1g02140' => 'nnu', 'Nn4g26168' => 'nnu', 'Nn5g26754' => 'nnu', 'Oeu001433.1' => 'oeu', 'Oeu010299.2' => 'oeu', 'Oeu011171.1' => 'oeu', 'Oeu037675.1' => 'oeu', 'Oeu038359.1' => 'oeu', 'Oeu063834.1' => 'oeu', 'Oeu063835.1' => 'oeu', 'Os05g0312000' => 'osa', 'Os07g0211101' => 'osa', 'Os07g0211200' => 'osa', 'Os07g0681500' => 'osa', 'Peaxi162Scf00095g01015' => 'pax', 'Peaxi162Scf00104g00329' => 'pax', 'Peaxi162Scf00161g00137' => 'pax', 'PGR004G1665' => 'pgr', 'PGR031G2937' => 'pgr', 'PGR119G2145' => 'pgr', 'PGSC0003DMG400004351' => 'stu', 'PGSC0003DMG400014625' => 'stu', 'PGSC0003DMG401000943' => 'stu', 'Phvul.001G148600' => 'pvu', 'Phvul.004G001700' => 'pvu', 'Phvul.006G154900' => 'pvu', 'Phvul.008G078200' => 'pvu', 'Phvul.011G136500' => 'pvu', 'Potri.002G215600' => 'ptr', 'Potri.008G201600' => 'ptr', 'Potri.014G138400' => 'ptr', 'Potri.016G142500' => 'ptr', 'Pp3c16_10580' => 'ppa', 'Pp3c5_25280' => 'ppa', 'Prupe.1G150000' => 'ppe', 'Prupe.1G150100' => 'ppe', 'Prupe.6G299600' => 'ppe', 'Prupe.8G245000' => 'ppe', 'Psat0s4927g0040' => 'psa', 'Psat1g052080' => 'psa', 'Psat1g183800' => 'psa', 'Psat3g113840' => 'psa', 'Psat3g126120' => 'psa', 'Psat3g126160' => 'psa', 'Psat3g158760' => 'psa', 'Psat3g158840' => 'psa', 'PSO170G2858' => 'pso', 'PSO339G0606' => 'pso', 'PSO384G4709' => 'pso', 'PSO407G0334' => 'pso', 'QL04p040276' => 'qlo', 'QL06p005458' => 'qlo', 'QL06p005472' => 'qlo', 'QL07p030546' => 'qlo', 'QL07p031519' => 'qlo', 'QL09p050949' => 'qlo', 'QL09p050966' => 'qlo', 'QL09p051067' => 'qlo', 'QL12p022706' => 'qlo', 'RcHm_v2.0_Chr2g0119601' => 'rch', 'RcHm_v2.0_Chr3g0459591' => 'rch', 'RcHm_v2.0_Chr4g0418521' => 'rch', 'RcHm_v2.0_Chr4g0418531' => 'rch', 'RcHm_v2.0_Chr4g0418541' => 'rch', 'RcHm_v2.0_Chr6g0291641' => 'rch', 'Rhsim01G0086300' => 'rsi', 'Rhsim01G0276300' => 'rsi', 'Rhsim01G0276500' => 'rsi', 'Rhsim04G0207700' => 'rsi', 'Rhsim05G0234500' => 'rsi', 'Rhsim13G0022400' => 'rsi', 'Sabra02G0167900' => 'sbr', 'Sabra04G0158500' => 'sbr', 'Sabra08G0159800' => 'sbr', 'Sabra10G0011500' => 'sbr', 'Sabra14G0104400' => 'sbr', 'SalBow2G2440' => 'sbo', 'SalBow4G2265' => 'sbo', 'Sc02g0000060' => 'sci', 'Sc05g0005020' => 'sci', 'Sc13g0003890' => 'sci', 'Sed0014865' => 'sed', 'Sed0017224' => 'sed', 'Sed0026391' => 'sed', 'SEGI_00063' => 'sgi', 'SEGI_10967' => 'sgi', 'SEGI_17510' => 'sgi', 'SEGI_24396' => 'sgi', 'SEGI_39719' => 'sgi', 'SEGI_41392' => 'sgi', 'SGA_v2.0_scaffold11G05794' => 'sas', 'SGA_v2.0_scaffold142G35607' => 'sas', 'SGA_v2.0_scaffold1G00447' => 'sas', 'SHI15388' => 'shi', 'SHI15394' => 'shi', 'SHI15396' => 'shi', 'SHI15399' => 'shi', 'SMO343G0151' => 'smo', 'SMO367G1118' => 'smo', 'Solyc01g080200.3' => 'sly', 'Solyc06g008960.3' => 'sly', 'Solyc09g064780.3' => 'sly', 'Sopen01g031980' => 'spe', 'Sopen06g003710' => 'spe', 'Sopen09g026460' => 'spe', 'Sp3g21240' => 'spa', 'Sp4g30030' => 'spa', 'TAR365G0022' => 'tar', 'TAR365G1023' => 'tar', 'TAR365G1253' => 'tar', 'TAR623G0078' => 'tar', 'TAR623G1721' => 'tar', 'TAR633G0959' => 'tar', 'THA.LOC104802225' => 'tha', 'THA.LOC104804769' => 'tha', 'THA.LOC104808660' => 'tha', 'THA.LOC104812792' => 'tha', 'Thecc.01G284000' => 'tca', 'Thecc.04G220600' => 'tca', 'Thecc.05G268900' => 'tca', 'Thecc.08G171100' => 'tca', 'Thhalv10001284m.g' => 'esa', 'Thhalv10019912m.g' => 'esa', 'TPR.G14189' => 'tpr', 'TPR.G18110' => 'tpr', 'TPR.G18130' => 'tpr', 'TPR.G18131' => 'tpr', 'TPR.G18140' => 'tpr', 'TPR.G24282' => 'tpr', 'TPR.G25221' => 'tpr', 'TPR.G29267' => 'tpr', 'TPR.G35315' => 'tpr', 'TPR.G36173' => 'tpr', 'TWI09G0794' => 'twi', 'TWI59G1348' => 'twi', 'TWI74G0430' => 'twi', 'unitig_26.g8940' => 'ugi', 'unitig_749.g13744' => 'ugi', 'unitig_749.g13745' => 'ugi', 'vmacro08269' => 'vma', 'vmacro14937' => 'vma', 'vmacro20401' => 'vma', 'VMungo0464G1349' => 'vmu', 'VMungo0540G0289' => 'vmu', 'VMungo1215G1590' => 'vmu', 'VMungo1309G0221' => 'vmu', 'VMungo1309G2815' => 'vmu', 'VMungo1383G0239' => 'vmu', 'VMungo1383G2910' => 'vmu', 'Zm00001eb095270' => 'zma', 'Zm00001eb095280' => 'zma', 'Zm00001eb111630' => 'zma', 'Zm00001eb237080' => 'zma', 'Zm00001eb273740' => 'zma', 'Zm00001eb285040' => 'zma', 'Zm00001eb330790' => 'zma', 'Zm00001eb337380' => 'zma' ) $gf_id = 'HOM05D001484' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001484' ) $data_identifier = 'HOM05D001484' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 2, 'aly' => (int) 2, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 22, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 7, 'hma' => (int) 2, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 7, 'mtr' => (int) 10, 'cme' => (int) 2, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 4, 'ppa' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 4, 'qlo' => (int) 9, 'rch' => (int) 6, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 10, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 7, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb337380' $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' => 'HOM05D001484', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p31500' => 'bna', 'A05p00020' => 'bna', 'A07p08820' => 'bna', 'Aa31LG4G3300' => 'aar', 'Aa31LG8G10030' => 'aar', 'Actinidia00731' => 'ach', 'Actinidia11473' => 'ach', 'Actinidia23469' => 'ach', 'Actinidia24318' => 'ach', 'Actinidia40196' => 'ach', 'Actinidia40197' => 'ach', 'Actinidia40198' => 'ach', 'Ah.08g212990' => 'amhyb', 'Ah.15g091720' => 'amhyb', 'AL3G38260' => 'aly', 'AL4G47710' => 'aly', 'Aqoxy2G00671' => 'aox', 'Aqoxy2G03236' => 'aox', 'arahy.Tifrunner.gnm1.ann1.05IDCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KR684' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATY3SJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK6QJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6APGL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IDT7Z9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM073U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ0R87' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LE7RV4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT4QRX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V5ENPK' => 'arhy', 'AT2G48110' => 'ath', 'AT3G23590' => 'ath', 'ATR0626G186' => 'atr', 'ATR1127G141' => 'atr', 'Atru.chr4.2583' => 'acertr', 'Atru.chr5.1358' => 'acertr', 'Atru.chr5.1359' => 'acertr', 'Atru.chr8.46' => 'acertr', 'AUR62002640' => 'cqu', 'AUR62030055' => 'cqu', 'AUR62033713' => 'cqu', 'AUR62033714' => 'cqu', 'AUR62036795' => 'cqu', 'AUR62039891' => 'cqu', 'BcaB02g08737' => 'bca', 'BcaB04g20441' => 'bca', 'BcaB06g26509' => 'bca', 'BcaB06g26510' => 'bca', 'BcaB06g26511' => 'bca', 'BcaB06g26512' => 'bca', 'BcaB06g26513' => 'bca', 'BcaC02g12564' => 'bca', 'BcaC02g12565' => 'bca', 'BcaC02g12794' => 'bca', 'BcaC02g12795' => 'bca', 'BcaC02g12796' => 'bca', 'BcaC06g35541' => 'bca', 'BNapus_Darmor_BZH_scaffold_188p00080' => 'bna', 'BNapus_Darmor_BZH_scaffold_188p00090' => 'bna', 'BolC1t03972H' => 'bol', 'BolC1t03973H' => 'bol', 'BolC4t21680H' => 'bol', 'BolC7t41863H' => 'bol', 'BolSC55t61227H' => 'bol', 'BolSC55t61228H' => 'bol', 'BraA01t03278Z' => 'bra', 'BraA05t18998Z' => 'bra', 'BraA07t28673Z' => 'bra', 'C01p40150' => 'bna', 'C05p12370' => 'bna', 'C07p13680' => 'bna', 'CAN.G1006.16' => 'can', 'CAN.G1006.17' => 'can', 'CAN.G1170.2' => 'can', 'CAN.G962.7' => 'can', 'CANSAT25G2179' => 'cansat', 'CANSAT78G1573' => 'cansat', 'CARHR099510' => 'chi', 'CARHR143510' => 'chi', 'Carub.0003s2380' => 'cru', 'Carub.0004s3082' => 'cru', 'Ca_00614_v3' => 'car', 'Ca_07801_v3' => 'car', 'Ca_08567_v3' => 'car', 'Ca_09571_v3' => 'car', 'CBR_g19290' => 'cbr', 'Cc01_g19770' => 'ccan', 'Cc03_g03030' => 'ccan', 'CDE07G0968' => 'cde', 'CDE09G1441' => 'cde', 'Cfa006103' => 'cfa', 'Cfa015573' => 'cfa', 'Cfa016988' => 'cfa', 'Ciclev10006738m.g' => 'ccl', 'Ciclev10010920m.g' => 'ccl', 'Ciclev10018517m.g' => 'ccl', 'CiPaw.01G159200' => 'cil', 'CiPaw.02G091000' => 'cil', 'CiPaw.02G091100' => 'cil', 'CiPaw.08G103100' => 'cil', 'CiPaw.09G224900' => 'cil', 'ClCG06G005740' => 'cla', 'ClCG07G000090' => 'cla', 'ClCG07G000100' => 'cla', 'COL.COLO4_09143' => 'col', 'COL.COLO4_25124' => 'col', 'Cpa.g.sc16.34' => 'cpa', 'Cpa.g.sc3504.1' => 'cpa', 'Cpa.g.sc60.37' => 'cpa', 'CsaV3_6G018520' => 'csa', 'CsaV3_6G036860' => 'csa', 'CSS0001072' => 'camsi', 'CSS0020208' => 'camsi', 'CSS0021253' => 'camsi', 'CSS0022190' => 'camsi', 'CSS0036150' => 'camsi', 'CSS0040442' => 'camsi', 'CSS0042300' => 'camsi', 'CSS0045298' => 'camsi', 'DCAR_012449' => 'dca', 'DCAR_018405' => 'dca', 'DCAR_024573' => 'dca', 'DCAR_030591' => 'dca', 'Dinv16926' => 'din', 'Dinv32963' => 'din', 'Dinv38382' => 'din', 'Dinv38383' => 'din', 'Duzib133G0974' => 'dzi', 'Duzib138G1867' => 'dzi', 'Duzib211G0420' => 'dzi', 'Duzib212G0930' => 'dzi', 'ECA234G1645' => 'eca', 'ECA247G3467' => 'eca', 'ECA248G1703' => 'eca', 'EL10Ac3g06327' => 'bvu', 'EL10Ac7g17204' => 'bvu', 'Eucgr.A00855' => 'egr', 'Eucgr.A00858' => 'egr', 'Eucgr.H01520' => 'egr', 'Eucgr.H03604' => 'egr', 'Eucgr.L03465' => 'egr', 'Eucgr.L03466' => 'egr', 'FAN01G0988' => 'fan', 'FAN02G3892' => 'fan', 'FAN05G3381' => 'fan', 'FAN07G0967' => 'fan', 'FAN07G1493' => 'fan', 'FAN08G3125' => 'fan', 'FAN09G0402' => 'fan', 'FAN12G2594' => 'fan', 'FAN12G3879' => 'fan', 'FAN14G1546' => 'fan', 'FAN15G3626' => 'fan', 'FAN17G0588' => 'fan', 'FAN17G0609' => 'fan', 'FAN18G2817' => 'fan', 'FAN19G1305' => 'fan', 'FAN20G1787' => 'fan', 'FAN22G0073' => 'fan', 'FAN22G0352' => 'fan', 'FAN22G0368' => 'fan', 'FAN22G2273' => 'fan', 'FAN24G1998' => 'fan', 'FAN27G1317' => 'fan', 'FvH4_2g23980' => 'fve', 'FvH4_4g14380' => 'fve', 'FvH4_4g14390' => 'fve', 'FvH4_6g09250' => 'fve', 'Glyma.03G151100' => 'gma', 'Glyma.04G122550' => 'gma', 'Glyma.05G001600' => 'gma', 'Glyma.09G270766' => 'gma', 'Glyma.09G270832' => 'gma', 'Glyma.13G209800' => 'gma', 'Glyma.15G102800' => 'gma', 'Glyma.18G218900' => 'gma', 'Glyma.19G001500' => 'gma', 'Glyma.19G153600' => 'gma', 'Gohir.A02G028600' => 'ghi', 'Gohir.A08G045000' => 'ghi', 'Gohir.A11G120500' => 'ghi', 'Gohir.A12G006200' => 'ghi', 'Gohir.A12G006250' => 'ghi', 'Gohir.D02G036300' => 'ghi', 'Gohir.D08G054700' => 'ghi', 'Gohir.D11G125600' => 'ghi', 'Gohir.D12G005700' => 'ghi', 'Gorai.004G055200' => 'gra', 'Gorai.005G040400' => 'gra', 'Gorai.007G134500' => 'gra', 'Gorai.008G005500' => 'gra', 'GSVIVG01011094001' => 'vvi', 'GSVIVG01017879001' => 'vvi', 'GSVIVG01025988001' => 'vvi', 'GSVIVG01029847001' => 'vvi', 'HanXRQChr10g0282901' => 'han', 'HanXRQChr10g0310371' => 'han', 'HanXRQChr10g0315041' => 'han', 'HanXRQChr11g0327651' => 'han', 'HanXRQChr12g0359391' => 'han', 'Haze_00972' => 'cav', 'Haze_00973' => 'cav', 'Haze_00974' => 'cav', 'Haze_04747' => 'cav', 'Haze_04749' => 'cav', 'Haze_04750' => 'cav', 'Haze_21217' => 'cav', 'Hma1.2p1_1037F.1_g250680' => 'hma', 'Hma1.2p1_1644F.1_g295320' => 'hma', 'HPP92_011322' => 'vpl', 'HPP92_011323' => 'vpl', 'HPP92_011324' => 'vpl', 'HPP92_011325' => 'vpl', 'HPP92_011326' => 'vpl', 'Hund12205' => 'sun', 'Hund17957' => 'sun', 'Lalb_Chr06g0176771' => 'lal', 'Lalb_Chr18g0056021' => 'lal', 'Lalb_Chr18g0056031' => 'lal', 'Lalb_Chr18g0056041' => 'lal', 'Lalb_Chr20g0107751' => 'lal', 'Lalb_Chr20g0118371' => 'lal', 'Lj1g0010239' => 'lja', 'Lj1g0017101' => 'lja', 'Lj2A1178G40' => 'lonja', 'Lj2A54G84' => 'lonja', 'Lj2g0015248' => 'lja', 'Lj3A761T51' => 'lonja', 'Lj6g0018116' => 'lja', 'Lsat_1_v5_gn_4_136040' => 'lsa', 'Lsat_1_v5_gn_5_187461' => 'lsa', 'Lsat_1_v5_gn_5_77001' => 'lsa', 'Lsat_1_v5_gn_9_4461' => 'lsa', 'Manes.01G210100' => 'mes', 'Manes.03G185600' => 'mes', 'Manes.05G073300' => 'mes', 'Manes.09G120300' => 'mes', 'Manes.15G022100' => 'mes', 'Mapoly0096s0053' => 'mpo', 'MBI03_g14058_MAGBIO' => 'mbi', 'MBI03_g33876_MAGBIO' => 'mbi', 'MBI03_g36854_MAGBIO' => 'mbi', 'MBI17_g11997_MAGBIO' => 'mbi', 'MD03G1269000' => 'mdo', 'MD04G1179600' => 'mdo', 'MD11G1289800' => 'mdo', 'MD12G1194700' => 'mdo', 'MD13G1182100' => 'mdo', 'MD13G1182200' => 'mdo', 'MD16G1182600' => 'mdo', 'Medtr2g021400' => 'mtr', 'Medtr2g021470' => 'mtr', 'Medtr2g105810' => 'mtr', 'Medtr3g033580' => 'mtr', 'Medtr6g007970' => 'mtr', 'Medtr7g056330' => 'mtr', 'Medtr7g074290' => 'mtr', 'Medtr7g074380' => 'mtr', 'Medtr7g094550' => 'mtr', 'Medtr8g069995' => 'mtr', 'MELO3C014345.2' => 'cme', 'MELO3C021395.2' => 'cme', 'Migut.D00262' => 'egut', 'Migut.G00257' => 'egut', 'MSTRG.21575' => 'ama', 'MSTRG.3985' => 'ama', 'Nitab4.5_0000295g0140' => 'nta', 'Nitab4.5_0000732g0140' => 'nta', 'Nitab4.5_0003162g0020' => 'nta', 'Nitab4.5_0006180g0090' => 'nta', 'Nitab4.5_0006390g0010' => 'nta', 'Nitab4.5_0007392g0040' => 'nta', 'Nn1g02140' => 'nnu', 'Nn4g26168' => 'nnu', 'Nn5g26754' => 'nnu', 'Oeu001433.1' => 'oeu', 'Oeu010299.2' => 'oeu', 'Oeu011171.1' => 'oeu', 'Oeu037675.1' => 'oeu', 'Oeu038359.1' => 'oeu', 'Oeu063834.1' => 'oeu', 'Oeu063835.1' => 'oeu', 'Os05g0312000' => 'osa', 'Os07g0211101' => 'osa', 'Os07g0211200' => 'osa', 'Os07g0681500' => 'osa', 'Peaxi162Scf00095g01015' => 'pax', 'Peaxi162Scf00104g00329' => 'pax', 'Peaxi162Scf00161g00137' => 'pax', 'PGR004G1665' => 'pgr', 'PGR031G2937' => 'pgr', 'PGR119G2145' => 'pgr', 'PGSC0003DMG400004351' => 'stu', 'PGSC0003DMG400014625' => 'stu', 'PGSC0003DMG401000943' => 'stu', 'Phvul.001G148600' => 'pvu', 'Phvul.004G001700' => 'pvu', 'Phvul.006G154900' => 'pvu', 'Phvul.008G078200' => 'pvu', 'Phvul.011G136500' => 'pvu', 'Potri.002G215600' => 'ptr', 'Potri.008G201600' => 'ptr', 'Potri.014G138400' => 'ptr', 'Potri.016G142500' => 'ptr', 'Pp3c16_10580' => 'ppa', 'Pp3c5_25280' => 'ppa', 'Prupe.1G150000' => 'ppe', 'Prupe.1G150100' => 'ppe', 'Prupe.6G299600' => 'ppe', 'Prupe.8G245000' => 'ppe', 'Psat0s4927g0040' => 'psa', 'Psat1g052080' => 'psa', 'Psat1g183800' => 'psa', 'Psat3g113840' => 'psa', 'Psat3g126120' => 'psa', 'Psat3g126160' => 'psa', 'Psat3g158760' => 'psa', 'Psat3g158840' => 'psa', 'PSO170G2858' => 'pso', 'PSO339G0606' => 'pso', 'PSO384G4709' => 'pso', 'PSO407G0334' => 'pso', 'QL04p040276' => 'qlo', 'QL06p005458' => 'qlo', 'QL06p005472' => 'qlo', 'QL07p030546' => 'qlo', 'QL07p031519' => 'qlo', 'QL09p050949' => 'qlo', 'QL09p050966' => 'qlo', 'QL09p051067' => 'qlo', 'QL12p022706' => 'qlo', 'RcHm_v2.0_Chr2g0119601' => 'rch', 'RcHm_v2.0_Chr3g0459591' => 'rch', 'RcHm_v2.0_Chr4g0418521' => 'rch', 'RcHm_v2.0_Chr4g0418531' => 'rch', 'RcHm_v2.0_Chr4g0418541' => 'rch', 'RcHm_v2.0_Chr6g0291641' => 'rch', 'Rhsim01G0086300' => 'rsi', 'Rhsim01G0276300' => 'rsi', 'Rhsim01G0276500' => 'rsi', 'Rhsim04G0207700' => 'rsi', 'Rhsim05G0234500' => 'rsi', 'Rhsim13G0022400' => 'rsi', 'Sabra02G0167900' => 'sbr', 'Sabra04G0158500' => 'sbr', 'Sabra08G0159800' => 'sbr', 'Sabra10G0011500' => 'sbr', 'Sabra14G0104400' => 'sbr', 'SalBow2G2440' => 'sbo', 'SalBow4G2265' => 'sbo', 'Sc02g0000060' => 'sci', 'Sc05g0005020' => 'sci', 'Sc13g0003890' => 'sci', 'Sed0014865' => 'sed', 'Sed0017224' => 'sed', 'Sed0026391' => 'sed', 'SEGI_00063' => 'sgi', 'SEGI_10967' => 'sgi', 'SEGI_17510' => 'sgi', 'SEGI_24396' => 'sgi', 'SEGI_39719' => 'sgi', 'SEGI_41392' => 'sgi', 'SGA_v2.0_scaffold11G05794' => 'sas', 'SGA_v2.0_scaffold142G35607' => 'sas', 'SGA_v2.0_scaffold1G00447' => 'sas', 'SHI15388' => 'shi', 'SHI15394' => 'shi', 'SHI15396' => 'shi', 'SHI15399' => 'shi', 'SMO343G0151' => 'smo', 'SMO367G1118' => 'smo', 'Solyc01g080200.3' => 'sly', 'Solyc06g008960.3' => 'sly', 'Solyc09g064780.3' => 'sly', 'Sopen01g031980' => 'spe', 'Sopen06g003710' => 'spe', 'Sopen09g026460' => 'spe', 'Sp3g21240' => 'spa', 'Sp4g30030' => 'spa', 'TAR365G0022' => 'tar', 'TAR365G1023' => 'tar', 'TAR365G1253' => 'tar', 'TAR623G0078' => 'tar', 'TAR623G1721' => 'tar', 'TAR633G0959' => 'tar', 'THA.LOC104802225' => 'tha', 'THA.LOC104804769' => 'tha', 'THA.LOC104808660' => 'tha', 'THA.LOC104812792' => 'tha', 'Thecc.01G284000' => 'tca', 'Thecc.04G220600' => 'tca', 'Thecc.05G268900' => 'tca', 'Thecc.08G171100' => 'tca', 'Thhalv10001284m.g' => 'esa', 'Thhalv10019912m.g' => 'esa', 'TPR.G14189' => 'tpr', 'TPR.G18110' => 'tpr', 'TPR.G18130' => 'tpr', 'TPR.G18131' => 'tpr', 'TPR.G18140' => 'tpr', 'TPR.G24282' => 'tpr', 'TPR.G25221' => 'tpr', 'TPR.G29267' => 'tpr', 'TPR.G35315' => 'tpr', 'TPR.G36173' => 'tpr', 'TWI09G0794' => 'twi', 'TWI59G1348' => 'twi', 'TWI74G0430' => 'twi', 'unitig_26.g8940' => 'ugi', 'unitig_749.g13744' => 'ugi', 'unitig_749.g13745' => 'ugi', 'vmacro08269' => 'vma', 'vmacro14937' => 'vma', 'vmacro20401' => 'vma', 'VMungo0464G1349' => 'vmu', 'VMungo0540G0289' => 'vmu', 'VMungo1215G1590' => 'vmu', 'VMungo1309G0221' => 'vmu', 'VMungo1309G2815' => 'vmu', 'VMungo1383G0239' => 'vmu', 'VMungo1383G2910' => 'vmu', 'Zm00001eb095270' => 'zma', 'Zm00001eb095280' => 'zma', 'Zm00001eb111630' => 'zma', 'Zm00001eb237080' => 'zma', 'Zm00001eb273740' => 'zma', 'Zm00001eb285040' => 'zma', 'Zm00001eb330790' => 'zma', 'Zm00001eb337380' => 'zma' ), 'gf_id' => 'HOM05D001484', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001484' ), 'data_identifier' => 'HOM05D001484', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001484', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p31500' => 'bna', 'A05p00020' => 'bna', 'A07p08820' => 'bna', 'Aa31LG4G3300' => 'aar', 'Aa31LG8G10030' => 'aar', 'Actinidia00731' => 'ach', 'Actinidia11473' => 'ach', 'Actinidia23469' => 'ach', 'Actinidia24318' => 'ach', 'Actinidia40196' => 'ach', 'Actinidia40197' => 'ach', 'Actinidia40198' => 'ach', 'Ah.08g212990' => 'amhyb', 'Ah.15g091720' => 'amhyb', 'AL3G38260' => 'aly', 'AL4G47710' => 'aly', 'Aqoxy2G00671' => 'aox', 'Aqoxy2G03236' => 'aox', 'arahy.Tifrunner.gnm1.ann1.05IDCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KR684' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATY3SJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK6QJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6APGL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IDT7Z9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM073U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ0R87' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LE7RV4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT4QRX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V5ENPK' => 'arhy', 'AT2G48110' => 'ath', 'AT3G23590' => 'ath', 'ATR0626G186' => 'atr', 'ATR1127G141' => 'atr', 'Atru.chr4.2583' => 'acertr', 'Atru.chr5.1358' => 'acertr', 'Atru.chr5.1359' => 'acertr', 'Atru.chr8.46' => 'acertr', 'AUR62002640' => 'cqu', 'AUR62030055' => 'cqu', 'AUR62033713' => 'cqu', 'AUR62033714' => 'cqu', 'AUR62036795' => 'cqu', 'AUR62039891' => 'cqu', 'BcaB02g08737' => 'bca', 'BcaB04g20441' => 'bca', 'BcaB06g26509' => 'bca', 'BcaB06g26510' => 'bca', 'BcaB06g26511' => 'bca', 'BcaB06g26512' => 'bca', 'BcaB06g26513' => 'bca', 'BcaC02g12564' => 'bca', 'BcaC02g12565' => 'bca', 'BcaC02g12794' => 'bca', 'BcaC02g12795' => 'bca', 'BcaC02g12796' => 'bca', 'BcaC06g35541' => 'bca', 'BNapus_Darmor_BZH_scaffold_188p00080' => 'bna', 'BNapus_Darmor_BZH_scaffold_188p00090' => 'bna', 'BolC1t03972H' => 'bol', 'BolC1t03973H' => 'bol', 'BolC4t21680H' => 'bol', 'BolC7t41863H' => 'bol', 'BolSC55t61227H' => 'bol', 'BolSC55t61228H' => 'bol', 'BraA01t03278Z' => 'bra', 'BraA05t18998Z' => 'bra', 'BraA07t28673Z' => 'bra', 'C01p40150' => 'bna', 'C05p12370' => 'bna', 'C07p13680' => 'bna', 'CAN.G1006.16' => 'can', 'CAN.G1006.17' => 'can', 'CAN.G1170.2' => 'can', 'CAN.G962.7' => 'can', 'CANSAT25G2179' => 'cansat', 'CANSAT78G1573' => 'cansat', 'CARHR099510' => 'chi', 'CARHR143510' => 'chi', 'Carub.0003s2380' => 'cru', 'Carub.0004s3082' => 'cru', 'Ca_00614_v3' => 'car', 'Ca_07801_v3' => 'car', 'Ca_08567_v3' => 'car', 'Ca_09571_v3' => 'car', 'CBR_g19290' => 'cbr', 'Cc01_g19770' => 'ccan', 'Cc03_g03030' => 'ccan', 'CDE07G0968' => 'cde', 'CDE09G1441' => 'cde', 'Cfa006103' => 'cfa', 'Cfa015573' => 'cfa', 'Cfa016988' => 'cfa', 'Ciclev10006738m.g' => 'ccl', 'Ciclev10010920m.g' => 'ccl', 'Ciclev10018517m.g' => 'ccl', 'CiPaw.01G159200' => 'cil', 'CiPaw.02G091000' => 'cil', 'CiPaw.02G091100' => 'cil', 'CiPaw.08G103100' => 'cil', 'CiPaw.09G224900' => 'cil', 'ClCG06G005740' => 'cla', 'ClCG07G000090' => 'cla', 'ClCG07G000100' => 'cla', 'COL.COLO4_09143' => 'col', 'COL.COLO4_25124' => 'col', 'Cpa.g.sc16.34' => 'cpa', 'Cpa.g.sc3504.1' => 'cpa', 'Cpa.g.sc60.37' => 'cpa', 'CsaV3_6G018520' => 'csa', 'CsaV3_6G036860' => 'csa', 'CSS0001072' => 'camsi', 'CSS0020208' => 'camsi', 'CSS0021253' => 'camsi', 'CSS0022190' => 'camsi', 'CSS0036150' => 'camsi', 'CSS0040442' => 'camsi', 'CSS0042300' => 'camsi', 'CSS0045298' => 'camsi', 'DCAR_012449' => 'dca', 'DCAR_018405' => 'dca', 'DCAR_024573' => 'dca', 'DCAR_030591' => 'dca', 'Dinv16926' => 'din', 'Dinv32963' => 'din', 'Dinv38382' => 'din', 'Dinv38383' => 'din', 'Duzib133G0974' => 'dzi', 'Duzib138G1867' => 'dzi', 'Duzib211G0420' => 'dzi', 'Duzib212G0930' => 'dzi', 'ECA234G1645' => 'eca', 'ECA247G3467' => 'eca', 'ECA248G1703' => 'eca', 'EL10Ac3g06327' => 'bvu', 'EL10Ac7g17204' => 'bvu', 'Eucgr.A00855' => 'egr', 'Eucgr.A00858' => 'egr', 'Eucgr.H01520' => 'egr', 'Eucgr.H03604' => 'egr', 'Eucgr.L03465' => 'egr', 'Eucgr.L03466' => 'egr', 'FAN01G0988' => 'fan', 'FAN02G3892' => 'fan', 'FAN05G3381' => 'fan', 'FAN07G0967' => 'fan', 'FAN07G1493' => 'fan', 'FAN08G3125' => 'fan', 'FAN09G0402' => 'fan', 'FAN12G2594' => 'fan', 'FAN12G3879' => 'fan', 'FAN14G1546' => 'fan', 'FAN15G3626' => 'fan', 'FAN17G0588' => 'fan', 'FAN17G0609' => 'fan', 'FAN18G2817' => 'fan', 'FAN19G1305' => 'fan', 'FAN20G1787' => 'fan', 'FAN22G0073' => 'fan', 'FAN22G0352' => 'fan', 'FAN22G0368' => 'fan', 'FAN22G2273' => 'fan', 'FAN24G1998' => 'fan', 'FAN27G1317' => 'fan', 'FvH4_2g23980' => 'fve', 'FvH4_4g14380' => 'fve', 'FvH4_4g14390' => 'fve', 'FvH4_6g09250' => 'fve', 'Glyma.03G151100' => 'gma', 'Glyma.04G122550' => 'gma', 'Glyma.05G001600' => 'gma', 'Glyma.09G270766' => 'gma', 'Glyma.09G270832' => 'gma', 'Glyma.13G209800' => 'gma', 'Glyma.15G102800' => 'gma', 'Glyma.18G218900' => 'gma', 'Glyma.19G001500' => 'gma', 'Glyma.19G153600' => 'gma', 'Gohir.A02G028600' => 'ghi', 'Gohir.A08G045000' => 'ghi', 'Gohir.A11G120500' => 'ghi', 'Gohir.A12G006200' => 'ghi', 'Gohir.A12G006250' => 'ghi', 'Gohir.D02G036300' => 'ghi', 'Gohir.D08G054700' => 'ghi', 'Gohir.D11G125600' => 'ghi', 'Gohir.D12G005700' => 'ghi', 'Gorai.004G055200' => 'gra', 'Gorai.005G040400' => 'gra', 'Gorai.007G134500' => 'gra', 'Gorai.008G005500' => 'gra', 'GSVIVG01011094001' => 'vvi', 'GSVIVG01017879001' => 'vvi', 'GSVIVG01025988001' => 'vvi', 'GSVIVG01029847001' => 'vvi', 'HanXRQChr10g0282901' => 'han', 'HanXRQChr10g0310371' => 'han', 'HanXRQChr10g0315041' => 'han', 'HanXRQChr11g0327651' => 'han', 'HanXRQChr12g0359391' => 'han', 'Haze_00972' => 'cav', 'Haze_00973' => 'cav', 'Haze_00974' => 'cav', 'Haze_04747' => 'cav', 'Haze_04749' => 'cav', 'Haze_04750' => 'cav', 'Haze_21217' => 'cav', 'Hma1.2p1_1037F.1_g250680' => 'hma', 'Hma1.2p1_1644F.1_g295320' => 'hma', 'HPP92_011322' => 'vpl', 'HPP92_011323' => 'vpl', 'HPP92_011324' => 'vpl', 'HPP92_011325' => 'vpl', 'HPP92_011326' => 'vpl', 'Hund12205' => 'sun', 'Hund17957' => 'sun', 'Lalb_Chr06g0176771' => 'lal', 'Lalb_Chr18g0056021' => 'lal', 'Lalb_Chr18g0056031' => 'lal', 'Lalb_Chr18g0056041' => 'lal', 'Lalb_Chr20g0107751' => 'lal', 'Lalb_Chr20g0118371' => 'lal', 'Lj1g0010239' => 'lja', 'Lj1g0017101' => 'lja', 'Lj2A1178G40' => 'lonja', 'Lj2A54G84' => 'lonja', 'Lj2g0015248' => 'lja', 'Lj3A761T51' => 'lonja', 'Lj6g0018116' => 'lja', 'Lsat_1_v5_gn_4_136040' => 'lsa', 'Lsat_1_v5_gn_5_187461' => 'lsa', 'Lsat_1_v5_gn_5_77001' => 'lsa', 'Lsat_1_v5_gn_9_4461' => 'lsa', 'Manes.01G210100' => 'mes', 'Manes.03G185600' => 'mes', 'Manes.05G073300' => 'mes', 'Manes.09G120300' => 'mes', 'Manes.15G022100' => 'mes', 'Mapoly0096s0053' => 'mpo', 'MBI03_g14058_MAGBIO' => 'mbi', 'MBI03_g33876_MAGBIO' => 'mbi', 'MBI03_g36854_MAGBIO' => 'mbi', 'MBI17_g11997_MAGBIO' => 'mbi', 'MD03G1269000' => 'mdo', 'MD04G1179600' => 'mdo', 'MD11G1289800' => 'mdo', 'MD12G1194700' => 'mdo', 'MD13G1182100' => 'mdo', 'MD13G1182200' => 'mdo', 'MD16G1182600' => 'mdo', 'Medtr2g021400' => 'mtr', 'Medtr2g021470' => 'mtr', 'Medtr2g105810' => 'mtr', 'Medtr3g033580' => 'mtr', 'Medtr6g007970' => 'mtr', 'Medtr7g056330' => 'mtr', 'Medtr7g074290' => 'mtr', 'Medtr7g074380' => 'mtr', 'Medtr7g094550' => 'mtr', 'Medtr8g069995' => 'mtr', 'MELO3C014345.2' => 'cme', 'MELO3C021395.2' => 'cme', 'Migut.D00262' => 'egut', 'Migut.G00257' => 'egut', 'MSTRG.21575' => 'ama', 'MSTRG.3985' => 'ama', 'Nitab4.5_0000295g0140' => 'nta', 'Nitab4.5_0000732g0140' => 'nta', 'Nitab4.5_0003162g0020' => 'nta', 'Nitab4.5_0006180g0090' => 'nta', 'Nitab4.5_0006390g0010' => 'nta', 'Nitab4.5_0007392g0040' => 'nta', 'Nn1g02140' => 'nnu', 'Nn4g26168' => 'nnu', 'Nn5g26754' => 'nnu', 'Oeu001433.1' => 'oeu', 'Oeu010299.2' => 'oeu', 'Oeu011171.1' => 'oeu', 'Oeu037675.1' => 'oeu', 'Oeu038359.1' => 'oeu', 'Oeu063834.1' => 'oeu', 'Oeu063835.1' => 'oeu', 'Os05g0312000' => 'osa', 'Os07g0211101' => 'osa', 'Os07g0211200' => 'osa', 'Os07g0681500' => 'osa', 'Peaxi162Scf00095g01015' => 'pax', 'Peaxi162Scf00104g00329' => 'pax', 'Peaxi162Scf00161g00137' => 'pax', 'PGR004G1665' => 'pgr', 'PGR031G2937' => 'pgr', 'PGR119G2145' => 'pgr', 'PGSC0003DMG400004351' => 'stu', 'PGSC0003DMG400014625' => 'stu', 'PGSC0003DMG401000943' => 'stu', 'Phvul.001G148600' => 'pvu', 'Phvul.004G001700' => 'pvu', 'Phvul.006G154900' => 'pvu', 'Phvul.008G078200' => 'pvu', 'Phvul.011G136500' => 'pvu', 'Potri.002G215600' => 'ptr', 'Potri.008G201600' => 'ptr', 'Potri.014G138400' => 'ptr', 'Potri.016G142500' => 'ptr', 'Pp3c16_10580' => 'ppa', 'Pp3c5_25280' => 'ppa', 'Prupe.1G150000' => 'ppe', 'Prupe.1G150100' => 'ppe', 'Prupe.6G299600' => 'ppe', 'Prupe.8G245000' => 'ppe', 'Psat0s4927g0040' => 'psa', 'Psat1g052080' => 'psa', 'Psat1g183800' => 'psa', 'Psat3g113840' => 'psa', 'Psat3g126120' => 'psa', 'Psat3g126160' => 'psa', 'Psat3g158760' => 'psa', 'Psat3g158840' => 'psa', 'PSO170G2858' => 'pso', 'PSO339G0606' => 'pso', 'PSO384G4709' => 'pso', 'PSO407G0334' => 'pso', 'QL04p040276' => 'qlo', 'QL06p005458' => 'qlo', 'QL06p005472' => 'qlo', 'QL07p030546' => 'qlo', 'QL07p031519' => 'qlo', 'QL09p050949' => 'qlo', 'QL09p050966' => 'qlo', 'QL09p051067' => 'qlo', 'QL12p022706' => 'qlo', 'RcHm_v2.0_Chr2g0119601' => 'rch', 'RcHm_v2.0_Chr3g0459591' => 'rch', 'RcHm_v2.0_Chr4g0418521' => 'rch', 'RcHm_v2.0_Chr4g0418531' => 'rch', 'RcHm_v2.0_Chr4g0418541' => 'rch', 'RcHm_v2.0_Chr6g0291641' => 'rch', 'Rhsim01G0086300' => 'rsi', 'Rhsim01G0276300' => 'rsi', 'Rhsim01G0276500' => 'rsi', 'Rhsim04G0207700' => 'rsi', 'Rhsim05G0234500' => 'rsi', 'Rhsim13G0022400' => 'rsi', 'Sabra02G0167900' => 'sbr', 'Sabra04G0158500' => 'sbr', 'Sabra08G0159800' => 'sbr', 'Sabra10G0011500' => 'sbr', 'Sabra14G0104400' => 'sbr', 'SalBow2G2440' => 'sbo', 'SalBow4G2265' => 'sbo', 'Sc02g0000060' => 'sci', 'Sc05g0005020' => 'sci', 'Sc13g0003890' => 'sci', 'Sed0014865' => 'sed', 'Sed0017224' => 'sed', 'Sed0026391' => 'sed', 'SEGI_00063' => 'sgi', 'SEGI_10967' => 'sgi', 'SEGI_17510' => 'sgi', 'SEGI_24396' => 'sgi', 'SEGI_39719' => 'sgi', 'SEGI_41392' => 'sgi', 'SGA_v2.0_scaffold11G05794' => 'sas', 'SGA_v2.0_scaffold142G35607' => 'sas', 'SGA_v2.0_scaffold1G00447' => 'sas', 'SHI15388' => 'shi', 'SHI15394' => 'shi', 'SHI15396' => 'shi', 'SHI15399' => 'shi', 'SMO343G0151' => 'smo', 'SMO367G1118' => 'smo', 'Solyc01g080200.3' => 'sly', 'Solyc06g008960.3' => 'sly', 'Solyc09g064780.3' => 'sly', 'Sopen01g031980' => 'spe', 'Sopen06g003710' => 'spe', 'Sopen09g026460' => 'spe', 'Sp3g21240' => 'spa', 'Sp4g30030' => 'spa', 'TAR365G0022' => 'tar', 'TAR365G1023' => 'tar', 'TAR365G1253' => 'tar', 'TAR623G0078' => 'tar', 'TAR623G1721' => 'tar', 'TAR633G0959' => 'tar', 'THA.LOC104802225' => 'tha', 'THA.LOC104804769' => 'tha', 'THA.LOC104808660' => 'tha', 'THA.LOC104812792' => 'tha', 'Thecc.01G284000' => 'tca', 'Thecc.04G220600' => 'tca', 'Thecc.05G268900' => 'tca', 'Thecc.08G171100' => 'tca', 'Thhalv10001284m.g' => 'esa', 'Thhalv10019912m.g' => 'esa', 'TPR.G14189' => 'tpr', 'TPR.G18110' => 'tpr', 'TPR.G18130' => 'tpr', 'TPR.G18131' => 'tpr', 'TPR.G18140' => 'tpr', 'TPR.G24282' => 'tpr', 'TPR.G25221' => 'tpr', 'TPR.G29267' => 'tpr', 'TPR.G35315' => 'tpr', 'TPR.G36173' => 'tpr', 'TWI09G0794' => 'twi', 'TWI59G1348' => 'twi', 'TWI74G0430' => 'twi', 'unitig_26.g8940' => 'ugi', 'unitig_749.g13744' => 'ugi', 'unitig_749.g13745' => 'ugi', 'vmacro08269' => 'vma', 'vmacro14937' => 'vma', 'vmacro20401' => 'vma', 'VMungo0464G1349' => 'vmu', 'VMungo0540G0289' => 'vmu', 'VMungo1215G1590' => 'vmu', 'VMungo1309G0221' => 'vmu', 'VMungo1309G2815' => 'vmu', 'VMungo1383G0239' => 'vmu', 'VMungo1383G2910' => 'vmu', 'Zm00001eb095270' => 'zma', 'Zm00001eb095280' => 'zma', 'Zm00001eb111630' => 'zma', 'Zm00001eb237080' => 'zma', 'Zm00001eb273740' => 'zma', 'Zm00001eb285040' => 'zma', 'Zm00001eb330790' => 'zma', 'Zm00001eb337380' => 'zma' ) $gf_id = 'HOM05D001484' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001484' ) $data_identifier = 'HOM05D001484' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 2, 'aly' => (int) 2, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 22, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 7, 'hma' => (int) 2, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 7, 'mtr' => (int) 10, 'cme' => (int) 2, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 4, 'ppa' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 4, 'qlo' => (int) 9, 'rch' => (int) 6, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 10, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 7, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb337380' $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' => 'HOM05D001484', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p31500' => 'bna', 'A05p00020' => 'bna', 'A07p08820' => 'bna', 'Aa31LG4G3300' => 'aar', 'Aa31LG8G10030' => 'aar', 'Actinidia00731' => 'ach', 'Actinidia11473' => 'ach', 'Actinidia23469' => 'ach', 'Actinidia24318' => 'ach', 'Actinidia40196' => 'ach', 'Actinidia40197' => 'ach', 'Actinidia40198' => 'ach', 'Ah.08g212990' => 'amhyb', 'Ah.15g091720' => 'amhyb', 'AL3G38260' => 'aly', 'AL4G47710' => 'aly', 'Aqoxy2G00671' => 'aox', 'Aqoxy2G03236' => 'aox', 'arahy.Tifrunner.gnm1.ann1.05IDCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KR684' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATY3SJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK6QJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6APGL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IDT7Z9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM073U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ0R87' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LE7RV4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT4QRX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V5ENPK' => 'arhy', 'AT2G48110' => 'ath', 'AT3G23590' => 'ath', 'ATR0626G186' => 'atr', 'ATR1127G141' => 'atr', 'Atru.chr4.2583' => 'acertr', 'Atru.chr5.1358' => 'acertr', 'Atru.chr5.1359' => 'acertr', 'Atru.chr8.46' => 'acertr', 'AUR62002640' => 'cqu', 'AUR62030055' => 'cqu', 'AUR62033713' => 'cqu', 'AUR62033714' => 'cqu', 'AUR62036795' => 'cqu', 'AUR62039891' => 'cqu', 'BcaB02g08737' => 'bca', 'BcaB04g20441' => 'bca', 'BcaB06g26509' => 'bca', 'BcaB06g26510' => 'bca', 'BcaB06g26511' => 'bca', 'BcaB06g26512' => 'bca', 'BcaB06g26513' => 'bca', 'BcaC02g12564' => 'bca', 'BcaC02g12565' => 'bca', 'BcaC02g12794' => 'bca', 'BcaC02g12795' => 'bca', 'BcaC02g12796' => 'bca', 'BcaC06g35541' => 'bca', 'BNapus_Darmor_BZH_scaffold_188p00080' => 'bna', 'BNapus_Darmor_BZH_scaffold_188p00090' => 'bna', 'BolC1t03972H' => 'bol', 'BolC1t03973H' => 'bol', 'BolC4t21680H' => 'bol', 'BolC7t41863H' => 'bol', 'BolSC55t61227H' => 'bol', 'BolSC55t61228H' => 'bol', 'BraA01t03278Z' => 'bra', 'BraA05t18998Z' => 'bra', 'BraA07t28673Z' => 'bra', 'C01p40150' => 'bna', 'C05p12370' => 'bna', 'C07p13680' => 'bna', 'CAN.G1006.16' => 'can', 'CAN.G1006.17' => 'can', 'CAN.G1170.2' => 'can', 'CAN.G962.7' => 'can', 'CANSAT25G2179' => 'cansat', 'CANSAT78G1573' => 'cansat', 'CARHR099510' => 'chi', 'CARHR143510' => 'chi', 'Carub.0003s2380' => 'cru', 'Carub.0004s3082' => 'cru', 'Ca_00614_v3' => 'car', 'Ca_07801_v3' => 'car', 'Ca_08567_v3' => 'car', 'Ca_09571_v3' => 'car', 'CBR_g19290' => 'cbr', 'Cc01_g19770' => 'ccan', 'Cc03_g03030' => 'ccan', 'CDE07G0968' => 'cde', 'CDE09G1441' => 'cde', 'Cfa006103' => 'cfa', 'Cfa015573' => 'cfa', 'Cfa016988' => 'cfa', 'Ciclev10006738m.g' => 'ccl', 'Ciclev10010920m.g' => 'ccl', 'Ciclev10018517m.g' => 'ccl', 'CiPaw.01G159200' => 'cil', 'CiPaw.02G091000' => 'cil', 'CiPaw.02G091100' => 'cil', 'CiPaw.08G103100' => 'cil', 'CiPaw.09G224900' => 'cil', 'ClCG06G005740' => 'cla', 'ClCG07G000090' => 'cla', 'ClCG07G000100' => 'cla', 'COL.COLO4_09143' => 'col', 'COL.COLO4_25124' => 'col', 'Cpa.g.sc16.34' => 'cpa', 'Cpa.g.sc3504.1' => 'cpa', 'Cpa.g.sc60.37' => 'cpa', 'CsaV3_6G018520' => 'csa', 'CsaV3_6G036860' => 'csa', 'CSS0001072' => 'camsi', 'CSS0020208' => 'camsi', 'CSS0021253' => 'camsi', 'CSS0022190' => 'camsi', 'CSS0036150' => 'camsi', 'CSS0040442' => 'camsi', 'CSS0042300' => 'camsi', 'CSS0045298' => 'camsi', 'DCAR_012449' => 'dca', 'DCAR_018405' => 'dca', 'DCAR_024573' => 'dca', 'DCAR_030591' => 'dca', 'Dinv16926' => 'din', 'Dinv32963' => 'din', 'Dinv38382' => 'din', 'Dinv38383' => 'din', 'Duzib133G0974' => 'dzi', 'Duzib138G1867' => 'dzi', 'Duzib211G0420' => 'dzi', 'Duzib212G0930' => 'dzi', 'ECA234G1645' => 'eca', 'ECA247G3467' => 'eca', 'ECA248G1703' => 'eca', 'EL10Ac3g06327' => 'bvu', 'EL10Ac7g17204' => 'bvu', 'Eucgr.A00855' => 'egr', 'Eucgr.A00858' => 'egr', 'Eucgr.H01520' => 'egr', 'Eucgr.H03604' => 'egr', 'Eucgr.L03465' => 'egr', 'Eucgr.L03466' => 'egr', 'FAN01G0988' => 'fan', 'FAN02G3892' => 'fan', 'FAN05G3381' => 'fan', 'FAN07G0967' => 'fan', 'FAN07G1493' => 'fan', 'FAN08G3125' => 'fan', 'FAN09G0402' => 'fan', 'FAN12G2594' => 'fan', 'FAN12G3879' => 'fan', 'FAN14G1546' => 'fan', 'FAN15G3626' => 'fan', 'FAN17G0588' => 'fan', 'FAN17G0609' => 'fan', 'FAN18G2817' => 'fan', 'FAN19G1305' => 'fan', 'FAN20G1787' => 'fan', 'FAN22G0073' => 'fan', 'FAN22G0352' => 'fan', 'FAN22G0368' => 'fan', 'FAN22G2273' => 'fan', 'FAN24G1998' => 'fan', 'FAN27G1317' => 'fan', 'FvH4_2g23980' => 'fve', 'FvH4_4g14380' => 'fve', 'FvH4_4g14390' => 'fve', 'FvH4_6g09250' => 'fve', 'Glyma.03G151100' => 'gma', 'Glyma.04G122550' => 'gma', 'Glyma.05G001600' => 'gma', 'Glyma.09G270766' => 'gma', 'Glyma.09G270832' => 'gma', 'Glyma.13G209800' => 'gma', 'Glyma.15G102800' => 'gma', 'Glyma.18G218900' => 'gma', 'Glyma.19G001500' => 'gma', 'Glyma.19G153600' => 'gma', 'Gohir.A02G028600' => 'ghi', 'Gohir.A08G045000' => 'ghi', 'Gohir.A11G120500' => 'ghi', 'Gohir.A12G006200' => 'ghi', 'Gohir.A12G006250' => 'ghi', 'Gohir.D02G036300' => 'ghi', 'Gohir.D08G054700' => 'ghi', 'Gohir.D11G125600' => 'ghi', 'Gohir.D12G005700' => 'ghi', 'Gorai.004G055200' => 'gra', 'Gorai.005G040400' => 'gra', 'Gorai.007G134500' => 'gra', 'Gorai.008G005500' => 'gra', 'GSVIVG01011094001' => 'vvi', 'GSVIVG01017879001' => 'vvi', 'GSVIVG01025988001' => 'vvi', 'GSVIVG01029847001' => 'vvi', 'HanXRQChr10g0282901' => 'han', 'HanXRQChr10g0310371' => 'han', 'HanXRQChr10g0315041' => 'han', 'HanXRQChr11g0327651' => 'han', 'HanXRQChr12g0359391' => 'han', 'Haze_00972' => 'cav', 'Haze_00973' => 'cav', 'Haze_00974' => 'cav', 'Haze_04747' => 'cav', 'Haze_04749' => 'cav', 'Haze_04750' => 'cav', 'Haze_21217' => 'cav', 'Hma1.2p1_1037F.1_g250680' => 'hma', 'Hma1.2p1_1644F.1_g295320' => 'hma', 'HPP92_011322' => 'vpl', 'HPP92_011323' => 'vpl', 'HPP92_011324' => 'vpl', 'HPP92_011325' => 'vpl', 'HPP92_011326' => 'vpl', 'Hund12205' => 'sun', 'Hund17957' => 'sun', 'Lalb_Chr06g0176771' => 'lal', 'Lalb_Chr18g0056021' => 'lal', 'Lalb_Chr18g0056031' => 'lal', 'Lalb_Chr18g0056041' => 'lal', 'Lalb_Chr20g0107751' => 'lal', 'Lalb_Chr20g0118371' => 'lal', 'Lj1g0010239' => 'lja', 'Lj1g0017101' => 'lja', 'Lj2A1178G40' => 'lonja', 'Lj2A54G84' => 'lonja', 'Lj2g0015248' => 'lja', 'Lj3A761T51' => 'lonja', 'Lj6g0018116' => 'lja', 'Lsat_1_v5_gn_4_136040' => 'lsa', 'Lsat_1_v5_gn_5_187461' => 'lsa', 'Lsat_1_v5_gn_5_77001' => 'lsa', 'Lsat_1_v5_gn_9_4461' => 'lsa', 'Manes.01G210100' => 'mes', 'Manes.03G185600' => 'mes', 'Manes.05G073300' => 'mes', 'Manes.09G120300' => 'mes', 'Manes.15G022100' => 'mes', 'Mapoly0096s0053' => 'mpo', 'MBI03_g14058_MAGBIO' => 'mbi', 'MBI03_g33876_MAGBIO' => 'mbi', 'MBI03_g36854_MAGBIO' => 'mbi', 'MBI17_g11997_MAGBIO' => 'mbi', 'MD03G1269000' => 'mdo', 'MD04G1179600' => 'mdo', 'MD11G1289800' => 'mdo', 'MD12G1194700' => 'mdo', 'MD13G1182100' => 'mdo', 'MD13G1182200' => 'mdo', 'MD16G1182600' => 'mdo', 'Medtr2g021400' => 'mtr', 'Medtr2g021470' => 'mtr', 'Medtr2g105810' => 'mtr', 'Medtr3g033580' => 'mtr', 'Medtr6g007970' => 'mtr', 'Medtr7g056330' => 'mtr', 'Medtr7g074290' => 'mtr', 'Medtr7g074380' => 'mtr', 'Medtr7g094550' => 'mtr', 'Medtr8g069995' => 'mtr', 'MELO3C014345.2' => 'cme', 'MELO3C021395.2' => 'cme', 'Migut.D00262' => 'egut', 'Migut.G00257' => 'egut', 'MSTRG.21575' => 'ama', 'MSTRG.3985' => 'ama', 'Nitab4.5_0000295g0140' => 'nta', 'Nitab4.5_0000732g0140' => 'nta', 'Nitab4.5_0003162g0020' => 'nta', 'Nitab4.5_0006180g0090' => 'nta', 'Nitab4.5_0006390g0010' => 'nta', 'Nitab4.5_0007392g0040' => 'nta', 'Nn1g02140' => 'nnu', 'Nn4g26168' => 'nnu', 'Nn5g26754' => 'nnu', 'Oeu001433.1' => 'oeu', 'Oeu010299.2' => 'oeu', 'Oeu011171.1' => 'oeu', 'Oeu037675.1' => 'oeu', 'Oeu038359.1' => 'oeu', 'Oeu063834.1' => 'oeu', 'Oeu063835.1' => 'oeu', 'Os05g0312000' => 'osa', 'Os07g0211101' => 'osa', 'Os07g0211200' => 'osa', 'Os07g0681500' => 'osa', 'Peaxi162Scf00095g01015' => 'pax', 'Peaxi162Scf00104g00329' => 'pax', 'Peaxi162Scf00161g00137' => 'pax', 'PGR004G1665' => 'pgr', 'PGR031G2937' => 'pgr', 'PGR119G2145' => 'pgr', 'PGSC0003DMG400004351' => 'stu', 'PGSC0003DMG400014625' => 'stu', 'PGSC0003DMG401000943' => 'stu', 'Phvul.001G148600' => 'pvu', 'Phvul.004G001700' => 'pvu', 'Phvul.006G154900' => 'pvu', 'Phvul.008G078200' => 'pvu', 'Phvul.011G136500' => 'pvu', 'Potri.002G215600' => 'ptr', 'Potri.008G201600' => 'ptr', 'Potri.014G138400' => 'ptr', 'Potri.016G142500' => 'ptr', 'Pp3c16_10580' => 'ppa', 'Pp3c5_25280' => 'ppa', 'Prupe.1G150000' => 'ppe', 'Prupe.1G150100' => 'ppe', 'Prupe.6G299600' => 'ppe', 'Prupe.8G245000' => 'ppe', 'Psat0s4927g0040' => 'psa', 'Psat1g052080' => 'psa', 'Psat1g183800' => 'psa', 'Psat3g113840' => 'psa', 'Psat3g126120' => 'psa', 'Psat3g126160' => 'psa', 'Psat3g158760' => 'psa', 'Psat3g158840' => 'psa', 'PSO170G2858' => 'pso', 'PSO339G0606' => 'pso', 'PSO384G4709' => 'pso', 'PSO407G0334' => 'pso', 'QL04p040276' => 'qlo', 'QL06p005458' => 'qlo', 'QL06p005472' => 'qlo', 'QL07p030546' => 'qlo', 'QL07p031519' => 'qlo', 'QL09p050949' => 'qlo', 'QL09p050966' => 'qlo', 'QL09p051067' => 'qlo', 'QL12p022706' => 'qlo', 'RcHm_v2.0_Chr2g0119601' => 'rch', 'RcHm_v2.0_Chr3g0459591' => 'rch', 'RcHm_v2.0_Chr4g0418521' => 'rch', 'RcHm_v2.0_Chr4g0418531' => 'rch', 'RcHm_v2.0_Chr4g0418541' => 'rch', 'RcHm_v2.0_Chr6g0291641' => 'rch', 'Rhsim01G0086300' => 'rsi', 'Rhsim01G0276300' => 'rsi', 'Rhsim01G0276500' => 'rsi', 'Rhsim04G0207700' => 'rsi', 'Rhsim05G0234500' => 'rsi', 'Rhsim13G0022400' => 'rsi', 'Sabra02G0167900' => 'sbr', 'Sabra04G0158500' => 'sbr', 'Sabra08G0159800' => 'sbr', 'Sabra10G0011500' => 'sbr', 'Sabra14G0104400' => 'sbr', 'SalBow2G2440' => 'sbo', 'SalBow4G2265' => 'sbo', 'Sc02g0000060' => 'sci', 'Sc05g0005020' => 'sci', 'Sc13g0003890' => 'sci', 'Sed0014865' => 'sed', 'Sed0017224' => 'sed', 'Sed0026391' => 'sed', 'SEGI_00063' => 'sgi', 'SEGI_10967' => 'sgi', 'SEGI_17510' => 'sgi', 'SEGI_24396' => 'sgi', 'SEGI_39719' => 'sgi', 'SEGI_41392' => 'sgi', 'SGA_v2.0_scaffold11G05794' => 'sas', 'SGA_v2.0_scaffold142G35607' => 'sas', 'SGA_v2.0_scaffold1G00447' => 'sas', 'SHI15388' => 'shi', 'SHI15394' => 'shi', 'SHI15396' => 'shi', 'SHI15399' => 'shi', 'SMO343G0151' => 'smo', 'SMO367G1118' => 'smo', 'Solyc01g080200.3' => 'sly', 'Solyc06g008960.3' => 'sly', 'Solyc09g064780.3' => 'sly', 'Sopen01g031980' => 'spe', 'Sopen06g003710' => 'spe', 'Sopen09g026460' => 'spe', 'Sp3g21240' => 'spa', 'Sp4g30030' => 'spa', 'TAR365G0022' => 'tar', 'TAR365G1023' => 'tar', 'TAR365G1253' => 'tar', 'TAR623G0078' => 'tar', 'TAR623G1721' => 'tar', 'TAR633G0959' => 'tar', 'THA.LOC104802225' => 'tha', 'THA.LOC104804769' => 'tha', 'THA.LOC104808660' => 'tha', 'THA.LOC104812792' => 'tha', 'Thecc.01G284000' => 'tca', 'Thecc.04G220600' => 'tca', 'Thecc.05G268900' => 'tca', 'Thecc.08G171100' => 'tca', 'Thhalv10001284m.g' => 'esa', 'Thhalv10019912m.g' => 'esa', 'TPR.G14189' => 'tpr', 'TPR.G18110' => 'tpr', 'TPR.G18130' => 'tpr', 'TPR.G18131' => 'tpr', 'TPR.G18140' => 'tpr', 'TPR.G24282' => 'tpr', 'TPR.G25221' => 'tpr', 'TPR.G29267' => 'tpr', 'TPR.G35315' => 'tpr', 'TPR.G36173' => 'tpr', 'TWI09G0794' => 'twi', 'TWI59G1348' => 'twi', 'TWI74G0430' => 'twi', 'unitig_26.g8940' => 'ugi', 'unitig_749.g13744' => 'ugi', 'unitig_749.g13745' => 'ugi', 'vmacro08269' => 'vma', 'vmacro14937' => 'vma', 'vmacro20401' => 'vma', 'VMungo0464G1349' => 'vmu', 'VMungo0540G0289' => 'vmu', 'VMungo1215G1590' => 'vmu', 'VMungo1309G0221' => 'vmu', 'VMungo1309G2815' => 'vmu', 'VMungo1383G0239' => 'vmu', 'VMungo1383G2910' => 'vmu', 'Zm00001eb095270' => 'zma', 'Zm00001eb095280' => 'zma', 'Zm00001eb111630' => 'zma', 'Zm00001eb237080' => 'zma', 'Zm00001eb273740' => 'zma', 'Zm00001eb285040' => 'zma', 'Zm00001eb330790' => 'zma', 'Zm00001eb337380' => 'zma' ), 'gf_id' => 'HOM05D001484', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001484' ), 'data_identifier' => 'HOM05D001484', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001484', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p31500' => 'bna', 'A05p00020' => 'bna', 'A07p08820' => 'bna', 'Aa31LG4G3300' => 'aar', 'Aa31LG8G10030' => 'aar', 'Actinidia00731' => 'ach', 'Actinidia11473' => 'ach', 'Actinidia23469' => 'ach', 'Actinidia24318' => 'ach', 'Actinidia40196' => 'ach', 'Actinidia40197' => 'ach', 'Actinidia40198' => 'ach', 'Ah.08g212990' => 'amhyb', 'Ah.15g091720' => 'amhyb', 'AL3G38260' => 'aly', 'AL4G47710' => 'aly', 'Aqoxy2G00671' => 'aox', 'Aqoxy2G03236' => 'aox', 'arahy.Tifrunner.gnm1.ann1.05IDCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KR684' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATY3SJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK6QJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6APGL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IDT7Z9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM073U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ0R87' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LE7RV4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT4QRX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V5ENPK' => 'arhy', 'AT2G48110' => 'ath', 'AT3G23590' => 'ath', 'ATR0626G186' => 'atr', 'ATR1127G141' => 'atr', 'Atru.chr4.2583' => 'acertr', 'Atru.chr5.1358' => 'acertr', 'Atru.chr5.1359' => 'acertr', 'Atru.chr8.46' => 'acertr', 'AUR62002640' => 'cqu', 'AUR62030055' => 'cqu', 'AUR62033713' => 'cqu', 'AUR62033714' => 'cqu', 'AUR62036795' => 'cqu', 'AUR62039891' => 'cqu', 'BcaB02g08737' => 'bca', 'BcaB04g20441' => 'bca', 'BcaB06g26509' => 'bca', 'BcaB06g26510' => 'bca', 'BcaB06g26511' => 'bca', 'BcaB06g26512' => 'bca', 'BcaB06g26513' => 'bca', 'BcaC02g12564' => 'bca', 'BcaC02g12565' => 'bca', 'BcaC02g12794' => 'bca', 'BcaC02g12795' => 'bca', 'BcaC02g12796' => 'bca', 'BcaC06g35541' => 'bca', 'BNapus_Darmor_BZH_scaffold_188p00080' => 'bna', 'BNapus_Darmor_BZH_scaffold_188p00090' => 'bna', 'BolC1t03972H' => 'bol', 'BolC1t03973H' => 'bol', 'BolC4t21680H' => 'bol', 'BolC7t41863H' => 'bol', 'BolSC55t61227H' => 'bol', 'BolSC55t61228H' => 'bol', 'BraA01t03278Z' => 'bra', 'BraA05t18998Z' => 'bra', 'BraA07t28673Z' => 'bra', 'C01p40150' => 'bna', 'C05p12370' => 'bna', 'C07p13680' => 'bna', 'CAN.G1006.16' => 'can', 'CAN.G1006.17' => 'can', 'CAN.G1170.2' => 'can', 'CAN.G962.7' => 'can', 'CANSAT25G2179' => 'cansat', 'CANSAT78G1573' => 'cansat', 'CARHR099510' => 'chi', 'CARHR143510' => 'chi', 'Carub.0003s2380' => 'cru', 'Carub.0004s3082' => 'cru', 'Ca_00614_v3' => 'car', 'Ca_07801_v3' => 'car', 'Ca_08567_v3' => 'car', 'Ca_09571_v3' => 'car', 'CBR_g19290' => 'cbr', 'Cc01_g19770' => 'ccan', 'Cc03_g03030' => 'ccan', 'CDE07G0968' => 'cde', 'CDE09G1441' => 'cde', 'Cfa006103' => 'cfa', 'Cfa015573' => 'cfa', 'Cfa016988' => 'cfa', 'Ciclev10006738m.g' => 'ccl', 'Ciclev10010920m.g' => 'ccl', 'Ciclev10018517m.g' => 'ccl', 'CiPaw.01G159200' => 'cil', 'CiPaw.02G091000' => 'cil', 'CiPaw.02G091100' => 'cil', 'CiPaw.08G103100' => 'cil', 'CiPaw.09G224900' => 'cil', 'ClCG06G005740' => 'cla', 'ClCG07G000090' => 'cla', 'ClCG07G000100' => 'cla', 'COL.COLO4_09143' => 'col', 'COL.COLO4_25124' => 'col', 'Cpa.g.sc16.34' => 'cpa', 'Cpa.g.sc3504.1' => 'cpa', 'Cpa.g.sc60.37' => 'cpa', 'CsaV3_6G018520' => 'csa', 'CsaV3_6G036860' => 'csa', 'CSS0001072' => 'camsi', 'CSS0020208' => 'camsi', 'CSS0021253' => 'camsi', 'CSS0022190' => 'camsi', 'CSS0036150' => 'camsi', 'CSS0040442' => 'camsi', 'CSS0042300' => 'camsi', 'CSS0045298' => 'camsi', 'DCAR_012449' => 'dca', 'DCAR_018405' => 'dca', 'DCAR_024573' => 'dca', 'DCAR_030591' => 'dca', 'Dinv16926' => 'din', 'Dinv32963' => 'din', 'Dinv38382' => 'din', 'Dinv38383' => 'din', 'Duzib133G0974' => 'dzi', 'Duzib138G1867' => 'dzi', 'Duzib211G0420' => 'dzi', 'Duzib212G0930' => 'dzi', 'ECA234G1645' => 'eca', 'ECA247G3467' => 'eca', 'ECA248G1703' => 'eca', 'EL10Ac3g06327' => 'bvu', 'EL10Ac7g17204' => 'bvu', 'Eucgr.A00855' => 'egr', 'Eucgr.A00858' => 'egr', 'Eucgr.H01520' => 'egr', 'Eucgr.H03604' => 'egr', 'Eucgr.L03465' => 'egr', 'Eucgr.L03466' => 'egr', 'FAN01G0988' => 'fan', 'FAN02G3892' => 'fan', 'FAN05G3381' => 'fan', 'FAN07G0967' => 'fan', 'FAN07G1493' => 'fan', 'FAN08G3125' => 'fan', 'FAN09G0402' => 'fan', 'FAN12G2594' => 'fan', 'FAN12G3879' => 'fan', 'FAN14G1546' => 'fan', 'FAN15G3626' => 'fan', 'FAN17G0588' => 'fan', 'FAN17G0609' => 'fan', 'FAN18G2817' => 'fan', 'FAN19G1305' => 'fan', 'FAN20G1787' => 'fan', 'FAN22G0073' => 'fan', 'FAN22G0352' => 'fan', 'FAN22G0368' => 'fan', 'FAN22G2273' => 'fan', 'FAN24G1998' => 'fan', 'FAN27G1317' => 'fan', 'FvH4_2g23980' => 'fve', 'FvH4_4g14380' => 'fve', 'FvH4_4g14390' => 'fve', 'FvH4_6g09250' => 'fve', 'Glyma.03G151100' => 'gma', 'Glyma.04G122550' => 'gma', 'Glyma.05G001600' => 'gma', 'Glyma.09G270766' => 'gma', 'Glyma.09G270832' => 'gma', 'Glyma.13G209800' => 'gma', 'Glyma.15G102800' => 'gma', 'Glyma.18G218900' => 'gma', 'Glyma.19G001500' => 'gma', 'Glyma.19G153600' => 'gma', 'Gohir.A02G028600' => 'ghi', 'Gohir.A08G045000' => 'ghi', 'Gohir.A11G120500' => 'ghi', 'Gohir.A12G006200' => 'ghi', 'Gohir.A12G006250' => 'ghi', 'Gohir.D02G036300' => 'ghi', 'Gohir.D08G054700' => 'ghi', 'Gohir.D11G125600' => 'ghi', 'Gohir.D12G005700' => 'ghi', 'Gorai.004G055200' => 'gra', 'Gorai.005G040400' => 'gra', 'Gorai.007G134500' => 'gra', 'Gorai.008G005500' => 'gra', 'GSVIVG01011094001' => 'vvi', 'GSVIVG01017879001' => 'vvi', 'GSVIVG01025988001' => 'vvi', 'GSVIVG01029847001' => 'vvi', 'HanXRQChr10g0282901' => 'han', 'HanXRQChr10g0310371' => 'han', 'HanXRQChr10g0315041' => 'han', 'HanXRQChr11g0327651' => 'han', 'HanXRQChr12g0359391' => 'han', 'Haze_00972' => 'cav', 'Haze_00973' => 'cav', 'Haze_00974' => 'cav', 'Haze_04747' => 'cav', 'Haze_04749' => 'cav', 'Haze_04750' => 'cav', 'Haze_21217' => 'cav', 'Hma1.2p1_1037F.1_g250680' => 'hma', 'Hma1.2p1_1644F.1_g295320' => 'hma', 'HPP92_011322' => 'vpl', 'HPP92_011323' => 'vpl', 'HPP92_011324' => 'vpl', 'HPP92_011325' => 'vpl', 'HPP92_011326' => 'vpl', 'Hund12205' => 'sun', 'Hund17957' => 'sun', 'Lalb_Chr06g0176771' => 'lal', 'Lalb_Chr18g0056021' => 'lal', 'Lalb_Chr18g0056031' => 'lal', 'Lalb_Chr18g0056041' => 'lal', 'Lalb_Chr20g0107751' => 'lal', 'Lalb_Chr20g0118371' => 'lal', 'Lj1g0010239' => 'lja', 'Lj1g0017101' => 'lja', 'Lj2A1178G40' => 'lonja', 'Lj2A54G84' => 'lonja', 'Lj2g0015248' => 'lja', 'Lj3A761T51' => 'lonja', 'Lj6g0018116' => 'lja', 'Lsat_1_v5_gn_4_136040' => 'lsa', 'Lsat_1_v5_gn_5_187461' => 'lsa', 'Lsat_1_v5_gn_5_77001' => 'lsa', 'Lsat_1_v5_gn_9_4461' => 'lsa', 'Manes.01G210100' => 'mes', 'Manes.03G185600' => 'mes', 'Manes.05G073300' => 'mes', 'Manes.09G120300' => 'mes', 'Manes.15G022100' => 'mes', 'Mapoly0096s0053' => 'mpo', 'MBI03_g14058_MAGBIO' => 'mbi', 'MBI03_g33876_MAGBIO' => 'mbi', 'MBI03_g36854_MAGBIO' => 'mbi', 'MBI17_g11997_MAGBIO' => 'mbi', 'MD03G1269000' => 'mdo', 'MD04G1179600' => 'mdo', 'MD11G1289800' => 'mdo', 'MD12G1194700' => 'mdo', 'MD13G1182100' => 'mdo', 'MD13G1182200' => 'mdo', 'MD16G1182600' => 'mdo', 'Medtr2g021400' => 'mtr', 'Medtr2g021470' => 'mtr', 'Medtr2g105810' => 'mtr', 'Medtr3g033580' => 'mtr', 'Medtr6g007970' => 'mtr', 'Medtr7g056330' => 'mtr', 'Medtr7g074290' => 'mtr', 'Medtr7g074380' => 'mtr', 'Medtr7g094550' => 'mtr', 'Medtr8g069995' => 'mtr', 'MELO3C014345.2' => 'cme', 'MELO3C021395.2' => 'cme', 'Migut.D00262' => 'egut', 'Migut.G00257' => 'egut', 'MSTRG.21575' => 'ama', 'MSTRG.3985' => 'ama', 'Nitab4.5_0000295g0140' => 'nta', 'Nitab4.5_0000732g0140' => 'nta', 'Nitab4.5_0003162g0020' => 'nta', 'Nitab4.5_0006180g0090' => 'nta', 'Nitab4.5_0006390g0010' => 'nta', 'Nitab4.5_0007392g0040' => 'nta', 'Nn1g02140' => 'nnu', 'Nn4g26168' => 'nnu', 'Nn5g26754' => 'nnu', 'Oeu001433.1' => 'oeu', 'Oeu010299.2' => 'oeu', 'Oeu011171.1' => 'oeu', 'Oeu037675.1' => 'oeu', 'Oeu038359.1' => 'oeu', 'Oeu063834.1' => 'oeu', 'Oeu063835.1' => 'oeu', 'Os05g0312000' => 'osa', 'Os07g0211101' => 'osa', 'Os07g0211200' => 'osa', 'Os07g0681500' => 'osa', 'Peaxi162Scf00095g01015' => 'pax', 'Peaxi162Scf00104g00329' => 'pax', 'Peaxi162Scf00161g00137' => 'pax', 'PGR004G1665' => 'pgr', 'PGR031G2937' => 'pgr', 'PGR119G2145' => 'pgr', 'PGSC0003DMG400004351' => 'stu', 'PGSC0003DMG400014625' => 'stu', 'PGSC0003DMG401000943' => 'stu', 'Phvul.001G148600' => 'pvu', 'Phvul.004G001700' => 'pvu', 'Phvul.006G154900' => 'pvu', 'Phvul.008G078200' => 'pvu', 'Phvul.011G136500' => 'pvu', 'Potri.002G215600' => 'ptr', 'Potri.008G201600' => 'ptr', 'Potri.014G138400' => 'ptr', 'Potri.016G142500' => 'ptr', 'Pp3c16_10580' => 'ppa', 'Pp3c5_25280' => 'ppa', 'Prupe.1G150000' => 'ppe', 'Prupe.1G150100' => 'ppe', 'Prupe.6G299600' => 'ppe', 'Prupe.8G245000' => 'ppe', 'Psat0s4927g0040' => 'psa', 'Psat1g052080' => 'psa', 'Psat1g183800' => 'psa', 'Psat3g113840' => 'psa', 'Psat3g126120' => 'psa', 'Psat3g126160' => 'psa', 'Psat3g158760' => 'psa', 'Psat3g158840' => 'psa', 'PSO170G2858' => 'pso', 'PSO339G0606' => 'pso', 'PSO384G4709' => 'pso', 'PSO407G0334' => 'pso', 'QL04p040276' => 'qlo', 'QL06p005458' => 'qlo', 'QL06p005472' => 'qlo', 'QL07p030546' => 'qlo', 'QL07p031519' => 'qlo', 'QL09p050949' => 'qlo', 'QL09p050966' => 'qlo', 'QL09p051067' => 'qlo', 'QL12p022706' => 'qlo', 'RcHm_v2.0_Chr2g0119601' => 'rch', 'RcHm_v2.0_Chr3g0459591' => 'rch', 'RcHm_v2.0_Chr4g0418521' => 'rch', 'RcHm_v2.0_Chr4g0418531' => 'rch', 'RcHm_v2.0_Chr4g0418541' => 'rch', 'RcHm_v2.0_Chr6g0291641' => 'rch', 'Rhsim01G0086300' => 'rsi', 'Rhsim01G0276300' => 'rsi', 'Rhsim01G0276500' => 'rsi', 'Rhsim04G0207700' => 'rsi', 'Rhsim05G0234500' => 'rsi', 'Rhsim13G0022400' => 'rsi', 'Sabra02G0167900' => 'sbr', 'Sabra04G0158500' => 'sbr', 'Sabra08G0159800' => 'sbr', 'Sabra10G0011500' => 'sbr', 'Sabra14G0104400' => 'sbr', 'SalBow2G2440' => 'sbo', 'SalBow4G2265' => 'sbo', 'Sc02g0000060' => 'sci', 'Sc05g0005020' => 'sci', 'Sc13g0003890' => 'sci', 'Sed0014865' => 'sed', 'Sed0017224' => 'sed', 'Sed0026391' => 'sed', 'SEGI_00063' => 'sgi', 'SEGI_10967' => 'sgi', 'SEGI_17510' => 'sgi', 'SEGI_24396' => 'sgi', 'SEGI_39719' => 'sgi', 'SEGI_41392' => 'sgi', 'SGA_v2.0_scaffold11G05794' => 'sas', 'SGA_v2.0_scaffold142G35607' => 'sas', 'SGA_v2.0_scaffold1G00447' => 'sas', 'SHI15388' => 'shi', 'SHI15394' => 'shi', 'SHI15396' => 'shi', 'SHI15399' => 'shi', 'SMO343G0151' => 'smo', 'SMO367G1118' => 'smo', 'Solyc01g080200.3' => 'sly', 'Solyc06g008960.3' => 'sly', 'Solyc09g064780.3' => 'sly', 'Sopen01g031980' => 'spe', 'Sopen06g003710' => 'spe', 'Sopen09g026460' => 'spe', 'Sp3g21240' => 'spa', 'Sp4g30030' => 'spa', 'TAR365G0022' => 'tar', 'TAR365G1023' => 'tar', 'TAR365G1253' => 'tar', 'TAR623G0078' => 'tar', 'TAR623G1721' => 'tar', 'TAR633G0959' => 'tar', 'THA.LOC104802225' => 'tha', 'THA.LOC104804769' => 'tha', 'THA.LOC104808660' => 'tha', 'THA.LOC104812792' => 'tha', 'Thecc.01G284000' => 'tca', 'Thecc.04G220600' => 'tca', 'Thecc.05G268900' => 'tca', 'Thecc.08G171100' => 'tca', 'Thhalv10001284m.g' => 'esa', 'Thhalv10019912m.g' => 'esa', 'TPR.G14189' => 'tpr', 'TPR.G18110' => 'tpr', 'TPR.G18130' => 'tpr', 'TPR.G18131' => 'tpr', 'TPR.G18140' => 'tpr', 'TPR.G24282' => 'tpr', 'TPR.G25221' => 'tpr', 'TPR.G29267' => 'tpr', 'TPR.G35315' => 'tpr', 'TPR.G36173' => 'tpr', 'TWI09G0794' => 'twi', 'TWI59G1348' => 'twi', 'TWI74G0430' => 'twi', 'unitig_26.g8940' => 'ugi', 'unitig_749.g13744' => 'ugi', 'unitig_749.g13745' => 'ugi', 'vmacro08269' => 'vma', 'vmacro14937' => 'vma', 'vmacro20401' => 'vma', 'VMungo0464G1349' => 'vmu', 'VMungo0540G0289' => 'vmu', 'VMungo1215G1590' => 'vmu', 'VMungo1309G0221' => 'vmu', 'VMungo1309G2815' => 'vmu', 'VMungo1383G0239' => 'vmu', 'VMungo1383G2910' => 'vmu', 'Zm00001eb095270' => 'zma', 'Zm00001eb095280' => 'zma', 'Zm00001eb111630' => 'zma', 'Zm00001eb237080' => 'zma', 'Zm00001eb273740' => 'zma', 'Zm00001eb285040' => 'zma', 'Zm00001eb330790' => 'zma', 'Zm00001eb337380' => 'zma' ) $gf_id = 'HOM05D001484' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001484' ) $data_identifier = 'HOM05D001484' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 2, 'aly' => (int) 2, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 22, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 7, 'hma' => (int) 2, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 7, 'mtr' => (int) 10, 'cme' => (int) 2, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 4, 'ppa' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 4, 'qlo' => (int) 9, 'rch' => (int) 6, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 10, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 7, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb337380' $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' => 'HOM05D001484', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p31500' => 'bna', 'A05p00020' => 'bna', 'A07p08820' => 'bna', 'Aa31LG4G3300' => 'aar', 'Aa31LG8G10030' => 'aar', 'Actinidia00731' => 'ach', 'Actinidia11473' => 'ach', 'Actinidia23469' => 'ach', 'Actinidia24318' => 'ach', 'Actinidia40196' => 'ach', 'Actinidia40197' => 'ach', 'Actinidia40198' => 'ach', 'Ah.08g212990' => 'amhyb', 'Ah.15g091720' => 'amhyb', 'AL3G38260' => 'aly', 'AL4G47710' => 'aly', 'Aqoxy2G00671' => 'aox', 'Aqoxy2G03236' => 'aox', 'arahy.Tifrunner.gnm1.ann1.05IDCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KR684' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATY3SJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK6QJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6APGL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IDT7Z9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM073U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ0R87' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LE7RV4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT4QRX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V5ENPK' => 'arhy', 'AT2G48110' => 'ath', 'AT3G23590' => 'ath', 'ATR0626G186' => 'atr', 'ATR1127G141' => 'atr', 'Atru.chr4.2583' => 'acertr', 'Atru.chr5.1358' => 'acertr', 'Atru.chr5.1359' => 'acertr', 'Atru.chr8.46' => 'acertr', 'AUR62002640' => 'cqu', 'AUR62030055' => 'cqu', 'AUR62033713' => 'cqu', 'AUR62033714' => 'cqu', 'AUR62036795' => 'cqu', 'AUR62039891' => 'cqu', 'BcaB02g08737' => 'bca', 'BcaB04g20441' => 'bca', 'BcaB06g26509' => 'bca', 'BcaB06g26510' => 'bca', 'BcaB06g26511' => 'bca', 'BcaB06g26512' => 'bca', 'BcaB06g26513' => 'bca', 'BcaC02g12564' => 'bca', 'BcaC02g12565' => 'bca', 'BcaC02g12794' => 'bca', 'BcaC02g12795' => 'bca', 'BcaC02g12796' => 'bca', 'BcaC06g35541' => 'bca', 'BNapus_Darmor_BZH_scaffold_188p00080' => 'bna', 'BNapus_Darmor_BZH_scaffold_188p00090' => 'bna', 'BolC1t03972H' => 'bol', 'BolC1t03973H' => 'bol', 'BolC4t21680H' => 'bol', 'BolC7t41863H' => 'bol', 'BolSC55t61227H' => 'bol', 'BolSC55t61228H' => 'bol', 'BraA01t03278Z' => 'bra', 'BraA05t18998Z' => 'bra', 'BraA07t28673Z' => 'bra', 'C01p40150' => 'bna', 'C05p12370' => 'bna', 'C07p13680' => 'bna', 'CAN.G1006.16' => 'can', 'CAN.G1006.17' => 'can', 'CAN.G1170.2' => 'can', 'CAN.G962.7' => 'can', 'CANSAT25G2179' => 'cansat', 'CANSAT78G1573' => 'cansat', 'CARHR099510' => 'chi', 'CARHR143510' => 'chi', 'Carub.0003s2380' => 'cru', 'Carub.0004s3082' => 'cru', 'Ca_00614_v3' => 'car', 'Ca_07801_v3' => 'car', 'Ca_08567_v3' => 'car', 'Ca_09571_v3' => 'car', 'CBR_g19290' => 'cbr', 'Cc01_g19770' => 'ccan', 'Cc03_g03030' => 'ccan', 'CDE07G0968' => 'cde', 'CDE09G1441' => 'cde', 'Cfa006103' => 'cfa', 'Cfa015573' => 'cfa', 'Cfa016988' => 'cfa', 'Ciclev10006738m.g' => 'ccl', 'Ciclev10010920m.g' => 'ccl', 'Ciclev10018517m.g' => 'ccl', 'CiPaw.01G159200' => 'cil', 'CiPaw.02G091000' => 'cil', 'CiPaw.02G091100' => 'cil', 'CiPaw.08G103100' => 'cil', 'CiPaw.09G224900' => 'cil', 'ClCG06G005740' => 'cla', 'ClCG07G000090' => 'cla', 'ClCG07G000100' => 'cla', 'COL.COLO4_09143' => 'col', 'COL.COLO4_25124' => 'col', 'Cpa.g.sc16.34' => 'cpa', 'Cpa.g.sc3504.1' => 'cpa', 'Cpa.g.sc60.37' => 'cpa', 'CsaV3_6G018520' => 'csa', 'CsaV3_6G036860' => 'csa', 'CSS0001072' => 'camsi', 'CSS0020208' => 'camsi', 'CSS0021253' => 'camsi', 'CSS0022190' => 'camsi', 'CSS0036150' => 'camsi', 'CSS0040442' => 'camsi', 'CSS0042300' => 'camsi', 'CSS0045298' => 'camsi', 'DCAR_012449' => 'dca', 'DCAR_018405' => 'dca', 'DCAR_024573' => 'dca', 'DCAR_030591' => 'dca', 'Dinv16926' => 'din', 'Dinv32963' => 'din', 'Dinv38382' => 'din', 'Dinv38383' => 'din', 'Duzib133G0974' => 'dzi', 'Duzib138G1867' => 'dzi', 'Duzib211G0420' => 'dzi', 'Duzib212G0930' => 'dzi', 'ECA234G1645' => 'eca', 'ECA247G3467' => 'eca', 'ECA248G1703' => 'eca', 'EL10Ac3g06327' => 'bvu', 'EL10Ac7g17204' => 'bvu', 'Eucgr.A00855' => 'egr', 'Eucgr.A00858' => 'egr', 'Eucgr.H01520' => 'egr', 'Eucgr.H03604' => 'egr', 'Eucgr.L03465' => 'egr', 'Eucgr.L03466' => 'egr', 'FAN01G0988' => 'fan', 'FAN02G3892' => 'fan', 'FAN05G3381' => 'fan', 'FAN07G0967' => 'fan', 'FAN07G1493' => 'fan', 'FAN08G3125' => 'fan', 'FAN09G0402' => 'fan', 'FAN12G2594' => 'fan', 'FAN12G3879' => 'fan', 'FAN14G1546' => 'fan', 'FAN15G3626' => 'fan', 'FAN17G0588' => 'fan', 'FAN17G0609' => 'fan', 'FAN18G2817' => 'fan', 'FAN19G1305' => 'fan', 'FAN20G1787' => 'fan', 'FAN22G0073' => 'fan', 'FAN22G0352' => 'fan', 'FAN22G0368' => 'fan', 'FAN22G2273' => 'fan', 'FAN24G1998' => 'fan', 'FAN27G1317' => 'fan', 'FvH4_2g23980' => 'fve', 'FvH4_4g14380' => 'fve', 'FvH4_4g14390' => 'fve', 'FvH4_6g09250' => 'fve', 'Glyma.03G151100' => 'gma', 'Glyma.04G122550' => 'gma', 'Glyma.05G001600' => 'gma', 'Glyma.09G270766' => 'gma', 'Glyma.09G270832' => 'gma', 'Glyma.13G209800' => 'gma', 'Glyma.15G102800' => 'gma', 'Glyma.18G218900' => 'gma', 'Glyma.19G001500' => 'gma', 'Glyma.19G153600' => 'gma', 'Gohir.A02G028600' => 'ghi', 'Gohir.A08G045000' => 'ghi', 'Gohir.A11G120500' => 'ghi', 'Gohir.A12G006200' => 'ghi', 'Gohir.A12G006250' => 'ghi', 'Gohir.D02G036300' => 'ghi', 'Gohir.D08G054700' => 'ghi', 'Gohir.D11G125600' => 'ghi', 'Gohir.D12G005700' => 'ghi', 'Gorai.004G055200' => 'gra', 'Gorai.005G040400' => 'gra', 'Gorai.007G134500' => 'gra', 'Gorai.008G005500' => 'gra', 'GSVIVG01011094001' => 'vvi', 'GSVIVG01017879001' => 'vvi', 'GSVIVG01025988001' => 'vvi', 'GSVIVG01029847001' => 'vvi', 'HanXRQChr10g0282901' => 'han', 'HanXRQChr10g0310371' => 'han', 'HanXRQChr10g0315041' => 'han', 'HanXRQChr11g0327651' => 'han', 'HanXRQChr12g0359391' => 'han', 'Haze_00972' => 'cav', 'Haze_00973' => 'cav', 'Haze_00974' => 'cav', 'Haze_04747' => 'cav', 'Haze_04749' => 'cav', 'Haze_04750' => 'cav', 'Haze_21217' => 'cav', 'Hma1.2p1_1037F.1_g250680' => 'hma', 'Hma1.2p1_1644F.1_g295320' => 'hma', 'HPP92_011322' => 'vpl', 'HPP92_011323' => 'vpl', 'HPP92_011324' => 'vpl', 'HPP92_011325' => 'vpl', 'HPP92_011326' => 'vpl', 'Hund12205' => 'sun', 'Hund17957' => 'sun', 'Lalb_Chr06g0176771' => 'lal', 'Lalb_Chr18g0056021' => 'lal', 'Lalb_Chr18g0056031' => 'lal', 'Lalb_Chr18g0056041' => 'lal', 'Lalb_Chr20g0107751' => 'lal', 'Lalb_Chr20g0118371' => 'lal', 'Lj1g0010239' => 'lja', 'Lj1g0017101' => 'lja', 'Lj2A1178G40' => 'lonja', 'Lj2A54G84' => 'lonja', 'Lj2g0015248' => 'lja', 'Lj3A761T51' => 'lonja', 'Lj6g0018116' => 'lja', 'Lsat_1_v5_gn_4_136040' => 'lsa', 'Lsat_1_v5_gn_5_187461' => 'lsa', 'Lsat_1_v5_gn_5_77001' => 'lsa', 'Lsat_1_v5_gn_9_4461' => 'lsa', 'Manes.01G210100' => 'mes', 'Manes.03G185600' => 'mes', 'Manes.05G073300' => 'mes', 'Manes.09G120300' => 'mes', 'Manes.15G022100' => 'mes', 'Mapoly0096s0053' => 'mpo', 'MBI03_g14058_MAGBIO' => 'mbi', 'MBI03_g33876_MAGBIO' => 'mbi', 'MBI03_g36854_MAGBIO' => 'mbi', 'MBI17_g11997_MAGBIO' => 'mbi', 'MD03G1269000' => 'mdo', 'MD04G1179600' => 'mdo', 'MD11G1289800' => 'mdo', 'MD12G1194700' => 'mdo', 'MD13G1182100' => 'mdo', 'MD13G1182200' => 'mdo', 'MD16G1182600' => 'mdo', 'Medtr2g021400' => 'mtr', 'Medtr2g021470' => 'mtr', 'Medtr2g105810' => 'mtr', 'Medtr3g033580' => 'mtr', 'Medtr6g007970' => 'mtr', 'Medtr7g056330' => 'mtr', 'Medtr7g074290' => 'mtr', 'Medtr7g074380' => 'mtr', 'Medtr7g094550' => 'mtr', 'Medtr8g069995' => 'mtr', 'MELO3C014345.2' => 'cme', 'MELO3C021395.2' => 'cme', 'Migut.D00262' => 'egut', 'Migut.G00257' => 'egut', 'MSTRG.21575' => 'ama', 'MSTRG.3985' => 'ama', 'Nitab4.5_0000295g0140' => 'nta', 'Nitab4.5_0000732g0140' => 'nta', 'Nitab4.5_0003162g0020' => 'nta', 'Nitab4.5_0006180g0090' => 'nta', 'Nitab4.5_0006390g0010' => 'nta', 'Nitab4.5_0007392g0040' => 'nta', 'Nn1g02140' => 'nnu', 'Nn4g26168' => 'nnu', 'Nn5g26754' => 'nnu', 'Oeu001433.1' => 'oeu', 'Oeu010299.2' => 'oeu', 'Oeu011171.1' => 'oeu', 'Oeu037675.1' => 'oeu', 'Oeu038359.1' => 'oeu', 'Oeu063834.1' => 'oeu', 'Oeu063835.1' => 'oeu', 'Os05g0312000' => 'osa', 'Os07g0211101' => 'osa', 'Os07g0211200' => 'osa', 'Os07g0681500' => 'osa', 'Peaxi162Scf00095g01015' => 'pax', 'Peaxi162Scf00104g00329' => 'pax', 'Peaxi162Scf00161g00137' => 'pax', 'PGR004G1665' => 'pgr', 'PGR031G2937' => 'pgr', 'PGR119G2145' => 'pgr', 'PGSC0003DMG400004351' => 'stu', 'PGSC0003DMG400014625' => 'stu', 'PGSC0003DMG401000943' => 'stu', 'Phvul.001G148600' => 'pvu', 'Phvul.004G001700' => 'pvu', 'Phvul.006G154900' => 'pvu', 'Phvul.008G078200' => 'pvu', 'Phvul.011G136500' => 'pvu', 'Potri.002G215600' => 'ptr', 'Potri.008G201600' => 'ptr', 'Potri.014G138400' => 'ptr', 'Potri.016G142500' => 'ptr', 'Pp3c16_10580' => 'ppa', 'Pp3c5_25280' => 'ppa', 'Prupe.1G150000' => 'ppe', 'Prupe.1G150100' => 'ppe', 'Prupe.6G299600' => 'ppe', 'Prupe.8G245000' => 'ppe', 'Psat0s4927g0040' => 'psa', 'Psat1g052080' => 'psa', 'Psat1g183800' => 'psa', 'Psat3g113840' => 'psa', 'Psat3g126120' => 'psa', 'Psat3g126160' => 'psa', 'Psat3g158760' => 'psa', 'Psat3g158840' => 'psa', 'PSO170G2858' => 'pso', 'PSO339G0606' => 'pso', 'PSO384G4709' => 'pso', 'PSO407G0334' => 'pso', 'QL04p040276' => 'qlo', 'QL06p005458' => 'qlo', 'QL06p005472' => 'qlo', 'QL07p030546' => 'qlo', 'QL07p031519' => 'qlo', 'QL09p050949' => 'qlo', 'QL09p050966' => 'qlo', 'QL09p051067' => 'qlo', 'QL12p022706' => 'qlo', 'RcHm_v2.0_Chr2g0119601' => 'rch', 'RcHm_v2.0_Chr3g0459591' => 'rch', 'RcHm_v2.0_Chr4g0418521' => 'rch', 'RcHm_v2.0_Chr4g0418531' => 'rch', 'RcHm_v2.0_Chr4g0418541' => 'rch', 'RcHm_v2.0_Chr6g0291641' => 'rch', 'Rhsim01G0086300' => 'rsi', 'Rhsim01G0276300' => 'rsi', 'Rhsim01G0276500' => 'rsi', 'Rhsim04G0207700' => 'rsi', 'Rhsim05G0234500' => 'rsi', 'Rhsim13G0022400' => 'rsi', 'Sabra02G0167900' => 'sbr', 'Sabra04G0158500' => 'sbr', 'Sabra08G0159800' => 'sbr', 'Sabra10G0011500' => 'sbr', 'Sabra14G0104400' => 'sbr', 'SalBow2G2440' => 'sbo', 'SalBow4G2265' => 'sbo', 'Sc02g0000060' => 'sci', 'Sc05g0005020' => 'sci', 'Sc13g0003890' => 'sci', 'Sed0014865' => 'sed', 'Sed0017224' => 'sed', 'Sed0026391' => 'sed', 'SEGI_00063' => 'sgi', 'SEGI_10967' => 'sgi', 'SEGI_17510' => 'sgi', 'SEGI_24396' => 'sgi', 'SEGI_39719' => 'sgi', 'SEGI_41392' => 'sgi', 'SGA_v2.0_scaffold11G05794' => 'sas', 'SGA_v2.0_scaffold142G35607' => 'sas', 'SGA_v2.0_scaffold1G00447' => 'sas', 'SHI15388' => 'shi', 'SHI15394' => 'shi', 'SHI15396' => 'shi', 'SHI15399' => 'shi', 'SMO343G0151' => 'smo', 'SMO367G1118' => 'smo', 'Solyc01g080200.3' => 'sly', 'Solyc06g008960.3' => 'sly', 'Solyc09g064780.3' => 'sly', 'Sopen01g031980' => 'spe', 'Sopen06g003710' => 'spe', 'Sopen09g026460' => 'spe', 'Sp3g21240' => 'spa', 'Sp4g30030' => 'spa', 'TAR365G0022' => 'tar', 'TAR365G1023' => 'tar', 'TAR365G1253' => 'tar', 'TAR623G0078' => 'tar', 'TAR623G1721' => 'tar', 'TAR633G0959' => 'tar', 'THA.LOC104802225' => 'tha', 'THA.LOC104804769' => 'tha', 'THA.LOC104808660' => 'tha', 'THA.LOC104812792' => 'tha', 'Thecc.01G284000' => 'tca', 'Thecc.04G220600' => 'tca', 'Thecc.05G268900' => 'tca', 'Thecc.08G171100' => 'tca', 'Thhalv10001284m.g' => 'esa', 'Thhalv10019912m.g' => 'esa', 'TPR.G14189' => 'tpr', 'TPR.G18110' => 'tpr', 'TPR.G18130' => 'tpr', 'TPR.G18131' => 'tpr', 'TPR.G18140' => 'tpr', 'TPR.G24282' => 'tpr', 'TPR.G25221' => 'tpr', 'TPR.G29267' => 'tpr', 'TPR.G35315' => 'tpr', 'TPR.G36173' => 'tpr', 'TWI09G0794' => 'twi', 'TWI59G1348' => 'twi', 'TWI74G0430' => 'twi', 'unitig_26.g8940' => 'ugi', 'unitig_749.g13744' => 'ugi', 'unitig_749.g13745' => 'ugi', 'vmacro08269' => 'vma', 'vmacro14937' => 'vma', 'vmacro20401' => 'vma', 'VMungo0464G1349' => 'vmu', 'VMungo0540G0289' => 'vmu', 'VMungo1215G1590' => 'vmu', 'VMungo1309G0221' => 'vmu', 'VMungo1309G2815' => 'vmu', 'VMungo1383G0239' => 'vmu', 'VMungo1383G2910' => 'vmu', 'Zm00001eb095270' => 'zma', 'Zm00001eb095280' => 'zma', 'Zm00001eb111630' => 'zma', 'Zm00001eb237080' => 'zma', 'Zm00001eb273740' => 'zma', 'Zm00001eb285040' => 'zma', 'Zm00001eb330790' => 'zma', 'Zm00001eb337380' => 'zma' ), 'gf_id' => 'HOM05D001484', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001484' ), 'data_identifier' => 'HOM05D001484', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001484', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p31500' => 'bna', 'A05p00020' => 'bna', 'A07p08820' => 'bna', 'Aa31LG4G3300' => 'aar', 'Aa31LG8G10030' => 'aar', 'Actinidia00731' => 'ach', 'Actinidia11473' => 'ach', 'Actinidia23469' => 'ach', 'Actinidia24318' => 'ach', 'Actinidia40196' => 'ach', 'Actinidia40197' => 'ach', 'Actinidia40198' => 'ach', 'Ah.08g212990' => 'amhyb', 'Ah.15g091720' => 'amhyb', 'AL3G38260' => 'aly', 'AL4G47710' => 'aly', 'Aqoxy2G00671' => 'aox', 'Aqoxy2G03236' => 'aox', 'arahy.Tifrunner.gnm1.ann1.05IDCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KR684' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATY3SJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK6QJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6APGL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IDT7Z9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM073U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ0R87' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LE7RV4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT4QRX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V5ENPK' => 'arhy', 'AT2G48110' => 'ath', 'AT3G23590' => 'ath', 'ATR0626G186' => 'atr', 'ATR1127G141' => 'atr', 'Atru.chr4.2583' => 'acertr', 'Atru.chr5.1358' => 'acertr', 'Atru.chr5.1359' => 'acertr', 'Atru.chr8.46' => 'acertr', 'AUR62002640' => 'cqu', 'AUR62030055' => 'cqu', 'AUR62033713' => 'cqu', 'AUR62033714' => 'cqu', 'AUR62036795' => 'cqu', 'AUR62039891' => 'cqu', 'BcaB02g08737' => 'bca', 'BcaB04g20441' => 'bca', 'BcaB06g26509' => 'bca', 'BcaB06g26510' => 'bca', 'BcaB06g26511' => 'bca', 'BcaB06g26512' => 'bca', 'BcaB06g26513' => 'bca', 'BcaC02g12564' => 'bca', 'BcaC02g12565' => 'bca', 'BcaC02g12794' => 'bca', 'BcaC02g12795' => 'bca', 'BcaC02g12796' => 'bca', 'BcaC06g35541' => 'bca', 'BNapus_Darmor_BZH_scaffold_188p00080' => 'bna', 'BNapus_Darmor_BZH_scaffold_188p00090' => 'bna', 'BolC1t03972H' => 'bol', 'BolC1t03973H' => 'bol', 'BolC4t21680H' => 'bol', 'BolC7t41863H' => 'bol', 'BolSC55t61227H' => 'bol', 'BolSC55t61228H' => 'bol', 'BraA01t03278Z' => 'bra', 'BraA05t18998Z' => 'bra', 'BraA07t28673Z' => 'bra', 'C01p40150' => 'bna', 'C05p12370' => 'bna', 'C07p13680' => 'bna', 'CAN.G1006.16' => 'can', 'CAN.G1006.17' => 'can', 'CAN.G1170.2' => 'can', 'CAN.G962.7' => 'can', 'CANSAT25G2179' => 'cansat', 'CANSAT78G1573' => 'cansat', 'CARHR099510' => 'chi', 'CARHR143510' => 'chi', 'Carub.0003s2380' => 'cru', 'Carub.0004s3082' => 'cru', 'Ca_00614_v3' => 'car', 'Ca_07801_v3' => 'car', 'Ca_08567_v3' => 'car', 'Ca_09571_v3' => 'car', 'CBR_g19290' => 'cbr', 'Cc01_g19770' => 'ccan', 'Cc03_g03030' => 'ccan', 'CDE07G0968' => 'cde', 'CDE09G1441' => 'cde', 'Cfa006103' => 'cfa', 'Cfa015573' => 'cfa', 'Cfa016988' => 'cfa', 'Ciclev10006738m.g' => 'ccl', 'Ciclev10010920m.g' => 'ccl', 'Ciclev10018517m.g' => 'ccl', 'CiPaw.01G159200' => 'cil', 'CiPaw.02G091000' => 'cil', 'CiPaw.02G091100' => 'cil', 'CiPaw.08G103100' => 'cil', 'CiPaw.09G224900' => 'cil', 'ClCG06G005740' => 'cla', 'ClCG07G000090' => 'cla', 'ClCG07G000100' => 'cla', 'COL.COLO4_09143' => 'col', 'COL.COLO4_25124' => 'col', 'Cpa.g.sc16.34' => 'cpa', 'Cpa.g.sc3504.1' => 'cpa', 'Cpa.g.sc60.37' => 'cpa', 'CsaV3_6G018520' => 'csa', 'CsaV3_6G036860' => 'csa', 'CSS0001072' => 'camsi', 'CSS0020208' => 'camsi', 'CSS0021253' => 'camsi', 'CSS0022190' => 'camsi', 'CSS0036150' => 'camsi', 'CSS0040442' => 'camsi', 'CSS0042300' => 'camsi', 'CSS0045298' => 'camsi', 'DCAR_012449' => 'dca', 'DCAR_018405' => 'dca', 'DCAR_024573' => 'dca', 'DCAR_030591' => 'dca', 'Dinv16926' => 'din', 'Dinv32963' => 'din', 'Dinv38382' => 'din', 'Dinv38383' => 'din', 'Duzib133G0974' => 'dzi', 'Duzib138G1867' => 'dzi', 'Duzib211G0420' => 'dzi', 'Duzib212G0930' => 'dzi', 'ECA234G1645' => 'eca', 'ECA247G3467' => 'eca', 'ECA248G1703' => 'eca', 'EL10Ac3g06327' => 'bvu', 'EL10Ac7g17204' => 'bvu', 'Eucgr.A00855' => 'egr', 'Eucgr.A00858' => 'egr', 'Eucgr.H01520' => 'egr', 'Eucgr.H03604' => 'egr', 'Eucgr.L03465' => 'egr', 'Eucgr.L03466' => 'egr', 'FAN01G0988' => 'fan', 'FAN02G3892' => 'fan', 'FAN05G3381' => 'fan', 'FAN07G0967' => 'fan', 'FAN07G1493' => 'fan', 'FAN08G3125' => 'fan', 'FAN09G0402' => 'fan', 'FAN12G2594' => 'fan', 'FAN12G3879' => 'fan', 'FAN14G1546' => 'fan', 'FAN15G3626' => 'fan', 'FAN17G0588' => 'fan', 'FAN17G0609' => 'fan', 'FAN18G2817' => 'fan', 'FAN19G1305' => 'fan', 'FAN20G1787' => 'fan', 'FAN22G0073' => 'fan', 'FAN22G0352' => 'fan', 'FAN22G0368' => 'fan', 'FAN22G2273' => 'fan', 'FAN24G1998' => 'fan', 'FAN27G1317' => 'fan', 'FvH4_2g23980' => 'fve', 'FvH4_4g14380' => 'fve', 'FvH4_4g14390' => 'fve', 'FvH4_6g09250' => 'fve', 'Glyma.03G151100' => 'gma', 'Glyma.04G122550' => 'gma', 'Glyma.05G001600' => 'gma', 'Glyma.09G270766' => 'gma', 'Glyma.09G270832' => 'gma', 'Glyma.13G209800' => 'gma', 'Glyma.15G102800' => 'gma', 'Glyma.18G218900' => 'gma', 'Glyma.19G001500' => 'gma', 'Glyma.19G153600' => 'gma', 'Gohir.A02G028600' => 'ghi', 'Gohir.A08G045000' => 'ghi', 'Gohir.A11G120500' => 'ghi', 'Gohir.A12G006200' => 'ghi', 'Gohir.A12G006250' => 'ghi', 'Gohir.D02G036300' => 'ghi', 'Gohir.D08G054700' => 'ghi', 'Gohir.D11G125600' => 'ghi', 'Gohir.D12G005700' => 'ghi', 'Gorai.004G055200' => 'gra', 'Gorai.005G040400' => 'gra', 'Gorai.007G134500' => 'gra', 'Gorai.008G005500' => 'gra', 'GSVIVG01011094001' => 'vvi', 'GSVIVG01017879001' => 'vvi', 'GSVIVG01025988001' => 'vvi', 'GSVIVG01029847001' => 'vvi', 'HanXRQChr10g0282901' => 'han', 'HanXRQChr10g0310371' => 'han', 'HanXRQChr10g0315041' => 'han', 'HanXRQChr11g0327651' => 'han', 'HanXRQChr12g0359391' => 'han', 'Haze_00972' => 'cav', 'Haze_00973' => 'cav', 'Haze_00974' => 'cav', 'Haze_04747' => 'cav', 'Haze_04749' => 'cav', 'Haze_04750' => 'cav', 'Haze_21217' => 'cav', 'Hma1.2p1_1037F.1_g250680' => 'hma', 'Hma1.2p1_1644F.1_g295320' => 'hma', 'HPP92_011322' => 'vpl', 'HPP92_011323' => 'vpl', 'HPP92_011324' => 'vpl', 'HPP92_011325' => 'vpl', 'HPP92_011326' => 'vpl', 'Hund12205' => 'sun', 'Hund17957' => 'sun', 'Lalb_Chr06g0176771' => 'lal', 'Lalb_Chr18g0056021' => 'lal', 'Lalb_Chr18g0056031' => 'lal', 'Lalb_Chr18g0056041' => 'lal', 'Lalb_Chr20g0107751' => 'lal', 'Lalb_Chr20g0118371' => 'lal', 'Lj1g0010239' => 'lja', 'Lj1g0017101' => 'lja', 'Lj2A1178G40' => 'lonja', 'Lj2A54G84' => 'lonja', 'Lj2g0015248' => 'lja', 'Lj3A761T51' => 'lonja', 'Lj6g0018116' => 'lja', 'Lsat_1_v5_gn_4_136040' => 'lsa', 'Lsat_1_v5_gn_5_187461' => 'lsa', 'Lsat_1_v5_gn_5_77001' => 'lsa', 'Lsat_1_v5_gn_9_4461' => 'lsa', 'Manes.01G210100' => 'mes', 'Manes.03G185600' => 'mes', 'Manes.05G073300' => 'mes', 'Manes.09G120300' => 'mes', 'Manes.15G022100' => 'mes', 'Mapoly0096s0053' => 'mpo', 'MBI03_g14058_MAGBIO' => 'mbi', 'MBI03_g33876_MAGBIO' => 'mbi', 'MBI03_g36854_MAGBIO' => 'mbi', 'MBI17_g11997_MAGBIO' => 'mbi', 'MD03G1269000' => 'mdo', 'MD04G1179600' => 'mdo', 'MD11G1289800' => 'mdo', 'MD12G1194700' => 'mdo', 'MD13G1182100' => 'mdo', 'MD13G1182200' => 'mdo', 'MD16G1182600' => 'mdo', 'Medtr2g021400' => 'mtr', 'Medtr2g021470' => 'mtr', 'Medtr2g105810' => 'mtr', 'Medtr3g033580' => 'mtr', 'Medtr6g007970' => 'mtr', 'Medtr7g056330' => 'mtr', 'Medtr7g074290' => 'mtr', 'Medtr7g074380' => 'mtr', 'Medtr7g094550' => 'mtr', 'Medtr8g069995' => 'mtr', 'MELO3C014345.2' => 'cme', 'MELO3C021395.2' => 'cme', 'Migut.D00262' => 'egut', 'Migut.G00257' => 'egut', 'MSTRG.21575' => 'ama', 'MSTRG.3985' => 'ama', 'Nitab4.5_0000295g0140' => 'nta', 'Nitab4.5_0000732g0140' => 'nta', 'Nitab4.5_0003162g0020' => 'nta', 'Nitab4.5_0006180g0090' => 'nta', 'Nitab4.5_0006390g0010' => 'nta', 'Nitab4.5_0007392g0040' => 'nta', 'Nn1g02140' => 'nnu', 'Nn4g26168' => 'nnu', 'Nn5g26754' => 'nnu', 'Oeu001433.1' => 'oeu', 'Oeu010299.2' => 'oeu', 'Oeu011171.1' => 'oeu', 'Oeu037675.1' => 'oeu', 'Oeu038359.1' => 'oeu', 'Oeu063834.1' => 'oeu', 'Oeu063835.1' => 'oeu', 'Os05g0312000' => 'osa', 'Os07g0211101' => 'osa', 'Os07g0211200' => 'osa', 'Os07g0681500' => 'osa', 'Peaxi162Scf00095g01015' => 'pax', 'Peaxi162Scf00104g00329' => 'pax', 'Peaxi162Scf00161g00137' => 'pax', 'PGR004G1665' => 'pgr', 'PGR031G2937' => 'pgr', 'PGR119G2145' => 'pgr', 'PGSC0003DMG400004351' => 'stu', 'PGSC0003DMG400014625' => 'stu', 'PGSC0003DMG401000943' => 'stu', 'Phvul.001G148600' => 'pvu', 'Phvul.004G001700' => 'pvu', 'Phvul.006G154900' => 'pvu', 'Phvul.008G078200' => 'pvu', 'Phvul.011G136500' => 'pvu', 'Potri.002G215600' => 'ptr', 'Potri.008G201600' => 'ptr', 'Potri.014G138400' => 'ptr', 'Potri.016G142500' => 'ptr', 'Pp3c16_10580' => 'ppa', 'Pp3c5_25280' => 'ppa', 'Prupe.1G150000' => 'ppe', 'Prupe.1G150100' => 'ppe', 'Prupe.6G299600' => 'ppe', 'Prupe.8G245000' => 'ppe', 'Psat0s4927g0040' => 'psa', 'Psat1g052080' => 'psa', 'Psat1g183800' => 'psa', 'Psat3g113840' => 'psa', 'Psat3g126120' => 'psa', 'Psat3g126160' => 'psa', 'Psat3g158760' => 'psa', 'Psat3g158840' => 'psa', 'PSO170G2858' => 'pso', 'PSO339G0606' => 'pso', 'PSO384G4709' => 'pso', 'PSO407G0334' => 'pso', 'QL04p040276' => 'qlo', 'QL06p005458' => 'qlo', 'QL06p005472' => 'qlo', 'QL07p030546' => 'qlo', 'QL07p031519' => 'qlo', 'QL09p050949' => 'qlo', 'QL09p050966' => 'qlo', 'QL09p051067' => 'qlo', 'QL12p022706' => 'qlo', 'RcHm_v2.0_Chr2g0119601' => 'rch', 'RcHm_v2.0_Chr3g0459591' => 'rch', 'RcHm_v2.0_Chr4g0418521' => 'rch', 'RcHm_v2.0_Chr4g0418531' => 'rch', 'RcHm_v2.0_Chr4g0418541' => 'rch', 'RcHm_v2.0_Chr6g0291641' => 'rch', 'Rhsim01G0086300' => 'rsi', 'Rhsim01G0276300' => 'rsi', 'Rhsim01G0276500' => 'rsi', 'Rhsim04G0207700' => 'rsi', 'Rhsim05G0234500' => 'rsi', 'Rhsim13G0022400' => 'rsi', 'Sabra02G0167900' => 'sbr', 'Sabra04G0158500' => 'sbr', 'Sabra08G0159800' => 'sbr', 'Sabra10G0011500' => 'sbr', 'Sabra14G0104400' => 'sbr', 'SalBow2G2440' => 'sbo', 'SalBow4G2265' => 'sbo', 'Sc02g0000060' => 'sci', 'Sc05g0005020' => 'sci', 'Sc13g0003890' => 'sci', 'Sed0014865' => 'sed', 'Sed0017224' => 'sed', 'Sed0026391' => 'sed', 'SEGI_00063' => 'sgi', 'SEGI_10967' => 'sgi', 'SEGI_17510' => 'sgi', 'SEGI_24396' => 'sgi', 'SEGI_39719' => 'sgi', 'SEGI_41392' => 'sgi', 'SGA_v2.0_scaffold11G05794' => 'sas', 'SGA_v2.0_scaffold142G35607' => 'sas', 'SGA_v2.0_scaffold1G00447' => 'sas', 'SHI15388' => 'shi', 'SHI15394' => 'shi', 'SHI15396' => 'shi', 'SHI15399' => 'shi', 'SMO343G0151' => 'smo', 'SMO367G1118' => 'smo', 'Solyc01g080200.3' => 'sly', 'Solyc06g008960.3' => 'sly', 'Solyc09g064780.3' => 'sly', 'Sopen01g031980' => 'spe', 'Sopen06g003710' => 'spe', 'Sopen09g026460' => 'spe', 'Sp3g21240' => 'spa', 'Sp4g30030' => 'spa', 'TAR365G0022' => 'tar', 'TAR365G1023' => 'tar', 'TAR365G1253' => 'tar', 'TAR623G0078' => 'tar', 'TAR623G1721' => 'tar', 'TAR633G0959' => 'tar', 'THA.LOC104802225' => 'tha', 'THA.LOC104804769' => 'tha', 'THA.LOC104808660' => 'tha', 'THA.LOC104812792' => 'tha', 'Thecc.01G284000' => 'tca', 'Thecc.04G220600' => 'tca', 'Thecc.05G268900' => 'tca', 'Thecc.08G171100' => 'tca', 'Thhalv10001284m.g' => 'esa', 'Thhalv10019912m.g' => 'esa', 'TPR.G14189' => 'tpr', 'TPR.G18110' => 'tpr', 'TPR.G18130' => 'tpr', 'TPR.G18131' => 'tpr', 'TPR.G18140' => 'tpr', 'TPR.G24282' => 'tpr', 'TPR.G25221' => 'tpr', 'TPR.G29267' => 'tpr', 'TPR.G35315' => 'tpr', 'TPR.G36173' => 'tpr', 'TWI09G0794' => 'twi', 'TWI59G1348' => 'twi', 'TWI74G0430' => 'twi', 'unitig_26.g8940' => 'ugi', 'unitig_749.g13744' => 'ugi', 'unitig_749.g13745' => 'ugi', 'vmacro08269' => 'vma', 'vmacro14937' => 'vma', 'vmacro20401' => 'vma', 'VMungo0464G1349' => 'vmu', 'VMungo0540G0289' => 'vmu', 'VMungo1215G1590' => 'vmu', 'VMungo1309G0221' => 'vmu', 'VMungo1309G2815' => 'vmu', 'VMungo1383G0239' => 'vmu', 'VMungo1383G2910' => 'vmu', 'Zm00001eb095270' => 'zma', 'Zm00001eb095280' => 'zma', 'Zm00001eb111630' => 'zma', 'Zm00001eb237080' => 'zma', 'Zm00001eb273740' => 'zma', 'Zm00001eb285040' => 'zma', 'Zm00001eb330790' => 'zma', 'Zm00001eb337380' => 'zma' ) $gf_id = 'HOM05D001484' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001484' ) $data_identifier = 'HOM05D001484' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 2, 'aly' => (int) 2, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 22, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 7, 'hma' => (int) 2, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 7, 'mtr' => (int) 10, 'cme' => (int) 2, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 4, 'ppa' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 4, 'qlo' => (int) 9, 'rch' => (int) 6, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 10, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 7, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb337380' $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' => 'HOM05D001484', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p31500' => 'bna', 'A05p00020' => 'bna', 'A07p08820' => 'bna', 'Aa31LG4G3300' => 'aar', 'Aa31LG8G10030' => 'aar', 'Actinidia00731' => 'ach', 'Actinidia11473' => 'ach', 'Actinidia23469' => 'ach', 'Actinidia24318' => 'ach', 'Actinidia40196' => 'ach', 'Actinidia40197' => 'ach', 'Actinidia40198' => 'ach', 'Ah.08g212990' => 'amhyb', 'Ah.15g091720' => 'amhyb', 'AL3G38260' => 'aly', 'AL4G47710' => 'aly', 'Aqoxy2G00671' => 'aox', 'Aqoxy2G03236' => 'aox', 'arahy.Tifrunner.gnm1.ann1.05IDCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KR684' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATY3SJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK6QJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6APGL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IDT7Z9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM073U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ0R87' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LE7RV4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT4QRX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V5ENPK' => 'arhy', 'AT2G48110' => 'ath', 'AT3G23590' => 'ath', 'ATR0626G186' => 'atr', 'ATR1127G141' => 'atr', 'Atru.chr4.2583' => 'acertr', 'Atru.chr5.1358' => 'acertr', 'Atru.chr5.1359' => 'acertr', 'Atru.chr8.46' => 'acertr', 'AUR62002640' => 'cqu', 'AUR62030055' => 'cqu', 'AUR62033713' => 'cqu', 'AUR62033714' => 'cqu', 'AUR62036795' => 'cqu', 'AUR62039891' => 'cqu', 'BcaB02g08737' => 'bca', 'BcaB04g20441' => 'bca', 'BcaB06g26509' => 'bca', 'BcaB06g26510' => 'bca', 'BcaB06g26511' => 'bca', 'BcaB06g26512' => 'bca', 'BcaB06g26513' => 'bca', 'BcaC02g12564' => 'bca', 'BcaC02g12565' => 'bca', 'BcaC02g12794' => 'bca', 'BcaC02g12795' => 'bca', 'BcaC02g12796' => 'bca', 'BcaC06g35541' => 'bca', 'BNapus_Darmor_BZH_scaffold_188p00080' => 'bna', 'BNapus_Darmor_BZH_scaffold_188p00090' => 'bna', 'BolC1t03972H' => 'bol', 'BolC1t03973H' => 'bol', 'BolC4t21680H' => 'bol', 'BolC7t41863H' => 'bol', 'BolSC55t61227H' => 'bol', 'BolSC55t61228H' => 'bol', 'BraA01t03278Z' => 'bra', 'BraA05t18998Z' => 'bra', 'BraA07t28673Z' => 'bra', 'C01p40150' => 'bna', 'C05p12370' => 'bna', 'C07p13680' => 'bna', 'CAN.G1006.16' => 'can', 'CAN.G1006.17' => 'can', 'CAN.G1170.2' => 'can', 'CAN.G962.7' => 'can', 'CANSAT25G2179' => 'cansat', 'CANSAT78G1573' => 'cansat', 'CARHR099510' => 'chi', 'CARHR143510' => 'chi', 'Carub.0003s2380' => 'cru', 'Carub.0004s3082' => 'cru', 'Ca_00614_v3' => 'car', 'Ca_07801_v3' => 'car', 'Ca_08567_v3' => 'car', 'Ca_09571_v3' => 'car', 'CBR_g19290' => 'cbr', 'Cc01_g19770' => 'ccan', 'Cc03_g03030' => 'ccan', 'CDE07G0968' => 'cde', 'CDE09G1441' => 'cde', 'Cfa006103' => 'cfa', 'Cfa015573' => 'cfa', 'Cfa016988' => 'cfa', 'Ciclev10006738m.g' => 'ccl', 'Ciclev10010920m.g' => 'ccl', 'Ciclev10018517m.g' => 'ccl', 'CiPaw.01G159200' => 'cil', 'CiPaw.02G091000' => 'cil', 'CiPaw.02G091100' => 'cil', 'CiPaw.08G103100' => 'cil', 'CiPaw.09G224900' => 'cil', 'ClCG06G005740' => 'cla', 'ClCG07G000090' => 'cla', 'ClCG07G000100' => 'cla', 'COL.COLO4_09143' => 'col', 'COL.COLO4_25124' => 'col', 'Cpa.g.sc16.34' => 'cpa', 'Cpa.g.sc3504.1' => 'cpa', 'Cpa.g.sc60.37' => 'cpa', 'CsaV3_6G018520' => 'csa', 'CsaV3_6G036860' => 'csa', 'CSS0001072' => 'camsi', 'CSS0020208' => 'camsi', 'CSS0021253' => 'camsi', 'CSS0022190' => 'camsi', 'CSS0036150' => 'camsi', 'CSS0040442' => 'camsi', 'CSS0042300' => 'camsi', 'CSS0045298' => 'camsi', 'DCAR_012449' => 'dca', 'DCAR_018405' => 'dca', 'DCAR_024573' => 'dca', 'DCAR_030591' => 'dca', 'Dinv16926' => 'din', 'Dinv32963' => 'din', 'Dinv38382' => 'din', 'Dinv38383' => 'din', 'Duzib133G0974' => 'dzi', 'Duzib138G1867' => 'dzi', 'Duzib211G0420' => 'dzi', 'Duzib212G0930' => 'dzi', 'ECA234G1645' => 'eca', 'ECA247G3467' => 'eca', 'ECA248G1703' => 'eca', 'EL10Ac3g06327' => 'bvu', 'EL10Ac7g17204' => 'bvu', 'Eucgr.A00855' => 'egr', 'Eucgr.A00858' => 'egr', 'Eucgr.H01520' => 'egr', 'Eucgr.H03604' => 'egr', 'Eucgr.L03465' => 'egr', 'Eucgr.L03466' => 'egr', 'FAN01G0988' => 'fan', 'FAN02G3892' => 'fan', 'FAN05G3381' => 'fan', 'FAN07G0967' => 'fan', 'FAN07G1493' => 'fan', 'FAN08G3125' => 'fan', 'FAN09G0402' => 'fan', 'FAN12G2594' => 'fan', 'FAN12G3879' => 'fan', 'FAN14G1546' => 'fan', 'FAN15G3626' => 'fan', 'FAN17G0588' => 'fan', 'FAN17G0609' => 'fan', 'FAN18G2817' => 'fan', 'FAN19G1305' => 'fan', 'FAN20G1787' => 'fan', 'FAN22G0073' => 'fan', 'FAN22G0352' => 'fan', 'FAN22G0368' => 'fan', 'FAN22G2273' => 'fan', 'FAN24G1998' => 'fan', 'FAN27G1317' => 'fan', 'FvH4_2g23980' => 'fve', 'FvH4_4g14380' => 'fve', 'FvH4_4g14390' => 'fve', 'FvH4_6g09250' => 'fve', 'Glyma.03G151100' => 'gma', 'Glyma.04G122550' => 'gma', 'Glyma.05G001600' => 'gma', 'Glyma.09G270766' => 'gma', 'Glyma.09G270832' => 'gma', 'Glyma.13G209800' => 'gma', 'Glyma.15G102800' => 'gma', 'Glyma.18G218900' => 'gma', 'Glyma.19G001500' => 'gma', 'Glyma.19G153600' => 'gma', 'Gohir.A02G028600' => 'ghi', 'Gohir.A08G045000' => 'ghi', 'Gohir.A11G120500' => 'ghi', 'Gohir.A12G006200' => 'ghi', 'Gohir.A12G006250' => 'ghi', 'Gohir.D02G036300' => 'ghi', 'Gohir.D08G054700' => 'ghi', 'Gohir.D11G125600' => 'ghi', 'Gohir.D12G005700' => 'ghi', 'Gorai.004G055200' => 'gra', 'Gorai.005G040400' => 'gra', 'Gorai.007G134500' => 'gra', 'Gorai.008G005500' => 'gra', 'GSVIVG01011094001' => 'vvi', 'GSVIVG01017879001' => 'vvi', 'GSVIVG01025988001' => 'vvi', 'GSVIVG01029847001' => 'vvi', 'HanXRQChr10g0282901' => 'han', 'HanXRQChr10g0310371' => 'han', 'HanXRQChr10g0315041' => 'han', 'HanXRQChr11g0327651' => 'han', 'HanXRQChr12g0359391' => 'han', 'Haze_00972' => 'cav', 'Haze_00973' => 'cav', 'Haze_00974' => 'cav', 'Haze_04747' => 'cav', 'Haze_04749' => 'cav', 'Haze_04750' => 'cav', 'Haze_21217' => 'cav', 'Hma1.2p1_1037F.1_g250680' => 'hma', 'Hma1.2p1_1644F.1_g295320' => 'hma', 'HPP92_011322' => 'vpl', 'HPP92_011323' => 'vpl', 'HPP92_011324' => 'vpl', 'HPP92_011325' => 'vpl', 'HPP92_011326' => 'vpl', 'Hund12205' => 'sun', 'Hund17957' => 'sun', 'Lalb_Chr06g0176771' => 'lal', 'Lalb_Chr18g0056021' => 'lal', 'Lalb_Chr18g0056031' => 'lal', 'Lalb_Chr18g0056041' => 'lal', 'Lalb_Chr20g0107751' => 'lal', 'Lalb_Chr20g0118371' => 'lal', 'Lj1g0010239' => 'lja', 'Lj1g0017101' => 'lja', 'Lj2A1178G40' => 'lonja', 'Lj2A54G84' => 'lonja', 'Lj2g0015248' => 'lja', 'Lj3A761T51' => 'lonja', 'Lj6g0018116' => 'lja', 'Lsat_1_v5_gn_4_136040' => 'lsa', 'Lsat_1_v5_gn_5_187461' => 'lsa', 'Lsat_1_v5_gn_5_77001' => 'lsa', 'Lsat_1_v5_gn_9_4461' => 'lsa', 'Manes.01G210100' => 'mes', 'Manes.03G185600' => 'mes', 'Manes.05G073300' => 'mes', 'Manes.09G120300' => 'mes', 'Manes.15G022100' => 'mes', 'Mapoly0096s0053' => 'mpo', 'MBI03_g14058_MAGBIO' => 'mbi', 'MBI03_g33876_MAGBIO' => 'mbi', 'MBI03_g36854_MAGBIO' => 'mbi', 'MBI17_g11997_MAGBIO' => 'mbi', 'MD03G1269000' => 'mdo', 'MD04G1179600' => 'mdo', 'MD11G1289800' => 'mdo', 'MD12G1194700' => 'mdo', 'MD13G1182100' => 'mdo', 'MD13G1182200' => 'mdo', 'MD16G1182600' => 'mdo', 'Medtr2g021400' => 'mtr', 'Medtr2g021470' => 'mtr', 'Medtr2g105810' => 'mtr', 'Medtr3g033580' => 'mtr', 'Medtr6g007970' => 'mtr', 'Medtr7g056330' => 'mtr', 'Medtr7g074290' => 'mtr', 'Medtr7g074380' => 'mtr', 'Medtr7g094550' => 'mtr', 'Medtr8g069995' => 'mtr', 'MELO3C014345.2' => 'cme', 'MELO3C021395.2' => 'cme', 'Migut.D00262' => 'egut', 'Migut.G00257' => 'egut', 'MSTRG.21575' => 'ama', 'MSTRG.3985' => 'ama', 'Nitab4.5_0000295g0140' => 'nta', 'Nitab4.5_0000732g0140' => 'nta', 'Nitab4.5_0003162g0020' => 'nta', 'Nitab4.5_0006180g0090' => 'nta', 'Nitab4.5_0006390g0010' => 'nta', 'Nitab4.5_0007392g0040' => 'nta', 'Nn1g02140' => 'nnu', 'Nn4g26168' => 'nnu', 'Nn5g26754' => 'nnu', 'Oeu001433.1' => 'oeu', 'Oeu010299.2' => 'oeu', 'Oeu011171.1' => 'oeu', 'Oeu037675.1' => 'oeu', 'Oeu038359.1' => 'oeu', 'Oeu063834.1' => 'oeu', 'Oeu063835.1' => 'oeu', 'Os05g0312000' => 'osa', 'Os07g0211101' => 'osa', 'Os07g0211200' => 'osa', 'Os07g0681500' => 'osa', 'Peaxi162Scf00095g01015' => 'pax', 'Peaxi162Scf00104g00329' => 'pax', 'Peaxi162Scf00161g00137' => 'pax', 'PGR004G1665' => 'pgr', 'PGR031G2937' => 'pgr', 'PGR119G2145' => 'pgr', 'PGSC0003DMG400004351' => 'stu', 'PGSC0003DMG400014625' => 'stu', 'PGSC0003DMG401000943' => 'stu', 'Phvul.001G148600' => 'pvu', 'Phvul.004G001700' => 'pvu', 'Phvul.006G154900' => 'pvu', 'Phvul.008G078200' => 'pvu', 'Phvul.011G136500' => 'pvu', 'Potri.002G215600' => 'ptr', 'Potri.008G201600' => 'ptr', 'Potri.014G138400' => 'ptr', 'Potri.016G142500' => 'ptr', 'Pp3c16_10580' => 'ppa', 'Pp3c5_25280' => 'ppa', 'Prupe.1G150000' => 'ppe', 'Prupe.1G150100' => 'ppe', 'Prupe.6G299600' => 'ppe', 'Prupe.8G245000' => 'ppe', 'Psat0s4927g0040' => 'psa', 'Psat1g052080' => 'psa', 'Psat1g183800' => 'psa', 'Psat3g113840' => 'psa', 'Psat3g126120' => 'psa', 'Psat3g126160' => 'psa', 'Psat3g158760' => 'psa', 'Psat3g158840' => 'psa', 'PSO170G2858' => 'pso', 'PSO339G0606' => 'pso', 'PSO384G4709' => 'pso', 'PSO407G0334' => 'pso', 'QL04p040276' => 'qlo', 'QL06p005458' => 'qlo', 'QL06p005472' => 'qlo', 'QL07p030546' => 'qlo', 'QL07p031519' => 'qlo', 'QL09p050949' => 'qlo', 'QL09p050966' => 'qlo', 'QL09p051067' => 'qlo', 'QL12p022706' => 'qlo', 'RcHm_v2.0_Chr2g0119601' => 'rch', 'RcHm_v2.0_Chr3g0459591' => 'rch', 'RcHm_v2.0_Chr4g0418521' => 'rch', 'RcHm_v2.0_Chr4g0418531' => 'rch', 'RcHm_v2.0_Chr4g0418541' => 'rch', 'RcHm_v2.0_Chr6g0291641' => 'rch', 'Rhsim01G0086300' => 'rsi', 'Rhsim01G0276300' => 'rsi', 'Rhsim01G0276500' => 'rsi', 'Rhsim04G0207700' => 'rsi', 'Rhsim05G0234500' => 'rsi', 'Rhsim13G0022400' => 'rsi', 'Sabra02G0167900' => 'sbr', 'Sabra04G0158500' => 'sbr', 'Sabra08G0159800' => 'sbr', 'Sabra10G0011500' => 'sbr', 'Sabra14G0104400' => 'sbr', 'SalBow2G2440' => 'sbo', 'SalBow4G2265' => 'sbo', 'Sc02g0000060' => 'sci', 'Sc05g0005020' => 'sci', 'Sc13g0003890' => 'sci', 'Sed0014865' => 'sed', 'Sed0017224' => 'sed', 'Sed0026391' => 'sed', 'SEGI_00063' => 'sgi', 'SEGI_10967' => 'sgi', 'SEGI_17510' => 'sgi', 'SEGI_24396' => 'sgi', 'SEGI_39719' => 'sgi', 'SEGI_41392' => 'sgi', 'SGA_v2.0_scaffold11G05794' => 'sas', 'SGA_v2.0_scaffold142G35607' => 'sas', 'SGA_v2.0_scaffold1G00447' => 'sas', 'SHI15388' => 'shi', 'SHI15394' => 'shi', 'SHI15396' => 'shi', 'SHI15399' => 'shi', 'SMO343G0151' => 'smo', 'SMO367G1118' => 'smo', 'Solyc01g080200.3' => 'sly', 'Solyc06g008960.3' => 'sly', 'Solyc09g064780.3' => 'sly', 'Sopen01g031980' => 'spe', 'Sopen06g003710' => 'spe', 'Sopen09g026460' => 'spe', 'Sp3g21240' => 'spa', 'Sp4g30030' => 'spa', 'TAR365G0022' => 'tar', 'TAR365G1023' => 'tar', 'TAR365G1253' => 'tar', 'TAR623G0078' => 'tar', 'TAR623G1721' => 'tar', 'TAR633G0959' => 'tar', 'THA.LOC104802225' => 'tha', 'THA.LOC104804769' => 'tha', 'THA.LOC104808660' => 'tha', 'THA.LOC104812792' => 'tha', 'Thecc.01G284000' => 'tca', 'Thecc.04G220600' => 'tca', 'Thecc.05G268900' => 'tca', 'Thecc.08G171100' => 'tca', 'Thhalv10001284m.g' => 'esa', 'Thhalv10019912m.g' => 'esa', 'TPR.G14189' => 'tpr', 'TPR.G18110' => 'tpr', 'TPR.G18130' => 'tpr', 'TPR.G18131' => 'tpr', 'TPR.G18140' => 'tpr', 'TPR.G24282' => 'tpr', 'TPR.G25221' => 'tpr', 'TPR.G29267' => 'tpr', 'TPR.G35315' => 'tpr', 'TPR.G36173' => 'tpr', 'TWI09G0794' => 'twi', 'TWI59G1348' => 'twi', 'TWI74G0430' => 'twi', 'unitig_26.g8940' => 'ugi', 'unitig_749.g13744' => 'ugi', 'unitig_749.g13745' => 'ugi', 'vmacro08269' => 'vma', 'vmacro14937' => 'vma', 'vmacro20401' => 'vma', 'VMungo0464G1349' => 'vmu', 'VMungo0540G0289' => 'vmu', 'VMungo1215G1590' => 'vmu', 'VMungo1309G0221' => 'vmu', 'VMungo1309G2815' => 'vmu', 'VMungo1383G0239' => 'vmu', 'VMungo1383G2910' => 'vmu', 'Zm00001eb095270' => 'zma', 'Zm00001eb095280' => 'zma', 'Zm00001eb111630' => 'zma', 'Zm00001eb237080' => 'zma', 'Zm00001eb273740' => 'zma', 'Zm00001eb285040' => 'zma', 'Zm00001eb330790' => 'zma', 'Zm00001eb337380' => 'zma' ), 'gf_id' => 'HOM05D001484', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001484' ), 'data_identifier' => 'HOM05D001484', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001484', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p31500' => 'bna', 'A05p00020' => 'bna', 'A07p08820' => 'bna', 'Aa31LG4G3300' => 'aar', 'Aa31LG8G10030' => 'aar', 'Actinidia00731' => 'ach', 'Actinidia11473' => 'ach', 'Actinidia23469' => 'ach', 'Actinidia24318' => 'ach', 'Actinidia40196' => 'ach', 'Actinidia40197' => 'ach', 'Actinidia40198' => 'ach', 'Ah.08g212990' => 'amhyb', 'Ah.15g091720' => 'amhyb', 'AL3G38260' => 'aly', 'AL4G47710' => 'aly', 'Aqoxy2G00671' => 'aox', 'Aqoxy2G03236' => 'aox', 'arahy.Tifrunner.gnm1.ann1.05IDCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KR684' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATY3SJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK6QJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6APGL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IDT7Z9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM073U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ0R87' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LE7RV4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT4QRX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V5ENPK' => 'arhy', 'AT2G48110' => 'ath', 'AT3G23590' => 'ath', 'ATR0626G186' => 'atr', 'ATR1127G141' => 'atr', 'Atru.chr4.2583' => 'acertr', 'Atru.chr5.1358' => 'acertr', 'Atru.chr5.1359' => 'acertr', 'Atru.chr8.46' => 'acertr', 'AUR62002640' => 'cqu', 'AUR62030055' => 'cqu', 'AUR62033713' => 'cqu', 'AUR62033714' => 'cqu', 'AUR62036795' => 'cqu', 'AUR62039891' => 'cqu', 'BcaB02g08737' => 'bca', 'BcaB04g20441' => 'bca', 'BcaB06g26509' => 'bca', 'BcaB06g26510' => 'bca', 'BcaB06g26511' => 'bca', 'BcaB06g26512' => 'bca', 'BcaB06g26513' => 'bca', 'BcaC02g12564' => 'bca', 'BcaC02g12565' => 'bca', 'BcaC02g12794' => 'bca', 'BcaC02g12795' => 'bca', 'BcaC02g12796' => 'bca', 'BcaC06g35541' => 'bca', 'BNapus_Darmor_BZH_scaffold_188p00080' => 'bna', 'BNapus_Darmor_BZH_scaffold_188p00090' => 'bna', 'BolC1t03972H' => 'bol', 'BolC1t03973H' => 'bol', 'BolC4t21680H' => 'bol', 'BolC7t41863H' => 'bol', 'BolSC55t61227H' => 'bol', 'BolSC55t61228H' => 'bol', 'BraA01t03278Z' => 'bra', 'BraA05t18998Z' => 'bra', 'BraA07t28673Z' => 'bra', 'C01p40150' => 'bna', 'C05p12370' => 'bna', 'C07p13680' => 'bna', 'CAN.G1006.16' => 'can', 'CAN.G1006.17' => 'can', 'CAN.G1170.2' => 'can', 'CAN.G962.7' => 'can', 'CANSAT25G2179' => 'cansat', 'CANSAT78G1573' => 'cansat', 'CARHR099510' => 'chi', 'CARHR143510' => 'chi', 'Carub.0003s2380' => 'cru', 'Carub.0004s3082' => 'cru', 'Ca_00614_v3' => 'car', 'Ca_07801_v3' => 'car', 'Ca_08567_v3' => 'car', 'Ca_09571_v3' => 'car', 'CBR_g19290' => 'cbr', 'Cc01_g19770' => 'ccan', 'Cc03_g03030' => 'ccan', 'CDE07G0968' => 'cde', 'CDE09G1441' => 'cde', 'Cfa006103' => 'cfa', 'Cfa015573' => 'cfa', 'Cfa016988' => 'cfa', 'Ciclev10006738m.g' => 'ccl', 'Ciclev10010920m.g' => 'ccl', 'Ciclev10018517m.g' => 'ccl', 'CiPaw.01G159200' => 'cil', 'CiPaw.02G091000' => 'cil', 'CiPaw.02G091100' => 'cil', 'CiPaw.08G103100' => 'cil', 'CiPaw.09G224900' => 'cil', 'ClCG06G005740' => 'cla', 'ClCG07G000090' => 'cla', 'ClCG07G000100' => 'cla', 'COL.COLO4_09143' => 'col', 'COL.COLO4_25124' => 'col', 'Cpa.g.sc16.34' => 'cpa', 'Cpa.g.sc3504.1' => 'cpa', 'Cpa.g.sc60.37' => 'cpa', 'CsaV3_6G018520' => 'csa', 'CsaV3_6G036860' => 'csa', 'CSS0001072' => 'camsi', 'CSS0020208' => 'camsi', 'CSS0021253' => 'camsi', 'CSS0022190' => 'camsi', 'CSS0036150' => 'camsi', 'CSS0040442' => 'camsi', 'CSS0042300' => 'camsi', 'CSS0045298' => 'camsi', 'DCAR_012449' => 'dca', 'DCAR_018405' => 'dca', 'DCAR_024573' => 'dca', 'DCAR_030591' => 'dca', 'Dinv16926' => 'din', 'Dinv32963' => 'din', 'Dinv38382' => 'din', 'Dinv38383' => 'din', 'Duzib133G0974' => 'dzi', 'Duzib138G1867' => 'dzi', 'Duzib211G0420' => 'dzi', 'Duzib212G0930' => 'dzi', 'ECA234G1645' => 'eca', 'ECA247G3467' => 'eca', 'ECA248G1703' => 'eca', 'EL10Ac3g06327' => 'bvu', 'EL10Ac7g17204' => 'bvu', 'Eucgr.A00855' => 'egr', 'Eucgr.A00858' => 'egr', 'Eucgr.H01520' => 'egr', 'Eucgr.H03604' => 'egr', 'Eucgr.L03465' => 'egr', 'Eucgr.L03466' => 'egr', 'FAN01G0988' => 'fan', 'FAN02G3892' => 'fan', 'FAN05G3381' => 'fan', 'FAN07G0967' => 'fan', 'FAN07G1493' => 'fan', 'FAN08G3125' => 'fan', 'FAN09G0402' => 'fan', 'FAN12G2594' => 'fan', 'FAN12G3879' => 'fan', 'FAN14G1546' => 'fan', 'FAN15G3626' => 'fan', 'FAN17G0588' => 'fan', 'FAN17G0609' => 'fan', 'FAN18G2817' => 'fan', 'FAN19G1305' => 'fan', 'FAN20G1787' => 'fan', 'FAN22G0073' => 'fan', 'FAN22G0352' => 'fan', 'FAN22G0368' => 'fan', 'FAN22G2273' => 'fan', 'FAN24G1998' => 'fan', 'FAN27G1317' => 'fan', 'FvH4_2g23980' => 'fve', 'FvH4_4g14380' => 'fve', 'FvH4_4g14390' => 'fve', 'FvH4_6g09250' => 'fve', 'Glyma.03G151100' => 'gma', 'Glyma.04G122550' => 'gma', 'Glyma.05G001600' => 'gma', 'Glyma.09G270766' => 'gma', 'Glyma.09G270832' => 'gma', 'Glyma.13G209800' => 'gma', 'Glyma.15G102800' => 'gma', 'Glyma.18G218900' => 'gma', 'Glyma.19G001500' => 'gma', 'Glyma.19G153600' => 'gma', 'Gohir.A02G028600' => 'ghi', 'Gohir.A08G045000' => 'ghi', 'Gohir.A11G120500' => 'ghi', 'Gohir.A12G006200' => 'ghi', 'Gohir.A12G006250' => 'ghi', 'Gohir.D02G036300' => 'ghi', 'Gohir.D08G054700' => 'ghi', 'Gohir.D11G125600' => 'ghi', 'Gohir.D12G005700' => 'ghi', 'Gorai.004G055200' => 'gra', 'Gorai.005G040400' => 'gra', 'Gorai.007G134500' => 'gra', 'Gorai.008G005500' => 'gra', 'GSVIVG01011094001' => 'vvi', 'GSVIVG01017879001' => 'vvi', 'GSVIVG01025988001' => 'vvi', 'GSVIVG01029847001' => 'vvi', 'HanXRQChr10g0282901' => 'han', 'HanXRQChr10g0310371' => 'han', 'HanXRQChr10g0315041' => 'han', 'HanXRQChr11g0327651' => 'han', 'HanXRQChr12g0359391' => 'han', 'Haze_00972' => 'cav', 'Haze_00973' => 'cav', 'Haze_00974' => 'cav', 'Haze_04747' => 'cav', 'Haze_04749' => 'cav', 'Haze_04750' => 'cav', 'Haze_21217' => 'cav', 'Hma1.2p1_1037F.1_g250680' => 'hma', 'Hma1.2p1_1644F.1_g295320' => 'hma', 'HPP92_011322' => 'vpl', 'HPP92_011323' => 'vpl', 'HPP92_011324' => 'vpl', 'HPP92_011325' => 'vpl', 'HPP92_011326' => 'vpl', 'Hund12205' => 'sun', 'Hund17957' => 'sun', 'Lalb_Chr06g0176771' => 'lal', 'Lalb_Chr18g0056021' => 'lal', 'Lalb_Chr18g0056031' => 'lal', 'Lalb_Chr18g0056041' => 'lal', 'Lalb_Chr20g0107751' => 'lal', 'Lalb_Chr20g0118371' => 'lal', 'Lj1g0010239' => 'lja', 'Lj1g0017101' => 'lja', 'Lj2A1178G40' => 'lonja', 'Lj2A54G84' => 'lonja', 'Lj2g0015248' => 'lja', 'Lj3A761T51' => 'lonja', 'Lj6g0018116' => 'lja', 'Lsat_1_v5_gn_4_136040' => 'lsa', 'Lsat_1_v5_gn_5_187461' => 'lsa', 'Lsat_1_v5_gn_5_77001' => 'lsa', 'Lsat_1_v5_gn_9_4461' => 'lsa', 'Manes.01G210100' => 'mes', 'Manes.03G185600' => 'mes', 'Manes.05G073300' => 'mes', 'Manes.09G120300' => 'mes', 'Manes.15G022100' => 'mes', 'Mapoly0096s0053' => 'mpo', 'MBI03_g14058_MAGBIO' => 'mbi', 'MBI03_g33876_MAGBIO' => 'mbi', 'MBI03_g36854_MAGBIO' => 'mbi', 'MBI17_g11997_MAGBIO' => 'mbi', 'MD03G1269000' => 'mdo', 'MD04G1179600' => 'mdo', 'MD11G1289800' => 'mdo', 'MD12G1194700' => 'mdo', 'MD13G1182100' => 'mdo', 'MD13G1182200' => 'mdo', 'MD16G1182600' => 'mdo', 'Medtr2g021400' => 'mtr', 'Medtr2g021470' => 'mtr', 'Medtr2g105810' => 'mtr', 'Medtr3g033580' => 'mtr', 'Medtr6g007970' => 'mtr', 'Medtr7g056330' => 'mtr', 'Medtr7g074290' => 'mtr', 'Medtr7g074380' => 'mtr', 'Medtr7g094550' => 'mtr', 'Medtr8g069995' => 'mtr', 'MELO3C014345.2' => 'cme', 'MELO3C021395.2' => 'cme', 'Migut.D00262' => 'egut', 'Migut.G00257' => 'egut', 'MSTRG.21575' => 'ama', 'MSTRG.3985' => 'ama', 'Nitab4.5_0000295g0140' => 'nta', 'Nitab4.5_0000732g0140' => 'nta', 'Nitab4.5_0003162g0020' => 'nta', 'Nitab4.5_0006180g0090' => 'nta', 'Nitab4.5_0006390g0010' => 'nta', 'Nitab4.5_0007392g0040' => 'nta', 'Nn1g02140' => 'nnu', 'Nn4g26168' => 'nnu', 'Nn5g26754' => 'nnu', 'Oeu001433.1' => 'oeu', 'Oeu010299.2' => 'oeu', 'Oeu011171.1' => 'oeu', 'Oeu037675.1' => 'oeu', 'Oeu038359.1' => 'oeu', 'Oeu063834.1' => 'oeu', 'Oeu063835.1' => 'oeu', 'Os05g0312000' => 'osa', 'Os07g0211101' => 'osa', 'Os07g0211200' => 'osa', 'Os07g0681500' => 'osa', 'Peaxi162Scf00095g01015' => 'pax', 'Peaxi162Scf00104g00329' => 'pax', 'Peaxi162Scf00161g00137' => 'pax', 'PGR004G1665' => 'pgr', 'PGR031G2937' => 'pgr', 'PGR119G2145' => 'pgr', 'PGSC0003DMG400004351' => 'stu', 'PGSC0003DMG400014625' => 'stu', 'PGSC0003DMG401000943' => 'stu', 'Phvul.001G148600' => 'pvu', 'Phvul.004G001700' => 'pvu', 'Phvul.006G154900' => 'pvu', 'Phvul.008G078200' => 'pvu', 'Phvul.011G136500' => 'pvu', 'Potri.002G215600' => 'ptr', 'Potri.008G201600' => 'ptr', 'Potri.014G138400' => 'ptr', 'Potri.016G142500' => 'ptr', 'Pp3c16_10580' => 'ppa', 'Pp3c5_25280' => 'ppa', 'Prupe.1G150000' => 'ppe', 'Prupe.1G150100' => 'ppe', 'Prupe.6G299600' => 'ppe', 'Prupe.8G245000' => 'ppe', 'Psat0s4927g0040' => 'psa', 'Psat1g052080' => 'psa', 'Psat1g183800' => 'psa', 'Psat3g113840' => 'psa', 'Psat3g126120' => 'psa', 'Psat3g126160' => 'psa', 'Psat3g158760' => 'psa', 'Psat3g158840' => 'psa', 'PSO170G2858' => 'pso', 'PSO339G0606' => 'pso', 'PSO384G4709' => 'pso', 'PSO407G0334' => 'pso', 'QL04p040276' => 'qlo', 'QL06p005458' => 'qlo', 'QL06p005472' => 'qlo', 'QL07p030546' => 'qlo', 'QL07p031519' => 'qlo', 'QL09p050949' => 'qlo', 'QL09p050966' => 'qlo', 'QL09p051067' => 'qlo', 'QL12p022706' => 'qlo', 'RcHm_v2.0_Chr2g0119601' => 'rch', 'RcHm_v2.0_Chr3g0459591' => 'rch', 'RcHm_v2.0_Chr4g0418521' => 'rch', 'RcHm_v2.0_Chr4g0418531' => 'rch', 'RcHm_v2.0_Chr4g0418541' => 'rch', 'RcHm_v2.0_Chr6g0291641' => 'rch', 'Rhsim01G0086300' => 'rsi', 'Rhsim01G0276300' => 'rsi', 'Rhsim01G0276500' => 'rsi', 'Rhsim04G0207700' => 'rsi', 'Rhsim05G0234500' => 'rsi', 'Rhsim13G0022400' => 'rsi', 'Sabra02G0167900' => 'sbr', 'Sabra04G0158500' => 'sbr', 'Sabra08G0159800' => 'sbr', 'Sabra10G0011500' => 'sbr', 'Sabra14G0104400' => 'sbr', 'SalBow2G2440' => 'sbo', 'SalBow4G2265' => 'sbo', 'Sc02g0000060' => 'sci', 'Sc05g0005020' => 'sci', 'Sc13g0003890' => 'sci', 'Sed0014865' => 'sed', 'Sed0017224' => 'sed', 'Sed0026391' => 'sed', 'SEGI_00063' => 'sgi', 'SEGI_10967' => 'sgi', 'SEGI_17510' => 'sgi', 'SEGI_24396' => 'sgi', 'SEGI_39719' => 'sgi', 'SEGI_41392' => 'sgi', 'SGA_v2.0_scaffold11G05794' => 'sas', 'SGA_v2.0_scaffold142G35607' => 'sas', 'SGA_v2.0_scaffold1G00447' => 'sas', 'SHI15388' => 'shi', 'SHI15394' => 'shi', 'SHI15396' => 'shi', 'SHI15399' => 'shi', 'SMO343G0151' => 'smo', 'SMO367G1118' => 'smo', 'Solyc01g080200.3' => 'sly', 'Solyc06g008960.3' => 'sly', 'Solyc09g064780.3' => 'sly', 'Sopen01g031980' => 'spe', 'Sopen06g003710' => 'spe', 'Sopen09g026460' => 'spe', 'Sp3g21240' => 'spa', 'Sp4g30030' => 'spa', 'TAR365G0022' => 'tar', 'TAR365G1023' => 'tar', 'TAR365G1253' => 'tar', 'TAR623G0078' => 'tar', 'TAR623G1721' => 'tar', 'TAR633G0959' => 'tar', 'THA.LOC104802225' => 'tha', 'THA.LOC104804769' => 'tha', 'THA.LOC104808660' => 'tha', 'THA.LOC104812792' => 'tha', 'Thecc.01G284000' => 'tca', 'Thecc.04G220600' => 'tca', 'Thecc.05G268900' => 'tca', 'Thecc.08G171100' => 'tca', 'Thhalv10001284m.g' => 'esa', 'Thhalv10019912m.g' => 'esa', 'TPR.G14189' => 'tpr', 'TPR.G18110' => 'tpr', 'TPR.G18130' => 'tpr', 'TPR.G18131' => 'tpr', 'TPR.G18140' => 'tpr', 'TPR.G24282' => 'tpr', 'TPR.G25221' => 'tpr', 'TPR.G29267' => 'tpr', 'TPR.G35315' => 'tpr', 'TPR.G36173' => 'tpr', 'TWI09G0794' => 'twi', 'TWI59G1348' => 'twi', 'TWI74G0430' => 'twi', 'unitig_26.g8940' => 'ugi', 'unitig_749.g13744' => 'ugi', 'unitig_749.g13745' => 'ugi', 'vmacro08269' => 'vma', 'vmacro14937' => 'vma', 'vmacro20401' => 'vma', 'VMungo0464G1349' => 'vmu', 'VMungo0540G0289' => 'vmu', 'VMungo1215G1590' => 'vmu', 'VMungo1309G0221' => 'vmu', 'VMungo1309G2815' => 'vmu', 'VMungo1383G0239' => 'vmu', 'VMungo1383G2910' => 'vmu', 'Zm00001eb095270' => 'zma', 'Zm00001eb095280' => 'zma', 'Zm00001eb111630' => 'zma', 'Zm00001eb237080' => 'zma', 'Zm00001eb273740' => 'zma', 'Zm00001eb285040' => 'zma', 'Zm00001eb330790' => 'zma', 'Zm00001eb337380' => 'zma' ) $gf_id = 'HOM05D001484' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001484' ) $data_identifier = 'HOM05D001484' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 2, 'aly' => (int) 2, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 22, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 7, 'hma' => (int) 2, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 7, 'mtr' => (int) 10, 'cme' => (int) 2, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 4, 'ppa' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 4, 'qlo' => (int) 9, 'rch' => (int) 6, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 10, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 7, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb337380' $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' => 'HOM05D001484', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p31500' => 'bna', 'A05p00020' => 'bna', 'A07p08820' => 'bna', 'Aa31LG4G3300' => 'aar', 'Aa31LG8G10030' => 'aar', 'Actinidia00731' => 'ach', 'Actinidia11473' => 'ach', 'Actinidia23469' => 'ach', 'Actinidia24318' => 'ach', 'Actinidia40196' => 'ach', 'Actinidia40197' => 'ach', 'Actinidia40198' => 'ach', 'Ah.08g212990' => 'amhyb', 'Ah.15g091720' => 'amhyb', 'AL3G38260' => 'aly', 'AL4G47710' => 'aly', 'Aqoxy2G00671' => 'aox', 'Aqoxy2G03236' => 'aox', 'arahy.Tifrunner.gnm1.ann1.05IDCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KR684' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATY3SJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK6QJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6APGL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IDT7Z9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM073U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ0R87' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LE7RV4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT4QRX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V5ENPK' => 'arhy', 'AT2G48110' => 'ath', 'AT3G23590' => 'ath', 'ATR0626G186' => 'atr', 'ATR1127G141' => 'atr', 'Atru.chr4.2583' => 'acertr', 'Atru.chr5.1358' => 'acertr', 'Atru.chr5.1359' => 'acertr', 'Atru.chr8.46' => 'acertr', 'AUR62002640' => 'cqu', 'AUR62030055' => 'cqu', 'AUR62033713' => 'cqu', 'AUR62033714' => 'cqu', 'AUR62036795' => 'cqu', 'AUR62039891' => 'cqu', 'BcaB02g08737' => 'bca', 'BcaB04g20441' => 'bca', 'BcaB06g26509' => 'bca', 'BcaB06g26510' => 'bca', 'BcaB06g26511' => 'bca', 'BcaB06g26512' => 'bca', 'BcaB06g26513' => 'bca', 'BcaC02g12564' => 'bca', 'BcaC02g12565' => 'bca', 'BcaC02g12794' => 'bca', 'BcaC02g12795' => 'bca', 'BcaC02g12796' => 'bca', 'BcaC06g35541' => 'bca', 'BNapus_Darmor_BZH_scaffold_188p00080' => 'bna', 'BNapus_Darmor_BZH_scaffold_188p00090' => 'bna', 'BolC1t03972H' => 'bol', 'BolC1t03973H' => 'bol', 'BolC4t21680H' => 'bol', 'BolC7t41863H' => 'bol', 'BolSC55t61227H' => 'bol', 'BolSC55t61228H' => 'bol', 'BraA01t03278Z' => 'bra', 'BraA05t18998Z' => 'bra', 'BraA07t28673Z' => 'bra', 'C01p40150' => 'bna', 'C05p12370' => 'bna', 'C07p13680' => 'bna', 'CAN.G1006.16' => 'can', 'CAN.G1006.17' => 'can', 'CAN.G1170.2' => 'can', 'CAN.G962.7' => 'can', 'CANSAT25G2179' => 'cansat', 'CANSAT78G1573' => 'cansat', 'CARHR099510' => 'chi', 'CARHR143510' => 'chi', 'Carub.0003s2380' => 'cru', 'Carub.0004s3082' => 'cru', 'Ca_00614_v3' => 'car', 'Ca_07801_v3' => 'car', 'Ca_08567_v3' => 'car', 'Ca_09571_v3' => 'car', 'CBR_g19290' => 'cbr', 'Cc01_g19770' => 'ccan', 'Cc03_g03030' => 'ccan', 'CDE07G0968' => 'cde', 'CDE09G1441' => 'cde', 'Cfa006103' => 'cfa', 'Cfa015573' => 'cfa', 'Cfa016988' => 'cfa', 'Ciclev10006738m.g' => 'ccl', 'Ciclev10010920m.g' => 'ccl', 'Ciclev10018517m.g' => 'ccl', 'CiPaw.01G159200' => 'cil', 'CiPaw.02G091000' => 'cil', 'CiPaw.02G091100' => 'cil', 'CiPaw.08G103100' => 'cil', 'CiPaw.09G224900' => 'cil', 'ClCG06G005740' => 'cla', 'ClCG07G000090' => 'cla', 'ClCG07G000100' => 'cla', 'COL.COLO4_09143' => 'col', 'COL.COLO4_25124' => 'col', 'Cpa.g.sc16.34' => 'cpa', 'Cpa.g.sc3504.1' => 'cpa', 'Cpa.g.sc60.37' => 'cpa', 'CsaV3_6G018520' => 'csa', 'CsaV3_6G036860' => 'csa', 'CSS0001072' => 'camsi', 'CSS0020208' => 'camsi', 'CSS0021253' => 'camsi', 'CSS0022190' => 'camsi', 'CSS0036150' => 'camsi', 'CSS0040442' => 'camsi', 'CSS0042300' => 'camsi', 'CSS0045298' => 'camsi', 'DCAR_012449' => 'dca', 'DCAR_018405' => 'dca', 'DCAR_024573' => 'dca', 'DCAR_030591' => 'dca', 'Dinv16926' => 'din', 'Dinv32963' => 'din', 'Dinv38382' => 'din', 'Dinv38383' => 'din', 'Duzib133G0974' => 'dzi', 'Duzib138G1867' => 'dzi', 'Duzib211G0420' => 'dzi', 'Duzib212G0930' => 'dzi', 'ECA234G1645' => 'eca', 'ECA247G3467' => 'eca', 'ECA248G1703' => 'eca', 'EL10Ac3g06327' => 'bvu', 'EL10Ac7g17204' => 'bvu', 'Eucgr.A00855' => 'egr', 'Eucgr.A00858' => 'egr', 'Eucgr.H01520' => 'egr', 'Eucgr.H03604' => 'egr', 'Eucgr.L03465' => 'egr', 'Eucgr.L03466' => 'egr', 'FAN01G0988' => 'fan', 'FAN02G3892' => 'fan', 'FAN05G3381' => 'fan', 'FAN07G0967' => 'fan', 'FAN07G1493' => 'fan', 'FAN08G3125' => 'fan', 'FAN09G0402' => 'fan', 'FAN12G2594' => 'fan', 'FAN12G3879' => 'fan', 'FAN14G1546' => 'fan', 'FAN15G3626' => 'fan', 'FAN17G0588' => 'fan', 'FAN17G0609' => 'fan', 'FAN18G2817' => 'fan', 'FAN19G1305' => 'fan', 'FAN20G1787' => 'fan', 'FAN22G0073' => 'fan', 'FAN22G0352' => 'fan', 'FAN22G0368' => 'fan', 'FAN22G2273' => 'fan', 'FAN24G1998' => 'fan', 'FAN27G1317' => 'fan', 'FvH4_2g23980' => 'fve', 'FvH4_4g14380' => 'fve', 'FvH4_4g14390' => 'fve', 'FvH4_6g09250' => 'fve', 'Glyma.03G151100' => 'gma', 'Glyma.04G122550' => 'gma', 'Glyma.05G001600' => 'gma', 'Glyma.09G270766' => 'gma', 'Glyma.09G270832' => 'gma', 'Glyma.13G209800' => 'gma', 'Glyma.15G102800' => 'gma', 'Glyma.18G218900' => 'gma', 'Glyma.19G001500' => 'gma', 'Glyma.19G153600' => 'gma', 'Gohir.A02G028600' => 'ghi', 'Gohir.A08G045000' => 'ghi', 'Gohir.A11G120500' => 'ghi', 'Gohir.A12G006200' => 'ghi', 'Gohir.A12G006250' => 'ghi', 'Gohir.D02G036300' => 'ghi', 'Gohir.D08G054700' => 'ghi', 'Gohir.D11G125600' => 'ghi', 'Gohir.D12G005700' => 'ghi', 'Gorai.004G055200' => 'gra', 'Gorai.005G040400' => 'gra', 'Gorai.007G134500' => 'gra', 'Gorai.008G005500' => 'gra', 'GSVIVG01011094001' => 'vvi', 'GSVIVG01017879001' => 'vvi', 'GSVIVG01025988001' => 'vvi', 'GSVIVG01029847001' => 'vvi', 'HanXRQChr10g0282901' => 'han', 'HanXRQChr10g0310371' => 'han', 'HanXRQChr10g0315041' => 'han', 'HanXRQChr11g0327651' => 'han', 'HanXRQChr12g0359391' => 'han', 'Haze_00972' => 'cav', 'Haze_00973' => 'cav', 'Haze_00974' => 'cav', 'Haze_04747' => 'cav', 'Haze_04749' => 'cav', 'Haze_04750' => 'cav', 'Haze_21217' => 'cav', 'Hma1.2p1_1037F.1_g250680' => 'hma', 'Hma1.2p1_1644F.1_g295320' => 'hma', 'HPP92_011322' => 'vpl', 'HPP92_011323' => 'vpl', 'HPP92_011324' => 'vpl', 'HPP92_011325' => 'vpl', 'HPP92_011326' => 'vpl', 'Hund12205' => 'sun', 'Hund17957' => 'sun', 'Lalb_Chr06g0176771' => 'lal', 'Lalb_Chr18g0056021' => 'lal', 'Lalb_Chr18g0056031' => 'lal', 'Lalb_Chr18g0056041' => 'lal', 'Lalb_Chr20g0107751' => 'lal', 'Lalb_Chr20g0118371' => 'lal', 'Lj1g0010239' => 'lja', 'Lj1g0017101' => 'lja', 'Lj2A1178G40' => 'lonja', 'Lj2A54G84' => 'lonja', 'Lj2g0015248' => 'lja', 'Lj3A761T51' => 'lonja', 'Lj6g0018116' => 'lja', 'Lsat_1_v5_gn_4_136040' => 'lsa', 'Lsat_1_v5_gn_5_187461' => 'lsa', 'Lsat_1_v5_gn_5_77001' => 'lsa', 'Lsat_1_v5_gn_9_4461' => 'lsa', 'Manes.01G210100' => 'mes', 'Manes.03G185600' => 'mes', 'Manes.05G073300' => 'mes', 'Manes.09G120300' => 'mes', 'Manes.15G022100' => 'mes', 'Mapoly0096s0053' => 'mpo', 'MBI03_g14058_MAGBIO' => 'mbi', 'MBI03_g33876_MAGBIO' => 'mbi', 'MBI03_g36854_MAGBIO' => 'mbi', 'MBI17_g11997_MAGBIO' => 'mbi', 'MD03G1269000' => 'mdo', 'MD04G1179600' => 'mdo', 'MD11G1289800' => 'mdo', 'MD12G1194700' => 'mdo', 'MD13G1182100' => 'mdo', 'MD13G1182200' => 'mdo', 'MD16G1182600' => 'mdo', 'Medtr2g021400' => 'mtr', 'Medtr2g021470' => 'mtr', 'Medtr2g105810' => 'mtr', 'Medtr3g033580' => 'mtr', 'Medtr6g007970' => 'mtr', 'Medtr7g056330' => 'mtr', 'Medtr7g074290' => 'mtr', 'Medtr7g074380' => 'mtr', 'Medtr7g094550' => 'mtr', 'Medtr8g069995' => 'mtr', 'MELO3C014345.2' => 'cme', 'MELO3C021395.2' => 'cme', 'Migut.D00262' => 'egut', 'Migut.G00257' => 'egut', 'MSTRG.21575' => 'ama', 'MSTRG.3985' => 'ama', 'Nitab4.5_0000295g0140' => 'nta', 'Nitab4.5_0000732g0140' => 'nta', 'Nitab4.5_0003162g0020' => 'nta', 'Nitab4.5_0006180g0090' => 'nta', 'Nitab4.5_0006390g0010' => 'nta', 'Nitab4.5_0007392g0040' => 'nta', 'Nn1g02140' => 'nnu', 'Nn4g26168' => 'nnu', 'Nn5g26754' => 'nnu', 'Oeu001433.1' => 'oeu', 'Oeu010299.2' => 'oeu', 'Oeu011171.1' => 'oeu', 'Oeu037675.1' => 'oeu', 'Oeu038359.1' => 'oeu', 'Oeu063834.1' => 'oeu', 'Oeu063835.1' => 'oeu', 'Os05g0312000' => 'osa', 'Os07g0211101' => 'osa', 'Os07g0211200' => 'osa', 'Os07g0681500' => 'osa', 'Peaxi162Scf00095g01015' => 'pax', 'Peaxi162Scf00104g00329' => 'pax', 'Peaxi162Scf00161g00137' => 'pax', 'PGR004G1665' => 'pgr', 'PGR031G2937' => 'pgr', 'PGR119G2145' => 'pgr', 'PGSC0003DMG400004351' => 'stu', 'PGSC0003DMG400014625' => 'stu', 'PGSC0003DMG401000943' => 'stu', 'Phvul.001G148600' => 'pvu', 'Phvul.004G001700' => 'pvu', 'Phvul.006G154900' => 'pvu', 'Phvul.008G078200' => 'pvu', 'Phvul.011G136500' => 'pvu', 'Potri.002G215600' => 'ptr', 'Potri.008G201600' => 'ptr', 'Potri.014G138400' => 'ptr', 'Potri.016G142500' => 'ptr', 'Pp3c16_10580' => 'ppa', 'Pp3c5_25280' => 'ppa', 'Prupe.1G150000' => 'ppe', 'Prupe.1G150100' => 'ppe', 'Prupe.6G299600' => 'ppe', 'Prupe.8G245000' => 'ppe', 'Psat0s4927g0040' => 'psa', 'Psat1g052080' => 'psa', 'Psat1g183800' => 'psa', 'Psat3g113840' => 'psa', 'Psat3g126120' => 'psa', 'Psat3g126160' => 'psa', 'Psat3g158760' => 'psa', 'Psat3g158840' => 'psa', 'PSO170G2858' => 'pso', 'PSO339G0606' => 'pso', 'PSO384G4709' => 'pso', 'PSO407G0334' => 'pso', 'QL04p040276' => 'qlo', 'QL06p005458' => 'qlo', 'QL06p005472' => 'qlo', 'QL07p030546' => 'qlo', 'QL07p031519' => 'qlo', 'QL09p050949' => 'qlo', 'QL09p050966' => 'qlo', 'QL09p051067' => 'qlo', 'QL12p022706' => 'qlo', 'RcHm_v2.0_Chr2g0119601' => 'rch', 'RcHm_v2.0_Chr3g0459591' => 'rch', 'RcHm_v2.0_Chr4g0418521' => 'rch', 'RcHm_v2.0_Chr4g0418531' => 'rch', 'RcHm_v2.0_Chr4g0418541' => 'rch', 'RcHm_v2.0_Chr6g0291641' => 'rch', 'Rhsim01G0086300' => 'rsi', 'Rhsim01G0276300' => 'rsi', 'Rhsim01G0276500' => 'rsi', 'Rhsim04G0207700' => 'rsi', 'Rhsim05G0234500' => 'rsi', 'Rhsim13G0022400' => 'rsi', 'Sabra02G0167900' => 'sbr', 'Sabra04G0158500' => 'sbr', 'Sabra08G0159800' => 'sbr', 'Sabra10G0011500' => 'sbr', 'Sabra14G0104400' => 'sbr', 'SalBow2G2440' => 'sbo', 'SalBow4G2265' => 'sbo', 'Sc02g0000060' => 'sci', 'Sc05g0005020' => 'sci', 'Sc13g0003890' => 'sci', 'Sed0014865' => 'sed', 'Sed0017224' => 'sed', 'Sed0026391' => 'sed', 'SEGI_00063' => 'sgi', 'SEGI_10967' => 'sgi', 'SEGI_17510' => 'sgi', 'SEGI_24396' => 'sgi', 'SEGI_39719' => 'sgi', 'SEGI_41392' => 'sgi', 'SGA_v2.0_scaffold11G05794' => 'sas', 'SGA_v2.0_scaffold142G35607' => 'sas', 'SGA_v2.0_scaffold1G00447' => 'sas', 'SHI15388' => 'shi', 'SHI15394' => 'shi', 'SHI15396' => 'shi', 'SHI15399' => 'shi', 'SMO343G0151' => 'smo', 'SMO367G1118' => 'smo', 'Solyc01g080200.3' => 'sly', 'Solyc06g008960.3' => 'sly', 'Solyc09g064780.3' => 'sly', 'Sopen01g031980' => 'spe', 'Sopen06g003710' => 'spe', 'Sopen09g026460' => 'spe', 'Sp3g21240' => 'spa', 'Sp4g30030' => 'spa', 'TAR365G0022' => 'tar', 'TAR365G1023' => 'tar', 'TAR365G1253' => 'tar', 'TAR623G0078' => 'tar', 'TAR623G1721' => 'tar', 'TAR633G0959' => 'tar', 'THA.LOC104802225' => 'tha', 'THA.LOC104804769' => 'tha', 'THA.LOC104808660' => 'tha', 'THA.LOC104812792' => 'tha', 'Thecc.01G284000' => 'tca', 'Thecc.04G220600' => 'tca', 'Thecc.05G268900' => 'tca', 'Thecc.08G171100' => 'tca', 'Thhalv10001284m.g' => 'esa', 'Thhalv10019912m.g' => 'esa', 'TPR.G14189' => 'tpr', 'TPR.G18110' => 'tpr', 'TPR.G18130' => 'tpr', 'TPR.G18131' => 'tpr', 'TPR.G18140' => 'tpr', 'TPR.G24282' => 'tpr', 'TPR.G25221' => 'tpr', 'TPR.G29267' => 'tpr', 'TPR.G35315' => 'tpr', 'TPR.G36173' => 'tpr', 'TWI09G0794' => 'twi', 'TWI59G1348' => 'twi', 'TWI74G0430' => 'twi', 'unitig_26.g8940' => 'ugi', 'unitig_749.g13744' => 'ugi', 'unitig_749.g13745' => 'ugi', 'vmacro08269' => 'vma', 'vmacro14937' => 'vma', 'vmacro20401' => 'vma', 'VMungo0464G1349' => 'vmu', 'VMungo0540G0289' => 'vmu', 'VMungo1215G1590' => 'vmu', 'VMungo1309G0221' => 'vmu', 'VMungo1309G2815' => 'vmu', 'VMungo1383G0239' => 'vmu', 'VMungo1383G2910' => 'vmu', 'Zm00001eb095270' => 'zma', 'Zm00001eb095280' => 'zma', 'Zm00001eb111630' => 'zma', 'Zm00001eb237080' => 'zma', 'Zm00001eb273740' => 'zma', 'Zm00001eb285040' => 'zma', 'Zm00001eb330790' => 'zma', 'Zm00001eb337380' => 'zma' ), 'gf_id' => 'HOM05D001484', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001484' ), 'data_identifier' => 'HOM05D001484', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001484', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p31500' => 'bna', 'A05p00020' => 'bna', 'A07p08820' => 'bna', 'Aa31LG4G3300' => 'aar', 'Aa31LG8G10030' => 'aar', 'Actinidia00731' => 'ach', 'Actinidia11473' => 'ach', 'Actinidia23469' => 'ach', 'Actinidia24318' => 'ach', 'Actinidia40196' => 'ach', 'Actinidia40197' => 'ach', 'Actinidia40198' => 'ach', 'Ah.08g212990' => 'amhyb', 'Ah.15g091720' => 'amhyb', 'AL3G38260' => 'aly', 'AL4G47710' => 'aly', 'Aqoxy2G00671' => 'aox', 'Aqoxy2G03236' => 'aox', 'arahy.Tifrunner.gnm1.ann1.05IDCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KR684' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATY3SJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK6QJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6APGL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IDT7Z9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM073U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ0R87' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LE7RV4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT4QRX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V5ENPK' => 'arhy', 'AT2G48110' => 'ath', 'AT3G23590' => 'ath', 'ATR0626G186' => 'atr', 'ATR1127G141' => 'atr', 'Atru.chr4.2583' => 'acertr', 'Atru.chr5.1358' => 'acertr', 'Atru.chr5.1359' => 'acertr', 'Atru.chr8.46' => 'acertr', 'AUR62002640' => 'cqu', 'AUR62030055' => 'cqu', 'AUR62033713' => 'cqu', 'AUR62033714' => 'cqu', 'AUR62036795' => 'cqu', 'AUR62039891' => 'cqu', 'BcaB02g08737' => 'bca', 'BcaB04g20441' => 'bca', 'BcaB06g26509' => 'bca', 'BcaB06g26510' => 'bca', 'BcaB06g26511' => 'bca', 'BcaB06g26512' => 'bca', 'BcaB06g26513' => 'bca', 'BcaC02g12564' => 'bca', 'BcaC02g12565' => 'bca', 'BcaC02g12794' => 'bca', 'BcaC02g12795' => 'bca', 'BcaC02g12796' => 'bca', 'BcaC06g35541' => 'bca', 'BNapus_Darmor_BZH_scaffold_188p00080' => 'bna', 'BNapus_Darmor_BZH_scaffold_188p00090' => 'bna', 'BolC1t03972H' => 'bol', 'BolC1t03973H' => 'bol', 'BolC4t21680H' => 'bol', 'BolC7t41863H' => 'bol', 'BolSC55t61227H' => 'bol', 'BolSC55t61228H' => 'bol', 'BraA01t03278Z' => 'bra', 'BraA05t18998Z' => 'bra', 'BraA07t28673Z' => 'bra', 'C01p40150' => 'bna', 'C05p12370' => 'bna', 'C07p13680' => 'bna', 'CAN.G1006.16' => 'can', 'CAN.G1006.17' => 'can', 'CAN.G1170.2' => 'can', 'CAN.G962.7' => 'can', 'CANSAT25G2179' => 'cansat', 'CANSAT78G1573' => 'cansat', 'CARHR099510' => 'chi', 'CARHR143510' => 'chi', 'Carub.0003s2380' => 'cru', 'Carub.0004s3082' => 'cru', 'Ca_00614_v3' => 'car', 'Ca_07801_v3' => 'car', 'Ca_08567_v3' => 'car', 'Ca_09571_v3' => 'car', 'CBR_g19290' => 'cbr', 'Cc01_g19770' => 'ccan', 'Cc03_g03030' => 'ccan', 'CDE07G0968' => 'cde', 'CDE09G1441' => 'cde', 'Cfa006103' => 'cfa', 'Cfa015573' => 'cfa', 'Cfa016988' => 'cfa', 'Ciclev10006738m.g' => 'ccl', 'Ciclev10010920m.g' => 'ccl', 'Ciclev10018517m.g' => 'ccl', 'CiPaw.01G159200' => 'cil', 'CiPaw.02G091000' => 'cil', 'CiPaw.02G091100' => 'cil', 'CiPaw.08G103100' => 'cil', 'CiPaw.09G224900' => 'cil', 'ClCG06G005740' => 'cla', 'ClCG07G000090' => 'cla', 'ClCG07G000100' => 'cla', 'COL.COLO4_09143' => 'col', 'COL.COLO4_25124' => 'col', 'Cpa.g.sc16.34' => 'cpa', 'Cpa.g.sc3504.1' => 'cpa', 'Cpa.g.sc60.37' => 'cpa', 'CsaV3_6G018520' => 'csa', 'CsaV3_6G036860' => 'csa', 'CSS0001072' => 'camsi', 'CSS0020208' => 'camsi', 'CSS0021253' => 'camsi', 'CSS0022190' => 'camsi', 'CSS0036150' => 'camsi', 'CSS0040442' => 'camsi', 'CSS0042300' => 'camsi', 'CSS0045298' => 'camsi', 'DCAR_012449' => 'dca', 'DCAR_018405' => 'dca', 'DCAR_024573' => 'dca', 'DCAR_030591' => 'dca', 'Dinv16926' => 'din', 'Dinv32963' => 'din', 'Dinv38382' => 'din', 'Dinv38383' => 'din', 'Duzib133G0974' => 'dzi', 'Duzib138G1867' => 'dzi', 'Duzib211G0420' => 'dzi', 'Duzib212G0930' => 'dzi', 'ECA234G1645' => 'eca', 'ECA247G3467' => 'eca', 'ECA248G1703' => 'eca', 'EL10Ac3g06327' => 'bvu', 'EL10Ac7g17204' => 'bvu', 'Eucgr.A00855' => 'egr', 'Eucgr.A00858' => 'egr', 'Eucgr.H01520' => 'egr', 'Eucgr.H03604' => 'egr', 'Eucgr.L03465' => 'egr', 'Eucgr.L03466' => 'egr', 'FAN01G0988' => 'fan', 'FAN02G3892' => 'fan', 'FAN05G3381' => 'fan', 'FAN07G0967' => 'fan', 'FAN07G1493' => 'fan', 'FAN08G3125' => 'fan', 'FAN09G0402' => 'fan', 'FAN12G2594' => 'fan', 'FAN12G3879' => 'fan', 'FAN14G1546' => 'fan', 'FAN15G3626' => 'fan', 'FAN17G0588' => 'fan', 'FAN17G0609' => 'fan', 'FAN18G2817' => 'fan', 'FAN19G1305' => 'fan', 'FAN20G1787' => 'fan', 'FAN22G0073' => 'fan', 'FAN22G0352' => 'fan', 'FAN22G0368' => 'fan', 'FAN22G2273' => 'fan', 'FAN24G1998' => 'fan', 'FAN27G1317' => 'fan', 'FvH4_2g23980' => 'fve', 'FvH4_4g14380' => 'fve', 'FvH4_4g14390' => 'fve', 'FvH4_6g09250' => 'fve', 'Glyma.03G151100' => 'gma', 'Glyma.04G122550' => 'gma', 'Glyma.05G001600' => 'gma', 'Glyma.09G270766' => 'gma', 'Glyma.09G270832' => 'gma', 'Glyma.13G209800' => 'gma', 'Glyma.15G102800' => 'gma', 'Glyma.18G218900' => 'gma', 'Glyma.19G001500' => 'gma', 'Glyma.19G153600' => 'gma', 'Gohir.A02G028600' => 'ghi', 'Gohir.A08G045000' => 'ghi', 'Gohir.A11G120500' => 'ghi', 'Gohir.A12G006200' => 'ghi', 'Gohir.A12G006250' => 'ghi', 'Gohir.D02G036300' => 'ghi', 'Gohir.D08G054700' => 'ghi', 'Gohir.D11G125600' => 'ghi', 'Gohir.D12G005700' => 'ghi', 'Gorai.004G055200' => 'gra', 'Gorai.005G040400' => 'gra', 'Gorai.007G134500' => 'gra', 'Gorai.008G005500' => 'gra', 'GSVIVG01011094001' => 'vvi', 'GSVIVG01017879001' => 'vvi', 'GSVIVG01025988001' => 'vvi', 'GSVIVG01029847001' => 'vvi', 'HanXRQChr10g0282901' => 'han', 'HanXRQChr10g0310371' => 'han', 'HanXRQChr10g0315041' => 'han', 'HanXRQChr11g0327651' => 'han', 'HanXRQChr12g0359391' => 'han', 'Haze_00972' => 'cav', 'Haze_00973' => 'cav', 'Haze_00974' => 'cav', 'Haze_04747' => 'cav', 'Haze_04749' => 'cav', 'Haze_04750' => 'cav', 'Haze_21217' => 'cav', 'Hma1.2p1_1037F.1_g250680' => 'hma', 'Hma1.2p1_1644F.1_g295320' => 'hma', 'HPP92_011322' => 'vpl', 'HPP92_011323' => 'vpl', 'HPP92_011324' => 'vpl', 'HPP92_011325' => 'vpl', 'HPP92_011326' => 'vpl', 'Hund12205' => 'sun', 'Hund17957' => 'sun', 'Lalb_Chr06g0176771' => 'lal', 'Lalb_Chr18g0056021' => 'lal', 'Lalb_Chr18g0056031' => 'lal', 'Lalb_Chr18g0056041' => 'lal', 'Lalb_Chr20g0107751' => 'lal', 'Lalb_Chr20g0118371' => 'lal', 'Lj1g0010239' => 'lja', 'Lj1g0017101' => 'lja', 'Lj2A1178G40' => 'lonja', 'Lj2A54G84' => 'lonja', 'Lj2g0015248' => 'lja', 'Lj3A761T51' => 'lonja', 'Lj6g0018116' => 'lja', 'Lsat_1_v5_gn_4_136040' => 'lsa', 'Lsat_1_v5_gn_5_187461' => 'lsa', 'Lsat_1_v5_gn_5_77001' => 'lsa', 'Lsat_1_v5_gn_9_4461' => 'lsa', 'Manes.01G210100' => 'mes', 'Manes.03G185600' => 'mes', 'Manes.05G073300' => 'mes', 'Manes.09G120300' => 'mes', 'Manes.15G022100' => 'mes', 'Mapoly0096s0053' => 'mpo', 'MBI03_g14058_MAGBIO' => 'mbi', 'MBI03_g33876_MAGBIO' => 'mbi', 'MBI03_g36854_MAGBIO' => 'mbi', 'MBI17_g11997_MAGBIO' => 'mbi', 'MD03G1269000' => 'mdo', 'MD04G1179600' => 'mdo', 'MD11G1289800' => 'mdo', 'MD12G1194700' => 'mdo', 'MD13G1182100' => 'mdo', 'MD13G1182200' => 'mdo', 'MD16G1182600' => 'mdo', 'Medtr2g021400' => 'mtr', 'Medtr2g021470' => 'mtr', 'Medtr2g105810' => 'mtr', 'Medtr3g033580' => 'mtr', 'Medtr6g007970' => 'mtr', 'Medtr7g056330' => 'mtr', 'Medtr7g074290' => 'mtr', 'Medtr7g074380' => 'mtr', 'Medtr7g094550' => 'mtr', 'Medtr8g069995' => 'mtr', 'MELO3C014345.2' => 'cme', 'MELO3C021395.2' => 'cme', 'Migut.D00262' => 'egut', 'Migut.G00257' => 'egut', 'MSTRG.21575' => 'ama', 'MSTRG.3985' => 'ama', 'Nitab4.5_0000295g0140' => 'nta', 'Nitab4.5_0000732g0140' => 'nta', 'Nitab4.5_0003162g0020' => 'nta', 'Nitab4.5_0006180g0090' => 'nta', 'Nitab4.5_0006390g0010' => 'nta', 'Nitab4.5_0007392g0040' => 'nta', 'Nn1g02140' => 'nnu', 'Nn4g26168' => 'nnu', 'Nn5g26754' => 'nnu', 'Oeu001433.1' => 'oeu', 'Oeu010299.2' => 'oeu', 'Oeu011171.1' => 'oeu', 'Oeu037675.1' => 'oeu', 'Oeu038359.1' => 'oeu', 'Oeu063834.1' => 'oeu', 'Oeu063835.1' => 'oeu', 'Os05g0312000' => 'osa', 'Os07g0211101' => 'osa', 'Os07g0211200' => 'osa', 'Os07g0681500' => 'osa', 'Peaxi162Scf00095g01015' => 'pax', 'Peaxi162Scf00104g00329' => 'pax', 'Peaxi162Scf00161g00137' => 'pax', 'PGR004G1665' => 'pgr', 'PGR031G2937' => 'pgr', 'PGR119G2145' => 'pgr', 'PGSC0003DMG400004351' => 'stu', 'PGSC0003DMG400014625' => 'stu', 'PGSC0003DMG401000943' => 'stu', 'Phvul.001G148600' => 'pvu', 'Phvul.004G001700' => 'pvu', 'Phvul.006G154900' => 'pvu', 'Phvul.008G078200' => 'pvu', 'Phvul.011G136500' => 'pvu', 'Potri.002G215600' => 'ptr', 'Potri.008G201600' => 'ptr', 'Potri.014G138400' => 'ptr', 'Potri.016G142500' => 'ptr', 'Pp3c16_10580' => 'ppa', 'Pp3c5_25280' => 'ppa', 'Prupe.1G150000' => 'ppe', 'Prupe.1G150100' => 'ppe', 'Prupe.6G299600' => 'ppe', 'Prupe.8G245000' => 'ppe', 'Psat0s4927g0040' => 'psa', 'Psat1g052080' => 'psa', 'Psat1g183800' => 'psa', 'Psat3g113840' => 'psa', 'Psat3g126120' => 'psa', 'Psat3g126160' => 'psa', 'Psat3g158760' => 'psa', 'Psat3g158840' => 'psa', 'PSO170G2858' => 'pso', 'PSO339G0606' => 'pso', 'PSO384G4709' => 'pso', 'PSO407G0334' => 'pso', 'QL04p040276' => 'qlo', 'QL06p005458' => 'qlo', 'QL06p005472' => 'qlo', 'QL07p030546' => 'qlo', 'QL07p031519' => 'qlo', 'QL09p050949' => 'qlo', 'QL09p050966' => 'qlo', 'QL09p051067' => 'qlo', 'QL12p022706' => 'qlo', 'RcHm_v2.0_Chr2g0119601' => 'rch', 'RcHm_v2.0_Chr3g0459591' => 'rch', 'RcHm_v2.0_Chr4g0418521' => 'rch', 'RcHm_v2.0_Chr4g0418531' => 'rch', 'RcHm_v2.0_Chr4g0418541' => 'rch', 'RcHm_v2.0_Chr6g0291641' => 'rch', 'Rhsim01G0086300' => 'rsi', 'Rhsim01G0276300' => 'rsi', 'Rhsim01G0276500' => 'rsi', 'Rhsim04G0207700' => 'rsi', 'Rhsim05G0234500' => 'rsi', 'Rhsim13G0022400' => 'rsi', 'Sabra02G0167900' => 'sbr', 'Sabra04G0158500' => 'sbr', 'Sabra08G0159800' => 'sbr', 'Sabra10G0011500' => 'sbr', 'Sabra14G0104400' => 'sbr', 'SalBow2G2440' => 'sbo', 'SalBow4G2265' => 'sbo', 'Sc02g0000060' => 'sci', 'Sc05g0005020' => 'sci', 'Sc13g0003890' => 'sci', 'Sed0014865' => 'sed', 'Sed0017224' => 'sed', 'Sed0026391' => 'sed', 'SEGI_00063' => 'sgi', 'SEGI_10967' => 'sgi', 'SEGI_17510' => 'sgi', 'SEGI_24396' => 'sgi', 'SEGI_39719' => 'sgi', 'SEGI_41392' => 'sgi', 'SGA_v2.0_scaffold11G05794' => 'sas', 'SGA_v2.0_scaffold142G35607' => 'sas', 'SGA_v2.0_scaffold1G00447' => 'sas', 'SHI15388' => 'shi', 'SHI15394' => 'shi', 'SHI15396' => 'shi', 'SHI15399' => 'shi', 'SMO343G0151' => 'smo', 'SMO367G1118' => 'smo', 'Solyc01g080200.3' => 'sly', 'Solyc06g008960.3' => 'sly', 'Solyc09g064780.3' => 'sly', 'Sopen01g031980' => 'spe', 'Sopen06g003710' => 'spe', 'Sopen09g026460' => 'spe', 'Sp3g21240' => 'spa', 'Sp4g30030' => 'spa', 'TAR365G0022' => 'tar', 'TAR365G1023' => 'tar', 'TAR365G1253' => 'tar', 'TAR623G0078' => 'tar', 'TAR623G1721' => 'tar', 'TAR633G0959' => 'tar', 'THA.LOC104802225' => 'tha', 'THA.LOC104804769' => 'tha', 'THA.LOC104808660' => 'tha', 'THA.LOC104812792' => 'tha', 'Thecc.01G284000' => 'tca', 'Thecc.04G220600' => 'tca', 'Thecc.05G268900' => 'tca', 'Thecc.08G171100' => 'tca', 'Thhalv10001284m.g' => 'esa', 'Thhalv10019912m.g' => 'esa', 'TPR.G14189' => 'tpr', 'TPR.G18110' => 'tpr', 'TPR.G18130' => 'tpr', 'TPR.G18131' => 'tpr', 'TPR.G18140' => 'tpr', 'TPR.G24282' => 'tpr', 'TPR.G25221' => 'tpr', 'TPR.G29267' => 'tpr', 'TPR.G35315' => 'tpr', 'TPR.G36173' => 'tpr', 'TWI09G0794' => 'twi', 'TWI59G1348' => 'twi', 'TWI74G0430' => 'twi', 'unitig_26.g8940' => 'ugi', 'unitig_749.g13744' => 'ugi', 'unitig_749.g13745' => 'ugi', 'vmacro08269' => 'vma', 'vmacro14937' => 'vma', 'vmacro20401' => 'vma', 'VMungo0464G1349' => 'vmu', 'VMungo0540G0289' => 'vmu', 'VMungo1215G1590' => 'vmu', 'VMungo1309G0221' => 'vmu', 'VMungo1309G2815' => 'vmu', 'VMungo1383G0239' => 'vmu', 'VMungo1383G2910' => 'vmu', 'Zm00001eb095270' => 'zma', 'Zm00001eb095280' => 'zma', 'Zm00001eb111630' => 'zma', 'Zm00001eb237080' => 'zma', 'Zm00001eb273740' => 'zma', 'Zm00001eb285040' => 'zma', 'Zm00001eb330790' => 'zma', 'Zm00001eb337380' => 'zma' ) $gf_id = 'HOM05D001484' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001484' ) $data_identifier = 'HOM05D001484' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 2, 'aly' => (int) 2, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 22, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 7, 'hma' => (int) 2, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 7, 'mtr' => (int) 10, 'cme' => (int) 2, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 4, 'ppa' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 4, 'qlo' => (int) 9, 'rch' => (int) 6, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 10, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 7, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb337380' $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' => 'HOM05D001484', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p31500' => 'bna', 'A05p00020' => 'bna', 'A07p08820' => 'bna', 'Aa31LG4G3300' => 'aar', 'Aa31LG8G10030' => 'aar', 'Actinidia00731' => 'ach', 'Actinidia11473' => 'ach', 'Actinidia23469' => 'ach', 'Actinidia24318' => 'ach', 'Actinidia40196' => 'ach', 'Actinidia40197' => 'ach', 'Actinidia40198' => 'ach', 'Ah.08g212990' => 'amhyb', 'Ah.15g091720' => 'amhyb', 'AL3G38260' => 'aly', 'AL4G47710' => 'aly', 'Aqoxy2G00671' => 'aox', 'Aqoxy2G03236' => 'aox', 'arahy.Tifrunner.gnm1.ann1.05IDCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KR684' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATY3SJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK6QJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6APGL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IDT7Z9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM073U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ0R87' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LE7RV4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT4QRX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V5ENPK' => 'arhy', 'AT2G48110' => 'ath', 'AT3G23590' => 'ath', 'ATR0626G186' => 'atr', 'ATR1127G141' => 'atr', 'Atru.chr4.2583' => 'acertr', 'Atru.chr5.1358' => 'acertr', 'Atru.chr5.1359' => 'acertr', 'Atru.chr8.46' => 'acertr', 'AUR62002640' => 'cqu', 'AUR62030055' => 'cqu', 'AUR62033713' => 'cqu', 'AUR62033714' => 'cqu', 'AUR62036795' => 'cqu', 'AUR62039891' => 'cqu', 'BcaB02g08737' => 'bca', 'BcaB04g20441' => 'bca', 'BcaB06g26509' => 'bca', 'BcaB06g26510' => 'bca', 'BcaB06g26511' => 'bca', 'BcaB06g26512' => 'bca', 'BcaB06g26513' => 'bca', 'BcaC02g12564' => 'bca', 'BcaC02g12565' => 'bca', 'BcaC02g12794' => 'bca', 'BcaC02g12795' => 'bca', 'BcaC02g12796' => 'bca', 'BcaC06g35541' => 'bca', 'BNapus_Darmor_BZH_scaffold_188p00080' => 'bna', 'BNapus_Darmor_BZH_scaffold_188p00090' => 'bna', 'BolC1t03972H' => 'bol', 'BolC1t03973H' => 'bol', 'BolC4t21680H' => 'bol', 'BolC7t41863H' => 'bol', 'BolSC55t61227H' => 'bol', 'BolSC55t61228H' => 'bol', 'BraA01t03278Z' => 'bra', 'BraA05t18998Z' => 'bra', 'BraA07t28673Z' => 'bra', 'C01p40150' => 'bna', 'C05p12370' => 'bna', 'C07p13680' => 'bna', 'CAN.G1006.16' => 'can', 'CAN.G1006.17' => 'can', 'CAN.G1170.2' => 'can', 'CAN.G962.7' => 'can', 'CANSAT25G2179' => 'cansat', 'CANSAT78G1573' => 'cansat', 'CARHR099510' => 'chi', 'CARHR143510' => 'chi', 'Carub.0003s2380' => 'cru', 'Carub.0004s3082' => 'cru', 'Ca_00614_v3' => 'car', 'Ca_07801_v3' => 'car', 'Ca_08567_v3' => 'car', 'Ca_09571_v3' => 'car', 'CBR_g19290' => 'cbr', 'Cc01_g19770' => 'ccan', 'Cc03_g03030' => 'ccan', 'CDE07G0968' => 'cde', 'CDE09G1441' => 'cde', 'Cfa006103' => 'cfa', 'Cfa015573' => 'cfa', 'Cfa016988' => 'cfa', 'Ciclev10006738m.g' => 'ccl', 'Ciclev10010920m.g' => 'ccl', 'Ciclev10018517m.g' => 'ccl', 'CiPaw.01G159200' => 'cil', 'CiPaw.02G091000' => 'cil', 'CiPaw.02G091100' => 'cil', 'CiPaw.08G103100' => 'cil', 'CiPaw.09G224900' => 'cil', 'ClCG06G005740' => 'cla', 'ClCG07G000090' => 'cla', 'ClCG07G000100' => 'cla', 'COL.COLO4_09143' => 'col', 'COL.COLO4_25124' => 'col', 'Cpa.g.sc16.34' => 'cpa', 'Cpa.g.sc3504.1' => 'cpa', 'Cpa.g.sc60.37' => 'cpa', 'CsaV3_6G018520' => 'csa', 'CsaV3_6G036860' => 'csa', 'CSS0001072' => 'camsi', 'CSS0020208' => 'camsi', 'CSS0021253' => 'camsi', 'CSS0022190' => 'camsi', 'CSS0036150' => 'camsi', 'CSS0040442' => 'camsi', 'CSS0042300' => 'camsi', 'CSS0045298' => 'camsi', 'DCAR_012449' => 'dca', 'DCAR_018405' => 'dca', 'DCAR_024573' => 'dca', 'DCAR_030591' => 'dca', 'Dinv16926' => 'din', 'Dinv32963' => 'din', 'Dinv38382' => 'din', 'Dinv38383' => 'din', 'Duzib133G0974' => 'dzi', 'Duzib138G1867' => 'dzi', 'Duzib211G0420' => 'dzi', 'Duzib212G0930' => 'dzi', 'ECA234G1645' => 'eca', 'ECA247G3467' => 'eca', 'ECA248G1703' => 'eca', 'EL10Ac3g06327' => 'bvu', 'EL10Ac7g17204' => 'bvu', 'Eucgr.A00855' => 'egr', 'Eucgr.A00858' => 'egr', 'Eucgr.H01520' => 'egr', 'Eucgr.H03604' => 'egr', 'Eucgr.L03465' => 'egr', 'Eucgr.L03466' => 'egr', 'FAN01G0988' => 'fan', 'FAN02G3892' => 'fan', 'FAN05G3381' => 'fan', 'FAN07G0967' => 'fan', 'FAN07G1493' => 'fan', 'FAN08G3125' => 'fan', 'FAN09G0402' => 'fan', 'FAN12G2594' => 'fan', 'FAN12G3879' => 'fan', 'FAN14G1546' => 'fan', 'FAN15G3626' => 'fan', 'FAN17G0588' => 'fan', 'FAN17G0609' => 'fan', 'FAN18G2817' => 'fan', 'FAN19G1305' => 'fan', 'FAN20G1787' => 'fan', 'FAN22G0073' => 'fan', 'FAN22G0352' => 'fan', 'FAN22G0368' => 'fan', 'FAN22G2273' => 'fan', 'FAN24G1998' => 'fan', 'FAN27G1317' => 'fan', 'FvH4_2g23980' => 'fve', 'FvH4_4g14380' => 'fve', 'FvH4_4g14390' => 'fve', 'FvH4_6g09250' => 'fve', 'Glyma.03G151100' => 'gma', 'Glyma.04G122550' => 'gma', 'Glyma.05G001600' => 'gma', 'Glyma.09G270766' => 'gma', 'Glyma.09G270832' => 'gma', 'Glyma.13G209800' => 'gma', 'Glyma.15G102800' => 'gma', 'Glyma.18G218900' => 'gma', 'Glyma.19G001500' => 'gma', 'Glyma.19G153600' => 'gma', 'Gohir.A02G028600' => 'ghi', 'Gohir.A08G045000' => 'ghi', 'Gohir.A11G120500' => 'ghi', 'Gohir.A12G006200' => 'ghi', 'Gohir.A12G006250' => 'ghi', 'Gohir.D02G036300' => 'ghi', 'Gohir.D08G054700' => 'ghi', 'Gohir.D11G125600' => 'ghi', 'Gohir.D12G005700' => 'ghi', 'Gorai.004G055200' => 'gra', 'Gorai.005G040400' => 'gra', 'Gorai.007G134500' => 'gra', 'Gorai.008G005500' => 'gra', 'GSVIVG01011094001' => 'vvi', 'GSVIVG01017879001' => 'vvi', 'GSVIVG01025988001' => 'vvi', 'GSVIVG01029847001' => 'vvi', 'HanXRQChr10g0282901' => 'han', 'HanXRQChr10g0310371' => 'han', 'HanXRQChr10g0315041' => 'han', 'HanXRQChr11g0327651' => 'han', 'HanXRQChr12g0359391' => 'han', 'Haze_00972' => 'cav', 'Haze_00973' => 'cav', 'Haze_00974' => 'cav', 'Haze_04747' => 'cav', 'Haze_04749' => 'cav', 'Haze_04750' => 'cav', 'Haze_21217' => 'cav', 'Hma1.2p1_1037F.1_g250680' => 'hma', 'Hma1.2p1_1644F.1_g295320' => 'hma', 'HPP92_011322' => 'vpl', 'HPP92_011323' => 'vpl', 'HPP92_011324' => 'vpl', 'HPP92_011325' => 'vpl', 'HPP92_011326' => 'vpl', 'Hund12205' => 'sun', 'Hund17957' => 'sun', 'Lalb_Chr06g0176771' => 'lal', 'Lalb_Chr18g0056021' => 'lal', 'Lalb_Chr18g0056031' => 'lal', 'Lalb_Chr18g0056041' => 'lal', 'Lalb_Chr20g0107751' => 'lal', 'Lalb_Chr20g0118371' => 'lal', 'Lj1g0010239' => 'lja', 'Lj1g0017101' => 'lja', 'Lj2A1178G40' => 'lonja', 'Lj2A54G84' => 'lonja', 'Lj2g0015248' => 'lja', 'Lj3A761T51' => 'lonja', 'Lj6g0018116' => 'lja', 'Lsat_1_v5_gn_4_136040' => 'lsa', 'Lsat_1_v5_gn_5_187461' => 'lsa', 'Lsat_1_v5_gn_5_77001' => 'lsa', 'Lsat_1_v5_gn_9_4461' => 'lsa', 'Manes.01G210100' => 'mes', 'Manes.03G185600' => 'mes', 'Manes.05G073300' => 'mes', 'Manes.09G120300' => 'mes', 'Manes.15G022100' => 'mes', 'Mapoly0096s0053' => 'mpo', 'MBI03_g14058_MAGBIO' => 'mbi', 'MBI03_g33876_MAGBIO' => 'mbi', 'MBI03_g36854_MAGBIO' => 'mbi', 'MBI17_g11997_MAGBIO' => 'mbi', 'MD03G1269000' => 'mdo', 'MD04G1179600' => 'mdo', 'MD11G1289800' => 'mdo', 'MD12G1194700' => 'mdo', 'MD13G1182100' => 'mdo', 'MD13G1182200' => 'mdo', 'MD16G1182600' => 'mdo', 'Medtr2g021400' => 'mtr', 'Medtr2g021470' => 'mtr', 'Medtr2g105810' => 'mtr', 'Medtr3g033580' => 'mtr', 'Medtr6g007970' => 'mtr', 'Medtr7g056330' => 'mtr', 'Medtr7g074290' => 'mtr', 'Medtr7g074380' => 'mtr', 'Medtr7g094550' => 'mtr', 'Medtr8g069995' => 'mtr', 'MELO3C014345.2' => 'cme', 'MELO3C021395.2' => 'cme', 'Migut.D00262' => 'egut', 'Migut.G00257' => 'egut', 'MSTRG.21575' => 'ama', 'MSTRG.3985' => 'ama', 'Nitab4.5_0000295g0140' => 'nta', 'Nitab4.5_0000732g0140' => 'nta', 'Nitab4.5_0003162g0020' => 'nta', 'Nitab4.5_0006180g0090' => 'nta', 'Nitab4.5_0006390g0010' => 'nta', 'Nitab4.5_0007392g0040' => 'nta', 'Nn1g02140' => 'nnu', 'Nn4g26168' => 'nnu', 'Nn5g26754' => 'nnu', 'Oeu001433.1' => 'oeu', 'Oeu010299.2' => 'oeu', 'Oeu011171.1' => 'oeu', 'Oeu037675.1' => 'oeu', 'Oeu038359.1' => 'oeu', 'Oeu063834.1' => 'oeu', 'Oeu063835.1' => 'oeu', 'Os05g0312000' => 'osa', 'Os07g0211101' => 'osa', 'Os07g0211200' => 'osa', 'Os07g0681500' => 'osa', 'Peaxi162Scf00095g01015' => 'pax', 'Peaxi162Scf00104g00329' => 'pax', 'Peaxi162Scf00161g00137' => 'pax', 'PGR004G1665' => 'pgr', 'PGR031G2937' => 'pgr', 'PGR119G2145' => 'pgr', 'PGSC0003DMG400004351' => 'stu', 'PGSC0003DMG400014625' => 'stu', 'PGSC0003DMG401000943' => 'stu', 'Phvul.001G148600' => 'pvu', 'Phvul.004G001700' => 'pvu', 'Phvul.006G154900' => 'pvu', 'Phvul.008G078200' => 'pvu', 'Phvul.011G136500' => 'pvu', 'Potri.002G215600' => 'ptr', 'Potri.008G201600' => 'ptr', 'Potri.014G138400' => 'ptr', 'Potri.016G142500' => 'ptr', 'Pp3c16_10580' => 'ppa', 'Pp3c5_25280' => 'ppa', 'Prupe.1G150000' => 'ppe', 'Prupe.1G150100' => 'ppe', 'Prupe.6G299600' => 'ppe', 'Prupe.8G245000' => 'ppe', 'Psat0s4927g0040' => 'psa', 'Psat1g052080' => 'psa', 'Psat1g183800' => 'psa', 'Psat3g113840' => 'psa', 'Psat3g126120' => 'psa', 'Psat3g126160' => 'psa', 'Psat3g158760' => 'psa', 'Psat3g158840' => 'psa', 'PSO170G2858' => 'pso', 'PSO339G0606' => 'pso', 'PSO384G4709' => 'pso', 'PSO407G0334' => 'pso', 'QL04p040276' => 'qlo', 'QL06p005458' => 'qlo', 'QL06p005472' => 'qlo', 'QL07p030546' => 'qlo', 'QL07p031519' => 'qlo', 'QL09p050949' => 'qlo', 'QL09p050966' => 'qlo', 'QL09p051067' => 'qlo', 'QL12p022706' => 'qlo', 'RcHm_v2.0_Chr2g0119601' => 'rch', 'RcHm_v2.0_Chr3g0459591' => 'rch', 'RcHm_v2.0_Chr4g0418521' => 'rch', 'RcHm_v2.0_Chr4g0418531' => 'rch', 'RcHm_v2.0_Chr4g0418541' => 'rch', 'RcHm_v2.0_Chr6g0291641' => 'rch', 'Rhsim01G0086300' => 'rsi', 'Rhsim01G0276300' => 'rsi', 'Rhsim01G0276500' => 'rsi', 'Rhsim04G0207700' => 'rsi', 'Rhsim05G0234500' => 'rsi', 'Rhsim13G0022400' => 'rsi', 'Sabra02G0167900' => 'sbr', 'Sabra04G0158500' => 'sbr', 'Sabra08G0159800' => 'sbr', 'Sabra10G0011500' => 'sbr', 'Sabra14G0104400' => 'sbr', 'SalBow2G2440' => 'sbo', 'SalBow4G2265' => 'sbo', 'Sc02g0000060' => 'sci', 'Sc05g0005020' => 'sci', 'Sc13g0003890' => 'sci', 'Sed0014865' => 'sed', 'Sed0017224' => 'sed', 'Sed0026391' => 'sed', 'SEGI_00063' => 'sgi', 'SEGI_10967' => 'sgi', 'SEGI_17510' => 'sgi', 'SEGI_24396' => 'sgi', 'SEGI_39719' => 'sgi', 'SEGI_41392' => 'sgi', 'SGA_v2.0_scaffold11G05794' => 'sas', 'SGA_v2.0_scaffold142G35607' => 'sas', 'SGA_v2.0_scaffold1G00447' => 'sas', 'SHI15388' => 'shi', 'SHI15394' => 'shi', 'SHI15396' => 'shi', 'SHI15399' => 'shi', 'SMO343G0151' => 'smo', 'SMO367G1118' => 'smo', 'Solyc01g080200.3' => 'sly', 'Solyc06g008960.3' => 'sly', 'Solyc09g064780.3' => 'sly', 'Sopen01g031980' => 'spe', 'Sopen06g003710' => 'spe', 'Sopen09g026460' => 'spe', 'Sp3g21240' => 'spa', 'Sp4g30030' => 'spa', 'TAR365G0022' => 'tar', 'TAR365G1023' => 'tar', 'TAR365G1253' => 'tar', 'TAR623G0078' => 'tar', 'TAR623G1721' => 'tar', 'TAR633G0959' => 'tar', 'THA.LOC104802225' => 'tha', 'THA.LOC104804769' => 'tha', 'THA.LOC104808660' => 'tha', 'THA.LOC104812792' => 'tha', 'Thecc.01G284000' => 'tca', 'Thecc.04G220600' => 'tca', 'Thecc.05G268900' => 'tca', 'Thecc.08G171100' => 'tca', 'Thhalv10001284m.g' => 'esa', 'Thhalv10019912m.g' => 'esa', 'TPR.G14189' => 'tpr', 'TPR.G18110' => 'tpr', 'TPR.G18130' => 'tpr', 'TPR.G18131' => 'tpr', 'TPR.G18140' => 'tpr', 'TPR.G24282' => 'tpr', 'TPR.G25221' => 'tpr', 'TPR.G29267' => 'tpr', 'TPR.G35315' => 'tpr', 'TPR.G36173' => 'tpr', 'TWI09G0794' => 'twi', 'TWI59G1348' => 'twi', 'TWI74G0430' => 'twi', 'unitig_26.g8940' => 'ugi', 'unitig_749.g13744' => 'ugi', 'unitig_749.g13745' => 'ugi', 'vmacro08269' => 'vma', 'vmacro14937' => 'vma', 'vmacro20401' => 'vma', 'VMungo0464G1349' => 'vmu', 'VMungo0540G0289' => 'vmu', 'VMungo1215G1590' => 'vmu', 'VMungo1309G0221' => 'vmu', 'VMungo1309G2815' => 'vmu', 'VMungo1383G0239' => 'vmu', 'VMungo1383G2910' => 'vmu', 'Zm00001eb095270' => 'zma', 'Zm00001eb095280' => 'zma', 'Zm00001eb111630' => 'zma', 'Zm00001eb237080' => 'zma', 'Zm00001eb273740' => 'zma', 'Zm00001eb285040' => 'zma', 'Zm00001eb330790' => 'zma', 'Zm00001eb337380' => 'zma' ), 'gf_id' => 'HOM05D001484', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001484' ), 'data_identifier' => 'HOM05D001484', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001484', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p31500' => 'bna', 'A05p00020' => 'bna', 'A07p08820' => 'bna', 'Aa31LG4G3300' => 'aar', 'Aa31LG8G10030' => 'aar', 'Actinidia00731' => 'ach', 'Actinidia11473' => 'ach', 'Actinidia23469' => 'ach', 'Actinidia24318' => 'ach', 'Actinidia40196' => 'ach', 'Actinidia40197' => 'ach', 'Actinidia40198' => 'ach', 'Ah.08g212990' => 'amhyb', 'Ah.15g091720' => 'amhyb', 'AL3G38260' => 'aly', 'AL4G47710' => 'aly', 'Aqoxy2G00671' => 'aox', 'Aqoxy2G03236' => 'aox', 'arahy.Tifrunner.gnm1.ann1.05IDCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KR684' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATY3SJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK6QJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6APGL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IDT7Z9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM073U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ0R87' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LE7RV4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT4QRX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V5ENPK' => 'arhy', 'AT2G48110' => 'ath', 'AT3G23590' => 'ath', 'ATR0626G186' => 'atr', 'ATR1127G141' => 'atr', 'Atru.chr4.2583' => 'acertr', 'Atru.chr5.1358' => 'acertr', 'Atru.chr5.1359' => 'acertr', 'Atru.chr8.46' => 'acertr', 'AUR62002640' => 'cqu', 'AUR62030055' => 'cqu', 'AUR62033713' => 'cqu', 'AUR62033714' => 'cqu', 'AUR62036795' => 'cqu', 'AUR62039891' => 'cqu', 'BcaB02g08737' => 'bca', 'BcaB04g20441' => 'bca', 'BcaB06g26509' => 'bca', 'BcaB06g26510' => 'bca', 'BcaB06g26511' => 'bca', 'BcaB06g26512' => 'bca', 'BcaB06g26513' => 'bca', 'BcaC02g12564' => 'bca', 'BcaC02g12565' => 'bca', 'BcaC02g12794' => 'bca', 'BcaC02g12795' => 'bca', 'BcaC02g12796' => 'bca', 'BcaC06g35541' => 'bca', 'BNapus_Darmor_BZH_scaffold_188p00080' => 'bna', 'BNapus_Darmor_BZH_scaffold_188p00090' => 'bna', 'BolC1t03972H' => 'bol', 'BolC1t03973H' => 'bol', 'BolC4t21680H' => 'bol', 'BolC7t41863H' => 'bol', 'BolSC55t61227H' => 'bol', 'BolSC55t61228H' => 'bol', 'BraA01t03278Z' => 'bra', 'BraA05t18998Z' => 'bra', 'BraA07t28673Z' => 'bra', 'C01p40150' => 'bna', 'C05p12370' => 'bna', 'C07p13680' => 'bna', 'CAN.G1006.16' => 'can', 'CAN.G1006.17' => 'can', 'CAN.G1170.2' => 'can', 'CAN.G962.7' => 'can', 'CANSAT25G2179' => 'cansat', 'CANSAT78G1573' => 'cansat', 'CARHR099510' => 'chi', 'CARHR143510' => 'chi', 'Carub.0003s2380' => 'cru', 'Carub.0004s3082' => 'cru', 'Ca_00614_v3' => 'car', 'Ca_07801_v3' => 'car', 'Ca_08567_v3' => 'car', 'Ca_09571_v3' => 'car', 'CBR_g19290' => 'cbr', 'Cc01_g19770' => 'ccan', 'Cc03_g03030' => 'ccan', 'CDE07G0968' => 'cde', 'CDE09G1441' => 'cde', 'Cfa006103' => 'cfa', 'Cfa015573' => 'cfa', 'Cfa016988' => 'cfa', 'Ciclev10006738m.g' => 'ccl', 'Ciclev10010920m.g' => 'ccl', 'Ciclev10018517m.g' => 'ccl', 'CiPaw.01G159200' => 'cil', 'CiPaw.02G091000' => 'cil', 'CiPaw.02G091100' => 'cil', 'CiPaw.08G103100' => 'cil', 'CiPaw.09G224900' => 'cil', 'ClCG06G005740' => 'cla', 'ClCG07G000090' => 'cla', 'ClCG07G000100' => 'cla', 'COL.COLO4_09143' => 'col', 'COL.COLO4_25124' => 'col', 'Cpa.g.sc16.34' => 'cpa', 'Cpa.g.sc3504.1' => 'cpa', 'Cpa.g.sc60.37' => 'cpa', 'CsaV3_6G018520' => 'csa', 'CsaV3_6G036860' => 'csa', 'CSS0001072' => 'camsi', 'CSS0020208' => 'camsi', 'CSS0021253' => 'camsi', 'CSS0022190' => 'camsi', 'CSS0036150' => 'camsi', 'CSS0040442' => 'camsi', 'CSS0042300' => 'camsi', 'CSS0045298' => 'camsi', 'DCAR_012449' => 'dca', 'DCAR_018405' => 'dca', 'DCAR_024573' => 'dca', 'DCAR_030591' => 'dca', 'Dinv16926' => 'din', 'Dinv32963' => 'din', 'Dinv38382' => 'din', 'Dinv38383' => 'din', 'Duzib133G0974' => 'dzi', 'Duzib138G1867' => 'dzi', 'Duzib211G0420' => 'dzi', 'Duzib212G0930' => 'dzi', 'ECA234G1645' => 'eca', 'ECA247G3467' => 'eca', 'ECA248G1703' => 'eca', 'EL10Ac3g06327' => 'bvu', 'EL10Ac7g17204' => 'bvu', 'Eucgr.A00855' => 'egr', 'Eucgr.A00858' => 'egr', 'Eucgr.H01520' => 'egr', 'Eucgr.H03604' => 'egr', 'Eucgr.L03465' => 'egr', 'Eucgr.L03466' => 'egr', 'FAN01G0988' => 'fan', 'FAN02G3892' => 'fan', 'FAN05G3381' => 'fan', 'FAN07G0967' => 'fan', 'FAN07G1493' => 'fan', 'FAN08G3125' => 'fan', 'FAN09G0402' => 'fan', 'FAN12G2594' => 'fan', 'FAN12G3879' => 'fan', 'FAN14G1546' => 'fan', 'FAN15G3626' => 'fan', 'FAN17G0588' => 'fan', 'FAN17G0609' => 'fan', 'FAN18G2817' => 'fan', 'FAN19G1305' => 'fan', 'FAN20G1787' => 'fan', 'FAN22G0073' => 'fan', 'FAN22G0352' => 'fan', 'FAN22G0368' => 'fan', 'FAN22G2273' => 'fan', 'FAN24G1998' => 'fan', 'FAN27G1317' => 'fan', 'FvH4_2g23980' => 'fve', 'FvH4_4g14380' => 'fve', 'FvH4_4g14390' => 'fve', 'FvH4_6g09250' => 'fve', 'Glyma.03G151100' => 'gma', 'Glyma.04G122550' => 'gma', 'Glyma.05G001600' => 'gma', 'Glyma.09G270766' => 'gma', 'Glyma.09G270832' => 'gma', 'Glyma.13G209800' => 'gma', 'Glyma.15G102800' => 'gma', 'Glyma.18G218900' => 'gma', 'Glyma.19G001500' => 'gma', 'Glyma.19G153600' => 'gma', 'Gohir.A02G028600' => 'ghi', 'Gohir.A08G045000' => 'ghi', 'Gohir.A11G120500' => 'ghi', 'Gohir.A12G006200' => 'ghi', 'Gohir.A12G006250' => 'ghi', 'Gohir.D02G036300' => 'ghi', 'Gohir.D08G054700' => 'ghi', 'Gohir.D11G125600' => 'ghi', 'Gohir.D12G005700' => 'ghi', 'Gorai.004G055200' => 'gra', 'Gorai.005G040400' => 'gra', 'Gorai.007G134500' => 'gra', 'Gorai.008G005500' => 'gra', 'GSVIVG01011094001' => 'vvi', 'GSVIVG01017879001' => 'vvi', 'GSVIVG01025988001' => 'vvi', 'GSVIVG01029847001' => 'vvi', 'HanXRQChr10g0282901' => 'han', 'HanXRQChr10g0310371' => 'han', 'HanXRQChr10g0315041' => 'han', 'HanXRQChr11g0327651' => 'han', 'HanXRQChr12g0359391' => 'han', 'Haze_00972' => 'cav', 'Haze_00973' => 'cav', 'Haze_00974' => 'cav', 'Haze_04747' => 'cav', 'Haze_04749' => 'cav', 'Haze_04750' => 'cav', 'Haze_21217' => 'cav', 'Hma1.2p1_1037F.1_g250680' => 'hma', 'Hma1.2p1_1644F.1_g295320' => 'hma', 'HPP92_011322' => 'vpl', 'HPP92_011323' => 'vpl', 'HPP92_011324' => 'vpl', 'HPP92_011325' => 'vpl', 'HPP92_011326' => 'vpl', 'Hund12205' => 'sun', 'Hund17957' => 'sun', 'Lalb_Chr06g0176771' => 'lal', 'Lalb_Chr18g0056021' => 'lal', 'Lalb_Chr18g0056031' => 'lal', 'Lalb_Chr18g0056041' => 'lal', 'Lalb_Chr20g0107751' => 'lal', 'Lalb_Chr20g0118371' => 'lal', 'Lj1g0010239' => 'lja', 'Lj1g0017101' => 'lja', 'Lj2A1178G40' => 'lonja', 'Lj2A54G84' => 'lonja', 'Lj2g0015248' => 'lja', 'Lj3A761T51' => 'lonja', 'Lj6g0018116' => 'lja', 'Lsat_1_v5_gn_4_136040' => 'lsa', 'Lsat_1_v5_gn_5_187461' => 'lsa', 'Lsat_1_v5_gn_5_77001' => 'lsa', 'Lsat_1_v5_gn_9_4461' => 'lsa', 'Manes.01G210100' => 'mes', 'Manes.03G185600' => 'mes', 'Manes.05G073300' => 'mes', 'Manes.09G120300' => 'mes', 'Manes.15G022100' => 'mes', 'Mapoly0096s0053' => 'mpo', 'MBI03_g14058_MAGBIO' => 'mbi', 'MBI03_g33876_MAGBIO' => 'mbi', 'MBI03_g36854_MAGBIO' => 'mbi', 'MBI17_g11997_MAGBIO' => 'mbi', 'MD03G1269000' => 'mdo', 'MD04G1179600' => 'mdo', 'MD11G1289800' => 'mdo', 'MD12G1194700' => 'mdo', 'MD13G1182100' => 'mdo', 'MD13G1182200' => 'mdo', 'MD16G1182600' => 'mdo', 'Medtr2g021400' => 'mtr', 'Medtr2g021470' => 'mtr', 'Medtr2g105810' => 'mtr', 'Medtr3g033580' => 'mtr', 'Medtr6g007970' => 'mtr', 'Medtr7g056330' => 'mtr', 'Medtr7g074290' => 'mtr', 'Medtr7g074380' => 'mtr', 'Medtr7g094550' => 'mtr', 'Medtr8g069995' => 'mtr', 'MELO3C014345.2' => 'cme', 'MELO3C021395.2' => 'cme', 'Migut.D00262' => 'egut', 'Migut.G00257' => 'egut', 'MSTRG.21575' => 'ama', 'MSTRG.3985' => 'ama', 'Nitab4.5_0000295g0140' => 'nta', 'Nitab4.5_0000732g0140' => 'nta', 'Nitab4.5_0003162g0020' => 'nta', 'Nitab4.5_0006180g0090' => 'nta', 'Nitab4.5_0006390g0010' => 'nta', 'Nitab4.5_0007392g0040' => 'nta', 'Nn1g02140' => 'nnu', 'Nn4g26168' => 'nnu', 'Nn5g26754' => 'nnu', 'Oeu001433.1' => 'oeu', 'Oeu010299.2' => 'oeu', 'Oeu011171.1' => 'oeu', 'Oeu037675.1' => 'oeu', 'Oeu038359.1' => 'oeu', 'Oeu063834.1' => 'oeu', 'Oeu063835.1' => 'oeu', 'Os05g0312000' => 'osa', 'Os07g0211101' => 'osa', 'Os07g0211200' => 'osa', 'Os07g0681500' => 'osa', 'Peaxi162Scf00095g01015' => 'pax', 'Peaxi162Scf00104g00329' => 'pax', 'Peaxi162Scf00161g00137' => 'pax', 'PGR004G1665' => 'pgr', 'PGR031G2937' => 'pgr', 'PGR119G2145' => 'pgr', 'PGSC0003DMG400004351' => 'stu', 'PGSC0003DMG400014625' => 'stu', 'PGSC0003DMG401000943' => 'stu', 'Phvul.001G148600' => 'pvu', 'Phvul.004G001700' => 'pvu', 'Phvul.006G154900' => 'pvu', 'Phvul.008G078200' => 'pvu', 'Phvul.011G136500' => 'pvu', 'Potri.002G215600' => 'ptr', 'Potri.008G201600' => 'ptr', 'Potri.014G138400' => 'ptr', 'Potri.016G142500' => 'ptr', 'Pp3c16_10580' => 'ppa', 'Pp3c5_25280' => 'ppa', 'Prupe.1G150000' => 'ppe', 'Prupe.1G150100' => 'ppe', 'Prupe.6G299600' => 'ppe', 'Prupe.8G245000' => 'ppe', 'Psat0s4927g0040' => 'psa', 'Psat1g052080' => 'psa', 'Psat1g183800' => 'psa', 'Psat3g113840' => 'psa', 'Psat3g126120' => 'psa', 'Psat3g126160' => 'psa', 'Psat3g158760' => 'psa', 'Psat3g158840' => 'psa', 'PSO170G2858' => 'pso', 'PSO339G0606' => 'pso', 'PSO384G4709' => 'pso', 'PSO407G0334' => 'pso', 'QL04p040276' => 'qlo', 'QL06p005458' => 'qlo', 'QL06p005472' => 'qlo', 'QL07p030546' => 'qlo', 'QL07p031519' => 'qlo', 'QL09p050949' => 'qlo', 'QL09p050966' => 'qlo', 'QL09p051067' => 'qlo', 'QL12p022706' => 'qlo', 'RcHm_v2.0_Chr2g0119601' => 'rch', 'RcHm_v2.0_Chr3g0459591' => 'rch', 'RcHm_v2.0_Chr4g0418521' => 'rch', 'RcHm_v2.0_Chr4g0418531' => 'rch', 'RcHm_v2.0_Chr4g0418541' => 'rch', 'RcHm_v2.0_Chr6g0291641' => 'rch', 'Rhsim01G0086300' => 'rsi', 'Rhsim01G0276300' => 'rsi', 'Rhsim01G0276500' => 'rsi', 'Rhsim04G0207700' => 'rsi', 'Rhsim05G0234500' => 'rsi', 'Rhsim13G0022400' => 'rsi', 'Sabra02G0167900' => 'sbr', 'Sabra04G0158500' => 'sbr', 'Sabra08G0159800' => 'sbr', 'Sabra10G0011500' => 'sbr', 'Sabra14G0104400' => 'sbr', 'SalBow2G2440' => 'sbo', 'SalBow4G2265' => 'sbo', 'Sc02g0000060' => 'sci', 'Sc05g0005020' => 'sci', 'Sc13g0003890' => 'sci', 'Sed0014865' => 'sed', 'Sed0017224' => 'sed', 'Sed0026391' => 'sed', 'SEGI_00063' => 'sgi', 'SEGI_10967' => 'sgi', 'SEGI_17510' => 'sgi', 'SEGI_24396' => 'sgi', 'SEGI_39719' => 'sgi', 'SEGI_41392' => 'sgi', 'SGA_v2.0_scaffold11G05794' => 'sas', 'SGA_v2.0_scaffold142G35607' => 'sas', 'SGA_v2.0_scaffold1G00447' => 'sas', 'SHI15388' => 'shi', 'SHI15394' => 'shi', 'SHI15396' => 'shi', 'SHI15399' => 'shi', 'SMO343G0151' => 'smo', 'SMO367G1118' => 'smo', 'Solyc01g080200.3' => 'sly', 'Solyc06g008960.3' => 'sly', 'Solyc09g064780.3' => 'sly', 'Sopen01g031980' => 'spe', 'Sopen06g003710' => 'spe', 'Sopen09g026460' => 'spe', 'Sp3g21240' => 'spa', 'Sp4g30030' => 'spa', 'TAR365G0022' => 'tar', 'TAR365G1023' => 'tar', 'TAR365G1253' => 'tar', 'TAR623G0078' => 'tar', 'TAR623G1721' => 'tar', 'TAR633G0959' => 'tar', 'THA.LOC104802225' => 'tha', 'THA.LOC104804769' => 'tha', 'THA.LOC104808660' => 'tha', 'THA.LOC104812792' => 'tha', 'Thecc.01G284000' => 'tca', 'Thecc.04G220600' => 'tca', 'Thecc.05G268900' => 'tca', 'Thecc.08G171100' => 'tca', 'Thhalv10001284m.g' => 'esa', 'Thhalv10019912m.g' => 'esa', 'TPR.G14189' => 'tpr', 'TPR.G18110' => 'tpr', 'TPR.G18130' => 'tpr', 'TPR.G18131' => 'tpr', 'TPR.G18140' => 'tpr', 'TPR.G24282' => 'tpr', 'TPR.G25221' => 'tpr', 'TPR.G29267' => 'tpr', 'TPR.G35315' => 'tpr', 'TPR.G36173' => 'tpr', 'TWI09G0794' => 'twi', 'TWI59G1348' => 'twi', 'TWI74G0430' => 'twi', 'unitig_26.g8940' => 'ugi', 'unitig_749.g13744' => 'ugi', 'unitig_749.g13745' => 'ugi', 'vmacro08269' => 'vma', 'vmacro14937' => 'vma', 'vmacro20401' => 'vma', 'VMungo0464G1349' => 'vmu', 'VMungo0540G0289' => 'vmu', 'VMungo1215G1590' => 'vmu', 'VMungo1309G0221' => 'vmu', 'VMungo1309G2815' => 'vmu', 'VMungo1383G0239' => 'vmu', 'VMungo1383G2910' => 'vmu', 'Zm00001eb095270' => 'zma', 'Zm00001eb095280' => 'zma', 'Zm00001eb111630' => 'zma', 'Zm00001eb237080' => 'zma', 'Zm00001eb273740' => 'zma', 'Zm00001eb285040' => 'zma', 'Zm00001eb330790' => 'zma', 'Zm00001eb337380' => 'zma' ) $gf_id = 'HOM05D001484' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001484' ) $data_identifier = 'HOM05D001484' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 2, 'aly' => (int) 2, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 22, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 7, 'hma' => (int) 2, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 7, 'mtr' => (int) 10, 'cme' => (int) 2, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 4, 'ppa' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 4, 'qlo' => (int) 9, 'rch' => (int) 6, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 10, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 7, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb337380' $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' => 'HOM05D001484', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p31500' => 'bna', 'A05p00020' => 'bna', 'A07p08820' => 'bna', 'Aa31LG4G3300' => 'aar', 'Aa31LG8G10030' => 'aar', 'Actinidia00731' => 'ach', 'Actinidia11473' => 'ach', 'Actinidia23469' => 'ach', 'Actinidia24318' => 'ach', 'Actinidia40196' => 'ach', 'Actinidia40197' => 'ach', 'Actinidia40198' => 'ach', 'Ah.08g212990' => 'amhyb', 'Ah.15g091720' => 'amhyb', 'AL3G38260' => 'aly', 'AL4G47710' => 'aly', 'Aqoxy2G00671' => 'aox', 'Aqoxy2G03236' => 'aox', 'arahy.Tifrunner.gnm1.ann1.05IDCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KR684' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATY3SJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK6QJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6APGL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IDT7Z9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM073U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ0R87' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LE7RV4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT4QRX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V5ENPK' => 'arhy', 'AT2G48110' => 'ath', 'AT3G23590' => 'ath', 'ATR0626G186' => 'atr', 'ATR1127G141' => 'atr', 'Atru.chr4.2583' => 'acertr', 'Atru.chr5.1358' => 'acertr', 'Atru.chr5.1359' => 'acertr', 'Atru.chr8.46' => 'acertr', 'AUR62002640' => 'cqu', 'AUR62030055' => 'cqu', 'AUR62033713' => 'cqu', 'AUR62033714' => 'cqu', 'AUR62036795' => 'cqu', 'AUR62039891' => 'cqu', 'BcaB02g08737' => 'bca', 'BcaB04g20441' => 'bca', 'BcaB06g26509' => 'bca', 'BcaB06g26510' => 'bca', 'BcaB06g26511' => 'bca', 'BcaB06g26512' => 'bca', 'BcaB06g26513' => 'bca', 'BcaC02g12564' => 'bca', 'BcaC02g12565' => 'bca', 'BcaC02g12794' => 'bca', 'BcaC02g12795' => 'bca', 'BcaC02g12796' => 'bca', 'BcaC06g35541' => 'bca', 'BNapus_Darmor_BZH_scaffold_188p00080' => 'bna', 'BNapus_Darmor_BZH_scaffold_188p00090' => 'bna', 'BolC1t03972H' => 'bol', 'BolC1t03973H' => 'bol', 'BolC4t21680H' => 'bol', 'BolC7t41863H' => 'bol', 'BolSC55t61227H' => 'bol', 'BolSC55t61228H' => 'bol', 'BraA01t03278Z' => 'bra', 'BraA05t18998Z' => 'bra', 'BraA07t28673Z' => 'bra', 'C01p40150' => 'bna', 'C05p12370' => 'bna', 'C07p13680' => 'bna', 'CAN.G1006.16' => 'can', 'CAN.G1006.17' => 'can', 'CAN.G1170.2' => 'can', 'CAN.G962.7' => 'can', 'CANSAT25G2179' => 'cansat', 'CANSAT78G1573' => 'cansat', 'CARHR099510' => 'chi', 'CARHR143510' => 'chi', 'Carub.0003s2380' => 'cru', 'Carub.0004s3082' => 'cru', 'Ca_00614_v3' => 'car', 'Ca_07801_v3' => 'car', 'Ca_08567_v3' => 'car', 'Ca_09571_v3' => 'car', 'CBR_g19290' => 'cbr', 'Cc01_g19770' => 'ccan', 'Cc03_g03030' => 'ccan', 'CDE07G0968' => 'cde', 'CDE09G1441' => 'cde', 'Cfa006103' => 'cfa', 'Cfa015573' => 'cfa', 'Cfa016988' => 'cfa', 'Ciclev10006738m.g' => 'ccl', 'Ciclev10010920m.g' => 'ccl', 'Ciclev10018517m.g' => 'ccl', 'CiPaw.01G159200' => 'cil', 'CiPaw.02G091000' => 'cil', 'CiPaw.02G091100' => 'cil', 'CiPaw.08G103100' => 'cil', 'CiPaw.09G224900' => 'cil', 'ClCG06G005740' => 'cla', 'ClCG07G000090' => 'cla', 'ClCG07G000100' => 'cla', 'COL.COLO4_09143' => 'col', 'COL.COLO4_25124' => 'col', 'Cpa.g.sc16.34' => 'cpa', 'Cpa.g.sc3504.1' => 'cpa', 'Cpa.g.sc60.37' => 'cpa', 'CsaV3_6G018520' => 'csa', 'CsaV3_6G036860' => 'csa', 'CSS0001072' => 'camsi', 'CSS0020208' => 'camsi', 'CSS0021253' => 'camsi', 'CSS0022190' => 'camsi', 'CSS0036150' => 'camsi', 'CSS0040442' => 'camsi', 'CSS0042300' => 'camsi', 'CSS0045298' => 'camsi', 'DCAR_012449' => 'dca', 'DCAR_018405' => 'dca', 'DCAR_024573' => 'dca', 'DCAR_030591' => 'dca', 'Dinv16926' => 'din', 'Dinv32963' => 'din', 'Dinv38382' => 'din', 'Dinv38383' => 'din', 'Duzib133G0974' => 'dzi', 'Duzib138G1867' => 'dzi', 'Duzib211G0420' => 'dzi', 'Duzib212G0930' => 'dzi', 'ECA234G1645' => 'eca', 'ECA247G3467' => 'eca', 'ECA248G1703' => 'eca', 'EL10Ac3g06327' => 'bvu', 'EL10Ac7g17204' => 'bvu', 'Eucgr.A00855' => 'egr', 'Eucgr.A00858' => 'egr', 'Eucgr.H01520' => 'egr', 'Eucgr.H03604' => 'egr', 'Eucgr.L03465' => 'egr', 'Eucgr.L03466' => 'egr', 'FAN01G0988' => 'fan', 'FAN02G3892' => 'fan', 'FAN05G3381' => 'fan', 'FAN07G0967' => 'fan', 'FAN07G1493' => 'fan', 'FAN08G3125' => 'fan', 'FAN09G0402' => 'fan', 'FAN12G2594' => 'fan', 'FAN12G3879' => 'fan', 'FAN14G1546' => 'fan', 'FAN15G3626' => 'fan', 'FAN17G0588' => 'fan', 'FAN17G0609' => 'fan', 'FAN18G2817' => 'fan', 'FAN19G1305' => 'fan', 'FAN20G1787' => 'fan', 'FAN22G0073' => 'fan', 'FAN22G0352' => 'fan', 'FAN22G0368' => 'fan', 'FAN22G2273' => 'fan', 'FAN24G1998' => 'fan', 'FAN27G1317' => 'fan', 'FvH4_2g23980' => 'fve', 'FvH4_4g14380' => 'fve', 'FvH4_4g14390' => 'fve', 'FvH4_6g09250' => 'fve', 'Glyma.03G151100' => 'gma', 'Glyma.04G122550' => 'gma', 'Glyma.05G001600' => 'gma', 'Glyma.09G270766' => 'gma', 'Glyma.09G270832' => 'gma', 'Glyma.13G209800' => 'gma', 'Glyma.15G102800' => 'gma', 'Glyma.18G218900' => 'gma', 'Glyma.19G001500' => 'gma', 'Glyma.19G153600' => 'gma', 'Gohir.A02G028600' => 'ghi', 'Gohir.A08G045000' => 'ghi', 'Gohir.A11G120500' => 'ghi', 'Gohir.A12G006200' => 'ghi', 'Gohir.A12G006250' => 'ghi', 'Gohir.D02G036300' => 'ghi', 'Gohir.D08G054700' => 'ghi', 'Gohir.D11G125600' => 'ghi', 'Gohir.D12G005700' => 'ghi', 'Gorai.004G055200' => 'gra', 'Gorai.005G040400' => 'gra', 'Gorai.007G134500' => 'gra', 'Gorai.008G005500' => 'gra', 'GSVIVG01011094001' => 'vvi', 'GSVIVG01017879001' => 'vvi', 'GSVIVG01025988001' => 'vvi', 'GSVIVG01029847001' => 'vvi', 'HanXRQChr10g0282901' => 'han', 'HanXRQChr10g0310371' => 'han', 'HanXRQChr10g0315041' => 'han', 'HanXRQChr11g0327651' => 'han', 'HanXRQChr12g0359391' => 'han', 'Haze_00972' => 'cav', 'Haze_00973' => 'cav', 'Haze_00974' => 'cav', 'Haze_04747' => 'cav', 'Haze_04749' => 'cav', 'Haze_04750' => 'cav', 'Haze_21217' => 'cav', 'Hma1.2p1_1037F.1_g250680' => 'hma', 'Hma1.2p1_1644F.1_g295320' => 'hma', 'HPP92_011322' => 'vpl', 'HPP92_011323' => 'vpl', 'HPP92_011324' => 'vpl', 'HPP92_011325' => 'vpl', 'HPP92_011326' => 'vpl', 'Hund12205' => 'sun', 'Hund17957' => 'sun', 'Lalb_Chr06g0176771' => 'lal', 'Lalb_Chr18g0056021' => 'lal', 'Lalb_Chr18g0056031' => 'lal', 'Lalb_Chr18g0056041' => 'lal', 'Lalb_Chr20g0107751' => 'lal', 'Lalb_Chr20g0118371' => 'lal', 'Lj1g0010239' => 'lja', 'Lj1g0017101' => 'lja', 'Lj2A1178G40' => 'lonja', 'Lj2A54G84' => 'lonja', 'Lj2g0015248' => 'lja', 'Lj3A761T51' => 'lonja', 'Lj6g0018116' => 'lja', 'Lsat_1_v5_gn_4_136040' => 'lsa', 'Lsat_1_v5_gn_5_187461' => 'lsa', 'Lsat_1_v5_gn_5_77001' => 'lsa', 'Lsat_1_v5_gn_9_4461' => 'lsa', 'Manes.01G210100' => 'mes', 'Manes.03G185600' => 'mes', 'Manes.05G073300' => 'mes', 'Manes.09G120300' => 'mes', 'Manes.15G022100' => 'mes', 'Mapoly0096s0053' => 'mpo', 'MBI03_g14058_MAGBIO' => 'mbi', 'MBI03_g33876_MAGBIO' => 'mbi', 'MBI03_g36854_MAGBIO' => 'mbi', 'MBI17_g11997_MAGBIO' => 'mbi', 'MD03G1269000' => 'mdo', 'MD04G1179600' => 'mdo', 'MD11G1289800' => 'mdo', 'MD12G1194700' => 'mdo', 'MD13G1182100' => 'mdo', 'MD13G1182200' => 'mdo', 'MD16G1182600' => 'mdo', 'Medtr2g021400' => 'mtr', 'Medtr2g021470' => 'mtr', 'Medtr2g105810' => 'mtr', 'Medtr3g033580' => 'mtr', 'Medtr6g007970' => 'mtr', 'Medtr7g056330' => 'mtr', 'Medtr7g074290' => 'mtr', 'Medtr7g074380' => 'mtr', 'Medtr7g094550' => 'mtr', 'Medtr8g069995' => 'mtr', 'MELO3C014345.2' => 'cme', 'MELO3C021395.2' => 'cme', 'Migut.D00262' => 'egut', 'Migut.G00257' => 'egut', 'MSTRG.21575' => 'ama', 'MSTRG.3985' => 'ama', 'Nitab4.5_0000295g0140' => 'nta', 'Nitab4.5_0000732g0140' => 'nta', 'Nitab4.5_0003162g0020' => 'nta', 'Nitab4.5_0006180g0090' => 'nta', 'Nitab4.5_0006390g0010' => 'nta', 'Nitab4.5_0007392g0040' => 'nta', 'Nn1g02140' => 'nnu', 'Nn4g26168' => 'nnu', 'Nn5g26754' => 'nnu', 'Oeu001433.1' => 'oeu', 'Oeu010299.2' => 'oeu', 'Oeu011171.1' => 'oeu', 'Oeu037675.1' => 'oeu', 'Oeu038359.1' => 'oeu', 'Oeu063834.1' => 'oeu', 'Oeu063835.1' => 'oeu', 'Os05g0312000' => 'osa', 'Os07g0211101' => 'osa', 'Os07g0211200' => 'osa', 'Os07g0681500' => 'osa', 'Peaxi162Scf00095g01015' => 'pax', 'Peaxi162Scf00104g00329' => 'pax', 'Peaxi162Scf00161g00137' => 'pax', 'PGR004G1665' => 'pgr', 'PGR031G2937' => 'pgr', 'PGR119G2145' => 'pgr', 'PGSC0003DMG400004351' => 'stu', 'PGSC0003DMG400014625' => 'stu', 'PGSC0003DMG401000943' => 'stu', 'Phvul.001G148600' => 'pvu', 'Phvul.004G001700' => 'pvu', 'Phvul.006G154900' => 'pvu', 'Phvul.008G078200' => 'pvu', 'Phvul.011G136500' => 'pvu', 'Potri.002G215600' => 'ptr', 'Potri.008G201600' => 'ptr', 'Potri.014G138400' => 'ptr', 'Potri.016G142500' => 'ptr', 'Pp3c16_10580' => 'ppa', 'Pp3c5_25280' => 'ppa', 'Prupe.1G150000' => 'ppe', 'Prupe.1G150100' => 'ppe', 'Prupe.6G299600' => 'ppe', 'Prupe.8G245000' => 'ppe', 'Psat0s4927g0040' => 'psa', 'Psat1g052080' => 'psa', 'Psat1g183800' => 'psa', 'Psat3g113840' => 'psa', 'Psat3g126120' => 'psa', 'Psat3g126160' => 'psa', 'Psat3g158760' => 'psa', 'Psat3g158840' => 'psa', 'PSO170G2858' => 'pso', 'PSO339G0606' => 'pso', 'PSO384G4709' => 'pso', 'PSO407G0334' => 'pso', 'QL04p040276' => 'qlo', 'QL06p005458' => 'qlo', 'QL06p005472' => 'qlo', 'QL07p030546' => 'qlo', 'QL07p031519' => 'qlo', 'QL09p050949' => 'qlo', 'QL09p050966' => 'qlo', 'QL09p051067' => 'qlo', 'QL12p022706' => 'qlo', 'RcHm_v2.0_Chr2g0119601' => 'rch', 'RcHm_v2.0_Chr3g0459591' => 'rch', 'RcHm_v2.0_Chr4g0418521' => 'rch', 'RcHm_v2.0_Chr4g0418531' => 'rch', 'RcHm_v2.0_Chr4g0418541' => 'rch', 'RcHm_v2.0_Chr6g0291641' => 'rch', 'Rhsim01G0086300' => 'rsi', 'Rhsim01G0276300' => 'rsi', 'Rhsim01G0276500' => 'rsi', 'Rhsim04G0207700' => 'rsi', 'Rhsim05G0234500' => 'rsi', 'Rhsim13G0022400' => 'rsi', 'Sabra02G0167900' => 'sbr', 'Sabra04G0158500' => 'sbr', 'Sabra08G0159800' => 'sbr', 'Sabra10G0011500' => 'sbr', 'Sabra14G0104400' => 'sbr', 'SalBow2G2440' => 'sbo', 'SalBow4G2265' => 'sbo', 'Sc02g0000060' => 'sci', 'Sc05g0005020' => 'sci', 'Sc13g0003890' => 'sci', 'Sed0014865' => 'sed', 'Sed0017224' => 'sed', 'Sed0026391' => 'sed', 'SEGI_00063' => 'sgi', 'SEGI_10967' => 'sgi', 'SEGI_17510' => 'sgi', 'SEGI_24396' => 'sgi', 'SEGI_39719' => 'sgi', 'SEGI_41392' => 'sgi', 'SGA_v2.0_scaffold11G05794' => 'sas', 'SGA_v2.0_scaffold142G35607' => 'sas', 'SGA_v2.0_scaffold1G00447' => 'sas', 'SHI15388' => 'shi', 'SHI15394' => 'shi', 'SHI15396' => 'shi', 'SHI15399' => 'shi', 'SMO343G0151' => 'smo', 'SMO367G1118' => 'smo', 'Solyc01g080200.3' => 'sly', 'Solyc06g008960.3' => 'sly', 'Solyc09g064780.3' => 'sly', 'Sopen01g031980' => 'spe', 'Sopen06g003710' => 'spe', 'Sopen09g026460' => 'spe', 'Sp3g21240' => 'spa', 'Sp4g30030' => 'spa', 'TAR365G0022' => 'tar', 'TAR365G1023' => 'tar', 'TAR365G1253' => 'tar', 'TAR623G0078' => 'tar', 'TAR623G1721' => 'tar', 'TAR633G0959' => 'tar', 'THA.LOC104802225' => 'tha', 'THA.LOC104804769' => 'tha', 'THA.LOC104808660' => 'tha', 'THA.LOC104812792' => 'tha', 'Thecc.01G284000' => 'tca', 'Thecc.04G220600' => 'tca', 'Thecc.05G268900' => 'tca', 'Thecc.08G171100' => 'tca', 'Thhalv10001284m.g' => 'esa', 'Thhalv10019912m.g' => 'esa', 'TPR.G14189' => 'tpr', 'TPR.G18110' => 'tpr', 'TPR.G18130' => 'tpr', 'TPR.G18131' => 'tpr', 'TPR.G18140' => 'tpr', 'TPR.G24282' => 'tpr', 'TPR.G25221' => 'tpr', 'TPR.G29267' => 'tpr', 'TPR.G35315' => 'tpr', 'TPR.G36173' => 'tpr', 'TWI09G0794' => 'twi', 'TWI59G1348' => 'twi', 'TWI74G0430' => 'twi', 'unitig_26.g8940' => 'ugi', 'unitig_749.g13744' => 'ugi', 'unitig_749.g13745' => 'ugi', 'vmacro08269' => 'vma', 'vmacro14937' => 'vma', 'vmacro20401' => 'vma', 'VMungo0464G1349' => 'vmu', 'VMungo0540G0289' => 'vmu', 'VMungo1215G1590' => 'vmu', 'VMungo1309G0221' => 'vmu', 'VMungo1309G2815' => 'vmu', 'VMungo1383G0239' => 'vmu', 'VMungo1383G2910' => 'vmu', 'Zm00001eb095270' => 'zma', 'Zm00001eb095280' => 'zma', 'Zm00001eb111630' => 'zma', 'Zm00001eb237080' => 'zma', 'Zm00001eb273740' => 'zma', 'Zm00001eb285040' => 'zma', 'Zm00001eb330790' => 'zma', 'Zm00001eb337380' => 'zma' ), 'gf_id' => 'HOM05D001484', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001484' ), 'data_identifier' => 'HOM05D001484', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001484', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p31500' => 'bna', 'A05p00020' => 'bna', 'A07p08820' => 'bna', 'Aa31LG4G3300' => 'aar', 'Aa31LG8G10030' => 'aar', 'Actinidia00731' => 'ach', 'Actinidia11473' => 'ach', 'Actinidia23469' => 'ach', 'Actinidia24318' => 'ach', 'Actinidia40196' => 'ach', 'Actinidia40197' => 'ach', 'Actinidia40198' => 'ach', 'Ah.08g212990' => 'amhyb', 'Ah.15g091720' => 'amhyb', 'AL3G38260' => 'aly', 'AL4G47710' => 'aly', 'Aqoxy2G00671' => 'aox', 'Aqoxy2G03236' => 'aox', 'arahy.Tifrunner.gnm1.ann1.05IDCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KR684' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATY3SJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK6QJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6APGL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IDT7Z9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM073U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ0R87' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LE7RV4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT4QRX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V5ENPK' => 'arhy', 'AT2G48110' => 'ath', 'AT3G23590' => 'ath', 'ATR0626G186' => 'atr', 'ATR1127G141' => 'atr', 'Atru.chr4.2583' => 'acertr', 'Atru.chr5.1358' => 'acertr', 'Atru.chr5.1359' => 'acertr', 'Atru.chr8.46' => 'acertr', 'AUR62002640' => 'cqu', 'AUR62030055' => 'cqu', 'AUR62033713' => 'cqu', 'AUR62033714' => 'cqu', 'AUR62036795' => 'cqu', 'AUR62039891' => 'cqu', 'BcaB02g08737' => 'bca', 'BcaB04g20441' => 'bca', 'BcaB06g26509' => 'bca', 'BcaB06g26510' => 'bca', 'BcaB06g26511' => 'bca', 'BcaB06g26512' => 'bca', 'BcaB06g26513' => 'bca', 'BcaC02g12564' => 'bca', 'BcaC02g12565' => 'bca', 'BcaC02g12794' => 'bca', 'BcaC02g12795' => 'bca', 'BcaC02g12796' => 'bca', 'BcaC06g35541' => 'bca', 'BNapus_Darmor_BZH_scaffold_188p00080' => 'bna', 'BNapus_Darmor_BZH_scaffold_188p00090' => 'bna', 'BolC1t03972H' => 'bol', 'BolC1t03973H' => 'bol', 'BolC4t21680H' => 'bol', 'BolC7t41863H' => 'bol', 'BolSC55t61227H' => 'bol', 'BolSC55t61228H' => 'bol', 'BraA01t03278Z' => 'bra', 'BraA05t18998Z' => 'bra', 'BraA07t28673Z' => 'bra', 'C01p40150' => 'bna', 'C05p12370' => 'bna', 'C07p13680' => 'bna', 'CAN.G1006.16' => 'can', 'CAN.G1006.17' => 'can', 'CAN.G1170.2' => 'can', 'CAN.G962.7' => 'can', 'CANSAT25G2179' => 'cansat', 'CANSAT78G1573' => 'cansat', 'CARHR099510' => 'chi', 'CARHR143510' => 'chi', 'Carub.0003s2380' => 'cru', 'Carub.0004s3082' => 'cru', 'Ca_00614_v3' => 'car', 'Ca_07801_v3' => 'car', 'Ca_08567_v3' => 'car', 'Ca_09571_v3' => 'car', 'CBR_g19290' => 'cbr', 'Cc01_g19770' => 'ccan', 'Cc03_g03030' => 'ccan', 'CDE07G0968' => 'cde', 'CDE09G1441' => 'cde', 'Cfa006103' => 'cfa', 'Cfa015573' => 'cfa', 'Cfa016988' => 'cfa', 'Ciclev10006738m.g' => 'ccl', 'Ciclev10010920m.g' => 'ccl', 'Ciclev10018517m.g' => 'ccl', 'CiPaw.01G159200' => 'cil', 'CiPaw.02G091000' => 'cil', 'CiPaw.02G091100' => 'cil', 'CiPaw.08G103100' => 'cil', 'CiPaw.09G224900' => 'cil', 'ClCG06G005740' => 'cla', 'ClCG07G000090' => 'cla', 'ClCG07G000100' => 'cla', 'COL.COLO4_09143' => 'col', 'COL.COLO4_25124' => 'col', 'Cpa.g.sc16.34' => 'cpa', 'Cpa.g.sc3504.1' => 'cpa', 'Cpa.g.sc60.37' => 'cpa', 'CsaV3_6G018520' => 'csa', 'CsaV3_6G036860' => 'csa', 'CSS0001072' => 'camsi', 'CSS0020208' => 'camsi', 'CSS0021253' => 'camsi', 'CSS0022190' => 'camsi', 'CSS0036150' => 'camsi', 'CSS0040442' => 'camsi', 'CSS0042300' => 'camsi', 'CSS0045298' => 'camsi', 'DCAR_012449' => 'dca', 'DCAR_018405' => 'dca', 'DCAR_024573' => 'dca', 'DCAR_030591' => 'dca', 'Dinv16926' => 'din', 'Dinv32963' => 'din', 'Dinv38382' => 'din', 'Dinv38383' => 'din', 'Duzib133G0974' => 'dzi', 'Duzib138G1867' => 'dzi', 'Duzib211G0420' => 'dzi', 'Duzib212G0930' => 'dzi', 'ECA234G1645' => 'eca', 'ECA247G3467' => 'eca', 'ECA248G1703' => 'eca', 'EL10Ac3g06327' => 'bvu', 'EL10Ac7g17204' => 'bvu', 'Eucgr.A00855' => 'egr', 'Eucgr.A00858' => 'egr', 'Eucgr.H01520' => 'egr', 'Eucgr.H03604' => 'egr', 'Eucgr.L03465' => 'egr', 'Eucgr.L03466' => 'egr', 'FAN01G0988' => 'fan', 'FAN02G3892' => 'fan', 'FAN05G3381' => 'fan', 'FAN07G0967' => 'fan', 'FAN07G1493' => 'fan', 'FAN08G3125' => 'fan', 'FAN09G0402' => 'fan', 'FAN12G2594' => 'fan', 'FAN12G3879' => 'fan', 'FAN14G1546' => 'fan', 'FAN15G3626' => 'fan', 'FAN17G0588' => 'fan', 'FAN17G0609' => 'fan', 'FAN18G2817' => 'fan', 'FAN19G1305' => 'fan', 'FAN20G1787' => 'fan', 'FAN22G0073' => 'fan', 'FAN22G0352' => 'fan', 'FAN22G0368' => 'fan', 'FAN22G2273' => 'fan', 'FAN24G1998' => 'fan', 'FAN27G1317' => 'fan', 'FvH4_2g23980' => 'fve', 'FvH4_4g14380' => 'fve', 'FvH4_4g14390' => 'fve', 'FvH4_6g09250' => 'fve', 'Glyma.03G151100' => 'gma', 'Glyma.04G122550' => 'gma', 'Glyma.05G001600' => 'gma', 'Glyma.09G270766' => 'gma', 'Glyma.09G270832' => 'gma', 'Glyma.13G209800' => 'gma', 'Glyma.15G102800' => 'gma', 'Glyma.18G218900' => 'gma', 'Glyma.19G001500' => 'gma', 'Glyma.19G153600' => 'gma', 'Gohir.A02G028600' => 'ghi', 'Gohir.A08G045000' => 'ghi', 'Gohir.A11G120500' => 'ghi', 'Gohir.A12G006200' => 'ghi', 'Gohir.A12G006250' => 'ghi', 'Gohir.D02G036300' => 'ghi', 'Gohir.D08G054700' => 'ghi', 'Gohir.D11G125600' => 'ghi', 'Gohir.D12G005700' => 'ghi', 'Gorai.004G055200' => 'gra', 'Gorai.005G040400' => 'gra', 'Gorai.007G134500' => 'gra', 'Gorai.008G005500' => 'gra', 'GSVIVG01011094001' => 'vvi', 'GSVIVG01017879001' => 'vvi', 'GSVIVG01025988001' => 'vvi', 'GSVIVG01029847001' => 'vvi', 'HanXRQChr10g0282901' => 'han', 'HanXRQChr10g0310371' => 'han', 'HanXRQChr10g0315041' => 'han', 'HanXRQChr11g0327651' => 'han', 'HanXRQChr12g0359391' => 'han', 'Haze_00972' => 'cav', 'Haze_00973' => 'cav', 'Haze_00974' => 'cav', 'Haze_04747' => 'cav', 'Haze_04749' => 'cav', 'Haze_04750' => 'cav', 'Haze_21217' => 'cav', 'Hma1.2p1_1037F.1_g250680' => 'hma', 'Hma1.2p1_1644F.1_g295320' => 'hma', 'HPP92_011322' => 'vpl', 'HPP92_011323' => 'vpl', 'HPP92_011324' => 'vpl', 'HPP92_011325' => 'vpl', 'HPP92_011326' => 'vpl', 'Hund12205' => 'sun', 'Hund17957' => 'sun', 'Lalb_Chr06g0176771' => 'lal', 'Lalb_Chr18g0056021' => 'lal', 'Lalb_Chr18g0056031' => 'lal', 'Lalb_Chr18g0056041' => 'lal', 'Lalb_Chr20g0107751' => 'lal', 'Lalb_Chr20g0118371' => 'lal', 'Lj1g0010239' => 'lja', 'Lj1g0017101' => 'lja', 'Lj2A1178G40' => 'lonja', 'Lj2A54G84' => 'lonja', 'Lj2g0015248' => 'lja', 'Lj3A761T51' => 'lonja', 'Lj6g0018116' => 'lja', 'Lsat_1_v5_gn_4_136040' => 'lsa', 'Lsat_1_v5_gn_5_187461' => 'lsa', 'Lsat_1_v5_gn_5_77001' => 'lsa', 'Lsat_1_v5_gn_9_4461' => 'lsa', 'Manes.01G210100' => 'mes', 'Manes.03G185600' => 'mes', 'Manes.05G073300' => 'mes', 'Manes.09G120300' => 'mes', 'Manes.15G022100' => 'mes', 'Mapoly0096s0053' => 'mpo', 'MBI03_g14058_MAGBIO' => 'mbi', 'MBI03_g33876_MAGBIO' => 'mbi', 'MBI03_g36854_MAGBIO' => 'mbi', 'MBI17_g11997_MAGBIO' => 'mbi', 'MD03G1269000' => 'mdo', 'MD04G1179600' => 'mdo', 'MD11G1289800' => 'mdo', 'MD12G1194700' => 'mdo', 'MD13G1182100' => 'mdo', 'MD13G1182200' => 'mdo', 'MD16G1182600' => 'mdo', 'Medtr2g021400' => 'mtr', 'Medtr2g021470' => 'mtr', 'Medtr2g105810' => 'mtr', 'Medtr3g033580' => 'mtr', 'Medtr6g007970' => 'mtr', 'Medtr7g056330' => 'mtr', 'Medtr7g074290' => 'mtr', 'Medtr7g074380' => 'mtr', 'Medtr7g094550' => 'mtr', 'Medtr8g069995' => 'mtr', 'MELO3C014345.2' => 'cme', 'MELO3C021395.2' => 'cme', 'Migut.D00262' => 'egut', 'Migut.G00257' => 'egut', 'MSTRG.21575' => 'ama', 'MSTRG.3985' => 'ama', 'Nitab4.5_0000295g0140' => 'nta', 'Nitab4.5_0000732g0140' => 'nta', 'Nitab4.5_0003162g0020' => 'nta', 'Nitab4.5_0006180g0090' => 'nta', 'Nitab4.5_0006390g0010' => 'nta', 'Nitab4.5_0007392g0040' => 'nta', 'Nn1g02140' => 'nnu', 'Nn4g26168' => 'nnu', 'Nn5g26754' => 'nnu', 'Oeu001433.1' => 'oeu', 'Oeu010299.2' => 'oeu', 'Oeu011171.1' => 'oeu', 'Oeu037675.1' => 'oeu', 'Oeu038359.1' => 'oeu', 'Oeu063834.1' => 'oeu', 'Oeu063835.1' => 'oeu', 'Os05g0312000' => 'osa', 'Os07g0211101' => 'osa', 'Os07g0211200' => 'osa', 'Os07g0681500' => 'osa', 'Peaxi162Scf00095g01015' => 'pax', 'Peaxi162Scf00104g00329' => 'pax', 'Peaxi162Scf00161g00137' => 'pax', 'PGR004G1665' => 'pgr', 'PGR031G2937' => 'pgr', 'PGR119G2145' => 'pgr', 'PGSC0003DMG400004351' => 'stu', 'PGSC0003DMG400014625' => 'stu', 'PGSC0003DMG401000943' => 'stu', 'Phvul.001G148600' => 'pvu', 'Phvul.004G001700' => 'pvu', 'Phvul.006G154900' => 'pvu', 'Phvul.008G078200' => 'pvu', 'Phvul.011G136500' => 'pvu', 'Potri.002G215600' => 'ptr', 'Potri.008G201600' => 'ptr', 'Potri.014G138400' => 'ptr', 'Potri.016G142500' => 'ptr', 'Pp3c16_10580' => 'ppa', 'Pp3c5_25280' => 'ppa', 'Prupe.1G150000' => 'ppe', 'Prupe.1G150100' => 'ppe', 'Prupe.6G299600' => 'ppe', 'Prupe.8G245000' => 'ppe', 'Psat0s4927g0040' => 'psa', 'Psat1g052080' => 'psa', 'Psat1g183800' => 'psa', 'Psat3g113840' => 'psa', 'Psat3g126120' => 'psa', 'Psat3g126160' => 'psa', 'Psat3g158760' => 'psa', 'Psat3g158840' => 'psa', 'PSO170G2858' => 'pso', 'PSO339G0606' => 'pso', 'PSO384G4709' => 'pso', 'PSO407G0334' => 'pso', 'QL04p040276' => 'qlo', 'QL06p005458' => 'qlo', 'QL06p005472' => 'qlo', 'QL07p030546' => 'qlo', 'QL07p031519' => 'qlo', 'QL09p050949' => 'qlo', 'QL09p050966' => 'qlo', 'QL09p051067' => 'qlo', 'QL12p022706' => 'qlo', 'RcHm_v2.0_Chr2g0119601' => 'rch', 'RcHm_v2.0_Chr3g0459591' => 'rch', 'RcHm_v2.0_Chr4g0418521' => 'rch', 'RcHm_v2.0_Chr4g0418531' => 'rch', 'RcHm_v2.0_Chr4g0418541' => 'rch', 'RcHm_v2.0_Chr6g0291641' => 'rch', 'Rhsim01G0086300' => 'rsi', 'Rhsim01G0276300' => 'rsi', 'Rhsim01G0276500' => 'rsi', 'Rhsim04G0207700' => 'rsi', 'Rhsim05G0234500' => 'rsi', 'Rhsim13G0022400' => 'rsi', 'Sabra02G0167900' => 'sbr', 'Sabra04G0158500' => 'sbr', 'Sabra08G0159800' => 'sbr', 'Sabra10G0011500' => 'sbr', 'Sabra14G0104400' => 'sbr', 'SalBow2G2440' => 'sbo', 'SalBow4G2265' => 'sbo', 'Sc02g0000060' => 'sci', 'Sc05g0005020' => 'sci', 'Sc13g0003890' => 'sci', 'Sed0014865' => 'sed', 'Sed0017224' => 'sed', 'Sed0026391' => 'sed', 'SEGI_00063' => 'sgi', 'SEGI_10967' => 'sgi', 'SEGI_17510' => 'sgi', 'SEGI_24396' => 'sgi', 'SEGI_39719' => 'sgi', 'SEGI_41392' => 'sgi', 'SGA_v2.0_scaffold11G05794' => 'sas', 'SGA_v2.0_scaffold142G35607' => 'sas', 'SGA_v2.0_scaffold1G00447' => 'sas', 'SHI15388' => 'shi', 'SHI15394' => 'shi', 'SHI15396' => 'shi', 'SHI15399' => 'shi', 'SMO343G0151' => 'smo', 'SMO367G1118' => 'smo', 'Solyc01g080200.3' => 'sly', 'Solyc06g008960.3' => 'sly', 'Solyc09g064780.3' => 'sly', 'Sopen01g031980' => 'spe', 'Sopen06g003710' => 'spe', 'Sopen09g026460' => 'spe', 'Sp3g21240' => 'spa', 'Sp4g30030' => 'spa', 'TAR365G0022' => 'tar', 'TAR365G1023' => 'tar', 'TAR365G1253' => 'tar', 'TAR623G0078' => 'tar', 'TAR623G1721' => 'tar', 'TAR633G0959' => 'tar', 'THA.LOC104802225' => 'tha', 'THA.LOC104804769' => 'tha', 'THA.LOC104808660' => 'tha', 'THA.LOC104812792' => 'tha', 'Thecc.01G284000' => 'tca', 'Thecc.04G220600' => 'tca', 'Thecc.05G268900' => 'tca', 'Thecc.08G171100' => 'tca', 'Thhalv10001284m.g' => 'esa', 'Thhalv10019912m.g' => 'esa', 'TPR.G14189' => 'tpr', 'TPR.G18110' => 'tpr', 'TPR.G18130' => 'tpr', 'TPR.G18131' => 'tpr', 'TPR.G18140' => 'tpr', 'TPR.G24282' => 'tpr', 'TPR.G25221' => 'tpr', 'TPR.G29267' => 'tpr', 'TPR.G35315' => 'tpr', 'TPR.G36173' => 'tpr', 'TWI09G0794' => 'twi', 'TWI59G1348' => 'twi', 'TWI74G0430' => 'twi', 'unitig_26.g8940' => 'ugi', 'unitig_749.g13744' => 'ugi', 'unitig_749.g13745' => 'ugi', 'vmacro08269' => 'vma', 'vmacro14937' => 'vma', 'vmacro20401' => 'vma', 'VMungo0464G1349' => 'vmu', 'VMungo0540G0289' => 'vmu', 'VMungo1215G1590' => 'vmu', 'VMungo1309G0221' => 'vmu', 'VMungo1309G2815' => 'vmu', 'VMungo1383G0239' => 'vmu', 'VMungo1383G2910' => 'vmu', 'Zm00001eb095270' => 'zma', 'Zm00001eb095280' => 'zma', 'Zm00001eb111630' => 'zma', 'Zm00001eb237080' => 'zma', 'Zm00001eb273740' => 'zma', 'Zm00001eb285040' => 'zma', 'Zm00001eb330790' => 'zma', 'Zm00001eb337380' => 'zma' ) $gf_id = 'HOM05D001484' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001484' ) $data_identifier = 'HOM05D001484' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 2, 'aly' => (int) 2, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 22, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 7, 'hma' => (int) 2, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 7, 'mtr' => (int) 10, 'cme' => (int) 2, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 4, 'ppa' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 4, 'qlo' => (int) 9, 'rch' => (int) 6, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 10, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 7, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb337380' $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' => 'HOM05D001484', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p31500' => 'bna', 'A05p00020' => 'bna', 'A07p08820' => 'bna', 'Aa31LG4G3300' => 'aar', 'Aa31LG8G10030' => 'aar', 'Actinidia00731' => 'ach', 'Actinidia11473' => 'ach', 'Actinidia23469' => 'ach', 'Actinidia24318' => 'ach', 'Actinidia40196' => 'ach', 'Actinidia40197' => 'ach', 'Actinidia40198' => 'ach', 'Ah.08g212990' => 'amhyb', 'Ah.15g091720' => 'amhyb', 'AL3G38260' => 'aly', 'AL4G47710' => 'aly', 'Aqoxy2G00671' => 'aox', 'Aqoxy2G03236' => 'aox', 'arahy.Tifrunner.gnm1.ann1.05IDCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KR684' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATY3SJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK6QJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6APGL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IDT7Z9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM073U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ0R87' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LE7RV4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT4QRX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V5ENPK' => 'arhy', 'AT2G48110' => 'ath', 'AT3G23590' => 'ath', 'ATR0626G186' => 'atr', 'ATR1127G141' => 'atr', 'Atru.chr4.2583' => 'acertr', 'Atru.chr5.1358' => 'acertr', 'Atru.chr5.1359' => 'acertr', 'Atru.chr8.46' => 'acertr', 'AUR62002640' => 'cqu', 'AUR62030055' => 'cqu', 'AUR62033713' => 'cqu', 'AUR62033714' => 'cqu', 'AUR62036795' => 'cqu', 'AUR62039891' => 'cqu', 'BcaB02g08737' => 'bca', 'BcaB04g20441' => 'bca', 'BcaB06g26509' => 'bca', 'BcaB06g26510' => 'bca', 'BcaB06g26511' => 'bca', 'BcaB06g26512' => 'bca', 'BcaB06g26513' => 'bca', 'BcaC02g12564' => 'bca', 'BcaC02g12565' => 'bca', 'BcaC02g12794' => 'bca', 'BcaC02g12795' => 'bca', 'BcaC02g12796' => 'bca', 'BcaC06g35541' => 'bca', 'BNapus_Darmor_BZH_scaffold_188p00080' => 'bna', 'BNapus_Darmor_BZH_scaffold_188p00090' => 'bna', 'BolC1t03972H' => 'bol', 'BolC1t03973H' => 'bol', 'BolC4t21680H' => 'bol', 'BolC7t41863H' => 'bol', 'BolSC55t61227H' => 'bol', 'BolSC55t61228H' => 'bol', 'BraA01t03278Z' => 'bra', 'BraA05t18998Z' => 'bra', 'BraA07t28673Z' => 'bra', 'C01p40150' => 'bna', 'C05p12370' => 'bna', 'C07p13680' => 'bna', 'CAN.G1006.16' => 'can', 'CAN.G1006.17' => 'can', 'CAN.G1170.2' => 'can', 'CAN.G962.7' => 'can', 'CANSAT25G2179' => 'cansat', 'CANSAT78G1573' => 'cansat', 'CARHR099510' => 'chi', 'CARHR143510' => 'chi', 'Carub.0003s2380' => 'cru', 'Carub.0004s3082' => 'cru', 'Ca_00614_v3' => 'car', 'Ca_07801_v3' => 'car', 'Ca_08567_v3' => 'car', 'Ca_09571_v3' => 'car', 'CBR_g19290' => 'cbr', 'Cc01_g19770' => 'ccan', 'Cc03_g03030' => 'ccan', 'CDE07G0968' => 'cde', 'CDE09G1441' => 'cde', 'Cfa006103' => 'cfa', 'Cfa015573' => 'cfa', 'Cfa016988' => 'cfa', 'Ciclev10006738m.g' => 'ccl', 'Ciclev10010920m.g' => 'ccl', 'Ciclev10018517m.g' => 'ccl', 'CiPaw.01G159200' => 'cil', 'CiPaw.02G091000' => 'cil', 'CiPaw.02G091100' => 'cil', 'CiPaw.08G103100' => 'cil', 'CiPaw.09G224900' => 'cil', 'ClCG06G005740' => 'cla', 'ClCG07G000090' => 'cla', 'ClCG07G000100' => 'cla', 'COL.COLO4_09143' => 'col', 'COL.COLO4_25124' => 'col', 'Cpa.g.sc16.34' => 'cpa', 'Cpa.g.sc3504.1' => 'cpa', 'Cpa.g.sc60.37' => 'cpa', 'CsaV3_6G018520' => 'csa', 'CsaV3_6G036860' => 'csa', 'CSS0001072' => 'camsi', 'CSS0020208' => 'camsi', 'CSS0021253' => 'camsi', 'CSS0022190' => 'camsi', 'CSS0036150' => 'camsi', 'CSS0040442' => 'camsi', 'CSS0042300' => 'camsi', 'CSS0045298' => 'camsi', 'DCAR_012449' => 'dca', 'DCAR_018405' => 'dca', 'DCAR_024573' => 'dca', 'DCAR_030591' => 'dca', 'Dinv16926' => 'din', 'Dinv32963' => 'din', 'Dinv38382' => 'din', 'Dinv38383' => 'din', 'Duzib133G0974' => 'dzi', 'Duzib138G1867' => 'dzi', 'Duzib211G0420' => 'dzi', 'Duzib212G0930' => 'dzi', 'ECA234G1645' => 'eca', 'ECA247G3467' => 'eca', 'ECA248G1703' => 'eca', 'EL10Ac3g06327' => 'bvu', 'EL10Ac7g17204' => 'bvu', 'Eucgr.A00855' => 'egr', 'Eucgr.A00858' => 'egr', 'Eucgr.H01520' => 'egr', 'Eucgr.H03604' => 'egr', 'Eucgr.L03465' => 'egr', 'Eucgr.L03466' => 'egr', 'FAN01G0988' => 'fan', 'FAN02G3892' => 'fan', 'FAN05G3381' => 'fan', 'FAN07G0967' => 'fan', 'FAN07G1493' => 'fan', 'FAN08G3125' => 'fan', 'FAN09G0402' => 'fan', 'FAN12G2594' => 'fan', 'FAN12G3879' => 'fan', 'FAN14G1546' => 'fan', 'FAN15G3626' => 'fan', 'FAN17G0588' => 'fan', 'FAN17G0609' => 'fan', 'FAN18G2817' => 'fan', 'FAN19G1305' => 'fan', 'FAN20G1787' => 'fan', 'FAN22G0073' => 'fan', 'FAN22G0352' => 'fan', 'FAN22G0368' => 'fan', 'FAN22G2273' => 'fan', 'FAN24G1998' => 'fan', 'FAN27G1317' => 'fan', 'FvH4_2g23980' => 'fve', 'FvH4_4g14380' => 'fve', 'FvH4_4g14390' => 'fve', 'FvH4_6g09250' => 'fve', 'Glyma.03G151100' => 'gma', 'Glyma.04G122550' => 'gma', 'Glyma.05G001600' => 'gma', 'Glyma.09G270766' => 'gma', 'Glyma.09G270832' => 'gma', 'Glyma.13G209800' => 'gma', 'Glyma.15G102800' => 'gma', 'Glyma.18G218900' => 'gma', 'Glyma.19G001500' => 'gma', 'Glyma.19G153600' => 'gma', 'Gohir.A02G028600' => 'ghi', 'Gohir.A08G045000' => 'ghi', 'Gohir.A11G120500' => 'ghi', 'Gohir.A12G006200' => 'ghi', 'Gohir.A12G006250' => 'ghi', 'Gohir.D02G036300' => 'ghi', 'Gohir.D08G054700' => 'ghi', 'Gohir.D11G125600' => 'ghi', 'Gohir.D12G005700' => 'ghi', 'Gorai.004G055200' => 'gra', 'Gorai.005G040400' => 'gra', 'Gorai.007G134500' => 'gra', 'Gorai.008G005500' => 'gra', 'GSVIVG01011094001' => 'vvi', 'GSVIVG01017879001' => 'vvi', 'GSVIVG01025988001' => 'vvi', 'GSVIVG01029847001' => 'vvi', 'HanXRQChr10g0282901' => 'han', 'HanXRQChr10g0310371' => 'han', 'HanXRQChr10g0315041' => 'han', 'HanXRQChr11g0327651' => 'han', 'HanXRQChr12g0359391' => 'han', 'Haze_00972' => 'cav', 'Haze_00973' => 'cav', 'Haze_00974' => 'cav', 'Haze_04747' => 'cav', 'Haze_04749' => 'cav', 'Haze_04750' => 'cav', 'Haze_21217' => 'cav', 'Hma1.2p1_1037F.1_g250680' => 'hma', 'Hma1.2p1_1644F.1_g295320' => 'hma', 'HPP92_011322' => 'vpl', 'HPP92_011323' => 'vpl', 'HPP92_011324' => 'vpl', 'HPP92_011325' => 'vpl', 'HPP92_011326' => 'vpl', 'Hund12205' => 'sun', 'Hund17957' => 'sun', 'Lalb_Chr06g0176771' => 'lal', 'Lalb_Chr18g0056021' => 'lal', 'Lalb_Chr18g0056031' => 'lal', 'Lalb_Chr18g0056041' => 'lal', 'Lalb_Chr20g0107751' => 'lal', 'Lalb_Chr20g0118371' => 'lal', 'Lj1g0010239' => 'lja', 'Lj1g0017101' => 'lja', 'Lj2A1178G40' => 'lonja', 'Lj2A54G84' => 'lonja', 'Lj2g0015248' => 'lja', 'Lj3A761T51' => 'lonja', 'Lj6g0018116' => 'lja', 'Lsat_1_v5_gn_4_136040' => 'lsa', 'Lsat_1_v5_gn_5_187461' => 'lsa', 'Lsat_1_v5_gn_5_77001' => 'lsa', 'Lsat_1_v5_gn_9_4461' => 'lsa', 'Manes.01G210100' => 'mes', 'Manes.03G185600' => 'mes', 'Manes.05G073300' => 'mes', 'Manes.09G120300' => 'mes', 'Manes.15G022100' => 'mes', 'Mapoly0096s0053' => 'mpo', 'MBI03_g14058_MAGBIO' => 'mbi', 'MBI03_g33876_MAGBIO' => 'mbi', 'MBI03_g36854_MAGBIO' => 'mbi', 'MBI17_g11997_MAGBIO' => 'mbi', 'MD03G1269000' => 'mdo', 'MD04G1179600' => 'mdo', 'MD11G1289800' => 'mdo', 'MD12G1194700' => 'mdo', 'MD13G1182100' => 'mdo', 'MD13G1182200' => 'mdo', 'MD16G1182600' => 'mdo', 'Medtr2g021400' => 'mtr', 'Medtr2g021470' => 'mtr', 'Medtr2g105810' => 'mtr', 'Medtr3g033580' => 'mtr', 'Medtr6g007970' => 'mtr', 'Medtr7g056330' => 'mtr', 'Medtr7g074290' => 'mtr', 'Medtr7g074380' => 'mtr', 'Medtr7g094550' => 'mtr', 'Medtr8g069995' => 'mtr', 'MELO3C014345.2' => 'cme', 'MELO3C021395.2' => 'cme', 'Migut.D00262' => 'egut', 'Migut.G00257' => 'egut', 'MSTRG.21575' => 'ama', 'MSTRG.3985' => 'ama', 'Nitab4.5_0000295g0140' => 'nta', 'Nitab4.5_0000732g0140' => 'nta', 'Nitab4.5_0003162g0020' => 'nta', 'Nitab4.5_0006180g0090' => 'nta', 'Nitab4.5_0006390g0010' => 'nta', 'Nitab4.5_0007392g0040' => 'nta', 'Nn1g02140' => 'nnu', 'Nn4g26168' => 'nnu', 'Nn5g26754' => 'nnu', 'Oeu001433.1' => 'oeu', 'Oeu010299.2' => 'oeu', 'Oeu011171.1' => 'oeu', 'Oeu037675.1' => 'oeu', 'Oeu038359.1' => 'oeu', 'Oeu063834.1' => 'oeu', 'Oeu063835.1' => 'oeu', 'Os05g0312000' => 'osa', 'Os07g0211101' => 'osa', 'Os07g0211200' => 'osa', 'Os07g0681500' => 'osa', 'Peaxi162Scf00095g01015' => 'pax', 'Peaxi162Scf00104g00329' => 'pax', 'Peaxi162Scf00161g00137' => 'pax', 'PGR004G1665' => 'pgr', 'PGR031G2937' => 'pgr', 'PGR119G2145' => 'pgr', 'PGSC0003DMG400004351' => 'stu', 'PGSC0003DMG400014625' => 'stu', 'PGSC0003DMG401000943' => 'stu', 'Phvul.001G148600' => 'pvu', 'Phvul.004G001700' => 'pvu', 'Phvul.006G154900' => 'pvu', 'Phvul.008G078200' => 'pvu', 'Phvul.011G136500' => 'pvu', 'Potri.002G215600' => 'ptr', 'Potri.008G201600' => 'ptr', 'Potri.014G138400' => 'ptr', 'Potri.016G142500' => 'ptr', 'Pp3c16_10580' => 'ppa', 'Pp3c5_25280' => 'ppa', 'Prupe.1G150000' => 'ppe', 'Prupe.1G150100' => 'ppe', 'Prupe.6G299600' => 'ppe', 'Prupe.8G245000' => 'ppe', 'Psat0s4927g0040' => 'psa', 'Psat1g052080' => 'psa', 'Psat1g183800' => 'psa', 'Psat3g113840' => 'psa', 'Psat3g126120' => 'psa', 'Psat3g126160' => 'psa', 'Psat3g158760' => 'psa', 'Psat3g158840' => 'psa', 'PSO170G2858' => 'pso', 'PSO339G0606' => 'pso', 'PSO384G4709' => 'pso', 'PSO407G0334' => 'pso', 'QL04p040276' => 'qlo', 'QL06p005458' => 'qlo', 'QL06p005472' => 'qlo', 'QL07p030546' => 'qlo', 'QL07p031519' => 'qlo', 'QL09p050949' => 'qlo', 'QL09p050966' => 'qlo', 'QL09p051067' => 'qlo', 'QL12p022706' => 'qlo', 'RcHm_v2.0_Chr2g0119601' => 'rch', 'RcHm_v2.0_Chr3g0459591' => 'rch', 'RcHm_v2.0_Chr4g0418521' => 'rch', 'RcHm_v2.0_Chr4g0418531' => 'rch', 'RcHm_v2.0_Chr4g0418541' => 'rch', 'RcHm_v2.0_Chr6g0291641' => 'rch', 'Rhsim01G0086300' => 'rsi', 'Rhsim01G0276300' => 'rsi', 'Rhsim01G0276500' => 'rsi', 'Rhsim04G0207700' => 'rsi', 'Rhsim05G0234500' => 'rsi', 'Rhsim13G0022400' => 'rsi', 'Sabra02G0167900' => 'sbr', 'Sabra04G0158500' => 'sbr', 'Sabra08G0159800' => 'sbr', 'Sabra10G0011500' => 'sbr', 'Sabra14G0104400' => 'sbr', 'SalBow2G2440' => 'sbo', 'SalBow4G2265' => 'sbo', 'Sc02g0000060' => 'sci', 'Sc05g0005020' => 'sci', 'Sc13g0003890' => 'sci', 'Sed0014865' => 'sed', 'Sed0017224' => 'sed', 'Sed0026391' => 'sed', 'SEGI_00063' => 'sgi', 'SEGI_10967' => 'sgi', 'SEGI_17510' => 'sgi', 'SEGI_24396' => 'sgi', 'SEGI_39719' => 'sgi', 'SEGI_41392' => 'sgi', 'SGA_v2.0_scaffold11G05794' => 'sas', 'SGA_v2.0_scaffold142G35607' => 'sas', 'SGA_v2.0_scaffold1G00447' => 'sas', 'SHI15388' => 'shi', 'SHI15394' => 'shi', 'SHI15396' => 'shi', 'SHI15399' => 'shi', 'SMO343G0151' => 'smo', 'SMO367G1118' => 'smo', 'Solyc01g080200.3' => 'sly', 'Solyc06g008960.3' => 'sly', 'Solyc09g064780.3' => 'sly', 'Sopen01g031980' => 'spe', 'Sopen06g003710' => 'spe', 'Sopen09g026460' => 'spe', 'Sp3g21240' => 'spa', 'Sp4g30030' => 'spa', 'TAR365G0022' => 'tar', 'TAR365G1023' => 'tar', 'TAR365G1253' => 'tar', 'TAR623G0078' => 'tar', 'TAR623G1721' => 'tar', 'TAR633G0959' => 'tar', 'THA.LOC104802225' => 'tha', 'THA.LOC104804769' => 'tha', 'THA.LOC104808660' => 'tha', 'THA.LOC104812792' => 'tha', 'Thecc.01G284000' => 'tca', 'Thecc.04G220600' => 'tca', 'Thecc.05G268900' => 'tca', 'Thecc.08G171100' => 'tca', 'Thhalv10001284m.g' => 'esa', 'Thhalv10019912m.g' => 'esa', 'TPR.G14189' => 'tpr', 'TPR.G18110' => 'tpr', 'TPR.G18130' => 'tpr', 'TPR.G18131' => 'tpr', 'TPR.G18140' => 'tpr', 'TPR.G24282' => 'tpr', 'TPR.G25221' => 'tpr', 'TPR.G29267' => 'tpr', 'TPR.G35315' => 'tpr', 'TPR.G36173' => 'tpr', 'TWI09G0794' => 'twi', 'TWI59G1348' => 'twi', 'TWI74G0430' => 'twi', 'unitig_26.g8940' => 'ugi', 'unitig_749.g13744' => 'ugi', 'unitig_749.g13745' => 'ugi', 'vmacro08269' => 'vma', 'vmacro14937' => 'vma', 'vmacro20401' => 'vma', 'VMungo0464G1349' => 'vmu', 'VMungo0540G0289' => 'vmu', 'VMungo1215G1590' => 'vmu', 'VMungo1309G0221' => 'vmu', 'VMungo1309G2815' => 'vmu', 'VMungo1383G0239' => 'vmu', 'VMungo1383G2910' => 'vmu', 'Zm00001eb095270' => 'zma', 'Zm00001eb095280' => 'zma', 'Zm00001eb111630' => 'zma', 'Zm00001eb237080' => 'zma', 'Zm00001eb273740' => 'zma', 'Zm00001eb285040' => 'zma', 'Zm00001eb330790' => 'zma', 'Zm00001eb337380' => 'zma' ), 'gf_id' => 'HOM05D001484', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001484' ), 'data_identifier' => 'HOM05D001484', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001484', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p31500' => 'bna', 'A05p00020' => 'bna', 'A07p08820' => 'bna', 'Aa31LG4G3300' => 'aar', 'Aa31LG8G10030' => 'aar', 'Actinidia00731' => 'ach', 'Actinidia11473' => 'ach', 'Actinidia23469' => 'ach', 'Actinidia24318' => 'ach', 'Actinidia40196' => 'ach', 'Actinidia40197' => 'ach', 'Actinidia40198' => 'ach', 'Ah.08g212990' => 'amhyb', 'Ah.15g091720' => 'amhyb', 'AL3G38260' => 'aly', 'AL4G47710' => 'aly', 'Aqoxy2G00671' => 'aox', 'Aqoxy2G03236' => 'aox', 'arahy.Tifrunner.gnm1.ann1.05IDCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KR684' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATY3SJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK6QJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6APGL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IDT7Z9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM073U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ0R87' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LE7RV4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT4QRX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V5ENPK' => 'arhy', 'AT2G48110' => 'ath', 'AT3G23590' => 'ath', 'ATR0626G186' => 'atr', 'ATR1127G141' => 'atr', 'Atru.chr4.2583' => 'acertr', 'Atru.chr5.1358' => 'acertr', 'Atru.chr5.1359' => 'acertr', 'Atru.chr8.46' => 'acertr', 'AUR62002640' => 'cqu', 'AUR62030055' => 'cqu', 'AUR62033713' => 'cqu', 'AUR62033714' => 'cqu', 'AUR62036795' => 'cqu', 'AUR62039891' => 'cqu', 'BcaB02g08737' => 'bca', 'BcaB04g20441' => 'bca', 'BcaB06g26509' => 'bca', 'BcaB06g26510' => 'bca', 'BcaB06g26511' => 'bca', 'BcaB06g26512' => 'bca', 'BcaB06g26513' => 'bca', 'BcaC02g12564' => 'bca', 'BcaC02g12565' => 'bca', 'BcaC02g12794' => 'bca', 'BcaC02g12795' => 'bca', 'BcaC02g12796' => 'bca', 'BcaC06g35541' => 'bca', 'BNapus_Darmor_BZH_scaffold_188p00080' => 'bna', 'BNapus_Darmor_BZH_scaffold_188p00090' => 'bna', 'BolC1t03972H' => 'bol', 'BolC1t03973H' => 'bol', 'BolC4t21680H' => 'bol', 'BolC7t41863H' => 'bol', 'BolSC55t61227H' => 'bol', 'BolSC55t61228H' => 'bol', 'BraA01t03278Z' => 'bra', 'BraA05t18998Z' => 'bra', 'BraA07t28673Z' => 'bra', 'C01p40150' => 'bna', 'C05p12370' => 'bna', 'C07p13680' => 'bna', 'CAN.G1006.16' => 'can', 'CAN.G1006.17' => 'can', 'CAN.G1170.2' => 'can', 'CAN.G962.7' => 'can', 'CANSAT25G2179' => 'cansat', 'CANSAT78G1573' => 'cansat', 'CARHR099510' => 'chi', 'CARHR143510' => 'chi', 'Carub.0003s2380' => 'cru', 'Carub.0004s3082' => 'cru', 'Ca_00614_v3' => 'car', 'Ca_07801_v3' => 'car', 'Ca_08567_v3' => 'car', 'Ca_09571_v3' => 'car', 'CBR_g19290' => 'cbr', 'Cc01_g19770' => 'ccan', 'Cc03_g03030' => 'ccan', 'CDE07G0968' => 'cde', 'CDE09G1441' => 'cde', 'Cfa006103' => 'cfa', 'Cfa015573' => 'cfa', 'Cfa016988' => 'cfa', 'Ciclev10006738m.g' => 'ccl', 'Ciclev10010920m.g' => 'ccl', 'Ciclev10018517m.g' => 'ccl', 'CiPaw.01G159200' => 'cil', 'CiPaw.02G091000' => 'cil', 'CiPaw.02G091100' => 'cil', 'CiPaw.08G103100' => 'cil', 'CiPaw.09G224900' => 'cil', 'ClCG06G005740' => 'cla', 'ClCG07G000090' => 'cla', 'ClCG07G000100' => 'cla', 'COL.COLO4_09143' => 'col', 'COL.COLO4_25124' => 'col', 'Cpa.g.sc16.34' => 'cpa', 'Cpa.g.sc3504.1' => 'cpa', 'Cpa.g.sc60.37' => 'cpa', 'CsaV3_6G018520' => 'csa', 'CsaV3_6G036860' => 'csa', 'CSS0001072' => 'camsi', 'CSS0020208' => 'camsi', 'CSS0021253' => 'camsi', 'CSS0022190' => 'camsi', 'CSS0036150' => 'camsi', 'CSS0040442' => 'camsi', 'CSS0042300' => 'camsi', 'CSS0045298' => 'camsi', 'DCAR_012449' => 'dca', 'DCAR_018405' => 'dca', 'DCAR_024573' => 'dca', 'DCAR_030591' => 'dca', 'Dinv16926' => 'din', 'Dinv32963' => 'din', 'Dinv38382' => 'din', 'Dinv38383' => 'din', 'Duzib133G0974' => 'dzi', 'Duzib138G1867' => 'dzi', 'Duzib211G0420' => 'dzi', 'Duzib212G0930' => 'dzi', 'ECA234G1645' => 'eca', 'ECA247G3467' => 'eca', 'ECA248G1703' => 'eca', 'EL10Ac3g06327' => 'bvu', 'EL10Ac7g17204' => 'bvu', 'Eucgr.A00855' => 'egr', 'Eucgr.A00858' => 'egr', 'Eucgr.H01520' => 'egr', 'Eucgr.H03604' => 'egr', 'Eucgr.L03465' => 'egr', 'Eucgr.L03466' => 'egr', 'FAN01G0988' => 'fan', 'FAN02G3892' => 'fan', 'FAN05G3381' => 'fan', 'FAN07G0967' => 'fan', 'FAN07G1493' => 'fan', 'FAN08G3125' => 'fan', 'FAN09G0402' => 'fan', 'FAN12G2594' => 'fan', 'FAN12G3879' => 'fan', 'FAN14G1546' => 'fan', 'FAN15G3626' => 'fan', 'FAN17G0588' => 'fan', 'FAN17G0609' => 'fan', 'FAN18G2817' => 'fan', 'FAN19G1305' => 'fan', 'FAN20G1787' => 'fan', 'FAN22G0073' => 'fan', 'FAN22G0352' => 'fan', 'FAN22G0368' => 'fan', 'FAN22G2273' => 'fan', 'FAN24G1998' => 'fan', 'FAN27G1317' => 'fan', 'FvH4_2g23980' => 'fve', 'FvH4_4g14380' => 'fve', 'FvH4_4g14390' => 'fve', 'FvH4_6g09250' => 'fve', 'Glyma.03G151100' => 'gma', 'Glyma.04G122550' => 'gma', 'Glyma.05G001600' => 'gma', 'Glyma.09G270766' => 'gma', 'Glyma.09G270832' => 'gma', 'Glyma.13G209800' => 'gma', 'Glyma.15G102800' => 'gma', 'Glyma.18G218900' => 'gma', 'Glyma.19G001500' => 'gma', 'Glyma.19G153600' => 'gma', 'Gohir.A02G028600' => 'ghi', 'Gohir.A08G045000' => 'ghi', 'Gohir.A11G120500' => 'ghi', 'Gohir.A12G006200' => 'ghi', 'Gohir.A12G006250' => 'ghi', 'Gohir.D02G036300' => 'ghi', 'Gohir.D08G054700' => 'ghi', 'Gohir.D11G125600' => 'ghi', 'Gohir.D12G005700' => 'ghi', 'Gorai.004G055200' => 'gra', 'Gorai.005G040400' => 'gra', 'Gorai.007G134500' => 'gra', 'Gorai.008G005500' => 'gra', 'GSVIVG01011094001' => 'vvi', 'GSVIVG01017879001' => 'vvi', 'GSVIVG01025988001' => 'vvi', 'GSVIVG01029847001' => 'vvi', 'HanXRQChr10g0282901' => 'han', 'HanXRQChr10g0310371' => 'han', 'HanXRQChr10g0315041' => 'han', 'HanXRQChr11g0327651' => 'han', 'HanXRQChr12g0359391' => 'han', 'Haze_00972' => 'cav', 'Haze_00973' => 'cav', 'Haze_00974' => 'cav', 'Haze_04747' => 'cav', 'Haze_04749' => 'cav', 'Haze_04750' => 'cav', 'Haze_21217' => 'cav', 'Hma1.2p1_1037F.1_g250680' => 'hma', 'Hma1.2p1_1644F.1_g295320' => 'hma', 'HPP92_011322' => 'vpl', 'HPP92_011323' => 'vpl', 'HPP92_011324' => 'vpl', 'HPP92_011325' => 'vpl', 'HPP92_011326' => 'vpl', 'Hund12205' => 'sun', 'Hund17957' => 'sun', 'Lalb_Chr06g0176771' => 'lal', 'Lalb_Chr18g0056021' => 'lal', 'Lalb_Chr18g0056031' => 'lal', 'Lalb_Chr18g0056041' => 'lal', 'Lalb_Chr20g0107751' => 'lal', 'Lalb_Chr20g0118371' => 'lal', 'Lj1g0010239' => 'lja', 'Lj1g0017101' => 'lja', 'Lj2A1178G40' => 'lonja', 'Lj2A54G84' => 'lonja', 'Lj2g0015248' => 'lja', 'Lj3A761T51' => 'lonja', 'Lj6g0018116' => 'lja', 'Lsat_1_v5_gn_4_136040' => 'lsa', 'Lsat_1_v5_gn_5_187461' => 'lsa', 'Lsat_1_v5_gn_5_77001' => 'lsa', 'Lsat_1_v5_gn_9_4461' => 'lsa', 'Manes.01G210100' => 'mes', 'Manes.03G185600' => 'mes', 'Manes.05G073300' => 'mes', 'Manes.09G120300' => 'mes', 'Manes.15G022100' => 'mes', 'Mapoly0096s0053' => 'mpo', 'MBI03_g14058_MAGBIO' => 'mbi', 'MBI03_g33876_MAGBIO' => 'mbi', 'MBI03_g36854_MAGBIO' => 'mbi', 'MBI17_g11997_MAGBIO' => 'mbi', 'MD03G1269000' => 'mdo', 'MD04G1179600' => 'mdo', 'MD11G1289800' => 'mdo', 'MD12G1194700' => 'mdo', 'MD13G1182100' => 'mdo', 'MD13G1182200' => 'mdo', 'MD16G1182600' => 'mdo', 'Medtr2g021400' => 'mtr', 'Medtr2g021470' => 'mtr', 'Medtr2g105810' => 'mtr', 'Medtr3g033580' => 'mtr', 'Medtr6g007970' => 'mtr', 'Medtr7g056330' => 'mtr', 'Medtr7g074290' => 'mtr', 'Medtr7g074380' => 'mtr', 'Medtr7g094550' => 'mtr', 'Medtr8g069995' => 'mtr', 'MELO3C014345.2' => 'cme', 'MELO3C021395.2' => 'cme', 'Migut.D00262' => 'egut', 'Migut.G00257' => 'egut', 'MSTRG.21575' => 'ama', 'MSTRG.3985' => 'ama', 'Nitab4.5_0000295g0140' => 'nta', 'Nitab4.5_0000732g0140' => 'nta', 'Nitab4.5_0003162g0020' => 'nta', 'Nitab4.5_0006180g0090' => 'nta', 'Nitab4.5_0006390g0010' => 'nta', 'Nitab4.5_0007392g0040' => 'nta', 'Nn1g02140' => 'nnu', 'Nn4g26168' => 'nnu', 'Nn5g26754' => 'nnu', 'Oeu001433.1' => 'oeu', 'Oeu010299.2' => 'oeu', 'Oeu011171.1' => 'oeu', 'Oeu037675.1' => 'oeu', 'Oeu038359.1' => 'oeu', 'Oeu063834.1' => 'oeu', 'Oeu063835.1' => 'oeu', 'Os05g0312000' => 'osa', 'Os07g0211101' => 'osa', 'Os07g0211200' => 'osa', 'Os07g0681500' => 'osa', 'Peaxi162Scf00095g01015' => 'pax', 'Peaxi162Scf00104g00329' => 'pax', 'Peaxi162Scf00161g00137' => 'pax', 'PGR004G1665' => 'pgr', 'PGR031G2937' => 'pgr', 'PGR119G2145' => 'pgr', 'PGSC0003DMG400004351' => 'stu', 'PGSC0003DMG400014625' => 'stu', 'PGSC0003DMG401000943' => 'stu', 'Phvul.001G148600' => 'pvu', 'Phvul.004G001700' => 'pvu', 'Phvul.006G154900' => 'pvu', 'Phvul.008G078200' => 'pvu', 'Phvul.011G136500' => 'pvu', 'Potri.002G215600' => 'ptr', 'Potri.008G201600' => 'ptr', 'Potri.014G138400' => 'ptr', 'Potri.016G142500' => 'ptr', 'Pp3c16_10580' => 'ppa', 'Pp3c5_25280' => 'ppa', 'Prupe.1G150000' => 'ppe', 'Prupe.1G150100' => 'ppe', 'Prupe.6G299600' => 'ppe', 'Prupe.8G245000' => 'ppe', 'Psat0s4927g0040' => 'psa', 'Psat1g052080' => 'psa', 'Psat1g183800' => 'psa', 'Psat3g113840' => 'psa', 'Psat3g126120' => 'psa', 'Psat3g126160' => 'psa', 'Psat3g158760' => 'psa', 'Psat3g158840' => 'psa', 'PSO170G2858' => 'pso', 'PSO339G0606' => 'pso', 'PSO384G4709' => 'pso', 'PSO407G0334' => 'pso', 'QL04p040276' => 'qlo', 'QL06p005458' => 'qlo', 'QL06p005472' => 'qlo', 'QL07p030546' => 'qlo', 'QL07p031519' => 'qlo', 'QL09p050949' => 'qlo', 'QL09p050966' => 'qlo', 'QL09p051067' => 'qlo', 'QL12p022706' => 'qlo', 'RcHm_v2.0_Chr2g0119601' => 'rch', 'RcHm_v2.0_Chr3g0459591' => 'rch', 'RcHm_v2.0_Chr4g0418521' => 'rch', 'RcHm_v2.0_Chr4g0418531' => 'rch', 'RcHm_v2.0_Chr4g0418541' => 'rch', 'RcHm_v2.0_Chr6g0291641' => 'rch', 'Rhsim01G0086300' => 'rsi', 'Rhsim01G0276300' => 'rsi', 'Rhsim01G0276500' => 'rsi', 'Rhsim04G0207700' => 'rsi', 'Rhsim05G0234500' => 'rsi', 'Rhsim13G0022400' => 'rsi', 'Sabra02G0167900' => 'sbr', 'Sabra04G0158500' => 'sbr', 'Sabra08G0159800' => 'sbr', 'Sabra10G0011500' => 'sbr', 'Sabra14G0104400' => 'sbr', 'SalBow2G2440' => 'sbo', 'SalBow4G2265' => 'sbo', 'Sc02g0000060' => 'sci', 'Sc05g0005020' => 'sci', 'Sc13g0003890' => 'sci', 'Sed0014865' => 'sed', 'Sed0017224' => 'sed', 'Sed0026391' => 'sed', 'SEGI_00063' => 'sgi', 'SEGI_10967' => 'sgi', 'SEGI_17510' => 'sgi', 'SEGI_24396' => 'sgi', 'SEGI_39719' => 'sgi', 'SEGI_41392' => 'sgi', 'SGA_v2.0_scaffold11G05794' => 'sas', 'SGA_v2.0_scaffold142G35607' => 'sas', 'SGA_v2.0_scaffold1G00447' => 'sas', 'SHI15388' => 'shi', 'SHI15394' => 'shi', 'SHI15396' => 'shi', 'SHI15399' => 'shi', 'SMO343G0151' => 'smo', 'SMO367G1118' => 'smo', 'Solyc01g080200.3' => 'sly', 'Solyc06g008960.3' => 'sly', 'Solyc09g064780.3' => 'sly', 'Sopen01g031980' => 'spe', 'Sopen06g003710' => 'spe', 'Sopen09g026460' => 'spe', 'Sp3g21240' => 'spa', 'Sp4g30030' => 'spa', 'TAR365G0022' => 'tar', 'TAR365G1023' => 'tar', 'TAR365G1253' => 'tar', 'TAR623G0078' => 'tar', 'TAR623G1721' => 'tar', 'TAR633G0959' => 'tar', 'THA.LOC104802225' => 'tha', 'THA.LOC104804769' => 'tha', 'THA.LOC104808660' => 'tha', 'THA.LOC104812792' => 'tha', 'Thecc.01G284000' => 'tca', 'Thecc.04G220600' => 'tca', 'Thecc.05G268900' => 'tca', 'Thecc.08G171100' => 'tca', 'Thhalv10001284m.g' => 'esa', 'Thhalv10019912m.g' => 'esa', 'TPR.G14189' => 'tpr', 'TPR.G18110' => 'tpr', 'TPR.G18130' => 'tpr', 'TPR.G18131' => 'tpr', 'TPR.G18140' => 'tpr', 'TPR.G24282' => 'tpr', 'TPR.G25221' => 'tpr', 'TPR.G29267' => 'tpr', 'TPR.G35315' => 'tpr', 'TPR.G36173' => 'tpr', 'TWI09G0794' => 'twi', 'TWI59G1348' => 'twi', 'TWI74G0430' => 'twi', 'unitig_26.g8940' => 'ugi', 'unitig_749.g13744' => 'ugi', 'unitig_749.g13745' => 'ugi', 'vmacro08269' => 'vma', 'vmacro14937' => 'vma', 'vmacro20401' => 'vma', 'VMungo0464G1349' => 'vmu', 'VMungo0540G0289' => 'vmu', 'VMungo1215G1590' => 'vmu', 'VMungo1309G0221' => 'vmu', 'VMungo1309G2815' => 'vmu', 'VMungo1383G0239' => 'vmu', 'VMungo1383G2910' => 'vmu', 'Zm00001eb095270' => 'zma', 'Zm00001eb095280' => 'zma', 'Zm00001eb111630' => 'zma', 'Zm00001eb237080' => 'zma', 'Zm00001eb273740' => 'zma', 'Zm00001eb285040' => 'zma', 'Zm00001eb330790' => 'zma', 'Zm00001eb337380' => 'zma' ) $gf_id = 'HOM05D001484' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001484' ) $data_identifier = 'HOM05D001484' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 2, 'aly' => (int) 2, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 22, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 7, 'hma' => (int) 2, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 7, 'mtr' => (int) 10, 'cme' => (int) 2, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 4, 'ppa' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 4, 'qlo' => (int) 9, 'rch' => (int) 6, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 10, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 7, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb337380' $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' => 'HOM05D001484', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p31500' => 'bna', 'A05p00020' => 'bna', 'A07p08820' => 'bna', 'Aa31LG4G3300' => 'aar', 'Aa31LG8G10030' => 'aar', 'Actinidia00731' => 'ach', 'Actinidia11473' => 'ach', 'Actinidia23469' => 'ach', 'Actinidia24318' => 'ach', 'Actinidia40196' => 'ach', 'Actinidia40197' => 'ach', 'Actinidia40198' => 'ach', 'Ah.08g212990' => 'amhyb', 'Ah.15g091720' => 'amhyb', 'AL3G38260' => 'aly', 'AL4G47710' => 'aly', 'Aqoxy2G00671' => 'aox', 'Aqoxy2G03236' => 'aox', 'arahy.Tifrunner.gnm1.ann1.05IDCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KR684' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATY3SJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK6QJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6APGL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IDT7Z9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM073U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ0R87' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LE7RV4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT4QRX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V5ENPK' => 'arhy', 'AT2G48110' => 'ath', 'AT3G23590' => 'ath', 'ATR0626G186' => 'atr', 'ATR1127G141' => 'atr', 'Atru.chr4.2583' => 'acertr', 'Atru.chr5.1358' => 'acertr', 'Atru.chr5.1359' => 'acertr', 'Atru.chr8.46' => 'acertr', 'AUR62002640' => 'cqu', 'AUR62030055' => 'cqu', 'AUR62033713' => 'cqu', 'AUR62033714' => 'cqu', 'AUR62036795' => 'cqu', 'AUR62039891' => 'cqu', 'BcaB02g08737' => 'bca', 'BcaB04g20441' => 'bca', 'BcaB06g26509' => 'bca', 'BcaB06g26510' => 'bca', 'BcaB06g26511' => 'bca', 'BcaB06g26512' => 'bca', 'BcaB06g26513' => 'bca', 'BcaC02g12564' => 'bca', 'BcaC02g12565' => 'bca', 'BcaC02g12794' => 'bca', 'BcaC02g12795' => 'bca', 'BcaC02g12796' => 'bca', 'BcaC06g35541' => 'bca', 'BNapus_Darmor_BZH_scaffold_188p00080' => 'bna', 'BNapus_Darmor_BZH_scaffold_188p00090' => 'bna', 'BolC1t03972H' => 'bol', 'BolC1t03973H' => 'bol', 'BolC4t21680H' => 'bol', 'BolC7t41863H' => 'bol', 'BolSC55t61227H' => 'bol', 'BolSC55t61228H' => 'bol', 'BraA01t03278Z' => 'bra', 'BraA05t18998Z' => 'bra', 'BraA07t28673Z' => 'bra', 'C01p40150' => 'bna', 'C05p12370' => 'bna', 'C07p13680' => 'bna', 'CAN.G1006.16' => 'can', 'CAN.G1006.17' => 'can', 'CAN.G1170.2' => 'can', 'CAN.G962.7' => 'can', 'CANSAT25G2179' => 'cansat', 'CANSAT78G1573' => 'cansat', 'CARHR099510' => 'chi', 'CARHR143510' => 'chi', 'Carub.0003s2380' => 'cru', 'Carub.0004s3082' => 'cru', 'Ca_00614_v3' => 'car', 'Ca_07801_v3' => 'car', 'Ca_08567_v3' => 'car', 'Ca_09571_v3' => 'car', 'CBR_g19290' => 'cbr', 'Cc01_g19770' => 'ccan', 'Cc03_g03030' => 'ccan', 'CDE07G0968' => 'cde', 'CDE09G1441' => 'cde', 'Cfa006103' => 'cfa', 'Cfa015573' => 'cfa', 'Cfa016988' => 'cfa', 'Ciclev10006738m.g' => 'ccl', 'Ciclev10010920m.g' => 'ccl', 'Ciclev10018517m.g' => 'ccl', 'CiPaw.01G159200' => 'cil', 'CiPaw.02G091000' => 'cil', 'CiPaw.02G091100' => 'cil', 'CiPaw.08G103100' => 'cil', 'CiPaw.09G224900' => 'cil', 'ClCG06G005740' => 'cla', 'ClCG07G000090' => 'cla', 'ClCG07G000100' => 'cla', 'COL.COLO4_09143' => 'col', 'COL.COLO4_25124' => 'col', 'Cpa.g.sc16.34' => 'cpa', 'Cpa.g.sc3504.1' => 'cpa', 'Cpa.g.sc60.37' => 'cpa', 'CsaV3_6G018520' => 'csa', 'CsaV3_6G036860' => 'csa', 'CSS0001072' => 'camsi', 'CSS0020208' => 'camsi', 'CSS0021253' => 'camsi', 'CSS0022190' => 'camsi', 'CSS0036150' => 'camsi', 'CSS0040442' => 'camsi', 'CSS0042300' => 'camsi', 'CSS0045298' => 'camsi', 'DCAR_012449' => 'dca', 'DCAR_018405' => 'dca', 'DCAR_024573' => 'dca', 'DCAR_030591' => 'dca', 'Dinv16926' => 'din', 'Dinv32963' => 'din', 'Dinv38382' => 'din', 'Dinv38383' => 'din', 'Duzib133G0974' => 'dzi', 'Duzib138G1867' => 'dzi', 'Duzib211G0420' => 'dzi', 'Duzib212G0930' => 'dzi', 'ECA234G1645' => 'eca', 'ECA247G3467' => 'eca', 'ECA248G1703' => 'eca', 'EL10Ac3g06327' => 'bvu', 'EL10Ac7g17204' => 'bvu', 'Eucgr.A00855' => 'egr', 'Eucgr.A00858' => 'egr', 'Eucgr.H01520' => 'egr', 'Eucgr.H03604' => 'egr', 'Eucgr.L03465' => 'egr', 'Eucgr.L03466' => 'egr', 'FAN01G0988' => 'fan', 'FAN02G3892' => 'fan', 'FAN05G3381' => 'fan', 'FAN07G0967' => 'fan', 'FAN07G1493' => 'fan', 'FAN08G3125' => 'fan', 'FAN09G0402' => 'fan', 'FAN12G2594' => 'fan', 'FAN12G3879' => 'fan', 'FAN14G1546' => 'fan', 'FAN15G3626' => 'fan', 'FAN17G0588' => 'fan', 'FAN17G0609' => 'fan', 'FAN18G2817' => 'fan', 'FAN19G1305' => 'fan', 'FAN20G1787' => 'fan', 'FAN22G0073' => 'fan', 'FAN22G0352' => 'fan', 'FAN22G0368' => 'fan', 'FAN22G2273' => 'fan', 'FAN24G1998' => 'fan', 'FAN27G1317' => 'fan', 'FvH4_2g23980' => 'fve', 'FvH4_4g14380' => 'fve', 'FvH4_4g14390' => 'fve', 'FvH4_6g09250' => 'fve', 'Glyma.03G151100' => 'gma', 'Glyma.04G122550' => 'gma', 'Glyma.05G001600' => 'gma', 'Glyma.09G270766' => 'gma', 'Glyma.09G270832' => 'gma', 'Glyma.13G209800' => 'gma', 'Glyma.15G102800' => 'gma', 'Glyma.18G218900' => 'gma', 'Glyma.19G001500' => 'gma', 'Glyma.19G153600' => 'gma', 'Gohir.A02G028600' => 'ghi', 'Gohir.A08G045000' => 'ghi', 'Gohir.A11G120500' => 'ghi', 'Gohir.A12G006200' => 'ghi', 'Gohir.A12G006250' => 'ghi', 'Gohir.D02G036300' => 'ghi', 'Gohir.D08G054700' => 'ghi', 'Gohir.D11G125600' => 'ghi', 'Gohir.D12G005700' => 'ghi', 'Gorai.004G055200' => 'gra', 'Gorai.005G040400' => 'gra', 'Gorai.007G134500' => 'gra', 'Gorai.008G005500' => 'gra', 'GSVIVG01011094001' => 'vvi', 'GSVIVG01017879001' => 'vvi', 'GSVIVG01025988001' => 'vvi', 'GSVIVG01029847001' => 'vvi', 'HanXRQChr10g0282901' => 'han', 'HanXRQChr10g0310371' => 'han', 'HanXRQChr10g0315041' => 'han', 'HanXRQChr11g0327651' => 'han', 'HanXRQChr12g0359391' => 'han', 'Haze_00972' => 'cav', 'Haze_00973' => 'cav', 'Haze_00974' => 'cav', 'Haze_04747' => 'cav', 'Haze_04749' => 'cav', 'Haze_04750' => 'cav', 'Haze_21217' => 'cav', 'Hma1.2p1_1037F.1_g250680' => 'hma', 'Hma1.2p1_1644F.1_g295320' => 'hma', 'HPP92_011322' => 'vpl', 'HPP92_011323' => 'vpl', 'HPP92_011324' => 'vpl', 'HPP92_011325' => 'vpl', 'HPP92_011326' => 'vpl', 'Hund12205' => 'sun', 'Hund17957' => 'sun', 'Lalb_Chr06g0176771' => 'lal', 'Lalb_Chr18g0056021' => 'lal', 'Lalb_Chr18g0056031' => 'lal', 'Lalb_Chr18g0056041' => 'lal', 'Lalb_Chr20g0107751' => 'lal', 'Lalb_Chr20g0118371' => 'lal', 'Lj1g0010239' => 'lja', 'Lj1g0017101' => 'lja', 'Lj2A1178G40' => 'lonja', 'Lj2A54G84' => 'lonja', 'Lj2g0015248' => 'lja', 'Lj3A761T51' => 'lonja', 'Lj6g0018116' => 'lja', 'Lsat_1_v5_gn_4_136040' => 'lsa', 'Lsat_1_v5_gn_5_187461' => 'lsa', 'Lsat_1_v5_gn_5_77001' => 'lsa', 'Lsat_1_v5_gn_9_4461' => 'lsa', 'Manes.01G210100' => 'mes', 'Manes.03G185600' => 'mes', 'Manes.05G073300' => 'mes', 'Manes.09G120300' => 'mes', 'Manes.15G022100' => 'mes', 'Mapoly0096s0053' => 'mpo', 'MBI03_g14058_MAGBIO' => 'mbi', 'MBI03_g33876_MAGBIO' => 'mbi', 'MBI03_g36854_MAGBIO' => 'mbi', 'MBI17_g11997_MAGBIO' => 'mbi', 'MD03G1269000' => 'mdo', 'MD04G1179600' => 'mdo', 'MD11G1289800' => 'mdo', 'MD12G1194700' => 'mdo', 'MD13G1182100' => 'mdo', 'MD13G1182200' => 'mdo', 'MD16G1182600' => 'mdo', 'Medtr2g021400' => 'mtr', 'Medtr2g021470' => 'mtr', 'Medtr2g105810' => 'mtr', 'Medtr3g033580' => 'mtr', 'Medtr6g007970' => 'mtr', 'Medtr7g056330' => 'mtr', 'Medtr7g074290' => 'mtr', 'Medtr7g074380' => 'mtr', 'Medtr7g094550' => 'mtr', 'Medtr8g069995' => 'mtr', 'MELO3C014345.2' => 'cme', 'MELO3C021395.2' => 'cme', 'Migut.D00262' => 'egut', 'Migut.G00257' => 'egut', 'MSTRG.21575' => 'ama', 'MSTRG.3985' => 'ama', 'Nitab4.5_0000295g0140' => 'nta', 'Nitab4.5_0000732g0140' => 'nta', 'Nitab4.5_0003162g0020' => 'nta', 'Nitab4.5_0006180g0090' => 'nta', 'Nitab4.5_0006390g0010' => 'nta', 'Nitab4.5_0007392g0040' => 'nta', 'Nn1g02140' => 'nnu', 'Nn4g26168' => 'nnu', 'Nn5g26754' => 'nnu', 'Oeu001433.1' => 'oeu', 'Oeu010299.2' => 'oeu', 'Oeu011171.1' => 'oeu', 'Oeu037675.1' => 'oeu', 'Oeu038359.1' => 'oeu', 'Oeu063834.1' => 'oeu', 'Oeu063835.1' => 'oeu', 'Os05g0312000' => 'osa', 'Os07g0211101' => 'osa', 'Os07g0211200' => 'osa', 'Os07g0681500' => 'osa', 'Peaxi162Scf00095g01015' => 'pax', 'Peaxi162Scf00104g00329' => 'pax', 'Peaxi162Scf00161g00137' => 'pax', 'PGR004G1665' => 'pgr', 'PGR031G2937' => 'pgr', 'PGR119G2145' => 'pgr', 'PGSC0003DMG400004351' => 'stu', 'PGSC0003DMG400014625' => 'stu', 'PGSC0003DMG401000943' => 'stu', 'Phvul.001G148600' => 'pvu', 'Phvul.004G001700' => 'pvu', 'Phvul.006G154900' => 'pvu', 'Phvul.008G078200' => 'pvu', 'Phvul.011G136500' => 'pvu', 'Potri.002G215600' => 'ptr', 'Potri.008G201600' => 'ptr', 'Potri.014G138400' => 'ptr', 'Potri.016G142500' => 'ptr', 'Pp3c16_10580' => 'ppa', 'Pp3c5_25280' => 'ppa', 'Prupe.1G150000' => 'ppe', 'Prupe.1G150100' => 'ppe', 'Prupe.6G299600' => 'ppe', 'Prupe.8G245000' => 'ppe', 'Psat0s4927g0040' => 'psa', 'Psat1g052080' => 'psa', 'Psat1g183800' => 'psa', 'Psat3g113840' => 'psa', 'Psat3g126120' => 'psa', 'Psat3g126160' => 'psa', 'Psat3g158760' => 'psa', 'Psat3g158840' => 'psa', 'PSO170G2858' => 'pso', 'PSO339G0606' => 'pso', 'PSO384G4709' => 'pso', 'PSO407G0334' => 'pso', 'QL04p040276' => 'qlo', 'QL06p005458' => 'qlo', 'QL06p005472' => 'qlo', 'QL07p030546' => 'qlo', 'QL07p031519' => 'qlo', 'QL09p050949' => 'qlo', 'QL09p050966' => 'qlo', 'QL09p051067' => 'qlo', 'QL12p022706' => 'qlo', 'RcHm_v2.0_Chr2g0119601' => 'rch', 'RcHm_v2.0_Chr3g0459591' => 'rch', 'RcHm_v2.0_Chr4g0418521' => 'rch', 'RcHm_v2.0_Chr4g0418531' => 'rch', 'RcHm_v2.0_Chr4g0418541' => 'rch', 'RcHm_v2.0_Chr6g0291641' => 'rch', 'Rhsim01G0086300' => 'rsi', 'Rhsim01G0276300' => 'rsi', 'Rhsim01G0276500' => 'rsi', 'Rhsim04G0207700' => 'rsi', 'Rhsim05G0234500' => 'rsi', 'Rhsim13G0022400' => 'rsi', 'Sabra02G0167900' => 'sbr', 'Sabra04G0158500' => 'sbr', 'Sabra08G0159800' => 'sbr', 'Sabra10G0011500' => 'sbr', 'Sabra14G0104400' => 'sbr', 'SalBow2G2440' => 'sbo', 'SalBow4G2265' => 'sbo', 'Sc02g0000060' => 'sci', 'Sc05g0005020' => 'sci', 'Sc13g0003890' => 'sci', 'Sed0014865' => 'sed', 'Sed0017224' => 'sed', 'Sed0026391' => 'sed', 'SEGI_00063' => 'sgi', 'SEGI_10967' => 'sgi', 'SEGI_17510' => 'sgi', 'SEGI_24396' => 'sgi', 'SEGI_39719' => 'sgi', 'SEGI_41392' => 'sgi', 'SGA_v2.0_scaffold11G05794' => 'sas', 'SGA_v2.0_scaffold142G35607' => 'sas', 'SGA_v2.0_scaffold1G00447' => 'sas', 'SHI15388' => 'shi', 'SHI15394' => 'shi', 'SHI15396' => 'shi', 'SHI15399' => 'shi', 'SMO343G0151' => 'smo', 'SMO367G1118' => 'smo', 'Solyc01g080200.3' => 'sly', 'Solyc06g008960.3' => 'sly', 'Solyc09g064780.3' => 'sly', 'Sopen01g031980' => 'spe', 'Sopen06g003710' => 'spe', 'Sopen09g026460' => 'spe', 'Sp3g21240' => 'spa', 'Sp4g30030' => 'spa', 'TAR365G0022' => 'tar', 'TAR365G1023' => 'tar', 'TAR365G1253' => 'tar', 'TAR623G0078' => 'tar', 'TAR623G1721' => 'tar', 'TAR633G0959' => 'tar', 'THA.LOC104802225' => 'tha', 'THA.LOC104804769' => 'tha', 'THA.LOC104808660' => 'tha', 'THA.LOC104812792' => 'tha', 'Thecc.01G284000' => 'tca', 'Thecc.04G220600' => 'tca', 'Thecc.05G268900' => 'tca', 'Thecc.08G171100' => 'tca', 'Thhalv10001284m.g' => 'esa', 'Thhalv10019912m.g' => 'esa', 'TPR.G14189' => 'tpr', 'TPR.G18110' => 'tpr', 'TPR.G18130' => 'tpr', 'TPR.G18131' => 'tpr', 'TPR.G18140' => 'tpr', 'TPR.G24282' => 'tpr', 'TPR.G25221' => 'tpr', 'TPR.G29267' => 'tpr', 'TPR.G35315' => 'tpr', 'TPR.G36173' => 'tpr', 'TWI09G0794' => 'twi', 'TWI59G1348' => 'twi', 'TWI74G0430' => 'twi', 'unitig_26.g8940' => 'ugi', 'unitig_749.g13744' => 'ugi', 'unitig_749.g13745' => 'ugi', 'vmacro08269' => 'vma', 'vmacro14937' => 'vma', 'vmacro20401' => 'vma', 'VMungo0464G1349' => 'vmu', 'VMungo0540G0289' => 'vmu', 'VMungo1215G1590' => 'vmu', 'VMungo1309G0221' => 'vmu', 'VMungo1309G2815' => 'vmu', 'VMungo1383G0239' => 'vmu', 'VMungo1383G2910' => 'vmu', 'Zm00001eb095270' => 'zma', 'Zm00001eb095280' => 'zma', 'Zm00001eb111630' => 'zma', 'Zm00001eb237080' => 'zma', 'Zm00001eb273740' => 'zma', 'Zm00001eb285040' => 'zma', 'Zm00001eb330790' => 'zma', 'Zm00001eb337380' => 'zma' ), 'gf_id' => 'HOM05D001484', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001484' ), 'data_identifier' => 'HOM05D001484', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001484', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p31500' => 'bna', 'A05p00020' => 'bna', 'A07p08820' => 'bna', 'Aa31LG4G3300' => 'aar', 'Aa31LG8G10030' => 'aar', 'Actinidia00731' => 'ach', 'Actinidia11473' => 'ach', 'Actinidia23469' => 'ach', 'Actinidia24318' => 'ach', 'Actinidia40196' => 'ach', 'Actinidia40197' => 'ach', 'Actinidia40198' => 'ach', 'Ah.08g212990' => 'amhyb', 'Ah.15g091720' => 'amhyb', 'AL3G38260' => 'aly', 'AL4G47710' => 'aly', 'Aqoxy2G00671' => 'aox', 'Aqoxy2G03236' => 'aox', 'arahy.Tifrunner.gnm1.ann1.05IDCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KR684' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATY3SJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK6QJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6APGL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IDT7Z9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM073U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ0R87' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LE7RV4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT4QRX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V5ENPK' => 'arhy', 'AT2G48110' => 'ath', 'AT3G23590' => 'ath', 'ATR0626G186' => 'atr', 'ATR1127G141' => 'atr', 'Atru.chr4.2583' => 'acertr', 'Atru.chr5.1358' => 'acertr', 'Atru.chr5.1359' => 'acertr', 'Atru.chr8.46' => 'acertr', 'AUR62002640' => 'cqu', 'AUR62030055' => 'cqu', 'AUR62033713' => 'cqu', 'AUR62033714' => 'cqu', 'AUR62036795' => 'cqu', 'AUR62039891' => 'cqu', 'BcaB02g08737' => 'bca', 'BcaB04g20441' => 'bca', 'BcaB06g26509' => 'bca', 'BcaB06g26510' => 'bca', 'BcaB06g26511' => 'bca', 'BcaB06g26512' => 'bca', 'BcaB06g26513' => 'bca', 'BcaC02g12564' => 'bca', 'BcaC02g12565' => 'bca', 'BcaC02g12794' => 'bca', 'BcaC02g12795' => 'bca', 'BcaC02g12796' => 'bca', 'BcaC06g35541' => 'bca', 'BNapus_Darmor_BZH_scaffold_188p00080' => 'bna', 'BNapus_Darmor_BZH_scaffold_188p00090' => 'bna', 'BolC1t03972H' => 'bol', 'BolC1t03973H' => 'bol', 'BolC4t21680H' => 'bol', 'BolC7t41863H' => 'bol', 'BolSC55t61227H' => 'bol', 'BolSC55t61228H' => 'bol', 'BraA01t03278Z' => 'bra', 'BraA05t18998Z' => 'bra', 'BraA07t28673Z' => 'bra', 'C01p40150' => 'bna', 'C05p12370' => 'bna', 'C07p13680' => 'bna', 'CAN.G1006.16' => 'can', 'CAN.G1006.17' => 'can', 'CAN.G1170.2' => 'can', 'CAN.G962.7' => 'can', 'CANSAT25G2179' => 'cansat', 'CANSAT78G1573' => 'cansat', 'CARHR099510' => 'chi', 'CARHR143510' => 'chi', 'Carub.0003s2380' => 'cru', 'Carub.0004s3082' => 'cru', 'Ca_00614_v3' => 'car', 'Ca_07801_v3' => 'car', 'Ca_08567_v3' => 'car', 'Ca_09571_v3' => 'car', 'CBR_g19290' => 'cbr', 'Cc01_g19770' => 'ccan', 'Cc03_g03030' => 'ccan', 'CDE07G0968' => 'cde', 'CDE09G1441' => 'cde', 'Cfa006103' => 'cfa', 'Cfa015573' => 'cfa', 'Cfa016988' => 'cfa', 'Ciclev10006738m.g' => 'ccl', 'Ciclev10010920m.g' => 'ccl', 'Ciclev10018517m.g' => 'ccl', 'CiPaw.01G159200' => 'cil', 'CiPaw.02G091000' => 'cil', 'CiPaw.02G091100' => 'cil', 'CiPaw.08G103100' => 'cil', 'CiPaw.09G224900' => 'cil', 'ClCG06G005740' => 'cla', 'ClCG07G000090' => 'cla', 'ClCG07G000100' => 'cla', 'COL.COLO4_09143' => 'col', 'COL.COLO4_25124' => 'col', 'Cpa.g.sc16.34' => 'cpa', 'Cpa.g.sc3504.1' => 'cpa', 'Cpa.g.sc60.37' => 'cpa', 'CsaV3_6G018520' => 'csa', 'CsaV3_6G036860' => 'csa', 'CSS0001072' => 'camsi', 'CSS0020208' => 'camsi', 'CSS0021253' => 'camsi', 'CSS0022190' => 'camsi', 'CSS0036150' => 'camsi', 'CSS0040442' => 'camsi', 'CSS0042300' => 'camsi', 'CSS0045298' => 'camsi', 'DCAR_012449' => 'dca', 'DCAR_018405' => 'dca', 'DCAR_024573' => 'dca', 'DCAR_030591' => 'dca', 'Dinv16926' => 'din', 'Dinv32963' => 'din', 'Dinv38382' => 'din', 'Dinv38383' => 'din', 'Duzib133G0974' => 'dzi', 'Duzib138G1867' => 'dzi', 'Duzib211G0420' => 'dzi', 'Duzib212G0930' => 'dzi', 'ECA234G1645' => 'eca', 'ECA247G3467' => 'eca', 'ECA248G1703' => 'eca', 'EL10Ac3g06327' => 'bvu', 'EL10Ac7g17204' => 'bvu', 'Eucgr.A00855' => 'egr', 'Eucgr.A00858' => 'egr', 'Eucgr.H01520' => 'egr', 'Eucgr.H03604' => 'egr', 'Eucgr.L03465' => 'egr', 'Eucgr.L03466' => 'egr', 'FAN01G0988' => 'fan', 'FAN02G3892' => 'fan', 'FAN05G3381' => 'fan', 'FAN07G0967' => 'fan', 'FAN07G1493' => 'fan', 'FAN08G3125' => 'fan', 'FAN09G0402' => 'fan', 'FAN12G2594' => 'fan', 'FAN12G3879' => 'fan', 'FAN14G1546' => 'fan', 'FAN15G3626' => 'fan', 'FAN17G0588' => 'fan', 'FAN17G0609' => 'fan', 'FAN18G2817' => 'fan', 'FAN19G1305' => 'fan', 'FAN20G1787' => 'fan', 'FAN22G0073' => 'fan', 'FAN22G0352' => 'fan', 'FAN22G0368' => 'fan', 'FAN22G2273' => 'fan', 'FAN24G1998' => 'fan', 'FAN27G1317' => 'fan', 'FvH4_2g23980' => 'fve', 'FvH4_4g14380' => 'fve', 'FvH4_4g14390' => 'fve', 'FvH4_6g09250' => 'fve', 'Glyma.03G151100' => 'gma', 'Glyma.04G122550' => 'gma', 'Glyma.05G001600' => 'gma', 'Glyma.09G270766' => 'gma', 'Glyma.09G270832' => 'gma', 'Glyma.13G209800' => 'gma', 'Glyma.15G102800' => 'gma', 'Glyma.18G218900' => 'gma', 'Glyma.19G001500' => 'gma', 'Glyma.19G153600' => 'gma', 'Gohir.A02G028600' => 'ghi', 'Gohir.A08G045000' => 'ghi', 'Gohir.A11G120500' => 'ghi', 'Gohir.A12G006200' => 'ghi', 'Gohir.A12G006250' => 'ghi', 'Gohir.D02G036300' => 'ghi', 'Gohir.D08G054700' => 'ghi', 'Gohir.D11G125600' => 'ghi', 'Gohir.D12G005700' => 'ghi', 'Gorai.004G055200' => 'gra', 'Gorai.005G040400' => 'gra', 'Gorai.007G134500' => 'gra', 'Gorai.008G005500' => 'gra', 'GSVIVG01011094001' => 'vvi', 'GSVIVG01017879001' => 'vvi', 'GSVIVG01025988001' => 'vvi', 'GSVIVG01029847001' => 'vvi', 'HanXRQChr10g0282901' => 'han', 'HanXRQChr10g0310371' => 'han', 'HanXRQChr10g0315041' => 'han', 'HanXRQChr11g0327651' => 'han', 'HanXRQChr12g0359391' => 'han', 'Haze_00972' => 'cav', 'Haze_00973' => 'cav', 'Haze_00974' => 'cav', 'Haze_04747' => 'cav', 'Haze_04749' => 'cav', 'Haze_04750' => 'cav', 'Haze_21217' => 'cav', 'Hma1.2p1_1037F.1_g250680' => 'hma', 'Hma1.2p1_1644F.1_g295320' => 'hma', 'HPP92_011322' => 'vpl', 'HPP92_011323' => 'vpl', 'HPP92_011324' => 'vpl', 'HPP92_011325' => 'vpl', 'HPP92_011326' => 'vpl', 'Hund12205' => 'sun', 'Hund17957' => 'sun', 'Lalb_Chr06g0176771' => 'lal', 'Lalb_Chr18g0056021' => 'lal', 'Lalb_Chr18g0056031' => 'lal', 'Lalb_Chr18g0056041' => 'lal', 'Lalb_Chr20g0107751' => 'lal', 'Lalb_Chr20g0118371' => 'lal', 'Lj1g0010239' => 'lja', 'Lj1g0017101' => 'lja', 'Lj2A1178G40' => 'lonja', 'Lj2A54G84' => 'lonja', 'Lj2g0015248' => 'lja', 'Lj3A761T51' => 'lonja', 'Lj6g0018116' => 'lja', 'Lsat_1_v5_gn_4_136040' => 'lsa', 'Lsat_1_v5_gn_5_187461' => 'lsa', 'Lsat_1_v5_gn_5_77001' => 'lsa', 'Lsat_1_v5_gn_9_4461' => 'lsa', 'Manes.01G210100' => 'mes', 'Manes.03G185600' => 'mes', 'Manes.05G073300' => 'mes', 'Manes.09G120300' => 'mes', 'Manes.15G022100' => 'mes', 'Mapoly0096s0053' => 'mpo', 'MBI03_g14058_MAGBIO' => 'mbi', 'MBI03_g33876_MAGBIO' => 'mbi', 'MBI03_g36854_MAGBIO' => 'mbi', 'MBI17_g11997_MAGBIO' => 'mbi', 'MD03G1269000' => 'mdo', 'MD04G1179600' => 'mdo', 'MD11G1289800' => 'mdo', 'MD12G1194700' => 'mdo', 'MD13G1182100' => 'mdo', 'MD13G1182200' => 'mdo', 'MD16G1182600' => 'mdo', 'Medtr2g021400' => 'mtr', 'Medtr2g021470' => 'mtr', 'Medtr2g105810' => 'mtr', 'Medtr3g033580' => 'mtr', 'Medtr6g007970' => 'mtr', 'Medtr7g056330' => 'mtr', 'Medtr7g074290' => 'mtr', 'Medtr7g074380' => 'mtr', 'Medtr7g094550' => 'mtr', 'Medtr8g069995' => 'mtr', 'MELO3C014345.2' => 'cme', 'MELO3C021395.2' => 'cme', 'Migut.D00262' => 'egut', 'Migut.G00257' => 'egut', 'MSTRG.21575' => 'ama', 'MSTRG.3985' => 'ama', 'Nitab4.5_0000295g0140' => 'nta', 'Nitab4.5_0000732g0140' => 'nta', 'Nitab4.5_0003162g0020' => 'nta', 'Nitab4.5_0006180g0090' => 'nta', 'Nitab4.5_0006390g0010' => 'nta', 'Nitab4.5_0007392g0040' => 'nta', 'Nn1g02140' => 'nnu', 'Nn4g26168' => 'nnu', 'Nn5g26754' => 'nnu', 'Oeu001433.1' => 'oeu', 'Oeu010299.2' => 'oeu', 'Oeu011171.1' => 'oeu', 'Oeu037675.1' => 'oeu', 'Oeu038359.1' => 'oeu', 'Oeu063834.1' => 'oeu', 'Oeu063835.1' => 'oeu', 'Os05g0312000' => 'osa', 'Os07g0211101' => 'osa', 'Os07g0211200' => 'osa', 'Os07g0681500' => 'osa', 'Peaxi162Scf00095g01015' => 'pax', 'Peaxi162Scf00104g00329' => 'pax', 'Peaxi162Scf00161g00137' => 'pax', 'PGR004G1665' => 'pgr', 'PGR031G2937' => 'pgr', 'PGR119G2145' => 'pgr', 'PGSC0003DMG400004351' => 'stu', 'PGSC0003DMG400014625' => 'stu', 'PGSC0003DMG401000943' => 'stu', 'Phvul.001G148600' => 'pvu', 'Phvul.004G001700' => 'pvu', 'Phvul.006G154900' => 'pvu', 'Phvul.008G078200' => 'pvu', 'Phvul.011G136500' => 'pvu', 'Potri.002G215600' => 'ptr', 'Potri.008G201600' => 'ptr', 'Potri.014G138400' => 'ptr', 'Potri.016G142500' => 'ptr', 'Pp3c16_10580' => 'ppa', 'Pp3c5_25280' => 'ppa', 'Prupe.1G150000' => 'ppe', 'Prupe.1G150100' => 'ppe', 'Prupe.6G299600' => 'ppe', 'Prupe.8G245000' => 'ppe', 'Psat0s4927g0040' => 'psa', 'Psat1g052080' => 'psa', 'Psat1g183800' => 'psa', 'Psat3g113840' => 'psa', 'Psat3g126120' => 'psa', 'Psat3g126160' => 'psa', 'Psat3g158760' => 'psa', 'Psat3g158840' => 'psa', 'PSO170G2858' => 'pso', 'PSO339G0606' => 'pso', 'PSO384G4709' => 'pso', 'PSO407G0334' => 'pso', 'QL04p040276' => 'qlo', 'QL06p005458' => 'qlo', 'QL06p005472' => 'qlo', 'QL07p030546' => 'qlo', 'QL07p031519' => 'qlo', 'QL09p050949' => 'qlo', 'QL09p050966' => 'qlo', 'QL09p051067' => 'qlo', 'QL12p022706' => 'qlo', 'RcHm_v2.0_Chr2g0119601' => 'rch', 'RcHm_v2.0_Chr3g0459591' => 'rch', 'RcHm_v2.0_Chr4g0418521' => 'rch', 'RcHm_v2.0_Chr4g0418531' => 'rch', 'RcHm_v2.0_Chr4g0418541' => 'rch', 'RcHm_v2.0_Chr6g0291641' => 'rch', 'Rhsim01G0086300' => 'rsi', 'Rhsim01G0276300' => 'rsi', 'Rhsim01G0276500' => 'rsi', 'Rhsim04G0207700' => 'rsi', 'Rhsim05G0234500' => 'rsi', 'Rhsim13G0022400' => 'rsi', 'Sabra02G0167900' => 'sbr', 'Sabra04G0158500' => 'sbr', 'Sabra08G0159800' => 'sbr', 'Sabra10G0011500' => 'sbr', 'Sabra14G0104400' => 'sbr', 'SalBow2G2440' => 'sbo', 'SalBow4G2265' => 'sbo', 'Sc02g0000060' => 'sci', 'Sc05g0005020' => 'sci', 'Sc13g0003890' => 'sci', 'Sed0014865' => 'sed', 'Sed0017224' => 'sed', 'Sed0026391' => 'sed', 'SEGI_00063' => 'sgi', 'SEGI_10967' => 'sgi', 'SEGI_17510' => 'sgi', 'SEGI_24396' => 'sgi', 'SEGI_39719' => 'sgi', 'SEGI_41392' => 'sgi', 'SGA_v2.0_scaffold11G05794' => 'sas', 'SGA_v2.0_scaffold142G35607' => 'sas', 'SGA_v2.0_scaffold1G00447' => 'sas', 'SHI15388' => 'shi', 'SHI15394' => 'shi', 'SHI15396' => 'shi', 'SHI15399' => 'shi', 'SMO343G0151' => 'smo', 'SMO367G1118' => 'smo', 'Solyc01g080200.3' => 'sly', 'Solyc06g008960.3' => 'sly', 'Solyc09g064780.3' => 'sly', 'Sopen01g031980' => 'spe', 'Sopen06g003710' => 'spe', 'Sopen09g026460' => 'spe', 'Sp3g21240' => 'spa', 'Sp4g30030' => 'spa', 'TAR365G0022' => 'tar', 'TAR365G1023' => 'tar', 'TAR365G1253' => 'tar', 'TAR623G0078' => 'tar', 'TAR623G1721' => 'tar', 'TAR633G0959' => 'tar', 'THA.LOC104802225' => 'tha', 'THA.LOC104804769' => 'tha', 'THA.LOC104808660' => 'tha', 'THA.LOC104812792' => 'tha', 'Thecc.01G284000' => 'tca', 'Thecc.04G220600' => 'tca', 'Thecc.05G268900' => 'tca', 'Thecc.08G171100' => 'tca', 'Thhalv10001284m.g' => 'esa', 'Thhalv10019912m.g' => 'esa', 'TPR.G14189' => 'tpr', 'TPR.G18110' => 'tpr', 'TPR.G18130' => 'tpr', 'TPR.G18131' => 'tpr', 'TPR.G18140' => 'tpr', 'TPR.G24282' => 'tpr', 'TPR.G25221' => 'tpr', 'TPR.G29267' => 'tpr', 'TPR.G35315' => 'tpr', 'TPR.G36173' => 'tpr', 'TWI09G0794' => 'twi', 'TWI59G1348' => 'twi', 'TWI74G0430' => 'twi', 'unitig_26.g8940' => 'ugi', 'unitig_749.g13744' => 'ugi', 'unitig_749.g13745' => 'ugi', 'vmacro08269' => 'vma', 'vmacro14937' => 'vma', 'vmacro20401' => 'vma', 'VMungo0464G1349' => 'vmu', 'VMungo0540G0289' => 'vmu', 'VMungo1215G1590' => 'vmu', 'VMungo1309G0221' => 'vmu', 'VMungo1309G2815' => 'vmu', 'VMungo1383G0239' => 'vmu', 'VMungo1383G2910' => 'vmu', 'Zm00001eb095270' => 'zma', 'Zm00001eb095280' => 'zma', 'Zm00001eb111630' => 'zma', 'Zm00001eb237080' => 'zma', 'Zm00001eb273740' => 'zma', 'Zm00001eb285040' => 'zma', 'Zm00001eb330790' => 'zma', 'Zm00001eb337380' => 'zma' ) $gf_id = 'HOM05D001484' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001484' ) $data_identifier = 'HOM05D001484' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 2, 'aly' => (int) 2, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 22, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 7, 'hma' => (int) 2, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 7, 'mtr' => (int) 10, 'cme' => (int) 2, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 4, 'ppa' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 4, 'qlo' => (int) 9, 'rch' => (int) 6, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 10, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 7, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb337380' $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' => 'HOM05D001484', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p31500' => 'bna', 'A05p00020' => 'bna', 'A07p08820' => 'bna', 'Aa31LG4G3300' => 'aar', 'Aa31LG8G10030' => 'aar', 'Actinidia00731' => 'ach', 'Actinidia11473' => 'ach', 'Actinidia23469' => 'ach', 'Actinidia24318' => 'ach', 'Actinidia40196' => 'ach', 'Actinidia40197' => 'ach', 'Actinidia40198' => 'ach', 'Ah.08g212990' => 'amhyb', 'Ah.15g091720' => 'amhyb', 'AL3G38260' => 'aly', 'AL4G47710' => 'aly', 'Aqoxy2G00671' => 'aox', 'Aqoxy2G03236' => 'aox', 'arahy.Tifrunner.gnm1.ann1.05IDCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KR684' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATY3SJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK6QJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6APGL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IDT7Z9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM073U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ0R87' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LE7RV4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT4QRX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V5ENPK' => 'arhy', 'AT2G48110' => 'ath', 'AT3G23590' => 'ath', 'ATR0626G186' => 'atr', 'ATR1127G141' => 'atr', 'Atru.chr4.2583' => 'acertr', 'Atru.chr5.1358' => 'acertr', 'Atru.chr5.1359' => 'acertr', 'Atru.chr8.46' => 'acertr', 'AUR62002640' => 'cqu', 'AUR62030055' => 'cqu', 'AUR62033713' => 'cqu', 'AUR62033714' => 'cqu', 'AUR62036795' => 'cqu', 'AUR62039891' => 'cqu', 'BcaB02g08737' => 'bca', 'BcaB04g20441' => 'bca', 'BcaB06g26509' => 'bca', 'BcaB06g26510' => 'bca', 'BcaB06g26511' => 'bca', 'BcaB06g26512' => 'bca', 'BcaB06g26513' => 'bca', 'BcaC02g12564' => 'bca', 'BcaC02g12565' => 'bca', 'BcaC02g12794' => 'bca', 'BcaC02g12795' => 'bca', 'BcaC02g12796' => 'bca', 'BcaC06g35541' => 'bca', 'BNapus_Darmor_BZH_scaffold_188p00080' => 'bna', 'BNapus_Darmor_BZH_scaffold_188p00090' => 'bna', 'BolC1t03972H' => 'bol', 'BolC1t03973H' => 'bol', 'BolC4t21680H' => 'bol', 'BolC7t41863H' => 'bol', 'BolSC55t61227H' => 'bol', 'BolSC55t61228H' => 'bol', 'BraA01t03278Z' => 'bra', 'BraA05t18998Z' => 'bra', 'BraA07t28673Z' => 'bra', 'C01p40150' => 'bna', 'C05p12370' => 'bna', 'C07p13680' => 'bna', 'CAN.G1006.16' => 'can', 'CAN.G1006.17' => 'can', 'CAN.G1170.2' => 'can', 'CAN.G962.7' => 'can', 'CANSAT25G2179' => 'cansat', 'CANSAT78G1573' => 'cansat', 'CARHR099510' => 'chi', 'CARHR143510' => 'chi', 'Carub.0003s2380' => 'cru', 'Carub.0004s3082' => 'cru', 'Ca_00614_v3' => 'car', 'Ca_07801_v3' => 'car', 'Ca_08567_v3' => 'car', 'Ca_09571_v3' => 'car', 'CBR_g19290' => 'cbr', 'Cc01_g19770' => 'ccan', 'Cc03_g03030' => 'ccan', 'CDE07G0968' => 'cde', 'CDE09G1441' => 'cde', 'Cfa006103' => 'cfa', 'Cfa015573' => 'cfa', 'Cfa016988' => 'cfa', 'Ciclev10006738m.g' => 'ccl', 'Ciclev10010920m.g' => 'ccl', 'Ciclev10018517m.g' => 'ccl', 'CiPaw.01G159200' => 'cil', 'CiPaw.02G091000' => 'cil', 'CiPaw.02G091100' => 'cil', 'CiPaw.08G103100' => 'cil', 'CiPaw.09G224900' => 'cil', 'ClCG06G005740' => 'cla', 'ClCG07G000090' => 'cla', 'ClCG07G000100' => 'cla', 'COL.COLO4_09143' => 'col', 'COL.COLO4_25124' => 'col', 'Cpa.g.sc16.34' => 'cpa', 'Cpa.g.sc3504.1' => 'cpa', 'Cpa.g.sc60.37' => 'cpa', 'CsaV3_6G018520' => 'csa', 'CsaV3_6G036860' => 'csa', 'CSS0001072' => 'camsi', 'CSS0020208' => 'camsi', 'CSS0021253' => 'camsi', 'CSS0022190' => 'camsi', 'CSS0036150' => 'camsi', 'CSS0040442' => 'camsi', 'CSS0042300' => 'camsi', 'CSS0045298' => 'camsi', 'DCAR_012449' => 'dca', 'DCAR_018405' => 'dca', 'DCAR_024573' => 'dca', 'DCAR_030591' => 'dca', 'Dinv16926' => 'din', 'Dinv32963' => 'din', 'Dinv38382' => 'din', 'Dinv38383' => 'din', 'Duzib133G0974' => 'dzi', 'Duzib138G1867' => 'dzi', 'Duzib211G0420' => 'dzi', 'Duzib212G0930' => 'dzi', 'ECA234G1645' => 'eca', 'ECA247G3467' => 'eca', 'ECA248G1703' => 'eca', 'EL10Ac3g06327' => 'bvu', 'EL10Ac7g17204' => 'bvu', 'Eucgr.A00855' => 'egr', 'Eucgr.A00858' => 'egr', 'Eucgr.H01520' => 'egr', 'Eucgr.H03604' => 'egr', 'Eucgr.L03465' => 'egr', 'Eucgr.L03466' => 'egr', 'FAN01G0988' => 'fan', 'FAN02G3892' => 'fan', 'FAN05G3381' => 'fan', 'FAN07G0967' => 'fan', 'FAN07G1493' => 'fan', 'FAN08G3125' => 'fan', 'FAN09G0402' => 'fan', 'FAN12G2594' => 'fan', 'FAN12G3879' => 'fan', 'FAN14G1546' => 'fan', 'FAN15G3626' => 'fan', 'FAN17G0588' => 'fan', 'FAN17G0609' => 'fan', 'FAN18G2817' => 'fan', 'FAN19G1305' => 'fan', 'FAN20G1787' => 'fan', 'FAN22G0073' => 'fan', 'FAN22G0352' => 'fan', 'FAN22G0368' => 'fan', 'FAN22G2273' => 'fan', 'FAN24G1998' => 'fan', 'FAN27G1317' => 'fan', 'FvH4_2g23980' => 'fve', 'FvH4_4g14380' => 'fve', 'FvH4_4g14390' => 'fve', 'FvH4_6g09250' => 'fve', 'Glyma.03G151100' => 'gma', 'Glyma.04G122550' => 'gma', 'Glyma.05G001600' => 'gma', 'Glyma.09G270766' => 'gma', 'Glyma.09G270832' => 'gma', 'Glyma.13G209800' => 'gma', 'Glyma.15G102800' => 'gma', 'Glyma.18G218900' => 'gma', 'Glyma.19G001500' => 'gma', 'Glyma.19G153600' => 'gma', 'Gohir.A02G028600' => 'ghi', 'Gohir.A08G045000' => 'ghi', 'Gohir.A11G120500' => 'ghi', 'Gohir.A12G006200' => 'ghi', 'Gohir.A12G006250' => 'ghi', 'Gohir.D02G036300' => 'ghi', 'Gohir.D08G054700' => 'ghi', 'Gohir.D11G125600' => 'ghi', 'Gohir.D12G005700' => 'ghi', 'Gorai.004G055200' => 'gra', 'Gorai.005G040400' => 'gra', 'Gorai.007G134500' => 'gra', 'Gorai.008G005500' => 'gra', 'GSVIVG01011094001' => 'vvi', 'GSVIVG01017879001' => 'vvi', 'GSVIVG01025988001' => 'vvi', 'GSVIVG01029847001' => 'vvi', 'HanXRQChr10g0282901' => 'han', 'HanXRQChr10g0310371' => 'han', 'HanXRQChr10g0315041' => 'han', 'HanXRQChr11g0327651' => 'han', 'HanXRQChr12g0359391' => 'han', 'Haze_00972' => 'cav', 'Haze_00973' => 'cav', 'Haze_00974' => 'cav', 'Haze_04747' => 'cav', 'Haze_04749' => 'cav', 'Haze_04750' => 'cav', 'Haze_21217' => 'cav', 'Hma1.2p1_1037F.1_g250680' => 'hma', 'Hma1.2p1_1644F.1_g295320' => 'hma', 'HPP92_011322' => 'vpl', 'HPP92_011323' => 'vpl', 'HPP92_011324' => 'vpl', 'HPP92_011325' => 'vpl', 'HPP92_011326' => 'vpl', 'Hund12205' => 'sun', 'Hund17957' => 'sun', 'Lalb_Chr06g0176771' => 'lal', 'Lalb_Chr18g0056021' => 'lal', 'Lalb_Chr18g0056031' => 'lal', 'Lalb_Chr18g0056041' => 'lal', 'Lalb_Chr20g0107751' => 'lal', 'Lalb_Chr20g0118371' => 'lal', 'Lj1g0010239' => 'lja', 'Lj1g0017101' => 'lja', 'Lj2A1178G40' => 'lonja', 'Lj2A54G84' => 'lonja', 'Lj2g0015248' => 'lja', 'Lj3A761T51' => 'lonja', 'Lj6g0018116' => 'lja', 'Lsat_1_v5_gn_4_136040' => 'lsa', 'Lsat_1_v5_gn_5_187461' => 'lsa', 'Lsat_1_v5_gn_5_77001' => 'lsa', 'Lsat_1_v5_gn_9_4461' => 'lsa', 'Manes.01G210100' => 'mes', 'Manes.03G185600' => 'mes', 'Manes.05G073300' => 'mes', 'Manes.09G120300' => 'mes', 'Manes.15G022100' => 'mes', 'Mapoly0096s0053' => 'mpo', 'MBI03_g14058_MAGBIO' => 'mbi', 'MBI03_g33876_MAGBIO' => 'mbi', 'MBI03_g36854_MAGBIO' => 'mbi', 'MBI17_g11997_MAGBIO' => 'mbi', 'MD03G1269000' => 'mdo', 'MD04G1179600' => 'mdo', 'MD11G1289800' => 'mdo', 'MD12G1194700' => 'mdo', 'MD13G1182100' => 'mdo', 'MD13G1182200' => 'mdo', 'MD16G1182600' => 'mdo', 'Medtr2g021400' => 'mtr', 'Medtr2g021470' => 'mtr', 'Medtr2g105810' => 'mtr', 'Medtr3g033580' => 'mtr', 'Medtr6g007970' => 'mtr', 'Medtr7g056330' => 'mtr', 'Medtr7g074290' => 'mtr', 'Medtr7g074380' => 'mtr', 'Medtr7g094550' => 'mtr', 'Medtr8g069995' => 'mtr', 'MELO3C014345.2' => 'cme', 'MELO3C021395.2' => 'cme', 'Migut.D00262' => 'egut', 'Migut.G00257' => 'egut', 'MSTRG.21575' => 'ama', 'MSTRG.3985' => 'ama', 'Nitab4.5_0000295g0140' => 'nta', 'Nitab4.5_0000732g0140' => 'nta', 'Nitab4.5_0003162g0020' => 'nta', 'Nitab4.5_0006180g0090' => 'nta', 'Nitab4.5_0006390g0010' => 'nta', 'Nitab4.5_0007392g0040' => 'nta', 'Nn1g02140' => 'nnu', 'Nn4g26168' => 'nnu', 'Nn5g26754' => 'nnu', 'Oeu001433.1' => 'oeu', 'Oeu010299.2' => 'oeu', 'Oeu011171.1' => 'oeu', 'Oeu037675.1' => 'oeu', 'Oeu038359.1' => 'oeu', 'Oeu063834.1' => 'oeu', 'Oeu063835.1' => 'oeu', 'Os05g0312000' => 'osa', 'Os07g0211101' => 'osa', 'Os07g0211200' => 'osa', 'Os07g0681500' => 'osa', 'Peaxi162Scf00095g01015' => 'pax', 'Peaxi162Scf00104g00329' => 'pax', 'Peaxi162Scf00161g00137' => 'pax', 'PGR004G1665' => 'pgr', 'PGR031G2937' => 'pgr', 'PGR119G2145' => 'pgr', 'PGSC0003DMG400004351' => 'stu', 'PGSC0003DMG400014625' => 'stu', 'PGSC0003DMG401000943' => 'stu', 'Phvul.001G148600' => 'pvu', 'Phvul.004G001700' => 'pvu', 'Phvul.006G154900' => 'pvu', 'Phvul.008G078200' => 'pvu', 'Phvul.011G136500' => 'pvu', 'Potri.002G215600' => 'ptr', 'Potri.008G201600' => 'ptr', 'Potri.014G138400' => 'ptr', 'Potri.016G142500' => 'ptr', 'Pp3c16_10580' => 'ppa', 'Pp3c5_25280' => 'ppa', 'Prupe.1G150000' => 'ppe', 'Prupe.1G150100' => 'ppe', 'Prupe.6G299600' => 'ppe', 'Prupe.8G245000' => 'ppe', 'Psat0s4927g0040' => 'psa', 'Psat1g052080' => 'psa', 'Psat1g183800' => 'psa', 'Psat3g113840' => 'psa', 'Psat3g126120' => 'psa', 'Psat3g126160' => 'psa', 'Psat3g158760' => 'psa', 'Psat3g158840' => 'psa', 'PSO170G2858' => 'pso', 'PSO339G0606' => 'pso', 'PSO384G4709' => 'pso', 'PSO407G0334' => 'pso', 'QL04p040276' => 'qlo', 'QL06p005458' => 'qlo', 'QL06p005472' => 'qlo', 'QL07p030546' => 'qlo', 'QL07p031519' => 'qlo', 'QL09p050949' => 'qlo', 'QL09p050966' => 'qlo', 'QL09p051067' => 'qlo', 'QL12p022706' => 'qlo', 'RcHm_v2.0_Chr2g0119601' => 'rch', 'RcHm_v2.0_Chr3g0459591' => 'rch', 'RcHm_v2.0_Chr4g0418521' => 'rch', 'RcHm_v2.0_Chr4g0418531' => 'rch', 'RcHm_v2.0_Chr4g0418541' => 'rch', 'RcHm_v2.0_Chr6g0291641' => 'rch', 'Rhsim01G0086300' => 'rsi', 'Rhsim01G0276300' => 'rsi', 'Rhsim01G0276500' => 'rsi', 'Rhsim04G0207700' => 'rsi', 'Rhsim05G0234500' => 'rsi', 'Rhsim13G0022400' => 'rsi', 'Sabra02G0167900' => 'sbr', 'Sabra04G0158500' => 'sbr', 'Sabra08G0159800' => 'sbr', 'Sabra10G0011500' => 'sbr', 'Sabra14G0104400' => 'sbr', 'SalBow2G2440' => 'sbo', 'SalBow4G2265' => 'sbo', 'Sc02g0000060' => 'sci', 'Sc05g0005020' => 'sci', 'Sc13g0003890' => 'sci', 'Sed0014865' => 'sed', 'Sed0017224' => 'sed', 'Sed0026391' => 'sed', 'SEGI_00063' => 'sgi', 'SEGI_10967' => 'sgi', 'SEGI_17510' => 'sgi', 'SEGI_24396' => 'sgi', 'SEGI_39719' => 'sgi', 'SEGI_41392' => 'sgi', 'SGA_v2.0_scaffold11G05794' => 'sas', 'SGA_v2.0_scaffold142G35607' => 'sas', 'SGA_v2.0_scaffold1G00447' => 'sas', 'SHI15388' => 'shi', 'SHI15394' => 'shi', 'SHI15396' => 'shi', 'SHI15399' => 'shi', 'SMO343G0151' => 'smo', 'SMO367G1118' => 'smo', 'Solyc01g080200.3' => 'sly', 'Solyc06g008960.3' => 'sly', 'Solyc09g064780.3' => 'sly', 'Sopen01g031980' => 'spe', 'Sopen06g003710' => 'spe', 'Sopen09g026460' => 'spe', 'Sp3g21240' => 'spa', 'Sp4g30030' => 'spa', 'TAR365G0022' => 'tar', 'TAR365G1023' => 'tar', 'TAR365G1253' => 'tar', 'TAR623G0078' => 'tar', 'TAR623G1721' => 'tar', 'TAR633G0959' => 'tar', 'THA.LOC104802225' => 'tha', 'THA.LOC104804769' => 'tha', 'THA.LOC104808660' => 'tha', 'THA.LOC104812792' => 'tha', 'Thecc.01G284000' => 'tca', 'Thecc.04G220600' => 'tca', 'Thecc.05G268900' => 'tca', 'Thecc.08G171100' => 'tca', 'Thhalv10001284m.g' => 'esa', 'Thhalv10019912m.g' => 'esa', 'TPR.G14189' => 'tpr', 'TPR.G18110' => 'tpr', 'TPR.G18130' => 'tpr', 'TPR.G18131' => 'tpr', 'TPR.G18140' => 'tpr', 'TPR.G24282' => 'tpr', 'TPR.G25221' => 'tpr', 'TPR.G29267' => 'tpr', 'TPR.G35315' => 'tpr', 'TPR.G36173' => 'tpr', 'TWI09G0794' => 'twi', 'TWI59G1348' => 'twi', 'TWI74G0430' => 'twi', 'unitig_26.g8940' => 'ugi', 'unitig_749.g13744' => 'ugi', 'unitig_749.g13745' => 'ugi', 'vmacro08269' => 'vma', 'vmacro14937' => 'vma', 'vmacro20401' => 'vma', 'VMungo0464G1349' => 'vmu', 'VMungo0540G0289' => 'vmu', 'VMungo1215G1590' => 'vmu', 'VMungo1309G0221' => 'vmu', 'VMungo1309G2815' => 'vmu', 'VMungo1383G0239' => 'vmu', 'VMungo1383G2910' => 'vmu', 'Zm00001eb095270' => 'zma', 'Zm00001eb095280' => 'zma', 'Zm00001eb111630' => 'zma', 'Zm00001eb237080' => 'zma', 'Zm00001eb273740' => 'zma', 'Zm00001eb285040' => 'zma', 'Zm00001eb330790' => 'zma', 'Zm00001eb337380' => 'zma' ), 'gf_id' => 'HOM05D001484', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001484' ), 'data_identifier' => 'HOM05D001484', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001484', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p31500' => 'bna', 'A05p00020' => 'bna', 'A07p08820' => 'bna', 'Aa31LG4G3300' => 'aar', 'Aa31LG8G10030' => 'aar', 'Actinidia00731' => 'ach', 'Actinidia11473' => 'ach', 'Actinidia23469' => 'ach', 'Actinidia24318' => 'ach', 'Actinidia40196' => 'ach', 'Actinidia40197' => 'ach', 'Actinidia40198' => 'ach', 'Ah.08g212990' => 'amhyb', 'Ah.15g091720' => 'amhyb', 'AL3G38260' => 'aly', 'AL4G47710' => 'aly', 'Aqoxy2G00671' => 'aox', 'Aqoxy2G03236' => 'aox', 'arahy.Tifrunner.gnm1.ann1.05IDCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KR684' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATY3SJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK6QJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6APGL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IDT7Z9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM073U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ0R87' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LE7RV4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT4QRX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V5ENPK' => 'arhy', 'AT2G48110' => 'ath', 'AT3G23590' => 'ath', 'ATR0626G186' => 'atr', 'ATR1127G141' => 'atr', 'Atru.chr4.2583' => 'acertr', 'Atru.chr5.1358' => 'acertr', 'Atru.chr5.1359' => 'acertr', 'Atru.chr8.46' => 'acertr', 'AUR62002640' => 'cqu', 'AUR62030055' => 'cqu', 'AUR62033713' => 'cqu', 'AUR62033714' => 'cqu', 'AUR62036795' => 'cqu', 'AUR62039891' => 'cqu', 'BcaB02g08737' => 'bca', 'BcaB04g20441' => 'bca', 'BcaB06g26509' => 'bca', 'BcaB06g26510' => 'bca', 'BcaB06g26511' => 'bca', 'BcaB06g26512' => 'bca', 'BcaB06g26513' => 'bca', 'BcaC02g12564' => 'bca', 'BcaC02g12565' => 'bca', 'BcaC02g12794' => 'bca', 'BcaC02g12795' => 'bca', 'BcaC02g12796' => 'bca', 'BcaC06g35541' => 'bca', 'BNapus_Darmor_BZH_scaffold_188p00080' => 'bna', 'BNapus_Darmor_BZH_scaffold_188p00090' => 'bna', 'BolC1t03972H' => 'bol', 'BolC1t03973H' => 'bol', 'BolC4t21680H' => 'bol', 'BolC7t41863H' => 'bol', 'BolSC55t61227H' => 'bol', 'BolSC55t61228H' => 'bol', 'BraA01t03278Z' => 'bra', 'BraA05t18998Z' => 'bra', 'BraA07t28673Z' => 'bra', 'C01p40150' => 'bna', 'C05p12370' => 'bna', 'C07p13680' => 'bna', 'CAN.G1006.16' => 'can', 'CAN.G1006.17' => 'can', 'CAN.G1170.2' => 'can', 'CAN.G962.7' => 'can', 'CANSAT25G2179' => 'cansat', 'CANSAT78G1573' => 'cansat', 'CARHR099510' => 'chi', 'CARHR143510' => 'chi', 'Carub.0003s2380' => 'cru', 'Carub.0004s3082' => 'cru', 'Ca_00614_v3' => 'car', 'Ca_07801_v3' => 'car', 'Ca_08567_v3' => 'car', 'Ca_09571_v3' => 'car', 'CBR_g19290' => 'cbr', 'Cc01_g19770' => 'ccan', 'Cc03_g03030' => 'ccan', 'CDE07G0968' => 'cde', 'CDE09G1441' => 'cde', 'Cfa006103' => 'cfa', 'Cfa015573' => 'cfa', 'Cfa016988' => 'cfa', 'Ciclev10006738m.g' => 'ccl', 'Ciclev10010920m.g' => 'ccl', 'Ciclev10018517m.g' => 'ccl', 'CiPaw.01G159200' => 'cil', 'CiPaw.02G091000' => 'cil', 'CiPaw.02G091100' => 'cil', 'CiPaw.08G103100' => 'cil', 'CiPaw.09G224900' => 'cil', 'ClCG06G005740' => 'cla', 'ClCG07G000090' => 'cla', 'ClCG07G000100' => 'cla', 'COL.COLO4_09143' => 'col', 'COL.COLO4_25124' => 'col', 'Cpa.g.sc16.34' => 'cpa', 'Cpa.g.sc3504.1' => 'cpa', 'Cpa.g.sc60.37' => 'cpa', 'CsaV3_6G018520' => 'csa', 'CsaV3_6G036860' => 'csa', 'CSS0001072' => 'camsi', 'CSS0020208' => 'camsi', 'CSS0021253' => 'camsi', 'CSS0022190' => 'camsi', 'CSS0036150' => 'camsi', 'CSS0040442' => 'camsi', 'CSS0042300' => 'camsi', 'CSS0045298' => 'camsi', 'DCAR_012449' => 'dca', 'DCAR_018405' => 'dca', 'DCAR_024573' => 'dca', 'DCAR_030591' => 'dca', 'Dinv16926' => 'din', 'Dinv32963' => 'din', 'Dinv38382' => 'din', 'Dinv38383' => 'din', 'Duzib133G0974' => 'dzi', 'Duzib138G1867' => 'dzi', 'Duzib211G0420' => 'dzi', 'Duzib212G0930' => 'dzi', 'ECA234G1645' => 'eca', 'ECA247G3467' => 'eca', 'ECA248G1703' => 'eca', 'EL10Ac3g06327' => 'bvu', 'EL10Ac7g17204' => 'bvu', 'Eucgr.A00855' => 'egr', 'Eucgr.A00858' => 'egr', 'Eucgr.H01520' => 'egr', 'Eucgr.H03604' => 'egr', 'Eucgr.L03465' => 'egr', 'Eucgr.L03466' => 'egr', 'FAN01G0988' => 'fan', 'FAN02G3892' => 'fan', 'FAN05G3381' => 'fan', 'FAN07G0967' => 'fan', 'FAN07G1493' => 'fan', 'FAN08G3125' => 'fan', 'FAN09G0402' => 'fan', 'FAN12G2594' => 'fan', 'FAN12G3879' => 'fan', 'FAN14G1546' => 'fan', 'FAN15G3626' => 'fan', 'FAN17G0588' => 'fan', 'FAN17G0609' => 'fan', 'FAN18G2817' => 'fan', 'FAN19G1305' => 'fan', 'FAN20G1787' => 'fan', 'FAN22G0073' => 'fan', 'FAN22G0352' => 'fan', 'FAN22G0368' => 'fan', 'FAN22G2273' => 'fan', 'FAN24G1998' => 'fan', 'FAN27G1317' => 'fan', 'FvH4_2g23980' => 'fve', 'FvH4_4g14380' => 'fve', 'FvH4_4g14390' => 'fve', 'FvH4_6g09250' => 'fve', 'Glyma.03G151100' => 'gma', 'Glyma.04G122550' => 'gma', 'Glyma.05G001600' => 'gma', 'Glyma.09G270766' => 'gma', 'Glyma.09G270832' => 'gma', 'Glyma.13G209800' => 'gma', 'Glyma.15G102800' => 'gma', 'Glyma.18G218900' => 'gma', 'Glyma.19G001500' => 'gma', 'Glyma.19G153600' => 'gma', 'Gohir.A02G028600' => 'ghi', 'Gohir.A08G045000' => 'ghi', 'Gohir.A11G120500' => 'ghi', 'Gohir.A12G006200' => 'ghi', 'Gohir.A12G006250' => 'ghi', 'Gohir.D02G036300' => 'ghi', 'Gohir.D08G054700' => 'ghi', 'Gohir.D11G125600' => 'ghi', 'Gohir.D12G005700' => 'ghi', 'Gorai.004G055200' => 'gra', 'Gorai.005G040400' => 'gra', 'Gorai.007G134500' => 'gra', 'Gorai.008G005500' => 'gra', 'GSVIVG01011094001' => 'vvi', 'GSVIVG01017879001' => 'vvi', 'GSVIVG01025988001' => 'vvi', 'GSVIVG01029847001' => 'vvi', 'HanXRQChr10g0282901' => 'han', 'HanXRQChr10g0310371' => 'han', 'HanXRQChr10g0315041' => 'han', 'HanXRQChr11g0327651' => 'han', 'HanXRQChr12g0359391' => 'han', 'Haze_00972' => 'cav', 'Haze_00973' => 'cav', 'Haze_00974' => 'cav', 'Haze_04747' => 'cav', 'Haze_04749' => 'cav', 'Haze_04750' => 'cav', 'Haze_21217' => 'cav', 'Hma1.2p1_1037F.1_g250680' => 'hma', 'Hma1.2p1_1644F.1_g295320' => 'hma', 'HPP92_011322' => 'vpl', 'HPP92_011323' => 'vpl', 'HPP92_011324' => 'vpl', 'HPP92_011325' => 'vpl', 'HPP92_011326' => 'vpl', 'Hund12205' => 'sun', 'Hund17957' => 'sun', 'Lalb_Chr06g0176771' => 'lal', 'Lalb_Chr18g0056021' => 'lal', 'Lalb_Chr18g0056031' => 'lal', 'Lalb_Chr18g0056041' => 'lal', 'Lalb_Chr20g0107751' => 'lal', 'Lalb_Chr20g0118371' => 'lal', 'Lj1g0010239' => 'lja', 'Lj1g0017101' => 'lja', 'Lj2A1178G40' => 'lonja', 'Lj2A54G84' => 'lonja', 'Lj2g0015248' => 'lja', 'Lj3A761T51' => 'lonja', 'Lj6g0018116' => 'lja', 'Lsat_1_v5_gn_4_136040' => 'lsa', 'Lsat_1_v5_gn_5_187461' => 'lsa', 'Lsat_1_v5_gn_5_77001' => 'lsa', 'Lsat_1_v5_gn_9_4461' => 'lsa', 'Manes.01G210100' => 'mes', 'Manes.03G185600' => 'mes', 'Manes.05G073300' => 'mes', 'Manes.09G120300' => 'mes', 'Manes.15G022100' => 'mes', 'Mapoly0096s0053' => 'mpo', 'MBI03_g14058_MAGBIO' => 'mbi', 'MBI03_g33876_MAGBIO' => 'mbi', 'MBI03_g36854_MAGBIO' => 'mbi', 'MBI17_g11997_MAGBIO' => 'mbi', 'MD03G1269000' => 'mdo', 'MD04G1179600' => 'mdo', 'MD11G1289800' => 'mdo', 'MD12G1194700' => 'mdo', 'MD13G1182100' => 'mdo', 'MD13G1182200' => 'mdo', 'MD16G1182600' => 'mdo', 'Medtr2g021400' => 'mtr', 'Medtr2g021470' => 'mtr', 'Medtr2g105810' => 'mtr', 'Medtr3g033580' => 'mtr', 'Medtr6g007970' => 'mtr', 'Medtr7g056330' => 'mtr', 'Medtr7g074290' => 'mtr', 'Medtr7g074380' => 'mtr', 'Medtr7g094550' => 'mtr', 'Medtr8g069995' => 'mtr', 'MELO3C014345.2' => 'cme', 'MELO3C021395.2' => 'cme', 'Migut.D00262' => 'egut', 'Migut.G00257' => 'egut', 'MSTRG.21575' => 'ama', 'MSTRG.3985' => 'ama', 'Nitab4.5_0000295g0140' => 'nta', 'Nitab4.5_0000732g0140' => 'nta', 'Nitab4.5_0003162g0020' => 'nta', 'Nitab4.5_0006180g0090' => 'nta', 'Nitab4.5_0006390g0010' => 'nta', 'Nitab4.5_0007392g0040' => 'nta', 'Nn1g02140' => 'nnu', 'Nn4g26168' => 'nnu', 'Nn5g26754' => 'nnu', 'Oeu001433.1' => 'oeu', 'Oeu010299.2' => 'oeu', 'Oeu011171.1' => 'oeu', 'Oeu037675.1' => 'oeu', 'Oeu038359.1' => 'oeu', 'Oeu063834.1' => 'oeu', 'Oeu063835.1' => 'oeu', 'Os05g0312000' => 'osa', 'Os07g0211101' => 'osa', 'Os07g0211200' => 'osa', 'Os07g0681500' => 'osa', 'Peaxi162Scf00095g01015' => 'pax', 'Peaxi162Scf00104g00329' => 'pax', 'Peaxi162Scf00161g00137' => 'pax', 'PGR004G1665' => 'pgr', 'PGR031G2937' => 'pgr', 'PGR119G2145' => 'pgr', 'PGSC0003DMG400004351' => 'stu', 'PGSC0003DMG400014625' => 'stu', 'PGSC0003DMG401000943' => 'stu', 'Phvul.001G148600' => 'pvu', 'Phvul.004G001700' => 'pvu', 'Phvul.006G154900' => 'pvu', 'Phvul.008G078200' => 'pvu', 'Phvul.011G136500' => 'pvu', 'Potri.002G215600' => 'ptr', 'Potri.008G201600' => 'ptr', 'Potri.014G138400' => 'ptr', 'Potri.016G142500' => 'ptr', 'Pp3c16_10580' => 'ppa', 'Pp3c5_25280' => 'ppa', 'Prupe.1G150000' => 'ppe', 'Prupe.1G150100' => 'ppe', 'Prupe.6G299600' => 'ppe', 'Prupe.8G245000' => 'ppe', 'Psat0s4927g0040' => 'psa', 'Psat1g052080' => 'psa', 'Psat1g183800' => 'psa', 'Psat3g113840' => 'psa', 'Psat3g126120' => 'psa', 'Psat3g126160' => 'psa', 'Psat3g158760' => 'psa', 'Psat3g158840' => 'psa', 'PSO170G2858' => 'pso', 'PSO339G0606' => 'pso', 'PSO384G4709' => 'pso', 'PSO407G0334' => 'pso', 'QL04p040276' => 'qlo', 'QL06p005458' => 'qlo', 'QL06p005472' => 'qlo', 'QL07p030546' => 'qlo', 'QL07p031519' => 'qlo', 'QL09p050949' => 'qlo', 'QL09p050966' => 'qlo', 'QL09p051067' => 'qlo', 'QL12p022706' => 'qlo', 'RcHm_v2.0_Chr2g0119601' => 'rch', 'RcHm_v2.0_Chr3g0459591' => 'rch', 'RcHm_v2.0_Chr4g0418521' => 'rch', 'RcHm_v2.0_Chr4g0418531' => 'rch', 'RcHm_v2.0_Chr4g0418541' => 'rch', 'RcHm_v2.0_Chr6g0291641' => 'rch', 'Rhsim01G0086300' => 'rsi', 'Rhsim01G0276300' => 'rsi', 'Rhsim01G0276500' => 'rsi', 'Rhsim04G0207700' => 'rsi', 'Rhsim05G0234500' => 'rsi', 'Rhsim13G0022400' => 'rsi', 'Sabra02G0167900' => 'sbr', 'Sabra04G0158500' => 'sbr', 'Sabra08G0159800' => 'sbr', 'Sabra10G0011500' => 'sbr', 'Sabra14G0104400' => 'sbr', 'SalBow2G2440' => 'sbo', 'SalBow4G2265' => 'sbo', 'Sc02g0000060' => 'sci', 'Sc05g0005020' => 'sci', 'Sc13g0003890' => 'sci', 'Sed0014865' => 'sed', 'Sed0017224' => 'sed', 'Sed0026391' => 'sed', 'SEGI_00063' => 'sgi', 'SEGI_10967' => 'sgi', 'SEGI_17510' => 'sgi', 'SEGI_24396' => 'sgi', 'SEGI_39719' => 'sgi', 'SEGI_41392' => 'sgi', 'SGA_v2.0_scaffold11G05794' => 'sas', 'SGA_v2.0_scaffold142G35607' => 'sas', 'SGA_v2.0_scaffold1G00447' => 'sas', 'SHI15388' => 'shi', 'SHI15394' => 'shi', 'SHI15396' => 'shi', 'SHI15399' => 'shi', 'SMO343G0151' => 'smo', 'SMO367G1118' => 'smo', 'Solyc01g080200.3' => 'sly', 'Solyc06g008960.3' => 'sly', 'Solyc09g064780.3' => 'sly', 'Sopen01g031980' => 'spe', 'Sopen06g003710' => 'spe', 'Sopen09g026460' => 'spe', 'Sp3g21240' => 'spa', 'Sp4g30030' => 'spa', 'TAR365G0022' => 'tar', 'TAR365G1023' => 'tar', 'TAR365G1253' => 'tar', 'TAR623G0078' => 'tar', 'TAR623G1721' => 'tar', 'TAR633G0959' => 'tar', 'THA.LOC104802225' => 'tha', 'THA.LOC104804769' => 'tha', 'THA.LOC104808660' => 'tha', 'THA.LOC104812792' => 'tha', 'Thecc.01G284000' => 'tca', 'Thecc.04G220600' => 'tca', 'Thecc.05G268900' => 'tca', 'Thecc.08G171100' => 'tca', 'Thhalv10001284m.g' => 'esa', 'Thhalv10019912m.g' => 'esa', 'TPR.G14189' => 'tpr', 'TPR.G18110' => 'tpr', 'TPR.G18130' => 'tpr', 'TPR.G18131' => 'tpr', 'TPR.G18140' => 'tpr', 'TPR.G24282' => 'tpr', 'TPR.G25221' => 'tpr', 'TPR.G29267' => 'tpr', 'TPR.G35315' => 'tpr', 'TPR.G36173' => 'tpr', 'TWI09G0794' => 'twi', 'TWI59G1348' => 'twi', 'TWI74G0430' => 'twi', 'unitig_26.g8940' => 'ugi', 'unitig_749.g13744' => 'ugi', 'unitig_749.g13745' => 'ugi', 'vmacro08269' => 'vma', 'vmacro14937' => 'vma', 'vmacro20401' => 'vma', 'VMungo0464G1349' => 'vmu', 'VMungo0540G0289' => 'vmu', 'VMungo1215G1590' => 'vmu', 'VMungo1309G0221' => 'vmu', 'VMungo1309G2815' => 'vmu', 'VMungo1383G0239' => 'vmu', 'VMungo1383G2910' => 'vmu', 'Zm00001eb095270' => 'zma', 'Zm00001eb095280' => 'zma', 'Zm00001eb111630' => 'zma', 'Zm00001eb237080' => 'zma', 'Zm00001eb273740' => 'zma', 'Zm00001eb285040' => 'zma', 'Zm00001eb330790' => 'zma', 'Zm00001eb337380' => 'zma' ) $gf_id = 'HOM05D001484' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001484' ) $data_identifier = 'HOM05D001484' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 2, 'aly' => (int) 2, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 22, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 7, 'hma' => (int) 2, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 7, 'mtr' => (int) 10, 'cme' => (int) 2, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 4, 'ppa' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 4, 'qlo' => (int) 9, 'rch' => (int) 6, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 10, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 7, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb337380' $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' => 'HOM05D001484', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p31500' => 'bna', 'A05p00020' => 'bna', 'A07p08820' => 'bna', 'Aa31LG4G3300' => 'aar', 'Aa31LG8G10030' => 'aar', 'Actinidia00731' => 'ach', 'Actinidia11473' => 'ach', 'Actinidia23469' => 'ach', 'Actinidia24318' => 'ach', 'Actinidia40196' => 'ach', 'Actinidia40197' => 'ach', 'Actinidia40198' => 'ach', 'Ah.08g212990' => 'amhyb', 'Ah.15g091720' => 'amhyb', 'AL3G38260' => 'aly', 'AL4G47710' => 'aly', 'Aqoxy2G00671' => 'aox', 'Aqoxy2G03236' => 'aox', 'arahy.Tifrunner.gnm1.ann1.05IDCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KR684' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATY3SJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK6QJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6APGL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IDT7Z9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM073U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ0R87' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LE7RV4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT4QRX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V5ENPK' => 'arhy', 'AT2G48110' => 'ath', 'AT3G23590' => 'ath', 'ATR0626G186' => 'atr', 'ATR1127G141' => 'atr', 'Atru.chr4.2583' => 'acertr', 'Atru.chr5.1358' => 'acertr', 'Atru.chr5.1359' => 'acertr', 'Atru.chr8.46' => 'acertr', 'AUR62002640' => 'cqu', 'AUR62030055' => 'cqu', 'AUR62033713' => 'cqu', 'AUR62033714' => 'cqu', 'AUR62036795' => 'cqu', 'AUR62039891' => 'cqu', 'BcaB02g08737' => 'bca', 'BcaB04g20441' => 'bca', 'BcaB06g26509' => 'bca', 'BcaB06g26510' => 'bca', 'BcaB06g26511' => 'bca', 'BcaB06g26512' => 'bca', 'BcaB06g26513' => 'bca', 'BcaC02g12564' => 'bca', 'BcaC02g12565' => 'bca', 'BcaC02g12794' => 'bca', 'BcaC02g12795' => 'bca', 'BcaC02g12796' => 'bca', 'BcaC06g35541' => 'bca', 'BNapus_Darmor_BZH_scaffold_188p00080' => 'bna', 'BNapus_Darmor_BZH_scaffold_188p00090' => 'bna', 'BolC1t03972H' => 'bol', 'BolC1t03973H' => 'bol', 'BolC4t21680H' => 'bol', 'BolC7t41863H' => 'bol', 'BolSC55t61227H' => 'bol', 'BolSC55t61228H' => 'bol', 'BraA01t03278Z' => 'bra', 'BraA05t18998Z' => 'bra', 'BraA07t28673Z' => 'bra', 'C01p40150' => 'bna', 'C05p12370' => 'bna', 'C07p13680' => 'bna', 'CAN.G1006.16' => 'can', 'CAN.G1006.17' => 'can', 'CAN.G1170.2' => 'can', 'CAN.G962.7' => 'can', 'CANSAT25G2179' => 'cansat', 'CANSAT78G1573' => 'cansat', 'CARHR099510' => 'chi', 'CARHR143510' => 'chi', 'Carub.0003s2380' => 'cru', 'Carub.0004s3082' => 'cru', 'Ca_00614_v3' => 'car', 'Ca_07801_v3' => 'car', 'Ca_08567_v3' => 'car', 'Ca_09571_v3' => 'car', 'CBR_g19290' => 'cbr', 'Cc01_g19770' => 'ccan', 'Cc03_g03030' => 'ccan', 'CDE07G0968' => 'cde', 'CDE09G1441' => 'cde', 'Cfa006103' => 'cfa', 'Cfa015573' => 'cfa', 'Cfa016988' => 'cfa', 'Ciclev10006738m.g' => 'ccl', 'Ciclev10010920m.g' => 'ccl', 'Ciclev10018517m.g' => 'ccl', 'CiPaw.01G159200' => 'cil', 'CiPaw.02G091000' => 'cil', 'CiPaw.02G091100' => 'cil', 'CiPaw.08G103100' => 'cil', 'CiPaw.09G224900' => 'cil', 'ClCG06G005740' => 'cla', 'ClCG07G000090' => 'cla', 'ClCG07G000100' => 'cla', 'COL.COLO4_09143' => 'col', 'COL.COLO4_25124' => 'col', 'Cpa.g.sc16.34' => 'cpa', 'Cpa.g.sc3504.1' => 'cpa', 'Cpa.g.sc60.37' => 'cpa', 'CsaV3_6G018520' => 'csa', 'CsaV3_6G036860' => 'csa', 'CSS0001072' => 'camsi', 'CSS0020208' => 'camsi', 'CSS0021253' => 'camsi', 'CSS0022190' => 'camsi', 'CSS0036150' => 'camsi', 'CSS0040442' => 'camsi', 'CSS0042300' => 'camsi', 'CSS0045298' => 'camsi', 'DCAR_012449' => 'dca', 'DCAR_018405' => 'dca', 'DCAR_024573' => 'dca', 'DCAR_030591' => 'dca', 'Dinv16926' => 'din', 'Dinv32963' => 'din', 'Dinv38382' => 'din', 'Dinv38383' => 'din', 'Duzib133G0974' => 'dzi', 'Duzib138G1867' => 'dzi', 'Duzib211G0420' => 'dzi', 'Duzib212G0930' => 'dzi', 'ECA234G1645' => 'eca', 'ECA247G3467' => 'eca', 'ECA248G1703' => 'eca', 'EL10Ac3g06327' => 'bvu', 'EL10Ac7g17204' => 'bvu', 'Eucgr.A00855' => 'egr', 'Eucgr.A00858' => 'egr', 'Eucgr.H01520' => 'egr', 'Eucgr.H03604' => 'egr', 'Eucgr.L03465' => 'egr', 'Eucgr.L03466' => 'egr', 'FAN01G0988' => 'fan', 'FAN02G3892' => 'fan', 'FAN05G3381' => 'fan', 'FAN07G0967' => 'fan', 'FAN07G1493' => 'fan', 'FAN08G3125' => 'fan', 'FAN09G0402' => 'fan', 'FAN12G2594' => 'fan', 'FAN12G3879' => 'fan', 'FAN14G1546' => 'fan', 'FAN15G3626' => 'fan', 'FAN17G0588' => 'fan', 'FAN17G0609' => 'fan', 'FAN18G2817' => 'fan', 'FAN19G1305' => 'fan', 'FAN20G1787' => 'fan', 'FAN22G0073' => 'fan', 'FAN22G0352' => 'fan', 'FAN22G0368' => 'fan', 'FAN22G2273' => 'fan', 'FAN24G1998' => 'fan', 'FAN27G1317' => 'fan', 'FvH4_2g23980' => 'fve', 'FvH4_4g14380' => 'fve', 'FvH4_4g14390' => 'fve', 'FvH4_6g09250' => 'fve', 'Glyma.03G151100' => 'gma', 'Glyma.04G122550' => 'gma', 'Glyma.05G001600' => 'gma', 'Glyma.09G270766' => 'gma', 'Glyma.09G270832' => 'gma', 'Glyma.13G209800' => 'gma', 'Glyma.15G102800' => 'gma', 'Glyma.18G218900' => 'gma', 'Glyma.19G001500' => 'gma', 'Glyma.19G153600' => 'gma', 'Gohir.A02G028600' => 'ghi', 'Gohir.A08G045000' => 'ghi', 'Gohir.A11G120500' => 'ghi', 'Gohir.A12G006200' => 'ghi', 'Gohir.A12G006250' => 'ghi', 'Gohir.D02G036300' => 'ghi', 'Gohir.D08G054700' => 'ghi', 'Gohir.D11G125600' => 'ghi', 'Gohir.D12G005700' => 'ghi', 'Gorai.004G055200' => 'gra', 'Gorai.005G040400' => 'gra', 'Gorai.007G134500' => 'gra', 'Gorai.008G005500' => 'gra', 'GSVIVG01011094001' => 'vvi', 'GSVIVG01017879001' => 'vvi', 'GSVIVG01025988001' => 'vvi', 'GSVIVG01029847001' => 'vvi', 'HanXRQChr10g0282901' => 'han', 'HanXRQChr10g0310371' => 'han', 'HanXRQChr10g0315041' => 'han', 'HanXRQChr11g0327651' => 'han', 'HanXRQChr12g0359391' => 'han', 'Haze_00972' => 'cav', 'Haze_00973' => 'cav', 'Haze_00974' => 'cav', 'Haze_04747' => 'cav', 'Haze_04749' => 'cav', 'Haze_04750' => 'cav', 'Haze_21217' => 'cav', 'Hma1.2p1_1037F.1_g250680' => 'hma', 'Hma1.2p1_1644F.1_g295320' => 'hma', 'HPP92_011322' => 'vpl', 'HPP92_011323' => 'vpl', 'HPP92_011324' => 'vpl', 'HPP92_011325' => 'vpl', 'HPP92_011326' => 'vpl', 'Hund12205' => 'sun', 'Hund17957' => 'sun', 'Lalb_Chr06g0176771' => 'lal', 'Lalb_Chr18g0056021' => 'lal', 'Lalb_Chr18g0056031' => 'lal', 'Lalb_Chr18g0056041' => 'lal', 'Lalb_Chr20g0107751' => 'lal', 'Lalb_Chr20g0118371' => 'lal', 'Lj1g0010239' => 'lja', 'Lj1g0017101' => 'lja', 'Lj2A1178G40' => 'lonja', 'Lj2A54G84' => 'lonja', 'Lj2g0015248' => 'lja', 'Lj3A761T51' => 'lonja', 'Lj6g0018116' => 'lja', 'Lsat_1_v5_gn_4_136040' => 'lsa', 'Lsat_1_v5_gn_5_187461' => 'lsa', 'Lsat_1_v5_gn_5_77001' => 'lsa', 'Lsat_1_v5_gn_9_4461' => 'lsa', 'Manes.01G210100' => 'mes', 'Manes.03G185600' => 'mes', 'Manes.05G073300' => 'mes', 'Manes.09G120300' => 'mes', 'Manes.15G022100' => 'mes', 'Mapoly0096s0053' => 'mpo', 'MBI03_g14058_MAGBIO' => 'mbi', 'MBI03_g33876_MAGBIO' => 'mbi', 'MBI03_g36854_MAGBIO' => 'mbi', 'MBI17_g11997_MAGBIO' => 'mbi', 'MD03G1269000' => 'mdo', 'MD04G1179600' => 'mdo', 'MD11G1289800' => 'mdo', 'MD12G1194700' => 'mdo', 'MD13G1182100' => 'mdo', 'MD13G1182200' => 'mdo', 'MD16G1182600' => 'mdo', 'Medtr2g021400' => 'mtr', 'Medtr2g021470' => 'mtr', 'Medtr2g105810' => 'mtr', 'Medtr3g033580' => 'mtr', 'Medtr6g007970' => 'mtr', 'Medtr7g056330' => 'mtr', 'Medtr7g074290' => 'mtr', 'Medtr7g074380' => 'mtr', 'Medtr7g094550' => 'mtr', 'Medtr8g069995' => 'mtr', 'MELO3C014345.2' => 'cme', 'MELO3C021395.2' => 'cme', 'Migut.D00262' => 'egut', 'Migut.G00257' => 'egut', 'MSTRG.21575' => 'ama', 'MSTRG.3985' => 'ama', 'Nitab4.5_0000295g0140' => 'nta', 'Nitab4.5_0000732g0140' => 'nta', 'Nitab4.5_0003162g0020' => 'nta', 'Nitab4.5_0006180g0090' => 'nta', 'Nitab4.5_0006390g0010' => 'nta', 'Nitab4.5_0007392g0040' => 'nta', 'Nn1g02140' => 'nnu', 'Nn4g26168' => 'nnu', 'Nn5g26754' => 'nnu', 'Oeu001433.1' => 'oeu', 'Oeu010299.2' => 'oeu', 'Oeu011171.1' => 'oeu', 'Oeu037675.1' => 'oeu', 'Oeu038359.1' => 'oeu', 'Oeu063834.1' => 'oeu', 'Oeu063835.1' => 'oeu', 'Os05g0312000' => 'osa', 'Os07g0211101' => 'osa', 'Os07g0211200' => 'osa', 'Os07g0681500' => 'osa', 'Peaxi162Scf00095g01015' => 'pax', 'Peaxi162Scf00104g00329' => 'pax', 'Peaxi162Scf00161g00137' => 'pax', 'PGR004G1665' => 'pgr', 'PGR031G2937' => 'pgr', 'PGR119G2145' => 'pgr', 'PGSC0003DMG400004351' => 'stu', 'PGSC0003DMG400014625' => 'stu', 'PGSC0003DMG401000943' => 'stu', 'Phvul.001G148600' => 'pvu', 'Phvul.004G001700' => 'pvu', 'Phvul.006G154900' => 'pvu', 'Phvul.008G078200' => 'pvu', 'Phvul.011G136500' => 'pvu', 'Potri.002G215600' => 'ptr', 'Potri.008G201600' => 'ptr', 'Potri.014G138400' => 'ptr', 'Potri.016G142500' => 'ptr', 'Pp3c16_10580' => 'ppa', 'Pp3c5_25280' => 'ppa', 'Prupe.1G150000' => 'ppe', 'Prupe.1G150100' => 'ppe', 'Prupe.6G299600' => 'ppe', 'Prupe.8G245000' => 'ppe', 'Psat0s4927g0040' => 'psa', 'Psat1g052080' => 'psa', 'Psat1g183800' => 'psa', 'Psat3g113840' => 'psa', 'Psat3g126120' => 'psa', 'Psat3g126160' => 'psa', 'Psat3g158760' => 'psa', 'Psat3g158840' => 'psa', 'PSO170G2858' => 'pso', 'PSO339G0606' => 'pso', 'PSO384G4709' => 'pso', 'PSO407G0334' => 'pso', 'QL04p040276' => 'qlo', 'QL06p005458' => 'qlo', 'QL06p005472' => 'qlo', 'QL07p030546' => 'qlo', 'QL07p031519' => 'qlo', 'QL09p050949' => 'qlo', 'QL09p050966' => 'qlo', 'QL09p051067' => 'qlo', 'QL12p022706' => 'qlo', 'RcHm_v2.0_Chr2g0119601' => 'rch', 'RcHm_v2.0_Chr3g0459591' => 'rch', 'RcHm_v2.0_Chr4g0418521' => 'rch', 'RcHm_v2.0_Chr4g0418531' => 'rch', 'RcHm_v2.0_Chr4g0418541' => 'rch', 'RcHm_v2.0_Chr6g0291641' => 'rch', 'Rhsim01G0086300' => 'rsi', 'Rhsim01G0276300' => 'rsi', 'Rhsim01G0276500' => 'rsi', 'Rhsim04G0207700' => 'rsi', 'Rhsim05G0234500' => 'rsi', 'Rhsim13G0022400' => 'rsi', 'Sabra02G0167900' => 'sbr', 'Sabra04G0158500' => 'sbr', 'Sabra08G0159800' => 'sbr', 'Sabra10G0011500' => 'sbr', 'Sabra14G0104400' => 'sbr', 'SalBow2G2440' => 'sbo', 'SalBow4G2265' => 'sbo', 'Sc02g0000060' => 'sci', 'Sc05g0005020' => 'sci', 'Sc13g0003890' => 'sci', 'Sed0014865' => 'sed', 'Sed0017224' => 'sed', 'Sed0026391' => 'sed', 'SEGI_00063' => 'sgi', 'SEGI_10967' => 'sgi', 'SEGI_17510' => 'sgi', 'SEGI_24396' => 'sgi', 'SEGI_39719' => 'sgi', 'SEGI_41392' => 'sgi', 'SGA_v2.0_scaffold11G05794' => 'sas', 'SGA_v2.0_scaffold142G35607' => 'sas', 'SGA_v2.0_scaffold1G00447' => 'sas', 'SHI15388' => 'shi', 'SHI15394' => 'shi', 'SHI15396' => 'shi', 'SHI15399' => 'shi', 'SMO343G0151' => 'smo', 'SMO367G1118' => 'smo', 'Solyc01g080200.3' => 'sly', 'Solyc06g008960.3' => 'sly', 'Solyc09g064780.3' => 'sly', 'Sopen01g031980' => 'spe', 'Sopen06g003710' => 'spe', 'Sopen09g026460' => 'spe', 'Sp3g21240' => 'spa', 'Sp4g30030' => 'spa', 'TAR365G0022' => 'tar', 'TAR365G1023' => 'tar', 'TAR365G1253' => 'tar', 'TAR623G0078' => 'tar', 'TAR623G1721' => 'tar', 'TAR633G0959' => 'tar', 'THA.LOC104802225' => 'tha', 'THA.LOC104804769' => 'tha', 'THA.LOC104808660' => 'tha', 'THA.LOC104812792' => 'tha', 'Thecc.01G284000' => 'tca', 'Thecc.04G220600' => 'tca', 'Thecc.05G268900' => 'tca', 'Thecc.08G171100' => 'tca', 'Thhalv10001284m.g' => 'esa', 'Thhalv10019912m.g' => 'esa', 'TPR.G14189' => 'tpr', 'TPR.G18110' => 'tpr', 'TPR.G18130' => 'tpr', 'TPR.G18131' => 'tpr', 'TPR.G18140' => 'tpr', 'TPR.G24282' => 'tpr', 'TPR.G25221' => 'tpr', 'TPR.G29267' => 'tpr', 'TPR.G35315' => 'tpr', 'TPR.G36173' => 'tpr', 'TWI09G0794' => 'twi', 'TWI59G1348' => 'twi', 'TWI74G0430' => 'twi', 'unitig_26.g8940' => 'ugi', 'unitig_749.g13744' => 'ugi', 'unitig_749.g13745' => 'ugi', 'vmacro08269' => 'vma', 'vmacro14937' => 'vma', 'vmacro20401' => 'vma', 'VMungo0464G1349' => 'vmu', 'VMungo0540G0289' => 'vmu', 'VMungo1215G1590' => 'vmu', 'VMungo1309G0221' => 'vmu', 'VMungo1309G2815' => 'vmu', 'VMungo1383G0239' => 'vmu', 'VMungo1383G2910' => 'vmu', 'Zm00001eb095270' => 'zma', 'Zm00001eb095280' => 'zma', 'Zm00001eb111630' => 'zma', 'Zm00001eb237080' => 'zma', 'Zm00001eb273740' => 'zma', 'Zm00001eb285040' => 'zma', 'Zm00001eb330790' => 'zma', 'Zm00001eb337380' => 'zma' ), 'gf_id' => 'HOM05D001484', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001484' ), 'data_identifier' => 'HOM05D001484', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001484', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p31500' => 'bna', 'A05p00020' => 'bna', 'A07p08820' => 'bna', 'Aa31LG4G3300' => 'aar', 'Aa31LG8G10030' => 'aar', 'Actinidia00731' => 'ach', 'Actinidia11473' => 'ach', 'Actinidia23469' => 'ach', 'Actinidia24318' => 'ach', 'Actinidia40196' => 'ach', 'Actinidia40197' => 'ach', 'Actinidia40198' => 'ach', 'Ah.08g212990' => 'amhyb', 'Ah.15g091720' => 'amhyb', 'AL3G38260' => 'aly', 'AL4G47710' => 'aly', 'Aqoxy2G00671' => 'aox', 'Aqoxy2G03236' => 'aox', 'arahy.Tifrunner.gnm1.ann1.05IDCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KR684' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATY3SJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK6QJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6APGL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IDT7Z9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM073U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ0R87' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LE7RV4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT4QRX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V5ENPK' => 'arhy', 'AT2G48110' => 'ath', 'AT3G23590' => 'ath', 'ATR0626G186' => 'atr', 'ATR1127G141' => 'atr', 'Atru.chr4.2583' => 'acertr', 'Atru.chr5.1358' => 'acertr', 'Atru.chr5.1359' => 'acertr', 'Atru.chr8.46' => 'acertr', 'AUR62002640' => 'cqu', 'AUR62030055' => 'cqu', 'AUR62033713' => 'cqu', 'AUR62033714' => 'cqu', 'AUR62036795' => 'cqu', 'AUR62039891' => 'cqu', 'BcaB02g08737' => 'bca', 'BcaB04g20441' => 'bca', 'BcaB06g26509' => 'bca', 'BcaB06g26510' => 'bca', 'BcaB06g26511' => 'bca', 'BcaB06g26512' => 'bca', 'BcaB06g26513' => 'bca', 'BcaC02g12564' => 'bca', 'BcaC02g12565' => 'bca', 'BcaC02g12794' => 'bca', 'BcaC02g12795' => 'bca', 'BcaC02g12796' => 'bca', 'BcaC06g35541' => 'bca', 'BNapus_Darmor_BZH_scaffold_188p00080' => 'bna', 'BNapus_Darmor_BZH_scaffold_188p00090' => 'bna', 'BolC1t03972H' => 'bol', 'BolC1t03973H' => 'bol', 'BolC4t21680H' => 'bol', 'BolC7t41863H' => 'bol', 'BolSC55t61227H' => 'bol', 'BolSC55t61228H' => 'bol', 'BraA01t03278Z' => 'bra', 'BraA05t18998Z' => 'bra', 'BraA07t28673Z' => 'bra', 'C01p40150' => 'bna', 'C05p12370' => 'bna', 'C07p13680' => 'bna', 'CAN.G1006.16' => 'can', 'CAN.G1006.17' => 'can', 'CAN.G1170.2' => 'can', 'CAN.G962.7' => 'can', 'CANSAT25G2179' => 'cansat', 'CANSAT78G1573' => 'cansat', 'CARHR099510' => 'chi', 'CARHR143510' => 'chi', 'Carub.0003s2380' => 'cru', 'Carub.0004s3082' => 'cru', 'Ca_00614_v3' => 'car', 'Ca_07801_v3' => 'car', 'Ca_08567_v3' => 'car', 'Ca_09571_v3' => 'car', 'CBR_g19290' => 'cbr', 'Cc01_g19770' => 'ccan', 'Cc03_g03030' => 'ccan', 'CDE07G0968' => 'cde', 'CDE09G1441' => 'cde', 'Cfa006103' => 'cfa', 'Cfa015573' => 'cfa', 'Cfa016988' => 'cfa', 'Ciclev10006738m.g' => 'ccl', 'Ciclev10010920m.g' => 'ccl', 'Ciclev10018517m.g' => 'ccl', 'CiPaw.01G159200' => 'cil', 'CiPaw.02G091000' => 'cil', 'CiPaw.02G091100' => 'cil', 'CiPaw.08G103100' => 'cil', 'CiPaw.09G224900' => 'cil', 'ClCG06G005740' => 'cla', 'ClCG07G000090' => 'cla', 'ClCG07G000100' => 'cla', 'COL.COLO4_09143' => 'col', 'COL.COLO4_25124' => 'col', 'Cpa.g.sc16.34' => 'cpa', 'Cpa.g.sc3504.1' => 'cpa', 'Cpa.g.sc60.37' => 'cpa', 'CsaV3_6G018520' => 'csa', 'CsaV3_6G036860' => 'csa', 'CSS0001072' => 'camsi', 'CSS0020208' => 'camsi', 'CSS0021253' => 'camsi', 'CSS0022190' => 'camsi', 'CSS0036150' => 'camsi', 'CSS0040442' => 'camsi', 'CSS0042300' => 'camsi', 'CSS0045298' => 'camsi', 'DCAR_012449' => 'dca', 'DCAR_018405' => 'dca', 'DCAR_024573' => 'dca', 'DCAR_030591' => 'dca', 'Dinv16926' => 'din', 'Dinv32963' => 'din', 'Dinv38382' => 'din', 'Dinv38383' => 'din', 'Duzib133G0974' => 'dzi', 'Duzib138G1867' => 'dzi', 'Duzib211G0420' => 'dzi', 'Duzib212G0930' => 'dzi', 'ECA234G1645' => 'eca', 'ECA247G3467' => 'eca', 'ECA248G1703' => 'eca', 'EL10Ac3g06327' => 'bvu', 'EL10Ac7g17204' => 'bvu', 'Eucgr.A00855' => 'egr', 'Eucgr.A00858' => 'egr', 'Eucgr.H01520' => 'egr', 'Eucgr.H03604' => 'egr', 'Eucgr.L03465' => 'egr', 'Eucgr.L03466' => 'egr', 'FAN01G0988' => 'fan', 'FAN02G3892' => 'fan', 'FAN05G3381' => 'fan', 'FAN07G0967' => 'fan', 'FAN07G1493' => 'fan', 'FAN08G3125' => 'fan', 'FAN09G0402' => 'fan', 'FAN12G2594' => 'fan', 'FAN12G3879' => 'fan', 'FAN14G1546' => 'fan', 'FAN15G3626' => 'fan', 'FAN17G0588' => 'fan', 'FAN17G0609' => 'fan', 'FAN18G2817' => 'fan', 'FAN19G1305' => 'fan', 'FAN20G1787' => 'fan', 'FAN22G0073' => 'fan', 'FAN22G0352' => 'fan', 'FAN22G0368' => 'fan', 'FAN22G2273' => 'fan', 'FAN24G1998' => 'fan', 'FAN27G1317' => 'fan', 'FvH4_2g23980' => 'fve', 'FvH4_4g14380' => 'fve', 'FvH4_4g14390' => 'fve', 'FvH4_6g09250' => 'fve', 'Glyma.03G151100' => 'gma', 'Glyma.04G122550' => 'gma', 'Glyma.05G001600' => 'gma', 'Glyma.09G270766' => 'gma', 'Glyma.09G270832' => 'gma', 'Glyma.13G209800' => 'gma', 'Glyma.15G102800' => 'gma', 'Glyma.18G218900' => 'gma', 'Glyma.19G001500' => 'gma', 'Glyma.19G153600' => 'gma', 'Gohir.A02G028600' => 'ghi', 'Gohir.A08G045000' => 'ghi', 'Gohir.A11G120500' => 'ghi', 'Gohir.A12G006200' => 'ghi', 'Gohir.A12G006250' => 'ghi', 'Gohir.D02G036300' => 'ghi', 'Gohir.D08G054700' => 'ghi', 'Gohir.D11G125600' => 'ghi', 'Gohir.D12G005700' => 'ghi', 'Gorai.004G055200' => 'gra', 'Gorai.005G040400' => 'gra', 'Gorai.007G134500' => 'gra', 'Gorai.008G005500' => 'gra', 'GSVIVG01011094001' => 'vvi', 'GSVIVG01017879001' => 'vvi', 'GSVIVG01025988001' => 'vvi', 'GSVIVG01029847001' => 'vvi', 'HanXRQChr10g0282901' => 'han', 'HanXRQChr10g0310371' => 'han', 'HanXRQChr10g0315041' => 'han', 'HanXRQChr11g0327651' => 'han', 'HanXRQChr12g0359391' => 'han', 'Haze_00972' => 'cav', 'Haze_00973' => 'cav', 'Haze_00974' => 'cav', 'Haze_04747' => 'cav', 'Haze_04749' => 'cav', 'Haze_04750' => 'cav', 'Haze_21217' => 'cav', 'Hma1.2p1_1037F.1_g250680' => 'hma', 'Hma1.2p1_1644F.1_g295320' => 'hma', 'HPP92_011322' => 'vpl', 'HPP92_011323' => 'vpl', 'HPP92_011324' => 'vpl', 'HPP92_011325' => 'vpl', 'HPP92_011326' => 'vpl', 'Hund12205' => 'sun', 'Hund17957' => 'sun', 'Lalb_Chr06g0176771' => 'lal', 'Lalb_Chr18g0056021' => 'lal', 'Lalb_Chr18g0056031' => 'lal', 'Lalb_Chr18g0056041' => 'lal', 'Lalb_Chr20g0107751' => 'lal', 'Lalb_Chr20g0118371' => 'lal', 'Lj1g0010239' => 'lja', 'Lj1g0017101' => 'lja', 'Lj2A1178G40' => 'lonja', 'Lj2A54G84' => 'lonja', 'Lj2g0015248' => 'lja', 'Lj3A761T51' => 'lonja', 'Lj6g0018116' => 'lja', 'Lsat_1_v5_gn_4_136040' => 'lsa', 'Lsat_1_v5_gn_5_187461' => 'lsa', 'Lsat_1_v5_gn_5_77001' => 'lsa', 'Lsat_1_v5_gn_9_4461' => 'lsa', 'Manes.01G210100' => 'mes', 'Manes.03G185600' => 'mes', 'Manes.05G073300' => 'mes', 'Manes.09G120300' => 'mes', 'Manes.15G022100' => 'mes', 'Mapoly0096s0053' => 'mpo', 'MBI03_g14058_MAGBIO' => 'mbi', 'MBI03_g33876_MAGBIO' => 'mbi', 'MBI03_g36854_MAGBIO' => 'mbi', 'MBI17_g11997_MAGBIO' => 'mbi', 'MD03G1269000' => 'mdo', 'MD04G1179600' => 'mdo', 'MD11G1289800' => 'mdo', 'MD12G1194700' => 'mdo', 'MD13G1182100' => 'mdo', 'MD13G1182200' => 'mdo', 'MD16G1182600' => 'mdo', 'Medtr2g021400' => 'mtr', 'Medtr2g021470' => 'mtr', 'Medtr2g105810' => 'mtr', 'Medtr3g033580' => 'mtr', 'Medtr6g007970' => 'mtr', 'Medtr7g056330' => 'mtr', 'Medtr7g074290' => 'mtr', 'Medtr7g074380' => 'mtr', 'Medtr7g094550' => 'mtr', 'Medtr8g069995' => 'mtr', 'MELO3C014345.2' => 'cme', 'MELO3C021395.2' => 'cme', 'Migut.D00262' => 'egut', 'Migut.G00257' => 'egut', 'MSTRG.21575' => 'ama', 'MSTRG.3985' => 'ama', 'Nitab4.5_0000295g0140' => 'nta', 'Nitab4.5_0000732g0140' => 'nta', 'Nitab4.5_0003162g0020' => 'nta', 'Nitab4.5_0006180g0090' => 'nta', 'Nitab4.5_0006390g0010' => 'nta', 'Nitab4.5_0007392g0040' => 'nta', 'Nn1g02140' => 'nnu', 'Nn4g26168' => 'nnu', 'Nn5g26754' => 'nnu', 'Oeu001433.1' => 'oeu', 'Oeu010299.2' => 'oeu', 'Oeu011171.1' => 'oeu', 'Oeu037675.1' => 'oeu', 'Oeu038359.1' => 'oeu', 'Oeu063834.1' => 'oeu', 'Oeu063835.1' => 'oeu', 'Os05g0312000' => 'osa', 'Os07g0211101' => 'osa', 'Os07g0211200' => 'osa', 'Os07g0681500' => 'osa', 'Peaxi162Scf00095g01015' => 'pax', 'Peaxi162Scf00104g00329' => 'pax', 'Peaxi162Scf00161g00137' => 'pax', 'PGR004G1665' => 'pgr', 'PGR031G2937' => 'pgr', 'PGR119G2145' => 'pgr', 'PGSC0003DMG400004351' => 'stu', 'PGSC0003DMG400014625' => 'stu', 'PGSC0003DMG401000943' => 'stu', 'Phvul.001G148600' => 'pvu', 'Phvul.004G001700' => 'pvu', 'Phvul.006G154900' => 'pvu', 'Phvul.008G078200' => 'pvu', 'Phvul.011G136500' => 'pvu', 'Potri.002G215600' => 'ptr', 'Potri.008G201600' => 'ptr', 'Potri.014G138400' => 'ptr', 'Potri.016G142500' => 'ptr', 'Pp3c16_10580' => 'ppa', 'Pp3c5_25280' => 'ppa', 'Prupe.1G150000' => 'ppe', 'Prupe.1G150100' => 'ppe', 'Prupe.6G299600' => 'ppe', 'Prupe.8G245000' => 'ppe', 'Psat0s4927g0040' => 'psa', 'Psat1g052080' => 'psa', 'Psat1g183800' => 'psa', 'Psat3g113840' => 'psa', 'Psat3g126120' => 'psa', 'Psat3g126160' => 'psa', 'Psat3g158760' => 'psa', 'Psat3g158840' => 'psa', 'PSO170G2858' => 'pso', 'PSO339G0606' => 'pso', 'PSO384G4709' => 'pso', 'PSO407G0334' => 'pso', 'QL04p040276' => 'qlo', 'QL06p005458' => 'qlo', 'QL06p005472' => 'qlo', 'QL07p030546' => 'qlo', 'QL07p031519' => 'qlo', 'QL09p050949' => 'qlo', 'QL09p050966' => 'qlo', 'QL09p051067' => 'qlo', 'QL12p022706' => 'qlo', 'RcHm_v2.0_Chr2g0119601' => 'rch', 'RcHm_v2.0_Chr3g0459591' => 'rch', 'RcHm_v2.0_Chr4g0418521' => 'rch', 'RcHm_v2.0_Chr4g0418531' => 'rch', 'RcHm_v2.0_Chr4g0418541' => 'rch', 'RcHm_v2.0_Chr6g0291641' => 'rch', 'Rhsim01G0086300' => 'rsi', 'Rhsim01G0276300' => 'rsi', 'Rhsim01G0276500' => 'rsi', 'Rhsim04G0207700' => 'rsi', 'Rhsim05G0234500' => 'rsi', 'Rhsim13G0022400' => 'rsi', 'Sabra02G0167900' => 'sbr', 'Sabra04G0158500' => 'sbr', 'Sabra08G0159800' => 'sbr', 'Sabra10G0011500' => 'sbr', 'Sabra14G0104400' => 'sbr', 'SalBow2G2440' => 'sbo', 'SalBow4G2265' => 'sbo', 'Sc02g0000060' => 'sci', 'Sc05g0005020' => 'sci', 'Sc13g0003890' => 'sci', 'Sed0014865' => 'sed', 'Sed0017224' => 'sed', 'Sed0026391' => 'sed', 'SEGI_00063' => 'sgi', 'SEGI_10967' => 'sgi', 'SEGI_17510' => 'sgi', 'SEGI_24396' => 'sgi', 'SEGI_39719' => 'sgi', 'SEGI_41392' => 'sgi', 'SGA_v2.0_scaffold11G05794' => 'sas', 'SGA_v2.0_scaffold142G35607' => 'sas', 'SGA_v2.0_scaffold1G00447' => 'sas', 'SHI15388' => 'shi', 'SHI15394' => 'shi', 'SHI15396' => 'shi', 'SHI15399' => 'shi', 'SMO343G0151' => 'smo', 'SMO367G1118' => 'smo', 'Solyc01g080200.3' => 'sly', 'Solyc06g008960.3' => 'sly', 'Solyc09g064780.3' => 'sly', 'Sopen01g031980' => 'spe', 'Sopen06g003710' => 'spe', 'Sopen09g026460' => 'spe', 'Sp3g21240' => 'spa', 'Sp4g30030' => 'spa', 'TAR365G0022' => 'tar', 'TAR365G1023' => 'tar', 'TAR365G1253' => 'tar', 'TAR623G0078' => 'tar', 'TAR623G1721' => 'tar', 'TAR633G0959' => 'tar', 'THA.LOC104802225' => 'tha', 'THA.LOC104804769' => 'tha', 'THA.LOC104808660' => 'tha', 'THA.LOC104812792' => 'tha', 'Thecc.01G284000' => 'tca', 'Thecc.04G220600' => 'tca', 'Thecc.05G268900' => 'tca', 'Thecc.08G171100' => 'tca', 'Thhalv10001284m.g' => 'esa', 'Thhalv10019912m.g' => 'esa', 'TPR.G14189' => 'tpr', 'TPR.G18110' => 'tpr', 'TPR.G18130' => 'tpr', 'TPR.G18131' => 'tpr', 'TPR.G18140' => 'tpr', 'TPR.G24282' => 'tpr', 'TPR.G25221' => 'tpr', 'TPR.G29267' => 'tpr', 'TPR.G35315' => 'tpr', 'TPR.G36173' => 'tpr', 'TWI09G0794' => 'twi', 'TWI59G1348' => 'twi', 'TWI74G0430' => 'twi', 'unitig_26.g8940' => 'ugi', 'unitig_749.g13744' => 'ugi', 'unitig_749.g13745' => 'ugi', 'vmacro08269' => 'vma', 'vmacro14937' => 'vma', 'vmacro20401' => 'vma', 'VMungo0464G1349' => 'vmu', 'VMungo0540G0289' => 'vmu', 'VMungo1215G1590' => 'vmu', 'VMungo1309G0221' => 'vmu', 'VMungo1309G2815' => 'vmu', 'VMungo1383G0239' => 'vmu', 'VMungo1383G2910' => 'vmu', 'Zm00001eb095270' => 'zma', 'Zm00001eb095280' => 'zma', 'Zm00001eb111630' => 'zma', 'Zm00001eb237080' => 'zma', 'Zm00001eb273740' => 'zma', 'Zm00001eb285040' => 'zma', 'Zm00001eb330790' => 'zma', 'Zm00001eb337380' => 'zma' ) $gf_id = 'HOM05D001484' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001484' ) $data_identifier = 'HOM05D001484' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 2, 'aly' => (int) 2, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 22, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 7, 'hma' => (int) 2, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 7, 'mtr' => (int) 10, 'cme' => (int) 2, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 4, 'ppa' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 4, 'qlo' => (int) 9, 'rch' => (int) 6, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 10, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 7, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb337380' $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' => 'HOM05D001484', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p31500' => 'bna', 'A05p00020' => 'bna', 'A07p08820' => 'bna', 'Aa31LG4G3300' => 'aar', 'Aa31LG8G10030' => 'aar', 'Actinidia00731' => 'ach', 'Actinidia11473' => 'ach', 'Actinidia23469' => 'ach', 'Actinidia24318' => 'ach', 'Actinidia40196' => 'ach', 'Actinidia40197' => 'ach', 'Actinidia40198' => 'ach', 'Ah.08g212990' => 'amhyb', 'Ah.15g091720' => 'amhyb', 'AL3G38260' => 'aly', 'AL4G47710' => 'aly', 'Aqoxy2G00671' => 'aox', 'Aqoxy2G03236' => 'aox', 'arahy.Tifrunner.gnm1.ann1.05IDCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KR684' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATY3SJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK6QJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6APGL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IDT7Z9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM073U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ0R87' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LE7RV4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT4QRX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V5ENPK' => 'arhy', 'AT2G48110' => 'ath', 'AT3G23590' => 'ath', 'ATR0626G186' => 'atr', 'ATR1127G141' => 'atr', 'Atru.chr4.2583' => 'acertr', 'Atru.chr5.1358' => 'acertr', 'Atru.chr5.1359' => 'acertr', 'Atru.chr8.46' => 'acertr', 'AUR62002640' => 'cqu', 'AUR62030055' => 'cqu', 'AUR62033713' => 'cqu', 'AUR62033714' => 'cqu', 'AUR62036795' => 'cqu', 'AUR62039891' => 'cqu', 'BcaB02g08737' => 'bca', 'BcaB04g20441' => 'bca', 'BcaB06g26509' => 'bca', 'BcaB06g26510' => 'bca', 'BcaB06g26511' => 'bca', 'BcaB06g26512' => 'bca', 'BcaB06g26513' => 'bca', 'BcaC02g12564' => 'bca', 'BcaC02g12565' => 'bca', 'BcaC02g12794' => 'bca', 'BcaC02g12795' => 'bca', 'BcaC02g12796' => 'bca', 'BcaC06g35541' => 'bca', 'BNapus_Darmor_BZH_scaffold_188p00080' => 'bna', 'BNapus_Darmor_BZH_scaffold_188p00090' => 'bna', 'BolC1t03972H' => 'bol', 'BolC1t03973H' => 'bol', 'BolC4t21680H' => 'bol', 'BolC7t41863H' => 'bol', 'BolSC55t61227H' => 'bol', 'BolSC55t61228H' => 'bol', 'BraA01t03278Z' => 'bra', 'BraA05t18998Z' => 'bra', 'BraA07t28673Z' => 'bra', 'C01p40150' => 'bna', 'C05p12370' => 'bna', 'C07p13680' => 'bna', 'CAN.G1006.16' => 'can', 'CAN.G1006.17' => 'can', 'CAN.G1170.2' => 'can', 'CAN.G962.7' => 'can', 'CANSAT25G2179' => 'cansat', 'CANSAT78G1573' => 'cansat', 'CARHR099510' => 'chi', 'CARHR143510' => 'chi', 'Carub.0003s2380' => 'cru', 'Carub.0004s3082' => 'cru', 'Ca_00614_v3' => 'car', 'Ca_07801_v3' => 'car', 'Ca_08567_v3' => 'car', 'Ca_09571_v3' => 'car', 'CBR_g19290' => 'cbr', 'Cc01_g19770' => 'ccan', 'Cc03_g03030' => 'ccan', 'CDE07G0968' => 'cde', 'CDE09G1441' => 'cde', 'Cfa006103' => 'cfa', 'Cfa015573' => 'cfa', 'Cfa016988' => 'cfa', 'Ciclev10006738m.g' => 'ccl', 'Ciclev10010920m.g' => 'ccl', 'Ciclev10018517m.g' => 'ccl', 'CiPaw.01G159200' => 'cil', 'CiPaw.02G091000' => 'cil', 'CiPaw.02G091100' => 'cil', 'CiPaw.08G103100' => 'cil', 'CiPaw.09G224900' => 'cil', 'ClCG06G005740' => 'cla', 'ClCG07G000090' => 'cla', 'ClCG07G000100' => 'cla', 'COL.COLO4_09143' => 'col', 'COL.COLO4_25124' => 'col', 'Cpa.g.sc16.34' => 'cpa', 'Cpa.g.sc3504.1' => 'cpa', 'Cpa.g.sc60.37' => 'cpa', 'CsaV3_6G018520' => 'csa', 'CsaV3_6G036860' => 'csa', 'CSS0001072' => 'camsi', 'CSS0020208' => 'camsi', 'CSS0021253' => 'camsi', 'CSS0022190' => 'camsi', 'CSS0036150' => 'camsi', 'CSS0040442' => 'camsi', 'CSS0042300' => 'camsi', 'CSS0045298' => 'camsi', 'DCAR_012449' => 'dca', 'DCAR_018405' => 'dca', 'DCAR_024573' => 'dca', 'DCAR_030591' => 'dca', 'Dinv16926' => 'din', 'Dinv32963' => 'din', 'Dinv38382' => 'din', 'Dinv38383' => 'din', 'Duzib133G0974' => 'dzi', 'Duzib138G1867' => 'dzi', 'Duzib211G0420' => 'dzi', 'Duzib212G0930' => 'dzi', 'ECA234G1645' => 'eca', 'ECA247G3467' => 'eca', 'ECA248G1703' => 'eca', 'EL10Ac3g06327' => 'bvu', 'EL10Ac7g17204' => 'bvu', 'Eucgr.A00855' => 'egr', 'Eucgr.A00858' => 'egr', 'Eucgr.H01520' => 'egr', 'Eucgr.H03604' => 'egr', 'Eucgr.L03465' => 'egr', 'Eucgr.L03466' => 'egr', 'FAN01G0988' => 'fan', 'FAN02G3892' => 'fan', 'FAN05G3381' => 'fan', 'FAN07G0967' => 'fan', 'FAN07G1493' => 'fan', 'FAN08G3125' => 'fan', 'FAN09G0402' => 'fan', 'FAN12G2594' => 'fan', 'FAN12G3879' => 'fan', 'FAN14G1546' => 'fan', 'FAN15G3626' => 'fan', 'FAN17G0588' => 'fan', 'FAN17G0609' => 'fan', 'FAN18G2817' => 'fan', 'FAN19G1305' => 'fan', 'FAN20G1787' => 'fan', 'FAN22G0073' => 'fan', 'FAN22G0352' => 'fan', 'FAN22G0368' => 'fan', 'FAN22G2273' => 'fan', 'FAN24G1998' => 'fan', 'FAN27G1317' => 'fan', 'FvH4_2g23980' => 'fve', 'FvH4_4g14380' => 'fve', 'FvH4_4g14390' => 'fve', 'FvH4_6g09250' => 'fve', 'Glyma.03G151100' => 'gma', 'Glyma.04G122550' => 'gma', 'Glyma.05G001600' => 'gma', 'Glyma.09G270766' => 'gma', 'Glyma.09G270832' => 'gma', 'Glyma.13G209800' => 'gma', 'Glyma.15G102800' => 'gma', 'Glyma.18G218900' => 'gma', 'Glyma.19G001500' => 'gma', 'Glyma.19G153600' => 'gma', 'Gohir.A02G028600' => 'ghi', 'Gohir.A08G045000' => 'ghi', 'Gohir.A11G120500' => 'ghi', 'Gohir.A12G006200' => 'ghi', 'Gohir.A12G006250' => 'ghi', 'Gohir.D02G036300' => 'ghi', 'Gohir.D08G054700' => 'ghi', 'Gohir.D11G125600' => 'ghi', 'Gohir.D12G005700' => 'ghi', 'Gorai.004G055200' => 'gra', 'Gorai.005G040400' => 'gra', 'Gorai.007G134500' => 'gra', 'Gorai.008G005500' => 'gra', 'GSVIVG01011094001' => 'vvi', 'GSVIVG01017879001' => 'vvi', 'GSVIVG01025988001' => 'vvi', 'GSVIVG01029847001' => 'vvi', 'HanXRQChr10g0282901' => 'han', 'HanXRQChr10g0310371' => 'han', 'HanXRQChr10g0315041' => 'han', 'HanXRQChr11g0327651' => 'han', 'HanXRQChr12g0359391' => 'han', 'Haze_00972' => 'cav', 'Haze_00973' => 'cav', 'Haze_00974' => 'cav', 'Haze_04747' => 'cav', 'Haze_04749' => 'cav', 'Haze_04750' => 'cav', 'Haze_21217' => 'cav', 'Hma1.2p1_1037F.1_g250680' => 'hma', 'Hma1.2p1_1644F.1_g295320' => 'hma', 'HPP92_011322' => 'vpl', 'HPP92_011323' => 'vpl', 'HPP92_011324' => 'vpl', 'HPP92_011325' => 'vpl', 'HPP92_011326' => 'vpl', 'Hund12205' => 'sun', 'Hund17957' => 'sun', 'Lalb_Chr06g0176771' => 'lal', 'Lalb_Chr18g0056021' => 'lal', 'Lalb_Chr18g0056031' => 'lal', 'Lalb_Chr18g0056041' => 'lal', 'Lalb_Chr20g0107751' => 'lal', 'Lalb_Chr20g0118371' => 'lal', 'Lj1g0010239' => 'lja', 'Lj1g0017101' => 'lja', 'Lj2A1178G40' => 'lonja', 'Lj2A54G84' => 'lonja', 'Lj2g0015248' => 'lja', 'Lj3A761T51' => 'lonja', 'Lj6g0018116' => 'lja', 'Lsat_1_v5_gn_4_136040' => 'lsa', 'Lsat_1_v5_gn_5_187461' => 'lsa', 'Lsat_1_v5_gn_5_77001' => 'lsa', 'Lsat_1_v5_gn_9_4461' => 'lsa', 'Manes.01G210100' => 'mes', 'Manes.03G185600' => 'mes', 'Manes.05G073300' => 'mes', 'Manes.09G120300' => 'mes', 'Manes.15G022100' => 'mes', 'Mapoly0096s0053' => 'mpo', 'MBI03_g14058_MAGBIO' => 'mbi', 'MBI03_g33876_MAGBIO' => 'mbi', 'MBI03_g36854_MAGBIO' => 'mbi', 'MBI17_g11997_MAGBIO' => 'mbi', 'MD03G1269000' => 'mdo', 'MD04G1179600' => 'mdo', 'MD11G1289800' => 'mdo', 'MD12G1194700' => 'mdo', 'MD13G1182100' => 'mdo', 'MD13G1182200' => 'mdo', 'MD16G1182600' => 'mdo', 'Medtr2g021400' => 'mtr', 'Medtr2g021470' => 'mtr', 'Medtr2g105810' => 'mtr', 'Medtr3g033580' => 'mtr', 'Medtr6g007970' => 'mtr', 'Medtr7g056330' => 'mtr', 'Medtr7g074290' => 'mtr', 'Medtr7g074380' => 'mtr', 'Medtr7g094550' => 'mtr', 'Medtr8g069995' => 'mtr', 'MELO3C014345.2' => 'cme', 'MELO3C021395.2' => 'cme', 'Migut.D00262' => 'egut', 'Migut.G00257' => 'egut', 'MSTRG.21575' => 'ama', 'MSTRG.3985' => 'ama', 'Nitab4.5_0000295g0140' => 'nta', 'Nitab4.5_0000732g0140' => 'nta', 'Nitab4.5_0003162g0020' => 'nta', 'Nitab4.5_0006180g0090' => 'nta', 'Nitab4.5_0006390g0010' => 'nta', 'Nitab4.5_0007392g0040' => 'nta', 'Nn1g02140' => 'nnu', 'Nn4g26168' => 'nnu', 'Nn5g26754' => 'nnu', 'Oeu001433.1' => 'oeu', 'Oeu010299.2' => 'oeu', 'Oeu011171.1' => 'oeu', 'Oeu037675.1' => 'oeu', 'Oeu038359.1' => 'oeu', 'Oeu063834.1' => 'oeu', 'Oeu063835.1' => 'oeu', 'Os05g0312000' => 'osa', 'Os07g0211101' => 'osa', 'Os07g0211200' => 'osa', 'Os07g0681500' => 'osa', 'Peaxi162Scf00095g01015' => 'pax', 'Peaxi162Scf00104g00329' => 'pax', 'Peaxi162Scf00161g00137' => 'pax', 'PGR004G1665' => 'pgr', 'PGR031G2937' => 'pgr', 'PGR119G2145' => 'pgr', 'PGSC0003DMG400004351' => 'stu', 'PGSC0003DMG400014625' => 'stu', 'PGSC0003DMG401000943' => 'stu', 'Phvul.001G148600' => 'pvu', 'Phvul.004G001700' => 'pvu', 'Phvul.006G154900' => 'pvu', 'Phvul.008G078200' => 'pvu', 'Phvul.011G136500' => 'pvu', 'Potri.002G215600' => 'ptr', 'Potri.008G201600' => 'ptr', 'Potri.014G138400' => 'ptr', 'Potri.016G142500' => 'ptr', 'Pp3c16_10580' => 'ppa', 'Pp3c5_25280' => 'ppa', 'Prupe.1G150000' => 'ppe', 'Prupe.1G150100' => 'ppe', 'Prupe.6G299600' => 'ppe', 'Prupe.8G245000' => 'ppe', 'Psat0s4927g0040' => 'psa', 'Psat1g052080' => 'psa', 'Psat1g183800' => 'psa', 'Psat3g113840' => 'psa', 'Psat3g126120' => 'psa', 'Psat3g126160' => 'psa', 'Psat3g158760' => 'psa', 'Psat3g158840' => 'psa', 'PSO170G2858' => 'pso', 'PSO339G0606' => 'pso', 'PSO384G4709' => 'pso', 'PSO407G0334' => 'pso', 'QL04p040276' => 'qlo', 'QL06p005458' => 'qlo', 'QL06p005472' => 'qlo', 'QL07p030546' => 'qlo', 'QL07p031519' => 'qlo', 'QL09p050949' => 'qlo', 'QL09p050966' => 'qlo', 'QL09p051067' => 'qlo', 'QL12p022706' => 'qlo', 'RcHm_v2.0_Chr2g0119601' => 'rch', 'RcHm_v2.0_Chr3g0459591' => 'rch', 'RcHm_v2.0_Chr4g0418521' => 'rch', 'RcHm_v2.0_Chr4g0418531' => 'rch', 'RcHm_v2.0_Chr4g0418541' => 'rch', 'RcHm_v2.0_Chr6g0291641' => 'rch', 'Rhsim01G0086300' => 'rsi', 'Rhsim01G0276300' => 'rsi', 'Rhsim01G0276500' => 'rsi', 'Rhsim04G0207700' => 'rsi', 'Rhsim05G0234500' => 'rsi', 'Rhsim13G0022400' => 'rsi', 'Sabra02G0167900' => 'sbr', 'Sabra04G0158500' => 'sbr', 'Sabra08G0159800' => 'sbr', 'Sabra10G0011500' => 'sbr', 'Sabra14G0104400' => 'sbr', 'SalBow2G2440' => 'sbo', 'SalBow4G2265' => 'sbo', 'Sc02g0000060' => 'sci', 'Sc05g0005020' => 'sci', 'Sc13g0003890' => 'sci', 'Sed0014865' => 'sed', 'Sed0017224' => 'sed', 'Sed0026391' => 'sed', 'SEGI_00063' => 'sgi', 'SEGI_10967' => 'sgi', 'SEGI_17510' => 'sgi', 'SEGI_24396' => 'sgi', 'SEGI_39719' => 'sgi', 'SEGI_41392' => 'sgi', 'SGA_v2.0_scaffold11G05794' => 'sas', 'SGA_v2.0_scaffold142G35607' => 'sas', 'SGA_v2.0_scaffold1G00447' => 'sas', 'SHI15388' => 'shi', 'SHI15394' => 'shi', 'SHI15396' => 'shi', 'SHI15399' => 'shi', 'SMO343G0151' => 'smo', 'SMO367G1118' => 'smo', 'Solyc01g080200.3' => 'sly', 'Solyc06g008960.3' => 'sly', 'Solyc09g064780.3' => 'sly', 'Sopen01g031980' => 'spe', 'Sopen06g003710' => 'spe', 'Sopen09g026460' => 'spe', 'Sp3g21240' => 'spa', 'Sp4g30030' => 'spa', 'TAR365G0022' => 'tar', 'TAR365G1023' => 'tar', 'TAR365G1253' => 'tar', 'TAR623G0078' => 'tar', 'TAR623G1721' => 'tar', 'TAR633G0959' => 'tar', 'THA.LOC104802225' => 'tha', 'THA.LOC104804769' => 'tha', 'THA.LOC104808660' => 'tha', 'THA.LOC104812792' => 'tha', 'Thecc.01G284000' => 'tca', 'Thecc.04G220600' => 'tca', 'Thecc.05G268900' => 'tca', 'Thecc.08G171100' => 'tca', 'Thhalv10001284m.g' => 'esa', 'Thhalv10019912m.g' => 'esa', 'TPR.G14189' => 'tpr', 'TPR.G18110' => 'tpr', 'TPR.G18130' => 'tpr', 'TPR.G18131' => 'tpr', 'TPR.G18140' => 'tpr', 'TPR.G24282' => 'tpr', 'TPR.G25221' => 'tpr', 'TPR.G29267' => 'tpr', 'TPR.G35315' => 'tpr', 'TPR.G36173' => 'tpr', 'TWI09G0794' => 'twi', 'TWI59G1348' => 'twi', 'TWI74G0430' => 'twi', 'unitig_26.g8940' => 'ugi', 'unitig_749.g13744' => 'ugi', 'unitig_749.g13745' => 'ugi', 'vmacro08269' => 'vma', 'vmacro14937' => 'vma', 'vmacro20401' => 'vma', 'VMungo0464G1349' => 'vmu', 'VMungo0540G0289' => 'vmu', 'VMungo1215G1590' => 'vmu', 'VMungo1309G0221' => 'vmu', 'VMungo1309G2815' => 'vmu', 'VMungo1383G0239' => 'vmu', 'VMungo1383G2910' => 'vmu', 'Zm00001eb095270' => 'zma', 'Zm00001eb095280' => 'zma', 'Zm00001eb111630' => 'zma', 'Zm00001eb237080' => 'zma', 'Zm00001eb273740' => 'zma', 'Zm00001eb285040' => 'zma', 'Zm00001eb330790' => 'zma', 'Zm00001eb337380' => 'zma' ), 'gf_id' => 'HOM05D001484', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001484' ), 'data_identifier' => 'HOM05D001484', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001484', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p31500' => 'bna', 'A05p00020' => 'bna', 'A07p08820' => 'bna', 'Aa31LG4G3300' => 'aar', 'Aa31LG8G10030' => 'aar', 'Actinidia00731' => 'ach', 'Actinidia11473' => 'ach', 'Actinidia23469' => 'ach', 'Actinidia24318' => 'ach', 'Actinidia40196' => 'ach', 'Actinidia40197' => 'ach', 'Actinidia40198' => 'ach', 'Ah.08g212990' => 'amhyb', 'Ah.15g091720' => 'amhyb', 'AL3G38260' => 'aly', 'AL4G47710' => 'aly', 'Aqoxy2G00671' => 'aox', 'Aqoxy2G03236' => 'aox', 'arahy.Tifrunner.gnm1.ann1.05IDCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KR684' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATY3SJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK6QJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6APGL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IDT7Z9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM073U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ0R87' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LE7RV4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT4QRX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V5ENPK' => 'arhy', 'AT2G48110' => 'ath', 'AT3G23590' => 'ath', 'ATR0626G186' => 'atr', 'ATR1127G141' => 'atr', 'Atru.chr4.2583' => 'acertr', 'Atru.chr5.1358' => 'acertr', 'Atru.chr5.1359' => 'acertr', 'Atru.chr8.46' => 'acertr', 'AUR62002640' => 'cqu', 'AUR62030055' => 'cqu', 'AUR62033713' => 'cqu', 'AUR62033714' => 'cqu', 'AUR62036795' => 'cqu', 'AUR62039891' => 'cqu', 'BcaB02g08737' => 'bca', 'BcaB04g20441' => 'bca', 'BcaB06g26509' => 'bca', 'BcaB06g26510' => 'bca', 'BcaB06g26511' => 'bca', 'BcaB06g26512' => 'bca', 'BcaB06g26513' => 'bca', 'BcaC02g12564' => 'bca', 'BcaC02g12565' => 'bca', 'BcaC02g12794' => 'bca', 'BcaC02g12795' => 'bca', 'BcaC02g12796' => 'bca', 'BcaC06g35541' => 'bca', 'BNapus_Darmor_BZH_scaffold_188p00080' => 'bna', 'BNapus_Darmor_BZH_scaffold_188p00090' => 'bna', 'BolC1t03972H' => 'bol', 'BolC1t03973H' => 'bol', 'BolC4t21680H' => 'bol', 'BolC7t41863H' => 'bol', 'BolSC55t61227H' => 'bol', 'BolSC55t61228H' => 'bol', 'BraA01t03278Z' => 'bra', 'BraA05t18998Z' => 'bra', 'BraA07t28673Z' => 'bra', 'C01p40150' => 'bna', 'C05p12370' => 'bna', 'C07p13680' => 'bna', 'CAN.G1006.16' => 'can', 'CAN.G1006.17' => 'can', 'CAN.G1170.2' => 'can', 'CAN.G962.7' => 'can', 'CANSAT25G2179' => 'cansat', 'CANSAT78G1573' => 'cansat', 'CARHR099510' => 'chi', 'CARHR143510' => 'chi', 'Carub.0003s2380' => 'cru', 'Carub.0004s3082' => 'cru', 'Ca_00614_v3' => 'car', 'Ca_07801_v3' => 'car', 'Ca_08567_v3' => 'car', 'Ca_09571_v3' => 'car', 'CBR_g19290' => 'cbr', 'Cc01_g19770' => 'ccan', 'Cc03_g03030' => 'ccan', 'CDE07G0968' => 'cde', 'CDE09G1441' => 'cde', 'Cfa006103' => 'cfa', 'Cfa015573' => 'cfa', 'Cfa016988' => 'cfa', 'Ciclev10006738m.g' => 'ccl', 'Ciclev10010920m.g' => 'ccl', 'Ciclev10018517m.g' => 'ccl', 'CiPaw.01G159200' => 'cil', 'CiPaw.02G091000' => 'cil', 'CiPaw.02G091100' => 'cil', 'CiPaw.08G103100' => 'cil', 'CiPaw.09G224900' => 'cil', 'ClCG06G005740' => 'cla', 'ClCG07G000090' => 'cla', 'ClCG07G000100' => 'cla', 'COL.COLO4_09143' => 'col', 'COL.COLO4_25124' => 'col', 'Cpa.g.sc16.34' => 'cpa', 'Cpa.g.sc3504.1' => 'cpa', 'Cpa.g.sc60.37' => 'cpa', 'CsaV3_6G018520' => 'csa', 'CsaV3_6G036860' => 'csa', 'CSS0001072' => 'camsi', 'CSS0020208' => 'camsi', 'CSS0021253' => 'camsi', 'CSS0022190' => 'camsi', 'CSS0036150' => 'camsi', 'CSS0040442' => 'camsi', 'CSS0042300' => 'camsi', 'CSS0045298' => 'camsi', 'DCAR_012449' => 'dca', 'DCAR_018405' => 'dca', 'DCAR_024573' => 'dca', 'DCAR_030591' => 'dca', 'Dinv16926' => 'din', 'Dinv32963' => 'din', 'Dinv38382' => 'din', 'Dinv38383' => 'din', 'Duzib133G0974' => 'dzi', 'Duzib138G1867' => 'dzi', 'Duzib211G0420' => 'dzi', 'Duzib212G0930' => 'dzi', 'ECA234G1645' => 'eca', 'ECA247G3467' => 'eca', 'ECA248G1703' => 'eca', 'EL10Ac3g06327' => 'bvu', 'EL10Ac7g17204' => 'bvu', 'Eucgr.A00855' => 'egr', 'Eucgr.A00858' => 'egr', 'Eucgr.H01520' => 'egr', 'Eucgr.H03604' => 'egr', 'Eucgr.L03465' => 'egr', 'Eucgr.L03466' => 'egr', 'FAN01G0988' => 'fan', 'FAN02G3892' => 'fan', 'FAN05G3381' => 'fan', 'FAN07G0967' => 'fan', 'FAN07G1493' => 'fan', 'FAN08G3125' => 'fan', 'FAN09G0402' => 'fan', 'FAN12G2594' => 'fan', 'FAN12G3879' => 'fan', 'FAN14G1546' => 'fan', 'FAN15G3626' => 'fan', 'FAN17G0588' => 'fan', 'FAN17G0609' => 'fan', 'FAN18G2817' => 'fan', 'FAN19G1305' => 'fan', 'FAN20G1787' => 'fan', 'FAN22G0073' => 'fan', 'FAN22G0352' => 'fan', 'FAN22G0368' => 'fan', 'FAN22G2273' => 'fan', 'FAN24G1998' => 'fan', 'FAN27G1317' => 'fan', 'FvH4_2g23980' => 'fve', 'FvH4_4g14380' => 'fve', 'FvH4_4g14390' => 'fve', 'FvH4_6g09250' => 'fve', 'Glyma.03G151100' => 'gma', 'Glyma.04G122550' => 'gma', 'Glyma.05G001600' => 'gma', 'Glyma.09G270766' => 'gma', 'Glyma.09G270832' => 'gma', 'Glyma.13G209800' => 'gma', 'Glyma.15G102800' => 'gma', 'Glyma.18G218900' => 'gma', 'Glyma.19G001500' => 'gma', 'Glyma.19G153600' => 'gma', 'Gohir.A02G028600' => 'ghi', 'Gohir.A08G045000' => 'ghi', 'Gohir.A11G120500' => 'ghi', 'Gohir.A12G006200' => 'ghi', 'Gohir.A12G006250' => 'ghi', 'Gohir.D02G036300' => 'ghi', 'Gohir.D08G054700' => 'ghi', 'Gohir.D11G125600' => 'ghi', 'Gohir.D12G005700' => 'ghi', 'Gorai.004G055200' => 'gra', 'Gorai.005G040400' => 'gra', 'Gorai.007G134500' => 'gra', 'Gorai.008G005500' => 'gra', 'GSVIVG01011094001' => 'vvi', 'GSVIVG01017879001' => 'vvi', 'GSVIVG01025988001' => 'vvi', 'GSVIVG01029847001' => 'vvi', 'HanXRQChr10g0282901' => 'han', 'HanXRQChr10g0310371' => 'han', 'HanXRQChr10g0315041' => 'han', 'HanXRQChr11g0327651' => 'han', 'HanXRQChr12g0359391' => 'han', 'Haze_00972' => 'cav', 'Haze_00973' => 'cav', 'Haze_00974' => 'cav', 'Haze_04747' => 'cav', 'Haze_04749' => 'cav', 'Haze_04750' => 'cav', 'Haze_21217' => 'cav', 'Hma1.2p1_1037F.1_g250680' => 'hma', 'Hma1.2p1_1644F.1_g295320' => 'hma', 'HPP92_011322' => 'vpl', 'HPP92_011323' => 'vpl', 'HPP92_011324' => 'vpl', 'HPP92_011325' => 'vpl', 'HPP92_011326' => 'vpl', 'Hund12205' => 'sun', 'Hund17957' => 'sun', 'Lalb_Chr06g0176771' => 'lal', 'Lalb_Chr18g0056021' => 'lal', 'Lalb_Chr18g0056031' => 'lal', 'Lalb_Chr18g0056041' => 'lal', 'Lalb_Chr20g0107751' => 'lal', 'Lalb_Chr20g0118371' => 'lal', 'Lj1g0010239' => 'lja', 'Lj1g0017101' => 'lja', 'Lj2A1178G40' => 'lonja', 'Lj2A54G84' => 'lonja', 'Lj2g0015248' => 'lja', 'Lj3A761T51' => 'lonja', 'Lj6g0018116' => 'lja', 'Lsat_1_v5_gn_4_136040' => 'lsa', 'Lsat_1_v5_gn_5_187461' => 'lsa', 'Lsat_1_v5_gn_5_77001' => 'lsa', 'Lsat_1_v5_gn_9_4461' => 'lsa', 'Manes.01G210100' => 'mes', 'Manes.03G185600' => 'mes', 'Manes.05G073300' => 'mes', 'Manes.09G120300' => 'mes', 'Manes.15G022100' => 'mes', 'Mapoly0096s0053' => 'mpo', 'MBI03_g14058_MAGBIO' => 'mbi', 'MBI03_g33876_MAGBIO' => 'mbi', 'MBI03_g36854_MAGBIO' => 'mbi', 'MBI17_g11997_MAGBIO' => 'mbi', 'MD03G1269000' => 'mdo', 'MD04G1179600' => 'mdo', 'MD11G1289800' => 'mdo', 'MD12G1194700' => 'mdo', 'MD13G1182100' => 'mdo', 'MD13G1182200' => 'mdo', 'MD16G1182600' => 'mdo', 'Medtr2g021400' => 'mtr', 'Medtr2g021470' => 'mtr', 'Medtr2g105810' => 'mtr', 'Medtr3g033580' => 'mtr', 'Medtr6g007970' => 'mtr', 'Medtr7g056330' => 'mtr', 'Medtr7g074290' => 'mtr', 'Medtr7g074380' => 'mtr', 'Medtr7g094550' => 'mtr', 'Medtr8g069995' => 'mtr', 'MELO3C014345.2' => 'cme', 'MELO3C021395.2' => 'cme', 'Migut.D00262' => 'egut', 'Migut.G00257' => 'egut', 'MSTRG.21575' => 'ama', 'MSTRG.3985' => 'ama', 'Nitab4.5_0000295g0140' => 'nta', 'Nitab4.5_0000732g0140' => 'nta', 'Nitab4.5_0003162g0020' => 'nta', 'Nitab4.5_0006180g0090' => 'nta', 'Nitab4.5_0006390g0010' => 'nta', 'Nitab4.5_0007392g0040' => 'nta', 'Nn1g02140' => 'nnu', 'Nn4g26168' => 'nnu', 'Nn5g26754' => 'nnu', 'Oeu001433.1' => 'oeu', 'Oeu010299.2' => 'oeu', 'Oeu011171.1' => 'oeu', 'Oeu037675.1' => 'oeu', 'Oeu038359.1' => 'oeu', 'Oeu063834.1' => 'oeu', 'Oeu063835.1' => 'oeu', 'Os05g0312000' => 'osa', 'Os07g0211101' => 'osa', 'Os07g0211200' => 'osa', 'Os07g0681500' => 'osa', 'Peaxi162Scf00095g01015' => 'pax', 'Peaxi162Scf00104g00329' => 'pax', 'Peaxi162Scf00161g00137' => 'pax', 'PGR004G1665' => 'pgr', 'PGR031G2937' => 'pgr', 'PGR119G2145' => 'pgr', 'PGSC0003DMG400004351' => 'stu', 'PGSC0003DMG400014625' => 'stu', 'PGSC0003DMG401000943' => 'stu', 'Phvul.001G148600' => 'pvu', 'Phvul.004G001700' => 'pvu', 'Phvul.006G154900' => 'pvu', 'Phvul.008G078200' => 'pvu', 'Phvul.011G136500' => 'pvu', 'Potri.002G215600' => 'ptr', 'Potri.008G201600' => 'ptr', 'Potri.014G138400' => 'ptr', 'Potri.016G142500' => 'ptr', 'Pp3c16_10580' => 'ppa', 'Pp3c5_25280' => 'ppa', 'Prupe.1G150000' => 'ppe', 'Prupe.1G150100' => 'ppe', 'Prupe.6G299600' => 'ppe', 'Prupe.8G245000' => 'ppe', 'Psat0s4927g0040' => 'psa', 'Psat1g052080' => 'psa', 'Psat1g183800' => 'psa', 'Psat3g113840' => 'psa', 'Psat3g126120' => 'psa', 'Psat3g126160' => 'psa', 'Psat3g158760' => 'psa', 'Psat3g158840' => 'psa', 'PSO170G2858' => 'pso', 'PSO339G0606' => 'pso', 'PSO384G4709' => 'pso', 'PSO407G0334' => 'pso', 'QL04p040276' => 'qlo', 'QL06p005458' => 'qlo', 'QL06p005472' => 'qlo', 'QL07p030546' => 'qlo', 'QL07p031519' => 'qlo', 'QL09p050949' => 'qlo', 'QL09p050966' => 'qlo', 'QL09p051067' => 'qlo', 'QL12p022706' => 'qlo', 'RcHm_v2.0_Chr2g0119601' => 'rch', 'RcHm_v2.0_Chr3g0459591' => 'rch', 'RcHm_v2.0_Chr4g0418521' => 'rch', 'RcHm_v2.0_Chr4g0418531' => 'rch', 'RcHm_v2.0_Chr4g0418541' => 'rch', 'RcHm_v2.0_Chr6g0291641' => 'rch', 'Rhsim01G0086300' => 'rsi', 'Rhsim01G0276300' => 'rsi', 'Rhsim01G0276500' => 'rsi', 'Rhsim04G0207700' => 'rsi', 'Rhsim05G0234500' => 'rsi', 'Rhsim13G0022400' => 'rsi', 'Sabra02G0167900' => 'sbr', 'Sabra04G0158500' => 'sbr', 'Sabra08G0159800' => 'sbr', 'Sabra10G0011500' => 'sbr', 'Sabra14G0104400' => 'sbr', 'SalBow2G2440' => 'sbo', 'SalBow4G2265' => 'sbo', 'Sc02g0000060' => 'sci', 'Sc05g0005020' => 'sci', 'Sc13g0003890' => 'sci', 'Sed0014865' => 'sed', 'Sed0017224' => 'sed', 'Sed0026391' => 'sed', 'SEGI_00063' => 'sgi', 'SEGI_10967' => 'sgi', 'SEGI_17510' => 'sgi', 'SEGI_24396' => 'sgi', 'SEGI_39719' => 'sgi', 'SEGI_41392' => 'sgi', 'SGA_v2.0_scaffold11G05794' => 'sas', 'SGA_v2.0_scaffold142G35607' => 'sas', 'SGA_v2.0_scaffold1G00447' => 'sas', 'SHI15388' => 'shi', 'SHI15394' => 'shi', 'SHI15396' => 'shi', 'SHI15399' => 'shi', 'SMO343G0151' => 'smo', 'SMO367G1118' => 'smo', 'Solyc01g080200.3' => 'sly', 'Solyc06g008960.3' => 'sly', 'Solyc09g064780.3' => 'sly', 'Sopen01g031980' => 'spe', 'Sopen06g003710' => 'spe', 'Sopen09g026460' => 'spe', 'Sp3g21240' => 'spa', 'Sp4g30030' => 'spa', 'TAR365G0022' => 'tar', 'TAR365G1023' => 'tar', 'TAR365G1253' => 'tar', 'TAR623G0078' => 'tar', 'TAR623G1721' => 'tar', 'TAR633G0959' => 'tar', 'THA.LOC104802225' => 'tha', 'THA.LOC104804769' => 'tha', 'THA.LOC104808660' => 'tha', 'THA.LOC104812792' => 'tha', 'Thecc.01G284000' => 'tca', 'Thecc.04G220600' => 'tca', 'Thecc.05G268900' => 'tca', 'Thecc.08G171100' => 'tca', 'Thhalv10001284m.g' => 'esa', 'Thhalv10019912m.g' => 'esa', 'TPR.G14189' => 'tpr', 'TPR.G18110' => 'tpr', 'TPR.G18130' => 'tpr', 'TPR.G18131' => 'tpr', 'TPR.G18140' => 'tpr', 'TPR.G24282' => 'tpr', 'TPR.G25221' => 'tpr', 'TPR.G29267' => 'tpr', 'TPR.G35315' => 'tpr', 'TPR.G36173' => 'tpr', 'TWI09G0794' => 'twi', 'TWI59G1348' => 'twi', 'TWI74G0430' => 'twi', 'unitig_26.g8940' => 'ugi', 'unitig_749.g13744' => 'ugi', 'unitig_749.g13745' => 'ugi', 'vmacro08269' => 'vma', 'vmacro14937' => 'vma', 'vmacro20401' => 'vma', 'VMungo0464G1349' => 'vmu', 'VMungo0540G0289' => 'vmu', 'VMungo1215G1590' => 'vmu', 'VMungo1309G0221' => 'vmu', 'VMungo1309G2815' => 'vmu', 'VMungo1383G0239' => 'vmu', 'VMungo1383G2910' => 'vmu', 'Zm00001eb095270' => 'zma', 'Zm00001eb095280' => 'zma', 'Zm00001eb111630' => 'zma', 'Zm00001eb237080' => 'zma', 'Zm00001eb273740' => 'zma', 'Zm00001eb285040' => 'zma', 'Zm00001eb330790' => 'zma', 'Zm00001eb337380' => 'zma' ) $gf_id = 'HOM05D001484' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001484' ) $data_identifier = 'HOM05D001484' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 2, 'aly' => (int) 2, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 22, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 7, 'hma' => (int) 2, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 7, 'mtr' => (int) 10, 'cme' => (int) 2, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 4, 'ppa' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 4, 'qlo' => (int) 9, 'rch' => (int) 6, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 10, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 7, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb337380' $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' => 'HOM05D001484', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p31500' => 'bna', 'A05p00020' => 'bna', 'A07p08820' => 'bna', 'Aa31LG4G3300' => 'aar', 'Aa31LG8G10030' => 'aar', 'Actinidia00731' => 'ach', 'Actinidia11473' => 'ach', 'Actinidia23469' => 'ach', 'Actinidia24318' => 'ach', 'Actinidia40196' => 'ach', 'Actinidia40197' => 'ach', 'Actinidia40198' => 'ach', 'Ah.08g212990' => 'amhyb', 'Ah.15g091720' => 'amhyb', 'AL3G38260' => 'aly', 'AL4G47710' => 'aly', 'Aqoxy2G00671' => 'aox', 'Aqoxy2G03236' => 'aox', 'arahy.Tifrunner.gnm1.ann1.05IDCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KR684' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATY3SJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK6QJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6APGL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IDT7Z9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM073U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ0R87' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LE7RV4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT4QRX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V5ENPK' => 'arhy', 'AT2G48110' => 'ath', 'AT3G23590' => 'ath', 'ATR0626G186' => 'atr', 'ATR1127G141' => 'atr', 'Atru.chr4.2583' => 'acertr', 'Atru.chr5.1358' => 'acertr', 'Atru.chr5.1359' => 'acertr', 'Atru.chr8.46' => 'acertr', 'AUR62002640' => 'cqu', 'AUR62030055' => 'cqu', 'AUR62033713' => 'cqu', 'AUR62033714' => 'cqu', 'AUR62036795' => 'cqu', 'AUR62039891' => 'cqu', 'BcaB02g08737' => 'bca', 'BcaB04g20441' => 'bca', 'BcaB06g26509' => 'bca', 'BcaB06g26510' => 'bca', 'BcaB06g26511' => 'bca', 'BcaB06g26512' => 'bca', 'BcaB06g26513' => 'bca', 'BcaC02g12564' => 'bca', 'BcaC02g12565' => 'bca', 'BcaC02g12794' => 'bca', 'BcaC02g12795' => 'bca', 'BcaC02g12796' => 'bca', 'BcaC06g35541' => 'bca', 'BNapus_Darmor_BZH_scaffold_188p00080' => 'bna', 'BNapus_Darmor_BZH_scaffold_188p00090' => 'bna', 'BolC1t03972H' => 'bol', 'BolC1t03973H' => 'bol', 'BolC4t21680H' => 'bol', 'BolC7t41863H' => 'bol', 'BolSC55t61227H' => 'bol', 'BolSC55t61228H' => 'bol', 'BraA01t03278Z' => 'bra', 'BraA05t18998Z' => 'bra', 'BraA07t28673Z' => 'bra', 'C01p40150' => 'bna', 'C05p12370' => 'bna', 'C07p13680' => 'bna', 'CAN.G1006.16' => 'can', 'CAN.G1006.17' => 'can', 'CAN.G1170.2' => 'can', 'CAN.G962.7' => 'can', 'CANSAT25G2179' => 'cansat', 'CANSAT78G1573' => 'cansat', 'CARHR099510' => 'chi', 'CARHR143510' => 'chi', 'Carub.0003s2380' => 'cru', 'Carub.0004s3082' => 'cru', 'Ca_00614_v3' => 'car', 'Ca_07801_v3' => 'car', 'Ca_08567_v3' => 'car', 'Ca_09571_v3' => 'car', 'CBR_g19290' => 'cbr', 'Cc01_g19770' => 'ccan', 'Cc03_g03030' => 'ccan', 'CDE07G0968' => 'cde', 'CDE09G1441' => 'cde', 'Cfa006103' => 'cfa', 'Cfa015573' => 'cfa', 'Cfa016988' => 'cfa', 'Ciclev10006738m.g' => 'ccl', 'Ciclev10010920m.g' => 'ccl', 'Ciclev10018517m.g' => 'ccl', 'CiPaw.01G159200' => 'cil', 'CiPaw.02G091000' => 'cil', 'CiPaw.02G091100' => 'cil', 'CiPaw.08G103100' => 'cil', 'CiPaw.09G224900' => 'cil', 'ClCG06G005740' => 'cla', 'ClCG07G000090' => 'cla', 'ClCG07G000100' => 'cla', 'COL.COLO4_09143' => 'col', 'COL.COLO4_25124' => 'col', 'Cpa.g.sc16.34' => 'cpa', 'Cpa.g.sc3504.1' => 'cpa', 'Cpa.g.sc60.37' => 'cpa', 'CsaV3_6G018520' => 'csa', 'CsaV3_6G036860' => 'csa', 'CSS0001072' => 'camsi', 'CSS0020208' => 'camsi', 'CSS0021253' => 'camsi', 'CSS0022190' => 'camsi', 'CSS0036150' => 'camsi', 'CSS0040442' => 'camsi', 'CSS0042300' => 'camsi', 'CSS0045298' => 'camsi', 'DCAR_012449' => 'dca', 'DCAR_018405' => 'dca', 'DCAR_024573' => 'dca', 'DCAR_030591' => 'dca', 'Dinv16926' => 'din', 'Dinv32963' => 'din', 'Dinv38382' => 'din', 'Dinv38383' => 'din', 'Duzib133G0974' => 'dzi', 'Duzib138G1867' => 'dzi', 'Duzib211G0420' => 'dzi', 'Duzib212G0930' => 'dzi', 'ECA234G1645' => 'eca', 'ECA247G3467' => 'eca', 'ECA248G1703' => 'eca', 'EL10Ac3g06327' => 'bvu', 'EL10Ac7g17204' => 'bvu', 'Eucgr.A00855' => 'egr', 'Eucgr.A00858' => 'egr', 'Eucgr.H01520' => 'egr', 'Eucgr.H03604' => 'egr', 'Eucgr.L03465' => 'egr', 'Eucgr.L03466' => 'egr', 'FAN01G0988' => 'fan', 'FAN02G3892' => 'fan', 'FAN05G3381' => 'fan', 'FAN07G0967' => 'fan', 'FAN07G1493' => 'fan', 'FAN08G3125' => 'fan', 'FAN09G0402' => 'fan', 'FAN12G2594' => 'fan', 'FAN12G3879' => 'fan', 'FAN14G1546' => 'fan', 'FAN15G3626' => 'fan', 'FAN17G0588' => 'fan', 'FAN17G0609' => 'fan', 'FAN18G2817' => 'fan', 'FAN19G1305' => 'fan', 'FAN20G1787' => 'fan', 'FAN22G0073' => 'fan', 'FAN22G0352' => 'fan', 'FAN22G0368' => 'fan', 'FAN22G2273' => 'fan', 'FAN24G1998' => 'fan', 'FAN27G1317' => 'fan', 'FvH4_2g23980' => 'fve', 'FvH4_4g14380' => 'fve', 'FvH4_4g14390' => 'fve', 'FvH4_6g09250' => 'fve', 'Glyma.03G151100' => 'gma', 'Glyma.04G122550' => 'gma', 'Glyma.05G001600' => 'gma', 'Glyma.09G270766' => 'gma', 'Glyma.09G270832' => 'gma', 'Glyma.13G209800' => 'gma', 'Glyma.15G102800' => 'gma', 'Glyma.18G218900' => 'gma', 'Glyma.19G001500' => 'gma', 'Glyma.19G153600' => 'gma', 'Gohir.A02G028600' => 'ghi', 'Gohir.A08G045000' => 'ghi', 'Gohir.A11G120500' => 'ghi', 'Gohir.A12G006200' => 'ghi', 'Gohir.A12G006250' => 'ghi', 'Gohir.D02G036300' => 'ghi', 'Gohir.D08G054700' => 'ghi', 'Gohir.D11G125600' => 'ghi', 'Gohir.D12G005700' => 'ghi', 'Gorai.004G055200' => 'gra', 'Gorai.005G040400' => 'gra', 'Gorai.007G134500' => 'gra', 'Gorai.008G005500' => 'gra', 'GSVIVG01011094001' => 'vvi', 'GSVIVG01017879001' => 'vvi', 'GSVIVG01025988001' => 'vvi', 'GSVIVG01029847001' => 'vvi', 'HanXRQChr10g0282901' => 'han', 'HanXRQChr10g0310371' => 'han', 'HanXRQChr10g0315041' => 'han', 'HanXRQChr11g0327651' => 'han', 'HanXRQChr12g0359391' => 'han', 'Haze_00972' => 'cav', 'Haze_00973' => 'cav', 'Haze_00974' => 'cav', 'Haze_04747' => 'cav', 'Haze_04749' => 'cav', 'Haze_04750' => 'cav', 'Haze_21217' => 'cav', 'Hma1.2p1_1037F.1_g250680' => 'hma', 'Hma1.2p1_1644F.1_g295320' => 'hma', 'HPP92_011322' => 'vpl', 'HPP92_011323' => 'vpl', 'HPP92_011324' => 'vpl', 'HPP92_011325' => 'vpl', 'HPP92_011326' => 'vpl', 'Hund12205' => 'sun', 'Hund17957' => 'sun', 'Lalb_Chr06g0176771' => 'lal', 'Lalb_Chr18g0056021' => 'lal', 'Lalb_Chr18g0056031' => 'lal', 'Lalb_Chr18g0056041' => 'lal', 'Lalb_Chr20g0107751' => 'lal', 'Lalb_Chr20g0118371' => 'lal', 'Lj1g0010239' => 'lja', 'Lj1g0017101' => 'lja', 'Lj2A1178G40' => 'lonja', 'Lj2A54G84' => 'lonja', 'Lj2g0015248' => 'lja', 'Lj3A761T51' => 'lonja', 'Lj6g0018116' => 'lja', 'Lsat_1_v5_gn_4_136040' => 'lsa', 'Lsat_1_v5_gn_5_187461' => 'lsa', 'Lsat_1_v5_gn_5_77001' => 'lsa', 'Lsat_1_v5_gn_9_4461' => 'lsa', 'Manes.01G210100' => 'mes', 'Manes.03G185600' => 'mes', 'Manes.05G073300' => 'mes', 'Manes.09G120300' => 'mes', 'Manes.15G022100' => 'mes', 'Mapoly0096s0053' => 'mpo', 'MBI03_g14058_MAGBIO' => 'mbi', 'MBI03_g33876_MAGBIO' => 'mbi', 'MBI03_g36854_MAGBIO' => 'mbi', 'MBI17_g11997_MAGBIO' => 'mbi', 'MD03G1269000' => 'mdo', 'MD04G1179600' => 'mdo', 'MD11G1289800' => 'mdo', 'MD12G1194700' => 'mdo', 'MD13G1182100' => 'mdo', 'MD13G1182200' => 'mdo', 'MD16G1182600' => 'mdo', 'Medtr2g021400' => 'mtr', 'Medtr2g021470' => 'mtr', 'Medtr2g105810' => 'mtr', 'Medtr3g033580' => 'mtr', 'Medtr6g007970' => 'mtr', 'Medtr7g056330' => 'mtr', 'Medtr7g074290' => 'mtr', 'Medtr7g074380' => 'mtr', 'Medtr7g094550' => 'mtr', 'Medtr8g069995' => 'mtr', 'MELO3C014345.2' => 'cme', 'MELO3C021395.2' => 'cme', 'Migut.D00262' => 'egut', 'Migut.G00257' => 'egut', 'MSTRG.21575' => 'ama', 'MSTRG.3985' => 'ama', 'Nitab4.5_0000295g0140' => 'nta', 'Nitab4.5_0000732g0140' => 'nta', 'Nitab4.5_0003162g0020' => 'nta', 'Nitab4.5_0006180g0090' => 'nta', 'Nitab4.5_0006390g0010' => 'nta', 'Nitab4.5_0007392g0040' => 'nta', 'Nn1g02140' => 'nnu', 'Nn4g26168' => 'nnu', 'Nn5g26754' => 'nnu', 'Oeu001433.1' => 'oeu', 'Oeu010299.2' => 'oeu', 'Oeu011171.1' => 'oeu', 'Oeu037675.1' => 'oeu', 'Oeu038359.1' => 'oeu', 'Oeu063834.1' => 'oeu', 'Oeu063835.1' => 'oeu', 'Os05g0312000' => 'osa', 'Os07g0211101' => 'osa', 'Os07g0211200' => 'osa', 'Os07g0681500' => 'osa', 'Peaxi162Scf00095g01015' => 'pax', 'Peaxi162Scf00104g00329' => 'pax', 'Peaxi162Scf00161g00137' => 'pax', 'PGR004G1665' => 'pgr', 'PGR031G2937' => 'pgr', 'PGR119G2145' => 'pgr', 'PGSC0003DMG400004351' => 'stu', 'PGSC0003DMG400014625' => 'stu', 'PGSC0003DMG401000943' => 'stu', 'Phvul.001G148600' => 'pvu', 'Phvul.004G001700' => 'pvu', 'Phvul.006G154900' => 'pvu', 'Phvul.008G078200' => 'pvu', 'Phvul.011G136500' => 'pvu', 'Potri.002G215600' => 'ptr', 'Potri.008G201600' => 'ptr', 'Potri.014G138400' => 'ptr', 'Potri.016G142500' => 'ptr', 'Pp3c16_10580' => 'ppa', 'Pp3c5_25280' => 'ppa', 'Prupe.1G150000' => 'ppe', 'Prupe.1G150100' => 'ppe', 'Prupe.6G299600' => 'ppe', 'Prupe.8G245000' => 'ppe', 'Psat0s4927g0040' => 'psa', 'Psat1g052080' => 'psa', 'Psat1g183800' => 'psa', 'Psat3g113840' => 'psa', 'Psat3g126120' => 'psa', 'Psat3g126160' => 'psa', 'Psat3g158760' => 'psa', 'Psat3g158840' => 'psa', 'PSO170G2858' => 'pso', 'PSO339G0606' => 'pso', 'PSO384G4709' => 'pso', 'PSO407G0334' => 'pso', 'QL04p040276' => 'qlo', 'QL06p005458' => 'qlo', 'QL06p005472' => 'qlo', 'QL07p030546' => 'qlo', 'QL07p031519' => 'qlo', 'QL09p050949' => 'qlo', 'QL09p050966' => 'qlo', 'QL09p051067' => 'qlo', 'QL12p022706' => 'qlo', 'RcHm_v2.0_Chr2g0119601' => 'rch', 'RcHm_v2.0_Chr3g0459591' => 'rch', 'RcHm_v2.0_Chr4g0418521' => 'rch', 'RcHm_v2.0_Chr4g0418531' => 'rch', 'RcHm_v2.0_Chr4g0418541' => 'rch', 'RcHm_v2.0_Chr6g0291641' => 'rch', 'Rhsim01G0086300' => 'rsi', 'Rhsim01G0276300' => 'rsi', 'Rhsim01G0276500' => 'rsi', 'Rhsim04G0207700' => 'rsi', 'Rhsim05G0234500' => 'rsi', 'Rhsim13G0022400' => 'rsi', 'Sabra02G0167900' => 'sbr', 'Sabra04G0158500' => 'sbr', 'Sabra08G0159800' => 'sbr', 'Sabra10G0011500' => 'sbr', 'Sabra14G0104400' => 'sbr', 'SalBow2G2440' => 'sbo', 'SalBow4G2265' => 'sbo', 'Sc02g0000060' => 'sci', 'Sc05g0005020' => 'sci', 'Sc13g0003890' => 'sci', 'Sed0014865' => 'sed', 'Sed0017224' => 'sed', 'Sed0026391' => 'sed', 'SEGI_00063' => 'sgi', 'SEGI_10967' => 'sgi', 'SEGI_17510' => 'sgi', 'SEGI_24396' => 'sgi', 'SEGI_39719' => 'sgi', 'SEGI_41392' => 'sgi', 'SGA_v2.0_scaffold11G05794' => 'sas', 'SGA_v2.0_scaffold142G35607' => 'sas', 'SGA_v2.0_scaffold1G00447' => 'sas', 'SHI15388' => 'shi', 'SHI15394' => 'shi', 'SHI15396' => 'shi', 'SHI15399' => 'shi', 'SMO343G0151' => 'smo', 'SMO367G1118' => 'smo', 'Solyc01g080200.3' => 'sly', 'Solyc06g008960.3' => 'sly', 'Solyc09g064780.3' => 'sly', 'Sopen01g031980' => 'spe', 'Sopen06g003710' => 'spe', 'Sopen09g026460' => 'spe', 'Sp3g21240' => 'spa', 'Sp4g30030' => 'spa', 'TAR365G0022' => 'tar', 'TAR365G1023' => 'tar', 'TAR365G1253' => 'tar', 'TAR623G0078' => 'tar', 'TAR623G1721' => 'tar', 'TAR633G0959' => 'tar', 'THA.LOC104802225' => 'tha', 'THA.LOC104804769' => 'tha', 'THA.LOC104808660' => 'tha', 'THA.LOC104812792' => 'tha', 'Thecc.01G284000' => 'tca', 'Thecc.04G220600' => 'tca', 'Thecc.05G268900' => 'tca', 'Thecc.08G171100' => 'tca', 'Thhalv10001284m.g' => 'esa', 'Thhalv10019912m.g' => 'esa', 'TPR.G14189' => 'tpr', 'TPR.G18110' => 'tpr', 'TPR.G18130' => 'tpr', 'TPR.G18131' => 'tpr', 'TPR.G18140' => 'tpr', 'TPR.G24282' => 'tpr', 'TPR.G25221' => 'tpr', 'TPR.G29267' => 'tpr', 'TPR.G35315' => 'tpr', 'TPR.G36173' => 'tpr', 'TWI09G0794' => 'twi', 'TWI59G1348' => 'twi', 'TWI74G0430' => 'twi', 'unitig_26.g8940' => 'ugi', 'unitig_749.g13744' => 'ugi', 'unitig_749.g13745' => 'ugi', 'vmacro08269' => 'vma', 'vmacro14937' => 'vma', 'vmacro20401' => 'vma', 'VMungo0464G1349' => 'vmu', 'VMungo0540G0289' => 'vmu', 'VMungo1215G1590' => 'vmu', 'VMungo1309G0221' => 'vmu', 'VMungo1309G2815' => 'vmu', 'VMungo1383G0239' => 'vmu', 'VMungo1383G2910' => 'vmu', 'Zm00001eb095270' => 'zma', 'Zm00001eb095280' => 'zma', 'Zm00001eb111630' => 'zma', 'Zm00001eb237080' => 'zma', 'Zm00001eb273740' => 'zma', 'Zm00001eb285040' => 'zma', 'Zm00001eb330790' => 'zma', 'Zm00001eb337380' => 'zma' ), 'gf_id' => 'HOM05D001484', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001484' ), 'data_identifier' => 'HOM05D001484', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001484', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p31500' => 'bna', 'A05p00020' => 'bna', 'A07p08820' => 'bna', 'Aa31LG4G3300' => 'aar', 'Aa31LG8G10030' => 'aar', 'Actinidia00731' => 'ach', 'Actinidia11473' => 'ach', 'Actinidia23469' => 'ach', 'Actinidia24318' => 'ach', 'Actinidia40196' => 'ach', 'Actinidia40197' => 'ach', 'Actinidia40198' => 'ach', 'Ah.08g212990' => 'amhyb', 'Ah.15g091720' => 'amhyb', 'AL3G38260' => 'aly', 'AL4G47710' => 'aly', 'Aqoxy2G00671' => 'aox', 'Aqoxy2G03236' => 'aox', 'arahy.Tifrunner.gnm1.ann1.05IDCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KR684' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATY3SJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK6QJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6APGL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IDT7Z9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM073U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ0R87' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LE7RV4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT4QRX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V5ENPK' => 'arhy', 'AT2G48110' => 'ath', 'AT3G23590' => 'ath', 'ATR0626G186' => 'atr', 'ATR1127G141' => 'atr', 'Atru.chr4.2583' => 'acertr', 'Atru.chr5.1358' => 'acertr', 'Atru.chr5.1359' => 'acertr', 'Atru.chr8.46' => 'acertr', 'AUR62002640' => 'cqu', 'AUR62030055' => 'cqu', 'AUR62033713' => 'cqu', 'AUR62033714' => 'cqu', 'AUR62036795' => 'cqu', 'AUR62039891' => 'cqu', 'BcaB02g08737' => 'bca', 'BcaB04g20441' => 'bca', 'BcaB06g26509' => 'bca', 'BcaB06g26510' => 'bca', 'BcaB06g26511' => 'bca', 'BcaB06g26512' => 'bca', 'BcaB06g26513' => 'bca', 'BcaC02g12564' => 'bca', 'BcaC02g12565' => 'bca', 'BcaC02g12794' => 'bca', 'BcaC02g12795' => 'bca', 'BcaC02g12796' => 'bca', 'BcaC06g35541' => 'bca', 'BNapus_Darmor_BZH_scaffold_188p00080' => 'bna', 'BNapus_Darmor_BZH_scaffold_188p00090' => 'bna', 'BolC1t03972H' => 'bol', 'BolC1t03973H' => 'bol', 'BolC4t21680H' => 'bol', 'BolC7t41863H' => 'bol', 'BolSC55t61227H' => 'bol', 'BolSC55t61228H' => 'bol', 'BraA01t03278Z' => 'bra', 'BraA05t18998Z' => 'bra', 'BraA07t28673Z' => 'bra', 'C01p40150' => 'bna', 'C05p12370' => 'bna', 'C07p13680' => 'bna', 'CAN.G1006.16' => 'can', 'CAN.G1006.17' => 'can', 'CAN.G1170.2' => 'can', 'CAN.G962.7' => 'can', 'CANSAT25G2179' => 'cansat', 'CANSAT78G1573' => 'cansat', 'CARHR099510' => 'chi', 'CARHR143510' => 'chi', 'Carub.0003s2380' => 'cru', 'Carub.0004s3082' => 'cru', 'Ca_00614_v3' => 'car', 'Ca_07801_v3' => 'car', 'Ca_08567_v3' => 'car', 'Ca_09571_v3' => 'car', 'CBR_g19290' => 'cbr', 'Cc01_g19770' => 'ccan', 'Cc03_g03030' => 'ccan', 'CDE07G0968' => 'cde', 'CDE09G1441' => 'cde', 'Cfa006103' => 'cfa', 'Cfa015573' => 'cfa', 'Cfa016988' => 'cfa', 'Ciclev10006738m.g' => 'ccl', 'Ciclev10010920m.g' => 'ccl', 'Ciclev10018517m.g' => 'ccl', 'CiPaw.01G159200' => 'cil', 'CiPaw.02G091000' => 'cil', 'CiPaw.02G091100' => 'cil', 'CiPaw.08G103100' => 'cil', 'CiPaw.09G224900' => 'cil', 'ClCG06G005740' => 'cla', 'ClCG07G000090' => 'cla', 'ClCG07G000100' => 'cla', 'COL.COLO4_09143' => 'col', 'COL.COLO4_25124' => 'col', 'Cpa.g.sc16.34' => 'cpa', 'Cpa.g.sc3504.1' => 'cpa', 'Cpa.g.sc60.37' => 'cpa', 'CsaV3_6G018520' => 'csa', 'CsaV3_6G036860' => 'csa', 'CSS0001072' => 'camsi', 'CSS0020208' => 'camsi', 'CSS0021253' => 'camsi', 'CSS0022190' => 'camsi', 'CSS0036150' => 'camsi', 'CSS0040442' => 'camsi', 'CSS0042300' => 'camsi', 'CSS0045298' => 'camsi', 'DCAR_012449' => 'dca', 'DCAR_018405' => 'dca', 'DCAR_024573' => 'dca', 'DCAR_030591' => 'dca', 'Dinv16926' => 'din', 'Dinv32963' => 'din', 'Dinv38382' => 'din', 'Dinv38383' => 'din', 'Duzib133G0974' => 'dzi', 'Duzib138G1867' => 'dzi', 'Duzib211G0420' => 'dzi', 'Duzib212G0930' => 'dzi', 'ECA234G1645' => 'eca', 'ECA247G3467' => 'eca', 'ECA248G1703' => 'eca', 'EL10Ac3g06327' => 'bvu', 'EL10Ac7g17204' => 'bvu', 'Eucgr.A00855' => 'egr', 'Eucgr.A00858' => 'egr', 'Eucgr.H01520' => 'egr', 'Eucgr.H03604' => 'egr', 'Eucgr.L03465' => 'egr', 'Eucgr.L03466' => 'egr', 'FAN01G0988' => 'fan', 'FAN02G3892' => 'fan', 'FAN05G3381' => 'fan', 'FAN07G0967' => 'fan', 'FAN07G1493' => 'fan', 'FAN08G3125' => 'fan', 'FAN09G0402' => 'fan', 'FAN12G2594' => 'fan', 'FAN12G3879' => 'fan', 'FAN14G1546' => 'fan', 'FAN15G3626' => 'fan', 'FAN17G0588' => 'fan', 'FAN17G0609' => 'fan', 'FAN18G2817' => 'fan', 'FAN19G1305' => 'fan', 'FAN20G1787' => 'fan', 'FAN22G0073' => 'fan', 'FAN22G0352' => 'fan', 'FAN22G0368' => 'fan', 'FAN22G2273' => 'fan', 'FAN24G1998' => 'fan', 'FAN27G1317' => 'fan', 'FvH4_2g23980' => 'fve', 'FvH4_4g14380' => 'fve', 'FvH4_4g14390' => 'fve', 'FvH4_6g09250' => 'fve', 'Glyma.03G151100' => 'gma', 'Glyma.04G122550' => 'gma', 'Glyma.05G001600' => 'gma', 'Glyma.09G270766' => 'gma', 'Glyma.09G270832' => 'gma', 'Glyma.13G209800' => 'gma', 'Glyma.15G102800' => 'gma', 'Glyma.18G218900' => 'gma', 'Glyma.19G001500' => 'gma', 'Glyma.19G153600' => 'gma', 'Gohir.A02G028600' => 'ghi', 'Gohir.A08G045000' => 'ghi', 'Gohir.A11G120500' => 'ghi', 'Gohir.A12G006200' => 'ghi', 'Gohir.A12G006250' => 'ghi', 'Gohir.D02G036300' => 'ghi', 'Gohir.D08G054700' => 'ghi', 'Gohir.D11G125600' => 'ghi', 'Gohir.D12G005700' => 'ghi', 'Gorai.004G055200' => 'gra', 'Gorai.005G040400' => 'gra', 'Gorai.007G134500' => 'gra', 'Gorai.008G005500' => 'gra', 'GSVIVG01011094001' => 'vvi', 'GSVIVG01017879001' => 'vvi', 'GSVIVG01025988001' => 'vvi', 'GSVIVG01029847001' => 'vvi', 'HanXRQChr10g0282901' => 'han', 'HanXRQChr10g0310371' => 'han', 'HanXRQChr10g0315041' => 'han', 'HanXRQChr11g0327651' => 'han', 'HanXRQChr12g0359391' => 'han', 'Haze_00972' => 'cav', 'Haze_00973' => 'cav', 'Haze_00974' => 'cav', 'Haze_04747' => 'cav', 'Haze_04749' => 'cav', 'Haze_04750' => 'cav', 'Haze_21217' => 'cav', 'Hma1.2p1_1037F.1_g250680' => 'hma', 'Hma1.2p1_1644F.1_g295320' => 'hma', 'HPP92_011322' => 'vpl', 'HPP92_011323' => 'vpl', 'HPP92_011324' => 'vpl', 'HPP92_011325' => 'vpl', 'HPP92_011326' => 'vpl', 'Hund12205' => 'sun', 'Hund17957' => 'sun', 'Lalb_Chr06g0176771' => 'lal', 'Lalb_Chr18g0056021' => 'lal', 'Lalb_Chr18g0056031' => 'lal', 'Lalb_Chr18g0056041' => 'lal', 'Lalb_Chr20g0107751' => 'lal', 'Lalb_Chr20g0118371' => 'lal', 'Lj1g0010239' => 'lja', 'Lj1g0017101' => 'lja', 'Lj2A1178G40' => 'lonja', 'Lj2A54G84' => 'lonja', 'Lj2g0015248' => 'lja', 'Lj3A761T51' => 'lonja', 'Lj6g0018116' => 'lja', 'Lsat_1_v5_gn_4_136040' => 'lsa', 'Lsat_1_v5_gn_5_187461' => 'lsa', 'Lsat_1_v5_gn_5_77001' => 'lsa', 'Lsat_1_v5_gn_9_4461' => 'lsa', 'Manes.01G210100' => 'mes', 'Manes.03G185600' => 'mes', 'Manes.05G073300' => 'mes', 'Manes.09G120300' => 'mes', 'Manes.15G022100' => 'mes', 'Mapoly0096s0053' => 'mpo', 'MBI03_g14058_MAGBIO' => 'mbi', 'MBI03_g33876_MAGBIO' => 'mbi', 'MBI03_g36854_MAGBIO' => 'mbi', 'MBI17_g11997_MAGBIO' => 'mbi', 'MD03G1269000' => 'mdo', 'MD04G1179600' => 'mdo', 'MD11G1289800' => 'mdo', 'MD12G1194700' => 'mdo', 'MD13G1182100' => 'mdo', 'MD13G1182200' => 'mdo', 'MD16G1182600' => 'mdo', 'Medtr2g021400' => 'mtr', 'Medtr2g021470' => 'mtr', 'Medtr2g105810' => 'mtr', 'Medtr3g033580' => 'mtr', 'Medtr6g007970' => 'mtr', 'Medtr7g056330' => 'mtr', 'Medtr7g074290' => 'mtr', 'Medtr7g074380' => 'mtr', 'Medtr7g094550' => 'mtr', 'Medtr8g069995' => 'mtr', 'MELO3C014345.2' => 'cme', 'MELO3C021395.2' => 'cme', 'Migut.D00262' => 'egut', 'Migut.G00257' => 'egut', 'MSTRG.21575' => 'ama', 'MSTRG.3985' => 'ama', 'Nitab4.5_0000295g0140' => 'nta', 'Nitab4.5_0000732g0140' => 'nta', 'Nitab4.5_0003162g0020' => 'nta', 'Nitab4.5_0006180g0090' => 'nta', 'Nitab4.5_0006390g0010' => 'nta', 'Nitab4.5_0007392g0040' => 'nta', 'Nn1g02140' => 'nnu', 'Nn4g26168' => 'nnu', 'Nn5g26754' => 'nnu', 'Oeu001433.1' => 'oeu', 'Oeu010299.2' => 'oeu', 'Oeu011171.1' => 'oeu', 'Oeu037675.1' => 'oeu', 'Oeu038359.1' => 'oeu', 'Oeu063834.1' => 'oeu', 'Oeu063835.1' => 'oeu', 'Os05g0312000' => 'osa', 'Os07g0211101' => 'osa', 'Os07g0211200' => 'osa', 'Os07g0681500' => 'osa', 'Peaxi162Scf00095g01015' => 'pax', 'Peaxi162Scf00104g00329' => 'pax', 'Peaxi162Scf00161g00137' => 'pax', 'PGR004G1665' => 'pgr', 'PGR031G2937' => 'pgr', 'PGR119G2145' => 'pgr', 'PGSC0003DMG400004351' => 'stu', 'PGSC0003DMG400014625' => 'stu', 'PGSC0003DMG401000943' => 'stu', 'Phvul.001G148600' => 'pvu', 'Phvul.004G001700' => 'pvu', 'Phvul.006G154900' => 'pvu', 'Phvul.008G078200' => 'pvu', 'Phvul.011G136500' => 'pvu', 'Potri.002G215600' => 'ptr', 'Potri.008G201600' => 'ptr', 'Potri.014G138400' => 'ptr', 'Potri.016G142500' => 'ptr', 'Pp3c16_10580' => 'ppa', 'Pp3c5_25280' => 'ppa', 'Prupe.1G150000' => 'ppe', 'Prupe.1G150100' => 'ppe', 'Prupe.6G299600' => 'ppe', 'Prupe.8G245000' => 'ppe', 'Psat0s4927g0040' => 'psa', 'Psat1g052080' => 'psa', 'Psat1g183800' => 'psa', 'Psat3g113840' => 'psa', 'Psat3g126120' => 'psa', 'Psat3g126160' => 'psa', 'Psat3g158760' => 'psa', 'Psat3g158840' => 'psa', 'PSO170G2858' => 'pso', 'PSO339G0606' => 'pso', 'PSO384G4709' => 'pso', 'PSO407G0334' => 'pso', 'QL04p040276' => 'qlo', 'QL06p005458' => 'qlo', 'QL06p005472' => 'qlo', 'QL07p030546' => 'qlo', 'QL07p031519' => 'qlo', 'QL09p050949' => 'qlo', 'QL09p050966' => 'qlo', 'QL09p051067' => 'qlo', 'QL12p022706' => 'qlo', 'RcHm_v2.0_Chr2g0119601' => 'rch', 'RcHm_v2.0_Chr3g0459591' => 'rch', 'RcHm_v2.0_Chr4g0418521' => 'rch', 'RcHm_v2.0_Chr4g0418531' => 'rch', 'RcHm_v2.0_Chr4g0418541' => 'rch', 'RcHm_v2.0_Chr6g0291641' => 'rch', 'Rhsim01G0086300' => 'rsi', 'Rhsim01G0276300' => 'rsi', 'Rhsim01G0276500' => 'rsi', 'Rhsim04G0207700' => 'rsi', 'Rhsim05G0234500' => 'rsi', 'Rhsim13G0022400' => 'rsi', 'Sabra02G0167900' => 'sbr', 'Sabra04G0158500' => 'sbr', 'Sabra08G0159800' => 'sbr', 'Sabra10G0011500' => 'sbr', 'Sabra14G0104400' => 'sbr', 'SalBow2G2440' => 'sbo', 'SalBow4G2265' => 'sbo', 'Sc02g0000060' => 'sci', 'Sc05g0005020' => 'sci', 'Sc13g0003890' => 'sci', 'Sed0014865' => 'sed', 'Sed0017224' => 'sed', 'Sed0026391' => 'sed', 'SEGI_00063' => 'sgi', 'SEGI_10967' => 'sgi', 'SEGI_17510' => 'sgi', 'SEGI_24396' => 'sgi', 'SEGI_39719' => 'sgi', 'SEGI_41392' => 'sgi', 'SGA_v2.0_scaffold11G05794' => 'sas', 'SGA_v2.0_scaffold142G35607' => 'sas', 'SGA_v2.0_scaffold1G00447' => 'sas', 'SHI15388' => 'shi', 'SHI15394' => 'shi', 'SHI15396' => 'shi', 'SHI15399' => 'shi', 'SMO343G0151' => 'smo', 'SMO367G1118' => 'smo', 'Solyc01g080200.3' => 'sly', 'Solyc06g008960.3' => 'sly', 'Solyc09g064780.3' => 'sly', 'Sopen01g031980' => 'spe', 'Sopen06g003710' => 'spe', 'Sopen09g026460' => 'spe', 'Sp3g21240' => 'spa', 'Sp4g30030' => 'spa', 'TAR365G0022' => 'tar', 'TAR365G1023' => 'tar', 'TAR365G1253' => 'tar', 'TAR623G0078' => 'tar', 'TAR623G1721' => 'tar', 'TAR633G0959' => 'tar', 'THA.LOC104802225' => 'tha', 'THA.LOC104804769' => 'tha', 'THA.LOC104808660' => 'tha', 'THA.LOC104812792' => 'tha', 'Thecc.01G284000' => 'tca', 'Thecc.04G220600' => 'tca', 'Thecc.05G268900' => 'tca', 'Thecc.08G171100' => 'tca', 'Thhalv10001284m.g' => 'esa', 'Thhalv10019912m.g' => 'esa', 'TPR.G14189' => 'tpr', 'TPR.G18110' => 'tpr', 'TPR.G18130' => 'tpr', 'TPR.G18131' => 'tpr', 'TPR.G18140' => 'tpr', 'TPR.G24282' => 'tpr', 'TPR.G25221' => 'tpr', 'TPR.G29267' => 'tpr', 'TPR.G35315' => 'tpr', 'TPR.G36173' => 'tpr', 'TWI09G0794' => 'twi', 'TWI59G1348' => 'twi', 'TWI74G0430' => 'twi', 'unitig_26.g8940' => 'ugi', 'unitig_749.g13744' => 'ugi', 'unitig_749.g13745' => 'ugi', 'vmacro08269' => 'vma', 'vmacro14937' => 'vma', 'vmacro20401' => 'vma', 'VMungo0464G1349' => 'vmu', 'VMungo0540G0289' => 'vmu', 'VMungo1215G1590' => 'vmu', 'VMungo1309G0221' => 'vmu', 'VMungo1309G2815' => 'vmu', 'VMungo1383G0239' => 'vmu', 'VMungo1383G2910' => 'vmu', 'Zm00001eb095270' => 'zma', 'Zm00001eb095280' => 'zma', 'Zm00001eb111630' => 'zma', 'Zm00001eb237080' => 'zma', 'Zm00001eb273740' => 'zma', 'Zm00001eb285040' => 'zma', 'Zm00001eb330790' => 'zma', 'Zm00001eb337380' => 'zma' ) $gf_id = 'HOM05D001484' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001484' ) $data_identifier = 'HOM05D001484' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 2, 'aly' => (int) 2, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 22, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 7, 'hma' => (int) 2, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 7, 'mtr' => (int) 10, 'cme' => (int) 2, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 4, 'ppa' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 4, 'qlo' => (int) 9, 'rch' => (int) 6, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 10, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 7, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb337380' $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' => 'HOM05D001484', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p31500' => 'bna', 'A05p00020' => 'bna', 'A07p08820' => 'bna', 'Aa31LG4G3300' => 'aar', 'Aa31LG8G10030' => 'aar', 'Actinidia00731' => 'ach', 'Actinidia11473' => 'ach', 'Actinidia23469' => 'ach', 'Actinidia24318' => 'ach', 'Actinidia40196' => 'ach', 'Actinidia40197' => 'ach', 'Actinidia40198' => 'ach', 'Ah.08g212990' => 'amhyb', 'Ah.15g091720' => 'amhyb', 'AL3G38260' => 'aly', 'AL4G47710' => 'aly', 'Aqoxy2G00671' => 'aox', 'Aqoxy2G03236' => 'aox', 'arahy.Tifrunner.gnm1.ann1.05IDCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KR684' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATY3SJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK6QJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6APGL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IDT7Z9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM073U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ0R87' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LE7RV4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT4QRX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V5ENPK' => 'arhy', 'AT2G48110' => 'ath', 'AT3G23590' => 'ath', 'ATR0626G186' => 'atr', 'ATR1127G141' => 'atr', 'Atru.chr4.2583' => 'acertr', 'Atru.chr5.1358' => 'acertr', 'Atru.chr5.1359' => 'acertr', 'Atru.chr8.46' => 'acertr', 'AUR62002640' => 'cqu', 'AUR62030055' => 'cqu', 'AUR62033713' => 'cqu', 'AUR62033714' => 'cqu', 'AUR62036795' => 'cqu', 'AUR62039891' => 'cqu', 'BcaB02g08737' => 'bca', 'BcaB04g20441' => 'bca', 'BcaB06g26509' => 'bca', 'BcaB06g26510' => 'bca', 'BcaB06g26511' => 'bca', 'BcaB06g26512' => 'bca', 'BcaB06g26513' => 'bca', 'BcaC02g12564' => 'bca', 'BcaC02g12565' => 'bca', 'BcaC02g12794' => 'bca', 'BcaC02g12795' => 'bca', 'BcaC02g12796' => 'bca', 'BcaC06g35541' => 'bca', 'BNapus_Darmor_BZH_scaffold_188p00080' => 'bna', 'BNapus_Darmor_BZH_scaffold_188p00090' => 'bna', 'BolC1t03972H' => 'bol', 'BolC1t03973H' => 'bol', 'BolC4t21680H' => 'bol', 'BolC7t41863H' => 'bol', 'BolSC55t61227H' => 'bol', 'BolSC55t61228H' => 'bol', 'BraA01t03278Z' => 'bra', 'BraA05t18998Z' => 'bra', 'BraA07t28673Z' => 'bra', 'C01p40150' => 'bna', 'C05p12370' => 'bna', 'C07p13680' => 'bna', 'CAN.G1006.16' => 'can', 'CAN.G1006.17' => 'can', 'CAN.G1170.2' => 'can', 'CAN.G962.7' => 'can', 'CANSAT25G2179' => 'cansat', 'CANSAT78G1573' => 'cansat', 'CARHR099510' => 'chi', 'CARHR143510' => 'chi', 'Carub.0003s2380' => 'cru', 'Carub.0004s3082' => 'cru', 'Ca_00614_v3' => 'car', 'Ca_07801_v3' => 'car', 'Ca_08567_v3' => 'car', 'Ca_09571_v3' => 'car', 'CBR_g19290' => 'cbr', 'Cc01_g19770' => 'ccan', 'Cc03_g03030' => 'ccan', 'CDE07G0968' => 'cde', 'CDE09G1441' => 'cde', 'Cfa006103' => 'cfa', 'Cfa015573' => 'cfa', 'Cfa016988' => 'cfa', 'Ciclev10006738m.g' => 'ccl', 'Ciclev10010920m.g' => 'ccl', 'Ciclev10018517m.g' => 'ccl', 'CiPaw.01G159200' => 'cil', 'CiPaw.02G091000' => 'cil', 'CiPaw.02G091100' => 'cil', 'CiPaw.08G103100' => 'cil', 'CiPaw.09G224900' => 'cil', 'ClCG06G005740' => 'cla', 'ClCG07G000090' => 'cla', 'ClCG07G000100' => 'cla', 'COL.COLO4_09143' => 'col', 'COL.COLO4_25124' => 'col', 'Cpa.g.sc16.34' => 'cpa', 'Cpa.g.sc3504.1' => 'cpa', 'Cpa.g.sc60.37' => 'cpa', 'CsaV3_6G018520' => 'csa', 'CsaV3_6G036860' => 'csa', 'CSS0001072' => 'camsi', 'CSS0020208' => 'camsi', 'CSS0021253' => 'camsi', 'CSS0022190' => 'camsi', 'CSS0036150' => 'camsi', 'CSS0040442' => 'camsi', 'CSS0042300' => 'camsi', 'CSS0045298' => 'camsi', 'DCAR_012449' => 'dca', 'DCAR_018405' => 'dca', 'DCAR_024573' => 'dca', 'DCAR_030591' => 'dca', 'Dinv16926' => 'din', 'Dinv32963' => 'din', 'Dinv38382' => 'din', 'Dinv38383' => 'din', 'Duzib133G0974' => 'dzi', 'Duzib138G1867' => 'dzi', 'Duzib211G0420' => 'dzi', 'Duzib212G0930' => 'dzi', 'ECA234G1645' => 'eca', 'ECA247G3467' => 'eca', 'ECA248G1703' => 'eca', 'EL10Ac3g06327' => 'bvu', 'EL10Ac7g17204' => 'bvu', 'Eucgr.A00855' => 'egr', 'Eucgr.A00858' => 'egr', 'Eucgr.H01520' => 'egr', 'Eucgr.H03604' => 'egr', 'Eucgr.L03465' => 'egr', 'Eucgr.L03466' => 'egr', 'FAN01G0988' => 'fan', 'FAN02G3892' => 'fan', 'FAN05G3381' => 'fan', 'FAN07G0967' => 'fan', 'FAN07G1493' => 'fan', 'FAN08G3125' => 'fan', 'FAN09G0402' => 'fan', 'FAN12G2594' => 'fan', 'FAN12G3879' => 'fan', 'FAN14G1546' => 'fan', 'FAN15G3626' => 'fan', 'FAN17G0588' => 'fan', 'FAN17G0609' => 'fan', 'FAN18G2817' => 'fan', 'FAN19G1305' => 'fan', 'FAN20G1787' => 'fan', 'FAN22G0073' => 'fan', 'FAN22G0352' => 'fan', 'FAN22G0368' => 'fan', 'FAN22G2273' => 'fan', 'FAN24G1998' => 'fan', 'FAN27G1317' => 'fan', 'FvH4_2g23980' => 'fve', 'FvH4_4g14380' => 'fve', 'FvH4_4g14390' => 'fve', 'FvH4_6g09250' => 'fve', 'Glyma.03G151100' => 'gma', 'Glyma.04G122550' => 'gma', 'Glyma.05G001600' => 'gma', 'Glyma.09G270766' => 'gma', 'Glyma.09G270832' => 'gma', 'Glyma.13G209800' => 'gma', 'Glyma.15G102800' => 'gma', 'Glyma.18G218900' => 'gma', 'Glyma.19G001500' => 'gma', 'Glyma.19G153600' => 'gma', 'Gohir.A02G028600' => 'ghi', 'Gohir.A08G045000' => 'ghi', 'Gohir.A11G120500' => 'ghi', 'Gohir.A12G006200' => 'ghi', 'Gohir.A12G006250' => 'ghi', 'Gohir.D02G036300' => 'ghi', 'Gohir.D08G054700' => 'ghi', 'Gohir.D11G125600' => 'ghi', 'Gohir.D12G005700' => 'ghi', 'Gorai.004G055200' => 'gra', 'Gorai.005G040400' => 'gra', 'Gorai.007G134500' => 'gra', 'Gorai.008G005500' => 'gra', 'GSVIVG01011094001' => 'vvi', 'GSVIVG01017879001' => 'vvi', 'GSVIVG01025988001' => 'vvi', 'GSVIVG01029847001' => 'vvi', 'HanXRQChr10g0282901' => 'han', 'HanXRQChr10g0310371' => 'han', 'HanXRQChr10g0315041' => 'han', 'HanXRQChr11g0327651' => 'han', 'HanXRQChr12g0359391' => 'han', 'Haze_00972' => 'cav', 'Haze_00973' => 'cav', 'Haze_00974' => 'cav', 'Haze_04747' => 'cav', 'Haze_04749' => 'cav', 'Haze_04750' => 'cav', 'Haze_21217' => 'cav', 'Hma1.2p1_1037F.1_g250680' => 'hma', 'Hma1.2p1_1644F.1_g295320' => 'hma', 'HPP92_011322' => 'vpl', 'HPP92_011323' => 'vpl', 'HPP92_011324' => 'vpl', 'HPP92_011325' => 'vpl', 'HPP92_011326' => 'vpl', 'Hund12205' => 'sun', 'Hund17957' => 'sun', 'Lalb_Chr06g0176771' => 'lal', 'Lalb_Chr18g0056021' => 'lal', 'Lalb_Chr18g0056031' => 'lal', 'Lalb_Chr18g0056041' => 'lal', 'Lalb_Chr20g0107751' => 'lal', 'Lalb_Chr20g0118371' => 'lal', 'Lj1g0010239' => 'lja', 'Lj1g0017101' => 'lja', 'Lj2A1178G40' => 'lonja', 'Lj2A54G84' => 'lonja', 'Lj2g0015248' => 'lja', 'Lj3A761T51' => 'lonja', 'Lj6g0018116' => 'lja', 'Lsat_1_v5_gn_4_136040' => 'lsa', 'Lsat_1_v5_gn_5_187461' => 'lsa', 'Lsat_1_v5_gn_5_77001' => 'lsa', 'Lsat_1_v5_gn_9_4461' => 'lsa', 'Manes.01G210100' => 'mes', 'Manes.03G185600' => 'mes', 'Manes.05G073300' => 'mes', 'Manes.09G120300' => 'mes', 'Manes.15G022100' => 'mes', 'Mapoly0096s0053' => 'mpo', 'MBI03_g14058_MAGBIO' => 'mbi', 'MBI03_g33876_MAGBIO' => 'mbi', 'MBI03_g36854_MAGBIO' => 'mbi', 'MBI17_g11997_MAGBIO' => 'mbi', 'MD03G1269000' => 'mdo', 'MD04G1179600' => 'mdo', 'MD11G1289800' => 'mdo', 'MD12G1194700' => 'mdo', 'MD13G1182100' => 'mdo', 'MD13G1182200' => 'mdo', 'MD16G1182600' => 'mdo', 'Medtr2g021400' => 'mtr', 'Medtr2g021470' => 'mtr', 'Medtr2g105810' => 'mtr', 'Medtr3g033580' => 'mtr', 'Medtr6g007970' => 'mtr', 'Medtr7g056330' => 'mtr', 'Medtr7g074290' => 'mtr', 'Medtr7g074380' => 'mtr', 'Medtr7g094550' => 'mtr', 'Medtr8g069995' => 'mtr', 'MELO3C014345.2' => 'cme', 'MELO3C021395.2' => 'cme', 'Migut.D00262' => 'egut', 'Migut.G00257' => 'egut', 'MSTRG.21575' => 'ama', 'MSTRG.3985' => 'ama', 'Nitab4.5_0000295g0140' => 'nta', 'Nitab4.5_0000732g0140' => 'nta', 'Nitab4.5_0003162g0020' => 'nta', 'Nitab4.5_0006180g0090' => 'nta', 'Nitab4.5_0006390g0010' => 'nta', 'Nitab4.5_0007392g0040' => 'nta', 'Nn1g02140' => 'nnu', 'Nn4g26168' => 'nnu', 'Nn5g26754' => 'nnu', 'Oeu001433.1' => 'oeu', 'Oeu010299.2' => 'oeu', 'Oeu011171.1' => 'oeu', 'Oeu037675.1' => 'oeu', 'Oeu038359.1' => 'oeu', 'Oeu063834.1' => 'oeu', 'Oeu063835.1' => 'oeu', 'Os05g0312000' => 'osa', 'Os07g0211101' => 'osa', 'Os07g0211200' => 'osa', 'Os07g0681500' => 'osa', 'Peaxi162Scf00095g01015' => 'pax', 'Peaxi162Scf00104g00329' => 'pax', 'Peaxi162Scf00161g00137' => 'pax', 'PGR004G1665' => 'pgr', 'PGR031G2937' => 'pgr', 'PGR119G2145' => 'pgr', 'PGSC0003DMG400004351' => 'stu', 'PGSC0003DMG400014625' => 'stu', 'PGSC0003DMG401000943' => 'stu', 'Phvul.001G148600' => 'pvu', 'Phvul.004G001700' => 'pvu', 'Phvul.006G154900' => 'pvu', 'Phvul.008G078200' => 'pvu', 'Phvul.011G136500' => 'pvu', 'Potri.002G215600' => 'ptr', 'Potri.008G201600' => 'ptr', 'Potri.014G138400' => 'ptr', 'Potri.016G142500' => 'ptr', 'Pp3c16_10580' => 'ppa', 'Pp3c5_25280' => 'ppa', 'Prupe.1G150000' => 'ppe', 'Prupe.1G150100' => 'ppe', 'Prupe.6G299600' => 'ppe', 'Prupe.8G245000' => 'ppe', 'Psat0s4927g0040' => 'psa', 'Psat1g052080' => 'psa', 'Psat1g183800' => 'psa', 'Psat3g113840' => 'psa', 'Psat3g126120' => 'psa', 'Psat3g126160' => 'psa', 'Psat3g158760' => 'psa', 'Psat3g158840' => 'psa', 'PSO170G2858' => 'pso', 'PSO339G0606' => 'pso', 'PSO384G4709' => 'pso', 'PSO407G0334' => 'pso', 'QL04p040276' => 'qlo', 'QL06p005458' => 'qlo', 'QL06p005472' => 'qlo', 'QL07p030546' => 'qlo', 'QL07p031519' => 'qlo', 'QL09p050949' => 'qlo', 'QL09p050966' => 'qlo', 'QL09p051067' => 'qlo', 'QL12p022706' => 'qlo', 'RcHm_v2.0_Chr2g0119601' => 'rch', 'RcHm_v2.0_Chr3g0459591' => 'rch', 'RcHm_v2.0_Chr4g0418521' => 'rch', 'RcHm_v2.0_Chr4g0418531' => 'rch', 'RcHm_v2.0_Chr4g0418541' => 'rch', 'RcHm_v2.0_Chr6g0291641' => 'rch', 'Rhsim01G0086300' => 'rsi', 'Rhsim01G0276300' => 'rsi', 'Rhsim01G0276500' => 'rsi', 'Rhsim04G0207700' => 'rsi', 'Rhsim05G0234500' => 'rsi', 'Rhsim13G0022400' => 'rsi', 'Sabra02G0167900' => 'sbr', 'Sabra04G0158500' => 'sbr', 'Sabra08G0159800' => 'sbr', 'Sabra10G0011500' => 'sbr', 'Sabra14G0104400' => 'sbr', 'SalBow2G2440' => 'sbo', 'SalBow4G2265' => 'sbo', 'Sc02g0000060' => 'sci', 'Sc05g0005020' => 'sci', 'Sc13g0003890' => 'sci', 'Sed0014865' => 'sed', 'Sed0017224' => 'sed', 'Sed0026391' => 'sed', 'SEGI_00063' => 'sgi', 'SEGI_10967' => 'sgi', 'SEGI_17510' => 'sgi', 'SEGI_24396' => 'sgi', 'SEGI_39719' => 'sgi', 'SEGI_41392' => 'sgi', 'SGA_v2.0_scaffold11G05794' => 'sas', 'SGA_v2.0_scaffold142G35607' => 'sas', 'SGA_v2.0_scaffold1G00447' => 'sas', 'SHI15388' => 'shi', 'SHI15394' => 'shi', 'SHI15396' => 'shi', 'SHI15399' => 'shi', 'SMO343G0151' => 'smo', 'SMO367G1118' => 'smo', 'Solyc01g080200.3' => 'sly', 'Solyc06g008960.3' => 'sly', 'Solyc09g064780.3' => 'sly', 'Sopen01g031980' => 'spe', 'Sopen06g003710' => 'spe', 'Sopen09g026460' => 'spe', 'Sp3g21240' => 'spa', 'Sp4g30030' => 'spa', 'TAR365G0022' => 'tar', 'TAR365G1023' => 'tar', 'TAR365G1253' => 'tar', 'TAR623G0078' => 'tar', 'TAR623G1721' => 'tar', 'TAR633G0959' => 'tar', 'THA.LOC104802225' => 'tha', 'THA.LOC104804769' => 'tha', 'THA.LOC104808660' => 'tha', 'THA.LOC104812792' => 'tha', 'Thecc.01G284000' => 'tca', 'Thecc.04G220600' => 'tca', 'Thecc.05G268900' => 'tca', 'Thecc.08G171100' => 'tca', 'Thhalv10001284m.g' => 'esa', 'Thhalv10019912m.g' => 'esa', 'TPR.G14189' => 'tpr', 'TPR.G18110' => 'tpr', 'TPR.G18130' => 'tpr', 'TPR.G18131' => 'tpr', 'TPR.G18140' => 'tpr', 'TPR.G24282' => 'tpr', 'TPR.G25221' => 'tpr', 'TPR.G29267' => 'tpr', 'TPR.G35315' => 'tpr', 'TPR.G36173' => 'tpr', 'TWI09G0794' => 'twi', 'TWI59G1348' => 'twi', 'TWI74G0430' => 'twi', 'unitig_26.g8940' => 'ugi', 'unitig_749.g13744' => 'ugi', 'unitig_749.g13745' => 'ugi', 'vmacro08269' => 'vma', 'vmacro14937' => 'vma', 'vmacro20401' => 'vma', 'VMungo0464G1349' => 'vmu', 'VMungo0540G0289' => 'vmu', 'VMungo1215G1590' => 'vmu', 'VMungo1309G0221' => 'vmu', 'VMungo1309G2815' => 'vmu', 'VMungo1383G0239' => 'vmu', 'VMungo1383G2910' => 'vmu', 'Zm00001eb095270' => 'zma', 'Zm00001eb095280' => 'zma', 'Zm00001eb111630' => 'zma', 'Zm00001eb237080' => 'zma', 'Zm00001eb273740' => 'zma', 'Zm00001eb285040' => 'zma', 'Zm00001eb330790' => 'zma', 'Zm00001eb337380' => 'zma' ), 'gf_id' => 'HOM05D001484', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001484' ), 'data_identifier' => 'HOM05D001484', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001484', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p31500' => 'bna', 'A05p00020' => 'bna', 'A07p08820' => 'bna', 'Aa31LG4G3300' => 'aar', 'Aa31LG8G10030' => 'aar', 'Actinidia00731' => 'ach', 'Actinidia11473' => 'ach', 'Actinidia23469' => 'ach', 'Actinidia24318' => 'ach', 'Actinidia40196' => 'ach', 'Actinidia40197' => 'ach', 'Actinidia40198' => 'ach', 'Ah.08g212990' => 'amhyb', 'Ah.15g091720' => 'amhyb', 'AL3G38260' => 'aly', 'AL4G47710' => 'aly', 'Aqoxy2G00671' => 'aox', 'Aqoxy2G03236' => 'aox', 'arahy.Tifrunner.gnm1.ann1.05IDCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KR684' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATY3SJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK6QJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6APGL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IDT7Z9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM073U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ0R87' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LE7RV4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT4QRX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V5ENPK' => 'arhy', 'AT2G48110' => 'ath', 'AT3G23590' => 'ath', 'ATR0626G186' => 'atr', 'ATR1127G141' => 'atr', 'Atru.chr4.2583' => 'acertr', 'Atru.chr5.1358' => 'acertr', 'Atru.chr5.1359' => 'acertr', 'Atru.chr8.46' => 'acertr', 'AUR62002640' => 'cqu', 'AUR62030055' => 'cqu', 'AUR62033713' => 'cqu', 'AUR62033714' => 'cqu', 'AUR62036795' => 'cqu', 'AUR62039891' => 'cqu', 'BcaB02g08737' => 'bca', 'BcaB04g20441' => 'bca', 'BcaB06g26509' => 'bca', 'BcaB06g26510' => 'bca', 'BcaB06g26511' => 'bca', 'BcaB06g26512' => 'bca', 'BcaB06g26513' => 'bca', 'BcaC02g12564' => 'bca', 'BcaC02g12565' => 'bca', 'BcaC02g12794' => 'bca', 'BcaC02g12795' => 'bca', 'BcaC02g12796' => 'bca', 'BcaC06g35541' => 'bca', 'BNapus_Darmor_BZH_scaffold_188p00080' => 'bna', 'BNapus_Darmor_BZH_scaffold_188p00090' => 'bna', 'BolC1t03972H' => 'bol', 'BolC1t03973H' => 'bol', 'BolC4t21680H' => 'bol', 'BolC7t41863H' => 'bol', 'BolSC55t61227H' => 'bol', 'BolSC55t61228H' => 'bol', 'BraA01t03278Z' => 'bra', 'BraA05t18998Z' => 'bra', 'BraA07t28673Z' => 'bra', 'C01p40150' => 'bna', 'C05p12370' => 'bna', 'C07p13680' => 'bna', 'CAN.G1006.16' => 'can', 'CAN.G1006.17' => 'can', 'CAN.G1170.2' => 'can', 'CAN.G962.7' => 'can', 'CANSAT25G2179' => 'cansat', 'CANSAT78G1573' => 'cansat', 'CARHR099510' => 'chi', 'CARHR143510' => 'chi', 'Carub.0003s2380' => 'cru', 'Carub.0004s3082' => 'cru', 'Ca_00614_v3' => 'car', 'Ca_07801_v3' => 'car', 'Ca_08567_v3' => 'car', 'Ca_09571_v3' => 'car', 'CBR_g19290' => 'cbr', 'Cc01_g19770' => 'ccan', 'Cc03_g03030' => 'ccan', 'CDE07G0968' => 'cde', 'CDE09G1441' => 'cde', 'Cfa006103' => 'cfa', 'Cfa015573' => 'cfa', 'Cfa016988' => 'cfa', 'Ciclev10006738m.g' => 'ccl', 'Ciclev10010920m.g' => 'ccl', 'Ciclev10018517m.g' => 'ccl', 'CiPaw.01G159200' => 'cil', 'CiPaw.02G091000' => 'cil', 'CiPaw.02G091100' => 'cil', 'CiPaw.08G103100' => 'cil', 'CiPaw.09G224900' => 'cil', 'ClCG06G005740' => 'cla', 'ClCG07G000090' => 'cla', 'ClCG07G000100' => 'cla', 'COL.COLO4_09143' => 'col', 'COL.COLO4_25124' => 'col', 'Cpa.g.sc16.34' => 'cpa', 'Cpa.g.sc3504.1' => 'cpa', 'Cpa.g.sc60.37' => 'cpa', 'CsaV3_6G018520' => 'csa', 'CsaV3_6G036860' => 'csa', 'CSS0001072' => 'camsi', 'CSS0020208' => 'camsi', 'CSS0021253' => 'camsi', 'CSS0022190' => 'camsi', 'CSS0036150' => 'camsi', 'CSS0040442' => 'camsi', 'CSS0042300' => 'camsi', 'CSS0045298' => 'camsi', 'DCAR_012449' => 'dca', 'DCAR_018405' => 'dca', 'DCAR_024573' => 'dca', 'DCAR_030591' => 'dca', 'Dinv16926' => 'din', 'Dinv32963' => 'din', 'Dinv38382' => 'din', 'Dinv38383' => 'din', 'Duzib133G0974' => 'dzi', 'Duzib138G1867' => 'dzi', 'Duzib211G0420' => 'dzi', 'Duzib212G0930' => 'dzi', 'ECA234G1645' => 'eca', 'ECA247G3467' => 'eca', 'ECA248G1703' => 'eca', 'EL10Ac3g06327' => 'bvu', 'EL10Ac7g17204' => 'bvu', 'Eucgr.A00855' => 'egr', 'Eucgr.A00858' => 'egr', 'Eucgr.H01520' => 'egr', 'Eucgr.H03604' => 'egr', 'Eucgr.L03465' => 'egr', 'Eucgr.L03466' => 'egr', 'FAN01G0988' => 'fan', 'FAN02G3892' => 'fan', 'FAN05G3381' => 'fan', 'FAN07G0967' => 'fan', 'FAN07G1493' => 'fan', 'FAN08G3125' => 'fan', 'FAN09G0402' => 'fan', 'FAN12G2594' => 'fan', 'FAN12G3879' => 'fan', 'FAN14G1546' => 'fan', 'FAN15G3626' => 'fan', 'FAN17G0588' => 'fan', 'FAN17G0609' => 'fan', 'FAN18G2817' => 'fan', 'FAN19G1305' => 'fan', 'FAN20G1787' => 'fan', 'FAN22G0073' => 'fan', 'FAN22G0352' => 'fan', 'FAN22G0368' => 'fan', 'FAN22G2273' => 'fan', 'FAN24G1998' => 'fan', 'FAN27G1317' => 'fan', 'FvH4_2g23980' => 'fve', 'FvH4_4g14380' => 'fve', 'FvH4_4g14390' => 'fve', 'FvH4_6g09250' => 'fve', 'Glyma.03G151100' => 'gma', 'Glyma.04G122550' => 'gma', 'Glyma.05G001600' => 'gma', 'Glyma.09G270766' => 'gma', 'Glyma.09G270832' => 'gma', 'Glyma.13G209800' => 'gma', 'Glyma.15G102800' => 'gma', 'Glyma.18G218900' => 'gma', 'Glyma.19G001500' => 'gma', 'Glyma.19G153600' => 'gma', 'Gohir.A02G028600' => 'ghi', 'Gohir.A08G045000' => 'ghi', 'Gohir.A11G120500' => 'ghi', 'Gohir.A12G006200' => 'ghi', 'Gohir.A12G006250' => 'ghi', 'Gohir.D02G036300' => 'ghi', 'Gohir.D08G054700' => 'ghi', 'Gohir.D11G125600' => 'ghi', 'Gohir.D12G005700' => 'ghi', 'Gorai.004G055200' => 'gra', 'Gorai.005G040400' => 'gra', 'Gorai.007G134500' => 'gra', 'Gorai.008G005500' => 'gra', 'GSVIVG01011094001' => 'vvi', 'GSVIVG01017879001' => 'vvi', 'GSVIVG01025988001' => 'vvi', 'GSVIVG01029847001' => 'vvi', 'HanXRQChr10g0282901' => 'han', 'HanXRQChr10g0310371' => 'han', 'HanXRQChr10g0315041' => 'han', 'HanXRQChr11g0327651' => 'han', 'HanXRQChr12g0359391' => 'han', 'Haze_00972' => 'cav', 'Haze_00973' => 'cav', 'Haze_00974' => 'cav', 'Haze_04747' => 'cav', 'Haze_04749' => 'cav', 'Haze_04750' => 'cav', 'Haze_21217' => 'cav', 'Hma1.2p1_1037F.1_g250680' => 'hma', 'Hma1.2p1_1644F.1_g295320' => 'hma', 'HPP92_011322' => 'vpl', 'HPP92_011323' => 'vpl', 'HPP92_011324' => 'vpl', 'HPP92_011325' => 'vpl', 'HPP92_011326' => 'vpl', 'Hund12205' => 'sun', 'Hund17957' => 'sun', 'Lalb_Chr06g0176771' => 'lal', 'Lalb_Chr18g0056021' => 'lal', 'Lalb_Chr18g0056031' => 'lal', 'Lalb_Chr18g0056041' => 'lal', 'Lalb_Chr20g0107751' => 'lal', 'Lalb_Chr20g0118371' => 'lal', 'Lj1g0010239' => 'lja', 'Lj1g0017101' => 'lja', 'Lj2A1178G40' => 'lonja', 'Lj2A54G84' => 'lonja', 'Lj2g0015248' => 'lja', 'Lj3A761T51' => 'lonja', 'Lj6g0018116' => 'lja', 'Lsat_1_v5_gn_4_136040' => 'lsa', 'Lsat_1_v5_gn_5_187461' => 'lsa', 'Lsat_1_v5_gn_5_77001' => 'lsa', 'Lsat_1_v5_gn_9_4461' => 'lsa', 'Manes.01G210100' => 'mes', 'Manes.03G185600' => 'mes', 'Manes.05G073300' => 'mes', 'Manes.09G120300' => 'mes', 'Manes.15G022100' => 'mes', 'Mapoly0096s0053' => 'mpo', 'MBI03_g14058_MAGBIO' => 'mbi', 'MBI03_g33876_MAGBIO' => 'mbi', 'MBI03_g36854_MAGBIO' => 'mbi', 'MBI17_g11997_MAGBIO' => 'mbi', 'MD03G1269000' => 'mdo', 'MD04G1179600' => 'mdo', 'MD11G1289800' => 'mdo', 'MD12G1194700' => 'mdo', 'MD13G1182100' => 'mdo', 'MD13G1182200' => 'mdo', 'MD16G1182600' => 'mdo', 'Medtr2g021400' => 'mtr', 'Medtr2g021470' => 'mtr', 'Medtr2g105810' => 'mtr', 'Medtr3g033580' => 'mtr', 'Medtr6g007970' => 'mtr', 'Medtr7g056330' => 'mtr', 'Medtr7g074290' => 'mtr', 'Medtr7g074380' => 'mtr', 'Medtr7g094550' => 'mtr', 'Medtr8g069995' => 'mtr', 'MELO3C014345.2' => 'cme', 'MELO3C021395.2' => 'cme', 'Migut.D00262' => 'egut', 'Migut.G00257' => 'egut', 'MSTRG.21575' => 'ama', 'MSTRG.3985' => 'ama', 'Nitab4.5_0000295g0140' => 'nta', 'Nitab4.5_0000732g0140' => 'nta', 'Nitab4.5_0003162g0020' => 'nta', 'Nitab4.5_0006180g0090' => 'nta', 'Nitab4.5_0006390g0010' => 'nta', 'Nitab4.5_0007392g0040' => 'nta', 'Nn1g02140' => 'nnu', 'Nn4g26168' => 'nnu', 'Nn5g26754' => 'nnu', 'Oeu001433.1' => 'oeu', 'Oeu010299.2' => 'oeu', 'Oeu011171.1' => 'oeu', 'Oeu037675.1' => 'oeu', 'Oeu038359.1' => 'oeu', 'Oeu063834.1' => 'oeu', 'Oeu063835.1' => 'oeu', 'Os05g0312000' => 'osa', 'Os07g0211101' => 'osa', 'Os07g0211200' => 'osa', 'Os07g0681500' => 'osa', 'Peaxi162Scf00095g01015' => 'pax', 'Peaxi162Scf00104g00329' => 'pax', 'Peaxi162Scf00161g00137' => 'pax', 'PGR004G1665' => 'pgr', 'PGR031G2937' => 'pgr', 'PGR119G2145' => 'pgr', 'PGSC0003DMG400004351' => 'stu', 'PGSC0003DMG400014625' => 'stu', 'PGSC0003DMG401000943' => 'stu', 'Phvul.001G148600' => 'pvu', 'Phvul.004G001700' => 'pvu', 'Phvul.006G154900' => 'pvu', 'Phvul.008G078200' => 'pvu', 'Phvul.011G136500' => 'pvu', 'Potri.002G215600' => 'ptr', 'Potri.008G201600' => 'ptr', 'Potri.014G138400' => 'ptr', 'Potri.016G142500' => 'ptr', 'Pp3c16_10580' => 'ppa', 'Pp3c5_25280' => 'ppa', 'Prupe.1G150000' => 'ppe', 'Prupe.1G150100' => 'ppe', 'Prupe.6G299600' => 'ppe', 'Prupe.8G245000' => 'ppe', 'Psat0s4927g0040' => 'psa', 'Psat1g052080' => 'psa', 'Psat1g183800' => 'psa', 'Psat3g113840' => 'psa', 'Psat3g126120' => 'psa', 'Psat3g126160' => 'psa', 'Psat3g158760' => 'psa', 'Psat3g158840' => 'psa', 'PSO170G2858' => 'pso', 'PSO339G0606' => 'pso', 'PSO384G4709' => 'pso', 'PSO407G0334' => 'pso', 'QL04p040276' => 'qlo', 'QL06p005458' => 'qlo', 'QL06p005472' => 'qlo', 'QL07p030546' => 'qlo', 'QL07p031519' => 'qlo', 'QL09p050949' => 'qlo', 'QL09p050966' => 'qlo', 'QL09p051067' => 'qlo', 'QL12p022706' => 'qlo', 'RcHm_v2.0_Chr2g0119601' => 'rch', 'RcHm_v2.0_Chr3g0459591' => 'rch', 'RcHm_v2.0_Chr4g0418521' => 'rch', 'RcHm_v2.0_Chr4g0418531' => 'rch', 'RcHm_v2.0_Chr4g0418541' => 'rch', 'RcHm_v2.0_Chr6g0291641' => 'rch', 'Rhsim01G0086300' => 'rsi', 'Rhsim01G0276300' => 'rsi', 'Rhsim01G0276500' => 'rsi', 'Rhsim04G0207700' => 'rsi', 'Rhsim05G0234500' => 'rsi', 'Rhsim13G0022400' => 'rsi', 'Sabra02G0167900' => 'sbr', 'Sabra04G0158500' => 'sbr', 'Sabra08G0159800' => 'sbr', 'Sabra10G0011500' => 'sbr', 'Sabra14G0104400' => 'sbr', 'SalBow2G2440' => 'sbo', 'SalBow4G2265' => 'sbo', 'Sc02g0000060' => 'sci', 'Sc05g0005020' => 'sci', 'Sc13g0003890' => 'sci', 'Sed0014865' => 'sed', 'Sed0017224' => 'sed', 'Sed0026391' => 'sed', 'SEGI_00063' => 'sgi', 'SEGI_10967' => 'sgi', 'SEGI_17510' => 'sgi', 'SEGI_24396' => 'sgi', 'SEGI_39719' => 'sgi', 'SEGI_41392' => 'sgi', 'SGA_v2.0_scaffold11G05794' => 'sas', 'SGA_v2.0_scaffold142G35607' => 'sas', 'SGA_v2.0_scaffold1G00447' => 'sas', 'SHI15388' => 'shi', 'SHI15394' => 'shi', 'SHI15396' => 'shi', 'SHI15399' => 'shi', 'SMO343G0151' => 'smo', 'SMO367G1118' => 'smo', 'Solyc01g080200.3' => 'sly', 'Solyc06g008960.3' => 'sly', 'Solyc09g064780.3' => 'sly', 'Sopen01g031980' => 'spe', 'Sopen06g003710' => 'spe', 'Sopen09g026460' => 'spe', 'Sp3g21240' => 'spa', 'Sp4g30030' => 'spa', 'TAR365G0022' => 'tar', 'TAR365G1023' => 'tar', 'TAR365G1253' => 'tar', 'TAR623G0078' => 'tar', 'TAR623G1721' => 'tar', 'TAR633G0959' => 'tar', 'THA.LOC104802225' => 'tha', 'THA.LOC104804769' => 'tha', 'THA.LOC104808660' => 'tha', 'THA.LOC104812792' => 'tha', 'Thecc.01G284000' => 'tca', 'Thecc.04G220600' => 'tca', 'Thecc.05G268900' => 'tca', 'Thecc.08G171100' => 'tca', 'Thhalv10001284m.g' => 'esa', 'Thhalv10019912m.g' => 'esa', 'TPR.G14189' => 'tpr', 'TPR.G18110' => 'tpr', 'TPR.G18130' => 'tpr', 'TPR.G18131' => 'tpr', 'TPR.G18140' => 'tpr', 'TPR.G24282' => 'tpr', 'TPR.G25221' => 'tpr', 'TPR.G29267' => 'tpr', 'TPR.G35315' => 'tpr', 'TPR.G36173' => 'tpr', 'TWI09G0794' => 'twi', 'TWI59G1348' => 'twi', 'TWI74G0430' => 'twi', 'unitig_26.g8940' => 'ugi', 'unitig_749.g13744' => 'ugi', 'unitig_749.g13745' => 'ugi', 'vmacro08269' => 'vma', 'vmacro14937' => 'vma', 'vmacro20401' => 'vma', 'VMungo0464G1349' => 'vmu', 'VMungo0540G0289' => 'vmu', 'VMungo1215G1590' => 'vmu', 'VMungo1309G0221' => 'vmu', 'VMungo1309G2815' => 'vmu', 'VMungo1383G0239' => 'vmu', 'VMungo1383G2910' => 'vmu', 'Zm00001eb095270' => 'zma', 'Zm00001eb095280' => 'zma', 'Zm00001eb111630' => 'zma', 'Zm00001eb237080' => 'zma', 'Zm00001eb273740' => 'zma', 'Zm00001eb285040' => 'zma', 'Zm00001eb330790' => 'zma', 'Zm00001eb337380' => 'zma' ) $gf_id = 'HOM05D001484' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001484' ) $data_identifier = 'HOM05D001484' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 2, 'aly' => (int) 2, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 22, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 7, 'hma' => (int) 2, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 7, 'mtr' => (int) 10, 'cme' => (int) 2, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 4, 'ppa' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 4, 'qlo' => (int) 9, 'rch' => (int) 6, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 10, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 7, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb337380' $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' => 'HOM05D001484', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p31500' => 'bna', 'A05p00020' => 'bna', 'A07p08820' => 'bna', 'Aa31LG4G3300' => 'aar', 'Aa31LG8G10030' => 'aar', 'Actinidia00731' => 'ach', 'Actinidia11473' => 'ach', 'Actinidia23469' => 'ach', 'Actinidia24318' => 'ach', 'Actinidia40196' => 'ach', 'Actinidia40197' => 'ach', 'Actinidia40198' => 'ach', 'Ah.08g212990' => 'amhyb', 'Ah.15g091720' => 'amhyb', 'AL3G38260' => 'aly', 'AL4G47710' => 'aly', 'Aqoxy2G00671' => 'aox', 'Aqoxy2G03236' => 'aox', 'arahy.Tifrunner.gnm1.ann1.05IDCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KR684' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATY3SJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK6QJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6APGL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IDT7Z9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM073U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ0R87' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LE7RV4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT4QRX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V5ENPK' => 'arhy', 'AT2G48110' => 'ath', 'AT3G23590' => 'ath', 'ATR0626G186' => 'atr', 'ATR1127G141' => 'atr', 'Atru.chr4.2583' => 'acertr', 'Atru.chr5.1358' => 'acertr', 'Atru.chr5.1359' => 'acertr', 'Atru.chr8.46' => 'acertr', 'AUR62002640' => 'cqu', 'AUR62030055' => 'cqu', 'AUR62033713' => 'cqu', 'AUR62033714' => 'cqu', 'AUR62036795' => 'cqu', 'AUR62039891' => 'cqu', 'BcaB02g08737' => 'bca', 'BcaB04g20441' => 'bca', 'BcaB06g26509' => 'bca', 'BcaB06g26510' => 'bca', 'BcaB06g26511' => 'bca', 'BcaB06g26512' => 'bca', 'BcaB06g26513' => 'bca', 'BcaC02g12564' => 'bca', 'BcaC02g12565' => 'bca', 'BcaC02g12794' => 'bca', 'BcaC02g12795' => 'bca', 'BcaC02g12796' => 'bca', 'BcaC06g35541' => 'bca', 'BNapus_Darmor_BZH_scaffold_188p00080' => 'bna', 'BNapus_Darmor_BZH_scaffold_188p00090' => 'bna', 'BolC1t03972H' => 'bol', 'BolC1t03973H' => 'bol', 'BolC4t21680H' => 'bol', 'BolC7t41863H' => 'bol', 'BolSC55t61227H' => 'bol', 'BolSC55t61228H' => 'bol', 'BraA01t03278Z' => 'bra', 'BraA05t18998Z' => 'bra', 'BraA07t28673Z' => 'bra', 'C01p40150' => 'bna', 'C05p12370' => 'bna', 'C07p13680' => 'bna', 'CAN.G1006.16' => 'can', 'CAN.G1006.17' => 'can', 'CAN.G1170.2' => 'can', 'CAN.G962.7' => 'can', 'CANSAT25G2179' => 'cansat', 'CANSAT78G1573' => 'cansat', 'CARHR099510' => 'chi', 'CARHR143510' => 'chi', 'Carub.0003s2380' => 'cru', 'Carub.0004s3082' => 'cru', 'Ca_00614_v3' => 'car', 'Ca_07801_v3' => 'car', 'Ca_08567_v3' => 'car', 'Ca_09571_v3' => 'car', 'CBR_g19290' => 'cbr', 'Cc01_g19770' => 'ccan', 'Cc03_g03030' => 'ccan', 'CDE07G0968' => 'cde', 'CDE09G1441' => 'cde', 'Cfa006103' => 'cfa', 'Cfa015573' => 'cfa', 'Cfa016988' => 'cfa', 'Ciclev10006738m.g' => 'ccl', 'Ciclev10010920m.g' => 'ccl', 'Ciclev10018517m.g' => 'ccl', 'CiPaw.01G159200' => 'cil', 'CiPaw.02G091000' => 'cil', 'CiPaw.02G091100' => 'cil', 'CiPaw.08G103100' => 'cil', 'CiPaw.09G224900' => 'cil', 'ClCG06G005740' => 'cla', 'ClCG07G000090' => 'cla', 'ClCG07G000100' => 'cla', 'COL.COLO4_09143' => 'col', 'COL.COLO4_25124' => 'col', 'Cpa.g.sc16.34' => 'cpa', 'Cpa.g.sc3504.1' => 'cpa', 'Cpa.g.sc60.37' => 'cpa', 'CsaV3_6G018520' => 'csa', 'CsaV3_6G036860' => 'csa', 'CSS0001072' => 'camsi', 'CSS0020208' => 'camsi', 'CSS0021253' => 'camsi', 'CSS0022190' => 'camsi', 'CSS0036150' => 'camsi', 'CSS0040442' => 'camsi', 'CSS0042300' => 'camsi', 'CSS0045298' => 'camsi', 'DCAR_012449' => 'dca', 'DCAR_018405' => 'dca', 'DCAR_024573' => 'dca', 'DCAR_030591' => 'dca', 'Dinv16926' => 'din', 'Dinv32963' => 'din', 'Dinv38382' => 'din', 'Dinv38383' => 'din', 'Duzib133G0974' => 'dzi', 'Duzib138G1867' => 'dzi', 'Duzib211G0420' => 'dzi', 'Duzib212G0930' => 'dzi', 'ECA234G1645' => 'eca', 'ECA247G3467' => 'eca', 'ECA248G1703' => 'eca', 'EL10Ac3g06327' => 'bvu', 'EL10Ac7g17204' => 'bvu', 'Eucgr.A00855' => 'egr', 'Eucgr.A00858' => 'egr', 'Eucgr.H01520' => 'egr', 'Eucgr.H03604' => 'egr', 'Eucgr.L03465' => 'egr', 'Eucgr.L03466' => 'egr', 'FAN01G0988' => 'fan', 'FAN02G3892' => 'fan', 'FAN05G3381' => 'fan', 'FAN07G0967' => 'fan', 'FAN07G1493' => 'fan', 'FAN08G3125' => 'fan', 'FAN09G0402' => 'fan', 'FAN12G2594' => 'fan', 'FAN12G3879' => 'fan', 'FAN14G1546' => 'fan', 'FAN15G3626' => 'fan', 'FAN17G0588' => 'fan', 'FAN17G0609' => 'fan', 'FAN18G2817' => 'fan', 'FAN19G1305' => 'fan', 'FAN20G1787' => 'fan', 'FAN22G0073' => 'fan', 'FAN22G0352' => 'fan', 'FAN22G0368' => 'fan', 'FAN22G2273' => 'fan', 'FAN24G1998' => 'fan', 'FAN27G1317' => 'fan', 'FvH4_2g23980' => 'fve', 'FvH4_4g14380' => 'fve', 'FvH4_4g14390' => 'fve', 'FvH4_6g09250' => 'fve', 'Glyma.03G151100' => 'gma', 'Glyma.04G122550' => 'gma', 'Glyma.05G001600' => 'gma', 'Glyma.09G270766' => 'gma', 'Glyma.09G270832' => 'gma', 'Glyma.13G209800' => 'gma', 'Glyma.15G102800' => 'gma', 'Glyma.18G218900' => 'gma', 'Glyma.19G001500' => 'gma', 'Glyma.19G153600' => 'gma', 'Gohir.A02G028600' => 'ghi', 'Gohir.A08G045000' => 'ghi', 'Gohir.A11G120500' => 'ghi', 'Gohir.A12G006200' => 'ghi', 'Gohir.A12G006250' => 'ghi', 'Gohir.D02G036300' => 'ghi', 'Gohir.D08G054700' => 'ghi', 'Gohir.D11G125600' => 'ghi', 'Gohir.D12G005700' => 'ghi', 'Gorai.004G055200' => 'gra', 'Gorai.005G040400' => 'gra', 'Gorai.007G134500' => 'gra', 'Gorai.008G005500' => 'gra', 'GSVIVG01011094001' => 'vvi', 'GSVIVG01017879001' => 'vvi', 'GSVIVG01025988001' => 'vvi', 'GSVIVG01029847001' => 'vvi', 'HanXRQChr10g0282901' => 'han', 'HanXRQChr10g0310371' => 'han', 'HanXRQChr10g0315041' => 'han', 'HanXRQChr11g0327651' => 'han', 'HanXRQChr12g0359391' => 'han', 'Haze_00972' => 'cav', 'Haze_00973' => 'cav', 'Haze_00974' => 'cav', 'Haze_04747' => 'cav', 'Haze_04749' => 'cav', 'Haze_04750' => 'cav', 'Haze_21217' => 'cav', 'Hma1.2p1_1037F.1_g250680' => 'hma', 'Hma1.2p1_1644F.1_g295320' => 'hma', 'HPP92_011322' => 'vpl', 'HPP92_011323' => 'vpl', 'HPP92_011324' => 'vpl', 'HPP92_011325' => 'vpl', 'HPP92_011326' => 'vpl', 'Hund12205' => 'sun', 'Hund17957' => 'sun', 'Lalb_Chr06g0176771' => 'lal', 'Lalb_Chr18g0056021' => 'lal', 'Lalb_Chr18g0056031' => 'lal', 'Lalb_Chr18g0056041' => 'lal', 'Lalb_Chr20g0107751' => 'lal', 'Lalb_Chr20g0118371' => 'lal', 'Lj1g0010239' => 'lja', 'Lj1g0017101' => 'lja', 'Lj2A1178G40' => 'lonja', 'Lj2A54G84' => 'lonja', 'Lj2g0015248' => 'lja', 'Lj3A761T51' => 'lonja', 'Lj6g0018116' => 'lja', 'Lsat_1_v5_gn_4_136040' => 'lsa', 'Lsat_1_v5_gn_5_187461' => 'lsa', 'Lsat_1_v5_gn_5_77001' => 'lsa', 'Lsat_1_v5_gn_9_4461' => 'lsa', 'Manes.01G210100' => 'mes', 'Manes.03G185600' => 'mes', 'Manes.05G073300' => 'mes', 'Manes.09G120300' => 'mes', 'Manes.15G022100' => 'mes', 'Mapoly0096s0053' => 'mpo', 'MBI03_g14058_MAGBIO' => 'mbi', 'MBI03_g33876_MAGBIO' => 'mbi', 'MBI03_g36854_MAGBIO' => 'mbi', 'MBI17_g11997_MAGBIO' => 'mbi', 'MD03G1269000' => 'mdo', 'MD04G1179600' => 'mdo', 'MD11G1289800' => 'mdo', 'MD12G1194700' => 'mdo', 'MD13G1182100' => 'mdo', 'MD13G1182200' => 'mdo', 'MD16G1182600' => 'mdo', 'Medtr2g021400' => 'mtr', 'Medtr2g021470' => 'mtr', 'Medtr2g105810' => 'mtr', 'Medtr3g033580' => 'mtr', 'Medtr6g007970' => 'mtr', 'Medtr7g056330' => 'mtr', 'Medtr7g074290' => 'mtr', 'Medtr7g074380' => 'mtr', 'Medtr7g094550' => 'mtr', 'Medtr8g069995' => 'mtr', 'MELO3C014345.2' => 'cme', 'MELO3C021395.2' => 'cme', 'Migut.D00262' => 'egut', 'Migut.G00257' => 'egut', 'MSTRG.21575' => 'ama', 'MSTRG.3985' => 'ama', 'Nitab4.5_0000295g0140' => 'nta', 'Nitab4.5_0000732g0140' => 'nta', 'Nitab4.5_0003162g0020' => 'nta', 'Nitab4.5_0006180g0090' => 'nta', 'Nitab4.5_0006390g0010' => 'nta', 'Nitab4.5_0007392g0040' => 'nta', 'Nn1g02140' => 'nnu', 'Nn4g26168' => 'nnu', 'Nn5g26754' => 'nnu', 'Oeu001433.1' => 'oeu', 'Oeu010299.2' => 'oeu', 'Oeu011171.1' => 'oeu', 'Oeu037675.1' => 'oeu', 'Oeu038359.1' => 'oeu', 'Oeu063834.1' => 'oeu', 'Oeu063835.1' => 'oeu', 'Os05g0312000' => 'osa', 'Os07g0211101' => 'osa', 'Os07g0211200' => 'osa', 'Os07g0681500' => 'osa', 'Peaxi162Scf00095g01015' => 'pax', 'Peaxi162Scf00104g00329' => 'pax', 'Peaxi162Scf00161g00137' => 'pax', 'PGR004G1665' => 'pgr', 'PGR031G2937' => 'pgr', 'PGR119G2145' => 'pgr', 'PGSC0003DMG400004351' => 'stu', 'PGSC0003DMG400014625' => 'stu', 'PGSC0003DMG401000943' => 'stu', 'Phvul.001G148600' => 'pvu', 'Phvul.004G001700' => 'pvu', 'Phvul.006G154900' => 'pvu', 'Phvul.008G078200' => 'pvu', 'Phvul.011G136500' => 'pvu', 'Potri.002G215600' => 'ptr', 'Potri.008G201600' => 'ptr', 'Potri.014G138400' => 'ptr', 'Potri.016G142500' => 'ptr', 'Pp3c16_10580' => 'ppa', 'Pp3c5_25280' => 'ppa', 'Prupe.1G150000' => 'ppe', 'Prupe.1G150100' => 'ppe', 'Prupe.6G299600' => 'ppe', 'Prupe.8G245000' => 'ppe', 'Psat0s4927g0040' => 'psa', 'Psat1g052080' => 'psa', 'Psat1g183800' => 'psa', 'Psat3g113840' => 'psa', 'Psat3g126120' => 'psa', 'Psat3g126160' => 'psa', 'Psat3g158760' => 'psa', 'Psat3g158840' => 'psa', 'PSO170G2858' => 'pso', 'PSO339G0606' => 'pso', 'PSO384G4709' => 'pso', 'PSO407G0334' => 'pso', 'QL04p040276' => 'qlo', 'QL06p005458' => 'qlo', 'QL06p005472' => 'qlo', 'QL07p030546' => 'qlo', 'QL07p031519' => 'qlo', 'QL09p050949' => 'qlo', 'QL09p050966' => 'qlo', 'QL09p051067' => 'qlo', 'QL12p022706' => 'qlo', 'RcHm_v2.0_Chr2g0119601' => 'rch', 'RcHm_v2.0_Chr3g0459591' => 'rch', 'RcHm_v2.0_Chr4g0418521' => 'rch', 'RcHm_v2.0_Chr4g0418531' => 'rch', 'RcHm_v2.0_Chr4g0418541' => 'rch', 'RcHm_v2.0_Chr6g0291641' => 'rch', 'Rhsim01G0086300' => 'rsi', 'Rhsim01G0276300' => 'rsi', 'Rhsim01G0276500' => 'rsi', 'Rhsim04G0207700' => 'rsi', 'Rhsim05G0234500' => 'rsi', 'Rhsim13G0022400' => 'rsi', 'Sabra02G0167900' => 'sbr', 'Sabra04G0158500' => 'sbr', 'Sabra08G0159800' => 'sbr', 'Sabra10G0011500' => 'sbr', 'Sabra14G0104400' => 'sbr', 'SalBow2G2440' => 'sbo', 'SalBow4G2265' => 'sbo', 'Sc02g0000060' => 'sci', 'Sc05g0005020' => 'sci', 'Sc13g0003890' => 'sci', 'Sed0014865' => 'sed', 'Sed0017224' => 'sed', 'Sed0026391' => 'sed', 'SEGI_00063' => 'sgi', 'SEGI_10967' => 'sgi', 'SEGI_17510' => 'sgi', 'SEGI_24396' => 'sgi', 'SEGI_39719' => 'sgi', 'SEGI_41392' => 'sgi', 'SGA_v2.0_scaffold11G05794' => 'sas', 'SGA_v2.0_scaffold142G35607' => 'sas', 'SGA_v2.0_scaffold1G00447' => 'sas', 'SHI15388' => 'shi', 'SHI15394' => 'shi', 'SHI15396' => 'shi', 'SHI15399' => 'shi', 'SMO343G0151' => 'smo', 'SMO367G1118' => 'smo', 'Solyc01g080200.3' => 'sly', 'Solyc06g008960.3' => 'sly', 'Solyc09g064780.3' => 'sly', 'Sopen01g031980' => 'spe', 'Sopen06g003710' => 'spe', 'Sopen09g026460' => 'spe', 'Sp3g21240' => 'spa', 'Sp4g30030' => 'spa', 'TAR365G0022' => 'tar', 'TAR365G1023' => 'tar', 'TAR365G1253' => 'tar', 'TAR623G0078' => 'tar', 'TAR623G1721' => 'tar', 'TAR633G0959' => 'tar', 'THA.LOC104802225' => 'tha', 'THA.LOC104804769' => 'tha', 'THA.LOC104808660' => 'tha', 'THA.LOC104812792' => 'tha', 'Thecc.01G284000' => 'tca', 'Thecc.04G220600' => 'tca', 'Thecc.05G268900' => 'tca', 'Thecc.08G171100' => 'tca', 'Thhalv10001284m.g' => 'esa', 'Thhalv10019912m.g' => 'esa', 'TPR.G14189' => 'tpr', 'TPR.G18110' => 'tpr', 'TPR.G18130' => 'tpr', 'TPR.G18131' => 'tpr', 'TPR.G18140' => 'tpr', 'TPR.G24282' => 'tpr', 'TPR.G25221' => 'tpr', 'TPR.G29267' => 'tpr', 'TPR.G35315' => 'tpr', 'TPR.G36173' => 'tpr', 'TWI09G0794' => 'twi', 'TWI59G1348' => 'twi', 'TWI74G0430' => 'twi', 'unitig_26.g8940' => 'ugi', 'unitig_749.g13744' => 'ugi', 'unitig_749.g13745' => 'ugi', 'vmacro08269' => 'vma', 'vmacro14937' => 'vma', 'vmacro20401' => 'vma', 'VMungo0464G1349' => 'vmu', 'VMungo0540G0289' => 'vmu', 'VMungo1215G1590' => 'vmu', 'VMungo1309G0221' => 'vmu', 'VMungo1309G2815' => 'vmu', 'VMungo1383G0239' => 'vmu', 'VMungo1383G2910' => 'vmu', 'Zm00001eb095270' => 'zma', 'Zm00001eb095280' => 'zma', 'Zm00001eb111630' => 'zma', 'Zm00001eb237080' => 'zma', 'Zm00001eb273740' => 'zma', 'Zm00001eb285040' => 'zma', 'Zm00001eb330790' => 'zma', 'Zm00001eb337380' => 'zma' ), 'gf_id' => 'HOM05D001484', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001484' ), 'data_identifier' => 'HOM05D001484', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001484', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p31500' => 'bna', 'A05p00020' => 'bna', 'A07p08820' => 'bna', 'Aa31LG4G3300' => 'aar', 'Aa31LG8G10030' => 'aar', 'Actinidia00731' => 'ach', 'Actinidia11473' => 'ach', 'Actinidia23469' => 'ach', 'Actinidia24318' => 'ach', 'Actinidia40196' => 'ach', 'Actinidia40197' => 'ach', 'Actinidia40198' => 'ach', 'Ah.08g212990' => 'amhyb', 'Ah.15g091720' => 'amhyb', 'AL3G38260' => 'aly', 'AL4G47710' => 'aly', 'Aqoxy2G00671' => 'aox', 'Aqoxy2G03236' => 'aox', 'arahy.Tifrunner.gnm1.ann1.05IDCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KR684' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATY3SJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK6QJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6APGL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IDT7Z9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM073U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ0R87' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LE7RV4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT4QRX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V5ENPK' => 'arhy', 'AT2G48110' => 'ath', 'AT3G23590' => 'ath', 'ATR0626G186' => 'atr', 'ATR1127G141' => 'atr', 'Atru.chr4.2583' => 'acertr', 'Atru.chr5.1358' => 'acertr', 'Atru.chr5.1359' => 'acertr', 'Atru.chr8.46' => 'acertr', 'AUR62002640' => 'cqu', 'AUR62030055' => 'cqu', 'AUR62033713' => 'cqu', 'AUR62033714' => 'cqu', 'AUR62036795' => 'cqu', 'AUR62039891' => 'cqu', 'BcaB02g08737' => 'bca', 'BcaB04g20441' => 'bca', 'BcaB06g26509' => 'bca', 'BcaB06g26510' => 'bca', 'BcaB06g26511' => 'bca', 'BcaB06g26512' => 'bca', 'BcaB06g26513' => 'bca', 'BcaC02g12564' => 'bca', 'BcaC02g12565' => 'bca', 'BcaC02g12794' => 'bca', 'BcaC02g12795' => 'bca', 'BcaC02g12796' => 'bca', 'BcaC06g35541' => 'bca', 'BNapus_Darmor_BZH_scaffold_188p00080' => 'bna', 'BNapus_Darmor_BZH_scaffold_188p00090' => 'bna', 'BolC1t03972H' => 'bol', 'BolC1t03973H' => 'bol', 'BolC4t21680H' => 'bol', 'BolC7t41863H' => 'bol', 'BolSC55t61227H' => 'bol', 'BolSC55t61228H' => 'bol', 'BraA01t03278Z' => 'bra', 'BraA05t18998Z' => 'bra', 'BraA07t28673Z' => 'bra', 'C01p40150' => 'bna', 'C05p12370' => 'bna', 'C07p13680' => 'bna', 'CAN.G1006.16' => 'can', 'CAN.G1006.17' => 'can', 'CAN.G1170.2' => 'can', 'CAN.G962.7' => 'can', 'CANSAT25G2179' => 'cansat', 'CANSAT78G1573' => 'cansat', 'CARHR099510' => 'chi', 'CARHR143510' => 'chi', 'Carub.0003s2380' => 'cru', 'Carub.0004s3082' => 'cru', 'Ca_00614_v3' => 'car', 'Ca_07801_v3' => 'car', 'Ca_08567_v3' => 'car', 'Ca_09571_v3' => 'car', 'CBR_g19290' => 'cbr', 'Cc01_g19770' => 'ccan', 'Cc03_g03030' => 'ccan', 'CDE07G0968' => 'cde', 'CDE09G1441' => 'cde', 'Cfa006103' => 'cfa', 'Cfa015573' => 'cfa', 'Cfa016988' => 'cfa', 'Ciclev10006738m.g' => 'ccl', 'Ciclev10010920m.g' => 'ccl', 'Ciclev10018517m.g' => 'ccl', 'CiPaw.01G159200' => 'cil', 'CiPaw.02G091000' => 'cil', 'CiPaw.02G091100' => 'cil', 'CiPaw.08G103100' => 'cil', 'CiPaw.09G224900' => 'cil', 'ClCG06G005740' => 'cla', 'ClCG07G000090' => 'cla', 'ClCG07G000100' => 'cla', 'COL.COLO4_09143' => 'col', 'COL.COLO4_25124' => 'col', 'Cpa.g.sc16.34' => 'cpa', 'Cpa.g.sc3504.1' => 'cpa', 'Cpa.g.sc60.37' => 'cpa', 'CsaV3_6G018520' => 'csa', 'CsaV3_6G036860' => 'csa', 'CSS0001072' => 'camsi', 'CSS0020208' => 'camsi', 'CSS0021253' => 'camsi', 'CSS0022190' => 'camsi', 'CSS0036150' => 'camsi', 'CSS0040442' => 'camsi', 'CSS0042300' => 'camsi', 'CSS0045298' => 'camsi', 'DCAR_012449' => 'dca', 'DCAR_018405' => 'dca', 'DCAR_024573' => 'dca', 'DCAR_030591' => 'dca', 'Dinv16926' => 'din', 'Dinv32963' => 'din', 'Dinv38382' => 'din', 'Dinv38383' => 'din', 'Duzib133G0974' => 'dzi', 'Duzib138G1867' => 'dzi', 'Duzib211G0420' => 'dzi', 'Duzib212G0930' => 'dzi', 'ECA234G1645' => 'eca', 'ECA247G3467' => 'eca', 'ECA248G1703' => 'eca', 'EL10Ac3g06327' => 'bvu', 'EL10Ac7g17204' => 'bvu', 'Eucgr.A00855' => 'egr', 'Eucgr.A00858' => 'egr', 'Eucgr.H01520' => 'egr', 'Eucgr.H03604' => 'egr', 'Eucgr.L03465' => 'egr', 'Eucgr.L03466' => 'egr', 'FAN01G0988' => 'fan', 'FAN02G3892' => 'fan', 'FAN05G3381' => 'fan', 'FAN07G0967' => 'fan', 'FAN07G1493' => 'fan', 'FAN08G3125' => 'fan', 'FAN09G0402' => 'fan', 'FAN12G2594' => 'fan', 'FAN12G3879' => 'fan', 'FAN14G1546' => 'fan', 'FAN15G3626' => 'fan', 'FAN17G0588' => 'fan', 'FAN17G0609' => 'fan', 'FAN18G2817' => 'fan', 'FAN19G1305' => 'fan', 'FAN20G1787' => 'fan', 'FAN22G0073' => 'fan', 'FAN22G0352' => 'fan', 'FAN22G0368' => 'fan', 'FAN22G2273' => 'fan', 'FAN24G1998' => 'fan', 'FAN27G1317' => 'fan', 'FvH4_2g23980' => 'fve', 'FvH4_4g14380' => 'fve', 'FvH4_4g14390' => 'fve', 'FvH4_6g09250' => 'fve', 'Glyma.03G151100' => 'gma', 'Glyma.04G122550' => 'gma', 'Glyma.05G001600' => 'gma', 'Glyma.09G270766' => 'gma', 'Glyma.09G270832' => 'gma', 'Glyma.13G209800' => 'gma', 'Glyma.15G102800' => 'gma', 'Glyma.18G218900' => 'gma', 'Glyma.19G001500' => 'gma', 'Glyma.19G153600' => 'gma', 'Gohir.A02G028600' => 'ghi', 'Gohir.A08G045000' => 'ghi', 'Gohir.A11G120500' => 'ghi', 'Gohir.A12G006200' => 'ghi', 'Gohir.A12G006250' => 'ghi', 'Gohir.D02G036300' => 'ghi', 'Gohir.D08G054700' => 'ghi', 'Gohir.D11G125600' => 'ghi', 'Gohir.D12G005700' => 'ghi', 'Gorai.004G055200' => 'gra', 'Gorai.005G040400' => 'gra', 'Gorai.007G134500' => 'gra', 'Gorai.008G005500' => 'gra', 'GSVIVG01011094001' => 'vvi', 'GSVIVG01017879001' => 'vvi', 'GSVIVG01025988001' => 'vvi', 'GSVIVG01029847001' => 'vvi', 'HanXRQChr10g0282901' => 'han', 'HanXRQChr10g0310371' => 'han', 'HanXRQChr10g0315041' => 'han', 'HanXRQChr11g0327651' => 'han', 'HanXRQChr12g0359391' => 'han', 'Haze_00972' => 'cav', 'Haze_00973' => 'cav', 'Haze_00974' => 'cav', 'Haze_04747' => 'cav', 'Haze_04749' => 'cav', 'Haze_04750' => 'cav', 'Haze_21217' => 'cav', 'Hma1.2p1_1037F.1_g250680' => 'hma', 'Hma1.2p1_1644F.1_g295320' => 'hma', 'HPP92_011322' => 'vpl', 'HPP92_011323' => 'vpl', 'HPP92_011324' => 'vpl', 'HPP92_011325' => 'vpl', 'HPP92_011326' => 'vpl', 'Hund12205' => 'sun', 'Hund17957' => 'sun', 'Lalb_Chr06g0176771' => 'lal', 'Lalb_Chr18g0056021' => 'lal', 'Lalb_Chr18g0056031' => 'lal', 'Lalb_Chr18g0056041' => 'lal', 'Lalb_Chr20g0107751' => 'lal', 'Lalb_Chr20g0118371' => 'lal', 'Lj1g0010239' => 'lja', 'Lj1g0017101' => 'lja', 'Lj2A1178G40' => 'lonja', 'Lj2A54G84' => 'lonja', 'Lj2g0015248' => 'lja', 'Lj3A761T51' => 'lonja', 'Lj6g0018116' => 'lja', 'Lsat_1_v5_gn_4_136040' => 'lsa', 'Lsat_1_v5_gn_5_187461' => 'lsa', 'Lsat_1_v5_gn_5_77001' => 'lsa', 'Lsat_1_v5_gn_9_4461' => 'lsa', 'Manes.01G210100' => 'mes', 'Manes.03G185600' => 'mes', 'Manes.05G073300' => 'mes', 'Manes.09G120300' => 'mes', 'Manes.15G022100' => 'mes', 'Mapoly0096s0053' => 'mpo', 'MBI03_g14058_MAGBIO' => 'mbi', 'MBI03_g33876_MAGBIO' => 'mbi', 'MBI03_g36854_MAGBIO' => 'mbi', 'MBI17_g11997_MAGBIO' => 'mbi', 'MD03G1269000' => 'mdo', 'MD04G1179600' => 'mdo', 'MD11G1289800' => 'mdo', 'MD12G1194700' => 'mdo', 'MD13G1182100' => 'mdo', 'MD13G1182200' => 'mdo', 'MD16G1182600' => 'mdo', 'Medtr2g021400' => 'mtr', 'Medtr2g021470' => 'mtr', 'Medtr2g105810' => 'mtr', 'Medtr3g033580' => 'mtr', 'Medtr6g007970' => 'mtr', 'Medtr7g056330' => 'mtr', 'Medtr7g074290' => 'mtr', 'Medtr7g074380' => 'mtr', 'Medtr7g094550' => 'mtr', 'Medtr8g069995' => 'mtr', 'MELO3C014345.2' => 'cme', 'MELO3C021395.2' => 'cme', 'Migut.D00262' => 'egut', 'Migut.G00257' => 'egut', 'MSTRG.21575' => 'ama', 'MSTRG.3985' => 'ama', 'Nitab4.5_0000295g0140' => 'nta', 'Nitab4.5_0000732g0140' => 'nta', 'Nitab4.5_0003162g0020' => 'nta', 'Nitab4.5_0006180g0090' => 'nta', 'Nitab4.5_0006390g0010' => 'nta', 'Nitab4.5_0007392g0040' => 'nta', 'Nn1g02140' => 'nnu', 'Nn4g26168' => 'nnu', 'Nn5g26754' => 'nnu', 'Oeu001433.1' => 'oeu', 'Oeu010299.2' => 'oeu', 'Oeu011171.1' => 'oeu', 'Oeu037675.1' => 'oeu', 'Oeu038359.1' => 'oeu', 'Oeu063834.1' => 'oeu', 'Oeu063835.1' => 'oeu', 'Os05g0312000' => 'osa', 'Os07g0211101' => 'osa', 'Os07g0211200' => 'osa', 'Os07g0681500' => 'osa', 'Peaxi162Scf00095g01015' => 'pax', 'Peaxi162Scf00104g00329' => 'pax', 'Peaxi162Scf00161g00137' => 'pax', 'PGR004G1665' => 'pgr', 'PGR031G2937' => 'pgr', 'PGR119G2145' => 'pgr', 'PGSC0003DMG400004351' => 'stu', 'PGSC0003DMG400014625' => 'stu', 'PGSC0003DMG401000943' => 'stu', 'Phvul.001G148600' => 'pvu', 'Phvul.004G001700' => 'pvu', 'Phvul.006G154900' => 'pvu', 'Phvul.008G078200' => 'pvu', 'Phvul.011G136500' => 'pvu', 'Potri.002G215600' => 'ptr', 'Potri.008G201600' => 'ptr', 'Potri.014G138400' => 'ptr', 'Potri.016G142500' => 'ptr', 'Pp3c16_10580' => 'ppa', 'Pp3c5_25280' => 'ppa', 'Prupe.1G150000' => 'ppe', 'Prupe.1G150100' => 'ppe', 'Prupe.6G299600' => 'ppe', 'Prupe.8G245000' => 'ppe', 'Psat0s4927g0040' => 'psa', 'Psat1g052080' => 'psa', 'Psat1g183800' => 'psa', 'Psat3g113840' => 'psa', 'Psat3g126120' => 'psa', 'Psat3g126160' => 'psa', 'Psat3g158760' => 'psa', 'Psat3g158840' => 'psa', 'PSO170G2858' => 'pso', 'PSO339G0606' => 'pso', 'PSO384G4709' => 'pso', 'PSO407G0334' => 'pso', 'QL04p040276' => 'qlo', 'QL06p005458' => 'qlo', 'QL06p005472' => 'qlo', 'QL07p030546' => 'qlo', 'QL07p031519' => 'qlo', 'QL09p050949' => 'qlo', 'QL09p050966' => 'qlo', 'QL09p051067' => 'qlo', 'QL12p022706' => 'qlo', 'RcHm_v2.0_Chr2g0119601' => 'rch', 'RcHm_v2.0_Chr3g0459591' => 'rch', 'RcHm_v2.0_Chr4g0418521' => 'rch', 'RcHm_v2.0_Chr4g0418531' => 'rch', 'RcHm_v2.0_Chr4g0418541' => 'rch', 'RcHm_v2.0_Chr6g0291641' => 'rch', 'Rhsim01G0086300' => 'rsi', 'Rhsim01G0276300' => 'rsi', 'Rhsim01G0276500' => 'rsi', 'Rhsim04G0207700' => 'rsi', 'Rhsim05G0234500' => 'rsi', 'Rhsim13G0022400' => 'rsi', 'Sabra02G0167900' => 'sbr', 'Sabra04G0158500' => 'sbr', 'Sabra08G0159800' => 'sbr', 'Sabra10G0011500' => 'sbr', 'Sabra14G0104400' => 'sbr', 'SalBow2G2440' => 'sbo', 'SalBow4G2265' => 'sbo', 'Sc02g0000060' => 'sci', 'Sc05g0005020' => 'sci', 'Sc13g0003890' => 'sci', 'Sed0014865' => 'sed', 'Sed0017224' => 'sed', 'Sed0026391' => 'sed', 'SEGI_00063' => 'sgi', 'SEGI_10967' => 'sgi', 'SEGI_17510' => 'sgi', 'SEGI_24396' => 'sgi', 'SEGI_39719' => 'sgi', 'SEGI_41392' => 'sgi', 'SGA_v2.0_scaffold11G05794' => 'sas', 'SGA_v2.0_scaffold142G35607' => 'sas', 'SGA_v2.0_scaffold1G00447' => 'sas', 'SHI15388' => 'shi', 'SHI15394' => 'shi', 'SHI15396' => 'shi', 'SHI15399' => 'shi', 'SMO343G0151' => 'smo', 'SMO367G1118' => 'smo', 'Solyc01g080200.3' => 'sly', 'Solyc06g008960.3' => 'sly', 'Solyc09g064780.3' => 'sly', 'Sopen01g031980' => 'spe', 'Sopen06g003710' => 'spe', 'Sopen09g026460' => 'spe', 'Sp3g21240' => 'spa', 'Sp4g30030' => 'spa', 'TAR365G0022' => 'tar', 'TAR365G1023' => 'tar', 'TAR365G1253' => 'tar', 'TAR623G0078' => 'tar', 'TAR623G1721' => 'tar', 'TAR633G0959' => 'tar', 'THA.LOC104802225' => 'tha', 'THA.LOC104804769' => 'tha', 'THA.LOC104808660' => 'tha', 'THA.LOC104812792' => 'tha', 'Thecc.01G284000' => 'tca', 'Thecc.04G220600' => 'tca', 'Thecc.05G268900' => 'tca', 'Thecc.08G171100' => 'tca', 'Thhalv10001284m.g' => 'esa', 'Thhalv10019912m.g' => 'esa', 'TPR.G14189' => 'tpr', 'TPR.G18110' => 'tpr', 'TPR.G18130' => 'tpr', 'TPR.G18131' => 'tpr', 'TPR.G18140' => 'tpr', 'TPR.G24282' => 'tpr', 'TPR.G25221' => 'tpr', 'TPR.G29267' => 'tpr', 'TPR.G35315' => 'tpr', 'TPR.G36173' => 'tpr', 'TWI09G0794' => 'twi', 'TWI59G1348' => 'twi', 'TWI74G0430' => 'twi', 'unitig_26.g8940' => 'ugi', 'unitig_749.g13744' => 'ugi', 'unitig_749.g13745' => 'ugi', 'vmacro08269' => 'vma', 'vmacro14937' => 'vma', 'vmacro20401' => 'vma', 'VMungo0464G1349' => 'vmu', 'VMungo0540G0289' => 'vmu', 'VMungo1215G1590' => 'vmu', 'VMungo1309G0221' => 'vmu', 'VMungo1309G2815' => 'vmu', 'VMungo1383G0239' => 'vmu', 'VMungo1383G2910' => 'vmu', 'Zm00001eb095270' => 'zma', 'Zm00001eb095280' => 'zma', 'Zm00001eb111630' => 'zma', 'Zm00001eb237080' => 'zma', 'Zm00001eb273740' => 'zma', 'Zm00001eb285040' => 'zma', 'Zm00001eb330790' => 'zma', 'Zm00001eb337380' => 'zma' ) $gf_id = 'HOM05D001484' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001484' ) $data_identifier = 'HOM05D001484' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 2, 'aly' => (int) 2, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 22, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 7, 'hma' => (int) 2, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 7, 'mtr' => (int) 10, 'cme' => (int) 2, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 4, 'ppa' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 4, 'qlo' => (int) 9, 'rch' => (int) 6, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 10, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 7, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb337380' $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' => 'HOM05D001484', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p31500' => 'bna', 'A05p00020' => 'bna', 'A07p08820' => 'bna', 'Aa31LG4G3300' => 'aar', 'Aa31LG8G10030' => 'aar', 'Actinidia00731' => 'ach', 'Actinidia11473' => 'ach', 'Actinidia23469' => 'ach', 'Actinidia24318' => 'ach', 'Actinidia40196' => 'ach', 'Actinidia40197' => 'ach', 'Actinidia40198' => 'ach', 'Ah.08g212990' => 'amhyb', 'Ah.15g091720' => 'amhyb', 'AL3G38260' => 'aly', 'AL4G47710' => 'aly', 'Aqoxy2G00671' => 'aox', 'Aqoxy2G03236' => 'aox', 'arahy.Tifrunner.gnm1.ann1.05IDCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KR684' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATY3SJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK6QJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6APGL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IDT7Z9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM073U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ0R87' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LE7RV4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT4QRX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V5ENPK' => 'arhy', 'AT2G48110' => 'ath', 'AT3G23590' => 'ath', 'ATR0626G186' => 'atr', 'ATR1127G141' => 'atr', 'Atru.chr4.2583' => 'acertr', 'Atru.chr5.1358' => 'acertr', 'Atru.chr5.1359' => 'acertr', 'Atru.chr8.46' => 'acertr', 'AUR62002640' => 'cqu', 'AUR62030055' => 'cqu', 'AUR62033713' => 'cqu', 'AUR62033714' => 'cqu', 'AUR62036795' => 'cqu', 'AUR62039891' => 'cqu', 'BcaB02g08737' => 'bca', 'BcaB04g20441' => 'bca', 'BcaB06g26509' => 'bca', 'BcaB06g26510' => 'bca', 'BcaB06g26511' => 'bca', 'BcaB06g26512' => 'bca', 'BcaB06g26513' => 'bca', 'BcaC02g12564' => 'bca', 'BcaC02g12565' => 'bca', 'BcaC02g12794' => 'bca', 'BcaC02g12795' => 'bca', 'BcaC02g12796' => 'bca', 'BcaC06g35541' => 'bca', 'BNapus_Darmor_BZH_scaffold_188p00080' => 'bna', 'BNapus_Darmor_BZH_scaffold_188p00090' => 'bna', 'BolC1t03972H' => 'bol', 'BolC1t03973H' => 'bol', 'BolC4t21680H' => 'bol', 'BolC7t41863H' => 'bol', 'BolSC55t61227H' => 'bol', 'BolSC55t61228H' => 'bol', 'BraA01t03278Z' => 'bra', 'BraA05t18998Z' => 'bra', 'BraA07t28673Z' => 'bra', 'C01p40150' => 'bna', 'C05p12370' => 'bna', 'C07p13680' => 'bna', 'CAN.G1006.16' => 'can', 'CAN.G1006.17' => 'can', 'CAN.G1170.2' => 'can', 'CAN.G962.7' => 'can', 'CANSAT25G2179' => 'cansat', 'CANSAT78G1573' => 'cansat', 'CARHR099510' => 'chi', 'CARHR143510' => 'chi', 'Carub.0003s2380' => 'cru', 'Carub.0004s3082' => 'cru', 'Ca_00614_v3' => 'car', 'Ca_07801_v3' => 'car', 'Ca_08567_v3' => 'car', 'Ca_09571_v3' => 'car', 'CBR_g19290' => 'cbr', 'Cc01_g19770' => 'ccan', 'Cc03_g03030' => 'ccan', 'CDE07G0968' => 'cde', 'CDE09G1441' => 'cde', 'Cfa006103' => 'cfa', 'Cfa015573' => 'cfa', 'Cfa016988' => 'cfa', 'Ciclev10006738m.g' => 'ccl', 'Ciclev10010920m.g' => 'ccl', 'Ciclev10018517m.g' => 'ccl', 'CiPaw.01G159200' => 'cil', 'CiPaw.02G091000' => 'cil', 'CiPaw.02G091100' => 'cil', 'CiPaw.08G103100' => 'cil', 'CiPaw.09G224900' => 'cil', 'ClCG06G005740' => 'cla', 'ClCG07G000090' => 'cla', 'ClCG07G000100' => 'cla', 'COL.COLO4_09143' => 'col', 'COL.COLO4_25124' => 'col', 'Cpa.g.sc16.34' => 'cpa', 'Cpa.g.sc3504.1' => 'cpa', 'Cpa.g.sc60.37' => 'cpa', 'CsaV3_6G018520' => 'csa', 'CsaV3_6G036860' => 'csa', 'CSS0001072' => 'camsi', 'CSS0020208' => 'camsi', 'CSS0021253' => 'camsi', 'CSS0022190' => 'camsi', 'CSS0036150' => 'camsi', 'CSS0040442' => 'camsi', 'CSS0042300' => 'camsi', 'CSS0045298' => 'camsi', 'DCAR_012449' => 'dca', 'DCAR_018405' => 'dca', 'DCAR_024573' => 'dca', 'DCAR_030591' => 'dca', 'Dinv16926' => 'din', 'Dinv32963' => 'din', 'Dinv38382' => 'din', 'Dinv38383' => 'din', 'Duzib133G0974' => 'dzi', 'Duzib138G1867' => 'dzi', 'Duzib211G0420' => 'dzi', 'Duzib212G0930' => 'dzi', 'ECA234G1645' => 'eca', 'ECA247G3467' => 'eca', 'ECA248G1703' => 'eca', 'EL10Ac3g06327' => 'bvu', 'EL10Ac7g17204' => 'bvu', 'Eucgr.A00855' => 'egr', 'Eucgr.A00858' => 'egr', 'Eucgr.H01520' => 'egr', 'Eucgr.H03604' => 'egr', 'Eucgr.L03465' => 'egr', 'Eucgr.L03466' => 'egr', 'FAN01G0988' => 'fan', 'FAN02G3892' => 'fan', 'FAN05G3381' => 'fan', 'FAN07G0967' => 'fan', 'FAN07G1493' => 'fan', 'FAN08G3125' => 'fan', 'FAN09G0402' => 'fan', 'FAN12G2594' => 'fan', 'FAN12G3879' => 'fan', 'FAN14G1546' => 'fan', 'FAN15G3626' => 'fan', 'FAN17G0588' => 'fan', 'FAN17G0609' => 'fan', 'FAN18G2817' => 'fan', 'FAN19G1305' => 'fan', 'FAN20G1787' => 'fan', 'FAN22G0073' => 'fan', 'FAN22G0352' => 'fan', 'FAN22G0368' => 'fan', 'FAN22G2273' => 'fan', 'FAN24G1998' => 'fan', 'FAN27G1317' => 'fan', 'FvH4_2g23980' => 'fve', 'FvH4_4g14380' => 'fve', 'FvH4_4g14390' => 'fve', 'FvH4_6g09250' => 'fve', 'Glyma.03G151100' => 'gma', 'Glyma.04G122550' => 'gma', 'Glyma.05G001600' => 'gma', 'Glyma.09G270766' => 'gma', 'Glyma.09G270832' => 'gma', 'Glyma.13G209800' => 'gma', 'Glyma.15G102800' => 'gma', 'Glyma.18G218900' => 'gma', 'Glyma.19G001500' => 'gma', 'Glyma.19G153600' => 'gma', 'Gohir.A02G028600' => 'ghi', 'Gohir.A08G045000' => 'ghi', 'Gohir.A11G120500' => 'ghi', 'Gohir.A12G006200' => 'ghi', 'Gohir.A12G006250' => 'ghi', 'Gohir.D02G036300' => 'ghi', 'Gohir.D08G054700' => 'ghi', 'Gohir.D11G125600' => 'ghi', 'Gohir.D12G005700' => 'ghi', 'Gorai.004G055200' => 'gra', 'Gorai.005G040400' => 'gra', 'Gorai.007G134500' => 'gra', 'Gorai.008G005500' => 'gra', 'GSVIVG01011094001' => 'vvi', 'GSVIVG01017879001' => 'vvi', 'GSVIVG01025988001' => 'vvi', 'GSVIVG01029847001' => 'vvi', 'HanXRQChr10g0282901' => 'han', 'HanXRQChr10g0310371' => 'han', 'HanXRQChr10g0315041' => 'han', 'HanXRQChr11g0327651' => 'han', 'HanXRQChr12g0359391' => 'han', 'Haze_00972' => 'cav', 'Haze_00973' => 'cav', 'Haze_00974' => 'cav', 'Haze_04747' => 'cav', 'Haze_04749' => 'cav', 'Haze_04750' => 'cav', 'Haze_21217' => 'cav', 'Hma1.2p1_1037F.1_g250680' => 'hma', 'Hma1.2p1_1644F.1_g295320' => 'hma', 'HPP92_011322' => 'vpl', 'HPP92_011323' => 'vpl', 'HPP92_011324' => 'vpl', 'HPP92_011325' => 'vpl', 'HPP92_011326' => 'vpl', 'Hund12205' => 'sun', 'Hund17957' => 'sun', 'Lalb_Chr06g0176771' => 'lal', 'Lalb_Chr18g0056021' => 'lal', 'Lalb_Chr18g0056031' => 'lal', 'Lalb_Chr18g0056041' => 'lal', 'Lalb_Chr20g0107751' => 'lal', 'Lalb_Chr20g0118371' => 'lal', 'Lj1g0010239' => 'lja', 'Lj1g0017101' => 'lja', 'Lj2A1178G40' => 'lonja', 'Lj2A54G84' => 'lonja', 'Lj2g0015248' => 'lja', 'Lj3A761T51' => 'lonja', 'Lj6g0018116' => 'lja', 'Lsat_1_v5_gn_4_136040' => 'lsa', 'Lsat_1_v5_gn_5_187461' => 'lsa', 'Lsat_1_v5_gn_5_77001' => 'lsa', 'Lsat_1_v5_gn_9_4461' => 'lsa', 'Manes.01G210100' => 'mes', 'Manes.03G185600' => 'mes', 'Manes.05G073300' => 'mes', 'Manes.09G120300' => 'mes', 'Manes.15G022100' => 'mes', 'Mapoly0096s0053' => 'mpo', 'MBI03_g14058_MAGBIO' => 'mbi', 'MBI03_g33876_MAGBIO' => 'mbi', 'MBI03_g36854_MAGBIO' => 'mbi', 'MBI17_g11997_MAGBIO' => 'mbi', 'MD03G1269000' => 'mdo', 'MD04G1179600' => 'mdo', 'MD11G1289800' => 'mdo', 'MD12G1194700' => 'mdo', 'MD13G1182100' => 'mdo', 'MD13G1182200' => 'mdo', 'MD16G1182600' => 'mdo', 'Medtr2g021400' => 'mtr', 'Medtr2g021470' => 'mtr', 'Medtr2g105810' => 'mtr', 'Medtr3g033580' => 'mtr', 'Medtr6g007970' => 'mtr', 'Medtr7g056330' => 'mtr', 'Medtr7g074290' => 'mtr', 'Medtr7g074380' => 'mtr', 'Medtr7g094550' => 'mtr', 'Medtr8g069995' => 'mtr', 'MELO3C014345.2' => 'cme', 'MELO3C021395.2' => 'cme', 'Migut.D00262' => 'egut', 'Migut.G00257' => 'egut', 'MSTRG.21575' => 'ama', 'MSTRG.3985' => 'ama', 'Nitab4.5_0000295g0140' => 'nta', 'Nitab4.5_0000732g0140' => 'nta', 'Nitab4.5_0003162g0020' => 'nta', 'Nitab4.5_0006180g0090' => 'nta', 'Nitab4.5_0006390g0010' => 'nta', 'Nitab4.5_0007392g0040' => 'nta', 'Nn1g02140' => 'nnu', 'Nn4g26168' => 'nnu', 'Nn5g26754' => 'nnu', 'Oeu001433.1' => 'oeu', 'Oeu010299.2' => 'oeu', 'Oeu011171.1' => 'oeu', 'Oeu037675.1' => 'oeu', 'Oeu038359.1' => 'oeu', 'Oeu063834.1' => 'oeu', 'Oeu063835.1' => 'oeu', 'Os05g0312000' => 'osa', 'Os07g0211101' => 'osa', 'Os07g0211200' => 'osa', 'Os07g0681500' => 'osa', 'Peaxi162Scf00095g01015' => 'pax', 'Peaxi162Scf00104g00329' => 'pax', 'Peaxi162Scf00161g00137' => 'pax', 'PGR004G1665' => 'pgr', 'PGR031G2937' => 'pgr', 'PGR119G2145' => 'pgr', 'PGSC0003DMG400004351' => 'stu', 'PGSC0003DMG400014625' => 'stu', 'PGSC0003DMG401000943' => 'stu', 'Phvul.001G148600' => 'pvu', 'Phvul.004G001700' => 'pvu', 'Phvul.006G154900' => 'pvu', 'Phvul.008G078200' => 'pvu', 'Phvul.011G136500' => 'pvu', 'Potri.002G215600' => 'ptr', 'Potri.008G201600' => 'ptr', 'Potri.014G138400' => 'ptr', 'Potri.016G142500' => 'ptr', 'Pp3c16_10580' => 'ppa', 'Pp3c5_25280' => 'ppa', 'Prupe.1G150000' => 'ppe', 'Prupe.1G150100' => 'ppe', 'Prupe.6G299600' => 'ppe', 'Prupe.8G245000' => 'ppe', 'Psat0s4927g0040' => 'psa', 'Psat1g052080' => 'psa', 'Psat1g183800' => 'psa', 'Psat3g113840' => 'psa', 'Psat3g126120' => 'psa', 'Psat3g126160' => 'psa', 'Psat3g158760' => 'psa', 'Psat3g158840' => 'psa', 'PSO170G2858' => 'pso', 'PSO339G0606' => 'pso', 'PSO384G4709' => 'pso', 'PSO407G0334' => 'pso', 'QL04p040276' => 'qlo', 'QL06p005458' => 'qlo', 'QL06p005472' => 'qlo', 'QL07p030546' => 'qlo', 'QL07p031519' => 'qlo', 'QL09p050949' => 'qlo', 'QL09p050966' => 'qlo', 'QL09p051067' => 'qlo', 'QL12p022706' => 'qlo', 'RcHm_v2.0_Chr2g0119601' => 'rch', 'RcHm_v2.0_Chr3g0459591' => 'rch', 'RcHm_v2.0_Chr4g0418521' => 'rch', 'RcHm_v2.0_Chr4g0418531' => 'rch', 'RcHm_v2.0_Chr4g0418541' => 'rch', 'RcHm_v2.0_Chr6g0291641' => 'rch', 'Rhsim01G0086300' => 'rsi', 'Rhsim01G0276300' => 'rsi', 'Rhsim01G0276500' => 'rsi', 'Rhsim04G0207700' => 'rsi', 'Rhsim05G0234500' => 'rsi', 'Rhsim13G0022400' => 'rsi', 'Sabra02G0167900' => 'sbr', 'Sabra04G0158500' => 'sbr', 'Sabra08G0159800' => 'sbr', 'Sabra10G0011500' => 'sbr', 'Sabra14G0104400' => 'sbr', 'SalBow2G2440' => 'sbo', 'SalBow4G2265' => 'sbo', 'Sc02g0000060' => 'sci', 'Sc05g0005020' => 'sci', 'Sc13g0003890' => 'sci', 'Sed0014865' => 'sed', 'Sed0017224' => 'sed', 'Sed0026391' => 'sed', 'SEGI_00063' => 'sgi', 'SEGI_10967' => 'sgi', 'SEGI_17510' => 'sgi', 'SEGI_24396' => 'sgi', 'SEGI_39719' => 'sgi', 'SEGI_41392' => 'sgi', 'SGA_v2.0_scaffold11G05794' => 'sas', 'SGA_v2.0_scaffold142G35607' => 'sas', 'SGA_v2.0_scaffold1G00447' => 'sas', 'SHI15388' => 'shi', 'SHI15394' => 'shi', 'SHI15396' => 'shi', 'SHI15399' => 'shi', 'SMO343G0151' => 'smo', 'SMO367G1118' => 'smo', 'Solyc01g080200.3' => 'sly', 'Solyc06g008960.3' => 'sly', 'Solyc09g064780.3' => 'sly', 'Sopen01g031980' => 'spe', 'Sopen06g003710' => 'spe', 'Sopen09g026460' => 'spe', 'Sp3g21240' => 'spa', 'Sp4g30030' => 'spa', 'TAR365G0022' => 'tar', 'TAR365G1023' => 'tar', 'TAR365G1253' => 'tar', 'TAR623G0078' => 'tar', 'TAR623G1721' => 'tar', 'TAR633G0959' => 'tar', 'THA.LOC104802225' => 'tha', 'THA.LOC104804769' => 'tha', 'THA.LOC104808660' => 'tha', 'THA.LOC104812792' => 'tha', 'Thecc.01G284000' => 'tca', 'Thecc.04G220600' => 'tca', 'Thecc.05G268900' => 'tca', 'Thecc.08G171100' => 'tca', 'Thhalv10001284m.g' => 'esa', 'Thhalv10019912m.g' => 'esa', 'TPR.G14189' => 'tpr', 'TPR.G18110' => 'tpr', 'TPR.G18130' => 'tpr', 'TPR.G18131' => 'tpr', 'TPR.G18140' => 'tpr', 'TPR.G24282' => 'tpr', 'TPR.G25221' => 'tpr', 'TPR.G29267' => 'tpr', 'TPR.G35315' => 'tpr', 'TPR.G36173' => 'tpr', 'TWI09G0794' => 'twi', 'TWI59G1348' => 'twi', 'TWI74G0430' => 'twi', 'unitig_26.g8940' => 'ugi', 'unitig_749.g13744' => 'ugi', 'unitig_749.g13745' => 'ugi', 'vmacro08269' => 'vma', 'vmacro14937' => 'vma', 'vmacro20401' => 'vma', 'VMungo0464G1349' => 'vmu', 'VMungo0540G0289' => 'vmu', 'VMungo1215G1590' => 'vmu', 'VMungo1309G0221' => 'vmu', 'VMungo1309G2815' => 'vmu', 'VMungo1383G0239' => 'vmu', 'VMungo1383G2910' => 'vmu', 'Zm00001eb095270' => 'zma', 'Zm00001eb095280' => 'zma', 'Zm00001eb111630' => 'zma', 'Zm00001eb237080' => 'zma', 'Zm00001eb273740' => 'zma', 'Zm00001eb285040' => 'zma', 'Zm00001eb330790' => 'zma', 'Zm00001eb337380' => 'zma' ), 'gf_id' => 'HOM05D001484', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001484' ), 'data_identifier' => 'HOM05D001484', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001484', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p31500' => 'bna', 'A05p00020' => 'bna', 'A07p08820' => 'bna', 'Aa31LG4G3300' => 'aar', 'Aa31LG8G10030' => 'aar', 'Actinidia00731' => 'ach', 'Actinidia11473' => 'ach', 'Actinidia23469' => 'ach', 'Actinidia24318' => 'ach', 'Actinidia40196' => 'ach', 'Actinidia40197' => 'ach', 'Actinidia40198' => 'ach', 'Ah.08g212990' => 'amhyb', 'Ah.15g091720' => 'amhyb', 'AL3G38260' => 'aly', 'AL4G47710' => 'aly', 'Aqoxy2G00671' => 'aox', 'Aqoxy2G03236' => 'aox', 'arahy.Tifrunner.gnm1.ann1.05IDCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KR684' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATY3SJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK6QJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6APGL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IDT7Z9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM073U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ0R87' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LE7RV4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT4QRX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V5ENPK' => 'arhy', 'AT2G48110' => 'ath', 'AT3G23590' => 'ath', 'ATR0626G186' => 'atr', 'ATR1127G141' => 'atr', 'Atru.chr4.2583' => 'acertr', 'Atru.chr5.1358' => 'acertr', 'Atru.chr5.1359' => 'acertr', 'Atru.chr8.46' => 'acertr', 'AUR62002640' => 'cqu', 'AUR62030055' => 'cqu', 'AUR62033713' => 'cqu', 'AUR62033714' => 'cqu', 'AUR62036795' => 'cqu', 'AUR62039891' => 'cqu', 'BcaB02g08737' => 'bca', 'BcaB04g20441' => 'bca', 'BcaB06g26509' => 'bca', 'BcaB06g26510' => 'bca', 'BcaB06g26511' => 'bca', 'BcaB06g26512' => 'bca', 'BcaB06g26513' => 'bca', 'BcaC02g12564' => 'bca', 'BcaC02g12565' => 'bca', 'BcaC02g12794' => 'bca', 'BcaC02g12795' => 'bca', 'BcaC02g12796' => 'bca', 'BcaC06g35541' => 'bca', 'BNapus_Darmor_BZH_scaffold_188p00080' => 'bna', 'BNapus_Darmor_BZH_scaffold_188p00090' => 'bna', 'BolC1t03972H' => 'bol', 'BolC1t03973H' => 'bol', 'BolC4t21680H' => 'bol', 'BolC7t41863H' => 'bol', 'BolSC55t61227H' => 'bol', 'BolSC55t61228H' => 'bol', 'BraA01t03278Z' => 'bra', 'BraA05t18998Z' => 'bra', 'BraA07t28673Z' => 'bra', 'C01p40150' => 'bna', 'C05p12370' => 'bna', 'C07p13680' => 'bna', 'CAN.G1006.16' => 'can', 'CAN.G1006.17' => 'can', 'CAN.G1170.2' => 'can', 'CAN.G962.7' => 'can', 'CANSAT25G2179' => 'cansat', 'CANSAT78G1573' => 'cansat', 'CARHR099510' => 'chi', 'CARHR143510' => 'chi', 'Carub.0003s2380' => 'cru', 'Carub.0004s3082' => 'cru', 'Ca_00614_v3' => 'car', 'Ca_07801_v3' => 'car', 'Ca_08567_v3' => 'car', 'Ca_09571_v3' => 'car', 'CBR_g19290' => 'cbr', 'Cc01_g19770' => 'ccan', 'Cc03_g03030' => 'ccan', 'CDE07G0968' => 'cde', 'CDE09G1441' => 'cde', 'Cfa006103' => 'cfa', 'Cfa015573' => 'cfa', 'Cfa016988' => 'cfa', 'Ciclev10006738m.g' => 'ccl', 'Ciclev10010920m.g' => 'ccl', 'Ciclev10018517m.g' => 'ccl', 'CiPaw.01G159200' => 'cil', 'CiPaw.02G091000' => 'cil', 'CiPaw.02G091100' => 'cil', 'CiPaw.08G103100' => 'cil', 'CiPaw.09G224900' => 'cil', 'ClCG06G005740' => 'cla', 'ClCG07G000090' => 'cla', 'ClCG07G000100' => 'cla', 'COL.COLO4_09143' => 'col', 'COL.COLO4_25124' => 'col', 'Cpa.g.sc16.34' => 'cpa', 'Cpa.g.sc3504.1' => 'cpa', 'Cpa.g.sc60.37' => 'cpa', 'CsaV3_6G018520' => 'csa', 'CsaV3_6G036860' => 'csa', 'CSS0001072' => 'camsi', 'CSS0020208' => 'camsi', 'CSS0021253' => 'camsi', 'CSS0022190' => 'camsi', 'CSS0036150' => 'camsi', 'CSS0040442' => 'camsi', 'CSS0042300' => 'camsi', 'CSS0045298' => 'camsi', 'DCAR_012449' => 'dca', 'DCAR_018405' => 'dca', 'DCAR_024573' => 'dca', 'DCAR_030591' => 'dca', 'Dinv16926' => 'din', 'Dinv32963' => 'din', 'Dinv38382' => 'din', 'Dinv38383' => 'din', 'Duzib133G0974' => 'dzi', 'Duzib138G1867' => 'dzi', 'Duzib211G0420' => 'dzi', 'Duzib212G0930' => 'dzi', 'ECA234G1645' => 'eca', 'ECA247G3467' => 'eca', 'ECA248G1703' => 'eca', 'EL10Ac3g06327' => 'bvu', 'EL10Ac7g17204' => 'bvu', 'Eucgr.A00855' => 'egr', 'Eucgr.A00858' => 'egr', 'Eucgr.H01520' => 'egr', 'Eucgr.H03604' => 'egr', 'Eucgr.L03465' => 'egr', 'Eucgr.L03466' => 'egr', 'FAN01G0988' => 'fan', 'FAN02G3892' => 'fan', 'FAN05G3381' => 'fan', 'FAN07G0967' => 'fan', 'FAN07G1493' => 'fan', 'FAN08G3125' => 'fan', 'FAN09G0402' => 'fan', 'FAN12G2594' => 'fan', 'FAN12G3879' => 'fan', 'FAN14G1546' => 'fan', 'FAN15G3626' => 'fan', 'FAN17G0588' => 'fan', 'FAN17G0609' => 'fan', 'FAN18G2817' => 'fan', 'FAN19G1305' => 'fan', 'FAN20G1787' => 'fan', 'FAN22G0073' => 'fan', 'FAN22G0352' => 'fan', 'FAN22G0368' => 'fan', 'FAN22G2273' => 'fan', 'FAN24G1998' => 'fan', 'FAN27G1317' => 'fan', 'FvH4_2g23980' => 'fve', 'FvH4_4g14380' => 'fve', 'FvH4_4g14390' => 'fve', 'FvH4_6g09250' => 'fve', 'Glyma.03G151100' => 'gma', 'Glyma.04G122550' => 'gma', 'Glyma.05G001600' => 'gma', 'Glyma.09G270766' => 'gma', 'Glyma.09G270832' => 'gma', 'Glyma.13G209800' => 'gma', 'Glyma.15G102800' => 'gma', 'Glyma.18G218900' => 'gma', 'Glyma.19G001500' => 'gma', 'Glyma.19G153600' => 'gma', 'Gohir.A02G028600' => 'ghi', 'Gohir.A08G045000' => 'ghi', 'Gohir.A11G120500' => 'ghi', 'Gohir.A12G006200' => 'ghi', 'Gohir.A12G006250' => 'ghi', 'Gohir.D02G036300' => 'ghi', 'Gohir.D08G054700' => 'ghi', 'Gohir.D11G125600' => 'ghi', 'Gohir.D12G005700' => 'ghi', 'Gorai.004G055200' => 'gra', 'Gorai.005G040400' => 'gra', 'Gorai.007G134500' => 'gra', 'Gorai.008G005500' => 'gra', 'GSVIVG01011094001' => 'vvi', 'GSVIVG01017879001' => 'vvi', 'GSVIVG01025988001' => 'vvi', 'GSVIVG01029847001' => 'vvi', 'HanXRQChr10g0282901' => 'han', 'HanXRQChr10g0310371' => 'han', 'HanXRQChr10g0315041' => 'han', 'HanXRQChr11g0327651' => 'han', 'HanXRQChr12g0359391' => 'han', 'Haze_00972' => 'cav', 'Haze_00973' => 'cav', 'Haze_00974' => 'cav', 'Haze_04747' => 'cav', 'Haze_04749' => 'cav', 'Haze_04750' => 'cav', 'Haze_21217' => 'cav', 'Hma1.2p1_1037F.1_g250680' => 'hma', 'Hma1.2p1_1644F.1_g295320' => 'hma', 'HPP92_011322' => 'vpl', 'HPP92_011323' => 'vpl', 'HPP92_011324' => 'vpl', 'HPP92_011325' => 'vpl', 'HPP92_011326' => 'vpl', 'Hund12205' => 'sun', 'Hund17957' => 'sun', 'Lalb_Chr06g0176771' => 'lal', 'Lalb_Chr18g0056021' => 'lal', 'Lalb_Chr18g0056031' => 'lal', 'Lalb_Chr18g0056041' => 'lal', 'Lalb_Chr20g0107751' => 'lal', 'Lalb_Chr20g0118371' => 'lal', 'Lj1g0010239' => 'lja', 'Lj1g0017101' => 'lja', 'Lj2A1178G40' => 'lonja', 'Lj2A54G84' => 'lonja', 'Lj2g0015248' => 'lja', 'Lj3A761T51' => 'lonja', 'Lj6g0018116' => 'lja', 'Lsat_1_v5_gn_4_136040' => 'lsa', 'Lsat_1_v5_gn_5_187461' => 'lsa', 'Lsat_1_v5_gn_5_77001' => 'lsa', 'Lsat_1_v5_gn_9_4461' => 'lsa', 'Manes.01G210100' => 'mes', 'Manes.03G185600' => 'mes', 'Manes.05G073300' => 'mes', 'Manes.09G120300' => 'mes', 'Manes.15G022100' => 'mes', 'Mapoly0096s0053' => 'mpo', 'MBI03_g14058_MAGBIO' => 'mbi', 'MBI03_g33876_MAGBIO' => 'mbi', 'MBI03_g36854_MAGBIO' => 'mbi', 'MBI17_g11997_MAGBIO' => 'mbi', 'MD03G1269000' => 'mdo', 'MD04G1179600' => 'mdo', 'MD11G1289800' => 'mdo', 'MD12G1194700' => 'mdo', 'MD13G1182100' => 'mdo', 'MD13G1182200' => 'mdo', 'MD16G1182600' => 'mdo', 'Medtr2g021400' => 'mtr', 'Medtr2g021470' => 'mtr', 'Medtr2g105810' => 'mtr', 'Medtr3g033580' => 'mtr', 'Medtr6g007970' => 'mtr', 'Medtr7g056330' => 'mtr', 'Medtr7g074290' => 'mtr', 'Medtr7g074380' => 'mtr', 'Medtr7g094550' => 'mtr', 'Medtr8g069995' => 'mtr', 'MELO3C014345.2' => 'cme', 'MELO3C021395.2' => 'cme', 'Migut.D00262' => 'egut', 'Migut.G00257' => 'egut', 'MSTRG.21575' => 'ama', 'MSTRG.3985' => 'ama', 'Nitab4.5_0000295g0140' => 'nta', 'Nitab4.5_0000732g0140' => 'nta', 'Nitab4.5_0003162g0020' => 'nta', 'Nitab4.5_0006180g0090' => 'nta', 'Nitab4.5_0006390g0010' => 'nta', 'Nitab4.5_0007392g0040' => 'nta', 'Nn1g02140' => 'nnu', 'Nn4g26168' => 'nnu', 'Nn5g26754' => 'nnu', 'Oeu001433.1' => 'oeu', 'Oeu010299.2' => 'oeu', 'Oeu011171.1' => 'oeu', 'Oeu037675.1' => 'oeu', 'Oeu038359.1' => 'oeu', 'Oeu063834.1' => 'oeu', 'Oeu063835.1' => 'oeu', 'Os05g0312000' => 'osa', 'Os07g0211101' => 'osa', 'Os07g0211200' => 'osa', 'Os07g0681500' => 'osa', 'Peaxi162Scf00095g01015' => 'pax', 'Peaxi162Scf00104g00329' => 'pax', 'Peaxi162Scf00161g00137' => 'pax', 'PGR004G1665' => 'pgr', 'PGR031G2937' => 'pgr', 'PGR119G2145' => 'pgr', 'PGSC0003DMG400004351' => 'stu', 'PGSC0003DMG400014625' => 'stu', 'PGSC0003DMG401000943' => 'stu', 'Phvul.001G148600' => 'pvu', 'Phvul.004G001700' => 'pvu', 'Phvul.006G154900' => 'pvu', 'Phvul.008G078200' => 'pvu', 'Phvul.011G136500' => 'pvu', 'Potri.002G215600' => 'ptr', 'Potri.008G201600' => 'ptr', 'Potri.014G138400' => 'ptr', 'Potri.016G142500' => 'ptr', 'Pp3c16_10580' => 'ppa', 'Pp3c5_25280' => 'ppa', 'Prupe.1G150000' => 'ppe', 'Prupe.1G150100' => 'ppe', 'Prupe.6G299600' => 'ppe', 'Prupe.8G245000' => 'ppe', 'Psat0s4927g0040' => 'psa', 'Psat1g052080' => 'psa', 'Psat1g183800' => 'psa', 'Psat3g113840' => 'psa', 'Psat3g126120' => 'psa', 'Psat3g126160' => 'psa', 'Psat3g158760' => 'psa', 'Psat3g158840' => 'psa', 'PSO170G2858' => 'pso', 'PSO339G0606' => 'pso', 'PSO384G4709' => 'pso', 'PSO407G0334' => 'pso', 'QL04p040276' => 'qlo', 'QL06p005458' => 'qlo', 'QL06p005472' => 'qlo', 'QL07p030546' => 'qlo', 'QL07p031519' => 'qlo', 'QL09p050949' => 'qlo', 'QL09p050966' => 'qlo', 'QL09p051067' => 'qlo', 'QL12p022706' => 'qlo', 'RcHm_v2.0_Chr2g0119601' => 'rch', 'RcHm_v2.0_Chr3g0459591' => 'rch', 'RcHm_v2.0_Chr4g0418521' => 'rch', 'RcHm_v2.0_Chr4g0418531' => 'rch', 'RcHm_v2.0_Chr4g0418541' => 'rch', 'RcHm_v2.0_Chr6g0291641' => 'rch', 'Rhsim01G0086300' => 'rsi', 'Rhsim01G0276300' => 'rsi', 'Rhsim01G0276500' => 'rsi', 'Rhsim04G0207700' => 'rsi', 'Rhsim05G0234500' => 'rsi', 'Rhsim13G0022400' => 'rsi', 'Sabra02G0167900' => 'sbr', 'Sabra04G0158500' => 'sbr', 'Sabra08G0159800' => 'sbr', 'Sabra10G0011500' => 'sbr', 'Sabra14G0104400' => 'sbr', 'SalBow2G2440' => 'sbo', 'SalBow4G2265' => 'sbo', 'Sc02g0000060' => 'sci', 'Sc05g0005020' => 'sci', 'Sc13g0003890' => 'sci', 'Sed0014865' => 'sed', 'Sed0017224' => 'sed', 'Sed0026391' => 'sed', 'SEGI_00063' => 'sgi', 'SEGI_10967' => 'sgi', 'SEGI_17510' => 'sgi', 'SEGI_24396' => 'sgi', 'SEGI_39719' => 'sgi', 'SEGI_41392' => 'sgi', 'SGA_v2.0_scaffold11G05794' => 'sas', 'SGA_v2.0_scaffold142G35607' => 'sas', 'SGA_v2.0_scaffold1G00447' => 'sas', 'SHI15388' => 'shi', 'SHI15394' => 'shi', 'SHI15396' => 'shi', 'SHI15399' => 'shi', 'SMO343G0151' => 'smo', 'SMO367G1118' => 'smo', 'Solyc01g080200.3' => 'sly', 'Solyc06g008960.3' => 'sly', 'Solyc09g064780.3' => 'sly', 'Sopen01g031980' => 'spe', 'Sopen06g003710' => 'spe', 'Sopen09g026460' => 'spe', 'Sp3g21240' => 'spa', 'Sp4g30030' => 'spa', 'TAR365G0022' => 'tar', 'TAR365G1023' => 'tar', 'TAR365G1253' => 'tar', 'TAR623G0078' => 'tar', 'TAR623G1721' => 'tar', 'TAR633G0959' => 'tar', 'THA.LOC104802225' => 'tha', 'THA.LOC104804769' => 'tha', 'THA.LOC104808660' => 'tha', 'THA.LOC104812792' => 'tha', 'Thecc.01G284000' => 'tca', 'Thecc.04G220600' => 'tca', 'Thecc.05G268900' => 'tca', 'Thecc.08G171100' => 'tca', 'Thhalv10001284m.g' => 'esa', 'Thhalv10019912m.g' => 'esa', 'TPR.G14189' => 'tpr', 'TPR.G18110' => 'tpr', 'TPR.G18130' => 'tpr', 'TPR.G18131' => 'tpr', 'TPR.G18140' => 'tpr', 'TPR.G24282' => 'tpr', 'TPR.G25221' => 'tpr', 'TPR.G29267' => 'tpr', 'TPR.G35315' => 'tpr', 'TPR.G36173' => 'tpr', 'TWI09G0794' => 'twi', 'TWI59G1348' => 'twi', 'TWI74G0430' => 'twi', 'unitig_26.g8940' => 'ugi', 'unitig_749.g13744' => 'ugi', 'unitig_749.g13745' => 'ugi', 'vmacro08269' => 'vma', 'vmacro14937' => 'vma', 'vmacro20401' => 'vma', 'VMungo0464G1349' => 'vmu', 'VMungo0540G0289' => 'vmu', 'VMungo1215G1590' => 'vmu', 'VMungo1309G0221' => 'vmu', 'VMungo1309G2815' => 'vmu', 'VMungo1383G0239' => 'vmu', 'VMungo1383G2910' => 'vmu', 'Zm00001eb095270' => 'zma', 'Zm00001eb095280' => 'zma', 'Zm00001eb111630' => 'zma', 'Zm00001eb237080' => 'zma', 'Zm00001eb273740' => 'zma', 'Zm00001eb285040' => 'zma', 'Zm00001eb330790' => 'zma', 'Zm00001eb337380' => 'zma' ) $gf_id = 'HOM05D001484' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001484' ) $data_identifier = 'HOM05D001484' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 2, 'aly' => (int) 2, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 22, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 7, 'hma' => (int) 2, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 7, 'mtr' => (int) 10, 'cme' => (int) 2, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 4, 'ppa' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 4, 'qlo' => (int) 9, 'rch' => (int) 6, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 10, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 7, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb337380' $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' => 'HOM05D001484', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p31500' => 'bna', 'A05p00020' => 'bna', 'A07p08820' => 'bna', 'Aa31LG4G3300' => 'aar', 'Aa31LG8G10030' => 'aar', 'Actinidia00731' => 'ach', 'Actinidia11473' => 'ach', 'Actinidia23469' => 'ach', 'Actinidia24318' => 'ach', 'Actinidia40196' => 'ach', 'Actinidia40197' => 'ach', 'Actinidia40198' => 'ach', 'Ah.08g212990' => 'amhyb', 'Ah.15g091720' => 'amhyb', 'AL3G38260' => 'aly', 'AL4G47710' => 'aly', 'Aqoxy2G00671' => 'aox', 'Aqoxy2G03236' => 'aox', 'arahy.Tifrunner.gnm1.ann1.05IDCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KR684' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATY3SJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK6QJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6APGL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IDT7Z9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM073U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ0R87' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LE7RV4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT4QRX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V5ENPK' => 'arhy', 'AT2G48110' => 'ath', 'AT3G23590' => 'ath', 'ATR0626G186' => 'atr', 'ATR1127G141' => 'atr', 'Atru.chr4.2583' => 'acertr', 'Atru.chr5.1358' => 'acertr', 'Atru.chr5.1359' => 'acertr', 'Atru.chr8.46' => 'acertr', 'AUR62002640' => 'cqu', 'AUR62030055' => 'cqu', 'AUR62033713' => 'cqu', 'AUR62033714' => 'cqu', 'AUR62036795' => 'cqu', 'AUR62039891' => 'cqu', 'BcaB02g08737' => 'bca', 'BcaB04g20441' => 'bca', 'BcaB06g26509' => 'bca', 'BcaB06g26510' => 'bca', 'BcaB06g26511' => 'bca', 'BcaB06g26512' => 'bca', 'BcaB06g26513' => 'bca', 'BcaC02g12564' => 'bca', 'BcaC02g12565' => 'bca', 'BcaC02g12794' => 'bca', 'BcaC02g12795' => 'bca', 'BcaC02g12796' => 'bca', 'BcaC06g35541' => 'bca', 'BNapus_Darmor_BZH_scaffold_188p00080' => 'bna', 'BNapus_Darmor_BZH_scaffold_188p00090' => 'bna', 'BolC1t03972H' => 'bol', 'BolC1t03973H' => 'bol', 'BolC4t21680H' => 'bol', 'BolC7t41863H' => 'bol', 'BolSC55t61227H' => 'bol', 'BolSC55t61228H' => 'bol', 'BraA01t03278Z' => 'bra', 'BraA05t18998Z' => 'bra', 'BraA07t28673Z' => 'bra', 'C01p40150' => 'bna', 'C05p12370' => 'bna', 'C07p13680' => 'bna', 'CAN.G1006.16' => 'can', 'CAN.G1006.17' => 'can', 'CAN.G1170.2' => 'can', 'CAN.G962.7' => 'can', 'CANSAT25G2179' => 'cansat', 'CANSAT78G1573' => 'cansat', 'CARHR099510' => 'chi', 'CARHR143510' => 'chi', 'Carub.0003s2380' => 'cru', 'Carub.0004s3082' => 'cru', 'Ca_00614_v3' => 'car', 'Ca_07801_v3' => 'car', 'Ca_08567_v3' => 'car', 'Ca_09571_v3' => 'car', 'CBR_g19290' => 'cbr', 'Cc01_g19770' => 'ccan', 'Cc03_g03030' => 'ccan', 'CDE07G0968' => 'cde', 'CDE09G1441' => 'cde', 'Cfa006103' => 'cfa', 'Cfa015573' => 'cfa', 'Cfa016988' => 'cfa', 'Ciclev10006738m.g' => 'ccl', 'Ciclev10010920m.g' => 'ccl', 'Ciclev10018517m.g' => 'ccl', 'CiPaw.01G159200' => 'cil', 'CiPaw.02G091000' => 'cil', 'CiPaw.02G091100' => 'cil', 'CiPaw.08G103100' => 'cil', 'CiPaw.09G224900' => 'cil', 'ClCG06G005740' => 'cla', 'ClCG07G000090' => 'cla', 'ClCG07G000100' => 'cla', 'COL.COLO4_09143' => 'col', 'COL.COLO4_25124' => 'col', 'Cpa.g.sc16.34' => 'cpa', 'Cpa.g.sc3504.1' => 'cpa', 'Cpa.g.sc60.37' => 'cpa', 'CsaV3_6G018520' => 'csa', 'CsaV3_6G036860' => 'csa', 'CSS0001072' => 'camsi', 'CSS0020208' => 'camsi', 'CSS0021253' => 'camsi', 'CSS0022190' => 'camsi', 'CSS0036150' => 'camsi', 'CSS0040442' => 'camsi', 'CSS0042300' => 'camsi', 'CSS0045298' => 'camsi', 'DCAR_012449' => 'dca', 'DCAR_018405' => 'dca', 'DCAR_024573' => 'dca', 'DCAR_030591' => 'dca', 'Dinv16926' => 'din', 'Dinv32963' => 'din', 'Dinv38382' => 'din', 'Dinv38383' => 'din', 'Duzib133G0974' => 'dzi', 'Duzib138G1867' => 'dzi', 'Duzib211G0420' => 'dzi', 'Duzib212G0930' => 'dzi', 'ECA234G1645' => 'eca', 'ECA247G3467' => 'eca', 'ECA248G1703' => 'eca', 'EL10Ac3g06327' => 'bvu', 'EL10Ac7g17204' => 'bvu', 'Eucgr.A00855' => 'egr', 'Eucgr.A00858' => 'egr', 'Eucgr.H01520' => 'egr', 'Eucgr.H03604' => 'egr', 'Eucgr.L03465' => 'egr', 'Eucgr.L03466' => 'egr', 'FAN01G0988' => 'fan', 'FAN02G3892' => 'fan', 'FAN05G3381' => 'fan', 'FAN07G0967' => 'fan', 'FAN07G1493' => 'fan', 'FAN08G3125' => 'fan', 'FAN09G0402' => 'fan', 'FAN12G2594' => 'fan', 'FAN12G3879' => 'fan', 'FAN14G1546' => 'fan', 'FAN15G3626' => 'fan', 'FAN17G0588' => 'fan', 'FAN17G0609' => 'fan', 'FAN18G2817' => 'fan', 'FAN19G1305' => 'fan', 'FAN20G1787' => 'fan', 'FAN22G0073' => 'fan', 'FAN22G0352' => 'fan', 'FAN22G0368' => 'fan', 'FAN22G2273' => 'fan', 'FAN24G1998' => 'fan', 'FAN27G1317' => 'fan', 'FvH4_2g23980' => 'fve', 'FvH4_4g14380' => 'fve', 'FvH4_4g14390' => 'fve', 'FvH4_6g09250' => 'fve', 'Glyma.03G151100' => 'gma', 'Glyma.04G122550' => 'gma', 'Glyma.05G001600' => 'gma', 'Glyma.09G270766' => 'gma', 'Glyma.09G270832' => 'gma', 'Glyma.13G209800' => 'gma', 'Glyma.15G102800' => 'gma', 'Glyma.18G218900' => 'gma', 'Glyma.19G001500' => 'gma', 'Glyma.19G153600' => 'gma', 'Gohir.A02G028600' => 'ghi', 'Gohir.A08G045000' => 'ghi', 'Gohir.A11G120500' => 'ghi', 'Gohir.A12G006200' => 'ghi', 'Gohir.A12G006250' => 'ghi', 'Gohir.D02G036300' => 'ghi', 'Gohir.D08G054700' => 'ghi', 'Gohir.D11G125600' => 'ghi', 'Gohir.D12G005700' => 'ghi', 'Gorai.004G055200' => 'gra', 'Gorai.005G040400' => 'gra', 'Gorai.007G134500' => 'gra', 'Gorai.008G005500' => 'gra', 'GSVIVG01011094001' => 'vvi', 'GSVIVG01017879001' => 'vvi', 'GSVIVG01025988001' => 'vvi', 'GSVIVG01029847001' => 'vvi', 'HanXRQChr10g0282901' => 'han', 'HanXRQChr10g0310371' => 'han', 'HanXRQChr10g0315041' => 'han', 'HanXRQChr11g0327651' => 'han', 'HanXRQChr12g0359391' => 'han', 'Haze_00972' => 'cav', 'Haze_00973' => 'cav', 'Haze_00974' => 'cav', 'Haze_04747' => 'cav', 'Haze_04749' => 'cav', 'Haze_04750' => 'cav', 'Haze_21217' => 'cav', 'Hma1.2p1_1037F.1_g250680' => 'hma', 'Hma1.2p1_1644F.1_g295320' => 'hma', 'HPP92_011322' => 'vpl', 'HPP92_011323' => 'vpl', 'HPP92_011324' => 'vpl', 'HPP92_011325' => 'vpl', 'HPP92_011326' => 'vpl', 'Hund12205' => 'sun', 'Hund17957' => 'sun', 'Lalb_Chr06g0176771' => 'lal', 'Lalb_Chr18g0056021' => 'lal', 'Lalb_Chr18g0056031' => 'lal', 'Lalb_Chr18g0056041' => 'lal', 'Lalb_Chr20g0107751' => 'lal', 'Lalb_Chr20g0118371' => 'lal', 'Lj1g0010239' => 'lja', 'Lj1g0017101' => 'lja', 'Lj2A1178G40' => 'lonja', 'Lj2A54G84' => 'lonja', 'Lj2g0015248' => 'lja', 'Lj3A761T51' => 'lonja', 'Lj6g0018116' => 'lja', 'Lsat_1_v5_gn_4_136040' => 'lsa', 'Lsat_1_v5_gn_5_187461' => 'lsa', 'Lsat_1_v5_gn_5_77001' => 'lsa', 'Lsat_1_v5_gn_9_4461' => 'lsa', 'Manes.01G210100' => 'mes', 'Manes.03G185600' => 'mes', 'Manes.05G073300' => 'mes', 'Manes.09G120300' => 'mes', 'Manes.15G022100' => 'mes', 'Mapoly0096s0053' => 'mpo', 'MBI03_g14058_MAGBIO' => 'mbi', 'MBI03_g33876_MAGBIO' => 'mbi', 'MBI03_g36854_MAGBIO' => 'mbi', 'MBI17_g11997_MAGBIO' => 'mbi', 'MD03G1269000' => 'mdo', 'MD04G1179600' => 'mdo', 'MD11G1289800' => 'mdo', 'MD12G1194700' => 'mdo', 'MD13G1182100' => 'mdo', 'MD13G1182200' => 'mdo', 'MD16G1182600' => 'mdo', 'Medtr2g021400' => 'mtr', 'Medtr2g021470' => 'mtr', 'Medtr2g105810' => 'mtr', 'Medtr3g033580' => 'mtr', 'Medtr6g007970' => 'mtr', 'Medtr7g056330' => 'mtr', 'Medtr7g074290' => 'mtr', 'Medtr7g074380' => 'mtr', 'Medtr7g094550' => 'mtr', 'Medtr8g069995' => 'mtr', 'MELO3C014345.2' => 'cme', 'MELO3C021395.2' => 'cme', 'Migut.D00262' => 'egut', 'Migut.G00257' => 'egut', 'MSTRG.21575' => 'ama', 'MSTRG.3985' => 'ama', 'Nitab4.5_0000295g0140' => 'nta', 'Nitab4.5_0000732g0140' => 'nta', 'Nitab4.5_0003162g0020' => 'nta', 'Nitab4.5_0006180g0090' => 'nta', 'Nitab4.5_0006390g0010' => 'nta', 'Nitab4.5_0007392g0040' => 'nta', 'Nn1g02140' => 'nnu', 'Nn4g26168' => 'nnu', 'Nn5g26754' => 'nnu', 'Oeu001433.1' => 'oeu', 'Oeu010299.2' => 'oeu', 'Oeu011171.1' => 'oeu', 'Oeu037675.1' => 'oeu', 'Oeu038359.1' => 'oeu', 'Oeu063834.1' => 'oeu', 'Oeu063835.1' => 'oeu', 'Os05g0312000' => 'osa', 'Os07g0211101' => 'osa', 'Os07g0211200' => 'osa', 'Os07g0681500' => 'osa', 'Peaxi162Scf00095g01015' => 'pax', 'Peaxi162Scf00104g00329' => 'pax', 'Peaxi162Scf00161g00137' => 'pax', 'PGR004G1665' => 'pgr', 'PGR031G2937' => 'pgr', 'PGR119G2145' => 'pgr', 'PGSC0003DMG400004351' => 'stu', 'PGSC0003DMG400014625' => 'stu', 'PGSC0003DMG401000943' => 'stu', 'Phvul.001G148600' => 'pvu', 'Phvul.004G001700' => 'pvu', 'Phvul.006G154900' => 'pvu', 'Phvul.008G078200' => 'pvu', 'Phvul.011G136500' => 'pvu', 'Potri.002G215600' => 'ptr', 'Potri.008G201600' => 'ptr', 'Potri.014G138400' => 'ptr', 'Potri.016G142500' => 'ptr', 'Pp3c16_10580' => 'ppa', 'Pp3c5_25280' => 'ppa', 'Prupe.1G150000' => 'ppe', 'Prupe.1G150100' => 'ppe', 'Prupe.6G299600' => 'ppe', 'Prupe.8G245000' => 'ppe', 'Psat0s4927g0040' => 'psa', 'Psat1g052080' => 'psa', 'Psat1g183800' => 'psa', 'Psat3g113840' => 'psa', 'Psat3g126120' => 'psa', 'Psat3g126160' => 'psa', 'Psat3g158760' => 'psa', 'Psat3g158840' => 'psa', 'PSO170G2858' => 'pso', 'PSO339G0606' => 'pso', 'PSO384G4709' => 'pso', 'PSO407G0334' => 'pso', 'QL04p040276' => 'qlo', 'QL06p005458' => 'qlo', 'QL06p005472' => 'qlo', 'QL07p030546' => 'qlo', 'QL07p031519' => 'qlo', 'QL09p050949' => 'qlo', 'QL09p050966' => 'qlo', 'QL09p051067' => 'qlo', 'QL12p022706' => 'qlo', 'RcHm_v2.0_Chr2g0119601' => 'rch', 'RcHm_v2.0_Chr3g0459591' => 'rch', 'RcHm_v2.0_Chr4g0418521' => 'rch', 'RcHm_v2.0_Chr4g0418531' => 'rch', 'RcHm_v2.0_Chr4g0418541' => 'rch', 'RcHm_v2.0_Chr6g0291641' => 'rch', 'Rhsim01G0086300' => 'rsi', 'Rhsim01G0276300' => 'rsi', 'Rhsim01G0276500' => 'rsi', 'Rhsim04G0207700' => 'rsi', 'Rhsim05G0234500' => 'rsi', 'Rhsim13G0022400' => 'rsi', 'Sabra02G0167900' => 'sbr', 'Sabra04G0158500' => 'sbr', 'Sabra08G0159800' => 'sbr', 'Sabra10G0011500' => 'sbr', 'Sabra14G0104400' => 'sbr', 'SalBow2G2440' => 'sbo', 'SalBow4G2265' => 'sbo', 'Sc02g0000060' => 'sci', 'Sc05g0005020' => 'sci', 'Sc13g0003890' => 'sci', 'Sed0014865' => 'sed', 'Sed0017224' => 'sed', 'Sed0026391' => 'sed', 'SEGI_00063' => 'sgi', 'SEGI_10967' => 'sgi', 'SEGI_17510' => 'sgi', 'SEGI_24396' => 'sgi', 'SEGI_39719' => 'sgi', 'SEGI_41392' => 'sgi', 'SGA_v2.0_scaffold11G05794' => 'sas', 'SGA_v2.0_scaffold142G35607' => 'sas', 'SGA_v2.0_scaffold1G00447' => 'sas', 'SHI15388' => 'shi', 'SHI15394' => 'shi', 'SHI15396' => 'shi', 'SHI15399' => 'shi', 'SMO343G0151' => 'smo', 'SMO367G1118' => 'smo', 'Solyc01g080200.3' => 'sly', 'Solyc06g008960.3' => 'sly', 'Solyc09g064780.3' => 'sly', 'Sopen01g031980' => 'spe', 'Sopen06g003710' => 'spe', 'Sopen09g026460' => 'spe', 'Sp3g21240' => 'spa', 'Sp4g30030' => 'spa', 'TAR365G0022' => 'tar', 'TAR365G1023' => 'tar', 'TAR365G1253' => 'tar', 'TAR623G0078' => 'tar', 'TAR623G1721' => 'tar', 'TAR633G0959' => 'tar', 'THA.LOC104802225' => 'tha', 'THA.LOC104804769' => 'tha', 'THA.LOC104808660' => 'tha', 'THA.LOC104812792' => 'tha', 'Thecc.01G284000' => 'tca', 'Thecc.04G220600' => 'tca', 'Thecc.05G268900' => 'tca', 'Thecc.08G171100' => 'tca', 'Thhalv10001284m.g' => 'esa', 'Thhalv10019912m.g' => 'esa', 'TPR.G14189' => 'tpr', 'TPR.G18110' => 'tpr', 'TPR.G18130' => 'tpr', 'TPR.G18131' => 'tpr', 'TPR.G18140' => 'tpr', 'TPR.G24282' => 'tpr', 'TPR.G25221' => 'tpr', 'TPR.G29267' => 'tpr', 'TPR.G35315' => 'tpr', 'TPR.G36173' => 'tpr', 'TWI09G0794' => 'twi', 'TWI59G1348' => 'twi', 'TWI74G0430' => 'twi', 'unitig_26.g8940' => 'ugi', 'unitig_749.g13744' => 'ugi', 'unitig_749.g13745' => 'ugi', 'vmacro08269' => 'vma', 'vmacro14937' => 'vma', 'vmacro20401' => 'vma', 'VMungo0464G1349' => 'vmu', 'VMungo0540G0289' => 'vmu', 'VMungo1215G1590' => 'vmu', 'VMungo1309G0221' => 'vmu', 'VMungo1309G2815' => 'vmu', 'VMungo1383G0239' => 'vmu', 'VMungo1383G2910' => 'vmu', 'Zm00001eb095270' => 'zma', 'Zm00001eb095280' => 'zma', 'Zm00001eb111630' => 'zma', 'Zm00001eb237080' => 'zma', 'Zm00001eb273740' => 'zma', 'Zm00001eb285040' => 'zma', 'Zm00001eb330790' => 'zma', 'Zm00001eb337380' => 'zma' ), 'gf_id' => 'HOM05D001484', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001484' ), 'data_identifier' => 'HOM05D001484', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001484', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p31500' => 'bna', 'A05p00020' => 'bna', 'A07p08820' => 'bna', 'Aa31LG4G3300' => 'aar', 'Aa31LG8G10030' => 'aar', 'Actinidia00731' => 'ach', 'Actinidia11473' => 'ach', 'Actinidia23469' => 'ach', 'Actinidia24318' => 'ach', 'Actinidia40196' => 'ach', 'Actinidia40197' => 'ach', 'Actinidia40198' => 'ach', 'Ah.08g212990' => 'amhyb', 'Ah.15g091720' => 'amhyb', 'AL3G38260' => 'aly', 'AL4G47710' => 'aly', 'Aqoxy2G00671' => 'aox', 'Aqoxy2G03236' => 'aox', 'arahy.Tifrunner.gnm1.ann1.05IDCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KR684' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATY3SJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK6QJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6APGL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IDT7Z9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM073U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ0R87' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LE7RV4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT4QRX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V5ENPK' => 'arhy', 'AT2G48110' => 'ath', 'AT3G23590' => 'ath', 'ATR0626G186' => 'atr', 'ATR1127G141' => 'atr', 'Atru.chr4.2583' => 'acertr', 'Atru.chr5.1358' => 'acertr', 'Atru.chr5.1359' => 'acertr', 'Atru.chr8.46' => 'acertr', 'AUR62002640' => 'cqu', 'AUR62030055' => 'cqu', 'AUR62033713' => 'cqu', 'AUR62033714' => 'cqu', 'AUR62036795' => 'cqu', 'AUR62039891' => 'cqu', 'BcaB02g08737' => 'bca', 'BcaB04g20441' => 'bca', 'BcaB06g26509' => 'bca', 'BcaB06g26510' => 'bca', 'BcaB06g26511' => 'bca', 'BcaB06g26512' => 'bca', 'BcaB06g26513' => 'bca', 'BcaC02g12564' => 'bca', 'BcaC02g12565' => 'bca', 'BcaC02g12794' => 'bca', 'BcaC02g12795' => 'bca', 'BcaC02g12796' => 'bca', 'BcaC06g35541' => 'bca', 'BNapus_Darmor_BZH_scaffold_188p00080' => 'bna', 'BNapus_Darmor_BZH_scaffold_188p00090' => 'bna', 'BolC1t03972H' => 'bol', 'BolC1t03973H' => 'bol', 'BolC4t21680H' => 'bol', 'BolC7t41863H' => 'bol', 'BolSC55t61227H' => 'bol', 'BolSC55t61228H' => 'bol', 'BraA01t03278Z' => 'bra', 'BraA05t18998Z' => 'bra', 'BraA07t28673Z' => 'bra', 'C01p40150' => 'bna', 'C05p12370' => 'bna', 'C07p13680' => 'bna', 'CAN.G1006.16' => 'can', 'CAN.G1006.17' => 'can', 'CAN.G1170.2' => 'can', 'CAN.G962.7' => 'can', 'CANSAT25G2179' => 'cansat', 'CANSAT78G1573' => 'cansat', 'CARHR099510' => 'chi', 'CARHR143510' => 'chi', 'Carub.0003s2380' => 'cru', 'Carub.0004s3082' => 'cru', 'Ca_00614_v3' => 'car', 'Ca_07801_v3' => 'car', 'Ca_08567_v3' => 'car', 'Ca_09571_v3' => 'car', 'CBR_g19290' => 'cbr', 'Cc01_g19770' => 'ccan', 'Cc03_g03030' => 'ccan', 'CDE07G0968' => 'cde', 'CDE09G1441' => 'cde', 'Cfa006103' => 'cfa', 'Cfa015573' => 'cfa', 'Cfa016988' => 'cfa', 'Ciclev10006738m.g' => 'ccl', 'Ciclev10010920m.g' => 'ccl', 'Ciclev10018517m.g' => 'ccl', 'CiPaw.01G159200' => 'cil', 'CiPaw.02G091000' => 'cil', 'CiPaw.02G091100' => 'cil', 'CiPaw.08G103100' => 'cil', 'CiPaw.09G224900' => 'cil', 'ClCG06G005740' => 'cla', 'ClCG07G000090' => 'cla', 'ClCG07G000100' => 'cla', 'COL.COLO4_09143' => 'col', 'COL.COLO4_25124' => 'col', 'Cpa.g.sc16.34' => 'cpa', 'Cpa.g.sc3504.1' => 'cpa', 'Cpa.g.sc60.37' => 'cpa', 'CsaV3_6G018520' => 'csa', 'CsaV3_6G036860' => 'csa', 'CSS0001072' => 'camsi', 'CSS0020208' => 'camsi', 'CSS0021253' => 'camsi', 'CSS0022190' => 'camsi', 'CSS0036150' => 'camsi', 'CSS0040442' => 'camsi', 'CSS0042300' => 'camsi', 'CSS0045298' => 'camsi', 'DCAR_012449' => 'dca', 'DCAR_018405' => 'dca', 'DCAR_024573' => 'dca', 'DCAR_030591' => 'dca', 'Dinv16926' => 'din', 'Dinv32963' => 'din', 'Dinv38382' => 'din', 'Dinv38383' => 'din', 'Duzib133G0974' => 'dzi', 'Duzib138G1867' => 'dzi', 'Duzib211G0420' => 'dzi', 'Duzib212G0930' => 'dzi', 'ECA234G1645' => 'eca', 'ECA247G3467' => 'eca', 'ECA248G1703' => 'eca', 'EL10Ac3g06327' => 'bvu', 'EL10Ac7g17204' => 'bvu', 'Eucgr.A00855' => 'egr', 'Eucgr.A00858' => 'egr', 'Eucgr.H01520' => 'egr', 'Eucgr.H03604' => 'egr', 'Eucgr.L03465' => 'egr', 'Eucgr.L03466' => 'egr', 'FAN01G0988' => 'fan', 'FAN02G3892' => 'fan', 'FAN05G3381' => 'fan', 'FAN07G0967' => 'fan', 'FAN07G1493' => 'fan', 'FAN08G3125' => 'fan', 'FAN09G0402' => 'fan', 'FAN12G2594' => 'fan', 'FAN12G3879' => 'fan', 'FAN14G1546' => 'fan', 'FAN15G3626' => 'fan', 'FAN17G0588' => 'fan', 'FAN17G0609' => 'fan', 'FAN18G2817' => 'fan', 'FAN19G1305' => 'fan', 'FAN20G1787' => 'fan', 'FAN22G0073' => 'fan', 'FAN22G0352' => 'fan', 'FAN22G0368' => 'fan', 'FAN22G2273' => 'fan', 'FAN24G1998' => 'fan', 'FAN27G1317' => 'fan', 'FvH4_2g23980' => 'fve', 'FvH4_4g14380' => 'fve', 'FvH4_4g14390' => 'fve', 'FvH4_6g09250' => 'fve', 'Glyma.03G151100' => 'gma', 'Glyma.04G122550' => 'gma', 'Glyma.05G001600' => 'gma', 'Glyma.09G270766' => 'gma', 'Glyma.09G270832' => 'gma', 'Glyma.13G209800' => 'gma', 'Glyma.15G102800' => 'gma', 'Glyma.18G218900' => 'gma', 'Glyma.19G001500' => 'gma', 'Glyma.19G153600' => 'gma', 'Gohir.A02G028600' => 'ghi', 'Gohir.A08G045000' => 'ghi', 'Gohir.A11G120500' => 'ghi', 'Gohir.A12G006200' => 'ghi', 'Gohir.A12G006250' => 'ghi', 'Gohir.D02G036300' => 'ghi', 'Gohir.D08G054700' => 'ghi', 'Gohir.D11G125600' => 'ghi', 'Gohir.D12G005700' => 'ghi', 'Gorai.004G055200' => 'gra', 'Gorai.005G040400' => 'gra', 'Gorai.007G134500' => 'gra', 'Gorai.008G005500' => 'gra', 'GSVIVG01011094001' => 'vvi', 'GSVIVG01017879001' => 'vvi', 'GSVIVG01025988001' => 'vvi', 'GSVIVG01029847001' => 'vvi', 'HanXRQChr10g0282901' => 'han', 'HanXRQChr10g0310371' => 'han', 'HanXRQChr10g0315041' => 'han', 'HanXRQChr11g0327651' => 'han', 'HanXRQChr12g0359391' => 'han', 'Haze_00972' => 'cav', 'Haze_00973' => 'cav', 'Haze_00974' => 'cav', 'Haze_04747' => 'cav', 'Haze_04749' => 'cav', 'Haze_04750' => 'cav', 'Haze_21217' => 'cav', 'Hma1.2p1_1037F.1_g250680' => 'hma', 'Hma1.2p1_1644F.1_g295320' => 'hma', 'HPP92_011322' => 'vpl', 'HPP92_011323' => 'vpl', 'HPP92_011324' => 'vpl', 'HPP92_011325' => 'vpl', 'HPP92_011326' => 'vpl', 'Hund12205' => 'sun', 'Hund17957' => 'sun', 'Lalb_Chr06g0176771' => 'lal', 'Lalb_Chr18g0056021' => 'lal', 'Lalb_Chr18g0056031' => 'lal', 'Lalb_Chr18g0056041' => 'lal', 'Lalb_Chr20g0107751' => 'lal', 'Lalb_Chr20g0118371' => 'lal', 'Lj1g0010239' => 'lja', 'Lj1g0017101' => 'lja', 'Lj2A1178G40' => 'lonja', 'Lj2A54G84' => 'lonja', 'Lj2g0015248' => 'lja', 'Lj3A761T51' => 'lonja', 'Lj6g0018116' => 'lja', 'Lsat_1_v5_gn_4_136040' => 'lsa', 'Lsat_1_v5_gn_5_187461' => 'lsa', 'Lsat_1_v5_gn_5_77001' => 'lsa', 'Lsat_1_v5_gn_9_4461' => 'lsa', 'Manes.01G210100' => 'mes', 'Manes.03G185600' => 'mes', 'Manes.05G073300' => 'mes', 'Manes.09G120300' => 'mes', 'Manes.15G022100' => 'mes', 'Mapoly0096s0053' => 'mpo', 'MBI03_g14058_MAGBIO' => 'mbi', 'MBI03_g33876_MAGBIO' => 'mbi', 'MBI03_g36854_MAGBIO' => 'mbi', 'MBI17_g11997_MAGBIO' => 'mbi', 'MD03G1269000' => 'mdo', 'MD04G1179600' => 'mdo', 'MD11G1289800' => 'mdo', 'MD12G1194700' => 'mdo', 'MD13G1182100' => 'mdo', 'MD13G1182200' => 'mdo', 'MD16G1182600' => 'mdo', 'Medtr2g021400' => 'mtr', 'Medtr2g021470' => 'mtr', 'Medtr2g105810' => 'mtr', 'Medtr3g033580' => 'mtr', 'Medtr6g007970' => 'mtr', 'Medtr7g056330' => 'mtr', 'Medtr7g074290' => 'mtr', 'Medtr7g074380' => 'mtr', 'Medtr7g094550' => 'mtr', 'Medtr8g069995' => 'mtr', 'MELO3C014345.2' => 'cme', 'MELO3C021395.2' => 'cme', 'Migut.D00262' => 'egut', 'Migut.G00257' => 'egut', 'MSTRG.21575' => 'ama', 'MSTRG.3985' => 'ama', 'Nitab4.5_0000295g0140' => 'nta', 'Nitab4.5_0000732g0140' => 'nta', 'Nitab4.5_0003162g0020' => 'nta', 'Nitab4.5_0006180g0090' => 'nta', 'Nitab4.5_0006390g0010' => 'nta', 'Nitab4.5_0007392g0040' => 'nta', 'Nn1g02140' => 'nnu', 'Nn4g26168' => 'nnu', 'Nn5g26754' => 'nnu', 'Oeu001433.1' => 'oeu', 'Oeu010299.2' => 'oeu', 'Oeu011171.1' => 'oeu', 'Oeu037675.1' => 'oeu', 'Oeu038359.1' => 'oeu', 'Oeu063834.1' => 'oeu', 'Oeu063835.1' => 'oeu', 'Os05g0312000' => 'osa', 'Os07g0211101' => 'osa', 'Os07g0211200' => 'osa', 'Os07g0681500' => 'osa', 'Peaxi162Scf00095g01015' => 'pax', 'Peaxi162Scf00104g00329' => 'pax', 'Peaxi162Scf00161g00137' => 'pax', 'PGR004G1665' => 'pgr', 'PGR031G2937' => 'pgr', 'PGR119G2145' => 'pgr', 'PGSC0003DMG400004351' => 'stu', 'PGSC0003DMG400014625' => 'stu', 'PGSC0003DMG401000943' => 'stu', 'Phvul.001G148600' => 'pvu', 'Phvul.004G001700' => 'pvu', 'Phvul.006G154900' => 'pvu', 'Phvul.008G078200' => 'pvu', 'Phvul.011G136500' => 'pvu', 'Potri.002G215600' => 'ptr', 'Potri.008G201600' => 'ptr', 'Potri.014G138400' => 'ptr', 'Potri.016G142500' => 'ptr', 'Pp3c16_10580' => 'ppa', 'Pp3c5_25280' => 'ppa', 'Prupe.1G150000' => 'ppe', 'Prupe.1G150100' => 'ppe', 'Prupe.6G299600' => 'ppe', 'Prupe.8G245000' => 'ppe', 'Psat0s4927g0040' => 'psa', 'Psat1g052080' => 'psa', 'Psat1g183800' => 'psa', 'Psat3g113840' => 'psa', 'Psat3g126120' => 'psa', 'Psat3g126160' => 'psa', 'Psat3g158760' => 'psa', 'Psat3g158840' => 'psa', 'PSO170G2858' => 'pso', 'PSO339G0606' => 'pso', 'PSO384G4709' => 'pso', 'PSO407G0334' => 'pso', 'QL04p040276' => 'qlo', 'QL06p005458' => 'qlo', 'QL06p005472' => 'qlo', 'QL07p030546' => 'qlo', 'QL07p031519' => 'qlo', 'QL09p050949' => 'qlo', 'QL09p050966' => 'qlo', 'QL09p051067' => 'qlo', 'QL12p022706' => 'qlo', 'RcHm_v2.0_Chr2g0119601' => 'rch', 'RcHm_v2.0_Chr3g0459591' => 'rch', 'RcHm_v2.0_Chr4g0418521' => 'rch', 'RcHm_v2.0_Chr4g0418531' => 'rch', 'RcHm_v2.0_Chr4g0418541' => 'rch', 'RcHm_v2.0_Chr6g0291641' => 'rch', 'Rhsim01G0086300' => 'rsi', 'Rhsim01G0276300' => 'rsi', 'Rhsim01G0276500' => 'rsi', 'Rhsim04G0207700' => 'rsi', 'Rhsim05G0234500' => 'rsi', 'Rhsim13G0022400' => 'rsi', 'Sabra02G0167900' => 'sbr', 'Sabra04G0158500' => 'sbr', 'Sabra08G0159800' => 'sbr', 'Sabra10G0011500' => 'sbr', 'Sabra14G0104400' => 'sbr', 'SalBow2G2440' => 'sbo', 'SalBow4G2265' => 'sbo', 'Sc02g0000060' => 'sci', 'Sc05g0005020' => 'sci', 'Sc13g0003890' => 'sci', 'Sed0014865' => 'sed', 'Sed0017224' => 'sed', 'Sed0026391' => 'sed', 'SEGI_00063' => 'sgi', 'SEGI_10967' => 'sgi', 'SEGI_17510' => 'sgi', 'SEGI_24396' => 'sgi', 'SEGI_39719' => 'sgi', 'SEGI_41392' => 'sgi', 'SGA_v2.0_scaffold11G05794' => 'sas', 'SGA_v2.0_scaffold142G35607' => 'sas', 'SGA_v2.0_scaffold1G00447' => 'sas', 'SHI15388' => 'shi', 'SHI15394' => 'shi', 'SHI15396' => 'shi', 'SHI15399' => 'shi', 'SMO343G0151' => 'smo', 'SMO367G1118' => 'smo', 'Solyc01g080200.3' => 'sly', 'Solyc06g008960.3' => 'sly', 'Solyc09g064780.3' => 'sly', 'Sopen01g031980' => 'spe', 'Sopen06g003710' => 'spe', 'Sopen09g026460' => 'spe', 'Sp3g21240' => 'spa', 'Sp4g30030' => 'spa', 'TAR365G0022' => 'tar', 'TAR365G1023' => 'tar', 'TAR365G1253' => 'tar', 'TAR623G0078' => 'tar', 'TAR623G1721' => 'tar', 'TAR633G0959' => 'tar', 'THA.LOC104802225' => 'tha', 'THA.LOC104804769' => 'tha', 'THA.LOC104808660' => 'tha', 'THA.LOC104812792' => 'tha', 'Thecc.01G284000' => 'tca', 'Thecc.04G220600' => 'tca', 'Thecc.05G268900' => 'tca', 'Thecc.08G171100' => 'tca', 'Thhalv10001284m.g' => 'esa', 'Thhalv10019912m.g' => 'esa', 'TPR.G14189' => 'tpr', 'TPR.G18110' => 'tpr', 'TPR.G18130' => 'tpr', 'TPR.G18131' => 'tpr', 'TPR.G18140' => 'tpr', 'TPR.G24282' => 'tpr', 'TPR.G25221' => 'tpr', 'TPR.G29267' => 'tpr', 'TPR.G35315' => 'tpr', 'TPR.G36173' => 'tpr', 'TWI09G0794' => 'twi', 'TWI59G1348' => 'twi', 'TWI74G0430' => 'twi', 'unitig_26.g8940' => 'ugi', 'unitig_749.g13744' => 'ugi', 'unitig_749.g13745' => 'ugi', 'vmacro08269' => 'vma', 'vmacro14937' => 'vma', 'vmacro20401' => 'vma', 'VMungo0464G1349' => 'vmu', 'VMungo0540G0289' => 'vmu', 'VMungo1215G1590' => 'vmu', 'VMungo1309G0221' => 'vmu', 'VMungo1309G2815' => 'vmu', 'VMungo1383G0239' => 'vmu', 'VMungo1383G2910' => 'vmu', 'Zm00001eb095270' => 'zma', 'Zm00001eb095280' => 'zma', 'Zm00001eb111630' => 'zma', 'Zm00001eb237080' => 'zma', 'Zm00001eb273740' => 'zma', 'Zm00001eb285040' => 'zma', 'Zm00001eb330790' => 'zma', 'Zm00001eb337380' => 'zma' ) $gf_id = 'HOM05D001484' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001484' ) $data_identifier = 'HOM05D001484' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 2, 'aly' => (int) 2, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 22, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 7, 'hma' => (int) 2, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 7, 'mtr' => (int) 10, 'cme' => (int) 2, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 4, 'ppa' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 4, 'qlo' => (int) 9, 'rch' => (int) 6, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 10, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 7, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb337380' $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' => 'HOM05D001484', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p31500' => 'bna', 'A05p00020' => 'bna', 'A07p08820' => 'bna', 'Aa31LG4G3300' => 'aar', 'Aa31LG8G10030' => 'aar', 'Actinidia00731' => 'ach', 'Actinidia11473' => 'ach', 'Actinidia23469' => 'ach', 'Actinidia24318' => 'ach', 'Actinidia40196' => 'ach', 'Actinidia40197' => 'ach', 'Actinidia40198' => 'ach', 'Ah.08g212990' => 'amhyb', 'Ah.15g091720' => 'amhyb', 'AL3G38260' => 'aly', 'AL4G47710' => 'aly', 'Aqoxy2G00671' => 'aox', 'Aqoxy2G03236' => 'aox', 'arahy.Tifrunner.gnm1.ann1.05IDCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KR684' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATY3SJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK6QJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6APGL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IDT7Z9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM073U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ0R87' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LE7RV4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT4QRX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V5ENPK' => 'arhy', 'AT2G48110' => 'ath', 'AT3G23590' => 'ath', 'ATR0626G186' => 'atr', 'ATR1127G141' => 'atr', 'Atru.chr4.2583' => 'acertr', 'Atru.chr5.1358' => 'acertr', 'Atru.chr5.1359' => 'acertr', 'Atru.chr8.46' => 'acertr', 'AUR62002640' => 'cqu', 'AUR62030055' => 'cqu', 'AUR62033713' => 'cqu', 'AUR62033714' => 'cqu', 'AUR62036795' => 'cqu', 'AUR62039891' => 'cqu', 'BcaB02g08737' => 'bca', 'BcaB04g20441' => 'bca', 'BcaB06g26509' => 'bca', 'BcaB06g26510' => 'bca', 'BcaB06g26511' => 'bca', 'BcaB06g26512' => 'bca', 'BcaB06g26513' => 'bca', 'BcaC02g12564' => 'bca', 'BcaC02g12565' => 'bca', 'BcaC02g12794' => 'bca', 'BcaC02g12795' => 'bca', 'BcaC02g12796' => 'bca', 'BcaC06g35541' => 'bca', 'BNapus_Darmor_BZH_scaffold_188p00080' => 'bna', 'BNapus_Darmor_BZH_scaffold_188p00090' => 'bna', 'BolC1t03972H' => 'bol', 'BolC1t03973H' => 'bol', 'BolC4t21680H' => 'bol', 'BolC7t41863H' => 'bol', 'BolSC55t61227H' => 'bol', 'BolSC55t61228H' => 'bol', 'BraA01t03278Z' => 'bra', 'BraA05t18998Z' => 'bra', 'BraA07t28673Z' => 'bra', 'C01p40150' => 'bna', 'C05p12370' => 'bna', 'C07p13680' => 'bna', 'CAN.G1006.16' => 'can', 'CAN.G1006.17' => 'can', 'CAN.G1170.2' => 'can', 'CAN.G962.7' => 'can', 'CANSAT25G2179' => 'cansat', 'CANSAT78G1573' => 'cansat', 'CARHR099510' => 'chi', 'CARHR143510' => 'chi', 'Carub.0003s2380' => 'cru', 'Carub.0004s3082' => 'cru', 'Ca_00614_v3' => 'car', 'Ca_07801_v3' => 'car', 'Ca_08567_v3' => 'car', 'Ca_09571_v3' => 'car', 'CBR_g19290' => 'cbr', 'Cc01_g19770' => 'ccan', 'Cc03_g03030' => 'ccan', 'CDE07G0968' => 'cde', 'CDE09G1441' => 'cde', 'Cfa006103' => 'cfa', 'Cfa015573' => 'cfa', 'Cfa016988' => 'cfa', 'Ciclev10006738m.g' => 'ccl', 'Ciclev10010920m.g' => 'ccl', 'Ciclev10018517m.g' => 'ccl', 'CiPaw.01G159200' => 'cil', 'CiPaw.02G091000' => 'cil', 'CiPaw.02G091100' => 'cil', 'CiPaw.08G103100' => 'cil', 'CiPaw.09G224900' => 'cil', 'ClCG06G005740' => 'cla', 'ClCG07G000090' => 'cla', 'ClCG07G000100' => 'cla', 'COL.COLO4_09143' => 'col', 'COL.COLO4_25124' => 'col', 'Cpa.g.sc16.34' => 'cpa', 'Cpa.g.sc3504.1' => 'cpa', 'Cpa.g.sc60.37' => 'cpa', 'CsaV3_6G018520' => 'csa', 'CsaV3_6G036860' => 'csa', 'CSS0001072' => 'camsi', 'CSS0020208' => 'camsi', 'CSS0021253' => 'camsi', 'CSS0022190' => 'camsi', 'CSS0036150' => 'camsi', 'CSS0040442' => 'camsi', 'CSS0042300' => 'camsi', 'CSS0045298' => 'camsi', 'DCAR_012449' => 'dca', 'DCAR_018405' => 'dca', 'DCAR_024573' => 'dca', 'DCAR_030591' => 'dca', 'Dinv16926' => 'din', 'Dinv32963' => 'din', 'Dinv38382' => 'din', 'Dinv38383' => 'din', 'Duzib133G0974' => 'dzi', 'Duzib138G1867' => 'dzi', 'Duzib211G0420' => 'dzi', 'Duzib212G0930' => 'dzi', 'ECA234G1645' => 'eca', 'ECA247G3467' => 'eca', 'ECA248G1703' => 'eca', 'EL10Ac3g06327' => 'bvu', 'EL10Ac7g17204' => 'bvu', 'Eucgr.A00855' => 'egr', 'Eucgr.A00858' => 'egr', 'Eucgr.H01520' => 'egr', 'Eucgr.H03604' => 'egr', 'Eucgr.L03465' => 'egr', 'Eucgr.L03466' => 'egr', 'FAN01G0988' => 'fan', 'FAN02G3892' => 'fan', 'FAN05G3381' => 'fan', 'FAN07G0967' => 'fan', 'FAN07G1493' => 'fan', 'FAN08G3125' => 'fan', 'FAN09G0402' => 'fan', 'FAN12G2594' => 'fan', 'FAN12G3879' => 'fan', 'FAN14G1546' => 'fan', 'FAN15G3626' => 'fan', 'FAN17G0588' => 'fan', 'FAN17G0609' => 'fan', 'FAN18G2817' => 'fan', 'FAN19G1305' => 'fan', 'FAN20G1787' => 'fan', 'FAN22G0073' => 'fan', 'FAN22G0352' => 'fan', 'FAN22G0368' => 'fan', 'FAN22G2273' => 'fan', 'FAN24G1998' => 'fan', 'FAN27G1317' => 'fan', 'FvH4_2g23980' => 'fve', 'FvH4_4g14380' => 'fve', 'FvH4_4g14390' => 'fve', 'FvH4_6g09250' => 'fve', 'Glyma.03G151100' => 'gma', 'Glyma.04G122550' => 'gma', 'Glyma.05G001600' => 'gma', 'Glyma.09G270766' => 'gma', 'Glyma.09G270832' => 'gma', 'Glyma.13G209800' => 'gma', 'Glyma.15G102800' => 'gma', 'Glyma.18G218900' => 'gma', 'Glyma.19G001500' => 'gma', 'Glyma.19G153600' => 'gma', 'Gohir.A02G028600' => 'ghi', 'Gohir.A08G045000' => 'ghi', 'Gohir.A11G120500' => 'ghi', 'Gohir.A12G006200' => 'ghi', 'Gohir.A12G006250' => 'ghi', 'Gohir.D02G036300' => 'ghi', 'Gohir.D08G054700' => 'ghi', 'Gohir.D11G125600' => 'ghi', 'Gohir.D12G005700' => 'ghi', 'Gorai.004G055200' => 'gra', 'Gorai.005G040400' => 'gra', 'Gorai.007G134500' => 'gra', 'Gorai.008G005500' => 'gra', 'GSVIVG01011094001' => 'vvi', 'GSVIVG01017879001' => 'vvi', 'GSVIVG01025988001' => 'vvi', 'GSVIVG01029847001' => 'vvi', 'HanXRQChr10g0282901' => 'han', 'HanXRQChr10g0310371' => 'han', 'HanXRQChr10g0315041' => 'han', 'HanXRQChr11g0327651' => 'han', 'HanXRQChr12g0359391' => 'han', 'Haze_00972' => 'cav', 'Haze_00973' => 'cav', 'Haze_00974' => 'cav', 'Haze_04747' => 'cav', 'Haze_04749' => 'cav', 'Haze_04750' => 'cav', 'Haze_21217' => 'cav', 'Hma1.2p1_1037F.1_g250680' => 'hma', 'Hma1.2p1_1644F.1_g295320' => 'hma', 'HPP92_011322' => 'vpl', 'HPP92_011323' => 'vpl', 'HPP92_011324' => 'vpl', 'HPP92_011325' => 'vpl', 'HPP92_011326' => 'vpl', 'Hund12205' => 'sun', 'Hund17957' => 'sun', 'Lalb_Chr06g0176771' => 'lal', 'Lalb_Chr18g0056021' => 'lal', 'Lalb_Chr18g0056031' => 'lal', 'Lalb_Chr18g0056041' => 'lal', 'Lalb_Chr20g0107751' => 'lal', 'Lalb_Chr20g0118371' => 'lal', 'Lj1g0010239' => 'lja', 'Lj1g0017101' => 'lja', 'Lj2A1178G40' => 'lonja', 'Lj2A54G84' => 'lonja', 'Lj2g0015248' => 'lja', 'Lj3A761T51' => 'lonja', 'Lj6g0018116' => 'lja', 'Lsat_1_v5_gn_4_136040' => 'lsa', 'Lsat_1_v5_gn_5_187461' => 'lsa', 'Lsat_1_v5_gn_5_77001' => 'lsa', 'Lsat_1_v5_gn_9_4461' => 'lsa', 'Manes.01G210100' => 'mes', 'Manes.03G185600' => 'mes', 'Manes.05G073300' => 'mes', 'Manes.09G120300' => 'mes', 'Manes.15G022100' => 'mes', 'Mapoly0096s0053' => 'mpo', 'MBI03_g14058_MAGBIO' => 'mbi', 'MBI03_g33876_MAGBIO' => 'mbi', 'MBI03_g36854_MAGBIO' => 'mbi', 'MBI17_g11997_MAGBIO' => 'mbi', 'MD03G1269000' => 'mdo', 'MD04G1179600' => 'mdo', 'MD11G1289800' => 'mdo', 'MD12G1194700' => 'mdo', 'MD13G1182100' => 'mdo', 'MD13G1182200' => 'mdo', 'MD16G1182600' => 'mdo', 'Medtr2g021400' => 'mtr', 'Medtr2g021470' => 'mtr', 'Medtr2g105810' => 'mtr', 'Medtr3g033580' => 'mtr', 'Medtr6g007970' => 'mtr', 'Medtr7g056330' => 'mtr', 'Medtr7g074290' => 'mtr', 'Medtr7g074380' => 'mtr', 'Medtr7g094550' => 'mtr', 'Medtr8g069995' => 'mtr', 'MELO3C014345.2' => 'cme', 'MELO3C021395.2' => 'cme', 'Migut.D00262' => 'egut', 'Migut.G00257' => 'egut', 'MSTRG.21575' => 'ama', 'MSTRG.3985' => 'ama', 'Nitab4.5_0000295g0140' => 'nta', 'Nitab4.5_0000732g0140' => 'nta', 'Nitab4.5_0003162g0020' => 'nta', 'Nitab4.5_0006180g0090' => 'nta', 'Nitab4.5_0006390g0010' => 'nta', 'Nitab4.5_0007392g0040' => 'nta', 'Nn1g02140' => 'nnu', 'Nn4g26168' => 'nnu', 'Nn5g26754' => 'nnu', 'Oeu001433.1' => 'oeu', 'Oeu010299.2' => 'oeu', 'Oeu011171.1' => 'oeu', 'Oeu037675.1' => 'oeu', 'Oeu038359.1' => 'oeu', 'Oeu063834.1' => 'oeu', 'Oeu063835.1' => 'oeu', 'Os05g0312000' => 'osa', 'Os07g0211101' => 'osa', 'Os07g0211200' => 'osa', 'Os07g0681500' => 'osa', 'Peaxi162Scf00095g01015' => 'pax', 'Peaxi162Scf00104g00329' => 'pax', 'Peaxi162Scf00161g00137' => 'pax', 'PGR004G1665' => 'pgr', 'PGR031G2937' => 'pgr', 'PGR119G2145' => 'pgr', 'PGSC0003DMG400004351' => 'stu', 'PGSC0003DMG400014625' => 'stu', 'PGSC0003DMG401000943' => 'stu', 'Phvul.001G148600' => 'pvu', 'Phvul.004G001700' => 'pvu', 'Phvul.006G154900' => 'pvu', 'Phvul.008G078200' => 'pvu', 'Phvul.011G136500' => 'pvu', 'Potri.002G215600' => 'ptr', 'Potri.008G201600' => 'ptr', 'Potri.014G138400' => 'ptr', 'Potri.016G142500' => 'ptr', 'Pp3c16_10580' => 'ppa', 'Pp3c5_25280' => 'ppa', 'Prupe.1G150000' => 'ppe', 'Prupe.1G150100' => 'ppe', 'Prupe.6G299600' => 'ppe', 'Prupe.8G245000' => 'ppe', 'Psat0s4927g0040' => 'psa', 'Psat1g052080' => 'psa', 'Psat1g183800' => 'psa', 'Psat3g113840' => 'psa', 'Psat3g126120' => 'psa', 'Psat3g126160' => 'psa', 'Psat3g158760' => 'psa', 'Psat3g158840' => 'psa', 'PSO170G2858' => 'pso', 'PSO339G0606' => 'pso', 'PSO384G4709' => 'pso', 'PSO407G0334' => 'pso', 'QL04p040276' => 'qlo', 'QL06p005458' => 'qlo', 'QL06p005472' => 'qlo', 'QL07p030546' => 'qlo', 'QL07p031519' => 'qlo', 'QL09p050949' => 'qlo', 'QL09p050966' => 'qlo', 'QL09p051067' => 'qlo', 'QL12p022706' => 'qlo', 'RcHm_v2.0_Chr2g0119601' => 'rch', 'RcHm_v2.0_Chr3g0459591' => 'rch', 'RcHm_v2.0_Chr4g0418521' => 'rch', 'RcHm_v2.0_Chr4g0418531' => 'rch', 'RcHm_v2.0_Chr4g0418541' => 'rch', 'RcHm_v2.0_Chr6g0291641' => 'rch', 'Rhsim01G0086300' => 'rsi', 'Rhsim01G0276300' => 'rsi', 'Rhsim01G0276500' => 'rsi', 'Rhsim04G0207700' => 'rsi', 'Rhsim05G0234500' => 'rsi', 'Rhsim13G0022400' => 'rsi', 'Sabra02G0167900' => 'sbr', 'Sabra04G0158500' => 'sbr', 'Sabra08G0159800' => 'sbr', 'Sabra10G0011500' => 'sbr', 'Sabra14G0104400' => 'sbr', 'SalBow2G2440' => 'sbo', 'SalBow4G2265' => 'sbo', 'Sc02g0000060' => 'sci', 'Sc05g0005020' => 'sci', 'Sc13g0003890' => 'sci', 'Sed0014865' => 'sed', 'Sed0017224' => 'sed', 'Sed0026391' => 'sed', 'SEGI_00063' => 'sgi', 'SEGI_10967' => 'sgi', 'SEGI_17510' => 'sgi', 'SEGI_24396' => 'sgi', 'SEGI_39719' => 'sgi', 'SEGI_41392' => 'sgi', 'SGA_v2.0_scaffold11G05794' => 'sas', 'SGA_v2.0_scaffold142G35607' => 'sas', 'SGA_v2.0_scaffold1G00447' => 'sas', 'SHI15388' => 'shi', 'SHI15394' => 'shi', 'SHI15396' => 'shi', 'SHI15399' => 'shi', 'SMO343G0151' => 'smo', 'SMO367G1118' => 'smo', 'Solyc01g080200.3' => 'sly', 'Solyc06g008960.3' => 'sly', 'Solyc09g064780.3' => 'sly', 'Sopen01g031980' => 'spe', 'Sopen06g003710' => 'spe', 'Sopen09g026460' => 'spe', 'Sp3g21240' => 'spa', 'Sp4g30030' => 'spa', 'TAR365G0022' => 'tar', 'TAR365G1023' => 'tar', 'TAR365G1253' => 'tar', 'TAR623G0078' => 'tar', 'TAR623G1721' => 'tar', 'TAR633G0959' => 'tar', 'THA.LOC104802225' => 'tha', 'THA.LOC104804769' => 'tha', 'THA.LOC104808660' => 'tha', 'THA.LOC104812792' => 'tha', 'Thecc.01G284000' => 'tca', 'Thecc.04G220600' => 'tca', 'Thecc.05G268900' => 'tca', 'Thecc.08G171100' => 'tca', 'Thhalv10001284m.g' => 'esa', 'Thhalv10019912m.g' => 'esa', 'TPR.G14189' => 'tpr', 'TPR.G18110' => 'tpr', 'TPR.G18130' => 'tpr', 'TPR.G18131' => 'tpr', 'TPR.G18140' => 'tpr', 'TPR.G24282' => 'tpr', 'TPR.G25221' => 'tpr', 'TPR.G29267' => 'tpr', 'TPR.G35315' => 'tpr', 'TPR.G36173' => 'tpr', 'TWI09G0794' => 'twi', 'TWI59G1348' => 'twi', 'TWI74G0430' => 'twi', 'unitig_26.g8940' => 'ugi', 'unitig_749.g13744' => 'ugi', 'unitig_749.g13745' => 'ugi', 'vmacro08269' => 'vma', 'vmacro14937' => 'vma', 'vmacro20401' => 'vma', 'VMungo0464G1349' => 'vmu', 'VMungo0540G0289' => 'vmu', 'VMungo1215G1590' => 'vmu', 'VMungo1309G0221' => 'vmu', 'VMungo1309G2815' => 'vmu', 'VMungo1383G0239' => 'vmu', 'VMungo1383G2910' => 'vmu', 'Zm00001eb095270' => 'zma', 'Zm00001eb095280' => 'zma', 'Zm00001eb111630' => 'zma', 'Zm00001eb237080' => 'zma', 'Zm00001eb273740' => 'zma', 'Zm00001eb285040' => 'zma', 'Zm00001eb330790' => 'zma', 'Zm00001eb337380' => 'zma' ), 'gf_id' => 'HOM05D001484', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001484' ), 'data_identifier' => 'HOM05D001484', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001484', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p31500' => 'bna', 'A05p00020' => 'bna', 'A07p08820' => 'bna', 'Aa31LG4G3300' => 'aar', 'Aa31LG8G10030' => 'aar', 'Actinidia00731' => 'ach', 'Actinidia11473' => 'ach', 'Actinidia23469' => 'ach', 'Actinidia24318' => 'ach', 'Actinidia40196' => 'ach', 'Actinidia40197' => 'ach', 'Actinidia40198' => 'ach', 'Ah.08g212990' => 'amhyb', 'Ah.15g091720' => 'amhyb', 'AL3G38260' => 'aly', 'AL4G47710' => 'aly', 'Aqoxy2G00671' => 'aox', 'Aqoxy2G03236' => 'aox', 'arahy.Tifrunner.gnm1.ann1.05IDCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KR684' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATY3SJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK6QJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6APGL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IDT7Z9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM073U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ0R87' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LE7RV4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT4QRX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V5ENPK' => 'arhy', 'AT2G48110' => 'ath', 'AT3G23590' => 'ath', 'ATR0626G186' => 'atr', 'ATR1127G141' => 'atr', 'Atru.chr4.2583' => 'acertr', 'Atru.chr5.1358' => 'acertr', 'Atru.chr5.1359' => 'acertr', 'Atru.chr8.46' => 'acertr', 'AUR62002640' => 'cqu', 'AUR62030055' => 'cqu', 'AUR62033713' => 'cqu', 'AUR62033714' => 'cqu', 'AUR62036795' => 'cqu', 'AUR62039891' => 'cqu', 'BcaB02g08737' => 'bca', 'BcaB04g20441' => 'bca', 'BcaB06g26509' => 'bca', 'BcaB06g26510' => 'bca', 'BcaB06g26511' => 'bca', 'BcaB06g26512' => 'bca', 'BcaB06g26513' => 'bca', 'BcaC02g12564' => 'bca', 'BcaC02g12565' => 'bca', 'BcaC02g12794' => 'bca', 'BcaC02g12795' => 'bca', 'BcaC02g12796' => 'bca', 'BcaC06g35541' => 'bca', 'BNapus_Darmor_BZH_scaffold_188p00080' => 'bna', 'BNapus_Darmor_BZH_scaffold_188p00090' => 'bna', 'BolC1t03972H' => 'bol', 'BolC1t03973H' => 'bol', 'BolC4t21680H' => 'bol', 'BolC7t41863H' => 'bol', 'BolSC55t61227H' => 'bol', 'BolSC55t61228H' => 'bol', 'BraA01t03278Z' => 'bra', 'BraA05t18998Z' => 'bra', 'BraA07t28673Z' => 'bra', 'C01p40150' => 'bna', 'C05p12370' => 'bna', 'C07p13680' => 'bna', 'CAN.G1006.16' => 'can', 'CAN.G1006.17' => 'can', 'CAN.G1170.2' => 'can', 'CAN.G962.7' => 'can', 'CANSAT25G2179' => 'cansat', 'CANSAT78G1573' => 'cansat', 'CARHR099510' => 'chi', 'CARHR143510' => 'chi', 'Carub.0003s2380' => 'cru', 'Carub.0004s3082' => 'cru', 'Ca_00614_v3' => 'car', 'Ca_07801_v3' => 'car', 'Ca_08567_v3' => 'car', 'Ca_09571_v3' => 'car', 'CBR_g19290' => 'cbr', 'Cc01_g19770' => 'ccan', 'Cc03_g03030' => 'ccan', 'CDE07G0968' => 'cde', 'CDE09G1441' => 'cde', 'Cfa006103' => 'cfa', 'Cfa015573' => 'cfa', 'Cfa016988' => 'cfa', 'Ciclev10006738m.g' => 'ccl', 'Ciclev10010920m.g' => 'ccl', 'Ciclev10018517m.g' => 'ccl', 'CiPaw.01G159200' => 'cil', 'CiPaw.02G091000' => 'cil', 'CiPaw.02G091100' => 'cil', 'CiPaw.08G103100' => 'cil', 'CiPaw.09G224900' => 'cil', 'ClCG06G005740' => 'cla', 'ClCG07G000090' => 'cla', 'ClCG07G000100' => 'cla', 'COL.COLO4_09143' => 'col', 'COL.COLO4_25124' => 'col', 'Cpa.g.sc16.34' => 'cpa', 'Cpa.g.sc3504.1' => 'cpa', 'Cpa.g.sc60.37' => 'cpa', 'CsaV3_6G018520' => 'csa', 'CsaV3_6G036860' => 'csa', 'CSS0001072' => 'camsi', 'CSS0020208' => 'camsi', 'CSS0021253' => 'camsi', 'CSS0022190' => 'camsi', 'CSS0036150' => 'camsi', 'CSS0040442' => 'camsi', 'CSS0042300' => 'camsi', 'CSS0045298' => 'camsi', 'DCAR_012449' => 'dca', 'DCAR_018405' => 'dca', 'DCAR_024573' => 'dca', 'DCAR_030591' => 'dca', 'Dinv16926' => 'din', 'Dinv32963' => 'din', 'Dinv38382' => 'din', 'Dinv38383' => 'din', 'Duzib133G0974' => 'dzi', 'Duzib138G1867' => 'dzi', 'Duzib211G0420' => 'dzi', 'Duzib212G0930' => 'dzi', 'ECA234G1645' => 'eca', 'ECA247G3467' => 'eca', 'ECA248G1703' => 'eca', 'EL10Ac3g06327' => 'bvu', 'EL10Ac7g17204' => 'bvu', 'Eucgr.A00855' => 'egr', 'Eucgr.A00858' => 'egr', 'Eucgr.H01520' => 'egr', 'Eucgr.H03604' => 'egr', 'Eucgr.L03465' => 'egr', 'Eucgr.L03466' => 'egr', 'FAN01G0988' => 'fan', 'FAN02G3892' => 'fan', 'FAN05G3381' => 'fan', 'FAN07G0967' => 'fan', 'FAN07G1493' => 'fan', 'FAN08G3125' => 'fan', 'FAN09G0402' => 'fan', 'FAN12G2594' => 'fan', 'FAN12G3879' => 'fan', 'FAN14G1546' => 'fan', 'FAN15G3626' => 'fan', 'FAN17G0588' => 'fan', 'FAN17G0609' => 'fan', 'FAN18G2817' => 'fan', 'FAN19G1305' => 'fan', 'FAN20G1787' => 'fan', 'FAN22G0073' => 'fan', 'FAN22G0352' => 'fan', 'FAN22G0368' => 'fan', 'FAN22G2273' => 'fan', 'FAN24G1998' => 'fan', 'FAN27G1317' => 'fan', 'FvH4_2g23980' => 'fve', 'FvH4_4g14380' => 'fve', 'FvH4_4g14390' => 'fve', 'FvH4_6g09250' => 'fve', 'Glyma.03G151100' => 'gma', 'Glyma.04G122550' => 'gma', 'Glyma.05G001600' => 'gma', 'Glyma.09G270766' => 'gma', 'Glyma.09G270832' => 'gma', 'Glyma.13G209800' => 'gma', 'Glyma.15G102800' => 'gma', 'Glyma.18G218900' => 'gma', 'Glyma.19G001500' => 'gma', 'Glyma.19G153600' => 'gma', 'Gohir.A02G028600' => 'ghi', 'Gohir.A08G045000' => 'ghi', 'Gohir.A11G120500' => 'ghi', 'Gohir.A12G006200' => 'ghi', 'Gohir.A12G006250' => 'ghi', 'Gohir.D02G036300' => 'ghi', 'Gohir.D08G054700' => 'ghi', 'Gohir.D11G125600' => 'ghi', 'Gohir.D12G005700' => 'ghi', 'Gorai.004G055200' => 'gra', 'Gorai.005G040400' => 'gra', 'Gorai.007G134500' => 'gra', 'Gorai.008G005500' => 'gra', 'GSVIVG01011094001' => 'vvi', 'GSVIVG01017879001' => 'vvi', 'GSVIVG01025988001' => 'vvi', 'GSVIVG01029847001' => 'vvi', 'HanXRQChr10g0282901' => 'han', 'HanXRQChr10g0310371' => 'han', 'HanXRQChr10g0315041' => 'han', 'HanXRQChr11g0327651' => 'han', 'HanXRQChr12g0359391' => 'han', 'Haze_00972' => 'cav', 'Haze_00973' => 'cav', 'Haze_00974' => 'cav', 'Haze_04747' => 'cav', 'Haze_04749' => 'cav', 'Haze_04750' => 'cav', 'Haze_21217' => 'cav', 'Hma1.2p1_1037F.1_g250680' => 'hma', 'Hma1.2p1_1644F.1_g295320' => 'hma', 'HPP92_011322' => 'vpl', 'HPP92_011323' => 'vpl', 'HPP92_011324' => 'vpl', 'HPP92_011325' => 'vpl', 'HPP92_011326' => 'vpl', 'Hund12205' => 'sun', 'Hund17957' => 'sun', 'Lalb_Chr06g0176771' => 'lal', 'Lalb_Chr18g0056021' => 'lal', 'Lalb_Chr18g0056031' => 'lal', 'Lalb_Chr18g0056041' => 'lal', 'Lalb_Chr20g0107751' => 'lal', 'Lalb_Chr20g0118371' => 'lal', 'Lj1g0010239' => 'lja', 'Lj1g0017101' => 'lja', 'Lj2A1178G40' => 'lonja', 'Lj2A54G84' => 'lonja', 'Lj2g0015248' => 'lja', 'Lj3A761T51' => 'lonja', 'Lj6g0018116' => 'lja', 'Lsat_1_v5_gn_4_136040' => 'lsa', 'Lsat_1_v5_gn_5_187461' => 'lsa', 'Lsat_1_v5_gn_5_77001' => 'lsa', 'Lsat_1_v5_gn_9_4461' => 'lsa', 'Manes.01G210100' => 'mes', 'Manes.03G185600' => 'mes', 'Manes.05G073300' => 'mes', 'Manes.09G120300' => 'mes', 'Manes.15G022100' => 'mes', 'Mapoly0096s0053' => 'mpo', 'MBI03_g14058_MAGBIO' => 'mbi', 'MBI03_g33876_MAGBIO' => 'mbi', 'MBI03_g36854_MAGBIO' => 'mbi', 'MBI17_g11997_MAGBIO' => 'mbi', 'MD03G1269000' => 'mdo', 'MD04G1179600' => 'mdo', 'MD11G1289800' => 'mdo', 'MD12G1194700' => 'mdo', 'MD13G1182100' => 'mdo', 'MD13G1182200' => 'mdo', 'MD16G1182600' => 'mdo', 'Medtr2g021400' => 'mtr', 'Medtr2g021470' => 'mtr', 'Medtr2g105810' => 'mtr', 'Medtr3g033580' => 'mtr', 'Medtr6g007970' => 'mtr', 'Medtr7g056330' => 'mtr', 'Medtr7g074290' => 'mtr', 'Medtr7g074380' => 'mtr', 'Medtr7g094550' => 'mtr', 'Medtr8g069995' => 'mtr', 'MELO3C014345.2' => 'cme', 'MELO3C021395.2' => 'cme', 'Migut.D00262' => 'egut', 'Migut.G00257' => 'egut', 'MSTRG.21575' => 'ama', 'MSTRG.3985' => 'ama', 'Nitab4.5_0000295g0140' => 'nta', 'Nitab4.5_0000732g0140' => 'nta', 'Nitab4.5_0003162g0020' => 'nta', 'Nitab4.5_0006180g0090' => 'nta', 'Nitab4.5_0006390g0010' => 'nta', 'Nitab4.5_0007392g0040' => 'nta', 'Nn1g02140' => 'nnu', 'Nn4g26168' => 'nnu', 'Nn5g26754' => 'nnu', 'Oeu001433.1' => 'oeu', 'Oeu010299.2' => 'oeu', 'Oeu011171.1' => 'oeu', 'Oeu037675.1' => 'oeu', 'Oeu038359.1' => 'oeu', 'Oeu063834.1' => 'oeu', 'Oeu063835.1' => 'oeu', 'Os05g0312000' => 'osa', 'Os07g0211101' => 'osa', 'Os07g0211200' => 'osa', 'Os07g0681500' => 'osa', 'Peaxi162Scf00095g01015' => 'pax', 'Peaxi162Scf00104g00329' => 'pax', 'Peaxi162Scf00161g00137' => 'pax', 'PGR004G1665' => 'pgr', 'PGR031G2937' => 'pgr', 'PGR119G2145' => 'pgr', 'PGSC0003DMG400004351' => 'stu', 'PGSC0003DMG400014625' => 'stu', 'PGSC0003DMG401000943' => 'stu', 'Phvul.001G148600' => 'pvu', 'Phvul.004G001700' => 'pvu', 'Phvul.006G154900' => 'pvu', 'Phvul.008G078200' => 'pvu', 'Phvul.011G136500' => 'pvu', 'Potri.002G215600' => 'ptr', 'Potri.008G201600' => 'ptr', 'Potri.014G138400' => 'ptr', 'Potri.016G142500' => 'ptr', 'Pp3c16_10580' => 'ppa', 'Pp3c5_25280' => 'ppa', 'Prupe.1G150000' => 'ppe', 'Prupe.1G150100' => 'ppe', 'Prupe.6G299600' => 'ppe', 'Prupe.8G245000' => 'ppe', 'Psat0s4927g0040' => 'psa', 'Psat1g052080' => 'psa', 'Psat1g183800' => 'psa', 'Psat3g113840' => 'psa', 'Psat3g126120' => 'psa', 'Psat3g126160' => 'psa', 'Psat3g158760' => 'psa', 'Psat3g158840' => 'psa', 'PSO170G2858' => 'pso', 'PSO339G0606' => 'pso', 'PSO384G4709' => 'pso', 'PSO407G0334' => 'pso', 'QL04p040276' => 'qlo', 'QL06p005458' => 'qlo', 'QL06p005472' => 'qlo', 'QL07p030546' => 'qlo', 'QL07p031519' => 'qlo', 'QL09p050949' => 'qlo', 'QL09p050966' => 'qlo', 'QL09p051067' => 'qlo', 'QL12p022706' => 'qlo', 'RcHm_v2.0_Chr2g0119601' => 'rch', 'RcHm_v2.0_Chr3g0459591' => 'rch', 'RcHm_v2.0_Chr4g0418521' => 'rch', 'RcHm_v2.0_Chr4g0418531' => 'rch', 'RcHm_v2.0_Chr4g0418541' => 'rch', 'RcHm_v2.0_Chr6g0291641' => 'rch', 'Rhsim01G0086300' => 'rsi', 'Rhsim01G0276300' => 'rsi', 'Rhsim01G0276500' => 'rsi', 'Rhsim04G0207700' => 'rsi', 'Rhsim05G0234500' => 'rsi', 'Rhsim13G0022400' => 'rsi', 'Sabra02G0167900' => 'sbr', 'Sabra04G0158500' => 'sbr', 'Sabra08G0159800' => 'sbr', 'Sabra10G0011500' => 'sbr', 'Sabra14G0104400' => 'sbr', 'SalBow2G2440' => 'sbo', 'SalBow4G2265' => 'sbo', 'Sc02g0000060' => 'sci', 'Sc05g0005020' => 'sci', 'Sc13g0003890' => 'sci', 'Sed0014865' => 'sed', 'Sed0017224' => 'sed', 'Sed0026391' => 'sed', 'SEGI_00063' => 'sgi', 'SEGI_10967' => 'sgi', 'SEGI_17510' => 'sgi', 'SEGI_24396' => 'sgi', 'SEGI_39719' => 'sgi', 'SEGI_41392' => 'sgi', 'SGA_v2.0_scaffold11G05794' => 'sas', 'SGA_v2.0_scaffold142G35607' => 'sas', 'SGA_v2.0_scaffold1G00447' => 'sas', 'SHI15388' => 'shi', 'SHI15394' => 'shi', 'SHI15396' => 'shi', 'SHI15399' => 'shi', 'SMO343G0151' => 'smo', 'SMO367G1118' => 'smo', 'Solyc01g080200.3' => 'sly', 'Solyc06g008960.3' => 'sly', 'Solyc09g064780.3' => 'sly', 'Sopen01g031980' => 'spe', 'Sopen06g003710' => 'spe', 'Sopen09g026460' => 'spe', 'Sp3g21240' => 'spa', 'Sp4g30030' => 'spa', 'TAR365G0022' => 'tar', 'TAR365G1023' => 'tar', 'TAR365G1253' => 'tar', 'TAR623G0078' => 'tar', 'TAR623G1721' => 'tar', 'TAR633G0959' => 'tar', 'THA.LOC104802225' => 'tha', 'THA.LOC104804769' => 'tha', 'THA.LOC104808660' => 'tha', 'THA.LOC104812792' => 'tha', 'Thecc.01G284000' => 'tca', 'Thecc.04G220600' => 'tca', 'Thecc.05G268900' => 'tca', 'Thecc.08G171100' => 'tca', 'Thhalv10001284m.g' => 'esa', 'Thhalv10019912m.g' => 'esa', 'TPR.G14189' => 'tpr', 'TPR.G18110' => 'tpr', 'TPR.G18130' => 'tpr', 'TPR.G18131' => 'tpr', 'TPR.G18140' => 'tpr', 'TPR.G24282' => 'tpr', 'TPR.G25221' => 'tpr', 'TPR.G29267' => 'tpr', 'TPR.G35315' => 'tpr', 'TPR.G36173' => 'tpr', 'TWI09G0794' => 'twi', 'TWI59G1348' => 'twi', 'TWI74G0430' => 'twi', 'unitig_26.g8940' => 'ugi', 'unitig_749.g13744' => 'ugi', 'unitig_749.g13745' => 'ugi', 'vmacro08269' => 'vma', 'vmacro14937' => 'vma', 'vmacro20401' => 'vma', 'VMungo0464G1349' => 'vmu', 'VMungo0540G0289' => 'vmu', 'VMungo1215G1590' => 'vmu', 'VMungo1309G0221' => 'vmu', 'VMungo1309G2815' => 'vmu', 'VMungo1383G0239' => 'vmu', 'VMungo1383G2910' => 'vmu', 'Zm00001eb095270' => 'zma', 'Zm00001eb095280' => 'zma', 'Zm00001eb111630' => 'zma', 'Zm00001eb237080' => 'zma', 'Zm00001eb273740' => 'zma', 'Zm00001eb285040' => 'zma', 'Zm00001eb330790' => 'zma', 'Zm00001eb337380' => 'zma' ) $gf_id = 'HOM05D001484' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001484' ) $data_identifier = 'HOM05D001484' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 2, 'aly' => (int) 2, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 22, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 7, 'hma' => (int) 2, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 7, 'mtr' => (int) 10, 'cme' => (int) 2, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 4, 'ppa' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 4, 'qlo' => (int) 9, 'rch' => (int) 6, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 10, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 7, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb337380' $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' => 'HOM05D001484', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p31500' => 'bna', 'A05p00020' => 'bna', 'A07p08820' => 'bna', 'Aa31LG4G3300' => 'aar', 'Aa31LG8G10030' => 'aar', 'Actinidia00731' => 'ach', 'Actinidia11473' => 'ach', 'Actinidia23469' => 'ach', 'Actinidia24318' => 'ach', 'Actinidia40196' => 'ach', 'Actinidia40197' => 'ach', 'Actinidia40198' => 'ach', 'Ah.08g212990' => 'amhyb', 'Ah.15g091720' => 'amhyb', 'AL3G38260' => 'aly', 'AL4G47710' => 'aly', 'Aqoxy2G00671' => 'aox', 'Aqoxy2G03236' => 'aox', 'arahy.Tifrunner.gnm1.ann1.05IDCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KR684' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATY3SJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK6QJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6APGL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IDT7Z9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM073U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ0R87' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LE7RV4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT4QRX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V5ENPK' => 'arhy', 'AT2G48110' => 'ath', 'AT3G23590' => 'ath', 'ATR0626G186' => 'atr', 'ATR1127G141' => 'atr', 'Atru.chr4.2583' => 'acertr', 'Atru.chr5.1358' => 'acertr', 'Atru.chr5.1359' => 'acertr', 'Atru.chr8.46' => 'acertr', 'AUR62002640' => 'cqu', 'AUR62030055' => 'cqu', 'AUR62033713' => 'cqu', 'AUR62033714' => 'cqu', 'AUR62036795' => 'cqu', 'AUR62039891' => 'cqu', 'BcaB02g08737' => 'bca', 'BcaB04g20441' => 'bca', 'BcaB06g26509' => 'bca', 'BcaB06g26510' => 'bca', 'BcaB06g26511' => 'bca', 'BcaB06g26512' => 'bca', 'BcaB06g26513' => 'bca', 'BcaC02g12564' => 'bca', 'BcaC02g12565' => 'bca', 'BcaC02g12794' => 'bca', 'BcaC02g12795' => 'bca', 'BcaC02g12796' => 'bca', 'BcaC06g35541' => 'bca', 'BNapus_Darmor_BZH_scaffold_188p00080' => 'bna', 'BNapus_Darmor_BZH_scaffold_188p00090' => 'bna', 'BolC1t03972H' => 'bol', 'BolC1t03973H' => 'bol', 'BolC4t21680H' => 'bol', 'BolC7t41863H' => 'bol', 'BolSC55t61227H' => 'bol', 'BolSC55t61228H' => 'bol', 'BraA01t03278Z' => 'bra', 'BraA05t18998Z' => 'bra', 'BraA07t28673Z' => 'bra', 'C01p40150' => 'bna', 'C05p12370' => 'bna', 'C07p13680' => 'bna', 'CAN.G1006.16' => 'can', 'CAN.G1006.17' => 'can', 'CAN.G1170.2' => 'can', 'CAN.G962.7' => 'can', 'CANSAT25G2179' => 'cansat', 'CANSAT78G1573' => 'cansat', 'CARHR099510' => 'chi', 'CARHR143510' => 'chi', 'Carub.0003s2380' => 'cru', 'Carub.0004s3082' => 'cru', 'Ca_00614_v3' => 'car', 'Ca_07801_v3' => 'car', 'Ca_08567_v3' => 'car', 'Ca_09571_v3' => 'car', 'CBR_g19290' => 'cbr', 'Cc01_g19770' => 'ccan', 'Cc03_g03030' => 'ccan', 'CDE07G0968' => 'cde', 'CDE09G1441' => 'cde', 'Cfa006103' => 'cfa', 'Cfa015573' => 'cfa', 'Cfa016988' => 'cfa', 'Ciclev10006738m.g' => 'ccl', 'Ciclev10010920m.g' => 'ccl', 'Ciclev10018517m.g' => 'ccl', 'CiPaw.01G159200' => 'cil', 'CiPaw.02G091000' => 'cil', 'CiPaw.02G091100' => 'cil', 'CiPaw.08G103100' => 'cil', 'CiPaw.09G224900' => 'cil', 'ClCG06G005740' => 'cla', 'ClCG07G000090' => 'cla', 'ClCG07G000100' => 'cla', 'COL.COLO4_09143' => 'col', 'COL.COLO4_25124' => 'col', 'Cpa.g.sc16.34' => 'cpa', 'Cpa.g.sc3504.1' => 'cpa', 'Cpa.g.sc60.37' => 'cpa', 'CsaV3_6G018520' => 'csa', 'CsaV3_6G036860' => 'csa', 'CSS0001072' => 'camsi', 'CSS0020208' => 'camsi', 'CSS0021253' => 'camsi', 'CSS0022190' => 'camsi', 'CSS0036150' => 'camsi', 'CSS0040442' => 'camsi', 'CSS0042300' => 'camsi', 'CSS0045298' => 'camsi', 'DCAR_012449' => 'dca', 'DCAR_018405' => 'dca', 'DCAR_024573' => 'dca', 'DCAR_030591' => 'dca', 'Dinv16926' => 'din', 'Dinv32963' => 'din', 'Dinv38382' => 'din', 'Dinv38383' => 'din', 'Duzib133G0974' => 'dzi', 'Duzib138G1867' => 'dzi', 'Duzib211G0420' => 'dzi', 'Duzib212G0930' => 'dzi', 'ECA234G1645' => 'eca', 'ECA247G3467' => 'eca', 'ECA248G1703' => 'eca', 'EL10Ac3g06327' => 'bvu', 'EL10Ac7g17204' => 'bvu', 'Eucgr.A00855' => 'egr', 'Eucgr.A00858' => 'egr', 'Eucgr.H01520' => 'egr', 'Eucgr.H03604' => 'egr', 'Eucgr.L03465' => 'egr', 'Eucgr.L03466' => 'egr', 'FAN01G0988' => 'fan', 'FAN02G3892' => 'fan', 'FAN05G3381' => 'fan', 'FAN07G0967' => 'fan', 'FAN07G1493' => 'fan', 'FAN08G3125' => 'fan', 'FAN09G0402' => 'fan', 'FAN12G2594' => 'fan', 'FAN12G3879' => 'fan', 'FAN14G1546' => 'fan', 'FAN15G3626' => 'fan', 'FAN17G0588' => 'fan', 'FAN17G0609' => 'fan', 'FAN18G2817' => 'fan', 'FAN19G1305' => 'fan', 'FAN20G1787' => 'fan', 'FAN22G0073' => 'fan', 'FAN22G0352' => 'fan', 'FAN22G0368' => 'fan', 'FAN22G2273' => 'fan', 'FAN24G1998' => 'fan', 'FAN27G1317' => 'fan', 'FvH4_2g23980' => 'fve', 'FvH4_4g14380' => 'fve', 'FvH4_4g14390' => 'fve', 'FvH4_6g09250' => 'fve', 'Glyma.03G151100' => 'gma', 'Glyma.04G122550' => 'gma', 'Glyma.05G001600' => 'gma', 'Glyma.09G270766' => 'gma', 'Glyma.09G270832' => 'gma', 'Glyma.13G209800' => 'gma', 'Glyma.15G102800' => 'gma', 'Glyma.18G218900' => 'gma', 'Glyma.19G001500' => 'gma', 'Glyma.19G153600' => 'gma', 'Gohir.A02G028600' => 'ghi', 'Gohir.A08G045000' => 'ghi', 'Gohir.A11G120500' => 'ghi', 'Gohir.A12G006200' => 'ghi', 'Gohir.A12G006250' => 'ghi', 'Gohir.D02G036300' => 'ghi', 'Gohir.D08G054700' => 'ghi', 'Gohir.D11G125600' => 'ghi', 'Gohir.D12G005700' => 'ghi', 'Gorai.004G055200' => 'gra', 'Gorai.005G040400' => 'gra', 'Gorai.007G134500' => 'gra', 'Gorai.008G005500' => 'gra', 'GSVIVG01011094001' => 'vvi', 'GSVIVG01017879001' => 'vvi', 'GSVIVG01025988001' => 'vvi', 'GSVIVG01029847001' => 'vvi', 'HanXRQChr10g0282901' => 'han', 'HanXRQChr10g0310371' => 'han', 'HanXRQChr10g0315041' => 'han', 'HanXRQChr11g0327651' => 'han', 'HanXRQChr12g0359391' => 'han', 'Haze_00972' => 'cav', 'Haze_00973' => 'cav', 'Haze_00974' => 'cav', 'Haze_04747' => 'cav', 'Haze_04749' => 'cav', 'Haze_04750' => 'cav', 'Haze_21217' => 'cav', 'Hma1.2p1_1037F.1_g250680' => 'hma', 'Hma1.2p1_1644F.1_g295320' => 'hma', 'HPP92_011322' => 'vpl', 'HPP92_011323' => 'vpl', 'HPP92_011324' => 'vpl', 'HPP92_011325' => 'vpl', 'HPP92_011326' => 'vpl', 'Hund12205' => 'sun', 'Hund17957' => 'sun', 'Lalb_Chr06g0176771' => 'lal', 'Lalb_Chr18g0056021' => 'lal', 'Lalb_Chr18g0056031' => 'lal', 'Lalb_Chr18g0056041' => 'lal', 'Lalb_Chr20g0107751' => 'lal', 'Lalb_Chr20g0118371' => 'lal', 'Lj1g0010239' => 'lja', 'Lj1g0017101' => 'lja', 'Lj2A1178G40' => 'lonja', 'Lj2A54G84' => 'lonja', 'Lj2g0015248' => 'lja', 'Lj3A761T51' => 'lonja', 'Lj6g0018116' => 'lja', 'Lsat_1_v5_gn_4_136040' => 'lsa', 'Lsat_1_v5_gn_5_187461' => 'lsa', 'Lsat_1_v5_gn_5_77001' => 'lsa', 'Lsat_1_v5_gn_9_4461' => 'lsa', 'Manes.01G210100' => 'mes', 'Manes.03G185600' => 'mes', 'Manes.05G073300' => 'mes', 'Manes.09G120300' => 'mes', 'Manes.15G022100' => 'mes', 'Mapoly0096s0053' => 'mpo', 'MBI03_g14058_MAGBIO' => 'mbi', 'MBI03_g33876_MAGBIO' => 'mbi', 'MBI03_g36854_MAGBIO' => 'mbi', 'MBI17_g11997_MAGBIO' => 'mbi', 'MD03G1269000' => 'mdo', 'MD04G1179600' => 'mdo', 'MD11G1289800' => 'mdo', 'MD12G1194700' => 'mdo', 'MD13G1182100' => 'mdo', 'MD13G1182200' => 'mdo', 'MD16G1182600' => 'mdo', 'Medtr2g021400' => 'mtr', 'Medtr2g021470' => 'mtr', 'Medtr2g105810' => 'mtr', 'Medtr3g033580' => 'mtr', 'Medtr6g007970' => 'mtr', 'Medtr7g056330' => 'mtr', 'Medtr7g074290' => 'mtr', 'Medtr7g074380' => 'mtr', 'Medtr7g094550' => 'mtr', 'Medtr8g069995' => 'mtr', 'MELO3C014345.2' => 'cme', 'MELO3C021395.2' => 'cme', 'Migut.D00262' => 'egut', 'Migut.G00257' => 'egut', 'MSTRG.21575' => 'ama', 'MSTRG.3985' => 'ama', 'Nitab4.5_0000295g0140' => 'nta', 'Nitab4.5_0000732g0140' => 'nta', 'Nitab4.5_0003162g0020' => 'nta', 'Nitab4.5_0006180g0090' => 'nta', 'Nitab4.5_0006390g0010' => 'nta', 'Nitab4.5_0007392g0040' => 'nta', 'Nn1g02140' => 'nnu', 'Nn4g26168' => 'nnu', 'Nn5g26754' => 'nnu', 'Oeu001433.1' => 'oeu', 'Oeu010299.2' => 'oeu', 'Oeu011171.1' => 'oeu', 'Oeu037675.1' => 'oeu', 'Oeu038359.1' => 'oeu', 'Oeu063834.1' => 'oeu', 'Oeu063835.1' => 'oeu', 'Os05g0312000' => 'osa', 'Os07g0211101' => 'osa', 'Os07g0211200' => 'osa', 'Os07g0681500' => 'osa', 'Peaxi162Scf00095g01015' => 'pax', 'Peaxi162Scf00104g00329' => 'pax', 'Peaxi162Scf00161g00137' => 'pax', 'PGR004G1665' => 'pgr', 'PGR031G2937' => 'pgr', 'PGR119G2145' => 'pgr', 'PGSC0003DMG400004351' => 'stu', 'PGSC0003DMG400014625' => 'stu', 'PGSC0003DMG401000943' => 'stu', 'Phvul.001G148600' => 'pvu', 'Phvul.004G001700' => 'pvu', 'Phvul.006G154900' => 'pvu', 'Phvul.008G078200' => 'pvu', 'Phvul.011G136500' => 'pvu', 'Potri.002G215600' => 'ptr', 'Potri.008G201600' => 'ptr', 'Potri.014G138400' => 'ptr', 'Potri.016G142500' => 'ptr', 'Pp3c16_10580' => 'ppa', 'Pp3c5_25280' => 'ppa', 'Prupe.1G150000' => 'ppe', 'Prupe.1G150100' => 'ppe', 'Prupe.6G299600' => 'ppe', 'Prupe.8G245000' => 'ppe', 'Psat0s4927g0040' => 'psa', 'Psat1g052080' => 'psa', 'Psat1g183800' => 'psa', 'Psat3g113840' => 'psa', 'Psat3g126120' => 'psa', 'Psat3g126160' => 'psa', 'Psat3g158760' => 'psa', 'Psat3g158840' => 'psa', 'PSO170G2858' => 'pso', 'PSO339G0606' => 'pso', 'PSO384G4709' => 'pso', 'PSO407G0334' => 'pso', 'QL04p040276' => 'qlo', 'QL06p005458' => 'qlo', 'QL06p005472' => 'qlo', 'QL07p030546' => 'qlo', 'QL07p031519' => 'qlo', 'QL09p050949' => 'qlo', 'QL09p050966' => 'qlo', 'QL09p051067' => 'qlo', 'QL12p022706' => 'qlo', 'RcHm_v2.0_Chr2g0119601' => 'rch', 'RcHm_v2.0_Chr3g0459591' => 'rch', 'RcHm_v2.0_Chr4g0418521' => 'rch', 'RcHm_v2.0_Chr4g0418531' => 'rch', 'RcHm_v2.0_Chr4g0418541' => 'rch', 'RcHm_v2.0_Chr6g0291641' => 'rch', 'Rhsim01G0086300' => 'rsi', 'Rhsim01G0276300' => 'rsi', 'Rhsim01G0276500' => 'rsi', 'Rhsim04G0207700' => 'rsi', 'Rhsim05G0234500' => 'rsi', 'Rhsim13G0022400' => 'rsi', 'Sabra02G0167900' => 'sbr', 'Sabra04G0158500' => 'sbr', 'Sabra08G0159800' => 'sbr', 'Sabra10G0011500' => 'sbr', 'Sabra14G0104400' => 'sbr', 'SalBow2G2440' => 'sbo', 'SalBow4G2265' => 'sbo', 'Sc02g0000060' => 'sci', 'Sc05g0005020' => 'sci', 'Sc13g0003890' => 'sci', 'Sed0014865' => 'sed', 'Sed0017224' => 'sed', 'Sed0026391' => 'sed', 'SEGI_00063' => 'sgi', 'SEGI_10967' => 'sgi', 'SEGI_17510' => 'sgi', 'SEGI_24396' => 'sgi', 'SEGI_39719' => 'sgi', 'SEGI_41392' => 'sgi', 'SGA_v2.0_scaffold11G05794' => 'sas', 'SGA_v2.0_scaffold142G35607' => 'sas', 'SGA_v2.0_scaffold1G00447' => 'sas', 'SHI15388' => 'shi', 'SHI15394' => 'shi', 'SHI15396' => 'shi', 'SHI15399' => 'shi', 'SMO343G0151' => 'smo', 'SMO367G1118' => 'smo', 'Solyc01g080200.3' => 'sly', 'Solyc06g008960.3' => 'sly', 'Solyc09g064780.3' => 'sly', 'Sopen01g031980' => 'spe', 'Sopen06g003710' => 'spe', 'Sopen09g026460' => 'spe', 'Sp3g21240' => 'spa', 'Sp4g30030' => 'spa', 'TAR365G0022' => 'tar', 'TAR365G1023' => 'tar', 'TAR365G1253' => 'tar', 'TAR623G0078' => 'tar', 'TAR623G1721' => 'tar', 'TAR633G0959' => 'tar', 'THA.LOC104802225' => 'tha', 'THA.LOC104804769' => 'tha', 'THA.LOC104808660' => 'tha', 'THA.LOC104812792' => 'tha', 'Thecc.01G284000' => 'tca', 'Thecc.04G220600' => 'tca', 'Thecc.05G268900' => 'tca', 'Thecc.08G171100' => 'tca', 'Thhalv10001284m.g' => 'esa', 'Thhalv10019912m.g' => 'esa', 'TPR.G14189' => 'tpr', 'TPR.G18110' => 'tpr', 'TPR.G18130' => 'tpr', 'TPR.G18131' => 'tpr', 'TPR.G18140' => 'tpr', 'TPR.G24282' => 'tpr', 'TPR.G25221' => 'tpr', 'TPR.G29267' => 'tpr', 'TPR.G35315' => 'tpr', 'TPR.G36173' => 'tpr', 'TWI09G0794' => 'twi', 'TWI59G1348' => 'twi', 'TWI74G0430' => 'twi', 'unitig_26.g8940' => 'ugi', 'unitig_749.g13744' => 'ugi', 'unitig_749.g13745' => 'ugi', 'vmacro08269' => 'vma', 'vmacro14937' => 'vma', 'vmacro20401' => 'vma', 'VMungo0464G1349' => 'vmu', 'VMungo0540G0289' => 'vmu', 'VMungo1215G1590' => 'vmu', 'VMungo1309G0221' => 'vmu', 'VMungo1309G2815' => 'vmu', 'VMungo1383G0239' => 'vmu', 'VMungo1383G2910' => 'vmu', 'Zm00001eb095270' => 'zma', 'Zm00001eb095280' => 'zma', 'Zm00001eb111630' => 'zma', 'Zm00001eb237080' => 'zma', 'Zm00001eb273740' => 'zma', 'Zm00001eb285040' => 'zma', 'Zm00001eb330790' => 'zma', 'Zm00001eb337380' => 'zma' ), 'gf_id' => 'HOM05D001484', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001484' ), 'data_identifier' => 'HOM05D001484', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001484', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p31500' => 'bna', 'A05p00020' => 'bna', 'A07p08820' => 'bna', 'Aa31LG4G3300' => 'aar', 'Aa31LG8G10030' => 'aar', 'Actinidia00731' => 'ach', 'Actinidia11473' => 'ach', 'Actinidia23469' => 'ach', 'Actinidia24318' => 'ach', 'Actinidia40196' => 'ach', 'Actinidia40197' => 'ach', 'Actinidia40198' => 'ach', 'Ah.08g212990' => 'amhyb', 'Ah.15g091720' => 'amhyb', 'AL3G38260' => 'aly', 'AL4G47710' => 'aly', 'Aqoxy2G00671' => 'aox', 'Aqoxy2G03236' => 'aox', 'arahy.Tifrunner.gnm1.ann1.05IDCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KR684' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATY3SJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK6QJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6APGL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IDT7Z9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM073U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ0R87' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LE7RV4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT4QRX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V5ENPK' => 'arhy', 'AT2G48110' => 'ath', 'AT3G23590' => 'ath', 'ATR0626G186' => 'atr', 'ATR1127G141' => 'atr', 'Atru.chr4.2583' => 'acertr', 'Atru.chr5.1358' => 'acertr', 'Atru.chr5.1359' => 'acertr', 'Atru.chr8.46' => 'acertr', 'AUR62002640' => 'cqu', 'AUR62030055' => 'cqu', 'AUR62033713' => 'cqu', 'AUR62033714' => 'cqu', 'AUR62036795' => 'cqu', 'AUR62039891' => 'cqu', 'BcaB02g08737' => 'bca', 'BcaB04g20441' => 'bca', 'BcaB06g26509' => 'bca', 'BcaB06g26510' => 'bca', 'BcaB06g26511' => 'bca', 'BcaB06g26512' => 'bca', 'BcaB06g26513' => 'bca', 'BcaC02g12564' => 'bca', 'BcaC02g12565' => 'bca', 'BcaC02g12794' => 'bca', 'BcaC02g12795' => 'bca', 'BcaC02g12796' => 'bca', 'BcaC06g35541' => 'bca', 'BNapus_Darmor_BZH_scaffold_188p00080' => 'bna', 'BNapus_Darmor_BZH_scaffold_188p00090' => 'bna', 'BolC1t03972H' => 'bol', 'BolC1t03973H' => 'bol', 'BolC4t21680H' => 'bol', 'BolC7t41863H' => 'bol', 'BolSC55t61227H' => 'bol', 'BolSC55t61228H' => 'bol', 'BraA01t03278Z' => 'bra', 'BraA05t18998Z' => 'bra', 'BraA07t28673Z' => 'bra', 'C01p40150' => 'bna', 'C05p12370' => 'bna', 'C07p13680' => 'bna', 'CAN.G1006.16' => 'can', 'CAN.G1006.17' => 'can', 'CAN.G1170.2' => 'can', 'CAN.G962.7' => 'can', 'CANSAT25G2179' => 'cansat', 'CANSAT78G1573' => 'cansat', 'CARHR099510' => 'chi', 'CARHR143510' => 'chi', 'Carub.0003s2380' => 'cru', 'Carub.0004s3082' => 'cru', 'Ca_00614_v3' => 'car', 'Ca_07801_v3' => 'car', 'Ca_08567_v3' => 'car', 'Ca_09571_v3' => 'car', 'CBR_g19290' => 'cbr', 'Cc01_g19770' => 'ccan', 'Cc03_g03030' => 'ccan', 'CDE07G0968' => 'cde', 'CDE09G1441' => 'cde', 'Cfa006103' => 'cfa', 'Cfa015573' => 'cfa', 'Cfa016988' => 'cfa', 'Ciclev10006738m.g' => 'ccl', 'Ciclev10010920m.g' => 'ccl', 'Ciclev10018517m.g' => 'ccl', 'CiPaw.01G159200' => 'cil', 'CiPaw.02G091000' => 'cil', 'CiPaw.02G091100' => 'cil', 'CiPaw.08G103100' => 'cil', 'CiPaw.09G224900' => 'cil', 'ClCG06G005740' => 'cla', 'ClCG07G000090' => 'cla', 'ClCG07G000100' => 'cla', 'COL.COLO4_09143' => 'col', 'COL.COLO4_25124' => 'col', 'Cpa.g.sc16.34' => 'cpa', 'Cpa.g.sc3504.1' => 'cpa', 'Cpa.g.sc60.37' => 'cpa', 'CsaV3_6G018520' => 'csa', 'CsaV3_6G036860' => 'csa', 'CSS0001072' => 'camsi', 'CSS0020208' => 'camsi', 'CSS0021253' => 'camsi', 'CSS0022190' => 'camsi', 'CSS0036150' => 'camsi', 'CSS0040442' => 'camsi', 'CSS0042300' => 'camsi', 'CSS0045298' => 'camsi', 'DCAR_012449' => 'dca', 'DCAR_018405' => 'dca', 'DCAR_024573' => 'dca', 'DCAR_030591' => 'dca', 'Dinv16926' => 'din', 'Dinv32963' => 'din', 'Dinv38382' => 'din', 'Dinv38383' => 'din', 'Duzib133G0974' => 'dzi', 'Duzib138G1867' => 'dzi', 'Duzib211G0420' => 'dzi', 'Duzib212G0930' => 'dzi', 'ECA234G1645' => 'eca', 'ECA247G3467' => 'eca', 'ECA248G1703' => 'eca', 'EL10Ac3g06327' => 'bvu', 'EL10Ac7g17204' => 'bvu', 'Eucgr.A00855' => 'egr', 'Eucgr.A00858' => 'egr', 'Eucgr.H01520' => 'egr', 'Eucgr.H03604' => 'egr', 'Eucgr.L03465' => 'egr', 'Eucgr.L03466' => 'egr', 'FAN01G0988' => 'fan', 'FAN02G3892' => 'fan', 'FAN05G3381' => 'fan', 'FAN07G0967' => 'fan', 'FAN07G1493' => 'fan', 'FAN08G3125' => 'fan', 'FAN09G0402' => 'fan', 'FAN12G2594' => 'fan', 'FAN12G3879' => 'fan', 'FAN14G1546' => 'fan', 'FAN15G3626' => 'fan', 'FAN17G0588' => 'fan', 'FAN17G0609' => 'fan', 'FAN18G2817' => 'fan', 'FAN19G1305' => 'fan', 'FAN20G1787' => 'fan', 'FAN22G0073' => 'fan', 'FAN22G0352' => 'fan', 'FAN22G0368' => 'fan', 'FAN22G2273' => 'fan', 'FAN24G1998' => 'fan', 'FAN27G1317' => 'fan', 'FvH4_2g23980' => 'fve', 'FvH4_4g14380' => 'fve', 'FvH4_4g14390' => 'fve', 'FvH4_6g09250' => 'fve', 'Glyma.03G151100' => 'gma', 'Glyma.04G122550' => 'gma', 'Glyma.05G001600' => 'gma', 'Glyma.09G270766' => 'gma', 'Glyma.09G270832' => 'gma', 'Glyma.13G209800' => 'gma', 'Glyma.15G102800' => 'gma', 'Glyma.18G218900' => 'gma', 'Glyma.19G001500' => 'gma', 'Glyma.19G153600' => 'gma', 'Gohir.A02G028600' => 'ghi', 'Gohir.A08G045000' => 'ghi', 'Gohir.A11G120500' => 'ghi', 'Gohir.A12G006200' => 'ghi', 'Gohir.A12G006250' => 'ghi', 'Gohir.D02G036300' => 'ghi', 'Gohir.D08G054700' => 'ghi', 'Gohir.D11G125600' => 'ghi', 'Gohir.D12G005700' => 'ghi', 'Gorai.004G055200' => 'gra', 'Gorai.005G040400' => 'gra', 'Gorai.007G134500' => 'gra', 'Gorai.008G005500' => 'gra', 'GSVIVG01011094001' => 'vvi', 'GSVIVG01017879001' => 'vvi', 'GSVIVG01025988001' => 'vvi', 'GSVIVG01029847001' => 'vvi', 'HanXRQChr10g0282901' => 'han', 'HanXRQChr10g0310371' => 'han', 'HanXRQChr10g0315041' => 'han', 'HanXRQChr11g0327651' => 'han', 'HanXRQChr12g0359391' => 'han', 'Haze_00972' => 'cav', 'Haze_00973' => 'cav', 'Haze_00974' => 'cav', 'Haze_04747' => 'cav', 'Haze_04749' => 'cav', 'Haze_04750' => 'cav', 'Haze_21217' => 'cav', 'Hma1.2p1_1037F.1_g250680' => 'hma', 'Hma1.2p1_1644F.1_g295320' => 'hma', 'HPP92_011322' => 'vpl', 'HPP92_011323' => 'vpl', 'HPP92_011324' => 'vpl', 'HPP92_011325' => 'vpl', 'HPP92_011326' => 'vpl', 'Hund12205' => 'sun', 'Hund17957' => 'sun', 'Lalb_Chr06g0176771' => 'lal', 'Lalb_Chr18g0056021' => 'lal', 'Lalb_Chr18g0056031' => 'lal', 'Lalb_Chr18g0056041' => 'lal', 'Lalb_Chr20g0107751' => 'lal', 'Lalb_Chr20g0118371' => 'lal', 'Lj1g0010239' => 'lja', 'Lj1g0017101' => 'lja', 'Lj2A1178G40' => 'lonja', 'Lj2A54G84' => 'lonja', 'Lj2g0015248' => 'lja', 'Lj3A761T51' => 'lonja', 'Lj6g0018116' => 'lja', 'Lsat_1_v5_gn_4_136040' => 'lsa', 'Lsat_1_v5_gn_5_187461' => 'lsa', 'Lsat_1_v5_gn_5_77001' => 'lsa', 'Lsat_1_v5_gn_9_4461' => 'lsa', 'Manes.01G210100' => 'mes', 'Manes.03G185600' => 'mes', 'Manes.05G073300' => 'mes', 'Manes.09G120300' => 'mes', 'Manes.15G022100' => 'mes', 'Mapoly0096s0053' => 'mpo', 'MBI03_g14058_MAGBIO' => 'mbi', 'MBI03_g33876_MAGBIO' => 'mbi', 'MBI03_g36854_MAGBIO' => 'mbi', 'MBI17_g11997_MAGBIO' => 'mbi', 'MD03G1269000' => 'mdo', 'MD04G1179600' => 'mdo', 'MD11G1289800' => 'mdo', 'MD12G1194700' => 'mdo', 'MD13G1182100' => 'mdo', 'MD13G1182200' => 'mdo', 'MD16G1182600' => 'mdo', 'Medtr2g021400' => 'mtr', 'Medtr2g021470' => 'mtr', 'Medtr2g105810' => 'mtr', 'Medtr3g033580' => 'mtr', 'Medtr6g007970' => 'mtr', 'Medtr7g056330' => 'mtr', 'Medtr7g074290' => 'mtr', 'Medtr7g074380' => 'mtr', 'Medtr7g094550' => 'mtr', 'Medtr8g069995' => 'mtr', 'MELO3C014345.2' => 'cme', 'MELO3C021395.2' => 'cme', 'Migut.D00262' => 'egut', 'Migut.G00257' => 'egut', 'MSTRG.21575' => 'ama', 'MSTRG.3985' => 'ama', 'Nitab4.5_0000295g0140' => 'nta', 'Nitab4.5_0000732g0140' => 'nta', 'Nitab4.5_0003162g0020' => 'nta', 'Nitab4.5_0006180g0090' => 'nta', 'Nitab4.5_0006390g0010' => 'nta', 'Nitab4.5_0007392g0040' => 'nta', 'Nn1g02140' => 'nnu', 'Nn4g26168' => 'nnu', 'Nn5g26754' => 'nnu', 'Oeu001433.1' => 'oeu', 'Oeu010299.2' => 'oeu', 'Oeu011171.1' => 'oeu', 'Oeu037675.1' => 'oeu', 'Oeu038359.1' => 'oeu', 'Oeu063834.1' => 'oeu', 'Oeu063835.1' => 'oeu', 'Os05g0312000' => 'osa', 'Os07g0211101' => 'osa', 'Os07g0211200' => 'osa', 'Os07g0681500' => 'osa', 'Peaxi162Scf00095g01015' => 'pax', 'Peaxi162Scf00104g00329' => 'pax', 'Peaxi162Scf00161g00137' => 'pax', 'PGR004G1665' => 'pgr', 'PGR031G2937' => 'pgr', 'PGR119G2145' => 'pgr', 'PGSC0003DMG400004351' => 'stu', 'PGSC0003DMG400014625' => 'stu', 'PGSC0003DMG401000943' => 'stu', 'Phvul.001G148600' => 'pvu', 'Phvul.004G001700' => 'pvu', 'Phvul.006G154900' => 'pvu', 'Phvul.008G078200' => 'pvu', 'Phvul.011G136500' => 'pvu', 'Potri.002G215600' => 'ptr', 'Potri.008G201600' => 'ptr', 'Potri.014G138400' => 'ptr', 'Potri.016G142500' => 'ptr', 'Pp3c16_10580' => 'ppa', 'Pp3c5_25280' => 'ppa', 'Prupe.1G150000' => 'ppe', 'Prupe.1G150100' => 'ppe', 'Prupe.6G299600' => 'ppe', 'Prupe.8G245000' => 'ppe', 'Psat0s4927g0040' => 'psa', 'Psat1g052080' => 'psa', 'Psat1g183800' => 'psa', 'Psat3g113840' => 'psa', 'Psat3g126120' => 'psa', 'Psat3g126160' => 'psa', 'Psat3g158760' => 'psa', 'Psat3g158840' => 'psa', 'PSO170G2858' => 'pso', 'PSO339G0606' => 'pso', 'PSO384G4709' => 'pso', 'PSO407G0334' => 'pso', 'QL04p040276' => 'qlo', 'QL06p005458' => 'qlo', 'QL06p005472' => 'qlo', 'QL07p030546' => 'qlo', 'QL07p031519' => 'qlo', 'QL09p050949' => 'qlo', 'QL09p050966' => 'qlo', 'QL09p051067' => 'qlo', 'QL12p022706' => 'qlo', 'RcHm_v2.0_Chr2g0119601' => 'rch', 'RcHm_v2.0_Chr3g0459591' => 'rch', 'RcHm_v2.0_Chr4g0418521' => 'rch', 'RcHm_v2.0_Chr4g0418531' => 'rch', 'RcHm_v2.0_Chr4g0418541' => 'rch', 'RcHm_v2.0_Chr6g0291641' => 'rch', 'Rhsim01G0086300' => 'rsi', 'Rhsim01G0276300' => 'rsi', 'Rhsim01G0276500' => 'rsi', 'Rhsim04G0207700' => 'rsi', 'Rhsim05G0234500' => 'rsi', 'Rhsim13G0022400' => 'rsi', 'Sabra02G0167900' => 'sbr', 'Sabra04G0158500' => 'sbr', 'Sabra08G0159800' => 'sbr', 'Sabra10G0011500' => 'sbr', 'Sabra14G0104400' => 'sbr', 'SalBow2G2440' => 'sbo', 'SalBow4G2265' => 'sbo', 'Sc02g0000060' => 'sci', 'Sc05g0005020' => 'sci', 'Sc13g0003890' => 'sci', 'Sed0014865' => 'sed', 'Sed0017224' => 'sed', 'Sed0026391' => 'sed', 'SEGI_00063' => 'sgi', 'SEGI_10967' => 'sgi', 'SEGI_17510' => 'sgi', 'SEGI_24396' => 'sgi', 'SEGI_39719' => 'sgi', 'SEGI_41392' => 'sgi', 'SGA_v2.0_scaffold11G05794' => 'sas', 'SGA_v2.0_scaffold142G35607' => 'sas', 'SGA_v2.0_scaffold1G00447' => 'sas', 'SHI15388' => 'shi', 'SHI15394' => 'shi', 'SHI15396' => 'shi', 'SHI15399' => 'shi', 'SMO343G0151' => 'smo', 'SMO367G1118' => 'smo', 'Solyc01g080200.3' => 'sly', 'Solyc06g008960.3' => 'sly', 'Solyc09g064780.3' => 'sly', 'Sopen01g031980' => 'spe', 'Sopen06g003710' => 'spe', 'Sopen09g026460' => 'spe', 'Sp3g21240' => 'spa', 'Sp4g30030' => 'spa', 'TAR365G0022' => 'tar', 'TAR365G1023' => 'tar', 'TAR365G1253' => 'tar', 'TAR623G0078' => 'tar', 'TAR623G1721' => 'tar', 'TAR633G0959' => 'tar', 'THA.LOC104802225' => 'tha', 'THA.LOC104804769' => 'tha', 'THA.LOC104808660' => 'tha', 'THA.LOC104812792' => 'tha', 'Thecc.01G284000' => 'tca', 'Thecc.04G220600' => 'tca', 'Thecc.05G268900' => 'tca', 'Thecc.08G171100' => 'tca', 'Thhalv10001284m.g' => 'esa', 'Thhalv10019912m.g' => 'esa', 'TPR.G14189' => 'tpr', 'TPR.G18110' => 'tpr', 'TPR.G18130' => 'tpr', 'TPR.G18131' => 'tpr', 'TPR.G18140' => 'tpr', 'TPR.G24282' => 'tpr', 'TPR.G25221' => 'tpr', 'TPR.G29267' => 'tpr', 'TPR.G35315' => 'tpr', 'TPR.G36173' => 'tpr', 'TWI09G0794' => 'twi', 'TWI59G1348' => 'twi', 'TWI74G0430' => 'twi', 'unitig_26.g8940' => 'ugi', 'unitig_749.g13744' => 'ugi', 'unitig_749.g13745' => 'ugi', 'vmacro08269' => 'vma', 'vmacro14937' => 'vma', 'vmacro20401' => 'vma', 'VMungo0464G1349' => 'vmu', 'VMungo0540G0289' => 'vmu', 'VMungo1215G1590' => 'vmu', 'VMungo1309G0221' => 'vmu', 'VMungo1309G2815' => 'vmu', 'VMungo1383G0239' => 'vmu', 'VMungo1383G2910' => 'vmu', 'Zm00001eb095270' => 'zma', 'Zm00001eb095280' => 'zma', 'Zm00001eb111630' => 'zma', 'Zm00001eb237080' => 'zma', 'Zm00001eb273740' => 'zma', 'Zm00001eb285040' => 'zma', 'Zm00001eb330790' => 'zma', 'Zm00001eb337380' => 'zma' ) $gf_id = 'HOM05D001484' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001484' ) $data_identifier = 'HOM05D001484' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 2, 'aly' => (int) 2, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 22, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 7, 'hma' => (int) 2, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 7, 'mtr' => (int) 10, 'cme' => (int) 2, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 4, 'ppa' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 4, 'qlo' => (int) 9, 'rch' => (int) 6, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 10, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 7, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb337380' $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' => 'HOM05D001484', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p31500' => 'bna', 'A05p00020' => 'bna', 'A07p08820' => 'bna', 'Aa31LG4G3300' => 'aar', 'Aa31LG8G10030' => 'aar', 'Actinidia00731' => 'ach', 'Actinidia11473' => 'ach', 'Actinidia23469' => 'ach', 'Actinidia24318' => 'ach', 'Actinidia40196' => 'ach', 'Actinidia40197' => 'ach', 'Actinidia40198' => 'ach', 'Ah.08g212990' => 'amhyb', 'Ah.15g091720' => 'amhyb', 'AL3G38260' => 'aly', 'AL4G47710' => 'aly', 'Aqoxy2G00671' => 'aox', 'Aqoxy2G03236' => 'aox', 'arahy.Tifrunner.gnm1.ann1.05IDCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KR684' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATY3SJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK6QJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6APGL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IDT7Z9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM073U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ0R87' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LE7RV4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT4QRX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V5ENPK' => 'arhy', 'AT2G48110' => 'ath', 'AT3G23590' => 'ath', 'ATR0626G186' => 'atr', 'ATR1127G141' => 'atr', 'Atru.chr4.2583' => 'acertr', 'Atru.chr5.1358' => 'acertr', 'Atru.chr5.1359' => 'acertr', 'Atru.chr8.46' => 'acertr', 'AUR62002640' => 'cqu', 'AUR62030055' => 'cqu', 'AUR62033713' => 'cqu', 'AUR62033714' => 'cqu', 'AUR62036795' => 'cqu', 'AUR62039891' => 'cqu', 'BcaB02g08737' => 'bca', 'BcaB04g20441' => 'bca', 'BcaB06g26509' => 'bca', 'BcaB06g26510' => 'bca', 'BcaB06g26511' => 'bca', 'BcaB06g26512' => 'bca', 'BcaB06g26513' => 'bca', 'BcaC02g12564' => 'bca', 'BcaC02g12565' => 'bca', 'BcaC02g12794' => 'bca', 'BcaC02g12795' => 'bca', 'BcaC02g12796' => 'bca', 'BcaC06g35541' => 'bca', 'BNapus_Darmor_BZH_scaffold_188p00080' => 'bna', 'BNapus_Darmor_BZH_scaffold_188p00090' => 'bna', 'BolC1t03972H' => 'bol', 'BolC1t03973H' => 'bol', 'BolC4t21680H' => 'bol', 'BolC7t41863H' => 'bol', 'BolSC55t61227H' => 'bol', 'BolSC55t61228H' => 'bol', 'BraA01t03278Z' => 'bra', 'BraA05t18998Z' => 'bra', 'BraA07t28673Z' => 'bra', 'C01p40150' => 'bna', 'C05p12370' => 'bna', 'C07p13680' => 'bna', 'CAN.G1006.16' => 'can', 'CAN.G1006.17' => 'can', 'CAN.G1170.2' => 'can', 'CAN.G962.7' => 'can', 'CANSAT25G2179' => 'cansat', 'CANSAT78G1573' => 'cansat', 'CARHR099510' => 'chi', 'CARHR143510' => 'chi', 'Carub.0003s2380' => 'cru', 'Carub.0004s3082' => 'cru', 'Ca_00614_v3' => 'car', 'Ca_07801_v3' => 'car', 'Ca_08567_v3' => 'car', 'Ca_09571_v3' => 'car', 'CBR_g19290' => 'cbr', 'Cc01_g19770' => 'ccan', 'Cc03_g03030' => 'ccan', 'CDE07G0968' => 'cde', 'CDE09G1441' => 'cde', 'Cfa006103' => 'cfa', 'Cfa015573' => 'cfa', 'Cfa016988' => 'cfa', 'Ciclev10006738m.g' => 'ccl', 'Ciclev10010920m.g' => 'ccl', 'Ciclev10018517m.g' => 'ccl', 'CiPaw.01G159200' => 'cil', 'CiPaw.02G091000' => 'cil', 'CiPaw.02G091100' => 'cil', 'CiPaw.08G103100' => 'cil', 'CiPaw.09G224900' => 'cil', 'ClCG06G005740' => 'cla', 'ClCG07G000090' => 'cla', 'ClCG07G000100' => 'cla', 'COL.COLO4_09143' => 'col', 'COL.COLO4_25124' => 'col', 'Cpa.g.sc16.34' => 'cpa', 'Cpa.g.sc3504.1' => 'cpa', 'Cpa.g.sc60.37' => 'cpa', 'CsaV3_6G018520' => 'csa', 'CsaV3_6G036860' => 'csa', 'CSS0001072' => 'camsi', 'CSS0020208' => 'camsi', 'CSS0021253' => 'camsi', 'CSS0022190' => 'camsi', 'CSS0036150' => 'camsi', 'CSS0040442' => 'camsi', 'CSS0042300' => 'camsi', 'CSS0045298' => 'camsi', 'DCAR_012449' => 'dca', 'DCAR_018405' => 'dca', 'DCAR_024573' => 'dca', 'DCAR_030591' => 'dca', 'Dinv16926' => 'din', 'Dinv32963' => 'din', 'Dinv38382' => 'din', 'Dinv38383' => 'din', 'Duzib133G0974' => 'dzi', 'Duzib138G1867' => 'dzi', 'Duzib211G0420' => 'dzi', 'Duzib212G0930' => 'dzi', 'ECA234G1645' => 'eca', 'ECA247G3467' => 'eca', 'ECA248G1703' => 'eca', 'EL10Ac3g06327' => 'bvu', 'EL10Ac7g17204' => 'bvu', 'Eucgr.A00855' => 'egr', 'Eucgr.A00858' => 'egr', 'Eucgr.H01520' => 'egr', 'Eucgr.H03604' => 'egr', 'Eucgr.L03465' => 'egr', 'Eucgr.L03466' => 'egr', 'FAN01G0988' => 'fan', 'FAN02G3892' => 'fan', 'FAN05G3381' => 'fan', 'FAN07G0967' => 'fan', 'FAN07G1493' => 'fan', 'FAN08G3125' => 'fan', 'FAN09G0402' => 'fan', 'FAN12G2594' => 'fan', 'FAN12G3879' => 'fan', 'FAN14G1546' => 'fan', 'FAN15G3626' => 'fan', 'FAN17G0588' => 'fan', 'FAN17G0609' => 'fan', 'FAN18G2817' => 'fan', 'FAN19G1305' => 'fan', 'FAN20G1787' => 'fan', 'FAN22G0073' => 'fan', 'FAN22G0352' => 'fan', 'FAN22G0368' => 'fan', 'FAN22G2273' => 'fan', 'FAN24G1998' => 'fan', 'FAN27G1317' => 'fan', 'FvH4_2g23980' => 'fve', 'FvH4_4g14380' => 'fve', 'FvH4_4g14390' => 'fve', 'FvH4_6g09250' => 'fve', 'Glyma.03G151100' => 'gma', 'Glyma.04G122550' => 'gma', 'Glyma.05G001600' => 'gma', 'Glyma.09G270766' => 'gma', 'Glyma.09G270832' => 'gma', 'Glyma.13G209800' => 'gma', 'Glyma.15G102800' => 'gma', 'Glyma.18G218900' => 'gma', 'Glyma.19G001500' => 'gma', 'Glyma.19G153600' => 'gma', 'Gohir.A02G028600' => 'ghi', 'Gohir.A08G045000' => 'ghi', 'Gohir.A11G120500' => 'ghi', 'Gohir.A12G006200' => 'ghi', 'Gohir.A12G006250' => 'ghi', 'Gohir.D02G036300' => 'ghi', 'Gohir.D08G054700' => 'ghi', 'Gohir.D11G125600' => 'ghi', 'Gohir.D12G005700' => 'ghi', 'Gorai.004G055200' => 'gra', 'Gorai.005G040400' => 'gra', 'Gorai.007G134500' => 'gra', 'Gorai.008G005500' => 'gra', 'GSVIVG01011094001' => 'vvi', 'GSVIVG01017879001' => 'vvi', 'GSVIVG01025988001' => 'vvi', 'GSVIVG01029847001' => 'vvi', 'HanXRQChr10g0282901' => 'han', 'HanXRQChr10g0310371' => 'han', 'HanXRQChr10g0315041' => 'han', 'HanXRQChr11g0327651' => 'han', 'HanXRQChr12g0359391' => 'han', 'Haze_00972' => 'cav', 'Haze_00973' => 'cav', 'Haze_00974' => 'cav', 'Haze_04747' => 'cav', 'Haze_04749' => 'cav', 'Haze_04750' => 'cav', 'Haze_21217' => 'cav', 'Hma1.2p1_1037F.1_g250680' => 'hma', 'Hma1.2p1_1644F.1_g295320' => 'hma', 'HPP92_011322' => 'vpl', 'HPP92_011323' => 'vpl', 'HPP92_011324' => 'vpl', 'HPP92_011325' => 'vpl', 'HPP92_011326' => 'vpl', 'Hund12205' => 'sun', 'Hund17957' => 'sun', 'Lalb_Chr06g0176771' => 'lal', 'Lalb_Chr18g0056021' => 'lal', 'Lalb_Chr18g0056031' => 'lal', 'Lalb_Chr18g0056041' => 'lal', 'Lalb_Chr20g0107751' => 'lal', 'Lalb_Chr20g0118371' => 'lal', 'Lj1g0010239' => 'lja', 'Lj1g0017101' => 'lja', 'Lj2A1178G40' => 'lonja', 'Lj2A54G84' => 'lonja', 'Lj2g0015248' => 'lja', 'Lj3A761T51' => 'lonja', 'Lj6g0018116' => 'lja', 'Lsat_1_v5_gn_4_136040' => 'lsa', 'Lsat_1_v5_gn_5_187461' => 'lsa', 'Lsat_1_v5_gn_5_77001' => 'lsa', 'Lsat_1_v5_gn_9_4461' => 'lsa', 'Manes.01G210100' => 'mes', 'Manes.03G185600' => 'mes', 'Manes.05G073300' => 'mes', 'Manes.09G120300' => 'mes', 'Manes.15G022100' => 'mes', 'Mapoly0096s0053' => 'mpo', 'MBI03_g14058_MAGBIO' => 'mbi', 'MBI03_g33876_MAGBIO' => 'mbi', 'MBI03_g36854_MAGBIO' => 'mbi', 'MBI17_g11997_MAGBIO' => 'mbi', 'MD03G1269000' => 'mdo', 'MD04G1179600' => 'mdo', 'MD11G1289800' => 'mdo', 'MD12G1194700' => 'mdo', 'MD13G1182100' => 'mdo', 'MD13G1182200' => 'mdo', 'MD16G1182600' => 'mdo', 'Medtr2g021400' => 'mtr', 'Medtr2g021470' => 'mtr', 'Medtr2g105810' => 'mtr', 'Medtr3g033580' => 'mtr', 'Medtr6g007970' => 'mtr', 'Medtr7g056330' => 'mtr', 'Medtr7g074290' => 'mtr', 'Medtr7g074380' => 'mtr', 'Medtr7g094550' => 'mtr', 'Medtr8g069995' => 'mtr', 'MELO3C014345.2' => 'cme', 'MELO3C021395.2' => 'cme', 'Migut.D00262' => 'egut', 'Migut.G00257' => 'egut', 'MSTRG.21575' => 'ama', 'MSTRG.3985' => 'ama', 'Nitab4.5_0000295g0140' => 'nta', 'Nitab4.5_0000732g0140' => 'nta', 'Nitab4.5_0003162g0020' => 'nta', 'Nitab4.5_0006180g0090' => 'nta', 'Nitab4.5_0006390g0010' => 'nta', 'Nitab4.5_0007392g0040' => 'nta', 'Nn1g02140' => 'nnu', 'Nn4g26168' => 'nnu', 'Nn5g26754' => 'nnu', 'Oeu001433.1' => 'oeu', 'Oeu010299.2' => 'oeu', 'Oeu011171.1' => 'oeu', 'Oeu037675.1' => 'oeu', 'Oeu038359.1' => 'oeu', 'Oeu063834.1' => 'oeu', 'Oeu063835.1' => 'oeu', 'Os05g0312000' => 'osa', 'Os07g0211101' => 'osa', 'Os07g0211200' => 'osa', 'Os07g0681500' => 'osa', 'Peaxi162Scf00095g01015' => 'pax', 'Peaxi162Scf00104g00329' => 'pax', 'Peaxi162Scf00161g00137' => 'pax', 'PGR004G1665' => 'pgr', 'PGR031G2937' => 'pgr', 'PGR119G2145' => 'pgr', 'PGSC0003DMG400004351' => 'stu', 'PGSC0003DMG400014625' => 'stu', 'PGSC0003DMG401000943' => 'stu', 'Phvul.001G148600' => 'pvu', 'Phvul.004G001700' => 'pvu', 'Phvul.006G154900' => 'pvu', 'Phvul.008G078200' => 'pvu', 'Phvul.011G136500' => 'pvu', 'Potri.002G215600' => 'ptr', 'Potri.008G201600' => 'ptr', 'Potri.014G138400' => 'ptr', 'Potri.016G142500' => 'ptr', 'Pp3c16_10580' => 'ppa', 'Pp3c5_25280' => 'ppa', 'Prupe.1G150000' => 'ppe', 'Prupe.1G150100' => 'ppe', 'Prupe.6G299600' => 'ppe', 'Prupe.8G245000' => 'ppe', 'Psat0s4927g0040' => 'psa', 'Psat1g052080' => 'psa', 'Psat1g183800' => 'psa', 'Psat3g113840' => 'psa', 'Psat3g126120' => 'psa', 'Psat3g126160' => 'psa', 'Psat3g158760' => 'psa', 'Psat3g158840' => 'psa', 'PSO170G2858' => 'pso', 'PSO339G0606' => 'pso', 'PSO384G4709' => 'pso', 'PSO407G0334' => 'pso', 'QL04p040276' => 'qlo', 'QL06p005458' => 'qlo', 'QL06p005472' => 'qlo', 'QL07p030546' => 'qlo', 'QL07p031519' => 'qlo', 'QL09p050949' => 'qlo', 'QL09p050966' => 'qlo', 'QL09p051067' => 'qlo', 'QL12p022706' => 'qlo', 'RcHm_v2.0_Chr2g0119601' => 'rch', 'RcHm_v2.0_Chr3g0459591' => 'rch', 'RcHm_v2.0_Chr4g0418521' => 'rch', 'RcHm_v2.0_Chr4g0418531' => 'rch', 'RcHm_v2.0_Chr4g0418541' => 'rch', 'RcHm_v2.0_Chr6g0291641' => 'rch', 'Rhsim01G0086300' => 'rsi', 'Rhsim01G0276300' => 'rsi', 'Rhsim01G0276500' => 'rsi', 'Rhsim04G0207700' => 'rsi', 'Rhsim05G0234500' => 'rsi', 'Rhsim13G0022400' => 'rsi', 'Sabra02G0167900' => 'sbr', 'Sabra04G0158500' => 'sbr', 'Sabra08G0159800' => 'sbr', 'Sabra10G0011500' => 'sbr', 'Sabra14G0104400' => 'sbr', 'SalBow2G2440' => 'sbo', 'SalBow4G2265' => 'sbo', 'Sc02g0000060' => 'sci', 'Sc05g0005020' => 'sci', 'Sc13g0003890' => 'sci', 'Sed0014865' => 'sed', 'Sed0017224' => 'sed', 'Sed0026391' => 'sed', 'SEGI_00063' => 'sgi', 'SEGI_10967' => 'sgi', 'SEGI_17510' => 'sgi', 'SEGI_24396' => 'sgi', 'SEGI_39719' => 'sgi', 'SEGI_41392' => 'sgi', 'SGA_v2.0_scaffold11G05794' => 'sas', 'SGA_v2.0_scaffold142G35607' => 'sas', 'SGA_v2.0_scaffold1G00447' => 'sas', 'SHI15388' => 'shi', 'SHI15394' => 'shi', 'SHI15396' => 'shi', 'SHI15399' => 'shi', 'SMO343G0151' => 'smo', 'SMO367G1118' => 'smo', 'Solyc01g080200.3' => 'sly', 'Solyc06g008960.3' => 'sly', 'Solyc09g064780.3' => 'sly', 'Sopen01g031980' => 'spe', 'Sopen06g003710' => 'spe', 'Sopen09g026460' => 'spe', 'Sp3g21240' => 'spa', 'Sp4g30030' => 'spa', 'TAR365G0022' => 'tar', 'TAR365G1023' => 'tar', 'TAR365G1253' => 'tar', 'TAR623G0078' => 'tar', 'TAR623G1721' => 'tar', 'TAR633G0959' => 'tar', 'THA.LOC104802225' => 'tha', 'THA.LOC104804769' => 'tha', 'THA.LOC104808660' => 'tha', 'THA.LOC104812792' => 'tha', 'Thecc.01G284000' => 'tca', 'Thecc.04G220600' => 'tca', 'Thecc.05G268900' => 'tca', 'Thecc.08G171100' => 'tca', 'Thhalv10001284m.g' => 'esa', 'Thhalv10019912m.g' => 'esa', 'TPR.G14189' => 'tpr', 'TPR.G18110' => 'tpr', 'TPR.G18130' => 'tpr', 'TPR.G18131' => 'tpr', 'TPR.G18140' => 'tpr', 'TPR.G24282' => 'tpr', 'TPR.G25221' => 'tpr', 'TPR.G29267' => 'tpr', 'TPR.G35315' => 'tpr', 'TPR.G36173' => 'tpr', 'TWI09G0794' => 'twi', 'TWI59G1348' => 'twi', 'TWI74G0430' => 'twi', 'unitig_26.g8940' => 'ugi', 'unitig_749.g13744' => 'ugi', 'unitig_749.g13745' => 'ugi', 'vmacro08269' => 'vma', 'vmacro14937' => 'vma', 'vmacro20401' => 'vma', 'VMungo0464G1349' => 'vmu', 'VMungo0540G0289' => 'vmu', 'VMungo1215G1590' => 'vmu', 'VMungo1309G0221' => 'vmu', 'VMungo1309G2815' => 'vmu', 'VMungo1383G0239' => 'vmu', 'VMungo1383G2910' => 'vmu', 'Zm00001eb095270' => 'zma', 'Zm00001eb095280' => 'zma', 'Zm00001eb111630' => 'zma', 'Zm00001eb237080' => 'zma', 'Zm00001eb273740' => 'zma', 'Zm00001eb285040' => 'zma', 'Zm00001eb330790' => 'zma', 'Zm00001eb337380' => 'zma' ), 'gf_id' => 'HOM05D001484', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001484' ), 'data_identifier' => 'HOM05D001484', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001484', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p31500' => 'bna', 'A05p00020' => 'bna', 'A07p08820' => 'bna', 'Aa31LG4G3300' => 'aar', 'Aa31LG8G10030' => 'aar', 'Actinidia00731' => 'ach', 'Actinidia11473' => 'ach', 'Actinidia23469' => 'ach', 'Actinidia24318' => 'ach', 'Actinidia40196' => 'ach', 'Actinidia40197' => 'ach', 'Actinidia40198' => 'ach', 'Ah.08g212990' => 'amhyb', 'Ah.15g091720' => 'amhyb', 'AL3G38260' => 'aly', 'AL4G47710' => 'aly', 'Aqoxy2G00671' => 'aox', 'Aqoxy2G03236' => 'aox', 'arahy.Tifrunner.gnm1.ann1.05IDCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KR684' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATY3SJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK6QJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6APGL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IDT7Z9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM073U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ0R87' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LE7RV4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT4QRX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V5ENPK' => 'arhy', 'AT2G48110' => 'ath', 'AT3G23590' => 'ath', 'ATR0626G186' => 'atr', 'ATR1127G141' => 'atr', 'Atru.chr4.2583' => 'acertr', 'Atru.chr5.1358' => 'acertr', 'Atru.chr5.1359' => 'acertr', 'Atru.chr8.46' => 'acertr', 'AUR62002640' => 'cqu', 'AUR62030055' => 'cqu', 'AUR62033713' => 'cqu', 'AUR62033714' => 'cqu', 'AUR62036795' => 'cqu', 'AUR62039891' => 'cqu', 'BcaB02g08737' => 'bca', 'BcaB04g20441' => 'bca', 'BcaB06g26509' => 'bca', 'BcaB06g26510' => 'bca', 'BcaB06g26511' => 'bca', 'BcaB06g26512' => 'bca', 'BcaB06g26513' => 'bca', 'BcaC02g12564' => 'bca', 'BcaC02g12565' => 'bca', 'BcaC02g12794' => 'bca', 'BcaC02g12795' => 'bca', 'BcaC02g12796' => 'bca', 'BcaC06g35541' => 'bca', 'BNapus_Darmor_BZH_scaffold_188p00080' => 'bna', 'BNapus_Darmor_BZH_scaffold_188p00090' => 'bna', 'BolC1t03972H' => 'bol', 'BolC1t03973H' => 'bol', 'BolC4t21680H' => 'bol', 'BolC7t41863H' => 'bol', 'BolSC55t61227H' => 'bol', 'BolSC55t61228H' => 'bol', 'BraA01t03278Z' => 'bra', 'BraA05t18998Z' => 'bra', 'BraA07t28673Z' => 'bra', 'C01p40150' => 'bna', 'C05p12370' => 'bna', 'C07p13680' => 'bna', 'CAN.G1006.16' => 'can', 'CAN.G1006.17' => 'can', 'CAN.G1170.2' => 'can', 'CAN.G962.7' => 'can', 'CANSAT25G2179' => 'cansat', 'CANSAT78G1573' => 'cansat', 'CARHR099510' => 'chi', 'CARHR143510' => 'chi', 'Carub.0003s2380' => 'cru', 'Carub.0004s3082' => 'cru', 'Ca_00614_v3' => 'car', 'Ca_07801_v3' => 'car', 'Ca_08567_v3' => 'car', 'Ca_09571_v3' => 'car', 'CBR_g19290' => 'cbr', 'Cc01_g19770' => 'ccan', 'Cc03_g03030' => 'ccan', 'CDE07G0968' => 'cde', 'CDE09G1441' => 'cde', 'Cfa006103' => 'cfa', 'Cfa015573' => 'cfa', 'Cfa016988' => 'cfa', 'Ciclev10006738m.g' => 'ccl', 'Ciclev10010920m.g' => 'ccl', 'Ciclev10018517m.g' => 'ccl', 'CiPaw.01G159200' => 'cil', 'CiPaw.02G091000' => 'cil', 'CiPaw.02G091100' => 'cil', 'CiPaw.08G103100' => 'cil', 'CiPaw.09G224900' => 'cil', 'ClCG06G005740' => 'cla', 'ClCG07G000090' => 'cla', 'ClCG07G000100' => 'cla', 'COL.COLO4_09143' => 'col', 'COL.COLO4_25124' => 'col', 'Cpa.g.sc16.34' => 'cpa', 'Cpa.g.sc3504.1' => 'cpa', 'Cpa.g.sc60.37' => 'cpa', 'CsaV3_6G018520' => 'csa', 'CsaV3_6G036860' => 'csa', 'CSS0001072' => 'camsi', 'CSS0020208' => 'camsi', 'CSS0021253' => 'camsi', 'CSS0022190' => 'camsi', 'CSS0036150' => 'camsi', 'CSS0040442' => 'camsi', 'CSS0042300' => 'camsi', 'CSS0045298' => 'camsi', 'DCAR_012449' => 'dca', 'DCAR_018405' => 'dca', 'DCAR_024573' => 'dca', 'DCAR_030591' => 'dca', 'Dinv16926' => 'din', 'Dinv32963' => 'din', 'Dinv38382' => 'din', 'Dinv38383' => 'din', 'Duzib133G0974' => 'dzi', 'Duzib138G1867' => 'dzi', 'Duzib211G0420' => 'dzi', 'Duzib212G0930' => 'dzi', 'ECA234G1645' => 'eca', 'ECA247G3467' => 'eca', 'ECA248G1703' => 'eca', 'EL10Ac3g06327' => 'bvu', 'EL10Ac7g17204' => 'bvu', 'Eucgr.A00855' => 'egr', 'Eucgr.A00858' => 'egr', 'Eucgr.H01520' => 'egr', 'Eucgr.H03604' => 'egr', 'Eucgr.L03465' => 'egr', 'Eucgr.L03466' => 'egr', 'FAN01G0988' => 'fan', 'FAN02G3892' => 'fan', 'FAN05G3381' => 'fan', 'FAN07G0967' => 'fan', 'FAN07G1493' => 'fan', 'FAN08G3125' => 'fan', 'FAN09G0402' => 'fan', 'FAN12G2594' => 'fan', 'FAN12G3879' => 'fan', 'FAN14G1546' => 'fan', 'FAN15G3626' => 'fan', 'FAN17G0588' => 'fan', 'FAN17G0609' => 'fan', 'FAN18G2817' => 'fan', 'FAN19G1305' => 'fan', 'FAN20G1787' => 'fan', 'FAN22G0073' => 'fan', 'FAN22G0352' => 'fan', 'FAN22G0368' => 'fan', 'FAN22G2273' => 'fan', 'FAN24G1998' => 'fan', 'FAN27G1317' => 'fan', 'FvH4_2g23980' => 'fve', 'FvH4_4g14380' => 'fve', 'FvH4_4g14390' => 'fve', 'FvH4_6g09250' => 'fve', 'Glyma.03G151100' => 'gma', 'Glyma.04G122550' => 'gma', 'Glyma.05G001600' => 'gma', 'Glyma.09G270766' => 'gma', 'Glyma.09G270832' => 'gma', 'Glyma.13G209800' => 'gma', 'Glyma.15G102800' => 'gma', 'Glyma.18G218900' => 'gma', 'Glyma.19G001500' => 'gma', 'Glyma.19G153600' => 'gma', 'Gohir.A02G028600' => 'ghi', 'Gohir.A08G045000' => 'ghi', 'Gohir.A11G120500' => 'ghi', 'Gohir.A12G006200' => 'ghi', 'Gohir.A12G006250' => 'ghi', 'Gohir.D02G036300' => 'ghi', 'Gohir.D08G054700' => 'ghi', 'Gohir.D11G125600' => 'ghi', 'Gohir.D12G005700' => 'ghi', 'Gorai.004G055200' => 'gra', 'Gorai.005G040400' => 'gra', 'Gorai.007G134500' => 'gra', 'Gorai.008G005500' => 'gra', 'GSVIVG01011094001' => 'vvi', 'GSVIVG01017879001' => 'vvi', 'GSVIVG01025988001' => 'vvi', 'GSVIVG01029847001' => 'vvi', 'HanXRQChr10g0282901' => 'han', 'HanXRQChr10g0310371' => 'han', 'HanXRQChr10g0315041' => 'han', 'HanXRQChr11g0327651' => 'han', 'HanXRQChr12g0359391' => 'han', 'Haze_00972' => 'cav', 'Haze_00973' => 'cav', 'Haze_00974' => 'cav', 'Haze_04747' => 'cav', 'Haze_04749' => 'cav', 'Haze_04750' => 'cav', 'Haze_21217' => 'cav', 'Hma1.2p1_1037F.1_g250680' => 'hma', 'Hma1.2p1_1644F.1_g295320' => 'hma', 'HPP92_011322' => 'vpl', 'HPP92_011323' => 'vpl', 'HPP92_011324' => 'vpl', 'HPP92_011325' => 'vpl', 'HPP92_011326' => 'vpl', 'Hund12205' => 'sun', 'Hund17957' => 'sun', 'Lalb_Chr06g0176771' => 'lal', 'Lalb_Chr18g0056021' => 'lal', 'Lalb_Chr18g0056031' => 'lal', 'Lalb_Chr18g0056041' => 'lal', 'Lalb_Chr20g0107751' => 'lal', 'Lalb_Chr20g0118371' => 'lal', 'Lj1g0010239' => 'lja', 'Lj1g0017101' => 'lja', 'Lj2A1178G40' => 'lonja', 'Lj2A54G84' => 'lonja', 'Lj2g0015248' => 'lja', 'Lj3A761T51' => 'lonja', 'Lj6g0018116' => 'lja', 'Lsat_1_v5_gn_4_136040' => 'lsa', 'Lsat_1_v5_gn_5_187461' => 'lsa', 'Lsat_1_v5_gn_5_77001' => 'lsa', 'Lsat_1_v5_gn_9_4461' => 'lsa', 'Manes.01G210100' => 'mes', 'Manes.03G185600' => 'mes', 'Manes.05G073300' => 'mes', 'Manes.09G120300' => 'mes', 'Manes.15G022100' => 'mes', 'Mapoly0096s0053' => 'mpo', 'MBI03_g14058_MAGBIO' => 'mbi', 'MBI03_g33876_MAGBIO' => 'mbi', 'MBI03_g36854_MAGBIO' => 'mbi', 'MBI17_g11997_MAGBIO' => 'mbi', 'MD03G1269000' => 'mdo', 'MD04G1179600' => 'mdo', 'MD11G1289800' => 'mdo', 'MD12G1194700' => 'mdo', 'MD13G1182100' => 'mdo', 'MD13G1182200' => 'mdo', 'MD16G1182600' => 'mdo', 'Medtr2g021400' => 'mtr', 'Medtr2g021470' => 'mtr', 'Medtr2g105810' => 'mtr', 'Medtr3g033580' => 'mtr', 'Medtr6g007970' => 'mtr', 'Medtr7g056330' => 'mtr', 'Medtr7g074290' => 'mtr', 'Medtr7g074380' => 'mtr', 'Medtr7g094550' => 'mtr', 'Medtr8g069995' => 'mtr', 'MELO3C014345.2' => 'cme', 'MELO3C021395.2' => 'cme', 'Migut.D00262' => 'egut', 'Migut.G00257' => 'egut', 'MSTRG.21575' => 'ama', 'MSTRG.3985' => 'ama', 'Nitab4.5_0000295g0140' => 'nta', 'Nitab4.5_0000732g0140' => 'nta', 'Nitab4.5_0003162g0020' => 'nta', 'Nitab4.5_0006180g0090' => 'nta', 'Nitab4.5_0006390g0010' => 'nta', 'Nitab4.5_0007392g0040' => 'nta', 'Nn1g02140' => 'nnu', 'Nn4g26168' => 'nnu', 'Nn5g26754' => 'nnu', 'Oeu001433.1' => 'oeu', 'Oeu010299.2' => 'oeu', 'Oeu011171.1' => 'oeu', 'Oeu037675.1' => 'oeu', 'Oeu038359.1' => 'oeu', 'Oeu063834.1' => 'oeu', 'Oeu063835.1' => 'oeu', 'Os05g0312000' => 'osa', 'Os07g0211101' => 'osa', 'Os07g0211200' => 'osa', 'Os07g0681500' => 'osa', 'Peaxi162Scf00095g01015' => 'pax', 'Peaxi162Scf00104g00329' => 'pax', 'Peaxi162Scf00161g00137' => 'pax', 'PGR004G1665' => 'pgr', 'PGR031G2937' => 'pgr', 'PGR119G2145' => 'pgr', 'PGSC0003DMG400004351' => 'stu', 'PGSC0003DMG400014625' => 'stu', 'PGSC0003DMG401000943' => 'stu', 'Phvul.001G148600' => 'pvu', 'Phvul.004G001700' => 'pvu', 'Phvul.006G154900' => 'pvu', 'Phvul.008G078200' => 'pvu', 'Phvul.011G136500' => 'pvu', 'Potri.002G215600' => 'ptr', 'Potri.008G201600' => 'ptr', 'Potri.014G138400' => 'ptr', 'Potri.016G142500' => 'ptr', 'Pp3c16_10580' => 'ppa', 'Pp3c5_25280' => 'ppa', 'Prupe.1G150000' => 'ppe', 'Prupe.1G150100' => 'ppe', 'Prupe.6G299600' => 'ppe', 'Prupe.8G245000' => 'ppe', 'Psat0s4927g0040' => 'psa', 'Psat1g052080' => 'psa', 'Psat1g183800' => 'psa', 'Psat3g113840' => 'psa', 'Psat3g126120' => 'psa', 'Psat3g126160' => 'psa', 'Psat3g158760' => 'psa', 'Psat3g158840' => 'psa', 'PSO170G2858' => 'pso', 'PSO339G0606' => 'pso', 'PSO384G4709' => 'pso', 'PSO407G0334' => 'pso', 'QL04p040276' => 'qlo', 'QL06p005458' => 'qlo', 'QL06p005472' => 'qlo', 'QL07p030546' => 'qlo', 'QL07p031519' => 'qlo', 'QL09p050949' => 'qlo', 'QL09p050966' => 'qlo', 'QL09p051067' => 'qlo', 'QL12p022706' => 'qlo', 'RcHm_v2.0_Chr2g0119601' => 'rch', 'RcHm_v2.0_Chr3g0459591' => 'rch', 'RcHm_v2.0_Chr4g0418521' => 'rch', 'RcHm_v2.0_Chr4g0418531' => 'rch', 'RcHm_v2.0_Chr4g0418541' => 'rch', 'RcHm_v2.0_Chr6g0291641' => 'rch', 'Rhsim01G0086300' => 'rsi', 'Rhsim01G0276300' => 'rsi', 'Rhsim01G0276500' => 'rsi', 'Rhsim04G0207700' => 'rsi', 'Rhsim05G0234500' => 'rsi', 'Rhsim13G0022400' => 'rsi', 'Sabra02G0167900' => 'sbr', 'Sabra04G0158500' => 'sbr', 'Sabra08G0159800' => 'sbr', 'Sabra10G0011500' => 'sbr', 'Sabra14G0104400' => 'sbr', 'SalBow2G2440' => 'sbo', 'SalBow4G2265' => 'sbo', 'Sc02g0000060' => 'sci', 'Sc05g0005020' => 'sci', 'Sc13g0003890' => 'sci', 'Sed0014865' => 'sed', 'Sed0017224' => 'sed', 'Sed0026391' => 'sed', 'SEGI_00063' => 'sgi', 'SEGI_10967' => 'sgi', 'SEGI_17510' => 'sgi', 'SEGI_24396' => 'sgi', 'SEGI_39719' => 'sgi', 'SEGI_41392' => 'sgi', 'SGA_v2.0_scaffold11G05794' => 'sas', 'SGA_v2.0_scaffold142G35607' => 'sas', 'SGA_v2.0_scaffold1G00447' => 'sas', 'SHI15388' => 'shi', 'SHI15394' => 'shi', 'SHI15396' => 'shi', 'SHI15399' => 'shi', 'SMO343G0151' => 'smo', 'SMO367G1118' => 'smo', 'Solyc01g080200.3' => 'sly', 'Solyc06g008960.3' => 'sly', 'Solyc09g064780.3' => 'sly', 'Sopen01g031980' => 'spe', 'Sopen06g003710' => 'spe', 'Sopen09g026460' => 'spe', 'Sp3g21240' => 'spa', 'Sp4g30030' => 'spa', 'TAR365G0022' => 'tar', 'TAR365G1023' => 'tar', 'TAR365G1253' => 'tar', 'TAR623G0078' => 'tar', 'TAR623G1721' => 'tar', 'TAR633G0959' => 'tar', 'THA.LOC104802225' => 'tha', 'THA.LOC104804769' => 'tha', 'THA.LOC104808660' => 'tha', 'THA.LOC104812792' => 'tha', 'Thecc.01G284000' => 'tca', 'Thecc.04G220600' => 'tca', 'Thecc.05G268900' => 'tca', 'Thecc.08G171100' => 'tca', 'Thhalv10001284m.g' => 'esa', 'Thhalv10019912m.g' => 'esa', 'TPR.G14189' => 'tpr', 'TPR.G18110' => 'tpr', 'TPR.G18130' => 'tpr', 'TPR.G18131' => 'tpr', 'TPR.G18140' => 'tpr', 'TPR.G24282' => 'tpr', 'TPR.G25221' => 'tpr', 'TPR.G29267' => 'tpr', 'TPR.G35315' => 'tpr', 'TPR.G36173' => 'tpr', 'TWI09G0794' => 'twi', 'TWI59G1348' => 'twi', 'TWI74G0430' => 'twi', 'unitig_26.g8940' => 'ugi', 'unitig_749.g13744' => 'ugi', 'unitig_749.g13745' => 'ugi', 'vmacro08269' => 'vma', 'vmacro14937' => 'vma', 'vmacro20401' => 'vma', 'VMungo0464G1349' => 'vmu', 'VMungo0540G0289' => 'vmu', 'VMungo1215G1590' => 'vmu', 'VMungo1309G0221' => 'vmu', 'VMungo1309G2815' => 'vmu', 'VMungo1383G0239' => 'vmu', 'VMungo1383G2910' => 'vmu', 'Zm00001eb095270' => 'zma', 'Zm00001eb095280' => 'zma', 'Zm00001eb111630' => 'zma', 'Zm00001eb237080' => 'zma', 'Zm00001eb273740' => 'zma', 'Zm00001eb285040' => 'zma', 'Zm00001eb330790' => 'zma', 'Zm00001eb337380' => 'zma' ) $gf_id = 'HOM05D001484' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001484' ) $data_identifier = 'HOM05D001484' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 2, 'aly' => (int) 2, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 22, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 7, 'hma' => (int) 2, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 7, 'mtr' => (int) 10, 'cme' => (int) 2, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 4, 'ppa' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 4, 'qlo' => (int) 9, 'rch' => (int) 6, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 10, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 7, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb337380' $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' => 'HOM05D001484', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p31500' => 'bna', 'A05p00020' => 'bna', 'A07p08820' => 'bna', 'Aa31LG4G3300' => 'aar', 'Aa31LG8G10030' => 'aar', 'Actinidia00731' => 'ach', 'Actinidia11473' => 'ach', 'Actinidia23469' => 'ach', 'Actinidia24318' => 'ach', 'Actinidia40196' => 'ach', 'Actinidia40197' => 'ach', 'Actinidia40198' => 'ach', 'Ah.08g212990' => 'amhyb', 'Ah.15g091720' => 'amhyb', 'AL3G38260' => 'aly', 'AL4G47710' => 'aly', 'Aqoxy2G00671' => 'aox', 'Aqoxy2G03236' => 'aox', 'arahy.Tifrunner.gnm1.ann1.05IDCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KR684' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATY3SJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK6QJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6APGL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IDT7Z9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM073U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ0R87' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LE7RV4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT4QRX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V5ENPK' => 'arhy', 'AT2G48110' => 'ath', 'AT3G23590' => 'ath', 'ATR0626G186' => 'atr', 'ATR1127G141' => 'atr', 'Atru.chr4.2583' => 'acertr', 'Atru.chr5.1358' => 'acertr', 'Atru.chr5.1359' => 'acertr', 'Atru.chr8.46' => 'acertr', 'AUR62002640' => 'cqu', 'AUR62030055' => 'cqu', 'AUR62033713' => 'cqu', 'AUR62033714' => 'cqu', 'AUR62036795' => 'cqu', 'AUR62039891' => 'cqu', 'BcaB02g08737' => 'bca', 'BcaB04g20441' => 'bca', 'BcaB06g26509' => 'bca', 'BcaB06g26510' => 'bca', 'BcaB06g26511' => 'bca', 'BcaB06g26512' => 'bca', 'BcaB06g26513' => 'bca', 'BcaC02g12564' => 'bca', 'BcaC02g12565' => 'bca', 'BcaC02g12794' => 'bca', 'BcaC02g12795' => 'bca', 'BcaC02g12796' => 'bca', 'BcaC06g35541' => 'bca', 'BNapus_Darmor_BZH_scaffold_188p00080' => 'bna', 'BNapus_Darmor_BZH_scaffold_188p00090' => 'bna', 'BolC1t03972H' => 'bol', 'BolC1t03973H' => 'bol', 'BolC4t21680H' => 'bol', 'BolC7t41863H' => 'bol', 'BolSC55t61227H' => 'bol', 'BolSC55t61228H' => 'bol', 'BraA01t03278Z' => 'bra', 'BraA05t18998Z' => 'bra', 'BraA07t28673Z' => 'bra', 'C01p40150' => 'bna', 'C05p12370' => 'bna', 'C07p13680' => 'bna', 'CAN.G1006.16' => 'can', 'CAN.G1006.17' => 'can', 'CAN.G1170.2' => 'can', 'CAN.G962.7' => 'can', 'CANSAT25G2179' => 'cansat', 'CANSAT78G1573' => 'cansat', 'CARHR099510' => 'chi', 'CARHR143510' => 'chi', 'Carub.0003s2380' => 'cru', 'Carub.0004s3082' => 'cru', 'Ca_00614_v3' => 'car', 'Ca_07801_v3' => 'car', 'Ca_08567_v3' => 'car', 'Ca_09571_v3' => 'car', 'CBR_g19290' => 'cbr', 'Cc01_g19770' => 'ccan', 'Cc03_g03030' => 'ccan', 'CDE07G0968' => 'cde', 'CDE09G1441' => 'cde', 'Cfa006103' => 'cfa', 'Cfa015573' => 'cfa', 'Cfa016988' => 'cfa', 'Ciclev10006738m.g' => 'ccl', 'Ciclev10010920m.g' => 'ccl', 'Ciclev10018517m.g' => 'ccl', 'CiPaw.01G159200' => 'cil', 'CiPaw.02G091000' => 'cil', 'CiPaw.02G091100' => 'cil', 'CiPaw.08G103100' => 'cil', 'CiPaw.09G224900' => 'cil', 'ClCG06G005740' => 'cla', 'ClCG07G000090' => 'cla', 'ClCG07G000100' => 'cla', 'COL.COLO4_09143' => 'col', 'COL.COLO4_25124' => 'col', 'Cpa.g.sc16.34' => 'cpa', 'Cpa.g.sc3504.1' => 'cpa', 'Cpa.g.sc60.37' => 'cpa', 'CsaV3_6G018520' => 'csa', 'CsaV3_6G036860' => 'csa', 'CSS0001072' => 'camsi', 'CSS0020208' => 'camsi', 'CSS0021253' => 'camsi', 'CSS0022190' => 'camsi', 'CSS0036150' => 'camsi', 'CSS0040442' => 'camsi', 'CSS0042300' => 'camsi', 'CSS0045298' => 'camsi', 'DCAR_012449' => 'dca', 'DCAR_018405' => 'dca', 'DCAR_024573' => 'dca', 'DCAR_030591' => 'dca', 'Dinv16926' => 'din', 'Dinv32963' => 'din', 'Dinv38382' => 'din', 'Dinv38383' => 'din', 'Duzib133G0974' => 'dzi', 'Duzib138G1867' => 'dzi', 'Duzib211G0420' => 'dzi', 'Duzib212G0930' => 'dzi', 'ECA234G1645' => 'eca', 'ECA247G3467' => 'eca', 'ECA248G1703' => 'eca', 'EL10Ac3g06327' => 'bvu', 'EL10Ac7g17204' => 'bvu', 'Eucgr.A00855' => 'egr', 'Eucgr.A00858' => 'egr', 'Eucgr.H01520' => 'egr', 'Eucgr.H03604' => 'egr', 'Eucgr.L03465' => 'egr', 'Eucgr.L03466' => 'egr', 'FAN01G0988' => 'fan', 'FAN02G3892' => 'fan', 'FAN05G3381' => 'fan', 'FAN07G0967' => 'fan', 'FAN07G1493' => 'fan', 'FAN08G3125' => 'fan', 'FAN09G0402' => 'fan', 'FAN12G2594' => 'fan', 'FAN12G3879' => 'fan', 'FAN14G1546' => 'fan', 'FAN15G3626' => 'fan', 'FAN17G0588' => 'fan', 'FAN17G0609' => 'fan', 'FAN18G2817' => 'fan', 'FAN19G1305' => 'fan', 'FAN20G1787' => 'fan', 'FAN22G0073' => 'fan', 'FAN22G0352' => 'fan', 'FAN22G0368' => 'fan', 'FAN22G2273' => 'fan', 'FAN24G1998' => 'fan', 'FAN27G1317' => 'fan', 'FvH4_2g23980' => 'fve', 'FvH4_4g14380' => 'fve', 'FvH4_4g14390' => 'fve', 'FvH4_6g09250' => 'fve', 'Glyma.03G151100' => 'gma', 'Glyma.04G122550' => 'gma', 'Glyma.05G001600' => 'gma', 'Glyma.09G270766' => 'gma', 'Glyma.09G270832' => 'gma', 'Glyma.13G209800' => 'gma', 'Glyma.15G102800' => 'gma', 'Glyma.18G218900' => 'gma', 'Glyma.19G001500' => 'gma', 'Glyma.19G153600' => 'gma', 'Gohir.A02G028600' => 'ghi', 'Gohir.A08G045000' => 'ghi', 'Gohir.A11G120500' => 'ghi', 'Gohir.A12G006200' => 'ghi', 'Gohir.A12G006250' => 'ghi', 'Gohir.D02G036300' => 'ghi', 'Gohir.D08G054700' => 'ghi', 'Gohir.D11G125600' => 'ghi', 'Gohir.D12G005700' => 'ghi', 'Gorai.004G055200' => 'gra', 'Gorai.005G040400' => 'gra', 'Gorai.007G134500' => 'gra', 'Gorai.008G005500' => 'gra', 'GSVIVG01011094001' => 'vvi', 'GSVIVG01017879001' => 'vvi', 'GSVIVG01025988001' => 'vvi', 'GSVIVG01029847001' => 'vvi', 'HanXRQChr10g0282901' => 'han', 'HanXRQChr10g0310371' => 'han', 'HanXRQChr10g0315041' => 'han', 'HanXRQChr11g0327651' => 'han', 'HanXRQChr12g0359391' => 'han', 'Haze_00972' => 'cav', 'Haze_00973' => 'cav', 'Haze_00974' => 'cav', 'Haze_04747' => 'cav', 'Haze_04749' => 'cav', 'Haze_04750' => 'cav', 'Haze_21217' => 'cav', 'Hma1.2p1_1037F.1_g250680' => 'hma', 'Hma1.2p1_1644F.1_g295320' => 'hma', 'HPP92_011322' => 'vpl', 'HPP92_011323' => 'vpl', 'HPP92_011324' => 'vpl', 'HPP92_011325' => 'vpl', 'HPP92_011326' => 'vpl', 'Hund12205' => 'sun', 'Hund17957' => 'sun', 'Lalb_Chr06g0176771' => 'lal', 'Lalb_Chr18g0056021' => 'lal', 'Lalb_Chr18g0056031' => 'lal', 'Lalb_Chr18g0056041' => 'lal', 'Lalb_Chr20g0107751' => 'lal', 'Lalb_Chr20g0118371' => 'lal', 'Lj1g0010239' => 'lja', 'Lj1g0017101' => 'lja', 'Lj2A1178G40' => 'lonja', 'Lj2A54G84' => 'lonja', 'Lj2g0015248' => 'lja', 'Lj3A761T51' => 'lonja', 'Lj6g0018116' => 'lja', 'Lsat_1_v5_gn_4_136040' => 'lsa', 'Lsat_1_v5_gn_5_187461' => 'lsa', 'Lsat_1_v5_gn_5_77001' => 'lsa', 'Lsat_1_v5_gn_9_4461' => 'lsa', 'Manes.01G210100' => 'mes', 'Manes.03G185600' => 'mes', 'Manes.05G073300' => 'mes', 'Manes.09G120300' => 'mes', 'Manes.15G022100' => 'mes', 'Mapoly0096s0053' => 'mpo', 'MBI03_g14058_MAGBIO' => 'mbi', 'MBI03_g33876_MAGBIO' => 'mbi', 'MBI03_g36854_MAGBIO' => 'mbi', 'MBI17_g11997_MAGBIO' => 'mbi', 'MD03G1269000' => 'mdo', 'MD04G1179600' => 'mdo', 'MD11G1289800' => 'mdo', 'MD12G1194700' => 'mdo', 'MD13G1182100' => 'mdo', 'MD13G1182200' => 'mdo', 'MD16G1182600' => 'mdo', 'Medtr2g021400' => 'mtr', 'Medtr2g021470' => 'mtr', 'Medtr2g105810' => 'mtr', 'Medtr3g033580' => 'mtr', 'Medtr6g007970' => 'mtr', 'Medtr7g056330' => 'mtr', 'Medtr7g074290' => 'mtr', 'Medtr7g074380' => 'mtr', 'Medtr7g094550' => 'mtr', 'Medtr8g069995' => 'mtr', 'MELO3C014345.2' => 'cme', 'MELO3C021395.2' => 'cme', 'Migut.D00262' => 'egut', 'Migut.G00257' => 'egut', 'MSTRG.21575' => 'ama', 'MSTRG.3985' => 'ama', 'Nitab4.5_0000295g0140' => 'nta', 'Nitab4.5_0000732g0140' => 'nta', 'Nitab4.5_0003162g0020' => 'nta', 'Nitab4.5_0006180g0090' => 'nta', 'Nitab4.5_0006390g0010' => 'nta', 'Nitab4.5_0007392g0040' => 'nta', 'Nn1g02140' => 'nnu', 'Nn4g26168' => 'nnu', 'Nn5g26754' => 'nnu', 'Oeu001433.1' => 'oeu', 'Oeu010299.2' => 'oeu', 'Oeu011171.1' => 'oeu', 'Oeu037675.1' => 'oeu', 'Oeu038359.1' => 'oeu', 'Oeu063834.1' => 'oeu', 'Oeu063835.1' => 'oeu', 'Os05g0312000' => 'osa', 'Os07g0211101' => 'osa', 'Os07g0211200' => 'osa', 'Os07g0681500' => 'osa', 'Peaxi162Scf00095g01015' => 'pax', 'Peaxi162Scf00104g00329' => 'pax', 'Peaxi162Scf00161g00137' => 'pax', 'PGR004G1665' => 'pgr', 'PGR031G2937' => 'pgr', 'PGR119G2145' => 'pgr', 'PGSC0003DMG400004351' => 'stu', 'PGSC0003DMG400014625' => 'stu', 'PGSC0003DMG401000943' => 'stu', 'Phvul.001G148600' => 'pvu', 'Phvul.004G001700' => 'pvu', 'Phvul.006G154900' => 'pvu', 'Phvul.008G078200' => 'pvu', 'Phvul.011G136500' => 'pvu', 'Potri.002G215600' => 'ptr', 'Potri.008G201600' => 'ptr', 'Potri.014G138400' => 'ptr', 'Potri.016G142500' => 'ptr', 'Pp3c16_10580' => 'ppa', 'Pp3c5_25280' => 'ppa', 'Prupe.1G150000' => 'ppe', 'Prupe.1G150100' => 'ppe', 'Prupe.6G299600' => 'ppe', 'Prupe.8G245000' => 'ppe', 'Psat0s4927g0040' => 'psa', 'Psat1g052080' => 'psa', 'Psat1g183800' => 'psa', 'Psat3g113840' => 'psa', 'Psat3g126120' => 'psa', 'Psat3g126160' => 'psa', 'Psat3g158760' => 'psa', 'Psat3g158840' => 'psa', 'PSO170G2858' => 'pso', 'PSO339G0606' => 'pso', 'PSO384G4709' => 'pso', 'PSO407G0334' => 'pso', 'QL04p040276' => 'qlo', 'QL06p005458' => 'qlo', 'QL06p005472' => 'qlo', 'QL07p030546' => 'qlo', 'QL07p031519' => 'qlo', 'QL09p050949' => 'qlo', 'QL09p050966' => 'qlo', 'QL09p051067' => 'qlo', 'QL12p022706' => 'qlo', 'RcHm_v2.0_Chr2g0119601' => 'rch', 'RcHm_v2.0_Chr3g0459591' => 'rch', 'RcHm_v2.0_Chr4g0418521' => 'rch', 'RcHm_v2.0_Chr4g0418531' => 'rch', 'RcHm_v2.0_Chr4g0418541' => 'rch', 'RcHm_v2.0_Chr6g0291641' => 'rch', 'Rhsim01G0086300' => 'rsi', 'Rhsim01G0276300' => 'rsi', 'Rhsim01G0276500' => 'rsi', 'Rhsim04G0207700' => 'rsi', 'Rhsim05G0234500' => 'rsi', 'Rhsim13G0022400' => 'rsi', 'Sabra02G0167900' => 'sbr', 'Sabra04G0158500' => 'sbr', 'Sabra08G0159800' => 'sbr', 'Sabra10G0011500' => 'sbr', 'Sabra14G0104400' => 'sbr', 'SalBow2G2440' => 'sbo', 'SalBow4G2265' => 'sbo', 'Sc02g0000060' => 'sci', 'Sc05g0005020' => 'sci', 'Sc13g0003890' => 'sci', 'Sed0014865' => 'sed', 'Sed0017224' => 'sed', 'Sed0026391' => 'sed', 'SEGI_00063' => 'sgi', 'SEGI_10967' => 'sgi', 'SEGI_17510' => 'sgi', 'SEGI_24396' => 'sgi', 'SEGI_39719' => 'sgi', 'SEGI_41392' => 'sgi', 'SGA_v2.0_scaffold11G05794' => 'sas', 'SGA_v2.0_scaffold142G35607' => 'sas', 'SGA_v2.0_scaffold1G00447' => 'sas', 'SHI15388' => 'shi', 'SHI15394' => 'shi', 'SHI15396' => 'shi', 'SHI15399' => 'shi', 'SMO343G0151' => 'smo', 'SMO367G1118' => 'smo', 'Solyc01g080200.3' => 'sly', 'Solyc06g008960.3' => 'sly', 'Solyc09g064780.3' => 'sly', 'Sopen01g031980' => 'spe', 'Sopen06g003710' => 'spe', 'Sopen09g026460' => 'spe', 'Sp3g21240' => 'spa', 'Sp4g30030' => 'spa', 'TAR365G0022' => 'tar', 'TAR365G1023' => 'tar', 'TAR365G1253' => 'tar', 'TAR623G0078' => 'tar', 'TAR623G1721' => 'tar', 'TAR633G0959' => 'tar', 'THA.LOC104802225' => 'tha', 'THA.LOC104804769' => 'tha', 'THA.LOC104808660' => 'tha', 'THA.LOC104812792' => 'tha', 'Thecc.01G284000' => 'tca', 'Thecc.04G220600' => 'tca', 'Thecc.05G268900' => 'tca', 'Thecc.08G171100' => 'tca', 'Thhalv10001284m.g' => 'esa', 'Thhalv10019912m.g' => 'esa', 'TPR.G14189' => 'tpr', 'TPR.G18110' => 'tpr', 'TPR.G18130' => 'tpr', 'TPR.G18131' => 'tpr', 'TPR.G18140' => 'tpr', 'TPR.G24282' => 'tpr', 'TPR.G25221' => 'tpr', 'TPR.G29267' => 'tpr', 'TPR.G35315' => 'tpr', 'TPR.G36173' => 'tpr', 'TWI09G0794' => 'twi', 'TWI59G1348' => 'twi', 'TWI74G0430' => 'twi', 'unitig_26.g8940' => 'ugi', 'unitig_749.g13744' => 'ugi', 'unitig_749.g13745' => 'ugi', 'vmacro08269' => 'vma', 'vmacro14937' => 'vma', 'vmacro20401' => 'vma', 'VMungo0464G1349' => 'vmu', 'VMungo0540G0289' => 'vmu', 'VMungo1215G1590' => 'vmu', 'VMungo1309G0221' => 'vmu', 'VMungo1309G2815' => 'vmu', 'VMungo1383G0239' => 'vmu', 'VMungo1383G2910' => 'vmu', 'Zm00001eb095270' => 'zma', 'Zm00001eb095280' => 'zma', 'Zm00001eb111630' => 'zma', 'Zm00001eb237080' => 'zma', 'Zm00001eb273740' => 'zma', 'Zm00001eb285040' => 'zma', 'Zm00001eb330790' => 'zma', 'Zm00001eb337380' => 'zma' ), 'gf_id' => 'HOM05D001484', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001484' ), 'data_identifier' => 'HOM05D001484', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001484', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p31500' => 'bna', 'A05p00020' => 'bna', 'A07p08820' => 'bna', 'Aa31LG4G3300' => 'aar', 'Aa31LG8G10030' => 'aar', 'Actinidia00731' => 'ach', 'Actinidia11473' => 'ach', 'Actinidia23469' => 'ach', 'Actinidia24318' => 'ach', 'Actinidia40196' => 'ach', 'Actinidia40197' => 'ach', 'Actinidia40198' => 'ach', 'Ah.08g212990' => 'amhyb', 'Ah.15g091720' => 'amhyb', 'AL3G38260' => 'aly', 'AL4G47710' => 'aly', 'Aqoxy2G00671' => 'aox', 'Aqoxy2G03236' => 'aox', 'arahy.Tifrunner.gnm1.ann1.05IDCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KR684' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATY3SJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK6QJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6APGL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IDT7Z9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM073U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ0R87' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LE7RV4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT4QRX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V5ENPK' => 'arhy', 'AT2G48110' => 'ath', 'AT3G23590' => 'ath', 'ATR0626G186' => 'atr', 'ATR1127G141' => 'atr', 'Atru.chr4.2583' => 'acertr', 'Atru.chr5.1358' => 'acertr', 'Atru.chr5.1359' => 'acertr', 'Atru.chr8.46' => 'acertr', 'AUR62002640' => 'cqu', 'AUR62030055' => 'cqu', 'AUR62033713' => 'cqu', 'AUR62033714' => 'cqu', 'AUR62036795' => 'cqu', 'AUR62039891' => 'cqu', 'BcaB02g08737' => 'bca', 'BcaB04g20441' => 'bca', 'BcaB06g26509' => 'bca', 'BcaB06g26510' => 'bca', 'BcaB06g26511' => 'bca', 'BcaB06g26512' => 'bca', 'BcaB06g26513' => 'bca', 'BcaC02g12564' => 'bca', 'BcaC02g12565' => 'bca', 'BcaC02g12794' => 'bca', 'BcaC02g12795' => 'bca', 'BcaC02g12796' => 'bca', 'BcaC06g35541' => 'bca', 'BNapus_Darmor_BZH_scaffold_188p00080' => 'bna', 'BNapus_Darmor_BZH_scaffold_188p00090' => 'bna', 'BolC1t03972H' => 'bol', 'BolC1t03973H' => 'bol', 'BolC4t21680H' => 'bol', 'BolC7t41863H' => 'bol', 'BolSC55t61227H' => 'bol', 'BolSC55t61228H' => 'bol', 'BraA01t03278Z' => 'bra', 'BraA05t18998Z' => 'bra', 'BraA07t28673Z' => 'bra', 'C01p40150' => 'bna', 'C05p12370' => 'bna', 'C07p13680' => 'bna', 'CAN.G1006.16' => 'can', 'CAN.G1006.17' => 'can', 'CAN.G1170.2' => 'can', 'CAN.G962.7' => 'can', 'CANSAT25G2179' => 'cansat', 'CANSAT78G1573' => 'cansat', 'CARHR099510' => 'chi', 'CARHR143510' => 'chi', 'Carub.0003s2380' => 'cru', 'Carub.0004s3082' => 'cru', 'Ca_00614_v3' => 'car', 'Ca_07801_v3' => 'car', 'Ca_08567_v3' => 'car', 'Ca_09571_v3' => 'car', 'CBR_g19290' => 'cbr', 'Cc01_g19770' => 'ccan', 'Cc03_g03030' => 'ccan', 'CDE07G0968' => 'cde', 'CDE09G1441' => 'cde', 'Cfa006103' => 'cfa', 'Cfa015573' => 'cfa', 'Cfa016988' => 'cfa', 'Ciclev10006738m.g' => 'ccl', 'Ciclev10010920m.g' => 'ccl', 'Ciclev10018517m.g' => 'ccl', 'CiPaw.01G159200' => 'cil', 'CiPaw.02G091000' => 'cil', 'CiPaw.02G091100' => 'cil', 'CiPaw.08G103100' => 'cil', 'CiPaw.09G224900' => 'cil', 'ClCG06G005740' => 'cla', 'ClCG07G000090' => 'cla', 'ClCG07G000100' => 'cla', 'COL.COLO4_09143' => 'col', 'COL.COLO4_25124' => 'col', 'Cpa.g.sc16.34' => 'cpa', 'Cpa.g.sc3504.1' => 'cpa', 'Cpa.g.sc60.37' => 'cpa', 'CsaV3_6G018520' => 'csa', 'CsaV3_6G036860' => 'csa', 'CSS0001072' => 'camsi', 'CSS0020208' => 'camsi', 'CSS0021253' => 'camsi', 'CSS0022190' => 'camsi', 'CSS0036150' => 'camsi', 'CSS0040442' => 'camsi', 'CSS0042300' => 'camsi', 'CSS0045298' => 'camsi', 'DCAR_012449' => 'dca', 'DCAR_018405' => 'dca', 'DCAR_024573' => 'dca', 'DCAR_030591' => 'dca', 'Dinv16926' => 'din', 'Dinv32963' => 'din', 'Dinv38382' => 'din', 'Dinv38383' => 'din', 'Duzib133G0974' => 'dzi', 'Duzib138G1867' => 'dzi', 'Duzib211G0420' => 'dzi', 'Duzib212G0930' => 'dzi', 'ECA234G1645' => 'eca', 'ECA247G3467' => 'eca', 'ECA248G1703' => 'eca', 'EL10Ac3g06327' => 'bvu', 'EL10Ac7g17204' => 'bvu', 'Eucgr.A00855' => 'egr', 'Eucgr.A00858' => 'egr', 'Eucgr.H01520' => 'egr', 'Eucgr.H03604' => 'egr', 'Eucgr.L03465' => 'egr', 'Eucgr.L03466' => 'egr', 'FAN01G0988' => 'fan', 'FAN02G3892' => 'fan', 'FAN05G3381' => 'fan', 'FAN07G0967' => 'fan', 'FAN07G1493' => 'fan', 'FAN08G3125' => 'fan', 'FAN09G0402' => 'fan', 'FAN12G2594' => 'fan', 'FAN12G3879' => 'fan', 'FAN14G1546' => 'fan', 'FAN15G3626' => 'fan', 'FAN17G0588' => 'fan', 'FAN17G0609' => 'fan', 'FAN18G2817' => 'fan', 'FAN19G1305' => 'fan', 'FAN20G1787' => 'fan', 'FAN22G0073' => 'fan', 'FAN22G0352' => 'fan', 'FAN22G0368' => 'fan', 'FAN22G2273' => 'fan', 'FAN24G1998' => 'fan', 'FAN27G1317' => 'fan', 'FvH4_2g23980' => 'fve', 'FvH4_4g14380' => 'fve', 'FvH4_4g14390' => 'fve', 'FvH4_6g09250' => 'fve', 'Glyma.03G151100' => 'gma', 'Glyma.04G122550' => 'gma', 'Glyma.05G001600' => 'gma', 'Glyma.09G270766' => 'gma', 'Glyma.09G270832' => 'gma', 'Glyma.13G209800' => 'gma', 'Glyma.15G102800' => 'gma', 'Glyma.18G218900' => 'gma', 'Glyma.19G001500' => 'gma', 'Glyma.19G153600' => 'gma', 'Gohir.A02G028600' => 'ghi', 'Gohir.A08G045000' => 'ghi', 'Gohir.A11G120500' => 'ghi', 'Gohir.A12G006200' => 'ghi', 'Gohir.A12G006250' => 'ghi', 'Gohir.D02G036300' => 'ghi', 'Gohir.D08G054700' => 'ghi', 'Gohir.D11G125600' => 'ghi', 'Gohir.D12G005700' => 'ghi', 'Gorai.004G055200' => 'gra', 'Gorai.005G040400' => 'gra', 'Gorai.007G134500' => 'gra', 'Gorai.008G005500' => 'gra', 'GSVIVG01011094001' => 'vvi', 'GSVIVG01017879001' => 'vvi', 'GSVIVG01025988001' => 'vvi', 'GSVIVG01029847001' => 'vvi', 'HanXRQChr10g0282901' => 'han', 'HanXRQChr10g0310371' => 'han', 'HanXRQChr10g0315041' => 'han', 'HanXRQChr11g0327651' => 'han', 'HanXRQChr12g0359391' => 'han', 'Haze_00972' => 'cav', 'Haze_00973' => 'cav', 'Haze_00974' => 'cav', 'Haze_04747' => 'cav', 'Haze_04749' => 'cav', 'Haze_04750' => 'cav', 'Haze_21217' => 'cav', 'Hma1.2p1_1037F.1_g250680' => 'hma', 'Hma1.2p1_1644F.1_g295320' => 'hma', 'HPP92_011322' => 'vpl', 'HPP92_011323' => 'vpl', 'HPP92_011324' => 'vpl', 'HPP92_011325' => 'vpl', 'HPP92_011326' => 'vpl', 'Hund12205' => 'sun', 'Hund17957' => 'sun', 'Lalb_Chr06g0176771' => 'lal', 'Lalb_Chr18g0056021' => 'lal', 'Lalb_Chr18g0056031' => 'lal', 'Lalb_Chr18g0056041' => 'lal', 'Lalb_Chr20g0107751' => 'lal', 'Lalb_Chr20g0118371' => 'lal', 'Lj1g0010239' => 'lja', 'Lj1g0017101' => 'lja', 'Lj2A1178G40' => 'lonja', 'Lj2A54G84' => 'lonja', 'Lj2g0015248' => 'lja', 'Lj3A761T51' => 'lonja', 'Lj6g0018116' => 'lja', 'Lsat_1_v5_gn_4_136040' => 'lsa', 'Lsat_1_v5_gn_5_187461' => 'lsa', 'Lsat_1_v5_gn_5_77001' => 'lsa', 'Lsat_1_v5_gn_9_4461' => 'lsa', 'Manes.01G210100' => 'mes', 'Manes.03G185600' => 'mes', 'Manes.05G073300' => 'mes', 'Manes.09G120300' => 'mes', 'Manes.15G022100' => 'mes', 'Mapoly0096s0053' => 'mpo', 'MBI03_g14058_MAGBIO' => 'mbi', 'MBI03_g33876_MAGBIO' => 'mbi', 'MBI03_g36854_MAGBIO' => 'mbi', 'MBI17_g11997_MAGBIO' => 'mbi', 'MD03G1269000' => 'mdo', 'MD04G1179600' => 'mdo', 'MD11G1289800' => 'mdo', 'MD12G1194700' => 'mdo', 'MD13G1182100' => 'mdo', 'MD13G1182200' => 'mdo', 'MD16G1182600' => 'mdo', 'Medtr2g021400' => 'mtr', 'Medtr2g021470' => 'mtr', 'Medtr2g105810' => 'mtr', 'Medtr3g033580' => 'mtr', 'Medtr6g007970' => 'mtr', 'Medtr7g056330' => 'mtr', 'Medtr7g074290' => 'mtr', 'Medtr7g074380' => 'mtr', 'Medtr7g094550' => 'mtr', 'Medtr8g069995' => 'mtr', 'MELO3C014345.2' => 'cme', 'MELO3C021395.2' => 'cme', 'Migut.D00262' => 'egut', 'Migut.G00257' => 'egut', 'MSTRG.21575' => 'ama', 'MSTRG.3985' => 'ama', 'Nitab4.5_0000295g0140' => 'nta', 'Nitab4.5_0000732g0140' => 'nta', 'Nitab4.5_0003162g0020' => 'nta', 'Nitab4.5_0006180g0090' => 'nta', 'Nitab4.5_0006390g0010' => 'nta', 'Nitab4.5_0007392g0040' => 'nta', 'Nn1g02140' => 'nnu', 'Nn4g26168' => 'nnu', 'Nn5g26754' => 'nnu', 'Oeu001433.1' => 'oeu', 'Oeu010299.2' => 'oeu', 'Oeu011171.1' => 'oeu', 'Oeu037675.1' => 'oeu', 'Oeu038359.1' => 'oeu', 'Oeu063834.1' => 'oeu', 'Oeu063835.1' => 'oeu', 'Os05g0312000' => 'osa', 'Os07g0211101' => 'osa', 'Os07g0211200' => 'osa', 'Os07g0681500' => 'osa', 'Peaxi162Scf00095g01015' => 'pax', 'Peaxi162Scf00104g00329' => 'pax', 'Peaxi162Scf00161g00137' => 'pax', 'PGR004G1665' => 'pgr', 'PGR031G2937' => 'pgr', 'PGR119G2145' => 'pgr', 'PGSC0003DMG400004351' => 'stu', 'PGSC0003DMG400014625' => 'stu', 'PGSC0003DMG401000943' => 'stu', 'Phvul.001G148600' => 'pvu', 'Phvul.004G001700' => 'pvu', 'Phvul.006G154900' => 'pvu', 'Phvul.008G078200' => 'pvu', 'Phvul.011G136500' => 'pvu', 'Potri.002G215600' => 'ptr', 'Potri.008G201600' => 'ptr', 'Potri.014G138400' => 'ptr', 'Potri.016G142500' => 'ptr', 'Pp3c16_10580' => 'ppa', 'Pp3c5_25280' => 'ppa', 'Prupe.1G150000' => 'ppe', 'Prupe.1G150100' => 'ppe', 'Prupe.6G299600' => 'ppe', 'Prupe.8G245000' => 'ppe', 'Psat0s4927g0040' => 'psa', 'Psat1g052080' => 'psa', 'Psat1g183800' => 'psa', 'Psat3g113840' => 'psa', 'Psat3g126120' => 'psa', 'Psat3g126160' => 'psa', 'Psat3g158760' => 'psa', 'Psat3g158840' => 'psa', 'PSO170G2858' => 'pso', 'PSO339G0606' => 'pso', 'PSO384G4709' => 'pso', 'PSO407G0334' => 'pso', 'QL04p040276' => 'qlo', 'QL06p005458' => 'qlo', 'QL06p005472' => 'qlo', 'QL07p030546' => 'qlo', 'QL07p031519' => 'qlo', 'QL09p050949' => 'qlo', 'QL09p050966' => 'qlo', 'QL09p051067' => 'qlo', 'QL12p022706' => 'qlo', 'RcHm_v2.0_Chr2g0119601' => 'rch', 'RcHm_v2.0_Chr3g0459591' => 'rch', 'RcHm_v2.0_Chr4g0418521' => 'rch', 'RcHm_v2.0_Chr4g0418531' => 'rch', 'RcHm_v2.0_Chr4g0418541' => 'rch', 'RcHm_v2.0_Chr6g0291641' => 'rch', 'Rhsim01G0086300' => 'rsi', 'Rhsim01G0276300' => 'rsi', 'Rhsim01G0276500' => 'rsi', 'Rhsim04G0207700' => 'rsi', 'Rhsim05G0234500' => 'rsi', 'Rhsim13G0022400' => 'rsi', 'Sabra02G0167900' => 'sbr', 'Sabra04G0158500' => 'sbr', 'Sabra08G0159800' => 'sbr', 'Sabra10G0011500' => 'sbr', 'Sabra14G0104400' => 'sbr', 'SalBow2G2440' => 'sbo', 'SalBow4G2265' => 'sbo', 'Sc02g0000060' => 'sci', 'Sc05g0005020' => 'sci', 'Sc13g0003890' => 'sci', 'Sed0014865' => 'sed', 'Sed0017224' => 'sed', 'Sed0026391' => 'sed', 'SEGI_00063' => 'sgi', 'SEGI_10967' => 'sgi', 'SEGI_17510' => 'sgi', 'SEGI_24396' => 'sgi', 'SEGI_39719' => 'sgi', 'SEGI_41392' => 'sgi', 'SGA_v2.0_scaffold11G05794' => 'sas', 'SGA_v2.0_scaffold142G35607' => 'sas', 'SGA_v2.0_scaffold1G00447' => 'sas', 'SHI15388' => 'shi', 'SHI15394' => 'shi', 'SHI15396' => 'shi', 'SHI15399' => 'shi', 'SMO343G0151' => 'smo', 'SMO367G1118' => 'smo', 'Solyc01g080200.3' => 'sly', 'Solyc06g008960.3' => 'sly', 'Solyc09g064780.3' => 'sly', 'Sopen01g031980' => 'spe', 'Sopen06g003710' => 'spe', 'Sopen09g026460' => 'spe', 'Sp3g21240' => 'spa', 'Sp4g30030' => 'spa', 'TAR365G0022' => 'tar', 'TAR365G1023' => 'tar', 'TAR365G1253' => 'tar', 'TAR623G0078' => 'tar', 'TAR623G1721' => 'tar', 'TAR633G0959' => 'tar', 'THA.LOC104802225' => 'tha', 'THA.LOC104804769' => 'tha', 'THA.LOC104808660' => 'tha', 'THA.LOC104812792' => 'tha', 'Thecc.01G284000' => 'tca', 'Thecc.04G220600' => 'tca', 'Thecc.05G268900' => 'tca', 'Thecc.08G171100' => 'tca', 'Thhalv10001284m.g' => 'esa', 'Thhalv10019912m.g' => 'esa', 'TPR.G14189' => 'tpr', 'TPR.G18110' => 'tpr', 'TPR.G18130' => 'tpr', 'TPR.G18131' => 'tpr', 'TPR.G18140' => 'tpr', 'TPR.G24282' => 'tpr', 'TPR.G25221' => 'tpr', 'TPR.G29267' => 'tpr', 'TPR.G35315' => 'tpr', 'TPR.G36173' => 'tpr', 'TWI09G0794' => 'twi', 'TWI59G1348' => 'twi', 'TWI74G0430' => 'twi', 'unitig_26.g8940' => 'ugi', 'unitig_749.g13744' => 'ugi', 'unitig_749.g13745' => 'ugi', 'vmacro08269' => 'vma', 'vmacro14937' => 'vma', 'vmacro20401' => 'vma', 'VMungo0464G1349' => 'vmu', 'VMungo0540G0289' => 'vmu', 'VMungo1215G1590' => 'vmu', 'VMungo1309G0221' => 'vmu', 'VMungo1309G2815' => 'vmu', 'VMungo1383G0239' => 'vmu', 'VMungo1383G2910' => 'vmu', 'Zm00001eb095270' => 'zma', 'Zm00001eb095280' => 'zma', 'Zm00001eb111630' => 'zma', 'Zm00001eb237080' => 'zma', 'Zm00001eb273740' => 'zma', 'Zm00001eb285040' => 'zma', 'Zm00001eb330790' => 'zma', 'Zm00001eb337380' => 'zma' ) $gf_id = 'HOM05D001484' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001484' ) $data_identifier = 'HOM05D001484' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 2, 'aly' => (int) 2, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 22, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 7, 'hma' => (int) 2, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 7, 'mtr' => (int) 10, 'cme' => (int) 2, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 4, 'ppa' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 4, 'qlo' => (int) 9, 'rch' => (int) 6, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 10, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 7, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb337380' $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' => 'HOM05D001484', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p31500' => 'bna', 'A05p00020' => 'bna', 'A07p08820' => 'bna', 'Aa31LG4G3300' => 'aar', 'Aa31LG8G10030' => 'aar', 'Actinidia00731' => 'ach', 'Actinidia11473' => 'ach', 'Actinidia23469' => 'ach', 'Actinidia24318' => 'ach', 'Actinidia40196' => 'ach', 'Actinidia40197' => 'ach', 'Actinidia40198' => 'ach', 'Ah.08g212990' => 'amhyb', 'Ah.15g091720' => 'amhyb', 'AL3G38260' => 'aly', 'AL4G47710' => 'aly', 'Aqoxy2G00671' => 'aox', 'Aqoxy2G03236' => 'aox', 'arahy.Tifrunner.gnm1.ann1.05IDCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KR684' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATY3SJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK6QJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6APGL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IDT7Z9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM073U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ0R87' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LE7RV4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT4QRX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V5ENPK' => 'arhy', 'AT2G48110' => 'ath', 'AT3G23590' => 'ath', 'ATR0626G186' => 'atr', 'ATR1127G141' => 'atr', 'Atru.chr4.2583' => 'acertr', 'Atru.chr5.1358' => 'acertr', 'Atru.chr5.1359' => 'acertr', 'Atru.chr8.46' => 'acertr', 'AUR62002640' => 'cqu', 'AUR62030055' => 'cqu', 'AUR62033713' => 'cqu', 'AUR62033714' => 'cqu', 'AUR62036795' => 'cqu', 'AUR62039891' => 'cqu', 'BcaB02g08737' => 'bca', 'BcaB04g20441' => 'bca', 'BcaB06g26509' => 'bca', 'BcaB06g26510' => 'bca', 'BcaB06g26511' => 'bca', 'BcaB06g26512' => 'bca', 'BcaB06g26513' => 'bca', 'BcaC02g12564' => 'bca', 'BcaC02g12565' => 'bca', 'BcaC02g12794' => 'bca', 'BcaC02g12795' => 'bca', 'BcaC02g12796' => 'bca', 'BcaC06g35541' => 'bca', 'BNapus_Darmor_BZH_scaffold_188p00080' => 'bna', 'BNapus_Darmor_BZH_scaffold_188p00090' => 'bna', 'BolC1t03972H' => 'bol', 'BolC1t03973H' => 'bol', 'BolC4t21680H' => 'bol', 'BolC7t41863H' => 'bol', 'BolSC55t61227H' => 'bol', 'BolSC55t61228H' => 'bol', 'BraA01t03278Z' => 'bra', 'BraA05t18998Z' => 'bra', 'BraA07t28673Z' => 'bra', 'C01p40150' => 'bna', 'C05p12370' => 'bna', 'C07p13680' => 'bna', 'CAN.G1006.16' => 'can', 'CAN.G1006.17' => 'can', 'CAN.G1170.2' => 'can', 'CAN.G962.7' => 'can', 'CANSAT25G2179' => 'cansat', 'CANSAT78G1573' => 'cansat', 'CARHR099510' => 'chi', 'CARHR143510' => 'chi', 'Carub.0003s2380' => 'cru', 'Carub.0004s3082' => 'cru', 'Ca_00614_v3' => 'car', 'Ca_07801_v3' => 'car', 'Ca_08567_v3' => 'car', 'Ca_09571_v3' => 'car', 'CBR_g19290' => 'cbr', 'Cc01_g19770' => 'ccan', 'Cc03_g03030' => 'ccan', 'CDE07G0968' => 'cde', 'CDE09G1441' => 'cde', 'Cfa006103' => 'cfa', 'Cfa015573' => 'cfa', 'Cfa016988' => 'cfa', 'Ciclev10006738m.g' => 'ccl', 'Ciclev10010920m.g' => 'ccl', 'Ciclev10018517m.g' => 'ccl', 'CiPaw.01G159200' => 'cil', 'CiPaw.02G091000' => 'cil', 'CiPaw.02G091100' => 'cil', 'CiPaw.08G103100' => 'cil', 'CiPaw.09G224900' => 'cil', 'ClCG06G005740' => 'cla', 'ClCG07G000090' => 'cla', 'ClCG07G000100' => 'cla', 'COL.COLO4_09143' => 'col', 'COL.COLO4_25124' => 'col', 'Cpa.g.sc16.34' => 'cpa', 'Cpa.g.sc3504.1' => 'cpa', 'Cpa.g.sc60.37' => 'cpa', 'CsaV3_6G018520' => 'csa', 'CsaV3_6G036860' => 'csa', 'CSS0001072' => 'camsi', 'CSS0020208' => 'camsi', 'CSS0021253' => 'camsi', 'CSS0022190' => 'camsi', 'CSS0036150' => 'camsi', 'CSS0040442' => 'camsi', 'CSS0042300' => 'camsi', 'CSS0045298' => 'camsi', 'DCAR_012449' => 'dca', 'DCAR_018405' => 'dca', 'DCAR_024573' => 'dca', 'DCAR_030591' => 'dca', 'Dinv16926' => 'din', 'Dinv32963' => 'din', 'Dinv38382' => 'din', 'Dinv38383' => 'din', 'Duzib133G0974' => 'dzi', 'Duzib138G1867' => 'dzi', 'Duzib211G0420' => 'dzi', 'Duzib212G0930' => 'dzi', 'ECA234G1645' => 'eca', 'ECA247G3467' => 'eca', 'ECA248G1703' => 'eca', 'EL10Ac3g06327' => 'bvu', 'EL10Ac7g17204' => 'bvu', 'Eucgr.A00855' => 'egr', 'Eucgr.A00858' => 'egr', 'Eucgr.H01520' => 'egr', 'Eucgr.H03604' => 'egr', 'Eucgr.L03465' => 'egr', 'Eucgr.L03466' => 'egr', 'FAN01G0988' => 'fan', 'FAN02G3892' => 'fan', 'FAN05G3381' => 'fan', 'FAN07G0967' => 'fan', 'FAN07G1493' => 'fan', 'FAN08G3125' => 'fan', 'FAN09G0402' => 'fan', 'FAN12G2594' => 'fan', 'FAN12G3879' => 'fan', 'FAN14G1546' => 'fan', 'FAN15G3626' => 'fan', 'FAN17G0588' => 'fan', 'FAN17G0609' => 'fan', 'FAN18G2817' => 'fan', 'FAN19G1305' => 'fan', 'FAN20G1787' => 'fan', 'FAN22G0073' => 'fan', 'FAN22G0352' => 'fan', 'FAN22G0368' => 'fan', 'FAN22G2273' => 'fan', 'FAN24G1998' => 'fan', 'FAN27G1317' => 'fan', 'FvH4_2g23980' => 'fve', 'FvH4_4g14380' => 'fve', 'FvH4_4g14390' => 'fve', 'FvH4_6g09250' => 'fve', 'Glyma.03G151100' => 'gma', 'Glyma.04G122550' => 'gma', 'Glyma.05G001600' => 'gma', 'Glyma.09G270766' => 'gma', 'Glyma.09G270832' => 'gma', 'Glyma.13G209800' => 'gma', 'Glyma.15G102800' => 'gma', 'Glyma.18G218900' => 'gma', 'Glyma.19G001500' => 'gma', 'Glyma.19G153600' => 'gma', 'Gohir.A02G028600' => 'ghi', 'Gohir.A08G045000' => 'ghi', 'Gohir.A11G120500' => 'ghi', 'Gohir.A12G006200' => 'ghi', 'Gohir.A12G006250' => 'ghi', 'Gohir.D02G036300' => 'ghi', 'Gohir.D08G054700' => 'ghi', 'Gohir.D11G125600' => 'ghi', 'Gohir.D12G005700' => 'ghi', 'Gorai.004G055200' => 'gra', 'Gorai.005G040400' => 'gra', 'Gorai.007G134500' => 'gra', 'Gorai.008G005500' => 'gra', 'GSVIVG01011094001' => 'vvi', 'GSVIVG01017879001' => 'vvi', 'GSVIVG01025988001' => 'vvi', 'GSVIVG01029847001' => 'vvi', 'HanXRQChr10g0282901' => 'han', 'HanXRQChr10g0310371' => 'han', 'HanXRQChr10g0315041' => 'han', 'HanXRQChr11g0327651' => 'han', 'HanXRQChr12g0359391' => 'han', 'Haze_00972' => 'cav', 'Haze_00973' => 'cav', 'Haze_00974' => 'cav', 'Haze_04747' => 'cav', 'Haze_04749' => 'cav', 'Haze_04750' => 'cav', 'Haze_21217' => 'cav', 'Hma1.2p1_1037F.1_g250680' => 'hma', 'Hma1.2p1_1644F.1_g295320' => 'hma', 'HPP92_011322' => 'vpl', 'HPP92_011323' => 'vpl', 'HPP92_011324' => 'vpl', 'HPP92_011325' => 'vpl', 'HPP92_011326' => 'vpl', 'Hund12205' => 'sun', 'Hund17957' => 'sun', 'Lalb_Chr06g0176771' => 'lal', 'Lalb_Chr18g0056021' => 'lal', 'Lalb_Chr18g0056031' => 'lal', 'Lalb_Chr18g0056041' => 'lal', 'Lalb_Chr20g0107751' => 'lal', 'Lalb_Chr20g0118371' => 'lal', 'Lj1g0010239' => 'lja', 'Lj1g0017101' => 'lja', 'Lj2A1178G40' => 'lonja', 'Lj2A54G84' => 'lonja', 'Lj2g0015248' => 'lja', 'Lj3A761T51' => 'lonja', 'Lj6g0018116' => 'lja', 'Lsat_1_v5_gn_4_136040' => 'lsa', 'Lsat_1_v5_gn_5_187461' => 'lsa', 'Lsat_1_v5_gn_5_77001' => 'lsa', 'Lsat_1_v5_gn_9_4461' => 'lsa', 'Manes.01G210100' => 'mes', 'Manes.03G185600' => 'mes', 'Manes.05G073300' => 'mes', 'Manes.09G120300' => 'mes', 'Manes.15G022100' => 'mes', 'Mapoly0096s0053' => 'mpo', 'MBI03_g14058_MAGBIO' => 'mbi', 'MBI03_g33876_MAGBIO' => 'mbi', 'MBI03_g36854_MAGBIO' => 'mbi', 'MBI17_g11997_MAGBIO' => 'mbi', 'MD03G1269000' => 'mdo', 'MD04G1179600' => 'mdo', 'MD11G1289800' => 'mdo', 'MD12G1194700' => 'mdo', 'MD13G1182100' => 'mdo', 'MD13G1182200' => 'mdo', 'MD16G1182600' => 'mdo', 'Medtr2g021400' => 'mtr', 'Medtr2g021470' => 'mtr', 'Medtr2g105810' => 'mtr', 'Medtr3g033580' => 'mtr', 'Medtr6g007970' => 'mtr', 'Medtr7g056330' => 'mtr', 'Medtr7g074290' => 'mtr', 'Medtr7g074380' => 'mtr', 'Medtr7g094550' => 'mtr', 'Medtr8g069995' => 'mtr', 'MELO3C014345.2' => 'cme', 'MELO3C021395.2' => 'cme', 'Migut.D00262' => 'egut', 'Migut.G00257' => 'egut', 'MSTRG.21575' => 'ama', 'MSTRG.3985' => 'ama', 'Nitab4.5_0000295g0140' => 'nta', 'Nitab4.5_0000732g0140' => 'nta', 'Nitab4.5_0003162g0020' => 'nta', 'Nitab4.5_0006180g0090' => 'nta', 'Nitab4.5_0006390g0010' => 'nta', 'Nitab4.5_0007392g0040' => 'nta', 'Nn1g02140' => 'nnu', 'Nn4g26168' => 'nnu', 'Nn5g26754' => 'nnu', 'Oeu001433.1' => 'oeu', 'Oeu010299.2' => 'oeu', 'Oeu011171.1' => 'oeu', 'Oeu037675.1' => 'oeu', 'Oeu038359.1' => 'oeu', 'Oeu063834.1' => 'oeu', 'Oeu063835.1' => 'oeu', 'Os05g0312000' => 'osa', 'Os07g0211101' => 'osa', 'Os07g0211200' => 'osa', 'Os07g0681500' => 'osa', 'Peaxi162Scf00095g01015' => 'pax', 'Peaxi162Scf00104g00329' => 'pax', 'Peaxi162Scf00161g00137' => 'pax', 'PGR004G1665' => 'pgr', 'PGR031G2937' => 'pgr', 'PGR119G2145' => 'pgr', 'PGSC0003DMG400004351' => 'stu', 'PGSC0003DMG400014625' => 'stu', 'PGSC0003DMG401000943' => 'stu', 'Phvul.001G148600' => 'pvu', 'Phvul.004G001700' => 'pvu', 'Phvul.006G154900' => 'pvu', 'Phvul.008G078200' => 'pvu', 'Phvul.011G136500' => 'pvu', 'Potri.002G215600' => 'ptr', 'Potri.008G201600' => 'ptr', 'Potri.014G138400' => 'ptr', 'Potri.016G142500' => 'ptr', 'Pp3c16_10580' => 'ppa', 'Pp3c5_25280' => 'ppa', 'Prupe.1G150000' => 'ppe', 'Prupe.1G150100' => 'ppe', 'Prupe.6G299600' => 'ppe', 'Prupe.8G245000' => 'ppe', 'Psat0s4927g0040' => 'psa', 'Psat1g052080' => 'psa', 'Psat1g183800' => 'psa', 'Psat3g113840' => 'psa', 'Psat3g126120' => 'psa', 'Psat3g126160' => 'psa', 'Psat3g158760' => 'psa', 'Psat3g158840' => 'psa', 'PSO170G2858' => 'pso', 'PSO339G0606' => 'pso', 'PSO384G4709' => 'pso', 'PSO407G0334' => 'pso', 'QL04p040276' => 'qlo', 'QL06p005458' => 'qlo', 'QL06p005472' => 'qlo', 'QL07p030546' => 'qlo', 'QL07p031519' => 'qlo', 'QL09p050949' => 'qlo', 'QL09p050966' => 'qlo', 'QL09p051067' => 'qlo', 'QL12p022706' => 'qlo', 'RcHm_v2.0_Chr2g0119601' => 'rch', 'RcHm_v2.0_Chr3g0459591' => 'rch', 'RcHm_v2.0_Chr4g0418521' => 'rch', 'RcHm_v2.0_Chr4g0418531' => 'rch', 'RcHm_v2.0_Chr4g0418541' => 'rch', 'RcHm_v2.0_Chr6g0291641' => 'rch', 'Rhsim01G0086300' => 'rsi', 'Rhsim01G0276300' => 'rsi', 'Rhsim01G0276500' => 'rsi', 'Rhsim04G0207700' => 'rsi', 'Rhsim05G0234500' => 'rsi', 'Rhsim13G0022400' => 'rsi', 'Sabra02G0167900' => 'sbr', 'Sabra04G0158500' => 'sbr', 'Sabra08G0159800' => 'sbr', 'Sabra10G0011500' => 'sbr', 'Sabra14G0104400' => 'sbr', 'SalBow2G2440' => 'sbo', 'SalBow4G2265' => 'sbo', 'Sc02g0000060' => 'sci', 'Sc05g0005020' => 'sci', 'Sc13g0003890' => 'sci', 'Sed0014865' => 'sed', 'Sed0017224' => 'sed', 'Sed0026391' => 'sed', 'SEGI_00063' => 'sgi', 'SEGI_10967' => 'sgi', 'SEGI_17510' => 'sgi', 'SEGI_24396' => 'sgi', 'SEGI_39719' => 'sgi', 'SEGI_41392' => 'sgi', 'SGA_v2.0_scaffold11G05794' => 'sas', 'SGA_v2.0_scaffold142G35607' => 'sas', 'SGA_v2.0_scaffold1G00447' => 'sas', 'SHI15388' => 'shi', 'SHI15394' => 'shi', 'SHI15396' => 'shi', 'SHI15399' => 'shi', 'SMO343G0151' => 'smo', 'SMO367G1118' => 'smo', 'Solyc01g080200.3' => 'sly', 'Solyc06g008960.3' => 'sly', 'Solyc09g064780.3' => 'sly', 'Sopen01g031980' => 'spe', 'Sopen06g003710' => 'spe', 'Sopen09g026460' => 'spe', 'Sp3g21240' => 'spa', 'Sp4g30030' => 'spa', 'TAR365G0022' => 'tar', 'TAR365G1023' => 'tar', 'TAR365G1253' => 'tar', 'TAR623G0078' => 'tar', 'TAR623G1721' => 'tar', 'TAR633G0959' => 'tar', 'THA.LOC104802225' => 'tha', 'THA.LOC104804769' => 'tha', 'THA.LOC104808660' => 'tha', 'THA.LOC104812792' => 'tha', 'Thecc.01G284000' => 'tca', 'Thecc.04G220600' => 'tca', 'Thecc.05G268900' => 'tca', 'Thecc.08G171100' => 'tca', 'Thhalv10001284m.g' => 'esa', 'Thhalv10019912m.g' => 'esa', 'TPR.G14189' => 'tpr', 'TPR.G18110' => 'tpr', 'TPR.G18130' => 'tpr', 'TPR.G18131' => 'tpr', 'TPR.G18140' => 'tpr', 'TPR.G24282' => 'tpr', 'TPR.G25221' => 'tpr', 'TPR.G29267' => 'tpr', 'TPR.G35315' => 'tpr', 'TPR.G36173' => 'tpr', 'TWI09G0794' => 'twi', 'TWI59G1348' => 'twi', 'TWI74G0430' => 'twi', 'unitig_26.g8940' => 'ugi', 'unitig_749.g13744' => 'ugi', 'unitig_749.g13745' => 'ugi', 'vmacro08269' => 'vma', 'vmacro14937' => 'vma', 'vmacro20401' => 'vma', 'VMungo0464G1349' => 'vmu', 'VMungo0540G0289' => 'vmu', 'VMungo1215G1590' => 'vmu', 'VMungo1309G0221' => 'vmu', 'VMungo1309G2815' => 'vmu', 'VMungo1383G0239' => 'vmu', 'VMungo1383G2910' => 'vmu', 'Zm00001eb095270' => 'zma', 'Zm00001eb095280' => 'zma', 'Zm00001eb111630' => 'zma', 'Zm00001eb237080' => 'zma', 'Zm00001eb273740' => 'zma', 'Zm00001eb285040' => 'zma', 'Zm00001eb330790' => 'zma', 'Zm00001eb337380' => 'zma' ), 'gf_id' => 'HOM05D001484', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001484' ), 'data_identifier' => 'HOM05D001484', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001484', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p31500' => 'bna', 'A05p00020' => 'bna', 'A07p08820' => 'bna', 'Aa31LG4G3300' => 'aar', 'Aa31LG8G10030' => 'aar', 'Actinidia00731' => 'ach', 'Actinidia11473' => 'ach', 'Actinidia23469' => 'ach', 'Actinidia24318' => 'ach', 'Actinidia40196' => 'ach', 'Actinidia40197' => 'ach', 'Actinidia40198' => 'ach', 'Ah.08g212990' => 'amhyb', 'Ah.15g091720' => 'amhyb', 'AL3G38260' => 'aly', 'AL4G47710' => 'aly', 'Aqoxy2G00671' => 'aox', 'Aqoxy2G03236' => 'aox', 'arahy.Tifrunner.gnm1.ann1.05IDCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KR684' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATY3SJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK6QJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6APGL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IDT7Z9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM073U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ0R87' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LE7RV4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT4QRX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V5ENPK' => 'arhy', 'AT2G48110' => 'ath', 'AT3G23590' => 'ath', 'ATR0626G186' => 'atr', 'ATR1127G141' => 'atr', 'Atru.chr4.2583' => 'acertr', 'Atru.chr5.1358' => 'acertr', 'Atru.chr5.1359' => 'acertr', 'Atru.chr8.46' => 'acertr', 'AUR62002640' => 'cqu', 'AUR62030055' => 'cqu', 'AUR62033713' => 'cqu', 'AUR62033714' => 'cqu', 'AUR62036795' => 'cqu', 'AUR62039891' => 'cqu', 'BcaB02g08737' => 'bca', 'BcaB04g20441' => 'bca', 'BcaB06g26509' => 'bca', 'BcaB06g26510' => 'bca', 'BcaB06g26511' => 'bca', 'BcaB06g26512' => 'bca', 'BcaB06g26513' => 'bca', 'BcaC02g12564' => 'bca', 'BcaC02g12565' => 'bca', 'BcaC02g12794' => 'bca', 'BcaC02g12795' => 'bca', 'BcaC02g12796' => 'bca', 'BcaC06g35541' => 'bca', 'BNapus_Darmor_BZH_scaffold_188p00080' => 'bna', 'BNapus_Darmor_BZH_scaffold_188p00090' => 'bna', 'BolC1t03972H' => 'bol', 'BolC1t03973H' => 'bol', 'BolC4t21680H' => 'bol', 'BolC7t41863H' => 'bol', 'BolSC55t61227H' => 'bol', 'BolSC55t61228H' => 'bol', 'BraA01t03278Z' => 'bra', 'BraA05t18998Z' => 'bra', 'BraA07t28673Z' => 'bra', 'C01p40150' => 'bna', 'C05p12370' => 'bna', 'C07p13680' => 'bna', 'CAN.G1006.16' => 'can', 'CAN.G1006.17' => 'can', 'CAN.G1170.2' => 'can', 'CAN.G962.7' => 'can', 'CANSAT25G2179' => 'cansat', 'CANSAT78G1573' => 'cansat', 'CARHR099510' => 'chi', 'CARHR143510' => 'chi', 'Carub.0003s2380' => 'cru', 'Carub.0004s3082' => 'cru', 'Ca_00614_v3' => 'car', 'Ca_07801_v3' => 'car', 'Ca_08567_v3' => 'car', 'Ca_09571_v3' => 'car', 'CBR_g19290' => 'cbr', 'Cc01_g19770' => 'ccan', 'Cc03_g03030' => 'ccan', 'CDE07G0968' => 'cde', 'CDE09G1441' => 'cde', 'Cfa006103' => 'cfa', 'Cfa015573' => 'cfa', 'Cfa016988' => 'cfa', 'Ciclev10006738m.g' => 'ccl', 'Ciclev10010920m.g' => 'ccl', 'Ciclev10018517m.g' => 'ccl', 'CiPaw.01G159200' => 'cil', 'CiPaw.02G091000' => 'cil', 'CiPaw.02G091100' => 'cil', 'CiPaw.08G103100' => 'cil', 'CiPaw.09G224900' => 'cil', 'ClCG06G005740' => 'cla', 'ClCG07G000090' => 'cla', 'ClCG07G000100' => 'cla', 'COL.COLO4_09143' => 'col', 'COL.COLO4_25124' => 'col', 'Cpa.g.sc16.34' => 'cpa', 'Cpa.g.sc3504.1' => 'cpa', 'Cpa.g.sc60.37' => 'cpa', 'CsaV3_6G018520' => 'csa', 'CsaV3_6G036860' => 'csa', 'CSS0001072' => 'camsi', 'CSS0020208' => 'camsi', 'CSS0021253' => 'camsi', 'CSS0022190' => 'camsi', 'CSS0036150' => 'camsi', 'CSS0040442' => 'camsi', 'CSS0042300' => 'camsi', 'CSS0045298' => 'camsi', 'DCAR_012449' => 'dca', 'DCAR_018405' => 'dca', 'DCAR_024573' => 'dca', 'DCAR_030591' => 'dca', 'Dinv16926' => 'din', 'Dinv32963' => 'din', 'Dinv38382' => 'din', 'Dinv38383' => 'din', 'Duzib133G0974' => 'dzi', 'Duzib138G1867' => 'dzi', 'Duzib211G0420' => 'dzi', 'Duzib212G0930' => 'dzi', 'ECA234G1645' => 'eca', 'ECA247G3467' => 'eca', 'ECA248G1703' => 'eca', 'EL10Ac3g06327' => 'bvu', 'EL10Ac7g17204' => 'bvu', 'Eucgr.A00855' => 'egr', 'Eucgr.A00858' => 'egr', 'Eucgr.H01520' => 'egr', 'Eucgr.H03604' => 'egr', 'Eucgr.L03465' => 'egr', 'Eucgr.L03466' => 'egr', 'FAN01G0988' => 'fan', 'FAN02G3892' => 'fan', 'FAN05G3381' => 'fan', 'FAN07G0967' => 'fan', 'FAN07G1493' => 'fan', 'FAN08G3125' => 'fan', 'FAN09G0402' => 'fan', 'FAN12G2594' => 'fan', 'FAN12G3879' => 'fan', 'FAN14G1546' => 'fan', 'FAN15G3626' => 'fan', 'FAN17G0588' => 'fan', 'FAN17G0609' => 'fan', 'FAN18G2817' => 'fan', 'FAN19G1305' => 'fan', 'FAN20G1787' => 'fan', 'FAN22G0073' => 'fan', 'FAN22G0352' => 'fan', 'FAN22G0368' => 'fan', 'FAN22G2273' => 'fan', 'FAN24G1998' => 'fan', 'FAN27G1317' => 'fan', 'FvH4_2g23980' => 'fve', 'FvH4_4g14380' => 'fve', 'FvH4_4g14390' => 'fve', 'FvH4_6g09250' => 'fve', 'Glyma.03G151100' => 'gma', 'Glyma.04G122550' => 'gma', 'Glyma.05G001600' => 'gma', 'Glyma.09G270766' => 'gma', 'Glyma.09G270832' => 'gma', 'Glyma.13G209800' => 'gma', 'Glyma.15G102800' => 'gma', 'Glyma.18G218900' => 'gma', 'Glyma.19G001500' => 'gma', 'Glyma.19G153600' => 'gma', 'Gohir.A02G028600' => 'ghi', 'Gohir.A08G045000' => 'ghi', 'Gohir.A11G120500' => 'ghi', 'Gohir.A12G006200' => 'ghi', 'Gohir.A12G006250' => 'ghi', 'Gohir.D02G036300' => 'ghi', 'Gohir.D08G054700' => 'ghi', 'Gohir.D11G125600' => 'ghi', 'Gohir.D12G005700' => 'ghi', 'Gorai.004G055200' => 'gra', 'Gorai.005G040400' => 'gra', 'Gorai.007G134500' => 'gra', 'Gorai.008G005500' => 'gra', 'GSVIVG01011094001' => 'vvi', 'GSVIVG01017879001' => 'vvi', 'GSVIVG01025988001' => 'vvi', 'GSVIVG01029847001' => 'vvi', 'HanXRQChr10g0282901' => 'han', 'HanXRQChr10g0310371' => 'han', 'HanXRQChr10g0315041' => 'han', 'HanXRQChr11g0327651' => 'han', 'HanXRQChr12g0359391' => 'han', 'Haze_00972' => 'cav', 'Haze_00973' => 'cav', 'Haze_00974' => 'cav', 'Haze_04747' => 'cav', 'Haze_04749' => 'cav', 'Haze_04750' => 'cav', 'Haze_21217' => 'cav', 'Hma1.2p1_1037F.1_g250680' => 'hma', 'Hma1.2p1_1644F.1_g295320' => 'hma', 'HPP92_011322' => 'vpl', 'HPP92_011323' => 'vpl', 'HPP92_011324' => 'vpl', 'HPP92_011325' => 'vpl', 'HPP92_011326' => 'vpl', 'Hund12205' => 'sun', 'Hund17957' => 'sun', 'Lalb_Chr06g0176771' => 'lal', 'Lalb_Chr18g0056021' => 'lal', 'Lalb_Chr18g0056031' => 'lal', 'Lalb_Chr18g0056041' => 'lal', 'Lalb_Chr20g0107751' => 'lal', 'Lalb_Chr20g0118371' => 'lal', 'Lj1g0010239' => 'lja', 'Lj1g0017101' => 'lja', 'Lj2A1178G40' => 'lonja', 'Lj2A54G84' => 'lonja', 'Lj2g0015248' => 'lja', 'Lj3A761T51' => 'lonja', 'Lj6g0018116' => 'lja', 'Lsat_1_v5_gn_4_136040' => 'lsa', 'Lsat_1_v5_gn_5_187461' => 'lsa', 'Lsat_1_v5_gn_5_77001' => 'lsa', 'Lsat_1_v5_gn_9_4461' => 'lsa', 'Manes.01G210100' => 'mes', 'Manes.03G185600' => 'mes', 'Manes.05G073300' => 'mes', 'Manes.09G120300' => 'mes', 'Manes.15G022100' => 'mes', 'Mapoly0096s0053' => 'mpo', 'MBI03_g14058_MAGBIO' => 'mbi', 'MBI03_g33876_MAGBIO' => 'mbi', 'MBI03_g36854_MAGBIO' => 'mbi', 'MBI17_g11997_MAGBIO' => 'mbi', 'MD03G1269000' => 'mdo', 'MD04G1179600' => 'mdo', 'MD11G1289800' => 'mdo', 'MD12G1194700' => 'mdo', 'MD13G1182100' => 'mdo', 'MD13G1182200' => 'mdo', 'MD16G1182600' => 'mdo', 'Medtr2g021400' => 'mtr', 'Medtr2g021470' => 'mtr', 'Medtr2g105810' => 'mtr', 'Medtr3g033580' => 'mtr', 'Medtr6g007970' => 'mtr', 'Medtr7g056330' => 'mtr', 'Medtr7g074290' => 'mtr', 'Medtr7g074380' => 'mtr', 'Medtr7g094550' => 'mtr', 'Medtr8g069995' => 'mtr', 'MELO3C014345.2' => 'cme', 'MELO3C021395.2' => 'cme', 'Migut.D00262' => 'egut', 'Migut.G00257' => 'egut', 'MSTRG.21575' => 'ama', 'MSTRG.3985' => 'ama', 'Nitab4.5_0000295g0140' => 'nta', 'Nitab4.5_0000732g0140' => 'nta', 'Nitab4.5_0003162g0020' => 'nta', 'Nitab4.5_0006180g0090' => 'nta', 'Nitab4.5_0006390g0010' => 'nta', 'Nitab4.5_0007392g0040' => 'nta', 'Nn1g02140' => 'nnu', 'Nn4g26168' => 'nnu', 'Nn5g26754' => 'nnu', 'Oeu001433.1' => 'oeu', 'Oeu010299.2' => 'oeu', 'Oeu011171.1' => 'oeu', 'Oeu037675.1' => 'oeu', 'Oeu038359.1' => 'oeu', 'Oeu063834.1' => 'oeu', 'Oeu063835.1' => 'oeu', 'Os05g0312000' => 'osa', 'Os07g0211101' => 'osa', 'Os07g0211200' => 'osa', 'Os07g0681500' => 'osa', 'Peaxi162Scf00095g01015' => 'pax', 'Peaxi162Scf00104g00329' => 'pax', 'Peaxi162Scf00161g00137' => 'pax', 'PGR004G1665' => 'pgr', 'PGR031G2937' => 'pgr', 'PGR119G2145' => 'pgr', 'PGSC0003DMG400004351' => 'stu', 'PGSC0003DMG400014625' => 'stu', 'PGSC0003DMG401000943' => 'stu', 'Phvul.001G148600' => 'pvu', 'Phvul.004G001700' => 'pvu', 'Phvul.006G154900' => 'pvu', 'Phvul.008G078200' => 'pvu', 'Phvul.011G136500' => 'pvu', 'Potri.002G215600' => 'ptr', 'Potri.008G201600' => 'ptr', 'Potri.014G138400' => 'ptr', 'Potri.016G142500' => 'ptr', 'Pp3c16_10580' => 'ppa', 'Pp3c5_25280' => 'ppa', 'Prupe.1G150000' => 'ppe', 'Prupe.1G150100' => 'ppe', 'Prupe.6G299600' => 'ppe', 'Prupe.8G245000' => 'ppe', 'Psat0s4927g0040' => 'psa', 'Psat1g052080' => 'psa', 'Psat1g183800' => 'psa', 'Psat3g113840' => 'psa', 'Psat3g126120' => 'psa', 'Psat3g126160' => 'psa', 'Psat3g158760' => 'psa', 'Psat3g158840' => 'psa', 'PSO170G2858' => 'pso', 'PSO339G0606' => 'pso', 'PSO384G4709' => 'pso', 'PSO407G0334' => 'pso', 'QL04p040276' => 'qlo', 'QL06p005458' => 'qlo', 'QL06p005472' => 'qlo', 'QL07p030546' => 'qlo', 'QL07p031519' => 'qlo', 'QL09p050949' => 'qlo', 'QL09p050966' => 'qlo', 'QL09p051067' => 'qlo', 'QL12p022706' => 'qlo', 'RcHm_v2.0_Chr2g0119601' => 'rch', 'RcHm_v2.0_Chr3g0459591' => 'rch', 'RcHm_v2.0_Chr4g0418521' => 'rch', 'RcHm_v2.0_Chr4g0418531' => 'rch', 'RcHm_v2.0_Chr4g0418541' => 'rch', 'RcHm_v2.0_Chr6g0291641' => 'rch', 'Rhsim01G0086300' => 'rsi', 'Rhsim01G0276300' => 'rsi', 'Rhsim01G0276500' => 'rsi', 'Rhsim04G0207700' => 'rsi', 'Rhsim05G0234500' => 'rsi', 'Rhsim13G0022400' => 'rsi', 'Sabra02G0167900' => 'sbr', 'Sabra04G0158500' => 'sbr', 'Sabra08G0159800' => 'sbr', 'Sabra10G0011500' => 'sbr', 'Sabra14G0104400' => 'sbr', 'SalBow2G2440' => 'sbo', 'SalBow4G2265' => 'sbo', 'Sc02g0000060' => 'sci', 'Sc05g0005020' => 'sci', 'Sc13g0003890' => 'sci', 'Sed0014865' => 'sed', 'Sed0017224' => 'sed', 'Sed0026391' => 'sed', 'SEGI_00063' => 'sgi', 'SEGI_10967' => 'sgi', 'SEGI_17510' => 'sgi', 'SEGI_24396' => 'sgi', 'SEGI_39719' => 'sgi', 'SEGI_41392' => 'sgi', 'SGA_v2.0_scaffold11G05794' => 'sas', 'SGA_v2.0_scaffold142G35607' => 'sas', 'SGA_v2.0_scaffold1G00447' => 'sas', 'SHI15388' => 'shi', 'SHI15394' => 'shi', 'SHI15396' => 'shi', 'SHI15399' => 'shi', 'SMO343G0151' => 'smo', 'SMO367G1118' => 'smo', 'Solyc01g080200.3' => 'sly', 'Solyc06g008960.3' => 'sly', 'Solyc09g064780.3' => 'sly', 'Sopen01g031980' => 'spe', 'Sopen06g003710' => 'spe', 'Sopen09g026460' => 'spe', 'Sp3g21240' => 'spa', 'Sp4g30030' => 'spa', 'TAR365G0022' => 'tar', 'TAR365G1023' => 'tar', 'TAR365G1253' => 'tar', 'TAR623G0078' => 'tar', 'TAR623G1721' => 'tar', 'TAR633G0959' => 'tar', 'THA.LOC104802225' => 'tha', 'THA.LOC104804769' => 'tha', 'THA.LOC104808660' => 'tha', 'THA.LOC104812792' => 'tha', 'Thecc.01G284000' => 'tca', 'Thecc.04G220600' => 'tca', 'Thecc.05G268900' => 'tca', 'Thecc.08G171100' => 'tca', 'Thhalv10001284m.g' => 'esa', 'Thhalv10019912m.g' => 'esa', 'TPR.G14189' => 'tpr', 'TPR.G18110' => 'tpr', 'TPR.G18130' => 'tpr', 'TPR.G18131' => 'tpr', 'TPR.G18140' => 'tpr', 'TPR.G24282' => 'tpr', 'TPR.G25221' => 'tpr', 'TPR.G29267' => 'tpr', 'TPR.G35315' => 'tpr', 'TPR.G36173' => 'tpr', 'TWI09G0794' => 'twi', 'TWI59G1348' => 'twi', 'TWI74G0430' => 'twi', 'unitig_26.g8940' => 'ugi', 'unitig_749.g13744' => 'ugi', 'unitig_749.g13745' => 'ugi', 'vmacro08269' => 'vma', 'vmacro14937' => 'vma', 'vmacro20401' => 'vma', 'VMungo0464G1349' => 'vmu', 'VMungo0540G0289' => 'vmu', 'VMungo1215G1590' => 'vmu', 'VMungo1309G0221' => 'vmu', 'VMungo1309G2815' => 'vmu', 'VMungo1383G0239' => 'vmu', 'VMungo1383G2910' => 'vmu', 'Zm00001eb095270' => 'zma', 'Zm00001eb095280' => 'zma', 'Zm00001eb111630' => 'zma', 'Zm00001eb237080' => 'zma', 'Zm00001eb273740' => 'zma', 'Zm00001eb285040' => 'zma', 'Zm00001eb330790' => 'zma', 'Zm00001eb337380' => 'zma' ) $gf_id = 'HOM05D001484' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001484' ) $data_identifier = 'HOM05D001484' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 2, 'aly' => (int) 2, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 22, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 7, 'hma' => (int) 2, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 7, 'mtr' => (int) 10, 'cme' => (int) 2, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 4, 'ppa' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 4, 'qlo' => (int) 9, 'rch' => (int) 6, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 10, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 7, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb337380' $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' => 'HOM05D001484', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p31500' => 'bna', 'A05p00020' => 'bna', 'A07p08820' => 'bna', 'Aa31LG4G3300' => 'aar', 'Aa31LG8G10030' => 'aar', 'Actinidia00731' => 'ach', 'Actinidia11473' => 'ach', 'Actinidia23469' => 'ach', 'Actinidia24318' => 'ach', 'Actinidia40196' => 'ach', 'Actinidia40197' => 'ach', 'Actinidia40198' => 'ach', 'Ah.08g212990' => 'amhyb', 'Ah.15g091720' => 'amhyb', 'AL3G38260' => 'aly', 'AL4G47710' => 'aly', 'Aqoxy2G00671' => 'aox', 'Aqoxy2G03236' => 'aox', 'arahy.Tifrunner.gnm1.ann1.05IDCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KR684' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATY3SJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK6QJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6APGL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IDT7Z9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM073U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ0R87' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LE7RV4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT4QRX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V5ENPK' => 'arhy', 'AT2G48110' => 'ath', 'AT3G23590' => 'ath', 'ATR0626G186' => 'atr', 'ATR1127G141' => 'atr', 'Atru.chr4.2583' => 'acertr', 'Atru.chr5.1358' => 'acertr', 'Atru.chr5.1359' => 'acertr', 'Atru.chr8.46' => 'acertr', 'AUR62002640' => 'cqu', 'AUR62030055' => 'cqu', 'AUR62033713' => 'cqu', 'AUR62033714' => 'cqu', 'AUR62036795' => 'cqu', 'AUR62039891' => 'cqu', 'BcaB02g08737' => 'bca', 'BcaB04g20441' => 'bca', 'BcaB06g26509' => 'bca', 'BcaB06g26510' => 'bca', 'BcaB06g26511' => 'bca', 'BcaB06g26512' => 'bca', 'BcaB06g26513' => 'bca', 'BcaC02g12564' => 'bca', 'BcaC02g12565' => 'bca', 'BcaC02g12794' => 'bca', 'BcaC02g12795' => 'bca', 'BcaC02g12796' => 'bca', 'BcaC06g35541' => 'bca', 'BNapus_Darmor_BZH_scaffold_188p00080' => 'bna', 'BNapus_Darmor_BZH_scaffold_188p00090' => 'bna', 'BolC1t03972H' => 'bol', 'BolC1t03973H' => 'bol', 'BolC4t21680H' => 'bol', 'BolC7t41863H' => 'bol', 'BolSC55t61227H' => 'bol', 'BolSC55t61228H' => 'bol', 'BraA01t03278Z' => 'bra', 'BraA05t18998Z' => 'bra', 'BraA07t28673Z' => 'bra', 'C01p40150' => 'bna', 'C05p12370' => 'bna', 'C07p13680' => 'bna', 'CAN.G1006.16' => 'can', 'CAN.G1006.17' => 'can', 'CAN.G1170.2' => 'can', 'CAN.G962.7' => 'can', 'CANSAT25G2179' => 'cansat', 'CANSAT78G1573' => 'cansat', 'CARHR099510' => 'chi', 'CARHR143510' => 'chi', 'Carub.0003s2380' => 'cru', 'Carub.0004s3082' => 'cru', 'Ca_00614_v3' => 'car', 'Ca_07801_v3' => 'car', 'Ca_08567_v3' => 'car', 'Ca_09571_v3' => 'car', 'CBR_g19290' => 'cbr', 'Cc01_g19770' => 'ccan', 'Cc03_g03030' => 'ccan', 'CDE07G0968' => 'cde', 'CDE09G1441' => 'cde', 'Cfa006103' => 'cfa', 'Cfa015573' => 'cfa', 'Cfa016988' => 'cfa', 'Ciclev10006738m.g' => 'ccl', 'Ciclev10010920m.g' => 'ccl', 'Ciclev10018517m.g' => 'ccl', 'CiPaw.01G159200' => 'cil', 'CiPaw.02G091000' => 'cil', 'CiPaw.02G091100' => 'cil', 'CiPaw.08G103100' => 'cil', 'CiPaw.09G224900' => 'cil', 'ClCG06G005740' => 'cla', 'ClCG07G000090' => 'cla', 'ClCG07G000100' => 'cla', 'COL.COLO4_09143' => 'col', 'COL.COLO4_25124' => 'col', 'Cpa.g.sc16.34' => 'cpa', 'Cpa.g.sc3504.1' => 'cpa', 'Cpa.g.sc60.37' => 'cpa', 'CsaV3_6G018520' => 'csa', 'CsaV3_6G036860' => 'csa', 'CSS0001072' => 'camsi', 'CSS0020208' => 'camsi', 'CSS0021253' => 'camsi', 'CSS0022190' => 'camsi', 'CSS0036150' => 'camsi', 'CSS0040442' => 'camsi', 'CSS0042300' => 'camsi', 'CSS0045298' => 'camsi', 'DCAR_012449' => 'dca', 'DCAR_018405' => 'dca', 'DCAR_024573' => 'dca', 'DCAR_030591' => 'dca', 'Dinv16926' => 'din', 'Dinv32963' => 'din', 'Dinv38382' => 'din', 'Dinv38383' => 'din', 'Duzib133G0974' => 'dzi', 'Duzib138G1867' => 'dzi', 'Duzib211G0420' => 'dzi', 'Duzib212G0930' => 'dzi', 'ECA234G1645' => 'eca', 'ECA247G3467' => 'eca', 'ECA248G1703' => 'eca', 'EL10Ac3g06327' => 'bvu', 'EL10Ac7g17204' => 'bvu', 'Eucgr.A00855' => 'egr', 'Eucgr.A00858' => 'egr', 'Eucgr.H01520' => 'egr', 'Eucgr.H03604' => 'egr', 'Eucgr.L03465' => 'egr', 'Eucgr.L03466' => 'egr', 'FAN01G0988' => 'fan', 'FAN02G3892' => 'fan', 'FAN05G3381' => 'fan', 'FAN07G0967' => 'fan', 'FAN07G1493' => 'fan', 'FAN08G3125' => 'fan', 'FAN09G0402' => 'fan', 'FAN12G2594' => 'fan', 'FAN12G3879' => 'fan', 'FAN14G1546' => 'fan', 'FAN15G3626' => 'fan', 'FAN17G0588' => 'fan', 'FAN17G0609' => 'fan', 'FAN18G2817' => 'fan', 'FAN19G1305' => 'fan', 'FAN20G1787' => 'fan', 'FAN22G0073' => 'fan', 'FAN22G0352' => 'fan', 'FAN22G0368' => 'fan', 'FAN22G2273' => 'fan', 'FAN24G1998' => 'fan', 'FAN27G1317' => 'fan', 'FvH4_2g23980' => 'fve', 'FvH4_4g14380' => 'fve', 'FvH4_4g14390' => 'fve', 'FvH4_6g09250' => 'fve', 'Glyma.03G151100' => 'gma', 'Glyma.04G122550' => 'gma', 'Glyma.05G001600' => 'gma', 'Glyma.09G270766' => 'gma', 'Glyma.09G270832' => 'gma', 'Glyma.13G209800' => 'gma', 'Glyma.15G102800' => 'gma', 'Glyma.18G218900' => 'gma', 'Glyma.19G001500' => 'gma', 'Glyma.19G153600' => 'gma', 'Gohir.A02G028600' => 'ghi', 'Gohir.A08G045000' => 'ghi', 'Gohir.A11G120500' => 'ghi', 'Gohir.A12G006200' => 'ghi', 'Gohir.A12G006250' => 'ghi', 'Gohir.D02G036300' => 'ghi', 'Gohir.D08G054700' => 'ghi', 'Gohir.D11G125600' => 'ghi', 'Gohir.D12G005700' => 'ghi', 'Gorai.004G055200' => 'gra', 'Gorai.005G040400' => 'gra', 'Gorai.007G134500' => 'gra', 'Gorai.008G005500' => 'gra', 'GSVIVG01011094001' => 'vvi', 'GSVIVG01017879001' => 'vvi', 'GSVIVG01025988001' => 'vvi', 'GSVIVG01029847001' => 'vvi', 'HanXRQChr10g0282901' => 'han', 'HanXRQChr10g0310371' => 'han', 'HanXRQChr10g0315041' => 'han', 'HanXRQChr11g0327651' => 'han', 'HanXRQChr12g0359391' => 'han', 'Haze_00972' => 'cav', 'Haze_00973' => 'cav', 'Haze_00974' => 'cav', 'Haze_04747' => 'cav', 'Haze_04749' => 'cav', 'Haze_04750' => 'cav', 'Haze_21217' => 'cav', 'Hma1.2p1_1037F.1_g250680' => 'hma', 'Hma1.2p1_1644F.1_g295320' => 'hma', 'HPP92_011322' => 'vpl', 'HPP92_011323' => 'vpl', 'HPP92_011324' => 'vpl', 'HPP92_011325' => 'vpl', 'HPP92_011326' => 'vpl', 'Hund12205' => 'sun', 'Hund17957' => 'sun', 'Lalb_Chr06g0176771' => 'lal', 'Lalb_Chr18g0056021' => 'lal', 'Lalb_Chr18g0056031' => 'lal', 'Lalb_Chr18g0056041' => 'lal', 'Lalb_Chr20g0107751' => 'lal', 'Lalb_Chr20g0118371' => 'lal', 'Lj1g0010239' => 'lja', 'Lj1g0017101' => 'lja', 'Lj2A1178G40' => 'lonja', 'Lj2A54G84' => 'lonja', 'Lj2g0015248' => 'lja', 'Lj3A761T51' => 'lonja', 'Lj6g0018116' => 'lja', 'Lsat_1_v5_gn_4_136040' => 'lsa', 'Lsat_1_v5_gn_5_187461' => 'lsa', 'Lsat_1_v5_gn_5_77001' => 'lsa', 'Lsat_1_v5_gn_9_4461' => 'lsa', 'Manes.01G210100' => 'mes', 'Manes.03G185600' => 'mes', 'Manes.05G073300' => 'mes', 'Manes.09G120300' => 'mes', 'Manes.15G022100' => 'mes', 'Mapoly0096s0053' => 'mpo', 'MBI03_g14058_MAGBIO' => 'mbi', 'MBI03_g33876_MAGBIO' => 'mbi', 'MBI03_g36854_MAGBIO' => 'mbi', 'MBI17_g11997_MAGBIO' => 'mbi', 'MD03G1269000' => 'mdo', 'MD04G1179600' => 'mdo', 'MD11G1289800' => 'mdo', 'MD12G1194700' => 'mdo', 'MD13G1182100' => 'mdo', 'MD13G1182200' => 'mdo', 'MD16G1182600' => 'mdo', 'Medtr2g021400' => 'mtr', 'Medtr2g021470' => 'mtr', 'Medtr2g105810' => 'mtr', 'Medtr3g033580' => 'mtr', 'Medtr6g007970' => 'mtr', 'Medtr7g056330' => 'mtr', 'Medtr7g074290' => 'mtr', 'Medtr7g074380' => 'mtr', 'Medtr7g094550' => 'mtr', 'Medtr8g069995' => 'mtr', 'MELO3C014345.2' => 'cme', 'MELO3C021395.2' => 'cme', 'Migut.D00262' => 'egut', 'Migut.G00257' => 'egut', 'MSTRG.21575' => 'ama', 'MSTRG.3985' => 'ama', 'Nitab4.5_0000295g0140' => 'nta', 'Nitab4.5_0000732g0140' => 'nta', 'Nitab4.5_0003162g0020' => 'nta', 'Nitab4.5_0006180g0090' => 'nta', 'Nitab4.5_0006390g0010' => 'nta', 'Nitab4.5_0007392g0040' => 'nta', 'Nn1g02140' => 'nnu', 'Nn4g26168' => 'nnu', 'Nn5g26754' => 'nnu', 'Oeu001433.1' => 'oeu', 'Oeu010299.2' => 'oeu', 'Oeu011171.1' => 'oeu', 'Oeu037675.1' => 'oeu', 'Oeu038359.1' => 'oeu', 'Oeu063834.1' => 'oeu', 'Oeu063835.1' => 'oeu', 'Os05g0312000' => 'osa', 'Os07g0211101' => 'osa', 'Os07g0211200' => 'osa', 'Os07g0681500' => 'osa', 'Peaxi162Scf00095g01015' => 'pax', 'Peaxi162Scf00104g00329' => 'pax', 'Peaxi162Scf00161g00137' => 'pax', 'PGR004G1665' => 'pgr', 'PGR031G2937' => 'pgr', 'PGR119G2145' => 'pgr', 'PGSC0003DMG400004351' => 'stu', 'PGSC0003DMG400014625' => 'stu', 'PGSC0003DMG401000943' => 'stu', 'Phvul.001G148600' => 'pvu', 'Phvul.004G001700' => 'pvu', 'Phvul.006G154900' => 'pvu', 'Phvul.008G078200' => 'pvu', 'Phvul.011G136500' => 'pvu', 'Potri.002G215600' => 'ptr', 'Potri.008G201600' => 'ptr', 'Potri.014G138400' => 'ptr', 'Potri.016G142500' => 'ptr', 'Pp3c16_10580' => 'ppa', 'Pp3c5_25280' => 'ppa', 'Prupe.1G150000' => 'ppe', 'Prupe.1G150100' => 'ppe', 'Prupe.6G299600' => 'ppe', 'Prupe.8G245000' => 'ppe', 'Psat0s4927g0040' => 'psa', 'Psat1g052080' => 'psa', 'Psat1g183800' => 'psa', 'Psat3g113840' => 'psa', 'Psat3g126120' => 'psa', 'Psat3g126160' => 'psa', 'Psat3g158760' => 'psa', 'Psat3g158840' => 'psa', 'PSO170G2858' => 'pso', 'PSO339G0606' => 'pso', 'PSO384G4709' => 'pso', 'PSO407G0334' => 'pso', 'QL04p040276' => 'qlo', 'QL06p005458' => 'qlo', 'QL06p005472' => 'qlo', 'QL07p030546' => 'qlo', 'QL07p031519' => 'qlo', 'QL09p050949' => 'qlo', 'QL09p050966' => 'qlo', 'QL09p051067' => 'qlo', 'QL12p022706' => 'qlo', 'RcHm_v2.0_Chr2g0119601' => 'rch', 'RcHm_v2.0_Chr3g0459591' => 'rch', 'RcHm_v2.0_Chr4g0418521' => 'rch', 'RcHm_v2.0_Chr4g0418531' => 'rch', 'RcHm_v2.0_Chr4g0418541' => 'rch', 'RcHm_v2.0_Chr6g0291641' => 'rch', 'Rhsim01G0086300' => 'rsi', 'Rhsim01G0276300' => 'rsi', 'Rhsim01G0276500' => 'rsi', 'Rhsim04G0207700' => 'rsi', 'Rhsim05G0234500' => 'rsi', 'Rhsim13G0022400' => 'rsi', 'Sabra02G0167900' => 'sbr', 'Sabra04G0158500' => 'sbr', 'Sabra08G0159800' => 'sbr', 'Sabra10G0011500' => 'sbr', 'Sabra14G0104400' => 'sbr', 'SalBow2G2440' => 'sbo', 'SalBow4G2265' => 'sbo', 'Sc02g0000060' => 'sci', 'Sc05g0005020' => 'sci', 'Sc13g0003890' => 'sci', 'Sed0014865' => 'sed', 'Sed0017224' => 'sed', 'Sed0026391' => 'sed', 'SEGI_00063' => 'sgi', 'SEGI_10967' => 'sgi', 'SEGI_17510' => 'sgi', 'SEGI_24396' => 'sgi', 'SEGI_39719' => 'sgi', 'SEGI_41392' => 'sgi', 'SGA_v2.0_scaffold11G05794' => 'sas', 'SGA_v2.0_scaffold142G35607' => 'sas', 'SGA_v2.0_scaffold1G00447' => 'sas', 'SHI15388' => 'shi', 'SHI15394' => 'shi', 'SHI15396' => 'shi', 'SHI15399' => 'shi', 'SMO343G0151' => 'smo', 'SMO367G1118' => 'smo', 'Solyc01g080200.3' => 'sly', 'Solyc06g008960.3' => 'sly', 'Solyc09g064780.3' => 'sly', 'Sopen01g031980' => 'spe', 'Sopen06g003710' => 'spe', 'Sopen09g026460' => 'spe', 'Sp3g21240' => 'spa', 'Sp4g30030' => 'spa', 'TAR365G0022' => 'tar', 'TAR365G1023' => 'tar', 'TAR365G1253' => 'tar', 'TAR623G0078' => 'tar', 'TAR623G1721' => 'tar', 'TAR633G0959' => 'tar', 'THA.LOC104802225' => 'tha', 'THA.LOC104804769' => 'tha', 'THA.LOC104808660' => 'tha', 'THA.LOC104812792' => 'tha', 'Thecc.01G284000' => 'tca', 'Thecc.04G220600' => 'tca', 'Thecc.05G268900' => 'tca', 'Thecc.08G171100' => 'tca', 'Thhalv10001284m.g' => 'esa', 'Thhalv10019912m.g' => 'esa', 'TPR.G14189' => 'tpr', 'TPR.G18110' => 'tpr', 'TPR.G18130' => 'tpr', 'TPR.G18131' => 'tpr', 'TPR.G18140' => 'tpr', 'TPR.G24282' => 'tpr', 'TPR.G25221' => 'tpr', 'TPR.G29267' => 'tpr', 'TPR.G35315' => 'tpr', 'TPR.G36173' => 'tpr', 'TWI09G0794' => 'twi', 'TWI59G1348' => 'twi', 'TWI74G0430' => 'twi', 'unitig_26.g8940' => 'ugi', 'unitig_749.g13744' => 'ugi', 'unitig_749.g13745' => 'ugi', 'vmacro08269' => 'vma', 'vmacro14937' => 'vma', 'vmacro20401' => 'vma', 'VMungo0464G1349' => 'vmu', 'VMungo0540G0289' => 'vmu', 'VMungo1215G1590' => 'vmu', 'VMungo1309G0221' => 'vmu', 'VMungo1309G2815' => 'vmu', 'VMungo1383G0239' => 'vmu', 'VMungo1383G2910' => 'vmu', 'Zm00001eb095270' => 'zma', 'Zm00001eb095280' => 'zma', 'Zm00001eb111630' => 'zma', 'Zm00001eb237080' => 'zma', 'Zm00001eb273740' => 'zma', 'Zm00001eb285040' => 'zma', 'Zm00001eb330790' => 'zma', 'Zm00001eb337380' => 'zma' ), 'gf_id' => 'HOM05D001484', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001484' ), 'data_identifier' => 'HOM05D001484', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001484', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p31500' => 'bna', 'A05p00020' => 'bna', 'A07p08820' => 'bna', 'Aa31LG4G3300' => 'aar', 'Aa31LG8G10030' => 'aar', 'Actinidia00731' => 'ach', 'Actinidia11473' => 'ach', 'Actinidia23469' => 'ach', 'Actinidia24318' => 'ach', 'Actinidia40196' => 'ach', 'Actinidia40197' => 'ach', 'Actinidia40198' => 'ach', 'Ah.08g212990' => 'amhyb', 'Ah.15g091720' => 'amhyb', 'AL3G38260' => 'aly', 'AL4G47710' => 'aly', 'Aqoxy2G00671' => 'aox', 'Aqoxy2G03236' => 'aox', 'arahy.Tifrunner.gnm1.ann1.05IDCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KR684' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATY3SJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK6QJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6APGL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IDT7Z9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM073U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ0R87' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LE7RV4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT4QRX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V5ENPK' => 'arhy', 'AT2G48110' => 'ath', 'AT3G23590' => 'ath', 'ATR0626G186' => 'atr', 'ATR1127G141' => 'atr', 'Atru.chr4.2583' => 'acertr', 'Atru.chr5.1358' => 'acertr', 'Atru.chr5.1359' => 'acertr', 'Atru.chr8.46' => 'acertr', 'AUR62002640' => 'cqu', 'AUR62030055' => 'cqu', 'AUR62033713' => 'cqu', 'AUR62033714' => 'cqu', 'AUR62036795' => 'cqu', 'AUR62039891' => 'cqu', 'BcaB02g08737' => 'bca', 'BcaB04g20441' => 'bca', 'BcaB06g26509' => 'bca', 'BcaB06g26510' => 'bca', 'BcaB06g26511' => 'bca', 'BcaB06g26512' => 'bca', 'BcaB06g26513' => 'bca', 'BcaC02g12564' => 'bca', 'BcaC02g12565' => 'bca', 'BcaC02g12794' => 'bca', 'BcaC02g12795' => 'bca', 'BcaC02g12796' => 'bca', 'BcaC06g35541' => 'bca', 'BNapus_Darmor_BZH_scaffold_188p00080' => 'bna', 'BNapus_Darmor_BZH_scaffold_188p00090' => 'bna', 'BolC1t03972H' => 'bol', 'BolC1t03973H' => 'bol', 'BolC4t21680H' => 'bol', 'BolC7t41863H' => 'bol', 'BolSC55t61227H' => 'bol', 'BolSC55t61228H' => 'bol', 'BraA01t03278Z' => 'bra', 'BraA05t18998Z' => 'bra', 'BraA07t28673Z' => 'bra', 'C01p40150' => 'bna', 'C05p12370' => 'bna', 'C07p13680' => 'bna', 'CAN.G1006.16' => 'can', 'CAN.G1006.17' => 'can', 'CAN.G1170.2' => 'can', 'CAN.G962.7' => 'can', 'CANSAT25G2179' => 'cansat', 'CANSAT78G1573' => 'cansat', 'CARHR099510' => 'chi', 'CARHR143510' => 'chi', 'Carub.0003s2380' => 'cru', 'Carub.0004s3082' => 'cru', 'Ca_00614_v3' => 'car', 'Ca_07801_v3' => 'car', 'Ca_08567_v3' => 'car', 'Ca_09571_v3' => 'car', 'CBR_g19290' => 'cbr', 'Cc01_g19770' => 'ccan', 'Cc03_g03030' => 'ccan', 'CDE07G0968' => 'cde', 'CDE09G1441' => 'cde', 'Cfa006103' => 'cfa', 'Cfa015573' => 'cfa', 'Cfa016988' => 'cfa', 'Ciclev10006738m.g' => 'ccl', 'Ciclev10010920m.g' => 'ccl', 'Ciclev10018517m.g' => 'ccl', 'CiPaw.01G159200' => 'cil', 'CiPaw.02G091000' => 'cil', 'CiPaw.02G091100' => 'cil', 'CiPaw.08G103100' => 'cil', 'CiPaw.09G224900' => 'cil', 'ClCG06G005740' => 'cla', 'ClCG07G000090' => 'cla', 'ClCG07G000100' => 'cla', 'COL.COLO4_09143' => 'col', 'COL.COLO4_25124' => 'col', 'Cpa.g.sc16.34' => 'cpa', 'Cpa.g.sc3504.1' => 'cpa', 'Cpa.g.sc60.37' => 'cpa', 'CsaV3_6G018520' => 'csa', 'CsaV3_6G036860' => 'csa', 'CSS0001072' => 'camsi', 'CSS0020208' => 'camsi', 'CSS0021253' => 'camsi', 'CSS0022190' => 'camsi', 'CSS0036150' => 'camsi', 'CSS0040442' => 'camsi', 'CSS0042300' => 'camsi', 'CSS0045298' => 'camsi', 'DCAR_012449' => 'dca', 'DCAR_018405' => 'dca', 'DCAR_024573' => 'dca', 'DCAR_030591' => 'dca', 'Dinv16926' => 'din', 'Dinv32963' => 'din', 'Dinv38382' => 'din', 'Dinv38383' => 'din', 'Duzib133G0974' => 'dzi', 'Duzib138G1867' => 'dzi', 'Duzib211G0420' => 'dzi', 'Duzib212G0930' => 'dzi', 'ECA234G1645' => 'eca', 'ECA247G3467' => 'eca', 'ECA248G1703' => 'eca', 'EL10Ac3g06327' => 'bvu', 'EL10Ac7g17204' => 'bvu', 'Eucgr.A00855' => 'egr', 'Eucgr.A00858' => 'egr', 'Eucgr.H01520' => 'egr', 'Eucgr.H03604' => 'egr', 'Eucgr.L03465' => 'egr', 'Eucgr.L03466' => 'egr', 'FAN01G0988' => 'fan', 'FAN02G3892' => 'fan', 'FAN05G3381' => 'fan', 'FAN07G0967' => 'fan', 'FAN07G1493' => 'fan', 'FAN08G3125' => 'fan', 'FAN09G0402' => 'fan', 'FAN12G2594' => 'fan', 'FAN12G3879' => 'fan', 'FAN14G1546' => 'fan', 'FAN15G3626' => 'fan', 'FAN17G0588' => 'fan', 'FAN17G0609' => 'fan', 'FAN18G2817' => 'fan', 'FAN19G1305' => 'fan', 'FAN20G1787' => 'fan', 'FAN22G0073' => 'fan', 'FAN22G0352' => 'fan', 'FAN22G0368' => 'fan', 'FAN22G2273' => 'fan', 'FAN24G1998' => 'fan', 'FAN27G1317' => 'fan', 'FvH4_2g23980' => 'fve', 'FvH4_4g14380' => 'fve', 'FvH4_4g14390' => 'fve', 'FvH4_6g09250' => 'fve', 'Glyma.03G151100' => 'gma', 'Glyma.04G122550' => 'gma', 'Glyma.05G001600' => 'gma', 'Glyma.09G270766' => 'gma', 'Glyma.09G270832' => 'gma', 'Glyma.13G209800' => 'gma', 'Glyma.15G102800' => 'gma', 'Glyma.18G218900' => 'gma', 'Glyma.19G001500' => 'gma', 'Glyma.19G153600' => 'gma', 'Gohir.A02G028600' => 'ghi', 'Gohir.A08G045000' => 'ghi', 'Gohir.A11G120500' => 'ghi', 'Gohir.A12G006200' => 'ghi', 'Gohir.A12G006250' => 'ghi', 'Gohir.D02G036300' => 'ghi', 'Gohir.D08G054700' => 'ghi', 'Gohir.D11G125600' => 'ghi', 'Gohir.D12G005700' => 'ghi', 'Gorai.004G055200' => 'gra', 'Gorai.005G040400' => 'gra', 'Gorai.007G134500' => 'gra', 'Gorai.008G005500' => 'gra', 'GSVIVG01011094001' => 'vvi', 'GSVIVG01017879001' => 'vvi', 'GSVIVG01025988001' => 'vvi', 'GSVIVG01029847001' => 'vvi', 'HanXRQChr10g0282901' => 'han', 'HanXRQChr10g0310371' => 'han', 'HanXRQChr10g0315041' => 'han', 'HanXRQChr11g0327651' => 'han', 'HanXRQChr12g0359391' => 'han', 'Haze_00972' => 'cav', 'Haze_00973' => 'cav', 'Haze_00974' => 'cav', 'Haze_04747' => 'cav', 'Haze_04749' => 'cav', 'Haze_04750' => 'cav', 'Haze_21217' => 'cav', 'Hma1.2p1_1037F.1_g250680' => 'hma', 'Hma1.2p1_1644F.1_g295320' => 'hma', 'HPP92_011322' => 'vpl', 'HPP92_011323' => 'vpl', 'HPP92_011324' => 'vpl', 'HPP92_011325' => 'vpl', 'HPP92_011326' => 'vpl', 'Hund12205' => 'sun', 'Hund17957' => 'sun', 'Lalb_Chr06g0176771' => 'lal', 'Lalb_Chr18g0056021' => 'lal', 'Lalb_Chr18g0056031' => 'lal', 'Lalb_Chr18g0056041' => 'lal', 'Lalb_Chr20g0107751' => 'lal', 'Lalb_Chr20g0118371' => 'lal', 'Lj1g0010239' => 'lja', 'Lj1g0017101' => 'lja', 'Lj2A1178G40' => 'lonja', 'Lj2A54G84' => 'lonja', 'Lj2g0015248' => 'lja', 'Lj3A761T51' => 'lonja', 'Lj6g0018116' => 'lja', 'Lsat_1_v5_gn_4_136040' => 'lsa', 'Lsat_1_v5_gn_5_187461' => 'lsa', 'Lsat_1_v5_gn_5_77001' => 'lsa', 'Lsat_1_v5_gn_9_4461' => 'lsa', 'Manes.01G210100' => 'mes', 'Manes.03G185600' => 'mes', 'Manes.05G073300' => 'mes', 'Manes.09G120300' => 'mes', 'Manes.15G022100' => 'mes', 'Mapoly0096s0053' => 'mpo', 'MBI03_g14058_MAGBIO' => 'mbi', 'MBI03_g33876_MAGBIO' => 'mbi', 'MBI03_g36854_MAGBIO' => 'mbi', 'MBI17_g11997_MAGBIO' => 'mbi', 'MD03G1269000' => 'mdo', 'MD04G1179600' => 'mdo', 'MD11G1289800' => 'mdo', 'MD12G1194700' => 'mdo', 'MD13G1182100' => 'mdo', 'MD13G1182200' => 'mdo', 'MD16G1182600' => 'mdo', 'Medtr2g021400' => 'mtr', 'Medtr2g021470' => 'mtr', 'Medtr2g105810' => 'mtr', 'Medtr3g033580' => 'mtr', 'Medtr6g007970' => 'mtr', 'Medtr7g056330' => 'mtr', 'Medtr7g074290' => 'mtr', 'Medtr7g074380' => 'mtr', 'Medtr7g094550' => 'mtr', 'Medtr8g069995' => 'mtr', 'MELO3C014345.2' => 'cme', 'MELO3C021395.2' => 'cme', 'Migut.D00262' => 'egut', 'Migut.G00257' => 'egut', 'MSTRG.21575' => 'ama', 'MSTRG.3985' => 'ama', 'Nitab4.5_0000295g0140' => 'nta', 'Nitab4.5_0000732g0140' => 'nta', 'Nitab4.5_0003162g0020' => 'nta', 'Nitab4.5_0006180g0090' => 'nta', 'Nitab4.5_0006390g0010' => 'nta', 'Nitab4.5_0007392g0040' => 'nta', 'Nn1g02140' => 'nnu', 'Nn4g26168' => 'nnu', 'Nn5g26754' => 'nnu', 'Oeu001433.1' => 'oeu', 'Oeu010299.2' => 'oeu', 'Oeu011171.1' => 'oeu', 'Oeu037675.1' => 'oeu', 'Oeu038359.1' => 'oeu', 'Oeu063834.1' => 'oeu', 'Oeu063835.1' => 'oeu', 'Os05g0312000' => 'osa', 'Os07g0211101' => 'osa', 'Os07g0211200' => 'osa', 'Os07g0681500' => 'osa', 'Peaxi162Scf00095g01015' => 'pax', 'Peaxi162Scf00104g00329' => 'pax', 'Peaxi162Scf00161g00137' => 'pax', 'PGR004G1665' => 'pgr', 'PGR031G2937' => 'pgr', 'PGR119G2145' => 'pgr', 'PGSC0003DMG400004351' => 'stu', 'PGSC0003DMG400014625' => 'stu', 'PGSC0003DMG401000943' => 'stu', 'Phvul.001G148600' => 'pvu', 'Phvul.004G001700' => 'pvu', 'Phvul.006G154900' => 'pvu', 'Phvul.008G078200' => 'pvu', 'Phvul.011G136500' => 'pvu', 'Potri.002G215600' => 'ptr', 'Potri.008G201600' => 'ptr', 'Potri.014G138400' => 'ptr', 'Potri.016G142500' => 'ptr', 'Pp3c16_10580' => 'ppa', 'Pp3c5_25280' => 'ppa', 'Prupe.1G150000' => 'ppe', 'Prupe.1G150100' => 'ppe', 'Prupe.6G299600' => 'ppe', 'Prupe.8G245000' => 'ppe', 'Psat0s4927g0040' => 'psa', 'Psat1g052080' => 'psa', 'Psat1g183800' => 'psa', 'Psat3g113840' => 'psa', 'Psat3g126120' => 'psa', 'Psat3g126160' => 'psa', 'Psat3g158760' => 'psa', 'Psat3g158840' => 'psa', 'PSO170G2858' => 'pso', 'PSO339G0606' => 'pso', 'PSO384G4709' => 'pso', 'PSO407G0334' => 'pso', 'QL04p040276' => 'qlo', 'QL06p005458' => 'qlo', 'QL06p005472' => 'qlo', 'QL07p030546' => 'qlo', 'QL07p031519' => 'qlo', 'QL09p050949' => 'qlo', 'QL09p050966' => 'qlo', 'QL09p051067' => 'qlo', 'QL12p022706' => 'qlo', 'RcHm_v2.0_Chr2g0119601' => 'rch', 'RcHm_v2.0_Chr3g0459591' => 'rch', 'RcHm_v2.0_Chr4g0418521' => 'rch', 'RcHm_v2.0_Chr4g0418531' => 'rch', 'RcHm_v2.0_Chr4g0418541' => 'rch', 'RcHm_v2.0_Chr6g0291641' => 'rch', 'Rhsim01G0086300' => 'rsi', 'Rhsim01G0276300' => 'rsi', 'Rhsim01G0276500' => 'rsi', 'Rhsim04G0207700' => 'rsi', 'Rhsim05G0234500' => 'rsi', 'Rhsim13G0022400' => 'rsi', 'Sabra02G0167900' => 'sbr', 'Sabra04G0158500' => 'sbr', 'Sabra08G0159800' => 'sbr', 'Sabra10G0011500' => 'sbr', 'Sabra14G0104400' => 'sbr', 'SalBow2G2440' => 'sbo', 'SalBow4G2265' => 'sbo', 'Sc02g0000060' => 'sci', 'Sc05g0005020' => 'sci', 'Sc13g0003890' => 'sci', 'Sed0014865' => 'sed', 'Sed0017224' => 'sed', 'Sed0026391' => 'sed', 'SEGI_00063' => 'sgi', 'SEGI_10967' => 'sgi', 'SEGI_17510' => 'sgi', 'SEGI_24396' => 'sgi', 'SEGI_39719' => 'sgi', 'SEGI_41392' => 'sgi', 'SGA_v2.0_scaffold11G05794' => 'sas', 'SGA_v2.0_scaffold142G35607' => 'sas', 'SGA_v2.0_scaffold1G00447' => 'sas', 'SHI15388' => 'shi', 'SHI15394' => 'shi', 'SHI15396' => 'shi', 'SHI15399' => 'shi', 'SMO343G0151' => 'smo', 'SMO367G1118' => 'smo', 'Solyc01g080200.3' => 'sly', 'Solyc06g008960.3' => 'sly', 'Solyc09g064780.3' => 'sly', 'Sopen01g031980' => 'spe', 'Sopen06g003710' => 'spe', 'Sopen09g026460' => 'spe', 'Sp3g21240' => 'spa', 'Sp4g30030' => 'spa', 'TAR365G0022' => 'tar', 'TAR365G1023' => 'tar', 'TAR365G1253' => 'tar', 'TAR623G0078' => 'tar', 'TAR623G1721' => 'tar', 'TAR633G0959' => 'tar', 'THA.LOC104802225' => 'tha', 'THA.LOC104804769' => 'tha', 'THA.LOC104808660' => 'tha', 'THA.LOC104812792' => 'tha', 'Thecc.01G284000' => 'tca', 'Thecc.04G220600' => 'tca', 'Thecc.05G268900' => 'tca', 'Thecc.08G171100' => 'tca', 'Thhalv10001284m.g' => 'esa', 'Thhalv10019912m.g' => 'esa', 'TPR.G14189' => 'tpr', 'TPR.G18110' => 'tpr', 'TPR.G18130' => 'tpr', 'TPR.G18131' => 'tpr', 'TPR.G18140' => 'tpr', 'TPR.G24282' => 'tpr', 'TPR.G25221' => 'tpr', 'TPR.G29267' => 'tpr', 'TPR.G35315' => 'tpr', 'TPR.G36173' => 'tpr', 'TWI09G0794' => 'twi', 'TWI59G1348' => 'twi', 'TWI74G0430' => 'twi', 'unitig_26.g8940' => 'ugi', 'unitig_749.g13744' => 'ugi', 'unitig_749.g13745' => 'ugi', 'vmacro08269' => 'vma', 'vmacro14937' => 'vma', 'vmacro20401' => 'vma', 'VMungo0464G1349' => 'vmu', 'VMungo0540G0289' => 'vmu', 'VMungo1215G1590' => 'vmu', 'VMungo1309G0221' => 'vmu', 'VMungo1309G2815' => 'vmu', 'VMungo1383G0239' => 'vmu', 'VMungo1383G2910' => 'vmu', 'Zm00001eb095270' => 'zma', 'Zm00001eb095280' => 'zma', 'Zm00001eb111630' => 'zma', 'Zm00001eb237080' => 'zma', 'Zm00001eb273740' => 'zma', 'Zm00001eb285040' => 'zma', 'Zm00001eb330790' => 'zma', 'Zm00001eb337380' => 'zma' ) $gf_id = 'HOM05D001484' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001484' ) $data_identifier = 'HOM05D001484' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 2, 'aly' => (int) 2, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 22, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 7, 'hma' => (int) 2, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 7, 'mtr' => (int) 10, 'cme' => (int) 2, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 4, 'ppa' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 4, 'qlo' => (int) 9, 'rch' => (int) 6, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 10, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 7, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb337380' $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' => 'HOM05D001484', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p31500' => 'bna', 'A05p00020' => 'bna', 'A07p08820' => 'bna', 'Aa31LG4G3300' => 'aar', 'Aa31LG8G10030' => 'aar', 'Actinidia00731' => 'ach', 'Actinidia11473' => 'ach', 'Actinidia23469' => 'ach', 'Actinidia24318' => 'ach', 'Actinidia40196' => 'ach', 'Actinidia40197' => 'ach', 'Actinidia40198' => 'ach', 'Ah.08g212990' => 'amhyb', 'Ah.15g091720' => 'amhyb', 'AL3G38260' => 'aly', 'AL4G47710' => 'aly', 'Aqoxy2G00671' => 'aox', 'Aqoxy2G03236' => 'aox', 'arahy.Tifrunner.gnm1.ann1.05IDCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KR684' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATY3SJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK6QJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6APGL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IDT7Z9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM073U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ0R87' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LE7RV4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT4QRX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V5ENPK' => 'arhy', 'AT2G48110' => 'ath', 'AT3G23590' => 'ath', 'ATR0626G186' => 'atr', 'ATR1127G141' => 'atr', 'Atru.chr4.2583' => 'acertr', 'Atru.chr5.1358' => 'acertr', 'Atru.chr5.1359' => 'acertr', 'Atru.chr8.46' => 'acertr', 'AUR62002640' => 'cqu', 'AUR62030055' => 'cqu', 'AUR62033713' => 'cqu', 'AUR62033714' => 'cqu', 'AUR62036795' => 'cqu', 'AUR62039891' => 'cqu', 'BcaB02g08737' => 'bca', 'BcaB04g20441' => 'bca', 'BcaB06g26509' => 'bca', 'BcaB06g26510' => 'bca', 'BcaB06g26511' => 'bca', 'BcaB06g26512' => 'bca', 'BcaB06g26513' => 'bca', 'BcaC02g12564' => 'bca', 'BcaC02g12565' => 'bca', 'BcaC02g12794' => 'bca', 'BcaC02g12795' => 'bca', 'BcaC02g12796' => 'bca', 'BcaC06g35541' => 'bca', 'BNapus_Darmor_BZH_scaffold_188p00080' => 'bna', 'BNapus_Darmor_BZH_scaffold_188p00090' => 'bna', 'BolC1t03972H' => 'bol', 'BolC1t03973H' => 'bol', 'BolC4t21680H' => 'bol', 'BolC7t41863H' => 'bol', 'BolSC55t61227H' => 'bol', 'BolSC55t61228H' => 'bol', 'BraA01t03278Z' => 'bra', 'BraA05t18998Z' => 'bra', 'BraA07t28673Z' => 'bra', 'C01p40150' => 'bna', 'C05p12370' => 'bna', 'C07p13680' => 'bna', 'CAN.G1006.16' => 'can', 'CAN.G1006.17' => 'can', 'CAN.G1170.2' => 'can', 'CAN.G962.7' => 'can', 'CANSAT25G2179' => 'cansat', 'CANSAT78G1573' => 'cansat', 'CARHR099510' => 'chi', 'CARHR143510' => 'chi', 'Carub.0003s2380' => 'cru', 'Carub.0004s3082' => 'cru', 'Ca_00614_v3' => 'car', 'Ca_07801_v3' => 'car', 'Ca_08567_v3' => 'car', 'Ca_09571_v3' => 'car', 'CBR_g19290' => 'cbr', 'Cc01_g19770' => 'ccan', 'Cc03_g03030' => 'ccan', 'CDE07G0968' => 'cde', 'CDE09G1441' => 'cde', 'Cfa006103' => 'cfa', 'Cfa015573' => 'cfa', 'Cfa016988' => 'cfa', 'Ciclev10006738m.g' => 'ccl', 'Ciclev10010920m.g' => 'ccl', 'Ciclev10018517m.g' => 'ccl', 'CiPaw.01G159200' => 'cil', 'CiPaw.02G091000' => 'cil', 'CiPaw.02G091100' => 'cil', 'CiPaw.08G103100' => 'cil', 'CiPaw.09G224900' => 'cil', 'ClCG06G005740' => 'cla', 'ClCG07G000090' => 'cla', 'ClCG07G000100' => 'cla', 'COL.COLO4_09143' => 'col', 'COL.COLO4_25124' => 'col', 'Cpa.g.sc16.34' => 'cpa', 'Cpa.g.sc3504.1' => 'cpa', 'Cpa.g.sc60.37' => 'cpa', 'CsaV3_6G018520' => 'csa', 'CsaV3_6G036860' => 'csa', 'CSS0001072' => 'camsi', 'CSS0020208' => 'camsi', 'CSS0021253' => 'camsi', 'CSS0022190' => 'camsi', 'CSS0036150' => 'camsi', 'CSS0040442' => 'camsi', 'CSS0042300' => 'camsi', 'CSS0045298' => 'camsi', 'DCAR_012449' => 'dca', 'DCAR_018405' => 'dca', 'DCAR_024573' => 'dca', 'DCAR_030591' => 'dca', 'Dinv16926' => 'din', 'Dinv32963' => 'din', 'Dinv38382' => 'din', 'Dinv38383' => 'din', 'Duzib133G0974' => 'dzi', 'Duzib138G1867' => 'dzi', 'Duzib211G0420' => 'dzi', 'Duzib212G0930' => 'dzi', 'ECA234G1645' => 'eca', 'ECA247G3467' => 'eca', 'ECA248G1703' => 'eca', 'EL10Ac3g06327' => 'bvu', 'EL10Ac7g17204' => 'bvu', 'Eucgr.A00855' => 'egr', 'Eucgr.A00858' => 'egr', 'Eucgr.H01520' => 'egr', 'Eucgr.H03604' => 'egr', 'Eucgr.L03465' => 'egr', 'Eucgr.L03466' => 'egr', 'FAN01G0988' => 'fan', 'FAN02G3892' => 'fan', 'FAN05G3381' => 'fan', 'FAN07G0967' => 'fan', 'FAN07G1493' => 'fan', 'FAN08G3125' => 'fan', 'FAN09G0402' => 'fan', 'FAN12G2594' => 'fan', 'FAN12G3879' => 'fan', 'FAN14G1546' => 'fan', 'FAN15G3626' => 'fan', 'FAN17G0588' => 'fan', 'FAN17G0609' => 'fan', 'FAN18G2817' => 'fan', 'FAN19G1305' => 'fan', 'FAN20G1787' => 'fan', 'FAN22G0073' => 'fan', 'FAN22G0352' => 'fan', 'FAN22G0368' => 'fan', 'FAN22G2273' => 'fan', 'FAN24G1998' => 'fan', 'FAN27G1317' => 'fan', 'FvH4_2g23980' => 'fve', 'FvH4_4g14380' => 'fve', 'FvH4_4g14390' => 'fve', 'FvH4_6g09250' => 'fve', 'Glyma.03G151100' => 'gma', 'Glyma.04G122550' => 'gma', 'Glyma.05G001600' => 'gma', 'Glyma.09G270766' => 'gma', 'Glyma.09G270832' => 'gma', 'Glyma.13G209800' => 'gma', 'Glyma.15G102800' => 'gma', 'Glyma.18G218900' => 'gma', 'Glyma.19G001500' => 'gma', 'Glyma.19G153600' => 'gma', 'Gohir.A02G028600' => 'ghi', 'Gohir.A08G045000' => 'ghi', 'Gohir.A11G120500' => 'ghi', 'Gohir.A12G006200' => 'ghi', 'Gohir.A12G006250' => 'ghi', 'Gohir.D02G036300' => 'ghi', 'Gohir.D08G054700' => 'ghi', 'Gohir.D11G125600' => 'ghi', 'Gohir.D12G005700' => 'ghi', 'Gorai.004G055200' => 'gra', 'Gorai.005G040400' => 'gra', 'Gorai.007G134500' => 'gra', 'Gorai.008G005500' => 'gra', 'GSVIVG01011094001' => 'vvi', 'GSVIVG01017879001' => 'vvi', 'GSVIVG01025988001' => 'vvi', 'GSVIVG01029847001' => 'vvi', 'HanXRQChr10g0282901' => 'han', 'HanXRQChr10g0310371' => 'han', 'HanXRQChr10g0315041' => 'han', 'HanXRQChr11g0327651' => 'han', 'HanXRQChr12g0359391' => 'han', 'Haze_00972' => 'cav', 'Haze_00973' => 'cav', 'Haze_00974' => 'cav', 'Haze_04747' => 'cav', 'Haze_04749' => 'cav', 'Haze_04750' => 'cav', 'Haze_21217' => 'cav', 'Hma1.2p1_1037F.1_g250680' => 'hma', 'Hma1.2p1_1644F.1_g295320' => 'hma', 'HPP92_011322' => 'vpl', 'HPP92_011323' => 'vpl', 'HPP92_011324' => 'vpl', 'HPP92_011325' => 'vpl', 'HPP92_011326' => 'vpl', 'Hund12205' => 'sun', 'Hund17957' => 'sun', 'Lalb_Chr06g0176771' => 'lal', 'Lalb_Chr18g0056021' => 'lal', 'Lalb_Chr18g0056031' => 'lal', 'Lalb_Chr18g0056041' => 'lal', 'Lalb_Chr20g0107751' => 'lal', 'Lalb_Chr20g0118371' => 'lal', 'Lj1g0010239' => 'lja', 'Lj1g0017101' => 'lja', 'Lj2A1178G40' => 'lonja', 'Lj2A54G84' => 'lonja', 'Lj2g0015248' => 'lja', 'Lj3A761T51' => 'lonja', 'Lj6g0018116' => 'lja', 'Lsat_1_v5_gn_4_136040' => 'lsa', 'Lsat_1_v5_gn_5_187461' => 'lsa', 'Lsat_1_v5_gn_5_77001' => 'lsa', 'Lsat_1_v5_gn_9_4461' => 'lsa', 'Manes.01G210100' => 'mes', 'Manes.03G185600' => 'mes', 'Manes.05G073300' => 'mes', 'Manes.09G120300' => 'mes', 'Manes.15G022100' => 'mes', 'Mapoly0096s0053' => 'mpo', 'MBI03_g14058_MAGBIO' => 'mbi', 'MBI03_g33876_MAGBIO' => 'mbi', 'MBI03_g36854_MAGBIO' => 'mbi', 'MBI17_g11997_MAGBIO' => 'mbi', 'MD03G1269000' => 'mdo', 'MD04G1179600' => 'mdo', 'MD11G1289800' => 'mdo', 'MD12G1194700' => 'mdo', 'MD13G1182100' => 'mdo', 'MD13G1182200' => 'mdo', 'MD16G1182600' => 'mdo', 'Medtr2g021400' => 'mtr', 'Medtr2g021470' => 'mtr', 'Medtr2g105810' => 'mtr', 'Medtr3g033580' => 'mtr', 'Medtr6g007970' => 'mtr', 'Medtr7g056330' => 'mtr', 'Medtr7g074290' => 'mtr', 'Medtr7g074380' => 'mtr', 'Medtr7g094550' => 'mtr', 'Medtr8g069995' => 'mtr', 'MELO3C014345.2' => 'cme', 'MELO3C021395.2' => 'cme', 'Migut.D00262' => 'egut', 'Migut.G00257' => 'egut', 'MSTRG.21575' => 'ama', 'MSTRG.3985' => 'ama', 'Nitab4.5_0000295g0140' => 'nta', 'Nitab4.5_0000732g0140' => 'nta', 'Nitab4.5_0003162g0020' => 'nta', 'Nitab4.5_0006180g0090' => 'nta', 'Nitab4.5_0006390g0010' => 'nta', 'Nitab4.5_0007392g0040' => 'nta', 'Nn1g02140' => 'nnu', 'Nn4g26168' => 'nnu', 'Nn5g26754' => 'nnu', 'Oeu001433.1' => 'oeu', 'Oeu010299.2' => 'oeu', 'Oeu011171.1' => 'oeu', 'Oeu037675.1' => 'oeu', 'Oeu038359.1' => 'oeu', 'Oeu063834.1' => 'oeu', 'Oeu063835.1' => 'oeu', 'Os05g0312000' => 'osa', 'Os07g0211101' => 'osa', 'Os07g0211200' => 'osa', 'Os07g0681500' => 'osa', 'Peaxi162Scf00095g01015' => 'pax', 'Peaxi162Scf00104g00329' => 'pax', 'Peaxi162Scf00161g00137' => 'pax', 'PGR004G1665' => 'pgr', 'PGR031G2937' => 'pgr', 'PGR119G2145' => 'pgr', 'PGSC0003DMG400004351' => 'stu', 'PGSC0003DMG400014625' => 'stu', 'PGSC0003DMG401000943' => 'stu', 'Phvul.001G148600' => 'pvu', 'Phvul.004G001700' => 'pvu', 'Phvul.006G154900' => 'pvu', 'Phvul.008G078200' => 'pvu', 'Phvul.011G136500' => 'pvu', 'Potri.002G215600' => 'ptr', 'Potri.008G201600' => 'ptr', 'Potri.014G138400' => 'ptr', 'Potri.016G142500' => 'ptr', 'Pp3c16_10580' => 'ppa', 'Pp3c5_25280' => 'ppa', 'Prupe.1G150000' => 'ppe', 'Prupe.1G150100' => 'ppe', 'Prupe.6G299600' => 'ppe', 'Prupe.8G245000' => 'ppe', 'Psat0s4927g0040' => 'psa', 'Psat1g052080' => 'psa', 'Psat1g183800' => 'psa', 'Psat3g113840' => 'psa', 'Psat3g126120' => 'psa', 'Psat3g126160' => 'psa', 'Psat3g158760' => 'psa', 'Psat3g158840' => 'psa', 'PSO170G2858' => 'pso', 'PSO339G0606' => 'pso', 'PSO384G4709' => 'pso', 'PSO407G0334' => 'pso', 'QL04p040276' => 'qlo', 'QL06p005458' => 'qlo', 'QL06p005472' => 'qlo', 'QL07p030546' => 'qlo', 'QL07p031519' => 'qlo', 'QL09p050949' => 'qlo', 'QL09p050966' => 'qlo', 'QL09p051067' => 'qlo', 'QL12p022706' => 'qlo', 'RcHm_v2.0_Chr2g0119601' => 'rch', 'RcHm_v2.0_Chr3g0459591' => 'rch', 'RcHm_v2.0_Chr4g0418521' => 'rch', 'RcHm_v2.0_Chr4g0418531' => 'rch', 'RcHm_v2.0_Chr4g0418541' => 'rch', 'RcHm_v2.0_Chr6g0291641' => 'rch', 'Rhsim01G0086300' => 'rsi', 'Rhsim01G0276300' => 'rsi', 'Rhsim01G0276500' => 'rsi', 'Rhsim04G0207700' => 'rsi', 'Rhsim05G0234500' => 'rsi', 'Rhsim13G0022400' => 'rsi', 'Sabra02G0167900' => 'sbr', 'Sabra04G0158500' => 'sbr', 'Sabra08G0159800' => 'sbr', 'Sabra10G0011500' => 'sbr', 'Sabra14G0104400' => 'sbr', 'SalBow2G2440' => 'sbo', 'SalBow4G2265' => 'sbo', 'Sc02g0000060' => 'sci', 'Sc05g0005020' => 'sci', 'Sc13g0003890' => 'sci', 'Sed0014865' => 'sed', 'Sed0017224' => 'sed', 'Sed0026391' => 'sed', 'SEGI_00063' => 'sgi', 'SEGI_10967' => 'sgi', 'SEGI_17510' => 'sgi', 'SEGI_24396' => 'sgi', 'SEGI_39719' => 'sgi', 'SEGI_41392' => 'sgi', 'SGA_v2.0_scaffold11G05794' => 'sas', 'SGA_v2.0_scaffold142G35607' => 'sas', 'SGA_v2.0_scaffold1G00447' => 'sas', 'SHI15388' => 'shi', 'SHI15394' => 'shi', 'SHI15396' => 'shi', 'SHI15399' => 'shi', 'SMO343G0151' => 'smo', 'SMO367G1118' => 'smo', 'Solyc01g080200.3' => 'sly', 'Solyc06g008960.3' => 'sly', 'Solyc09g064780.3' => 'sly', 'Sopen01g031980' => 'spe', 'Sopen06g003710' => 'spe', 'Sopen09g026460' => 'spe', 'Sp3g21240' => 'spa', 'Sp4g30030' => 'spa', 'TAR365G0022' => 'tar', 'TAR365G1023' => 'tar', 'TAR365G1253' => 'tar', 'TAR623G0078' => 'tar', 'TAR623G1721' => 'tar', 'TAR633G0959' => 'tar', 'THA.LOC104802225' => 'tha', 'THA.LOC104804769' => 'tha', 'THA.LOC104808660' => 'tha', 'THA.LOC104812792' => 'tha', 'Thecc.01G284000' => 'tca', 'Thecc.04G220600' => 'tca', 'Thecc.05G268900' => 'tca', 'Thecc.08G171100' => 'tca', 'Thhalv10001284m.g' => 'esa', 'Thhalv10019912m.g' => 'esa', 'TPR.G14189' => 'tpr', 'TPR.G18110' => 'tpr', 'TPR.G18130' => 'tpr', 'TPR.G18131' => 'tpr', 'TPR.G18140' => 'tpr', 'TPR.G24282' => 'tpr', 'TPR.G25221' => 'tpr', 'TPR.G29267' => 'tpr', 'TPR.G35315' => 'tpr', 'TPR.G36173' => 'tpr', 'TWI09G0794' => 'twi', 'TWI59G1348' => 'twi', 'TWI74G0430' => 'twi', 'unitig_26.g8940' => 'ugi', 'unitig_749.g13744' => 'ugi', 'unitig_749.g13745' => 'ugi', 'vmacro08269' => 'vma', 'vmacro14937' => 'vma', 'vmacro20401' => 'vma', 'VMungo0464G1349' => 'vmu', 'VMungo0540G0289' => 'vmu', 'VMungo1215G1590' => 'vmu', 'VMungo1309G0221' => 'vmu', 'VMungo1309G2815' => 'vmu', 'VMungo1383G0239' => 'vmu', 'VMungo1383G2910' => 'vmu', 'Zm00001eb095270' => 'zma', 'Zm00001eb095280' => 'zma', 'Zm00001eb111630' => 'zma', 'Zm00001eb237080' => 'zma', 'Zm00001eb273740' => 'zma', 'Zm00001eb285040' => 'zma', 'Zm00001eb330790' => 'zma', 'Zm00001eb337380' => 'zma' ), 'gf_id' => 'HOM05D001484', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001484' ), 'data_identifier' => 'HOM05D001484', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001484', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p31500' => 'bna', 'A05p00020' => 'bna', 'A07p08820' => 'bna', 'Aa31LG4G3300' => 'aar', 'Aa31LG8G10030' => 'aar', 'Actinidia00731' => 'ach', 'Actinidia11473' => 'ach', 'Actinidia23469' => 'ach', 'Actinidia24318' => 'ach', 'Actinidia40196' => 'ach', 'Actinidia40197' => 'ach', 'Actinidia40198' => 'ach', 'Ah.08g212990' => 'amhyb', 'Ah.15g091720' => 'amhyb', 'AL3G38260' => 'aly', 'AL4G47710' => 'aly', 'Aqoxy2G00671' => 'aox', 'Aqoxy2G03236' => 'aox', 'arahy.Tifrunner.gnm1.ann1.05IDCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KR684' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATY3SJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK6QJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6APGL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IDT7Z9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM073U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ0R87' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LE7RV4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT4QRX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V5ENPK' => 'arhy', 'AT2G48110' => 'ath', 'AT3G23590' => 'ath', 'ATR0626G186' => 'atr', 'ATR1127G141' => 'atr', 'Atru.chr4.2583' => 'acertr', 'Atru.chr5.1358' => 'acertr', 'Atru.chr5.1359' => 'acertr', 'Atru.chr8.46' => 'acertr', 'AUR62002640' => 'cqu', 'AUR62030055' => 'cqu', 'AUR62033713' => 'cqu', 'AUR62033714' => 'cqu', 'AUR62036795' => 'cqu', 'AUR62039891' => 'cqu', 'BcaB02g08737' => 'bca', 'BcaB04g20441' => 'bca', 'BcaB06g26509' => 'bca', 'BcaB06g26510' => 'bca', 'BcaB06g26511' => 'bca', 'BcaB06g26512' => 'bca', 'BcaB06g26513' => 'bca', 'BcaC02g12564' => 'bca', 'BcaC02g12565' => 'bca', 'BcaC02g12794' => 'bca', 'BcaC02g12795' => 'bca', 'BcaC02g12796' => 'bca', 'BcaC06g35541' => 'bca', 'BNapus_Darmor_BZH_scaffold_188p00080' => 'bna', 'BNapus_Darmor_BZH_scaffold_188p00090' => 'bna', 'BolC1t03972H' => 'bol', 'BolC1t03973H' => 'bol', 'BolC4t21680H' => 'bol', 'BolC7t41863H' => 'bol', 'BolSC55t61227H' => 'bol', 'BolSC55t61228H' => 'bol', 'BraA01t03278Z' => 'bra', 'BraA05t18998Z' => 'bra', 'BraA07t28673Z' => 'bra', 'C01p40150' => 'bna', 'C05p12370' => 'bna', 'C07p13680' => 'bna', 'CAN.G1006.16' => 'can', 'CAN.G1006.17' => 'can', 'CAN.G1170.2' => 'can', 'CAN.G962.7' => 'can', 'CANSAT25G2179' => 'cansat', 'CANSAT78G1573' => 'cansat', 'CARHR099510' => 'chi', 'CARHR143510' => 'chi', 'Carub.0003s2380' => 'cru', 'Carub.0004s3082' => 'cru', 'Ca_00614_v3' => 'car', 'Ca_07801_v3' => 'car', 'Ca_08567_v3' => 'car', 'Ca_09571_v3' => 'car', 'CBR_g19290' => 'cbr', 'Cc01_g19770' => 'ccan', 'Cc03_g03030' => 'ccan', 'CDE07G0968' => 'cde', 'CDE09G1441' => 'cde', 'Cfa006103' => 'cfa', 'Cfa015573' => 'cfa', 'Cfa016988' => 'cfa', 'Ciclev10006738m.g' => 'ccl', 'Ciclev10010920m.g' => 'ccl', 'Ciclev10018517m.g' => 'ccl', 'CiPaw.01G159200' => 'cil', 'CiPaw.02G091000' => 'cil', 'CiPaw.02G091100' => 'cil', 'CiPaw.08G103100' => 'cil', 'CiPaw.09G224900' => 'cil', 'ClCG06G005740' => 'cla', 'ClCG07G000090' => 'cla', 'ClCG07G000100' => 'cla', 'COL.COLO4_09143' => 'col', 'COL.COLO4_25124' => 'col', 'Cpa.g.sc16.34' => 'cpa', 'Cpa.g.sc3504.1' => 'cpa', 'Cpa.g.sc60.37' => 'cpa', 'CsaV3_6G018520' => 'csa', 'CsaV3_6G036860' => 'csa', 'CSS0001072' => 'camsi', 'CSS0020208' => 'camsi', 'CSS0021253' => 'camsi', 'CSS0022190' => 'camsi', 'CSS0036150' => 'camsi', 'CSS0040442' => 'camsi', 'CSS0042300' => 'camsi', 'CSS0045298' => 'camsi', 'DCAR_012449' => 'dca', 'DCAR_018405' => 'dca', 'DCAR_024573' => 'dca', 'DCAR_030591' => 'dca', 'Dinv16926' => 'din', 'Dinv32963' => 'din', 'Dinv38382' => 'din', 'Dinv38383' => 'din', 'Duzib133G0974' => 'dzi', 'Duzib138G1867' => 'dzi', 'Duzib211G0420' => 'dzi', 'Duzib212G0930' => 'dzi', 'ECA234G1645' => 'eca', 'ECA247G3467' => 'eca', 'ECA248G1703' => 'eca', 'EL10Ac3g06327' => 'bvu', 'EL10Ac7g17204' => 'bvu', 'Eucgr.A00855' => 'egr', 'Eucgr.A00858' => 'egr', 'Eucgr.H01520' => 'egr', 'Eucgr.H03604' => 'egr', 'Eucgr.L03465' => 'egr', 'Eucgr.L03466' => 'egr', 'FAN01G0988' => 'fan', 'FAN02G3892' => 'fan', 'FAN05G3381' => 'fan', 'FAN07G0967' => 'fan', 'FAN07G1493' => 'fan', 'FAN08G3125' => 'fan', 'FAN09G0402' => 'fan', 'FAN12G2594' => 'fan', 'FAN12G3879' => 'fan', 'FAN14G1546' => 'fan', 'FAN15G3626' => 'fan', 'FAN17G0588' => 'fan', 'FAN17G0609' => 'fan', 'FAN18G2817' => 'fan', 'FAN19G1305' => 'fan', 'FAN20G1787' => 'fan', 'FAN22G0073' => 'fan', 'FAN22G0352' => 'fan', 'FAN22G0368' => 'fan', 'FAN22G2273' => 'fan', 'FAN24G1998' => 'fan', 'FAN27G1317' => 'fan', 'FvH4_2g23980' => 'fve', 'FvH4_4g14380' => 'fve', 'FvH4_4g14390' => 'fve', 'FvH4_6g09250' => 'fve', 'Glyma.03G151100' => 'gma', 'Glyma.04G122550' => 'gma', 'Glyma.05G001600' => 'gma', 'Glyma.09G270766' => 'gma', 'Glyma.09G270832' => 'gma', 'Glyma.13G209800' => 'gma', 'Glyma.15G102800' => 'gma', 'Glyma.18G218900' => 'gma', 'Glyma.19G001500' => 'gma', 'Glyma.19G153600' => 'gma', 'Gohir.A02G028600' => 'ghi', 'Gohir.A08G045000' => 'ghi', 'Gohir.A11G120500' => 'ghi', 'Gohir.A12G006200' => 'ghi', 'Gohir.A12G006250' => 'ghi', 'Gohir.D02G036300' => 'ghi', 'Gohir.D08G054700' => 'ghi', 'Gohir.D11G125600' => 'ghi', 'Gohir.D12G005700' => 'ghi', 'Gorai.004G055200' => 'gra', 'Gorai.005G040400' => 'gra', 'Gorai.007G134500' => 'gra', 'Gorai.008G005500' => 'gra', 'GSVIVG01011094001' => 'vvi', 'GSVIVG01017879001' => 'vvi', 'GSVIVG01025988001' => 'vvi', 'GSVIVG01029847001' => 'vvi', 'HanXRQChr10g0282901' => 'han', 'HanXRQChr10g0310371' => 'han', 'HanXRQChr10g0315041' => 'han', 'HanXRQChr11g0327651' => 'han', 'HanXRQChr12g0359391' => 'han', 'Haze_00972' => 'cav', 'Haze_00973' => 'cav', 'Haze_00974' => 'cav', 'Haze_04747' => 'cav', 'Haze_04749' => 'cav', 'Haze_04750' => 'cav', 'Haze_21217' => 'cav', 'Hma1.2p1_1037F.1_g250680' => 'hma', 'Hma1.2p1_1644F.1_g295320' => 'hma', 'HPP92_011322' => 'vpl', 'HPP92_011323' => 'vpl', 'HPP92_011324' => 'vpl', 'HPP92_011325' => 'vpl', 'HPP92_011326' => 'vpl', 'Hund12205' => 'sun', 'Hund17957' => 'sun', 'Lalb_Chr06g0176771' => 'lal', 'Lalb_Chr18g0056021' => 'lal', 'Lalb_Chr18g0056031' => 'lal', 'Lalb_Chr18g0056041' => 'lal', 'Lalb_Chr20g0107751' => 'lal', 'Lalb_Chr20g0118371' => 'lal', 'Lj1g0010239' => 'lja', 'Lj1g0017101' => 'lja', 'Lj2A1178G40' => 'lonja', 'Lj2A54G84' => 'lonja', 'Lj2g0015248' => 'lja', 'Lj3A761T51' => 'lonja', 'Lj6g0018116' => 'lja', 'Lsat_1_v5_gn_4_136040' => 'lsa', 'Lsat_1_v5_gn_5_187461' => 'lsa', 'Lsat_1_v5_gn_5_77001' => 'lsa', 'Lsat_1_v5_gn_9_4461' => 'lsa', 'Manes.01G210100' => 'mes', 'Manes.03G185600' => 'mes', 'Manes.05G073300' => 'mes', 'Manes.09G120300' => 'mes', 'Manes.15G022100' => 'mes', 'Mapoly0096s0053' => 'mpo', 'MBI03_g14058_MAGBIO' => 'mbi', 'MBI03_g33876_MAGBIO' => 'mbi', 'MBI03_g36854_MAGBIO' => 'mbi', 'MBI17_g11997_MAGBIO' => 'mbi', 'MD03G1269000' => 'mdo', 'MD04G1179600' => 'mdo', 'MD11G1289800' => 'mdo', 'MD12G1194700' => 'mdo', 'MD13G1182100' => 'mdo', 'MD13G1182200' => 'mdo', 'MD16G1182600' => 'mdo', 'Medtr2g021400' => 'mtr', 'Medtr2g021470' => 'mtr', 'Medtr2g105810' => 'mtr', 'Medtr3g033580' => 'mtr', 'Medtr6g007970' => 'mtr', 'Medtr7g056330' => 'mtr', 'Medtr7g074290' => 'mtr', 'Medtr7g074380' => 'mtr', 'Medtr7g094550' => 'mtr', 'Medtr8g069995' => 'mtr', 'MELO3C014345.2' => 'cme', 'MELO3C021395.2' => 'cme', 'Migut.D00262' => 'egut', 'Migut.G00257' => 'egut', 'MSTRG.21575' => 'ama', 'MSTRG.3985' => 'ama', 'Nitab4.5_0000295g0140' => 'nta', 'Nitab4.5_0000732g0140' => 'nta', 'Nitab4.5_0003162g0020' => 'nta', 'Nitab4.5_0006180g0090' => 'nta', 'Nitab4.5_0006390g0010' => 'nta', 'Nitab4.5_0007392g0040' => 'nta', 'Nn1g02140' => 'nnu', 'Nn4g26168' => 'nnu', 'Nn5g26754' => 'nnu', 'Oeu001433.1' => 'oeu', 'Oeu010299.2' => 'oeu', 'Oeu011171.1' => 'oeu', 'Oeu037675.1' => 'oeu', 'Oeu038359.1' => 'oeu', 'Oeu063834.1' => 'oeu', 'Oeu063835.1' => 'oeu', 'Os05g0312000' => 'osa', 'Os07g0211101' => 'osa', 'Os07g0211200' => 'osa', 'Os07g0681500' => 'osa', 'Peaxi162Scf00095g01015' => 'pax', 'Peaxi162Scf00104g00329' => 'pax', 'Peaxi162Scf00161g00137' => 'pax', 'PGR004G1665' => 'pgr', 'PGR031G2937' => 'pgr', 'PGR119G2145' => 'pgr', 'PGSC0003DMG400004351' => 'stu', 'PGSC0003DMG400014625' => 'stu', 'PGSC0003DMG401000943' => 'stu', 'Phvul.001G148600' => 'pvu', 'Phvul.004G001700' => 'pvu', 'Phvul.006G154900' => 'pvu', 'Phvul.008G078200' => 'pvu', 'Phvul.011G136500' => 'pvu', 'Potri.002G215600' => 'ptr', 'Potri.008G201600' => 'ptr', 'Potri.014G138400' => 'ptr', 'Potri.016G142500' => 'ptr', 'Pp3c16_10580' => 'ppa', 'Pp3c5_25280' => 'ppa', 'Prupe.1G150000' => 'ppe', 'Prupe.1G150100' => 'ppe', 'Prupe.6G299600' => 'ppe', 'Prupe.8G245000' => 'ppe', 'Psat0s4927g0040' => 'psa', 'Psat1g052080' => 'psa', 'Psat1g183800' => 'psa', 'Psat3g113840' => 'psa', 'Psat3g126120' => 'psa', 'Psat3g126160' => 'psa', 'Psat3g158760' => 'psa', 'Psat3g158840' => 'psa', 'PSO170G2858' => 'pso', 'PSO339G0606' => 'pso', 'PSO384G4709' => 'pso', 'PSO407G0334' => 'pso', 'QL04p040276' => 'qlo', 'QL06p005458' => 'qlo', 'QL06p005472' => 'qlo', 'QL07p030546' => 'qlo', 'QL07p031519' => 'qlo', 'QL09p050949' => 'qlo', 'QL09p050966' => 'qlo', 'QL09p051067' => 'qlo', 'QL12p022706' => 'qlo', 'RcHm_v2.0_Chr2g0119601' => 'rch', 'RcHm_v2.0_Chr3g0459591' => 'rch', 'RcHm_v2.0_Chr4g0418521' => 'rch', 'RcHm_v2.0_Chr4g0418531' => 'rch', 'RcHm_v2.0_Chr4g0418541' => 'rch', 'RcHm_v2.0_Chr6g0291641' => 'rch', 'Rhsim01G0086300' => 'rsi', 'Rhsim01G0276300' => 'rsi', 'Rhsim01G0276500' => 'rsi', 'Rhsim04G0207700' => 'rsi', 'Rhsim05G0234500' => 'rsi', 'Rhsim13G0022400' => 'rsi', 'Sabra02G0167900' => 'sbr', 'Sabra04G0158500' => 'sbr', 'Sabra08G0159800' => 'sbr', 'Sabra10G0011500' => 'sbr', 'Sabra14G0104400' => 'sbr', 'SalBow2G2440' => 'sbo', 'SalBow4G2265' => 'sbo', 'Sc02g0000060' => 'sci', 'Sc05g0005020' => 'sci', 'Sc13g0003890' => 'sci', 'Sed0014865' => 'sed', 'Sed0017224' => 'sed', 'Sed0026391' => 'sed', 'SEGI_00063' => 'sgi', 'SEGI_10967' => 'sgi', 'SEGI_17510' => 'sgi', 'SEGI_24396' => 'sgi', 'SEGI_39719' => 'sgi', 'SEGI_41392' => 'sgi', 'SGA_v2.0_scaffold11G05794' => 'sas', 'SGA_v2.0_scaffold142G35607' => 'sas', 'SGA_v2.0_scaffold1G00447' => 'sas', 'SHI15388' => 'shi', 'SHI15394' => 'shi', 'SHI15396' => 'shi', 'SHI15399' => 'shi', 'SMO343G0151' => 'smo', 'SMO367G1118' => 'smo', 'Solyc01g080200.3' => 'sly', 'Solyc06g008960.3' => 'sly', 'Solyc09g064780.3' => 'sly', 'Sopen01g031980' => 'spe', 'Sopen06g003710' => 'spe', 'Sopen09g026460' => 'spe', 'Sp3g21240' => 'spa', 'Sp4g30030' => 'spa', 'TAR365G0022' => 'tar', 'TAR365G1023' => 'tar', 'TAR365G1253' => 'tar', 'TAR623G0078' => 'tar', 'TAR623G1721' => 'tar', 'TAR633G0959' => 'tar', 'THA.LOC104802225' => 'tha', 'THA.LOC104804769' => 'tha', 'THA.LOC104808660' => 'tha', 'THA.LOC104812792' => 'tha', 'Thecc.01G284000' => 'tca', 'Thecc.04G220600' => 'tca', 'Thecc.05G268900' => 'tca', 'Thecc.08G171100' => 'tca', 'Thhalv10001284m.g' => 'esa', 'Thhalv10019912m.g' => 'esa', 'TPR.G14189' => 'tpr', 'TPR.G18110' => 'tpr', 'TPR.G18130' => 'tpr', 'TPR.G18131' => 'tpr', 'TPR.G18140' => 'tpr', 'TPR.G24282' => 'tpr', 'TPR.G25221' => 'tpr', 'TPR.G29267' => 'tpr', 'TPR.G35315' => 'tpr', 'TPR.G36173' => 'tpr', 'TWI09G0794' => 'twi', 'TWI59G1348' => 'twi', 'TWI74G0430' => 'twi', 'unitig_26.g8940' => 'ugi', 'unitig_749.g13744' => 'ugi', 'unitig_749.g13745' => 'ugi', 'vmacro08269' => 'vma', 'vmacro14937' => 'vma', 'vmacro20401' => 'vma', 'VMungo0464G1349' => 'vmu', 'VMungo0540G0289' => 'vmu', 'VMungo1215G1590' => 'vmu', 'VMungo1309G0221' => 'vmu', 'VMungo1309G2815' => 'vmu', 'VMungo1383G0239' => 'vmu', 'VMungo1383G2910' => 'vmu', 'Zm00001eb095270' => 'zma', 'Zm00001eb095280' => 'zma', 'Zm00001eb111630' => 'zma', 'Zm00001eb237080' => 'zma', 'Zm00001eb273740' => 'zma', 'Zm00001eb285040' => 'zma', 'Zm00001eb330790' => 'zma', 'Zm00001eb337380' => 'zma' ) $gf_id = 'HOM05D001484' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001484' ) $data_identifier = 'HOM05D001484' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 2, 'aly' => (int) 2, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 22, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 7, 'hma' => (int) 2, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 7, 'mtr' => (int) 10, 'cme' => (int) 2, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 4, 'ppa' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 4, 'qlo' => (int) 9, 'rch' => (int) 6, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 10, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 7, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb337380' $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' => 'HOM05D001484', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p31500' => 'bna', 'A05p00020' => 'bna', 'A07p08820' => 'bna', 'Aa31LG4G3300' => 'aar', 'Aa31LG8G10030' => 'aar', 'Actinidia00731' => 'ach', 'Actinidia11473' => 'ach', 'Actinidia23469' => 'ach', 'Actinidia24318' => 'ach', 'Actinidia40196' => 'ach', 'Actinidia40197' => 'ach', 'Actinidia40198' => 'ach', 'Ah.08g212990' => 'amhyb', 'Ah.15g091720' => 'amhyb', 'AL3G38260' => 'aly', 'AL4G47710' => 'aly', 'Aqoxy2G00671' => 'aox', 'Aqoxy2G03236' => 'aox', 'arahy.Tifrunner.gnm1.ann1.05IDCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KR684' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATY3SJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK6QJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6APGL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IDT7Z9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM073U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ0R87' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LE7RV4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT4QRX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V5ENPK' => 'arhy', 'AT2G48110' => 'ath', 'AT3G23590' => 'ath', 'ATR0626G186' => 'atr', 'ATR1127G141' => 'atr', 'Atru.chr4.2583' => 'acertr', 'Atru.chr5.1358' => 'acertr', 'Atru.chr5.1359' => 'acertr', 'Atru.chr8.46' => 'acertr', 'AUR62002640' => 'cqu', 'AUR62030055' => 'cqu', 'AUR62033713' => 'cqu', 'AUR62033714' => 'cqu', 'AUR62036795' => 'cqu', 'AUR62039891' => 'cqu', 'BcaB02g08737' => 'bca', 'BcaB04g20441' => 'bca', 'BcaB06g26509' => 'bca', 'BcaB06g26510' => 'bca', 'BcaB06g26511' => 'bca', 'BcaB06g26512' => 'bca', 'BcaB06g26513' => 'bca', 'BcaC02g12564' => 'bca', 'BcaC02g12565' => 'bca', 'BcaC02g12794' => 'bca', 'BcaC02g12795' => 'bca', 'BcaC02g12796' => 'bca', 'BcaC06g35541' => 'bca', 'BNapus_Darmor_BZH_scaffold_188p00080' => 'bna', 'BNapus_Darmor_BZH_scaffold_188p00090' => 'bna', 'BolC1t03972H' => 'bol', 'BolC1t03973H' => 'bol', 'BolC4t21680H' => 'bol', 'BolC7t41863H' => 'bol', 'BolSC55t61227H' => 'bol', 'BolSC55t61228H' => 'bol', 'BraA01t03278Z' => 'bra', 'BraA05t18998Z' => 'bra', 'BraA07t28673Z' => 'bra', 'C01p40150' => 'bna', 'C05p12370' => 'bna', 'C07p13680' => 'bna', 'CAN.G1006.16' => 'can', 'CAN.G1006.17' => 'can', 'CAN.G1170.2' => 'can', 'CAN.G962.7' => 'can', 'CANSAT25G2179' => 'cansat', 'CANSAT78G1573' => 'cansat', 'CARHR099510' => 'chi', 'CARHR143510' => 'chi', 'Carub.0003s2380' => 'cru', 'Carub.0004s3082' => 'cru', 'Ca_00614_v3' => 'car', 'Ca_07801_v3' => 'car', 'Ca_08567_v3' => 'car', 'Ca_09571_v3' => 'car', 'CBR_g19290' => 'cbr', 'Cc01_g19770' => 'ccan', 'Cc03_g03030' => 'ccan', 'CDE07G0968' => 'cde', 'CDE09G1441' => 'cde', 'Cfa006103' => 'cfa', 'Cfa015573' => 'cfa', 'Cfa016988' => 'cfa', 'Ciclev10006738m.g' => 'ccl', 'Ciclev10010920m.g' => 'ccl', 'Ciclev10018517m.g' => 'ccl', 'CiPaw.01G159200' => 'cil', 'CiPaw.02G091000' => 'cil', 'CiPaw.02G091100' => 'cil', 'CiPaw.08G103100' => 'cil', 'CiPaw.09G224900' => 'cil', 'ClCG06G005740' => 'cla', 'ClCG07G000090' => 'cla', 'ClCG07G000100' => 'cla', 'COL.COLO4_09143' => 'col', 'COL.COLO4_25124' => 'col', 'Cpa.g.sc16.34' => 'cpa', 'Cpa.g.sc3504.1' => 'cpa', 'Cpa.g.sc60.37' => 'cpa', 'CsaV3_6G018520' => 'csa', 'CsaV3_6G036860' => 'csa', 'CSS0001072' => 'camsi', 'CSS0020208' => 'camsi', 'CSS0021253' => 'camsi', 'CSS0022190' => 'camsi', 'CSS0036150' => 'camsi', 'CSS0040442' => 'camsi', 'CSS0042300' => 'camsi', 'CSS0045298' => 'camsi', 'DCAR_012449' => 'dca', 'DCAR_018405' => 'dca', 'DCAR_024573' => 'dca', 'DCAR_030591' => 'dca', 'Dinv16926' => 'din', 'Dinv32963' => 'din', 'Dinv38382' => 'din', 'Dinv38383' => 'din', 'Duzib133G0974' => 'dzi', 'Duzib138G1867' => 'dzi', 'Duzib211G0420' => 'dzi', 'Duzib212G0930' => 'dzi', 'ECA234G1645' => 'eca', 'ECA247G3467' => 'eca', 'ECA248G1703' => 'eca', 'EL10Ac3g06327' => 'bvu', 'EL10Ac7g17204' => 'bvu', 'Eucgr.A00855' => 'egr', 'Eucgr.A00858' => 'egr', 'Eucgr.H01520' => 'egr', 'Eucgr.H03604' => 'egr', 'Eucgr.L03465' => 'egr', 'Eucgr.L03466' => 'egr', 'FAN01G0988' => 'fan', 'FAN02G3892' => 'fan', 'FAN05G3381' => 'fan', 'FAN07G0967' => 'fan', 'FAN07G1493' => 'fan', 'FAN08G3125' => 'fan', 'FAN09G0402' => 'fan', 'FAN12G2594' => 'fan', 'FAN12G3879' => 'fan', 'FAN14G1546' => 'fan', 'FAN15G3626' => 'fan', 'FAN17G0588' => 'fan', 'FAN17G0609' => 'fan', 'FAN18G2817' => 'fan', 'FAN19G1305' => 'fan', 'FAN20G1787' => 'fan', 'FAN22G0073' => 'fan', 'FAN22G0352' => 'fan', 'FAN22G0368' => 'fan', 'FAN22G2273' => 'fan', 'FAN24G1998' => 'fan', 'FAN27G1317' => 'fan', 'FvH4_2g23980' => 'fve', 'FvH4_4g14380' => 'fve', 'FvH4_4g14390' => 'fve', 'FvH4_6g09250' => 'fve', 'Glyma.03G151100' => 'gma', 'Glyma.04G122550' => 'gma', 'Glyma.05G001600' => 'gma', 'Glyma.09G270766' => 'gma', 'Glyma.09G270832' => 'gma', 'Glyma.13G209800' => 'gma', 'Glyma.15G102800' => 'gma', 'Glyma.18G218900' => 'gma', 'Glyma.19G001500' => 'gma', 'Glyma.19G153600' => 'gma', 'Gohir.A02G028600' => 'ghi', 'Gohir.A08G045000' => 'ghi', 'Gohir.A11G120500' => 'ghi', 'Gohir.A12G006200' => 'ghi', 'Gohir.A12G006250' => 'ghi', 'Gohir.D02G036300' => 'ghi', 'Gohir.D08G054700' => 'ghi', 'Gohir.D11G125600' => 'ghi', 'Gohir.D12G005700' => 'ghi', 'Gorai.004G055200' => 'gra', 'Gorai.005G040400' => 'gra', 'Gorai.007G134500' => 'gra', 'Gorai.008G005500' => 'gra', 'GSVIVG01011094001' => 'vvi', 'GSVIVG01017879001' => 'vvi', 'GSVIVG01025988001' => 'vvi', 'GSVIVG01029847001' => 'vvi', 'HanXRQChr10g0282901' => 'han', 'HanXRQChr10g0310371' => 'han', 'HanXRQChr10g0315041' => 'han', 'HanXRQChr11g0327651' => 'han', 'HanXRQChr12g0359391' => 'han', 'Haze_00972' => 'cav', 'Haze_00973' => 'cav', 'Haze_00974' => 'cav', 'Haze_04747' => 'cav', 'Haze_04749' => 'cav', 'Haze_04750' => 'cav', 'Haze_21217' => 'cav', 'Hma1.2p1_1037F.1_g250680' => 'hma', 'Hma1.2p1_1644F.1_g295320' => 'hma', 'HPP92_011322' => 'vpl', 'HPP92_011323' => 'vpl', 'HPP92_011324' => 'vpl', 'HPP92_011325' => 'vpl', 'HPP92_011326' => 'vpl', 'Hund12205' => 'sun', 'Hund17957' => 'sun', 'Lalb_Chr06g0176771' => 'lal', 'Lalb_Chr18g0056021' => 'lal', 'Lalb_Chr18g0056031' => 'lal', 'Lalb_Chr18g0056041' => 'lal', 'Lalb_Chr20g0107751' => 'lal', 'Lalb_Chr20g0118371' => 'lal', 'Lj1g0010239' => 'lja', 'Lj1g0017101' => 'lja', 'Lj2A1178G40' => 'lonja', 'Lj2A54G84' => 'lonja', 'Lj2g0015248' => 'lja', 'Lj3A761T51' => 'lonja', 'Lj6g0018116' => 'lja', 'Lsat_1_v5_gn_4_136040' => 'lsa', 'Lsat_1_v5_gn_5_187461' => 'lsa', 'Lsat_1_v5_gn_5_77001' => 'lsa', 'Lsat_1_v5_gn_9_4461' => 'lsa', 'Manes.01G210100' => 'mes', 'Manes.03G185600' => 'mes', 'Manes.05G073300' => 'mes', 'Manes.09G120300' => 'mes', 'Manes.15G022100' => 'mes', 'Mapoly0096s0053' => 'mpo', 'MBI03_g14058_MAGBIO' => 'mbi', 'MBI03_g33876_MAGBIO' => 'mbi', 'MBI03_g36854_MAGBIO' => 'mbi', 'MBI17_g11997_MAGBIO' => 'mbi', 'MD03G1269000' => 'mdo', 'MD04G1179600' => 'mdo', 'MD11G1289800' => 'mdo', 'MD12G1194700' => 'mdo', 'MD13G1182100' => 'mdo', 'MD13G1182200' => 'mdo', 'MD16G1182600' => 'mdo', 'Medtr2g021400' => 'mtr', 'Medtr2g021470' => 'mtr', 'Medtr2g105810' => 'mtr', 'Medtr3g033580' => 'mtr', 'Medtr6g007970' => 'mtr', 'Medtr7g056330' => 'mtr', 'Medtr7g074290' => 'mtr', 'Medtr7g074380' => 'mtr', 'Medtr7g094550' => 'mtr', 'Medtr8g069995' => 'mtr', 'MELO3C014345.2' => 'cme', 'MELO3C021395.2' => 'cme', 'Migut.D00262' => 'egut', 'Migut.G00257' => 'egut', 'MSTRG.21575' => 'ama', 'MSTRG.3985' => 'ama', 'Nitab4.5_0000295g0140' => 'nta', 'Nitab4.5_0000732g0140' => 'nta', 'Nitab4.5_0003162g0020' => 'nta', 'Nitab4.5_0006180g0090' => 'nta', 'Nitab4.5_0006390g0010' => 'nta', 'Nitab4.5_0007392g0040' => 'nta', 'Nn1g02140' => 'nnu', 'Nn4g26168' => 'nnu', 'Nn5g26754' => 'nnu', 'Oeu001433.1' => 'oeu', 'Oeu010299.2' => 'oeu', 'Oeu011171.1' => 'oeu', 'Oeu037675.1' => 'oeu', 'Oeu038359.1' => 'oeu', 'Oeu063834.1' => 'oeu', 'Oeu063835.1' => 'oeu', 'Os05g0312000' => 'osa', 'Os07g0211101' => 'osa', 'Os07g0211200' => 'osa', 'Os07g0681500' => 'osa', 'Peaxi162Scf00095g01015' => 'pax', 'Peaxi162Scf00104g00329' => 'pax', 'Peaxi162Scf00161g00137' => 'pax', 'PGR004G1665' => 'pgr', 'PGR031G2937' => 'pgr', 'PGR119G2145' => 'pgr', 'PGSC0003DMG400004351' => 'stu', 'PGSC0003DMG400014625' => 'stu', 'PGSC0003DMG401000943' => 'stu', 'Phvul.001G148600' => 'pvu', 'Phvul.004G001700' => 'pvu', 'Phvul.006G154900' => 'pvu', 'Phvul.008G078200' => 'pvu', 'Phvul.011G136500' => 'pvu', 'Potri.002G215600' => 'ptr', 'Potri.008G201600' => 'ptr', 'Potri.014G138400' => 'ptr', 'Potri.016G142500' => 'ptr', 'Pp3c16_10580' => 'ppa', 'Pp3c5_25280' => 'ppa', 'Prupe.1G150000' => 'ppe', 'Prupe.1G150100' => 'ppe', 'Prupe.6G299600' => 'ppe', 'Prupe.8G245000' => 'ppe', 'Psat0s4927g0040' => 'psa', 'Psat1g052080' => 'psa', 'Psat1g183800' => 'psa', 'Psat3g113840' => 'psa', 'Psat3g126120' => 'psa', 'Psat3g126160' => 'psa', 'Psat3g158760' => 'psa', 'Psat3g158840' => 'psa', 'PSO170G2858' => 'pso', 'PSO339G0606' => 'pso', 'PSO384G4709' => 'pso', 'PSO407G0334' => 'pso', 'QL04p040276' => 'qlo', 'QL06p005458' => 'qlo', 'QL06p005472' => 'qlo', 'QL07p030546' => 'qlo', 'QL07p031519' => 'qlo', 'QL09p050949' => 'qlo', 'QL09p050966' => 'qlo', 'QL09p051067' => 'qlo', 'QL12p022706' => 'qlo', 'RcHm_v2.0_Chr2g0119601' => 'rch', 'RcHm_v2.0_Chr3g0459591' => 'rch', 'RcHm_v2.0_Chr4g0418521' => 'rch', 'RcHm_v2.0_Chr4g0418531' => 'rch', 'RcHm_v2.0_Chr4g0418541' => 'rch', 'RcHm_v2.0_Chr6g0291641' => 'rch', 'Rhsim01G0086300' => 'rsi', 'Rhsim01G0276300' => 'rsi', 'Rhsim01G0276500' => 'rsi', 'Rhsim04G0207700' => 'rsi', 'Rhsim05G0234500' => 'rsi', 'Rhsim13G0022400' => 'rsi', 'Sabra02G0167900' => 'sbr', 'Sabra04G0158500' => 'sbr', 'Sabra08G0159800' => 'sbr', 'Sabra10G0011500' => 'sbr', 'Sabra14G0104400' => 'sbr', 'SalBow2G2440' => 'sbo', 'SalBow4G2265' => 'sbo', 'Sc02g0000060' => 'sci', 'Sc05g0005020' => 'sci', 'Sc13g0003890' => 'sci', 'Sed0014865' => 'sed', 'Sed0017224' => 'sed', 'Sed0026391' => 'sed', 'SEGI_00063' => 'sgi', 'SEGI_10967' => 'sgi', 'SEGI_17510' => 'sgi', 'SEGI_24396' => 'sgi', 'SEGI_39719' => 'sgi', 'SEGI_41392' => 'sgi', 'SGA_v2.0_scaffold11G05794' => 'sas', 'SGA_v2.0_scaffold142G35607' => 'sas', 'SGA_v2.0_scaffold1G00447' => 'sas', 'SHI15388' => 'shi', 'SHI15394' => 'shi', 'SHI15396' => 'shi', 'SHI15399' => 'shi', 'SMO343G0151' => 'smo', 'SMO367G1118' => 'smo', 'Solyc01g080200.3' => 'sly', 'Solyc06g008960.3' => 'sly', 'Solyc09g064780.3' => 'sly', 'Sopen01g031980' => 'spe', 'Sopen06g003710' => 'spe', 'Sopen09g026460' => 'spe', 'Sp3g21240' => 'spa', 'Sp4g30030' => 'spa', 'TAR365G0022' => 'tar', 'TAR365G1023' => 'tar', 'TAR365G1253' => 'tar', 'TAR623G0078' => 'tar', 'TAR623G1721' => 'tar', 'TAR633G0959' => 'tar', 'THA.LOC104802225' => 'tha', 'THA.LOC104804769' => 'tha', 'THA.LOC104808660' => 'tha', 'THA.LOC104812792' => 'tha', 'Thecc.01G284000' => 'tca', 'Thecc.04G220600' => 'tca', 'Thecc.05G268900' => 'tca', 'Thecc.08G171100' => 'tca', 'Thhalv10001284m.g' => 'esa', 'Thhalv10019912m.g' => 'esa', 'TPR.G14189' => 'tpr', 'TPR.G18110' => 'tpr', 'TPR.G18130' => 'tpr', 'TPR.G18131' => 'tpr', 'TPR.G18140' => 'tpr', 'TPR.G24282' => 'tpr', 'TPR.G25221' => 'tpr', 'TPR.G29267' => 'tpr', 'TPR.G35315' => 'tpr', 'TPR.G36173' => 'tpr', 'TWI09G0794' => 'twi', 'TWI59G1348' => 'twi', 'TWI74G0430' => 'twi', 'unitig_26.g8940' => 'ugi', 'unitig_749.g13744' => 'ugi', 'unitig_749.g13745' => 'ugi', 'vmacro08269' => 'vma', 'vmacro14937' => 'vma', 'vmacro20401' => 'vma', 'VMungo0464G1349' => 'vmu', 'VMungo0540G0289' => 'vmu', 'VMungo1215G1590' => 'vmu', 'VMungo1309G0221' => 'vmu', 'VMungo1309G2815' => 'vmu', 'VMungo1383G0239' => 'vmu', 'VMungo1383G2910' => 'vmu', 'Zm00001eb095270' => 'zma', 'Zm00001eb095280' => 'zma', 'Zm00001eb111630' => 'zma', 'Zm00001eb237080' => 'zma', 'Zm00001eb273740' => 'zma', 'Zm00001eb285040' => 'zma', 'Zm00001eb330790' => 'zma', 'Zm00001eb337380' => 'zma' ), 'gf_id' => 'HOM05D001484', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001484' ), 'data_identifier' => 'HOM05D001484', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001484', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p31500' => 'bna', 'A05p00020' => 'bna', 'A07p08820' => 'bna', 'Aa31LG4G3300' => 'aar', 'Aa31LG8G10030' => 'aar', 'Actinidia00731' => 'ach', 'Actinidia11473' => 'ach', 'Actinidia23469' => 'ach', 'Actinidia24318' => 'ach', 'Actinidia40196' => 'ach', 'Actinidia40197' => 'ach', 'Actinidia40198' => 'ach', 'Ah.08g212990' => 'amhyb', 'Ah.15g091720' => 'amhyb', 'AL3G38260' => 'aly', 'AL4G47710' => 'aly', 'Aqoxy2G00671' => 'aox', 'Aqoxy2G03236' => 'aox', 'arahy.Tifrunner.gnm1.ann1.05IDCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KR684' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATY3SJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK6QJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6APGL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IDT7Z9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM073U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ0R87' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LE7RV4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT4QRX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V5ENPK' => 'arhy', 'AT2G48110' => 'ath', 'AT3G23590' => 'ath', 'ATR0626G186' => 'atr', 'ATR1127G141' => 'atr', 'Atru.chr4.2583' => 'acertr', 'Atru.chr5.1358' => 'acertr', 'Atru.chr5.1359' => 'acertr', 'Atru.chr8.46' => 'acertr', 'AUR62002640' => 'cqu', 'AUR62030055' => 'cqu', 'AUR62033713' => 'cqu', 'AUR62033714' => 'cqu', 'AUR62036795' => 'cqu', 'AUR62039891' => 'cqu', 'BcaB02g08737' => 'bca', 'BcaB04g20441' => 'bca', 'BcaB06g26509' => 'bca', 'BcaB06g26510' => 'bca', 'BcaB06g26511' => 'bca', 'BcaB06g26512' => 'bca', 'BcaB06g26513' => 'bca', 'BcaC02g12564' => 'bca', 'BcaC02g12565' => 'bca', 'BcaC02g12794' => 'bca', 'BcaC02g12795' => 'bca', 'BcaC02g12796' => 'bca', 'BcaC06g35541' => 'bca', 'BNapus_Darmor_BZH_scaffold_188p00080' => 'bna', 'BNapus_Darmor_BZH_scaffold_188p00090' => 'bna', 'BolC1t03972H' => 'bol', 'BolC1t03973H' => 'bol', 'BolC4t21680H' => 'bol', 'BolC7t41863H' => 'bol', 'BolSC55t61227H' => 'bol', 'BolSC55t61228H' => 'bol', 'BraA01t03278Z' => 'bra', 'BraA05t18998Z' => 'bra', 'BraA07t28673Z' => 'bra', 'C01p40150' => 'bna', 'C05p12370' => 'bna', 'C07p13680' => 'bna', 'CAN.G1006.16' => 'can', 'CAN.G1006.17' => 'can', 'CAN.G1170.2' => 'can', 'CAN.G962.7' => 'can', 'CANSAT25G2179' => 'cansat', 'CANSAT78G1573' => 'cansat', 'CARHR099510' => 'chi', 'CARHR143510' => 'chi', 'Carub.0003s2380' => 'cru', 'Carub.0004s3082' => 'cru', 'Ca_00614_v3' => 'car', 'Ca_07801_v3' => 'car', 'Ca_08567_v3' => 'car', 'Ca_09571_v3' => 'car', 'CBR_g19290' => 'cbr', 'Cc01_g19770' => 'ccan', 'Cc03_g03030' => 'ccan', 'CDE07G0968' => 'cde', 'CDE09G1441' => 'cde', 'Cfa006103' => 'cfa', 'Cfa015573' => 'cfa', 'Cfa016988' => 'cfa', 'Ciclev10006738m.g' => 'ccl', 'Ciclev10010920m.g' => 'ccl', 'Ciclev10018517m.g' => 'ccl', 'CiPaw.01G159200' => 'cil', 'CiPaw.02G091000' => 'cil', 'CiPaw.02G091100' => 'cil', 'CiPaw.08G103100' => 'cil', 'CiPaw.09G224900' => 'cil', 'ClCG06G005740' => 'cla', 'ClCG07G000090' => 'cla', 'ClCG07G000100' => 'cla', 'COL.COLO4_09143' => 'col', 'COL.COLO4_25124' => 'col', 'Cpa.g.sc16.34' => 'cpa', 'Cpa.g.sc3504.1' => 'cpa', 'Cpa.g.sc60.37' => 'cpa', 'CsaV3_6G018520' => 'csa', 'CsaV3_6G036860' => 'csa', 'CSS0001072' => 'camsi', 'CSS0020208' => 'camsi', 'CSS0021253' => 'camsi', 'CSS0022190' => 'camsi', 'CSS0036150' => 'camsi', 'CSS0040442' => 'camsi', 'CSS0042300' => 'camsi', 'CSS0045298' => 'camsi', 'DCAR_012449' => 'dca', 'DCAR_018405' => 'dca', 'DCAR_024573' => 'dca', 'DCAR_030591' => 'dca', 'Dinv16926' => 'din', 'Dinv32963' => 'din', 'Dinv38382' => 'din', 'Dinv38383' => 'din', 'Duzib133G0974' => 'dzi', 'Duzib138G1867' => 'dzi', 'Duzib211G0420' => 'dzi', 'Duzib212G0930' => 'dzi', 'ECA234G1645' => 'eca', 'ECA247G3467' => 'eca', 'ECA248G1703' => 'eca', 'EL10Ac3g06327' => 'bvu', 'EL10Ac7g17204' => 'bvu', 'Eucgr.A00855' => 'egr', 'Eucgr.A00858' => 'egr', 'Eucgr.H01520' => 'egr', 'Eucgr.H03604' => 'egr', 'Eucgr.L03465' => 'egr', 'Eucgr.L03466' => 'egr', 'FAN01G0988' => 'fan', 'FAN02G3892' => 'fan', 'FAN05G3381' => 'fan', 'FAN07G0967' => 'fan', 'FAN07G1493' => 'fan', 'FAN08G3125' => 'fan', 'FAN09G0402' => 'fan', 'FAN12G2594' => 'fan', 'FAN12G3879' => 'fan', 'FAN14G1546' => 'fan', 'FAN15G3626' => 'fan', 'FAN17G0588' => 'fan', 'FAN17G0609' => 'fan', 'FAN18G2817' => 'fan', 'FAN19G1305' => 'fan', 'FAN20G1787' => 'fan', 'FAN22G0073' => 'fan', 'FAN22G0352' => 'fan', 'FAN22G0368' => 'fan', 'FAN22G2273' => 'fan', 'FAN24G1998' => 'fan', 'FAN27G1317' => 'fan', 'FvH4_2g23980' => 'fve', 'FvH4_4g14380' => 'fve', 'FvH4_4g14390' => 'fve', 'FvH4_6g09250' => 'fve', 'Glyma.03G151100' => 'gma', 'Glyma.04G122550' => 'gma', 'Glyma.05G001600' => 'gma', 'Glyma.09G270766' => 'gma', 'Glyma.09G270832' => 'gma', 'Glyma.13G209800' => 'gma', 'Glyma.15G102800' => 'gma', 'Glyma.18G218900' => 'gma', 'Glyma.19G001500' => 'gma', 'Glyma.19G153600' => 'gma', 'Gohir.A02G028600' => 'ghi', 'Gohir.A08G045000' => 'ghi', 'Gohir.A11G120500' => 'ghi', 'Gohir.A12G006200' => 'ghi', 'Gohir.A12G006250' => 'ghi', 'Gohir.D02G036300' => 'ghi', 'Gohir.D08G054700' => 'ghi', 'Gohir.D11G125600' => 'ghi', 'Gohir.D12G005700' => 'ghi', 'Gorai.004G055200' => 'gra', 'Gorai.005G040400' => 'gra', 'Gorai.007G134500' => 'gra', 'Gorai.008G005500' => 'gra', 'GSVIVG01011094001' => 'vvi', 'GSVIVG01017879001' => 'vvi', 'GSVIVG01025988001' => 'vvi', 'GSVIVG01029847001' => 'vvi', 'HanXRQChr10g0282901' => 'han', 'HanXRQChr10g0310371' => 'han', 'HanXRQChr10g0315041' => 'han', 'HanXRQChr11g0327651' => 'han', 'HanXRQChr12g0359391' => 'han', 'Haze_00972' => 'cav', 'Haze_00973' => 'cav', 'Haze_00974' => 'cav', 'Haze_04747' => 'cav', 'Haze_04749' => 'cav', 'Haze_04750' => 'cav', 'Haze_21217' => 'cav', 'Hma1.2p1_1037F.1_g250680' => 'hma', 'Hma1.2p1_1644F.1_g295320' => 'hma', 'HPP92_011322' => 'vpl', 'HPP92_011323' => 'vpl', 'HPP92_011324' => 'vpl', 'HPP92_011325' => 'vpl', 'HPP92_011326' => 'vpl', 'Hund12205' => 'sun', 'Hund17957' => 'sun', 'Lalb_Chr06g0176771' => 'lal', 'Lalb_Chr18g0056021' => 'lal', 'Lalb_Chr18g0056031' => 'lal', 'Lalb_Chr18g0056041' => 'lal', 'Lalb_Chr20g0107751' => 'lal', 'Lalb_Chr20g0118371' => 'lal', 'Lj1g0010239' => 'lja', 'Lj1g0017101' => 'lja', 'Lj2A1178G40' => 'lonja', 'Lj2A54G84' => 'lonja', 'Lj2g0015248' => 'lja', 'Lj3A761T51' => 'lonja', 'Lj6g0018116' => 'lja', 'Lsat_1_v5_gn_4_136040' => 'lsa', 'Lsat_1_v5_gn_5_187461' => 'lsa', 'Lsat_1_v5_gn_5_77001' => 'lsa', 'Lsat_1_v5_gn_9_4461' => 'lsa', 'Manes.01G210100' => 'mes', 'Manes.03G185600' => 'mes', 'Manes.05G073300' => 'mes', 'Manes.09G120300' => 'mes', 'Manes.15G022100' => 'mes', 'Mapoly0096s0053' => 'mpo', 'MBI03_g14058_MAGBIO' => 'mbi', 'MBI03_g33876_MAGBIO' => 'mbi', 'MBI03_g36854_MAGBIO' => 'mbi', 'MBI17_g11997_MAGBIO' => 'mbi', 'MD03G1269000' => 'mdo', 'MD04G1179600' => 'mdo', 'MD11G1289800' => 'mdo', 'MD12G1194700' => 'mdo', 'MD13G1182100' => 'mdo', 'MD13G1182200' => 'mdo', 'MD16G1182600' => 'mdo', 'Medtr2g021400' => 'mtr', 'Medtr2g021470' => 'mtr', 'Medtr2g105810' => 'mtr', 'Medtr3g033580' => 'mtr', 'Medtr6g007970' => 'mtr', 'Medtr7g056330' => 'mtr', 'Medtr7g074290' => 'mtr', 'Medtr7g074380' => 'mtr', 'Medtr7g094550' => 'mtr', 'Medtr8g069995' => 'mtr', 'MELO3C014345.2' => 'cme', 'MELO3C021395.2' => 'cme', 'Migut.D00262' => 'egut', 'Migut.G00257' => 'egut', 'MSTRG.21575' => 'ama', 'MSTRG.3985' => 'ama', 'Nitab4.5_0000295g0140' => 'nta', 'Nitab4.5_0000732g0140' => 'nta', 'Nitab4.5_0003162g0020' => 'nta', 'Nitab4.5_0006180g0090' => 'nta', 'Nitab4.5_0006390g0010' => 'nta', 'Nitab4.5_0007392g0040' => 'nta', 'Nn1g02140' => 'nnu', 'Nn4g26168' => 'nnu', 'Nn5g26754' => 'nnu', 'Oeu001433.1' => 'oeu', 'Oeu010299.2' => 'oeu', 'Oeu011171.1' => 'oeu', 'Oeu037675.1' => 'oeu', 'Oeu038359.1' => 'oeu', 'Oeu063834.1' => 'oeu', 'Oeu063835.1' => 'oeu', 'Os05g0312000' => 'osa', 'Os07g0211101' => 'osa', 'Os07g0211200' => 'osa', 'Os07g0681500' => 'osa', 'Peaxi162Scf00095g01015' => 'pax', 'Peaxi162Scf00104g00329' => 'pax', 'Peaxi162Scf00161g00137' => 'pax', 'PGR004G1665' => 'pgr', 'PGR031G2937' => 'pgr', 'PGR119G2145' => 'pgr', 'PGSC0003DMG400004351' => 'stu', 'PGSC0003DMG400014625' => 'stu', 'PGSC0003DMG401000943' => 'stu', 'Phvul.001G148600' => 'pvu', 'Phvul.004G001700' => 'pvu', 'Phvul.006G154900' => 'pvu', 'Phvul.008G078200' => 'pvu', 'Phvul.011G136500' => 'pvu', 'Potri.002G215600' => 'ptr', 'Potri.008G201600' => 'ptr', 'Potri.014G138400' => 'ptr', 'Potri.016G142500' => 'ptr', 'Pp3c16_10580' => 'ppa', 'Pp3c5_25280' => 'ppa', 'Prupe.1G150000' => 'ppe', 'Prupe.1G150100' => 'ppe', 'Prupe.6G299600' => 'ppe', 'Prupe.8G245000' => 'ppe', 'Psat0s4927g0040' => 'psa', 'Psat1g052080' => 'psa', 'Psat1g183800' => 'psa', 'Psat3g113840' => 'psa', 'Psat3g126120' => 'psa', 'Psat3g126160' => 'psa', 'Psat3g158760' => 'psa', 'Psat3g158840' => 'psa', 'PSO170G2858' => 'pso', 'PSO339G0606' => 'pso', 'PSO384G4709' => 'pso', 'PSO407G0334' => 'pso', 'QL04p040276' => 'qlo', 'QL06p005458' => 'qlo', 'QL06p005472' => 'qlo', 'QL07p030546' => 'qlo', 'QL07p031519' => 'qlo', 'QL09p050949' => 'qlo', 'QL09p050966' => 'qlo', 'QL09p051067' => 'qlo', 'QL12p022706' => 'qlo', 'RcHm_v2.0_Chr2g0119601' => 'rch', 'RcHm_v2.0_Chr3g0459591' => 'rch', 'RcHm_v2.0_Chr4g0418521' => 'rch', 'RcHm_v2.0_Chr4g0418531' => 'rch', 'RcHm_v2.0_Chr4g0418541' => 'rch', 'RcHm_v2.0_Chr6g0291641' => 'rch', 'Rhsim01G0086300' => 'rsi', 'Rhsim01G0276300' => 'rsi', 'Rhsim01G0276500' => 'rsi', 'Rhsim04G0207700' => 'rsi', 'Rhsim05G0234500' => 'rsi', 'Rhsim13G0022400' => 'rsi', 'Sabra02G0167900' => 'sbr', 'Sabra04G0158500' => 'sbr', 'Sabra08G0159800' => 'sbr', 'Sabra10G0011500' => 'sbr', 'Sabra14G0104400' => 'sbr', 'SalBow2G2440' => 'sbo', 'SalBow4G2265' => 'sbo', 'Sc02g0000060' => 'sci', 'Sc05g0005020' => 'sci', 'Sc13g0003890' => 'sci', 'Sed0014865' => 'sed', 'Sed0017224' => 'sed', 'Sed0026391' => 'sed', 'SEGI_00063' => 'sgi', 'SEGI_10967' => 'sgi', 'SEGI_17510' => 'sgi', 'SEGI_24396' => 'sgi', 'SEGI_39719' => 'sgi', 'SEGI_41392' => 'sgi', 'SGA_v2.0_scaffold11G05794' => 'sas', 'SGA_v2.0_scaffold142G35607' => 'sas', 'SGA_v2.0_scaffold1G00447' => 'sas', 'SHI15388' => 'shi', 'SHI15394' => 'shi', 'SHI15396' => 'shi', 'SHI15399' => 'shi', 'SMO343G0151' => 'smo', 'SMO367G1118' => 'smo', 'Solyc01g080200.3' => 'sly', 'Solyc06g008960.3' => 'sly', 'Solyc09g064780.3' => 'sly', 'Sopen01g031980' => 'spe', 'Sopen06g003710' => 'spe', 'Sopen09g026460' => 'spe', 'Sp3g21240' => 'spa', 'Sp4g30030' => 'spa', 'TAR365G0022' => 'tar', 'TAR365G1023' => 'tar', 'TAR365G1253' => 'tar', 'TAR623G0078' => 'tar', 'TAR623G1721' => 'tar', 'TAR633G0959' => 'tar', 'THA.LOC104802225' => 'tha', 'THA.LOC104804769' => 'tha', 'THA.LOC104808660' => 'tha', 'THA.LOC104812792' => 'tha', 'Thecc.01G284000' => 'tca', 'Thecc.04G220600' => 'tca', 'Thecc.05G268900' => 'tca', 'Thecc.08G171100' => 'tca', 'Thhalv10001284m.g' => 'esa', 'Thhalv10019912m.g' => 'esa', 'TPR.G14189' => 'tpr', 'TPR.G18110' => 'tpr', 'TPR.G18130' => 'tpr', 'TPR.G18131' => 'tpr', 'TPR.G18140' => 'tpr', 'TPR.G24282' => 'tpr', 'TPR.G25221' => 'tpr', 'TPR.G29267' => 'tpr', 'TPR.G35315' => 'tpr', 'TPR.G36173' => 'tpr', 'TWI09G0794' => 'twi', 'TWI59G1348' => 'twi', 'TWI74G0430' => 'twi', 'unitig_26.g8940' => 'ugi', 'unitig_749.g13744' => 'ugi', 'unitig_749.g13745' => 'ugi', 'vmacro08269' => 'vma', 'vmacro14937' => 'vma', 'vmacro20401' => 'vma', 'VMungo0464G1349' => 'vmu', 'VMungo0540G0289' => 'vmu', 'VMungo1215G1590' => 'vmu', 'VMungo1309G0221' => 'vmu', 'VMungo1309G2815' => 'vmu', 'VMungo1383G0239' => 'vmu', 'VMungo1383G2910' => 'vmu', 'Zm00001eb095270' => 'zma', 'Zm00001eb095280' => 'zma', 'Zm00001eb111630' => 'zma', 'Zm00001eb237080' => 'zma', 'Zm00001eb273740' => 'zma', 'Zm00001eb285040' => 'zma', 'Zm00001eb330790' => 'zma', 'Zm00001eb337380' => 'zma' ) $gf_id = 'HOM05D001484' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001484' ) $data_identifier = 'HOM05D001484' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 2, 'aly' => (int) 2, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 22, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 7, 'hma' => (int) 2, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 7, 'mtr' => (int) 10, 'cme' => (int) 2, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 4, 'ppa' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 4, 'qlo' => (int) 9, 'rch' => (int) 6, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 10, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 7, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb337380' $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' => 'HOM05D001484', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p31500' => 'bna', 'A05p00020' => 'bna', 'A07p08820' => 'bna', 'Aa31LG4G3300' => 'aar', 'Aa31LG8G10030' => 'aar', 'Actinidia00731' => 'ach', 'Actinidia11473' => 'ach', 'Actinidia23469' => 'ach', 'Actinidia24318' => 'ach', 'Actinidia40196' => 'ach', 'Actinidia40197' => 'ach', 'Actinidia40198' => 'ach', 'Ah.08g212990' => 'amhyb', 'Ah.15g091720' => 'amhyb', 'AL3G38260' => 'aly', 'AL4G47710' => 'aly', 'Aqoxy2G00671' => 'aox', 'Aqoxy2G03236' => 'aox', 'arahy.Tifrunner.gnm1.ann1.05IDCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KR684' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATY3SJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK6QJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6APGL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IDT7Z9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM073U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ0R87' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LE7RV4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT4QRX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V5ENPK' => 'arhy', 'AT2G48110' => 'ath', 'AT3G23590' => 'ath', 'ATR0626G186' => 'atr', 'ATR1127G141' => 'atr', 'Atru.chr4.2583' => 'acertr', 'Atru.chr5.1358' => 'acertr', 'Atru.chr5.1359' => 'acertr', 'Atru.chr8.46' => 'acertr', 'AUR62002640' => 'cqu', 'AUR62030055' => 'cqu', 'AUR62033713' => 'cqu', 'AUR62033714' => 'cqu', 'AUR62036795' => 'cqu', 'AUR62039891' => 'cqu', 'BcaB02g08737' => 'bca', 'BcaB04g20441' => 'bca', 'BcaB06g26509' => 'bca', 'BcaB06g26510' => 'bca', 'BcaB06g26511' => 'bca', 'BcaB06g26512' => 'bca', 'BcaB06g26513' => 'bca', 'BcaC02g12564' => 'bca', 'BcaC02g12565' => 'bca', 'BcaC02g12794' => 'bca', 'BcaC02g12795' => 'bca', 'BcaC02g12796' => 'bca', 'BcaC06g35541' => 'bca', 'BNapus_Darmor_BZH_scaffold_188p00080' => 'bna', 'BNapus_Darmor_BZH_scaffold_188p00090' => 'bna', 'BolC1t03972H' => 'bol', 'BolC1t03973H' => 'bol', 'BolC4t21680H' => 'bol', 'BolC7t41863H' => 'bol', 'BolSC55t61227H' => 'bol', 'BolSC55t61228H' => 'bol', 'BraA01t03278Z' => 'bra', 'BraA05t18998Z' => 'bra', 'BraA07t28673Z' => 'bra', 'C01p40150' => 'bna', 'C05p12370' => 'bna', 'C07p13680' => 'bna', 'CAN.G1006.16' => 'can', 'CAN.G1006.17' => 'can', 'CAN.G1170.2' => 'can', 'CAN.G962.7' => 'can', 'CANSAT25G2179' => 'cansat', 'CANSAT78G1573' => 'cansat', 'CARHR099510' => 'chi', 'CARHR143510' => 'chi', 'Carub.0003s2380' => 'cru', 'Carub.0004s3082' => 'cru', 'Ca_00614_v3' => 'car', 'Ca_07801_v3' => 'car', 'Ca_08567_v3' => 'car', 'Ca_09571_v3' => 'car', 'CBR_g19290' => 'cbr', 'Cc01_g19770' => 'ccan', 'Cc03_g03030' => 'ccan', 'CDE07G0968' => 'cde', 'CDE09G1441' => 'cde', 'Cfa006103' => 'cfa', 'Cfa015573' => 'cfa', 'Cfa016988' => 'cfa', 'Ciclev10006738m.g' => 'ccl', 'Ciclev10010920m.g' => 'ccl', 'Ciclev10018517m.g' => 'ccl', 'CiPaw.01G159200' => 'cil', 'CiPaw.02G091000' => 'cil', 'CiPaw.02G091100' => 'cil', 'CiPaw.08G103100' => 'cil', 'CiPaw.09G224900' => 'cil', 'ClCG06G005740' => 'cla', 'ClCG07G000090' => 'cla', 'ClCG07G000100' => 'cla', 'COL.COLO4_09143' => 'col', 'COL.COLO4_25124' => 'col', 'Cpa.g.sc16.34' => 'cpa', 'Cpa.g.sc3504.1' => 'cpa', 'Cpa.g.sc60.37' => 'cpa', 'CsaV3_6G018520' => 'csa', 'CsaV3_6G036860' => 'csa', 'CSS0001072' => 'camsi', 'CSS0020208' => 'camsi', 'CSS0021253' => 'camsi', 'CSS0022190' => 'camsi', 'CSS0036150' => 'camsi', 'CSS0040442' => 'camsi', 'CSS0042300' => 'camsi', 'CSS0045298' => 'camsi', 'DCAR_012449' => 'dca', 'DCAR_018405' => 'dca', 'DCAR_024573' => 'dca', 'DCAR_030591' => 'dca', 'Dinv16926' => 'din', 'Dinv32963' => 'din', 'Dinv38382' => 'din', 'Dinv38383' => 'din', 'Duzib133G0974' => 'dzi', 'Duzib138G1867' => 'dzi', 'Duzib211G0420' => 'dzi', 'Duzib212G0930' => 'dzi', 'ECA234G1645' => 'eca', 'ECA247G3467' => 'eca', 'ECA248G1703' => 'eca', 'EL10Ac3g06327' => 'bvu', 'EL10Ac7g17204' => 'bvu', 'Eucgr.A00855' => 'egr', 'Eucgr.A00858' => 'egr', 'Eucgr.H01520' => 'egr', 'Eucgr.H03604' => 'egr', 'Eucgr.L03465' => 'egr', 'Eucgr.L03466' => 'egr', 'FAN01G0988' => 'fan', 'FAN02G3892' => 'fan', 'FAN05G3381' => 'fan', 'FAN07G0967' => 'fan', 'FAN07G1493' => 'fan', 'FAN08G3125' => 'fan', 'FAN09G0402' => 'fan', 'FAN12G2594' => 'fan', 'FAN12G3879' => 'fan', 'FAN14G1546' => 'fan', 'FAN15G3626' => 'fan', 'FAN17G0588' => 'fan', 'FAN17G0609' => 'fan', 'FAN18G2817' => 'fan', 'FAN19G1305' => 'fan', 'FAN20G1787' => 'fan', 'FAN22G0073' => 'fan', 'FAN22G0352' => 'fan', 'FAN22G0368' => 'fan', 'FAN22G2273' => 'fan', 'FAN24G1998' => 'fan', 'FAN27G1317' => 'fan', 'FvH4_2g23980' => 'fve', 'FvH4_4g14380' => 'fve', 'FvH4_4g14390' => 'fve', 'FvH4_6g09250' => 'fve', 'Glyma.03G151100' => 'gma', 'Glyma.04G122550' => 'gma', 'Glyma.05G001600' => 'gma', 'Glyma.09G270766' => 'gma', 'Glyma.09G270832' => 'gma', 'Glyma.13G209800' => 'gma', 'Glyma.15G102800' => 'gma', 'Glyma.18G218900' => 'gma', 'Glyma.19G001500' => 'gma', 'Glyma.19G153600' => 'gma', 'Gohir.A02G028600' => 'ghi', 'Gohir.A08G045000' => 'ghi', 'Gohir.A11G120500' => 'ghi', 'Gohir.A12G006200' => 'ghi', 'Gohir.A12G006250' => 'ghi', 'Gohir.D02G036300' => 'ghi', 'Gohir.D08G054700' => 'ghi', 'Gohir.D11G125600' => 'ghi', 'Gohir.D12G005700' => 'ghi', 'Gorai.004G055200' => 'gra', 'Gorai.005G040400' => 'gra', 'Gorai.007G134500' => 'gra', 'Gorai.008G005500' => 'gra', 'GSVIVG01011094001' => 'vvi', 'GSVIVG01017879001' => 'vvi', 'GSVIVG01025988001' => 'vvi', 'GSVIVG01029847001' => 'vvi', 'HanXRQChr10g0282901' => 'han', 'HanXRQChr10g0310371' => 'han', 'HanXRQChr10g0315041' => 'han', 'HanXRQChr11g0327651' => 'han', 'HanXRQChr12g0359391' => 'han', 'Haze_00972' => 'cav', 'Haze_00973' => 'cav', 'Haze_00974' => 'cav', 'Haze_04747' => 'cav', 'Haze_04749' => 'cav', 'Haze_04750' => 'cav', 'Haze_21217' => 'cav', 'Hma1.2p1_1037F.1_g250680' => 'hma', 'Hma1.2p1_1644F.1_g295320' => 'hma', 'HPP92_011322' => 'vpl', 'HPP92_011323' => 'vpl', 'HPP92_011324' => 'vpl', 'HPP92_011325' => 'vpl', 'HPP92_011326' => 'vpl', 'Hund12205' => 'sun', 'Hund17957' => 'sun', 'Lalb_Chr06g0176771' => 'lal', 'Lalb_Chr18g0056021' => 'lal', 'Lalb_Chr18g0056031' => 'lal', 'Lalb_Chr18g0056041' => 'lal', 'Lalb_Chr20g0107751' => 'lal', 'Lalb_Chr20g0118371' => 'lal', 'Lj1g0010239' => 'lja', 'Lj1g0017101' => 'lja', 'Lj2A1178G40' => 'lonja', 'Lj2A54G84' => 'lonja', 'Lj2g0015248' => 'lja', 'Lj3A761T51' => 'lonja', 'Lj6g0018116' => 'lja', 'Lsat_1_v5_gn_4_136040' => 'lsa', 'Lsat_1_v5_gn_5_187461' => 'lsa', 'Lsat_1_v5_gn_5_77001' => 'lsa', 'Lsat_1_v5_gn_9_4461' => 'lsa', 'Manes.01G210100' => 'mes', 'Manes.03G185600' => 'mes', 'Manes.05G073300' => 'mes', 'Manes.09G120300' => 'mes', 'Manes.15G022100' => 'mes', 'Mapoly0096s0053' => 'mpo', 'MBI03_g14058_MAGBIO' => 'mbi', 'MBI03_g33876_MAGBIO' => 'mbi', 'MBI03_g36854_MAGBIO' => 'mbi', 'MBI17_g11997_MAGBIO' => 'mbi', 'MD03G1269000' => 'mdo', 'MD04G1179600' => 'mdo', 'MD11G1289800' => 'mdo', 'MD12G1194700' => 'mdo', 'MD13G1182100' => 'mdo', 'MD13G1182200' => 'mdo', 'MD16G1182600' => 'mdo', 'Medtr2g021400' => 'mtr', 'Medtr2g021470' => 'mtr', 'Medtr2g105810' => 'mtr', 'Medtr3g033580' => 'mtr', 'Medtr6g007970' => 'mtr', 'Medtr7g056330' => 'mtr', 'Medtr7g074290' => 'mtr', 'Medtr7g074380' => 'mtr', 'Medtr7g094550' => 'mtr', 'Medtr8g069995' => 'mtr', 'MELO3C014345.2' => 'cme', 'MELO3C021395.2' => 'cme', 'Migut.D00262' => 'egut', 'Migut.G00257' => 'egut', 'MSTRG.21575' => 'ama', 'MSTRG.3985' => 'ama', 'Nitab4.5_0000295g0140' => 'nta', 'Nitab4.5_0000732g0140' => 'nta', 'Nitab4.5_0003162g0020' => 'nta', 'Nitab4.5_0006180g0090' => 'nta', 'Nitab4.5_0006390g0010' => 'nta', 'Nitab4.5_0007392g0040' => 'nta', 'Nn1g02140' => 'nnu', 'Nn4g26168' => 'nnu', 'Nn5g26754' => 'nnu', 'Oeu001433.1' => 'oeu', 'Oeu010299.2' => 'oeu', 'Oeu011171.1' => 'oeu', 'Oeu037675.1' => 'oeu', 'Oeu038359.1' => 'oeu', 'Oeu063834.1' => 'oeu', 'Oeu063835.1' => 'oeu', 'Os05g0312000' => 'osa', 'Os07g0211101' => 'osa', 'Os07g0211200' => 'osa', 'Os07g0681500' => 'osa', 'Peaxi162Scf00095g01015' => 'pax', 'Peaxi162Scf00104g00329' => 'pax', 'Peaxi162Scf00161g00137' => 'pax', 'PGR004G1665' => 'pgr', 'PGR031G2937' => 'pgr', 'PGR119G2145' => 'pgr', 'PGSC0003DMG400004351' => 'stu', 'PGSC0003DMG400014625' => 'stu', 'PGSC0003DMG401000943' => 'stu', 'Phvul.001G148600' => 'pvu', 'Phvul.004G001700' => 'pvu', 'Phvul.006G154900' => 'pvu', 'Phvul.008G078200' => 'pvu', 'Phvul.011G136500' => 'pvu', 'Potri.002G215600' => 'ptr', 'Potri.008G201600' => 'ptr', 'Potri.014G138400' => 'ptr', 'Potri.016G142500' => 'ptr', 'Pp3c16_10580' => 'ppa', 'Pp3c5_25280' => 'ppa', 'Prupe.1G150000' => 'ppe', 'Prupe.1G150100' => 'ppe', 'Prupe.6G299600' => 'ppe', 'Prupe.8G245000' => 'ppe', 'Psat0s4927g0040' => 'psa', 'Psat1g052080' => 'psa', 'Psat1g183800' => 'psa', 'Psat3g113840' => 'psa', 'Psat3g126120' => 'psa', 'Psat3g126160' => 'psa', 'Psat3g158760' => 'psa', 'Psat3g158840' => 'psa', 'PSO170G2858' => 'pso', 'PSO339G0606' => 'pso', 'PSO384G4709' => 'pso', 'PSO407G0334' => 'pso', 'QL04p040276' => 'qlo', 'QL06p005458' => 'qlo', 'QL06p005472' => 'qlo', 'QL07p030546' => 'qlo', 'QL07p031519' => 'qlo', 'QL09p050949' => 'qlo', 'QL09p050966' => 'qlo', 'QL09p051067' => 'qlo', 'QL12p022706' => 'qlo', 'RcHm_v2.0_Chr2g0119601' => 'rch', 'RcHm_v2.0_Chr3g0459591' => 'rch', 'RcHm_v2.0_Chr4g0418521' => 'rch', 'RcHm_v2.0_Chr4g0418531' => 'rch', 'RcHm_v2.0_Chr4g0418541' => 'rch', 'RcHm_v2.0_Chr6g0291641' => 'rch', 'Rhsim01G0086300' => 'rsi', 'Rhsim01G0276300' => 'rsi', 'Rhsim01G0276500' => 'rsi', 'Rhsim04G0207700' => 'rsi', 'Rhsim05G0234500' => 'rsi', 'Rhsim13G0022400' => 'rsi', 'Sabra02G0167900' => 'sbr', 'Sabra04G0158500' => 'sbr', 'Sabra08G0159800' => 'sbr', 'Sabra10G0011500' => 'sbr', 'Sabra14G0104400' => 'sbr', 'SalBow2G2440' => 'sbo', 'SalBow4G2265' => 'sbo', 'Sc02g0000060' => 'sci', 'Sc05g0005020' => 'sci', 'Sc13g0003890' => 'sci', 'Sed0014865' => 'sed', 'Sed0017224' => 'sed', 'Sed0026391' => 'sed', 'SEGI_00063' => 'sgi', 'SEGI_10967' => 'sgi', 'SEGI_17510' => 'sgi', 'SEGI_24396' => 'sgi', 'SEGI_39719' => 'sgi', 'SEGI_41392' => 'sgi', 'SGA_v2.0_scaffold11G05794' => 'sas', 'SGA_v2.0_scaffold142G35607' => 'sas', 'SGA_v2.0_scaffold1G00447' => 'sas', 'SHI15388' => 'shi', 'SHI15394' => 'shi', 'SHI15396' => 'shi', 'SHI15399' => 'shi', 'SMO343G0151' => 'smo', 'SMO367G1118' => 'smo', 'Solyc01g080200.3' => 'sly', 'Solyc06g008960.3' => 'sly', 'Solyc09g064780.3' => 'sly', 'Sopen01g031980' => 'spe', 'Sopen06g003710' => 'spe', 'Sopen09g026460' => 'spe', 'Sp3g21240' => 'spa', 'Sp4g30030' => 'spa', 'TAR365G0022' => 'tar', 'TAR365G1023' => 'tar', 'TAR365G1253' => 'tar', 'TAR623G0078' => 'tar', 'TAR623G1721' => 'tar', 'TAR633G0959' => 'tar', 'THA.LOC104802225' => 'tha', 'THA.LOC104804769' => 'tha', 'THA.LOC104808660' => 'tha', 'THA.LOC104812792' => 'tha', 'Thecc.01G284000' => 'tca', 'Thecc.04G220600' => 'tca', 'Thecc.05G268900' => 'tca', 'Thecc.08G171100' => 'tca', 'Thhalv10001284m.g' => 'esa', 'Thhalv10019912m.g' => 'esa', 'TPR.G14189' => 'tpr', 'TPR.G18110' => 'tpr', 'TPR.G18130' => 'tpr', 'TPR.G18131' => 'tpr', 'TPR.G18140' => 'tpr', 'TPR.G24282' => 'tpr', 'TPR.G25221' => 'tpr', 'TPR.G29267' => 'tpr', 'TPR.G35315' => 'tpr', 'TPR.G36173' => 'tpr', 'TWI09G0794' => 'twi', 'TWI59G1348' => 'twi', 'TWI74G0430' => 'twi', 'unitig_26.g8940' => 'ugi', 'unitig_749.g13744' => 'ugi', 'unitig_749.g13745' => 'ugi', 'vmacro08269' => 'vma', 'vmacro14937' => 'vma', 'vmacro20401' => 'vma', 'VMungo0464G1349' => 'vmu', 'VMungo0540G0289' => 'vmu', 'VMungo1215G1590' => 'vmu', 'VMungo1309G0221' => 'vmu', 'VMungo1309G2815' => 'vmu', 'VMungo1383G0239' => 'vmu', 'VMungo1383G2910' => 'vmu', 'Zm00001eb095270' => 'zma', 'Zm00001eb095280' => 'zma', 'Zm00001eb111630' => 'zma', 'Zm00001eb237080' => 'zma', 'Zm00001eb273740' => 'zma', 'Zm00001eb285040' => 'zma', 'Zm00001eb330790' => 'zma', 'Zm00001eb337380' => 'zma' ), 'gf_id' => 'HOM05D001484', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001484' ), 'data_identifier' => 'HOM05D001484', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001484', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p31500' => 'bna', 'A05p00020' => 'bna', 'A07p08820' => 'bna', 'Aa31LG4G3300' => 'aar', 'Aa31LG8G10030' => 'aar', 'Actinidia00731' => 'ach', 'Actinidia11473' => 'ach', 'Actinidia23469' => 'ach', 'Actinidia24318' => 'ach', 'Actinidia40196' => 'ach', 'Actinidia40197' => 'ach', 'Actinidia40198' => 'ach', 'Ah.08g212990' => 'amhyb', 'Ah.15g091720' => 'amhyb', 'AL3G38260' => 'aly', 'AL4G47710' => 'aly', 'Aqoxy2G00671' => 'aox', 'Aqoxy2G03236' => 'aox', 'arahy.Tifrunner.gnm1.ann1.05IDCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KR684' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATY3SJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK6QJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6APGL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IDT7Z9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM073U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ0R87' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LE7RV4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT4QRX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V5ENPK' => 'arhy', 'AT2G48110' => 'ath', 'AT3G23590' => 'ath', 'ATR0626G186' => 'atr', 'ATR1127G141' => 'atr', 'Atru.chr4.2583' => 'acertr', 'Atru.chr5.1358' => 'acertr', 'Atru.chr5.1359' => 'acertr', 'Atru.chr8.46' => 'acertr', 'AUR62002640' => 'cqu', 'AUR62030055' => 'cqu', 'AUR62033713' => 'cqu', 'AUR62033714' => 'cqu', 'AUR62036795' => 'cqu', 'AUR62039891' => 'cqu', 'BcaB02g08737' => 'bca', 'BcaB04g20441' => 'bca', 'BcaB06g26509' => 'bca', 'BcaB06g26510' => 'bca', 'BcaB06g26511' => 'bca', 'BcaB06g26512' => 'bca', 'BcaB06g26513' => 'bca', 'BcaC02g12564' => 'bca', 'BcaC02g12565' => 'bca', 'BcaC02g12794' => 'bca', 'BcaC02g12795' => 'bca', 'BcaC02g12796' => 'bca', 'BcaC06g35541' => 'bca', 'BNapus_Darmor_BZH_scaffold_188p00080' => 'bna', 'BNapus_Darmor_BZH_scaffold_188p00090' => 'bna', 'BolC1t03972H' => 'bol', 'BolC1t03973H' => 'bol', 'BolC4t21680H' => 'bol', 'BolC7t41863H' => 'bol', 'BolSC55t61227H' => 'bol', 'BolSC55t61228H' => 'bol', 'BraA01t03278Z' => 'bra', 'BraA05t18998Z' => 'bra', 'BraA07t28673Z' => 'bra', 'C01p40150' => 'bna', 'C05p12370' => 'bna', 'C07p13680' => 'bna', 'CAN.G1006.16' => 'can', 'CAN.G1006.17' => 'can', 'CAN.G1170.2' => 'can', 'CAN.G962.7' => 'can', 'CANSAT25G2179' => 'cansat', 'CANSAT78G1573' => 'cansat', 'CARHR099510' => 'chi', 'CARHR143510' => 'chi', 'Carub.0003s2380' => 'cru', 'Carub.0004s3082' => 'cru', 'Ca_00614_v3' => 'car', 'Ca_07801_v3' => 'car', 'Ca_08567_v3' => 'car', 'Ca_09571_v3' => 'car', 'CBR_g19290' => 'cbr', 'Cc01_g19770' => 'ccan', 'Cc03_g03030' => 'ccan', 'CDE07G0968' => 'cde', 'CDE09G1441' => 'cde', 'Cfa006103' => 'cfa', 'Cfa015573' => 'cfa', 'Cfa016988' => 'cfa', 'Ciclev10006738m.g' => 'ccl', 'Ciclev10010920m.g' => 'ccl', 'Ciclev10018517m.g' => 'ccl', 'CiPaw.01G159200' => 'cil', 'CiPaw.02G091000' => 'cil', 'CiPaw.02G091100' => 'cil', 'CiPaw.08G103100' => 'cil', 'CiPaw.09G224900' => 'cil', 'ClCG06G005740' => 'cla', 'ClCG07G000090' => 'cla', 'ClCG07G000100' => 'cla', 'COL.COLO4_09143' => 'col', 'COL.COLO4_25124' => 'col', 'Cpa.g.sc16.34' => 'cpa', 'Cpa.g.sc3504.1' => 'cpa', 'Cpa.g.sc60.37' => 'cpa', 'CsaV3_6G018520' => 'csa', 'CsaV3_6G036860' => 'csa', 'CSS0001072' => 'camsi', 'CSS0020208' => 'camsi', 'CSS0021253' => 'camsi', 'CSS0022190' => 'camsi', 'CSS0036150' => 'camsi', 'CSS0040442' => 'camsi', 'CSS0042300' => 'camsi', 'CSS0045298' => 'camsi', 'DCAR_012449' => 'dca', 'DCAR_018405' => 'dca', 'DCAR_024573' => 'dca', 'DCAR_030591' => 'dca', 'Dinv16926' => 'din', 'Dinv32963' => 'din', 'Dinv38382' => 'din', 'Dinv38383' => 'din', 'Duzib133G0974' => 'dzi', 'Duzib138G1867' => 'dzi', 'Duzib211G0420' => 'dzi', 'Duzib212G0930' => 'dzi', 'ECA234G1645' => 'eca', 'ECA247G3467' => 'eca', 'ECA248G1703' => 'eca', 'EL10Ac3g06327' => 'bvu', 'EL10Ac7g17204' => 'bvu', 'Eucgr.A00855' => 'egr', 'Eucgr.A00858' => 'egr', 'Eucgr.H01520' => 'egr', 'Eucgr.H03604' => 'egr', 'Eucgr.L03465' => 'egr', 'Eucgr.L03466' => 'egr', 'FAN01G0988' => 'fan', 'FAN02G3892' => 'fan', 'FAN05G3381' => 'fan', 'FAN07G0967' => 'fan', 'FAN07G1493' => 'fan', 'FAN08G3125' => 'fan', 'FAN09G0402' => 'fan', 'FAN12G2594' => 'fan', 'FAN12G3879' => 'fan', 'FAN14G1546' => 'fan', 'FAN15G3626' => 'fan', 'FAN17G0588' => 'fan', 'FAN17G0609' => 'fan', 'FAN18G2817' => 'fan', 'FAN19G1305' => 'fan', 'FAN20G1787' => 'fan', 'FAN22G0073' => 'fan', 'FAN22G0352' => 'fan', 'FAN22G0368' => 'fan', 'FAN22G2273' => 'fan', 'FAN24G1998' => 'fan', 'FAN27G1317' => 'fan', 'FvH4_2g23980' => 'fve', 'FvH4_4g14380' => 'fve', 'FvH4_4g14390' => 'fve', 'FvH4_6g09250' => 'fve', 'Glyma.03G151100' => 'gma', 'Glyma.04G122550' => 'gma', 'Glyma.05G001600' => 'gma', 'Glyma.09G270766' => 'gma', 'Glyma.09G270832' => 'gma', 'Glyma.13G209800' => 'gma', 'Glyma.15G102800' => 'gma', 'Glyma.18G218900' => 'gma', 'Glyma.19G001500' => 'gma', 'Glyma.19G153600' => 'gma', 'Gohir.A02G028600' => 'ghi', 'Gohir.A08G045000' => 'ghi', 'Gohir.A11G120500' => 'ghi', 'Gohir.A12G006200' => 'ghi', 'Gohir.A12G006250' => 'ghi', 'Gohir.D02G036300' => 'ghi', 'Gohir.D08G054700' => 'ghi', 'Gohir.D11G125600' => 'ghi', 'Gohir.D12G005700' => 'ghi', 'Gorai.004G055200' => 'gra', 'Gorai.005G040400' => 'gra', 'Gorai.007G134500' => 'gra', 'Gorai.008G005500' => 'gra', 'GSVIVG01011094001' => 'vvi', 'GSVIVG01017879001' => 'vvi', 'GSVIVG01025988001' => 'vvi', 'GSVIVG01029847001' => 'vvi', 'HanXRQChr10g0282901' => 'han', 'HanXRQChr10g0310371' => 'han', 'HanXRQChr10g0315041' => 'han', 'HanXRQChr11g0327651' => 'han', 'HanXRQChr12g0359391' => 'han', 'Haze_00972' => 'cav', 'Haze_00973' => 'cav', 'Haze_00974' => 'cav', 'Haze_04747' => 'cav', 'Haze_04749' => 'cav', 'Haze_04750' => 'cav', 'Haze_21217' => 'cav', 'Hma1.2p1_1037F.1_g250680' => 'hma', 'Hma1.2p1_1644F.1_g295320' => 'hma', 'HPP92_011322' => 'vpl', 'HPP92_011323' => 'vpl', 'HPP92_011324' => 'vpl', 'HPP92_011325' => 'vpl', 'HPP92_011326' => 'vpl', 'Hund12205' => 'sun', 'Hund17957' => 'sun', 'Lalb_Chr06g0176771' => 'lal', 'Lalb_Chr18g0056021' => 'lal', 'Lalb_Chr18g0056031' => 'lal', 'Lalb_Chr18g0056041' => 'lal', 'Lalb_Chr20g0107751' => 'lal', 'Lalb_Chr20g0118371' => 'lal', 'Lj1g0010239' => 'lja', 'Lj1g0017101' => 'lja', 'Lj2A1178G40' => 'lonja', 'Lj2A54G84' => 'lonja', 'Lj2g0015248' => 'lja', 'Lj3A761T51' => 'lonja', 'Lj6g0018116' => 'lja', 'Lsat_1_v5_gn_4_136040' => 'lsa', 'Lsat_1_v5_gn_5_187461' => 'lsa', 'Lsat_1_v5_gn_5_77001' => 'lsa', 'Lsat_1_v5_gn_9_4461' => 'lsa', 'Manes.01G210100' => 'mes', 'Manes.03G185600' => 'mes', 'Manes.05G073300' => 'mes', 'Manes.09G120300' => 'mes', 'Manes.15G022100' => 'mes', 'Mapoly0096s0053' => 'mpo', 'MBI03_g14058_MAGBIO' => 'mbi', 'MBI03_g33876_MAGBIO' => 'mbi', 'MBI03_g36854_MAGBIO' => 'mbi', 'MBI17_g11997_MAGBIO' => 'mbi', 'MD03G1269000' => 'mdo', 'MD04G1179600' => 'mdo', 'MD11G1289800' => 'mdo', 'MD12G1194700' => 'mdo', 'MD13G1182100' => 'mdo', 'MD13G1182200' => 'mdo', 'MD16G1182600' => 'mdo', 'Medtr2g021400' => 'mtr', 'Medtr2g021470' => 'mtr', 'Medtr2g105810' => 'mtr', 'Medtr3g033580' => 'mtr', 'Medtr6g007970' => 'mtr', 'Medtr7g056330' => 'mtr', 'Medtr7g074290' => 'mtr', 'Medtr7g074380' => 'mtr', 'Medtr7g094550' => 'mtr', 'Medtr8g069995' => 'mtr', 'MELO3C014345.2' => 'cme', 'MELO3C021395.2' => 'cme', 'Migut.D00262' => 'egut', 'Migut.G00257' => 'egut', 'MSTRG.21575' => 'ama', 'MSTRG.3985' => 'ama', 'Nitab4.5_0000295g0140' => 'nta', 'Nitab4.5_0000732g0140' => 'nta', 'Nitab4.5_0003162g0020' => 'nta', 'Nitab4.5_0006180g0090' => 'nta', 'Nitab4.5_0006390g0010' => 'nta', 'Nitab4.5_0007392g0040' => 'nta', 'Nn1g02140' => 'nnu', 'Nn4g26168' => 'nnu', 'Nn5g26754' => 'nnu', 'Oeu001433.1' => 'oeu', 'Oeu010299.2' => 'oeu', 'Oeu011171.1' => 'oeu', 'Oeu037675.1' => 'oeu', 'Oeu038359.1' => 'oeu', 'Oeu063834.1' => 'oeu', 'Oeu063835.1' => 'oeu', 'Os05g0312000' => 'osa', 'Os07g0211101' => 'osa', 'Os07g0211200' => 'osa', 'Os07g0681500' => 'osa', 'Peaxi162Scf00095g01015' => 'pax', 'Peaxi162Scf00104g00329' => 'pax', 'Peaxi162Scf00161g00137' => 'pax', 'PGR004G1665' => 'pgr', 'PGR031G2937' => 'pgr', 'PGR119G2145' => 'pgr', 'PGSC0003DMG400004351' => 'stu', 'PGSC0003DMG400014625' => 'stu', 'PGSC0003DMG401000943' => 'stu', 'Phvul.001G148600' => 'pvu', 'Phvul.004G001700' => 'pvu', 'Phvul.006G154900' => 'pvu', 'Phvul.008G078200' => 'pvu', 'Phvul.011G136500' => 'pvu', 'Potri.002G215600' => 'ptr', 'Potri.008G201600' => 'ptr', 'Potri.014G138400' => 'ptr', 'Potri.016G142500' => 'ptr', 'Pp3c16_10580' => 'ppa', 'Pp3c5_25280' => 'ppa', 'Prupe.1G150000' => 'ppe', 'Prupe.1G150100' => 'ppe', 'Prupe.6G299600' => 'ppe', 'Prupe.8G245000' => 'ppe', 'Psat0s4927g0040' => 'psa', 'Psat1g052080' => 'psa', 'Psat1g183800' => 'psa', 'Psat3g113840' => 'psa', 'Psat3g126120' => 'psa', 'Psat3g126160' => 'psa', 'Psat3g158760' => 'psa', 'Psat3g158840' => 'psa', 'PSO170G2858' => 'pso', 'PSO339G0606' => 'pso', 'PSO384G4709' => 'pso', 'PSO407G0334' => 'pso', 'QL04p040276' => 'qlo', 'QL06p005458' => 'qlo', 'QL06p005472' => 'qlo', 'QL07p030546' => 'qlo', 'QL07p031519' => 'qlo', 'QL09p050949' => 'qlo', 'QL09p050966' => 'qlo', 'QL09p051067' => 'qlo', 'QL12p022706' => 'qlo', 'RcHm_v2.0_Chr2g0119601' => 'rch', 'RcHm_v2.0_Chr3g0459591' => 'rch', 'RcHm_v2.0_Chr4g0418521' => 'rch', 'RcHm_v2.0_Chr4g0418531' => 'rch', 'RcHm_v2.0_Chr4g0418541' => 'rch', 'RcHm_v2.0_Chr6g0291641' => 'rch', 'Rhsim01G0086300' => 'rsi', 'Rhsim01G0276300' => 'rsi', 'Rhsim01G0276500' => 'rsi', 'Rhsim04G0207700' => 'rsi', 'Rhsim05G0234500' => 'rsi', 'Rhsim13G0022400' => 'rsi', 'Sabra02G0167900' => 'sbr', 'Sabra04G0158500' => 'sbr', 'Sabra08G0159800' => 'sbr', 'Sabra10G0011500' => 'sbr', 'Sabra14G0104400' => 'sbr', 'SalBow2G2440' => 'sbo', 'SalBow4G2265' => 'sbo', 'Sc02g0000060' => 'sci', 'Sc05g0005020' => 'sci', 'Sc13g0003890' => 'sci', 'Sed0014865' => 'sed', 'Sed0017224' => 'sed', 'Sed0026391' => 'sed', 'SEGI_00063' => 'sgi', 'SEGI_10967' => 'sgi', 'SEGI_17510' => 'sgi', 'SEGI_24396' => 'sgi', 'SEGI_39719' => 'sgi', 'SEGI_41392' => 'sgi', 'SGA_v2.0_scaffold11G05794' => 'sas', 'SGA_v2.0_scaffold142G35607' => 'sas', 'SGA_v2.0_scaffold1G00447' => 'sas', 'SHI15388' => 'shi', 'SHI15394' => 'shi', 'SHI15396' => 'shi', 'SHI15399' => 'shi', 'SMO343G0151' => 'smo', 'SMO367G1118' => 'smo', 'Solyc01g080200.3' => 'sly', 'Solyc06g008960.3' => 'sly', 'Solyc09g064780.3' => 'sly', 'Sopen01g031980' => 'spe', 'Sopen06g003710' => 'spe', 'Sopen09g026460' => 'spe', 'Sp3g21240' => 'spa', 'Sp4g30030' => 'spa', 'TAR365G0022' => 'tar', 'TAR365G1023' => 'tar', 'TAR365G1253' => 'tar', 'TAR623G0078' => 'tar', 'TAR623G1721' => 'tar', 'TAR633G0959' => 'tar', 'THA.LOC104802225' => 'tha', 'THA.LOC104804769' => 'tha', 'THA.LOC104808660' => 'tha', 'THA.LOC104812792' => 'tha', 'Thecc.01G284000' => 'tca', 'Thecc.04G220600' => 'tca', 'Thecc.05G268900' => 'tca', 'Thecc.08G171100' => 'tca', 'Thhalv10001284m.g' => 'esa', 'Thhalv10019912m.g' => 'esa', 'TPR.G14189' => 'tpr', 'TPR.G18110' => 'tpr', 'TPR.G18130' => 'tpr', 'TPR.G18131' => 'tpr', 'TPR.G18140' => 'tpr', 'TPR.G24282' => 'tpr', 'TPR.G25221' => 'tpr', 'TPR.G29267' => 'tpr', 'TPR.G35315' => 'tpr', 'TPR.G36173' => 'tpr', 'TWI09G0794' => 'twi', 'TWI59G1348' => 'twi', 'TWI74G0430' => 'twi', 'unitig_26.g8940' => 'ugi', 'unitig_749.g13744' => 'ugi', 'unitig_749.g13745' => 'ugi', 'vmacro08269' => 'vma', 'vmacro14937' => 'vma', 'vmacro20401' => 'vma', 'VMungo0464G1349' => 'vmu', 'VMungo0540G0289' => 'vmu', 'VMungo1215G1590' => 'vmu', 'VMungo1309G0221' => 'vmu', 'VMungo1309G2815' => 'vmu', 'VMungo1383G0239' => 'vmu', 'VMungo1383G2910' => 'vmu', 'Zm00001eb095270' => 'zma', 'Zm00001eb095280' => 'zma', 'Zm00001eb111630' => 'zma', 'Zm00001eb237080' => 'zma', 'Zm00001eb273740' => 'zma', 'Zm00001eb285040' => 'zma', 'Zm00001eb330790' => 'zma', 'Zm00001eb337380' => 'zma' ) $gf_id = 'HOM05D001484' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001484' ) $data_identifier = 'HOM05D001484' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 2, 'aly' => (int) 2, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 22, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 7, 'hma' => (int) 2, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 7, 'mtr' => (int) 10, 'cme' => (int) 2, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 4, 'ppa' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 4, 'qlo' => (int) 9, 'rch' => (int) 6, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 10, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 7, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb337380' $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' => 'HOM05D001484', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p31500' => 'bna', 'A05p00020' => 'bna', 'A07p08820' => 'bna', 'Aa31LG4G3300' => 'aar', 'Aa31LG8G10030' => 'aar', 'Actinidia00731' => 'ach', 'Actinidia11473' => 'ach', 'Actinidia23469' => 'ach', 'Actinidia24318' => 'ach', 'Actinidia40196' => 'ach', 'Actinidia40197' => 'ach', 'Actinidia40198' => 'ach', 'Ah.08g212990' => 'amhyb', 'Ah.15g091720' => 'amhyb', 'AL3G38260' => 'aly', 'AL4G47710' => 'aly', 'Aqoxy2G00671' => 'aox', 'Aqoxy2G03236' => 'aox', 'arahy.Tifrunner.gnm1.ann1.05IDCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KR684' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATY3SJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK6QJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6APGL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IDT7Z9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM073U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ0R87' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LE7RV4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT4QRX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V5ENPK' => 'arhy', 'AT2G48110' => 'ath', 'AT3G23590' => 'ath', 'ATR0626G186' => 'atr', 'ATR1127G141' => 'atr', 'Atru.chr4.2583' => 'acertr', 'Atru.chr5.1358' => 'acertr', 'Atru.chr5.1359' => 'acertr', 'Atru.chr8.46' => 'acertr', 'AUR62002640' => 'cqu', 'AUR62030055' => 'cqu', 'AUR62033713' => 'cqu', 'AUR62033714' => 'cqu', 'AUR62036795' => 'cqu', 'AUR62039891' => 'cqu', 'BcaB02g08737' => 'bca', 'BcaB04g20441' => 'bca', 'BcaB06g26509' => 'bca', 'BcaB06g26510' => 'bca', 'BcaB06g26511' => 'bca', 'BcaB06g26512' => 'bca', 'BcaB06g26513' => 'bca', 'BcaC02g12564' => 'bca', 'BcaC02g12565' => 'bca', 'BcaC02g12794' => 'bca', 'BcaC02g12795' => 'bca', 'BcaC02g12796' => 'bca', 'BcaC06g35541' => 'bca', 'BNapus_Darmor_BZH_scaffold_188p00080' => 'bna', 'BNapus_Darmor_BZH_scaffold_188p00090' => 'bna', 'BolC1t03972H' => 'bol', 'BolC1t03973H' => 'bol', 'BolC4t21680H' => 'bol', 'BolC7t41863H' => 'bol', 'BolSC55t61227H' => 'bol', 'BolSC55t61228H' => 'bol', 'BraA01t03278Z' => 'bra', 'BraA05t18998Z' => 'bra', 'BraA07t28673Z' => 'bra', 'C01p40150' => 'bna', 'C05p12370' => 'bna', 'C07p13680' => 'bna', 'CAN.G1006.16' => 'can', 'CAN.G1006.17' => 'can', 'CAN.G1170.2' => 'can', 'CAN.G962.7' => 'can', 'CANSAT25G2179' => 'cansat', 'CANSAT78G1573' => 'cansat', 'CARHR099510' => 'chi', 'CARHR143510' => 'chi', 'Carub.0003s2380' => 'cru', 'Carub.0004s3082' => 'cru', 'Ca_00614_v3' => 'car', 'Ca_07801_v3' => 'car', 'Ca_08567_v3' => 'car', 'Ca_09571_v3' => 'car', 'CBR_g19290' => 'cbr', 'Cc01_g19770' => 'ccan', 'Cc03_g03030' => 'ccan', 'CDE07G0968' => 'cde', 'CDE09G1441' => 'cde', 'Cfa006103' => 'cfa', 'Cfa015573' => 'cfa', 'Cfa016988' => 'cfa', 'Ciclev10006738m.g' => 'ccl', 'Ciclev10010920m.g' => 'ccl', 'Ciclev10018517m.g' => 'ccl', 'CiPaw.01G159200' => 'cil', 'CiPaw.02G091000' => 'cil', 'CiPaw.02G091100' => 'cil', 'CiPaw.08G103100' => 'cil', 'CiPaw.09G224900' => 'cil', 'ClCG06G005740' => 'cla', 'ClCG07G000090' => 'cla', 'ClCG07G000100' => 'cla', 'COL.COLO4_09143' => 'col', 'COL.COLO4_25124' => 'col', 'Cpa.g.sc16.34' => 'cpa', 'Cpa.g.sc3504.1' => 'cpa', 'Cpa.g.sc60.37' => 'cpa', 'CsaV3_6G018520' => 'csa', 'CsaV3_6G036860' => 'csa', 'CSS0001072' => 'camsi', 'CSS0020208' => 'camsi', 'CSS0021253' => 'camsi', 'CSS0022190' => 'camsi', 'CSS0036150' => 'camsi', 'CSS0040442' => 'camsi', 'CSS0042300' => 'camsi', 'CSS0045298' => 'camsi', 'DCAR_012449' => 'dca', 'DCAR_018405' => 'dca', 'DCAR_024573' => 'dca', 'DCAR_030591' => 'dca', 'Dinv16926' => 'din', 'Dinv32963' => 'din', 'Dinv38382' => 'din', 'Dinv38383' => 'din', 'Duzib133G0974' => 'dzi', 'Duzib138G1867' => 'dzi', 'Duzib211G0420' => 'dzi', 'Duzib212G0930' => 'dzi', 'ECA234G1645' => 'eca', 'ECA247G3467' => 'eca', 'ECA248G1703' => 'eca', 'EL10Ac3g06327' => 'bvu', 'EL10Ac7g17204' => 'bvu', 'Eucgr.A00855' => 'egr', 'Eucgr.A00858' => 'egr', 'Eucgr.H01520' => 'egr', 'Eucgr.H03604' => 'egr', 'Eucgr.L03465' => 'egr', 'Eucgr.L03466' => 'egr', 'FAN01G0988' => 'fan', 'FAN02G3892' => 'fan', 'FAN05G3381' => 'fan', 'FAN07G0967' => 'fan', 'FAN07G1493' => 'fan', 'FAN08G3125' => 'fan', 'FAN09G0402' => 'fan', 'FAN12G2594' => 'fan', 'FAN12G3879' => 'fan', 'FAN14G1546' => 'fan', 'FAN15G3626' => 'fan', 'FAN17G0588' => 'fan', 'FAN17G0609' => 'fan', 'FAN18G2817' => 'fan', 'FAN19G1305' => 'fan', 'FAN20G1787' => 'fan', 'FAN22G0073' => 'fan', 'FAN22G0352' => 'fan', 'FAN22G0368' => 'fan', 'FAN22G2273' => 'fan', 'FAN24G1998' => 'fan', 'FAN27G1317' => 'fan', 'FvH4_2g23980' => 'fve', 'FvH4_4g14380' => 'fve', 'FvH4_4g14390' => 'fve', 'FvH4_6g09250' => 'fve', 'Glyma.03G151100' => 'gma', 'Glyma.04G122550' => 'gma', 'Glyma.05G001600' => 'gma', 'Glyma.09G270766' => 'gma', 'Glyma.09G270832' => 'gma', 'Glyma.13G209800' => 'gma', 'Glyma.15G102800' => 'gma', 'Glyma.18G218900' => 'gma', 'Glyma.19G001500' => 'gma', 'Glyma.19G153600' => 'gma', 'Gohir.A02G028600' => 'ghi', 'Gohir.A08G045000' => 'ghi', 'Gohir.A11G120500' => 'ghi', 'Gohir.A12G006200' => 'ghi', 'Gohir.A12G006250' => 'ghi', 'Gohir.D02G036300' => 'ghi', 'Gohir.D08G054700' => 'ghi', 'Gohir.D11G125600' => 'ghi', 'Gohir.D12G005700' => 'ghi', 'Gorai.004G055200' => 'gra', 'Gorai.005G040400' => 'gra', 'Gorai.007G134500' => 'gra', 'Gorai.008G005500' => 'gra', 'GSVIVG01011094001' => 'vvi', 'GSVIVG01017879001' => 'vvi', 'GSVIVG01025988001' => 'vvi', 'GSVIVG01029847001' => 'vvi', 'HanXRQChr10g0282901' => 'han', 'HanXRQChr10g0310371' => 'han', 'HanXRQChr10g0315041' => 'han', 'HanXRQChr11g0327651' => 'han', 'HanXRQChr12g0359391' => 'han', 'Haze_00972' => 'cav', 'Haze_00973' => 'cav', 'Haze_00974' => 'cav', 'Haze_04747' => 'cav', 'Haze_04749' => 'cav', 'Haze_04750' => 'cav', 'Haze_21217' => 'cav', 'Hma1.2p1_1037F.1_g250680' => 'hma', 'Hma1.2p1_1644F.1_g295320' => 'hma', 'HPP92_011322' => 'vpl', 'HPP92_011323' => 'vpl', 'HPP92_011324' => 'vpl', 'HPP92_011325' => 'vpl', 'HPP92_011326' => 'vpl', 'Hund12205' => 'sun', 'Hund17957' => 'sun', 'Lalb_Chr06g0176771' => 'lal', 'Lalb_Chr18g0056021' => 'lal', 'Lalb_Chr18g0056031' => 'lal', 'Lalb_Chr18g0056041' => 'lal', 'Lalb_Chr20g0107751' => 'lal', 'Lalb_Chr20g0118371' => 'lal', 'Lj1g0010239' => 'lja', 'Lj1g0017101' => 'lja', 'Lj2A1178G40' => 'lonja', 'Lj2A54G84' => 'lonja', 'Lj2g0015248' => 'lja', 'Lj3A761T51' => 'lonja', 'Lj6g0018116' => 'lja', 'Lsat_1_v5_gn_4_136040' => 'lsa', 'Lsat_1_v5_gn_5_187461' => 'lsa', 'Lsat_1_v5_gn_5_77001' => 'lsa', 'Lsat_1_v5_gn_9_4461' => 'lsa', 'Manes.01G210100' => 'mes', 'Manes.03G185600' => 'mes', 'Manes.05G073300' => 'mes', 'Manes.09G120300' => 'mes', 'Manes.15G022100' => 'mes', 'Mapoly0096s0053' => 'mpo', 'MBI03_g14058_MAGBIO' => 'mbi', 'MBI03_g33876_MAGBIO' => 'mbi', 'MBI03_g36854_MAGBIO' => 'mbi', 'MBI17_g11997_MAGBIO' => 'mbi', 'MD03G1269000' => 'mdo', 'MD04G1179600' => 'mdo', 'MD11G1289800' => 'mdo', 'MD12G1194700' => 'mdo', 'MD13G1182100' => 'mdo', 'MD13G1182200' => 'mdo', 'MD16G1182600' => 'mdo', 'Medtr2g021400' => 'mtr', 'Medtr2g021470' => 'mtr', 'Medtr2g105810' => 'mtr', 'Medtr3g033580' => 'mtr', 'Medtr6g007970' => 'mtr', 'Medtr7g056330' => 'mtr', 'Medtr7g074290' => 'mtr', 'Medtr7g074380' => 'mtr', 'Medtr7g094550' => 'mtr', 'Medtr8g069995' => 'mtr', 'MELO3C014345.2' => 'cme', 'MELO3C021395.2' => 'cme', 'Migut.D00262' => 'egut', 'Migut.G00257' => 'egut', 'MSTRG.21575' => 'ama', 'MSTRG.3985' => 'ama', 'Nitab4.5_0000295g0140' => 'nta', 'Nitab4.5_0000732g0140' => 'nta', 'Nitab4.5_0003162g0020' => 'nta', 'Nitab4.5_0006180g0090' => 'nta', 'Nitab4.5_0006390g0010' => 'nta', 'Nitab4.5_0007392g0040' => 'nta', 'Nn1g02140' => 'nnu', 'Nn4g26168' => 'nnu', 'Nn5g26754' => 'nnu', 'Oeu001433.1' => 'oeu', 'Oeu010299.2' => 'oeu', 'Oeu011171.1' => 'oeu', 'Oeu037675.1' => 'oeu', 'Oeu038359.1' => 'oeu', 'Oeu063834.1' => 'oeu', 'Oeu063835.1' => 'oeu', 'Os05g0312000' => 'osa', 'Os07g0211101' => 'osa', 'Os07g0211200' => 'osa', 'Os07g0681500' => 'osa', 'Peaxi162Scf00095g01015' => 'pax', 'Peaxi162Scf00104g00329' => 'pax', 'Peaxi162Scf00161g00137' => 'pax', 'PGR004G1665' => 'pgr', 'PGR031G2937' => 'pgr', 'PGR119G2145' => 'pgr', 'PGSC0003DMG400004351' => 'stu', 'PGSC0003DMG400014625' => 'stu', 'PGSC0003DMG401000943' => 'stu', 'Phvul.001G148600' => 'pvu', 'Phvul.004G001700' => 'pvu', 'Phvul.006G154900' => 'pvu', 'Phvul.008G078200' => 'pvu', 'Phvul.011G136500' => 'pvu', 'Potri.002G215600' => 'ptr', 'Potri.008G201600' => 'ptr', 'Potri.014G138400' => 'ptr', 'Potri.016G142500' => 'ptr', 'Pp3c16_10580' => 'ppa', 'Pp3c5_25280' => 'ppa', 'Prupe.1G150000' => 'ppe', 'Prupe.1G150100' => 'ppe', 'Prupe.6G299600' => 'ppe', 'Prupe.8G245000' => 'ppe', 'Psat0s4927g0040' => 'psa', 'Psat1g052080' => 'psa', 'Psat1g183800' => 'psa', 'Psat3g113840' => 'psa', 'Psat3g126120' => 'psa', 'Psat3g126160' => 'psa', 'Psat3g158760' => 'psa', 'Psat3g158840' => 'psa', 'PSO170G2858' => 'pso', 'PSO339G0606' => 'pso', 'PSO384G4709' => 'pso', 'PSO407G0334' => 'pso', 'QL04p040276' => 'qlo', 'QL06p005458' => 'qlo', 'QL06p005472' => 'qlo', 'QL07p030546' => 'qlo', 'QL07p031519' => 'qlo', 'QL09p050949' => 'qlo', 'QL09p050966' => 'qlo', 'QL09p051067' => 'qlo', 'QL12p022706' => 'qlo', 'RcHm_v2.0_Chr2g0119601' => 'rch', 'RcHm_v2.0_Chr3g0459591' => 'rch', 'RcHm_v2.0_Chr4g0418521' => 'rch', 'RcHm_v2.0_Chr4g0418531' => 'rch', 'RcHm_v2.0_Chr4g0418541' => 'rch', 'RcHm_v2.0_Chr6g0291641' => 'rch', 'Rhsim01G0086300' => 'rsi', 'Rhsim01G0276300' => 'rsi', 'Rhsim01G0276500' => 'rsi', 'Rhsim04G0207700' => 'rsi', 'Rhsim05G0234500' => 'rsi', 'Rhsim13G0022400' => 'rsi', 'Sabra02G0167900' => 'sbr', 'Sabra04G0158500' => 'sbr', 'Sabra08G0159800' => 'sbr', 'Sabra10G0011500' => 'sbr', 'Sabra14G0104400' => 'sbr', 'SalBow2G2440' => 'sbo', 'SalBow4G2265' => 'sbo', 'Sc02g0000060' => 'sci', 'Sc05g0005020' => 'sci', 'Sc13g0003890' => 'sci', 'Sed0014865' => 'sed', 'Sed0017224' => 'sed', 'Sed0026391' => 'sed', 'SEGI_00063' => 'sgi', 'SEGI_10967' => 'sgi', 'SEGI_17510' => 'sgi', 'SEGI_24396' => 'sgi', 'SEGI_39719' => 'sgi', 'SEGI_41392' => 'sgi', 'SGA_v2.0_scaffold11G05794' => 'sas', 'SGA_v2.0_scaffold142G35607' => 'sas', 'SGA_v2.0_scaffold1G00447' => 'sas', 'SHI15388' => 'shi', 'SHI15394' => 'shi', 'SHI15396' => 'shi', 'SHI15399' => 'shi', 'SMO343G0151' => 'smo', 'SMO367G1118' => 'smo', 'Solyc01g080200.3' => 'sly', 'Solyc06g008960.3' => 'sly', 'Solyc09g064780.3' => 'sly', 'Sopen01g031980' => 'spe', 'Sopen06g003710' => 'spe', 'Sopen09g026460' => 'spe', 'Sp3g21240' => 'spa', 'Sp4g30030' => 'spa', 'TAR365G0022' => 'tar', 'TAR365G1023' => 'tar', 'TAR365G1253' => 'tar', 'TAR623G0078' => 'tar', 'TAR623G1721' => 'tar', 'TAR633G0959' => 'tar', 'THA.LOC104802225' => 'tha', 'THA.LOC104804769' => 'tha', 'THA.LOC104808660' => 'tha', 'THA.LOC104812792' => 'tha', 'Thecc.01G284000' => 'tca', 'Thecc.04G220600' => 'tca', 'Thecc.05G268900' => 'tca', 'Thecc.08G171100' => 'tca', 'Thhalv10001284m.g' => 'esa', 'Thhalv10019912m.g' => 'esa', 'TPR.G14189' => 'tpr', 'TPR.G18110' => 'tpr', 'TPR.G18130' => 'tpr', 'TPR.G18131' => 'tpr', 'TPR.G18140' => 'tpr', 'TPR.G24282' => 'tpr', 'TPR.G25221' => 'tpr', 'TPR.G29267' => 'tpr', 'TPR.G35315' => 'tpr', 'TPR.G36173' => 'tpr', 'TWI09G0794' => 'twi', 'TWI59G1348' => 'twi', 'TWI74G0430' => 'twi', 'unitig_26.g8940' => 'ugi', 'unitig_749.g13744' => 'ugi', 'unitig_749.g13745' => 'ugi', 'vmacro08269' => 'vma', 'vmacro14937' => 'vma', 'vmacro20401' => 'vma', 'VMungo0464G1349' => 'vmu', 'VMungo0540G0289' => 'vmu', 'VMungo1215G1590' => 'vmu', 'VMungo1309G0221' => 'vmu', 'VMungo1309G2815' => 'vmu', 'VMungo1383G0239' => 'vmu', 'VMungo1383G2910' => 'vmu', 'Zm00001eb095270' => 'zma', 'Zm00001eb095280' => 'zma', 'Zm00001eb111630' => 'zma', 'Zm00001eb237080' => 'zma', 'Zm00001eb273740' => 'zma', 'Zm00001eb285040' => 'zma', 'Zm00001eb330790' => 'zma', 'Zm00001eb337380' => 'zma' ), 'gf_id' => 'HOM05D001484', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001484' ), 'data_identifier' => 'HOM05D001484', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001484', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p31500' => 'bna', 'A05p00020' => 'bna', 'A07p08820' => 'bna', 'Aa31LG4G3300' => 'aar', 'Aa31LG8G10030' => 'aar', 'Actinidia00731' => 'ach', 'Actinidia11473' => 'ach', 'Actinidia23469' => 'ach', 'Actinidia24318' => 'ach', 'Actinidia40196' => 'ach', 'Actinidia40197' => 'ach', 'Actinidia40198' => 'ach', 'Ah.08g212990' => 'amhyb', 'Ah.15g091720' => 'amhyb', 'AL3G38260' => 'aly', 'AL4G47710' => 'aly', 'Aqoxy2G00671' => 'aox', 'Aqoxy2G03236' => 'aox', 'arahy.Tifrunner.gnm1.ann1.05IDCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KR684' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATY3SJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK6QJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6APGL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IDT7Z9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM073U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ0R87' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LE7RV4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT4QRX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V5ENPK' => 'arhy', 'AT2G48110' => 'ath', 'AT3G23590' => 'ath', 'ATR0626G186' => 'atr', 'ATR1127G141' => 'atr', 'Atru.chr4.2583' => 'acertr', 'Atru.chr5.1358' => 'acertr', 'Atru.chr5.1359' => 'acertr', 'Atru.chr8.46' => 'acertr', 'AUR62002640' => 'cqu', 'AUR62030055' => 'cqu', 'AUR62033713' => 'cqu', 'AUR62033714' => 'cqu', 'AUR62036795' => 'cqu', 'AUR62039891' => 'cqu', 'BcaB02g08737' => 'bca', 'BcaB04g20441' => 'bca', 'BcaB06g26509' => 'bca', 'BcaB06g26510' => 'bca', 'BcaB06g26511' => 'bca', 'BcaB06g26512' => 'bca', 'BcaB06g26513' => 'bca', 'BcaC02g12564' => 'bca', 'BcaC02g12565' => 'bca', 'BcaC02g12794' => 'bca', 'BcaC02g12795' => 'bca', 'BcaC02g12796' => 'bca', 'BcaC06g35541' => 'bca', 'BNapus_Darmor_BZH_scaffold_188p00080' => 'bna', 'BNapus_Darmor_BZH_scaffold_188p00090' => 'bna', 'BolC1t03972H' => 'bol', 'BolC1t03973H' => 'bol', 'BolC4t21680H' => 'bol', 'BolC7t41863H' => 'bol', 'BolSC55t61227H' => 'bol', 'BolSC55t61228H' => 'bol', 'BraA01t03278Z' => 'bra', 'BraA05t18998Z' => 'bra', 'BraA07t28673Z' => 'bra', 'C01p40150' => 'bna', 'C05p12370' => 'bna', 'C07p13680' => 'bna', 'CAN.G1006.16' => 'can', 'CAN.G1006.17' => 'can', 'CAN.G1170.2' => 'can', 'CAN.G962.7' => 'can', 'CANSAT25G2179' => 'cansat', 'CANSAT78G1573' => 'cansat', 'CARHR099510' => 'chi', 'CARHR143510' => 'chi', 'Carub.0003s2380' => 'cru', 'Carub.0004s3082' => 'cru', 'Ca_00614_v3' => 'car', 'Ca_07801_v3' => 'car', 'Ca_08567_v3' => 'car', 'Ca_09571_v3' => 'car', 'CBR_g19290' => 'cbr', 'Cc01_g19770' => 'ccan', 'Cc03_g03030' => 'ccan', 'CDE07G0968' => 'cde', 'CDE09G1441' => 'cde', 'Cfa006103' => 'cfa', 'Cfa015573' => 'cfa', 'Cfa016988' => 'cfa', 'Ciclev10006738m.g' => 'ccl', 'Ciclev10010920m.g' => 'ccl', 'Ciclev10018517m.g' => 'ccl', 'CiPaw.01G159200' => 'cil', 'CiPaw.02G091000' => 'cil', 'CiPaw.02G091100' => 'cil', 'CiPaw.08G103100' => 'cil', 'CiPaw.09G224900' => 'cil', 'ClCG06G005740' => 'cla', 'ClCG07G000090' => 'cla', 'ClCG07G000100' => 'cla', 'COL.COLO4_09143' => 'col', 'COL.COLO4_25124' => 'col', 'Cpa.g.sc16.34' => 'cpa', 'Cpa.g.sc3504.1' => 'cpa', 'Cpa.g.sc60.37' => 'cpa', 'CsaV3_6G018520' => 'csa', 'CsaV3_6G036860' => 'csa', 'CSS0001072' => 'camsi', 'CSS0020208' => 'camsi', 'CSS0021253' => 'camsi', 'CSS0022190' => 'camsi', 'CSS0036150' => 'camsi', 'CSS0040442' => 'camsi', 'CSS0042300' => 'camsi', 'CSS0045298' => 'camsi', 'DCAR_012449' => 'dca', 'DCAR_018405' => 'dca', 'DCAR_024573' => 'dca', 'DCAR_030591' => 'dca', 'Dinv16926' => 'din', 'Dinv32963' => 'din', 'Dinv38382' => 'din', 'Dinv38383' => 'din', 'Duzib133G0974' => 'dzi', 'Duzib138G1867' => 'dzi', 'Duzib211G0420' => 'dzi', 'Duzib212G0930' => 'dzi', 'ECA234G1645' => 'eca', 'ECA247G3467' => 'eca', 'ECA248G1703' => 'eca', 'EL10Ac3g06327' => 'bvu', 'EL10Ac7g17204' => 'bvu', 'Eucgr.A00855' => 'egr', 'Eucgr.A00858' => 'egr', 'Eucgr.H01520' => 'egr', 'Eucgr.H03604' => 'egr', 'Eucgr.L03465' => 'egr', 'Eucgr.L03466' => 'egr', 'FAN01G0988' => 'fan', 'FAN02G3892' => 'fan', 'FAN05G3381' => 'fan', 'FAN07G0967' => 'fan', 'FAN07G1493' => 'fan', 'FAN08G3125' => 'fan', 'FAN09G0402' => 'fan', 'FAN12G2594' => 'fan', 'FAN12G3879' => 'fan', 'FAN14G1546' => 'fan', 'FAN15G3626' => 'fan', 'FAN17G0588' => 'fan', 'FAN17G0609' => 'fan', 'FAN18G2817' => 'fan', 'FAN19G1305' => 'fan', 'FAN20G1787' => 'fan', 'FAN22G0073' => 'fan', 'FAN22G0352' => 'fan', 'FAN22G0368' => 'fan', 'FAN22G2273' => 'fan', 'FAN24G1998' => 'fan', 'FAN27G1317' => 'fan', 'FvH4_2g23980' => 'fve', 'FvH4_4g14380' => 'fve', 'FvH4_4g14390' => 'fve', 'FvH4_6g09250' => 'fve', 'Glyma.03G151100' => 'gma', 'Glyma.04G122550' => 'gma', 'Glyma.05G001600' => 'gma', 'Glyma.09G270766' => 'gma', 'Glyma.09G270832' => 'gma', 'Glyma.13G209800' => 'gma', 'Glyma.15G102800' => 'gma', 'Glyma.18G218900' => 'gma', 'Glyma.19G001500' => 'gma', 'Glyma.19G153600' => 'gma', 'Gohir.A02G028600' => 'ghi', 'Gohir.A08G045000' => 'ghi', 'Gohir.A11G120500' => 'ghi', 'Gohir.A12G006200' => 'ghi', 'Gohir.A12G006250' => 'ghi', 'Gohir.D02G036300' => 'ghi', 'Gohir.D08G054700' => 'ghi', 'Gohir.D11G125600' => 'ghi', 'Gohir.D12G005700' => 'ghi', 'Gorai.004G055200' => 'gra', 'Gorai.005G040400' => 'gra', 'Gorai.007G134500' => 'gra', 'Gorai.008G005500' => 'gra', 'GSVIVG01011094001' => 'vvi', 'GSVIVG01017879001' => 'vvi', 'GSVIVG01025988001' => 'vvi', 'GSVIVG01029847001' => 'vvi', 'HanXRQChr10g0282901' => 'han', 'HanXRQChr10g0310371' => 'han', 'HanXRQChr10g0315041' => 'han', 'HanXRQChr11g0327651' => 'han', 'HanXRQChr12g0359391' => 'han', 'Haze_00972' => 'cav', 'Haze_00973' => 'cav', 'Haze_00974' => 'cav', 'Haze_04747' => 'cav', 'Haze_04749' => 'cav', 'Haze_04750' => 'cav', 'Haze_21217' => 'cav', 'Hma1.2p1_1037F.1_g250680' => 'hma', 'Hma1.2p1_1644F.1_g295320' => 'hma', 'HPP92_011322' => 'vpl', 'HPP92_011323' => 'vpl', 'HPP92_011324' => 'vpl', 'HPP92_011325' => 'vpl', 'HPP92_011326' => 'vpl', 'Hund12205' => 'sun', 'Hund17957' => 'sun', 'Lalb_Chr06g0176771' => 'lal', 'Lalb_Chr18g0056021' => 'lal', 'Lalb_Chr18g0056031' => 'lal', 'Lalb_Chr18g0056041' => 'lal', 'Lalb_Chr20g0107751' => 'lal', 'Lalb_Chr20g0118371' => 'lal', 'Lj1g0010239' => 'lja', 'Lj1g0017101' => 'lja', 'Lj2A1178G40' => 'lonja', 'Lj2A54G84' => 'lonja', 'Lj2g0015248' => 'lja', 'Lj3A761T51' => 'lonja', 'Lj6g0018116' => 'lja', 'Lsat_1_v5_gn_4_136040' => 'lsa', 'Lsat_1_v5_gn_5_187461' => 'lsa', 'Lsat_1_v5_gn_5_77001' => 'lsa', 'Lsat_1_v5_gn_9_4461' => 'lsa', 'Manes.01G210100' => 'mes', 'Manes.03G185600' => 'mes', 'Manes.05G073300' => 'mes', 'Manes.09G120300' => 'mes', 'Manes.15G022100' => 'mes', 'Mapoly0096s0053' => 'mpo', 'MBI03_g14058_MAGBIO' => 'mbi', 'MBI03_g33876_MAGBIO' => 'mbi', 'MBI03_g36854_MAGBIO' => 'mbi', 'MBI17_g11997_MAGBIO' => 'mbi', 'MD03G1269000' => 'mdo', 'MD04G1179600' => 'mdo', 'MD11G1289800' => 'mdo', 'MD12G1194700' => 'mdo', 'MD13G1182100' => 'mdo', 'MD13G1182200' => 'mdo', 'MD16G1182600' => 'mdo', 'Medtr2g021400' => 'mtr', 'Medtr2g021470' => 'mtr', 'Medtr2g105810' => 'mtr', 'Medtr3g033580' => 'mtr', 'Medtr6g007970' => 'mtr', 'Medtr7g056330' => 'mtr', 'Medtr7g074290' => 'mtr', 'Medtr7g074380' => 'mtr', 'Medtr7g094550' => 'mtr', 'Medtr8g069995' => 'mtr', 'MELO3C014345.2' => 'cme', 'MELO3C021395.2' => 'cme', 'Migut.D00262' => 'egut', 'Migut.G00257' => 'egut', 'MSTRG.21575' => 'ama', 'MSTRG.3985' => 'ama', 'Nitab4.5_0000295g0140' => 'nta', 'Nitab4.5_0000732g0140' => 'nta', 'Nitab4.5_0003162g0020' => 'nta', 'Nitab4.5_0006180g0090' => 'nta', 'Nitab4.5_0006390g0010' => 'nta', 'Nitab4.5_0007392g0040' => 'nta', 'Nn1g02140' => 'nnu', 'Nn4g26168' => 'nnu', 'Nn5g26754' => 'nnu', 'Oeu001433.1' => 'oeu', 'Oeu010299.2' => 'oeu', 'Oeu011171.1' => 'oeu', 'Oeu037675.1' => 'oeu', 'Oeu038359.1' => 'oeu', 'Oeu063834.1' => 'oeu', 'Oeu063835.1' => 'oeu', 'Os05g0312000' => 'osa', 'Os07g0211101' => 'osa', 'Os07g0211200' => 'osa', 'Os07g0681500' => 'osa', 'Peaxi162Scf00095g01015' => 'pax', 'Peaxi162Scf00104g00329' => 'pax', 'Peaxi162Scf00161g00137' => 'pax', 'PGR004G1665' => 'pgr', 'PGR031G2937' => 'pgr', 'PGR119G2145' => 'pgr', 'PGSC0003DMG400004351' => 'stu', 'PGSC0003DMG400014625' => 'stu', 'PGSC0003DMG401000943' => 'stu', 'Phvul.001G148600' => 'pvu', 'Phvul.004G001700' => 'pvu', 'Phvul.006G154900' => 'pvu', 'Phvul.008G078200' => 'pvu', 'Phvul.011G136500' => 'pvu', 'Potri.002G215600' => 'ptr', 'Potri.008G201600' => 'ptr', 'Potri.014G138400' => 'ptr', 'Potri.016G142500' => 'ptr', 'Pp3c16_10580' => 'ppa', 'Pp3c5_25280' => 'ppa', 'Prupe.1G150000' => 'ppe', 'Prupe.1G150100' => 'ppe', 'Prupe.6G299600' => 'ppe', 'Prupe.8G245000' => 'ppe', 'Psat0s4927g0040' => 'psa', 'Psat1g052080' => 'psa', 'Psat1g183800' => 'psa', 'Psat3g113840' => 'psa', 'Psat3g126120' => 'psa', 'Psat3g126160' => 'psa', 'Psat3g158760' => 'psa', 'Psat3g158840' => 'psa', 'PSO170G2858' => 'pso', 'PSO339G0606' => 'pso', 'PSO384G4709' => 'pso', 'PSO407G0334' => 'pso', 'QL04p040276' => 'qlo', 'QL06p005458' => 'qlo', 'QL06p005472' => 'qlo', 'QL07p030546' => 'qlo', 'QL07p031519' => 'qlo', 'QL09p050949' => 'qlo', 'QL09p050966' => 'qlo', 'QL09p051067' => 'qlo', 'QL12p022706' => 'qlo', 'RcHm_v2.0_Chr2g0119601' => 'rch', 'RcHm_v2.0_Chr3g0459591' => 'rch', 'RcHm_v2.0_Chr4g0418521' => 'rch', 'RcHm_v2.0_Chr4g0418531' => 'rch', 'RcHm_v2.0_Chr4g0418541' => 'rch', 'RcHm_v2.0_Chr6g0291641' => 'rch', 'Rhsim01G0086300' => 'rsi', 'Rhsim01G0276300' => 'rsi', 'Rhsim01G0276500' => 'rsi', 'Rhsim04G0207700' => 'rsi', 'Rhsim05G0234500' => 'rsi', 'Rhsim13G0022400' => 'rsi', 'Sabra02G0167900' => 'sbr', 'Sabra04G0158500' => 'sbr', 'Sabra08G0159800' => 'sbr', 'Sabra10G0011500' => 'sbr', 'Sabra14G0104400' => 'sbr', 'SalBow2G2440' => 'sbo', 'SalBow4G2265' => 'sbo', 'Sc02g0000060' => 'sci', 'Sc05g0005020' => 'sci', 'Sc13g0003890' => 'sci', 'Sed0014865' => 'sed', 'Sed0017224' => 'sed', 'Sed0026391' => 'sed', 'SEGI_00063' => 'sgi', 'SEGI_10967' => 'sgi', 'SEGI_17510' => 'sgi', 'SEGI_24396' => 'sgi', 'SEGI_39719' => 'sgi', 'SEGI_41392' => 'sgi', 'SGA_v2.0_scaffold11G05794' => 'sas', 'SGA_v2.0_scaffold142G35607' => 'sas', 'SGA_v2.0_scaffold1G00447' => 'sas', 'SHI15388' => 'shi', 'SHI15394' => 'shi', 'SHI15396' => 'shi', 'SHI15399' => 'shi', 'SMO343G0151' => 'smo', 'SMO367G1118' => 'smo', 'Solyc01g080200.3' => 'sly', 'Solyc06g008960.3' => 'sly', 'Solyc09g064780.3' => 'sly', 'Sopen01g031980' => 'spe', 'Sopen06g003710' => 'spe', 'Sopen09g026460' => 'spe', 'Sp3g21240' => 'spa', 'Sp4g30030' => 'spa', 'TAR365G0022' => 'tar', 'TAR365G1023' => 'tar', 'TAR365G1253' => 'tar', 'TAR623G0078' => 'tar', 'TAR623G1721' => 'tar', 'TAR633G0959' => 'tar', 'THA.LOC104802225' => 'tha', 'THA.LOC104804769' => 'tha', 'THA.LOC104808660' => 'tha', 'THA.LOC104812792' => 'tha', 'Thecc.01G284000' => 'tca', 'Thecc.04G220600' => 'tca', 'Thecc.05G268900' => 'tca', 'Thecc.08G171100' => 'tca', 'Thhalv10001284m.g' => 'esa', 'Thhalv10019912m.g' => 'esa', 'TPR.G14189' => 'tpr', 'TPR.G18110' => 'tpr', 'TPR.G18130' => 'tpr', 'TPR.G18131' => 'tpr', 'TPR.G18140' => 'tpr', 'TPR.G24282' => 'tpr', 'TPR.G25221' => 'tpr', 'TPR.G29267' => 'tpr', 'TPR.G35315' => 'tpr', 'TPR.G36173' => 'tpr', 'TWI09G0794' => 'twi', 'TWI59G1348' => 'twi', 'TWI74G0430' => 'twi', 'unitig_26.g8940' => 'ugi', 'unitig_749.g13744' => 'ugi', 'unitig_749.g13745' => 'ugi', 'vmacro08269' => 'vma', 'vmacro14937' => 'vma', 'vmacro20401' => 'vma', 'VMungo0464G1349' => 'vmu', 'VMungo0540G0289' => 'vmu', 'VMungo1215G1590' => 'vmu', 'VMungo1309G0221' => 'vmu', 'VMungo1309G2815' => 'vmu', 'VMungo1383G0239' => 'vmu', 'VMungo1383G2910' => 'vmu', 'Zm00001eb095270' => 'zma', 'Zm00001eb095280' => 'zma', 'Zm00001eb111630' => 'zma', 'Zm00001eb237080' => 'zma', 'Zm00001eb273740' => 'zma', 'Zm00001eb285040' => 'zma', 'Zm00001eb330790' => 'zma', 'Zm00001eb337380' => 'zma' ) $gf_id = 'HOM05D001484' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001484' ) $data_identifier = 'HOM05D001484' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 2, 'aly' => (int) 2, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 22, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 7, 'hma' => (int) 2, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 7, 'mtr' => (int) 10, 'cme' => (int) 2, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 4, 'ppa' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 4, 'qlo' => (int) 9, 'rch' => (int) 6, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 10, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 7, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb337380' $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' => 'HOM05D001484', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p31500' => 'bna', 'A05p00020' => 'bna', 'A07p08820' => 'bna', 'Aa31LG4G3300' => 'aar', 'Aa31LG8G10030' => 'aar', 'Actinidia00731' => 'ach', 'Actinidia11473' => 'ach', 'Actinidia23469' => 'ach', 'Actinidia24318' => 'ach', 'Actinidia40196' => 'ach', 'Actinidia40197' => 'ach', 'Actinidia40198' => 'ach', 'Ah.08g212990' => 'amhyb', 'Ah.15g091720' => 'amhyb', 'AL3G38260' => 'aly', 'AL4G47710' => 'aly', 'Aqoxy2G00671' => 'aox', 'Aqoxy2G03236' => 'aox', 'arahy.Tifrunner.gnm1.ann1.05IDCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KR684' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATY3SJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK6QJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6APGL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IDT7Z9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM073U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ0R87' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LE7RV4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT4QRX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V5ENPK' => 'arhy', 'AT2G48110' => 'ath', 'AT3G23590' => 'ath', 'ATR0626G186' => 'atr', 'ATR1127G141' => 'atr', 'Atru.chr4.2583' => 'acertr', 'Atru.chr5.1358' => 'acertr', 'Atru.chr5.1359' => 'acertr', 'Atru.chr8.46' => 'acertr', 'AUR62002640' => 'cqu', 'AUR62030055' => 'cqu', 'AUR62033713' => 'cqu', 'AUR62033714' => 'cqu', 'AUR62036795' => 'cqu', 'AUR62039891' => 'cqu', 'BcaB02g08737' => 'bca', 'BcaB04g20441' => 'bca', 'BcaB06g26509' => 'bca', 'BcaB06g26510' => 'bca', 'BcaB06g26511' => 'bca', 'BcaB06g26512' => 'bca', 'BcaB06g26513' => 'bca', 'BcaC02g12564' => 'bca', 'BcaC02g12565' => 'bca', 'BcaC02g12794' => 'bca', 'BcaC02g12795' => 'bca', 'BcaC02g12796' => 'bca', 'BcaC06g35541' => 'bca', 'BNapus_Darmor_BZH_scaffold_188p00080' => 'bna', 'BNapus_Darmor_BZH_scaffold_188p00090' => 'bna', 'BolC1t03972H' => 'bol', 'BolC1t03973H' => 'bol', 'BolC4t21680H' => 'bol', 'BolC7t41863H' => 'bol', 'BolSC55t61227H' => 'bol', 'BolSC55t61228H' => 'bol', 'BraA01t03278Z' => 'bra', 'BraA05t18998Z' => 'bra', 'BraA07t28673Z' => 'bra', 'C01p40150' => 'bna', 'C05p12370' => 'bna', 'C07p13680' => 'bna', 'CAN.G1006.16' => 'can', 'CAN.G1006.17' => 'can', 'CAN.G1170.2' => 'can', 'CAN.G962.7' => 'can', 'CANSAT25G2179' => 'cansat', 'CANSAT78G1573' => 'cansat', 'CARHR099510' => 'chi', 'CARHR143510' => 'chi', 'Carub.0003s2380' => 'cru', 'Carub.0004s3082' => 'cru', 'Ca_00614_v3' => 'car', 'Ca_07801_v3' => 'car', 'Ca_08567_v3' => 'car', 'Ca_09571_v3' => 'car', 'CBR_g19290' => 'cbr', 'Cc01_g19770' => 'ccan', 'Cc03_g03030' => 'ccan', 'CDE07G0968' => 'cde', 'CDE09G1441' => 'cde', 'Cfa006103' => 'cfa', 'Cfa015573' => 'cfa', 'Cfa016988' => 'cfa', 'Ciclev10006738m.g' => 'ccl', 'Ciclev10010920m.g' => 'ccl', 'Ciclev10018517m.g' => 'ccl', 'CiPaw.01G159200' => 'cil', 'CiPaw.02G091000' => 'cil', 'CiPaw.02G091100' => 'cil', 'CiPaw.08G103100' => 'cil', 'CiPaw.09G224900' => 'cil', 'ClCG06G005740' => 'cla', 'ClCG07G000090' => 'cla', 'ClCG07G000100' => 'cla', 'COL.COLO4_09143' => 'col', 'COL.COLO4_25124' => 'col', 'Cpa.g.sc16.34' => 'cpa', 'Cpa.g.sc3504.1' => 'cpa', 'Cpa.g.sc60.37' => 'cpa', 'CsaV3_6G018520' => 'csa', 'CsaV3_6G036860' => 'csa', 'CSS0001072' => 'camsi', 'CSS0020208' => 'camsi', 'CSS0021253' => 'camsi', 'CSS0022190' => 'camsi', 'CSS0036150' => 'camsi', 'CSS0040442' => 'camsi', 'CSS0042300' => 'camsi', 'CSS0045298' => 'camsi', 'DCAR_012449' => 'dca', 'DCAR_018405' => 'dca', 'DCAR_024573' => 'dca', 'DCAR_030591' => 'dca', 'Dinv16926' => 'din', 'Dinv32963' => 'din', 'Dinv38382' => 'din', 'Dinv38383' => 'din', 'Duzib133G0974' => 'dzi', 'Duzib138G1867' => 'dzi', 'Duzib211G0420' => 'dzi', 'Duzib212G0930' => 'dzi', 'ECA234G1645' => 'eca', 'ECA247G3467' => 'eca', 'ECA248G1703' => 'eca', 'EL10Ac3g06327' => 'bvu', 'EL10Ac7g17204' => 'bvu', 'Eucgr.A00855' => 'egr', 'Eucgr.A00858' => 'egr', 'Eucgr.H01520' => 'egr', 'Eucgr.H03604' => 'egr', 'Eucgr.L03465' => 'egr', 'Eucgr.L03466' => 'egr', 'FAN01G0988' => 'fan', 'FAN02G3892' => 'fan', 'FAN05G3381' => 'fan', 'FAN07G0967' => 'fan', 'FAN07G1493' => 'fan', 'FAN08G3125' => 'fan', 'FAN09G0402' => 'fan', 'FAN12G2594' => 'fan', 'FAN12G3879' => 'fan', 'FAN14G1546' => 'fan', 'FAN15G3626' => 'fan', 'FAN17G0588' => 'fan', 'FAN17G0609' => 'fan', 'FAN18G2817' => 'fan', 'FAN19G1305' => 'fan', 'FAN20G1787' => 'fan', 'FAN22G0073' => 'fan', 'FAN22G0352' => 'fan', 'FAN22G0368' => 'fan', 'FAN22G2273' => 'fan', 'FAN24G1998' => 'fan', 'FAN27G1317' => 'fan', 'FvH4_2g23980' => 'fve', 'FvH4_4g14380' => 'fve', 'FvH4_4g14390' => 'fve', 'FvH4_6g09250' => 'fve', 'Glyma.03G151100' => 'gma', 'Glyma.04G122550' => 'gma', 'Glyma.05G001600' => 'gma', 'Glyma.09G270766' => 'gma', 'Glyma.09G270832' => 'gma', 'Glyma.13G209800' => 'gma', 'Glyma.15G102800' => 'gma', 'Glyma.18G218900' => 'gma', 'Glyma.19G001500' => 'gma', 'Glyma.19G153600' => 'gma', 'Gohir.A02G028600' => 'ghi', 'Gohir.A08G045000' => 'ghi', 'Gohir.A11G120500' => 'ghi', 'Gohir.A12G006200' => 'ghi', 'Gohir.A12G006250' => 'ghi', 'Gohir.D02G036300' => 'ghi', 'Gohir.D08G054700' => 'ghi', 'Gohir.D11G125600' => 'ghi', 'Gohir.D12G005700' => 'ghi', 'Gorai.004G055200' => 'gra', 'Gorai.005G040400' => 'gra', 'Gorai.007G134500' => 'gra', 'Gorai.008G005500' => 'gra', 'GSVIVG01011094001' => 'vvi', 'GSVIVG01017879001' => 'vvi', 'GSVIVG01025988001' => 'vvi', 'GSVIVG01029847001' => 'vvi', 'HanXRQChr10g0282901' => 'han', 'HanXRQChr10g0310371' => 'han', 'HanXRQChr10g0315041' => 'han', 'HanXRQChr11g0327651' => 'han', 'HanXRQChr12g0359391' => 'han', 'Haze_00972' => 'cav', 'Haze_00973' => 'cav', 'Haze_00974' => 'cav', 'Haze_04747' => 'cav', 'Haze_04749' => 'cav', 'Haze_04750' => 'cav', 'Haze_21217' => 'cav', 'Hma1.2p1_1037F.1_g250680' => 'hma', 'Hma1.2p1_1644F.1_g295320' => 'hma', 'HPP92_011322' => 'vpl', 'HPP92_011323' => 'vpl', 'HPP92_011324' => 'vpl', 'HPP92_011325' => 'vpl', 'HPP92_011326' => 'vpl', 'Hund12205' => 'sun', 'Hund17957' => 'sun', 'Lalb_Chr06g0176771' => 'lal', 'Lalb_Chr18g0056021' => 'lal', 'Lalb_Chr18g0056031' => 'lal', 'Lalb_Chr18g0056041' => 'lal', 'Lalb_Chr20g0107751' => 'lal', 'Lalb_Chr20g0118371' => 'lal', 'Lj1g0010239' => 'lja', 'Lj1g0017101' => 'lja', 'Lj2A1178G40' => 'lonja', 'Lj2A54G84' => 'lonja', 'Lj2g0015248' => 'lja', 'Lj3A761T51' => 'lonja', 'Lj6g0018116' => 'lja', 'Lsat_1_v5_gn_4_136040' => 'lsa', 'Lsat_1_v5_gn_5_187461' => 'lsa', 'Lsat_1_v5_gn_5_77001' => 'lsa', 'Lsat_1_v5_gn_9_4461' => 'lsa', 'Manes.01G210100' => 'mes', 'Manes.03G185600' => 'mes', 'Manes.05G073300' => 'mes', 'Manes.09G120300' => 'mes', 'Manes.15G022100' => 'mes', 'Mapoly0096s0053' => 'mpo', 'MBI03_g14058_MAGBIO' => 'mbi', 'MBI03_g33876_MAGBIO' => 'mbi', 'MBI03_g36854_MAGBIO' => 'mbi', 'MBI17_g11997_MAGBIO' => 'mbi', 'MD03G1269000' => 'mdo', 'MD04G1179600' => 'mdo', 'MD11G1289800' => 'mdo', 'MD12G1194700' => 'mdo', 'MD13G1182100' => 'mdo', 'MD13G1182200' => 'mdo', 'MD16G1182600' => 'mdo', 'Medtr2g021400' => 'mtr', 'Medtr2g021470' => 'mtr', 'Medtr2g105810' => 'mtr', 'Medtr3g033580' => 'mtr', 'Medtr6g007970' => 'mtr', 'Medtr7g056330' => 'mtr', 'Medtr7g074290' => 'mtr', 'Medtr7g074380' => 'mtr', 'Medtr7g094550' => 'mtr', 'Medtr8g069995' => 'mtr', 'MELO3C014345.2' => 'cme', 'MELO3C021395.2' => 'cme', 'Migut.D00262' => 'egut', 'Migut.G00257' => 'egut', 'MSTRG.21575' => 'ama', 'MSTRG.3985' => 'ama', 'Nitab4.5_0000295g0140' => 'nta', 'Nitab4.5_0000732g0140' => 'nta', 'Nitab4.5_0003162g0020' => 'nta', 'Nitab4.5_0006180g0090' => 'nta', 'Nitab4.5_0006390g0010' => 'nta', 'Nitab4.5_0007392g0040' => 'nta', 'Nn1g02140' => 'nnu', 'Nn4g26168' => 'nnu', 'Nn5g26754' => 'nnu', 'Oeu001433.1' => 'oeu', 'Oeu010299.2' => 'oeu', 'Oeu011171.1' => 'oeu', 'Oeu037675.1' => 'oeu', 'Oeu038359.1' => 'oeu', 'Oeu063834.1' => 'oeu', 'Oeu063835.1' => 'oeu', 'Os05g0312000' => 'osa', 'Os07g0211101' => 'osa', 'Os07g0211200' => 'osa', 'Os07g0681500' => 'osa', 'Peaxi162Scf00095g01015' => 'pax', 'Peaxi162Scf00104g00329' => 'pax', 'Peaxi162Scf00161g00137' => 'pax', 'PGR004G1665' => 'pgr', 'PGR031G2937' => 'pgr', 'PGR119G2145' => 'pgr', 'PGSC0003DMG400004351' => 'stu', 'PGSC0003DMG400014625' => 'stu', 'PGSC0003DMG401000943' => 'stu', 'Phvul.001G148600' => 'pvu', 'Phvul.004G001700' => 'pvu', 'Phvul.006G154900' => 'pvu', 'Phvul.008G078200' => 'pvu', 'Phvul.011G136500' => 'pvu', 'Potri.002G215600' => 'ptr', 'Potri.008G201600' => 'ptr', 'Potri.014G138400' => 'ptr', 'Potri.016G142500' => 'ptr', 'Pp3c16_10580' => 'ppa', 'Pp3c5_25280' => 'ppa', 'Prupe.1G150000' => 'ppe', 'Prupe.1G150100' => 'ppe', 'Prupe.6G299600' => 'ppe', 'Prupe.8G245000' => 'ppe', 'Psat0s4927g0040' => 'psa', 'Psat1g052080' => 'psa', 'Psat1g183800' => 'psa', 'Psat3g113840' => 'psa', 'Psat3g126120' => 'psa', 'Psat3g126160' => 'psa', 'Psat3g158760' => 'psa', 'Psat3g158840' => 'psa', 'PSO170G2858' => 'pso', 'PSO339G0606' => 'pso', 'PSO384G4709' => 'pso', 'PSO407G0334' => 'pso', 'QL04p040276' => 'qlo', 'QL06p005458' => 'qlo', 'QL06p005472' => 'qlo', 'QL07p030546' => 'qlo', 'QL07p031519' => 'qlo', 'QL09p050949' => 'qlo', 'QL09p050966' => 'qlo', 'QL09p051067' => 'qlo', 'QL12p022706' => 'qlo', 'RcHm_v2.0_Chr2g0119601' => 'rch', 'RcHm_v2.0_Chr3g0459591' => 'rch', 'RcHm_v2.0_Chr4g0418521' => 'rch', 'RcHm_v2.0_Chr4g0418531' => 'rch', 'RcHm_v2.0_Chr4g0418541' => 'rch', 'RcHm_v2.0_Chr6g0291641' => 'rch', 'Rhsim01G0086300' => 'rsi', 'Rhsim01G0276300' => 'rsi', 'Rhsim01G0276500' => 'rsi', 'Rhsim04G0207700' => 'rsi', 'Rhsim05G0234500' => 'rsi', 'Rhsim13G0022400' => 'rsi', 'Sabra02G0167900' => 'sbr', 'Sabra04G0158500' => 'sbr', 'Sabra08G0159800' => 'sbr', 'Sabra10G0011500' => 'sbr', 'Sabra14G0104400' => 'sbr', 'SalBow2G2440' => 'sbo', 'SalBow4G2265' => 'sbo', 'Sc02g0000060' => 'sci', 'Sc05g0005020' => 'sci', 'Sc13g0003890' => 'sci', 'Sed0014865' => 'sed', 'Sed0017224' => 'sed', 'Sed0026391' => 'sed', 'SEGI_00063' => 'sgi', 'SEGI_10967' => 'sgi', 'SEGI_17510' => 'sgi', 'SEGI_24396' => 'sgi', 'SEGI_39719' => 'sgi', 'SEGI_41392' => 'sgi', 'SGA_v2.0_scaffold11G05794' => 'sas', 'SGA_v2.0_scaffold142G35607' => 'sas', 'SGA_v2.0_scaffold1G00447' => 'sas', 'SHI15388' => 'shi', 'SHI15394' => 'shi', 'SHI15396' => 'shi', 'SHI15399' => 'shi', 'SMO343G0151' => 'smo', 'SMO367G1118' => 'smo', 'Solyc01g080200.3' => 'sly', 'Solyc06g008960.3' => 'sly', 'Solyc09g064780.3' => 'sly', 'Sopen01g031980' => 'spe', 'Sopen06g003710' => 'spe', 'Sopen09g026460' => 'spe', 'Sp3g21240' => 'spa', 'Sp4g30030' => 'spa', 'TAR365G0022' => 'tar', 'TAR365G1023' => 'tar', 'TAR365G1253' => 'tar', 'TAR623G0078' => 'tar', 'TAR623G1721' => 'tar', 'TAR633G0959' => 'tar', 'THA.LOC104802225' => 'tha', 'THA.LOC104804769' => 'tha', 'THA.LOC104808660' => 'tha', 'THA.LOC104812792' => 'tha', 'Thecc.01G284000' => 'tca', 'Thecc.04G220600' => 'tca', 'Thecc.05G268900' => 'tca', 'Thecc.08G171100' => 'tca', 'Thhalv10001284m.g' => 'esa', 'Thhalv10019912m.g' => 'esa', 'TPR.G14189' => 'tpr', 'TPR.G18110' => 'tpr', 'TPR.G18130' => 'tpr', 'TPR.G18131' => 'tpr', 'TPR.G18140' => 'tpr', 'TPR.G24282' => 'tpr', 'TPR.G25221' => 'tpr', 'TPR.G29267' => 'tpr', 'TPR.G35315' => 'tpr', 'TPR.G36173' => 'tpr', 'TWI09G0794' => 'twi', 'TWI59G1348' => 'twi', 'TWI74G0430' => 'twi', 'unitig_26.g8940' => 'ugi', 'unitig_749.g13744' => 'ugi', 'unitig_749.g13745' => 'ugi', 'vmacro08269' => 'vma', 'vmacro14937' => 'vma', 'vmacro20401' => 'vma', 'VMungo0464G1349' => 'vmu', 'VMungo0540G0289' => 'vmu', 'VMungo1215G1590' => 'vmu', 'VMungo1309G0221' => 'vmu', 'VMungo1309G2815' => 'vmu', 'VMungo1383G0239' => 'vmu', 'VMungo1383G2910' => 'vmu', 'Zm00001eb095270' => 'zma', 'Zm00001eb095280' => 'zma', 'Zm00001eb111630' => 'zma', 'Zm00001eb237080' => 'zma', 'Zm00001eb273740' => 'zma', 'Zm00001eb285040' => 'zma', 'Zm00001eb330790' => 'zma', 'Zm00001eb337380' => 'zma' ), 'gf_id' => 'HOM05D001484', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001484' ), 'data_identifier' => 'HOM05D001484', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001484', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p31500' => 'bna', 'A05p00020' => 'bna', 'A07p08820' => 'bna', 'Aa31LG4G3300' => 'aar', 'Aa31LG8G10030' => 'aar', 'Actinidia00731' => 'ach', 'Actinidia11473' => 'ach', 'Actinidia23469' => 'ach', 'Actinidia24318' => 'ach', 'Actinidia40196' => 'ach', 'Actinidia40197' => 'ach', 'Actinidia40198' => 'ach', 'Ah.08g212990' => 'amhyb', 'Ah.15g091720' => 'amhyb', 'AL3G38260' => 'aly', 'AL4G47710' => 'aly', 'Aqoxy2G00671' => 'aox', 'Aqoxy2G03236' => 'aox', 'arahy.Tifrunner.gnm1.ann1.05IDCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KR684' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATY3SJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK6QJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6APGL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IDT7Z9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM073U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ0R87' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LE7RV4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT4QRX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V5ENPK' => 'arhy', 'AT2G48110' => 'ath', 'AT3G23590' => 'ath', 'ATR0626G186' => 'atr', 'ATR1127G141' => 'atr', 'Atru.chr4.2583' => 'acertr', 'Atru.chr5.1358' => 'acertr', 'Atru.chr5.1359' => 'acertr', 'Atru.chr8.46' => 'acertr', 'AUR62002640' => 'cqu', 'AUR62030055' => 'cqu', 'AUR62033713' => 'cqu', 'AUR62033714' => 'cqu', 'AUR62036795' => 'cqu', 'AUR62039891' => 'cqu', 'BcaB02g08737' => 'bca', 'BcaB04g20441' => 'bca', 'BcaB06g26509' => 'bca', 'BcaB06g26510' => 'bca', 'BcaB06g26511' => 'bca', 'BcaB06g26512' => 'bca', 'BcaB06g26513' => 'bca', 'BcaC02g12564' => 'bca', 'BcaC02g12565' => 'bca', 'BcaC02g12794' => 'bca', 'BcaC02g12795' => 'bca', 'BcaC02g12796' => 'bca', 'BcaC06g35541' => 'bca', 'BNapus_Darmor_BZH_scaffold_188p00080' => 'bna', 'BNapus_Darmor_BZH_scaffold_188p00090' => 'bna', 'BolC1t03972H' => 'bol', 'BolC1t03973H' => 'bol', 'BolC4t21680H' => 'bol', 'BolC7t41863H' => 'bol', 'BolSC55t61227H' => 'bol', 'BolSC55t61228H' => 'bol', 'BraA01t03278Z' => 'bra', 'BraA05t18998Z' => 'bra', 'BraA07t28673Z' => 'bra', 'C01p40150' => 'bna', 'C05p12370' => 'bna', 'C07p13680' => 'bna', 'CAN.G1006.16' => 'can', 'CAN.G1006.17' => 'can', 'CAN.G1170.2' => 'can', 'CAN.G962.7' => 'can', 'CANSAT25G2179' => 'cansat', 'CANSAT78G1573' => 'cansat', 'CARHR099510' => 'chi', 'CARHR143510' => 'chi', 'Carub.0003s2380' => 'cru', 'Carub.0004s3082' => 'cru', 'Ca_00614_v3' => 'car', 'Ca_07801_v3' => 'car', 'Ca_08567_v3' => 'car', 'Ca_09571_v3' => 'car', 'CBR_g19290' => 'cbr', 'Cc01_g19770' => 'ccan', 'Cc03_g03030' => 'ccan', 'CDE07G0968' => 'cde', 'CDE09G1441' => 'cde', 'Cfa006103' => 'cfa', 'Cfa015573' => 'cfa', 'Cfa016988' => 'cfa', 'Ciclev10006738m.g' => 'ccl', 'Ciclev10010920m.g' => 'ccl', 'Ciclev10018517m.g' => 'ccl', 'CiPaw.01G159200' => 'cil', 'CiPaw.02G091000' => 'cil', 'CiPaw.02G091100' => 'cil', 'CiPaw.08G103100' => 'cil', 'CiPaw.09G224900' => 'cil', 'ClCG06G005740' => 'cla', 'ClCG07G000090' => 'cla', 'ClCG07G000100' => 'cla', 'COL.COLO4_09143' => 'col', 'COL.COLO4_25124' => 'col', 'Cpa.g.sc16.34' => 'cpa', 'Cpa.g.sc3504.1' => 'cpa', 'Cpa.g.sc60.37' => 'cpa', 'CsaV3_6G018520' => 'csa', 'CsaV3_6G036860' => 'csa', 'CSS0001072' => 'camsi', 'CSS0020208' => 'camsi', 'CSS0021253' => 'camsi', 'CSS0022190' => 'camsi', 'CSS0036150' => 'camsi', 'CSS0040442' => 'camsi', 'CSS0042300' => 'camsi', 'CSS0045298' => 'camsi', 'DCAR_012449' => 'dca', 'DCAR_018405' => 'dca', 'DCAR_024573' => 'dca', 'DCAR_030591' => 'dca', 'Dinv16926' => 'din', 'Dinv32963' => 'din', 'Dinv38382' => 'din', 'Dinv38383' => 'din', 'Duzib133G0974' => 'dzi', 'Duzib138G1867' => 'dzi', 'Duzib211G0420' => 'dzi', 'Duzib212G0930' => 'dzi', 'ECA234G1645' => 'eca', 'ECA247G3467' => 'eca', 'ECA248G1703' => 'eca', 'EL10Ac3g06327' => 'bvu', 'EL10Ac7g17204' => 'bvu', 'Eucgr.A00855' => 'egr', 'Eucgr.A00858' => 'egr', 'Eucgr.H01520' => 'egr', 'Eucgr.H03604' => 'egr', 'Eucgr.L03465' => 'egr', 'Eucgr.L03466' => 'egr', 'FAN01G0988' => 'fan', 'FAN02G3892' => 'fan', 'FAN05G3381' => 'fan', 'FAN07G0967' => 'fan', 'FAN07G1493' => 'fan', 'FAN08G3125' => 'fan', 'FAN09G0402' => 'fan', 'FAN12G2594' => 'fan', 'FAN12G3879' => 'fan', 'FAN14G1546' => 'fan', 'FAN15G3626' => 'fan', 'FAN17G0588' => 'fan', 'FAN17G0609' => 'fan', 'FAN18G2817' => 'fan', 'FAN19G1305' => 'fan', 'FAN20G1787' => 'fan', 'FAN22G0073' => 'fan', 'FAN22G0352' => 'fan', 'FAN22G0368' => 'fan', 'FAN22G2273' => 'fan', 'FAN24G1998' => 'fan', 'FAN27G1317' => 'fan', 'FvH4_2g23980' => 'fve', 'FvH4_4g14380' => 'fve', 'FvH4_4g14390' => 'fve', 'FvH4_6g09250' => 'fve', 'Glyma.03G151100' => 'gma', 'Glyma.04G122550' => 'gma', 'Glyma.05G001600' => 'gma', 'Glyma.09G270766' => 'gma', 'Glyma.09G270832' => 'gma', 'Glyma.13G209800' => 'gma', 'Glyma.15G102800' => 'gma', 'Glyma.18G218900' => 'gma', 'Glyma.19G001500' => 'gma', 'Glyma.19G153600' => 'gma', 'Gohir.A02G028600' => 'ghi', 'Gohir.A08G045000' => 'ghi', 'Gohir.A11G120500' => 'ghi', 'Gohir.A12G006200' => 'ghi', 'Gohir.A12G006250' => 'ghi', 'Gohir.D02G036300' => 'ghi', 'Gohir.D08G054700' => 'ghi', 'Gohir.D11G125600' => 'ghi', 'Gohir.D12G005700' => 'ghi', 'Gorai.004G055200' => 'gra', 'Gorai.005G040400' => 'gra', 'Gorai.007G134500' => 'gra', 'Gorai.008G005500' => 'gra', 'GSVIVG01011094001' => 'vvi', 'GSVIVG01017879001' => 'vvi', 'GSVIVG01025988001' => 'vvi', 'GSVIVG01029847001' => 'vvi', 'HanXRQChr10g0282901' => 'han', 'HanXRQChr10g0310371' => 'han', 'HanXRQChr10g0315041' => 'han', 'HanXRQChr11g0327651' => 'han', 'HanXRQChr12g0359391' => 'han', 'Haze_00972' => 'cav', 'Haze_00973' => 'cav', 'Haze_00974' => 'cav', 'Haze_04747' => 'cav', 'Haze_04749' => 'cav', 'Haze_04750' => 'cav', 'Haze_21217' => 'cav', 'Hma1.2p1_1037F.1_g250680' => 'hma', 'Hma1.2p1_1644F.1_g295320' => 'hma', 'HPP92_011322' => 'vpl', 'HPP92_011323' => 'vpl', 'HPP92_011324' => 'vpl', 'HPP92_011325' => 'vpl', 'HPP92_011326' => 'vpl', 'Hund12205' => 'sun', 'Hund17957' => 'sun', 'Lalb_Chr06g0176771' => 'lal', 'Lalb_Chr18g0056021' => 'lal', 'Lalb_Chr18g0056031' => 'lal', 'Lalb_Chr18g0056041' => 'lal', 'Lalb_Chr20g0107751' => 'lal', 'Lalb_Chr20g0118371' => 'lal', 'Lj1g0010239' => 'lja', 'Lj1g0017101' => 'lja', 'Lj2A1178G40' => 'lonja', 'Lj2A54G84' => 'lonja', 'Lj2g0015248' => 'lja', 'Lj3A761T51' => 'lonja', 'Lj6g0018116' => 'lja', 'Lsat_1_v5_gn_4_136040' => 'lsa', 'Lsat_1_v5_gn_5_187461' => 'lsa', 'Lsat_1_v5_gn_5_77001' => 'lsa', 'Lsat_1_v5_gn_9_4461' => 'lsa', 'Manes.01G210100' => 'mes', 'Manes.03G185600' => 'mes', 'Manes.05G073300' => 'mes', 'Manes.09G120300' => 'mes', 'Manes.15G022100' => 'mes', 'Mapoly0096s0053' => 'mpo', 'MBI03_g14058_MAGBIO' => 'mbi', 'MBI03_g33876_MAGBIO' => 'mbi', 'MBI03_g36854_MAGBIO' => 'mbi', 'MBI17_g11997_MAGBIO' => 'mbi', 'MD03G1269000' => 'mdo', 'MD04G1179600' => 'mdo', 'MD11G1289800' => 'mdo', 'MD12G1194700' => 'mdo', 'MD13G1182100' => 'mdo', 'MD13G1182200' => 'mdo', 'MD16G1182600' => 'mdo', 'Medtr2g021400' => 'mtr', 'Medtr2g021470' => 'mtr', 'Medtr2g105810' => 'mtr', 'Medtr3g033580' => 'mtr', 'Medtr6g007970' => 'mtr', 'Medtr7g056330' => 'mtr', 'Medtr7g074290' => 'mtr', 'Medtr7g074380' => 'mtr', 'Medtr7g094550' => 'mtr', 'Medtr8g069995' => 'mtr', 'MELO3C014345.2' => 'cme', 'MELO3C021395.2' => 'cme', 'Migut.D00262' => 'egut', 'Migut.G00257' => 'egut', 'MSTRG.21575' => 'ama', 'MSTRG.3985' => 'ama', 'Nitab4.5_0000295g0140' => 'nta', 'Nitab4.5_0000732g0140' => 'nta', 'Nitab4.5_0003162g0020' => 'nta', 'Nitab4.5_0006180g0090' => 'nta', 'Nitab4.5_0006390g0010' => 'nta', 'Nitab4.5_0007392g0040' => 'nta', 'Nn1g02140' => 'nnu', 'Nn4g26168' => 'nnu', 'Nn5g26754' => 'nnu', 'Oeu001433.1' => 'oeu', 'Oeu010299.2' => 'oeu', 'Oeu011171.1' => 'oeu', 'Oeu037675.1' => 'oeu', 'Oeu038359.1' => 'oeu', 'Oeu063834.1' => 'oeu', 'Oeu063835.1' => 'oeu', 'Os05g0312000' => 'osa', 'Os07g0211101' => 'osa', 'Os07g0211200' => 'osa', 'Os07g0681500' => 'osa', 'Peaxi162Scf00095g01015' => 'pax', 'Peaxi162Scf00104g00329' => 'pax', 'Peaxi162Scf00161g00137' => 'pax', 'PGR004G1665' => 'pgr', 'PGR031G2937' => 'pgr', 'PGR119G2145' => 'pgr', 'PGSC0003DMG400004351' => 'stu', 'PGSC0003DMG400014625' => 'stu', 'PGSC0003DMG401000943' => 'stu', 'Phvul.001G148600' => 'pvu', 'Phvul.004G001700' => 'pvu', 'Phvul.006G154900' => 'pvu', 'Phvul.008G078200' => 'pvu', 'Phvul.011G136500' => 'pvu', 'Potri.002G215600' => 'ptr', 'Potri.008G201600' => 'ptr', 'Potri.014G138400' => 'ptr', 'Potri.016G142500' => 'ptr', 'Pp3c16_10580' => 'ppa', 'Pp3c5_25280' => 'ppa', 'Prupe.1G150000' => 'ppe', 'Prupe.1G150100' => 'ppe', 'Prupe.6G299600' => 'ppe', 'Prupe.8G245000' => 'ppe', 'Psat0s4927g0040' => 'psa', 'Psat1g052080' => 'psa', 'Psat1g183800' => 'psa', 'Psat3g113840' => 'psa', 'Psat3g126120' => 'psa', 'Psat3g126160' => 'psa', 'Psat3g158760' => 'psa', 'Psat3g158840' => 'psa', 'PSO170G2858' => 'pso', 'PSO339G0606' => 'pso', 'PSO384G4709' => 'pso', 'PSO407G0334' => 'pso', 'QL04p040276' => 'qlo', 'QL06p005458' => 'qlo', 'QL06p005472' => 'qlo', 'QL07p030546' => 'qlo', 'QL07p031519' => 'qlo', 'QL09p050949' => 'qlo', 'QL09p050966' => 'qlo', 'QL09p051067' => 'qlo', 'QL12p022706' => 'qlo', 'RcHm_v2.0_Chr2g0119601' => 'rch', 'RcHm_v2.0_Chr3g0459591' => 'rch', 'RcHm_v2.0_Chr4g0418521' => 'rch', 'RcHm_v2.0_Chr4g0418531' => 'rch', 'RcHm_v2.0_Chr4g0418541' => 'rch', 'RcHm_v2.0_Chr6g0291641' => 'rch', 'Rhsim01G0086300' => 'rsi', 'Rhsim01G0276300' => 'rsi', 'Rhsim01G0276500' => 'rsi', 'Rhsim04G0207700' => 'rsi', 'Rhsim05G0234500' => 'rsi', 'Rhsim13G0022400' => 'rsi', 'Sabra02G0167900' => 'sbr', 'Sabra04G0158500' => 'sbr', 'Sabra08G0159800' => 'sbr', 'Sabra10G0011500' => 'sbr', 'Sabra14G0104400' => 'sbr', 'SalBow2G2440' => 'sbo', 'SalBow4G2265' => 'sbo', 'Sc02g0000060' => 'sci', 'Sc05g0005020' => 'sci', 'Sc13g0003890' => 'sci', 'Sed0014865' => 'sed', 'Sed0017224' => 'sed', 'Sed0026391' => 'sed', 'SEGI_00063' => 'sgi', 'SEGI_10967' => 'sgi', 'SEGI_17510' => 'sgi', 'SEGI_24396' => 'sgi', 'SEGI_39719' => 'sgi', 'SEGI_41392' => 'sgi', 'SGA_v2.0_scaffold11G05794' => 'sas', 'SGA_v2.0_scaffold142G35607' => 'sas', 'SGA_v2.0_scaffold1G00447' => 'sas', 'SHI15388' => 'shi', 'SHI15394' => 'shi', 'SHI15396' => 'shi', 'SHI15399' => 'shi', 'SMO343G0151' => 'smo', 'SMO367G1118' => 'smo', 'Solyc01g080200.3' => 'sly', 'Solyc06g008960.3' => 'sly', 'Solyc09g064780.3' => 'sly', 'Sopen01g031980' => 'spe', 'Sopen06g003710' => 'spe', 'Sopen09g026460' => 'spe', 'Sp3g21240' => 'spa', 'Sp4g30030' => 'spa', 'TAR365G0022' => 'tar', 'TAR365G1023' => 'tar', 'TAR365G1253' => 'tar', 'TAR623G0078' => 'tar', 'TAR623G1721' => 'tar', 'TAR633G0959' => 'tar', 'THA.LOC104802225' => 'tha', 'THA.LOC104804769' => 'tha', 'THA.LOC104808660' => 'tha', 'THA.LOC104812792' => 'tha', 'Thecc.01G284000' => 'tca', 'Thecc.04G220600' => 'tca', 'Thecc.05G268900' => 'tca', 'Thecc.08G171100' => 'tca', 'Thhalv10001284m.g' => 'esa', 'Thhalv10019912m.g' => 'esa', 'TPR.G14189' => 'tpr', 'TPR.G18110' => 'tpr', 'TPR.G18130' => 'tpr', 'TPR.G18131' => 'tpr', 'TPR.G18140' => 'tpr', 'TPR.G24282' => 'tpr', 'TPR.G25221' => 'tpr', 'TPR.G29267' => 'tpr', 'TPR.G35315' => 'tpr', 'TPR.G36173' => 'tpr', 'TWI09G0794' => 'twi', 'TWI59G1348' => 'twi', 'TWI74G0430' => 'twi', 'unitig_26.g8940' => 'ugi', 'unitig_749.g13744' => 'ugi', 'unitig_749.g13745' => 'ugi', 'vmacro08269' => 'vma', 'vmacro14937' => 'vma', 'vmacro20401' => 'vma', 'VMungo0464G1349' => 'vmu', 'VMungo0540G0289' => 'vmu', 'VMungo1215G1590' => 'vmu', 'VMungo1309G0221' => 'vmu', 'VMungo1309G2815' => 'vmu', 'VMungo1383G0239' => 'vmu', 'VMungo1383G2910' => 'vmu', 'Zm00001eb095270' => 'zma', 'Zm00001eb095280' => 'zma', 'Zm00001eb111630' => 'zma', 'Zm00001eb237080' => 'zma', 'Zm00001eb273740' => 'zma', 'Zm00001eb285040' => 'zma', 'Zm00001eb330790' => 'zma', 'Zm00001eb337380' => 'zma' ) $gf_id = 'HOM05D001484' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001484' ) $data_identifier = 'HOM05D001484' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 2, 'aly' => (int) 2, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 22, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 7, 'hma' => (int) 2, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 7, 'mtr' => (int) 10, 'cme' => (int) 2, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 4, 'ppa' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 4, 'qlo' => (int) 9, 'rch' => (int) 6, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 10, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 7, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb337380' $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' => 'HOM05D001484', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p31500' => 'bna', 'A05p00020' => 'bna', 'A07p08820' => 'bna', 'Aa31LG4G3300' => 'aar', 'Aa31LG8G10030' => 'aar', 'Actinidia00731' => 'ach', 'Actinidia11473' => 'ach', 'Actinidia23469' => 'ach', 'Actinidia24318' => 'ach', 'Actinidia40196' => 'ach', 'Actinidia40197' => 'ach', 'Actinidia40198' => 'ach', 'Ah.08g212990' => 'amhyb', 'Ah.15g091720' => 'amhyb', 'AL3G38260' => 'aly', 'AL4G47710' => 'aly', 'Aqoxy2G00671' => 'aox', 'Aqoxy2G03236' => 'aox', 'arahy.Tifrunner.gnm1.ann1.05IDCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KR684' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATY3SJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK6QJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6APGL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IDT7Z9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM073U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ0R87' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LE7RV4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT4QRX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V5ENPK' => 'arhy', 'AT2G48110' => 'ath', 'AT3G23590' => 'ath', 'ATR0626G186' => 'atr', 'ATR1127G141' => 'atr', 'Atru.chr4.2583' => 'acertr', 'Atru.chr5.1358' => 'acertr', 'Atru.chr5.1359' => 'acertr', 'Atru.chr8.46' => 'acertr', 'AUR62002640' => 'cqu', 'AUR62030055' => 'cqu', 'AUR62033713' => 'cqu', 'AUR62033714' => 'cqu', 'AUR62036795' => 'cqu', 'AUR62039891' => 'cqu', 'BcaB02g08737' => 'bca', 'BcaB04g20441' => 'bca', 'BcaB06g26509' => 'bca', 'BcaB06g26510' => 'bca', 'BcaB06g26511' => 'bca', 'BcaB06g26512' => 'bca', 'BcaB06g26513' => 'bca', 'BcaC02g12564' => 'bca', 'BcaC02g12565' => 'bca', 'BcaC02g12794' => 'bca', 'BcaC02g12795' => 'bca', 'BcaC02g12796' => 'bca', 'BcaC06g35541' => 'bca', 'BNapus_Darmor_BZH_scaffold_188p00080' => 'bna', 'BNapus_Darmor_BZH_scaffold_188p00090' => 'bna', 'BolC1t03972H' => 'bol', 'BolC1t03973H' => 'bol', 'BolC4t21680H' => 'bol', 'BolC7t41863H' => 'bol', 'BolSC55t61227H' => 'bol', 'BolSC55t61228H' => 'bol', 'BraA01t03278Z' => 'bra', 'BraA05t18998Z' => 'bra', 'BraA07t28673Z' => 'bra', 'C01p40150' => 'bna', 'C05p12370' => 'bna', 'C07p13680' => 'bna', 'CAN.G1006.16' => 'can', 'CAN.G1006.17' => 'can', 'CAN.G1170.2' => 'can', 'CAN.G962.7' => 'can', 'CANSAT25G2179' => 'cansat', 'CANSAT78G1573' => 'cansat', 'CARHR099510' => 'chi', 'CARHR143510' => 'chi', 'Carub.0003s2380' => 'cru', 'Carub.0004s3082' => 'cru', 'Ca_00614_v3' => 'car', 'Ca_07801_v3' => 'car', 'Ca_08567_v3' => 'car', 'Ca_09571_v3' => 'car', 'CBR_g19290' => 'cbr', 'Cc01_g19770' => 'ccan', 'Cc03_g03030' => 'ccan', 'CDE07G0968' => 'cde', 'CDE09G1441' => 'cde', 'Cfa006103' => 'cfa', 'Cfa015573' => 'cfa', 'Cfa016988' => 'cfa', 'Ciclev10006738m.g' => 'ccl', 'Ciclev10010920m.g' => 'ccl', 'Ciclev10018517m.g' => 'ccl', 'CiPaw.01G159200' => 'cil', 'CiPaw.02G091000' => 'cil', 'CiPaw.02G091100' => 'cil', 'CiPaw.08G103100' => 'cil', 'CiPaw.09G224900' => 'cil', 'ClCG06G005740' => 'cla', 'ClCG07G000090' => 'cla', 'ClCG07G000100' => 'cla', 'COL.COLO4_09143' => 'col', 'COL.COLO4_25124' => 'col', 'Cpa.g.sc16.34' => 'cpa', 'Cpa.g.sc3504.1' => 'cpa', 'Cpa.g.sc60.37' => 'cpa', 'CsaV3_6G018520' => 'csa', 'CsaV3_6G036860' => 'csa', 'CSS0001072' => 'camsi', 'CSS0020208' => 'camsi', 'CSS0021253' => 'camsi', 'CSS0022190' => 'camsi', 'CSS0036150' => 'camsi', 'CSS0040442' => 'camsi', 'CSS0042300' => 'camsi', 'CSS0045298' => 'camsi', 'DCAR_012449' => 'dca', 'DCAR_018405' => 'dca', 'DCAR_024573' => 'dca', 'DCAR_030591' => 'dca', 'Dinv16926' => 'din', 'Dinv32963' => 'din', 'Dinv38382' => 'din', 'Dinv38383' => 'din', 'Duzib133G0974' => 'dzi', 'Duzib138G1867' => 'dzi', 'Duzib211G0420' => 'dzi', 'Duzib212G0930' => 'dzi', 'ECA234G1645' => 'eca', 'ECA247G3467' => 'eca', 'ECA248G1703' => 'eca', 'EL10Ac3g06327' => 'bvu', 'EL10Ac7g17204' => 'bvu', 'Eucgr.A00855' => 'egr', 'Eucgr.A00858' => 'egr', 'Eucgr.H01520' => 'egr', 'Eucgr.H03604' => 'egr', 'Eucgr.L03465' => 'egr', 'Eucgr.L03466' => 'egr', 'FAN01G0988' => 'fan', 'FAN02G3892' => 'fan', 'FAN05G3381' => 'fan', 'FAN07G0967' => 'fan', 'FAN07G1493' => 'fan', 'FAN08G3125' => 'fan', 'FAN09G0402' => 'fan', 'FAN12G2594' => 'fan', 'FAN12G3879' => 'fan', 'FAN14G1546' => 'fan', 'FAN15G3626' => 'fan', 'FAN17G0588' => 'fan', 'FAN17G0609' => 'fan', 'FAN18G2817' => 'fan', 'FAN19G1305' => 'fan', 'FAN20G1787' => 'fan', 'FAN22G0073' => 'fan', 'FAN22G0352' => 'fan', 'FAN22G0368' => 'fan', 'FAN22G2273' => 'fan', 'FAN24G1998' => 'fan', 'FAN27G1317' => 'fan', 'FvH4_2g23980' => 'fve', 'FvH4_4g14380' => 'fve', 'FvH4_4g14390' => 'fve', 'FvH4_6g09250' => 'fve', 'Glyma.03G151100' => 'gma', 'Glyma.04G122550' => 'gma', 'Glyma.05G001600' => 'gma', 'Glyma.09G270766' => 'gma', 'Glyma.09G270832' => 'gma', 'Glyma.13G209800' => 'gma', 'Glyma.15G102800' => 'gma', 'Glyma.18G218900' => 'gma', 'Glyma.19G001500' => 'gma', 'Glyma.19G153600' => 'gma', 'Gohir.A02G028600' => 'ghi', 'Gohir.A08G045000' => 'ghi', 'Gohir.A11G120500' => 'ghi', 'Gohir.A12G006200' => 'ghi', 'Gohir.A12G006250' => 'ghi', 'Gohir.D02G036300' => 'ghi', 'Gohir.D08G054700' => 'ghi', 'Gohir.D11G125600' => 'ghi', 'Gohir.D12G005700' => 'ghi', 'Gorai.004G055200' => 'gra', 'Gorai.005G040400' => 'gra', 'Gorai.007G134500' => 'gra', 'Gorai.008G005500' => 'gra', 'GSVIVG01011094001' => 'vvi', 'GSVIVG01017879001' => 'vvi', 'GSVIVG01025988001' => 'vvi', 'GSVIVG01029847001' => 'vvi', 'HanXRQChr10g0282901' => 'han', 'HanXRQChr10g0310371' => 'han', 'HanXRQChr10g0315041' => 'han', 'HanXRQChr11g0327651' => 'han', 'HanXRQChr12g0359391' => 'han', 'Haze_00972' => 'cav', 'Haze_00973' => 'cav', 'Haze_00974' => 'cav', 'Haze_04747' => 'cav', 'Haze_04749' => 'cav', 'Haze_04750' => 'cav', 'Haze_21217' => 'cav', 'Hma1.2p1_1037F.1_g250680' => 'hma', 'Hma1.2p1_1644F.1_g295320' => 'hma', 'HPP92_011322' => 'vpl', 'HPP92_011323' => 'vpl', 'HPP92_011324' => 'vpl', 'HPP92_011325' => 'vpl', 'HPP92_011326' => 'vpl', 'Hund12205' => 'sun', 'Hund17957' => 'sun', 'Lalb_Chr06g0176771' => 'lal', 'Lalb_Chr18g0056021' => 'lal', 'Lalb_Chr18g0056031' => 'lal', 'Lalb_Chr18g0056041' => 'lal', 'Lalb_Chr20g0107751' => 'lal', 'Lalb_Chr20g0118371' => 'lal', 'Lj1g0010239' => 'lja', 'Lj1g0017101' => 'lja', 'Lj2A1178G40' => 'lonja', 'Lj2A54G84' => 'lonja', 'Lj2g0015248' => 'lja', 'Lj3A761T51' => 'lonja', 'Lj6g0018116' => 'lja', 'Lsat_1_v5_gn_4_136040' => 'lsa', 'Lsat_1_v5_gn_5_187461' => 'lsa', 'Lsat_1_v5_gn_5_77001' => 'lsa', 'Lsat_1_v5_gn_9_4461' => 'lsa', 'Manes.01G210100' => 'mes', 'Manes.03G185600' => 'mes', 'Manes.05G073300' => 'mes', 'Manes.09G120300' => 'mes', 'Manes.15G022100' => 'mes', 'Mapoly0096s0053' => 'mpo', 'MBI03_g14058_MAGBIO' => 'mbi', 'MBI03_g33876_MAGBIO' => 'mbi', 'MBI03_g36854_MAGBIO' => 'mbi', 'MBI17_g11997_MAGBIO' => 'mbi', 'MD03G1269000' => 'mdo', 'MD04G1179600' => 'mdo', 'MD11G1289800' => 'mdo', 'MD12G1194700' => 'mdo', 'MD13G1182100' => 'mdo', 'MD13G1182200' => 'mdo', 'MD16G1182600' => 'mdo', 'Medtr2g021400' => 'mtr', 'Medtr2g021470' => 'mtr', 'Medtr2g105810' => 'mtr', 'Medtr3g033580' => 'mtr', 'Medtr6g007970' => 'mtr', 'Medtr7g056330' => 'mtr', 'Medtr7g074290' => 'mtr', 'Medtr7g074380' => 'mtr', 'Medtr7g094550' => 'mtr', 'Medtr8g069995' => 'mtr', 'MELO3C014345.2' => 'cme', 'MELO3C021395.2' => 'cme', 'Migut.D00262' => 'egut', 'Migut.G00257' => 'egut', 'MSTRG.21575' => 'ama', 'MSTRG.3985' => 'ama', 'Nitab4.5_0000295g0140' => 'nta', 'Nitab4.5_0000732g0140' => 'nta', 'Nitab4.5_0003162g0020' => 'nta', 'Nitab4.5_0006180g0090' => 'nta', 'Nitab4.5_0006390g0010' => 'nta', 'Nitab4.5_0007392g0040' => 'nta', 'Nn1g02140' => 'nnu', 'Nn4g26168' => 'nnu', 'Nn5g26754' => 'nnu', 'Oeu001433.1' => 'oeu', 'Oeu010299.2' => 'oeu', 'Oeu011171.1' => 'oeu', 'Oeu037675.1' => 'oeu', 'Oeu038359.1' => 'oeu', 'Oeu063834.1' => 'oeu', 'Oeu063835.1' => 'oeu', 'Os05g0312000' => 'osa', 'Os07g0211101' => 'osa', 'Os07g0211200' => 'osa', 'Os07g0681500' => 'osa', 'Peaxi162Scf00095g01015' => 'pax', 'Peaxi162Scf00104g00329' => 'pax', 'Peaxi162Scf00161g00137' => 'pax', 'PGR004G1665' => 'pgr', 'PGR031G2937' => 'pgr', 'PGR119G2145' => 'pgr', 'PGSC0003DMG400004351' => 'stu', 'PGSC0003DMG400014625' => 'stu', 'PGSC0003DMG401000943' => 'stu', 'Phvul.001G148600' => 'pvu', 'Phvul.004G001700' => 'pvu', 'Phvul.006G154900' => 'pvu', 'Phvul.008G078200' => 'pvu', 'Phvul.011G136500' => 'pvu', 'Potri.002G215600' => 'ptr', 'Potri.008G201600' => 'ptr', 'Potri.014G138400' => 'ptr', 'Potri.016G142500' => 'ptr', 'Pp3c16_10580' => 'ppa', 'Pp3c5_25280' => 'ppa', 'Prupe.1G150000' => 'ppe', 'Prupe.1G150100' => 'ppe', 'Prupe.6G299600' => 'ppe', 'Prupe.8G245000' => 'ppe', 'Psat0s4927g0040' => 'psa', 'Psat1g052080' => 'psa', 'Psat1g183800' => 'psa', 'Psat3g113840' => 'psa', 'Psat3g126120' => 'psa', 'Psat3g126160' => 'psa', 'Psat3g158760' => 'psa', 'Psat3g158840' => 'psa', 'PSO170G2858' => 'pso', 'PSO339G0606' => 'pso', 'PSO384G4709' => 'pso', 'PSO407G0334' => 'pso', 'QL04p040276' => 'qlo', 'QL06p005458' => 'qlo', 'QL06p005472' => 'qlo', 'QL07p030546' => 'qlo', 'QL07p031519' => 'qlo', 'QL09p050949' => 'qlo', 'QL09p050966' => 'qlo', 'QL09p051067' => 'qlo', 'QL12p022706' => 'qlo', 'RcHm_v2.0_Chr2g0119601' => 'rch', 'RcHm_v2.0_Chr3g0459591' => 'rch', 'RcHm_v2.0_Chr4g0418521' => 'rch', 'RcHm_v2.0_Chr4g0418531' => 'rch', 'RcHm_v2.0_Chr4g0418541' => 'rch', 'RcHm_v2.0_Chr6g0291641' => 'rch', 'Rhsim01G0086300' => 'rsi', 'Rhsim01G0276300' => 'rsi', 'Rhsim01G0276500' => 'rsi', 'Rhsim04G0207700' => 'rsi', 'Rhsim05G0234500' => 'rsi', 'Rhsim13G0022400' => 'rsi', 'Sabra02G0167900' => 'sbr', 'Sabra04G0158500' => 'sbr', 'Sabra08G0159800' => 'sbr', 'Sabra10G0011500' => 'sbr', 'Sabra14G0104400' => 'sbr', 'SalBow2G2440' => 'sbo', 'SalBow4G2265' => 'sbo', 'Sc02g0000060' => 'sci', 'Sc05g0005020' => 'sci', 'Sc13g0003890' => 'sci', 'Sed0014865' => 'sed', 'Sed0017224' => 'sed', 'Sed0026391' => 'sed', 'SEGI_00063' => 'sgi', 'SEGI_10967' => 'sgi', 'SEGI_17510' => 'sgi', 'SEGI_24396' => 'sgi', 'SEGI_39719' => 'sgi', 'SEGI_41392' => 'sgi', 'SGA_v2.0_scaffold11G05794' => 'sas', 'SGA_v2.0_scaffold142G35607' => 'sas', 'SGA_v2.0_scaffold1G00447' => 'sas', 'SHI15388' => 'shi', 'SHI15394' => 'shi', 'SHI15396' => 'shi', 'SHI15399' => 'shi', 'SMO343G0151' => 'smo', 'SMO367G1118' => 'smo', 'Solyc01g080200.3' => 'sly', 'Solyc06g008960.3' => 'sly', 'Solyc09g064780.3' => 'sly', 'Sopen01g031980' => 'spe', 'Sopen06g003710' => 'spe', 'Sopen09g026460' => 'spe', 'Sp3g21240' => 'spa', 'Sp4g30030' => 'spa', 'TAR365G0022' => 'tar', 'TAR365G1023' => 'tar', 'TAR365G1253' => 'tar', 'TAR623G0078' => 'tar', 'TAR623G1721' => 'tar', 'TAR633G0959' => 'tar', 'THA.LOC104802225' => 'tha', 'THA.LOC104804769' => 'tha', 'THA.LOC104808660' => 'tha', 'THA.LOC104812792' => 'tha', 'Thecc.01G284000' => 'tca', 'Thecc.04G220600' => 'tca', 'Thecc.05G268900' => 'tca', 'Thecc.08G171100' => 'tca', 'Thhalv10001284m.g' => 'esa', 'Thhalv10019912m.g' => 'esa', 'TPR.G14189' => 'tpr', 'TPR.G18110' => 'tpr', 'TPR.G18130' => 'tpr', 'TPR.G18131' => 'tpr', 'TPR.G18140' => 'tpr', 'TPR.G24282' => 'tpr', 'TPR.G25221' => 'tpr', 'TPR.G29267' => 'tpr', 'TPR.G35315' => 'tpr', 'TPR.G36173' => 'tpr', 'TWI09G0794' => 'twi', 'TWI59G1348' => 'twi', 'TWI74G0430' => 'twi', 'unitig_26.g8940' => 'ugi', 'unitig_749.g13744' => 'ugi', 'unitig_749.g13745' => 'ugi', 'vmacro08269' => 'vma', 'vmacro14937' => 'vma', 'vmacro20401' => 'vma', 'VMungo0464G1349' => 'vmu', 'VMungo0540G0289' => 'vmu', 'VMungo1215G1590' => 'vmu', 'VMungo1309G0221' => 'vmu', 'VMungo1309G2815' => 'vmu', 'VMungo1383G0239' => 'vmu', 'VMungo1383G2910' => 'vmu', 'Zm00001eb095270' => 'zma', 'Zm00001eb095280' => 'zma', 'Zm00001eb111630' => 'zma', 'Zm00001eb237080' => 'zma', 'Zm00001eb273740' => 'zma', 'Zm00001eb285040' => 'zma', 'Zm00001eb330790' => 'zma', 'Zm00001eb337380' => 'zma' ), 'gf_id' => 'HOM05D001484', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001484' ), 'data_identifier' => 'HOM05D001484', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001484', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p31500' => 'bna', 'A05p00020' => 'bna', 'A07p08820' => 'bna', 'Aa31LG4G3300' => 'aar', 'Aa31LG8G10030' => 'aar', 'Actinidia00731' => 'ach', 'Actinidia11473' => 'ach', 'Actinidia23469' => 'ach', 'Actinidia24318' => 'ach', 'Actinidia40196' => 'ach', 'Actinidia40197' => 'ach', 'Actinidia40198' => 'ach', 'Ah.08g212990' => 'amhyb', 'Ah.15g091720' => 'amhyb', 'AL3G38260' => 'aly', 'AL4G47710' => 'aly', 'Aqoxy2G00671' => 'aox', 'Aqoxy2G03236' => 'aox', 'arahy.Tifrunner.gnm1.ann1.05IDCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KR684' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATY3SJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK6QJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6APGL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IDT7Z9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM073U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ0R87' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LE7RV4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT4QRX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V5ENPK' => 'arhy', 'AT2G48110' => 'ath', 'AT3G23590' => 'ath', 'ATR0626G186' => 'atr', 'ATR1127G141' => 'atr', 'Atru.chr4.2583' => 'acertr', 'Atru.chr5.1358' => 'acertr', 'Atru.chr5.1359' => 'acertr', 'Atru.chr8.46' => 'acertr', 'AUR62002640' => 'cqu', 'AUR62030055' => 'cqu', 'AUR62033713' => 'cqu', 'AUR62033714' => 'cqu', 'AUR62036795' => 'cqu', 'AUR62039891' => 'cqu', 'BcaB02g08737' => 'bca', 'BcaB04g20441' => 'bca', 'BcaB06g26509' => 'bca', 'BcaB06g26510' => 'bca', 'BcaB06g26511' => 'bca', 'BcaB06g26512' => 'bca', 'BcaB06g26513' => 'bca', 'BcaC02g12564' => 'bca', 'BcaC02g12565' => 'bca', 'BcaC02g12794' => 'bca', 'BcaC02g12795' => 'bca', 'BcaC02g12796' => 'bca', 'BcaC06g35541' => 'bca', 'BNapus_Darmor_BZH_scaffold_188p00080' => 'bna', 'BNapus_Darmor_BZH_scaffold_188p00090' => 'bna', 'BolC1t03972H' => 'bol', 'BolC1t03973H' => 'bol', 'BolC4t21680H' => 'bol', 'BolC7t41863H' => 'bol', 'BolSC55t61227H' => 'bol', 'BolSC55t61228H' => 'bol', 'BraA01t03278Z' => 'bra', 'BraA05t18998Z' => 'bra', 'BraA07t28673Z' => 'bra', 'C01p40150' => 'bna', 'C05p12370' => 'bna', 'C07p13680' => 'bna', 'CAN.G1006.16' => 'can', 'CAN.G1006.17' => 'can', 'CAN.G1170.2' => 'can', 'CAN.G962.7' => 'can', 'CANSAT25G2179' => 'cansat', 'CANSAT78G1573' => 'cansat', 'CARHR099510' => 'chi', 'CARHR143510' => 'chi', 'Carub.0003s2380' => 'cru', 'Carub.0004s3082' => 'cru', 'Ca_00614_v3' => 'car', 'Ca_07801_v3' => 'car', 'Ca_08567_v3' => 'car', 'Ca_09571_v3' => 'car', 'CBR_g19290' => 'cbr', 'Cc01_g19770' => 'ccan', 'Cc03_g03030' => 'ccan', 'CDE07G0968' => 'cde', 'CDE09G1441' => 'cde', 'Cfa006103' => 'cfa', 'Cfa015573' => 'cfa', 'Cfa016988' => 'cfa', 'Ciclev10006738m.g' => 'ccl', 'Ciclev10010920m.g' => 'ccl', 'Ciclev10018517m.g' => 'ccl', 'CiPaw.01G159200' => 'cil', 'CiPaw.02G091000' => 'cil', 'CiPaw.02G091100' => 'cil', 'CiPaw.08G103100' => 'cil', 'CiPaw.09G224900' => 'cil', 'ClCG06G005740' => 'cla', 'ClCG07G000090' => 'cla', 'ClCG07G000100' => 'cla', 'COL.COLO4_09143' => 'col', 'COL.COLO4_25124' => 'col', 'Cpa.g.sc16.34' => 'cpa', 'Cpa.g.sc3504.1' => 'cpa', 'Cpa.g.sc60.37' => 'cpa', 'CsaV3_6G018520' => 'csa', 'CsaV3_6G036860' => 'csa', 'CSS0001072' => 'camsi', 'CSS0020208' => 'camsi', 'CSS0021253' => 'camsi', 'CSS0022190' => 'camsi', 'CSS0036150' => 'camsi', 'CSS0040442' => 'camsi', 'CSS0042300' => 'camsi', 'CSS0045298' => 'camsi', 'DCAR_012449' => 'dca', 'DCAR_018405' => 'dca', 'DCAR_024573' => 'dca', 'DCAR_030591' => 'dca', 'Dinv16926' => 'din', 'Dinv32963' => 'din', 'Dinv38382' => 'din', 'Dinv38383' => 'din', 'Duzib133G0974' => 'dzi', 'Duzib138G1867' => 'dzi', 'Duzib211G0420' => 'dzi', 'Duzib212G0930' => 'dzi', 'ECA234G1645' => 'eca', 'ECA247G3467' => 'eca', 'ECA248G1703' => 'eca', 'EL10Ac3g06327' => 'bvu', 'EL10Ac7g17204' => 'bvu', 'Eucgr.A00855' => 'egr', 'Eucgr.A00858' => 'egr', 'Eucgr.H01520' => 'egr', 'Eucgr.H03604' => 'egr', 'Eucgr.L03465' => 'egr', 'Eucgr.L03466' => 'egr', 'FAN01G0988' => 'fan', 'FAN02G3892' => 'fan', 'FAN05G3381' => 'fan', 'FAN07G0967' => 'fan', 'FAN07G1493' => 'fan', 'FAN08G3125' => 'fan', 'FAN09G0402' => 'fan', 'FAN12G2594' => 'fan', 'FAN12G3879' => 'fan', 'FAN14G1546' => 'fan', 'FAN15G3626' => 'fan', 'FAN17G0588' => 'fan', 'FAN17G0609' => 'fan', 'FAN18G2817' => 'fan', 'FAN19G1305' => 'fan', 'FAN20G1787' => 'fan', 'FAN22G0073' => 'fan', 'FAN22G0352' => 'fan', 'FAN22G0368' => 'fan', 'FAN22G2273' => 'fan', 'FAN24G1998' => 'fan', 'FAN27G1317' => 'fan', 'FvH4_2g23980' => 'fve', 'FvH4_4g14380' => 'fve', 'FvH4_4g14390' => 'fve', 'FvH4_6g09250' => 'fve', 'Glyma.03G151100' => 'gma', 'Glyma.04G122550' => 'gma', 'Glyma.05G001600' => 'gma', 'Glyma.09G270766' => 'gma', 'Glyma.09G270832' => 'gma', 'Glyma.13G209800' => 'gma', 'Glyma.15G102800' => 'gma', 'Glyma.18G218900' => 'gma', 'Glyma.19G001500' => 'gma', 'Glyma.19G153600' => 'gma', 'Gohir.A02G028600' => 'ghi', 'Gohir.A08G045000' => 'ghi', 'Gohir.A11G120500' => 'ghi', 'Gohir.A12G006200' => 'ghi', 'Gohir.A12G006250' => 'ghi', 'Gohir.D02G036300' => 'ghi', 'Gohir.D08G054700' => 'ghi', 'Gohir.D11G125600' => 'ghi', 'Gohir.D12G005700' => 'ghi', 'Gorai.004G055200' => 'gra', 'Gorai.005G040400' => 'gra', 'Gorai.007G134500' => 'gra', 'Gorai.008G005500' => 'gra', 'GSVIVG01011094001' => 'vvi', 'GSVIVG01017879001' => 'vvi', 'GSVIVG01025988001' => 'vvi', 'GSVIVG01029847001' => 'vvi', 'HanXRQChr10g0282901' => 'han', 'HanXRQChr10g0310371' => 'han', 'HanXRQChr10g0315041' => 'han', 'HanXRQChr11g0327651' => 'han', 'HanXRQChr12g0359391' => 'han', 'Haze_00972' => 'cav', 'Haze_00973' => 'cav', 'Haze_00974' => 'cav', 'Haze_04747' => 'cav', 'Haze_04749' => 'cav', 'Haze_04750' => 'cav', 'Haze_21217' => 'cav', 'Hma1.2p1_1037F.1_g250680' => 'hma', 'Hma1.2p1_1644F.1_g295320' => 'hma', 'HPP92_011322' => 'vpl', 'HPP92_011323' => 'vpl', 'HPP92_011324' => 'vpl', 'HPP92_011325' => 'vpl', 'HPP92_011326' => 'vpl', 'Hund12205' => 'sun', 'Hund17957' => 'sun', 'Lalb_Chr06g0176771' => 'lal', 'Lalb_Chr18g0056021' => 'lal', 'Lalb_Chr18g0056031' => 'lal', 'Lalb_Chr18g0056041' => 'lal', 'Lalb_Chr20g0107751' => 'lal', 'Lalb_Chr20g0118371' => 'lal', 'Lj1g0010239' => 'lja', 'Lj1g0017101' => 'lja', 'Lj2A1178G40' => 'lonja', 'Lj2A54G84' => 'lonja', 'Lj2g0015248' => 'lja', 'Lj3A761T51' => 'lonja', 'Lj6g0018116' => 'lja', 'Lsat_1_v5_gn_4_136040' => 'lsa', 'Lsat_1_v5_gn_5_187461' => 'lsa', 'Lsat_1_v5_gn_5_77001' => 'lsa', 'Lsat_1_v5_gn_9_4461' => 'lsa', 'Manes.01G210100' => 'mes', 'Manes.03G185600' => 'mes', 'Manes.05G073300' => 'mes', 'Manes.09G120300' => 'mes', 'Manes.15G022100' => 'mes', 'Mapoly0096s0053' => 'mpo', 'MBI03_g14058_MAGBIO' => 'mbi', 'MBI03_g33876_MAGBIO' => 'mbi', 'MBI03_g36854_MAGBIO' => 'mbi', 'MBI17_g11997_MAGBIO' => 'mbi', 'MD03G1269000' => 'mdo', 'MD04G1179600' => 'mdo', 'MD11G1289800' => 'mdo', 'MD12G1194700' => 'mdo', 'MD13G1182100' => 'mdo', 'MD13G1182200' => 'mdo', 'MD16G1182600' => 'mdo', 'Medtr2g021400' => 'mtr', 'Medtr2g021470' => 'mtr', 'Medtr2g105810' => 'mtr', 'Medtr3g033580' => 'mtr', 'Medtr6g007970' => 'mtr', 'Medtr7g056330' => 'mtr', 'Medtr7g074290' => 'mtr', 'Medtr7g074380' => 'mtr', 'Medtr7g094550' => 'mtr', 'Medtr8g069995' => 'mtr', 'MELO3C014345.2' => 'cme', 'MELO3C021395.2' => 'cme', 'Migut.D00262' => 'egut', 'Migut.G00257' => 'egut', 'MSTRG.21575' => 'ama', 'MSTRG.3985' => 'ama', 'Nitab4.5_0000295g0140' => 'nta', 'Nitab4.5_0000732g0140' => 'nta', 'Nitab4.5_0003162g0020' => 'nta', 'Nitab4.5_0006180g0090' => 'nta', 'Nitab4.5_0006390g0010' => 'nta', 'Nitab4.5_0007392g0040' => 'nta', 'Nn1g02140' => 'nnu', 'Nn4g26168' => 'nnu', 'Nn5g26754' => 'nnu', 'Oeu001433.1' => 'oeu', 'Oeu010299.2' => 'oeu', 'Oeu011171.1' => 'oeu', 'Oeu037675.1' => 'oeu', 'Oeu038359.1' => 'oeu', 'Oeu063834.1' => 'oeu', 'Oeu063835.1' => 'oeu', 'Os05g0312000' => 'osa', 'Os07g0211101' => 'osa', 'Os07g0211200' => 'osa', 'Os07g0681500' => 'osa', 'Peaxi162Scf00095g01015' => 'pax', 'Peaxi162Scf00104g00329' => 'pax', 'Peaxi162Scf00161g00137' => 'pax', 'PGR004G1665' => 'pgr', 'PGR031G2937' => 'pgr', 'PGR119G2145' => 'pgr', 'PGSC0003DMG400004351' => 'stu', 'PGSC0003DMG400014625' => 'stu', 'PGSC0003DMG401000943' => 'stu', 'Phvul.001G148600' => 'pvu', 'Phvul.004G001700' => 'pvu', 'Phvul.006G154900' => 'pvu', 'Phvul.008G078200' => 'pvu', 'Phvul.011G136500' => 'pvu', 'Potri.002G215600' => 'ptr', 'Potri.008G201600' => 'ptr', 'Potri.014G138400' => 'ptr', 'Potri.016G142500' => 'ptr', 'Pp3c16_10580' => 'ppa', 'Pp3c5_25280' => 'ppa', 'Prupe.1G150000' => 'ppe', 'Prupe.1G150100' => 'ppe', 'Prupe.6G299600' => 'ppe', 'Prupe.8G245000' => 'ppe', 'Psat0s4927g0040' => 'psa', 'Psat1g052080' => 'psa', 'Psat1g183800' => 'psa', 'Psat3g113840' => 'psa', 'Psat3g126120' => 'psa', 'Psat3g126160' => 'psa', 'Psat3g158760' => 'psa', 'Psat3g158840' => 'psa', 'PSO170G2858' => 'pso', 'PSO339G0606' => 'pso', 'PSO384G4709' => 'pso', 'PSO407G0334' => 'pso', 'QL04p040276' => 'qlo', 'QL06p005458' => 'qlo', 'QL06p005472' => 'qlo', 'QL07p030546' => 'qlo', 'QL07p031519' => 'qlo', 'QL09p050949' => 'qlo', 'QL09p050966' => 'qlo', 'QL09p051067' => 'qlo', 'QL12p022706' => 'qlo', 'RcHm_v2.0_Chr2g0119601' => 'rch', 'RcHm_v2.0_Chr3g0459591' => 'rch', 'RcHm_v2.0_Chr4g0418521' => 'rch', 'RcHm_v2.0_Chr4g0418531' => 'rch', 'RcHm_v2.0_Chr4g0418541' => 'rch', 'RcHm_v2.0_Chr6g0291641' => 'rch', 'Rhsim01G0086300' => 'rsi', 'Rhsim01G0276300' => 'rsi', 'Rhsim01G0276500' => 'rsi', 'Rhsim04G0207700' => 'rsi', 'Rhsim05G0234500' => 'rsi', 'Rhsim13G0022400' => 'rsi', 'Sabra02G0167900' => 'sbr', 'Sabra04G0158500' => 'sbr', 'Sabra08G0159800' => 'sbr', 'Sabra10G0011500' => 'sbr', 'Sabra14G0104400' => 'sbr', 'SalBow2G2440' => 'sbo', 'SalBow4G2265' => 'sbo', 'Sc02g0000060' => 'sci', 'Sc05g0005020' => 'sci', 'Sc13g0003890' => 'sci', 'Sed0014865' => 'sed', 'Sed0017224' => 'sed', 'Sed0026391' => 'sed', 'SEGI_00063' => 'sgi', 'SEGI_10967' => 'sgi', 'SEGI_17510' => 'sgi', 'SEGI_24396' => 'sgi', 'SEGI_39719' => 'sgi', 'SEGI_41392' => 'sgi', 'SGA_v2.0_scaffold11G05794' => 'sas', 'SGA_v2.0_scaffold142G35607' => 'sas', 'SGA_v2.0_scaffold1G00447' => 'sas', 'SHI15388' => 'shi', 'SHI15394' => 'shi', 'SHI15396' => 'shi', 'SHI15399' => 'shi', 'SMO343G0151' => 'smo', 'SMO367G1118' => 'smo', 'Solyc01g080200.3' => 'sly', 'Solyc06g008960.3' => 'sly', 'Solyc09g064780.3' => 'sly', 'Sopen01g031980' => 'spe', 'Sopen06g003710' => 'spe', 'Sopen09g026460' => 'spe', 'Sp3g21240' => 'spa', 'Sp4g30030' => 'spa', 'TAR365G0022' => 'tar', 'TAR365G1023' => 'tar', 'TAR365G1253' => 'tar', 'TAR623G0078' => 'tar', 'TAR623G1721' => 'tar', 'TAR633G0959' => 'tar', 'THA.LOC104802225' => 'tha', 'THA.LOC104804769' => 'tha', 'THA.LOC104808660' => 'tha', 'THA.LOC104812792' => 'tha', 'Thecc.01G284000' => 'tca', 'Thecc.04G220600' => 'tca', 'Thecc.05G268900' => 'tca', 'Thecc.08G171100' => 'tca', 'Thhalv10001284m.g' => 'esa', 'Thhalv10019912m.g' => 'esa', 'TPR.G14189' => 'tpr', 'TPR.G18110' => 'tpr', 'TPR.G18130' => 'tpr', 'TPR.G18131' => 'tpr', 'TPR.G18140' => 'tpr', 'TPR.G24282' => 'tpr', 'TPR.G25221' => 'tpr', 'TPR.G29267' => 'tpr', 'TPR.G35315' => 'tpr', 'TPR.G36173' => 'tpr', 'TWI09G0794' => 'twi', 'TWI59G1348' => 'twi', 'TWI74G0430' => 'twi', 'unitig_26.g8940' => 'ugi', 'unitig_749.g13744' => 'ugi', 'unitig_749.g13745' => 'ugi', 'vmacro08269' => 'vma', 'vmacro14937' => 'vma', 'vmacro20401' => 'vma', 'VMungo0464G1349' => 'vmu', 'VMungo0540G0289' => 'vmu', 'VMungo1215G1590' => 'vmu', 'VMungo1309G0221' => 'vmu', 'VMungo1309G2815' => 'vmu', 'VMungo1383G0239' => 'vmu', 'VMungo1383G2910' => 'vmu', 'Zm00001eb095270' => 'zma', 'Zm00001eb095280' => 'zma', 'Zm00001eb111630' => 'zma', 'Zm00001eb237080' => 'zma', 'Zm00001eb273740' => 'zma', 'Zm00001eb285040' => 'zma', 'Zm00001eb330790' => 'zma', 'Zm00001eb337380' => 'zma' ) $gf_id = 'HOM05D001484' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001484' ) $data_identifier = 'HOM05D001484' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 2, 'aly' => (int) 2, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 22, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 7, 'hma' => (int) 2, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 7, 'mtr' => (int) 10, 'cme' => (int) 2, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 4, 'ppa' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 4, 'qlo' => (int) 9, 'rch' => (int) 6, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 10, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 7, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb337380' $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' => 'HOM05D001484', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p31500' => 'bna', 'A05p00020' => 'bna', 'A07p08820' => 'bna', 'Aa31LG4G3300' => 'aar', 'Aa31LG8G10030' => 'aar', 'Actinidia00731' => 'ach', 'Actinidia11473' => 'ach', 'Actinidia23469' => 'ach', 'Actinidia24318' => 'ach', 'Actinidia40196' => 'ach', 'Actinidia40197' => 'ach', 'Actinidia40198' => 'ach', 'Ah.08g212990' => 'amhyb', 'Ah.15g091720' => 'amhyb', 'AL3G38260' => 'aly', 'AL4G47710' => 'aly', 'Aqoxy2G00671' => 'aox', 'Aqoxy2G03236' => 'aox', 'arahy.Tifrunner.gnm1.ann1.05IDCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KR684' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATY3SJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK6QJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6APGL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IDT7Z9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM073U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ0R87' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LE7RV4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT4QRX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V5ENPK' => 'arhy', 'AT2G48110' => 'ath', 'AT3G23590' => 'ath', 'ATR0626G186' => 'atr', 'ATR1127G141' => 'atr', 'Atru.chr4.2583' => 'acertr', 'Atru.chr5.1358' => 'acertr', 'Atru.chr5.1359' => 'acertr', 'Atru.chr8.46' => 'acertr', 'AUR62002640' => 'cqu', 'AUR62030055' => 'cqu', 'AUR62033713' => 'cqu', 'AUR62033714' => 'cqu', 'AUR62036795' => 'cqu', 'AUR62039891' => 'cqu', 'BcaB02g08737' => 'bca', 'BcaB04g20441' => 'bca', 'BcaB06g26509' => 'bca', 'BcaB06g26510' => 'bca', 'BcaB06g26511' => 'bca', 'BcaB06g26512' => 'bca', 'BcaB06g26513' => 'bca', 'BcaC02g12564' => 'bca', 'BcaC02g12565' => 'bca', 'BcaC02g12794' => 'bca', 'BcaC02g12795' => 'bca', 'BcaC02g12796' => 'bca', 'BcaC06g35541' => 'bca', 'BNapus_Darmor_BZH_scaffold_188p00080' => 'bna', 'BNapus_Darmor_BZH_scaffold_188p00090' => 'bna', 'BolC1t03972H' => 'bol', 'BolC1t03973H' => 'bol', 'BolC4t21680H' => 'bol', 'BolC7t41863H' => 'bol', 'BolSC55t61227H' => 'bol', 'BolSC55t61228H' => 'bol', 'BraA01t03278Z' => 'bra', 'BraA05t18998Z' => 'bra', 'BraA07t28673Z' => 'bra', 'C01p40150' => 'bna', 'C05p12370' => 'bna', 'C07p13680' => 'bna', 'CAN.G1006.16' => 'can', 'CAN.G1006.17' => 'can', 'CAN.G1170.2' => 'can', 'CAN.G962.7' => 'can', 'CANSAT25G2179' => 'cansat', 'CANSAT78G1573' => 'cansat', 'CARHR099510' => 'chi', 'CARHR143510' => 'chi', 'Carub.0003s2380' => 'cru', 'Carub.0004s3082' => 'cru', 'Ca_00614_v3' => 'car', 'Ca_07801_v3' => 'car', 'Ca_08567_v3' => 'car', 'Ca_09571_v3' => 'car', 'CBR_g19290' => 'cbr', 'Cc01_g19770' => 'ccan', 'Cc03_g03030' => 'ccan', 'CDE07G0968' => 'cde', 'CDE09G1441' => 'cde', 'Cfa006103' => 'cfa', 'Cfa015573' => 'cfa', 'Cfa016988' => 'cfa', 'Ciclev10006738m.g' => 'ccl', 'Ciclev10010920m.g' => 'ccl', 'Ciclev10018517m.g' => 'ccl', 'CiPaw.01G159200' => 'cil', 'CiPaw.02G091000' => 'cil', 'CiPaw.02G091100' => 'cil', 'CiPaw.08G103100' => 'cil', 'CiPaw.09G224900' => 'cil', 'ClCG06G005740' => 'cla', 'ClCG07G000090' => 'cla', 'ClCG07G000100' => 'cla', 'COL.COLO4_09143' => 'col', 'COL.COLO4_25124' => 'col', 'Cpa.g.sc16.34' => 'cpa', 'Cpa.g.sc3504.1' => 'cpa', 'Cpa.g.sc60.37' => 'cpa', 'CsaV3_6G018520' => 'csa', 'CsaV3_6G036860' => 'csa', 'CSS0001072' => 'camsi', 'CSS0020208' => 'camsi', 'CSS0021253' => 'camsi', 'CSS0022190' => 'camsi', 'CSS0036150' => 'camsi', 'CSS0040442' => 'camsi', 'CSS0042300' => 'camsi', 'CSS0045298' => 'camsi', 'DCAR_012449' => 'dca', 'DCAR_018405' => 'dca', 'DCAR_024573' => 'dca', 'DCAR_030591' => 'dca', 'Dinv16926' => 'din', 'Dinv32963' => 'din', 'Dinv38382' => 'din', 'Dinv38383' => 'din', 'Duzib133G0974' => 'dzi', 'Duzib138G1867' => 'dzi', 'Duzib211G0420' => 'dzi', 'Duzib212G0930' => 'dzi', 'ECA234G1645' => 'eca', 'ECA247G3467' => 'eca', 'ECA248G1703' => 'eca', 'EL10Ac3g06327' => 'bvu', 'EL10Ac7g17204' => 'bvu', 'Eucgr.A00855' => 'egr', 'Eucgr.A00858' => 'egr', 'Eucgr.H01520' => 'egr', 'Eucgr.H03604' => 'egr', 'Eucgr.L03465' => 'egr', 'Eucgr.L03466' => 'egr', 'FAN01G0988' => 'fan', 'FAN02G3892' => 'fan', 'FAN05G3381' => 'fan', 'FAN07G0967' => 'fan', 'FAN07G1493' => 'fan', 'FAN08G3125' => 'fan', 'FAN09G0402' => 'fan', 'FAN12G2594' => 'fan', 'FAN12G3879' => 'fan', 'FAN14G1546' => 'fan', 'FAN15G3626' => 'fan', 'FAN17G0588' => 'fan', 'FAN17G0609' => 'fan', 'FAN18G2817' => 'fan', 'FAN19G1305' => 'fan', 'FAN20G1787' => 'fan', 'FAN22G0073' => 'fan', 'FAN22G0352' => 'fan', 'FAN22G0368' => 'fan', 'FAN22G2273' => 'fan', 'FAN24G1998' => 'fan', 'FAN27G1317' => 'fan', 'FvH4_2g23980' => 'fve', 'FvH4_4g14380' => 'fve', 'FvH4_4g14390' => 'fve', 'FvH4_6g09250' => 'fve', 'Glyma.03G151100' => 'gma', 'Glyma.04G122550' => 'gma', 'Glyma.05G001600' => 'gma', 'Glyma.09G270766' => 'gma', 'Glyma.09G270832' => 'gma', 'Glyma.13G209800' => 'gma', 'Glyma.15G102800' => 'gma', 'Glyma.18G218900' => 'gma', 'Glyma.19G001500' => 'gma', 'Glyma.19G153600' => 'gma', 'Gohir.A02G028600' => 'ghi', 'Gohir.A08G045000' => 'ghi', 'Gohir.A11G120500' => 'ghi', 'Gohir.A12G006200' => 'ghi', 'Gohir.A12G006250' => 'ghi', 'Gohir.D02G036300' => 'ghi', 'Gohir.D08G054700' => 'ghi', 'Gohir.D11G125600' => 'ghi', 'Gohir.D12G005700' => 'ghi', 'Gorai.004G055200' => 'gra', 'Gorai.005G040400' => 'gra', 'Gorai.007G134500' => 'gra', 'Gorai.008G005500' => 'gra', 'GSVIVG01011094001' => 'vvi', 'GSVIVG01017879001' => 'vvi', 'GSVIVG01025988001' => 'vvi', 'GSVIVG01029847001' => 'vvi', 'HanXRQChr10g0282901' => 'han', 'HanXRQChr10g0310371' => 'han', 'HanXRQChr10g0315041' => 'han', 'HanXRQChr11g0327651' => 'han', 'HanXRQChr12g0359391' => 'han', 'Haze_00972' => 'cav', 'Haze_00973' => 'cav', 'Haze_00974' => 'cav', 'Haze_04747' => 'cav', 'Haze_04749' => 'cav', 'Haze_04750' => 'cav', 'Haze_21217' => 'cav', 'Hma1.2p1_1037F.1_g250680' => 'hma', 'Hma1.2p1_1644F.1_g295320' => 'hma', 'HPP92_011322' => 'vpl', 'HPP92_011323' => 'vpl', 'HPP92_011324' => 'vpl', 'HPP92_011325' => 'vpl', 'HPP92_011326' => 'vpl', 'Hund12205' => 'sun', 'Hund17957' => 'sun', 'Lalb_Chr06g0176771' => 'lal', 'Lalb_Chr18g0056021' => 'lal', 'Lalb_Chr18g0056031' => 'lal', 'Lalb_Chr18g0056041' => 'lal', 'Lalb_Chr20g0107751' => 'lal', 'Lalb_Chr20g0118371' => 'lal', 'Lj1g0010239' => 'lja', 'Lj1g0017101' => 'lja', 'Lj2A1178G40' => 'lonja', 'Lj2A54G84' => 'lonja', 'Lj2g0015248' => 'lja', 'Lj3A761T51' => 'lonja', 'Lj6g0018116' => 'lja', 'Lsat_1_v5_gn_4_136040' => 'lsa', 'Lsat_1_v5_gn_5_187461' => 'lsa', 'Lsat_1_v5_gn_5_77001' => 'lsa', 'Lsat_1_v5_gn_9_4461' => 'lsa', 'Manes.01G210100' => 'mes', 'Manes.03G185600' => 'mes', 'Manes.05G073300' => 'mes', 'Manes.09G120300' => 'mes', 'Manes.15G022100' => 'mes', 'Mapoly0096s0053' => 'mpo', 'MBI03_g14058_MAGBIO' => 'mbi', 'MBI03_g33876_MAGBIO' => 'mbi', 'MBI03_g36854_MAGBIO' => 'mbi', 'MBI17_g11997_MAGBIO' => 'mbi', 'MD03G1269000' => 'mdo', 'MD04G1179600' => 'mdo', 'MD11G1289800' => 'mdo', 'MD12G1194700' => 'mdo', 'MD13G1182100' => 'mdo', 'MD13G1182200' => 'mdo', 'MD16G1182600' => 'mdo', 'Medtr2g021400' => 'mtr', 'Medtr2g021470' => 'mtr', 'Medtr2g105810' => 'mtr', 'Medtr3g033580' => 'mtr', 'Medtr6g007970' => 'mtr', 'Medtr7g056330' => 'mtr', 'Medtr7g074290' => 'mtr', 'Medtr7g074380' => 'mtr', 'Medtr7g094550' => 'mtr', 'Medtr8g069995' => 'mtr', 'MELO3C014345.2' => 'cme', 'MELO3C021395.2' => 'cme', 'Migut.D00262' => 'egut', 'Migut.G00257' => 'egut', 'MSTRG.21575' => 'ama', 'MSTRG.3985' => 'ama', 'Nitab4.5_0000295g0140' => 'nta', 'Nitab4.5_0000732g0140' => 'nta', 'Nitab4.5_0003162g0020' => 'nta', 'Nitab4.5_0006180g0090' => 'nta', 'Nitab4.5_0006390g0010' => 'nta', 'Nitab4.5_0007392g0040' => 'nta', 'Nn1g02140' => 'nnu', 'Nn4g26168' => 'nnu', 'Nn5g26754' => 'nnu', 'Oeu001433.1' => 'oeu', 'Oeu010299.2' => 'oeu', 'Oeu011171.1' => 'oeu', 'Oeu037675.1' => 'oeu', 'Oeu038359.1' => 'oeu', 'Oeu063834.1' => 'oeu', 'Oeu063835.1' => 'oeu', 'Os05g0312000' => 'osa', 'Os07g0211101' => 'osa', 'Os07g0211200' => 'osa', 'Os07g0681500' => 'osa', 'Peaxi162Scf00095g01015' => 'pax', 'Peaxi162Scf00104g00329' => 'pax', 'Peaxi162Scf00161g00137' => 'pax', 'PGR004G1665' => 'pgr', 'PGR031G2937' => 'pgr', 'PGR119G2145' => 'pgr', 'PGSC0003DMG400004351' => 'stu', 'PGSC0003DMG400014625' => 'stu', 'PGSC0003DMG401000943' => 'stu', 'Phvul.001G148600' => 'pvu', 'Phvul.004G001700' => 'pvu', 'Phvul.006G154900' => 'pvu', 'Phvul.008G078200' => 'pvu', 'Phvul.011G136500' => 'pvu', 'Potri.002G215600' => 'ptr', 'Potri.008G201600' => 'ptr', 'Potri.014G138400' => 'ptr', 'Potri.016G142500' => 'ptr', 'Pp3c16_10580' => 'ppa', 'Pp3c5_25280' => 'ppa', 'Prupe.1G150000' => 'ppe', 'Prupe.1G150100' => 'ppe', 'Prupe.6G299600' => 'ppe', 'Prupe.8G245000' => 'ppe', 'Psat0s4927g0040' => 'psa', 'Psat1g052080' => 'psa', 'Psat1g183800' => 'psa', 'Psat3g113840' => 'psa', 'Psat3g126120' => 'psa', 'Psat3g126160' => 'psa', 'Psat3g158760' => 'psa', 'Psat3g158840' => 'psa', 'PSO170G2858' => 'pso', 'PSO339G0606' => 'pso', 'PSO384G4709' => 'pso', 'PSO407G0334' => 'pso', 'QL04p040276' => 'qlo', 'QL06p005458' => 'qlo', 'QL06p005472' => 'qlo', 'QL07p030546' => 'qlo', 'QL07p031519' => 'qlo', 'QL09p050949' => 'qlo', 'QL09p050966' => 'qlo', 'QL09p051067' => 'qlo', 'QL12p022706' => 'qlo', 'RcHm_v2.0_Chr2g0119601' => 'rch', 'RcHm_v2.0_Chr3g0459591' => 'rch', 'RcHm_v2.0_Chr4g0418521' => 'rch', 'RcHm_v2.0_Chr4g0418531' => 'rch', 'RcHm_v2.0_Chr4g0418541' => 'rch', 'RcHm_v2.0_Chr6g0291641' => 'rch', 'Rhsim01G0086300' => 'rsi', 'Rhsim01G0276300' => 'rsi', 'Rhsim01G0276500' => 'rsi', 'Rhsim04G0207700' => 'rsi', 'Rhsim05G0234500' => 'rsi', 'Rhsim13G0022400' => 'rsi', 'Sabra02G0167900' => 'sbr', 'Sabra04G0158500' => 'sbr', 'Sabra08G0159800' => 'sbr', 'Sabra10G0011500' => 'sbr', 'Sabra14G0104400' => 'sbr', 'SalBow2G2440' => 'sbo', 'SalBow4G2265' => 'sbo', 'Sc02g0000060' => 'sci', 'Sc05g0005020' => 'sci', 'Sc13g0003890' => 'sci', 'Sed0014865' => 'sed', 'Sed0017224' => 'sed', 'Sed0026391' => 'sed', 'SEGI_00063' => 'sgi', 'SEGI_10967' => 'sgi', 'SEGI_17510' => 'sgi', 'SEGI_24396' => 'sgi', 'SEGI_39719' => 'sgi', 'SEGI_41392' => 'sgi', 'SGA_v2.0_scaffold11G05794' => 'sas', 'SGA_v2.0_scaffold142G35607' => 'sas', 'SGA_v2.0_scaffold1G00447' => 'sas', 'SHI15388' => 'shi', 'SHI15394' => 'shi', 'SHI15396' => 'shi', 'SHI15399' => 'shi', 'SMO343G0151' => 'smo', 'SMO367G1118' => 'smo', 'Solyc01g080200.3' => 'sly', 'Solyc06g008960.3' => 'sly', 'Solyc09g064780.3' => 'sly', 'Sopen01g031980' => 'spe', 'Sopen06g003710' => 'spe', 'Sopen09g026460' => 'spe', 'Sp3g21240' => 'spa', 'Sp4g30030' => 'spa', 'TAR365G0022' => 'tar', 'TAR365G1023' => 'tar', 'TAR365G1253' => 'tar', 'TAR623G0078' => 'tar', 'TAR623G1721' => 'tar', 'TAR633G0959' => 'tar', 'THA.LOC104802225' => 'tha', 'THA.LOC104804769' => 'tha', 'THA.LOC104808660' => 'tha', 'THA.LOC104812792' => 'tha', 'Thecc.01G284000' => 'tca', 'Thecc.04G220600' => 'tca', 'Thecc.05G268900' => 'tca', 'Thecc.08G171100' => 'tca', 'Thhalv10001284m.g' => 'esa', 'Thhalv10019912m.g' => 'esa', 'TPR.G14189' => 'tpr', 'TPR.G18110' => 'tpr', 'TPR.G18130' => 'tpr', 'TPR.G18131' => 'tpr', 'TPR.G18140' => 'tpr', 'TPR.G24282' => 'tpr', 'TPR.G25221' => 'tpr', 'TPR.G29267' => 'tpr', 'TPR.G35315' => 'tpr', 'TPR.G36173' => 'tpr', 'TWI09G0794' => 'twi', 'TWI59G1348' => 'twi', 'TWI74G0430' => 'twi', 'unitig_26.g8940' => 'ugi', 'unitig_749.g13744' => 'ugi', 'unitig_749.g13745' => 'ugi', 'vmacro08269' => 'vma', 'vmacro14937' => 'vma', 'vmacro20401' => 'vma', 'VMungo0464G1349' => 'vmu', 'VMungo0540G0289' => 'vmu', 'VMungo1215G1590' => 'vmu', 'VMungo1309G0221' => 'vmu', 'VMungo1309G2815' => 'vmu', 'VMungo1383G0239' => 'vmu', 'VMungo1383G2910' => 'vmu', 'Zm00001eb095270' => 'zma', 'Zm00001eb095280' => 'zma', 'Zm00001eb111630' => 'zma', 'Zm00001eb237080' => 'zma', 'Zm00001eb273740' => 'zma', 'Zm00001eb285040' => 'zma', 'Zm00001eb330790' => 'zma', 'Zm00001eb337380' => 'zma' ), 'gf_id' => 'HOM05D001484', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001484' ), 'data_identifier' => 'HOM05D001484', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001484', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p31500' => 'bna', 'A05p00020' => 'bna', 'A07p08820' => 'bna', 'Aa31LG4G3300' => 'aar', 'Aa31LG8G10030' => 'aar', 'Actinidia00731' => 'ach', 'Actinidia11473' => 'ach', 'Actinidia23469' => 'ach', 'Actinidia24318' => 'ach', 'Actinidia40196' => 'ach', 'Actinidia40197' => 'ach', 'Actinidia40198' => 'ach', 'Ah.08g212990' => 'amhyb', 'Ah.15g091720' => 'amhyb', 'AL3G38260' => 'aly', 'AL4G47710' => 'aly', 'Aqoxy2G00671' => 'aox', 'Aqoxy2G03236' => 'aox', 'arahy.Tifrunner.gnm1.ann1.05IDCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KR684' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATY3SJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK6QJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6APGL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IDT7Z9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM073U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ0R87' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LE7RV4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT4QRX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V5ENPK' => 'arhy', 'AT2G48110' => 'ath', 'AT3G23590' => 'ath', 'ATR0626G186' => 'atr', 'ATR1127G141' => 'atr', 'Atru.chr4.2583' => 'acertr', 'Atru.chr5.1358' => 'acertr', 'Atru.chr5.1359' => 'acertr', 'Atru.chr8.46' => 'acertr', 'AUR62002640' => 'cqu', 'AUR62030055' => 'cqu', 'AUR62033713' => 'cqu', 'AUR62033714' => 'cqu', 'AUR62036795' => 'cqu', 'AUR62039891' => 'cqu', 'BcaB02g08737' => 'bca', 'BcaB04g20441' => 'bca', 'BcaB06g26509' => 'bca', 'BcaB06g26510' => 'bca', 'BcaB06g26511' => 'bca', 'BcaB06g26512' => 'bca', 'BcaB06g26513' => 'bca', 'BcaC02g12564' => 'bca', 'BcaC02g12565' => 'bca', 'BcaC02g12794' => 'bca', 'BcaC02g12795' => 'bca', 'BcaC02g12796' => 'bca', 'BcaC06g35541' => 'bca', 'BNapus_Darmor_BZH_scaffold_188p00080' => 'bna', 'BNapus_Darmor_BZH_scaffold_188p00090' => 'bna', 'BolC1t03972H' => 'bol', 'BolC1t03973H' => 'bol', 'BolC4t21680H' => 'bol', 'BolC7t41863H' => 'bol', 'BolSC55t61227H' => 'bol', 'BolSC55t61228H' => 'bol', 'BraA01t03278Z' => 'bra', 'BraA05t18998Z' => 'bra', 'BraA07t28673Z' => 'bra', 'C01p40150' => 'bna', 'C05p12370' => 'bna', 'C07p13680' => 'bna', 'CAN.G1006.16' => 'can', 'CAN.G1006.17' => 'can', 'CAN.G1170.2' => 'can', 'CAN.G962.7' => 'can', 'CANSAT25G2179' => 'cansat', 'CANSAT78G1573' => 'cansat', 'CARHR099510' => 'chi', 'CARHR143510' => 'chi', 'Carub.0003s2380' => 'cru', 'Carub.0004s3082' => 'cru', 'Ca_00614_v3' => 'car', 'Ca_07801_v3' => 'car', 'Ca_08567_v3' => 'car', 'Ca_09571_v3' => 'car', 'CBR_g19290' => 'cbr', 'Cc01_g19770' => 'ccan', 'Cc03_g03030' => 'ccan', 'CDE07G0968' => 'cde', 'CDE09G1441' => 'cde', 'Cfa006103' => 'cfa', 'Cfa015573' => 'cfa', 'Cfa016988' => 'cfa', 'Ciclev10006738m.g' => 'ccl', 'Ciclev10010920m.g' => 'ccl', 'Ciclev10018517m.g' => 'ccl', 'CiPaw.01G159200' => 'cil', 'CiPaw.02G091000' => 'cil', 'CiPaw.02G091100' => 'cil', 'CiPaw.08G103100' => 'cil', 'CiPaw.09G224900' => 'cil', 'ClCG06G005740' => 'cla', 'ClCG07G000090' => 'cla', 'ClCG07G000100' => 'cla', 'COL.COLO4_09143' => 'col', 'COL.COLO4_25124' => 'col', 'Cpa.g.sc16.34' => 'cpa', 'Cpa.g.sc3504.1' => 'cpa', 'Cpa.g.sc60.37' => 'cpa', 'CsaV3_6G018520' => 'csa', 'CsaV3_6G036860' => 'csa', 'CSS0001072' => 'camsi', 'CSS0020208' => 'camsi', 'CSS0021253' => 'camsi', 'CSS0022190' => 'camsi', 'CSS0036150' => 'camsi', 'CSS0040442' => 'camsi', 'CSS0042300' => 'camsi', 'CSS0045298' => 'camsi', 'DCAR_012449' => 'dca', 'DCAR_018405' => 'dca', 'DCAR_024573' => 'dca', 'DCAR_030591' => 'dca', 'Dinv16926' => 'din', 'Dinv32963' => 'din', 'Dinv38382' => 'din', 'Dinv38383' => 'din', 'Duzib133G0974' => 'dzi', 'Duzib138G1867' => 'dzi', 'Duzib211G0420' => 'dzi', 'Duzib212G0930' => 'dzi', 'ECA234G1645' => 'eca', 'ECA247G3467' => 'eca', 'ECA248G1703' => 'eca', 'EL10Ac3g06327' => 'bvu', 'EL10Ac7g17204' => 'bvu', 'Eucgr.A00855' => 'egr', 'Eucgr.A00858' => 'egr', 'Eucgr.H01520' => 'egr', 'Eucgr.H03604' => 'egr', 'Eucgr.L03465' => 'egr', 'Eucgr.L03466' => 'egr', 'FAN01G0988' => 'fan', 'FAN02G3892' => 'fan', 'FAN05G3381' => 'fan', 'FAN07G0967' => 'fan', 'FAN07G1493' => 'fan', 'FAN08G3125' => 'fan', 'FAN09G0402' => 'fan', 'FAN12G2594' => 'fan', 'FAN12G3879' => 'fan', 'FAN14G1546' => 'fan', 'FAN15G3626' => 'fan', 'FAN17G0588' => 'fan', 'FAN17G0609' => 'fan', 'FAN18G2817' => 'fan', 'FAN19G1305' => 'fan', 'FAN20G1787' => 'fan', 'FAN22G0073' => 'fan', 'FAN22G0352' => 'fan', 'FAN22G0368' => 'fan', 'FAN22G2273' => 'fan', 'FAN24G1998' => 'fan', 'FAN27G1317' => 'fan', 'FvH4_2g23980' => 'fve', 'FvH4_4g14380' => 'fve', 'FvH4_4g14390' => 'fve', 'FvH4_6g09250' => 'fve', 'Glyma.03G151100' => 'gma', 'Glyma.04G122550' => 'gma', 'Glyma.05G001600' => 'gma', 'Glyma.09G270766' => 'gma', 'Glyma.09G270832' => 'gma', 'Glyma.13G209800' => 'gma', 'Glyma.15G102800' => 'gma', 'Glyma.18G218900' => 'gma', 'Glyma.19G001500' => 'gma', 'Glyma.19G153600' => 'gma', 'Gohir.A02G028600' => 'ghi', 'Gohir.A08G045000' => 'ghi', 'Gohir.A11G120500' => 'ghi', 'Gohir.A12G006200' => 'ghi', 'Gohir.A12G006250' => 'ghi', 'Gohir.D02G036300' => 'ghi', 'Gohir.D08G054700' => 'ghi', 'Gohir.D11G125600' => 'ghi', 'Gohir.D12G005700' => 'ghi', 'Gorai.004G055200' => 'gra', 'Gorai.005G040400' => 'gra', 'Gorai.007G134500' => 'gra', 'Gorai.008G005500' => 'gra', 'GSVIVG01011094001' => 'vvi', 'GSVIVG01017879001' => 'vvi', 'GSVIVG01025988001' => 'vvi', 'GSVIVG01029847001' => 'vvi', 'HanXRQChr10g0282901' => 'han', 'HanXRQChr10g0310371' => 'han', 'HanXRQChr10g0315041' => 'han', 'HanXRQChr11g0327651' => 'han', 'HanXRQChr12g0359391' => 'han', 'Haze_00972' => 'cav', 'Haze_00973' => 'cav', 'Haze_00974' => 'cav', 'Haze_04747' => 'cav', 'Haze_04749' => 'cav', 'Haze_04750' => 'cav', 'Haze_21217' => 'cav', 'Hma1.2p1_1037F.1_g250680' => 'hma', 'Hma1.2p1_1644F.1_g295320' => 'hma', 'HPP92_011322' => 'vpl', 'HPP92_011323' => 'vpl', 'HPP92_011324' => 'vpl', 'HPP92_011325' => 'vpl', 'HPP92_011326' => 'vpl', 'Hund12205' => 'sun', 'Hund17957' => 'sun', 'Lalb_Chr06g0176771' => 'lal', 'Lalb_Chr18g0056021' => 'lal', 'Lalb_Chr18g0056031' => 'lal', 'Lalb_Chr18g0056041' => 'lal', 'Lalb_Chr20g0107751' => 'lal', 'Lalb_Chr20g0118371' => 'lal', 'Lj1g0010239' => 'lja', 'Lj1g0017101' => 'lja', 'Lj2A1178G40' => 'lonja', 'Lj2A54G84' => 'lonja', 'Lj2g0015248' => 'lja', 'Lj3A761T51' => 'lonja', 'Lj6g0018116' => 'lja', 'Lsat_1_v5_gn_4_136040' => 'lsa', 'Lsat_1_v5_gn_5_187461' => 'lsa', 'Lsat_1_v5_gn_5_77001' => 'lsa', 'Lsat_1_v5_gn_9_4461' => 'lsa', 'Manes.01G210100' => 'mes', 'Manes.03G185600' => 'mes', 'Manes.05G073300' => 'mes', 'Manes.09G120300' => 'mes', 'Manes.15G022100' => 'mes', 'Mapoly0096s0053' => 'mpo', 'MBI03_g14058_MAGBIO' => 'mbi', 'MBI03_g33876_MAGBIO' => 'mbi', 'MBI03_g36854_MAGBIO' => 'mbi', 'MBI17_g11997_MAGBIO' => 'mbi', 'MD03G1269000' => 'mdo', 'MD04G1179600' => 'mdo', 'MD11G1289800' => 'mdo', 'MD12G1194700' => 'mdo', 'MD13G1182100' => 'mdo', 'MD13G1182200' => 'mdo', 'MD16G1182600' => 'mdo', 'Medtr2g021400' => 'mtr', 'Medtr2g021470' => 'mtr', 'Medtr2g105810' => 'mtr', 'Medtr3g033580' => 'mtr', 'Medtr6g007970' => 'mtr', 'Medtr7g056330' => 'mtr', 'Medtr7g074290' => 'mtr', 'Medtr7g074380' => 'mtr', 'Medtr7g094550' => 'mtr', 'Medtr8g069995' => 'mtr', 'MELO3C014345.2' => 'cme', 'MELO3C021395.2' => 'cme', 'Migut.D00262' => 'egut', 'Migut.G00257' => 'egut', 'MSTRG.21575' => 'ama', 'MSTRG.3985' => 'ama', 'Nitab4.5_0000295g0140' => 'nta', 'Nitab4.5_0000732g0140' => 'nta', 'Nitab4.5_0003162g0020' => 'nta', 'Nitab4.5_0006180g0090' => 'nta', 'Nitab4.5_0006390g0010' => 'nta', 'Nitab4.5_0007392g0040' => 'nta', 'Nn1g02140' => 'nnu', 'Nn4g26168' => 'nnu', 'Nn5g26754' => 'nnu', 'Oeu001433.1' => 'oeu', 'Oeu010299.2' => 'oeu', 'Oeu011171.1' => 'oeu', 'Oeu037675.1' => 'oeu', 'Oeu038359.1' => 'oeu', 'Oeu063834.1' => 'oeu', 'Oeu063835.1' => 'oeu', 'Os05g0312000' => 'osa', 'Os07g0211101' => 'osa', 'Os07g0211200' => 'osa', 'Os07g0681500' => 'osa', 'Peaxi162Scf00095g01015' => 'pax', 'Peaxi162Scf00104g00329' => 'pax', 'Peaxi162Scf00161g00137' => 'pax', 'PGR004G1665' => 'pgr', 'PGR031G2937' => 'pgr', 'PGR119G2145' => 'pgr', 'PGSC0003DMG400004351' => 'stu', 'PGSC0003DMG400014625' => 'stu', 'PGSC0003DMG401000943' => 'stu', 'Phvul.001G148600' => 'pvu', 'Phvul.004G001700' => 'pvu', 'Phvul.006G154900' => 'pvu', 'Phvul.008G078200' => 'pvu', 'Phvul.011G136500' => 'pvu', 'Potri.002G215600' => 'ptr', 'Potri.008G201600' => 'ptr', 'Potri.014G138400' => 'ptr', 'Potri.016G142500' => 'ptr', 'Pp3c16_10580' => 'ppa', 'Pp3c5_25280' => 'ppa', 'Prupe.1G150000' => 'ppe', 'Prupe.1G150100' => 'ppe', 'Prupe.6G299600' => 'ppe', 'Prupe.8G245000' => 'ppe', 'Psat0s4927g0040' => 'psa', 'Psat1g052080' => 'psa', 'Psat1g183800' => 'psa', 'Psat3g113840' => 'psa', 'Psat3g126120' => 'psa', 'Psat3g126160' => 'psa', 'Psat3g158760' => 'psa', 'Psat3g158840' => 'psa', 'PSO170G2858' => 'pso', 'PSO339G0606' => 'pso', 'PSO384G4709' => 'pso', 'PSO407G0334' => 'pso', 'QL04p040276' => 'qlo', 'QL06p005458' => 'qlo', 'QL06p005472' => 'qlo', 'QL07p030546' => 'qlo', 'QL07p031519' => 'qlo', 'QL09p050949' => 'qlo', 'QL09p050966' => 'qlo', 'QL09p051067' => 'qlo', 'QL12p022706' => 'qlo', 'RcHm_v2.0_Chr2g0119601' => 'rch', 'RcHm_v2.0_Chr3g0459591' => 'rch', 'RcHm_v2.0_Chr4g0418521' => 'rch', 'RcHm_v2.0_Chr4g0418531' => 'rch', 'RcHm_v2.0_Chr4g0418541' => 'rch', 'RcHm_v2.0_Chr6g0291641' => 'rch', 'Rhsim01G0086300' => 'rsi', 'Rhsim01G0276300' => 'rsi', 'Rhsim01G0276500' => 'rsi', 'Rhsim04G0207700' => 'rsi', 'Rhsim05G0234500' => 'rsi', 'Rhsim13G0022400' => 'rsi', 'Sabra02G0167900' => 'sbr', 'Sabra04G0158500' => 'sbr', 'Sabra08G0159800' => 'sbr', 'Sabra10G0011500' => 'sbr', 'Sabra14G0104400' => 'sbr', 'SalBow2G2440' => 'sbo', 'SalBow4G2265' => 'sbo', 'Sc02g0000060' => 'sci', 'Sc05g0005020' => 'sci', 'Sc13g0003890' => 'sci', 'Sed0014865' => 'sed', 'Sed0017224' => 'sed', 'Sed0026391' => 'sed', 'SEGI_00063' => 'sgi', 'SEGI_10967' => 'sgi', 'SEGI_17510' => 'sgi', 'SEGI_24396' => 'sgi', 'SEGI_39719' => 'sgi', 'SEGI_41392' => 'sgi', 'SGA_v2.0_scaffold11G05794' => 'sas', 'SGA_v2.0_scaffold142G35607' => 'sas', 'SGA_v2.0_scaffold1G00447' => 'sas', 'SHI15388' => 'shi', 'SHI15394' => 'shi', 'SHI15396' => 'shi', 'SHI15399' => 'shi', 'SMO343G0151' => 'smo', 'SMO367G1118' => 'smo', 'Solyc01g080200.3' => 'sly', 'Solyc06g008960.3' => 'sly', 'Solyc09g064780.3' => 'sly', 'Sopen01g031980' => 'spe', 'Sopen06g003710' => 'spe', 'Sopen09g026460' => 'spe', 'Sp3g21240' => 'spa', 'Sp4g30030' => 'spa', 'TAR365G0022' => 'tar', 'TAR365G1023' => 'tar', 'TAR365G1253' => 'tar', 'TAR623G0078' => 'tar', 'TAR623G1721' => 'tar', 'TAR633G0959' => 'tar', 'THA.LOC104802225' => 'tha', 'THA.LOC104804769' => 'tha', 'THA.LOC104808660' => 'tha', 'THA.LOC104812792' => 'tha', 'Thecc.01G284000' => 'tca', 'Thecc.04G220600' => 'tca', 'Thecc.05G268900' => 'tca', 'Thecc.08G171100' => 'tca', 'Thhalv10001284m.g' => 'esa', 'Thhalv10019912m.g' => 'esa', 'TPR.G14189' => 'tpr', 'TPR.G18110' => 'tpr', 'TPR.G18130' => 'tpr', 'TPR.G18131' => 'tpr', 'TPR.G18140' => 'tpr', 'TPR.G24282' => 'tpr', 'TPR.G25221' => 'tpr', 'TPR.G29267' => 'tpr', 'TPR.G35315' => 'tpr', 'TPR.G36173' => 'tpr', 'TWI09G0794' => 'twi', 'TWI59G1348' => 'twi', 'TWI74G0430' => 'twi', 'unitig_26.g8940' => 'ugi', 'unitig_749.g13744' => 'ugi', 'unitig_749.g13745' => 'ugi', 'vmacro08269' => 'vma', 'vmacro14937' => 'vma', 'vmacro20401' => 'vma', 'VMungo0464G1349' => 'vmu', 'VMungo0540G0289' => 'vmu', 'VMungo1215G1590' => 'vmu', 'VMungo1309G0221' => 'vmu', 'VMungo1309G2815' => 'vmu', 'VMungo1383G0239' => 'vmu', 'VMungo1383G2910' => 'vmu', 'Zm00001eb095270' => 'zma', 'Zm00001eb095280' => 'zma', 'Zm00001eb111630' => 'zma', 'Zm00001eb237080' => 'zma', 'Zm00001eb273740' => 'zma', 'Zm00001eb285040' => 'zma', 'Zm00001eb330790' => 'zma', 'Zm00001eb337380' => 'zma' ) $gf_id = 'HOM05D001484' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001484' ) $data_identifier = 'HOM05D001484' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 2, 'aly' => (int) 2, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 22, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 7, 'hma' => (int) 2, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 7, 'mtr' => (int) 10, 'cme' => (int) 2, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 4, 'ppa' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 4, 'qlo' => (int) 9, 'rch' => (int) 6, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 10, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 7, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb337380' $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' => 'HOM05D001484', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p31500' => 'bna', 'A05p00020' => 'bna', 'A07p08820' => 'bna', 'Aa31LG4G3300' => 'aar', 'Aa31LG8G10030' => 'aar', 'Actinidia00731' => 'ach', 'Actinidia11473' => 'ach', 'Actinidia23469' => 'ach', 'Actinidia24318' => 'ach', 'Actinidia40196' => 'ach', 'Actinidia40197' => 'ach', 'Actinidia40198' => 'ach', 'Ah.08g212990' => 'amhyb', 'Ah.15g091720' => 'amhyb', 'AL3G38260' => 'aly', 'AL4G47710' => 'aly', 'Aqoxy2G00671' => 'aox', 'Aqoxy2G03236' => 'aox', 'arahy.Tifrunner.gnm1.ann1.05IDCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KR684' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATY3SJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK6QJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6APGL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IDT7Z9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM073U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ0R87' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LE7RV4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT4QRX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V5ENPK' => 'arhy', 'AT2G48110' => 'ath', 'AT3G23590' => 'ath', 'ATR0626G186' => 'atr', 'ATR1127G141' => 'atr', 'Atru.chr4.2583' => 'acertr', 'Atru.chr5.1358' => 'acertr', 'Atru.chr5.1359' => 'acertr', 'Atru.chr8.46' => 'acertr', 'AUR62002640' => 'cqu', 'AUR62030055' => 'cqu', 'AUR62033713' => 'cqu', 'AUR62033714' => 'cqu', 'AUR62036795' => 'cqu', 'AUR62039891' => 'cqu', 'BcaB02g08737' => 'bca', 'BcaB04g20441' => 'bca', 'BcaB06g26509' => 'bca', 'BcaB06g26510' => 'bca', 'BcaB06g26511' => 'bca', 'BcaB06g26512' => 'bca', 'BcaB06g26513' => 'bca', 'BcaC02g12564' => 'bca', 'BcaC02g12565' => 'bca', 'BcaC02g12794' => 'bca', 'BcaC02g12795' => 'bca', 'BcaC02g12796' => 'bca', 'BcaC06g35541' => 'bca', 'BNapus_Darmor_BZH_scaffold_188p00080' => 'bna', 'BNapus_Darmor_BZH_scaffold_188p00090' => 'bna', 'BolC1t03972H' => 'bol', 'BolC1t03973H' => 'bol', 'BolC4t21680H' => 'bol', 'BolC7t41863H' => 'bol', 'BolSC55t61227H' => 'bol', 'BolSC55t61228H' => 'bol', 'BraA01t03278Z' => 'bra', 'BraA05t18998Z' => 'bra', 'BraA07t28673Z' => 'bra', 'C01p40150' => 'bna', 'C05p12370' => 'bna', 'C07p13680' => 'bna', 'CAN.G1006.16' => 'can', 'CAN.G1006.17' => 'can', 'CAN.G1170.2' => 'can', 'CAN.G962.7' => 'can', 'CANSAT25G2179' => 'cansat', 'CANSAT78G1573' => 'cansat', 'CARHR099510' => 'chi', 'CARHR143510' => 'chi', 'Carub.0003s2380' => 'cru', 'Carub.0004s3082' => 'cru', 'Ca_00614_v3' => 'car', 'Ca_07801_v3' => 'car', 'Ca_08567_v3' => 'car', 'Ca_09571_v3' => 'car', 'CBR_g19290' => 'cbr', 'Cc01_g19770' => 'ccan', 'Cc03_g03030' => 'ccan', 'CDE07G0968' => 'cde', 'CDE09G1441' => 'cde', 'Cfa006103' => 'cfa', 'Cfa015573' => 'cfa', 'Cfa016988' => 'cfa', 'Ciclev10006738m.g' => 'ccl', 'Ciclev10010920m.g' => 'ccl', 'Ciclev10018517m.g' => 'ccl', 'CiPaw.01G159200' => 'cil', 'CiPaw.02G091000' => 'cil', 'CiPaw.02G091100' => 'cil', 'CiPaw.08G103100' => 'cil', 'CiPaw.09G224900' => 'cil', 'ClCG06G005740' => 'cla', 'ClCG07G000090' => 'cla', 'ClCG07G000100' => 'cla', 'COL.COLO4_09143' => 'col', 'COL.COLO4_25124' => 'col', 'Cpa.g.sc16.34' => 'cpa', 'Cpa.g.sc3504.1' => 'cpa', 'Cpa.g.sc60.37' => 'cpa', 'CsaV3_6G018520' => 'csa', 'CsaV3_6G036860' => 'csa', 'CSS0001072' => 'camsi', 'CSS0020208' => 'camsi', 'CSS0021253' => 'camsi', 'CSS0022190' => 'camsi', 'CSS0036150' => 'camsi', 'CSS0040442' => 'camsi', 'CSS0042300' => 'camsi', 'CSS0045298' => 'camsi', 'DCAR_012449' => 'dca', 'DCAR_018405' => 'dca', 'DCAR_024573' => 'dca', 'DCAR_030591' => 'dca', 'Dinv16926' => 'din', 'Dinv32963' => 'din', 'Dinv38382' => 'din', 'Dinv38383' => 'din', 'Duzib133G0974' => 'dzi', 'Duzib138G1867' => 'dzi', 'Duzib211G0420' => 'dzi', 'Duzib212G0930' => 'dzi', 'ECA234G1645' => 'eca', 'ECA247G3467' => 'eca', 'ECA248G1703' => 'eca', 'EL10Ac3g06327' => 'bvu', 'EL10Ac7g17204' => 'bvu', 'Eucgr.A00855' => 'egr', 'Eucgr.A00858' => 'egr', 'Eucgr.H01520' => 'egr', 'Eucgr.H03604' => 'egr', 'Eucgr.L03465' => 'egr', 'Eucgr.L03466' => 'egr', 'FAN01G0988' => 'fan', 'FAN02G3892' => 'fan', 'FAN05G3381' => 'fan', 'FAN07G0967' => 'fan', 'FAN07G1493' => 'fan', 'FAN08G3125' => 'fan', 'FAN09G0402' => 'fan', 'FAN12G2594' => 'fan', 'FAN12G3879' => 'fan', 'FAN14G1546' => 'fan', 'FAN15G3626' => 'fan', 'FAN17G0588' => 'fan', 'FAN17G0609' => 'fan', 'FAN18G2817' => 'fan', 'FAN19G1305' => 'fan', 'FAN20G1787' => 'fan', 'FAN22G0073' => 'fan', 'FAN22G0352' => 'fan', 'FAN22G0368' => 'fan', 'FAN22G2273' => 'fan', 'FAN24G1998' => 'fan', 'FAN27G1317' => 'fan', 'FvH4_2g23980' => 'fve', 'FvH4_4g14380' => 'fve', 'FvH4_4g14390' => 'fve', 'FvH4_6g09250' => 'fve', 'Glyma.03G151100' => 'gma', 'Glyma.04G122550' => 'gma', 'Glyma.05G001600' => 'gma', 'Glyma.09G270766' => 'gma', 'Glyma.09G270832' => 'gma', 'Glyma.13G209800' => 'gma', 'Glyma.15G102800' => 'gma', 'Glyma.18G218900' => 'gma', 'Glyma.19G001500' => 'gma', 'Glyma.19G153600' => 'gma', 'Gohir.A02G028600' => 'ghi', 'Gohir.A08G045000' => 'ghi', 'Gohir.A11G120500' => 'ghi', 'Gohir.A12G006200' => 'ghi', 'Gohir.A12G006250' => 'ghi', 'Gohir.D02G036300' => 'ghi', 'Gohir.D08G054700' => 'ghi', 'Gohir.D11G125600' => 'ghi', 'Gohir.D12G005700' => 'ghi', 'Gorai.004G055200' => 'gra', 'Gorai.005G040400' => 'gra', 'Gorai.007G134500' => 'gra', 'Gorai.008G005500' => 'gra', 'GSVIVG01011094001' => 'vvi', 'GSVIVG01017879001' => 'vvi', 'GSVIVG01025988001' => 'vvi', 'GSVIVG01029847001' => 'vvi', 'HanXRQChr10g0282901' => 'han', 'HanXRQChr10g0310371' => 'han', 'HanXRQChr10g0315041' => 'han', 'HanXRQChr11g0327651' => 'han', 'HanXRQChr12g0359391' => 'han', 'Haze_00972' => 'cav', 'Haze_00973' => 'cav', 'Haze_00974' => 'cav', 'Haze_04747' => 'cav', 'Haze_04749' => 'cav', 'Haze_04750' => 'cav', 'Haze_21217' => 'cav', 'Hma1.2p1_1037F.1_g250680' => 'hma', 'Hma1.2p1_1644F.1_g295320' => 'hma', 'HPP92_011322' => 'vpl', 'HPP92_011323' => 'vpl', 'HPP92_011324' => 'vpl', 'HPP92_011325' => 'vpl', 'HPP92_011326' => 'vpl', 'Hund12205' => 'sun', 'Hund17957' => 'sun', 'Lalb_Chr06g0176771' => 'lal', 'Lalb_Chr18g0056021' => 'lal', 'Lalb_Chr18g0056031' => 'lal', 'Lalb_Chr18g0056041' => 'lal', 'Lalb_Chr20g0107751' => 'lal', 'Lalb_Chr20g0118371' => 'lal', 'Lj1g0010239' => 'lja', 'Lj1g0017101' => 'lja', 'Lj2A1178G40' => 'lonja', 'Lj2A54G84' => 'lonja', 'Lj2g0015248' => 'lja', 'Lj3A761T51' => 'lonja', 'Lj6g0018116' => 'lja', 'Lsat_1_v5_gn_4_136040' => 'lsa', 'Lsat_1_v5_gn_5_187461' => 'lsa', 'Lsat_1_v5_gn_5_77001' => 'lsa', 'Lsat_1_v5_gn_9_4461' => 'lsa', 'Manes.01G210100' => 'mes', 'Manes.03G185600' => 'mes', 'Manes.05G073300' => 'mes', 'Manes.09G120300' => 'mes', 'Manes.15G022100' => 'mes', 'Mapoly0096s0053' => 'mpo', 'MBI03_g14058_MAGBIO' => 'mbi', 'MBI03_g33876_MAGBIO' => 'mbi', 'MBI03_g36854_MAGBIO' => 'mbi', 'MBI17_g11997_MAGBIO' => 'mbi', 'MD03G1269000' => 'mdo', 'MD04G1179600' => 'mdo', 'MD11G1289800' => 'mdo', 'MD12G1194700' => 'mdo', 'MD13G1182100' => 'mdo', 'MD13G1182200' => 'mdo', 'MD16G1182600' => 'mdo', 'Medtr2g021400' => 'mtr', 'Medtr2g021470' => 'mtr', 'Medtr2g105810' => 'mtr', 'Medtr3g033580' => 'mtr', 'Medtr6g007970' => 'mtr', 'Medtr7g056330' => 'mtr', 'Medtr7g074290' => 'mtr', 'Medtr7g074380' => 'mtr', 'Medtr7g094550' => 'mtr', 'Medtr8g069995' => 'mtr', 'MELO3C014345.2' => 'cme', 'MELO3C021395.2' => 'cme', 'Migut.D00262' => 'egut', 'Migut.G00257' => 'egut', 'MSTRG.21575' => 'ama', 'MSTRG.3985' => 'ama', 'Nitab4.5_0000295g0140' => 'nta', 'Nitab4.5_0000732g0140' => 'nta', 'Nitab4.5_0003162g0020' => 'nta', 'Nitab4.5_0006180g0090' => 'nta', 'Nitab4.5_0006390g0010' => 'nta', 'Nitab4.5_0007392g0040' => 'nta', 'Nn1g02140' => 'nnu', 'Nn4g26168' => 'nnu', 'Nn5g26754' => 'nnu', 'Oeu001433.1' => 'oeu', 'Oeu010299.2' => 'oeu', 'Oeu011171.1' => 'oeu', 'Oeu037675.1' => 'oeu', 'Oeu038359.1' => 'oeu', 'Oeu063834.1' => 'oeu', 'Oeu063835.1' => 'oeu', 'Os05g0312000' => 'osa', 'Os07g0211101' => 'osa', 'Os07g0211200' => 'osa', 'Os07g0681500' => 'osa', 'Peaxi162Scf00095g01015' => 'pax', 'Peaxi162Scf00104g00329' => 'pax', 'Peaxi162Scf00161g00137' => 'pax', 'PGR004G1665' => 'pgr', 'PGR031G2937' => 'pgr', 'PGR119G2145' => 'pgr', 'PGSC0003DMG400004351' => 'stu', 'PGSC0003DMG400014625' => 'stu', 'PGSC0003DMG401000943' => 'stu', 'Phvul.001G148600' => 'pvu', 'Phvul.004G001700' => 'pvu', 'Phvul.006G154900' => 'pvu', 'Phvul.008G078200' => 'pvu', 'Phvul.011G136500' => 'pvu', 'Potri.002G215600' => 'ptr', 'Potri.008G201600' => 'ptr', 'Potri.014G138400' => 'ptr', 'Potri.016G142500' => 'ptr', 'Pp3c16_10580' => 'ppa', 'Pp3c5_25280' => 'ppa', 'Prupe.1G150000' => 'ppe', 'Prupe.1G150100' => 'ppe', 'Prupe.6G299600' => 'ppe', 'Prupe.8G245000' => 'ppe', 'Psat0s4927g0040' => 'psa', 'Psat1g052080' => 'psa', 'Psat1g183800' => 'psa', 'Psat3g113840' => 'psa', 'Psat3g126120' => 'psa', 'Psat3g126160' => 'psa', 'Psat3g158760' => 'psa', 'Psat3g158840' => 'psa', 'PSO170G2858' => 'pso', 'PSO339G0606' => 'pso', 'PSO384G4709' => 'pso', 'PSO407G0334' => 'pso', 'QL04p040276' => 'qlo', 'QL06p005458' => 'qlo', 'QL06p005472' => 'qlo', 'QL07p030546' => 'qlo', 'QL07p031519' => 'qlo', 'QL09p050949' => 'qlo', 'QL09p050966' => 'qlo', 'QL09p051067' => 'qlo', 'QL12p022706' => 'qlo', 'RcHm_v2.0_Chr2g0119601' => 'rch', 'RcHm_v2.0_Chr3g0459591' => 'rch', 'RcHm_v2.0_Chr4g0418521' => 'rch', 'RcHm_v2.0_Chr4g0418531' => 'rch', 'RcHm_v2.0_Chr4g0418541' => 'rch', 'RcHm_v2.0_Chr6g0291641' => 'rch', 'Rhsim01G0086300' => 'rsi', 'Rhsim01G0276300' => 'rsi', 'Rhsim01G0276500' => 'rsi', 'Rhsim04G0207700' => 'rsi', 'Rhsim05G0234500' => 'rsi', 'Rhsim13G0022400' => 'rsi', 'Sabra02G0167900' => 'sbr', 'Sabra04G0158500' => 'sbr', 'Sabra08G0159800' => 'sbr', 'Sabra10G0011500' => 'sbr', 'Sabra14G0104400' => 'sbr', 'SalBow2G2440' => 'sbo', 'SalBow4G2265' => 'sbo', 'Sc02g0000060' => 'sci', 'Sc05g0005020' => 'sci', 'Sc13g0003890' => 'sci', 'Sed0014865' => 'sed', 'Sed0017224' => 'sed', 'Sed0026391' => 'sed', 'SEGI_00063' => 'sgi', 'SEGI_10967' => 'sgi', 'SEGI_17510' => 'sgi', 'SEGI_24396' => 'sgi', 'SEGI_39719' => 'sgi', 'SEGI_41392' => 'sgi', 'SGA_v2.0_scaffold11G05794' => 'sas', 'SGA_v2.0_scaffold142G35607' => 'sas', 'SGA_v2.0_scaffold1G00447' => 'sas', 'SHI15388' => 'shi', 'SHI15394' => 'shi', 'SHI15396' => 'shi', 'SHI15399' => 'shi', 'SMO343G0151' => 'smo', 'SMO367G1118' => 'smo', 'Solyc01g080200.3' => 'sly', 'Solyc06g008960.3' => 'sly', 'Solyc09g064780.3' => 'sly', 'Sopen01g031980' => 'spe', 'Sopen06g003710' => 'spe', 'Sopen09g026460' => 'spe', 'Sp3g21240' => 'spa', 'Sp4g30030' => 'spa', 'TAR365G0022' => 'tar', 'TAR365G1023' => 'tar', 'TAR365G1253' => 'tar', 'TAR623G0078' => 'tar', 'TAR623G1721' => 'tar', 'TAR633G0959' => 'tar', 'THA.LOC104802225' => 'tha', 'THA.LOC104804769' => 'tha', 'THA.LOC104808660' => 'tha', 'THA.LOC104812792' => 'tha', 'Thecc.01G284000' => 'tca', 'Thecc.04G220600' => 'tca', 'Thecc.05G268900' => 'tca', 'Thecc.08G171100' => 'tca', 'Thhalv10001284m.g' => 'esa', 'Thhalv10019912m.g' => 'esa', 'TPR.G14189' => 'tpr', 'TPR.G18110' => 'tpr', 'TPR.G18130' => 'tpr', 'TPR.G18131' => 'tpr', 'TPR.G18140' => 'tpr', 'TPR.G24282' => 'tpr', 'TPR.G25221' => 'tpr', 'TPR.G29267' => 'tpr', 'TPR.G35315' => 'tpr', 'TPR.G36173' => 'tpr', 'TWI09G0794' => 'twi', 'TWI59G1348' => 'twi', 'TWI74G0430' => 'twi', 'unitig_26.g8940' => 'ugi', 'unitig_749.g13744' => 'ugi', 'unitig_749.g13745' => 'ugi', 'vmacro08269' => 'vma', 'vmacro14937' => 'vma', 'vmacro20401' => 'vma', 'VMungo0464G1349' => 'vmu', 'VMungo0540G0289' => 'vmu', 'VMungo1215G1590' => 'vmu', 'VMungo1309G0221' => 'vmu', 'VMungo1309G2815' => 'vmu', 'VMungo1383G0239' => 'vmu', 'VMungo1383G2910' => 'vmu', 'Zm00001eb095270' => 'zma', 'Zm00001eb095280' => 'zma', 'Zm00001eb111630' => 'zma', 'Zm00001eb237080' => 'zma', 'Zm00001eb273740' => 'zma', 'Zm00001eb285040' => 'zma', 'Zm00001eb330790' => 'zma', 'Zm00001eb337380' => 'zma' ), 'gf_id' => 'HOM05D001484', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001484' ), 'data_identifier' => 'HOM05D001484', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001484', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p31500' => 'bna', 'A05p00020' => 'bna', 'A07p08820' => 'bna', 'Aa31LG4G3300' => 'aar', 'Aa31LG8G10030' => 'aar', 'Actinidia00731' => 'ach', 'Actinidia11473' => 'ach', 'Actinidia23469' => 'ach', 'Actinidia24318' => 'ach', 'Actinidia40196' => 'ach', 'Actinidia40197' => 'ach', 'Actinidia40198' => 'ach', 'Ah.08g212990' => 'amhyb', 'Ah.15g091720' => 'amhyb', 'AL3G38260' => 'aly', 'AL4G47710' => 'aly', 'Aqoxy2G00671' => 'aox', 'Aqoxy2G03236' => 'aox', 'arahy.Tifrunner.gnm1.ann1.05IDCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KR684' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATY3SJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK6QJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6APGL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IDT7Z9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM073U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ0R87' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LE7RV4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT4QRX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V5ENPK' => 'arhy', 'AT2G48110' => 'ath', 'AT3G23590' => 'ath', 'ATR0626G186' => 'atr', 'ATR1127G141' => 'atr', 'Atru.chr4.2583' => 'acertr', 'Atru.chr5.1358' => 'acertr', 'Atru.chr5.1359' => 'acertr', 'Atru.chr8.46' => 'acertr', 'AUR62002640' => 'cqu', 'AUR62030055' => 'cqu', 'AUR62033713' => 'cqu', 'AUR62033714' => 'cqu', 'AUR62036795' => 'cqu', 'AUR62039891' => 'cqu', 'BcaB02g08737' => 'bca', 'BcaB04g20441' => 'bca', 'BcaB06g26509' => 'bca', 'BcaB06g26510' => 'bca', 'BcaB06g26511' => 'bca', 'BcaB06g26512' => 'bca', 'BcaB06g26513' => 'bca', 'BcaC02g12564' => 'bca', 'BcaC02g12565' => 'bca', 'BcaC02g12794' => 'bca', 'BcaC02g12795' => 'bca', 'BcaC02g12796' => 'bca', 'BcaC06g35541' => 'bca', 'BNapus_Darmor_BZH_scaffold_188p00080' => 'bna', 'BNapus_Darmor_BZH_scaffold_188p00090' => 'bna', 'BolC1t03972H' => 'bol', 'BolC1t03973H' => 'bol', 'BolC4t21680H' => 'bol', 'BolC7t41863H' => 'bol', 'BolSC55t61227H' => 'bol', 'BolSC55t61228H' => 'bol', 'BraA01t03278Z' => 'bra', 'BraA05t18998Z' => 'bra', 'BraA07t28673Z' => 'bra', 'C01p40150' => 'bna', 'C05p12370' => 'bna', 'C07p13680' => 'bna', 'CAN.G1006.16' => 'can', 'CAN.G1006.17' => 'can', 'CAN.G1170.2' => 'can', 'CAN.G962.7' => 'can', 'CANSAT25G2179' => 'cansat', 'CANSAT78G1573' => 'cansat', 'CARHR099510' => 'chi', 'CARHR143510' => 'chi', 'Carub.0003s2380' => 'cru', 'Carub.0004s3082' => 'cru', 'Ca_00614_v3' => 'car', 'Ca_07801_v3' => 'car', 'Ca_08567_v3' => 'car', 'Ca_09571_v3' => 'car', 'CBR_g19290' => 'cbr', 'Cc01_g19770' => 'ccan', 'Cc03_g03030' => 'ccan', 'CDE07G0968' => 'cde', 'CDE09G1441' => 'cde', 'Cfa006103' => 'cfa', 'Cfa015573' => 'cfa', 'Cfa016988' => 'cfa', 'Ciclev10006738m.g' => 'ccl', 'Ciclev10010920m.g' => 'ccl', 'Ciclev10018517m.g' => 'ccl', 'CiPaw.01G159200' => 'cil', 'CiPaw.02G091000' => 'cil', 'CiPaw.02G091100' => 'cil', 'CiPaw.08G103100' => 'cil', 'CiPaw.09G224900' => 'cil', 'ClCG06G005740' => 'cla', 'ClCG07G000090' => 'cla', 'ClCG07G000100' => 'cla', 'COL.COLO4_09143' => 'col', 'COL.COLO4_25124' => 'col', 'Cpa.g.sc16.34' => 'cpa', 'Cpa.g.sc3504.1' => 'cpa', 'Cpa.g.sc60.37' => 'cpa', 'CsaV3_6G018520' => 'csa', 'CsaV3_6G036860' => 'csa', 'CSS0001072' => 'camsi', 'CSS0020208' => 'camsi', 'CSS0021253' => 'camsi', 'CSS0022190' => 'camsi', 'CSS0036150' => 'camsi', 'CSS0040442' => 'camsi', 'CSS0042300' => 'camsi', 'CSS0045298' => 'camsi', 'DCAR_012449' => 'dca', 'DCAR_018405' => 'dca', 'DCAR_024573' => 'dca', 'DCAR_030591' => 'dca', 'Dinv16926' => 'din', 'Dinv32963' => 'din', 'Dinv38382' => 'din', 'Dinv38383' => 'din', 'Duzib133G0974' => 'dzi', 'Duzib138G1867' => 'dzi', 'Duzib211G0420' => 'dzi', 'Duzib212G0930' => 'dzi', 'ECA234G1645' => 'eca', 'ECA247G3467' => 'eca', 'ECA248G1703' => 'eca', 'EL10Ac3g06327' => 'bvu', 'EL10Ac7g17204' => 'bvu', 'Eucgr.A00855' => 'egr', 'Eucgr.A00858' => 'egr', 'Eucgr.H01520' => 'egr', 'Eucgr.H03604' => 'egr', 'Eucgr.L03465' => 'egr', 'Eucgr.L03466' => 'egr', 'FAN01G0988' => 'fan', 'FAN02G3892' => 'fan', 'FAN05G3381' => 'fan', 'FAN07G0967' => 'fan', 'FAN07G1493' => 'fan', 'FAN08G3125' => 'fan', 'FAN09G0402' => 'fan', 'FAN12G2594' => 'fan', 'FAN12G3879' => 'fan', 'FAN14G1546' => 'fan', 'FAN15G3626' => 'fan', 'FAN17G0588' => 'fan', 'FAN17G0609' => 'fan', 'FAN18G2817' => 'fan', 'FAN19G1305' => 'fan', 'FAN20G1787' => 'fan', 'FAN22G0073' => 'fan', 'FAN22G0352' => 'fan', 'FAN22G0368' => 'fan', 'FAN22G2273' => 'fan', 'FAN24G1998' => 'fan', 'FAN27G1317' => 'fan', 'FvH4_2g23980' => 'fve', 'FvH4_4g14380' => 'fve', 'FvH4_4g14390' => 'fve', 'FvH4_6g09250' => 'fve', 'Glyma.03G151100' => 'gma', 'Glyma.04G122550' => 'gma', 'Glyma.05G001600' => 'gma', 'Glyma.09G270766' => 'gma', 'Glyma.09G270832' => 'gma', 'Glyma.13G209800' => 'gma', 'Glyma.15G102800' => 'gma', 'Glyma.18G218900' => 'gma', 'Glyma.19G001500' => 'gma', 'Glyma.19G153600' => 'gma', 'Gohir.A02G028600' => 'ghi', 'Gohir.A08G045000' => 'ghi', 'Gohir.A11G120500' => 'ghi', 'Gohir.A12G006200' => 'ghi', 'Gohir.A12G006250' => 'ghi', 'Gohir.D02G036300' => 'ghi', 'Gohir.D08G054700' => 'ghi', 'Gohir.D11G125600' => 'ghi', 'Gohir.D12G005700' => 'ghi', 'Gorai.004G055200' => 'gra', 'Gorai.005G040400' => 'gra', 'Gorai.007G134500' => 'gra', 'Gorai.008G005500' => 'gra', 'GSVIVG01011094001' => 'vvi', 'GSVIVG01017879001' => 'vvi', 'GSVIVG01025988001' => 'vvi', 'GSVIVG01029847001' => 'vvi', 'HanXRQChr10g0282901' => 'han', 'HanXRQChr10g0310371' => 'han', 'HanXRQChr10g0315041' => 'han', 'HanXRQChr11g0327651' => 'han', 'HanXRQChr12g0359391' => 'han', 'Haze_00972' => 'cav', 'Haze_00973' => 'cav', 'Haze_00974' => 'cav', 'Haze_04747' => 'cav', 'Haze_04749' => 'cav', 'Haze_04750' => 'cav', 'Haze_21217' => 'cav', 'Hma1.2p1_1037F.1_g250680' => 'hma', 'Hma1.2p1_1644F.1_g295320' => 'hma', 'HPP92_011322' => 'vpl', 'HPP92_011323' => 'vpl', 'HPP92_011324' => 'vpl', 'HPP92_011325' => 'vpl', 'HPP92_011326' => 'vpl', 'Hund12205' => 'sun', 'Hund17957' => 'sun', 'Lalb_Chr06g0176771' => 'lal', 'Lalb_Chr18g0056021' => 'lal', 'Lalb_Chr18g0056031' => 'lal', 'Lalb_Chr18g0056041' => 'lal', 'Lalb_Chr20g0107751' => 'lal', 'Lalb_Chr20g0118371' => 'lal', 'Lj1g0010239' => 'lja', 'Lj1g0017101' => 'lja', 'Lj2A1178G40' => 'lonja', 'Lj2A54G84' => 'lonja', 'Lj2g0015248' => 'lja', 'Lj3A761T51' => 'lonja', 'Lj6g0018116' => 'lja', 'Lsat_1_v5_gn_4_136040' => 'lsa', 'Lsat_1_v5_gn_5_187461' => 'lsa', 'Lsat_1_v5_gn_5_77001' => 'lsa', 'Lsat_1_v5_gn_9_4461' => 'lsa', 'Manes.01G210100' => 'mes', 'Manes.03G185600' => 'mes', 'Manes.05G073300' => 'mes', 'Manes.09G120300' => 'mes', 'Manes.15G022100' => 'mes', 'Mapoly0096s0053' => 'mpo', 'MBI03_g14058_MAGBIO' => 'mbi', 'MBI03_g33876_MAGBIO' => 'mbi', 'MBI03_g36854_MAGBIO' => 'mbi', 'MBI17_g11997_MAGBIO' => 'mbi', 'MD03G1269000' => 'mdo', 'MD04G1179600' => 'mdo', 'MD11G1289800' => 'mdo', 'MD12G1194700' => 'mdo', 'MD13G1182100' => 'mdo', 'MD13G1182200' => 'mdo', 'MD16G1182600' => 'mdo', 'Medtr2g021400' => 'mtr', 'Medtr2g021470' => 'mtr', 'Medtr2g105810' => 'mtr', 'Medtr3g033580' => 'mtr', 'Medtr6g007970' => 'mtr', 'Medtr7g056330' => 'mtr', 'Medtr7g074290' => 'mtr', 'Medtr7g074380' => 'mtr', 'Medtr7g094550' => 'mtr', 'Medtr8g069995' => 'mtr', 'MELO3C014345.2' => 'cme', 'MELO3C021395.2' => 'cme', 'Migut.D00262' => 'egut', 'Migut.G00257' => 'egut', 'MSTRG.21575' => 'ama', 'MSTRG.3985' => 'ama', 'Nitab4.5_0000295g0140' => 'nta', 'Nitab4.5_0000732g0140' => 'nta', 'Nitab4.5_0003162g0020' => 'nta', 'Nitab4.5_0006180g0090' => 'nta', 'Nitab4.5_0006390g0010' => 'nta', 'Nitab4.5_0007392g0040' => 'nta', 'Nn1g02140' => 'nnu', 'Nn4g26168' => 'nnu', 'Nn5g26754' => 'nnu', 'Oeu001433.1' => 'oeu', 'Oeu010299.2' => 'oeu', 'Oeu011171.1' => 'oeu', 'Oeu037675.1' => 'oeu', 'Oeu038359.1' => 'oeu', 'Oeu063834.1' => 'oeu', 'Oeu063835.1' => 'oeu', 'Os05g0312000' => 'osa', 'Os07g0211101' => 'osa', 'Os07g0211200' => 'osa', 'Os07g0681500' => 'osa', 'Peaxi162Scf00095g01015' => 'pax', 'Peaxi162Scf00104g00329' => 'pax', 'Peaxi162Scf00161g00137' => 'pax', 'PGR004G1665' => 'pgr', 'PGR031G2937' => 'pgr', 'PGR119G2145' => 'pgr', 'PGSC0003DMG400004351' => 'stu', 'PGSC0003DMG400014625' => 'stu', 'PGSC0003DMG401000943' => 'stu', 'Phvul.001G148600' => 'pvu', 'Phvul.004G001700' => 'pvu', 'Phvul.006G154900' => 'pvu', 'Phvul.008G078200' => 'pvu', 'Phvul.011G136500' => 'pvu', 'Potri.002G215600' => 'ptr', 'Potri.008G201600' => 'ptr', 'Potri.014G138400' => 'ptr', 'Potri.016G142500' => 'ptr', 'Pp3c16_10580' => 'ppa', 'Pp3c5_25280' => 'ppa', 'Prupe.1G150000' => 'ppe', 'Prupe.1G150100' => 'ppe', 'Prupe.6G299600' => 'ppe', 'Prupe.8G245000' => 'ppe', 'Psat0s4927g0040' => 'psa', 'Psat1g052080' => 'psa', 'Psat1g183800' => 'psa', 'Psat3g113840' => 'psa', 'Psat3g126120' => 'psa', 'Psat3g126160' => 'psa', 'Psat3g158760' => 'psa', 'Psat3g158840' => 'psa', 'PSO170G2858' => 'pso', 'PSO339G0606' => 'pso', 'PSO384G4709' => 'pso', 'PSO407G0334' => 'pso', 'QL04p040276' => 'qlo', 'QL06p005458' => 'qlo', 'QL06p005472' => 'qlo', 'QL07p030546' => 'qlo', 'QL07p031519' => 'qlo', 'QL09p050949' => 'qlo', 'QL09p050966' => 'qlo', 'QL09p051067' => 'qlo', 'QL12p022706' => 'qlo', 'RcHm_v2.0_Chr2g0119601' => 'rch', 'RcHm_v2.0_Chr3g0459591' => 'rch', 'RcHm_v2.0_Chr4g0418521' => 'rch', 'RcHm_v2.0_Chr4g0418531' => 'rch', 'RcHm_v2.0_Chr4g0418541' => 'rch', 'RcHm_v2.0_Chr6g0291641' => 'rch', 'Rhsim01G0086300' => 'rsi', 'Rhsim01G0276300' => 'rsi', 'Rhsim01G0276500' => 'rsi', 'Rhsim04G0207700' => 'rsi', 'Rhsim05G0234500' => 'rsi', 'Rhsim13G0022400' => 'rsi', 'Sabra02G0167900' => 'sbr', 'Sabra04G0158500' => 'sbr', 'Sabra08G0159800' => 'sbr', 'Sabra10G0011500' => 'sbr', 'Sabra14G0104400' => 'sbr', 'SalBow2G2440' => 'sbo', 'SalBow4G2265' => 'sbo', 'Sc02g0000060' => 'sci', 'Sc05g0005020' => 'sci', 'Sc13g0003890' => 'sci', 'Sed0014865' => 'sed', 'Sed0017224' => 'sed', 'Sed0026391' => 'sed', 'SEGI_00063' => 'sgi', 'SEGI_10967' => 'sgi', 'SEGI_17510' => 'sgi', 'SEGI_24396' => 'sgi', 'SEGI_39719' => 'sgi', 'SEGI_41392' => 'sgi', 'SGA_v2.0_scaffold11G05794' => 'sas', 'SGA_v2.0_scaffold142G35607' => 'sas', 'SGA_v2.0_scaffold1G00447' => 'sas', 'SHI15388' => 'shi', 'SHI15394' => 'shi', 'SHI15396' => 'shi', 'SHI15399' => 'shi', 'SMO343G0151' => 'smo', 'SMO367G1118' => 'smo', 'Solyc01g080200.3' => 'sly', 'Solyc06g008960.3' => 'sly', 'Solyc09g064780.3' => 'sly', 'Sopen01g031980' => 'spe', 'Sopen06g003710' => 'spe', 'Sopen09g026460' => 'spe', 'Sp3g21240' => 'spa', 'Sp4g30030' => 'spa', 'TAR365G0022' => 'tar', 'TAR365G1023' => 'tar', 'TAR365G1253' => 'tar', 'TAR623G0078' => 'tar', 'TAR623G1721' => 'tar', 'TAR633G0959' => 'tar', 'THA.LOC104802225' => 'tha', 'THA.LOC104804769' => 'tha', 'THA.LOC104808660' => 'tha', 'THA.LOC104812792' => 'tha', 'Thecc.01G284000' => 'tca', 'Thecc.04G220600' => 'tca', 'Thecc.05G268900' => 'tca', 'Thecc.08G171100' => 'tca', 'Thhalv10001284m.g' => 'esa', 'Thhalv10019912m.g' => 'esa', 'TPR.G14189' => 'tpr', 'TPR.G18110' => 'tpr', 'TPR.G18130' => 'tpr', 'TPR.G18131' => 'tpr', 'TPR.G18140' => 'tpr', 'TPR.G24282' => 'tpr', 'TPR.G25221' => 'tpr', 'TPR.G29267' => 'tpr', 'TPR.G35315' => 'tpr', 'TPR.G36173' => 'tpr', 'TWI09G0794' => 'twi', 'TWI59G1348' => 'twi', 'TWI74G0430' => 'twi', 'unitig_26.g8940' => 'ugi', 'unitig_749.g13744' => 'ugi', 'unitig_749.g13745' => 'ugi', 'vmacro08269' => 'vma', 'vmacro14937' => 'vma', 'vmacro20401' => 'vma', 'VMungo0464G1349' => 'vmu', 'VMungo0540G0289' => 'vmu', 'VMungo1215G1590' => 'vmu', 'VMungo1309G0221' => 'vmu', 'VMungo1309G2815' => 'vmu', 'VMungo1383G0239' => 'vmu', 'VMungo1383G2910' => 'vmu', 'Zm00001eb095270' => 'zma', 'Zm00001eb095280' => 'zma', 'Zm00001eb111630' => 'zma', 'Zm00001eb237080' => 'zma', 'Zm00001eb273740' => 'zma', 'Zm00001eb285040' => 'zma', 'Zm00001eb330790' => 'zma', 'Zm00001eb337380' => 'zma' ) $gf_id = 'HOM05D001484' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001484' ) $data_identifier = 'HOM05D001484' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 2, 'aly' => (int) 2, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 22, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 7, 'hma' => (int) 2, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 7, 'mtr' => (int) 10, 'cme' => (int) 2, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 4, 'ppa' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 4, 'qlo' => (int) 9, 'rch' => (int) 6, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 10, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 7, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb337380' $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' => 'HOM05D001484', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p31500' => 'bna', 'A05p00020' => 'bna', 'A07p08820' => 'bna', 'Aa31LG4G3300' => 'aar', 'Aa31LG8G10030' => 'aar', 'Actinidia00731' => 'ach', 'Actinidia11473' => 'ach', 'Actinidia23469' => 'ach', 'Actinidia24318' => 'ach', 'Actinidia40196' => 'ach', 'Actinidia40197' => 'ach', 'Actinidia40198' => 'ach', 'Ah.08g212990' => 'amhyb', 'Ah.15g091720' => 'amhyb', 'AL3G38260' => 'aly', 'AL4G47710' => 'aly', 'Aqoxy2G00671' => 'aox', 'Aqoxy2G03236' => 'aox', 'arahy.Tifrunner.gnm1.ann1.05IDCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KR684' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATY3SJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK6QJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6APGL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IDT7Z9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM073U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ0R87' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LE7RV4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT4QRX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V5ENPK' => 'arhy', 'AT2G48110' => 'ath', 'AT3G23590' => 'ath', 'ATR0626G186' => 'atr', 'ATR1127G141' => 'atr', 'Atru.chr4.2583' => 'acertr', 'Atru.chr5.1358' => 'acertr', 'Atru.chr5.1359' => 'acertr', 'Atru.chr8.46' => 'acertr', 'AUR62002640' => 'cqu', 'AUR62030055' => 'cqu', 'AUR62033713' => 'cqu', 'AUR62033714' => 'cqu', 'AUR62036795' => 'cqu', 'AUR62039891' => 'cqu', 'BcaB02g08737' => 'bca', 'BcaB04g20441' => 'bca', 'BcaB06g26509' => 'bca', 'BcaB06g26510' => 'bca', 'BcaB06g26511' => 'bca', 'BcaB06g26512' => 'bca', 'BcaB06g26513' => 'bca', 'BcaC02g12564' => 'bca', 'BcaC02g12565' => 'bca', 'BcaC02g12794' => 'bca', 'BcaC02g12795' => 'bca', 'BcaC02g12796' => 'bca', 'BcaC06g35541' => 'bca', 'BNapus_Darmor_BZH_scaffold_188p00080' => 'bna', 'BNapus_Darmor_BZH_scaffold_188p00090' => 'bna', 'BolC1t03972H' => 'bol', 'BolC1t03973H' => 'bol', 'BolC4t21680H' => 'bol', 'BolC7t41863H' => 'bol', 'BolSC55t61227H' => 'bol', 'BolSC55t61228H' => 'bol', 'BraA01t03278Z' => 'bra', 'BraA05t18998Z' => 'bra', 'BraA07t28673Z' => 'bra', 'C01p40150' => 'bna', 'C05p12370' => 'bna', 'C07p13680' => 'bna', 'CAN.G1006.16' => 'can', 'CAN.G1006.17' => 'can', 'CAN.G1170.2' => 'can', 'CAN.G962.7' => 'can', 'CANSAT25G2179' => 'cansat', 'CANSAT78G1573' => 'cansat', 'CARHR099510' => 'chi', 'CARHR143510' => 'chi', 'Carub.0003s2380' => 'cru', 'Carub.0004s3082' => 'cru', 'Ca_00614_v3' => 'car', 'Ca_07801_v3' => 'car', 'Ca_08567_v3' => 'car', 'Ca_09571_v3' => 'car', 'CBR_g19290' => 'cbr', 'Cc01_g19770' => 'ccan', 'Cc03_g03030' => 'ccan', 'CDE07G0968' => 'cde', 'CDE09G1441' => 'cde', 'Cfa006103' => 'cfa', 'Cfa015573' => 'cfa', 'Cfa016988' => 'cfa', 'Ciclev10006738m.g' => 'ccl', 'Ciclev10010920m.g' => 'ccl', 'Ciclev10018517m.g' => 'ccl', 'CiPaw.01G159200' => 'cil', 'CiPaw.02G091000' => 'cil', 'CiPaw.02G091100' => 'cil', 'CiPaw.08G103100' => 'cil', 'CiPaw.09G224900' => 'cil', 'ClCG06G005740' => 'cla', 'ClCG07G000090' => 'cla', 'ClCG07G000100' => 'cla', 'COL.COLO4_09143' => 'col', 'COL.COLO4_25124' => 'col', 'Cpa.g.sc16.34' => 'cpa', 'Cpa.g.sc3504.1' => 'cpa', 'Cpa.g.sc60.37' => 'cpa', 'CsaV3_6G018520' => 'csa', 'CsaV3_6G036860' => 'csa', 'CSS0001072' => 'camsi', 'CSS0020208' => 'camsi', 'CSS0021253' => 'camsi', 'CSS0022190' => 'camsi', 'CSS0036150' => 'camsi', 'CSS0040442' => 'camsi', 'CSS0042300' => 'camsi', 'CSS0045298' => 'camsi', 'DCAR_012449' => 'dca', 'DCAR_018405' => 'dca', 'DCAR_024573' => 'dca', 'DCAR_030591' => 'dca', 'Dinv16926' => 'din', 'Dinv32963' => 'din', 'Dinv38382' => 'din', 'Dinv38383' => 'din', 'Duzib133G0974' => 'dzi', 'Duzib138G1867' => 'dzi', 'Duzib211G0420' => 'dzi', 'Duzib212G0930' => 'dzi', 'ECA234G1645' => 'eca', 'ECA247G3467' => 'eca', 'ECA248G1703' => 'eca', 'EL10Ac3g06327' => 'bvu', 'EL10Ac7g17204' => 'bvu', 'Eucgr.A00855' => 'egr', 'Eucgr.A00858' => 'egr', 'Eucgr.H01520' => 'egr', 'Eucgr.H03604' => 'egr', 'Eucgr.L03465' => 'egr', 'Eucgr.L03466' => 'egr', 'FAN01G0988' => 'fan', 'FAN02G3892' => 'fan', 'FAN05G3381' => 'fan', 'FAN07G0967' => 'fan', 'FAN07G1493' => 'fan', 'FAN08G3125' => 'fan', 'FAN09G0402' => 'fan', 'FAN12G2594' => 'fan', 'FAN12G3879' => 'fan', 'FAN14G1546' => 'fan', 'FAN15G3626' => 'fan', 'FAN17G0588' => 'fan', 'FAN17G0609' => 'fan', 'FAN18G2817' => 'fan', 'FAN19G1305' => 'fan', 'FAN20G1787' => 'fan', 'FAN22G0073' => 'fan', 'FAN22G0352' => 'fan', 'FAN22G0368' => 'fan', 'FAN22G2273' => 'fan', 'FAN24G1998' => 'fan', 'FAN27G1317' => 'fan', 'FvH4_2g23980' => 'fve', 'FvH4_4g14380' => 'fve', 'FvH4_4g14390' => 'fve', 'FvH4_6g09250' => 'fve', 'Glyma.03G151100' => 'gma', 'Glyma.04G122550' => 'gma', 'Glyma.05G001600' => 'gma', 'Glyma.09G270766' => 'gma', 'Glyma.09G270832' => 'gma', 'Glyma.13G209800' => 'gma', 'Glyma.15G102800' => 'gma', 'Glyma.18G218900' => 'gma', 'Glyma.19G001500' => 'gma', 'Glyma.19G153600' => 'gma', 'Gohir.A02G028600' => 'ghi', 'Gohir.A08G045000' => 'ghi', 'Gohir.A11G120500' => 'ghi', 'Gohir.A12G006200' => 'ghi', 'Gohir.A12G006250' => 'ghi', 'Gohir.D02G036300' => 'ghi', 'Gohir.D08G054700' => 'ghi', 'Gohir.D11G125600' => 'ghi', 'Gohir.D12G005700' => 'ghi', 'Gorai.004G055200' => 'gra', 'Gorai.005G040400' => 'gra', 'Gorai.007G134500' => 'gra', 'Gorai.008G005500' => 'gra', 'GSVIVG01011094001' => 'vvi', 'GSVIVG01017879001' => 'vvi', 'GSVIVG01025988001' => 'vvi', 'GSVIVG01029847001' => 'vvi', 'HanXRQChr10g0282901' => 'han', 'HanXRQChr10g0310371' => 'han', 'HanXRQChr10g0315041' => 'han', 'HanXRQChr11g0327651' => 'han', 'HanXRQChr12g0359391' => 'han', 'Haze_00972' => 'cav', 'Haze_00973' => 'cav', 'Haze_00974' => 'cav', 'Haze_04747' => 'cav', 'Haze_04749' => 'cav', 'Haze_04750' => 'cav', 'Haze_21217' => 'cav', 'Hma1.2p1_1037F.1_g250680' => 'hma', 'Hma1.2p1_1644F.1_g295320' => 'hma', 'HPP92_011322' => 'vpl', 'HPP92_011323' => 'vpl', 'HPP92_011324' => 'vpl', 'HPP92_011325' => 'vpl', 'HPP92_011326' => 'vpl', 'Hund12205' => 'sun', 'Hund17957' => 'sun', 'Lalb_Chr06g0176771' => 'lal', 'Lalb_Chr18g0056021' => 'lal', 'Lalb_Chr18g0056031' => 'lal', 'Lalb_Chr18g0056041' => 'lal', 'Lalb_Chr20g0107751' => 'lal', 'Lalb_Chr20g0118371' => 'lal', 'Lj1g0010239' => 'lja', 'Lj1g0017101' => 'lja', 'Lj2A1178G40' => 'lonja', 'Lj2A54G84' => 'lonja', 'Lj2g0015248' => 'lja', 'Lj3A761T51' => 'lonja', 'Lj6g0018116' => 'lja', 'Lsat_1_v5_gn_4_136040' => 'lsa', 'Lsat_1_v5_gn_5_187461' => 'lsa', 'Lsat_1_v5_gn_5_77001' => 'lsa', 'Lsat_1_v5_gn_9_4461' => 'lsa', 'Manes.01G210100' => 'mes', 'Manes.03G185600' => 'mes', 'Manes.05G073300' => 'mes', 'Manes.09G120300' => 'mes', 'Manes.15G022100' => 'mes', 'Mapoly0096s0053' => 'mpo', 'MBI03_g14058_MAGBIO' => 'mbi', 'MBI03_g33876_MAGBIO' => 'mbi', 'MBI03_g36854_MAGBIO' => 'mbi', 'MBI17_g11997_MAGBIO' => 'mbi', 'MD03G1269000' => 'mdo', 'MD04G1179600' => 'mdo', 'MD11G1289800' => 'mdo', 'MD12G1194700' => 'mdo', 'MD13G1182100' => 'mdo', 'MD13G1182200' => 'mdo', 'MD16G1182600' => 'mdo', 'Medtr2g021400' => 'mtr', 'Medtr2g021470' => 'mtr', 'Medtr2g105810' => 'mtr', 'Medtr3g033580' => 'mtr', 'Medtr6g007970' => 'mtr', 'Medtr7g056330' => 'mtr', 'Medtr7g074290' => 'mtr', 'Medtr7g074380' => 'mtr', 'Medtr7g094550' => 'mtr', 'Medtr8g069995' => 'mtr', 'MELO3C014345.2' => 'cme', 'MELO3C021395.2' => 'cme', 'Migut.D00262' => 'egut', 'Migut.G00257' => 'egut', 'MSTRG.21575' => 'ama', 'MSTRG.3985' => 'ama', 'Nitab4.5_0000295g0140' => 'nta', 'Nitab4.5_0000732g0140' => 'nta', 'Nitab4.5_0003162g0020' => 'nta', 'Nitab4.5_0006180g0090' => 'nta', 'Nitab4.5_0006390g0010' => 'nta', 'Nitab4.5_0007392g0040' => 'nta', 'Nn1g02140' => 'nnu', 'Nn4g26168' => 'nnu', 'Nn5g26754' => 'nnu', 'Oeu001433.1' => 'oeu', 'Oeu010299.2' => 'oeu', 'Oeu011171.1' => 'oeu', 'Oeu037675.1' => 'oeu', 'Oeu038359.1' => 'oeu', 'Oeu063834.1' => 'oeu', 'Oeu063835.1' => 'oeu', 'Os05g0312000' => 'osa', 'Os07g0211101' => 'osa', 'Os07g0211200' => 'osa', 'Os07g0681500' => 'osa', 'Peaxi162Scf00095g01015' => 'pax', 'Peaxi162Scf00104g00329' => 'pax', 'Peaxi162Scf00161g00137' => 'pax', 'PGR004G1665' => 'pgr', 'PGR031G2937' => 'pgr', 'PGR119G2145' => 'pgr', 'PGSC0003DMG400004351' => 'stu', 'PGSC0003DMG400014625' => 'stu', 'PGSC0003DMG401000943' => 'stu', 'Phvul.001G148600' => 'pvu', 'Phvul.004G001700' => 'pvu', 'Phvul.006G154900' => 'pvu', 'Phvul.008G078200' => 'pvu', 'Phvul.011G136500' => 'pvu', 'Potri.002G215600' => 'ptr', 'Potri.008G201600' => 'ptr', 'Potri.014G138400' => 'ptr', 'Potri.016G142500' => 'ptr', 'Pp3c16_10580' => 'ppa', 'Pp3c5_25280' => 'ppa', 'Prupe.1G150000' => 'ppe', 'Prupe.1G150100' => 'ppe', 'Prupe.6G299600' => 'ppe', 'Prupe.8G245000' => 'ppe', 'Psat0s4927g0040' => 'psa', 'Psat1g052080' => 'psa', 'Psat1g183800' => 'psa', 'Psat3g113840' => 'psa', 'Psat3g126120' => 'psa', 'Psat3g126160' => 'psa', 'Psat3g158760' => 'psa', 'Psat3g158840' => 'psa', 'PSO170G2858' => 'pso', 'PSO339G0606' => 'pso', 'PSO384G4709' => 'pso', 'PSO407G0334' => 'pso', 'QL04p040276' => 'qlo', 'QL06p005458' => 'qlo', 'QL06p005472' => 'qlo', 'QL07p030546' => 'qlo', 'QL07p031519' => 'qlo', 'QL09p050949' => 'qlo', 'QL09p050966' => 'qlo', 'QL09p051067' => 'qlo', 'QL12p022706' => 'qlo', 'RcHm_v2.0_Chr2g0119601' => 'rch', 'RcHm_v2.0_Chr3g0459591' => 'rch', 'RcHm_v2.0_Chr4g0418521' => 'rch', 'RcHm_v2.0_Chr4g0418531' => 'rch', 'RcHm_v2.0_Chr4g0418541' => 'rch', 'RcHm_v2.0_Chr6g0291641' => 'rch', 'Rhsim01G0086300' => 'rsi', 'Rhsim01G0276300' => 'rsi', 'Rhsim01G0276500' => 'rsi', 'Rhsim04G0207700' => 'rsi', 'Rhsim05G0234500' => 'rsi', 'Rhsim13G0022400' => 'rsi', 'Sabra02G0167900' => 'sbr', 'Sabra04G0158500' => 'sbr', 'Sabra08G0159800' => 'sbr', 'Sabra10G0011500' => 'sbr', 'Sabra14G0104400' => 'sbr', 'SalBow2G2440' => 'sbo', 'SalBow4G2265' => 'sbo', 'Sc02g0000060' => 'sci', 'Sc05g0005020' => 'sci', 'Sc13g0003890' => 'sci', 'Sed0014865' => 'sed', 'Sed0017224' => 'sed', 'Sed0026391' => 'sed', 'SEGI_00063' => 'sgi', 'SEGI_10967' => 'sgi', 'SEGI_17510' => 'sgi', 'SEGI_24396' => 'sgi', 'SEGI_39719' => 'sgi', 'SEGI_41392' => 'sgi', 'SGA_v2.0_scaffold11G05794' => 'sas', 'SGA_v2.0_scaffold142G35607' => 'sas', 'SGA_v2.0_scaffold1G00447' => 'sas', 'SHI15388' => 'shi', 'SHI15394' => 'shi', 'SHI15396' => 'shi', 'SHI15399' => 'shi', 'SMO343G0151' => 'smo', 'SMO367G1118' => 'smo', 'Solyc01g080200.3' => 'sly', 'Solyc06g008960.3' => 'sly', 'Solyc09g064780.3' => 'sly', 'Sopen01g031980' => 'spe', 'Sopen06g003710' => 'spe', 'Sopen09g026460' => 'spe', 'Sp3g21240' => 'spa', 'Sp4g30030' => 'spa', 'TAR365G0022' => 'tar', 'TAR365G1023' => 'tar', 'TAR365G1253' => 'tar', 'TAR623G0078' => 'tar', 'TAR623G1721' => 'tar', 'TAR633G0959' => 'tar', 'THA.LOC104802225' => 'tha', 'THA.LOC104804769' => 'tha', 'THA.LOC104808660' => 'tha', 'THA.LOC104812792' => 'tha', 'Thecc.01G284000' => 'tca', 'Thecc.04G220600' => 'tca', 'Thecc.05G268900' => 'tca', 'Thecc.08G171100' => 'tca', 'Thhalv10001284m.g' => 'esa', 'Thhalv10019912m.g' => 'esa', 'TPR.G14189' => 'tpr', 'TPR.G18110' => 'tpr', 'TPR.G18130' => 'tpr', 'TPR.G18131' => 'tpr', 'TPR.G18140' => 'tpr', 'TPR.G24282' => 'tpr', 'TPR.G25221' => 'tpr', 'TPR.G29267' => 'tpr', 'TPR.G35315' => 'tpr', 'TPR.G36173' => 'tpr', 'TWI09G0794' => 'twi', 'TWI59G1348' => 'twi', 'TWI74G0430' => 'twi', 'unitig_26.g8940' => 'ugi', 'unitig_749.g13744' => 'ugi', 'unitig_749.g13745' => 'ugi', 'vmacro08269' => 'vma', 'vmacro14937' => 'vma', 'vmacro20401' => 'vma', 'VMungo0464G1349' => 'vmu', 'VMungo0540G0289' => 'vmu', 'VMungo1215G1590' => 'vmu', 'VMungo1309G0221' => 'vmu', 'VMungo1309G2815' => 'vmu', 'VMungo1383G0239' => 'vmu', 'VMungo1383G2910' => 'vmu', 'Zm00001eb095270' => 'zma', 'Zm00001eb095280' => 'zma', 'Zm00001eb111630' => 'zma', 'Zm00001eb237080' => 'zma', 'Zm00001eb273740' => 'zma', 'Zm00001eb285040' => 'zma', 'Zm00001eb330790' => 'zma', 'Zm00001eb337380' => 'zma' ), 'gf_id' => 'HOM05D001484', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001484' ), 'data_identifier' => 'HOM05D001484', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001484', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p31500' => 'bna', 'A05p00020' => 'bna', 'A07p08820' => 'bna', 'Aa31LG4G3300' => 'aar', 'Aa31LG8G10030' => 'aar', 'Actinidia00731' => 'ach', 'Actinidia11473' => 'ach', 'Actinidia23469' => 'ach', 'Actinidia24318' => 'ach', 'Actinidia40196' => 'ach', 'Actinidia40197' => 'ach', 'Actinidia40198' => 'ach', 'Ah.08g212990' => 'amhyb', 'Ah.15g091720' => 'amhyb', 'AL3G38260' => 'aly', 'AL4G47710' => 'aly', 'Aqoxy2G00671' => 'aox', 'Aqoxy2G03236' => 'aox', 'arahy.Tifrunner.gnm1.ann1.05IDCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KR684' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATY3SJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK6QJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6APGL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IDT7Z9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM073U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ0R87' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LE7RV4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT4QRX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V5ENPK' => 'arhy', 'AT2G48110' => 'ath', 'AT3G23590' => 'ath', 'ATR0626G186' => 'atr', 'ATR1127G141' => 'atr', 'Atru.chr4.2583' => 'acertr', 'Atru.chr5.1358' => 'acertr', 'Atru.chr5.1359' => 'acertr', 'Atru.chr8.46' => 'acertr', 'AUR62002640' => 'cqu', 'AUR62030055' => 'cqu', 'AUR62033713' => 'cqu', 'AUR62033714' => 'cqu', 'AUR62036795' => 'cqu', 'AUR62039891' => 'cqu', 'BcaB02g08737' => 'bca', 'BcaB04g20441' => 'bca', 'BcaB06g26509' => 'bca', 'BcaB06g26510' => 'bca', 'BcaB06g26511' => 'bca', 'BcaB06g26512' => 'bca', 'BcaB06g26513' => 'bca', 'BcaC02g12564' => 'bca', 'BcaC02g12565' => 'bca', 'BcaC02g12794' => 'bca', 'BcaC02g12795' => 'bca', 'BcaC02g12796' => 'bca', 'BcaC06g35541' => 'bca', 'BNapus_Darmor_BZH_scaffold_188p00080' => 'bna', 'BNapus_Darmor_BZH_scaffold_188p00090' => 'bna', 'BolC1t03972H' => 'bol', 'BolC1t03973H' => 'bol', 'BolC4t21680H' => 'bol', 'BolC7t41863H' => 'bol', 'BolSC55t61227H' => 'bol', 'BolSC55t61228H' => 'bol', 'BraA01t03278Z' => 'bra', 'BraA05t18998Z' => 'bra', 'BraA07t28673Z' => 'bra', 'C01p40150' => 'bna', 'C05p12370' => 'bna', 'C07p13680' => 'bna', 'CAN.G1006.16' => 'can', 'CAN.G1006.17' => 'can', 'CAN.G1170.2' => 'can', 'CAN.G962.7' => 'can', 'CANSAT25G2179' => 'cansat', 'CANSAT78G1573' => 'cansat', 'CARHR099510' => 'chi', 'CARHR143510' => 'chi', 'Carub.0003s2380' => 'cru', 'Carub.0004s3082' => 'cru', 'Ca_00614_v3' => 'car', 'Ca_07801_v3' => 'car', 'Ca_08567_v3' => 'car', 'Ca_09571_v3' => 'car', 'CBR_g19290' => 'cbr', 'Cc01_g19770' => 'ccan', 'Cc03_g03030' => 'ccan', 'CDE07G0968' => 'cde', 'CDE09G1441' => 'cde', 'Cfa006103' => 'cfa', 'Cfa015573' => 'cfa', 'Cfa016988' => 'cfa', 'Ciclev10006738m.g' => 'ccl', 'Ciclev10010920m.g' => 'ccl', 'Ciclev10018517m.g' => 'ccl', 'CiPaw.01G159200' => 'cil', 'CiPaw.02G091000' => 'cil', 'CiPaw.02G091100' => 'cil', 'CiPaw.08G103100' => 'cil', 'CiPaw.09G224900' => 'cil', 'ClCG06G005740' => 'cla', 'ClCG07G000090' => 'cla', 'ClCG07G000100' => 'cla', 'COL.COLO4_09143' => 'col', 'COL.COLO4_25124' => 'col', 'Cpa.g.sc16.34' => 'cpa', 'Cpa.g.sc3504.1' => 'cpa', 'Cpa.g.sc60.37' => 'cpa', 'CsaV3_6G018520' => 'csa', 'CsaV3_6G036860' => 'csa', 'CSS0001072' => 'camsi', 'CSS0020208' => 'camsi', 'CSS0021253' => 'camsi', 'CSS0022190' => 'camsi', 'CSS0036150' => 'camsi', 'CSS0040442' => 'camsi', 'CSS0042300' => 'camsi', 'CSS0045298' => 'camsi', 'DCAR_012449' => 'dca', 'DCAR_018405' => 'dca', 'DCAR_024573' => 'dca', 'DCAR_030591' => 'dca', 'Dinv16926' => 'din', 'Dinv32963' => 'din', 'Dinv38382' => 'din', 'Dinv38383' => 'din', 'Duzib133G0974' => 'dzi', 'Duzib138G1867' => 'dzi', 'Duzib211G0420' => 'dzi', 'Duzib212G0930' => 'dzi', 'ECA234G1645' => 'eca', 'ECA247G3467' => 'eca', 'ECA248G1703' => 'eca', 'EL10Ac3g06327' => 'bvu', 'EL10Ac7g17204' => 'bvu', 'Eucgr.A00855' => 'egr', 'Eucgr.A00858' => 'egr', 'Eucgr.H01520' => 'egr', 'Eucgr.H03604' => 'egr', 'Eucgr.L03465' => 'egr', 'Eucgr.L03466' => 'egr', 'FAN01G0988' => 'fan', 'FAN02G3892' => 'fan', 'FAN05G3381' => 'fan', 'FAN07G0967' => 'fan', 'FAN07G1493' => 'fan', 'FAN08G3125' => 'fan', 'FAN09G0402' => 'fan', 'FAN12G2594' => 'fan', 'FAN12G3879' => 'fan', 'FAN14G1546' => 'fan', 'FAN15G3626' => 'fan', 'FAN17G0588' => 'fan', 'FAN17G0609' => 'fan', 'FAN18G2817' => 'fan', 'FAN19G1305' => 'fan', 'FAN20G1787' => 'fan', 'FAN22G0073' => 'fan', 'FAN22G0352' => 'fan', 'FAN22G0368' => 'fan', 'FAN22G2273' => 'fan', 'FAN24G1998' => 'fan', 'FAN27G1317' => 'fan', 'FvH4_2g23980' => 'fve', 'FvH4_4g14380' => 'fve', 'FvH4_4g14390' => 'fve', 'FvH4_6g09250' => 'fve', 'Glyma.03G151100' => 'gma', 'Glyma.04G122550' => 'gma', 'Glyma.05G001600' => 'gma', 'Glyma.09G270766' => 'gma', 'Glyma.09G270832' => 'gma', 'Glyma.13G209800' => 'gma', 'Glyma.15G102800' => 'gma', 'Glyma.18G218900' => 'gma', 'Glyma.19G001500' => 'gma', 'Glyma.19G153600' => 'gma', 'Gohir.A02G028600' => 'ghi', 'Gohir.A08G045000' => 'ghi', 'Gohir.A11G120500' => 'ghi', 'Gohir.A12G006200' => 'ghi', 'Gohir.A12G006250' => 'ghi', 'Gohir.D02G036300' => 'ghi', 'Gohir.D08G054700' => 'ghi', 'Gohir.D11G125600' => 'ghi', 'Gohir.D12G005700' => 'ghi', 'Gorai.004G055200' => 'gra', 'Gorai.005G040400' => 'gra', 'Gorai.007G134500' => 'gra', 'Gorai.008G005500' => 'gra', 'GSVIVG01011094001' => 'vvi', 'GSVIVG01017879001' => 'vvi', 'GSVIVG01025988001' => 'vvi', 'GSVIVG01029847001' => 'vvi', 'HanXRQChr10g0282901' => 'han', 'HanXRQChr10g0310371' => 'han', 'HanXRQChr10g0315041' => 'han', 'HanXRQChr11g0327651' => 'han', 'HanXRQChr12g0359391' => 'han', 'Haze_00972' => 'cav', 'Haze_00973' => 'cav', 'Haze_00974' => 'cav', 'Haze_04747' => 'cav', 'Haze_04749' => 'cav', 'Haze_04750' => 'cav', 'Haze_21217' => 'cav', 'Hma1.2p1_1037F.1_g250680' => 'hma', 'Hma1.2p1_1644F.1_g295320' => 'hma', 'HPP92_011322' => 'vpl', 'HPP92_011323' => 'vpl', 'HPP92_011324' => 'vpl', 'HPP92_011325' => 'vpl', 'HPP92_011326' => 'vpl', 'Hund12205' => 'sun', 'Hund17957' => 'sun', 'Lalb_Chr06g0176771' => 'lal', 'Lalb_Chr18g0056021' => 'lal', 'Lalb_Chr18g0056031' => 'lal', 'Lalb_Chr18g0056041' => 'lal', 'Lalb_Chr20g0107751' => 'lal', 'Lalb_Chr20g0118371' => 'lal', 'Lj1g0010239' => 'lja', 'Lj1g0017101' => 'lja', 'Lj2A1178G40' => 'lonja', 'Lj2A54G84' => 'lonja', 'Lj2g0015248' => 'lja', 'Lj3A761T51' => 'lonja', 'Lj6g0018116' => 'lja', 'Lsat_1_v5_gn_4_136040' => 'lsa', 'Lsat_1_v5_gn_5_187461' => 'lsa', 'Lsat_1_v5_gn_5_77001' => 'lsa', 'Lsat_1_v5_gn_9_4461' => 'lsa', 'Manes.01G210100' => 'mes', 'Manes.03G185600' => 'mes', 'Manes.05G073300' => 'mes', 'Manes.09G120300' => 'mes', 'Manes.15G022100' => 'mes', 'Mapoly0096s0053' => 'mpo', 'MBI03_g14058_MAGBIO' => 'mbi', 'MBI03_g33876_MAGBIO' => 'mbi', 'MBI03_g36854_MAGBIO' => 'mbi', 'MBI17_g11997_MAGBIO' => 'mbi', 'MD03G1269000' => 'mdo', 'MD04G1179600' => 'mdo', 'MD11G1289800' => 'mdo', 'MD12G1194700' => 'mdo', 'MD13G1182100' => 'mdo', 'MD13G1182200' => 'mdo', 'MD16G1182600' => 'mdo', 'Medtr2g021400' => 'mtr', 'Medtr2g021470' => 'mtr', 'Medtr2g105810' => 'mtr', 'Medtr3g033580' => 'mtr', 'Medtr6g007970' => 'mtr', 'Medtr7g056330' => 'mtr', 'Medtr7g074290' => 'mtr', 'Medtr7g074380' => 'mtr', 'Medtr7g094550' => 'mtr', 'Medtr8g069995' => 'mtr', 'MELO3C014345.2' => 'cme', 'MELO3C021395.2' => 'cme', 'Migut.D00262' => 'egut', 'Migut.G00257' => 'egut', 'MSTRG.21575' => 'ama', 'MSTRG.3985' => 'ama', 'Nitab4.5_0000295g0140' => 'nta', 'Nitab4.5_0000732g0140' => 'nta', 'Nitab4.5_0003162g0020' => 'nta', 'Nitab4.5_0006180g0090' => 'nta', 'Nitab4.5_0006390g0010' => 'nta', 'Nitab4.5_0007392g0040' => 'nta', 'Nn1g02140' => 'nnu', 'Nn4g26168' => 'nnu', 'Nn5g26754' => 'nnu', 'Oeu001433.1' => 'oeu', 'Oeu010299.2' => 'oeu', 'Oeu011171.1' => 'oeu', 'Oeu037675.1' => 'oeu', 'Oeu038359.1' => 'oeu', 'Oeu063834.1' => 'oeu', 'Oeu063835.1' => 'oeu', 'Os05g0312000' => 'osa', 'Os07g0211101' => 'osa', 'Os07g0211200' => 'osa', 'Os07g0681500' => 'osa', 'Peaxi162Scf00095g01015' => 'pax', 'Peaxi162Scf00104g00329' => 'pax', 'Peaxi162Scf00161g00137' => 'pax', 'PGR004G1665' => 'pgr', 'PGR031G2937' => 'pgr', 'PGR119G2145' => 'pgr', 'PGSC0003DMG400004351' => 'stu', 'PGSC0003DMG400014625' => 'stu', 'PGSC0003DMG401000943' => 'stu', 'Phvul.001G148600' => 'pvu', 'Phvul.004G001700' => 'pvu', 'Phvul.006G154900' => 'pvu', 'Phvul.008G078200' => 'pvu', 'Phvul.011G136500' => 'pvu', 'Potri.002G215600' => 'ptr', 'Potri.008G201600' => 'ptr', 'Potri.014G138400' => 'ptr', 'Potri.016G142500' => 'ptr', 'Pp3c16_10580' => 'ppa', 'Pp3c5_25280' => 'ppa', 'Prupe.1G150000' => 'ppe', 'Prupe.1G150100' => 'ppe', 'Prupe.6G299600' => 'ppe', 'Prupe.8G245000' => 'ppe', 'Psat0s4927g0040' => 'psa', 'Psat1g052080' => 'psa', 'Psat1g183800' => 'psa', 'Psat3g113840' => 'psa', 'Psat3g126120' => 'psa', 'Psat3g126160' => 'psa', 'Psat3g158760' => 'psa', 'Psat3g158840' => 'psa', 'PSO170G2858' => 'pso', 'PSO339G0606' => 'pso', 'PSO384G4709' => 'pso', 'PSO407G0334' => 'pso', 'QL04p040276' => 'qlo', 'QL06p005458' => 'qlo', 'QL06p005472' => 'qlo', 'QL07p030546' => 'qlo', 'QL07p031519' => 'qlo', 'QL09p050949' => 'qlo', 'QL09p050966' => 'qlo', 'QL09p051067' => 'qlo', 'QL12p022706' => 'qlo', 'RcHm_v2.0_Chr2g0119601' => 'rch', 'RcHm_v2.0_Chr3g0459591' => 'rch', 'RcHm_v2.0_Chr4g0418521' => 'rch', 'RcHm_v2.0_Chr4g0418531' => 'rch', 'RcHm_v2.0_Chr4g0418541' => 'rch', 'RcHm_v2.0_Chr6g0291641' => 'rch', 'Rhsim01G0086300' => 'rsi', 'Rhsim01G0276300' => 'rsi', 'Rhsim01G0276500' => 'rsi', 'Rhsim04G0207700' => 'rsi', 'Rhsim05G0234500' => 'rsi', 'Rhsim13G0022400' => 'rsi', 'Sabra02G0167900' => 'sbr', 'Sabra04G0158500' => 'sbr', 'Sabra08G0159800' => 'sbr', 'Sabra10G0011500' => 'sbr', 'Sabra14G0104400' => 'sbr', 'SalBow2G2440' => 'sbo', 'SalBow4G2265' => 'sbo', 'Sc02g0000060' => 'sci', 'Sc05g0005020' => 'sci', 'Sc13g0003890' => 'sci', 'Sed0014865' => 'sed', 'Sed0017224' => 'sed', 'Sed0026391' => 'sed', 'SEGI_00063' => 'sgi', 'SEGI_10967' => 'sgi', 'SEGI_17510' => 'sgi', 'SEGI_24396' => 'sgi', 'SEGI_39719' => 'sgi', 'SEGI_41392' => 'sgi', 'SGA_v2.0_scaffold11G05794' => 'sas', 'SGA_v2.0_scaffold142G35607' => 'sas', 'SGA_v2.0_scaffold1G00447' => 'sas', 'SHI15388' => 'shi', 'SHI15394' => 'shi', 'SHI15396' => 'shi', 'SHI15399' => 'shi', 'SMO343G0151' => 'smo', 'SMO367G1118' => 'smo', 'Solyc01g080200.3' => 'sly', 'Solyc06g008960.3' => 'sly', 'Solyc09g064780.3' => 'sly', 'Sopen01g031980' => 'spe', 'Sopen06g003710' => 'spe', 'Sopen09g026460' => 'spe', 'Sp3g21240' => 'spa', 'Sp4g30030' => 'spa', 'TAR365G0022' => 'tar', 'TAR365G1023' => 'tar', 'TAR365G1253' => 'tar', 'TAR623G0078' => 'tar', 'TAR623G1721' => 'tar', 'TAR633G0959' => 'tar', 'THA.LOC104802225' => 'tha', 'THA.LOC104804769' => 'tha', 'THA.LOC104808660' => 'tha', 'THA.LOC104812792' => 'tha', 'Thecc.01G284000' => 'tca', 'Thecc.04G220600' => 'tca', 'Thecc.05G268900' => 'tca', 'Thecc.08G171100' => 'tca', 'Thhalv10001284m.g' => 'esa', 'Thhalv10019912m.g' => 'esa', 'TPR.G14189' => 'tpr', 'TPR.G18110' => 'tpr', 'TPR.G18130' => 'tpr', 'TPR.G18131' => 'tpr', 'TPR.G18140' => 'tpr', 'TPR.G24282' => 'tpr', 'TPR.G25221' => 'tpr', 'TPR.G29267' => 'tpr', 'TPR.G35315' => 'tpr', 'TPR.G36173' => 'tpr', 'TWI09G0794' => 'twi', 'TWI59G1348' => 'twi', 'TWI74G0430' => 'twi', 'unitig_26.g8940' => 'ugi', 'unitig_749.g13744' => 'ugi', 'unitig_749.g13745' => 'ugi', 'vmacro08269' => 'vma', 'vmacro14937' => 'vma', 'vmacro20401' => 'vma', 'VMungo0464G1349' => 'vmu', 'VMungo0540G0289' => 'vmu', 'VMungo1215G1590' => 'vmu', 'VMungo1309G0221' => 'vmu', 'VMungo1309G2815' => 'vmu', 'VMungo1383G0239' => 'vmu', 'VMungo1383G2910' => 'vmu', 'Zm00001eb095270' => 'zma', 'Zm00001eb095280' => 'zma', 'Zm00001eb111630' => 'zma', 'Zm00001eb237080' => 'zma', 'Zm00001eb273740' => 'zma', 'Zm00001eb285040' => 'zma', 'Zm00001eb330790' => 'zma', 'Zm00001eb337380' => 'zma' ) $gf_id = 'HOM05D001484' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001484' ) $data_identifier = 'HOM05D001484' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 2, 'aly' => (int) 2, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 22, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 7, 'hma' => (int) 2, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 7, 'mtr' => (int) 10, 'cme' => (int) 2, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 4, 'ppa' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 4, 'qlo' => (int) 9, 'rch' => (int) 6, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 10, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 7, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb337380' $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' => 'HOM05D001484', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p31500' => 'bna', 'A05p00020' => 'bna', 'A07p08820' => 'bna', 'Aa31LG4G3300' => 'aar', 'Aa31LG8G10030' => 'aar', 'Actinidia00731' => 'ach', 'Actinidia11473' => 'ach', 'Actinidia23469' => 'ach', 'Actinidia24318' => 'ach', 'Actinidia40196' => 'ach', 'Actinidia40197' => 'ach', 'Actinidia40198' => 'ach', 'Ah.08g212990' => 'amhyb', 'Ah.15g091720' => 'amhyb', 'AL3G38260' => 'aly', 'AL4G47710' => 'aly', 'Aqoxy2G00671' => 'aox', 'Aqoxy2G03236' => 'aox', 'arahy.Tifrunner.gnm1.ann1.05IDCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KR684' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATY3SJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK6QJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6APGL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IDT7Z9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM073U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ0R87' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LE7RV4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT4QRX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V5ENPK' => 'arhy', 'AT2G48110' => 'ath', 'AT3G23590' => 'ath', 'ATR0626G186' => 'atr', 'ATR1127G141' => 'atr', 'Atru.chr4.2583' => 'acertr', 'Atru.chr5.1358' => 'acertr', 'Atru.chr5.1359' => 'acertr', 'Atru.chr8.46' => 'acertr', 'AUR62002640' => 'cqu', 'AUR62030055' => 'cqu', 'AUR62033713' => 'cqu', 'AUR62033714' => 'cqu', 'AUR62036795' => 'cqu', 'AUR62039891' => 'cqu', 'BcaB02g08737' => 'bca', 'BcaB04g20441' => 'bca', 'BcaB06g26509' => 'bca', 'BcaB06g26510' => 'bca', 'BcaB06g26511' => 'bca', 'BcaB06g26512' => 'bca', 'BcaB06g26513' => 'bca', 'BcaC02g12564' => 'bca', 'BcaC02g12565' => 'bca', 'BcaC02g12794' => 'bca', 'BcaC02g12795' => 'bca', 'BcaC02g12796' => 'bca', 'BcaC06g35541' => 'bca', 'BNapus_Darmor_BZH_scaffold_188p00080' => 'bna', 'BNapus_Darmor_BZH_scaffold_188p00090' => 'bna', 'BolC1t03972H' => 'bol', 'BolC1t03973H' => 'bol', 'BolC4t21680H' => 'bol', 'BolC7t41863H' => 'bol', 'BolSC55t61227H' => 'bol', 'BolSC55t61228H' => 'bol', 'BraA01t03278Z' => 'bra', 'BraA05t18998Z' => 'bra', 'BraA07t28673Z' => 'bra', 'C01p40150' => 'bna', 'C05p12370' => 'bna', 'C07p13680' => 'bna', 'CAN.G1006.16' => 'can', 'CAN.G1006.17' => 'can', 'CAN.G1170.2' => 'can', 'CAN.G962.7' => 'can', 'CANSAT25G2179' => 'cansat', 'CANSAT78G1573' => 'cansat', 'CARHR099510' => 'chi', 'CARHR143510' => 'chi', 'Carub.0003s2380' => 'cru', 'Carub.0004s3082' => 'cru', 'Ca_00614_v3' => 'car', 'Ca_07801_v3' => 'car', 'Ca_08567_v3' => 'car', 'Ca_09571_v3' => 'car', 'CBR_g19290' => 'cbr', 'Cc01_g19770' => 'ccan', 'Cc03_g03030' => 'ccan', 'CDE07G0968' => 'cde', 'CDE09G1441' => 'cde', 'Cfa006103' => 'cfa', 'Cfa015573' => 'cfa', 'Cfa016988' => 'cfa', 'Ciclev10006738m.g' => 'ccl', 'Ciclev10010920m.g' => 'ccl', 'Ciclev10018517m.g' => 'ccl', 'CiPaw.01G159200' => 'cil', 'CiPaw.02G091000' => 'cil', 'CiPaw.02G091100' => 'cil', 'CiPaw.08G103100' => 'cil', 'CiPaw.09G224900' => 'cil', 'ClCG06G005740' => 'cla', 'ClCG07G000090' => 'cla', 'ClCG07G000100' => 'cla', 'COL.COLO4_09143' => 'col', 'COL.COLO4_25124' => 'col', 'Cpa.g.sc16.34' => 'cpa', 'Cpa.g.sc3504.1' => 'cpa', 'Cpa.g.sc60.37' => 'cpa', 'CsaV3_6G018520' => 'csa', 'CsaV3_6G036860' => 'csa', 'CSS0001072' => 'camsi', 'CSS0020208' => 'camsi', 'CSS0021253' => 'camsi', 'CSS0022190' => 'camsi', 'CSS0036150' => 'camsi', 'CSS0040442' => 'camsi', 'CSS0042300' => 'camsi', 'CSS0045298' => 'camsi', 'DCAR_012449' => 'dca', 'DCAR_018405' => 'dca', 'DCAR_024573' => 'dca', 'DCAR_030591' => 'dca', 'Dinv16926' => 'din', 'Dinv32963' => 'din', 'Dinv38382' => 'din', 'Dinv38383' => 'din', 'Duzib133G0974' => 'dzi', 'Duzib138G1867' => 'dzi', 'Duzib211G0420' => 'dzi', 'Duzib212G0930' => 'dzi', 'ECA234G1645' => 'eca', 'ECA247G3467' => 'eca', 'ECA248G1703' => 'eca', 'EL10Ac3g06327' => 'bvu', 'EL10Ac7g17204' => 'bvu', 'Eucgr.A00855' => 'egr', 'Eucgr.A00858' => 'egr', 'Eucgr.H01520' => 'egr', 'Eucgr.H03604' => 'egr', 'Eucgr.L03465' => 'egr', 'Eucgr.L03466' => 'egr', 'FAN01G0988' => 'fan', 'FAN02G3892' => 'fan', 'FAN05G3381' => 'fan', 'FAN07G0967' => 'fan', 'FAN07G1493' => 'fan', 'FAN08G3125' => 'fan', 'FAN09G0402' => 'fan', 'FAN12G2594' => 'fan', 'FAN12G3879' => 'fan', 'FAN14G1546' => 'fan', 'FAN15G3626' => 'fan', 'FAN17G0588' => 'fan', 'FAN17G0609' => 'fan', 'FAN18G2817' => 'fan', 'FAN19G1305' => 'fan', 'FAN20G1787' => 'fan', 'FAN22G0073' => 'fan', 'FAN22G0352' => 'fan', 'FAN22G0368' => 'fan', 'FAN22G2273' => 'fan', 'FAN24G1998' => 'fan', 'FAN27G1317' => 'fan', 'FvH4_2g23980' => 'fve', 'FvH4_4g14380' => 'fve', 'FvH4_4g14390' => 'fve', 'FvH4_6g09250' => 'fve', 'Glyma.03G151100' => 'gma', 'Glyma.04G122550' => 'gma', 'Glyma.05G001600' => 'gma', 'Glyma.09G270766' => 'gma', 'Glyma.09G270832' => 'gma', 'Glyma.13G209800' => 'gma', 'Glyma.15G102800' => 'gma', 'Glyma.18G218900' => 'gma', 'Glyma.19G001500' => 'gma', 'Glyma.19G153600' => 'gma', 'Gohir.A02G028600' => 'ghi', 'Gohir.A08G045000' => 'ghi', 'Gohir.A11G120500' => 'ghi', 'Gohir.A12G006200' => 'ghi', 'Gohir.A12G006250' => 'ghi', 'Gohir.D02G036300' => 'ghi', 'Gohir.D08G054700' => 'ghi', 'Gohir.D11G125600' => 'ghi', 'Gohir.D12G005700' => 'ghi', 'Gorai.004G055200' => 'gra', 'Gorai.005G040400' => 'gra', 'Gorai.007G134500' => 'gra', 'Gorai.008G005500' => 'gra', 'GSVIVG01011094001' => 'vvi', 'GSVIVG01017879001' => 'vvi', 'GSVIVG01025988001' => 'vvi', 'GSVIVG01029847001' => 'vvi', 'HanXRQChr10g0282901' => 'han', 'HanXRQChr10g0310371' => 'han', 'HanXRQChr10g0315041' => 'han', 'HanXRQChr11g0327651' => 'han', 'HanXRQChr12g0359391' => 'han', 'Haze_00972' => 'cav', 'Haze_00973' => 'cav', 'Haze_00974' => 'cav', 'Haze_04747' => 'cav', 'Haze_04749' => 'cav', 'Haze_04750' => 'cav', 'Haze_21217' => 'cav', 'Hma1.2p1_1037F.1_g250680' => 'hma', 'Hma1.2p1_1644F.1_g295320' => 'hma', 'HPP92_011322' => 'vpl', 'HPP92_011323' => 'vpl', 'HPP92_011324' => 'vpl', 'HPP92_011325' => 'vpl', 'HPP92_011326' => 'vpl', 'Hund12205' => 'sun', 'Hund17957' => 'sun', 'Lalb_Chr06g0176771' => 'lal', 'Lalb_Chr18g0056021' => 'lal', 'Lalb_Chr18g0056031' => 'lal', 'Lalb_Chr18g0056041' => 'lal', 'Lalb_Chr20g0107751' => 'lal', 'Lalb_Chr20g0118371' => 'lal', 'Lj1g0010239' => 'lja', 'Lj1g0017101' => 'lja', 'Lj2A1178G40' => 'lonja', 'Lj2A54G84' => 'lonja', 'Lj2g0015248' => 'lja', 'Lj3A761T51' => 'lonja', 'Lj6g0018116' => 'lja', 'Lsat_1_v5_gn_4_136040' => 'lsa', 'Lsat_1_v5_gn_5_187461' => 'lsa', 'Lsat_1_v5_gn_5_77001' => 'lsa', 'Lsat_1_v5_gn_9_4461' => 'lsa', 'Manes.01G210100' => 'mes', 'Manes.03G185600' => 'mes', 'Manes.05G073300' => 'mes', 'Manes.09G120300' => 'mes', 'Manes.15G022100' => 'mes', 'Mapoly0096s0053' => 'mpo', 'MBI03_g14058_MAGBIO' => 'mbi', 'MBI03_g33876_MAGBIO' => 'mbi', 'MBI03_g36854_MAGBIO' => 'mbi', 'MBI17_g11997_MAGBIO' => 'mbi', 'MD03G1269000' => 'mdo', 'MD04G1179600' => 'mdo', 'MD11G1289800' => 'mdo', 'MD12G1194700' => 'mdo', 'MD13G1182100' => 'mdo', 'MD13G1182200' => 'mdo', 'MD16G1182600' => 'mdo', 'Medtr2g021400' => 'mtr', 'Medtr2g021470' => 'mtr', 'Medtr2g105810' => 'mtr', 'Medtr3g033580' => 'mtr', 'Medtr6g007970' => 'mtr', 'Medtr7g056330' => 'mtr', 'Medtr7g074290' => 'mtr', 'Medtr7g074380' => 'mtr', 'Medtr7g094550' => 'mtr', 'Medtr8g069995' => 'mtr', 'MELO3C014345.2' => 'cme', 'MELO3C021395.2' => 'cme', 'Migut.D00262' => 'egut', 'Migut.G00257' => 'egut', 'MSTRG.21575' => 'ama', 'MSTRG.3985' => 'ama', 'Nitab4.5_0000295g0140' => 'nta', 'Nitab4.5_0000732g0140' => 'nta', 'Nitab4.5_0003162g0020' => 'nta', 'Nitab4.5_0006180g0090' => 'nta', 'Nitab4.5_0006390g0010' => 'nta', 'Nitab4.5_0007392g0040' => 'nta', 'Nn1g02140' => 'nnu', 'Nn4g26168' => 'nnu', 'Nn5g26754' => 'nnu', 'Oeu001433.1' => 'oeu', 'Oeu010299.2' => 'oeu', 'Oeu011171.1' => 'oeu', 'Oeu037675.1' => 'oeu', 'Oeu038359.1' => 'oeu', 'Oeu063834.1' => 'oeu', 'Oeu063835.1' => 'oeu', 'Os05g0312000' => 'osa', 'Os07g0211101' => 'osa', 'Os07g0211200' => 'osa', 'Os07g0681500' => 'osa', 'Peaxi162Scf00095g01015' => 'pax', 'Peaxi162Scf00104g00329' => 'pax', 'Peaxi162Scf00161g00137' => 'pax', 'PGR004G1665' => 'pgr', 'PGR031G2937' => 'pgr', 'PGR119G2145' => 'pgr', 'PGSC0003DMG400004351' => 'stu', 'PGSC0003DMG400014625' => 'stu', 'PGSC0003DMG401000943' => 'stu', 'Phvul.001G148600' => 'pvu', 'Phvul.004G001700' => 'pvu', 'Phvul.006G154900' => 'pvu', 'Phvul.008G078200' => 'pvu', 'Phvul.011G136500' => 'pvu', 'Potri.002G215600' => 'ptr', 'Potri.008G201600' => 'ptr', 'Potri.014G138400' => 'ptr', 'Potri.016G142500' => 'ptr', 'Pp3c16_10580' => 'ppa', 'Pp3c5_25280' => 'ppa', 'Prupe.1G150000' => 'ppe', 'Prupe.1G150100' => 'ppe', 'Prupe.6G299600' => 'ppe', 'Prupe.8G245000' => 'ppe', 'Psat0s4927g0040' => 'psa', 'Psat1g052080' => 'psa', 'Psat1g183800' => 'psa', 'Psat3g113840' => 'psa', 'Psat3g126120' => 'psa', 'Psat3g126160' => 'psa', 'Psat3g158760' => 'psa', 'Psat3g158840' => 'psa', 'PSO170G2858' => 'pso', 'PSO339G0606' => 'pso', 'PSO384G4709' => 'pso', 'PSO407G0334' => 'pso', 'QL04p040276' => 'qlo', 'QL06p005458' => 'qlo', 'QL06p005472' => 'qlo', 'QL07p030546' => 'qlo', 'QL07p031519' => 'qlo', 'QL09p050949' => 'qlo', 'QL09p050966' => 'qlo', 'QL09p051067' => 'qlo', 'QL12p022706' => 'qlo', 'RcHm_v2.0_Chr2g0119601' => 'rch', 'RcHm_v2.0_Chr3g0459591' => 'rch', 'RcHm_v2.0_Chr4g0418521' => 'rch', 'RcHm_v2.0_Chr4g0418531' => 'rch', 'RcHm_v2.0_Chr4g0418541' => 'rch', 'RcHm_v2.0_Chr6g0291641' => 'rch', 'Rhsim01G0086300' => 'rsi', 'Rhsim01G0276300' => 'rsi', 'Rhsim01G0276500' => 'rsi', 'Rhsim04G0207700' => 'rsi', 'Rhsim05G0234500' => 'rsi', 'Rhsim13G0022400' => 'rsi', 'Sabra02G0167900' => 'sbr', 'Sabra04G0158500' => 'sbr', 'Sabra08G0159800' => 'sbr', 'Sabra10G0011500' => 'sbr', 'Sabra14G0104400' => 'sbr', 'SalBow2G2440' => 'sbo', 'SalBow4G2265' => 'sbo', 'Sc02g0000060' => 'sci', 'Sc05g0005020' => 'sci', 'Sc13g0003890' => 'sci', 'Sed0014865' => 'sed', 'Sed0017224' => 'sed', 'Sed0026391' => 'sed', 'SEGI_00063' => 'sgi', 'SEGI_10967' => 'sgi', 'SEGI_17510' => 'sgi', 'SEGI_24396' => 'sgi', 'SEGI_39719' => 'sgi', 'SEGI_41392' => 'sgi', 'SGA_v2.0_scaffold11G05794' => 'sas', 'SGA_v2.0_scaffold142G35607' => 'sas', 'SGA_v2.0_scaffold1G00447' => 'sas', 'SHI15388' => 'shi', 'SHI15394' => 'shi', 'SHI15396' => 'shi', 'SHI15399' => 'shi', 'SMO343G0151' => 'smo', 'SMO367G1118' => 'smo', 'Solyc01g080200.3' => 'sly', 'Solyc06g008960.3' => 'sly', 'Solyc09g064780.3' => 'sly', 'Sopen01g031980' => 'spe', 'Sopen06g003710' => 'spe', 'Sopen09g026460' => 'spe', 'Sp3g21240' => 'spa', 'Sp4g30030' => 'spa', 'TAR365G0022' => 'tar', 'TAR365G1023' => 'tar', 'TAR365G1253' => 'tar', 'TAR623G0078' => 'tar', 'TAR623G1721' => 'tar', 'TAR633G0959' => 'tar', 'THA.LOC104802225' => 'tha', 'THA.LOC104804769' => 'tha', 'THA.LOC104808660' => 'tha', 'THA.LOC104812792' => 'tha', 'Thecc.01G284000' => 'tca', 'Thecc.04G220600' => 'tca', 'Thecc.05G268900' => 'tca', 'Thecc.08G171100' => 'tca', 'Thhalv10001284m.g' => 'esa', 'Thhalv10019912m.g' => 'esa', 'TPR.G14189' => 'tpr', 'TPR.G18110' => 'tpr', 'TPR.G18130' => 'tpr', 'TPR.G18131' => 'tpr', 'TPR.G18140' => 'tpr', 'TPR.G24282' => 'tpr', 'TPR.G25221' => 'tpr', 'TPR.G29267' => 'tpr', 'TPR.G35315' => 'tpr', 'TPR.G36173' => 'tpr', 'TWI09G0794' => 'twi', 'TWI59G1348' => 'twi', 'TWI74G0430' => 'twi', 'unitig_26.g8940' => 'ugi', 'unitig_749.g13744' => 'ugi', 'unitig_749.g13745' => 'ugi', 'vmacro08269' => 'vma', 'vmacro14937' => 'vma', 'vmacro20401' => 'vma', 'VMungo0464G1349' => 'vmu', 'VMungo0540G0289' => 'vmu', 'VMungo1215G1590' => 'vmu', 'VMungo1309G0221' => 'vmu', 'VMungo1309G2815' => 'vmu', 'VMungo1383G0239' => 'vmu', 'VMungo1383G2910' => 'vmu', 'Zm00001eb095270' => 'zma', 'Zm00001eb095280' => 'zma', 'Zm00001eb111630' => 'zma', 'Zm00001eb237080' => 'zma', 'Zm00001eb273740' => 'zma', 'Zm00001eb285040' => 'zma', 'Zm00001eb330790' => 'zma', 'Zm00001eb337380' => 'zma' ), 'gf_id' => 'HOM05D001484', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001484' ), 'data_identifier' => 'HOM05D001484', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001484', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p31500' => 'bna', 'A05p00020' => 'bna', 'A07p08820' => 'bna', 'Aa31LG4G3300' => 'aar', 'Aa31LG8G10030' => 'aar', 'Actinidia00731' => 'ach', 'Actinidia11473' => 'ach', 'Actinidia23469' => 'ach', 'Actinidia24318' => 'ach', 'Actinidia40196' => 'ach', 'Actinidia40197' => 'ach', 'Actinidia40198' => 'ach', 'Ah.08g212990' => 'amhyb', 'Ah.15g091720' => 'amhyb', 'AL3G38260' => 'aly', 'AL4G47710' => 'aly', 'Aqoxy2G00671' => 'aox', 'Aqoxy2G03236' => 'aox', 'arahy.Tifrunner.gnm1.ann1.05IDCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KR684' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATY3SJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK6QJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6APGL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IDT7Z9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM073U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ0R87' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LE7RV4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT4QRX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V5ENPK' => 'arhy', 'AT2G48110' => 'ath', 'AT3G23590' => 'ath', 'ATR0626G186' => 'atr', 'ATR1127G141' => 'atr', 'Atru.chr4.2583' => 'acertr', 'Atru.chr5.1358' => 'acertr', 'Atru.chr5.1359' => 'acertr', 'Atru.chr8.46' => 'acertr', 'AUR62002640' => 'cqu', 'AUR62030055' => 'cqu', 'AUR62033713' => 'cqu', 'AUR62033714' => 'cqu', 'AUR62036795' => 'cqu', 'AUR62039891' => 'cqu', 'BcaB02g08737' => 'bca', 'BcaB04g20441' => 'bca', 'BcaB06g26509' => 'bca', 'BcaB06g26510' => 'bca', 'BcaB06g26511' => 'bca', 'BcaB06g26512' => 'bca', 'BcaB06g26513' => 'bca', 'BcaC02g12564' => 'bca', 'BcaC02g12565' => 'bca', 'BcaC02g12794' => 'bca', 'BcaC02g12795' => 'bca', 'BcaC02g12796' => 'bca', 'BcaC06g35541' => 'bca', 'BNapus_Darmor_BZH_scaffold_188p00080' => 'bna', 'BNapus_Darmor_BZH_scaffold_188p00090' => 'bna', 'BolC1t03972H' => 'bol', 'BolC1t03973H' => 'bol', 'BolC4t21680H' => 'bol', 'BolC7t41863H' => 'bol', 'BolSC55t61227H' => 'bol', 'BolSC55t61228H' => 'bol', 'BraA01t03278Z' => 'bra', 'BraA05t18998Z' => 'bra', 'BraA07t28673Z' => 'bra', 'C01p40150' => 'bna', 'C05p12370' => 'bna', 'C07p13680' => 'bna', 'CAN.G1006.16' => 'can', 'CAN.G1006.17' => 'can', 'CAN.G1170.2' => 'can', 'CAN.G962.7' => 'can', 'CANSAT25G2179' => 'cansat', 'CANSAT78G1573' => 'cansat', 'CARHR099510' => 'chi', 'CARHR143510' => 'chi', 'Carub.0003s2380' => 'cru', 'Carub.0004s3082' => 'cru', 'Ca_00614_v3' => 'car', 'Ca_07801_v3' => 'car', 'Ca_08567_v3' => 'car', 'Ca_09571_v3' => 'car', 'CBR_g19290' => 'cbr', 'Cc01_g19770' => 'ccan', 'Cc03_g03030' => 'ccan', 'CDE07G0968' => 'cde', 'CDE09G1441' => 'cde', 'Cfa006103' => 'cfa', 'Cfa015573' => 'cfa', 'Cfa016988' => 'cfa', 'Ciclev10006738m.g' => 'ccl', 'Ciclev10010920m.g' => 'ccl', 'Ciclev10018517m.g' => 'ccl', 'CiPaw.01G159200' => 'cil', 'CiPaw.02G091000' => 'cil', 'CiPaw.02G091100' => 'cil', 'CiPaw.08G103100' => 'cil', 'CiPaw.09G224900' => 'cil', 'ClCG06G005740' => 'cla', 'ClCG07G000090' => 'cla', 'ClCG07G000100' => 'cla', 'COL.COLO4_09143' => 'col', 'COL.COLO4_25124' => 'col', 'Cpa.g.sc16.34' => 'cpa', 'Cpa.g.sc3504.1' => 'cpa', 'Cpa.g.sc60.37' => 'cpa', 'CsaV3_6G018520' => 'csa', 'CsaV3_6G036860' => 'csa', 'CSS0001072' => 'camsi', 'CSS0020208' => 'camsi', 'CSS0021253' => 'camsi', 'CSS0022190' => 'camsi', 'CSS0036150' => 'camsi', 'CSS0040442' => 'camsi', 'CSS0042300' => 'camsi', 'CSS0045298' => 'camsi', 'DCAR_012449' => 'dca', 'DCAR_018405' => 'dca', 'DCAR_024573' => 'dca', 'DCAR_030591' => 'dca', 'Dinv16926' => 'din', 'Dinv32963' => 'din', 'Dinv38382' => 'din', 'Dinv38383' => 'din', 'Duzib133G0974' => 'dzi', 'Duzib138G1867' => 'dzi', 'Duzib211G0420' => 'dzi', 'Duzib212G0930' => 'dzi', 'ECA234G1645' => 'eca', 'ECA247G3467' => 'eca', 'ECA248G1703' => 'eca', 'EL10Ac3g06327' => 'bvu', 'EL10Ac7g17204' => 'bvu', 'Eucgr.A00855' => 'egr', 'Eucgr.A00858' => 'egr', 'Eucgr.H01520' => 'egr', 'Eucgr.H03604' => 'egr', 'Eucgr.L03465' => 'egr', 'Eucgr.L03466' => 'egr', 'FAN01G0988' => 'fan', 'FAN02G3892' => 'fan', 'FAN05G3381' => 'fan', 'FAN07G0967' => 'fan', 'FAN07G1493' => 'fan', 'FAN08G3125' => 'fan', 'FAN09G0402' => 'fan', 'FAN12G2594' => 'fan', 'FAN12G3879' => 'fan', 'FAN14G1546' => 'fan', 'FAN15G3626' => 'fan', 'FAN17G0588' => 'fan', 'FAN17G0609' => 'fan', 'FAN18G2817' => 'fan', 'FAN19G1305' => 'fan', 'FAN20G1787' => 'fan', 'FAN22G0073' => 'fan', 'FAN22G0352' => 'fan', 'FAN22G0368' => 'fan', 'FAN22G2273' => 'fan', 'FAN24G1998' => 'fan', 'FAN27G1317' => 'fan', 'FvH4_2g23980' => 'fve', 'FvH4_4g14380' => 'fve', 'FvH4_4g14390' => 'fve', 'FvH4_6g09250' => 'fve', 'Glyma.03G151100' => 'gma', 'Glyma.04G122550' => 'gma', 'Glyma.05G001600' => 'gma', 'Glyma.09G270766' => 'gma', 'Glyma.09G270832' => 'gma', 'Glyma.13G209800' => 'gma', 'Glyma.15G102800' => 'gma', 'Glyma.18G218900' => 'gma', 'Glyma.19G001500' => 'gma', 'Glyma.19G153600' => 'gma', 'Gohir.A02G028600' => 'ghi', 'Gohir.A08G045000' => 'ghi', 'Gohir.A11G120500' => 'ghi', 'Gohir.A12G006200' => 'ghi', 'Gohir.A12G006250' => 'ghi', 'Gohir.D02G036300' => 'ghi', 'Gohir.D08G054700' => 'ghi', 'Gohir.D11G125600' => 'ghi', 'Gohir.D12G005700' => 'ghi', 'Gorai.004G055200' => 'gra', 'Gorai.005G040400' => 'gra', 'Gorai.007G134500' => 'gra', 'Gorai.008G005500' => 'gra', 'GSVIVG01011094001' => 'vvi', 'GSVIVG01017879001' => 'vvi', 'GSVIVG01025988001' => 'vvi', 'GSVIVG01029847001' => 'vvi', 'HanXRQChr10g0282901' => 'han', 'HanXRQChr10g0310371' => 'han', 'HanXRQChr10g0315041' => 'han', 'HanXRQChr11g0327651' => 'han', 'HanXRQChr12g0359391' => 'han', 'Haze_00972' => 'cav', 'Haze_00973' => 'cav', 'Haze_00974' => 'cav', 'Haze_04747' => 'cav', 'Haze_04749' => 'cav', 'Haze_04750' => 'cav', 'Haze_21217' => 'cav', 'Hma1.2p1_1037F.1_g250680' => 'hma', 'Hma1.2p1_1644F.1_g295320' => 'hma', 'HPP92_011322' => 'vpl', 'HPP92_011323' => 'vpl', 'HPP92_011324' => 'vpl', 'HPP92_011325' => 'vpl', 'HPP92_011326' => 'vpl', 'Hund12205' => 'sun', 'Hund17957' => 'sun', 'Lalb_Chr06g0176771' => 'lal', 'Lalb_Chr18g0056021' => 'lal', 'Lalb_Chr18g0056031' => 'lal', 'Lalb_Chr18g0056041' => 'lal', 'Lalb_Chr20g0107751' => 'lal', 'Lalb_Chr20g0118371' => 'lal', 'Lj1g0010239' => 'lja', 'Lj1g0017101' => 'lja', 'Lj2A1178G40' => 'lonja', 'Lj2A54G84' => 'lonja', 'Lj2g0015248' => 'lja', 'Lj3A761T51' => 'lonja', 'Lj6g0018116' => 'lja', 'Lsat_1_v5_gn_4_136040' => 'lsa', 'Lsat_1_v5_gn_5_187461' => 'lsa', 'Lsat_1_v5_gn_5_77001' => 'lsa', 'Lsat_1_v5_gn_9_4461' => 'lsa', 'Manes.01G210100' => 'mes', 'Manes.03G185600' => 'mes', 'Manes.05G073300' => 'mes', 'Manes.09G120300' => 'mes', 'Manes.15G022100' => 'mes', 'Mapoly0096s0053' => 'mpo', 'MBI03_g14058_MAGBIO' => 'mbi', 'MBI03_g33876_MAGBIO' => 'mbi', 'MBI03_g36854_MAGBIO' => 'mbi', 'MBI17_g11997_MAGBIO' => 'mbi', 'MD03G1269000' => 'mdo', 'MD04G1179600' => 'mdo', 'MD11G1289800' => 'mdo', 'MD12G1194700' => 'mdo', 'MD13G1182100' => 'mdo', 'MD13G1182200' => 'mdo', 'MD16G1182600' => 'mdo', 'Medtr2g021400' => 'mtr', 'Medtr2g021470' => 'mtr', 'Medtr2g105810' => 'mtr', 'Medtr3g033580' => 'mtr', 'Medtr6g007970' => 'mtr', 'Medtr7g056330' => 'mtr', 'Medtr7g074290' => 'mtr', 'Medtr7g074380' => 'mtr', 'Medtr7g094550' => 'mtr', 'Medtr8g069995' => 'mtr', 'MELO3C014345.2' => 'cme', 'MELO3C021395.2' => 'cme', 'Migut.D00262' => 'egut', 'Migut.G00257' => 'egut', 'MSTRG.21575' => 'ama', 'MSTRG.3985' => 'ama', 'Nitab4.5_0000295g0140' => 'nta', 'Nitab4.5_0000732g0140' => 'nta', 'Nitab4.5_0003162g0020' => 'nta', 'Nitab4.5_0006180g0090' => 'nta', 'Nitab4.5_0006390g0010' => 'nta', 'Nitab4.5_0007392g0040' => 'nta', 'Nn1g02140' => 'nnu', 'Nn4g26168' => 'nnu', 'Nn5g26754' => 'nnu', 'Oeu001433.1' => 'oeu', 'Oeu010299.2' => 'oeu', 'Oeu011171.1' => 'oeu', 'Oeu037675.1' => 'oeu', 'Oeu038359.1' => 'oeu', 'Oeu063834.1' => 'oeu', 'Oeu063835.1' => 'oeu', 'Os05g0312000' => 'osa', 'Os07g0211101' => 'osa', 'Os07g0211200' => 'osa', 'Os07g0681500' => 'osa', 'Peaxi162Scf00095g01015' => 'pax', 'Peaxi162Scf00104g00329' => 'pax', 'Peaxi162Scf00161g00137' => 'pax', 'PGR004G1665' => 'pgr', 'PGR031G2937' => 'pgr', 'PGR119G2145' => 'pgr', 'PGSC0003DMG400004351' => 'stu', 'PGSC0003DMG400014625' => 'stu', 'PGSC0003DMG401000943' => 'stu', 'Phvul.001G148600' => 'pvu', 'Phvul.004G001700' => 'pvu', 'Phvul.006G154900' => 'pvu', 'Phvul.008G078200' => 'pvu', 'Phvul.011G136500' => 'pvu', 'Potri.002G215600' => 'ptr', 'Potri.008G201600' => 'ptr', 'Potri.014G138400' => 'ptr', 'Potri.016G142500' => 'ptr', 'Pp3c16_10580' => 'ppa', 'Pp3c5_25280' => 'ppa', 'Prupe.1G150000' => 'ppe', 'Prupe.1G150100' => 'ppe', 'Prupe.6G299600' => 'ppe', 'Prupe.8G245000' => 'ppe', 'Psat0s4927g0040' => 'psa', 'Psat1g052080' => 'psa', 'Psat1g183800' => 'psa', 'Psat3g113840' => 'psa', 'Psat3g126120' => 'psa', 'Psat3g126160' => 'psa', 'Psat3g158760' => 'psa', 'Psat3g158840' => 'psa', 'PSO170G2858' => 'pso', 'PSO339G0606' => 'pso', 'PSO384G4709' => 'pso', 'PSO407G0334' => 'pso', 'QL04p040276' => 'qlo', 'QL06p005458' => 'qlo', 'QL06p005472' => 'qlo', 'QL07p030546' => 'qlo', 'QL07p031519' => 'qlo', 'QL09p050949' => 'qlo', 'QL09p050966' => 'qlo', 'QL09p051067' => 'qlo', 'QL12p022706' => 'qlo', 'RcHm_v2.0_Chr2g0119601' => 'rch', 'RcHm_v2.0_Chr3g0459591' => 'rch', 'RcHm_v2.0_Chr4g0418521' => 'rch', 'RcHm_v2.0_Chr4g0418531' => 'rch', 'RcHm_v2.0_Chr4g0418541' => 'rch', 'RcHm_v2.0_Chr6g0291641' => 'rch', 'Rhsim01G0086300' => 'rsi', 'Rhsim01G0276300' => 'rsi', 'Rhsim01G0276500' => 'rsi', 'Rhsim04G0207700' => 'rsi', 'Rhsim05G0234500' => 'rsi', 'Rhsim13G0022400' => 'rsi', 'Sabra02G0167900' => 'sbr', 'Sabra04G0158500' => 'sbr', 'Sabra08G0159800' => 'sbr', 'Sabra10G0011500' => 'sbr', 'Sabra14G0104400' => 'sbr', 'SalBow2G2440' => 'sbo', 'SalBow4G2265' => 'sbo', 'Sc02g0000060' => 'sci', 'Sc05g0005020' => 'sci', 'Sc13g0003890' => 'sci', 'Sed0014865' => 'sed', 'Sed0017224' => 'sed', 'Sed0026391' => 'sed', 'SEGI_00063' => 'sgi', 'SEGI_10967' => 'sgi', 'SEGI_17510' => 'sgi', 'SEGI_24396' => 'sgi', 'SEGI_39719' => 'sgi', 'SEGI_41392' => 'sgi', 'SGA_v2.0_scaffold11G05794' => 'sas', 'SGA_v2.0_scaffold142G35607' => 'sas', 'SGA_v2.0_scaffold1G00447' => 'sas', 'SHI15388' => 'shi', 'SHI15394' => 'shi', 'SHI15396' => 'shi', 'SHI15399' => 'shi', 'SMO343G0151' => 'smo', 'SMO367G1118' => 'smo', 'Solyc01g080200.3' => 'sly', 'Solyc06g008960.3' => 'sly', 'Solyc09g064780.3' => 'sly', 'Sopen01g031980' => 'spe', 'Sopen06g003710' => 'spe', 'Sopen09g026460' => 'spe', 'Sp3g21240' => 'spa', 'Sp4g30030' => 'spa', 'TAR365G0022' => 'tar', 'TAR365G1023' => 'tar', 'TAR365G1253' => 'tar', 'TAR623G0078' => 'tar', 'TAR623G1721' => 'tar', 'TAR633G0959' => 'tar', 'THA.LOC104802225' => 'tha', 'THA.LOC104804769' => 'tha', 'THA.LOC104808660' => 'tha', 'THA.LOC104812792' => 'tha', 'Thecc.01G284000' => 'tca', 'Thecc.04G220600' => 'tca', 'Thecc.05G268900' => 'tca', 'Thecc.08G171100' => 'tca', 'Thhalv10001284m.g' => 'esa', 'Thhalv10019912m.g' => 'esa', 'TPR.G14189' => 'tpr', 'TPR.G18110' => 'tpr', 'TPR.G18130' => 'tpr', 'TPR.G18131' => 'tpr', 'TPR.G18140' => 'tpr', 'TPR.G24282' => 'tpr', 'TPR.G25221' => 'tpr', 'TPR.G29267' => 'tpr', 'TPR.G35315' => 'tpr', 'TPR.G36173' => 'tpr', 'TWI09G0794' => 'twi', 'TWI59G1348' => 'twi', 'TWI74G0430' => 'twi', 'unitig_26.g8940' => 'ugi', 'unitig_749.g13744' => 'ugi', 'unitig_749.g13745' => 'ugi', 'vmacro08269' => 'vma', 'vmacro14937' => 'vma', 'vmacro20401' => 'vma', 'VMungo0464G1349' => 'vmu', 'VMungo0540G0289' => 'vmu', 'VMungo1215G1590' => 'vmu', 'VMungo1309G0221' => 'vmu', 'VMungo1309G2815' => 'vmu', 'VMungo1383G0239' => 'vmu', 'VMungo1383G2910' => 'vmu', 'Zm00001eb095270' => 'zma', 'Zm00001eb095280' => 'zma', 'Zm00001eb111630' => 'zma', 'Zm00001eb237080' => 'zma', 'Zm00001eb273740' => 'zma', 'Zm00001eb285040' => 'zma', 'Zm00001eb330790' => 'zma', 'Zm00001eb337380' => 'zma' ) $gf_id = 'HOM05D001484' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001484' ) $data_identifier = 'HOM05D001484' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 2, 'aly' => (int) 2, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 22, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 7, 'hma' => (int) 2, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 7, 'mtr' => (int) 10, 'cme' => (int) 2, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 4, 'ppa' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 4, 'qlo' => (int) 9, 'rch' => (int) 6, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 10, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 7, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb337380' $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' => 'HOM05D001484', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p31500' => 'bna', 'A05p00020' => 'bna', 'A07p08820' => 'bna', 'Aa31LG4G3300' => 'aar', 'Aa31LG8G10030' => 'aar', 'Actinidia00731' => 'ach', 'Actinidia11473' => 'ach', 'Actinidia23469' => 'ach', 'Actinidia24318' => 'ach', 'Actinidia40196' => 'ach', 'Actinidia40197' => 'ach', 'Actinidia40198' => 'ach', 'Ah.08g212990' => 'amhyb', 'Ah.15g091720' => 'amhyb', 'AL3G38260' => 'aly', 'AL4G47710' => 'aly', 'Aqoxy2G00671' => 'aox', 'Aqoxy2G03236' => 'aox', 'arahy.Tifrunner.gnm1.ann1.05IDCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KR684' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATY3SJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK6QJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6APGL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IDT7Z9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM073U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ0R87' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LE7RV4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT4QRX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V5ENPK' => 'arhy', 'AT2G48110' => 'ath', 'AT3G23590' => 'ath', 'ATR0626G186' => 'atr', 'ATR1127G141' => 'atr', 'Atru.chr4.2583' => 'acertr', 'Atru.chr5.1358' => 'acertr', 'Atru.chr5.1359' => 'acertr', 'Atru.chr8.46' => 'acertr', 'AUR62002640' => 'cqu', 'AUR62030055' => 'cqu', 'AUR62033713' => 'cqu', 'AUR62033714' => 'cqu', 'AUR62036795' => 'cqu', 'AUR62039891' => 'cqu', 'BcaB02g08737' => 'bca', 'BcaB04g20441' => 'bca', 'BcaB06g26509' => 'bca', 'BcaB06g26510' => 'bca', 'BcaB06g26511' => 'bca', 'BcaB06g26512' => 'bca', 'BcaB06g26513' => 'bca', 'BcaC02g12564' => 'bca', 'BcaC02g12565' => 'bca', 'BcaC02g12794' => 'bca', 'BcaC02g12795' => 'bca', 'BcaC02g12796' => 'bca', 'BcaC06g35541' => 'bca', 'BNapus_Darmor_BZH_scaffold_188p00080' => 'bna', 'BNapus_Darmor_BZH_scaffold_188p00090' => 'bna', 'BolC1t03972H' => 'bol', 'BolC1t03973H' => 'bol', 'BolC4t21680H' => 'bol', 'BolC7t41863H' => 'bol', 'BolSC55t61227H' => 'bol', 'BolSC55t61228H' => 'bol', 'BraA01t03278Z' => 'bra', 'BraA05t18998Z' => 'bra', 'BraA07t28673Z' => 'bra', 'C01p40150' => 'bna', 'C05p12370' => 'bna', 'C07p13680' => 'bna', 'CAN.G1006.16' => 'can', 'CAN.G1006.17' => 'can', 'CAN.G1170.2' => 'can', 'CAN.G962.7' => 'can', 'CANSAT25G2179' => 'cansat', 'CANSAT78G1573' => 'cansat', 'CARHR099510' => 'chi', 'CARHR143510' => 'chi', 'Carub.0003s2380' => 'cru', 'Carub.0004s3082' => 'cru', 'Ca_00614_v3' => 'car', 'Ca_07801_v3' => 'car', 'Ca_08567_v3' => 'car', 'Ca_09571_v3' => 'car', 'CBR_g19290' => 'cbr', 'Cc01_g19770' => 'ccan', 'Cc03_g03030' => 'ccan', 'CDE07G0968' => 'cde', 'CDE09G1441' => 'cde', 'Cfa006103' => 'cfa', 'Cfa015573' => 'cfa', 'Cfa016988' => 'cfa', 'Ciclev10006738m.g' => 'ccl', 'Ciclev10010920m.g' => 'ccl', 'Ciclev10018517m.g' => 'ccl', 'CiPaw.01G159200' => 'cil', 'CiPaw.02G091000' => 'cil', 'CiPaw.02G091100' => 'cil', 'CiPaw.08G103100' => 'cil', 'CiPaw.09G224900' => 'cil', 'ClCG06G005740' => 'cla', 'ClCG07G000090' => 'cla', 'ClCG07G000100' => 'cla', 'COL.COLO4_09143' => 'col', 'COL.COLO4_25124' => 'col', 'Cpa.g.sc16.34' => 'cpa', 'Cpa.g.sc3504.1' => 'cpa', 'Cpa.g.sc60.37' => 'cpa', 'CsaV3_6G018520' => 'csa', 'CsaV3_6G036860' => 'csa', 'CSS0001072' => 'camsi', 'CSS0020208' => 'camsi', 'CSS0021253' => 'camsi', 'CSS0022190' => 'camsi', 'CSS0036150' => 'camsi', 'CSS0040442' => 'camsi', 'CSS0042300' => 'camsi', 'CSS0045298' => 'camsi', 'DCAR_012449' => 'dca', 'DCAR_018405' => 'dca', 'DCAR_024573' => 'dca', 'DCAR_030591' => 'dca', 'Dinv16926' => 'din', 'Dinv32963' => 'din', 'Dinv38382' => 'din', 'Dinv38383' => 'din', 'Duzib133G0974' => 'dzi', 'Duzib138G1867' => 'dzi', 'Duzib211G0420' => 'dzi', 'Duzib212G0930' => 'dzi', 'ECA234G1645' => 'eca', 'ECA247G3467' => 'eca', 'ECA248G1703' => 'eca', 'EL10Ac3g06327' => 'bvu', 'EL10Ac7g17204' => 'bvu', 'Eucgr.A00855' => 'egr', 'Eucgr.A00858' => 'egr', 'Eucgr.H01520' => 'egr', 'Eucgr.H03604' => 'egr', 'Eucgr.L03465' => 'egr', 'Eucgr.L03466' => 'egr', 'FAN01G0988' => 'fan', 'FAN02G3892' => 'fan', 'FAN05G3381' => 'fan', 'FAN07G0967' => 'fan', 'FAN07G1493' => 'fan', 'FAN08G3125' => 'fan', 'FAN09G0402' => 'fan', 'FAN12G2594' => 'fan', 'FAN12G3879' => 'fan', 'FAN14G1546' => 'fan', 'FAN15G3626' => 'fan', 'FAN17G0588' => 'fan', 'FAN17G0609' => 'fan', 'FAN18G2817' => 'fan', 'FAN19G1305' => 'fan', 'FAN20G1787' => 'fan', 'FAN22G0073' => 'fan', 'FAN22G0352' => 'fan', 'FAN22G0368' => 'fan', 'FAN22G2273' => 'fan', 'FAN24G1998' => 'fan', 'FAN27G1317' => 'fan', 'FvH4_2g23980' => 'fve', 'FvH4_4g14380' => 'fve', 'FvH4_4g14390' => 'fve', 'FvH4_6g09250' => 'fve', 'Glyma.03G151100' => 'gma', 'Glyma.04G122550' => 'gma', 'Glyma.05G001600' => 'gma', 'Glyma.09G270766' => 'gma', 'Glyma.09G270832' => 'gma', 'Glyma.13G209800' => 'gma', 'Glyma.15G102800' => 'gma', 'Glyma.18G218900' => 'gma', 'Glyma.19G001500' => 'gma', 'Glyma.19G153600' => 'gma', 'Gohir.A02G028600' => 'ghi', 'Gohir.A08G045000' => 'ghi', 'Gohir.A11G120500' => 'ghi', 'Gohir.A12G006200' => 'ghi', 'Gohir.A12G006250' => 'ghi', 'Gohir.D02G036300' => 'ghi', 'Gohir.D08G054700' => 'ghi', 'Gohir.D11G125600' => 'ghi', 'Gohir.D12G005700' => 'ghi', 'Gorai.004G055200' => 'gra', 'Gorai.005G040400' => 'gra', 'Gorai.007G134500' => 'gra', 'Gorai.008G005500' => 'gra', 'GSVIVG01011094001' => 'vvi', 'GSVIVG01017879001' => 'vvi', 'GSVIVG01025988001' => 'vvi', 'GSVIVG01029847001' => 'vvi', 'HanXRQChr10g0282901' => 'han', 'HanXRQChr10g0310371' => 'han', 'HanXRQChr10g0315041' => 'han', 'HanXRQChr11g0327651' => 'han', 'HanXRQChr12g0359391' => 'han', 'Haze_00972' => 'cav', 'Haze_00973' => 'cav', 'Haze_00974' => 'cav', 'Haze_04747' => 'cav', 'Haze_04749' => 'cav', 'Haze_04750' => 'cav', 'Haze_21217' => 'cav', 'Hma1.2p1_1037F.1_g250680' => 'hma', 'Hma1.2p1_1644F.1_g295320' => 'hma', 'HPP92_011322' => 'vpl', 'HPP92_011323' => 'vpl', 'HPP92_011324' => 'vpl', 'HPP92_011325' => 'vpl', 'HPP92_011326' => 'vpl', 'Hund12205' => 'sun', 'Hund17957' => 'sun', 'Lalb_Chr06g0176771' => 'lal', 'Lalb_Chr18g0056021' => 'lal', 'Lalb_Chr18g0056031' => 'lal', 'Lalb_Chr18g0056041' => 'lal', 'Lalb_Chr20g0107751' => 'lal', 'Lalb_Chr20g0118371' => 'lal', 'Lj1g0010239' => 'lja', 'Lj1g0017101' => 'lja', 'Lj2A1178G40' => 'lonja', 'Lj2A54G84' => 'lonja', 'Lj2g0015248' => 'lja', 'Lj3A761T51' => 'lonja', 'Lj6g0018116' => 'lja', 'Lsat_1_v5_gn_4_136040' => 'lsa', 'Lsat_1_v5_gn_5_187461' => 'lsa', 'Lsat_1_v5_gn_5_77001' => 'lsa', 'Lsat_1_v5_gn_9_4461' => 'lsa', 'Manes.01G210100' => 'mes', 'Manes.03G185600' => 'mes', 'Manes.05G073300' => 'mes', 'Manes.09G120300' => 'mes', 'Manes.15G022100' => 'mes', 'Mapoly0096s0053' => 'mpo', 'MBI03_g14058_MAGBIO' => 'mbi', 'MBI03_g33876_MAGBIO' => 'mbi', 'MBI03_g36854_MAGBIO' => 'mbi', 'MBI17_g11997_MAGBIO' => 'mbi', 'MD03G1269000' => 'mdo', 'MD04G1179600' => 'mdo', 'MD11G1289800' => 'mdo', 'MD12G1194700' => 'mdo', 'MD13G1182100' => 'mdo', 'MD13G1182200' => 'mdo', 'MD16G1182600' => 'mdo', 'Medtr2g021400' => 'mtr', 'Medtr2g021470' => 'mtr', 'Medtr2g105810' => 'mtr', 'Medtr3g033580' => 'mtr', 'Medtr6g007970' => 'mtr', 'Medtr7g056330' => 'mtr', 'Medtr7g074290' => 'mtr', 'Medtr7g074380' => 'mtr', 'Medtr7g094550' => 'mtr', 'Medtr8g069995' => 'mtr', 'MELO3C014345.2' => 'cme', 'MELO3C021395.2' => 'cme', 'Migut.D00262' => 'egut', 'Migut.G00257' => 'egut', 'MSTRG.21575' => 'ama', 'MSTRG.3985' => 'ama', 'Nitab4.5_0000295g0140' => 'nta', 'Nitab4.5_0000732g0140' => 'nta', 'Nitab4.5_0003162g0020' => 'nta', 'Nitab4.5_0006180g0090' => 'nta', 'Nitab4.5_0006390g0010' => 'nta', 'Nitab4.5_0007392g0040' => 'nta', 'Nn1g02140' => 'nnu', 'Nn4g26168' => 'nnu', 'Nn5g26754' => 'nnu', 'Oeu001433.1' => 'oeu', 'Oeu010299.2' => 'oeu', 'Oeu011171.1' => 'oeu', 'Oeu037675.1' => 'oeu', 'Oeu038359.1' => 'oeu', 'Oeu063834.1' => 'oeu', 'Oeu063835.1' => 'oeu', 'Os05g0312000' => 'osa', 'Os07g0211101' => 'osa', 'Os07g0211200' => 'osa', 'Os07g0681500' => 'osa', 'Peaxi162Scf00095g01015' => 'pax', 'Peaxi162Scf00104g00329' => 'pax', 'Peaxi162Scf00161g00137' => 'pax', 'PGR004G1665' => 'pgr', 'PGR031G2937' => 'pgr', 'PGR119G2145' => 'pgr', 'PGSC0003DMG400004351' => 'stu', 'PGSC0003DMG400014625' => 'stu', 'PGSC0003DMG401000943' => 'stu', 'Phvul.001G148600' => 'pvu', 'Phvul.004G001700' => 'pvu', 'Phvul.006G154900' => 'pvu', 'Phvul.008G078200' => 'pvu', 'Phvul.011G136500' => 'pvu', 'Potri.002G215600' => 'ptr', 'Potri.008G201600' => 'ptr', 'Potri.014G138400' => 'ptr', 'Potri.016G142500' => 'ptr', 'Pp3c16_10580' => 'ppa', 'Pp3c5_25280' => 'ppa', 'Prupe.1G150000' => 'ppe', 'Prupe.1G150100' => 'ppe', 'Prupe.6G299600' => 'ppe', 'Prupe.8G245000' => 'ppe', 'Psat0s4927g0040' => 'psa', 'Psat1g052080' => 'psa', 'Psat1g183800' => 'psa', 'Psat3g113840' => 'psa', 'Psat3g126120' => 'psa', 'Psat3g126160' => 'psa', 'Psat3g158760' => 'psa', 'Psat3g158840' => 'psa', 'PSO170G2858' => 'pso', 'PSO339G0606' => 'pso', 'PSO384G4709' => 'pso', 'PSO407G0334' => 'pso', 'QL04p040276' => 'qlo', 'QL06p005458' => 'qlo', 'QL06p005472' => 'qlo', 'QL07p030546' => 'qlo', 'QL07p031519' => 'qlo', 'QL09p050949' => 'qlo', 'QL09p050966' => 'qlo', 'QL09p051067' => 'qlo', 'QL12p022706' => 'qlo', 'RcHm_v2.0_Chr2g0119601' => 'rch', 'RcHm_v2.0_Chr3g0459591' => 'rch', 'RcHm_v2.0_Chr4g0418521' => 'rch', 'RcHm_v2.0_Chr4g0418531' => 'rch', 'RcHm_v2.0_Chr4g0418541' => 'rch', 'RcHm_v2.0_Chr6g0291641' => 'rch', 'Rhsim01G0086300' => 'rsi', 'Rhsim01G0276300' => 'rsi', 'Rhsim01G0276500' => 'rsi', 'Rhsim04G0207700' => 'rsi', 'Rhsim05G0234500' => 'rsi', 'Rhsim13G0022400' => 'rsi', 'Sabra02G0167900' => 'sbr', 'Sabra04G0158500' => 'sbr', 'Sabra08G0159800' => 'sbr', 'Sabra10G0011500' => 'sbr', 'Sabra14G0104400' => 'sbr', 'SalBow2G2440' => 'sbo', 'SalBow4G2265' => 'sbo', 'Sc02g0000060' => 'sci', 'Sc05g0005020' => 'sci', 'Sc13g0003890' => 'sci', 'Sed0014865' => 'sed', 'Sed0017224' => 'sed', 'Sed0026391' => 'sed', 'SEGI_00063' => 'sgi', 'SEGI_10967' => 'sgi', 'SEGI_17510' => 'sgi', 'SEGI_24396' => 'sgi', 'SEGI_39719' => 'sgi', 'SEGI_41392' => 'sgi', 'SGA_v2.0_scaffold11G05794' => 'sas', 'SGA_v2.0_scaffold142G35607' => 'sas', 'SGA_v2.0_scaffold1G00447' => 'sas', 'SHI15388' => 'shi', 'SHI15394' => 'shi', 'SHI15396' => 'shi', 'SHI15399' => 'shi', 'SMO343G0151' => 'smo', 'SMO367G1118' => 'smo', 'Solyc01g080200.3' => 'sly', 'Solyc06g008960.3' => 'sly', 'Solyc09g064780.3' => 'sly', 'Sopen01g031980' => 'spe', 'Sopen06g003710' => 'spe', 'Sopen09g026460' => 'spe', 'Sp3g21240' => 'spa', 'Sp4g30030' => 'spa', 'TAR365G0022' => 'tar', 'TAR365G1023' => 'tar', 'TAR365G1253' => 'tar', 'TAR623G0078' => 'tar', 'TAR623G1721' => 'tar', 'TAR633G0959' => 'tar', 'THA.LOC104802225' => 'tha', 'THA.LOC104804769' => 'tha', 'THA.LOC104808660' => 'tha', 'THA.LOC104812792' => 'tha', 'Thecc.01G284000' => 'tca', 'Thecc.04G220600' => 'tca', 'Thecc.05G268900' => 'tca', 'Thecc.08G171100' => 'tca', 'Thhalv10001284m.g' => 'esa', 'Thhalv10019912m.g' => 'esa', 'TPR.G14189' => 'tpr', 'TPR.G18110' => 'tpr', 'TPR.G18130' => 'tpr', 'TPR.G18131' => 'tpr', 'TPR.G18140' => 'tpr', 'TPR.G24282' => 'tpr', 'TPR.G25221' => 'tpr', 'TPR.G29267' => 'tpr', 'TPR.G35315' => 'tpr', 'TPR.G36173' => 'tpr', 'TWI09G0794' => 'twi', 'TWI59G1348' => 'twi', 'TWI74G0430' => 'twi', 'unitig_26.g8940' => 'ugi', 'unitig_749.g13744' => 'ugi', 'unitig_749.g13745' => 'ugi', 'vmacro08269' => 'vma', 'vmacro14937' => 'vma', 'vmacro20401' => 'vma', 'VMungo0464G1349' => 'vmu', 'VMungo0540G0289' => 'vmu', 'VMungo1215G1590' => 'vmu', 'VMungo1309G0221' => 'vmu', 'VMungo1309G2815' => 'vmu', 'VMungo1383G0239' => 'vmu', 'VMungo1383G2910' => 'vmu', 'Zm00001eb095270' => 'zma', 'Zm00001eb095280' => 'zma', 'Zm00001eb111630' => 'zma', 'Zm00001eb237080' => 'zma', 'Zm00001eb273740' => 'zma', 'Zm00001eb285040' => 'zma', 'Zm00001eb330790' => 'zma', 'Zm00001eb337380' => 'zma' ), 'gf_id' => 'HOM05D001484', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001484' ), 'data_identifier' => 'HOM05D001484', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001484', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p31500' => 'bna', 'A05p00020' => 'bna', 'A07p08820' => 'bna', 'Aa31LG4G3300' => 'aar', 'Aa31LG8G10030' => 'aar', 'Actinidia00731' => 'ach', 'Actinidia11473' => 'ach', 'Actinidia23469' => 'ach', 'Actinidia24318' => 'ach', 'Actinidia40196' => 'ach', 'Actinidia40197' => 'ach', 'Actinidia40198' => 'ach', 'Ah.08g212990' => 'amhyb', 'Ah.15g091720' => 'amhyb', 'AL3G38260' => 'aly', 'AL4G47710' => 'aly', 'Aqoxy2G00671' => 'aox', 'Aqoxy2G03236' => 'aox', 'arahy.Tifrunner.gnm1.ann1.05IDCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KR684' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATY3SJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK6QJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6APGL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IDT7Z9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM073U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ0R87' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LE7RV4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT4QRX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V5ENPK' => 'arhy', 'AT2G48110' => 'ath', 'AT3G23590' => 'ath', 'ATR0626G186' => 'atr', 'ATR1127G141' => 'atr', 'Atru.chr4.2583' => 'acertr', 'Atru.chr5.1358' => 'acertr', 'Atru.chr5.1359' => 'acertr', 'Atru.chr8.46' => 'acertr', 'AUR62002640' => 'cqu', 'AUR62030055' => 'cqu', 'AUR62033713' => 'cqu', 'AUR62033714' => 'cqu', 'AUR62036795' => 'cqu', 'AUR62039891' => 'cqu', 'BcaB02g08737' => 'bca', 'BcaB04g20441' => 'bca', 'BcaB06g26509' => 'bca', 'BcaB06g26510' => 'bca', 'BcaB06g26511' => 'bca', 'BcaB06g26512' => 'bca', 'BcaB06g26513' => 'bca', 'BcaC02g12564' => 'bca', 'BcaC02g12565' => 'bca', 'BcaC02g12794' => 'bca', 'BcaC02g12795' => 'bca', 'BcaC02g12796' => 'bca', 'BcaC06g35541' => 'bca', 'BNapus_Darmor_BZH_scaffold_188p00080' => 'bna', 'BNapus_Darmor_BZH_scaffold_188p00090' => 'bna', 'BolC1t03972H' => 'bol', 'BolC1t03973H' => 'bol', 'BolC4t21680H' => 'bol', 'BolC7t41863H' => 'bol', 'BolSC55t61227H' => 'bol', 'BolSC55t61228H' => 'bol', 'BraA01t03278Z' => 'bra', 'BraA05t18998Z' => 'bra', 'BraA07t28673Z' => 'bra', 'C01p40150' => 'bna', 'C05p12370' => 'bna', 'C07p13680' => 'bna', 'CAN.G1006.16' => 'can', 'CAN.G1006.17' => 'can', 'CAN.G1170.2' => 'can', 'CAN.G962.7' => 'can', 'CANSAT25G2179' => 'cansat', 'CANSAT78G1573' => 'cansat', 'CARHR099510' => 'chi', 'CARHR143510' => 'chi', 'Carub.0003s2380' => 'cru', 'Carub.0004s3082' => 'cru', 'Ca_00614_v3' => 'car', 'Ca_07801_v3' => 'car', 'Ca_08567_v3' => 'car', 'Ca_09571_v3' => 'car', 'CBR_g19290' => 'cbr', 'Cc01_g19770' => 'ccan', 'Cc03_g03030' => 'ccan', 'CDE07G0968' => 'cde', 'CDE09G1441' => 'cde', 'Cfa006103' => 'cfa', 'Cfa015573' => 'cfa', 'Cfa016988' => 'cfa', 'Ciclev10006738m.g' => 'ccl', 'Ciclev10010920m.g' => 'ccl', 'Ciclev10018517m.g' => 'ccl', 'CiPaw.01G159200' => 'cil', 'CiPaw.02G091000' => 'cil', 'CiPaw.02G091100' => 'cil', 'CiPaw.08G103100' => 'cil', 'CiPaw.09G224900' => 'cil', 'ClCG06G005740' => 'cla', 'ClCG07G000090' => 'cla', 'ClCG07G000100' => 'cla', 'COL.COLO4_09143' => 'col', 'COL.COLO4_25124' => 'col', 'Cpa.g.sc16.34' => 'cpa', 'Cpa.g.sc3504.1' => 'cpa', 'Cpa.g.sc60.37' => 'cpa', 'CsaV3_6G018520' => 'csa', 'CsaV3_6G036860' => 'csa', 'CSS0001072' => 'camsi', 'CSS0020208' => 'camsi', 'CSS0021253' => 'camsi', 'CSS0022190' => 'camsi', 'CSS0036150' => 'camsi', 'CSS0040442' => 'camsi', 'CSS0042300' => 'camsi', 'CSS0045298' => 'camsi', 'DCAR_012449' => 'dca', 'DCAR_018405' => 'dca', 'DCAR_024573' => 'dca', 'DCAR_030591' => 'dca', 'Dinv16926' => 'din', 'Dinv32963' => 'din', 'Dinv38382' => 'din', 'Dinv38383' => 'din', 'Duzib133G0974' => 'dzi', 'Duzib138G1867' => 'dzi', 'Duzib211G0420' => 'dzi', 'Duzib212G0930' => 'dzi', 'ECA234G1645' => 'eca', 'ECA247G3467' => 'eca', 'ECA248G1703' => 'eca', 'EL10Ac3g06327' => 'bvu', 'EL10Ac7g17204' => 'bvu', 'Eucgr.A00855' => 'egr', 'Eucgr.A00858' => 'egr', 'Eucgr.H01520' => 'egr', 'Eucgr.H03604' => 'egr', 'Eucgr.L03465' => 'egr', 'Eucgr.L03466' => 'egr', 'FAN01G0988' => 'fan', 'FAN02G3892' => 'fan', 'FAN05G3381' => 'fan', 'FAN07G0967' => 'fan', 'FAN07G1493' => 'fan', 'FAN08G3125' => 'fan', 'FAN09G0402' => 'fan', 'FAN12G2594' => 'fan', 'FAN12G3879' => 'fan', 'FAN14G1546' => 'fan', 'FAN15G3626' => 'fan', 'FAN17G0588' => 'fan', 'FAN17G0609' => 'fan', 'FAN18G2817' => 'fan', 'FAN19G1305' => 'fan', 'FAN20G1787' => 'fan', 'FAN22G0073' => 'fan', 'FAN22G0352' => 'fan', 'FAN22G0368' => 'fan', 'FAN22G2273' => 'fan', 'FAN24G1998' => 'fan', 'FAN27G1317' => 'fan', 'FvH4_2g23980' => 'fve', 'FvH4_4g14380' => 'fve', 'FvH4_4g14390' => 'fve', 'FvH4_6g09250' => 'fve', 'Glyma.03G151100' => 'gma', 'Glyma.04G122550' => 'gma', 'Glyma.05G001600' => 'gma', 'Glyma.09G270766' => 'gma', 'Glyma.09G270832' => 'gma', 'Glyma.13G209800' => 'gma', 'Glyma.15G102800' => 'gma', 'Glyma.18G218900' => 'gma', 'Glyma.19G001500' => 'gma', 'Glyma.19G153600' => 'gma', 'Gohir.A02G028600' => 'ghi', 'Gohir.A08G045000' => 'ghi', 'Gohir.A11G120500' => 'ghi', 'Gohir.A12G006200' => 'ghi', 'Gohir.A12G006250' => 'ghi', 'Gohir.D02G036300' => 'ghi', 'Gohir.D08G054700' => 'ghi', 'Gohir.D11G125600' => 'ghi', 'Gohir.D12G005700' => 'ghi', 'Gorai.004G055200' => 'gra', 'Gorai.005G040400' => 'gra', 'Gorai.007G134500' => 'gra', 'Gorai.008G005500' => 'gra', 'GSVIVG01011094001' => 'vvi', 'GSVIVG01017879001' => 'vvi', 'GSVIVG01025988001' => 'vvi', 'GSVIVG01029847001' => 'vvi', 'HanXRQChr10g0282901' => 'han', 'HanXRQChr10g0310371' => 'han', 'HanXRQChr10g0315041' => 'han', 'HanXRQChr11g0327651' => 'han', 'HanXRQChr12g0359391' => 'han', 'Haze_00972' => 'cav', 'Haze_00973' => 'cav', 'Haze_00974' => 'cav', 'Haze_04747' => 'cav', 'Haze_04749' => 'cav', 'Haze_04750' => 'cav', 'Haze_21217' => 'cav', 'Hma1.2p1_1037F.1_g250680' => 'hma', 'Hma1.2p1_1644F.1_g295320' => 'hma', 'HPP92_011322' => 'vpl', 'HPP92_011323' => 'vpl', 'HPP92_011324' => 'vpl', 'HPP92_011325' => 'vpl', 'HPP92_011326' => 'vpl', 'Hund12205' => 'sun', 'Hund17957' => 'sun', 'Lalb_Chr06g0176771' => 'lal', 'Lalb_Chr18g0056021' => 'lal', 'Lalb_Chr18g0056031' => 'lal', 'Lalb_Chr18g0056041' => 'lal', 'Lalb_Chr20g0107751' => 'lal', 'Lalb_Chr20g0118371' => 'lal', 'Lj1g0010239' => 'lja', 'Lj1g0017101' => 'lja', 'Lj2A1178G40' => 'lonja', 'Lj2A54G84' => 'lonja', 'Lj2g0015248' => 'lja', 'Lj3A761T51' => 'lonja', 'Lj6g0018116' => 'lja', 'Lsat_1_v5_gn_4_136040' => 'lsa', 'Lsat_1_v5_gn_5_187461' => 'lsa', 'Lsat_1_v5_gn_5_77001' => 'lsa', 'Lsat_1_v5_gn_9_4461' => 'lsa', 'Manes.01G210100' => 'mes', 'Manes.03G185600' => 'mes', 'Manes.05G073300' => 'mes', 'Manes.09G120300' => 'mes', 'Manes.15G022100' => 'mes', 'Mapoly0096s0053' => 'mpo', 'MBI03_g14058_MAGBIO' => 'mbi', 'MBI03_g33876_MAGBIO' => 'mbi', 'MBI03_g36854_MAGBIO' => 'mbi', 'MBI17_g11997_MAGBIO' => 'mbi', 'MD03G1269000' => 'mdo', 'MD04G1179600' => 'mdo', 'MD11G1289800' => 'mdo', 'MD12G1194700' => 'mdo', 'MD13G1182100' => 'mdo', 'MD13G1182200' => 'mdo', 'MD16G1182600' => 'mdo', 'Medtr2g021400' => 'mtr', 'Medtr2g021470' => 'mtr', 'Medtr2g105810' => 'mtr', 'Medtr3g033580' => 'mtr', 'Medtr6g007970' => 'mtr', 'Medtr7g056330' => 'mtr', 'Medtr7g074290' => 'mtr', 'Medtr7g074380' => 'mtr', 'Medtr7g094550' => 'mtr', 'Medtr8g069995' => 'mtr', 'MELO3C014345.2' => 'cme', 'MELO3C021395.2' => 'cme', 'Migut.D00262' => 'egut', 'Migut.G00257' => 'egut', 'MSTRG.21575' => 'ama', 'MSTRG.3985' => 'ama', 'Nitab4.5_0000295g0140' => 'nta', 'Nitab4.5_0000732g0140' => 'nta', 'Nitab4.5_0003162g0020' => 'nta', 'Nitab4.5_0006180g0090' => 'nta', 'Nitab4.5_0006390g0010' => 'nta', 'Nitab4.5_0007392g0040' => 'nta', 'Nn1g02140' => 'nnu', 'Nn4g26168' => 'nnu', 'Nn5g26754' => 'nnu', 'Oeu001433.1' => 'oeu', 'Oeu010299.2' => 'oeu', 'Oeu011171.1' => 'oeu', 'Oeu037675.1' => 'oeu', 'Oeu038359.1' => 'oeu', 'Oeu063834.1' => 'oeu', 'Oeu063835.1' => 'oeu', 'Os05g0312000' => 'osa', 'Os07g0211101' => 'osa', 'Os07g0211200' => 'osa', 'Os07g0681500' => 'osa', 'Peaxi162Scf00095g01015' => 'pax', 'Peaxi162Scf00104g00329' => 'pax', 'Peaxi162Scf00161g00137' => 'pax', 'PGR004G1665' => 'pgr', 'PGR031G2937' => 'pgr', 'PGR119G2145' => 'pgr', 'PGSC0003DMG400004351' => 'stu', 'PGSC0003DMG400014625' => 'stu', 'PGSC0003DMG401000943' => 'stu', 'Phvul.001G148600' => 'pvu', 'Phvul.004G001700' => 'pvu', 'Phvul.006G154900' => 'pvu', 'Phvul.008G078200' => 'pvu', 'Phvul.011G136500' => 'pvu', 'Potri.002G215600' => 'ptr', 'Potri.008G201600' => 'ptr', 'Potri.014G138400' => 'ptr', 'Potri.016G142500' => 'ptr', 'Pp3c16_10580' => 'ppa', 'Pp3c5_25280' => 'ppa', 'Prupe.1G150000' => 'ppe', 'Prupe.1G150100' => 'ppe', 'Prupe.6G299600' => 'ppe', 'Prupe.8G245000' => 'ppe', 'Psat0s4927g0040' => 'psa', 'Psat1g052080' => 'psa', 'Psat1g183800' => 'psa', 'Psat3g113840' => 'psa', 'Psat3g126120' => 'psa', 'Psat3g126160' => 'psa', 'Psat3g158760' => 'psa', 'Psat3g158840' => 'psa', 'PSO170G2858' => 'pso', 'PSO339G0606' => 'pso', 'PSO384G4709' => 'pso', 'PSO407G0334' => 'pso', 'QL04p040276' => 'qlo', 'QL06p005458' => 'qlo', 'QL06p005472' => 'qlo', 'QL07p030546' => 'qlo', 'QL07p031519' => 'qlo', 'QL09p050949' => 'qlo', 'QL09p050966' => 'qlo', 'QL09p051067' => 'qlo', 'QL12p022706' => 'qlo', 'RcHm_v2.0_Chr2g0119601' => 'rch', 'RcHm_v2.0_Chr3g0459591' => 'rch', 'RcHm_v2.0_Chr4g0418521' => 'rch', 'RcHm_v2.0_Chr4g0418531' => 'rch', 'RcHm_v2.0_Chr4g0418541' => 'rch', 'RcHm_v2.0_Chr6g0291641' => 'rch', 'Rhsim01G0086300' => 'rsi', 'Rhsim01G0276300' => 'rsi', 'Rhsim01G0276500' => 'rsi', 'Rhsim04G0207700' => 'rsi', 'Rhsim05G0234500' => 'rsi', 'Rhsim13G0022400' => 'rsi', 'Sabra02G0167900' => 'sbr', 'Sabra04G0158500' => 'sbr', 'Sabra08G0159800' => 'sbr', 'Sabra10G0011500' => 'sbr', 'Sabra14G0104400' => 'sbr', 'SalBow2G2440' => 'sbo', 'SalBow4G2265' => 'sbo', 'Sc02g0000060' => 'sci', 'Sc05g0005020' => 'sci', 'Sc13g0003890' => 'sci', 'Sed0014865' => 'sed', 'Sed0017224' => 'sed', 'Sed0026391' => 'sed', 'SEGI_00063' => 'sgi', 'SEGI_10967' => 'sgi', 'SEGI_17510' => 'sgi', 'SEGI_24396' => 'sgi', 'SEGI_39719' => 'sgi', 'SEGI_41392' => 'sgi', 'SGA_v2.0_scaffold11G05794' => 'sas', 'SGA_v2.0_scaffold142G35607' => 'sas', 'SGA_v2.0_scaffold1G00447' => 'sas', 'SHI15388' => 'shi', 'SHI15394' => 'shi', 'SHI15396' => 'shi', 'SHI15399' => 'shi', 'SMO343G0151' => 'smo', 'SMO367G1118' => 'smo', 'Solyc01g080200.3' => 'sly', 'Solyc06g008960.3' => 'sly', 'Solyc09g064780.3' => 'sly', 'Sopen01g031980' => 'spe', 'Sopen06g003710' => 'spe', 'Sopen09g026460' => 'spe', 'Sp3g21240' => 'spa', 'Sp4g30030' => 'spa', 'TAR365G0022' => 'tar', 'TAR365G1023' => 'tar', 'TAR365G1253' => 'tar', 'TAR623G0078' => 'tar', 'TAR623G1721' => 'tar', 'TAR633G0959' => 'tar', 'THA.LOC104802225' => 'tha', 'THA.LOC104804769' => 'tha', 'THA.LOC104808660' => 'tha', 'THA.LOC104812792' => 'tha', 'Thecc.01G284000' => 'tca', 'Thecc.04G220600' => 'tca', 'Thecc.05G268900' => 'tca', 'Thecc.08G171100' => 'tca', 'Thhalv10001284m.g' => 'esa', 'Thhalv10019912m.g' => 'esa', 'TPR.G14189' => 'tpr', 'TPR.G18110' => 'tpr', 'TPR.G18130' => 'tpr', 'TPR.G18131' => 'tpr', 'TPR.G18140' => 'tpr', 'TPR.G24282' => 'tpr', 'TPR.G25221' => 'tpr', 'TPR.G29267' => 'tpr', 'TPR.G35315' => 'tpr', 'TPR.G36173' => 'tpr', 'TWI09G0794' => 'twi', 'TWI59G1348' => 'twi', 'TWI74G0430' => 'twi', 'unitig_26.g8940' => 'ugi', 'unitig_749.g13744' => 'ugi', 'unitig_749.g13745' => 'ugi', 'vmacro08269' => 'vma', 'vmacro14937' => 'vma', 'vmacro20401' => 'vma', 'VMungo0464G1349' => 'vmu', 'VMungo0540G0289' => 'vmu', 'VMungo1215G1590' => 'vmu', 'VMungo1309G0221' => 'vmu', 'VMungo1309G2815' => 'vmu', 'VMungo1383G0239' => 'vmu', 'VMungo1383G2910' => 'vmu', 'Zm00001eb095270' => 'zma', 'Zm00001eb095280' => 'zma', 'Zm00001eb111630' => 'zma', 'Zm00001eb237080' => 'zma', 'Zm00001eb273740' => 'zma', 'Zm00001eb285040' => 'zma', 'Zm00001eb330790' => 'zma', 'Zm00001eb337380' => 'zma' ) $gf_id = 'HOM05D001484' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001484' ) $data_identifier = 'HOM05D001484' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 2, 'aly' => (int) 2, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 22, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 7, 'hma' => (int) 2, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 7, 'mtr' => (int) 10, 'cme' => (int) 2, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 4, 'ppa' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 4, 'qlo' => (int) 9, 'rch' => (int) 6, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 10, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 7, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb337380' $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' => 'HOM05D001484', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p31500' => 'bna', 'A05p00020' => 'bna', 'A07p08820' => 'bna', 'Aa31LG4G3300' => 'aar', 'Aa31LG8G10030' => 'aar', 'Actinidia00731' => 'ach', 'Actinidia11473' => 'ach', 'Actinidia23469' => 'ach', 'Actinidia24318' => 'ach', 'Actinidia40196' => 'ach', 'Actinidia40197' => 'ach', 'Actinidia40198' => 'ach', 'Ah.08g212990' => 'amhyb', 'Ah.15g091720' => 'amhyb', 'AL3G38260' => 'aly', 'AL4G47710' => 'aly', 'Aqoxy2G00671' => 'aox', 'Aqoxy2G03236' => 'aox', 'arahy.Tifrunner.gnm1.ann1.05IDCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KR684' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATY3SJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK6QJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6APGL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IDT7Z9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM073U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ0R87' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LE7RV4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT4QRX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V5ENPK' => 'arhy', 'AT2G48110' => 'ath', 'AT3G23590' => 'ath', 'ATR0626G186' => 'atr', 'ATR1127G141' => 'atr', 'Atru.chr4.2583' => 'acertr', 'Atru.chr5.1358' => 'acertr', 'Atru.chr5.1359' => 'acertr', 'Atru.chr8.46' => 'acertr', 'AUR62002640' => 'cqu', 'AUR62030055' => 'cqu', 'AUR62033713' => 'cqu', 'AUR62033714' => 'cqu', 'AUR62036795' => 'cqu', 'AUR62039891' => 'cqu', 'BcaB02g08737' => 'bca', 'BcaB04g20441' => 'bca', 'BcaB06g26509' => 'bca', 'BcaB06g26510' => 'bca', 'BcaB06g26511' => 'bca', 'BcaB06g26512' => 'bca', 'BcaB06g26513' => 'bca', 'BcaC02g12564' => 'bca', 'BcaC02g12565' => 'bca', 'BcaC02g12794' => 'bca', 'BcaC02g12795' => 'bca', 'BcaC02g12796' => 'bca', 'BcaC06g35541' => 'bca', 'BNapus_Darmor_BZH_scaffold_188p00080' => 'bna', 'BNapus_Darmor_BZH_scaffold_188p00090' => 'bna', 'BolC1t03972H' => 'bol', 'BolC1t03973H' => 'bol', 'BolC4t21680H' => 'bol', 'BolC7t41863H' => 'bol', 'BolSC55t61227H' => 'bol', 'BolSC55t61228H' => 'bol', 'BraA01t03278Z' => 'bra', 'BraA05t18998Z' => 'bra', 'BraA07t28673Z' => 'bra', 'C01p40150' => 'bna', 'C05p12370' => 'bna', 'C07p13680' => 'bna', 'CAN.G1006.16' => 'can', 'CAN.G1006.17' => 'can', 'CAN.G1170.2' => 'can', 'CAN.G962.7' => 'can', 'CANSAT25G2179' => 'cansat', 'CANSAT78G1573' => 'cansat', 'CARHR099510' => 'chi', 'CARHR143510' => 'chi', 'Carub.0003s2380' => 'cru', 'Carub.0004s3082' => 'cru', 'Ca_00614_v3' => 'car', 'Ca_07801_v3' => 'car', 'Ca_08567_v3' => 'car', 'Ca_09571_v3' => 'car', 'CBR_g19290' => 'cbr', 'Cc01_g19770' => 'ccan', 'Cc03_g03030' => 'ccan', 'CDE07G0968' => 'cde', 'CDE09G1441' => 'cde', 'Cfa006103' => 'cfa', 'Cfa015573' => 'cfa', 'Cfa016988' => 'cfa', 'Ciclev10006738m.g' => 'ccl', 'Ciclev10010920m.g' => 'ccl', 'Ciclev10018517m.g' => 'ccl', 'CiPaw.01G159200' => 'cil', 'CiPaw.02G091000' => 'cil', 'CiPaw.02G091100' => 'cil', 'CiPaw.08G103100' => 'cil', 'CiPaw.09G224900' => 'cil', 'ClCG06G005740' => 'cla', 'ClCG07G000090' => 'cla', 'ClCG07G000100' => 'cla', 'COL.COLO4_09143' => 'col', 'COL.COLO4_25124' => 'col', 'Cpa.g.sc16.34' => 'cpa', 'Cpa.g.sc3504.1' => 'cpa', 'Cpa.g.sc60.37' => 'cpa', 'CsaV3_6G018520' => 'csa', 'CsaV3_6G036860' => 'csa', 'CSS0001072' => 'camsi', 'CSS0020208' => 'camsi', 'CSS0021253' => 'camsi', 'CSS0022190' => 'camsi', 'CSS0036150' => 'camsi', 'CSS0040442' => 'camsi', 'CSS0042300' => 'camsi', 'CSS0045298' => 'camsi', 'DCAR_012449' => 'dca', 'DCAR_018405' => 'dca', 'DCAR_024573' => 'dca', 'DCAR_030591' => 'dca', 'Dinv16926' => 'din', 'Dinv32963' => 'din', 'Dinv38382' => 'din', 'Dinv38383' => 'din', 'Duzib133G0974' => 'dzi', 'Duzib138G1867' => 'dzi', 'Duzib211G0420' => 'dzi', 'Duzib212G0930' => 'dzi', 'ECA234G1645' => 'eca', 'ECA247G3467' => 'eca', 'ECA248G1703' => 'eca', 'EL10Ac3g06327' => 'bvu', 'EL10Ac7g17204' => 'bvu', 'Eucgr.A00855' => 'egr', 'Eucgr.A00858' => 'egr', 'Eucgr.H01520' => 'egr', 'Eucgr.H03604' => 'egr', 'Eucgr.L03465' => 'egr', 'Eucgr.L03466' => 'egr', 'FAN01G0988' => 'fan', 'FAN02G3892' => 'fan', 'FAN05G3381' => 'fan', 'FAN07G0967' => 'fan', 'FAN07G1493' => 'fan', 'FAN08G3125' => 'fan', 'FAN09G0402' => 'fan', 'FAN12G2594' => 'fan', 'FAN12G3879' => 'fan', 'FAN14G1546' => 'fan', 'FAN15G3626' => 'fan', 'FAN17G0588' => 'fan', 'FAN17G0609' => 'fan', 'FAN18G2817' => 'fan', 'FAN19G1305' => 'fan', 'FAN20G1787' => 'fan', 'FAN22G0073' => 'fan', 'FAN22G0352' => 'fan', 'FAN22G0368' => 'fan', 'FAN22G2273' => 'fan', 'FAN24G1998' => 'fan', 'FAN27G1317' => 'fan', 'FvH4_2g23980' => 'fve', 'FvH4_4g14380' => 'fve', 'FvH4_4g14390' => 'fve', 'FvH4_6g09250' => 'fve', 'Glyma.03G151100' => 'gma', 'Glyma.04G122550' => 'gma', 'Glyma.05G001600' => 'gma', 'Glyma.09G270766' => 'gma', 'Glyma.09G270832' => 'gma', 'Glyma.13G209800' => 'gma', 'Glyma.15G102800' => 'gma', 'Glyma.18G218900' => 'gma', 'Glyma.19G001500' => 'gma', 'Glyma.19G153600' => 'gma', 'Gohir.A02G028600' => 'ghi', 'Gohir.A08G045000' => 'ghi', 'Gohir.A11G120500' => 'ghi', 'Gohir.A12G006200' => 'ghi', 'Gohir.A12G006250' => 'ghi', 'Gohir.D02G036300' => 'ghi', 'Gohir.D08G054700' => 'ghi', 'Gohir.D11G125600' => 'ghi', 'Gohir.D12G005700' => 'ghi', 'Gorai.004G055200' => 'gra', 'Gorai.005G040400' => 'gra', 'Gorai.007G134500' => 'gra', 'Gorai.008G005500' => 'gra', 'GSVIVG01011094001' => 'vvi', 'GSVIVG01017879001' => 'vvi', 'GSVIVG01025988001' => 'vvi', 'GSVIVG01029847001' => 'vvi', 'HanXRQChr10g0282901' => 'han', 'HanXRQChr10g0310371' => 'han', 'HanXRQChr10g0315041' => 'han', 'HanXRQChr11g0327651' => 'han', 'HanXRQChr12g0359391' => 'han', 'Haze_00972' => 'cav', 'Haze_00973' => 'cav', 'Haze_00974' => 'cav', 'Haze_04747' => 'cav', 'Haze_04749' => 'cav', 'Haze_04750' => 'cav', 'Haze_21217' => 'cav', 'Hma1.2p1_1037F.1_g250680' => 'hma', 'Hma1.2p1_1644F.1_g295320' => 'hma', 'HPP92_011322' => 'vpl', 'HPP92_011323' => 'vpl', 'HPP92_011324' => 'vpl', 'HPP92_011325' => 'vpl', 'HPP92_011326' => 'vpl', 'Hund12205' => 'sun', 'Hund17957' => 'sun', 'Lalb_Chr06g0176771' => 'lal', 'Lalb_Chr18g0056021' => 'lal', 'Lalb_Chr18g0056031' => 'lal', 'Lalb_Chr18g0056041' => 'lal', 'Lalb_Chr20g0107751' => 'lal', 'Lalb_Chr20g0118371' => 'lal', 'Lj1g0010239' => 'lja', 'Lj1g0017101' => 'lja', 'Lj2A1178G40' => 'lonja', 'Lj2A54G84' => 'lonja', 'Lj2g0015248' => 'lja', 'Lj3A761T51' => 'lonja', 'Lj6g0018116' => 'lja', 'Lsat_1_v5_gn_4_136040' => 'lsa', 'Lsat_1_v5_gn_5_187461' => 'lsa', 'Lsat_1_v5_gn_5_77001' => 'lsa', 'Lsat_1_v5_gn_9_4461' => 'lsa', 'Manes.01G210100' => 'mes', 'Manes.03G185600' => 'mes', 'Manes.05G073300' => 'mes', 'Manes.09G120300' => 'mes', 'Manes.15G022100' => 'mes', 'Mapoly0096s0053' => 'mpo', 'MBI03_g14058_MAGBIO' => 'mbi', 'MBI03_g33876_MAGBIO' => 'mbi', 'MBI03_g36854_MAGBIO' => 'mbi', 'MBI17_g11997_MAGBIO' => 'mbi', 'MD03G1269000' => 'mdo', 'MD04G1179600' => 'mdo', 'MD11G1289800' => 'mdo', 'MD12G1194700' => 'mdo', 'MD13G1182100' => 'mdo', 'MD13G1182200' => 'mdo', 'MD16G1182600' => 'mdo', 'Medtr2g021400' => 'mtr', 'Medtr2g021470' => 'mtr', 'Medtr2g105810' => 'mtr', 'Medtr3g033580' => 'mtr', 'Medtr6g007970' => 'mtr', 'Medtr7g056330' => 'mtr', 'Medtr7g074290' => 'mtr', 'Medtr7g074380' => 'mtr', 'Medtr7g094550' => 'mtr', 'Medtr8g069995' => 'mtr', 'MELO3C014345.2' => 'cme', 'MELO3C021395.2' => 'cme', 'Migut.D00262' => 'egut', 'Migut.G00257' => 'egut', 'MSTRG.21575' => 'ama', 'MSTRG.3985' => 'ama', 'Nitab4.5_0000295g0140' => 'nta', 'Nitab4.5_0000732g0140' => 'nta', 'Nitab4.5_0003162g0020' => 'nta', 'Nitab4.5_0006180g0090' => 'nta', 'Nitab4.5_0006390g0010' => 'nta', 'Nitab4.5_0007392g0040' => 'nta', 'Nn1g02140' => 'nnu', 'Nn4g26168' => 'nnu', 'Nn5g26754' => 'nnu', 'Oeu001433.1' => 'oeu', 'Oeu010299.2' => 'oeu', 'Oeu011171.1' => 'oeu', 'Oeu037675.1' => 'oeu', 'Oeu038359.1' => 'oeu', 'Oeu063834.1' => 'oeu', 'Oeu063835.1' => 'oeu', 'Os05g0312000' => 'osa', 'Os07g0211101' => 'osa', 'Os07g0211200' => 'osa', 'Os07g0681500' => 'osa', 'Peaxi162Scf00095g01015' => 'pax', 'Peaxi162Scf00104g00329' => 'pax', 'Peaxi162Scf00161g00137' => 'pax', 'PGR004G1665' => 'pgr', 'PGR031G2937' => 'pgr', 'PGR119G2145' => 'pgr', 'PGSC0003DMG400004351' => 'stu', 'PGSC0003DMG400014625' => 'stu', 'PGSC0003DMG401000943' => 'stu', 'Phvul.001G148600' => 'pvu', 'Phvul.004G001700' => 'pvu', 'Phvul.006G154900' => 'pvu', 'Phvul.008G078200' => 'pvu', 'Phvul.011G136500' => 'pvu', 'Potri.002G215600' => 'ptr', 'Potri.008G201600' => 'ptr', 'Potri.014G138400' => 'ptr', 'Potri.016G142500' => 'ptr', 'Pp3c16_10580' => 'ppa', 'Pp3c5_25280' => 'ppa', 'Prupe.1G150000' => 'ppe', 'Prupe.1G150100' => 'ppe', 'Prupe.6G299600' => 'ppe', 'Prupe.8G245000' => 'ppe', 'Psat0s4927g0040' => 'psa', 'Psat1g052080' => 'psa', 'Psat1g183800' => 'psa', 'Psat3g113840' => 'psa', 'Psat3g126120' => 'psa', 'Psat3g126160' => 'psa', 'Psat3g158760' => 'psa', 'Psat3g158840' => 'psa', 'PSO170G2858' => 'pso', 'PSO339G0606' => 'pso', 'PSO384G4709' => 'pso', 'PSO407G0334' => 'pso', 'QL04p040276' => 'qlo', 'QL06p005458' => 'qlo', 'QL06p005472' => 'qlo', 'QL07p030546' => 'qlo', 'QL07p031519' => 'qlo', 'QL09p050949' => 'qlo', 'QL09p050966' => 'qlo', 'QL09p051067' => 'qlo', 'QL12p022706' => 'qlo', 'RcHm_v2.0_Chr2g0119601' => 'rch', 'RcHm_v2.0_Chr3g0459591' => 'rch', 'RcHm_v2.0_Chr4g0418521' => 'rch', 'RcHm_v2.0_Chr4g0418531' => 'rch', 'RcHm_v2.0_Chr4g0418541' => 'rch', 'RcHm_v2.0_Chr6g0291641' => 'rch', 'Rhsim01G0086300' => 'rsi', 'Rhsim01G0276300' => 'rsi', 'Rhsim01G0276500' => 'rsi', 'Rhsim04G0207700' => 'rsi', 'Rhsim05G0234500' => 'rsi', 'Rhsim13G0022400' => 'rsi', 'Sabra02G0167900' => 'sbr', 'Sabra04G0158500' => 'sbr', 'Sabra08G0159800' => 'sbr', 'Sabra10G0011500' => 'sbr', 'Sabra14G0104400' => 'sbr', 'SalBow2G2440' => 'sbo', 'SalBow4G2265' => 'sbo', 'Sc02g0000060' => 'sci', 'Sc05g0005020' => 'sci', 'Sc13g0003890' => 'sci', 'Sed0014865' => 'sed', 'Sed0017224' => 'sed', 'Sed0026391' => 'sed', 'SEGI_00063' => 'sgi', 'SEGI_10967' => 'sgi', 'SEGI_17510' => 'sgi', 'SEGI_24396' => 'sgi', 'SEGI_39719' => 'sgi', 'SEGI_41392' => 'sgi', 'SGA_v2.0_scaffold11G05794' => 'sas', 'SGA_v2.0_scaffold142G35607' => 'sas', 'SGA_v2.0_scaffold1G00447' => 'sas', 'SHI15388' => 'shi', 'SHI15394' => 'shi', 'SHI15396' => 'shi', 'SHI15399' => 'shi', 'SMO343G0151' => 'smo', 'SMO367G1118' => 'smo', 'Solyc01g080200.3' => 'sly', 'Solyc06g008960.3' => 'sly', 'Solyc09g064780.3' => 'sly', 'Sopen01g031980' => 'spe', 'Sopen06g003710' => 'spe', 'Sopen09g026460' => 'spe', 'Sp3g21240' => 'spa', 'Sp4g30030' => 'spa', 'TAR365G0022' => 'tar', 'TAR365G1023' => 'tar', 'TAR365G1253' => 'tar', 'TAR623G0078' => 'tar', 'TAR623G1721' => 'tar', 'TAR633G0959' => 'tar', 'THA.LOC104802225' => 'tha', 'THA.LOC104804769' => 'tha', 'THA.LOC104808660' => 'tha', 'THA.LOC104812792' => 'tha', 'Thecc.01G284000' => 'tca', 'Thecc.04G220600' => 'tca', 'Thecc.05G268900' => 'tca', 'Thecc.08G171100' => 'tca', 'Thhalv10001284m.g' => 'esa', 'Thhalv10019912m.g' => 'esa', 'TPR.G14189' => 'tpr', 'TPR.G18110' => 'tpr', 'TPR.G18130' => 'tpr', 'TPR.G18131' => 'tpr', 'TPR.G18140' => 'tpr', 'TPR.G24282' => 'tpr', 'TPR.G25221' => 'tpr', 'TPR.G29267' => 'tpr', 'TPR.G35315' => 'tpr', 'TPR.G36173' => 'tpr', 'TWI09G0794' => 'twi', 'TWI59G1348' => 'twi', 'TWI74G0430' => 'twi', 'unitig_26.g8940' => 'ugi', 'unitig_749.g13744' => 'ugi', 'unitig_749.g13745' => 'ugi', 'vmacro08269' => 'vma', 'vmacro14937' => 'vma', 'vmacro20401' => 'vma', 'VMungo0464G1349' => 'vmu', 'VMungo0540G0289' => 'vmu', 'VMungo1215G1590' => 'vmu', 'VMungo1309G0221' => 'vmu', 'VMungo1309G2815' => 'vmu', 'VMungo1383G0239' => 'vmu', 'VMungo1383G2910' => 'vmu', 'Zm00001eb095270' => 'zma', 'Zm00001eb095280' => 'zma', 'Zm00001eb111630' => 'zma', 'Zm00001eb237080' => 'zma', 'Zm00001eb273740' => 'zma', 'Zm00001eb285040' => 'zma', 'Zm00001eb330790' => 'zma', 'Zm00001eb337380' => 'zma' ), 'gf_id' => 'HOM05D001484', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001484' ), 'data_identifier' => 'HOM05D001484', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001484', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p31500' => 'bna', 'A05p00020' => 'bna', 'A07p08820' => 'bna', 'Aa31LG4G3300' => 'aar', 'Aa31LG8G10030' => 'aar', 'Actinidia00731' => 'ach', 'Actinidia11473' => 'ach', 'Actinidia23469' => 'ach', 'Actinidia24318' => 'ach', 'Actinidia40196' => 'ach', 'Actinidia40197' => 'ach', 'Actinidia40198' => 'ach', 'Ah.08g212990' => 'amhyb', 'Ah.15g091720' => 'amhyb', 'AL3G38260' => 'aly', 'AL4G47710' => 'aly', 'Aqoxy2G00671' => 'aox', 'Aqoxy2G03236' => 'aox', 'arahy.Tifrunner.gnm1.ann1.05IDCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KR684' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATY3SJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK6QJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6APGL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IDT7Z9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM073U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ0R87' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LE7RV4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT4QRX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V5ENPK' => 'arhy', 'AT2G48110' => 'ath', 'AT3G23590' => 'ath', 'ATR0626G186' => 'atr', 'ATR1127G141' => 'atr', 'Atru.chr4.2583' => 'acertr', 'Atru.chr5.1358' => 'acertr', 'Atru.chr5.1359' => 'acertr', 'Atru.chr8.46' => 'acertr', 'AUR62002640' => 'cqu', 'AUR62030055' => 'cqu', 'AUR62033713' => 'cqu', 'AUR62033714' => 'cqu', 'AUR62036795' => 'cqu', 'AUR62039891' => 'cqu', 'BcaB02g08737' => 'bca', 'BcaB04g20441' => 'bca', 'BcaB06g26509' => 'bca', 'BcaB06g26510' => 'bca', 'BcaB06g26511' => 'bca', 'BcaB06g26512' => 'bca', 'BcaB06g26513' => 'bca', 'BcaC02g12564' => 'bca', 'BcaC02g12565' => 'bca', 'BcaC02g12794' => 'bca', 'BcaC02g12795' => 'bca', 'BcaC02g12796' => 'bca', 'BcaC06g35541' => 'bca', 'BNapus_Darmor_BZH_scaffold_188p00080' => 'bna', 'BNapus_Darmor_BZH_scaffold_188p00090' => 'bna', 'BolC1t03972H' => 'bol', 'BolC1t03973H' => 'bol', 'BolC4t21680H' => 'bol', 'BolC7t41863H' => 'bol', 'BolSC55t61227H' => 'bol', 'BolSC55t61228H' => 'bol', 'BraA01t03278Z' => 'bra', 'BraA05t18998Z' => 'bra', 'BraA07t28673Z' => 'bra', 'C01p40150' => 'bna', 'C05p12370' => 'bna', 'C07p13680' => 'bna', 'CAN.G1006.16' => 'can', 'CAN.G1006.17' => 'can', 'CAN.G1170.2' => 'can', 'CAN.G962.7' => 'can', 'CANSAT25G2179' => 'cansat', 'CANSAT78G1573' => 'cansat', 'CARHR099510' => 'chi', 'CARHR143510' => 'chi', 'Carub.0003s2380' => 'cru', 'Carub.0004s3082' => 'cru', 'Ca_00614_v3' => 'car', 'Ca_07801_v3' => 'car', 'Ca_08567_v3' => 'car', 'Ca_09571_v3' => 'car', 'CBR_g19290' => 'cbr', 'Cc01_g19770' => 'ccan', 'Cc03_g03030' => 'ccan', 'CDE07G0968' => 'cde', 'CDE09G1441' => 'cde', 'Cfa006103' => 'cfa', 'Cfa015573' => 'cfa', 'Cfa016988' => 'cfa', 'Ciclev10006738m.g' => 'ccl', 'Ciclev10010920m.g' => 'ccl', 'Ciclev10018517m.g' => 'ccl', 'CiPaw.01G159200' => 'cil', 'CiPaw.02G091000' => 'cil', 'CiPaw.02G091100' => 'cil', 'CiPaw.08G103100' => 'cil', 'CiPaw.09G224900' => 'cil', 'ClCG06G005740' => 'cla', 'ClCG07G000090' => 'cla', 'ClCG07G000100' => 'cla', 'COL.COLO4_09143' => 'col', 'COL.COLO4_25124' => 'col', 'Cpa.g.sc16.34' => 'cpa', 'Cpa.g.sc3504.1' => 'cpa', 'Cpa.g.sc60.37' => 'cpa', 'CsaV3_6G018520' => 'csa', 'CsaV3_6G036860' => 'csa', 'CSS0001072' => 'camsi', 'CSS0020208' => 'camsi', 'CSS0021253' => 'camsi', 'CSS0022190' => 'camsi', 'CSS0036150' => 'camsi', 'CSS0040442' => 'camsi', 'CSS0042300' => 'camsi', 'CSS0045298' => 'camsi', 'DCAR_012449' => 'dca', 'DCAR_018405' => 'dca', 'DCAR_024573' => 'dca', 'DCAR_030591' => 'dca', 'Dinv16926' => 'din', 'Dinv32963' => 'din', 'Dinv38382' => 'din', 'Dinv38383' => 'din', 'Duzib133G0974' => 'dzi', 'Duzib138G1867' => 'dzi', 'Duzib211G0420' => 'dzi', 'Duzib212G0930' => 'dzi', 'ECA234G1645' => 'eca', 'ECA247G3467' => 'eca', 'ECA248G1703' => 'eca', 'EL10Ac3g06327' => 'bvu', 'EL10Ac7g17204' => 'bvu', 'Eucgr.A00855' => 'egr', 'Eucgr.A00858' => 'egr', 'Eucgr.H01520' => 'egr', 'Eucgr.H03604' => 'egr', 'Eucgr.L03465' => 'egr', 'Eucgr.L03466' => 'egr', 'FAN01G0988' => 'fan', 'FAN02G3892' => 'fan', 'FAN05G3381' => 'fan', 'FAN07G0967' => 'fan', 'FAN07G1493' => 'fan', 'FAN08G3125' => 'fan', 'FAN09G0402' => 'fan', 'FAN12G2594' => 'fan', 'FAN12G3879' => 'fan', 'FAN14G1546' => 'fan', 'FAN15G3626' => 'fan', 'FAN17G0588' => 'fan', 'FAN17G0609' => 'fan', 'FAN18G2817' => 'fan', 'FAN19G1305' => 'fan', 'FAN20G1787' => 'fan', 'FAN22G0073' => 'fan', 'FAN22G0352' => 'fan', 'FAN22G0368' => 'fan', 'FAN22G2273' => 'fan', 'FAN24G1998' => 'fan', 'FAN27G1317' => 'fan', 'FvH4_2g23980' => 'fve', 'FvH4_4g14380' => 'fve', 'FvH4_4g14390' => 'fve', 'FvH4_6g09250' => 'fve', 'Glyma.03G151100' => 'gma', 'Glyma.04G122550' => 'gma', 'Glyma.05G001600' => 'gma', 'Glyma.09G270766' => 'gma', 'Glyma.09G270832' => 'gma', 'Glyma.13G209800' => 'gma', 'Glyma.15G102800' => 'gma', 'Glyma.18G218900' => 'gma', 'Glyma.19G001500' => 'gma', 'Glyma.19G153600' => 'gma', 'Gohir.A02G028600' => 'ghi', 'Gohir.A08G045000' => 'ghi', 'Gohir.A11G120500' => 'ghi', 'Gohir.A12G006200' => 'ghi', 'Gohir.A12G006250' => 'ghi', 'Gohir.D02G036300' => 'ghi', 'Gohir.D08G054700' => 'ghi', 'Gohir.D11G125600' => 'ghi', 'Gohir.D12G005700' => 'ghi', 'Gorai.004G055200' => 'gra', 'Gorai.005G040400' => 'gra', 'Gorai.007G134500' => 'gra', 'Gorai.008G005500' => 'gra', 'GSVIVG01011094001' => 'vvi', 'GSVIVG01017879001' => 'vvi', 'GSVIVG01025988001' => 'vvi', 'GSVIVG01029847001' => 'vvi', 'HanXRQChr10g0282901' => 'han', 'HanXRQChr10g0310371' => 'han', 'HanXRQChr10g0315041' => 'han', 'HanXRQChr11g0327651' => 'han', 'HanXRQChr12g0359391' => 'han', 'Haze_00972' => 'cav', 'Haze_00973' => 'cav', 'Haze_00974' => 'cav', 'Haze_04747' => 'cav', 'Haze_04749' => 'cav', 'Haze_04750' => 'cav', 'Haze_21217' => 'cav', 'Hma1.2p1_1037F.1_g250680' => 'hma', 'Hma1.2p1_1644F.1_g295320' => 'hma', 'HPP92_011322' => 'vpl', 'HPP92_011323' => 'vpl', 'HPP92_011324' => 'vpl', 'HPP92_011325' => 'vpl', 'HPP92_011326' => 'vpl', 'Hund12205' => 'sun', 'Hund17957' => 'sun', 'Lalb_Chr06g0176771' => 'lal', 'Lalb_Chr18g0056021' => 'lal', 'Lalb_Chr18g0056031' => 'lal', 'Lalb_Chr18g0056041' => 'lal', 'Lalb_Chr20g0107751' => 'lal', 'Lalb_Chr20g0118371' => 'lal', 'Lj1g0010239' => 'lja', 'Lj1g0017101' => 'lja', 'Lj2A1178G40' => 'lonja', 'Lj2A54G84' => 'lonja', 'Lj2g0015248' => 'lja', 'Lj3A761T51' => 'lonja', 'Lj6g0018116' => 'lja', 'Lsat_1_v5_gn_4_136040' => 'lsa', 'Lsat_1_v5_gn_5_187461' => 'lsa', 'Lsat_1_v5_gn_5_77001' => 'lsa', 'Lsat_1_v5_gn_9_4461' => 'lsa', 'Manes.01G210100' => 'mes', 'Manes.03G185600' => 'mes', 'Manes.05G073300' => 'mes', 'Manes.09G120300' => 'mes', 'Manes.15G022100' => 'mes', 'Mapoly0096s0053' => 'mpo', 'MBI03_g14058_MAGBIO' => 'mbi', 'MBI03_g33876_MAGBIO' => 'mbi', 'MBI03_g36854_MAGBIO' => 'mbi', 'MBI17_g11997_MAGBIO' => 'mbi', 'MD03G1269000' => 'mdo', 'MD04G1179600' => 'mdo', 'MD11G1289800' => 'mdo', 'MD12G1194700' => 'mdo', 'MD13G1182100' => 'mdo', 'MD13G1182200' => 'mdo', 'MD16G1182600' => 'mdo', 'Medtr2g021400' => 'mtr', 'Medtr2g021470' => 'mtr', 'Medtr2g105810' => 'mtr', 'Medtr3g033580' => 'mtr', 'Medtr6g007970' => 'mtr', 'Medtr7g056330' => 'mtr', 'Medtr7g074290' => 'mtr', 'Medtr7g074380' => 'mtr', 'Medtr7g094550' => 'mtr', 'Medtr8g069995' => 'mtr', 'MELO3C014345.2' => 'cme', 'MELO3C021395.2' => 'cme', 'Migut.D00262' => 'egut', 'Migut.G00257' => 'egut', 'MSTRG.21575' => 'ama', 'MSTRG.3985' => 'ama', 'Nitab4.5_0000295g0140' => 'nta', 'Nitab4.5_0000732g0140' => 'nta', 'Nitab4.5_0003162g0020' => 'nta', 'Nitab4.5_0006180g0090' => 'nta', 'Nitab4.5_0006390g0010' => 'nta', 'Nitab4.5_0007392g0040' => 'nta', 'Nn1g02140' => 'nnu', 'Nn4g26168' => 'nnu', 'Nn5g26754' => 'nnu', 'Oeu001433.1' => 'oeu', 'Oeu010299.2' => 'oeu', 'Oeu011171.1' => 'oeu', 'Oeu037675.1' => 'oeu', 'Oeu038359.1' => 'oeu', 'Oeu063834.1' => 'oeu', 'Oeu063835.1' => 'oeu', 'Os05g0312000' => 'osa', 'Os07g0211101' => 'osa', 'Os07g0211200' => 'osa', 'Os07g0681500' => 'osa', 'Peaxi162Scf00095g01015' => 'pax', 'Peaxi162Scf00104g00329' => 'pax', 'Peaxi162Scf00161g00137' => 'pax', 'PGR004G1665' => 'pgr', 'PGR031G2937' => 'pgr', 'PGR119G2145' => 'pgr', 'PGSC0003DMG400004351' => 'stu', 'PGSC0003DMG400014625' => 'stu', 'PGSC0003DMG401000943' => 'stu', 'Phvul.001G148600' => 'pvu', 'Phvul.004G001700' => 'pvu', 'Phvul.006G154900' => 'pvu', 'Phvul.008G078200' => 'pvu', 'Phvul.011G136500' => 'pvu', 'Potri.002G215600' => 'ptr', 'Potri.008G201600' => 'ptr', 'Potri.014G138400' => 'ptr', 'Potri.016G142500' => 'ptr', 'Pp3c16_10580' => 'ppa', 'Pp3c5_25280' => 'ppa', 'Prupe.1G150000' => 'ppe', 'Prupe.1G150100' => 'ppe', 'Prupe.6G299600' => 'ppe', 'Prupe.8G245000' => 'ppe', 'Psat0s4927g0040' => 'psa', 'Psat1g052080' => 'psa', 'Psat1g183800' => 'psa', 'Psat3g113840' => 'psa', 'Psat3g126120' => 'psa', 'Psat3g126160' => 'psa', 'Psat3g158760' => 'psa', 'Psat3g158840' => 'psa', 'PSO170G2858' => 'pso', 'PSO339G0606' => 'pso', 'PSO384G4709' => 'pso', 'PSO407G0334' => 'pso', 'QL04p040276' => 'qlo', 'QL06p005458' => 'qlo', 'QL06p005472' => 'qlo', 'QL07p030546' => 'qlo', 'QL07p031519' => 'qlo', 'QL09p050949' => 'qlo', 'QL09p050966' => 'qlo', 'QL09p051067' => 'qlo', 'QL12p022706' => 'qlo', 'RcHm_v2.0_Chr2g0119601' => 'rch', 'RcHm_v2.0_Chr3g0459591' => 'rch', 'RcHm_v2.0_Chr4g0418521' => 'rch', 'RcHm_v2.0_Chr4g0418531' => 'rch', 'RcHm_v2.0_Chr4g0418541' => 'rch', 'RcHm_v2.0_Chr6g0291641' => 'rch', 'Rhsim01G0086300' => 'rsi', 'Rhsim01G0276300' => 'rsi', 'Rhsim01G0276500' => 'rsi', 'Rhsim04G0207700' => 'rsi', 'Rhsim05G0234500' => 'rsi', 'Rhsim13G0022400' => 'rsi', 'Sabra02G0167900' => 'sbr', 'Sabra04G0158500' => 'sbr', 'Sabra08G0159800' => 'sbr', 'Sabra10G0011500' => 'sbr', 'Sabra14G0104400' => 'sbr', 'SalBow2G2440' => 'sbo', 'SalBow4G2265' => 'sbo', 'Sc02g0000060' => 'sci', 'Sc05g0005020' => 'sci', 'Sc13g0003890' => 'sci', 'Sed0014865' => 'sed', 'Sed0017224' => 'sed', 'Sed0026391' => 'sed', 'SEGI_00063' => 'sgi', 'SEGI_10967' => 'sgi', 'SEGI_17510' => 'sgi', 'SEGI_24396' => 'sgi', 'SEGI_39719' => 'sgi', 'SEGI_41392' => 'sgi', 'SGA_v2.0_scaffold11G05794' => 'sas', 'SGA_v2.0_scaffold142G35607' => 'sas', 'SGA_v2.0_scaffold1G00447' => 'sas', 'SHI15388' => 'shi', 'SHI15394' => 'shi', 'SHI15396' => 'shi', 'SHI15399' => 'shi', 'SMO343G0151' => 'smo', 'SMO367G1118' => 'smo', 'Solyc01g080200.3' => 'sly', 'Solyc06g008960.3' => 'sly', 'Solyc09g064780.3' => 'sly', 'Sopen01g031980' => 'spe', 'Sopen06g003710' => 'spe', 'Sopen09g026460' => 'spe', 'Sp3g21240' => 'spa', 'Sp4g30030' => 'spa', 'TAR365G0022' => 'tar', 'TAR365G1023' => 'tar', 'TAR365G1253' => 'tar', 'TAR623G0078' => 'tar', 'TAR623G1721' => 'tar', 'TAR633G0959' => 'tar', 'THA.LOC104802225' => 'tha', 'THA.LOC104804769' => 'tha', 'THA.LOC104808660' => 'tha', 'THA.LOC104812792' => 'tha', 'Thecc.01G284000' => 'tca', 'Thecc.04G220600' => 'tca', 'Thecc.05G268900' => 'tca', 'Thecc.08G171100' => 'tca', 'Thhalv10001284m.g' => 'esa', 'Thhalv10019912m.g' => 'esa', 'TPR.G14189' => 'tpr', 'TPR.G18110' => 'tpr', 'TPR.G18130' => 'tpr', 'TPR.G18131' => 'tpr', 'TPR.G18140' => 'tpr', 'TPR.G24282' => 'tpr', 'TPR.G25221' => 'tpr', 'TPR.G29267' => 'tpr', 'TPR.G35315' => 'tpr', 'TPR.G36173' => 'tpr', 'TWI09G0794' => 'twi', 'TWI59G1348' => 'twi', 'TWI74G0430' => 'twi', 'unitig_26.g8940' => 'ugi', 'unitig_749.g13744' => 'ugi', 'unitig_749.g13745' => 'ugi', 'vmacro08269' => 'vma', 'vmacro14937' => 'vma', 'vmacro20401' => 'vma', 'VMungo0464G1349' => 'vmu', 'VMungo0540G0289' => 'vmu', 'VMungo1215G1590' => 'vmu', 'VMungo1309G0221' => 'vmu', 'VMungo1309G2815' => 'vmu', 'VMungo1383G0239' => 'vmu', 'VMungo1383G2910' => 'vmu', 'Zm00001eb095270' => 'zma', 'Zm00001eb095280' => 'zma', 'Zm00001eb111630' => 'zma', 'Zm00001eb237080' => 'zma', 'Zm00001eb273740' => 'zma', 'Zm00001eb285040' => 'zma', 'Zm00001eb330790' => 'zma', 'Zm00001eb337380' => 'zma' ) $gf_id = 'HOM05D001484' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001484' ) $data_identifier = 'HOM05D001484' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 2, 'aly' => (int) 2, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 22, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 7, 'hma' => (int) 2, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 7, 'mtr' => (int) 10, 'cme' => (int) 2, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 4, 'ppa' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 4, 'qlo' => (int) 9, 'rch' => (int) 6, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 10, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 7, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb337380' $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' => 'HOM05D001484', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p31500' => 'bna', 'A05p00020' => 'bna', 'A07p08820' => 'bna', 'Aa31LG4G3300' => 'aar', 'Aa31LG8G10030' => 'aar', 'Actinidia00731' => 'ach', 'Actinidia11473' => 'ach', 'Actinidia23469' => 'ach', 'Actinidia24318' => 'ach', 'Actinidia40196' => 'ach', 'Actinidia40197' => 'ach', 'Actinidia40198' => 'ach', 'Ah.08g212990' => 'amhyb', 'Ah.15g091720' => 'amhyb', 'AL3G38260' => 'aly', 'AL4G47710' => 'aly', 'Aqoxy2G00671' => 'aox', 'Aqoxy2G03236' => 'aox', 'arahy.Tifrunner.gnm1.ann1.05IDCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KR684' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATY3SJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK6QJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6APGL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IDT7Z9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM073U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ0R87' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LE7RV4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT4QRX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V5ENPK' => 'arhy', 'AT2G48110' => 'ath', 'AT3G23590' => 'ath', 'ATR0626G186' => 'atr', 'ATR1127G141' => 'atr', 'Atru.chr4.2583' => 'acertr', 'Atru.chr5.1358' => 'acertr', 'Atru.chr5.1359' => 'acertr', 'Atru.chr8.46' => 'acertr', 'AUR62002640' => 'cqu', 'AUR62030055' => 'cqu', 'AUR62033713' => 'cqu', 'AUR62033714' => 'cqu', 'AUR62036795' => 'cqu', 'AUR62039891' => 'cqu', 'BcaB02g08737' => 'bca', 'BcaB04g20441' => 'bca', 'BcaB06g26509' => 'bca', 'BcaB06g26510' => 'bca', 'BcaB06g26511' => 'bca', 'BcaB06g26512' => 'bca', 'BcaB06g26513' => 'bca', 'BcaC02g12564' => 'bca', 'BcaC02g12565' => 'bca', 'BcaC02g12794' => 'bca', 'BcaC02g12795' => 'bca', 'BcaC02g12796' => 'bca', 'BcaC06g35541' => 'bca', 'BNapus_Darmor_BZH_scaffold_188p00080' => 'bna', 'BNapus_Darmor_BZH_scaffold_188p00090' => 'bna', 'BolC1t03972H' => 'bol', 'BolC1t03973H' => 'bol', 'BolC4t21680H' => 'bol', 'BolC7t41863H' => 'bol', 'BolSC55t61227H' => 'bol', 'BolSC55t61228H' => 'bol', 'BraA01t03278Z' => 'bra', 'BraA05t18998Z' => 'bra', 'BraA07t28673Z' => 'bra', 'C01p40150' => 'bna', 'C05p12370' => 'bna', 'C07p13680' => 'bna', 'CAN.G1006.16' => 'can', 'CAN.G1006.17' => 'can', 'CAN.G1170.2' => 'can', 'CAN.G962.7' => 'can', 'CANSAT25G2179' => 'cansat', 'CANSAT78G1573' => 'cansat', 'CARHR099510' => 'chi', 'CARHR143510' => 'chi', 'Carub.0003s2380' => 'cru', 'Carub.0004s3082' => 'cru', 'Ca_00614_v3' => 'car', 'Ca_07801_v3' => 'car', 'Ca_08567_v3' => 'car', 'Ca_09571_v3' => 'car', 'CBR_g19290' => 'cbr', 'Cc01_g19770' => 'ccan', 'Cc03_g03030' => 'ccan', 'CDE07G0968' => 'cde', 'CDE09G1441' => 'cde', 'Cfa006103' => 'cfa', 'Cfa015573' => 'cfa', 'Cfa016988' => 'cfa', 'Ciclev10006738m.g' => 'ccl', 'Ciclev10010920m.g' => 'ccl', 'Ciclev10018517m.g' => 'ccl', 'CiPaw.01G159200' => 'cil', 'CiPaw.02G091000' => 'cil', 'CiPaw.02G091100' => 'cil', 'CiPaw.08G103100' => 'cil', 'CiPaw.09G224900' => 'cil', 'ClCG06G005740' => 'cla', 'ClCG07G000090' => 'cla', 'ClCG07G000100' => 'cla', 'COL.COLO4_09143' => 'col', 'COL.COLO4_25124' => 'col', 'Cpa.g.sc16.34' => 'cpa', 'Cpa.g.sc3504.1' => 'cpa', 'Cpa.g.sc60.37' => 'cpa', 'CsaV3_6G018520' => 'csa', 'CsaV3_6G036860' => 'csa', 'CSS0001072' => 'camsi', 'CSS0020208' => 'camsi', 'CSS0021253' => 'camsi', 'CSS0022190' => 'camsi', 'CSS0036150' => 'camsi', 'CSS0040442' => 'camsi', 'CSS0042300' => 'camsi', 'CSS0045298' => 'camsi', 'DCAR_012449' => 'dca', 'DCAR_018405' => 'dca', 'DCAR_024573' => 'dca', 'DCAR_030591' => 'dca', 'Dinv16926' => 'din', 'Dinv32963' => 'din', 'Dinv38382' => 'din', 'Dinv38383' => 'din', 'Duzib133G0974' => 'dzi', 'Duzib138G1867' => 'dzi', 'Duzib211G0420' => 'dzi', 'Duzib212G0930' => 'dzi', 'ECA234G1645' => 'eca', 'ECA247G3467' => 'eca', 'ECA248G1703' => 'eca', 'EL10Ac3g06327' => 'bvu', 'EL10Ac7g17204' => 'bvu', 'Eucgr.A00855' => 'egr', 'Eucgr.A00858' => 'egr', 'Eucgr.H01520' => 'egr', 'Eucgr.H03604' => 'egr', 'Eucgr.L03465' => 'egr', 'Eucgr.L03466' => 'egr', 'FAN01G0988' => 'fan', 'FAN02G3892' => 'fan', 'FAN05G3381' => 'fan', 'FAN07G0967' => 'fan', 'FAN07G1493' => 'fan', 'FAN08G3125' => 'fan', 'FAN09G0402' => 'fan', 'FAN12G2594' => 'fan', 'FAN12G3879' => 'fan', 'FAN14G1546' => 'fan', 'FAN15G3626' => 'fan', 'FAN17G0588' => 'fan', 'FAN17G0609' => 'fan', 'FAN18G2817' => 'fan', 'FAN19G1305' => 'fan', 'FAN20G1787' => 'fan', 'FAN22G0073' => 'fan', 'FAN22G0352' => 'fan', 'FAN22G0368' => 'fan', 'FAN22G2273' => 'fan', 'FAN24G1998' => 'fan', 'FAN27G1317' => 'fan', 'FvH4_2g23980' => 'fve', 'FvH4_4g14380' => 'fve', 'FvH4_4g14390' => 'fve', 'FvH4_6g09250' => 'fve', 'Glyma.03G151100' => 'gma', 'Glyma.04G122550' => 'gma', 'Glyma.05G001600' => 'gma', 'Glyma.09G270766' => 'gma', 'Glyma.09G270832' => 'gma', 'Glyma.13G209800' => 'gma', 'Glyma.15G102800' => 'gma', 'Glyma.18G218900' => 'gma', 'Glyma.19G001500' => 'gma', 'Glyma.19G153600' => 'gma', 'Gohir.A02G028600' => 'ghi', 'Gohir.A08G045000' => 'ghi', 'Gohir.A11G120500' => 'ghi', 'Gohir.A12G006200' => 'ghi', 'Gohir.A12G006250' => 'ghi', 'Gohir.D02G036300' => 'ghi', 'Gohir.D08G054700' => 'ghi', 'Gohir.D11G125600' => 'ghi', 'Gohir.D12G005700' => 'ghi', 'Gorai.004G055200' => 'gra', 'Gorai.005G040400' => 'gra', 'Gorai.007G134500' => 'gra', 'Gorai.008G005500' => 'gra', 'GSVIVG01011094001' => 'vvi', 'GSVIVG01017879001' => 'vvi', 'GSVIVG01025988001' => 'vvi', 'GSVIVG01029847001' => 'vvi', 'HanXRQChr10g0282901' => 'han', 'HanXRQChr10g0310371' => 'han', 'HanXRQChr10g0315041' => 'han', 'HanXRQChr11g0327651' => 'han', 'HanXRQChr12g0359391' => 'han', 'Haze_00972' => 'cav', 'Haze_00973' => 'cav', 'Haze_00974' => 'cav', 'Haze_04747' => 'cav', 'Haze_04749' => 'cav', 'Haze_04750' => 'cav', 'Haze_21217' => 'cav', 'Hma1.2p1_1037F.1_g250680' => 'hma', 'Hma1.2p1_1644F.1_g295320' => 'hma', 'HPP92_011322' => 'vpl', 'HPP92_011323' => 'vpl', 'HPP92_011324' => 'vpl', 'HPP92_011325' => 'vpl', 'HPP92_011326' => 'vpl', 'Hund12205' => 'sun', 'Hund17957' => 'sun', 'Lalb_Chr06g0176771' => 'lal', 'Lalb_Chr18g0056021' => 'lal', 'Lalb_Chr18g0056031' => 'lal', 'Lalb_Chr18g0056041' => 'lal', 'Lalb_Chr20g0107751' => 'lal', 'Lalb_Chr20g0118371' => 'lal', 'Lj1g0010239' => 'lja', 'Lj1g0017101' => 'lja', 'Lj2A1178G40' => 'lonja', 'Lj2A54G84' => 'lonja', 'Lj2g0015248' => 'lja', 'Lj3A761T51' => 'lonja', 'Lj6g0018116' => 'lja', 'Lsat_1_v5_gn_4_136040' => 'lsa', 'Lsat_1_v5_gn_5_187461' => 'lsa', 'Lsat_1_v5_gn_5_77001' => 'lsa', 'Lsat_1_v5_gn_9_4461' => 'lsa', 'Manes.01G210100' => 'mes', 'Manes.03G185600' => 'mes', 'Manes.05G073300' => 'mes', 'Manes.09G120300' => 'mes', 'Manes.15G022100' => 'mes', 'Mapoly0096s0053' => 'mpo', 'MBI03_g14058_MAGBIO' => 'mbi', 'MBI03_g33876_MAGBIO' => 'mbi', 'MBI03_g36854_MAGBIO' => 'mbi', 'MBI17_g11997_MAGBIO' => 'mbi', 'MD03G1269000' => 'mdo', 'MD04G1179600' => 'mdo', 'MD11G1289800' => 'mdo', 'MD12G1194700' => 'mdo', 'MD13G1182100' => 'mdo', 'MD13G1182200' => 'mdo', 'MD16G1182600' => 'mdo', 'Medtr2g021400' => 'mtr', 'Medtr2g021470' => 'mtr', 'Medtr2g105810' => 'mtr', 'Medtr3g033580' => 'mtr', 'Medtr6g007970' => 'mtr', 'Medtr7g056330' => 'mtr', 'Medtr7g074290' => 'mtr', 'Medtr7g074380' => 'mtr', 'Medtr7g094550' => 'mtr', 'Medtr8g069995' => 'mtr', 'MELO3C014345.2' => 'cme', 'MELO3C021395.2' => 'cme', 'Migut.D00262' => 'egut', 'Migut.G00257' => 'egut', 'MSTRG.21575' => 'ama', 'MSTRG.3985' => 'ama', 'Nitab4.5_0000295g0140' => 'nta', 'Nitab4.5_0000732g0140' => 'nta', 'Nitab4.5_0003162g0020' => 'nta', 'Nitab4.5_0006180g0090' => 'nta', 'Nitab4.5_0006390g0010' => 'nta', 'Nitab4.5_0007392g0040' => 'nta', 'Nn1g02140' => 'nnu', 'Nn4g26168' => 'nnu', 'Nn5g26754' => 'nnu', 'Oeu001433.1' => 'oeu', 'Oeu010299.2' => 'oeu', 'Oeu011171.1' => 'oeu', 'Oeu037675.1' => 'oeu', 'Oeu038359.1' => 'oeu', 'Oeu063834.1' => 'oeu', 'Oeu063835.1' => 'oeu', 'Os05g0312000' => 'osa', 'Os07g0211101' => 'osa', 'Os07g0211200' => 'osa', 'Os07g0681500' => 'osa', 'Peaxi162Scf00095g01015' => 'pax', 'Peaxi162Scf00104g00329' => 'pax', 'Peaxi162Scf00161g00137' => 'pax', 'PGR004G1665' => 'pgr', 'PGR031G2937' => 'pgr', 'PGR119G2145' => 'pgr', 'PGSC0003DMG400004351' => 'stu', 'PGSC0003DMG400014625' => 'stu', 'PGSC0003DMG401000943' => 'stu', 'Phvul.001G148600' => 'pvu', 'Phvul.004G001700' => 'pvu', 'Phvul.006G154900' => 'pvu', 'Phvul.008G078200' => 'pvu', 'Phvul.011G136500' => 'pvu', 'Potri.002G215600' => 'ptr', 'Potri.008G201600' => 'ptr', 'Potri.014G138400' => 'ptr', 'Potri.016G142500' => 'ptr', 'Pp3c16_10580' => 'ppa', 'Pp3c5_25280' => 'ppa', 'Prupe.1G150000' => 'ppe', 'Prupe.1G150100' => 'ppe', 'Prupe.6G299600' => 'ppe', 'Prupe.8G245000' => 'ppe', 'Psat0s4927g0040' => 'psa', 'Psat1g052080' => 'psa', 'Psat1g183800' => 'psa', 'Psat3g113840' => 'psa', 'Psat3g126120' => 'psa', 'Psat3g126160' => 'psa', 'Psat3g158760' => 'psa', 'Psat3g158840' => 'psa', 'PSO170G2858' => 'pso', 'PSO339G0606' => 'pso', 'PSO384G4709' => 'pso', 'PSO407G0334' => 'pso', 'QL04p040276' => 'qlo', 'QL06p005458' => 'qlo', 'QL06p005472' => 'qlo', 'QL07p030546' => 'qlo', 'QL07p031519' => 'qlo', 'QL09p050949' => 'qlo', 'QL09p050966' => 'qlo', 'QL09p051067' => 'qlo', 'QL12p022706' => 'qlo', 'RcHm_v2.0_Chr2g0119601' => 'rch', 'RcHm_v2.0_Chr3g0459591' => 'rch', 'RcHm_v2.0_Chr4g0418521' => 'rch', 'RcHm_v2.0_Chr4g0418531' => 'rch', 'RcHm_v2.0_Chr4g0418541' => 'rch', 'RcHm_v2.0_Chr6g0291641' => 'rch', 'Rhsim01G0086300' => 'rsi', 'Rhsim01G0276300' => 'rsi', 'Rhsim01G0276500' => 'rsi', 'Rhsim04G0207700' => 'rsi', 'Rhsim05G0234500' => 'rsi', 'Rhsim13G0022400' => 'rsi', 'Sabra02G0167900' => 'sbr', 'Sabra04G0158500' => 'sbr', 'Sabra08G0159800' => 'sbr', 'Sabra10G0011500' => 'sbr', 'Sabra14G0104400' => 'sbr', 'SalBow2G2440' => 'sbo', 'SalBow4G2265' => 'sbo', 'Sc02g0000060' => 'sci', 'Sc05g0005020' => 'sci', 'Sc13g0003890' => 'sci', 'Sed0014865' => 'sed', 'Sed0017224' => 'sed', 'Sed0026391' => 'sed', 'SEGI_00063' => 'sgi', 'SEGI_10967' => 'sgi', 'SEGI_17510' => 'sgi', 'SEGI_24396' => 'sgi', 'SEGI_39719' => 'sgi', 'SEGI_41392' => 'sgi', 'SGA_v2.0_scaffold11G05794' => 'sas', 'SGA_v2.0_scaffold142G35607' => 'sas', 'SGA_v2.0_scaffold1G00447' => 'sas', 'SHI15388' => 'shi', 'SHI15394' => 'shi', 'SHI15396' => 'shi', 'SHI15399' => 'shi', 'SMO343G0151' => 'smo', 'SMO367G1118' => 'smo', 'Solyc01g080200.3' => 'sly', 'Solyc06g008960.3' => 'sly', 'Solyc09g064780.3' => 'sly', 'Sopen01g031980' => 'spe', 'Sopen06g003710' => 'spe', 'Sopen09g026460' => 'spe', 'Sp3g21240' => 'spa', 'Sp4g30030' => 'spa', 'TAR365G0022' => 'tar', 'TAR365G1023' => 'tar', 'TAR365G1253' => 'tar', 'TAR623G0078' => 'tar', 'TAR623G1721' => 'tar', 'TAR633G0959' => 'tar', 'THA.LOC104802225' => 'tha', 'THA.LOC104804769' => 'tha', 'THA.LOC104808660' => 'tha', 'THA.LOC104812792' => 'tha', 'Thecc.01G284000' => 'tca', 'Thecc.04G220600' => 'tca', 'Thecc.05G268900' => 'tca', 'Thecc.08G171100' => 'tca', 'Thhalv10001284m.g' => 'esa', 'Thhalv10019912m.g' => 'esa', 'TPR.G14189' => 'tpr', 'TPR.G18110' => 'tpr', 'TPR.G18130' => 'tpr', 'TPR.G18131' => 'tpr', 'TPR.G18140' => 'tpr', 'TPR.G24282' => 'tpr', 'TPR.G25221' => 'tpr', 'TPR.G29267' => 'tpr', 'TPR.G35315' => 'tpr', 'TPR.G36173' => 'tpr', 'TWI09G0794' => 'twi', 'TWI59G1348' => 'twi', 'TWI74G0430' => 'twi', 'unitig_26.g8940' => 'ugi', 'unitig_749.g13744' => 'ugi', 'unitig_749.g13745' => 'ugi', 'vmacro08269' => 'vma', 'vmacro14937' => 'vma', 'vmacro20401' => 'vma', 'VMungo0464G1349' => 'vmu', 'VMungo0540G0289' => 'vmu', 'VMungo1215G1590' => 'vmu', 'VMungo1309G0221' => 'vmu', 'VMungo1309G2815' => 'vmu', 'VMungo1383G0239' => 'vmu', 'VMungo1383G2910' => 'vmu', 'Zm00001eb095270' => 'zma', 'Zm00001eb095280' => 'zma', 'Zm00001eb111630' => 'zma', 'Zm00001eb237080' => 'zma', 'Zm00001eb273740' => 'zma', 'Zm00001eb285040' => 'zma', 'Zm00001eb330790' => 'zma', 'Zm00001eb337380' => 'zma' ), 'gf_id' => 'HOM05D001484', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001484' ), 'data_identifier' => 'HOM05D001484', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001484', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p31500' => 'bna', 'A05p00020' => 'bna', 'A07p08820' => 'bna', 'Aa31LG4G3300' => 'aar', 'Aa31LG8G10030' => 'aar', 'Actinidia00731' => 'ach', 'Actinidia11473' => 'ach', 'Actinidia23469' => 'ach', 'Actinidia24318' => 'ach', 'Actinidia40196' => 'ach', 'Actinidia40197' => 'ach', 'Actinidia40198' => 'ach', 'Ah.08g212990' => 'amhyb', 'Ah.15g091720' => 'amhyb', 'AL3G38260' => 'aly', 'AL4G47710' => 'aly', 'Aqoxy2G00671' => 'aox', 'Aqoxy2G03236' => 'aox', 'arahy.Tifrunner.gnm1.ann1.05IDCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KR684' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATY3SJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK6QJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6APGL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IDT7Z9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM073U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ0R87' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LE7RV4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT4QRX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V5ENPK' => 'arhy', 'AT2G48110' => 'ath', 'AT3G23590' => 'ath', 'ATR0626G186' => 'atr', 'ATR1127G141' => 'atr', 'Atru.chr4.2583' => 'acertr', 'Atru.chr5.1358' => 'acertr', 'Atru.chr5.1359' => 'acertr', 'Atru.chr8.46' => 'acertr', 'AUR62002640' => 'cqu', 'AUR62030055' => 'cqu', 'AUR62033713' => 'cqu', 'AUR62033714' => 'cqu', 'AUR62036795' => 'cqu', 'AUR62039891' => 'cqu', 'BcaB02g08737' => 'bca', 'BcaB04g20441' => 'bca', 'BcaB06g26509' => 'bca', 'BcaB06g26510' => 'bca', 'BcaB06g26511' => 'bca', 'BcaB06g26512' => 'bca', 'BcaB06g26513' => 'bca', 'BcaC02g12564' => 'bca', 'BcaC02g12565' => 'bca', 'BcaC02g12794' => 'bca', 'BcaC02g12795' => 'bca', 'BcaC02g12796' => 'bca', 'BcaC06g35541' => 'bca', 'BNapus_Darmor_BZH_scaffold_188p00080' => 'bna', 'BNapus_Darmor_BZH_scaffold_188p00090' => 'bna', 'BolC1t03972H' => 'bol', 'BolC1t03973H' => 'bol', 'BolC4t21680H' => 'bol', 'BolC7t41863H' => 'bol', 'BolSC55t61227H' => 'bol', 'BolSC55t61228H' => 'bol', 'BraA01t03278Z' => 'bra', 'BraA05t18998Z' => 'bra', 'BraA07t28673Z' => 'bra', 'C01p40150' => 'bna', 'C05p12370' => 'bna', 'C07p13680' => 'bna', 'CAN.G1006.16' => 'can', 'CAN.G1006.17' => 'can', 'CAN.G1170.2' => 'can', 'CAN.G962.7' => 'can', 'CANSAT25G2179' => 'cansat', 'CANSAT78G1573' => 'cansat', 'CARHR099510' => 'chi', 'CARHR143510' => 'chi', 'Carub.0003s2380' => 'cru', 'Carub.0004s3082' => 'cru', 'Ca_00614_v3' => 'car', 'Ca_07801_v3' => 'car', 'Ca_08567_v3' => 'car', 'Ca_09571_v3' => 'car', 'CBR_g19290' => 'cbr', 'Cc01_g19770' => 'ccan', 'Cc03_g03030' => 'ccan', 'CDE07G0968' => 'cde', 'CDE09G1441' => 'cde', 'Cfa006103' => 'cfa', 'Cfa015573' => 'cfa', 'Cfa016988' => 'cfa', 'Ciclev10006738m.g' => 'ccl', 'Ciclev10010920m.g' => 'ccl', 'Ciclev10018517m.g' => 'ccl', 'CiPaw.01G159200' => 'cil', 'CiPaw.02G091000' => 'cil', 'CiPaw.02G091100' => 'cil', 'CiPaw.08G103100' => 'cil', 'CiPaw.09G224900' => 'cil', 'ClCG06G005740' => 'cla', 'ClCG07G000090' => 'cla', 'ClCG07G000100' => 'cla', 'COL.COLO4_09143' => 'col', 'COL.COLO4_25124' => 'col', 'Cpa.g.sc16.34' => 'cpa', 'Cpa.g.sc3504.1' => 'cpa', 'Cpa.g.sc60.37' => 'cpa', 'CsaV3_6G018520' => 'csa', 'CsaV3_6G036860' => 'csa', 'CSS0001072' => 'camsi', 'CSS0020208' => 'camsi', 'CSS0021253' => 'camsi', 'CSS0022190' => 'camsi', 'CSS0036150' => 'camsi', 'CSS0040442' => 'camsi', 'CSS0042300' => 'camsi', 'CSS0045298' => 'camsi', 'DCAR_012449' => 'dca', 'DCAR_018405' => 'dca', 'DCAR_024573' => 'dca', 'DCAR_030591' => 'dca', 'Dinv16926' => 'din', 'Dinv32963' => 'din', 'Dinv38382' => 'din', 'Dinv38383' => 'din', 'Duzib133G0974' => 'dzi', 'Duzib138G1867' => 'dzi', 'Duzib211G0420' => 'dzi', 'Duzib212G0930' => 'dzi', 'ECA234G1645' => 'eca', 'ECA247G3467' => 'eca', 'ECA248G1703' => 'eca', 'EL10Ac3g06327' => 'bvu', 'EL10Ac7g17204' => 'bvu', 'Eucgr.A00855' => 'egr', 'Eucgr.A00858' => 'egr', 'Eucgr.H01520' => 'egr', 'Eucgr.H03604' => 'egr', 'Eucgr.L03465' => 'egr', 'Eucgr.L03466' => 'egr', 'FAN01G0988' => 'fan', 'FAN02G3892' => 'fan', 'FAN05G3381' => 'fan', 'FAN07G0967' => 'fan', 'FAN07G1493' => 'fan', 'FAN08G3125' => 'fan', 'FAN09G0402' => 'fan', 'FAN12G2594' => 'fan', 'FAN12G3879' => 'fan', 'FAN14G1546' => 'fan', 'FAN15G3626' => 'fan', 'FAN17G0588' => 'fan', 'FAN17G0609' => 'fan', 'FAN18G2817' => 'fan', 'FAN19G1305' => 'fan', 'FAN20G1787' => 'fan', 'FAN22G0073' => 'fan', 'FAN22G0352' => 'fan', 'FAN22G0368' => 'fan', 'FAN22G2273' => 'fan', 'FAN24G1998' => 'fan', 'FAN27G1317' => 'fan', 'FvH4_2g23980' => 'fve', 'FvH4_4g14380' => 'fve', 'FvH4_4g14390' => 'fve', 'FvH4_6g09250' => 'fve', 'Glyma.03G151100' => 'gma', 'Glyma.04G122550' => 'gma', 'Glyma.05G001600' => 'gma', 'Glyma.09G270766' => 'gma', 'Glyma.09G270832' => 'gma', 'Glyma.13G209800' => 'gma', 'Glyma.15G102800' => 'gma', 'Glyma.18G218900' => 'gma', 'Glyma.19G001500' => 'gma', 'Glyma.19G153600' => 'gma', 'Gohir.A02G028600' => 'ghi', 'Gohir.A08G045000' => 'ghi', 'Gohir.A11G120500' => 'ghi', 'Gohir.A12G006200' => 'ghi', 'Gohir.A12G006250' => 'ghi', 'Gohir.D02G036300' => 'ghi', 'Gohir.D08G054700' => 'ghi', 'Gohir.D11G125600' => 'ghi', 'Gohir.D12G005700' => 'ghi', 'Gorai.004G055200' => 'gra', 'Gorai.005G040400' => 'gra', 'Gorai.007G134500' => 'gra', 'Gorai.008G005500' => 'gra', 'GSVIVG01011094001' => 'vvi', 'GSVIVG01017879001' => 'vvi', 'GSVIVG01025988001' => 'vvi', 'GSVIVG01029847001' => 'vvi', 'HanXRQChr10g0282901' => 'han', 'HanXRQChr10g0310371' => 'han', 'HanXRQChr10g0315041' => 'han', 'HanXRQChr11g0327651' => 'han', 'HanXRQChr12g0359391' => 'han', 'Haze_00972' => 'cav', 'Haze_00973' => 'cav', 'Haze_00974' => 'cav', 'Haze_04747' => 'cav', 'Haze_04749' => 'cav', 'Haze_04750' => 'cav', 'Haze_21217' => 'cav', 'Hma1.2p1_1037F.1_g250680' => 'hma', 'Hma1.2p1_1644F.1_g295320' => 'hma', 'HPP92_011322' => 'vpl', 'HPP92_011323' => 'vpl', 'HPP92_011324' => 'vpl', 'HPP92_011325' => 'vpl', 'HPP92_011326' => 'vpl', 'Hund12205' => 'sun', 'Hund17957' => 'sun', 'Lalb_Chr06g0176771' => 'lal', 'Lalb_Chr18g0056021' => 'lal', 'Lalb_Chr18g0056031' => 'lal', 'Lalb_Chr18g0056041' => 'lal', 'Lalb_Chr20g0107751' => 'lal', 'Lalb_Chr20g0118371' => 'lal', 'Lj1g0010239' => 'lja', 'Lj1g0017101' => 'lja', 'Lj2A1178G40' => 'lonja', 'Lj2A54G84' => 'lonja', 'Lj2g0015248' => 'lja', 'Lj3A761T51' => 'lonja', 'Lj6g0018116' => 'lja', 'Lsat_1_v5_gn_4_136040' => 'lsa', 'Lsat_1_v5_gn_5_187461' => 'lsa', 'Lsat_1_v5_gn_5_77001' => 'lsa', 'Lsat_1_v5_gn_9_4461' => 'lsa', 'Manes.01G210100' => 'mes', 'Manes.03G185600' => 'mes', 'Manes.05G073300' => 'mes', 'Manes.09G120300' => 'mes', 'Manes.15G022100' => 'mes', 'Mapoly0096s0053' => 'mpo', 'MBI03_g14058_MAGBIO' => 'mbi', 'MBI03_g33876_MAGBIO' => 'mbi', 'MBI03_g36854_MAGBIO' => 'mbi', 'MBI17_g11997_MAGBIO' => 'mbi', 'MD03G1269000' => 'mdo', 'MD04G1179600' => 'mdo', 'MD11G1289800' => 'mdo', 'MD12G1194700' => 'mdo', 'MD13G1182100' => 'mdo', 'MD13G1182200' => 'mdo', 'MD16G1182600' => 'mdo', 'Medtr2g021400' => 'mtr', 'Medtr2g021470' => 'mtr', 'Medtr2g105810' => 'mtr', 'Medtr3g033580' => 'mtr', 'Medtr6g007970' => 'mtr', 'Medtr7g056330' => 'mtr', 'Medtr7g074290' => 'mtr', 'Medtr7g074380' => 'mtr', 'Medtr7g094550' => 'mtr', 'Medtr8g069995' => 'mtr', 'MELO3C014345.2' => 'cme', 'MELO3C021395.2' => 'cme', 'Migut.D00262' => 'egut', 'Migut.G00257' => 'egut', 'MSTRG.21575' => 'ama', 'MSTRG.3985' => 'ama', 'Nitab4.5_0000295g0140' => 'nta', 'Nitab4.5_0000732g0140' => 'nta', 'Nitab4.5_0003162g0020' => 'nta', 'Nitab4.5_0006180g0090' => 'nta', 'Nitab4.5_0006390g0010' => 'nta', 'Nitab4.5_0007392g0040' => 'nta', 'Nn1g02140' => 'nnu', 'Nn4g26168' => 'nnu', 'Nn5g26754' => 'nnu', 'Oeu001433.1' => 'oeu', 'Oeu010299.2' => 'oeu', 'Oeu011171.1' => 'oeu', 'Oeu037675.1' => 'oeu', 'Oeu038359.1' => 'oeu', 'Oeu063834.1' => 'oeu', 'Oeu063835.1' => 'oeu', 'Os05g0312000' => 'osa', 'Os07g0211101' => 'osa', 'Os07g0211200' => 'osa', 'Os07g0681500' => 'osa', 'Peaxi162Scf00095g01015' => 'pax', 'Peaxi162Scf00104g00329' => 'pax', 'Peaxi162Scf00161g00137' => 'pax', 'PGR004G1665' => 'pgr', 'PGR031G2937' => 'pgr', 'PGR119G2145' => 'pgr', 'PGSC0003DMG400004351' => 'stu', 'PGSC0003DMG400014625' => 'stu', 'PGSC0003DMG401000943' => 'stu', 'Phvul.001G148600' => 'pvu', 'Phvul.004G001700' => 'pvu', 'Phvul.006G154900' => 'pvu', 'Phvul.008G078200' => 'pvu', 'Phvul.011G136500' => 'pvu', 'Potri.002G215600' => 'ptr', 'Potri.008G201600' => 'ptr', 'Potri.014G138400' => 'ptr', 'Potri.016G142500' => 'ptr', 'Pp3c16_10580' => 'ppa', 'Pp3c5_25280' => 'ppa', 'Prupe.1G150000' => 'ppe', 'Prupe.1G150100' => 'ppe', 'Prupe.6G299600' => 'ppe', 'Prupe.8G245000' => 'ppe', 'Psat0s4927g0040' => 'psa', 'Psat1g052080' => 'psa', 'Psat1g183800' => 'psa', 'Psat3g113840' => 'psa', 'Psat3g126120' => 'psa', 'Psat3g126160' => 'psa', 'Psat3g158760' => 'psa', 'Psat3g158840' => 'psa', 'PSO170G2858' => 'pso', 'PSO339G0606' => 'pso', 'PSO384G4709' => 'pso', 'PSO407G0334' => 'pso', 'QL04p040276' => 'qlo', 'QL06p005458' => 'qlo', 'QL06p005472' => 'qlo', 'QL07p030546' => 'qlo', 'QL07p031519' => 'qlo', 'QL09p050949' => 'qlo', 'QL09p050966' => 'qlo', 'QL09p051067' => 'qlo', 'QL12p022706' => 'qlo', 'RcHm_v2.0_Chr2g0119601' => 'rch', 'RcHm_v2.0_Chr3g0459591' => 'rch', 'RcHm_v2.0_Chr4g0418521' => 'rch', 'RcHm_v2.0_Chr4g0418531' => 'rch', 'RcHm_v2.0_Chr4g0418541' => 'rch', 'RcHm_v2.0_Chr6g0291641' => 'rch', 'Rhsim01G0086300' => 'rsi', 'Rhsim01G0276300' => 'rsi', 'Rhsim01G0276500' => 'rsi', 'Rhsim04G0207700' => 'rsi', 'Rhsim05G0234500' => 'rsi', 'Rhsim13G0022400' => 'rsi', 'Sabra02G0167900' => 'sbr', 'Sabra04G0158500' => 'sbr', 'Sabra08G0159800' => 'sbr', 'Sabra10G0011500' => 'sbr', 'Sabra14G0104400' => 'sbr', 'SalBow2G2440' => 'sbo', 'SalBow4G2265' => 'sbo', 'Sc02g0000060' => 'sci', 'Sc05g0005020' => 'sci', 'Sc13g0003890' => 'sci', 'Sed0014865' => 'sed', 'Sed0017224' => 'sed', 'Sed0026391' => 'sed', 'SEGI_00063' => 'sgi', 'SEGI_10967' => 'sgi', 'SEGI_17510' => 'sgi', 'SEGI_24396' => 'sgi', 'SEGI_39719' => 'sgi', 'SEGI_41392' => 'sgi', 'SGA_v2.0_scaffold11G05794' => 'sas', 'SGA_v2.0_scaffold142G35607' => 'sas', 'SGA_v2.0_scaffold1G00447' => 'sas', 'SHI15388' => 'shi', 'SHI15394' => 'shi', 'SHI15396' => 'shi', 'SHI15399' => 'shi', 'SMO343G0151' => 'smo', 'SMO367G1118' => 'smo', 'Solyc01g080200.3' => 'sly', 'Solyc06g008960.3' => 'sly', 'Solyc09g064780.3' => 'sly', 'Sopen01g031980' => 'spe', 'Sopen06g003710' => 'spe', 'Sopen09g026460' => 'spe', 'Sp3g21240' => 'spa', 'Sp4g30030' => 'spa', 'TAR365G0022' => 'tar', 'TAR365G1023' => 'tar', 'TAR365G1253' => 'tar', 'TAR623G0078' => 'tar', 'TAR623G1721' => 'tar', 'TAR633G0959' => 'tar', 'THA.LOC104802225' => 'tha', 'THA.LOC104804769' => 'tha', 'THA.LOC104808660' => 'tha', 'THA.LOC104812792' => 'tha', 'Thecc.01G284000' => 'tca', 'Thecc.04G220600' => 'tca', 'Thecc.05G268900' => 'tca', 'Thecc.08G171100' => 'tca', 'Thhalv10001284m.g' => 'esa', 'Thhalv10019912m.g' => 'esa', 'TPR.G14189' => 'tpr', 'TPR.G18110' => 'tpr', 'TPR.G18130' => 'tpr', 'TPR.G18131' => 'tpr', 'TPR.G18140' => 'tpr', 'TPR.G24282' => 'tpr', 'TPR.G25221' => 'tpr', 'TPR.G29267' => 'tpr', 'TPR.G35315' => 'tpr', 'TPR.G36173' => 'tpr', 'TWI09G0794' => 'twi', 'TWI59G1348' => 'twi', 'TWI74G0430' => 'twi', 'unitig_26.g8940' => 'ugi', 'unitig_749.g13744' => 'ugi', 'unitig_749.g13745' => 'ugi', 'vmacro08269' => 'vma', 'vmacro14937' => 'vma', 'vmacro20401' => 'vma', 'VMungo0464G1349' => 'vmu', 'VMungo0540G0289' => 'vmu', 'VMungo1215G1590' => 'vmu', 'VMungo1309G0221' => 'vmu', 'VMungo1309G2815' => 'vmu', 'VMungo1383G0239' => 'vmu', 'VMungo1383G2910' => 'vmu', 'Zm00001eb095270' => 'zma', 'Zm00001eb095280' => 'zma', 'Zm00001eb111630' => 'zma', 'Zm00001eb237080' => 'zma', 'Zm00001eb273740' => 'zma', 'Zm00001eb285040' => 'zma', 'Zm00001eb330790' => 'zma', 'Zm00001eb337380' => 'zma' ) $gf_id = 'HOM05D001484' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001484' ) $data_identifier = 'HOM05D001484' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 2, 'aly' => (int) 2, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 22, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 7, 'hma' => (int) 2, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 7, 'mtr' => (int) 10, 'cme' => (int) 2, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 4, 'ppa' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 4, 'qlo' => (int) 9, 'rch' => (int) 6, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 10, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 7, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb337380' $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' => 'HOM05D001484', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p31500' => 'bna', 'A05p00020' => 'bna', 'A07p08820' => 'bna', 'Aa31LG4G3300' => 'aar', 'Aa31LG8G10030' => 'aar', 'Actinidia00731' => 'ach', 'Actinidia11473' => 'ach', 'Actinidia23469' => 'ach', 'Actinidia24318' => 'ach', 'Actinidia40196' => 'ach', 'Actinidia40197' => 'ach', 'Actinidia40198' => 'ach', 'Ah.08g212990' => 'amhyb', 'Ah.15g091720' => 'amhyb', 'AL3G38260' => 'aly', 'AL4G47710' => 'aly', 'Aqoxy2G00671' => 'aox', 'Aqoxy2G03236' => 'aox', 'arahy.Tifrunner.gnm1.ann1.05IDCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KR684' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATY3SJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK6QJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6APGL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IDT7Z9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM073U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ0R87' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LE7RV4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT4QRX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V5ENPK' => 'arhy', 'AT2G48110' => 'ath', 'AT3G23590' => 'ath', 'ATR0626G186' => 'atr', 'ATR1127G141' => 'atr', 'Atru.chr4.2583' => 'acertr', 'Atru.chr5.1358' => 'acertr', 'Atru.chr5.1359' => 'acertr', 'Atru.chr8.46' => 'acertr', 'AUR62002640' => 'cqu', 'AUR62030055' => 'cqu', 'AUR62033713' => 'cqu', 'AUR62033714' => 'cqu', 'AUR62036795' => 'cqu', 'AUR62039891' => 'cqu', 'BcaB02g08737' => 'bca', 'BcaB04g20441' => 'bca', 'BcaB06g26509' => 'bca', 'BcaB06g26510' => 'bca', 'BcaB06g26511' => 'bca', 'BcaB06g26512' => 'bca', 'BcaB06g26513' => 'bca', 'BcaC02g12564' => 'bca', 'BcaC02g12565' => 'bca', 'BcaC02g12794' => 'bca', 'BcaC02g12795' => 'bca', 'BcaC02g12796' => 'bca', 'BcaC06g35541' => 'bca', 'BNapus_Darmor_BZH_scaffold_188p00080' => 'bna', 'BNapus_Darmor_BZH_scaffold_188p00090' => 'bna', 'BolC1t03972H' => 'bol', 'BolC1t03973H' => 'bol', 'BolC4t21680H' => 'bol', 'BolC7t41863H' => 'bol', 'BolSC55t61227H' => 'bol', 'BolSC55t61228H' => 'bol', 'BraA01t03278Z' => 'bra', 'BraA05t18998Z' => 'bra', 'BraA07t28673Z' => 'bra', 'C01p40150' => 'bna', 'C05p12370' => 'bna', 'C07p13680' => 'bna', 'CAN.G1006.16' => 'can', 'CAN.G1006.17' => 'can', 'CAN.G1170.2' => 'can', 'CAN.G962.7' => 'can', 'CANSAT25G2179' => 'cansat', 'CANSAT78G1573' => 'cansat', 'CARHR099510' => 'chi', 'CARHR143510' => 'chi', 'Carub.0003s2380' => 'cru', 'Carub.0004s3082' => 'cru', 'Ca_00614_v3' => 'car', 'Ca_07801_v3' => 'car', 'Ca_08567_v3' => 'car', 'Ca_09571_v3' => 'car', 'CBR_g19290' => 'cbr', 'Cc01_g19770' => 'ccan', 'Cc03_g03030' => 'ccan', 'CDE07G0968' => 'cde', 'CDE09G1441' => 'cde', 'Cfa006103' => 'cfa', 'Cfa015573' => 'cfa', 'Cfa016988' => 'cfa', 'Ciclev10006738m.g' => 'ccl', 'Ciclev10010920m.g' => 'ccl', 'Ciclev10018517m.g' => 'ccl', 'CiPaw.01G159200' => 'cil', 'CiPaw.02G091000' => 'cil', 'CiPaw.02G091100' => 'cil', 'CiPaw.08G103100' => 'cil', 'CiPaw.09G224900' => 'cil', 'ClCG06G005740' => 'cla', 'ClCG07G000090' => 'cla', 'ClCG07G000100' => 'cla', 'COL.COLO4_09143' => 'col', 'COL.COLO4_25124' => 'col', 'Cpa.g.sc16.34' => 'cpa', 'Cpa.g.sc3504.1' => 'cpa', 'Cpa.g.sc60.37' => 'cpa', 'CsaV3_6G018520' => 'csa', 'CsaV3_6G036860' => 'csa', 'CSS0001072' => 'camsi', 'CSS0020208' => 'camsi', 'CSS0021253' => 'camsi', 'CSS0022190' => 'camsi', 'CSS0036150' => 'camsi', 'CSS0040442' => 'camsi', 'CSS0042300' => 'camsi', 'CSS0045298' => 'camsi', 'DCAR_012449' => 'dca', 'DCAR_018405' => 'dca', 'DCAR_024573' => 'dca', 'DCAR_030591' => 'dca', 'Dinv16926' => 'din', 'Dinv32963' => 'din', 'Dinv38382' => 'din', 'Dinv38383' => 'din', 'Duzib133G0974' => 'dzi', 'Duzib138G1867' => 'dzi', 'Duzib211G0420' => 'dzi', 'Duzib212G0930' => 'dzi', 'ECA234G1645' => 'eca', 'ECA247G3467' => 'eca', 'ECA248G1703' => 'eca', 'EL10Ac3g06327' => 'bvu', 'EL10Ac7g17204' => 'bvu', 'Eucgr.A00855' => 'egr', 'Eucgr.A00858' => 'egr', 'Eucgr.H01520' => 'egr', 'Eucgr.H03604' => 'egr', 'Eucgr.L03465' => 'egr', 'Eucgr.L03466' => 'egr', 'FAN01G0988' => 'fan', 'FAN02G3892' => 'fan', 'FAN05G3381' => 'fan', 'FAN07G0967' => 'fan', 'FAN07G1493' => 'fan', 'FAN08G3125' => 'fan', 'FAN09G0402' => 'fan', 'FAN12G2594' => 'fan', 'FAN12G3879' => 'fan', 'FAN14G1546' => 'fan', 'FAN15G3626' => 'fan', 'FAN17G0588' => 'fan', 'FAN17G0609' => 'fan', 'FAN18G2817' => 'fan', 'FAN19G1305' => 'fan', 'FAN20G1787' => 'fan', 'FAN22G0073' => 'fan', 'FAN22G0352' => 'fan', 'FAN22G0368' => 'fan', 'FAN22G2273' => 'fan', 'FAN24G1998' => 'fan', 'FAN27G1317' => 'fan', 'FvH4_2g23980' => 'fve', 'FvH4_4g14380' => 'fve', 'FvH4_4g14390' => 'fve', 'FvH4_6g09250' => 'fve', 'Glyma.03G151100' => 'gma', 'Glyma.04G122550' => 'gma', 'Glyma.05G001600' => 'gma', 'Glyma.09G270766' => 'gma', 'Glyma.09G270832' => 'gma', 'Glyma.13G209800' => 'gma', 'Glyma.15G102800' => 'gma', 'Glyma.18G218900' => 'gma', 'Glyma.19G001500' => 'gma', 'Glyma.19G153600' => 'gma', 'Gohir.A02G028600' => 'ghi', 'Gohir.A08G045000' => 'ghi', 'Gohir.A11G120500' => 'ghi', 'Gohir.A12G006200' => 'ghi', 'Gohir.A12G006250' => 'ghi', 'Gohir.D02G036300' => 'ghi', 'Gohir.D08G054700' => 'ghi', 'Gohir.D11G125600' => 'ghi', 'Gohir.D12G005700' => 'ghi', 'Gorai.004G055200' => 'gra', 'Gorai.005G040400' => 'gra', 'Gorai.007G134500' => 'gra', 'Gorai.008G005500' => 'gra', 'GSVIVG01011094001' => 'vvi', 'GSVIVG01017879001' => 'vvi', 'GSVIVG01025988001' => 'vvi', 'GSVIVG01029847001' => 'vvi', 'HanXRQChr10g0282901' => 'han', 'HanXRQChr10g0310371' => 'han', 'HanXRQChr10g0315041' => 'han', 'HanXRQChr11g0327651' => 'han', 'HanXRQChr12g0359391' => 'han', 'Haze_00972' => 'cav', 'Haze_00973' => 'cav', 'Haze_00974' => 'cav', 'Haze_04747' => 'cav', 'Haze_04749' => 'cav', 'Haze_04750' => 'cav', 'Haze_21217' => 'cav', 'Hma1.2p1_1037F.1_g250680' => 'hma', 'Hma1.2p1_1644F.1_g295320' => 'hma', 'HPP92_011322' => 'vpl', 'HPP92_011323' => 'vpl', 'HPP92_011324' => 'vpl', 'HPP92_011325' => 'vpl', 'HPP92_011326' => 'vpl', 'Hund12205' => 'sun', 'Hund17957' => 'sun', 'Lalb_Chr06g0176771' => 'lal', 'Lalb_Chr18g0056021' => 'lal', 'Lalb_Chr18g0056031' => 'lal', 'Lalb_Chr18g0056041' => 'lal', 'Lalb_Chr20g0107751' => 'lal', 'Lalb_Chr20g0118371' => 'lal', 'Lj1g0010239' => 'lja', 'Lj1g0017101' => 'lja', 'Lj2A1178G40' => 'lonja', 'Lj2A54G84' => 'lonja', 'Lj2g0015248' => 'lja', 'Lj3A761T51' => 'lonja', 'Lj6g0018116' => 'lja', 'Lsat_1_v5_gn_4_136040' => 'lsa', 'Lsat_1_v5_gn_5_187461' => 'lsa', 'Lsat_1_v5_gn_5_77001' => 'lsa', 'Lsat_1_v5_gn_9_4461' => 'lsa', 'Manes.01G210100' => 'mes', 'Manes.03G185600' => 'mes', 'Manes.05G073300' => 'mes', 'Manes.09G120300' => 'mes', 'Manes.15G022100' => 'mes', 'Mapoly0096s0053' => 'mpo', 'MBI03_g14058_MAGBIO' => 'mbi', 'MBI03_g33876_MAGBIO' => 'mbi', 'MBI03_g36854_MAGBIO' => 'mbi', 'MBI17_g11997_MAGBIO' => 'mbi', 'MD03G1269000' => 'mdo', 'MD04G1179600' => 'mdo', 'MD11G1289800' => 'mdo', 'MD12G1194700' => 'mdo', 'MD13G1182100' => 'mdo', 'MD13G1182200' => 'mdo', 'MD16G1182600' => 'mdo', 'Medtr2g021400' => 'mtr', 'Medtr2g021470' => 'mtr', 'Medtr2g105810' => 'mtr', 'Medtr3g033580' => 'mtr', 'Medtr6g007970' => 'mtr', 'Medtr7g056330' => 'mtr', 'Medtr7g074290' => 'mtr', 'Medtr7g074380' => 'mtr', 'Medtr7g094550' => 'mtr', 'Medtr8g069995' => 'mtr', 'MELO3C014345.2' => 'cme', 'MELO3C021395.2' => 'cme', 'Migut.D00262' => 'egut', 'Migut.G00257' => 'egut', 'MSTRG.21575' => 'ama', 'MSTRG.3985' => 'ama', 'Nitab4.5_0000295g0140' => 'nta', 'Nitab4.5_0000732g0140' => 'nta', 'Nitab4.5_0003162g0020' => 'nta', 'Nitab4.5_0006180g0090' => 'nta', 'Nitab4.5_0006390g0010' => 'nta', 'Nitab4.5_0007392g0040' => 'nta', 'Nn1g02140' => 'nnu', 'Nn4g26168' => 'nnu', 'Nn5g26754' => 'nnu', 'Oeu001433.1' => 'oeu', 'Oeu010299.2' => 'oeu', 'Oeu011171.1' => 'oeu', 'Oeu037675.1' => 'oeu', 'Oeu038359.1' => 'oeu', 'Oeu063834.1' => 'oeu', 'Oeu063835.1' => 'oeu', 'Os05g0312000' => 'osa', 'Os07g0211101' => 'osa', 'Os07g0211200' => 'osa', 'Os07g0681500' => 'osa', 'Peaxi162Scf00095g01015' => 'pax', 'Peaxi162Scf00104g00329' => 'pax', 'Peaxi162Scf00161g00137' => 'pax', 'PGR004G1665' => 'pgr', 'PGR031G2937' => 'pgr', 'PGR119G2145' => 'pgr', 'PGSC0003DMG400004351' => 'stu', 'PGSC0003DMG400014625' => 'stu', 'PGSC0003DMG401000943' => 'stu', 'Phvul.001G148600' => 'pvu', 'Phvul.004G001700' => 'pvu', 'Phvul.006G154900' => 'pvu', 'Phvul.008G078200' => 'pvu', 'Phvul.011G136500' => 'pvu', 'Potri.002G215600' => 'ptr', 'Potri.008G201600' => 'ptr', 'Potri.014G138400' => 'ptr', 'Potri.016G142500' => 'ptr', 'Pp3c16_10580' => 'ppa', 'Pp3c5_25280' => 'ppa', 'Prupe.1G150000' => 'ppe', 'Prupe.1G150100' => 'ppe', 'Prupe.6G299600' => 'ppe', 'Prupe.8G245000' => 'ppe', 'Psat0s4927g0040' => 'psa', 'Psat1g052080' => 'psa', 'Psat1g183800' => 'psa', 'Psat3g113840' => 'psa', 'Psat3g126120' => 'psa', 'Psat3g126160' => 'psa', 'Psat3g158760' => 'psa', 'Psat3g158840' => 'psa', 'PSO170G2858' => 'pso', 'PSO339G0606' => 'pso', 'PSO384G4709' => 'pso', 'PSO407G0334' => 'pso', 'QL04p040276' => 'qlo', 'QL06p005458' => 'qlo', 'QL06p005472' => 'qlo', 'QL07p030546' => 'qlo', 'QL07p031519' => 'qlo', 'QL09p050949' => 'qlo', 'QL09p050966' => 'qlo', 'QL09p051067' => 'qlo', 'QL12p022706' => 'qlo', 'RcHm_v2.0_Chr2g0119601' => 'rch', 'RcHm_v2.0_Chr3g0459591' => 'rch', 'RcHm_v2.0_Chr4g0418521' => 'rch', 'RcHm_v2.0_Chr4g0418531' => 'rch', 'RcHm_v2.0_Chr4g0418541' => 'rch', 'RcHm_v2.0_Chr6g0291641' => 'rch', 'Rhsim01G0086300' => 'rsi', 'Rhsim01G0276300' => 'rsi', 'Rhsim01G0276500' => 'rsi', 'Rhsim04G0207700' => 'rsi', 'Rhsim05G0234500' => 'rsi', 'Rhsim13G0022400' => 'rsi', 'Sabra02G0167900' => 'sbr', 'Sabra04G0158500' => 'sbr', 'Sabra08G0159800' => 'sbr', 'Sabra10G0011500' => 'sbr', 'Sabra14G0104400' => 'sbr', 'SalBow2G2440' => 'sbo', 'SalBow4G2265' => 'sbo', 'Sc02g0000060' => 'sci', 'Sc05g0005020' => 'sci', 'Sc13g0003890' => 'sci', 'Sed0014865' => 'sed', 'Sed0017224' => 'sed', 'Sed0026391' => 'sed', 'SEGI_00063' => 'sgi', 'SEGI_10967' => 'sgi', 'SEGI_17510' => 'sgi', 'SEGI_24396' => 'sgi', 'SEGI_39719' => 'sgi', 'SEGI_41392' => 'sgi', 'SGA_v2.0_scaffold11G05794' => 'sas', 'SGA_v2.0_scaffold142G35607' => 'sas', 'SGA_v2.0_scaffold1G00447' => 'sas', 'SHI15388' => 'shi', 'SHI15394' => 'shi', 'SHI15396' => 'shi', 'SHI15399' => 'shi', 'SMO343G0151' => 'smo', 'SMO367G1118' => 'smo', 'Solyc01g080200.3' => 'sly', 'Solyc06g008960.3' => 'sly', 'Solyc09g064780.3' => 'sly', 'Sopen01g031980' => 'spe', 'Sopen06g003710' => 'spe', 'Sopen09g026460' => 'spe', 'Sp3g21240' => 'spa', 'Sp4g30030' => 'spa', 'TAR365G0022' => 'tar', 'TAR365G1023' => 'tar', 'TAR365G1253' => 'tar', 'TAR623G0078' => 'tar', 'TAR623G1721' => 'tar', 'TAR633G0959' => 'tar', 'THA.LOC104802225' => 'tha', 'THA.LOC104804769' => 'tha', 'THA.LOC104808660' => 'tha', 'THA.LOC104812792' => 'tha', 'Thecc.01G284000' => 'tca', 'Thecc.04G220600' => 'tca', 'Thecc.05G268900' => 'tca', 'Thecc.08G171100' => 'tca', 'Thhalv10001284m.g' => 'esa', 'Thhalv10019912m.g' => 'esa', 'TPR.G14189' => 'tpr', 'TPR.G18110' => 'tpr', 'TPR.G18130' => 'tpr', 'TPR.G18131' => 'tpr', 'TPR.G18140' => 'tpr', 'TPR.G24282' => 'tpr', 'TPR.G25221' => 'tpr', 'TPR.G29267' => 'tpr', 'TPR.G35315' => 'tpr', 'TPR.G36173' => 'tpr', 'TWI09G0794' => 'twi', 'TWI59G1348' => 'twi', 'TWI74G0430' => 'twi', 'unitig_26.g8940' => 'ugi', 'unitig_749.g13744' => 'ugi', 'unitig_749.g13745' => 'ugi', 'vmacro08269' => 'vma', 'vmacro14937' => 'vma', 'vmacro20401' => 'vma', 'VMungo0464G1349' => 'vmu', 'VMungo0540G0289' => 'vmu', 'VMungo1215G1590' => 'vmu', 'VMungo1309G0221' => 'vmu', 'VMungo1309G2815' => 'vmu', 'VMungo1383G0239' => 'vmu', 'VMungo1383G2910' => 'vmu', 'Zm00001eb095270' => 'zma', 'Zm00001eb095280' => 'zma', 'Zm00001eb111630' => 'zma', 'Zm00001eb237080' => 'zma', 'Zm00001eb273740' => 'zma', 'Zm00001eb285040' => 'zma', 'Zm00001eb330790' => 'zma', 'Zm00001eb337380' => 'zma' ), 'gf_id' => 'HOM05D001484', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001484' ), 'data_identifier' => 'HOM05D001484', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001484', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p31500' => 'bna', 'A05p00020' => 'bna', 'A07p08820' => 'bna', 'Aa31LG4G3300' => 'aar', 'Aa31LG8G10030' => 'aar', 'Actinidia00731' => 'ach', 'Actinidia11473' => 'ach', 'Actinidia23469' => 'ach', 'Actinidia24318' => 'ach', 'Actinidia40196' => 'ach', 'Actinidia40197' => 'ach', 'Actinidia40198' => 'ach', 'Ah.08g212990' => 'amhyb', 'Ah.15g091720' => 'amhyb', 'AL3G38260' => 'aly', 'AL4G47710' => 'aly', 'Aqoxy2G00671' => 'aox', 'Aqoxy2G03236' => 'aox', 'arahy.Tifrunner.gnm1.ann1.05IDCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KR684' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATY3SJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK6QJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6APGL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IDT7Z9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM073U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ0R87' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LE7RV4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT4QRX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V5ENPK' => 'arhy', 'AT2G48110' => 'ath', 'AT3G23590' => 'ath', 'ATR0626G186' => 'atr', 'ATR1127G141' => 'atr', 'Atru.chr4.2583' => 'acertr', 'Atru.chr5.1358' => 'acertr', 'Atru.chr5.1359' => 'acertr', 'Atru.chr8.46' => 'acertr', 'AUR62002640' => 'cqu', 'AUR62030055' => 'cqu', 'AUR62033713' => 'cqu', 'AUR62033714' => 'cqu', 'AUR62036795' => 'cqu', 'AUR62039891' => 'cqu', 'BcaB02g08737' => 'bca', 'BcaB04g20441' => 'bca', 'BcaB06g26509' => 'bca', 'BcaB06g26510' => 'bca', 'BcaB06g26511' => 'bca', 'BcaB06g26512' => 'bca', 'BcaB06g26513' => 'bca', 'BcaC02g12564' => 'bca', 'BcaC02g12565' => 'bca', 'BcaC02g12794' => 'bca', 'BcaC02g12795' => 'bca', 'BcaC02g12796' => 'bca', 'BcaC06g35541' => 'bca', 'BNapus_Darmor_BZH_scaffold_188p00080' => 'bna', 'BNapus_Darmor_BZH_scaffold_188p00090' => 'bna', 'BolC1t03972H' => 'bol', 'BolC1t03973H' => 'bol', 'BolC4t21680H' => 'bol', 'BolC7t41863H' => 'bol', 'BolSC55t61227H' => 'bol', 'BolSC55t61228H' => 'bol', 'BraA01t03278Z' => 'bra', 'BraA05t18998Z' => 'bra', 'BraA07t28673Z' => 'bra', 'C01p40150' => 'bna', 'C05p12370' => 'bna', 'C07p13680' => 'bna', 'CAN.G1006.16' => 'can', 'CAN.G1006.17' => 'can', 'CAN.G1170.2' => 'can', 'CAN.G962.7' => 'can', 'CANSAT25G2179' => 'cansat', 'CANSAT78G1573' => 'cansat', 'CARHR099510' => 'chi', 'CARHR143510' => 'chi', 'Carub.0003s2380' => 'cru', 'Carub.0004s3082' => 'cru', 'Ca_00614_v3' => 'car', 'Ca_07801_v3' => 'car', 'Ca_08567_v3' => 'car', 'Ca_09571_v3' => 'car', 'CBR_g19290' => 'cbr', 'Cc01_g19770' => 'ccan', 'Cc03_g03030' => 'ccan', 'CDE07G0968' => 'cde', 'CDE09G1441' => 'cde', 'Cfa006103' => 'cfa', 'Cfa015573' => 'cfa', 'Cfa016988' => 'cfa', 'Ciclev10006738m.g' => 'ccl', 'Ciclev10010920m.g' => 'ccl', 'Ciclev10018517m.g' => 'ccl', 'CiPaw.01G159200' => 'cil', 'CiPaw.02G091000' => 'cil', 'CiPaw.02G091100' => 'cil', 'CiPaw.08G103100' => 'cil', 'CiPaw.09G224900' => 'cil', 'ClCG06G005740' => 'cla', 'ClCG07G000090' => 'cla', 'ClCG07G000100' => 'cla', 'COL.COLO4_09143' => 'col', 'COL.COLO4_25124' => 'col', 'Cpa.g.sc16.34' => 'cpa', 'Cpa.g.sc3504.1' => 'cpa', 'Cpa.g.sc60.37' => 'cpa', 'CsaV3_6G018520' => 'csa', 'CsaV3_6G036860' => 'csa', 'CSS0001072' => 'camsi', 'CSS0020208' => 'camsi', 'CSS0021253' => 'camsi', 'CSS0022190' => 'camsi', 'CSS0036150' => 'camsi', 'CSS0040442' => 'camsi', 'CSS0042300' => 'camsi', 'CSS0045298' => 'camsi', 'DCAR_012449' => 'dca', 'DCAR_018405' => 'dca', 'DCAR_024573' => 'dca', 'DCAR_030591' => 'dca', 'Dinv16926' => 'din', 'Dinv32963' => 'din', 'Dinv38382' => 'din', 'Dinv38383' => 'din', 'Duzib133G0974' => 'dzi', 'Duzib138G1867' => 'dzi', 'Duzib211G0420' => 'dzi', 'Duzib212G0930' => 'dzi', 'ECA234G1645' => 'eca', 'ECA247G3467' => 'eca', 'ECA248G1703' => 'eca', 'EL10Ac3g06327' => 'bvu', 'EL10Ac7g17204' => 'bvu', 'Eucgr.A00855' => 'egr', 'Eucgr.A00858' => 'egr', 'Eucgr.H01520' => 'egr', 'Eucgr.H03604' => 'egr', 'Eucgr.L03465' => 'egr', 'Eucgr.L03466' => 'egr', 'FAN01G0988' => 'fan', 'FAN02G3892' => 'fan', 'FAN05G3381' => 'fan', 'FAN07G0967' => 'fan', 'FAN07G1493' => 'fan', 'FAN08G3125' => 'fan', 'FAN09G0402' => 'fan', 'FAN12G2594' => 'fan', 'FAN12G3879' => 'fan', 'FAN14G1546' => 'fan', 'FAN15G3626' => 'fan', 'FAN17G0588' => 'fan', 'FAN17G0609' => 'fan', 'FAN18G2817' => 'fan', 'FAN19G1305' => 'fan', 'FAN20G1787' => 'fan', 'FAN22G0073' => 'fan', 'FAN22G0352' => 'fan', 'FAN22G0368' => 'fan', 'FAN22G2273' => 'fan', 'FAN24G1998' => 'fan', 'FAN27G1317' => 'fan', 'FvH4_2g23980' => 'fve', 'FvH4_4g14380' => 'fve', 'FvH4_4g14390' => 'fve', 'FvH4_6g09250' => 'fve', 'Glyma.03G151100' => 'gma', 'Glyma.04G122550' => 'gma', 'Glyma.05G001600' => 'gma', 'Glyma.09G270766' => 'gma', 'Glyma.09G270832' => 'gma', 'Glyma.13G209800' => 'gma', 'Glyma.15G102800' => 'gma', 'Glyma.18G218900' => 'gma', 'Glyma.19G001500' => 'gma', 'Glyma.19G153600' => 'gma', 'Gohir.A02G028600' => 'ghi', 'Gohir.A08G045000' => 'ghi', 'Gohir.A11G120500' => 'ghi', 'Gohir.A12G006200' => 'ghi', 'Gohir.A12G006250' => 'ghi', 'Gohir.D02G036300' => 'ghi', 'Gohir.D08G054700' => 'ghi', 'Gohir.D11G125600' => 'ghi', 'Gohir.D12G005700' => 'ghi', 'Gorai.004G055200' => 'gra', 'Gorai.005G040400' => 'gra', 'Gorai.007G134500' => 'gra', 'Gorai.008G005500' => 'gra', 'GSVIVG01011094001' => 'vvi', 'GSVIVG01017879001' => 'vvi', 'GSVIVG01025988001' => 'vvi', 'GSVIVG01029847001' => 'vvi', 'HanXRQChr10g0282901' => 'han', 'HanXRQChr10g0310371' => 'han', 'HanXRQChr10g0315041' => 'han', 'HanXRQChr11g0327651' => 'han', 'HanXRQChr12g0359391' => 'han', 'Haze_00972' => 'cav', 'Haze_00973' => 'cav', 'Haze_00974' => 'cav', 'Haze_04747' => 'cav', 'Haze_04749' => 'cav', 'Haze_04750' => 'cav', 'Haze_21217' => 'cav', 'Hma1.2p1_1037F.1_g250680' => 'hma', 'Hma1.2p1_1644F.1_g295320' => 'hma', 'HPP92_011322' => 'vpl', 'HPP92_011323' => 'vpl', 'HPP92_011324' => 'vpl', 'HPP92_011325' => 'vpl', 'HPP92_011326' => 'vpl', 'Hund12205' => 'sun', 'Hund17957' => 'sun', 'Lalb_Chr06g0176771' => 'lal', 'Lalb_Chr18g0056021' => 'lal', 'Lalb_Chr18g0056031' => 'lal', 'Lalb_Chr18g0056041' => 'lal', 'Lalb_Chr20g0107751' => 'lal', 'Lalb_Chr20g0118371' => 'lal', 'Lj1g0010239' => 'lja', 'Lj1g0017101' => 'lja', 'Lj2A1178G40' => 'lonja', 'Lj2A54G84' => 'lonja', 'Lj2g0015248' => 'lja', 'Lj3A761T51' => 'lonja', 'Lj6g0018116' => 'lja', 'Lsat_1_v5_gn_4_136040' => 'lsa', 'Lsat_1_v5_gn_5_187461' => 'lsa', 'Lsat_1_v5_gn_5_77001' => 'lsa', 'Lsat_1_v5_gn_9_4461' => 'lsa', 'Manes.01G210100' => 'mes', 'Manes.03G185600' => 'mes', 'Manes.05G073300' => 'mes', 'Manes.09G120300' => 'mes', 'Manes.15G022100' => 'mes', 'Mapoly0096s0053' => 'mpo', 'MBI03_g14058_MAGBIO' => 'mbi', 'MBI03_g33876_MAGBIO' => 'mbi', 'MBI03_g36854_MAGBIO' => 'mbi', 'MBI17_g11997_MAGBIO' => 'mbi', 'MD03G1269000' => 'mdo', 'MD04G1179600' => 'mdo', 'MD11G1289800' => 'mdo', 'MD12G1194700' => 'mdo', 'MD13G1182100' => 'mdo', 'MD13G1182200' => 'mdo', 'MD16G1182600' => 'mdo', 'Medtr2g021400' => 'mtr', 'Medtr2g021470' => 'mtr', 'Medtr2g105810' => 'mtr', 'Medtr3g033580' => 'mtr', 'Medtr6g007970' => 'mtr', 'Medtr7g056330' => 'mtr', 'Medtr7g074290' => 'mtr', 'Medtr7g074380' => 'mtr', 'Medtr7g094550' => 'mtr', 'Medtr8g069995' => 'mtr', 'MELO3C014345.2' => 'cme', 'MELO3C021395.2' => 'cme', 'Migut.D00262' => 'egut', 'Migut.G00257' => 'egut', 'MSTRG.21575' => 'ama', 'MSTRG.3985' => 'ama', 'Nitab4.5_0000295g0140' => 'nta', 'Nitab4.5_0000732g0140' => 'nta', 'Nitab4.5_0003162g0020' => 'nta', 'Nitab4.5_0006180g0090' => 'nta', 'Nitab4.5_0006390g0010' => 'nta', 'Nitab4.5_0007392g0040' => 'nta', 'Nn1g02140' => 'nnu', 'Nn4g26168' => 'nnu', 'Nn5g26754' => 'nnu', 'Oeu001433.1' => 'oeu', 'Oeu010299.2' => 'oeu', 'Oeu011171.1' => 'oeu', 'Oeu037675.1' => 'oeu', 'Oeu038359.1' => 'oeu', 'Oeu063834.1' => 'oeu', 'Oeu063835.1' => 'oeu', 'Os05g0312000' => 'osa', 'Os07g0211101' => 'osa', 'Os07g0211200' => 'osa', 'Os07g0681500' => 'osa', 'Peaxi162Scf00095g01015' => 'pax', 'Peaxi162Scf00104g00329' => 'pax', 'Peaxi162Scf00161g00137' => 'pax', 'PGR004G1665' => 'pgr', 'PGR031G2937' => 'pgr', 'PGR119G2145' => 'pgr', 'PGSC0003DMG400004351' => 'stu', 'PGSC0003DMG400014625' => 'stu', 'PGSC0003DMG401000943' => 'stu', 'Phvul.001G148600' => 'pvu', 'Phvul.004G001700' => 'pvu', 'Phvul.006G154900' => 'pvu', 'Phvul.008G078200' => 'pvu', 'Phvul.011G136500' => 'pvu', 'Potri.002G215600' => 'ptr', 'Potri.008G201600' => 'ptr', 'Potri.014G138400' => 'ptr', 'Potri.016G142500' => 'ptr', 'Pp3c16_10580' => 'ppa', 'Pp3c5_25280' => 'ppa', 'Prupe.1G150000' => 'ppe', 'Prupe.1G150100' => 'ppe', 'Prupe.6G299600' => 'ppe', 'Prupe.8G245000' => 'ppe', 'Psat0s4927g0040' => 'psa', 'Psat1g052080' => 'psa', 'Psat1g183800' => 'psa', 'Psat3g113840' => 'psa', 'Psat3g126120' => 'psa', 'Psat3g126160' => 'psa', 'Psat3g158760' => 'psa', 'Psat3g158840' => 'psa', 'PSO170G2858' => 'pso', 'PSO339G0606' => 'pso', 'PSO384G4709' => 'pso', 'PSO407G0334' => 'pso', 'QL04p040276' => 'qlo', 'QL06p005458' => 'qlo', 'QL06p005472' => 'qlo', 'QL07p030546' => 'qlo', 'QL07p031519' => 'qlo', 'QL09p050949' => 'qlo', 'QL09p050966' => 'qlo', 'QL09p051067' => 'qlo', 'QL12p022706' => 'qlo', 'RcHm_v2.0_Chr2g0119601' => 'rch', 'RcHm_v2.0_Chr3g0459591' => 'rch', 'RcHm_v2.0_Chr4g0418521' => 'rch', 'RcHm_v2.0_Chr4g0418531' => 'rch', 'RcHm_v2.0_Chr4g0418541' => 'rch', 'RcHm_v2.0_Chr6g0291641' => 'rch', 'Rhsim01G0086300' => 'rsi', 'Rhsim01G0276300' => 'rsi', 'Rhsim01G0276500' => 'rsi', 'Rhsim04G0207700' => 'rsi', 'Rhsim05G0234500' => 'rsi', 'Rhsim13G0022400' => 'rsi', 'Sabra02G0167900' => 'sbr', 'Sabra04G0158500' => 'sbr', 'Sabra08G0159800' => 'sbr', 'Sabra10G0011500' => 'sbr', 'Sabra14G0104400' => 'sbr', 'SalBow2G2440' => 'sbo', 'SalBow4G2265' => 'sbo', 'Sc02g0000060' => 'sci', 'Sc05g0005020' => 'sci', 'Sc13g0003890' => 'sci', 'Sed0014865' => 'sed', 'Sed0017224' => 'sed', 'Sed0026391' => 'sed', 'SEGI_00063' => 'sgi', 'SEGI_10967' => 'sgi', 'SEGI_17510' => 'sgi', 'SEGI_24396' => 'sgi', 'SEGI_39719' => 'sgi', 'SEGI_41392' => 'sgi', 'SGA_v2.0_scaffold11G05794' => 'sas', 'SGA_v2.0_scaffold142G35607' => 'sas', 'SGA_v2.0_scaffold1G00447' => 'sas', 'SHI15388' => 'shi', 'SHI15394' => 'shi', 'SHI15396' => 'shi', 'SHI15399' => 'shi', 'SMO343G0151' => 'smo', 'SMO367G1118' => 'smo', 'Solyc01g080200.3' => 'sly', 'Solyc06g008960.3' => 'sly', 'Solyc09g064780.3' => 'sly', 'Sopen01g031980' => 'spe', 'Sopen06g003710' => 'spe', 'Sopen09g026460' => 'spe', 'Sp3g21240' => 'spa', 'Sp4g30030' => 'spa', 'TAR365G0022' => 'tar', 'TAR365G1023' => 'tar', 'TAR365G1253' => 'tar', 'TAR623G0078' => 'tar', 'TAR623G1721' => 'tar', 'TAR633G0959' => 'tar', 'THA.LOC104802225' => 'tha', 'THA.LOC104804769' => 'tha', 'THA.LOC104808660' => 'tha', 'THA.LOC104812792' => 'tha', 'Thecc.01G284000' => 'tca', 'Thecc.04G220600' => 'tca', 'Thecc.05G268900' => 'tca', 'Thecc.08G171100' => 'tca', 'Thhalv10001284m.g' => 'esa', 'Thhalv10019912m.g' => 'esa', 'TPR.G14189' => 'tpr', 'TPR.G18110' => 'tpr', 'TPR.G18130' => 'tpr', 'TPR.G18131' => 'tpr', 'TPR.G18140' => 'tpr', 'TPR.G24282' => 'tpr', 'TPR.G25221' => 'tpr', 'TPR.G29267' => 'tpr', 'TPR.G35315' => 'tpr', 'TPR.G36173' => 'tpr', 'TWI09G0794' => 'twi', 'TWI59G1348' => 'twi', 'TWI74G0430' => 'twi', 'unitig_26.g8940' => 'ugi', 'unitig_749.g13744' => 'ugi', 'unitig_749.g13745' => 'ugi', 'vmacro08269' => 'vma', 'vmacro14937' => 'vma', 'vmacro20401' => 'vma', 'VMungo0464G1349' => 'vmu', 'VMungo0540G0289' => 'vmu', 'VMungo1215G1590' => 'vmu', 'VMungo1309G0221' => 'vmu', 'VMungo1309G2815' => 'vmu', 'VMungo1383G0239' => 'vmu', 'VMungo1383G2910' => 'vmu', 'Zm00001eb095270' => 'zma', 'Zm00001eb095280' => 'zma', 'Zm00001eb111630' => 'zma', 'Zm00001eb237080' => 'zma', 'Zm00001eb273740' => 'zma', 'Zm00001eb285040' => 'zma', 'Zm00001eb330790' => 'zma', 'Zm00001eb337380' => 'zma' ) $gf_id = 'HOM05D001484' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001484' ) $data_identifier = 'HOM05D001484' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 2, 'aly' => (int) 2, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 22, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 7, 'hma' => (int) 2, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 7, 'mtr' => (int) 10, 'cme' => (int) 2, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 4, 'ppa' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 4, 'qlo' => (int) 9, 'rch' => (int) 6, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 10, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 7, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb337380' $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' => 'HOM05D001484', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p31500' => 'bna', 'A05p00020' => 'bna', 'A07p08820' => 'bna', 'Aa31LG4G3300' => 'aar', 'Aa31LG8G10030' => 'aar', 'Actinidia00731' => 'ach', 'Actinidia11473' => 'ach', 'Actinidia23469' => 'ach', 'Actinidia24318' => 'ach', 'Actinidia40196' => 'ach', 'Actinidia40197' => 'ach', 'Actinidia40198' => 'ach', 'Ah.08g212990' => 'amhyb', 'Ah.15g091720' => 'amhyb', 'AL3G38260' => 'aly', 'AL4G47710' => 'aly', 'Aqoxy2G00671' => 'aox', 'Aqoxy2G03236' => 'aox', 'arahy.Tifrunner.gnm1.ann1.05IDCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KR684' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATY3SJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK6QJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6APGL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IDT7Z9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM073U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ0R87' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LE7RV4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT4QRX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V5ENPK' => 'arhy', 'AT2G48110' => 'ath', 'AT3G23590' => 'ath', 'ATR0626G186' => 'atr', 'ATR1127G141' => 'atr', 'Atru.chr4.2583' => 'acertr', 'Atru.chr5.1358' => 'acertr', 'Atru.chr5.1359' => 'acertr', 'Atru.chr8.46' => 'acertr', 'AUR62002640' => 'cqu', 'AUR62030055' => 'cqu', 'AUR62033713' => 'cqu', 'AUR62033714' => 'cqu', 'AUR62036795' => 'cqu', 'AUR62039891' => 'cqu', 'BcaB02g08737' => 'bca', 'BcaB04g20441' => 'bca', 'BcaB06g26509' => 'bca', 'BcaB06g26510' => 'bca', 'BcaB06g26511' => 'bca', 'BcaB06g26512' => 'bca', 'BcaB06g26513' => 'bca', 'BcaC02g12564' => 'bca', 'BcaC02g12565' => 'bca', 'BcaC02g12794' => 'bca', 'BcaC02g12795' => 'bca', 'BcaC02g12796' => 'bca', 'BcaC06g35541' => 'bca', 'BNapus_Darmor_BZH_scaffold_188p00080' => 'bna', 'BNapus_Darmor_BZH_scaffold_188p00090' => 'bna', 'BolC1t03972H' => 'bol', 'BolC1t03973H' => 'bol', 'BolC4t21680H' => 'bol', 'BolC7t41863H' => 'bol', 'BolSC55t61227H' => 'bol', 'BolSC55t61228H' => 'bol', 'BraA01t03278Z' => 'bra', 'BraA05t18998Z' => 'bra', 'BraA07t28673Z' => 'bra', 'C01p40150' => 'bna', 'C05p12370' => 'bna', 'C07p13680' => 'bna', 'CAN.G1006.16' => 'can', 'CAN.G1006.17' => 'can', 'CAN.G1170.2' => 'can', 'CAN.G962.7' => 'can', 'CANSAT25G2179' => 'cansat', 'CANSAT78G1573' => 'cansat', 'CARHR099510' => 'chi', 'CARHR143510' => 'chi', 'Carub.0003s2380' => 'cru', 'Carub.0004s3082' => 'cru', 'Ca_00614_v3' => 'car', 'Ca_07801_v3' => 'car', 'Ca_08567_v3' => 'car', 'Ca_09571_v3' => 'car', 'CBR_g19290' => 'cbr', 'Cc01_g19770' => 'ccan', 'Cc03_g03030' => 'ccan', 'CDE07G0968' => 'cde', 'CDE09G1441' => 'cde', 'Cfa006103' => 'cfa', 'Cfa015573' => 'cfa', 'Cfa016988' => 'cfa', 'Ciclev10006738m.g' => 'ccl', 'Ciclev10010920m.g' => 'ccl', 'Ciclev10018517m.g' => 'ccl', 'CiPaw.01G159200' => 'cil', 'CiPaw.02G091000' => 'cil', 'CiPaw.02G091100' => 'cil', 'CiPaw.08G103100' => 'cil', 'CiPaw.09G224900' => 'cil', 'ClCG06G005740' => 'cla', 'ClCG07G000090' => 'cla', 'ClCG07G000100' => 'cla', 'COL.COLO4_09143' => 'col', 'COL.COLO4_25124' => 'col', 'Cpa.g.sc16.34' => 'cpa', 'Cpa.g.sc3504.1' => 'cpa', 'Cpa.g.sc60.37' => 'cpa', 'CsaV3_6G018520' => 'csa', 'CsaV3_6G036860' => 'csa', 'CSS0001072' => 'camsi', 'CSS0020208' => 'camsi', 'CSS0021253' => 'camsi', 'CSS0022190' => 'camsi', 'CSS0036150' => 'camsi', 'CSS0040442' => 'camsi', 'CSS0042300' => 'camsi', 'CSS0045298' => 'camsi', 'DCAR_012449' => 'dca', 'DCAR_018405' => 'dca', 'DCAR_024573' => 'dca', 'DCAR_030591' => 'dca', 'Dinv16926' => 'din', 'Dinv32963' => 'din', 'Dinv38382' => 'din', 'Dinv38383' => 'din', 'Duzib133G0974' => 'dzi', 'Duzib138G1867' => 'dzi', 'Duzib211G0420' => 'dzi', 'Duzib212G0930' => 'dzi', 'ECA234G1645' => 'eca', 'ECA247G3467' => 'eca', 'ECA248G1703' => 'eca', 'EL10Ac3g06327' => 'bvu', 'EL10Ac7g17204' => 'bvu', 'Eucgr.A00855' => 'egr', 'Eucgr.A00858' => 'egr', 'Eucgr.H01520' => 'egr', 'Eucgr.H03604' => 'egr', 'Eucgr.L03465' => 'egr', 'Eucgr.L03466' => 'egr', 'FAN01G0988' => 'fan', 'FAN02G3892' => 'fan', 'FAN05G3381' => 'fan', 'FAN07G0967' => 'fan', 'FAN07G1493' => 'fan', 'FAN08G3125' => 'fan', 'FAN09G0402' => 'fan', 'FAN12G2594' => 'fan', 'FAN12G3879' => 'fan', 'FAN14G1546' => 'fan', 'FAN15G3626' => 'fan', 'FAN17G0588' => 'fan', 'FAN17G0609' => 'fan', 'FAN18G2817' => 'fan', 'FAN19G1305' => 'fan', 'FAN20G1787' => 'fan', 'FAN22G0073' => 'fan', 'FAN22G0352' => 'fan', 'FAN22G0368' => 'fan', 'FAN22G2273' => 'fan', 'FAN24G1998' => 'fan', 'FAN27G1317' => 'fan', 'FvH4_2g23980' => 'fve', 'FvH4_4g14380' => 'fve', 'FvH4_4g14390' => 'fve', 'FvH4_6g09250' => 'fve', 'Glyma.03G151100' => 'gma', 'Glyma.04G122550' => 'gma', 'Glyma.05G001600' => 'gma', 'Glyma.09G270766' => 'gma', 'Glyma.09G270832' => 'gma', 'Glyma.13G209800' => 'gma', 'Glyma.15G102800' => 'gma', 'Glyma.18G218900' => 'gma', 'Glyma.19G001500' => 'gma', 'Glyma.19G153600' => 'gma', 'Gohir.A02G028600' => 'ghi', 'Gohir.A08G045000' => 'ghi', 'Gohir.A11G120500' => 'ghi', 'Gohir.A12G006200' => 'ghi', 'Gohir.A12G006250' => 'ghi', 'Gohir.D02G036300' => 'ghi', 'Gohir.D08G054700' => 'ghi', 'Gohir.D11G125600' => 'ghi', 'Gohir.D12G005700' => 'ghi', 'Gorai.004G055200' => 'gra', 'Gorai.005G040400' => 'gra', 'Gorai.007G134500' => 'gra', 'Gorai.008G005500' => 'gra', 'GSVIVG01011094001' => 'vvi', 'GSVIVG01017879001' => 'vvi', 'GSVIVG01025988001' => 'vvi', 'GSVIVG01029847001' => 'vvi', 'HanXRQChr10g0282901' => 'han', 'HanXRQChr10g0310371' => 'han', 'HanXRQChr10g0315041' => 'han', 'HanXRQChr11g0327651' => 'han', 'HanXRQChr12g0359391' => 'han', 'Haze_00972' => 'cav', 'Haze_00973' => 'cav', 'Haze_00974' => 'cav', 'Haze_04747' => 'cav', 'Haze_04749' => 'cav', 'Haze_04750' => 'cav', 'Haze_21217' => 'cav', 'Hma1.2p1_1037F.1_g250680' => 'hma', 'Hma1.2p1_1644F.1_g295320' => 'hma', 'HPP92_011322' => 'vpl', 'HPP92_011323' => 'vpl', 'HPP92_011324' => 'vpl', 'HPP92_011325' => 'vpl', 'HPP92_011326' => 'vpl', 'Hund12205' => 'sun', 'Hund17957' => 'sun', 'Lalb_Chr06g0176771' => 'lal', 'Lalb_Chr18g0056021' => 'lal', 'Lalb_Chr18g0056031' => 'lal', 'Lalb_Chr18g0056041' => 'lal', 'Lalb_Chr20g0107751' => 'lal', 'Lalb_Chr20g0118371' => 'lal', 'Lj1g0010239' => 'lja', 'Lj1g0017101' => 'lja', 'Lj2A1178G40' => 'lonja', 'Lj2A54G84' => 'lonja', 'Lj2g0015248' => 'lja', 'Lj3A761T51' => 'lonja', 'Lj6g0018116' => 'lja', 'Lsat_1_v5_gn_4_136040' => 'lsa', 'Lsat_1_v5_gn_5_187461' => 'lsa', 'Lsat_1_v5_gn_5_77001' => 'lsa', 'Lsat_1_v5_gn_9_4461' => 'lsa', 'Manes.01G210100' => 'mes', 'Manes.03G185600' => 'mes', 'Manes.05G073300' => 'mes', 'Manes.09G120300' => 'mes', 'Manes.15G022100' => 'mes', 'Mapoly0096s0053' => 'mpo', 'MBI03_g14058_MAGBIO' => 'mbi', 'MBI03_g33876_MAGBIO' => 'mbi', 'MBI03_g36854_MAGBIO' => 'mbi', 'MBI17_g11997_MAGBIO' => 'mbi', 'MD03G1269000' => 'mdo', 'MD04G1179600' => 'mdo', 'MD11G1289800' => 'mdo', 'MD12G1194700' => 'mdo', 'MD13G1182100' => 'mdo', 'MD13G1182200' => 'mdo', 'MD16G1182600' => 'mdo', 'Medtr2g021400' => 'mtr', 'Medtr2g021470' => 'mtr', 'Medtr2g105810' => 'mtr', 'Medtr3g033580' => 'mtr', 'Medtr6g007970' => 'mtr', 'Medtr7g056330' => 'mtr', 'Medtr7g074290' => 'mtr', 'Medtr7g074380' => 'mtr', 'Medtr7g094550' => 'mtr', 'Medtr8g069995' => 'mtr', 'MELO3C014345.2' => 'cme', 'MELO3C021395.2' => 'cme', 'Migut.D00262' => 'egut', 'Migut.G00257' => 'egut', 'MSTRG.21575' => 'ama', 'MSTRG.3985' => 'ama', 'Nitab4.5_0000295g0140' => 'nta', 'Nitab4.5_0000732g0140' => 'nta', 'Nitab4.5_0003162g0020' => 'nta', 'Nitab4.5_0006180g0090' => 'nta', 'Nitab4.5_0006390g0010' => 'nta', 'Nitab4.5_0007392g0040' => 'nta', 'Nn1g02140' => 'nnu', 'Nn4g26168' => 'nnu', 'Nn5g26754' => 'nnu', 'Oeu001433.1' => 'oeu', 'Oeu010299.2' => 'oeu', 'Oeu011171.1' => 'oeu', 'Oeu037675.1' => 'oeu', 'Oeu038359.1' => 'oeu', 'Oeu063834.1' => 'oeu', 'Oeu063835.1' => 'oeu', 'Os05g0312000' => 'osa', 'Os07g0211101' => 'osa', 'Os07g0211200' => 'osa', 'Os07g0681500' => 'osa', 'Peaxi162Scf00095g01015' => 'pax', 'Peaxi162Scf00104g00329' => 'pax', 'Peaxi162Scf00161g00137' => 'pax', 'PGR004G1665' => 'pgr', 'PGR031G2937' => 'pgr', 'PGR119G2145' => 'pgr', 'PGSC0003DMG400004351' => 'stu', 'PGSC0003DMG400014625' => 'stu', 'PGSC0003DMG401000943' => 'stu', 'Phvul.001G148600' => 'pvu', 'Phvul.004G001700' => 'pvu', 'Phvul.006G154900' => 'pvu', 'Phvul.008G078200' => 'pvu', 'Phvul.011G136500' => 'pvu', 'Potri.002G215600' => 'ptr', 'Potri.008G201600' => 'ptr', 'Potri.014G138400' => 'ptr', 'Potri.016G142500' => 'ptr', 'Pp3c16_10580' => 'ppa', 'Pp3c5_25280' => 'ppa', 'Prupe.1G150000' => 'ppe', 'Prupe.1G150100' => 'ppe', 'Prupe.6G299600' => 'ppe', 'Prupe.8G245000' => 'ppe', 'Psat0s4927g0040' => 'psa', 'Psat1g052080' => 'psa', 'Psat1g183800' => 'psa', 'Psat3g113840' => 'psa', 'Psat3g126120' => 'psa', 'Psat3g126160' => 'psa', 'Psat3g158760' => 'psa', 'Psat3g158840' => 'psa', 'PSO170G2858' => 'pso', 'PSO339G0606' => 'pso', 'PSO384G4709' => 'pso', 'PSO407G0334' => 'pso', 'QL04p040276' => 'qlo', 'QL06p005458' => 'qlo', 'QL06p005472' => 'qlo', 'QL07p030546' => 'qlo', 'QL07p031519' => 'qlo', 'QL09p050949' => 'qlo', 'QL09p050966' => 'qlo', 'QL09p051067' => 'qlo', 'QL12p022706' => 'qlo', 'RcHm_v2.0_Chr2g0119601' => 'rch', 'RcHm_v2.0_Chr3g0459591' => 'rch', 'RcHm_v2.0_Chr4g0418521' => 'rch', 'RcHm_v2.0_Chr4g0418531' => 'rch', 'RcHm_v2.0_Chr4g0418541' => 'rch', 'RcHm_v2.0_Chr6g0291641' => 'rch', 'Rhsim01G0086300' => 'rsi', 'Rhsim01G0276300' => 'rsi', 'Rhsim01G0276500' => 'rsi', 'Rhsim04G0207700' => 'rsi', 'Rhsim05G0234500' => 'rsi', 'Rhsim13G0022400' => 'rsi', 'Sabra02G0167900' => 'sbr', 'Sabra04G0158500' => 'sbr', 'Sabra08G0159800' => 'sbr', 'Sabra10G0011500' => 'sbr', 'Sabra14G0104400' => 'sbr', 'SalBow2G2440' => 'sbo', 'SalBow4G2265' => 'sbo', 'Sc02g0000060' => 'sci', 'Sc05g0005020' => 'sci', 'Sc13g0003890' => 'sci', 'Sed0014865' => 'sed', 'Sed0017224' => 'sed', 'Sed0026391' => 'sed', 'SEGI_00063' => 'sgi', 'SEGI_10967' => 'sgi', 'SEGI_17510' => 'sgi', 'SEGI_24396' => 'sgi', 'SEGI_39719' => 'sgi', 'SEGI_41392' => 'sgi', 'SGA_v2.0_scaffold11G05794' => 'sas', 'SGA_v2.0_scaffold142G35607' => 'sas', 'SGA_v2.0_scaffold1G00447' => 'sas', 'SHI15388' => 'shi', 'SHI15394' => 'shi', 'SHI15396' => 'shi', 'SHI15399' => 'shi', 'SMO343G0151' => 'smo', 'SMO367G1118' => 'smo', 'Solyc01g080200.3' => 'sly', 'Solyc06g008960.3' => 'sly', 'Solyc09g064780.3' => 'sly', 'Sopen01g031980' => 'spe', 'Sopen06g003710' => 'spe', 'Sopen09g026460' => 'spe', 'Sp3g21240' => 'spa', 'Sp4g30030' => 'spa', 'TAR365G0022' => 'tar', 'TAR365G1023' => 'tar', 'TAR365G1253' => 'tar', 'TAR623G0078' => 'tar', 'TAR623G1721' => 'tar', 'TAR633G0959' => 'tar', 'THA.LOC104802225' => 'tha', 'THA.LOC104804769' => 'tha', 'THA.LOC104808660' => 'tha', 'THA.LOC104812792' => 'tha', 'Thecc.01G284000' => 'tca', 'Thecc.04G220600' => 'tca', 'Thecc.05G268900' => 'tca', 'Thecc.08G171100' => 'tca', 'Thhalv10001284m.g' => 'esa', 'Thhalv10019912m.g' => 'esa', 'TPR.G14189' => 'tpr', 'TPR.G18110' => 'tpr', 'TPR.G18130' => 'tpr', 'TPR.G18131' => 'tpr', 'TPR.G18140' => 'tpr', 'TPR.G24282' => 'tpr', 'TPR.G25221' => 'tpr', 'TPR.G29267' => 'tpr', 'TPR.G35315' => 'tpr', 'TPR.G36173' => 'tpr', 'TWI09G0794' => 'twi', 'TWI59G1348' => 'twi', 'TWI74G0430' => 'twi', 'unitig_26.g8940' => 'ugi', 'unitig_749.g13744' => 'ugi', 'unitig_749.g13745' => 'ugi', 'vmacro08269' => 'vma', 'vmacro14937' => 'vma', 'vmacro20401' => 'vma', 'VMungo0464G1349' => 'vmu', 'VMungo0540G0289' => 'vmu', 'VMungo1215G1590' => 'vmu', 'VMungo1309G0221' => 'vmu', 'VMungo1309G2815' => 'vmu', 'VMungo1383G0239' => 'vmu', 'VMungo1383G2910' => 'vmu', 'Zm00001eb095270' => 'zma', 'Zm00001eb095280' => 'zma', 'Zm00001eb111630' => 'zma', 'Zm00001eb237080' => 'zma', 'Zm00001eb273740' => 'zma', 'Zm00001eb285040' => 'zma', 'Zm00001eb330790' => 'zma', 'Zm00001eb337380' => 'zma' ), 'gf_id' => 'HOM05D001484', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001484' ), 'data_identifier' => 'HOM05D001484', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001484', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p31500' => 'bna', 'A05p00020' => 'bna', 'A07p08820' => 'bna', 'Aa31LG4G3300' => 'aar', 'Aa31LG8G10030' => 'aar', 'Actinidia00731' => 'ach', 'Actinidia11473' => 'ach', 'Actinidia23469' => 'ach', 'Actinidia24318' => 'ach', 'Actinidia40196' => 'ach', 'Actinidia40197' => 'ach', 'Actinidia40198' => 'ach', 'Ah.08g212990' => 'amhyb', 'Ah.15g091720' => 'amhyb', 'AL3G38260' => 'aly', 'AL4G47710' => 'aly', 'Aqoxy2G00671' => 'aox', 'Aqoxy2G03236' => 'aox', 'arahy.Tifrunner.gnm1.ann1.05IDCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KR684' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATY3SJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK6QJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6APGL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IDT7Z9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM073U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ0R87' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LE7RV4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT4QRX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V5ENPK' => 'arhy', 'AT2G48110' => 'ath', 'AT3G23590' => 'ath', 'ATR0626G186' => 'atr', 'ATR1127G141' => 'atr', 'Atru.chr4.2583' => 'acertr', 'Atru.chr5.1358' => 'acertr', 'Atru.chr5.1359' => 'acertr', 'Atru.chr8.46' => 'acertr', 'AUR62002640' => 'cqu', 'AUR62030055' => 'cqu', 'AUR62033713' => 'cqu', 'AUR62033714' => 'cqu', 'AUR62036795' => 'cqu', 'AUR62039891' => 'cqu', 'BcaB02g08737' => 'bca', 'BcaB04g20441' => 'bca', 'BcaB06g26509' => 'bca', 'BcaB06g26510' => 'bca', 'BcaB06g26511' => 'bca', 'BcaB06g26512' => 'bca', 'BcaB06g26513' => 'bca', 'BcaC02g12564' => 'bca', 'BcaC02g12565' => 'bca', 'BcaC02g12794' => 'bca', 'BcaC02g12795' => 'bca', 'BcaC02g12796' => 'bca', 'BcaC06g35541' => 'bca', 'BNapus_Darmor_BZH_scaffold_188p00080' => 'bna', 'BNapus_Darmor_BZH_scaffold_188p00090' => 'bna', 'BolC1t03972H' => 'bol', 'BolC1t03973H' => 'bol', 'BolC4t21680H' => 'bol', 'BolC7t41863H' => 'bol', 'BolSC55t61227H' => 'bol', 'BolSC55t61228H' => 'bol', 'BraA01t03278Z' => 'bra', 'BraA05t18998Z' => 'bra', 'BraA07t28673Z' => 'bra', 'C01p40150' => 'bna', 'C05p12370' => 'bna', 'C07p13680' => 'bna', 'CAN.G1006.16' => 'can', 'CAN.G1006.17' => 'can', 'CAN.G1170.2' => 'can', 'CAN.G962.7' => 'can', 'CANSAT25G2179' => 'cansat', 'CANSAT78G1573' => 'cansat', 'CARHR099510' => 'chi', 'CARHR143510' => 'chi', 'Carub.0003s2380' => 'cru', 'Carub.0004s3082' => 'cru', 'Ca_00614_v3' => 'car', 'Ca_07801_v3' => 'car', 'Ca_08567_v3' => 'car', 'Ca_09571_v3' => 'car', 'CBR_g19290' => 'cbr', 'Cc01_g19770' => 'ccan', 'Cc03_g03030' => 'ccan', 'CDE07G0968' => 'cde', 'CDE09G1441' => 'cde', 'Cfa006103' => 'cfa', 'Cfa015573' => 'cfa', 'Cfa016988' => 'cfa', 'Ciclev10006738m.g' => 'ccl', 'Ciclev10010920m.g' => 'ccl', 'Ciclev10018517m.g' => 'ccl', 'CiPaw.01G159200' => 'cil', 'CiPaw.02G091000' => 'cil', 'CiPaw.02G091100' => 'cil', 'CiPaw.08G103100' => 'cil', 'CiPaw.09G224900' => 'cil', 'ClCG06G005740' => 'cla', 'ClCG07G000090' => 'cla', 'ClCG07G000100' => 'cla', 'COL.COLO4_09143' => 'col', 'COL.COLO4_25124' => 'col', 'Cpa.g.sc16.34' => 'cpa', 'Cpa.g.sc3504.1' => 'cpa', 'Cpa.g.sc60.37' => 'cpa', 'CsaV3_6G018520' => 'csa', 'CsaV3_6G036860' => 'csa', 'CSS0001072' => 'camsi', 'CSS0020208' => 'camsi', 'CSS0021253' => 'camsi', 'CSS0022190' => 'camsi', 'CSS0036150' => 'camsi', 'CSS0040442' => 'camsi', 'CSS0042300' => 'camsi', 'CSS0045298' => 'camsi', 'DCAR_012449' => 'dca', 'DCAR_018405' => 'dca', 'DCAR_024573' => 'dca', 'DCAR_030591' => 'dca', 'Dinv16926' => 'din', 'Dinv32963' => 'din', 'Dinv38382' => 'din', 'Dinv38383' => 'din', 'Duzib133G0974' => 'dzi', 'Duzib138G1867' => 'dzi', 'Duzib211G0420' => 'dzi', 'Duzib212G0930' => 'dzi', 'ECA234G1645' => 'eca', 'ECA247G3467' => 'eca', 'ECA248G1703' => 'eca', 'EL10Ac3g06327' => 'bvu', 'EL10Ac7g17204' => 'bvu', 'Eucgr.A00855' => 'egr', 'Eucgr.A00858' => 'egr', 'Eucgr.H01520' => 'egr', 'Eucgr.H03604' => 'egr', 'Eucgr.L03465' => 'egr', 'Eucgr.L03466' => 'egr', 'FAN01G0988' => 'fan', 'FAN02G3892' => 'fan', 'FAN05G3381' => 'fan', 'FAN07G0967' => 'fan', 'FAN07G1493' => 'fan', 'FAN08G3125' => 'fan', 'FAN09G0402' => 'fan', 'FAN12G2594' => 'fan', 'FAN12G3879' => 'fan', 'FAN14G1546' => 'fan', 'FAN15G3626' => 'fan', 'FAN17G0588' => 'fan', 'FAN17G0609' => 'fan', 'FAN18G2817' => 'fan', 'FAN19G1305' => 'fan', 'FAN20G1787' => 'fan', 'FAN22G0073' => 'fan', 'FAN22G0352' => 'fan', 'FAN22G0368' => 'fan', 'FAN22G2273' => 'fan', 'FAN24G1998' => 'fan', 'FAN27G1317' => 'fan', 'FvH4_2g23980' => 'fve', 'FvH4_4g14380' => 'fve', 'FvH4_4g14390' => 'fve', 'FvH4_6g09250' => 'fve', 'Glyma.03G151100' => 'gma', 'Glyma.04G122550' => 'gma', 'Glyma.05G001600' => 'gma', 'Glyma.09G270766' => 'gma', 'Glyma.09G270832' => 'gma', 'Glyma.13G209800' => 'gma', 'Glyma.15G102800' => 'gma', 'Glyma.18G218900' => 'gma', 'Glyma.19G001500' => 'gma', 'Glyma.19G153600' => 'gma', 'Gohir.A02G028600' => 'ghi', 'Gohir.A08G045000' => 'ghi', 'Gohir.A11G120500' => 'ghi', 'Gohir.A12G006200' => 'ghi', 'Gohir.A12G006250' => 'ghi', 'Gohir.D02G036300' => 'ghi', 'Gohir.D08G054700' => 'ghi', 'Gohir.D11G125600' => 'ghi', 'Gohir.D12G005700' => 'ghi', 'Gorai.004G055200' => 'gra', 'Gorai.005G040400' => 'gra', 'Gorai.007G134500' => 'gra', 'Gorai.008G005500' => 'gra', 'GSVIVG01011094001' => 'vvi', 'GSVIVG01017879001' => 'vvi', 'GSVIVG01025988001' => 'vvi', 'GSVIVG01029847001' => 'vvi', 'HanXRQChr10g0282901' => 'han', 'HanXRQChr10g0310371' => 'han', 'HanXRQChr10g0315041' => 'han', 'HanXRQChr11g0327651' => 'han', 'HanXRQChr12g0359391' => 'han', 'Haze_00972' => 'cav', 'Haze_00973' => 'cav', 'Haze_00974' => 'cav', 'Haze_04747' => 'cav', 'Haze_04749' => 'cav', 'Haze_04750' => 'cav', 'Haze_21217' => 'cav', 'Hma1.2p1_1037F.1_g250680' => 'hma', 'Hma1.2p1_1644F.1_g295320' => 'hma', 'HPP92_011322' => 'vpl', 'HPP92_011323' => 'vpl', 'HPP92_011324' => 'vpl', 'HPP92_011325' => 'vpl', 'HPP92_011326' => 'vpl', 'Hund12205' => 'sun', 'Hund17957' => 'sun', 'Lalb_Chr06g0176771' => 'lal', 'Lalb_Chr18g0056021' => 'lal', 'Lalb_Chr18g0056031' => 'lal', 'Lalb_Chr18g0056041' => 'lal', 'Lalb_Chr20g0107751' => 'lal', 'Lalb_Chr20g0118371' => 'lal', 'Lj1g0010239' => 'lja', 'Lj1g0017101' => 'lja', 'Lj2A1178G40' => 'lonja', 'Lj2A54G84' => 'lonja', 'Lj2g0015248' => 'lja', 'Lj3A761T51' => 'lonja', 'Lj6g0018116' => 'lja', 'Lsat_1_v5_gn_4_136040' => 'lsa', 'Lsat_1_v5_gn_5_187461' => 'lsa', 'Lsat_1_v5_gn_5_77001' => 'lsa', 'Lsat_1_v5_gn_9_4461' => 'lsa', 'Manes.01G210100' => 'mes', 'Manes.03G185600' => 'mes', 'Manes.05G073300' => 'mes', 'Manes.09G120300' => 'mes', 'Manes.15G022100' => 'mes', 'Mapoly0096s0053' => 'mpo', 'MBI03_g14058_MAGBIO' => 'mbi', 'MBI03_g33876_MAGBIO' => 'mbi', 'MBI03_g36854_MAGBIO' => 'mbi', 'MBI17_g11997_MAGBIO' => 'mbi', 'MD03G1269000' => 'mdo', 'MD04G1179600' => 'mdo', 'MD11G1289800' => 'mdo', 'MD12G1194700' => 'mdo', 'MD13G1182100' => 'mdo', 'MD13G1182200' => 'mdo', 'MD16G1182600' => 'mdo', 'Medtr2g021400' => 'mtr', 'Medtr2g021470' => 'mtr', 'Medtr2g105810' => 'mtr', 'Medtr3g033580' => 'mtr', 'Medtr6g007970' => 'mtr', 'Medtr7g056330' => 'mtr', 'Medtr7g074290' => 'mtr', 'Medtr7g074380' => 'mtr', 'Medtr7g094550' => 'mtr', 'Medtr8g069995' => 'mtr', 'MELO3C014345.2' => 'cme', 'MELO3C021395.2' => 'cme', 'Migut.D00262' => 'egut', 'Migut.G00257' => 'egut', 'MSTRG.21575' => 'ama', 'MSTRG.3985' => 'ama', 'Nitab4.5_0000295g0140' => 'nta', 'Nitab4.5_0000732g0140' => 'nta', 'Nitab4.5_0003162g0020' => 'nta', 'Nitab4.5_0006180g0090' => 'nta', 'Nitab4.5_0006390g0010' => 'nta', 'Nitab4.5_0007392g0040' => 'nta', 'Nn1g02140' => 'nnu', 'Nn4g26168' => 'nnu', 'Nn5g26754' => 'nnu', 'Oeu001433.1' => 'oeu', 'Oeu010299.2' => 'oeu', 'Oeu011171.1' => 'oeu', 'Oeu037675.1' => 'oeu', 'Oeu038359.1' => 'oeu', 'Oeu063834.1' => 'oeu', 'Oeu063835.1' => 'oeu', 'Os05g0312000' => 'osa', 'Os07g0211101' => 'osa', 'Os07g0211200' => 'osa', 'Os07g0681500' => 'osa', 'Peaxi162Scf00095g01015' => 'pax', 'Peaxi162Scf00104g00329' => 'pax', 'Peaxi162Scf00161g00137' => 'pax', 'PGR004G1665' => 'pgr', 'PGR031G2937' => 'pgr', 'PGR119G2145' => 'pgr', 'PGSC0003DMG400004351' => 'stu', 'PGSC0003DMG400014625' => 'stu', 'PGSC0003DMG401000943' => 'stu', 'Phvul.001G148600' => 'pvu', 'Phvul.004G001700' => 'pvu', 'Phvul.006G154900' => 'pvu', 'Phvul.008G078200' => 'pvu', 'Phvul.011G136500' => 'pvu', 'Potri.002G215600' => 'ptr', 'Potri.008G201600' => 'ptr', 'Potri.014G138400' => 'ptr', 'Potri.016G142500' => 'ptr', 'Pp3c16_10580' => 'ppa', 'Pp3c5_25280' => 'ppa', 'Prupe.1G150000' => 'ppe', 'Prupe.1G150100' => 'ppe', 'Prupe.6G299600' => 'ppe', 'Prupe.8G245000' => 'ppe', 'Psat0s4927g0040' => 'psa', 'Psat1g052080' => 'psa', 'Psat1g183800' => 'psa', 'Psat3g113840' => 'psa', 'Psat3g126120' => 'psa', 'Psat3g126160' => 'psa', 'Psat3g158760' => 'psa', 'Psat3g158840' => 'psa', 'PSO170G2858' => 'pso', 'PSO339G0606' => 'pso', 'PSO384G4709' => 'pso', 'PSO407G0334' => 'pso', 'QL04p040276' => 'qlo', 'QL06p005458' => 'qlo', 'QL06p005472' => 'qlo', 'QL07p030546' => 'qlo', 'QL07p031519' => 'qlo', 'QL09p050949' => 'qlo', 'QL09p050966' => 'qlo', 'QL09p051067' => 'qlo', 'QL12p022706' => 'qlo', 'RcHm_v2.0_Chr2g0119601' => 'rch', 'RcHm_v2.0_Chr3g0459591' => 'rch', 'RcHm_v2.0_Chr4g0418521' => 'rch', 'RcHm_v2.0_Chr4g0418531' => 'rch', 'RcHm_v2.0_Chr4g0418541' => 'rch', 'RcHm_v2.0_Chr6g0291641' => 'rch', 'Rhsim01G0086300' => 'rsi', 'Rhsim01G0276300' => 'rsi', 'Rhsim01G0276500' => 'rsi', 'Rhsim04G0207700' => 'rsi', 'Rhsim05G0234500' => 'rsi', 'Rhsim13G0022400' => 'rsi', 'Sabra02G0167900' => 'sbr', 'Sabra04G0158500' => 'sbr', 'Sabra08G0159800' => 'sbr', 'Sabra10G0011500' => 'sbr', 'Sabra14G0104400' => 'sbr', 'SalBow2G2440' => 'sbo', 'SalBow4G2265' => 'sbo', 'Sc02g0000060' => 'sci', 'Sc05g0005020' => 'sci', 'Sc13g0003890' => 'sci', 'Sed0014865' => 'sed', 'Sed0017224' => 'sed', 'Sed0026391' => 'sed', 'SEGI_00063' => 'sgi', 'SEGI_10967' => 'sgi', 'SEGI_17510' => 'sgi', 'SEGI_24396' => 'sgi', 'SEGI_39719' => 'sgi', 'SEGI_41392' => 'sgi', 'SGA_v2.0_scaffold11G05794' => 'sas', 'SGA_v2.0_scaffold142G35607' => 'sas', 'SGA_v2.0_scaffold1G00447' => 'sas', 'SHI15388' => 'shi', 'SHI15394' => 'shi', 'SHI15396' => 'shi', 'SHI15399' => 'shi', 'SMO343G0151' => 'smo', 'SMO367G1118' => 'smo', 'Solyc01g080200.3' => 'sly', 'Solyc06g008960.3' => 'sly', 'Solyc09g064780.3' => 'sly', 'Sopen01g031980' => 'spe', 'Sopen06g003710' => 'spe', 'Sopen09g026460' => 'spe', 'Sp3g21240' => 'spa', 'Sp4g30030' => 'spa', 'TAR365G0022' => 'tar', 'TAR365G1023' => 'tar', 'TAR365G1253' => 'tar', 'TAR623G0078' => 'tar', 'TAR623G1721' => 'tar', 'TAR633G0959' => 'tar', 'THA.LOC104802225' => 'tha', 'THA.LOC104804769' => 'tha', 'THA.LOC104808660' => 'tha', 'THA.LOC104812792' => 'tha', 'Thecc.01G284000' => 'tca', 'Thecc.04G220600' => 'tca', 'Thecc.05G268900' => 'tca', 'Thecc.08G171100' => 'tca', 'Thhalv10001284m.g' => 'esa', 'Thhalv10019912m.g' => 'esa', 'TPR.G14189' => 'tpr', 'TPR.G18110' => 'tpr', 'TPR.G18130' => 'tpr', 'TPR.G18131' => 'tpr', 'TPR.G18140' => 'tpr', 'TPR.G24282' => 'tpr', 'TPR.G25221' => 'tpr', 'TPR.G29267' => 'tpr', 'TPR.G35315' => 'tpr', 'TPR.G36173' => 'tpr', 'TWI09G0794' => 'twi', 'TWI59G1348' => 'twi', 'TWI74G0430' => 'twi', 'unitig_26.g8940' => 'ugi', 'unitig_749.g13744' => 'ugi', 'unitig_749.g13745' => 'ugi', 'vmacro08269' => 'vma', 'vmacro14937' => 'vma', 'vmacro20401' => 'vma', 'VMungo0464G1349' => 'vmu', 'VMungo0540G0289' => 'vmu', 'VMungo1215G1590' => 'vmu', 'VMungo1309G0221' => 'vmu', 'VMungo1309G2815' => 'vmu', 'VMungo1383G0239' => 'vmu', 'VMungo1383G2910' => 'vmu', 'Zm00001eb095270' => 'zma', 'Zm00001eb095280' => 'zma', 'Zm00001eb111630' => 'zma', 'Zm00001eb237080' => 'zma', 'Zm00001eb273740' => 'zma', 'Zm00001eb285040' => 'zma', 'Zm00001eb330790' => 'zma', 'Zm00001eb337380' => 'zma' ) $gf_id = 'HOM05D001484' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001484' ) $data_identifier = 'HOM05D001484' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 2, 'aly' => (int) 2, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 22, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 7, 'hma' => (int) 2, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 7, 'mtr' => (int) 10, 'cme' => (int) 2, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 4, 'ppa' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 4, 'qlo' => (int) 9, 'rch' => (int) 6, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 10, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 7, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb337380' $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' => 'HOM05D001484', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p31500' => 'bna', 'A05p00020' => 'bna', 'A07p08820' => 'bna', 'Aa31LG4G3300' => 'aar', 'Aa31LG8G10030' => 'aar', 'Actinidia00731' => 'ach', 'Actinidia11473' => 'ach', 'Actinidia23469' => 'ach', 'Actinidia24318' => 'ach', 'Actinidia40196' => 'ach', 'Actinidia40197' => 'ach', 'Actinidia40198' => 'ach', 'Ah.08g212990' => 'amhyb', 'Ah.15g091720' => 'amhyb', 'AL3G38260' => 'aly', 'AL4G47710' => 'aly', 'Aqoxy2G00671' => 'aox', 'Aqoxy2G03236' => 'aox', 'arahy.Tifrunner.gnm1.ann1.05IDCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KR684' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATY3SJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK6QJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6APGL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IDT7Z9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM073U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ0R87' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LE7RV4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT4QRX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V5ENPK' => 'arhy', 'AT2G48110' => 'ath', 'AT3G23590' => 'ath', 'ATR0626G186' => 'atr', 'ATR1127G141' => 'atr', 'Atru.chr4.2583' => 'acertr', 'Atru.chr5.1358' => 'acertr', 'Atru.chr5.1359' => 'acertr', 'Atru.chr8.46' => 'acertr', 'AUR62002640' => 'cqu', 'AUR62030055' => 'cqu', 'AUR62033713' => 'cqu', 'AUR62033714' => 'cqu', 'AUR62036795' => 'cqu', 'AUR62039891' => 'cqu', 'BcaB02g08737' => 'bca', 'BcaB04g20441' => 'bca', 'BcaB06g26509' => 'bca', 'BcaB06g26510' => 'bca', 'BcaB06g26511' => 'bca', 'BcaB06g26512' => 'bca', 'BcaB06g26513' => 'bca', 'BcaC02g12564' => 'bca', 'BcaC02g12565' => 'bca', 'BcaC02g12794' => 'bca', 'BcaC02g12795' => 'bca', 'BcaC02g12796' => 'bca', 'BcaC06g35541' => 'bca', 'BNapus_Darmor_BZH_scaffold_188p00080' => 'bna', 'BNapus_Darmor_BZH_scaffold_188p00090' => 'bna', 'BolC1t03972H' => 'bol', 'BolC1t03973H' => 'bol', 'BolC4t21680H' => 'bol', 'BolC7t41863H' => 'bol', 'BolSC55t61227H' => 'bol', 'BolSC55t61228H' => 'bol', 'BraA01t03278Z' => 'bra', 'BraA05t18998Z' => 'bra', 'BraA07t28673Z' => 'bra', 'C01p40150' => 'bna', 'C05p12370' => 'bna', 'C07p13680' => 'bna', 'CAN.G1006.16' => 'can', 'CAN.G1006.17' => 'can', 'CAN.G1170.2' => 'can', 'CAN.G962.7' => 'can', 'CANSAT25G2179' => 'cansat', 'CANSAT78G1573' => 'cansat', 'CARHR099510' => 'chi', 'CARHR143510' => 'chi', 'Carub.0003s2380' => 'cru', 'Carub.0004s3082' => 'cru', 'Ca_00614_v3' => 'car', 'Ca_07801_v3' => 'car', 'Ca_08567_v3' => 'car', 'Ca_09571_v3' => 'car', 'CBR_g19290' => 'cbr', 'Cc01_g19770' => 'ccan', 'Cc03_g03030' => 'ccan', 'CDE07G0968' => 'cde', 'CDE09G1441' => 'cde', 'Cfa006103' => 'cfa', 'Cfa015573' => 'cfa', 'Cfa016988' => 'cfa', 'Ciclev10006738m.g' => 'ccl', 'Ciclev10010920m.g' => 'ccl', 'Ciclev10018517m.g' => 'ccl', 'CiPaw.01G159200' => 'cil', 'CiPaw.02G091000' => 'cil', 'CiPaw.02G091100' => 'cil', 'CiPaw.08G103100' => 'cil', 'CiPaw.09G224900' => 'cil', 'ClCG06G005740' => 'cla', 'ClCG07G000090' => 'cla', 'ClCG07G000100' => 'cla', 'COL.COLO4_09143' => 'col', 'COL.COLO4_25124' => 'col', 'Cpa.g.sc16.34' => 'cpa', 'Cpa.g.sc3504.1' => 'cpa', 'Cpa.g.sc60.37' => 'cpa', 'CsaV3_6G018520' => 'csa', 'CsaV3_6G036860' => 'csa', 'CSS0001072' => 'camsi', 'CSS0020208' => 'camsi', 'CSS0021253' => 'camsi', 'CSS0022190' => 'camsi', 'CSS0036150' => 'camsi', 'CSS0040442' => 'camsi', 'CSS0042300' => 'camsi', 'CSS0045298' => 'camsi', 'DCAR_012449' => 'dca', 'DCAR_018405' => 'dca', 'DCAR_024573' => 'dca', 'DCAR_030591' => 'dca', 'Dinv16926' => 'din', 'Dinv32963' => 'din', 'Dinv38382' => 'din', 'Dinv38383' => 'din', 'Duzib133G0974' => 'dzi', 'Duzib138G1867' => 'dzi', 'Duzib211G0420' => 'dzi', 'Duzib212G0930' => 'dzi', 'ECA234G1645' => 'eca', 'ECA247G3467' => 'eca', 'ECA248G1703' => 'eca', 'EL10Ac3g06327' => 'bvu', 'EL10Ac7g17204' => 'bvu', 'Eucgr.A00855' => 'egr', 'Eucgr.A00858' => 'egr', 'Eucgr.H01520' => 'egr', 'Eucgr.H03604' => 'egr', 'Eucgr.L03465' => 'egr', 'Eucgr.L03466' => 'egr', 'FAN01G0988' => 'fan', 'FAN02G3892' => 'fan', 'FAN05G3381' => 'fan', 'FAN07G0967' => 'fan', 'FAN07G1493' => 'fan', 'FAN08G3125' => 'fan', 'FAN09G0402' => 'fan', 'FAN12G2594' => 'fan', 'FAN12G3879' => 'fan', 'FAN14G1546' => 'fan', 'FAN15G3626' => 'fan', 'FAN17G0588' => 'fan', 'FAN17G0609' => 'fan', 'FAN18G2817' => 'fan', 'FAN19G1305' => 'fan', 'FAN20G1787' => 'fan', 'FAN22G0073' => 'fan', 'FAN22G0352' => 'fan', 'FAN22G0368' => 'fan', 'FAN22G2273' => 'fan', 'FAN24G1998' => 'fan', 'FAN27G1317' => 'fan', 'FvH4_2g23980' => 'fve', 'FvH4_4g14380' => 'fve', 'FvH4_4g14390' => 'fve', 'FvH4_6g09250' => 'fve', 'Glyma.03G151100' => 'gma', 'Glyma.04G122550' => 'gma', 'Glyma.05G001600' => 'gma', 'Glyma.09G270766' => 'gma', 'Glyma.09G270832' => 'gma', 'Glyma.13G209800' => 'gma', 'Glyma.15G102800' => 'gma', 'Glyma.18G218900' => 'gma', 'Glyma.19G001500' => 'gma', 'Glyma.19G153600' => 'gma', 'Gohir.A02G028600' => 'ghi', 'Gohir.A08G045000' => 'ghi', 'Gohir.A11G120500' => 'ghi', 'Gohir.A12G006200' => 'ghi', 'Gohir.A12G006250' => 'ghi', 'Gohir.D02G036300' => 'ghi', 'Gohir.D08G054700' => 'ghi', 'Gohir.D11G125600' => 'ghi', 'Gohir.D12G005700' => 'ghi', 'Gorai.004G055200' => 'gra', 'Gorai.005G040400' => 'gra', 'Gorai.007G134500' => 'gra', 'Gorai.008G005500' => 'gra', 'GSVIVG01011094001' => 'vvi', 'GSVIVG01017879001' => 'vvi', 'GSVIVG01025988001' => 'vvi', 'GSVIVG01029847001' => 'vvi', 'HanXRQChr10g0282901' => 'han', 'HanXRQChr10g0310371' => 'han', 'HanXRQChr10g0315041' => 'han', 'HanXRQChr11g0327651' => 'han', 'HanXRQChr12g0359391' => 'han', 'Haze_00972' => 'cav', 'Haze_00973' => 'cav', 'Haze_00974' => 'cav', 'Haze_04747' => 'cav', 'Haze_04749' => 'cav', 'Haze_04750' => 'cav', 'Haze_21217' => 'cav', 'Hma1.2p1_1037F.1_g250680' => 'hma', 'Hma1.2p1_1644F.1_g295320' => 'hma', 'HPP92_011322' => 'vpl', 'HPP92_011323' => 'vpl', 'HPP92_011324' => 'vpl', 'HPP92_011325' => 'vpl', 'HPP92_011326' => 'vpl', 'Hund12205' => 'sun', 'Hund17957' => 'sun', 'Lalb_Chr06g0176771' => 'lal', 'Lalb_Chr18g0056021' => 'lal', 'Lalb_Chr18g0056031' => 'lal', 'Lalb_Chr18g0056041' => 'lal', 'Lalb_Chr20g0107751' => 'lal', 'Lalb_Chr20g0118371' => 'lal', 'Lj1g0010239' => 'lja', 'Lj1g0017101' => 'lja', 'Lj2A1178G40' => 'lonja', 'Lj2A54G84' => 'lonja', 'Lj2g0015248' => 'lja', 'Lj3A761T51' => 'lonja', 'Lj6g0018116' => 'lja', 'Lsat_1_v5_gn_4_136040' => 'lsa', 'Lsat_1_v5_gn_5_187461' => 'lsa', 'Lsat_1_v5_gn_5_77001' => 'lsa', 'Lsat_1_v5_gn_9_4461' => 'lsa', 'Manes.01G210100' => 'mes', 'Manes.03G185600' => 'mes', 'Manes.05G073300' => 'mes', 'Manes.09G120300' => 'mes', 'Manes.15G022100' => 'mes', 'Mapoly0096s0053' => 'mpo', 'MBI03_g14058_MAGBIO' => 'mbi', 'MBI03_g33876_MAGBIO' => 'mbi', 'MBI03_g36854_MAGBIO' => 'mbi', 'MBI17_g11997_MAGBIO' => 'mbi', 'MD03G1269000' => 'mdo', 'MD04G1179600' => 'mdo', 'MD11G1289800' => 'mdo', 'MD12G1194700' => 'mdo', 'MD13G1182100' => 'mdo', 'MD13G1182200' => 'mdo', 'MD16G1182600' => 'mdo', 'Medtr2g021400' => 'mtr', 'Medtr2g021470' => 'mtr', 'Medtr2g105810' => 'mtr', 'Medtr3g033580' => 'mtr', 'Medtr6g007970' => 'mtr', 'Medtr7g056330' => 'mtr', 'Medtr7g074290' => 'mtr', 'Medtr7g074380' => 'mtr', 'Medtr7g094550' => 'mtr', 'Medtr8g069995' => 'mtr', 'MELO3C014345.2' => 'cme', 'MELO3C021395.2' => 'cme', 'Migut.D00262' => 'egut', 'Migut.G00257' => 'egut', 'MSTRG.21575' => 'ama', 'MSTRG.3985' => 'ama', 'Nitab4.5_0000295g0140' => 'nta', 'Nitab4.5_0000732g0140' => 'nta', 'Nitab4.5_0003162g0020' => 'nta', 'Nitab4.5_0006180g0090' => 'nta', 'Nitab4.5_0006390g0010' => 'nta', 'Nitab4.5_0007392g0040' => 'nta', 'Nn1g02140' => 'nnu', 'Nn4g26168' => 'nnu', 'Nn5g26754' => 'nnu', 'Oeu001433.1' => 'oeu', 'Oeu010299.2' => 'oeu', 'Oeu011171.1' => 'oeu', 'Oeu037675.1' => 'oeu', 'Oeu038359.1' => 'oeu', 'Oeu063834.1' => 'oeu', 'Oeu063835.1' => 'oeu', 'Os05g0312000' => 'osa', 'Os07g0211101' => 'osa', 'Os07g0211200' => 'osa', 'Os07g0681500' => 'osa', 'Peaxi162Scf00095g01015' => 'pax', 'Peaxi162Scf00104g00329' => 'pax', 'Peaxi162Scf00161g00137' => 'pax', 'PGR004G1665' => 'pgr', 'PGR031G2937' => 'pgr', 'PGR119G2145' => 'pgr', 'PGSC0003DMG400004351' => 'stu', 'PGSC0003DMG400014625' => 'stu', 'PGSC0003DMG401000943' => 'stu', 'Phvul.001G148600' => 'pvu', 'Phvul.004G001700' => 'pvu', 'Phvul.006G154900' => 'pvu', 'Phvul.008G078200' => 'pvu', 'Phvul.011G136500' => 'pvu', 'Potri.002G215600' => 'ptr', 'Potri.008G201600' => 'ptr', 'Potri.014G138400' => 'ptr', 'Potri.016G142500' => 'ptr', 'Pp3c16_10580' => 'ppa', 'Pp3c5_25280' => 'ppa', 'Prupe.1G150000' => 'ppe', 'Prupe.1G150100' => 'ppe', 'Prupe.6G299600' => 'ppe', 'Prupe.8G245000' => 'ppe', 'Psat0s4927g0040' => 'psa', 'Psat1g052080' => 'psa', 'Psat1g183800' => 'psa', 'Psat3g113840' => 'psa', 'Psat3g126120' => 'psa', 'Psat3g126160' => 'psa', 'Psat3g158760' => 'psa', 'Psat3g158840' => 'psa', 'PSO170G2858' => 'pso', 'PSO339G0606' => 'pso', 'PSO384G4709' => 'pso', 'PSO407G0334' => 'pso', 'QL04p040276' => 'qlo', 'QL06p005458' => 'qlo', 'QL06p005472' => 'qlo', 'QL07p030546' => 'qlo', 'QL07p031519' => 'qlo', 'QL09p050949' => 'qlo', 'QL09p050966' => 'qlo', 'QL09p051067' => 'qlo', 'QL12p022706' => 'qlo', 'RcHm_v2.0_Chr2g0119601' => 'rch', 'RcHm_v2.0_Chr3g0459591' => 'rch', 'RcHm_v2.0_Chr4g0418521' => 'rch', 'RcHm_v2.0_Chr4g0418531' => 'rch', 'RcHm_v2.0_Chr4g0418541' => 'rch', 'RcHm_v2.0_Chr6g0291641' => 'rch', 'Rhsim01G0086300' => 'rsi', 'Rhsim01G0276300' => 'rsi', 'Rhsim01G0276500' => 'rsi', 'Rhsim04G0207700' => 'rsi', 'Rhsim05G0234500' => 'rsi', 'Rhsim13G0022400' => 'rsi', 'Sabra02G0167900' => 'sbr', 'Sabra04G0158500' => 'sbr', 'Sabra08G0159800' => 'sbr', 'Sabra10G0011500' => 'sbr', 'Sabra14G0104400' => 'sbr', 'SalBow2G2440' => 'sbo', 'SalBow4G2265' => 'sbo', 'Sc02g0000060' => 'sci', 'Sc05g0005020' => 'sci', 'Sc13g0003890' => 'sci', 'Sed0014865' => 'sed', 'Sed0017224' => 'sed', 'Sed0026391' => 'sed', 'SEGI_00063' => 'sgi', 'SEGI_10967' => 'sgi', 'SEGI_17510' => 'sgi', 'SEGI_24396' => 'sgi', 'SEGI_39719' => 'sgi', 'SEGI_41392' => 'sgi', 'SGA_v2.0_scaffold11G05794' => 'sas', 'SGA_v2.0_scaffold142G35607' => 'sas', 'SGA_v2.0_scaffold1G00447' => 'sas', 'SHI15388' => 'shi', 'SHI15394' => 'shi', 'SHI15396' => 'shi', 'SHI15399' => 'shi', 'SMO343G0151' => 'smo', 'SMO367G1118' => 'smo', 'Solyc01g080200.3' => 'sly', 'Solyc06g008960.3' => 'sly', 'Solyc09g064780.3' => 'sly', 'Sopen01g031980' => 'spe', 'Sopen06g003710' => 'spe', 'Sopen09g026460' => 'spe', 'Sp3g21240' => 'spa', 'Sp4g30030' => 'spa', 'TAR365G0022' => 'tar', 'TAR365G1023' => 'tar', 'TAR365G1253' => 'tar', 'TAR623G0078' => 'tar', 'TAR623G1721' => 'tar', 'TAR633G0959' => 'tar', 'THA.LOC104802225' => 'tha', 'THA.LOC104804769' => 'tha', 'THA.LOC104808660' => 'tha', 'THA.LOC104812792' => 'tha', 'Thecc.01G284000' => 'tca', 'Thecc.04G220600' => 'tca', 'Thecc.05G268900' => 'tca', 'Thecc.08G171100' => 'tca', 'Thhalv10001284m.g' => 'esa', 'Thhalv10019912m.g' => 'esa', 'TPR.G14189' => 'tpr', 'TPR.G18110' => 'tpr', 'TPR.G18130' => 'tpr', 'TPR.G18131' => 'tpr', 'TPR.G18140' => 'tpr', 'TPR.G24282' => 'tpr', 'TPR.G25221' => 'tpr', 'TPR.G29267' => 'tpr', 'TPR.G35315' => 'tpr', 'TPR.G36173' => 'tpr', 'TWI09G0794' => 'twi', 'TWI59G1348' => 'twi', 'TWI74G0430' => 'twi', 'unitig_26.g8940' => 'ugi', 'unitig_749.g13744' => 'ugi', 'unitig_749.g13745' => 'ugi', 'vmacro08269' => 'vma', 'vmacro14937' => 'vma', 'vmacro20401' => 'vma', 'VMungo0464G1349' => 'vmu', 'VMungo0540G0289' => 'vmu', 'VMungo1215G1590' => 'vmu', 'VMungo1309G0221' => 'vmu', 'VMungo1309G2815' => 'vmu', 'VMungo1383G0239' => 'vmu', 'VMungo1383G2910' => 'vmu', 'Zm00001eb095270' => 'zma', 'Zm00001eb095280' => 'zma', 'Zm00001eb111630' => 'zma', 'Zm00001eb237080' => 'zma', 'Zm00001eb273740' => 'zma', 'Zm00001eb285040' => 'zma', 'Zm00001eb330790' => 'zma', 'Zm00001eb337380' => 'zma' ), 'gf_id' => 'HOM05D001484', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001484' ), 'data_identifier' => 'HOM05D001484', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001484', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p31500' => 'bna', 'A05p00020' => 'bna', 'A07p08820' => 'bna', 'Aa31LG4G3300' => 'aar', 'Aa31LG8G10030' => 'aar', 'Actinidia00731' => 'ach', 'Actinidia11473' => 'ach', 'Actinidia23469' => 'ach', 'Actinidia24318' => 'ach', 'Actinidia40196' => 'ach', 'Actinidia40197' => 'ach', 'Actinidia40198' => 'ach', 'Ah.08g212990' => 'amhyb', 'Ah.15g091720' => 'amhyb', 'AL3G38260' => 'aly', 'AL4G47710' => 'aly', 'Aqoxy2G00671' => 'aox', 'Aqoxy2G03236' => 'aox', 'arahy.Tifrunner.gnm1.ann1.05IDCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KR684' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATY3SJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK6QJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6APGL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IDT7Z9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM073U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ0R87' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LE7RV4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT4QRX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V5ENPK' => 'arhy', 'AT2G48110' => 'ath', 'AT3G23590' => 'ath', 'ATR0626G186' => 'atr', 'ATR1127G141' => 'atr', 'Atru.chr4.2583' => 'acertr', 'Atru.chr5.1358' => 'acertr', 'Atru.chr5.1359' => 'acertr', 'Atru.chr8.46' => 'acertr', 'AUR62002640' => 'cqu', 'AUR62030055' => 'cqu', 'AUR62033713' => 'cqu', 'AUR62033714' => 'cqu', 'AUR62036795' => 'cqu', 'AUR62039891' => 'cqu', 'BcaB02g08737' => 'bca', 'BcaB04g20441' => 'bca', 'BcaB06g26509' => 'bca', 'BcaB06g26510' => 'bca', 'BcaB06g26511' => 'bca', 'BcaB06g26512' => 'bca', 'BcaB06g26513' => 'bca', 'BcaC02g12564' => 'bca', 'BcaC02g12565' => 'bca', 'BcaC02g12794' => 'bca', 'BcaC02g12795' => 'bca', 'BcaC02g12796' => 'bca', 'BcaC06g35541' => 'bca', 'BNapus_Darmor_BZH_scaffold_188p00080' => 'bna', 'BNapus_Darmor_BZH_scaffold_188p00090' => 'bna', 'BolC1t03972H' => 'bol', 'BolC1t03973H' => 'bol', 'BolC4t21680H' => 'bol', 'BolC7t41863H' => 'bol', 'BolSC55t61227H' => 'bol', 'BolSC55t61228H' => 'bol', 'BraA01t03278Z' => 'bra', 'BraA05t18998Z' => 'bra', 'BraA07t28673Z' => 'bra', 'C01p40150' => 'bna', 'C05p12370' => 'bna', 'C07p13680' => 'bna', 'CAN.G1006.16' => 'can', 'CAN.G1006.17' => 'can', 'CAN.G1170.2' => 'can', 'CAN.G962.7' => 'can', 'CANSAT25G2179' => 'cansat', 'CANSAT78G1573' => 'cansat', 'CARHR099510' => 'chi', 'CARHR143510' => 'chi', 'Carub.0003s2380' => 'cru', 'Carub.0004s3082' => 'cru', 'Ca_00614_v3' => 'car', 'Ca_07801_v3' => 'car', 'Ca_08567_v3' => 'car', 'Ca_09571_v3' => 'car', 'CBR_g19290' => 'cbr', 'Cc01_g19770' => 'ccan', 'Cc03_g03030' => 'ccan', 'CDE07G0968' => 'cde', 'CDE09G1441' => 'cde', 'Cfa006103' => 'cfa', 'Cfa015573' => 'cfa', 'Cfa016988' => 'cfa', 'Ciclev10006738m.g' => 'ccl', 'Ciclev10010920m.g' => 'ccl', 'Ciclev10018517m.g' => 'ccl', 'CiPaw.01G159200' => 'cil', 'CiPaw.02G091000' => 'cil', 'CiPaw.02G091100' => 'cil', 'CiPaw.08G103100' => 'cil', 'CiPaw.09G224900' => 'cil', 'ClCG06G005740' => 'cla', 'ClCG07G000090' => 'cla', 'ClCG07G000100' => 'cla', 'COL.COLO4_09143' => 'col', 'COL.COLO4_25124' => 'col', 'Cpa.g.sc16.34' => 'cpa', 'Cpa.g.sc3504.1' => 'cpa', 'Cpa.g.sc60.37' => 'cpa', 'CsaV3_6G018520' => 'csa', 'CsaV3_6G036860' => 'csa', 'CSS0001072' => 'camsi', 'CSS0020208' => 'camsi', 'CSS0021253' => 'camsi', 'CSS0022190' => 'camsi', 'CSS0036150' => 'camsi', 'CSS0040442' => 'camsi', 'CSS0042300' => 'camsi', 'CSS0045298' => 'camsi', 'DCAR_012449' => 'dca', 'DCAR_018405' => 'dca', 'DCAR_024573' => 'dca', 'DCAR_030591' => 'dca', 'Dinv16926' => 'din', 'Dinv32963' => 'din', 'Dinv38382' => 'din', 'Dinv38383' => 'din', 'Duzib133G0974' => 'dzi', 'Duzib138G1867' => 'dzi', 'Duzib211G0420' => 'dzi', 'Duzib212G0930' => 'dzi', 'ECA234G1645' => 'eca', 'ECA247G3467' => 'eca', 'ECA248G1703' => 'eca', 'EL10Ac3g06327' => 'bvu', 'EL10Ac7g17204' => 'bvu', 'Eucgr.A00855' => 'egr', 'Eucgr.A00858' => 'egr', 'Eucgr.H01520' => 'egr', 'Eucgr.H03604' => 'egr', 'Eucgr.L03465' => 'egr', 'Eucgr.L03466' => 'egr', 'FAN01G0988' => 'fan', 'FAN02G3892' => 'fan', 'FAN05G3381' => 'fan', 'FAN07G0967' => 'fan', 'FAN07G1493' => 'fan', 'FAN08G3125' => 'fan', 'FAN09G0402' => 'fan', 'FAN12G2594' => 'fan', 'FAN12G3879' => 'fan', 'FAN14G1546' => 'fan', 'FAN15G3626' => 'fan', 'FAN17G0588' => 'fan', 'FAN17G0609' => 'fan', 'FAN18G2817' => 'fan', 'FAN19G1305' => 'fan', 'FAN20G1787' => 'fan', 'FAN22G0073' => 'fan', 'FAN22G0352' => 'fan', 'FAN22G0368' => 'fan', 'FAN22G2273' => 'fan', 'FAN24G1998' => 'fan', 'FAN27G1317' => 'fan', 'FvH4_2g23980' => 'fve', 'FvH4_4g14380' => 'fve', 'FvH4_4g14390' => 'fve', 'FvH4_6g09250' => 'fve', 'Glyma.03G151100' => 'gma', 'Glyma.04G122550' => 'gma', 'Glyma.05G001600' => 'gma', 'Glyma.09G270766' => 'gma', 'Glyma.09G270832' => 'gma', 'Glyma.13G209800' => 'gma', 'Glyma.15G102800' => 'gma', 'Glyma.18G218900' => 'gma', 'Glyma.19G001500' => 'gma', 'Glyma.19G153600' => 'gma', 'Gohir.A02G028600' => 'ghi', 'Gohir.A08G045000' => 'ghi', 'Gohir.A11G120500' => 'ghi', 'Gohir.A12G006200' => 'ghi', 'Gohir.A12G006250' => 'ghi', 'Gohir.D02G036300' => 'ghi', 'Gohir.D08G054700' => 'ghi', 'Gohir.D11G125600' => 'ghi', 'Gohir.D12G005700' => 'ghi', 'Gorai.004G055200' => 'gra', 'Gorai.005G040400' => 'gra', 'Gorai.007G134500' => 'gra', 'Gorai.008G005500' => 'gra', 'GSVIVG01011094001' => 'vvi', 'GSVIVG01017879001' => 'vvi', 'GSVIVG01025988001' => 'vvi', 'GSVIVG01029847001' => 'vvi', 'HanXRQChr10g0282901' => 'han', 'HanXRQChr10g0310371' => 'han', 'HanXRQChr10g0315041' => 'han', 'HanXRQChr11g0327651' => 'han', 'HanXRQChr12g0359391' => 'han', 'Haze_00972' => 'cav', 'Haze_00973' => 'cav', 'Haze_00974' => 'cav', 'Haze_04747' => 'cav', 'Haze_04749' => 'cav', 'Haze_04750' => 'cav', 'Haze_21217' => 'cav', 'Hma1.2p1_1037F.1_g250680' => 'hma', 'Hma1.2p1_1644F.1_g295320' => 'hma', 'HPP92_011322' => 'vpl', 'HPP92_011323' => 'vpl', 'HPP92_011324' => 'vpl', 'HPP92_011325' => 'vpl', 'HPP92_011326' => 'vpl', 'Hund12205' => 'sun', 'Hund17957' => 'sun', 'Lalb_Chr06g0176771' => 'lal', 'Lalb_Chr18g0056021' => 'lal', 'Lalb_Chr18g0056031' => 'lal', 'Lalb_Chr18g0056041' => 'lal', 'Lalb_Chr20g0107751' => 'lal', 'Lalb_Chr20g0118371' => 'lal', 'Lj1g0010239' => 'lja', 'Lj1g0017101' => 'lja', 'Lj2A1178G40' => 'lonja', 'Lj2A54G84' => 'lonja', 'Lj2g0015248' => 'lja', 'Lj3A761T51' => 'lonja', 'Lj6g0018116' => 'lja', 'Lsat_1_v5_gn_4_136040' => 'lsa', 'Lsat_1_v5_gn_5_187461' => 'lsa', 'Lsat_1_v5_gn_5_77001' => 'lsa', 'Lsat_1_v5_gn_9_4461' => 'lsa', 'Manes.01G210100' => 'mes', 'Manes.03G185600' => 'mes', 'Manes.05G073300' => 'mes', 'Manes.09G120300' => 'mes', 'Manes.15G022100' => 'mes', 'Mapoly0096s0053' => 'mpo', 'MBI03_g14058_MAGBIO' => 'mbi', 'MBI03_g33876_MAGBIO' => 'mbi', 'MBI03_g36854_MAGBIO' => 'mbi', 'MBI17_g11997_MAGBIO' => 'mbi', 'MD03G1269000' => 'mdo', 'MD04G1179600' => 'mdo', 'MD11G1289800' => 'mdo', 'MD12G1194700' => 'mdo', 'MD13G1182100' => 'mdo', 'MD13G1182200' => 'mdo', 'MD16G1182600' => 'mdo', 'Medtr2g021400' => 'mtr', 'Medtr2g021470' => 'mtr', 'Medtr2g105810' => 'mtr', 'Medtr3g033580' => 'mtr', 'Medtr6g007970' => 'mtr', 'Medtr7g056330' => 'mtr', 'Medtr7g074290' => 'mtr', 'Medtr7g074380' => 'mtr', 'Medtr7g094550' => 'mtr', 'Medtr8g069995' => 'mtr', 'MELO3C014345.2' => 'cme', 'MELO3C021395.2' => 'cme', 'Migut.D00262' => 'egut', 'Migut.G00257' => 'egut', 'MSTRG.21575' => 'ama', 'MSTRG.3985' => 'ama', 'Nitab4.5_0000295g0140' => 'nta', 'Nitab4.5_0000732g0140' => 'nta', 'Nitab4.5_0003162g0020' => 'nta', 'Nitab4.5_0006180g0090' => 'nta', 'Nitab4.5_0006390g0010' => 'nta', 'Nitab4.5_0007392g0040' => 'nta', 'Nn1g02140' => 'nnu', 'Nn4g26168' => 'nnu', 'Nn5g26754' => 'nnu', 'Oeu001433.1' => 'oeu', 'Oeu010299.2' => 'oeu', 'Oeu011171.1' => 'oeu', 'Oeu037675.1' => 'oeu', 'Oeu038359.1' => 'oeu', 'Oeu063834.1' => 'oeu', 'Oeu063835.1' => 'oeu', 'Os05g0312000' => 'osa', 'Os07g0211101' => 'osa', 'Os07g0211200' => 'osa', 'Os07g0681500' => 'osa', 'Peaxi162Scf00095g01015' => 'pax', 'Peaxi162Scf00104g00329' => 'pax', 'Peaxi162Scf00161g00137' => 'pax', 'PGR004G1665' => 'pgr', 'PGR031G2937' => 'pgr', 'PGR119G2145' => 'pgr', 'PGSC0003DMG400004351' => 'stu', 'PGSC0003DMG400014625' => 'stu', 'PGSC0003DMG401000943' => 'stu', 'Phvul.001G148600' => 'pvu', 'Phvul.004G001700' => 'pvu', 'Phvul.006G154900' => 'pvu', 'Phvul.008G078200' => 'pvu', 'Phvul.011G136500' => 'pvu', 'Potri.002G215600' => 'ptr', 'Potri.008G201600' => 'ptr', 'Potri.014G138400' => 'ptr', 'Potri.016G142500' => 'ptr', 'Pp3c16_10580' => 'ppa', 'Pp3c5_25280' => 'ppa', 'Prupe.1G150000' => 'ppe', 'Prupe.1G150100' => 'ppe', 'Prupe.6G299600' => 'ppe', 'Prupe.8G245000' => 'ppe', 'Psat0s4927g0040' => 'psa', 'Psat1g052080' => 'psa', 'Psat1g183800' => 'psa', 'Psat3g113840' => 'psa', 'Psat3g126120' => 'psa', 'Psat3g126160' => 'psa', 'Psat3g158760' => 'psa', 'Psat3g158840' => 'psa', 'PSO170G2858' => 'pso', 'PSO339G0606' => 'pso', 'PSO384G4709' => 'pso', 'PSO407G0334' => 'pso', 'QL04p040276' => 'qlo', 'QL06p005458' => 'qlo', 'QL06p005472' => 'qlo', 'QL07p030546' => 'qlo', 'QL07p031519' => 'qlo', 'QL09p050949' => 'qlo', 'QL09p050966' => 'qlo', 'QL09p051067' => 'qlo', 'QL12p022706' => 'qlo', 'RcHm_v2.0_Chr2g0119601' => 'rch', 'RcHm_v2.0_Chr3g0459591' => 'rch', 'RcHm_v2.0_Chr4g0418521' => 'rch', 'RcHm_v2.0_Chr4g0418531' => 'rch', 'RcHm_v2.0_Chr4g0418541' => 'rch', 'RcHm_v2.0_Chr6g0291641' => 'rch', 'Rhsim01G0086300' => 'rsi', 'Rhsim01G0276300' => 'rsi', 'Rhsim01G0276500' => 'rsi', 'Rhsim04G0207700' => 'rsi', 'Rhsim05G0234500' => 'rsi', 'Rhsim13G0022400' => 'rsi', 'Sabra02G0167900' => 'sbr', 'Sabra04G0158500' => 'sbr', 'Sabra08G0159800' => 'sbr', 'Sabra10G0011500' => 'sbr', 'Sabra14G0104400' => 'sbr', 'SalBow2G2440' => 'sbo', 'SalBow4G2265' => 'sbo', 'Sc02g0000060' => 'sci', 'Sc05g0005020' => 'sci', 'Sc13g0003890' => 'sci', 'Sed0014865' => 'sed', 'Sed0017224' => 'sed', 'Sed0026391' => 'sed', 'SEGI_00063' => 'sgi', 'SEGI_10967' => 'sgi', 'SEGI_17510' => 'sgi', 'SEGI_24396' => 'sgi', 'SEGI_39719' => 'sgi', 'SEGI_41392' => 'sgi', 'SGA_v2.0_scaffold11G05794' => 'sas', 'SGA_v2.0_scaffold142G35607' => 'sas', 'SGA_v2.0_scaffold1G00447' => 'sas', 'SHI15388' => 'shi', 'SHI15394' => 'shi', 'SHI15396' => 'shi', 'SHI15399' => 'shi', 'SMO343G0151' => 'smo', 'SMO367G1118' => 'smo', 'Solyc01g080200.3' => 'sly', 'Solyc06g008960.3' => 'sly', 'Solyc09g064780.3' => 'sly', 'Sopen01g031980' => 'spe', 'Sopen06g003710' => 'spe', 'Sopen09g026460' => 'spe', 'Sp3g21240' => 'spa', 'Sp4g30030' => 'spa', 'TAR365G0022' => 'tar', 'TAR365G1023' => 'tar', 'TAR365G1253' => 'tar', 'TAR623G0078' => 'tar', 'TAR623G1721' => 'tar', 'TAR633G0959' => 'tar', 'THA.LOC104802225' => 'tha', 'THA.LOC104804769' => 'tha', 'THA.LOC104808660' => 'tha', 'THA.LOC104812792' => 'tha', 'Thecc.01G284000' => 'tca', 'Thecc.04G220600' => 'tca', 'Thecc.05G268900' => 'tca', 'Thecc.08G171100' => 'tca', 'Thhalv10001284m.g' => 'esa', 'Thhalv10019912m.g' => 'esa', 'TPR.G14189' => 'tpr', 'TPR.G18110' => 'tpr', 'TPR.G18130' => 'tpr', 'TPR.G18131' => 'tpr', 'TPR.G18140' => 'tpr', 'TPR.G24282' => 'tpr', 'TPR.G25221' => 'tpr', 'TPR.G29267' => 'tpr', 'TPR.G35315' => 'tpr', 'TPR.G36173' => 'tpr', 'TWI09G0794' => 'twi', 'TWI59G1348' => 'twi', 'TWI74G0430' => 'twi', 'unitig_26.g8940' => 'ugi', 'unitig_749.g13744' => 'ugi', 'unitig_749.g13745' => 'ugi', 'vmacro08269' => 'vma', 'vmacro14937' => 'vma', 'vmacro20401' => 'vma', 'VMungo0464G1349' => 'vmu', 'VMungo0540G0289' => 'vmu', 'VMungo1215G1590' => 'vmu', 'VMungo1309G0221' => 'vmu', 'VMungo1309G2815' => 'vmu', 'VMungo1383G0239' => 'vmu', 'VMungo1383G2910' => 'vmu', 'Zm00001eb095270' => 'zma', 'Zm00001eb095280' => 'zma', 'Zm00001eb111630' => 'zma', 'Zm00001eb237080' => 'zma', 'Zm00001eb273740' => 'zma', 'Zm00001eb285040' => 'zma', 'Zm00001eb330790' => 'zma', 'Zm00001eb337380' => 'zma' ) $gf_id = 'HOM05D001484' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001484' ) $data_identifier = 'HOM05D001484' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 2, 'aly' => (int) 2, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 22, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 7, 'hma' => (int) 2, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 7, 'mtr' => (int) 10, 'cme' => (int) 2, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 4, 'ppa' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 4, 'qlo' => (int) 9, 'rch' => (int) 6, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 10, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 7, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb337380' $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' => 'HOM05D001484', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p31500' => 'bna', 'A05p00020' => 'bna', 'A07p08820' => 'bna', 'Aa31LG4G3300' => 'aar', 'Aa31LG8G10030' => 'aar', 'Actinidia00731' => 'ach', 'Actinidia11473' => 'ach', 'Actinidia23469' => 'ach', 'Actinidia24318' => 'ach', 'Actinidia40196' => 'ach', 'Actinidia40197' => 'ach', 'Actinidia40198' => 'ach', 'Ah.08g212990' => 'amhyb', 'Ah.15g091720' => 'amhyb', 'AL3G38260' => 'aly', 'AL4G47710' => 'aly', 'Aqoxy2G00671' => 'aox', 'Aqoxy2G03236' => 'aox', 'arahy.Tifrunner.gnm1.ann1.05IDCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KR684' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATY3SJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK6QJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6APGL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IDT7Z9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM073U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ0R87' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LE7RV4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT4QRX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V5ENPK' => 'arhy', 'AT2G48110' => 'ath', 'AT3G23590' => 'ath', 'ATR0626G186' => 'atr', 'ATR1127G141' => 'atr', 'Atru.chr4.2583' => 'acertr', 'Atru.chr5.1358' => 'acertr', 'Atru.chr5.1359' => 'acertr', 'Atru.chr8.46' => 'acertr', 'AUR62002640' => 'cqu', 'AUR62030055' => 'cqu', 'AUR62033713' => 'cqu', 'AUR62033714' => 'cqu', 'AUR62036795' => 'cqu', 'AUR62039891' => 'cqu', 'BcaB02g08737' => 'bca', 'BcaB04g20441' => 'bca', 'BcaB06g26509' => 'bca', 'BcaB06g26510' => 'bca', 'BcaB06g26511' => 'bca', 'BcaB06g26512' => 'bca', 'BcaB06g26513' => 'bca', 'BcaC02g12564' => 'bca', 'BcaC02g12565' => 'bca', 'BcaC02g12794' => 'bca', 'BcaC02g12795' => 'bca', 'BcaC02g12796' => 'bca', 'BcaC06g35541' => 'bca', 'BNapus_Darmor_BZH_scaffold_188p00080' => 'bna', 'BNapus_Darmor_BZH_scaffold_188p00090' => 'bna', 'BolC1t03972H' => 'bol', 'BolC1t03973H' => 'bol', 'BolC4t21680H' => 'bol', 'BolC7t41863H' => 'bol', 'BolSC55t61227H' => 'bol', 'BolSC55t61228H' => 'bol', 'BraA01t03278Z' => 'bra', 'BraA05t18998Z' => 'bra', 'BraA07t28673Z' => 'bra', 'C01p40150' => 'bna', 'C05p12370' => 'bna', 'C07p13680' => 'bna', 'CAN.G1006.16' => 'can', 'CAN.G1006.17' => 'can', 'CAN.G1170.2' => 'can', 'CAN.G962.7' => 'can', 'CANSAT25G2179' => 'cansat', 'CANSAT78G1573' => 'cansat', 'CARHR099510' => 'chi', 'CARHR143510' => 'chi', 'Carub.0003s2380' => 'cru', 'Carub.0004s3082' => 'cru', 'Ca_00614_v3' => 'car', 'Ca_07801_v3' => 'car', 'Ca_08567_v3' => 'car', 'Ca_09571_v3' => 'car', 'CBR_g19290' => 'cbr', 'Cc01_g19770' => 'ccan', 'Cc03_g03030' => 'ccan', 'CDE07G0968' => 'cde', 'CDE09G1441' => 'cde', 'Cfa006103' => 'cfa', 'Cfa015573' => 'cfa', 'Cfa016988' => 'cfa', 'Ciclev10006738m.g' => 'ccl', 'Ciclev10010920m.g' => 'ccl', 'Ciclev10018517m.g' => 'ccl', 'CiPaw.01G159200' => 'cil', 'CiPaw.02G091000' => 'cil', 'CiPaw.02G091100' => 'cil', 'CiPaw.08G103100' => 'cil', 'CiPaw.09G224900' => 'cil', 'ClCG06G005740' => 'cla', 'ClCG07G000090' => 'cla', 'ClCG07G000100' => 'cla', 'COL.COLO4_09143' => 'col', 'COL.COLO4_25124' => 'col', 'Cpa.g.sc16.34' => 'cpa', 'Cpa.g.sc3504.1' => 'cpa', 'Cpa.g.sc60.37' => 'cpa', 'CsaV3_6G018520' => 'csa', 'CsaV3_6G036860' => 'csa', 'CSS0001072' => 'camsi', 'CSS0020208' => 'camsi', 'CSS0021253' => 'camsi', 'CSS0022190' => 'camsi', 'CSS0036150' => 'camsi', 'CSS0040442' => 'camsi', 'CSS0042300' => 'camsi', 'CSS0045298' => 'camsi', 'DCAR_012449' => 'dca', 'DCAR_018405' => 'dca', 'DCAR_024573' => 'dca', 'DCAR_030591' => 'dca', 'Dinv16926' => 'din', 'Dinv32963' => 'din', 'Dinv38382' => 'din', 'Dinv38383' => 'din', 'Duzib133G0974' => 'dzi', 'Duzib138G1867' => 'dzi', 'Duzib211G0420' => 'dzi', 'Duzib212G0930' => 'dzi', 'ECA234G1645' => 'eca', 'ECA247G3467' => 'eca', 'ECA248G1703' => 'eca', 'EL10Ac3g06327' => 'bvu', 'EL10Ac7g17204' => 'bvu', 'Eucgr.A00855' => 'egr', 'Eucgr.A00858' => 'egr', 'Eucgr.H01520' => 'egr', 'Eucgr.H03604' => 'egr', 'Eucgr.L03465' => 'egr', 'Eucgr.L03466' => 'egr', 'FAN01G0988' => 'fan', 'FAN02G3892' => 'fan', 'FAN05G3381' => 'fan', 'FAN07G0967' => 'fan', 'FAN07G1493' => 'fan', 'FAN08G3125' => 'fan', 'FAN09G0402' => 'fan', 'FAN12G2594' => 'fan', 'FAN12G3879' => 'fan', 'FAN14G1546' => 'fan', 'FAN15G3626' => 'fan', 'FAN17G0588' => 'fan', 'FAN17G0609' => 'fan', 'FAN18G2817' => 'fan', 'FAN19G1305' => 'fan', 'FAN20G1787' => 'fan', 'FAN22G0073' => 'fan', 'FAN22G0352' => 'fan', 'FAN22G0368' => 'fan', 'FAN22G2273' => 'fan', 'FAN24G1998' => 'fan', 'FAN27G1317' => 'fan', 'FvH4_2g23980' => 'fve', 'FvH4_4g14380' => 'fve', 'FvH4_4g14390' => 'fve', 'FvH4_6g09250' => 'fve', 'Glyma.03G151100' => 'gma', 'Glyma.04G122550' => 'gma', 'Glyma.05G001600' => 'gma', 'Glyma.09G270766' => 'gma', 'Glyma.09G270832' => 'gma', 'Glyma.13G209800' => 'gma', 'Glyma.15G102800' => 'gma', 'Glyma.18G218900' => 'gma', 'Glyma.19G001500' => 'gma', 'Glyma.19G153600' => 'gma', 'Gohir.A02G028600' => 'ghi', 'Gohir.A08G045000' => 'ghi', 'Gohir.A11G120500' => 'ghi', 'Gohir.A12G006200' => 'ghi', 'Gohir.A12G006250' => 'ghi', 'Gohir.D02G036300' => 'ghi', 'Gohir.D08G054700' => 'ghi', 'Gohir.D11G125600' => 'ghi', 'Gohir.D12G005700' => 'ghi', 'Gorai.004G055200' => 'gra', 'Gorai.005G040400' => 'gra', 'Gorai.007G134500' => 'gra', 'Gorai.008G005500' => 'gra', 'GSVIVG01011094001' => 'vvi', 'GSVIVG01017879001' => 'vvi', 'GSVIVG01025988001' => 'vvi', 'GSVIVG01029847001' => 'vvi', 'HanXRQChr10g0282901' => 'han', 'HanXRQChr10g0310371' => 'han', 'HanXRQChr10g0315041' => 'han', 'HanXRQChr11g0327651' => 'han', 'HanXRQChr12g0359391' => 'han', 'Haze_00972' => 'cav', 'Haze_00973' => 'cav', 'Haze_00974' => 'cav', 'Haze_04747' => 'cav', 'Haze_04749' => 'cav', 'Haze_04750' => 'cav', 'Haze_21217' => 'cav', 'Hma1.2p1_1037F.1_g250680' => 'hma', 'Hma1.2p1_1644F.1_g295320' => 'hma', 'HPP92_011322' => 'vpl', 'HPP92_011323' => 'vpl', 'HPP92_011324' => 'vpl', 'HPP92_011325' => 'vpl', 'HPP92_011326' => 'vpl', 'Hund12205' => 'sun', 'Hund17957' => 'sun', 'Lalb_Chr06g0176771' => 'lal', 'Lalb_Chr18g0056021' => 'lal', 'Lalb_Chr18g0056031' => 'lal', 'Lalb_Chr18g0056041' => 'lal', 'Lalb_Chr20g0107751' => 'lal', 'Lalb_Chr20g0118371' => 'lal', 'Lj1g0010239' => 'lja', 'Lj1g0017101' => 'lja', 'Lj2A1178G40' => 'lonja', 'Lj2A54G84' => 'lonja', 'Lj2g0015248' => 'lja', 'Lj3A761T51' => 'lonja', 'Lj6g0018116' => 'lja', 'Lsat_1_v5_gn_4_136040' => 'lsa', 'Lsat_1_v5_gn_5_187461' => 'lsa', 'Lsat_1_v5_gn_5_77001' => 'lsa', 'Lsat_1_v5_gn_9_4461' => 'lsa', 'Manes.01G210100' => 'mes', 'Manes.03G185600' => 'mes', 'Manes.05G073300' => 'mes', 'Manes.09G120300' => 'mes', 'Manes.15G022100' => 'mes', 'Mapoly0096s0053' => 'mpo', 'MBI03_g14058_MAGBIO' => 'mbi', 'MBI03_g33876_MAGBIO' => 'mbi', 'MBI03_g36854_MAGBIO' => 'mbi', 'MBI17_g11997_MAGBIO' => 'mbi', 'MD03G1269000' => 'mdo', 'MD04G1179600' => 'mdo', 'MD11G1289800' => 'mdo', 'MD12G1194700' => 'mdo', 'MD13G1182100' => 'mdo', 'MD13G1182200' => 'mdo', 'MD16G1182600' => 'mdo', 'Medtr2g021400' => 'mtr', 'Medtr2g021470' => 'mtr', 'Medtr2g105810' => 'mtr', 'Medtr3g033580' => 'mtr', 'Medtr6g007970' => 'mtr', 'Medtr7g056330' => 'mtr', 'Medtr7g074290' => 'mtr', 'Medtr7g074380' => 'mtr', 'Medtr7g094550' => 'mtr', 'Medtr8g069995' => 'mtr', 'MELO3C014345.2' => 'cme', 'MELO3C021395.2' => 'cme', 'Migut.D00262' => 'egut', 'Migut.G00257' => 'egut', 'MSTRG.21575' => 'ama', 'MSTRG.3985' => 'ama', 'Nitab4.5_0000295g0140' => 'nta', 'Nitab4.5_0000732g0140' => 'nta', 'Nitab4.5_0003162g0020' => 'nta', 'Nitab4.5_0006180g0090' => 'nta', 'Nitab4.5_0006390g0010' => 'nta', 'Nitab4.5_0007392g0040' => 'nta', 'Nn1g02140' => 'nnu', 'Nn4g26168' => 'nnu', 'Nn5g26754' => 'nnu', 'Oeu001433.1' => 'oeu', 'Oeu010299.2' => 'oeu', 'Oeu011171.1' => 'oeu', 'Oeu037675.1' => 'oeu', 'Oeu038359.1' => 'oeu', 'Oeu063834.1' => 'oeu', 'Oeu063835.1' => 'oeu', 'Os05g0312000' => 'osa', 'Os07g0211101' => 'osa', 'Os07g0211200' => 'osa', 'Os07g0681500' => 'osa', 'Peaxi162Scf00095g01015' => 'pax', 'Peaxi162Scf00104g00329' => 'pax', 'Peaxi162Scf00161g00137' => 'pax', 'PGR004G1665' => 'pgr', 'PGR031G2937' => 'pgr', 'PGR119G2145' => 'pgr', 'PGSC0003DMG400004351' => 'stu', 'PGSC0003DMG400014625' => 'stu', 'PGSC0003DMG401000943' => 'stu', 'Phvul.001G148600' => 'pvu', 'Phvul.004G001700' => 'pvu', 'Phvul.006G154900' => 'pvu', 'Phvul.008G078200' => 'pvu', 'Phvul.011G136500' => 'pvu', 'Potri.002G215600' => 'ptr', 'Potri.008G201600' => 'ptr', 'Potri.014G138400' => 'ptr', 'Potri.016G142500' => 'ptr', 'Pp3c16_10580' => 'ppa', 'Pp3c5_25280' => 'ppa', 'Prupe.1G150000' => 'ppe', 'Prupe.1G150100' => 'ppe', 'Prupe.6G299600' => 'ppe', 'Prupe.8G245000' => 'ppe', 'Psat0s4927g0040' => 'psa', 'Psat1g052080' => 'psa', 'Psat1g183800' => 'psa', 'Psat3g113840' => 'psa', 'Psat3g126120' => 'psa', 'Psat3g126160' => 'psa', 'Psat3g158760' => 'psa', 'Psat3g158840' => 'psa', 'PSO170G2858' => 'pso', 'PSO339G0606' => 'pso', 'PSO384G4709' => 'pso', 'PSO407G0334' => 'pso', 'QL04p040276' => 'qlo', 'QL06p005458' => 'qlo', 'QL06p005472' => 'qlo', 'QL07p030546' => 'qlo', 'QL07p031519' => 'qlo', 'QL09p050949' => 'qlo', 'QL09p050966' => 'qlo', 'QL09p051067' => 'qlo', 'QL12p022706' => 'qlo', 'RcHm_v2.0_Chr2g0119601' => 'rch', 'RcHm_v2.0_Chr3g0459591' => 'rch', 'RcHm_v2.0_Chr4g0418521' => 'rch', 'RcHm_v2.0_Chr4g0418531' => 'rch', 'RcHm_v2.0_Chr4g0418541' => 'rch', 'RcHm_v2.0_Chr6g0291641' => 'rch', 'Rhsim01G0086300' => 'rsi', 'Rhsim01G0276300' => 'rsi', 'Rhsim01G0276500' => 'rsi', 'Rhsim04G0207700' => 'rsi', 'Rhsim05G0234500' => 'rsi', 'Rhsim13G0022400' => 'rsi', 'Sabra02G0167900' => 'sbr', 'Sabra04G0158500' => 'sbr', 'Sabra08G0159800' => 'sbr', 'Sabra10G0011500' => 'sbr', 'Sabra14G0104400' => 'sbr', 'SalBow2G2440' => 'sbo', 'SalBow4G2265' => 'sbo', 'Sc02g0000060' => 'sci', 'Sc05g0005020' => 'sci', 'Sc13g0003890' => 'sci', 'Sed0014865' => 'sed', 'Sed0017224' => 'sed', 'Sed0026391' => 'sed', 'SEGI_00063' => 'sgi', 'SEGI_10967' => 'sgi', 'SEGI_17510' => 'sgi', 'SEGI_24396' => 'sgi', 'SEGI_39719' => 'sgi', 'SEGI_41392' => 'sgi', 'SGA_v2.0_scaffold11G05794' => 'sas', 'SGA_v2.0_scaffold142G35607' => 'sas', 'SGA_v2.0_scaffold1G00447' => 'sas', 'SHI15388' => 'shi', 'SHI15394' => 'shi', 'SHI15396' => 'shi', 'SHI15399' => 'shi', 'SMO343G0151' => 'smo', 'SMO367G1118' => 'smo', 'Solyc01g080200.3' => 'sly', 'Solyc06g008960.3' => 'sly', 'Solyc09g064780.3' => 'sly', 'Sopen01g031980' => 'spe', 'Sopen06g003710' => 'spe', 'Sopen09g026460' => 'spe', 'Sp3g21240' => 'spa', 'Sp4g30030' => 'spa', 'TAR365G0022' => 'tar', 'TAR365G1023' => 'tar', 'TAR365G1253' => 'tar', 'TAR623G0078' => 'tar', 'TAR623G1721' => 'tar', 'TAR633G0959' => 'tar', 'THA.LOC104802225' => 'tha', 'THA.LOC104804769' => 'tha', 'THA.LOC104808660' => 'tha', 'THA.LOC104812792' => 'tha', 'Thecc.01G284000' => 'tca', 'Thecc.04G220600' => 'tca', 'Thecc.05G268900' => 'tca', 'Thecc.08G171100' => 'tca', 'Thhalv10001284m.g' => 'esa', 'Thhalv10019912m.g' => 'esa', 'TPR.G14189' => 'tpr', 'TPR.G18110' => 'tpr', 'TPR.G18130' => 'tpr', 'TPR.G18131' => 'tpr', 'TPR.G18140' => 'tpr', 'TPR.G24282' => 'tpr', 'TPR.G25221' => 'tpr', 'TPR.G29267' => 'tpr', 'TPR.G35315' => 'tpr', 'TPR.G36173' => 'tpr', 'TWI09G0794' => 'twi', 'TWI59G1348' => 'twi', 'TWI74G0430' => 'twi', 'unitig_26.g8940' => 'ugi', 'unitig_749.g13744' => 'ugi', 'unitig_749.g13745' => 'ugi', 'vmacro08269' => 'vma', 'vmacro14937' => 'vma', 'vmacro20401' => 'vma', 'VMungo0464G1349' => 'vmu', 'VMungo0540G0289' => 'vmu', 'VMungo1215G1590' => 'vmu', 'VMungo1309G0221' => 'vmu', 'VMungo1309G2815' => 'vmu', 'VMungo1383G0239' => 'vmu', 'VMungo1383G2910' => 'vmu', 'Zm00001eb095270' => 'zma', 'Zm00001eb095280' => 'zma', 'Zm00001eb111630' => 'zma', 'Zm00001eb237080' => 'zma', 'Zm00001eb273740' => 'zma', 'Zm00001eb285040' => 'zma', 'Zm00001eb330790' => 'zma', 'Zm00001eb337380' => 'zma' ), 'gf_id' => 'HOM05D001484', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001484' ), 'data_identifier' => 'HOM05D001484', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001484', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p31500' => 'bna', 'A05p00020' => 'bna', 'A07p08820' => 'bna', 'Aa31LG4G3300' => 'aar', 'Aa31LG8G10030' => 'aar', 'Actinidia00731' => 'ach', 'Actinidia11473' => 'ach', 'Actinidia23469' => 'ach', 'Actinidia24318' => 'ach', 'Actinidia40196' => 'ach', 'Actinidia40197' => 'ach', 'Actinidia40198' => 'ach', 'Ah.08g212990' => 'amhyb', 'Ah.15g091720' => 'amhyb', 'AL3G38260' => 'aly', 'AL4G47710' => 'aly', 'Aqoxy2G00671' => 'aox', 'Aqoxy2G03236' => 'aox', 'arahy.Tifrunner.gnm1.ann1.05IDCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KR684' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATY3SJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK6QJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6APGL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IDT7Z9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM073U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ0R87' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LE7RV4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT4QRX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V5ENPK' => 'arhy', 'AT2G48110' => 'ath', 'AT3G23590' => 'ath', 'ATR0626G186' => 'atr', 'ATR1127G141' => 'atr', 'Atru.chr4.2583' => 'acertr', 'Atru.chr5.1358' => 'acertr', 'Atru.chr5.1359' => 'acertr', 'Atru.chr8.46' => 'acertr', 'AUR62002640' => 'cqu', 'AUR62030055' => 'cqu', 'AUR62033713' => 'cqu', 'AUR62033714' => 'cqu', 'AUR62036795' => 'cqu', 'AUR62039891' => 'cqu', 'BcaB02g08737' => 'bca', 'BcaB04g20441' => 'bca', 'BcaB06g26509' => 'bca', 'BcaB06g26510' => 'bca', 'BcaB06g26511' => 'bca', 'BcaB06g26512' => 'bca', 'BcaB06g26513' => 'bca', 'BcaC02g12564' => 'bca', 'BcaC02g12565' => 'bca', 'BcaC02g12794' => 'bca', 'BcaC02g12795' => 'bca', 'BcaC02g12796' => 'bca', 'BcaC06g35541' => 'bca', 'BNapus_Darmor_BZH_scaffold_188p00080' => 'bna', 'BNapus_Darmor_BZH_scaffold_188p00090' => 'bna', 'BolC1t03972H' => 'bol', 'BolC1t03973H' => 'bol', 'BolC4t21680H' => 'bol', 'BolC7t41863H' => 'bol', 'BolSC55t61227H' => 'bol', 'BolSC55t61228H' => 'bol', 'BraA01t03278Z' => 'bra', 'BraA05t18998Z' => 'bra', 'BraA07t28673Z' => 'bra', 'C01p40150' => 'bna', 'C05p12370' => 'bna', 'C07p13680' => 'bna', 'CAN.G1006.16' => 'can', 'CAN.G1006.17' => 'can', 'CAN.G1170.2' => 'can', 'CAN.G962.7' => 'can', 'CANSAT25G2179' => 'cansat', 'CANSAT78G1573' => 'cansat', 'CARHR099510' => 'chi', 'CARHR143510' => 'chi', 'Carub.0003s2380' => 'cru', 'Carub.0004s3082' => 'cru', 'Ca_00614_v3' => 'car', 'Ca_07801_v3' => 'car', 'Ca_08567_v3' => 'car', 'Ca_09571_v3' => 'car', 'CBR_g19290' => 'cbr', 'Cc01_g19770' => 'ccan', 'Cc03_g03030' => 'ccan', 'CDE07G0968' => 'cde', 'CDE09G1441' => 'cde', 'Cfa006103' => 'cfa', 'Cfa015573' => 'cfa', 'Cfa016988' => 'cfa', 'Ciclev10006738m.g' => 'ccl', 'Ciclev10010920m.g' => 'ccl', 'Ciclev10018517m.g' => 'ccl', 'CiPaw.01G159200' => 'cil', 'CiPaw.02G091000' => 'cil', 'CiPaw.02G091100' => 'cil', 'CiPaw.08G103100' => 'cil', 'CiPaw.09G224900' => 'cil', 'ClCG06G005740' => 'cla', 'ClCG07G000090' => 'cla', 'ClCG07G000100' => 'cla', 'COL.COLO4_09143' => 'col', 'COL.COLO4_25124' => 'col', 'Cpa.g.sc16.34' => 'cpa', 'Cpa.g.sc3504.1' => 'cpa', 'Cpa.g.sc60.37' => 'cpa', 'CsaV3_6G018520' => 'csa', 'CsaV3_6G036860' => 'csa', 'CSS0001072' => 'camsi', 'CSS0020208' => 'camsi', 'CSS0021253' => 'camsi', 'CSS0022190' => 'camsi', 'CSS0036150' => 'camsi', 'CSS0040442' => 'camsi', 'CSS0042300' => 'camsi', 'CSS0045298' => 'camsi', 'DCAR_012449' => 'dca', 'DCAR_018405' => 'dca', 'DCAR_024573' => 'dca', 'DCAR_030591' => 'dca', 'Dinv16926' => 'din', 'Dinv32963' => 'din', 'Dinv38382' => 'din', 'Dinv38383' => 'din', 'Duzib133G0974' => 'dzi', 'Duzib138G1867' => 'dzi', 'Duzib211G0420' => 'dzi', 'Duzib212G0930' => 'dzi', 'ECA234G1645' => 'eca', 'ECA247G3467' => 'eca', 'ECA248G1703' => 'eca', 'EL10Ac3g06327' => 'bvu', 'EL10Ac7g17204' => 'bvu', 'Eucgr.A00855' => 'egr', 'Eucgr.A00858' => 'egr', 'Eucgr.H01520' => 'egr', 'Eucgr.H03604' => 'egr', 'Eucgr.L03465' => 'egr', 'Eucgr.L03466' => 'egr', 'FAN01G0988' => 'fan', 'FAN02G3892' => 'fan', 'FAN05G3381' => 'fan', 'FAN07G0967' => 'fan', 'FAN07G1493' => 'fan', 'FAN08G3125' => 'fan', 'FAN09G0402' => 'fan', 'FAN12G2594' => 'fan', 'FAN12G3879' => 'fan', 'FAN14G1546' => 'fan', 'FAN15G3626' => 'fan', 'FAN17G0588' => 'fan', 'FAN17G0609' => 'fan', 'FAN18G2817' => 'fan', 'FAN19G1305' => 'fan', 'FAN20G1787' => 'fan', 'FAN22G0073' => 'fan', 'FAN22G0352' => 'fan', 'FAN22G0368' => 'fan', 'FAN22G2273' => 'fan', 'FAN24G1998' => 'fan', 'FAN27G1317' => 'fan', 'FvH4_2g23980' => 'fve', 'FvH4_4g14380' => 'fve', 'FvH4_4g14390' => 'fve', 'FvH4_6g09250' => 'fve', 'Glyma.03G151100' => 'gma', 'Glyma.04G122550' => 'gma', 'Glyma.05G001600' => 'gma', 'Glyma.09G270766' => 'gma', 'Glyma.09G270832' => 'gma', 'Glyma.13G209800' => 'gma', 'Glyma.15G102800' => 'gma', 'Glyma.18G218900' => 'gma', 'Glyma.19G001500' => 'gma', 'Glyma.19G153600' => 'gma', 'Gohir.A02G028600' => 'ghi', 'Gohir.A08G045000' => 'ghi', 'Gohir.A11G120500' => 'ghi', 'Gohir.A12G006200' => 'ghi', 'Gohir.A12G006250' => 'ghi', 'Gohir.D02G036300' => 'ghi', 'Gohir.D08G054700' => 'ghi', 'Gohir.D11G125600' => 'ghi', 'Gohir.D12G005700' => 'ghi', 'Gorai.004G055200' => 'gra', 'Gorai.005G040400' => 'gra', 'Gorai.007G134500' => 'gra', 'Gorai.008G005500' => 'gra', 'GSVIVG01011094001' => 'vvi', 'GSVIVG01017879001' => 'vvi', 'GSVIVG01025988001' => 'vvi', 'GSVIVG01029847001' => 'vvi', 'HanXRQChr10g0282901' => 'han', 'HanXRQChr10g0310371' => 'han', 'HanXRQChr10g0315041' => 'han', 'HanXRQChr11g0327651' => 'han', 'HanXRQChr12g0359391' => 'han', 'Haze_00972' => 'cav', 'Haze_00973' => 'cav', 'Haze_00974' => 'cav', 'Haze_04747' => 'cav', 'Haze_04749' => 'cav', 'Haze_04750' => 'cav', 'Haze_21217' => 'cav', 'Hma1.2p1_1037F.1_g250680' => 'hma', 'Hma1.2p1_1644F.1_g295320' => 'hma', 'HPP92_011322' => 'vpl', 'HPP92_011323' => 'vpl', 'HPP92_011324' => 'vpl', 'HPP92_011325' => 'vpl', 'HPP92_011326' => 'vpl', 'Hund12205' => 'sun', 'Hund17957' => 'sun', 'Lalb_Chr06g0176771' => 'lal', 'Lalb_Chr18g0056021' => 'lal', 'Lalb_Chr18g0056031' => 'lal', 'Lalb_Chr18g0056041' => 'lal', 'Lalb_Chr20g0107751' => 'lal', 'Lalb_Chr20g0118371' => 'lal', 'Lj1g0010239' => 'lja', 'Lj1g0017101' => 'lja', 'Lj2A1178G40' => 'lonja', 'Lj2A54G84' => 'lonja', 'Lj2g0015248' => 'lja', 'Lj3A761T51' => 'lonja', 'Lj6g0018116' => 'lja', 'Lsat_1_v5_gn_4_136040' => 'lsa', 'Lsat_1_v5_gn_5_187461' => 'lsa', 'Lsat_1_v5_gn_5_77001' => 'lsa', 'Lsat_1_v5_gn_9_4461' => 'lsa', 'Manes.01G210100' => 'mes', 'Manes.03G185600' => 'mes', 'Manes.05G073300' => 'mes', 'Manes.09G120300' => 'mes', 'Manes.15G022100' => 'mes', 'Mapoly0096s0053' => 'mpo', 'MBI03_g14058_MAGBIO' => 'mbi', 'MBI03_g33876_MAGBIO' => 'mbi', 'MBI03_g36854_MAGBIO' => 'mbi', 'MBI17_g11997_MAGBIO' => 'mbi', 'MD03G1269000' => 'mdo', 'MD04G1179600' => 'mdo', 'MD11G1289800' => 'mdo', 'MD12G1194700' => 'mdo', 'MD13G1182100' => 'mdo', 'MD13G1182200' => 'mdo', 'MD16G1182600' => 'mdo', 'Medtr2g021400' => 'mtr', 'Medtr2g021470' => 'mtr', 'Medtr2g105810' => 'mtr', 'Medtr3g033580' => 'mtr', 'Medtr6g007970' => 'mtr', 'Medtr7g056330' => 'mtr', 'Medtr7g074290' => 'mtr', 'Medtr7g074380' => 'mtr', 'Medtr7g094550' => 'mtr', 'Medtr8g069995' => 'mtr', 'MELO3C014345.2' => 'cme', 'MELO3C021395.2' => 'cme', 'Migut.D00262' => 'egut', 'Migut.G00257' => 'egut', 'MSTRG.21575' => 'ama', 'MSTRG.3985' => 'ama', 'Nitab4.5_0000295g0140' => 'nta', 'Nitab4.5_0000732g0140' => 'nta', 'Nitab4.5_0003162g0020' => 'nta', 'Nitab4.5_0006180g0090' => 'nta', 'Nitab4.5_0006390g0010' => 'nta', 'Nitab4.5_0007392g0040' => 'nta', 'Nn1g02140' => 'nnu', 'Nn4g26168' => 'nnu', 'Nn5g26754' => 'nnu', 'Oeu001433.1' => 'oeu', 'Oeu010299.2' => 'oeu', 'Oeu011171.1' => 'oeu', 'Oeu037675.1' => 'oeu', 'Oeu038359.1' => 'oeu', 'Oeu063834.1' => 'oeu', 'Oeu063835.1' => 'oeu', 'Os05g0312000' => 'osa', 'Os07g0211101' => 'osa', 'Os07g0211200' => 'osa', 'Os07g0681500' => 'osa', 'Peaxi162Scf00095g01015' => 'pax', 'Peaxi162Scf00104g00329' => 'pax', 'Peaxi162Scf00161g00137' => 'pax', 'PGR004G1665' => 'pgr', 'PGR031G2937' => 'pgr', 'PGR119G2145' => 'pgr', 'PGSC0003DMG400004351' => 'stu', 'PGSC0003DMG400014625' => 'stu', 'PGSC0003DMG401000943' => 'stu', 'Phvul.001G148600' => 'pvu', 'Phvul.004G001700' => 'pvu', 'Phvul.006G154900' => 'pvu', 'Phvul.008G078200' => 'pvu', 'Phvul.011G136500' => 'pvu', 'Potri.002G215600' => 'ptr', 'Potri.008G201600' => 'ptr', 'Potri.014G138400' => 'ptr', 'Potri.016G142500' => 'ptr', 'Pp3c16_10580' => 'ppa', 'Pp3c5_25280' => 'ppa', 'Prupe.1G150000' => 'ppe', 'Prupe.1G150100' => 'ppe', 'Prupe.6G299600' => 'ppe', 'Prupe.8G245000' => 'ppe', 'Psat0s4927g0040' => 'psa', 'Psat1g052080' => 'psa', 'Psat1g183800' => 'psa', 'Psat3g113840' => 'psa', 'Psat3g126120' => 'psa', 'Psat3g126160' => 'psa', 'Psat3g158760' => 'psa', 'Psat3g158840' => 'psa', 'PSO170G2858' => 'pso', 'PSO339G0606' => 'pso', 'PSO384G4709' => 'pso', 'PSO407G0334' => 'pso', 'QL04p040276' => 'qlo', 'QL06p005458' => 'qlo', 'QL06p005472' => 'qlo', 'QL07p030546' => 'qlo', 'QL07p031519' => 'qlo', 'QL09p050949' => 'qlo', 'QL09p050966' => 'qlo', 'QL09p051067' => 'qlo', 'QL12p022706' => 'qlo', 'RcHm_v2.0_Chr2g0119601' => 'rch', 'RcHm_v2.0_Chr3g0459591' => 'rch', 'RcHm_v2.0_Chr4g0418521' => 'rch', 'RcHm_v2.0_Chr4g0418531' => 'rch', 'RcHm_v2.0_Chr4g0418541' => 'rch', 'RcHm_v2.0_Chr6g0291641' => 'rch', 'Rhsim01G0086300' => 'rsi', 'Rhsim01G0276300' => 'rsi', 'Rhsim01G0276500' => 'rsi', 'Rhsim04G0207700' => 'rsi', 'Rhsim05G0234500' => 'rsi', 'Rhsim13G0022400' => 'rsi', 'Sabra02G0167900' => 'sbr', 'Sabra04G0158500' => 'sbr', 'Sabra08G0159800' => 'sbr', 'Sabra10G0011500' => 'sbr', 'Sabra14G0104400' => 'sbr', 'SalBow2G2440' => 'sbo', 'SalBow4G2265' => 'sbo', 'Sc02g0000060' => 'sci', 'Sc05g0005020' => 'sci', 'Sc13g0003890' => 'sci', 'Sed0014865' => 'sed', 'Sed0017224' => 'sed', 'Sed0026391' => 'sed', 'SEGI_00063' => 'sgi', 'SEGI_10967' => 'sgi', 'SEGI_17510' => 'sgi', 'SEGI_24396' => 'sgi', 'SEGI_39719' => 'sgi', 'SEGI_41392' => 'sgi', 'SGA_v2.0_scaffold11G05794' => 'sas', 'SGA_v2.0_scaffold142G35607' => 'sas', 'SGA_v2.0_scaffold1G00447' => 'sas', 'SHI15388' => 'shi', 'SHI15394' => 'shi', 'SHI15396' => 'shi', 'SHI15399' => 'shi', 'SMO343G0151' => 'smo', 'SMO367G1118' => 'smo', 'Solyc01g080200.3' => 'sly', 'Solyc06g008960.3' => 'sly', 'Solyc09g064780.3' => 'sly', 'Sopen01g031980' => 'spe', 'Sopen06g003710' => 'spe', 'Sopen09g026460' => 'spe', 'Sp3g21240' => 'spa', 'Sp4g30030' => 'spa', 'TAR365G0022' => 'tar', 'TAR365G1023' => 'tar', 'TAR365G1253' => 'tar', 'TAR623G0078' => 'tar', 'TAR623G1721' => 'tar', 'TAR633G0959' => 'tar', 'THA.LOC104802225' => 'tha', 'THA.LOC104804769' => 'tha', 'THA.LOC104808660' => 'tha', 'THA.LOC104812792' => 'tha', 'Thecc.01G284000' => 'tca', 'Thecc.04G220600' => 'tca', 'Thecc.05G268900' => 'tca', 'Thecc.08G171100' => 'tca', 'Thhalv10001284m.g' => 'esa', 'Thhalv10019912m.g' => 'esa', 'TPR.G14189' => 'tpr', 'TPR.G18110' => 'tpr', 'TPR.G18130' => 'tpr', 'TPR.G18131' => 'tpr', 'TPR.G18140' => 'tpr', 'TPR.G24282' => 'tpr', 'TPR.G25221' => 'tpr', 'TPR.G29267' => 'tpr', 'TPR.G35315' => 'tpr', 'TPR.G36173' => 'tpr', 'TWI09G0794' => 'twi', 'TWI59G1348' => 'twi', 'TWI74G0430' => 'twi', 'unitig_26.g8940' => 'ugi', 'unitig_749.g13744' => 'ugi', 'unitig_749.g13745' => 'ugi', 'vmacro08269' => 'vma', 'vmacro14937' => 'vma', 'vmacro20401' => 'vma', 'VMungo0464G1349' => 'vmu', 'VMungo0540G0289' => 'vmu', 'VMungo1215G1590' => 'vmu', 'VMungo1309G0221' => 'vmu', 'VMungo1309G2815' => 'vmu', 'VMungo1383G0239' => 'vmu', 'VMungo1383G2910' => 'vmu', 'Zm00001eb095270' => 'zma', 'Zm00001eb095280' => 'zma', 'Zm00001eb111630' => 'zma', 'Zm00001eb237080' => 'zma', 'Zm00001eb273740' => 'zma', 'Zm00001eb285040' => 'zma', 'Zm00001eb330790' => 'zma', 'Zm00001eb337380' => 'zma' ) $gf_id = 'HOM05D001484' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001484' ) $data_identifier = 'HOM05D001484' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 2, 'aly' => (int) 2, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 22, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 7, 'hma' => (int) 2, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 7, 'mtr' => (int) 10, 'cme' => (int) 2, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 4, 'ppa' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 4, 'qlo' => (int) 9, 'rch' => (int) 6, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 10, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 7, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb337380' $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' => 'HOM05D001484', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p31500' => 'bna', 'A05p00020' => 'bna', 'A07p08820' => 'bna', 'Aa31LG4G3300' => 'aar', 'Aa31LG8G10030' => 'aar', 'Actinidia00731' => 'ach', 'Actinidia11473' => 'ach', 'Actinidia23469' => 'ach', 'Actinidia24318' => 'ach', 'Actinidia40196' => 'ach', 'Actinidia40197' => 'ach', 'Actinidia40198' => 'ach', 'Ah.08g212990' => 'amhyb', 'Ah.15g091720' => 'amhyb', 'AL3G38260' => 'aly', 'AL4G47710' => 'aly', 'Aqoxy2G00671' => 'aox', 'Aqoxy2G03236' => 'aox', 'arahy.Tifrunner.gnm1.ann1.05IDCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KR684' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATY3SJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK6QJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6APGL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IDT7Z9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM073U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ0R87' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LE7RV4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT4QRX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V5ENPK' => 'arhy', 'AT2G48110' => 'ath', 'AT3G23590' => 'ath', 'ATR0626G186' => 'atr', 'ATR1127G141' => 'atr', 'Atru.chr4.2583' => 'acertr', 'Atru.chr5.1358' => 'acertr', 'Atru.chr5.1359' => 'acertr', 'Atru.chr8.46' => 'acertr', 'AUR62002640' => 'cqu', 'AUR62030055' => 'cqu', 'AUR62033713' => 'cqu', 'AUR62033714' => 'cqu', 'AUR62036795' => 'cqu', 'AUR62039891' => 'cqu', 'BcaB02g08737' => 'bca', 'BcaB04g20441' => 'bca', 'BcaB06g26509' => 'bca', 'BcaB06g26510' => 'bca', 'BcaB06g26511' => 'bca', 'BcaB06g26512' => 'bca', 'BcaB06g26513' => 'bca', 'BcaC02g12564' => 'bca', 'BcaC02g12565' => 'bca', 'BcaC02g12794' => 'bca', 'BcaC02g12795' => 'bca', 'BcaC02g12796' => 'bca', 'BcaC06g35541' => 'bca', 'BNapus_Darmor_BZH_scaffold_188p00080' => 'bna', 'BNapus_Darmor_BZH_scaffold_188p00090' => 'bna', 'BolC1t03972H' => 'bol', 'BolC1t03973H' => 'bol', 'BolC4t21680H' => 'bol', 'BolC7t41863H' => 'bol', 'BolSC55t61227H' => 'bol', 'BolSC55t61228H' => 'bol', 'BraA01t03278Z' => 'bra', 'BraA05t18998Z' => 'bra', 'BraA07t28673Z' => 'bra', 'C01p40150' => 'bna', 'C05p12370' => 'bna', 'C07p13680' => 'bna', 'CAN.G1006.16' => 'can', 'CAN.G1006.17' => 'can', 'CAN.G1170.2' => 'can', 'CAN.G962.7' => 'can', 'CANSAT25G2179' => 'cansat', 'CANSAT78G1573' => 'cansat', 'CARHR099510' => 'chi', 'CARHR143510' => 'chi', 'Carub.0003s2380' => 'cru', 'Carub.0004s3082' => 'cru', 'Ca_00614_v3' => 'car', 'Ca_07801_v3' => 'car', 'Ca_08567_v3' => 'car', 'Ca_09571_v3' => 'car', 'CBR_g19290' => 'cbr', 'Cc01_g19770' => 'ccan', 'Cc03_g03030' => 'ccan', 'CDE07G0968' => 'cde', 'CDE09G1441' => 'cde', 'Cfa006103' => 'cfa', 'Cfa015573' => 'cfa', 'Cfa016988' => 'cfa', 'Ciclev10006738m.g' => 'ccl', 'Ciclev10010920m.g' => 'ccl', 'Ciclev10018517m.g' => 'ccl', 'CiPaw.01G159200' => 'cil', 'CiPaw.02G091000' => 'cil', 'CiPaw.02G091100' => 'cil', 'CiPaw.08G103100' => 'cil', 'CiPaw.09G224900' => 'cil', 'ClCG06G005740' => 'cla', 'ClCG07G000090' => 'cla', 'ClCG07G000100' => 'cla', 'COL.COLO4_09143' => 'col', 'COL.COLO4_25124' => 'col', 'Cpa.g.sc16.34' => 'cpa', 'Cpa.g.sc3504.1' => 'cpa', 'Cpa.g.sc60.37' => 'cpa', 'CsaV3_6G018520' => 'csa', 'CsaV3_6G036860' => 'csa', 'CSS0001072' => 'camsi', 'CSS0020208' => 'camsi', 'CSS0021253' => 'camsi', 'CSS0022190' => 'camsi', 'CSS0036150' => 'camsi', 'CSS0040442' => 'camsi', 'CSS0042300' => 'camsi', 'CSS0045298' => 'camsi', 'DCAR_012449' => 'dca', 'DCAR_018405' => 'dca', 'DCAR_024573' => 'dca', 'DCAR_030591' => 'dca', 'Dinv16926' => 'din', 'Dinv32963' => 'din', 'Dinv38382' => 'din', 'Dinv38383' => 'din', 'Duzib133G0974' => 'dzi', 'Duzib138G1867' => 'dzi', 'Duzib211G0420' => 'dzi', 'Duzib212G0930' => 'dzi', 'ECA234G1645' => 'eca', 'ECA247G3467' => 'eca', 'ECA248G1703' => 'eca', 'EL10Ac3g06327' => 'bvu', 'EL10Ac7g17204' => 'bvu', 'Eucgr.A00855' => 'egr', 'Eucgr.A00858' => 'egr', 'Eucgr.H01520' => 'egr', 'Eucgr.H03604' => 'egr', 'Eucgr.L03465' => 'egr', 'Eucgr.L03466' => 'egr', 'FAN01G0988' => 'fan', 'FAN02G3892' => 'fan', 'FAN05G3381' => 'fan', 'FAN07G0967' => 'fan', 'FAN07G1493' => 'fan', 'FAN08G3125' => 'fan', 'FAN09G0402' => 'fan', 'FAN12G2594' => 'fan', 'FAN12G3879' => 'fan', 'FAN14G1546' => 'fan', 'FAN15G3626' => 'fan', 'FAN17G0588' => 'fan', 'FAN17G0609' => 'fan', 'FAN18G2817' => 'fan', 'FAN19G1305' => 'fan', 'FAN20G1787' => 'fan', 'FAN22G0073' => 'fan', 'FAN22G0352' => 'fan', 'FAN22G0368' => 'fan', 'FAN22G2273' => 'fan', 'FAN24G1998' => 'fan', 'FAN27G1317' => 'fan', 'FvH4_2g23980' => 'fve', 'FvH4_4g14380' => 'fve', 'FvH4_4g14390' => 'fve', 'FvH4_6g09250' => 'fve', 'Glyma.03G151100' => 'gma', 'Glyma.04G122550' => 'gma', 'Glyma.05G001600' => 'gma', 'Glyma.09G270766' => 'gma', 'Glyma.09G270832' => 'gma', 'Glyma.13G209800' => 'gma', 'Glyma.15G102800' => 'gma', 'Glyma.18G218900' => 'gma', 'Glyma.19G001500' => 'gma', 'Glyma.19G153600' => 'gma', 'Gohir.A02G028600' => 'ghi', 'Gohir.A08G045000' => 'ghi', 'Gohir.A11G120500' => 'ghi', 'Gohir.A12G006200' => 'ghi', 'Gohir.A12G006250' => 'ghi', 'Gohir.D02G036300' => 'ghi', 'Gohir.D08G054700' => 'ghi', 'Gohir.D11G125600' => 'ghi', 'Gohir.D12G005700' => 'ghi', 'Gorai.004G055200' => 'gra', 'Gorai.005G040400' => 'gra', 'Gorai.007G134500' => 'gra', 'Gorai.008G005500' => 'gra', 'GSVIVG01011094001' => 'vvi', 'GSVIVG01017879001' => 'vvi', 'GSVIVG01025988001' => 'vvi', 'GSVIVG01029847001' => 'vvi', 'HanXRQChr10g0282901' => 'han', 'HanXRQChr10g0310371' => 'han', 'HanXRQChr10g0315041' => 'han', 'HanXRQChr11g0327651' => 'han', 'HanXRQChr12g0359391' => 'han', 'Haze_00972' => 'cav', 'Haze_00973' => 'cav', 'Haze_00974' => 'cav', 'Haze_04747' => 'cav', 'Haze_04749' => 'cav', 'Haze_04750' => 'cav', 'Haze_21217' => 'cav', 'Hma1.2p1_1037F.1_g250680' => 'hma', 'Hma1.2p1_1644F.1_g295320' => 'hma', 'HPP92_011322' => 'vpl', 'HPP92_011323' => 'vpl', 'HPP92_011324' => 'vpl', 'HPP92_011325' => 'vpl', 'HPP92_011326' => 'vpl', 'Hund12205' => 'sun', 'Hund17957' => 'sun', 'Lalb_Chr06g0176771' => 'lal', 'Lalb_Chr18g0056021' => 'lal', 'Lalb_Chr18g0056031' => 'lal', 'Lalb_Chr18g0056041' => 'lal', 'Lalb_Chr20g0107751' => 'lal', 'Lalb_Chr20g0118371' => 'lal', 'Lj1g0010239' => 'lja', 'Lj1g0017101' => 'lja', 'Lj2A1178G40' => 'lonja', 'Lj2A54G84' => 'lonja', 'Lj2g0015248' => 'lja', 'Lj3A761T51' => 'lonja', 'Lj6g0018116' => 'lja', 'Lsat_1_v5_gn_4_136040' => 'lsa', 'Lsat_1_v5_gn_5_187461' => 'lsa', 'Lsat_1_v5_gn_5_77001' => 'lsa', 'Lsat_1_v5_gn_9_4461' => 'lsa', 'Manes.01G210100' => 'mes', 'Manes.03G185600' => 'mes', 'Manes.05G073300' => 'mes', 'Manes.09G120300' => 'mes', 'Manes.15G022100' => 'mes', 'Mapoly0096s0053' => 'mpo', 'MBI03_g14058_MAGBIO' => 'mbi', 'MBI03_g33876_MAGBIO' => 'mbi', 'MBI03_g36854_MAGBIO' => 'mbi', 'MBI17_g11997_MAGBIO' => 'mbi', 'MD03G1269000' => 'mdo', 'MD04G1179600' => 'mdo', 'MD11G1289800' => 'mdo', 'MD12G1194700' => 'mdo', 'MD13G1182100' => 'mdo', 'MD13G1182200' => 'mdo', 'MD16G1182600' => 'mdo', 'Medtr2g021400' => 'mtr', 'Medtr2g021470' => 'mtr', 'Medtr2g105810' => 'mtr', 'Medtr3g033580' => 'mtr', 'Medtr6g007970' => 'mtr', 'Medtr7g056330' => 'mtr', 'Medtr7g074290' => 'mtr', 'Medtr7g074380' => 'mtr', 'Medtr7g094550' => 'mtr', 'Medtr8g069995' => 'mtr', 'MELO3C014345.2' => 'cme', 'MELO3C021395.2' => 'cme', 'Migut.D00262' => 'egut', 'Migut.G00257' => 'egut', 'MSTRG.21575' => 'ama', 'MSTRG.3985' => 'ama', 'Nitab4.5_0000295g0140' => 'nta', 'Nitab4.5_0000732g0140' => 'nta', 'Nitab4.5_0003162g0020' => 'nta', 'Nitab4.5_0006180g0090' => 'nta', 'Nitab4.5_0006390g0010' => 'nta', 'Nitab4.5_0007392g0040' => 'nta', 'Nn1g02140' => 'nnu', 'Nn4g26168' => 'nnu', 'Nn5g26754' => 'nnu', 'Oeu001433.1' => 'oeu', 'Oeu010299.2' => 'oeu', 'Oeu011171.1' => 'oeu', 'Oeu037675.1' => 'oeu', 'Oeu038359.1' => 'oeu', 'Oeu063834.1' => 'oeu', 'Oeu063835.1' => 'oeu', 'Os05g0312000' => 'osa', 'Os07g0211101' => 'osa', 'Os07g0211200' => 'osa', 'Os07g0681500' => 'osa', 'Peaxi162Scf00095g01015' => 'pax', 'Peaxi162Scf00104g00329' => 'pax', 'Peaxi162Scf00161g00137' => 'pax', 'PGR004G1665' => 'pgr', 'PGR031G2937' => 'pgr', 'PGR119G2145' => 'pgr', 'PGSC0003DMG400004351' => 'stu', 'PGSC0003DMG400014625' => 'stu', 'PGSC0003DMG401000943' => 'stu', 'Phvul.001G148600' => 'pvu', 'Phvul.004G001700' => 'pvu', 'Phvul.006G154900' => 'pvu', 'Phvul.008G078200' => 'pvu', 'Phvul.011G136500' => 'pvu', 'Potri.002G215600' => 'ptr', 'Potri.008G201600' => 'ptr', 'Potri.014G138400' => 'ptr', 'Potri.016G142500' => 'ptr', 'Pp3c16_10580' => 'ppa', 'Pp3c5_25280' => 'ppa', 'Prupe.1G150000' => 'ppe', 'Prupe.1G150100' => 'ppe', 'Prupe.6G299600' => 'ppe', 'Prupe.8G245000' => 'ppe', 'Psat0s4927g0040' => 'psa', 'Psat1g052080' => 'psa', 'Psat1g183800' => 'psa', 'Psat3g113840' => 'psa', 'Psat3g126120' => 'psa', 'Psat3g126160' => 'psa', 'Psat3g158760' => 'psa', 'Psat3g158840' => 'psa', 'PSO170G2858' => 'pso', 'PSO339G0606' => 'pso', 'PSO384G4709' => 'pso', 'PSO407G0334' => 'pso', 'QL04p040276' => 'qlo', 'QL06p005458' => 'qlo', 'QL06p005472' => 'qlo', 'QL07p030546' => 'qlo', 'QL07p031519' => 'qlo', 'QL09p050949' => 'qlo', 'QL09p050966' => 'qlo', 'QL09p051067' => 'qlo', 'QL12p022706' => 'qlo', 'RcHm_v2.0_Chr2g0119601' => 'rch', 'RcHm_v2.0_Chr3g0459591' => 'rch', 'RcHm_v2.0_Chr4g0418521' => 'rch', 'RcHm_v2.0_Chr4g0418531' => 'rch', 'RcHm_v2.0_Chr4g0418541' => 'rch', 'RcHm_v2.0_Chr6g0291641' => 'rch', 'Rhsim01G0086300' => 'rsi', 'Rhsim01G0276300' => 'rsi', 'Rhsim01G0276500' => 'rsi', 'Rhsim04G0207700' => 'rsi', 'Rhsim05G0234500' => 'rsi', 'Rhsim13G0022400' => 'rsi', 'Sabra02G0167900' => 'sbr', 'Sabra04G0158500' => 'sbr', 'Sabra08G0159800' => 'sbr', 'Sabra10G0011500' => 'sbr', 'Sabra14G0104400' => 'sbr', 'SalBow2G2440' => 'sbo', 'SalBow4G2265' => 'sbo', 'Sc02g0000060' => 'sci', 'Sc05g0005020' => 'sci', 'Sc13g0003890' => 'sci', 'Sed0014865' => 'sed', 'Sed0017224' => 'sed', 'Sed0026391' => 'sed', 'SEGI_00063' => 'sgi', 'SEGI_10967' => 'sgi', 'SEGI_17510' => 'sgi', 'SEGI_24396' => 'sgi', 'SEGI_39719' => 'sgi', 'SEGI_41392' => 'sgi', 'SGA_v2.0_scaffold11G05794' => 'sas', 'SGA_v2.0_scaffold142G35607' => 'sas', 'SGA_v2.0_scaffold1G00447' => 'sas', 'SHI15388' => 'shi', 'SHI15394' => 'shi', 'SHI15396' => 'shi', 'SHI15399' => 'shi', 'SMO343G0151' => 'smo', 'SMO367G1118' => 'smo', 'Solyc01g080200.3' => 'sly', 'Solyc06g008960.3' => 'sly', 'Solyc09g064780.3' => 'sly', 'Sopen01g031980' => 'spe', 'Sopen06g003710' => 'spe', 'Sopen09g026460' => 'spe', 'Sp3g21240' => 'spa', 'Sp4g30030' => 'spa', 'TAR365G0022' => 'tar', 'TAR365G1023' => 'tar', 'TAR365G1253' => 'tar', 'TAR623G0078' => 'tar', 'TAR623G1721' => 'tar', 'TAR633G0959' => 'tar', 'THA.LOC104802225' => 'tha', 'THA.LOC104804769' => 'tha', 'THA.LOC104808660' => 'tha', 'THA.LOC104812792' => 'tha', 'Thecc.01G284000' => 'tca', 'Thecc.04G220600' => 'tca', 'Thecc.05G268900' => 'tca', 'Thecc.08G171100' => 'tca', 'Thhalv10001284m.g' => 'esa', 'Thhalv10019912m.g' => 'esa', 'TPR.G14189' => 'tpr', 'TPR.G18110' => 'tpr', 'TPR.G18130' => 'tpr', 'TPR.G18131' => 'tpr', 'TPR.G18140' => 'tpr', 'TPR.G24282' => 'tpr', 'TPR.G25221' => 'tpr', 'TPR.G29267' => 'tpr', 'TPR.G35315' => 'tpr', 'TPR.G36173' => 'tpr', 'TWI09G0794' => 'twi', 'TWI59G1348' => 'twi', 'TWI74G0430' => 'twi', 'unitig_26.g8940' => 'ugi', 'unitig_749.g13744' => 'ugi', 'unitig_749.g13745' => 'ugi', 'vmacro08269' => 'vma', 'vmacro14937' => 'vma', 'vmacro20401' => 'vma', 'VMungo0464G1349' => 'vmu', 'VMungo0540G0289' => 'vmu', 'VMungo1215G1590' => 'vmu', 'VMungo1309G0221' => 'vmu', 'VMungo1309G2815' => 'vmu', 'VMungo1383G0239' => 'vmu', 'VMungo1383G2910' => 'vmu', 'Zm00001eb095270' => 'zma', 'Zm00001eb095280' => 'zma', 'Zm00001eb111630' => 'zma', 'Zm00001eb237080' => 'zma', 'Zm00001eb273740' => 'zma', 'Zm00001eb285040' => 'zma', 'Zm00001eb330790' => 'zma', 'Zm00001eb337380' => 'zma' ), 'gf_id' => 'HOM05D001484', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001484' ), 'data_identifier' => 'HOM05D001484', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001484', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p31500' => 'bna', 'A05p00020' => 'bna', 'A07p08820' => 'bna', 'Aa31LG4G3300' => 'aar', 'Aa31LG8G10030' => 'aar', 'Actinidia00731' => 'ach', 'Actinidia11473' => 'ach', 'Actinidia23469' => 'ach', 'Actinidia24318' => 'ach', 'Actinidia40196' => 'ach', 'Actinidia40197' => 'ach', 'Actinidia40198' => 'ach', 'Ah.08g212990' => 'amhyb', 'Ah.15g091720' => 'amhyb', 'AL3G38260' => 'aly', 'AL4G47710' => 'aly', 'Aqoxy2G00671' => 'aox', 'Aqoxy2G03236' => 'aox', 'arahy.Tifrunner.gnm1.ann1.05IDCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KR684' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATY3SJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK6QJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6APGL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IDT7Z9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM073U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ0R87' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LE7RV4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT4QRX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V5ENPK' => 'arhy', 'AT2G48110' => 'ath', 'AT3G23590' => 'ath', 'ATR0626G186' => 'atr', 'ATR1127G141' => 'atr', 'Atru.chr4.2583' => 'acertr', 'Atru.chr5.1358' => 'acertr', 'Atru.chr5.1359' => 'acertr', 'Atru.chr8.46' => 'acertr', 'AUR62002640' => 'cqu', 'AUR62030055' => 'cqu', 'AUR62033713' => 'cqu', 'AUR62033714' => 'cqu', 'AUR62036795' => 'cqu', 'AUR62039891' => 'cqu', 'BcaB02g08737' => 'bca', 'BcaB04g20441' => 'bca', 'BcaB06g26509' => 'bca', 'BcaB06g26510' => 'bca', 'BcaB06g26511' => 'bca', 'BcaB06g26512' => 'bca', 'BcaB06g26513' => 'bca', 'BcaC02g12564' => 'bca', 'BcaC02g12565' => 'bca', 'BcaC02g12794' => 'bca', 'BcaC02g12795' => 'bca', 'BcaC02g12796' => 'bca', 'BcaC06g35541' => 'bca', 'BNapus_Darmor_BZH_scaffold_188p00080' => 'bna', 'BNapus_Darmor_BZH_scaffold_188p00090' => 'bna', 'BolC1t03972H' => 'bol', 'BolC1t03973H' => 'bol', 'BolC4t21680H' => 'bol', 'BolC7t41863H' => 'bol', 'BolSC55t61227H' => 'bol', 'BolSC55t61228H' => 'bol', 'BraA01t03278Z' => 'bra', 'BraA05t18998Z' => 'bra', 'BraA07t28673Z' => 'bra', 'C01p40150' => 'bna', 'C05p12370' => 'bna', 'C07p13680' => 'bna', 'CAN.G1006.16' => 'can', 'CAN.G1006.17' => 'can', 'CAN.G1170.2' => 'can', 'CAN.G962.7' => 'can', 'CANSAT25G2179' => 'cansat', 'CANSAT78G1573' => 'cansat', 'CARHR099510' => 'chi', 'CARHR143510' => 'chi', 'Carub.0003s2380' => 'cru', 'Carub.0004s3082' => 'cru', 'Ca_00614_v3' => 'car', 'Ca_07801_v3' => 'car', 'Ca_08567_v3' => 'car', 'Ca_09571_v3' => 'car', 'CBR_g19290' => 'cbr', 'Cc01_g19770' => 'ccan', 'Cc03_g03030' => 'ccan', 'CDE07G0968' => 'cde', 'CDE09G1441' => 'cde', 'Cfa006103' => 'cfa', 'Cfa015573' => 'cfa', 'Cfa016988' => 'cfa', 'Ciclev10006738m.g' => 'ccl', 'Ciclev10010920m.g' => 'ccl', 'Ciclev10018517m.g' => 'ccl', 'CiPaw.01G159200' => 'cil', 'CiPaw.02G091000' => 'cil', 'CiPaw.02G091100' => 'cil', 'CiPaw.08G103100' => 'cil', 'CiPaw.09G224900' => 'cil', 'ClCG06G005740' => 'cla', 'ClCG07G000090' => 'cla', 'ClCG07G000100' => 'cla', 'COL.COLO4_09143' => 'col', 'COL.COLO4_25124' => 'col', 'Cpa.g.sc16.34' => 'cpa', 'Cpa.g.sc3504.1' => 'cpa', 'Cpa.g.sc60.37' => 'cpa', 'CsaV3_6G018520' => 'csa', 'CsaV3_6G036860' => 'csa', 'CSS0001072' => 'camsi', 'CSS0020208' => 'camsi', 'CSS0021253' => 'camsi', 'CSS0022190' => 'camsi', 'CSS0036150' => 'camsi', 'CSS0040442' => 'camsi', 'CSS0042300' => 'camsi', 'CSS0045298' => 'camsi', 'DCAR_012449' => 'dca', 'DCAR_018405' => 'dca', 'DCAR_024573' => 'dca', 'DCAR_030591' => 'dca', 'Dinv16926' => 'din', 'Dinv32963' => 'din', 'Dinv38382' => 'din', 'Dinv38383' => 'din', 'Duzib133G0974' => 'dzi', 'Duzib138G1867' => 'dzi', 'Duzib211G0420' => 'dzi', 'Duzib212G0930' => 'dzi', 'ECA234G1645' => 'eca', 'ECA247G3467' => 'eca', 'ECA248G1703' => 'eca', 'EL10Ac3g06327' => 'bvu', 'EL10Ac7g17204' => 'bvu', 'Eucgr.A00855' => 'egr', 'Eucgr.A00858' => 'egr', 'Eucgr.H01520' => 'egr', 'Eucgr.H03604' => 'egr', 'Eucgr.L03465' => 'egr', 'Eucgr.L03466' => 'egr', 'FAN01G0988' => 'fan', 'FAN02G3892' => 'fan', 'FAN05G3381' => 'fan', 'FAN07G0967' => 'fan', 'FAN07G1493' => 'fan', 'FAN08G3125' => 'fan', 'FAN09G0402' => 'fan', 'FAN12G2594' => 'fan', 'FAN12G3879' => 'fan', 'FAN14G1546' => 'fan', 'FAN15G3626' => 'fan', 'FAN17G0588' => 'fan', 'FAN17G0609' => 'fan', 'FAN18G2817' => 'fan', 'FAN19G1305' => 'fan', 'FAN20G1787' => 'fan', 'FAN22G0073' => 'fan', 'FAN22G0352' => 'fan', 'FAN22G0368' => 'fan', 'FAN22G2273' => 'fan', 'FAN24G1998' => 'fan', 'FAN27G1317' => 'fan', 'FvH4_2g23980' => 'fve', 'FvH4_4g14380' => 'fve', 'FvH4_4g14390' => 'fve', 'FvH4_6g09250' => 'fve', 'Glyma.03G151100' => 'gma', 'Glyma.04G122550' => 'gma', 'Glyma.05G001600' => 'gma', 'Glyma.09G270766' => 'gma', 'Glyma.09G270832' => 'gma', 'Glyma.13G209800' => 'gma', 'Glyma.15G102800' => 'gma', 'Glyma.18G218900' => 'gma', 'Glyma.19G001500' => 'gma', 'Glyma.19G153600' => 'gma', 'Gohir.A02G028600' => 'ghi', 'Gohir.A08G045000' => 'ghi', 'Gohir.A11G120500' => 'ghi', 'Gohir.A12G006200' => 'ghi', 'Gohir.A12G006250' => 'ghi', 'Gohir.D02G036300' => 'ghi', 'Gohir.D08G054700' => 'ghi', 'Gohir.D11G125600' => 'ghi', 'Gohir.D12G005700' => 'ghi', 'Gorai.004G055200' => 'gra', 'Gorai.005G040400' => 'gra', 'Gorai.007G134500' => 'gra', 'Gorai.008G005500' => 'gra', 'GSVIVG01011094001' => 'vvi', 'GSVIVG01017879001' => 'vvi', 'GSVIVG01025988001' => 'vvi', 'GSVIVG01029847001' => 'vvi', 'HanXRQChr10g0282901' => 'han', 'HanXRQChr10g0310371' => 'han', 'HanXRQChr10g0315041' => 'han', 'HanXRQChr11g0327651' => 'han', 'HanXRQChr12g0359391' => 'han', 'Haze_00972' => 'cav', 'Haze_00973' => 'cav', 'Haze_00974' => 'cav', 'Haze_04747' => 'cav', 'Haze_04749' => 'cav', 'Haze_04750' => 'cav', 'Haze_21217' => 'cav', 'Hma1.2p1_1037F.1_g250680' => 'hma', 'Hma1.2p1_1644F.1_g295320' => 'hma', 'HPP92_011322' => 'vpl', 'HPP92_011323' => 'vpl', 'HPP92_011324' => 'vpl', 'HPP92_011325' => 'vpl', 'HPP92_011326' => 'vpl', 'Hund12205' => 'sun', 'Hund17957' => 'sun', 'Lalb_Chr06g0176771' => 'lal', 'Lalb_Chr18g0056021' => 'lal', 'Lalb_Chr18g0056031' => 'lal', 'Lalb_Chr18g0056041' => 'lal', 'Lalb_Chr20g0107751' => 'lal', 'Lalb_Chr20g0118371' => 'lal', 'Lj1g0010239' => 'lja', 'Lj1g0017101' => 'lja', 'Lj2A1178G40' => 'lonja', 'Lj2A54G84' => 'lonja', 'Lj2g0015248' => 'lja', 'Lj3A761T51' => 'lonja', 'Lj6g0018116' => 'lja', 'Lsat_1_v5_gn_4_136040' => 'lsa', 'Lsat_1_v5_gn_5_187461' => 'lsa', 'Lsat_1_v5_gn_5_77001' => 'lsa', 'Lsat_1_v5_gn_9_4461' => 'lsa', 'Manes.01G210100' => 'mes', 'Manes.03G185600' => 'mes', 'Manes.05G073300' => 'mes', 'Manes.09G120300' => 'mes', 'Manes.15G022100' => 'mes', 'Mapoly0096s0053' => 'mpo', 'MBI03_g14058_MAGBIO' => 'mbi', 'MBI03_g33876_MAGBIO' => 'mbi', 'MBI03_g36854_MAGBIO' => 'mbi', 'MBI17_g11997_MAGBIO' => 'mbi', 'MD03G1269000' => 'mdo', 'MD04G1179600' => 'mdo', 'MD11G1289800' => 'mdo', 'MD12G1194700' => 'mdo', 'MD13G1182100' => 'mdo', 'MD13G1182200' => 'mdo', 'MD16G1182600' => 'mdo', 'Medtr2g021400' => 'mtr', 'Medtr2g021470' => 'mtr', 'Medtr2g105810' => 'mtr', 'Medtr3g033580' => 'mtr', 'Medtr6g007970' => 'mtr', 'Medtr7g056330' => 'mtr', 'Medtr7g074290' => 'mtr', 'Medtr7g074380' => 'mtr', 'Medtr7g094550' => 'mtr', 'Medtr8g069995' => 'mtr', 'MELO3C014345.2' => 'cme', 'MELO3C021395.2' => 'cme', 'Migut.D00262' => 'egut', 'Migut.G00257' => 'egut', 'MSTRG.21575' => 'ama', 'MSTRG.3985' => 'ama', 'Nitab4.5_0000295g0140' => 'nta', 'Nitab4.5_0000732g0140' => 'nta', 'Nitab4.5_0003162g0020' => 'nta', 'Nitab4.5_0006180g0090' => 'nta', 'Nitab4.5_0006390g0010' => 'nta', 'Nitab4.5_0007392g0040' => 'nta', 'Nn1g02140' => 'nnu', 'Nn4g26168' => 'nnu', 'Nn5g26754' => 'nnu', 'Oeu001433.1' => 'oeu', 'Oeu010299.2' => 'oeu', 'Oeu011171.1' => 'oeu', 'Oeu037675.1' => 'oeu', 'Oeu038359.1' => 'oeu', 'Oeu063834.1' => 'oeu', 'Oeu063835.1' => 'oeu', 'Os05g0312000' => 'osa', 'Os07g0211101' => 'osa', 'Os07g0211200' => 'osa', 'Os07g0681500' => 'osa', 'Peaxi162Scf00095g01015' => 'pax', 'Peaxi162Scf00104g00329' => 'pax', 'Peaxi162Scf00161g00137' => 'pax', 'PGR004G1665' => 'pgr', 'PGR031G2937' => 'pgr', 'PGR119G2145' => 'pgr', 'PGSC0003DMG400004351' => 'stu', 'PGSC0003DMG400014625' => 'stu', 'PGSC0003DMG401000943' => 'stu', 'Phvul.001G148600' => 'pvu', 'Phvul.004G001700' => 'pvu', 'Phvul.006G154900' => 'pvu', 'Phvul.008G078200' => 'pvu', 'Phvul.011G136500' => 'pvu', 'Potri.002G215600' => 'ptr', 'Potri.008G201600' => 'ptr', 'Potri.014G138400' => 'ptr', 'Potri.016G142500' => 'ptr', 'Pp3c16_10580' => 'ppa', 'Pp3c5_25280' => 'ppa', 'Prupe.1G150000' => 'ppe', 'Prupe.1G150100' => 'ppe', 'Prupe.6G299600' => 'ppe', 'Prupe.8G245000' => 'ppe', 'Psat0s4927g0040' => 'psa', 'Psat1g052080' => 'psa', 'Psat1g183800' => 'psa', 'Psat3g113840' => 'psa', 'Psat3g126120' => 'psa', 'Psat3g126160' => 'psa', 'Psat3g158760' => 'psa', 'Psat3g158840' => 'psa', 'PSO170G2858' => 'pso', 'PSO339G0606' => 'pso', 'PSO384G4709' => 'pso', 'PSO407G0334' => 'pso', 'QL04p040276' => 'qlo', 'QL06p005458' => 'qlo', 'QL06p005472' => 'qlo', 'QL07p030546' => 'qlo', 'QL07p031519' => 'qlo', 'QL09p050949' => 'qlo', 'QL09p050966' => 'qlo', 'QL09p051067' => 'qlo', 'QL12p022706' => 'qlo', 'RcHm_v2.0_Chr2g0119601' => 'rch', 'RcHm_v2.0_Chr3g0459591' => 'rch', 'RcHm_v2.0_Chr4g0418521' => 'rch', 'RcHm_v2.0_Chr4g0418531' => 'rch', 'RcHm_v2.0_Chr4g0418541' => 'rch', 'RcHm_v2.0_Chr6g0291641' => 'rch', 'Rhsim01G0086300' => 'rsi', 'Rhsim01G0276300' => 'rsi', 'Rhsim01G0276500' => 'rsi', 'Rhsim04G0207700' => 'rsi', 'Rhsim05G0234500' => 'rsi', 'Rhsim13G0022400' => 'rsi', 'Sabra02G0167900' => 'sbr', 'Sabra04G0158500' => 'sbr', 'Sabra08G0159800' => 'sbr', 'Sabra10G0011500' => 'sbr', 'Sabra14G0104400' => 'sbr', 'SalBow2G2440' => 'sbo', 'SalBow4G2265' => 'sbo', 'Sc02g0000060' => 'sci', 'Sc05g0005020' => 'sci', 'Sc13g0003890' => 'sci', 'Sed0014865' => 'sed', 'Sed0017224' => 'sed', 'Sed0026391' => 'sed', 'SEGI_00063' => 'sgi', 'SEGI_10967' => 'sgi', 'SEGI_17510' => 'sgi', 'SEGI_24396' => 'sgi', 'SEGI_39719' => 'sgi', 'SEGI_41392' => 'sgi', 'SGA_v2.0_scaffold11G05794' => 'sas', 'SGA_v2.0_scaffold142G35607' => 'sas', 'SGA_v2.0_scaffold1G00447' => 'sas', 'SHI15388' => 'shi', 'SHI15394' => 'shi', 'SHI15396' => 'shi', 'SHI15399' => 'shi', 'SMO343G0151' => 'smo', 'SMO367G1118' => 'smo', 'Solyc01g080200.3' => 'sly', 'Solyc06g008960.3' => 'sly', 'Solyc09g064780.3' => 'sly', 'Sopen01g031980' => 'spe', 'Sopen06g003710' => 'spe', 'Sopen09g026460' => 'spe', 'Sp3g21240' => 'spa', 'Sp4g30030' => 'spa', 'TAR365G0022' => 'tar', 'TAR365G1023' => 'tar', 'TAR365G1253' => 'tar', 'TAR623G0078' => 'tar', 'TAR623G1721' => 'tar', 'TAR633G0959' => 'tar', 'THA.LOC104802225' => 'tha', 'THA.LOC104804769' => 'tha', 'THA.LOC104808660' => 'tha', 'THA.LOC104812792' => 'tha', 'Thecc.01G284000' => 'tca', 'Thecc.04G220600' => 'tca', 'Thecc.05G268900' => 'tca', 'Thecc.08G171100' => 'tca', 'Thhalv10001284m.g' => 'esa', 'Thhalv10019912m.g' => 'esa', 'TPR.G14189' => 'tpr', 'TPR.G18110' => 'tpr', 'TPR.G18130' => 'tpr', 'TPR.G18131' => 'tpr', 'TPR.G18140' => 'tpr', 'TPR.G24282' => 'tpr', 'TPR.G25221' => 'tpr', 'TPR.G29267' => 'tpr', 'TPR.G35315' => 'tpr', 'TPR.G36173' => 'tpr', 'TWI09G0794' => 'twi', 'TWI59G1348' => 'twi', 'TWI74G0430' => 'twi', 'unitig_26.g8940' => 'ugi', 'unitig_749.g13744' => 'ugi', 'unitig_749.g13745' => 'ugi', 'vmacro08269' => 'vma', 'vmacro14937' => 'vma', 'vmacro20401' => 'vma', 'VMungo0464G1349' => 'vmu', 'VMungo0540G0289' => 'vmu', 'VMungo1215G1590' => 'vmu', 'VMungo1309G0221' => 'vmu', 'VMungo1309G2815' => 'vmu', 'VMungo1383G0239' => 'vmu', 'VMungo1383G2910' => 'vmu', 'Zm00001eb095270' => 'zma', 'Zm00001eb095280' => 'zma', 'Zm00001eb111630' => 'zma', 'Zm00001eb237080' => 'zma', 'Zm00001eb273740' => 'zma', 'Zm00001eb285040' => 'zma', 'Zm00001eb330790' => 'zma', 'Zm00001eb337380' => 'zma' ) $gf_id = 'HOM05D001484' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001484' ) $data_identifier = 'HOM05D001484' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 2, 'aly' => (int) 2, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 22, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 7, 'hma' => (int) 2, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 7, 'mtr' => (int) 10, 'cme' => (int) 2, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 4, 'ppa' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 4, 'qlo' => (int) 9, 'rch' => (int) 6, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 10, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 7, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb337380' $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' => 'HOM05D001484', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p31500' => 'bna', 'A05p00020' => 'bna', 'A07p08820' => 'bna', 'Aa31LG4G3300' => 'aar', 'Aa31LG8G10030' => 'aar', 'Actinidia00731' => 'ach', 'Actinidia11473' => 'ach', 'Actinidia23469' => 'ach', 'Actinidia24318' => 'ach', 'Actinidia40196' => 'ach', 'Actinidia40197' => 'ach', 'Actinidia40198' => 'ach', 'Ah.08g212990' => 'amhyb', 'Ah.15g091720' => 'amhyb', 'AL3G38260' => 'aly', 'AL4G47710' => 'aly', 'Aqoxy2G00671' => 'aox', 'Aqoxy2G03236' => 'aox', 'arahy.Tifrunner.gnm1.ann1.05IDCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KR684' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATY3SJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK6QJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6APGL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IDT7Z9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM073U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ0R87' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LE7RV4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT4QRX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V5ENPK' => 'arhy', 'AT2G48110' => 'ath', 'AT3G23590' => 'ath', 'ATR0626G186' => 'atr', 'ATR1127G141' => 'atr', 'Atru.chr4.2583' => 'acertr', 'Atru.chr5.1358' => 'acertr', 'Atru.chr5.1359' => 'acertr', 'Atru.chr8.46' => 'acertr', 'AUR62002640' => 'cqu', 'AUR62030055' => 'cqu', 'AUR62033713' => 'cqu', 'AUR62033714' => 'cqu', 'AUR62036795' => 'cqu', 'AUR62039891' => 'cqu', 'BcaB02g08737' => 'bca', 'BcaB04g20441' => 'bca', 'BcaB06g26509' => 'bca', 'BcaB06g26510' => 'bca', 'BcaB06g26511' => 'bca', 'BcaB06g26512' => 'bca', 'BcaB06g26513' => 'bca', 'BcaC02g12564' => 'bca', 'BcaC02g12565' => 'bca', 'BcaC02g12794' => 'bca', 'BcaC02g12795' => 'bca', 'BcaC02g12796' => 'bca', 'BcaC06g35541' => 'bca', 'BNapus_Darmor_BZH_scaffold_188p00080' => 'bna', 'BNapus_Darmor_BZH_scaffold_188p00090' => 'bna', 'BolC1t03972H' => 'bol', 'BolC1t03973H' => 'bol', 'BolC4t21680H' => 'bol', 'BolC7t41863H' => 'bol', 'BolSC55t61227H' => 'bol', 'BolSC55t61228H' => 'bol', 'BraA01t03278Z' => 'bra', 'BraA05t18998Z' => 'bra', 'BraA07t28673Z' => 'bra', 'C01p40150' => 'bna', 'C05p12370' => 'bna', 'C07p13680' => 'bna', 'CAN.G1006.16' => 'can', 'CAN.G1006.17' => 'can', 'CAN.G1170.2' => 'can', 'CAN.G962.7' => 'can', 'CANSAT25G2179' => 'cansat', 'CANSAT78G1573' => 'cansat', 'CARHR099510' => 'chi', 'CARHR143510' => 'chi', 'Carub.0003s2380' => 'cru', 'Carub.0004s3082' => 'cru', 'Ca_00614_v3' => 'car', 'Ca_07801_v3' => 'car', 'Ca_08567_v3' => 'car', 'Ca_09571_v3' => 'car', 'CBR_g19290' => 'cbr', 'Cc01_g19770' => 'ccan', 'Cc03_g03030' => 'ccan', 'CDE07G0968' => 'cde', 'CDE09G1441' => 'cde', 'Cfa006103' => 'cfa', 'Cfa015573' => 'cfa', 'Cfa016988' => 'cfa', 'Ciclev10006738m.g' => 'ccl', 'Ciclev10010920m.g' => 'ccl', 'Ciclev10018517m.g' => 'ccl', 'CiPaw.01G159200' => 'cil', 'CiPaw.02G091000' => 'cil', 'CiPaw.02G091100' => 'cil', 'CiPaw.08G103100' => 'cil', 'CiPaw.09G224900' => 'cil', 'ClCG06G005740' => 'cla', 'ClCG07G000090' => 'cla', 'ClCG07G000100' => 'cla', 'COL.COLO4_09143' => 'col', 'COL.COLO4_25124' => 'col', 'Cpa.g.sc16.34' => 'cpa', 'Cpa.g.sc3504.1' => 'cpa', 'Cpa.g.sc60.37' => 'cpa', 'CsaV3_6G018520' => 'csa', 'CsaV3_6G036860' => 'csa', 'CSS0001072' => 'camsi', 'CSS0020208' => 'camsi', 'CSS0021253' => 'camsi', 'CSS0022190' => 'camsi', 'CSS0036150' => 'camsi', 'CSS0040442' => 'camsi', 'CSS0042300' => 'camsi', 'CSS0045298' => 'camsi', 'DCAR_012449' => 'dca', 'DCAR_018405' => 'dca', 'DCAR_024573' => 'dca', 'DCAR_030591' => 'dca', 'Dinv16926' => 'din', 'Dinv32963' => 'din', 'Dinv38382' => 'din', 'Dinv38383' => 'din', 'Duzib133G0974' => 'dzi', 'Duzib138G1867' => 'dzi', 'Duzib211G0420' => 'dzi', 'Duzib212G0930' => 'dzi', 'ECA234G1645' => 'eca', 'ECA247G3467' => 'eca', 'ECA248G1703' => 'eca', 'EL10Ac3g06327' => 'bvu', 'EL10Ac7g17204' => 'bvu', 'Eucgr.A00855' => 'egr', 'Eucgr.A00858' => 'egr', 'Eucgr.H01520' => 'egr', 'Eucgr.H03604' => 'egr', 'Eucgr.L03465' => 'egr', 'Eucgr.L03466' => 'egr', 'FAN01G0988' => 'fan', 'FAN02G3892' => 'fan', 'FAN05G3381' => 'fan', 'FAN07G0967' => 'fan', 'FAN07G1493' => 'fan', 'FAN08G3125' => 'fan', 'FAN09G0402' => 'fan', 'FAN12G2594' => 'fan', 'FAN12G3879' => 'fan', 'FAN14G1546' => 'fan', 'FAN15G3626' => 'fan', 'FAN17G0588' => 'fan', 'FAN17G0609' => 'fan', 'FAN18G2817' => 'fan', 'FAN19G1305' => 'fan', 'FAN20G1787' => 'fan', 'FAN22G0073' => 'fan', 'FAN22G0352' => 'fan', 'FAN22G0368' => 'fan', 'FAN22G2273' => 'fan', 'FAN24G1998' => 'fan', 'FAN27G1317' => 'fan', 'FvH4_2g23980' => 'fve', 'FvH4_4g14380' => 'fve', 'FvH4_4g14390' => 'fve', 'FvH4_6g09250' => 'fve', 'Glyma.03G151100' => 'gma', 'Glyma.04G122550' => 'gma', 'Glyma.05G001600' => 'gma', 'Glyma.09G270766' => 'gma', 'Glyma.09G270832' => 'gma', 'Glyma.13G209800' => 'gma', 'Glyma.15G102800' => 'gma', 'Glyma.18G218900' => 'gma', 'Glyma.19G001500' => 'gma', 'Glyma.19G153600' => 'gma', 'Gohir.A02G028600' => 'ghi', 'Gohir.A08G045000' => 'ghi', 'Gohir.A11G120500' => 'ghi', 'Gohir.A12G006200' => 'ghi', 'Gohir.A12G006250' => 'ghi', 'Gohir.D02G036300' => 'ghi', 'Gohir.D08G054700' => 'ghi', 'Gohir.D11G125600' => 'ghi', 'Gohir.D12G005700' => 'ghi', 'Gorai.004G055200' => 'gra', 'Gorai.005G040400' => 'gra', 'Gorai.007G134500' => 'gra', 'Gorai.008G005500' => 'gra', 'GSVIVG01011094001' => 'vvi', 'GSVIVG01017879001' => 'vvi', 'GSVIVG01025988001' => 'vvi', 'GSVIVG01029847001' => 'vvi', 'HanXRQChr10g0282901' => 'han', 'HanXRQChr10g0310371' => 'han', 'HanXRQChr10g0315041' => 'han', 'HanXRQChr11g0327651' => 'han', 'HanXRQChr12g0359391' => 'han', 'Haze_00972' => 'cav', 'Haze_00973' => 'cav', 'Haze_00974' => 'cav', 'Haze_04747' => 'cav', 'Haze_04749' => 'cav', 'Haze_04750' => 'cav', 'Haze_21217' => 'cav', 'Hma1.2p1_1037F.1_g250680' => 'hma', 'Hma1.2p1_1644F.1_g295320' => 'hma', 'HPP92_011322' => 'vpl', 'HPP92_011323' => 'vpl', 'HPP92_011324' => 'vpl', 'HPP92_011325' => 'vpl', 'HPP92_011326' => 'vpl', 'Hund12205' => 'sun', 'Hund17957' => 'sun', 'Lalb_Chr06g0176771' => 'lal', 'Lalb_Chr18g0056021' => 'lal', 'Lalb_Chr18g0056031' => 'lal', 'Lalb_Chr18g0056041' => 'lal', 'Lalb_Chr20g0107751' => 'lal', 'Lalb_Chr20g0118371' => 'lal', 'Lj1g0010239' => 'lja', 'Lj1g0017101' => 'lja', 'Lj2A1178G40' => 'lonja', 'Lj2A54G84' => 'lonja', 'Lj2g0015248' => 'lja', 'Lj3A761T51' => 'lonja', 'Lj6g0018116' => 'lja', 'Lsat_1_v5_gn_4_136040' => 'lsa', 'Lsat_1_v5_gn_5_187461' => 'lsa', 'Lsat_1_v5_gn_5_77001' => 'lsa', 'Lsat_1_v5_gn_9_4461' => 'lsa', 'Manes.01G210100' => 'mes', 'Manes.03G185600' => 'mes', 'Manes.05G073300' => 'mes', 'Manes.09G120300' => 'mes', 'Manes.15G022100' => 'mes', 'Mapoly0096s0053' => 'mpo', 'MBI03_g14058_MAGBIO' => 'mbi', 'MBI03_g33876_MAGBIO' => 'mbi', 'MBI03_g36854_MAGBIO' => 'mbi', 'MBI17_g11997_MAGBIO' => 'mbi', 'MD03G1269000' => 'mdo', 'MD04G1179600' => 'mdo', 'MD11G1289800' => 'mdo', 'MD12G1194700' => 'mdo', 'MD13G1182100' => 'mdo', 'MD13G1182200' => 'mdo', 'MD16G1182600' => 'mdo', 'Medtr2g021400' => 'mtr', 'Medtr2g021470' => 'mtr', 'Medtr2g105810' => 'mtr', 'Medtr3g033580' => 'mtr', 'Medtr6g007970' => 'mtr', 'Medtr7g056330' => 'mtr', 'Medtr7g074290' => 'mtr', 'Medtr7g074380' => 'mtr', 'Medtr7g094550' => 'mtr', 'Medtr8g069995' => 'mtr', 'MELO3C014345.2' => 'cme', 'MELO3C021395.2' => 'cme', 'Migut.D00262' => 'egut', 'Migut.G00257' => 'egut', 'MSTRG.21575' => 'ama', 'MSTRG.3985' => 'ama', 'Nitab4.5_0000295g0140' => 'nta', 'Nitab4.5_0000732g0140' => 'nta', 'Nitab4.5_0003162g0020' => 'nta', 'Nitab4.5_0006180g0090' => 'nta', 'Nitab4.5_0006390g0010' => 'nta', 'Nitab4.5_0007392g0040' => 'nta', 'Nn1g02140' => 'nnu', 'Nn4g26168' => 'nnu', 'Nn5g26754' => 'nnu', 'Oeu001433.1' => 'oeu', 'Oeu010299.2' => 'oeu', 'Oeu011171.1' => 'oeu', 'Oeu037675.1' => 'oeu', 'Oeu038359.1' => 'oeu', 'Oeu063834.1' => 'oeu', 'Oeu063835.1' => 'oeu', 'Os05g0312000' => 'osa', 'Os07g0211101' => 'osa', 'Os07g0211200' => 'osa', 'Os07g0681500' => 'osa', 'Peaxi162Scf00095g01015' => 'pax', 'Peaxi162Scf00104g00329' => 'pax', 'Peaxi162Scf00161g00137' => 'pax', 'PGR004G1665' => 'pgr', 'PGR031G2937' => 'pgr', 'PGR119G2145' => 'pgr', 'PGSC0003DMG400004351' => 'stu', 'PGSC0003DMG400014625' => 'stu', 'PGSC0003DMG401000943' => 'stu', 'Phvul.001G148600' => 'pvu', 'Phvul.004G001700' => 'pvu', 'Phvul.006G154900' => 'pvu', 'Phvul.008G078200' => 'pvu', 'Phvul.011G136500' => 'pvu', 'Potri.002G215600' => 'ptr', 'Potri.008G201600' => 'ptr', 'Potri.014G138400' => 'ptr', 'Potri.016G142500' => 'ptr', 'Pp3c16_10580' => 'ppa', 'Pp3c5_25280' => 'ppa', 'Prupe.1G150000' => 'ppe', 'Prupe.1G150100' => 'ppe', 'Prupe.6G299600' => 'ppe', 'Prupe.8G245000' => 'ppe', 'Psat0s4927g0040' => 'psa', 'Psat1g052080' => 'psa', 'Psat1g183800' => 'psa', 'Psat3g113840' => 'psa', 'Psat3g126120' => 'psa', 'Psat3g126160' => 'psa', 'Psat3g158760' => 'psa', 'Psat3g158840' => 'psa', 'PSO170G2858' => 'pso', 'PSO339G0606' => 'pso', 'PSO384G4709' => 'pso', 'PSO407G0334' => 'pso', 'QL04p040276' => 'qlo', 'QL06p005458' => 'qlo', 'QL06p005472' => 'qlo', 'QL07p030546' => 'qlo', 'QL07p031519' => 'qlo', 'QL09p050949' => 'qlo', 'QL09p050966' => 'qlo', 'QL09p051067' => 'qlo', 'QL12p022706' => 'qlo', 'RcHm_v2.0_Chr2g0119601' => 'rch', 'RcHm_v2.0_Chr3g0459591' => 'rch', 'RcHm_v2.0_Chr4g0418521' => 'rch', 'RcHm_v2.0_Chr4g0418531' => 'rch', 'RcHm_v2.0_Chr4g0418541' => 'rch', 'RcHm_v2.0_Chr6g0291641' => 'rch', 'Rhsim01G0086300' => 'rsi', 'Rhsim01G0276300' => 'rsi', 'Rhsim01G0276500' => 'rsi', 'Rhsim04G0207700' => 'rsi', 'Rhsim05G0234500' => 'rsi', 'Rhsim13G0022400' => 'rsi', 'Sabra02G0167900' => 'sbr', 'Sabra04G0158500' => 'sbr', 'Sabra08G0159800' => 'sbr', 'Sabra10G0011500' => 'sbr', 'Sabra14G0104400' => 'sbr', 'SalBow2G2440' => 'sbo', 'SalBow4G2265' => 'sbo', 'Sc02g0000060' => 'sci', 'Sc05g0005020' => 'sci', 'Sc13g0003890' => 'sci', 'Sed0014865' => 'sed', 'Sed0017224' => 'sed', 'Sed0026391' => 'sed', 'SEGI_00063' => 'sgi', 'SEGI_10967' => 'sgi', 'SEGI_17510' => 'sgi', 'SEGI_24396' => 'sgi', 'SEGI_39719' => 'sgi', 'SEGI_41392' => 'sgi', 'SGA_v2.0_scaffold11G05794' => 'sas', 'SGA_v2.0_scaffold142G35607' => 'sas', 'SGA_v2.0_scaffold1G00447' => 'sas', 'SHI15388' => 'shi', 'SHI15394' => 'shi', 'SHI15396' => 'shi', 'SHI15399' => 'shi', 'SMO343G0151' => 'smo', 'SMO367G1118' => 'smo', 'Solyc01g080200.3' => 'sly', 'Solyc06g008960.3' => 'sly', 'Solyc09g064780.3' => 'sly', 'Sopen01g031980' => 'spe', 'Sopen06g003710' => 'spe', 'Sopen09g026460' => 'spe', 'Sp3g21240' => 'spa', 'Sp4g30030' => 'spa', 'TAR365G0022' => 'tar', 'TAR365G1023' => 'tar', 'TAR365G1253' => 'tar', 'TAR623G0078' => 'tar', 'TAR623G1721' => 'tar', 'TAR633G0959' => 'tar', 'THA.LOC104802225' => 'tha', 'THA.LOC104804769' => 'tha', 'THA.LOC104808660' => 'tha', 'THA.LOC104812792' => 'tha', 'Thecc.01G284000' => 'tca', 'Thecc.04G220600' => 'tca', 'Thecc.05G268900' => 'tca', 'Thecc.08G171100' => 'tca', 'Thhalv10001284m.g' => 'esa', 'Thhalv10019912m.g' => 'esa', 'TPR.G14189' => 'tpr', 'TPR.G18110' => 'tpr', 'TPR.G18130' => 'tpr', 'TPR.G18131' => 'tpr', 'TPR.G18140' => 'tpr', 'TPR.G24282' => 'tpr', 'TPR.G25221' => 'tpr', 'TPR.G29267' => 'tpr', 'TPR.G35315' => 'tpr', 'TPR.G36173' => 'tpr', 'TWI09G0794' => 'twi', 'TWI59G1348' => 'twi', 'TWI74G0430' => 'twi', 'unitig_26.g8940' => 'ugi', 'unitig_749.g13744' => 'ugi', 'unitig_749.g13745' => 'ugi', 'vmacro08269' => 'vma', 'vmacro14937' => 'vma', 'vmacro20401' => 'vma', 'VMungo0464G1349' => 'vmu', 'VMungo0540G0289' => 'vmu', 'VMungo1215G1590' => 'vmu', 'VMungo1309G0221' => 'vmu', 'VMungo1309G2815' => 'vmu', 'VMungo1383G0239' => 'vmu', 'VMungo1383G2910' => 'vmu', 'Zm00001eb095270' => 'zma', 'Zm00001eb095280' => 'zma', 'Zm00001eb111630' => 'zma', 'Zm00001eb237080' => 'zma', 'Zm00001eb273740' => 'zma', 'Zm00001eb285040' => 'zma', 'Zm00001eb330790' => 'zma', 'Zm00001eb337380' => 'zma' ), 'gf_id' => 'HOM05D001484', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001484' ), 'data_identifier' => 'HOM05D001484', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001484', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p31500' => 'bna', 'A05p00020' => 'bna', 'A07p08820' => 'bna', 'Aa31LG4G3300' => 'aar', 'Aa31LG8G10030' => 'aar', 'Actinidia00731' => 'ach', 'Actinidia11473' => 'ach', 'Actinidia23469' => 'ach', 'Actinidia24318' => 'ach', 'Actinidia40196' => 'ach', 'Actinidia40197' => 'ach', 'Actinidia40198' => 'ach', 'Ah.08g212990' => 'amhyb', 'Ah.15g091720' => 'amhyb', 'AL3G38260' => 'aly', 'AL4G47710' => 'aly', 'Aqoxy2G00671' => 'aox', 'Aqoxy2G03236' => 'aox', 'arahy.Tifrunner.gnm1.ann1.05IDCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KR684' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATY3SJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK6QJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6APGL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IDT7Z9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM073U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ0R87' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LE7RV4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT4QRX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V5ENPK' => 'arhy', 'AT2G48110' => 'ath', 'AT3G23590' => 'ath', 'ATR0626G186' => 'atr', 'ATR1127G141' => 'atr', 'Atru.chr4.2583' => 'acertr', 'Atru.chr5.1358' => 'acertr', 'Atru.chr5.1359' => 'acertr', 'Atru.chr8.46' => 'acertr', 'AUR62002640' => 'cqu', 'AUR62030055' => 'cqu', 'AUR62033713' => 'cqu', 'AUR62033714' => 'cqu', 'AUR62036795' => 'cqu', 'AUR62039891' => 'cqu', 'BcaB02g08737' => 'bca', 'BcaB04g20441' => 'bca', 'BcaB06g26509' => 'bca', 'BcaB06g26510' => 'bca', 'BcaB06g26511' => 'bca', 'BcaB06g26512' => 'bca', 'BcaB06g26513' => 'bca', 'BcaC02g12564' => 'bca', 'BcaC02g12565' => 'bca', 'BcaC02g12794' => 'bca', 'BcaC02g12795' => 'bca', 'BcaC02g12796' => 'bca', 'BcaC06g35541' => 'bca', 'BNapus_Darmor_BZH_scaffold_188p00080' => 'bna', 'BNapus_Darmor_BZH_scaffold_188p00090' => 'bna', 'BolC1t03972H' => 'bol', 'BolC1t03973H' => 'bol', 'BolC4t21680H' => 'bol', 'BolC7t41863H' => 'bol', 'BolSC55t61227H' => 'bol', 'BolSC55t61228H' => 'bol', 'BraA01t03278Z' => 'bra', 'BraA05t18998Z' => 'bra', 'BraA07t28673Z' => 'bra', 'C01p40150' => 'bna', 'C05p12370' => 'bna', 'C07p13680' => 'bna', 'CAN.G1006.16' => 'can', 'CAN.G1006.17' => 'can', 'CAN.G1170.2' => 'can', 'CAN.G962.7' => 'can', 'CANSAT25G2179' => 'cansat', 'CANSAT78G1573' => 'cansat', 'CARHR099510' => 'chi', 'CARHR143510' => 'chi', 'Carub.0003s2380' => 'cru', 'Carub.0004s3082' => 'cru', 'Ca_00614_v3' => 'car', 'Ca_07801_v3' => 'car', 'Ca_08567_v3' => 'car', 'Ca_09571_v3' => 'car', 'CBR_g19290' => 'cbr', 'Cc01_g19770' => 'ccan', 'Cc03_g03030' => 'ccan', 'CDE07G0968' => 'cde', 'CDE09G1441' => 'cde', 'Cfa006103' => 'cfa', 'Cfa015573' => 'cfa', 'Cfa016988' => 'cfa', 'Ciclev10006738m.g' => 'ccl', 'Ciclev10010920m.g' => 'ccl', 'Ciclev10018517m.g' => 'ccl', 'CiPaw.01G159200' => 'cil', 'CiPaw.02G091000' => 'cil', 'CiPaw.02G091100' => 'cil', 'CiPaw.08G103100' => 'cil', 'CiPaw.09G224900' => 'cil', 'ClCG06G005740' => 'cla', 'ClCG07G000090' => 'cla', 'ClCG07G000100' => 'cla', 'COL.COLO4_09143' => 'col', 'COL.COLO4_25124' => 'col', 'Cpa.g.sc16.34' => 'cpa', 'Cpa.g.sc3504.1' => 'cpa', 'Cpa.g.sc60.37' => 'cpa', 'CsaV3_6G018520' => 'csa', 'CsaV3_6G036860' => 'csa', 'CSS0001072' => 'camsi', 'CSS0020208' => 'camsi', 'CSS0021253' => 'camsi', 'CSS0022190' => 'camsi', 'CSS0036150' => 'camsi', 'CSS0040442' => 'camsi', 'CSS0042300' => 'camsi', 'CSS0045298' => 'camsi', 'DCAR_012449' => 'dca', 'DCAR_018405' => 'dca', 'DCAR_024573' => 'dca', 'DCAR_030591' => 'dca', 'Dinv16926' => 'din', 'Dinv32963' => 'din', 'Dinv38382' => 'din', 'Dinv38383' => 'din', 'Duzib133G0974' => 'dzi', 'Duzib138G1867' => 'dzi', 'Duzib211G0420' => 'dzi', 'Duzib212G0930' => 'dzi', 'ECA234G1645' => 'eca', 'ECA247G3467' => 'eca', 'ECA248G1703' => 'eca', 'EL10Ac3g06327' => 'bvu', 'EL10Ac7g17204' => 'bvu', 'Eucgr.A00855' => 'egr', 'Eucgr.A00858' => 'egr', 'Eucgr.H01520' => 'egr', 'Eucgr.H03604' => 'egr', 'Eucgr.L03465' => 'egr', 'Eucgr.L03466' => 'egr', 'FAN01G0988' => 'fan', 'FAN02G3892' => 'fan', 'FAN05G3381' => 'fan', 'FAN07G0967' => 'fan', 'FAN07G1493' => 'fan', 'FAN08G3125' => 'fan', 'FAN09G0402' => 'fan', 'FAN12G2594' => 'fan', 'FAN12G3879' => 'fan', 'FAN14G1546' => 'fan', 'FAN15G3626' => 'fan', 'FAN17G0588' => 'fan', 'FAN17G0609' => 'fan', 'FAN18G2817' => 'fan', 'FAN19G1305' => 'fan', 'FAN20G1787' => 'fan', 'FAN22G0073' => 'fan', 'FAN22G0352' => 'fan', 'FAN22G0368' => 'fan', 'FAN22G2273' => 'fan', 'FAN24G1998' => 'fan', 'FAN27G1317' => 'fan', 'FvH4_2g23980' => 'fve', 'FvH4_4g14380' => 'fve', 'FvH4_4g14390' => 'fve', 'FvH4_6g09250' => 'fve', 'Glyma.03G151100' => 'gma', 'Glyma.04G122550' => 'gma', 'Glyma.05G001600' => 'gma', 'Glyma.09G270766' => 'gma', 'Glyma.09G270832' => 'gma', 'Glyma.13G209800' => 'gma', 'Glyma.15G102800' => 'gma', 'Glyma.18G218900' => 'gma', 'Glyma.19G001500' => 'gma', 'Glyma.19G153600' => 'gma', 'Gohir.A02G028600' => 'ghi', 'Gohir.A08G045000' => 'ghi', 'Gohir.A11G120500' => 'ghi', 'Gohir.A12G006200' => 'ghi', 'Gohir.A12G006250' => 'ghi', 'Gohir.D02G036300' => 'ghi', 'Gohir.D08G054700' => 'ghi', 'Gohir.D11G125600' => 'ghi', 'Gohir.D12G005700' => 'ghi', 'Gorai.004G055200' => 'gra', 'Gorai.005G040400' => 'gra', 'Gorai.007G134500' => 'gra', 'Gorai.008G005500' => 'gra', 'GSVIVG01011094001' => 'vvi', 'GSVIVG01017879001' => 'vvi', 'GSVIVG01025988001' => 'vvi', 'GSVIVG01029847001' => 'vvi', 'HanXRQChr10g0282901' => 'han', 'HanXRQChr10g0310371' => 'han', 'HanXRQChr10g0315041' => 'han', 'HanXRQChr11g0327651' => 'han', 'HanXRQChr12g0359391' => 'han', 'Haze_00972' => 'cav', 'Haze_00973' => 'cav', 'Haze_00974' => 'cav', 'Haze_04747' => 'cav', 'Haze_04749' => 'cav', 'Haze_04750' => 'cav', 'Haze_21217' => 'cav', 'Hma1.2p1_1037F.1_g250680' => 'hma', 'Hma1.2p1_1644F.1_g295320' => 'hma', 'HPP92_011322' => 'vpl', 'HPP92_011323' => 'vpl', 'HPP92_011324' => 'vpl', 'HPP92_011325' => 'vpl', 'HPP92_011326' => 'vpl', 'Hund12205' => 'sun', 'Hund17957' => 'sun', 'Lalb_Chr06g0176771' => 'lal', 'Lalb_Chr18g0056021' => 'lal', 'Lalb_Chr18g0056031' => 'lal', 'Lalb_Chr18g0056041' => 'lal', 'Lalb_Chr20g0107751' => 'lal', 'Lalb_Chr20g0118371' => 'lal', 'Lj1g0010239' => 'lja', 'Lj1g0017101' => 'lja', 'Lj2A1178G40' => 'lonja', 'Lj2A54G84' => 'lonja', 'Lj2g0015248' => 'lja', 'Lj3A761T51' => 'lonja', 'Lj6g0018116' => 'lja', 'Lsat_1_v5_gn_4_136040' => 'lsa', 'Lsat_1_v5_gn_5_187461' => 'lsa', 'Lsat_1_v5_gn_5_77001' => 'lsa', 'Lsat_1_v5_gn_9_4461' => 'lsa', 'Manes.01G210100' => 'mes', 'Manes.03G185600' => 'mes', 'Manes.05G073300' => 'mes', 'Manes.09G120300' => 'mes', 'Manes.15G022100' => 'mes', 'Mapoly0096s0053' => 'mpo', 'MBI03_g14058_MAGBIO' => 'mbi', 'MBI03_g33876_MAGBIO' => 'mbi', 'MBI03_g36854_MAGBIO' => 'mbi', 'MBI17_g11997_MAGBIO' => 'mbi', 'MD03G1269000' => 'mdo', 'MD04G1179600' => 'mdo', 'MD11G1289800' => 'mdo', 'MD12G1194700' => 'mdo', 'MD13G1182100' => 'mdo', 'MD13G1182200' => 'mdo', 'MD16G1182600' => 'mdo', 'Medtr2g021400' => 'mtr', 'Medtr2g021470' => 'mtr', 'Medtr2g105810' => 'mtr', 'Medtr3g033580' => 'mtr', 'Medtr6g007970' => 'mtr', 'Medtr7g056330' => 'mtr', 'Medtr7g074290' => 'mtr', 'Medtr7g074380' => 'mtr', 'Medtr7g094550' => 'mtr', 'Medtr8g069995' => 'mtr', 'MELO3C014345.2' => 'cme', 'MELO3C021395.2' => 'cme', 'Migut.D00262' => 'egut', 'Migut.G00257' => 'egut', 'MSTRG.21575' => 'ama', 'MSTRG.3985' => 'ama', 'Nitab4.5_0000295g0140' => 'nta', 'Nitab4.5_0000732g0140' => 'nta', 'Nitab4.5_0003162g0020' => 'nta', 'Nitab4.5_0006180g0090' => 'nta', 'Nitab4.5_0006390g0010' => 'nta', 'Nitab4.5_0007392g0040' => 'nta', 'Nn1g02140' => 'nnu', 'Nn4g26168' => 'nnu', 'Nn5g26754' => 'nnu', 'Oeu001433.1' => 'oeu', 'Oeu010299.2' => 'oeu', 'Oeu011171.1' => 'oeu', 'Oeu037675.1' => 'oeu', 'Oeu038359.1' => 'oeu', 'Oeu063834.1' => 'oeu', 'Oeu063835.1' => 'oeu', 'Os05g0312000' => 'osa', 'Os07g0211101' => 'osa', 'Os07g0211200' => 'osa', 'Os07g0681500' => 'osa', 'Peaxi162Scf00095g01015' => 'pax', 'Peaxi162Scf00104g00329' => 'pax', 'Peaxi162Scf00161g00137' => 'pax', 'PGR004G1665' => 'pgr', 'PGR031G2937' => 'pgr', 'PGR119G2145' => 'pgr', 'PGSC0003DMG400004351' => 'stu', 'PGSC0003DMG400014625' => 'stu', 'PGSC0003DMG401000943' => 'stu', 'Phvul.001G148600' => 'pvu', 'Phvul.004G001700' => 'pvu', 'Phvul.006G154900' => 'pvu', 'Phvul.008G078200' => 'pvu', 'Phvul.011G136500' => 'pvu', 'Potri.002G215600' => 'ptr', 'Potri.008G201600' => 'ptr', 'Potri.014G138400' => 'ptr', 'Potri.016G142500' => 'ptr', 'Pp3c16_10580' => 'ppa', 'Pp3c5_25280' => 'ppa', 'Prupe.1G150000' => 'ppe', 'Prupe.1G150100' => 'ppe', 'Prupe.6G299600' => 'ppe', 'Prupe.8G245000' => 'ppe', 'Psat0s4927g0040' => 'psa', 'Psat1g052080' => 'psa', 'Psat1g183800' => 'psa', 'Psat3g113840' => 'psa', 'Psat3g126120' => 'psa', 'Psat3g126160' => 'psa', 'Psat3g158760' => 'psa', 'Psat3g158840' => 'psa', 'PSO170G2858' => 'pso', 'PSO339G0606' => 'pso', 'PSO384G4709' => 'pso', 'PSO407G0334' => 'pso', 'QL04p040276' => 'qlo', 'QL06p005458' => 'qlo', 'QL06p005472' => 'qlo', 'QL07p030546' => 'qlo', 'QL07p031519' => 'qlo', 'QL09p050949' => 'qlo', 'QL09p050966' => 'qlo', 'QL09p051067' => 'qlo', 'QL12p022706' => 'qlo', 'RcHm_v2.0_Chr2g0119601' => 'rch', 'RcHm_v2.0_Chr3g0459591' => 'rch', 'RcHm_v2.0_Chr4g0418521' => 'rch', 'RcHm_v2.0_Chr4g0418531' => 'rch', 'RcHm_v2.0_Chr4g0418541' => 'rch', 'RcHm_v2.0_Chr6g0291641' => 'rch', 'Rhsim01G0086300' => 'rsi', 'Rhsim01G0276300' => 'rsi', 'Rhsim01G0276500' => 'rsi', 'Rhsim04G0207700' => 'rsi', 'Rhsim05G0234500' => 'rsi', 'Rhsim13G0022400' => 'rsi', 'Sabra02G0167900' => 'sbr', 'Sabra04G0158500' => 'sbr', 'Sabra08G0159800' => 'sbr', 'Sabra10G0011500' => 'sbr', 'Sabra14G0104400' => 'sbr', 'SalBow2G2440' => 'sbo', 'SalBow4G2265' => 'sbo', 'Sc02g0000060' => 'sci', 'Sc05g0005020' => 'sci', 'Sc13g0003890' => 'sci', 'Sed0014865' => 'sed', 'Sed0017224' => 'sed', 'Sed0026391' => 'sed', 'SEGI_00063' => 'sgi', 'SEGI_10967' => 'sgi', 'SEGI_17510' => 'sgi', 'SEGI_24396' => 'sgi', 'SEGI_39719' => 'sgi', 'SEGI_41392' => 'sgi', 'SGA_v2.0_scaffold11G05794' => 'sas', 'SGA_v2.0_scaffold142G35607' => 'sas', 'SGA_v2.0_scaffold1G00447' => 'sas', 'SHI15388' => 'shi', 'SHI15394' => 'shi', 'SHI15396' => 'shi', 'SHI15399' => 'shi', 'SMO343G0151' => 'smo', 'SMO367G1118' => 'smo', 'Solyc01g080200.3' => 'sly', 'Solyc06g008960.3' => 'sly', 'Solyc09g064780.3' => 'sly', 'Sopen01g031980' => 'spe', 'Sopen06g003710' => 'spe', 'Sopen09g026460' => 'spe', 'Sp3g21240' => 'spa', 'Sp4g30030' => 'spa', 'TAR365G0022' => 'tar', 'TAR365G1023' => 'tar', 'TAR365G1253' => 'tar', 'TAR623G0078' => 'tar', 'TAR623G1721' => 'tar', 'TAR633G0959' => 'tar', 'THA.LOC104802225' => 'tha', 'THA.LOC104804769' => 'tha', 'THA.LOC104808660' => 'tha', 'THA.LOC104812792' => 'tha', 'Thecc.01G284000' => 'tca', 'Thecc.04G220600' => 'tca', 'Thecc.05G268900' => 'tca', 'Thecc.08G171100' => 'tca', 'Thhalv10001284m.g' => 'esa', 'Thhalv10019912m.g' => 'esa', 'TPR.G14189' => 'tpr', 'TPR.G18110' => 'tpr', 'TPR.G18130' => 'tpr', 'TPR.G18131' => 'tpr', 'TPR.G18140' => 'tpr', 'TPR.G24282' => 'tpr', 'TPR.G25221' => 'tpr', 'TPR.G29267' => 'tpr', 'TPR.G35315' => 'tpr', 'TPR.G36173' => 'tpr', 'TWI09G0794' => 'twi', 'TWI59G1348' => 'twi', 'TWI74G0430' => 'twi', 'unitig_26.g8940' => 'ugi', 'unitig_749.g13744' => 'ugi', 'unitig_749.g13745' => 'ugi', 'vmacro08269' => 'vma', 'vmacro14937' => 'vma', 'vmacro20401' => 'vma', 'VMungo0464G1349' => 'vmu', 'VMungo0540G0289' => 'vmu', 'VMungo1215G1590' => 'vmu', 'VMungo1309G0221' => 'vmu', 'VMungo1309G2815' => 'vmu', 'VMungo1383G0239' => 'vmu', 'VMungo1383G2910' => 'vmu', 'Zm00001eb095270' => 'zma', 'Zm00001eb095280' => 'zma', 'Zm00001eb111630' => 'zma', 'Zm00001eb237080' => 'zma', 'Zm00001eb273740' => 'zma', 'Zm00001eb285040' => 'zma', 'Zm00001eb330790' => 'zma', 'Zm00001eb337380' => 'zma' ) $gf_id = 'HOM05D001484' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001484' ) $data_identifier = 'HOM05D001484' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 2, 'aly' => (int) 2, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 22, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 7, 'hma' => (int) 2, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 7, 'mtr' => (int) 10, 'cme' => (int) 2, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 4, 'ppa' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 4, 'qlo' => (int) 9, 'rch' => (int) 6, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 10, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 7, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb337380' $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' => 'HOM05D001484', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p31500' => 'bna', 'A05p00020' => 'bna', 'A07p08820' => 'bna', 'Aa31LG4G3300' => 'aar', 'Aa31LG8G10030' => 'aar', 'Actinidia00731' => 'ach', 'Actinidia11473' => 'ach', 'Actinidia23469' => 'ach', 'Actinidia24318' => 'ach', 'Actinidia40196' => 'ach', 'Actinidia40197' => 'ach', 'Actinidia40198' => 'ach', 'Ah.08g212990' => 'amhyb', 'Ah.15g091720' => 'amhyb', 'AL3G38260' => 'aly', 'AL4G47710' => 'aly', 'Aqoxy2G00671' => 'aox', 'Aqoxy2G03236' => 'aox', 'arahy.Tifrunner.gnm1.ann1.05IDCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KR684' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATY3SJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK6QJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6APGL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IDT7Z9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM073U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ0R87' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LE7RV4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT4QRX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V5ENPK' => 'arhy', 'AT2G48110' => 'ath', 'AT3G23590' => 'ath', 'ATR0626G186' => 'atr', 'ATR1127G141' => 'atr', 'Atru.chr4.2583' => 'acertr', 'Atru.chr5.1358' => 'acertr', 'Atru.chr5.1359' => 'acertr', 'Atru.chr8.46' => 'acertr', 'AUR62002640' => 'cqu', 'AUR62030055' => 'cqu', 'AUR62033713' => 'cqu', 'AUR62033714' => 'cqu', 'AUR62036795' => 'cqu', 'AUR62039891' => 'cqu', 'BcaB02g08737' => 'bca', 'BcaB04g20441' => 'bca', 'BcaB06g26509' => 'bca', 'BcaB06g26510' => 'bca', 'BcaB06g26511' => 'bca', 'BcaB06g26512' => 'bca', 'BcaB06g26513' => 'bca', 'BcaC02g12564' => 'bca', 'BcaC02g12565' => 'bca', 'BcaC02g12794' => 'bca', 'BcaC02g12795' => 'bca', 'BcaC02g12796' => 'bca', 'BcaC06g35541' => 'bca', 'BNapus_Darmor_BZH_scaffold_188p00080' => 'bna', 'BNapus_Darmor_BZH_scaffold_188p00090' => 'bna', 'BolC1t03972H' => 'bol', 'BolC1t03973H' => 'bol', 'BolC4t21680H' => 'bol', 'BolC7t41863H' => 'bol', 'BolSC55t61227H' => 'bol', 'BolSC55t61228H' => 'bol', 'BraA01t03278Z' => 'bra', 'BraA05t18998Z' => 'bra', 'BraA07t28673Z' => 'bra', 'C01p40150' => 'bna', 'C05p12370' => 'bna', 'C07p13680' => 'bna', 'CAN.G1006.16' => 'can', 'CAN.G1006.17' => 'can', 'CAN.G1170.2' => 'can', 'CAN.G962.7' => 'can', 'CANSAT25G2179' => 'cansat', 'CANSAT78G1573' => 'cansat', 'CARHR099510' => 'chi', 'CARHR143510' => 'chi', 'Carub.0003s2380' => 'cru', 'Carub.0004s3082' => 'cru', 'Ca_00614_v3' => 'car', 'Ca_07801_v3' => 'car', 'Ca_08567_v3' => 'car', 'Ca_09571_v3' => 'car', 'CBR_g19290' => 'cbr', 'Cc01_g19770' => 'ccan', 'Cc03_g03030' => 'ccan', 'CDE07G0968' => 'cde', 'CDE09G1441' => 'cde', 'Cfa006103' => 'cfa', 'Cfa015573' => 'cfa', 'Cfa016988' => 'cfa', 'Ciclev10006738m.g' => 'ccl', 'Ciclev10010920m.g' => 'ccl', 'Ciclev10018517m.g' => 'ccl', 'CiPaw.01G159200' => 'cil', 'CiPaw.02G091000' => 'cil', 'CiPaw.02G091100' => 'cil', 'CiPaw.08G103100' => 'cil', 'CiPaw.09G224900' => 'cil', 'ClCG06G005740' => 'cla', 'ClCG07G000090' => 'cla', 'ClCG07G000100' => 'cla', 'COL.COLO4_09143' => 'col', 'COL.COLO4_25124' => 'col', 'Cpa.g.sc16.34' => 'cpa', 'Cpa.g.sc3504.1' => 'cpa', 'Cpa.g.sc60.37' => 'cpa', 'CsaV3_6G018520' => 'csa', 'CsaV3_6G036860' => 'csa', 'CSS0001072' => 'camsi', 'CSS0020208' => 'camsi', 'CSS0021253' => 'camsi', 'CSS0022190' => 'camsi', 'CSS0036150' => 'camsi', 'CSS0040442' => 'camsi', 'CSS0042300' => 'camsi', 'CSS0045298' => 'camsi', 'DCAR_012449' => 'dca', 'DCAR_018405' => 'dca', 'DCAR_024573' => 'dca', 'DCAR_030591' => 'dca', 'Dinv16926' => 'din', 'Dinv32963' => 'din', 'Dinv38382' => 'din', 'Dinv38383' => 'din', 'Duzib133G0974' => 'dzi', 'Duzib138G1867' => 'dzi', 'Duzib211G0420' => 'dzi', 'Duzib212G0930' => 'dzi', 'ECA234G1645' => 'eca', 'ECA247G3467' => 'eca', 'ECA248G1703' => 'eca', 'EL10Ac3g06327' => 'bvu', 'EL10Ac7g17204' => 'bvu', 'Eucgr.A00855' => 'egr', 'Eucgr.A00858' => 'egr', 'Eucgr.H01520' => 'egr', 'Eucgr.H03604' => 'egr', 'Eucgr.L03465' => 'egr', 'Eucgr.L03466' => 'egr', 'FAN01G0988' => 'fan', 'FAN02G3892' => 'fan', 'FAN05G3381' => 'fan', 'FAN07G0967' => 'fan', 'FAN07G1493' => 'fan', 'FAN08G3125' => 'fan', 'FAN09G0402' => 'fan', 'FAN12G2594' => 'fan', 'FAN12G3879' => 'fan', 'FAN14G1546' => 'fan', 'FAN15G3626' => 'fan', 'FAN17G0588' => 'fan', 'FAN17G0609' => 'fan', 'FAN18G2817' => 'fan', 'FAN19G1305' => 'fan', 'FAN20G1787' => 'fan', 'FAN22G0073' => 'fan', 'FAN22G0352' => 'fan', 'FAN22G0368' => 'fan', 'FAN22G2273' => 'fan', 'FAN24G1998' => 'fan', 'FAN27G1317' => 'fan', 'FvH4_2g23980' => 'fve', 'FvH4_4g14380' => 'fve', 'FvH4_4g14390' => 'fve', 'FvH4_6g09250' => 'fve', 'Glyma.03G151100' => 'gma', 'Glyma.04G122550' => 'gma', 'Glyma.05G001600' => 'gma', 'Glyma.09G270766' => 'gma', 'Glyma.09G270832' => 'gma', 'Glyma.13G209800' => 'gma', 'Glyma.15G102800' => 'gma', 'Glyma.18G218900' => 'gma', 'Glyma.19G001500' => 'gma', 'Glyma.19G153600' => 'gma', 'Gohir.A02G028600' => 'ghi', 'Gohir.A08G045000' => 'ghi', 'Gohir.A11G120500' => 'ghi', 'Gohir.A12G006200' => 'ghi', 'Gohir.A12G006250' => 'ghi', 'Gohir.D02G036300' => 'ghi', 'Gohir.D08G054700' => 'ghi', 'Gohir.D11G125600' => 'ghi', 'Gohir.D12G005700' => 'ghi', 'Gorai.004G055200' => 'gra', 'Gorai.005G040400' => 'gra', 'Gorai.007G134500' => 'gra', 'Gorai.008G005500' => 'gra', 'GSVIVG01011094001' => 'vvi', 'GSVIVG01017879001' => 'vvi', 'GSVIVG01025988001' => 'vvi', 'GSVIVG01029847001' => 'vvi', 'HanXRQChr10g0282901' => 'han', 'HanXRQChr10g0310371' => 'han', 'HanXRQChr10g0315041' => 'han', 'HanXRQChr11g0327651' => 'han', 'HanXRQChr12g0359391' => 'han', 'Haze_00972' => 'cav', 'Haze_00973' => 'cav', 'Haze_00974' => 'cav', 'Haze_04747' => 'cav', 'Haze_04749' => 'cav', 'Haze_04750' => 'cav', 'Haze_21217' => 'cav', 'Hma1.2p1_1037F.1_g250680' => 'hma', 'Hma1.2p1_1644F.1_g295320' => 'hma', 'HPP92_011322' => 'vpl', 'HPP92_011323' => 'vpl', 'HPP92_011324' => 'vpl', 'HPP92_011325' => 'vpl', 'HPP92_011326' => 'vpl', 'Hund12205' => 'sun', 'Hund17957' => 'sun', 'Lalb_Chr06g0176771' => 'lal', 'Lalb_Chr18g0056021' => 'lal', 'Lalb_Chr18g0056031' => 'lal', 'Lalb_Chr18g0056041' => 'lal', 'Lalb_Chr20g0107751' => 'lal', 'Lalb_Chr20g0118371' => 'lal', 'Lj1g0010239' => 'lja', 'Lj1g0017101' => 'lja', 'Lj2A1178G40' => 'lonja', 'Lj2A54G84' => 'lonja', 'Lj2g0015248' => 'lja', 'Lj3A761T51' => 'lonja', 'Lj6g0018116' => 'lja', 'Lsat_1_v5_gn_4_136040' => 'lsa', 'Lsat_1_v5_gn_5_187461' => 'lsa', 'Lsat_1_v5_gn_5_77001' => 'lsa', 'Lsat_1_v5_gn_9_4461' => 'lsa', 'Manes.01G210100' => 'mes', 'Manes.03G185600' => 'mes', 'Manes.05G073300' => 'mes', 'Manes.09G120300' => 'mes', 'Manes.15G022100' => 'mes', 'Mapoly0096s0053' => 'mpo', 'MBI03_g14058_MAGBIO' => 'mbi', 'MBI03_g33876_MAGBIO' => 'mbi', 'MBI03_g36854_MAGBIO' => 'mbi', 'MBI17_g11997_MAGBIO' => 'mbi', 'MD03G1269000' => 'mdo', 'MD04G1179600' => 'mdo', 'MD11G1289800' => 'mdo', 'MD12G1194700' => 'mdo', 'MD13G1182100' => 'mdo', 'MD13G1182200' => 'mdo', 'MD16G1182600' => 'mdo', 'Medtr2g021400' => 'mtr', 'Medtr2g021470' => 'mtr', 'Medtr2g105810' => 'mtr', 'Medtr3g033580' => 'mtr', 'Medtr6g007970' => 'mtr', 'Medtr7g056330' => 'mtr', 'Medtr7g074290' => 'mtr', 'Medtr7g074380' => 'mtr', 'Medtr7g094550' => 'mtr', 'Medtr8g069995' => 'mtr', 'MELO3C014345.2' => 'cme', 'MELO3C021395.2' => 'cme', 'Migut.D00262' => 'egut', 'Migut.G00257' => 'egut', 'MSTRG.21575' => 'ama', 'MSTRG.3985' => 'ama', 'Nitab4.5_0000295g0140' => 'nta', 'Nitab4.5_0000732g0140' => 'nta', 'Nitab4.5_0003162g0020' => 'nta', 'Nitab4.5_0006180g0090' => 'nta', 'Nitab4.5_0006390g0010' => 'nta', 'Nitab4.5_0007392g0040' => 'nta', 'Nn1g02140' => 'nnu', 'Nn4g26168' => 'nnu', 'Nn5g26754' => 'nnu', 'Oeu001433.1' => 'oeu', 'Oeu010299.2' => 'oeu', 'Oeu011171.1' => 'oeu', 'Oeu037675.1' => 'oeu', 'Oeu038359.1' => 'oeu', 'Oeu063834.1' => 'oeu', 'Oeu063835.1' => 'oeu', 'Os05g0312000' => 'osa', 'Os07g0211101' => 'osa', 'Os07g0211200' => 'osa', 'Os07g0681500' => 'osa', 'Peaxi162Scf00095g01015' => 'pax', 'Peaxi162Scf00104g00329' => 'pax', 'Peaxi162Scf00161g00137' => 'pax', 'PGR004G1665' => 'pgr', 'PGR031G2937' => 'pgr', 'PGR119G2145' => 'pgr', 'PGSC0003DMG400004351' => 'stu', 'PGSC0003DMG400014625' => 'stu', 'PGSC0003DMG401000943' => 'stu', 'Phvul.001G148600' => 'pvu', 'Phvul.004G001700' => 'pvu', 'Phvul.006G154900' => 'pvu', 'Phvul.008G078200' => 'pvu', 'Phvul.011G136500' => 'pvu', 'Potri.002G215600' => 'ptr', 'Potri.008G201600' => 'ptr', 'Potri.014G138400' => 'ptr', 'Potri.016G142500' => 'ptr', 'Pp3c16_10580' => 'ppa', 'Pp3c5_25280' => 'ppa', 'Prupe.1G150000' => 'ppe', 'Prupe.1G150100' => 'ppe', 'Prupe.6G299600' => 'ppe', 'Prupe.8G245000' => 'ppe', 'Psat0s4927g0040' => 'psa', 'Psat1g052080' => 'psa', 'Psat1g183800' => 'psa', 'Psat3g113840' => 'psa', 'Psat3g126120' => 'psa', 'Psat3g126160' => 'psa', 'Psat3g158760' => 'psa', 'Psat3g158840' => 'psa', 'PSO170G2858' => 'pso', 'PSO339G0606' => 'pso', 'PSO384G4709' => 'pso', 'PSO407G0334' => 'pso', 'QL04p040276' => 'qlo', 'QL06p005458' => 'qlo', 'QL06p005472' => 'qlo', 'QL07p030546' => 'qlo', 'QL07p031519' => 'qlo', 'QL09p050949' => 'qlo', 'QL09p050966' => 'qlo', 'QL09p051067' => 'qlo', 'QL12p022706' => 'qlo', 'RcHm_v2.0_Chr2g0119601' => 'rch', 'RcHm_v2.0_Chr3g0459591' => 'rch', 'RcHm_v2.0_Chr4g0418521' => 'rch', 'RcHm_v2.0_Chr4g0418531' => 'rch', 'RcHm_v2.0_Chr4g0418541' => 'rch', 'RcHm_v2.0_Chr6g0291641' => 'rch', 'Rhsim01G0086300' => 'rsi', 'Rhsim01G0276300' => 'rsi', 'Rhsim01G0276500' => 'rsi', 'Rhsim04G0207700' => 'rsi', 'Rhsim05G0234500' => 'rsi', 'Rhsim13G0022400' => 'rsi', 'Sabra02G0167900' => 'sbr', 'Sabra04G0158500' => 'sbr', 'Sabra08G0159800' => 'sbr', 'Sabra10G0011500' => 'sbr', 'Sabra14G0104400' => 'sbr', 'SalBow2G2440' => 'sbo', 'SalBow4G2265' => 'sbo', 'Sc02g0000060' => 'sci', 'Sc05g0005020' => 'sci', 'Sc13g0003890' => 'sci', 'Sed0014865' => 'sed', 'Sed0017224' => 'sed', 'Sed0026391' => 'sed', 'SEGI_00063' => 'sgi', 'SEGI_10967' => 'sgi', 'SEGI_17510' => 'sgi', 'SEGI_24396' => 'sgi', 'SEGI_39719' => 'sgi', 'SEGI_41392' => 'sgi', 'SGA_v2.0_scaffold11G05794' => 'sas', 'SGA_v2.0_scaffold142G35607' => 'sas', 'SGA_v2.0_scaffold1G00447' => 'sas', 'SHI15388' => 'shi', 'SHI15394' => 'shi', 'SHI15396' => 'shi', 'SHI15399' => 'shi', 'SMO343G0151' => 'smo', 'SMO367G1118' => 'smo', 'Solyc01g080200.3' => 'sly', 'Solyc06g008960.3' => 'sly', 'Solyc09g064780.3' => 'sly', 'Sopen01g031980' => 'spe', 'Sopen06g003710' => 'spe', 'Sopen09g026460' => 'spe', 'Sp3g21240' => 'spa', 'Sp4g30030' => 'spa', 'TAR365G0022' => 'tar', 'TAR365G1023' => 'tar', 'TAR365G1253' => 'tar', 'TAR623G0078' => 'tar', 'TAR623G1721' => 'tar', 'TAR633G0959' => 'tar', 'THA.LOC104802225' => 'tha', 'THA.LOC104804769' => 'tha', 'THA.LOC104808660' => 'tha', 'THA.LOC104812792' => 'tha', 'Thecc.01G284000' => 'tca', 'Thecc.04G220600' => 'tca', 'Thecc.05G268900' => 'tca', 'Thecc.08G171100' => 'tca', 'Thhalv10001284m.g' => 'esa', 'Thhalv10019912m.g' => 'esa', 'TPR.G14189' => 'tpr', 'TPR.G18110' => 'tpr', 'TPR.G18130' => 'tpr', 'TPR.G18131' => 'tpr', 'TPR.G18140' => 'tpr', 'TPR.G24282' => 'tpr', 'TPR.G25221' => 'tpr', 'TPR.G29267' => 'tpr', 'TPR.G35315' => 'tpr', 'TPR.G36173' => 'tpr', 'TWI09G0794' => 'twi', 'TWI59G1348' => 'twi', 'TWI74G0430' => 'twi', 'unitig_26.g8940' => 'ugi', 'unitig_749.g13744' => 'ugi', 'unitig_749.g13745' => 'ugi', 'vmacro08269' => 'vma', 'vmacro14937' => 'vma', 'vmacro20401' => 'vma', 'VMungo0464G1349' => 'vmu', 'VMungo0540G0289' => 'vmu', 'VMungo1215G1590' => 'vmu', 'VMungo1309G0221' => 'vmu', 'VMungo1309G2815' => 'vmu', 'VMungo1383G0239' => 'vmu', 'VMungo1383G2910' => 'vmu', 'Zm00001eb095270' => 'zma', 'Zm00001eb095280' => 'zma', 'Zm00001eb111630' => 'zma', 'Zm00001eb237080' => 'zma', 'Zm00001eb273740' => 'zma', 'Zm00001eb285040' => 'zma', 'Zm00001eb330790' => 'zma', 'Zm00001eb337380' => 'zma' ), 'gf_id' => 'HOM05D001484', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001484' ), 'data_identifier' => 'HOM05D001484', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001484', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p31500' => 'bna', 'A05p00020' => 'bna', 'A07p08820' => 'bna', 'Aa31LG4G3300' => 'aar', 'Aa31LG8G10030' => 'aar', 'Actinidia00731' => 'ach', 'Actinidia11473' => 'ach', 'Actinidia23469' => 'ach', 'Actinidia24318' => 'ach', 'Actinidia40196' => 'ach', 'Actinidia40197' => 'ach', 'Actinidia40198' => 'ach', 'Ah.08g212990' => 'amhyb', 'Ah.15g091720' => 'amhyb', 'AL3G38260' => 'aly', 'AL4G47710' => 'aly', 'Aqoxy2G00671' => 'aox', 'Aqoxy2G03236' => 'aox', 'arahy.Tifrunner.gnm1.ann1.05IDCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KR684' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATY3SJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK6QJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6APGL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IDT7Z9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM073U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ0R87' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LE7RV4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT4QRX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V5ENPK' => 'arhy', 'AT2G48110' => 'ath', 'AT3G23590' => 'ath', 'ATR0626G186' => 'atr', 'ATR1127G141' => 'atr', 'Atru.chr4.2583' => 'acertr', 'Atru.chr5.1358' => 'acertr', 'Atru.chr5.1359' => 'acertr', 'Atru.chr8.46' => 'acertr', 'AUR62002640' => 'cqu', 'AUR62030055' => 'cqu', 'AUR62033713' => 'cqu', 'AUR62033714' => 'cqu', 'AUR62036795' => 'cqu', 'AUR62039891' => 'cqu', 'BcaB02g08737' => 'bca', 'BcaB04g20441' => 'bca', 'BcaB06g26509' => 'bca', 'BcaB06g26510' => 'bca', 'BcaB06g26511' => 'bca', 'BcaB06g26512' => 'bca', 'BcaB06g26513' => 'bca', 'BcaC02g12564' => 'bca', 'BcaC02g12565' => 'bca', 'BcaC02g12794' => 'bca', 'BcaC02g12795' => 'bca', 'BcaC02g12796' => 'bca', 'BcaC06g35541' => 'bca', 'BNapus_Darmor_BZH_scaffold_188p00080' => 'bna', 'BNapus_Darmor_BZH_scaffold_188p00090' => 'bna', 'BolC1t03972H' => 'bol', 'BolC1t03973H' => 'bol', 'BolC4t21680H' => 'bol', 'BolC7t41863H' => 'bol', 'BolSC55t61227H' => 'bol', 'BolSC55t61228H' => 'bol', 'BraA01t03278Z' => 'bra', 'BraA05t18998Z' => 'bra', 'BraA07t28673Z' => 'bra', 'C01p40150' => 'bna', 'C05p12370' => 'bna', 'C07p13680' => 'bna', 'CAN.G1006.16' => 'can', 'CAN.G1006.17' => 'can', 'CAN.G1170.2' => 'can', 'CAN.G962.7' => 'can', 'CANSAT25G2179' => 'cansat', 'CANSAT78G1573' => 'cansat', 'CARHR099510' => 'chi', 'CARHR143510' => 'chi', 'Carub.0003s2380' => 'cru', 'Carub.0004s3082' => 'cru', 'Ca_00614_v3' => 'car', 'Ca_07801_v3' => 'car', 'Ca_08567_v3' => 'car', 'Ca_09571_v3' => 'car', 'CBR_g19290' => 'cbr', 'Cc01_g19770' => 'ccan', 'Cc03_g03030' => 'ccan', 'CDE07G0968' => 'cde', 'CDE09G1441' => 'cde', 'Cfa006103' => 'cfa', 'Cfa015573' => 'cfa', 'Cfa016988' => 'cfa', 'Ciclev10006738m.g' => 'ccl', 'Ciclev10010920m.g' => 'ccl', 'Ciclev10018517m.g' => 'ccl', 'CiPaw.01G159200' => 'cil', 'CiPaw.02G091000' => 'cil', 'CiPaw.02G091100' => 'cil', 'CiPaw.08G103100' => 'cil', 'CiPaw.09G224900' => 'cil', 'ClCG06G005740' => 'cla', 'ClCG07G000090' => 'cla', 'ClCG07G000100' => 'cla', 'COL.COLO4_09143' => 'col', 'COL.COLO4_25124' => 'col', 'Cpa.g.sc16.34' => 'cpa', 'Cpa.g.sc3504.1' => 'cpa', 'Cpa.g.sc60.37' => 'cpa', 'CsaV3_6G018520' => 'csa', 'CsaV3_6G036860' => 'csa', 'CSS0001072' => 'camsi', 'CSS0020208' => 'camsi', 'CSS0021253' => 'camsi', 'CSS0022190' => 'camsi', 'CSS0036150' => 'camsi', 'CSS0040442' => 'camsi', 'CSS0042300' => 'camsi', 'CSS0045298' => 'camsi', 'DCAR_012449' => 'dca', 'DCAR_018405' => 'dca', 'DCAR_024573' => 'dca', 'DCAR_030591' => 'dca', 'Dinv16926' => 'din', 'Dinv32963' => 'din', 'Dinv38382' => 'din', 'Dinv38383' => 'din', 'Duzib133G0974' => 'dzi', 'Duzib138G1867' => 'dzi', 'Duzib211G0420' => 'dzi', 'Duzib212G0930' => 'dzi', 'ECA234G1645' => 'eca', 'ECA247G3467' => 'eca', 'ECA248G1703' => 'eca', 'EL10Ac3g06327' => 'bvu', 'EL10Ac7g17204' => 'bvu', 'Eucgr.A00855' => 'egr', 'Eucgr.A00858' => 'egr', 'Eucgr.H01520' => 'egr', 'Eucgr.H03604' => 'egr', 'Eucgr.L03465' => 'egr', 'Eucgr.L03466' => 'egr', 'FAN01G0988' => 'fan', 'FAN02G3892' => 'fan', 'FAN05G3381' => 'fan', 'FAN07G0967' => 'fan', 'FAN07G1493' => 'fan', 'FAN08G3125' => 'fan', 'FAN09G0402' => 'fan', 'FAN12G2594' => 'fan', 'FAN12G3879' => 'fan', 'FAN14G1546' => 'fan', 'FAN15G3626' => 'fan', 'FAN17G0588' => 'fan', 'FAN17G0609' => 'fan', 'FAN18G2817' => 'fan', 'FAN19G1305' => 'fan', 'FAN20G1787' => 'fan', 'FAN22G0073' => 'fan', 'FAN22G0352' => 'fan', 'FAN22G0368' => 'fan', 'FAN22G2273' => 'fan', 'FAN24G1998' => 'fan', 'FAN27G1317' => 'fan', 'FvH4_2g23980' => 'fve', 'FvH4_4g14380' => 'fve', 'FvH4_4g14390' => 'fve', 'FvH4_6g09250' => 'fve', 'Glyma.03G151100' => 'gma', 'Glyma.04G122550' => 'gma', 'Glyma.05G001600' => 'gma', 'Glyma.09G270766' => 'gma', 'Glyma.09G270832' => 'gma', 'Glyma.13G209800' => 'gma', 'Glyma.15G102800' => 'gma', 'Glyma.18G218900' => 'gma', 'Glyma.19G001500' => 'gma', 'Glyma.19G153600' => 'gma', 'Gohir.A02G028600' => 'ghi', 'Gohir.A08G045000' => 'ghi', 'Gohir.A11G120500' => 'ghi', 'Gohir.A12G006200' => 'ghi', 'Gohir.A12G006250' => 'ghi', 'Gohir.D02G036300' => 'ghi', 'Gohir.D08G054700' => 'ghi', 'Gohir.D11G125600' => 'ghi', 'Gohir.D12G005700' => 'ghi', 'Gorai.004G055200' => 'gra', 'Gorai.005G040400' => 'gra', 'Gorai.007G134500' => 'gra', 'Gorai.008G005500' => 'gra', 'GSVIVG01011094001' => 'vvi', 'GSVIVG01017879001' => 'vvi', 'GSVIVG01025988001' => 'vvi', 'GSVIVG01029847001' => 'vvi', 'HanXRQChr10g0282901' => 'han', 'HanXRQChr10g0310371' => 'han', 'HanXRQChr10g0315041' => 'han', 'HanXRQChr11g0327651' => 'han', 'HanXRQChr12g0359391' => 'han', 'Haze_00972' => 'cav', 'Haze_00973' => 'cav', 'Haze_00974' => 'cav', 'Haze_04747' => 'cav', 'Haze_04749' => 'cav', 'Haze_04750' => 'cav', 'Haze_21217' => 'cav', 'Hma1.2p1_1037F.1_g250680' => 'hma', 'Hma1.2p1_1644F.1_g295320' => 'hma', 'HPP92_011322' => 'vpl', 'HPP92_011323' => 'vpl', 'HPP92_011324' => 'vpl', 'HPP92_011325' => 'vpl', 'HPP92_011326' => 'vpl', 'Hund12205' => 'sun', 'Hund17957' => 'sun', 'Lalb_Chr06g0176771' => 'lal', 'Lalb_Chr18g0056021' => 'lal', 'Lalb_Chr18g0056031' => 'lal', 'Lalb_Chr18g0056041' => 'lal', 'Lalb_Chr20g0107751' => 'lal', 'Lalb_Chr20g0118371' => 'lal', 'Lj1g0010239' => 'lja', 'Lj1g0017101' => 'lja', 'Lj2A1178G40' => 'lonja', 'Lj2A54G84' => 'lonja', 'Lj2g0015248' => 'lja', 'Lj3A761T51' => 'lonja', 'Lj6g0018116' => 'lja', 'Lsat_1_v5_gn_4_136040' => 'lsa', 'Lsat_1_v5_gn_5_187461' => 'lsa', 'Lsat_1_v5_gn_5_77001' => 'lsa', 'Lsat_1_v5_gn_9_4461' => 'lsa', 'Manes.01G210100' => 'mes', 'Manes.03G185600' => 'mes', 'Manes.05G073300' => 'mes', 'Manes.09G120300' => 'mes', 'Manes.15G022100' => 'mes', 'Mapoly0096s0053' => 'mpo', 'MBI03_g14058_MAGBIO' => 'mbi', 'MBI03_g33876_MAGBIO' => 'mbi', 'MBI03_g36854_MAGBIO' => 'mbi', 'MBI17_g11997_MAGBIO' => 'mbi', 'MD03G1269000' => 'mdo', 'MD04G1179600' => 'mdo', 'MD11G1289800' => 'mdo', 'MD12G1194700' => 'mdo', 'MD13G1182100' => 'mdo', 'MD13G1182200' => 'mdo', 'MD16G1182600' => 'mdo', 'Medtr2g021400' => 'mtr', 'Medtr2g021470' => 'mtr', 'Medtr2g105810' => 'mtr', 'Medtr3g033580' => 'mtr', 'Medtr6g007970' => 'mtr', 'Medtr7g056330' => 'mtr', 'Medtr7g074290' => 'mtr', 'Medtr7g074380' => 'mtr', 'Medtr7g094550' => 'mtr', 'Medtr8g069995' => 'mtr', 'MELO3C014345.2' => 'cme', 'MELO3C021395.2' => 'cme', 'Migut.D00262' => 'egut', 'Migut.G00257' => 'egut', 'MSTRG.21575' => 'ama', 'MSTRG.3985' => 'ama', 'Nitab4.5_0000295g0140' => 'nta', 'Nitab4.5_0000732g0140' => 'nta', 'Nitab4.5_0003162g0020' => 'nta', 'Nitab4.5_0006180g0090' => 'nta', 'Nitab4.5_0006390g0010' => 'nta', 'Nitab4.5_0007392g0040' => 'nta', 'Nn1g02140' => 'nnu', 'Nn4g26168' => 'nnu', 'Nn5g26754' => 'nnu', 'Oeu001433.1' => 'oeu', 'Oeu010299.2' => 'oeu', 'Oeu011171.1' => 'oeu', 'Oeu037675.1' => 'oeu', 'Oeu038359.1' => 'oeu', 'Oeu063834.1' => 'oeu', 'Oeu063835.1' => 'oeu', 'Os05g0312000' => 'osa', 'Os07g0211101' => 'osa', 'Os07g0211200' => 'osa', 'Os07g0681500' => 'osa', 'Peaxi162Scf00095g01015' => 'pax', 'Peaxi162Scf00104g00329' => 'pax', 'Peaxi162Scf00161g00137' => 'pax', 'PGR004G1665' => 'pgr', 'PGR031G2937' => 'pgr', 'PGR119G2145' => 'pgr', 'PGSC0003DMG400004351' => 'stu', 'PGSC0003DMG400014625' => 'stu', 'PGSC0003DMG401000943' => 'stu', 'Phvul.001G148600' => 'pvu', 'Phvul.004G001700' => 'pvu', 'Phvul.006G154900' => 'pvu', 'Phvul.008G078200' => 'pvu', 'Phvul.011G136500' => 'pvu', 'Potri.002G215600' => 'ptr', 'Potri.008G201600' => 'ptr', 'Potri.014G138400' => 'ptr', 'Potri.016G142500' => 'ptr', 'Pp3c16_10580' => 'ppa', 'Pp3c5_25280' => 'ppa', 'Prupe.1G150000' => 'ppe', 'Prupe.1G150100' => 'ppe', 'Prupe.6G299600' => 'ppe', 'Prupe.8G245000' => 'ppe', 'Psat0s4927g0040' => 'psa', 'Psat1g052080' => 'psa', 'Psat1g183800' => 'psa', 'Psat3g113840' => 'psa', 'Psat3g126120' => 'psa', 'Psat3g126160' => 'psa', 'Psat3g158760' => 'psa', 'Psat3g158840' => 'psa', 'PSO170G2858' => 'pso', 'PSO339G0606' => 'pso', 'PSO384G4709' => 'pso', 'PSO407G0334' => 'pso', 'QL04p040276' => 'qlo', 'QL06p005458' => 'qlo', 'QL06p005472' => 'qlo', 'QL07p030546' => 'qlo', 'QL07p031519' => 'qlo', 'QL09p050949' => 'qlo', 'QL09p050966' => 'qlo', 'QL09p051067' => 'qlo', 'QL12p022706' => 'qlo', 'RcHm_v2.0_Chr2g0119601' => 'rch', 'RcHm_v2.0_Chr3g0459591' => 'rch', 'RcHm_v2.0_Chr4g0418521' => 'rch', 'RcHm_v2.0_Chr4g0418531' => 'rch', 'RcHm_v2.0_Chr4g0418541' => 'rch', 'RcHm_v2.0_Chr6g0291641' => 'rch', 'Rhsim01G0086300' => 'rsi', 'Rhsim01G0276300' => 'rsi', 'Rhsim01G0276500' => 'rsi', 'Rhsim04G0207700' => 'rsi', 'Rhsim05G0234500' => 'rsi', 'Rhsim13G0022400' => 'rsi', 'Sabra02G0167900' => 'sbr', 'Sabra04G0158500' => 'sbr', 'Sabra08G0159800' => 'sbr', 'Sabra10G0011500' => 'sbr', 'Sabra14G0104400' => 'sbr', 'SalBow2G2440' => 'sbo', 'SalBow4G2265' => 'sbo', 'Sc02g0000060' => 'sci', 'Sc05g0005020' => 'sci', 'Sc13g0003890' => 'sci', 'Sed0014865' => 'sed', 'Sed0017224' => 'sed', 'Sed0026391' => 'sed', 'SEGI_00063' => 'sgi', 'SEGI_10967' => 'sgi', 'SEGI_17510' => 'sgi', 'SEGI_24396' => 'sgi', 'SEGI_39719' => 'sgi', 'SEGI_41392' => 'sgi', 'SGA_v2.0_scaffold11G05794' => 'sas', 'SGA_v2.0_scaffold142G35607' => 'sas', 'SGA_v2.0_scaffold1G00447' => 'sas', 'SHI15388' => 'shi', 'SHI15394' => 'shi', 'SHI15396' => 'shi', 'SHI15399' => 'shi', 'SMO343G0151' => 'smo', 'SMO367G1118' => 'smo', 'Solyc01g080200.3' => 'sly', 'Solyc06g008960.3' => 'sly', 'Solyc09g064780.3' => 'sly', 'Sopen01g031980' => 'spe', 'Sopen06g003710' => 'spe', 'Sopen09g026460' => 'spe', 'Sp3g21240' => 'spa', 'Sp4g30030' => 'spa', 'TAR365G0022' => 'tar', 'TAR365G1023' => 'tar', 'TAR365G1253' => 'tar', 'TAR623G0078' => 'tar', 'TAR623G1721' => 'tar', 'TAR633G0959' => 'tar', 'THA.LOC104802225' => 'tha', 'THA.LOC104804769' => 'tha', 'THA.LOC104808660' => 'tha', 'THA.LOC104812792' => 'tha', 'Thecc.01G284000' => 'tca', 'Thecc.04G220600' => 'tca', 'Thecc.05G268900' => 'tca', 'Thecc.08G171100' => 'tca', 'Thhalv10001284m.g' => 'esa', 'Thhalv10019912m.g' => 'esa', 'TPR.G14189' => 'tpr', 'TPR.G18110' => 'tpr', 'TPR.G18130' => 'tpr', 'TPR.G18131' => 'tpr', 'TPR.G18140' => 'tpr', 'TPR.G24282' => 'tpr', 'TPR.G25221' => 'tpr', 'TPR.G29267' => 'tpr', 'TPR.G35315' => 'tpr', 'TPR.G36173' => 'tpr', 'TWI09G0794' => 'twi', 'TWI59G1348' => 'twi', 'TWI74G0430' => 'twi', 'unitig_26.g8940' => 'ugi', 'unitig_749.g13744' => 'ugi', 'unitig_749.g13745' => 'ugi', 'vmacro08269' => 'vma', 'vmacro14937' => 'vma', 'vmacro20401' => 'vma', 'VMungo0464G1349' => 'vmu', 'VMungo0540G0289' => 'vmu', 'VMungo1215G1590' => 'vmu', 'VMungo1309G0221' => 'vmu', 'VMungo1309G2815' => 'vmu', 'VMungo1383G0239' => 'vmu', 'VMungo1383G2910' => 'vmu', 'Zm00001eb095270' => 'zma', 'Zm00001eb095280' => 'zma', 'Zm00001eb111630' => 'zma', 'Zm00001eb237080' => 'zma', 'Zm00001eb273740' => 'zma', 'Zm00001eb285040' => 'zma', 'Zm00001eb330790' => 'zma', 'Zm00001eb337380' => 'zma' ) $gf_id = 'HOM05D001484' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001484' ) $data_identifier = 'HOM05D001484' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 2, 'aly' => (int) 2, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 22, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 7, 'hma' => (int) 2, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 7, 'mtr' => (int) 10, 'cme' => (int) 2, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 4, 'ppa' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 4, 'qlo' => (int) 9, 'rch' => (int) 6, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 10, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 7, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb337380' $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' => 'HOM05D001484', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p31500' => 'bna', 'A05p00020' => 'bna', 'A07p08820' => 'bna', 'Aa31LG4G3300' => 'aar', 'Aa31LG8G10030' => 'aar', 'Actinidia00731' => 'ach', 'Actinidia11473' => 'ach', 'Actinidia23469' => 'ach', 'Actinidia24318' => 'ach', 'Actinidia40196' => 'ach', 'Actinidia40197' => 'ach', 'Actinidia40198' => 'ach', 'Ah.08g212990' => 'amhyb', 'Ah.15g091720' => 'amhyb', 'AL3G38260' => 'aly', 'AL4G47710' => 'aly', 'Aqoxy2G00671' => 'aox', 'Aqoxy2G03236' => 'aox', 'arahy.Tifrunner.gnm1.ann1.05IDCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KR684' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATY3SJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK6QJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6APGL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IDT7Z9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM073U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ0R87' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LE7RV4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT4QRX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V5ENPK' => 'arhy', 'AT2G48110' => 'ath', 'AT3G23590' => 'ath', 'ATR0626G186' => 'atr', 'ATR1127G141' => 'atr', 'Atru.chr4.2583' => 'acertr', 'Atru.chr5.1358' => 'acertr', 'Atru.chr5.1359' => 'acertr', 'Atru.chr8.46' => 'acertr', 'AUR62002640' => 'cqu', 'AUR62030055' => 'cqu', 'AUR62033713' => 'cqu', 'AUR62033714' => 'cqu', 'AUR62036795' => 'cqu', 'AUR62039891' => 'cqu', 'BcaB02g08737' => 'bca', 'BcaB04g20441' => 'bca', 'BcaB06g26509' => 'bca', 'BcaB06g26510' => 'bca', 'BcaB06g26511' => 'bca', 'BcaB06g26512' => 'bca', 'BcaB06g26513' => 'bca', 'BcaC02g12564' => 'bca', 'BcaC02g12565' => 'bca', 'BcaC02g12794' => 'bca', 'BcaC02g12795' => 'bca', 'BcaC02g12796' => 'bca', 'BcaC06g35541' => 'bca', 'BNapus_Darmor_BZH_scaffold_188p00080' => 'bna', 'BNapus_Darmor_BZH_scaffold_188p00090' => 'bna', 'BolC1t03972H' => 'bol', 'BolC1t03973H' => 'bol', 'BolC4t21680H' => 'bol', 'BolC7t41863H' => 'bol', 'BolSC55t61227H' => 'bol', 'BolSC55t61228H' => 'bol', 'BraA01t03278Z' => 'bra', 'BraA05t18998Z' => 'bra', 'BraA07t28673Z' => 'bra', 'C01p40150' => 'bna', 'C05p12370' => 'bna', 'C07p13680' => 'bna', 'CAN.G1006.16' => 'can', 'CAN.G1006.17' => 'can', 'CAN.G1170.2' => 'can', 'CAN.G962.7' => 'can', 'CANSAT25G2179' => 'cansat', 'CANSAT78G1573' => 'cansat', 'CARHR099510' => 'chi', 'CARHR143510' => 'chi', 'Carub.0003s2380' => 'cru', 'Carub.0004s3082' => 'cru', 'Ca_00614_v3' => 'car', 'Ca_07801_v3' => 'car', 'Ca_08567_v3' => 'car', 'Ca_09571_v3' => 'car', 'CBR_g19290' => 'cbr', 'Cc01_g19770' => 'ccan', 'Cc03_g03030' => 'ccan', 'CDE07G0968' => 'cde', 'CDE09G1441' => 'cde', 'Cfa006103' => 'cfa', 'Cfa015573' => 'cfa', 'Cfa016988' => 'cfa', 'Ciclev10006738m.g' => 'ccl', 'Ciclev10010920m.g' => 'ccl', 'Ciclev10018517m.g' => 'ccl', 'CiPaw.01G159200' => 'cil', 'CiPaw.02G091000' => 'cil', 'CiPaw.02G091100' => 'cil', 'CiPaw.08G103100' => 'cil', 'CiPaw.09G224900' => 'cil', 'ClCG06G005740' => 'cla', 'ClCG07G000090' => 'cla', 'ClCG07G000100' => 'cla', 'COL.COLO4_09143' => 'col', 'COL.COLO4_25124' => 'col', 'Cpa.g.sc16.34' => 'cpa', 'Cpa.g.sc3504.1' => 'cpa', 'Cpa.g.sc60.37' => 'cpa', 'CsaV3_6G018520' => 'csa', 'CsaV3_6G036860' => 'csa', 'CSS0001072' => 'camsi', 'CSS0020208' => 'camsi', 'CSS0021253' => 'camsi', 'CSS0022190' => 'camsi', 'CSS0036150' => 'camsi', 'CSS0040442' => 'camsi', 'CSS0042300' => 'camsi', 'CSS0045298' => 'camsi', 'DCAR_012449' => 'dca', 'DCAR_018405' => 'dca', 'DCAR_024573' => 'dca', 'DCAR_030591' => 'dca', 'Dinv16926' => 'din', 'Dinv32963' => 'din', 'Dinv38382' => 'din', 'Dinv38383' => 'din', 'Duzib133G0974' => 'dzi', 'Duzib138G1867' => 'dzi', 'Duzib211G0420' => 'dzi', 'Duzib212G0930' => 'dzi', 'ECA234G1645' => 'eca', 'ECA247G3467' => 'eca', 'ECA248G1703' => 'eca', 'EL10Ac3g06327' => 'bvu', 'EL10Ac7g17204' => 'bvu', 'Eucgr.A00855' => 'egr', 'Eucgr.A00858' => 'egr', 'Eucgr.H01520' => 'egr', 'Eucgr.H03604' => 'egr', 'Eucgr.L03465' => 'egr', 'Eucgr.L03466' => 'egr', 'FAN01G0988' => 'fan', 'FAN02G3892' => 'fan', 'FAN05G3381' => 'fan', 'FAN07G0967' => 'fan', 'FAN07G1493' => 'fan', 'FAN08G3125' => 'fan', 'FAN09G0402' => 'fan', 'FAN12G2594' => 'fan', 'FAN12G3879' => 'fan', 'FAN14G1546' => 'fan', 'FAN15G3626' => 'fan', 'FAN17G0588' => 'fan', 'FAN17G0609' => 'fan', 'FAN18G2817' => 'fan', 'FAN19G1305' => 'fan', 'FAN20G1787' => 'fan', 'FAN22G0073' => 'fan', 'FAN22G0352' => 'fan', 'FAN22G0368' => 'fan', 'FAN22G2273' => 'fan', 'FAN24G1998' => 'fan', 'FAN27G1317' => 'fan', 'FvH4_2g23980' => 'fve', 'FvH4_4g14380' => 'fve', 'FvH4_4g14390' => 'fve', 'FvH4_6g09250' => 'fve', 'Glyma.03G151100' => 'gma', 'Glyma.04G122550' => 'gma', 'Glyma.05G001600' => 'gma', 'Glyma.09G270766' => 'gma', 'Glyma.09G270832' => 'gma', 'Glyma.13G209800' => 'gma', 'Glyma.15G102800' => 'gma', 'Glyma.18G218900' => 'gma', 'Glyma.19G001500' => 'gma', 'Glyma.19G153600' => 'gma', 'Gohir.A02G028600' => 'ghi', 'Gohir.A08G045000' => 'ghi', 'Gohir.A11G120500' => 'ghi', 'Gohir.A12G006200' => 'ghi', 'Gohir.A12G006250' => 'ghi', 'Gohir.D02G036300' => 'ghi', 'Gohir.D08G054700' => 'ghi', 'Gohir.D11G125600' => 'ghi', 'Gohir.D12G005700' => 'ghi', 'Gorai.004G055200' => 'gra', 'Gorai.005G040400' => 'gra', 'Gorai.007G134500' => 'gra', 'Gorai.008G005500' => 'gra', 'GSVIVG01011094001' => 'vvi', 'GSVIVG01017879001' => 'vvi', 'GSVIVG01025988001' => 'vvi', 'GSVIVG01029847001' => 'vvi', 'HanXRQChr10g0282901' => 'han', 'HanXRQChr10g0310371' => 'han', 'HanXRQChr10g0315041' => 'han', 'HanXRQChr11g0327651' => 'han', 'HanXRQChr12g0359391' => 'han', 'Haze_00972' => 'cav', 'Haze_00973' => 'cav', 'Haze_00974' => 'cav', 'Haze_04747' => 'cav', 'Haze_04749' => 'cav', 'Haze_04750' => 'cav', 'Haze_21217' => 'cav', 'Hma1.2p1_1037F.1_g250680' => 'hma', 'Hma1.2p1_1644F.1_g295320' => 'hma', 'HPP92_011322' => 'vpl', 'HPP92_011323' => 'vpl', 'HPP92_011324' => 'vpl', 'HPP92_011325' => 'vpl', 'HPP92_011326' => 'vpl', 'Hund12205' => 'sun', 'Hund17957' => 'sun', 'Lalb_Chr06g0176771' => 'lal', 'Lalb_Chr18g0056021' => 'lal', 'Lalb_Chr18g0056031' => 'lal', 'Lalb_Chr18g0056041' => 'lal', 'Lalb_Chr20g0107751' => 'lal', 'Lalb_Chr20g0118371' => 'lal', 'Lj1g0010239' => 'lja', 'Lj1g0017101' => 'lja', 'Lj2A1178G40' => 'lonja', 'Lj2A54G84' => 'lonja', 'Lj2g0015248' => 'lja', 'Lj3A761T51' => 'lonja', 'Lj6g0018116' => 'lja', 'Lsat_1_v5_gn_4_136040' => 'lsa', 'Lsat_1_v5_gn_5_187461' => 'lsa', 'Lsat_1_v5_gn_5_77001' => 'lsa', 'Lsat_1_v5_gn_9_4461' => 'lsa', 'Manes.01G210100' => 'mes', 'Manes.03G185600' => 'mes', 'Manes.05G073300' => 'mes', 'Manes.09G120300' => 'mes', 'Manes.15G022100' => 'mes', 'Mapoly0096s0053' => 'mpo', 'MBI03_g14058_MAGBIO' => 'mbi', 'MBI03_g33876_MAGBIO' => 'mbi', 'MBI03_g36854_MAGBIO' => 'mbi', 'MBI17_g11997_MAGBIO' => 'mbi', 'MD03G1269000' => 'mdo', 'MD04G1179600' => 'mdo', 'MD11G1289800' => 'mdo', 'MD12G1194700' => 'mdo', 'MD13G1182100' => 'mdo', 'MD13G1182200' => 'mdo', 'MD16G1182600' => 'mdo', 'Medtr2g021400' => 'mtr', 'Medtr2g021470' => 'mtr', 'Medtr2g105810' => 'mtr', 'Medtr3g033580' => 'mtr', 'Medtr6g007970' => 'mtr', 'Medtr7g056330' => 'mtr', 'Medtr7g074290' => 'mtr', 'Medtr7g074380' => 'mtr', 'Medtr7g094550' => 'mtr', 'Medtr8g069995' => 'mtr', 'MELO3C014345.2' => 'cme', 'MELO3C021395.2' => 'cme', 'Migut.D00262' => 'egut', 'Migut.G00257' => 'egut', 'MSTRG.21575' => 'ama', 'MSTRG.3985' => 'ama', 'Nitab4.5_0000295g0140' => 'nta', 'Nitab4.5_0000732g0140' => 'nta', 'Nitab4.5_0003162g0020' => 'nta', 'Nitab4.5_0006180g0090' => 'nta', 'Nitab4.5_0006390g0010' => 'nta', 'Nitab4.5_0007392g0040' => 'nta', 'Nn1g02140' => 'nnu', 'Nn4g26168' => 'nnu', 'Nn5g26754' => 'nnu', 'Oeu001433.1' => 'oeu', 'Oeu010299.2' => 'oeu', 'Oeu011171.1' => 'oeu', 'Oeu037675.1' => 'oeu', 'Oeu038359.1' => 'oeu', 'Oeu063834.1' => 'oeu', 'Oeu063835.1' => 'oeu', 'Os05g0312000' => 'osa', 'Os07g0211101' => 'osa', 'Os07g0211200' => 'osa', 'Os07g0681500' => 'osa', 'Peaxi162Scf00095g01015' => 'pax', 'Peaxi162Scf00104g00329' => 'pax', 'Peaxi162Scf00161g00137' => 'pax', 'PGR004G1665' => 'pgr', 'PGR031G2937' => 'pgr', 'PGR119G2145' => 'pgr', 'PGSC0003DMG400004351' => 'stu', 'PGSC0003DMG400014625' => 'stu', 'PGSC0003DMG401000943' => 'stu', 'Phvul.001G148600' => 'pvu', 'Phvul.004G001700' => 'pvu', 'Phvul.006G154900' => 'pvu', 'Phvul.008G078200' => 'pvu', 'Phvul.011G136500' => 'pvu', 'Potri.002G215600' => 'ptr', 'Potri.008G201600' => 'ptr', 'Potri.014G138400' => 'ptr', 'Potri.016G142500' => 'ptr', 'Pp3c16_10580' => 'ppa', 'Pp3c5_25280' => 'ppa', 'Prupe.1G150000' => 'ppe', 'Prupe.1G150100' => 'ppe', 'Prupe.6G299600' => 'ppe', 'Prupe.8G245000' => 'ppe', 'Psat0s4927g0040' => 'psa', 'Psat1g052080' => 'psa', 'Psat1g183800' => 'psa', 'Psat3g113840' => 'psa', 'Psat3g126120' => 'psa', 'Psat3g126160' => 'psa', 'Psat3g158760' => 'psa', 'Psat3g158840' => 'psa', 'PSO170G2858' => 'pso', 'PSO339G0606' => 'pso', 'PSO384G4709' => 'pso', 'PSO407G0334' => 'pso', 'QL04p040276' => 'qlo', 'QL06p005458' => 'qlo', 'QL06p005472' => 'qlo', 'QL07p030546' => 'qlo', 'QL07p031519' => 'qlo', 'QL09p050949' => 'qlo', 'QL09p050966' => 'qlo', 'QL09p051067' => 'qlo', 'QL12p022706' => 'qlo', 'RcHm_v2.0_Chr2g0119601' => 'rch', 'RcHm_v2.0_Chr3g0459591' => 'rch', 'RcHm_v2.0_Chr4g0418521' => 'rch', 'RcHm_v2.0_Chr4g0418531' => 'rch', 'RcHm_v2.0_Chr4g0418541' => 'rch', 'RcHm_v2.0_Chr6g0291641' => 'rch', 'Rhsim01G0086300' => 'rsi', 'Rhsim01G0276300' => 'rsi', 'Rhsim01G0276500' => 'rsi', 'Rhsim04G0207700' => 'rsi', 'Rhsim05G0234500' => 'rsi', 'Rhsim13G0022400' => 'rsi', 'Sabra02G0167900' => 'sbr', 'Sabra04G0158500' => 'sbr', 'Sabra08G0159800' => 'sbr', 'Sabra10G0011500' => 'sbr', 'Sabra14G0104400' => 'sbr', 'SalBow2G2440' => 'sbo', 'SalBow4G2265' => 'sbo', 'Sc02g0000060' => 'sci', 'Sc05g0005020' => 'sci', 'Sc13g0003890' => 'sci', 'Sed0014865' => 'sed', 'Sed0017224' => 'sed', 'Sed0026391' => 'sed', 'SEGI_00063' => 'sgi', 'SEGI_10967' => 'sgi', 'SEGI_17510' => 'sgi', 'SEGI_24396' => 'sgi', 'SEGI_39719' => 'sgi', 'SEGI_41392' => 'sgi', 'SGA_v2.0_scaffold11G05794' => 'sas', 'SGA_v2.0_scaffold142G35607' => 'sas', 'SGA_v2.0_scaffold1G00447' => 'sas', 'SHI15388' => 'shi', 'SHI15394' => 'shi', 'SHI15396' => 'shi', 'SHI15399' => 'shi', 'SMO343G0151' => 'smo', 'SMO367G1118' => 'smo', 'Solyc01g080200.3' => 'sly', 'Solyc06g008960.3' => 'sly', 'Solyc09g064780.3' => 'sly', 'Sopen01g031980' => 'spe', 'Sopen06g003710' => 'spe', 'Sopen09g026460' => 'spe', 'Sp3g21240' => 'spa', 'Sp4g30030' => 'spa', 'TAR365G0022' => 'tar', 'TAR365G1023' => 'tar', 'TAR365G1253' => 'tar', 'TAR623G0078' => 'tar', 'TAR623G1721' => 'tar', 'TAR633G0959' => 'tar', 'THA.LOC104802225' => 'tha', 'THA.LOC104804769' => 'tha', 'THA.LOC104808660' => 'tha', 'THA.LOC104812792' => 'tha', 'Thecc.01G284000' => 'tca', 'Thecc.04G220600' => 'tca', 'Thecc.05G268900' => 'tca', 'Thecc.08G171100' => 'tca', 'Thhalv10001284m.g' => 'esa', 'Thhalv10019912m.g' => 'esa', 'TPR.G14189' => 'tpr', 'TPR.G18110' => 'tpr', 'TPR.G18130' => 'tpr', 'TPR.G18131' => 'tpr', 'TPR.G18140' => 'tpr', 'TPR.G24282' => 'tpr', 'TPR.G25221' => 'tpr', 'TPR.G29267' => 'tpr', 'TPR.G35315' => 'tpr', 'TPR.G36173' => 'tpr', 'TWI09G0794' => 'twi', 'TWI59G1348' => 'twi', 'TWI74G0430' => 'twi', 'unitig_26.g8940' => 'ugi', 'unitig_749.g13744' => 'ugi', 'unitig_749.g13745' => 'ugi', 'vmacro08269' => 'vma', 'vmacro14937' => 'vma', 'vmacro20401' => 'vma', 'VMungo0464G1349' => 'vmu', 'VMungo0540G0289' => 'vmu', 'VMungo1215G1590' => 'vmu', 'VMungo1309G0221' => 'vmu', 'VMungo1309G2815' => 'vmu', 'VMungo1383G0239' => 'vmu', 'VMungo1383G2910' => 'vmu', 'Zm00001eb095270' => 'zma', 'Zm00001eb095280' => 'zma', 'Zm00001eb111630' => 'zma', 'Zm00001eb237080' => 'zma', 'Zm00001eb273740' => 'zma', 'Zm00001eb285040' => 'zma', 'Zm00001eb330790' => 'zma', 'Zm00001eb337380' => 'zma' ), 'gf_id' => 'HOM05D001484', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001484' ), 'data_identifier' => 'HOM05D001484', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001484', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p31500' => 'bna', 'A05p00020' => 'bna', 'A07p08820' => 'bna', 'Aa31LG4G3300' => 'aar', 'Aa31LG8G10030' => 'aar', 'Actinidia00731' => 'ach', 'Actinidia11473' => 'ach', 'Actinidia23469' => 'ach', 'Actinidia24318' => 'ach', 'Actinidia40196' => 'ach', 'Actinidia40197' => 'ach', 'Actinidia40198' => 'ach', 'Ah.08g212990' => 'amhyb', 'Ah.15g091720' => 'amhyb', 'AL3G38260' => 'aly', 'AL4G47710' => 'aly', 'Aqoxy2G00671' => 'aox', 'Aqoxy2G03236' => 'aox', 'arahy.Tifrunner.gnm1.ann1.05IDCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KR684' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATY3SJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK6QJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6APGL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IDT7Z9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM073U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ0R87' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LE7RV4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT4QRX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V5ENPK' => 'arhy', 'AT2G48110' => 'ath', 'AT3G23590' => 'ath', 'ATR0626G186' => 'atr', 'ATR1127G141' => 'atr', 'Atru.chr4.2583' => 'acertr', 'Atru.chr5.1358' => 'acertr', 'Atru.chr5.1359' => 'acertr', 'Atru.chr8.46' => 'acertr', 'AUR62002640' => 'cqu', 'AUR62030055' => 'cqu', 'AUR62033713' => 'cqu', 'AUR62033714' => 'cqu', 'AUR62036795' => 'cqu', 'AUR62039891' => 'cqu', 'BcaB02g08737' => 'bca', 'BcaB04g20441' => 'bca', 'BcaB06g26509' => 'bca', 'BcaB06g26510' => 'bca', 'BcaB06g26511' => 'bca', 'BcaB06g26512' => 'bca', 'BcaB06g26513' => 'bca', 'BcaC02g12564' => 'bca', 'BcaC02g12565' => 'bca', 'BcaC02g12794' => 'bca', 'BcaC02g12795' => 'bca', 'BcaC02g12796' => 'bca', 'BcaC06g35541' => 'bca', 'BNapus_Darmor_BZH_scaffold_188p00080' => 'bna', 'BNapus_Darmor_BZH_scaffold_188p00090' => 'bna', 'BolC1t03972H' => 'bol', 'BolC1t03973H' => 'bol', 'BolC4t21680H' => 'bol', 'BolC7t41863H' => 'bol', 'BolSC55t61227H' => 'bol', 'BolSC55t61228H' => 'bol', 'BraA01t03278Z' => 'bra', 'BraA05t18998Z' => 'bra', 'BraA07t28673Z' => 'bra', 'C01p40150' => 'bna', 'C05p12370' => 'bna', 'C07p13680' => 'bna', 'CAN.G1006.16' => 'can', 'CAN.G1006.17' => 'can', 'CAN.G1170.2' => 'can', 'CAN.G962.7' => 'can', 'CANSAT25G2179' => 'cansat', 'CANSAT78G1573' => 'cansat', 'CARHR099510' => 'chi', 'CARHR143510' => 'chi', 'Carub.0003s2380' => 'cru', 'Carub.0004s3082' => 'cru', 'Ca_00614_v3' => 'car', 'Ca_07801_v3' => 'car', 'Ca_08567_v3' => 'car', 'Ca_09571_v3' => 'car', 'CBR_g19290' => 'cbr', 'Cc01_g19770' => 'ccan', 'Cc03_g03030' => 'ccan', 'CDE07G0968' => 'cde', 'CDE09G1441' => 'cde', 'Cfa006103' => 'cfa', 'Cfa015573' => 'cfa', 'Cfa016988' => 'cfa', 'Ciclev10006738m.g' => 'ccl', 'Ciclev10010920m.g' => 'ccl', 'Ciclev10018517m.g' => 'ccl', 'CiPaw.01G159200' => 'cil', 'CiPaw.02G091000' => 'cil', 'CiPaw.02G091100' => 'cil', 'CiPaw.08G103100' => 'cil', 'CiPaw.09G224900' => 'cil', 'ClCG06G005740' => 'cla', 'ClCG07G000090' => 'cla', 'ClCG07G000100' => 'cla', 'COL.COLO4_09143' => 'col', 'COL.COLO4_25124' => 'col', 'Cpa.g.sc16.34' => 'cpa', 'Cpa.g.sc3504.1' => 'cpa', 'Cpa.g.sc60.37' => 'cpa', 'CsaV3_6G018520' => 'csa', 'CsaV3_6G036860' => 'csa', 'CSS0001072' => 'camsi', 'CSS0020208' => 'camsi', 'CSS0021253' => 'camsi', 'CSS0022190' => 'camsi', 'CSS0036150' => 'camsi', 'CSS0040442' => 'camsi', 'CSS0042300' => 'camsi', 'CSS0045298' => 'camsi', 'DCAR_012449' => 'dca', 'DCAR_018405' => 'dca', 'DCAR_024573' => 'dca', 'DCAR_030591' => 'dca', 'Dinv16926' => 'din', 'Dinv32963' => 'din', 'Dinv38382' => 'din', 'Dinv38383' => 'din', 'Duzib133G0974' => 'dzi', 'Duzib138G1867' => 'dzi', 'Duzib211G0420' => 'dzi', 'Duzib212G0930' => 'dzi', 'ECA234G1645' => 'eca', 'ECA247G3467' => 'eca', 'ECA248G1703' => 'eca', 'EL10Ac3g06327' => 'bvu', 'EL10Ac7g17204' => 'bvu', 'Eucgr.A00855' => 'egr', 'Eucgr.A00858' => 'egr', 'Eucgr.H01520' => 'egr', 'Eucgr.H03604' => 'egr', 'Eucgr.L03465' => 'egr', 'Eucgr.L03466' => 'egr', 'FAN01G0988' => 'fan', 'FAN02G3892' => 'fan', 'FAN05G3381' => 'fan', 'FAN07G0967' => 'fan', 'FAN07G1493' => 'fan', 'FAN08G3125' => 'fan', 'FAN09G0402' => 'fan', 'FAN12G2594' => 'fan', 'FAN12G3879' => 'fan', 'FAN14G1546' => 'fan', 'FAN15G3626' => 'fan', 'FAN17G0588' => 'fan', 'FAN17G0609' => 'fan', 'FAN18G2817' => 'fan', 'FAN19G1305' => 'fan', 'FAN20G1787' => 'fan', 'FAN22G0073' => 'fan', 'FAN22G0352' => 'fan', 'FAN22G0368' => 'fan', 'FAN22G2273' => 'fan', 'FAN24G1998' => 'fan', 'FAN27G1317' => 'fan', 'FvH4_2g23980' => 'fve', 'FvH4_4g14380' => 'fve', 'FvH4_4g14390' => 'fve', 'FvH4_6g09250' => 'fve', 'Glyma.03G151100' => 'gma', 'Glyma.04G122550' => 'gma', 'Glyma.05G001600' => 'gma', 'Glyma.09G270766' => 'gma', 'Glyma.09G270832' => 'gma', 'Glyma.13G209800' => 'gma', 'Glyma.15G102800' => 'gma', 'Glyma.18G218900' => 'gma', 'Glyma.19G001500' => 'gma', 'Glyma.19G153600' => 'gma', 'Gohir.A02G028600' => 'ghi', 'Gohir.A08G045000' => 'ghi', 'Gohir.A11G120500' => 'ghi', 'Gohir.A12G006200' => 'ghi', 'Gohir.A12G006250' => 'ghi', 'Gohir.D02G036300' => 'ghi', 'Gohir.D08G054700' => 'ghi', 'Gohir.D11G125600' => 'ghi', 'Gohir.D12G005700' => 'ghi', 'Gorai.004G055200' => 'gra', 'Gorai.005G040400' => 'gra', 'Gorai.007G134500' => 'gra', 'Gorai.008G005500' => 'gra', 'GSVIVG01011094001' => 'vvi', 'GSVIVG01017879001' => 'vvi', 'GSVIVG01025988001' => 'vvi', 'GSVIVG01029847001' => 'vvi', 'HanXRQChr10g0282901' => 'han', 'HanXRQChr10g0310371' => 'han', 'HanXRQChr10g0315041' => 'han', 'HanXRQChr11g0327651' => 'han', 'HanXRQChr12g0359391' => 'han', 'Haze_00972' => 'cav', 'Haze_00973' => 'cav', 'Haze_00974' => 'cav', 'Haze_04747' => 'cav', 'Haze_04749' => 'cav', 'Haze_04750' => 'cav', 'Haze_21217' => 'cav', 'Hma1.2p1_1037F.1_g250680' => 'hma', 'Hma1.2p1_1644F.1_g295320' => 'hma', 'HPP92_011322' => 'vpl', 'HPP92_011323' => 'vpl', 'HPP92_011324' => 'vpl', 'HPP92_011325' => 'vpl', 'HPP92_011326' => 'vpl', 'Hund12205' => 'sun', 'Hund17957' => 'sun', 'Lalb_Chr06g0176771' => 'lal', 'Lalb_Chr18g0056021' => 'lal', 'Lalb_Chr18g0056031' => 'lal', 'Lalb_Chr18g0056041' => 'lal', 'Lalb_Chr20g0107751' => 'lal', 'Lalb_Chr20g0118371' => 'lal', 'Lj1g0010239' => 'lja', 'Lj1g0017101' => 'lja', 'Lj2A1178G40' => 'lonja', 'Lj2A54G84' => 'lonja', 'Lj2g0015248' => 'lja', 'Lj3A761T51' => 'lonja', 'Lj6g0018116' => 'lja', 'Lsat_1_v5_gn_4_136040' => 'lsa', 'Lsat_1_v5_gn_5_187461' => 'lsa', 'Lsat_1_v5_gn_5_77001' => 'lsa', 'Lsat_1_v5_gn_9_4461' => 'lsa', 'Manes.01G210100' => 'mes', 'Manes.03G185600' => 'mes', 'Manes.05G073300' => 'mes', 'Manes.09G120300' => 'mes', 'Manes.15G022100' => 'mes', 'Mapoly0096s0053' => 'mpo', 'MBI03_g14058_MAGBIO' => 'mbi', 'MBI03_g33876_MAGBIO' => 'mbi', 'MBI03_g36854_MAGBIO' => 'mbi', 'MBI17_g11997_MAGBIO' => 'mbi', 'MD03G1269000' => 'mdo', 'MD04G1179600' => 'mdo', 'MD11G1289800' => 'mdo', 'MD12G1194700' => 'mdo', 'MD13G1182100' => 'mdo', 'MD13G1182200' => 'mdo', 'MD16G1182600' => 'mdo', 'Medtr2g021400' => 'mtr', 'Medtr2g021470' => 'mtr', 'Medtr2g105810' => 'mtr', 'Medtr3g033580' => 'mtr', 'Medtr6g007970' => 'mtr', 'Medtr7g056330' => 'mtr', 'Medtr7g074290' => 'mtr', 'Medtr7g074380' => 'mtr', 'Medtr7g094550' => 'mtr', 'Medtr8g069995' => 'mtr', 'MELO3C014345.2' => 'cme', 'MELO3C021395.2' => 'cme', 'Migut.D00262' => 'egut', 'Migut.G00257' => 'egut', 'MSTRG.21575' => 'ama', 'MSTRG.3985' => 'ama', 'Nitab4.5_0000295g0140' => 'nta', 'Nitab4.5_0000732g0140' => 'nta', 'Nitab4.5_0003162g0020' => 'nta', 'Nitab4.5_0006180g0090' => 'nta', 'Nitab4.5_0006390g0010' => 'nta', 'Nitab4.5_0007392g0040' => 'nta', 'Nn1g02140' => 'nnu', 'Nn4g26168' => 'nnu', 'Nn5g26754' => 'nnu', 'Oeu001433.1' => 'oeu', 'Oeu010299.2' => 'oeu', 'Oeu011171.1' => 'oeu', 'Oeu037675.1' => 'oeu', 'Oeu038359.1' => 'oeu', 'Oeu063834.1' => 'oeu', 'Oeu063835.1' => 'oeu', 'Os05g0312000' => 'osa', 'Os07g0211101' => 'osa', 'Os07g0211200' => 'osa', 'Os07g0681500' => 'osa', 'Peaxi162Scf00095g01015' => 'pax', 'Peaxi162Scf00104g00329' => 'pax', 'Peaxi162Scf00161g00137' => 'pax', 'PGR004G1665' => 'pgr', 'PGR031G2937' => 'pgr', 'PGR119G2145' => 'pgr', 'PGSC0003DMG400004351' => 'stu', 'PGSC0003DMG400014625' => 'stu', 'PGSC0003DMG401000943' => 'stu', 'Phvul.001G148600' => 'pvu', 'Phvul.004G001700' => 'pvu', 'Phvul.006G154900' => 'pvu', 'Phvul.008G078200' => 'pvu', 'Phvul.011G136500' => 'pvu', 'Potri.002G215600' => 'ptr', 'Potri.008G201600' => 'ptr', 'Potri.014G138400' => 'ptr', 'Potri.016G142500' => 'ptr', 'Pp3c16_10580' => 'ppa', 'Pp3c5_25280' => 'ppa', 'Prupe.1G150000' => 'ppe', 'Prupe.1G150100' => 'ppe', 'Prupe.6G299600' => 'ppe', 'Prupe.8G245000' => 'ppe', 'Psat0s4927g0040' => 'psa', 'Psat1g052080' => 'psa', 'Psat1g183800' => 'psa', 'Psat3g113840' => 'psa', 'Psat3g126120' => 'psa', 'Psat3g126160' => 'psa', 'Psat3g158760' => 'psa', 'Psat3g158840' => 'psa', 'PSO170G2858' => 'pso', 'PSO339G0606' => 'pso', 'PSO384G4709' => 'pso', 'PSO407G0334' => 'pso', 'QL04p040276' => 'qlo', 'QL06p005458' => 'qlo', 'QL06p005472' => 'qlo', 'QL07p030546' => 'qlo', 'QL07p031519' => 'qlo', 'QL09p050949' => 'qlo', 'QL09p050966' => 'qlo', 'QL09p051067' => 'qlo', 'QL12p022706' => 'qlo', 'RcHm_v2.0_Chr2g0119601' => 'rch', 'RcHm_v2.0_Chr3g0459591' => 'rch', 'RcHm_v2.0_Chr4g0418521' => 'rch', 'RcHm_v2.0_Chr4g0418531' => 'rch', 'RcHm_v2.0_Chr4g0418541' => 'rch', 'RcHm_v2.0_Chr6g0291641' => 'rch', 'Rhsim01G0086300' => 'rsi', 'Rhsim01G0276300' => 'rsi', 'Rhsim01G0276500' => 'rsi', 'Rhsim04G0207700' => 'rsi', 'Rhsim05G0234500' => 'rsi', 'Rhsim13G0022400' => 'rsi', 'Sabra02G0167900' => 'sbr', 'Sabra04G0158500' => 'sbr', 'Sabra08G0159800' => 'sbr', 'Sabra10G0011500' => 'sbr', 'Sabra14G0104400' => 'sbr', 'SalBow2G2440' => 'sbo', 'SalBow4G2265' => 'sbo', 'Sc02g0000060' => 'sci', 'Sc05g0005020' => 'sci', 'Sc13g0003890' => 'sci', 'Sed0014865' => 'sed', 'Sed0017224' => 'sed', 'Sed0026391' => 'sed', 'SEGI_00063' => 'sgi', 'SEGI_10967' => 'sgi', 'SEGI_17510' => 'sgi', 'SEGI_24396' => 'sgi', 'SEGI_39719' => 'sgi', 'SEGI_41392' => 'sgi', 'SGA_v2.0_scaffold11G05794' => 'sas', 'SGA_v2.0_scaffold142G35607' => 'sas', 'SGA_v2.0_scaffold1G00447' => 'sas', 'SHI15388' => 'shi', 'SHI15394' => 'shi', 'SHI15396' => 'shi', 'SHI15399' => 'shi', 'SMO343G0151' => 'smo', 'SMO367G1118' => 'smo', 'Solyc01g080200.3' => 'sly', 'Solyc06g008960.3' => 'sly', 'Solyc09g064780.3' => 'sly', 'Sopen01g031980' => 'spe', 'Sopen06g003710' => 'spe', 'Sopen09g026460' => 'spe', 'Sp3g21240' => 'spa', 'Sp4g30030' => 'spa', 'TAR365G0022' => 'tar', 'TAR365G1023' => 'tar', 'TAR365G1253' => 'tar', 'TAR623G0078' => 'tar', 'TAR623G1721' => 'tar', 'TAR633G0959' => 'tar', 'THA.LOC104802225' => 'tha', 'THA.LOC104804769' => 'tha', 'THA.LOC104808660' => 'tha', 'THA.LOC104812792' => 'tha', 'Thecc.01G284000' => 'tca', 'Thecc.04G220600' => 'tca', 'Thecc.05G268900' => 'tca', 'Thecc.08G171100' => 'tca', 'Thhalv10001284m.g' => 'esa', 'Thhalv10019912m.g' => 'esa', 'TPR.G14189' => 'tpr', 'TPR.G18110' => 'tpr', 'TPR.G18130' => 'tpr', 'TPR.G18131' => 'tpr', 'TPR.G18140' => 'tpr', 'TPR.G24282' => 'tpr', 'TPR.G25221' => 'tpr', 'TPR.G29267' => 'tpr', 'TPR.G35315' => 'tpr', 'TPR.G36173' => 'tpr', 'TWI09G0794' => 'twi', 'TWI59G1348' => 'twi', 'TWI74G0430' => 'twi', 'unitig_26.g8940' => 'ugi', 'unitig_749.g13744' => 'ugi', 'unitig_749.g13745' => 'ugi', 'vmacro08269' => 'vma', 'vmacro14937' => 'vma', 'vmacro20401' => 'vma', 'VMungo0464G1349' => 'vmu', 'VMungo0540G0289' => 'vmu', 'VMungo1215G1590' => 'vmu', 'VMungo1309G0221' => 'vmu', 'VMungo1309G2815' => 'vmu', 'VMungo1383G0239' => 'vmu', 'VMungo1383G2910' => 'vmu', 'Zm00001eb095270' => 'zma', 'Zm00001eb095280' => 'zma', 'Zm00001eb111630' => 'zma', 'Zm00001eb237080' => 'zma', 'Zm00001eb273740' => 'zma', 'Zm00001eb285040' => 'zma', 'Zm00001eb330790' => 'zma', 'Zm00001eb337380' => 'zma' ) $gf_id = 'HOM05D001484' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001484' ) $data_identifier = 'HOM05D001484' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 2, 'aly' => (int) 2, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 22, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 7, 'hma' => (int) 2, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 7, 'mtr' => (int) 10, 'cme' => (int) 2, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 4, 'ppa' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 4, 'qlo' => (int) 9, 'rch' => (int) 6, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 10, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 7, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb337380' $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' => 'HOM05D001484', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p31500' => 'bna', 'A05p00020' => 'bna', 'A07p08820' => 'bna', 'Aa31LG4G3300' => 'aar', 'Aa31LG8G10030' => 'aar', 'Actinidia00731' => 'ach', 'Actinidia11473' => 'ach', 'Actinidia23469' => 'ach', 'Actinidia24318' => 'ach', 'Actinidia40196' => 'ach', 'Actinidia40197' => 'ach', 'Actinidia40198' => 'ach', 'Ah.08g212990' => 'amhyb', 'Ah.15g091720' => 'amhyb', 'AL3G38260' => 'aly', 'AL4G47710' => 'aly', 'Aqoxy2G00671' => 'aox', 'Aqoxy2G03236' => 'aox', 'arahy.Tifrunner.gnm1.ann1.05IDCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KR684' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATY3SJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK6QJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6APGL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IDT7Z9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM073U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ0R87' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LE7RV4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT4QRX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V5ENPK' => 'arhy', 'AT2G48110' => 'ath', 'AT3G23590' => 'ath', 'ATR0626G186' => 'atr', 'ATR1127G141' => 'atr', 'Atru.chr4.2583' => 'acertr', 'Atru.chr5.1358' => 'acertr', 'Atru.chr5.1359' => 'acertr', 'Atru.chr8.46' => 'acertr', 'AUR62002640' => 'cqu', 'AUR62030055' => 'cqu', 'AUR62033713' => 'cqu', 'AUR62033714' => 'cqu', 'AUR62036795' => 'cqu', 'AUR62039891' => 'cqu', 'BcaB02g08737' => 'bca', 'BcaB04g20441' => 'bca', 'BcaB06g26509' => 'bca', 'BcaB06g26510' => 'bca', 'BcaB06g26511' => 'bca', 'BcaB06g26512' => 'bca', 'BcaB06g26513' => 'bca', 'BcaC02g12564' => 'bca', 'BcaC02g12565' => 'bca', 'BcaC02g12794' => 'bca', 'BcaC02g12795' => 'bca', 'BcaC02g12796' => 'bca', 'BcaC06g35541' => 'bca', 'BNapus_Darmor_BZH_scaffold_188p00080' => 'bna', 'BNapus_Darmor_BZH_scaffold_188p00090' => 'bna', 'BolC1t03972H' => 'bol', 'BolC1t03973H' => 'bol', 'BolC4t21680H' => 'bol', 'BolC7t41863H' => 'bol', 'BolSC55t61227H' => 'bol', 'BolSC55t61228H' => 'bol', 'BraA01t03278Z' => 'bra', 'BraA05t18998Z' => 'bra', 'BraA07t28673Z' => 'bra', 'C01p40150' => 'bna', 'C05p12370' => 'bna', 'C07p13680' => 'bna', 'CAN.G1006.16' => 'can', 'CAN.G1006.17' => 'can', 'CAN.G1170.2' => 'can', 'CAN.G962.7' => 'can', 'CANSAT25G2179' => 'cansat', 'CANSAT78G1573' => 'cansat', 'CARHR099510' => 'chi', 'CARHR143510' => 'chi', 'Carub.0003s2380' => 'cru', 'Carub.0004s3082' => 'cru', 'Ca_00614_v3' => 'car', 'Ca_07801_v3' => 'car', 'Ca_08567_v3' => 'car', 'Ca_09571_v3' => 'car', 'CBR_g19290' => 'cbr', 'Cc01_g19770' => 'ccan', 'Cc03_g03030' => 'ccan', 'CDE07G0968' => 'cde', 'CDE09G1441' => 'cde', 'Cfa006103' => 'cfa', 'Cfa015573' => 'cfa', 'Cfa016988' => 'cfa', 'Ciclev10006738m.g' => 'ccl', 'Ciclev10010920m.g' => 'ccl', 'Ciclev10018517m.g' => 'ccl', 'CiPaw.01G159200' => 'cil', 'CiPaw.02G091000' => 'cil', 'CiPaw.02G091100' => 'cil', 'CiPaw.08G103100' => 'cil', 'CiPaw.09G224900' => 'cil', 'ClCG06G005740' => 'cla', 'ClCG07G000090' => 'cla', 'ClCG07G000100' => 'cla', 'COL.COLO4_09143' => 'col', 'COL.COLO4_25124' => 'col', 'Cpa.g.sc16.34' => 'cpa', 'Cpa.g.sc3504.1' => 'cpa', 'Cpa.g.sc60.37' => 'cpa', 'CsaV3_6G018520' => 'csa', 'CsaV3_6G036860' => 'csa', 'CSS0001072' => 'camsi', 'CSS0020208' => 'camsi', 'CSS0021253' => 'camsi', 'CSS0022190' => 'camsi', 'CSS0036150' => 'camsi', 'CSS0040442' => 'camsi', 'CSS0042300' => 'camsi', 'CSS0045298' => 'camsi', 'DCAR_012449' => 'dca', 'DCAR_018405' => 'dca', 'DCAR_024573' => 'dca', 'DCAR_030591' => 'dca', 'Dinv16926' => 'din', 'Dinv32963' => 'din', 'Dinv38382' => 'din', 'Dinv38383' => 'din', 'Duzib133G0974' => 'dzi', 'Duzib138G1867' => 'dzi', 'Duzib211G0420' => 'dzi', 'Duzib212G0930' => 'dzi', 'ECA234G1645' => 'eca', 'ECA247G3467' => 'eca', 'ECA248G1703' => 'eca', 'EL10Ac3g06327' => 'bvu', 'EL10Ac7g17204' => 'bvu', 'Eucgr.A00855' => 'egr', 'Eucgr.A00858' => 'egr', 'Eucgr.H01520' => 'egr', 'Eucgr.H03604' => 'egr', 'Eucgr.L03465' => 'egr', 'Eucgr.L03466' => 'egr', 'FAN01G0988' => 'fan', 'FAN02G3892' => 'fan', 'FAN05G3381' => 'fan', 'FAN07G0967' => 'fan', 'FAN07G1493' => 'fan', 'FAN08G3125' => 'fan', 'FAN09G0402' => 'fan', 'FAN12G2594' => 'fan', 'FAN12G3879' => 'fan', 'FAN14G1546' => 'fan', 'FAN15G3626' => 'fan', 'FAN17G0588' => 'fan', 'FAN17G0609' => 'fan', 'FAN18G2817' => 'fan', 'FAN19G1305' => 'fan', 'FAN20G1787' => 'fan', 'FAN22G0073' => 'fan', 'FAN22G0352' => 'fan', 'FAN22G0368' => 'fan', 'FAN22G2273' => 'fan', 'FAN24G1998' => 'fan', 'FAN27G1317' => 'fan', 'FvH4_2g23980' => 'fve', 'FvH4_4g14380' => 'fve', 'FvH4_4g14390' => 'fve', 'FvH4_6g09250' => 'fve', 'Glyma.03G151100' => 'gma', 'Glyma.04G122550' => 'gma', 'Glyma.05G001600' => 'gma', 'Glyma.09G270766' => 'gma', 'Glyma.09G270832' => 'gma', 'Glyma.13G209800' => 'gma', 'Glyma.15G102800' => 'gma', 'Glyma.18G218900' => 'gma', 'Glyma.19G001500' => 'gma', 'Glyma.19G153600' => 'gma', 'Gohir.A02G028600' => 'ghi', 'Gohir.A08G045000' => 'ghi', 'Gohir.A11G120500' => 'ghi', 'Gohir.A12G006200' => 'ghi', 'Gohir.A12G006250' => 'ghi', 'Gohir.D02G036300' => 'ghi', 'Gohir.D08G054700' => 'ghi', 'Gohir.D11G125600' => 'ghi', 'Gohir.D12G005700' => 'ghi', 'Gorai.004G055200' => 'gra', 'Gorai.005G040400' => 'gra', 'Gorai.007G134500' => 'gra', 'Gorai.008G005500' => 'gra', 'GSVIVG01011094001' => 'vvi', 'GSVIVG01017879001' => 'vvi', 'GSVIVG01025988001' => 'vvi', 'GSVIVG01029847001' => 'vvi', 'HanXRQChr10g0282901' => 'han', 'HanXRQChr10g0310371' => 'han', 'HanXRQChr10g0315041' => 'han', 'HanXRQChr11g0327651' => 'han', 'HanXRQChr12g0359391' => 'han', 'Haze_00972' => 'cav', 'Haze_00973' => 'cav', 'Haze_00974' => 'cav', 'Haze_04747' => 'cav', 'Haze_04749' => 'cav', 'Haze_04750' => 'cav', 'Haze_21217' => 'cav', 'Hma1.2p1_1037F.1_g250680' => 'hma', 'Hma1.2p1_1644F.1_g295320' => 'hma', 'HPP92_011322' => 'vpl', 'HPP92_011323' => 'vpl', 'HPP92_011324' => 'vpl', 'HPP92_011325' => 'vpl', 'HPP92_011326' => 'vpl', 'Hund12205' => 'sun', 'Hund17957' => 'sun', 'Lalb_Chr06g0176771' => 'lal', 'Lalb_Chr18g0056021' => 'lal', 'Lalb_Chr18g0056031' => 'lal', 'Lalb_Chr18g0056041' => 'lal', 'Lalb_Chr20g0107751' => 'lal', 'Lalb_Chr20g0118371' => 'lal', 'Lj1g0010239' => 'lja', 'Lj1g0017101' => 'lja', 'Lj2A1178G40' => 'lonja', 'Lj2A54G84' => 'lonja', 'Lj2g0015248' => 'lja', 'Lj3A761T51' => 'lonja', 'Lj6g0018116' => 'lja', 'Lsat_1_v5_gn_4_136040' => 'lsa', 'Lsat_1_v5_gn_5_187461' => 'lsa', 'Lsat_1_v5_gn_5_77001' => 'lsa', 'Lsat_1_v5_gn_9_4461' => 'lsa', 'Manes.01G210100' => 'mes', 'Manes.03G185600' => 'mes', 'Manes.05G073300' => 'mes', 'Manes.09G120300' => 'mes', 'Manes.15G022100' => 'mes', 'Mapoly0096s0053' => 'mpo', 'MBI03_g14058_MAGBIO' => 'mbi', 'MBI03_g33876_MAGBIO' => 'mbi', 'MBI03_g36854_MAGBIO' => 'mbi', 'MBI17_g11997_MAGBIO' => 'mbi', 'MD03G1269000' => 'mdo', 'MD04G1179600' => 'mdo', 'MD11G1289800' => 'mdo', 'MD12G1194700' => 'mdo', 'MD13G1182100' => 'mdo', 'MD13G1182200' => 'mdo', 'MD16G1182600' => 'mdo', 'Medtr2g021400' => 'mtr', 'Medtr2g021470' => 'mtr', 'Medtr2g105810' => 'mtr', 'Medtr3g033580' => 'mtr', 'Medtr6g007970' => 'mtr', 'Medtr7g056330' => 'mtr', 'Medtr7g074290' => 'mtr', 'Medtr7g074380' => 'mtr', 'Medtr7g094550' => 'mtr', 'Medtr8g069995' => 'mtr', 'MELO3C014345.2' => 'cme', 'MELO3C021395.2' => 'cme', 'Migut.D00262' => 'egut', 'Migut.G00257' => 'egut', 'MSTRG.21575' => 'ama', 'MSTRG.3985' => 'ama', 'Nitab4.5_0000295g0140' => 'nta', 'Nitab4.5_0000732g0140' => 'nta', 'Nitab4.5_0003162g0020' => 'nta', 'Nitab4.5_0006180g0090' => 'nta', 'Nitab4.5_0006390g0010' => 'nta', 'Nitab4.5_0007392g0040' => 'nta', 'Nn1g02140' => 'nnu', 'Nn4g26168' => 'nnu', 'Nn5g26754' => 'nnu', 'Oeu001433.1' => 'oeu', 'Oeu010299.2' => 'oeu', 'Oeu011171.1' => 'oeu', 'Oeu037675.1' => 'oeu', 'Oeu038359.1' => 'oeu', 'Oeu063834.1' => 'oeu', 'Oeu063835.1' => 'oeu', 'Os05g0312000' => 'osa', 'Os07g0211101' => 'osa', 'Os07g0211200' => 'osa', 'Os07g0681500' => 'osa', 'Peaxi162Scf00095g01015' => 'pax', 'Peaxi162Scf00104g00329' => 'pax', 'Peaxi162Scf00161g00137' => 'pax', 'PGR004G1665' => 'pgr', 'PGR031G2937' => 'pgr', 'PGR119G2145' => 'pgr', 'PGSC0003DMG400004351' => 'stu', 'PGSC0003DMG400014625' => 'stu', 'PGSC0003DMG401000943' => 'stu', 'Phvul.001G148600' => 'pvu', 'Phvul.004G001700' => 'pvu', 'Phvul.006G154900' => 'pvu', 'Phvul.008G078200' => 'pvu', 'Phvul.011G136500' => 'pvu', 'Potri.002G215600' => 'ptr', 'Potri.008G201600' => 'ptr', 'Potri.014G138400' => 'ptr', 'Potri.016G142500' => 'ptr', 'Pp3c16_10580' => 'ppa', 'Pp3c5_25280' => 'ppa', 'Prupe.1G150000' => 'ppe', 'Prupe.1G150100' => 'ppe', 'Prupe.6G299600' => 'ppe', 'Prupe.8G245000' => 'ppe', 'Psat0s4927g0040' => 'psa', 'Psat1g052080' => 'psa', 'Psat1g183800' => 'psa', 'Psat3g113840' => 'psa', 'Psat3g126120' => 'psa', 'Psat3g126160' => 'psa', 'Psat3g158760' => 'psa', 'Psat3g158840' => 'psa', 'PSO170G2858' => 'pso', 'PSO339G0606' => 'pso', 'PSO384G4709' => 'pso', 'PSO407G0334' => 'pso', 'QL04p040276' => 'qlo', 'QL06p005458' => 'qlo', 'QL06p005472' => 'qlo', 'QL07p030546' => 'qlo', 'QL07p031519' => 'qlo', 'QL09p050949' => 'qlo', 'QL09p050966' => 'qlo', 'QL09p051067' => 'qlo', 'QL12p022706' => 'qlo', 'RcHm_v2.0_Chr2g0119601' => 'rch', 'RcHm_v2.0_Chr3g0459591' => 'rch', 'RcHm_v2.0_Chr4g0418521' => 'rch', 'RcHm_v2.0_Chr4g0418531' => 'rch', 'RcHm_v2.0_Chr4g0418541' => 'rch', 'RcHm_v2.0_Chr6g0291641' => 'rch', 'Rhsim01G0086300' => 'rsi', 'Rhsim01G0276300' => 'rsi', 'Rhsim01G0276500' => 'rsi', 'Rhsim04G0207700' => 'rsi', 'Rhsim05G0234500' => 'rsi', 'Rhsim13G0022400' => 'rsi', 'Sabra02G0167900' => 'sbr', 'Sabra04G0158500' => 'sbr', 'Sabra08G0159800' => 'sbr', 'Sabra10G0011500' => 'sbr', 'Sabra14G0104400' => 'sbr', 'SalBow2G2440' => 'sbo', 'SalBow4G2265' => 'sbo', 'Sc02g0000060' => 'sci', 'Sc05g0005020' => 'sci', 'Sc13g0003890' => 'sci', 'Sed0014865' => 'sed', 'Sed0017224' => 'sed', 'Sed0026391' => 'sed', 'SEGI_00063' => 'sgi', 'SEGI_10967' => 'sgi', 'SEGI_17510' => 'sgi', 'SEGI_24396' => 'sgi', 'SEGI_39719' => 'sgi', 'SEGI_41392' => 'sgi', 'SGA_v2.0_scaffold11G05794' => 'sas', 'SGA_v2.0_scaffold142G35607' => 'sas', 'SGA_v2.0_scaffold1G00447' => 'sas', 'SHI15388' => 'shi', 'SHI15394' => 'shi', 'SHI15396' => 'shi', 'SHI15399' => 'shi', 'SMO343G0151' => 'smo', 'SMO367G1118' => 'smo', 'Solyc01g080200.3' => 'sly', 'Solyc06g008960.3' => 'sly', 'Solyc09g064780.3' => 'sly', 'Sopen01g031980' => 'spe', 'Sopen06g003710' => 'spe', 'Sopen09g026460' => 'spe', 'Sp3g21240' => 'spa', 'Sp4g30030' => 'spa', 'TAR365G0022' => 'tar', 'TAR365G1023' => 'tar', 'TAR365G1253' => 'tar', 'TAR623G0078' => 'tar', 'TAR623G1721' => 'tar', 'TAR633G0959' => 'tar', 'THA.LOC104802225' => 'tha', 'THA.LOC104804769' => 'tha', 'THA.LOC104808660' => 'tha', 'THA.LOC104812792' => 'tha', 'Thecc.01G284000' => 'tca', 'Thecc.04G220600' => 'tca', 'Thecc.05G268900' => 'tca', 'Thecc.08G171100' => 'tca', 'Thhalv10001284m.g' => 'esa', 'Thhalv10019912m.g' => 'esa', 'TPR.G14189' => 'tpr', 'TPR.G18110' => 'tpr', 'TPR.G18130' => 'tpr', 'TPR.G18131' => 'tpr', 'TPR.G18140' => 'tpr', 'TPR.G24282' => 'tpr', 'TPR.G25221' => 'tpr', 'TPR.G29267' => 'tpr', 'TPR.G35315' => 'tpr', 'TPR.G36173' => 'tpr', 'TWI09G0794' => 'twi', 'TWI59G1348' => 'twi', 'TWI74G0430' => 'twi', 'unitig_26.g8940' => 'ugi', 'unitig_749.g13744' => 'ugi', 'unitig_749.g13745' => 'ugi', 'vmacro08269' => 'vma', 'vmacro14937' => 'vma', 'vmacro20401' => 'vma', 'VMungo0464G1349' => 'vmu', 'VMungo0540G0289' => 'vmu', 'VMungo1215G1590' => 'vmu', 'VMungo1309G0221' => 'vmu', 'VMungo1309G2815' => 'vmu', 'VMungo1383G0239' => 'vmu', 'VMungo1383G2910' => 'vmu', 'Zm00001eb095270' => 'zma', 'Zm00001eb095280' => 'zma', 'Zm00001eb111630' => 'zma', 'Zm00001eb237080' => 'zma', 'Zm00001eb273740' => 'zma', 'Zm00001eb285040' => 'zma', 'Zm00001eb330790' => 'zma', 'Zm00001eb337380' => 'zma' ), 'gf_id' => 'HOM05D001484', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001484' ), 'data_identifier' => 'HOM05D001484', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001484', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p31500' => 'bna', 'A05p00020' => 'bna', 'A07p08820' => 'bna', 'Aa31LG4G3300' => 'aar', 'Aa31LG8G10030' => 'aar', 'Actinidia00731' => 'ach', 'Actinidia11473' => 'ach', 'Actinidia23469' => 'ach', 'Actinidia24318' => 'ach', 'Actinidia40196' => 'ach', 'Actinidia40197' => 'ach', 'Actinidia40198' => 'ach', 'Ah.08g212990' => 'amhyb', 'Ah.15g091720' => 'amhyb', 'AL3G38260' => 'aly', 'AL4G47710' => 'aly', 'Aqoxy2G00671' => 'aox', 'Aqoxy2G03236' => 'aox', 'arahy.Tifrunner.gnm1.ann1.05IDCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KR684' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATY3SJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK6QJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6APGL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IDT7Z9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM073U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ0R87' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LE7RV4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT4QRX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V5ENPK' => 'arhy', 'AT2G48110' => 'ath', 'AT3G23590' => 'ath', 'ATR0626G186' => 'atr', 'ATR1127G141' => 'atr', 'Atru.chr4.2583' => 'acertr', 'Atru.chr5.1358' => 'acertr', 'Atru.chr5.1359' => 'acertr', 'Atru.chr8.46' => 'acertr', 'AUR62002640' => 'cqu', 'AUR62030055' => 'cqu', 'AUR62033713' => 'cqu', 'AUR62033714' => 'cqu', 'AUR62036795' => 'cqu', 'AUR62039891' => 'cqu', 'BcaB02g08737' => 'bca', 'BcaB04g20441' => 'bca', 'BcaB06g26509' => 'bca', 'BcaB06g26510' => 'bca', 'BcaB06g26511' => 'bca', 'BcaB06g26512' => 'bca', 'BcaB06g26513' => 'bca', 'BcaC02g12564' => 'bca', 'BcaC02g12565' => 'bca', 'BcaC02g12794' => 'bca', 'BcaC02g12795' => 'bca', 'BcaC02g12796' => 'bca', 'BcaC06g35541' => 'bca', 'BNapus_Darmor_BZH_scaffold_188p00080' => 'bna', 'BNapus_Darmor_BZH_scaffold_188p00090' => 'bna', 'BolC1t03972H' => 'bol', 'BolC1t03973H' => 'bol', 'BolC4t21680H' => 'bol', 'BolC7t41863H' => 'bol', 'BolSC55t61227H' => 'bol', 'BolSC55t61228H' => 'bol', 'BraA01t03278Z' => 'bra', 'BraA05t18998Z' => 'bra', 'BraA07t28673Z' => 'bra', 'C01p40150' => 'bna', 'C05p12370' => 'bna', 'C07p13680' => 'bna', 'CAN.G1006.16' => 'can', 'CAN.G1006.17' => 'can', 'CAN.G1170.2' => 'can', 'CAN.G962.7' => 'can', 'CANSAT25G2179' => 'cansat', 'CANSAT78G1573' => 'cansat', 'CARHR099510' => 'chi', 'CARHR143510' => 'chi', 'Carub.0003s2380' => 'cru', 'Carub.0004s3082' => 'cru', 'Ca_00614_v3' => 'car', 'Ca_07801_v3' => 'car', 'Ca_08567_v3' => 'car', 'Ca_09571_v3' => 'car', 'CBR_g19290' => 'cbr', 'Cc01_g19770' => 'ccan', 'Cc03_g03030' => 'ccan', 'CDE07G0968' => 'cde', 'CDE09G1441' => 'cde', 'Cfa006103' => 'cfa', 'Cfa015573' => 'cfa', 'Cfa016988' => 'cfa', 'Ciclev10006738m.g' => 'ccl', 'Ciclev10010920m.g' => 'ccl', 'Ciclev10018517m.g' => 'ccl', 'CiPaw.01G159200' => 'cil', 'CiPaw.02G091000' => 'cil', 'CiPaw.02G091100' => 'cil', 'CiPaw.08G103100' => 'cil', 'CiPaw.09G224900' => 'cil', 'ClCG06G005740' => 'cla', 'ClCG07G000090' => 'cla', 'ClCG07G000100' => 'cla', 'COL.COLO4_09143' => 'col', 'COL.COLO4_25124' => 'col', 'Cpa.g.sc16.34' => 'cpa', 'Cpa.g.sc3504.1' => 'cpa', 'Cpa.g.sc60.37' => 'cpa', 'CsaV3_6G018520' => 'csa', 'CsaV3_6G036860' => 'csa', 'CSS0001072' => 'camsi', 'CSS0020208' => 'camsi', 'CSS0021253' => 'camsi', 'CSS0022190' => 'camsi', 'CSS0036150' => 'camsi', 'CSS0040442' => 'camsi', 'CSS0042300' => 'camsi', 'CSS0045298' => 'camsi', 'DCAR_012449' => 'dca', 'DCAR_018405' => 'dca', 'DCAR_024573' => 'dca', 'DCAR_030591' => 'dca', 'Dinv16926' => 'din', 'Dinv32963' => 'din', 'Dinv38382' => 'din', 'Dinv38383' => 'din', 'Duzib133G0974' => 'dzi', 'Duzib138G1867' => 'dzi', 'Duzib211G0420' => 'dzi', 'Duzib212G0930' => 'dzi', 'ECA234G1645' => 'eca', 'ECA247G3467' => 'eca', 'ECA248G1703' => 'eca', 'EL10Ac3g06327' => 'bvu', 'EL10Ac7g17204' => 'bvu', 'Eucgr.A00855' => 'egr', 'Eucgr.A00858' => 'egr', 'Eucgr.H01520' => 'egr', 'Eucgr.H03604' => 'egr', 'Eucgr.L03465' => 'egr', 'Eucgr.L03466' => 'egr', 'FAN01G0988' => 'fan', 'FAN02G3892' => 'fan', 'FAN05G3381' => 'fan', 'FAN07G0967' => 'fan', 'FAN07G1493' => 'fan', 'FAN08G3125' => 'fan', 'FAN09G0402' => 'fan', 'FAN12G2594' => 'fan', 'FAN12G3879' => 'fan', 'FAN14G1546' => 'fan', 'FAN15G3626' => 'fan', 'FAN17G0588' => 'fan', 'FAN17G0609' => 'fan', 'FAN18G2817' => 'fan', 'FAN19G1305' => 'fan', 'FAN20G1787' => 'fan', 'FAN22G0073' => 'fan', 'FAN22G0352' => 'fan', 'FAN22G0368' => 'fan', 'FAN22G2273' => 'fan', 'FAN24G1998' => 'fan', 'FAN27G1317' => 'fan', 'FvH4_2g23980' => 'fve', 'FvH4_4g14380' => 'fve', 'FvH4_4g14390' => 'fve', 'FvH4_6g09250' => 'fve', 'Glyma.03G151100' => 'gma', 'Glyma.04G122550' => 'gma', 'Glyma.05G001600' => 'gma', 'Glyma.09G270766' => 'gma', 'Glyma.09G270832' => 'gma', 'Glyma.13G209800' => 'gma', 'Glyma.15G102800' => 'gma', 'Glyma.18G218900' => 'gma', 'Glyma.19G001500' => 'gma', 'Glyma.19G153600' => 'gma', 'Gohir.A02G028600' => 'ghi', 'Gohir.A08G045000' => 'ghi', 'Gohir.A11G120500' => 'ghi', 'Gohir.A12G006200' => 'ghi', 'Gohir.A12G006250' => 'ghi', 'Gohir.D02G036300' => 'ghi', 'Gohir.D08G054700' => 'ghi', 'Gohir.D11G125600' => 'ghi', 'Gohir.D12G005700' => 'ghi', 'Gorai.004G055200' => 'gra', 'Gorai.005G040400' => 'gra', 'Gorai.007G134500' => 'gra', 'Gorai.008G005500' => 'gra', 'GSVIVG01011094001' => 'vvi', 'GSVIVG01017879001' => 'vvi', 'GSVIVG01025988001' => 'vvi', 'GSVIVG01029847001' => 'vvi', 'HanXRQChr10g0282901' => 'han', 'HanXRQChr10g0310371' => 'han', 'HanXRQChr10g0315041' => 'han', 'HanXRQChr11g0327651' => 'han', 'HanXRQChr12g0359391' => 'han', 'Haze_00972' => 'cav', 'Haze_00973' => 'cav', 'Haze_00974' => 'cav', 'Haze_04747' => 'cav', 'Haze_04749' => 'cav', 'Haze_04750' => 'cav', 'Haze_21217' => 'cav', 'Hma1.2p1_1037F.1_g250680' => 'hma', 'Hma1.2p1_1644F.1_g295320' => 'hma', 'HPP92_011322' => 'vpl', 'HPP92_011323' => 'vpl', 'HPP92_011324' => 'vpl', 'HPP92_011325' => 'vpl', 'HPP92_011326' => 'vpl', 'Hund12205' => 'sun', 'Hund17957' => 'sun', 'Lalb_Chr06g0176771' => 'lal', 'Lalb_Chr18g0056021' => 'lal', 'Lalb_Chr18g0056031' => 'lal', 'Lalb_Chr18g0056041' => 'lal', 'Lalb_Chr20g0107751' => 'lal', 'Lalb_Chr20g0118371' => 'lal', 'Lj1g0010239' => 'lja', 'Lj1g0017101' => 'lja', 'Lj2A1178G40' => 'lonja', 'Lj2A54G84' => 'lonja', 'Lj2g0015248' => 'lja', 'Lj3A761T51' => 'lonja', 'Lj6g0018116' => 'lja', 'Lsat_1_v5_gn_4_136040' => 'lsa', 'Lsat_1_v5_gn_5_187461' => 'lsa', 'Lsat_1_v5_gn_5_77001' => 'lsa', 'Lsat_1_v5_gn_9_4461' => 'lsa', 'Manes.01G210100' => 'mes', 'Manes.03G185600' => 'mes', 'Manes.05G073300' => 'mes', 'Manes.09G120300' => 'mes', 'Manes.15G022100' => 'mes', 'Mapoly0096s0053' => 'mpo', 'MBI03_g14058_MAGBIO' => 'mbi', 'MBI03_g33876_MAGBIO' => 'mbi', 'MBI03_g36854_MAGBIO' => 'mbi', 'MBI17_g11997_MAGBIO' => 'mbi', 'MD03G1269000' => 'mdo', 'MD04G1179600' => 'mdo', 'MD11G1289800' => 'mdo', 'MD12G1194700' => 'mdo', 'MD13G1182100' => 'mdo', 'MD13G1182200' => 'mdo', 'MD16G1182600' => 'mdo', 'Medtr2g021400' => 'mtr', 'Medtr2g021470' => 'mtr', 'Medtr2g105810' => 'mtr', 'Medtr3g033580' => 'mtr', 'Medtr6g007970' => 'mtr', 'Medtr7g056330' => 'mtr', 'Medtr7g074290' => 'mtr', 'Medtr7g074380' => 'mtr', 'Medtr7g094550' => 'mtr', 'Medtr8g069995' => 'mtr', 'MELO3C014345.2' => 'cme', 'MELO3C021395.2' => 'cme', 'Migut.D00262' => 'egut', 'Migut.G00257' => 'egut', 'MSTRG.21575' => 'ama', 'MSTRG.3985' => 'ama', 'Nitab4.5_0000295g0140' => 'nta', 'Nitab4.5_0000732g0140' => 'nta', 'Nitab4.5_0003162g0020' => 'nta', 'Nitab4.5_0006180g0090' => 'nta', 'Nitab4.5_0006390g0010' => 'nta', 'Nitab4.5_0007392g0040' => 'nta', 'Nn1g02140' => 'nnu', 'Nn4g26168' => 'nnu', 'Nn5g26754' => 'nnu', 'Oeu001433.1' => 'oeu', 'Oeu010299.2' => 'oeu', 'Oeu011171.1' => 'oeu', 'Oeu037675.1' => 'oeu', 'Oeu038359.1' => 'oeu', 'Oeu063834.1' => 'oeu', 'Oeu063835.1' => 'oeu', 'Os05g0312000' => 'osa', 'Os07g0211101' => 'osa', 'Os07g0211200' => 'osa', 'Os07g0681500' => 'osa', 'Peaxi162Scf00095g01015' => 'pax', 'Peaxi162Scf00104g00329' => 'pax', 'Peaxi162Scf00161g00137' => 'pax', 'PGR004G1665' => 'pgr', 'PGR031G2937' => 'pgr', 'PGR119G2145' => 'pgr', 'PGSC0003DMG400004351' => 'stu', 'PGSC0003DMG400014625' => 'stu', 'PGSC0003DMG401000943' => 'stu', 'Phvul.001G148600' => 'pvu', 'Phvul.004G001700' => 'pvu', 'Phvul.006G154900' => 'pvu', 'Phvul.008G078200' => 'pvu', 'Phvul.011G136500' => 'pvu', 'Potri.002G215600' => 'ptr', 'Potri.008G201600' => 'ptr', 'Potri.014G138400' => 'ptr', 'Potri.016G142500' => 'ptr', 'Pp3c16_10580' => 'ppa', 'Pp3c5_25280' => 'ppa', 'Prupe.1G150000' => 'ppe', 'Prupe.1G150100' => 'ppe', 'Prupe.6G299600' => 'ppe', 'Prupe.8G245000' => 'ppe', 'Psat0s4927g0040' => 'psa', 'Psat1g052080' => 'psa', 'Psat1g183800' => 'psa', 'Psat3g113840' => 'psa', 'Psat3g126120' => 'psa', 'Psat3g126160' => 'psa', 'Psat3g158760' => 'psa', 'Psat3g158840' => 'psa', 'PSO170G2858' => 'pso', 'PSO339G0606' => 'pso', 'PSO384G4709' => 'pso', 'PSO407G0334' => 'pso', 'QL04p040276' => 'qlo', 'QL06p005458' => 'qlo', 'QL06p005472' => 'qlo', 'QL07p030546' => 'qlo', 'QL07p031519' => 'qlo', 'QL09p050949' => 'qlo', 'QL09p050966' => 'qlo', 'QL09p051067' => 'qlo', 'QL12p022706' => 'qlo', 'RcHm_v2.0_Chr2g0119601' => 'rch', 'RcHm_v2.0_Chr3g0459591' => 'rch', 'RcHm_v2.0_Chr4g0418521' => 'rch', 'RcHm_v2.0_Chr4g0418531' => 'rch', 'RcHm_v2.0_Chr4g0418541' => 'rch', 'RcHm_v2.0_Chr6g0291641' => 'rch', 'Rhsim01G0086300' => 'rsi', 'Rhsim01G0276300' => 'rsi', 'Rhsim01G0276500' => 'rsi', 'Rhsim04G0207700' => 'rsi', 'Rhsim05G0234500' => 'rsi', 'Rhsim13G0022400' => 'rsi', 'Sabra02G0167900' => 'sbr', 'Sabra04G0158500' => 'sbr', 'Sabra08G0159800' => 'sbr', 'Sabra10G0011500' => 'sbr', 'Sabra14G0104400' => 'sbr', 'SalBow2G2440' => 'sbo', 'SalBow4G2265' => 'sbo', 'Sc02g0000060' => 'sci', 'Sc05g0005020' => 'sci', 'Sc13g0003890' => 'sci', 'Sed0014865' => 'sed', 'Sed0017224' => 'sed', 'Sed0026391' => 'sed', 'SEGI_00063' => 'sgi', 'SEGI_10967' => 'sgi', 'SEGI_17510' => 'sgi', 'SEGI_24396' => 'sgi', 'SEGI_39719' => 'sgi', 'SEGI_41392' => 'sgi', 'SGA_v2.0_scaffold11G05794' => 'sas', 'SGA_v2.0_scaffold142G35607' => 'sas', 'SGA_v2.0_scaffold1G00447' => 'sas', 'SHI15388' => 'shi', 'SHI15394' => 'shi', 'SHI15396' => 'shi', 'SHI15399' => 'shi', 'SMO343G0151' => 'smo', 'SMO367G1118' => 'smo', 'Solyc01g080200.3' => 'sly', 'Solyc06g008960.3' => 'sly', 'Solyc09g064780.3' => 'sly', 'Sopen01g031980' => 'spe', 'Sopen06g003710' => 'spe', 'Sopen09g026460' => 'spe', 'Sp3g21240' => 'spa', 'Sp4g30030' => 'spa', 'TAR365G0022' => 'tar', 'TAR365G1023' => 'tar', 'TAR365G1253' => 'tar', 'TAR623G0078' => 'tar', 'TAR623G1721' => 'tar', 'TAR633G0959' => 'tar', 'THA.LOC104802225' => 'tha', 'THA.LOC104804769' => 'tha', 'THA.LOC104808660' => 'tha', 'THA.LOC104812792' => 'tha', 'Thecc.01G284000' => 'tca', 'Thecc.04G220600' => 'tca', 'Thecc.05G268900' => 'tca', 'Thecc.08G171100' => 'tca', 'Thhalv10001284m.g' => 'esa', 'Thhalv10019912m.g' => 'esa', 'TPR.G14189' => 'tpr', 'TPR.G18110' => 'tpr', 'TPR.G18130' => 'tpr', 'TPR.G18131' => 'tpr', 'TPR.G18140' => 'tpr', 'TPR.G24282' => 'tpr', 'TPR.G25221' => 'tpr', 'TPR.G29267' => 'tpr', 'TPR.G35315' => 'tpr', 'TPR.G36173' => 'tpr', 'TWI09G0794' => 'twi', 'TWI59G1348' => 'twi', 'TWI74G0430' => 'twi', 'unitig_26.g8940' => 'ugi', 'unitig_749.g13744' => 'ugi', 'unitig_749.g13745' => 'ugi', 'vmacro08269' => 'vma', 'vmacro14937' => 'vma', 'vmacro20401' => 'vma', 'VMungo0464G1349' => 'vmu', 'VMungo0540G0289' => 'vmu', 'VMungo1215G1590' => 'vmu', 'VMungo1309G0221' => 'vmu', 'VMungo1309G2815' => 'vmu', 'VMungo1383G0239' => 'vmu', 'VMungo1383G2910' => 'vmu', 'Zm00001eb095270' => 'zma', 'Zm00001eb095280' => 'zma', 'Zm00001eb111630' => 'zma', 'Zm00001eb237080' => 'zma', 'Zm00001eb273740' => 'zma', 'Zm00001eb285040' => 'zma', 'Zm00001eb330790' => 'zma', 'Zm00001eb337380' => 'zma' ) $gf_id = 'HOM05D001484' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001484' ) $data_identifier = 'HOM05D001484' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 2, 'aly' => (int) 2, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 22, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 7, 'hma' => (int) 2, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 7, 'mtr' => (int) 10, 'cme' => (int) 2, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 4, 'ppa' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 4, 'qlo' => (int) 9, 'rch' => (int) 6, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 10, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 7, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb337380' $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' => 'HOM05D001484', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p31500' => 'bna', 'A05p00020' => 'bna', 'A07p08820' => 'bna', 'Aa31LG4G3300' => 'aar', 'Aa31LG8G10030' => 'aar', 'Actinidia00731' => 'ach', 'Actinidia11473' => 'ach', 'Actinidia23469' => 'ach', 'Actinidia24318' => 'ach', 'Actinidia40196' => 'ach', 'Actinidia40197' => 'ach', 'Actinidia40198' => 'ach', 'Ah.08g212990' => 'amhyb', 'Ah.15g091720' => 'amhyb', 'AL3G38260' => 'aly', 'AL4G47710' => 'aly', 'Aqoxy2G00671' => 'aox', 'Aqoxy2G03236' => 'aox', 'arahy.Tifrunner.gnm1.ann1.05IDCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KR684' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATY3SJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK6QJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6APGL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IDT7Z9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM073U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ0R87' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LE7RV4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT4QRX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V5ENPK' => 'arhy', 'AT2G48110' => 'ath', 'AT3G23590' => 'ath', 'ATR0626G186' => 'atr', 'ATR1127G141' => 'atr', 'Atru.chr4.2583' => 'acertr', 'Atru.chr5.1358' => 'acertr', 'Atru.chr5.1359' => 'acertr', 'Atru.chr8.46' => 'acertr', 'AUR62002640' => 'cqu', 'AUR62030055' => 'cqu', 'AUR62033713' => 'cqu', 'AUR62033714' => 'cqu', 'AUR62036795' => 'cqu', 'AUR62039891' => 'cqu', 'BcaB02g08737' => 'bca', 'BcaB04g20441' => 'bca', 'BcaB06g26509' => 'bca', 'BcaB06g26510' => 'bca', 'BcaB06g26511' => 'bca', 'BcaB06g26512' => 'bca', 'BcaB06g26513' => 'bca', 'BcaC02g12564' => 'bca', 'BcaC02g12565' => 'bca', 'BcaC02g12794' => 'bca', 'BcaC02g12795' => 'bca', 'BcaC02g12796' => 'bca', 'BcaC06g35541' => 'bca', 'BNapus_Darmor_BZH_scaffold_188p00080' => 'bna', 'BNapus_Darmor_BZH_scaffold_188p00090' => 'bna', 'BolC1t03972H' => 'bol', 'BolC1t03973H' => 'bol', 'BolC4t21680H' => 'bol', 'BolC7t41863H' => 'bol', 'BolSC55t61227H' => 'bol', 'BolSC55t61228H' => 'bol', 'BraA01t03278Z' => 'bra', 'BraA05t18998Z' => 'bra', 'BraA07t28673Z' => 'bra', 'C01p40150' => 'bna', 'C05p12370' => 'bna', 'C07p13680' => 'bna', 'CAN.G1006.16' => 'can', 'CAN.G1006.17' => 'can', 'CAN.G1170.2' => 'can', 'CAN.G962.7' => 'can', 'CANSAT25G2179' => 'cansat', 'CANSAT78G1573' => 'cansat', 'CARHR099510' => 'chi', 'CARHR143510' => 'chi', 'Carub.0003s2380' => 'cru', 'Carub.0004s3082' => 'cru', 'Ca_00614_v3' => 'car', 'Ca_07801_v3' => 'car', 'Ca_08567_v3' => 'car', 'Ca_09571_v3' => 'car', 'CBR_g19290' => 'cbr', 'Cc01_g19770' => 'ccan', 'Cc03_g03030' => 'ccan', 'CDE07G0968' => 'cde', 'CDE09G1441' => 'cde', 'Cfa006103' => 'cfa', 'Cfa015573' => 'cfa', 'Cfa016988' => 'cfa', 'Ciclev10006738m.g' => 'ccl', 'Ciclev10010920m.g' => 'ccl', 'Ciclev10018517m.g' => 'ccl', 'CiPaw.01G159200' => 'cil', 'CiPaw.02G091000' => 'cil', 'CiPaw.02G091100' => 'cil', 'CiPaw.08G103100' => 'cil', 'CiPaw.09G224900' => 'cil', 'ClCG06G005740' => 'cla', 'ClCG07G000090' => 'cla', 'ClCG07G000100' => 'cla', 'COL.COLO4_09143' => 'col', 'COL.COLO4_25124' => 'col', 'Cpa.g.sc16.34' => 'cpa', 'Cpa.g.sc3504.1' => 'cpa', 'Cpa.g.sc60.37' => 'cpa', 'CsaV3_6G018520' => 'csa', 'CsaV3_6G036860' => 'csa', 'CSS0001072' => 'camsi', 'CSS0020208' => 'camsi', 'CSS0021253' => 'camsi', 'CSS0022190' => 'camsi', 'CSS0036150' => 'camsi', 'CSS0040442' => 'camsi', 'CSS0042300' => 'camsi', 'CSS0045298' => 'camsi', 'DCAR_012449' => 'dca', 'DCAR_018405' => 'dca', 'DCAR_024573' => 'dca', 'DCAR_030591' => 'dca', 'Dinv16926' => 'din', 'Dinv32963' => 'din', 'Dinv38382' => 'din', 'Dinv38383' => 'din', 'Duzib133G0974' => 'dzi', 'Duzib138G1867' => 'dzi', 'Duzib211G0420' => 'dzi', 'Duzib212G0930' => 'dzi', 'ECA234G1645' => 'eca', 'ECA247G3467' => 'eca', 'ECA248G1703' => 'eca', 'EL10Ac3g06327' => 'bvu', 'EL10Ac7g17204' => 'bvu', 'Eucgr.A00855' => 'egr', 'Eucgr.A00858' => 'egr', 'Eucgr.H01520' => 'egr', 'Eucgr.H03604' => 'egr', 'Eucgr.L03465' => 'egr', 'Eucgr.L03466' => 'egr', 'FAN01G0988' => 'fan', 'FAN02G3892' => 'fan', 'FAN05G3381' => 'fan', 'FAN07G0967' => 'fan', 'FAN07G1493' => 'fan', 'FAN08G3125' => 'fan', 'FAN09G0402' => 'fan', 'FAN12G2594' => 'fan', 'FAN12G3879' => 'fan', 'FAN14G1546' => 'fan', 'FAN15G3626' => 'fan', 'FAN17G0588' => 'fan', 'FAN17G0609' => 'fan', 'FAN18G2817' => 'fan', 'FAN19G1305' => 'fan', 'FAN20G1787' => 'fan', 'FAN22G0073' => 'fan', 'FAN22G0352' => 'fan', 'FAN22G0368' => 'fan', 'FAN22G2273' => 'fan', 'FAN24G1998' => 'fan', 'FAN27G1317' => 'fan', 'FvH4_2g23980' => 'fve', 'FvH4_4g14380' => 'fve', 'FvH4_4g14390' => 'fve', 'FvH4_6g09250' => 'fve', 'Glyma.03G151100' => 'gma', 'Glyma.04G122550' => 'gma', 'Glyma.05G001600' => 'gma', 'Glyma.09G270766' => 'gma', 'Glyma.09G270832' => 'gma', 'Glyma.13G209800' => 'gma', 'Glyma.15G102800' => 'gma', 'Glyma.18G218900' => 'gma', 'Glyma.19G001500' => 'gma', 'Glyma.19G153600' => 'gma', 'Gohir.A02G028600' => 'ghi', 'Gohir.A08G045000' => 'ghi', 'Gohir.A11G120500' => 'ghi', 'Gohir.A12G006200' => 'ghi', 'Gohir.A12G006250' => 'ghi', 'Gohir.D02G036300' => 'ghi', 'Gohir.D08G054700' => 'ghi', 'Gohir.D11G125600' => 'ghi', 'Gohir.D12G005700' => 'ghi', 'Gorai.004G055200' => 'gra', 'Gorai.005G040400' => 'gra', 'Gorai.007G134500' => 'gra', 'Gorai.008G005500' => 'gra', 'GSVIVG01011094001' => 'vvi', 'GSVIVG01017879001' => 'vvi', 'GSVIVG01025988001' => 'vvi', 'GSVIVG01029847001' => 'vvi', 'HanXRQChr10g0282901' => 'han', 'HanXRQChr10g0310371' => 'han', 'HanXRQChr10g0315041' => 'han', 'HanXRQChr11g0327651' => 'han', 'HanXRQChr12g0359391' => 'han', 'Haze_00972' => 'cav', 'Haze_00973' => 'cav', 'Haze_00974' => 'cav', 'Haze_04747' => 'cav', 'Haze_04749' => 'cav', 'Haze_04750' => 'cav', 'Haze_21217' => 'cav', 'Hma1.2p1_1037F.1_g250680' => 'hma', 'Hma1.2p1_1644F.1_g295320' => 'hma', 'HPP92_011322' => 'vpl', 'HPP92_011323' => 'vpl', 'HPP92_011324' => 'vpl', 'HPP92_011325' => 'vpl', 'HPP92_011326' => 'vpl', 'Hund12205' => 'sun', 'Hund17957' => 'sun', 'Lalb_Chr06g0176771' => 'lal', 'Lalb_Chr18g0056021' => 'lal', 'Lalb_Chr18g0056031' => 'lal', 'Lalb_Chr18g0056041' => 'lal', 'Lalb_Chr20g0107751' => 'lal', 'Lalb_Chr20g0118371' => 'lal', 'Lj1g0010239' => 'lja', 'Lj1g0017101' => 'lja', 'Lj2A1178G40' => 'lonja', 'Lj2A54G84' => 'lonja', 'Lj2g0015248' => 'lja', 'Lj3A761T51' => 'lonja', 'Lj6g0018116' => 'lja', 'Lsat_1_v5_gn_4_136040' => 'lsa', 'Lsat_1_v5_gn_5_187461' => 'lsa', 'Lsat_1_v5_gn_5_77001' => 'lsa', 'Lsat_1_v5_gn_9_4461' => 'lsa', 'Manes.01G210100' => 'mes', 'Manes.03G185600' => 'mes', 'Manes.05G073300' => 'mes', 'Manes.09G120300' => 'mes', 'Manes.15G022100' => 'mes', 'Mapoly0096s0053' => 'mpo', 'MBI03_g14058_MAGBIO' => 'mbi', 'MBI03_g33876_MAGBIO' => 'mbi', 'MBI03_g36854_MAGBIO' => 'mbi', 'MBI17_g11997_MAGBIO' => 'mbi', 'MD03G1269000' => 'mdo', 'MD04G1179600' => 'mdo', 'MD11G1289800' => 'mdo', 'MD12G1194700' => 'mdo', 'MD13G1182100' => 'mdo', 'MD13G1182200' => 'mdo', 'MD16G1182600' => 'mdo', 'Medtr2g021400' => 'mtr', 'Medtr2g021470' => 'mtr', 'Medtr2g105810' => 'mtr', 'Medtr3g033580' => 'mtr', 'Medtr6g007970' => 'mtr', 'Medtr7g056330' => 'mtr', 'Medtr7g074290' => 'mtr', 'Medtr7g074380' => 'mtr', 'Medtr7g094550' => 'mtr', 'Medtr8g069995' => 'mtr', 'MELO3C014345.2' => 'cme', 'MELO3C021395.2' => 'cme', 'Migut.D00262' => 'egut', 'Migut.G00257' => 'egut', 'MSTRG.21575' => 'ama', 'MSTRG.3985' => 'ama', 'Nitab4.5_0000295g0140' => 'nta', 'Nitab4.5_0000732g0140' => 'nta', 'Nitab4.5_0003162g0020' => 'nta', 'Nitab4.5_0006180g0090' => 'nta', 'Nitab4.5_0006390g0010' => 'nta', 'Nitab4.5_0007392g0040' => 'nta', 'Nn1g02140' => 'nnu', 'Nn4g26168' => 'nnu', 'Nn5g26754' => 'nnu', 'Oeu001433.1' => 'oeu', 'Oeu010299.2' => 'oeu', 'Oeu011171.1' => 'oeu', 'Oeu037675.1' => 'oeu', 'Oeu038359.1' => 'oeu', 'Oeu063834.1' => 'oeu', 'Oeu063835.1' => 'oeu', 'Os05g0312000' => 'osa', 'Os07g0211101' => 'osa', 'Os07g0211200' => 'osa', 'Os07g0681500' => 'osa', 'Peaxi162Scf00095g01015' => 'pax', 'Peaxi162Scf00104g00329' => 'pax', 'Peaxi162Scf00161g00137' => 'pax', 'PGR004G1665' => 'pgr', 'PGR031G2937' => 'pgr', 'PGR119G2145' => 'pgr', 'PGSC0003DMG400004351' => 'stu', 'PGSC0003DMG400014625' => 'stu', 'PGSC0003DMG401000943' => 'stu', 'Phvul.001G148600' => 'pvu', 'Phvul.004G001700' => 'pvu', 'Phvul.006G154900' => 'pvu', 'Phvul.008G078200' => 'pvu', 'Phvul.011G136500' => 'pvu', 'Potri.002G215600' => 'ptr', 'Potri.008G201600' => 'ptr', 'Potri.014G138400' => 'ptr', 'Potri.016G142500' => 'ptr', 'Pp3c16_10580' => 'ppa', 'Pp3c5_25280' => 'ppa', 'Prupe.1G150000' => 'ppe', 'Prupe.1G150100' => 'ppe', 'Prupe.6G299600' => 'ppe', 'Prupe.8G245000' => 'ppe', 'Psat0s4927g0040' => 'psa', 'Psat1g052080' => 'psa', 'Psat1g183800' => 'psa', 'Psat3g113840' => 'psa', 'Psat3g126120' => 'psa', 'Psat3g126160' => 'psa', 'Psat3g158760' => 'psa', 'Psat3g158840' => 'psa', 'PSO170G2858' => 'pso', 'PSO339G0606' => 'pso', 'PSO384G4709' => 'pso', 'PSO407G0334' => 'pso', 'QL04p040276' => 'qlo', 'QL06p005458' => 'qlo', 'QL06p005472' => 'qlo', 'QL07p030546' => 'qlo', 'QL07p031519' => 'qlo', 'QL09p050949' => 'qlo', 'QL09p050966' => 'qlo', 'QL09p051067' => 'qlo', 'QL12p022706' => 'qlo', 'RcHm_v2.0_Chr2g0119601' => 'rch', 'RcHm_v2.0_Chr3g0459591' => 'rch', 'RcHm_v2.0_Chr4g0418521' => 'rch', 'RcHm_v2.0_Chr4g0418531' => 'rch', 'RcHm_v2.0_Chr4g0418541' => 'rch', 'RcHm_v2.0_Chr6g0291641' => 'rch', 'Rhsim01G0086300' => 'rsi', 'Rhsim01G0276300' => 'rsi', 'Rhsim01G0276500' => 'rsi', 'Rhsim04G0207700' => 'rsi', 'Rhsim05G0234500' => 'rsi', 'Rhsim13G0022400' => 'rsi', 'Sabra02G0167900' => 'sbr', 'Sabra04G0158500' => 'sbr', 'Sabra08G0159800' => 'sbr', 'Sabra10G0011500' => 'sbr', 'Sabra14G0104400' => 'sbr', 'SalBow2G2440' => 'sbo', 'SalBow4G2265' => 'sbo', 'Sc02g0000060' => 'sci', 'Sc05g0005020' => 'sci', 'Sc13g0003890' => 'sci', 'Sed0014865' => 'sed', 'Sed0017224' => 'sed', 'Sed0026391' => 'sed', 'SEGI_00063' => 'sgi', 'SEGI_10967' => 'sgi', 'SEGI_17510' => 'sgi', 'SEGI_24396' => 'sgi', 'SEGI_39719' => 'sgi', 'SEGI_41392' => 'sgi', 'SGA_v2.0_scaffold11G05794' => 'sas', 'SGA_v2.0_scaffold142G35607' => 'sas', 'SGA_v2.0_scaffold1G00447' => 'sas', 'SHI15388' => 'shi', 'SHI15394' => 'shi', 'SHI15396' => 'shi', 'SHI15399' => 'shi', 'SMO343G0151' => 'smo', 'SMO367G1118' => 'smo', 'Solyc01g080200.3' => 'sly', 'Solyc06g008960.3' => 'sly', 'Solyc09g064780.3' => 'sly', 'Sopen01g031980' => 'spe', 'Sopen06g003710' => 'spe', 'Sopen09g026460' => 'spe', 'Sp3g21240' => 'spa', 'Sp4g30030' => 'spa', 'TAR365G0022' => 'tar', 'TAR365G1023' => 'tar', 'TAR365G1253' => 'tar', 'TAR623G0078' => 'tar', 'TAR623G1721' => 'tar', 'TAR633G0959' => 'tar', 'THA.LOC104802225' => 'tha', 'THA.LOC104804769' => 'tha', 'THA.LOC104808660' => 'tha', 'THA.LOC104812792' => 'tha', 'Thecc.01G284000' => 'tca', 'Thecc.04G220600' => 'tca', 'Thecc.05G268900' => 'tca', 'Thecc.08G171100' => 'tca', 'Thhalv10001284m.g' => 'esa', 'Thhalv10019912m.g' => 'esa', 'TPR.G14189' => 'tpr', 'TPR.G18110' => 'tpr', 'TPR.G18130' => 'tpr', 'TPR.G18131' => 'tpr', 'TPR.G18140' => 'tpr', 'TPR.G24282' => 'tpr', 'TPR.G25221' => 'tpr', 'TPR.G29267' => 'tpr', 'TPR.G35315' => 'tpr', 'TPR.G36173' => 'tpr', 'TWI09G0794' => 'twi', 'TWI59G1348' => 'twi', 'TWI74G0430' => 'twi', 'unitig_26.g8940' => 'ugi', 'unitig_749.g13744' => 'ugi', 'unitig_749.g13745' => 'ugi', 'vmacro08269' => 'vma', 'vmacro14937' => 'vma', 'vmacro20401' => 'vma', 'VMungo0464G1349' => 'vmu', 'VMungo0540G0289' => 'vmu', 'VMungo1215G1590' => 'vmu', 'VMungo1309G0221' => 'vmu', 'VMungo1309G2815' => 'vmu', 'VMungo1383G0239' => 'vmu', 'VMungo1383G2910' => 'vmu', 'Zm00001eb095270' => 'zma', 'Zm00001eb095280' => 'zma', 'Zm00001eb111630' => 'zma', 'Zm00001eb237080' => 'zma', 'Zm00001eb273740' => 'zma', 'Zm00001eb285040' => 'zma', 'Zm00001eb330790' => 'zma', 'Zm00001eb337380' => 'zma' ), 'gf_id' => 'HOM05D001484', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001484' ), 'data_identifier' => 'HOM05D001484', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001484', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p31500' => 'bna', 'A05p00020' => 'bna', 'A07p08820' => 'bna', 'Aa31LG4G3300' => 'aar', 'Aa31LG8G10030' => 'aar', 'Actinidia00731' => 'ach', 'Actinidia11473' => 'ach', 'Actinidia23469' => 'ach', 'Actinidia24318' => 'ach', 'Actinidia40196' => 'ach', 'Actinidia40197' => 'ach', 'Actinidia40198' => 'ach', 'Ah.08g212990' => 'amhyb', 'Ah.15g091720' => 'amhyb', 'AL3G38260' => 'aly', 'AL4G47710' => 'aly', 'Aqoxy2G00671' => 'aox', 'Aqoxy2G03236' => 'aox', 'arahy.Tifrunner.gnm1.ann1.05IDCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KR684' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATY3SJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK6QJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6APGL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IDT7Z9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM073U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ0R87' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LE7RV4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT4QRX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V5ENPK' => 'arhy', 'AT2G48110' => 'ath', 'AT3G23590' => 'ath', 'ATR0626G186' => 'atr', 'ATR1127G141' => 'atr', 'Atru.chr4.2583' => 'acertr', 'Atru.chr5.1358' => 'acertr', 'Atru.chr5.1359' => 'acertr', 'Atru.chr8.46' => 'acertr', 'AUR62002640' => 'cqu', 'AUR62030055' => 'cqu', 'AUR62033713' => 'cqu', 'AUR62033714' => 'cqu', 'AUR62036795' => 'cqu', 'AUR62039891' => 'cqu', 'BcaB02g08737' => 'bca', 'BcaB04g20441' => 'bca', 'BcaB06g26509' => 'bca', 'BcaB06g26510' => 'bca', 'BcaB06g26511' => 'bca', 'BcaB06g26512' => 'bca', 'BcaB06g26513' => 'bca', 'BcaC02g12564' => 'bca', 'BcaC02g12565' => 'bca', 'BcaC02g12794' => 'bca', 'BcaC02g12795' => 'bca', 'BcaC02g12796' => 'bca', 'BcaC06g35541' => 'bca', 'BNapus_Darmor_BZH_scaffold_188p00080' => 'bna', 'BNapus_Darmor_BZH_scaffold_188p00090' => 'bna', 'BolC1t03972H' => 'bol', 'BolC1t03973H' => 'bol', 'BolC4t21680H' => 'bol', 'BolC7t41863H' => 'bol', 'BolSC55t61227H' => 'bol', 'BolSC55t61228H' => 'bol', 'BraA01t03278Z' => 'bra', 'BraA05t18998Z' => 'bra', 'BraA07t28673Z' => 'bra', 'C01p40150' => 'bna', 'C05p12370' => 'bna', 'C07p13680' => 'bna', 'CAN.G1006.16' => 'can', 'CAN.G1006.17' => 'can', 'CAN.G1170.2' => 'can', 'CAN.G962.7' => 'can', 'CANSAT25G2179' => 'cansat', 'CANSAT78G1573' => 'cansat', 'CARHR099510' => 'chi', 'CARHR143510' => 'chi', 'Carub.0003s2380' => 'cru', 'Carub.0004s3082' => 'cru', 'Ca_00614_v3' => 'car', 'Ca_07801_v3' => 'car', 'Ca_08567_v3' => 'car', 'Ca_09571_v3' => 'car', 'CBR_g19290' => 'cbr', 'Cc01_g19770' => 'ccan', 'Cc03_g03030' => 'ccan', 'CDE07G0968' => 'cde', 'CDE09G1441' => 'cde', 'Cfa006103' => 'cfa', 'Cfa015573' => 'cfa', 'Cfa016988' => 'cfa', 'Ciclev10006738m.g' => 'ccl', 'Ciclev10010920m.g' => 'ccl', 'Ciclev10018517m.g' => 'ccl', 'CiPaw.01G159200' => 'cil', 'CiPaw.02G091000' => 'cil', 'CiPaw.02G091100' => 'cil', 'CiPaw.08G103100' => 'cil', 'CiPaw.09G224900' => 'cil', 'ClCG06G005740' => 'cla', 'ClCG07G000090' => 'cla', 'ClCG07G000100' => 'cla', 'COL.COLO4_09143' => 'col', 'COL.COLO4_25124' => 'col', 'Cpa.g.sc16.34' => 'cpa', 'Cpa.g.sc3504.1' => 'cpa', 'Cpa.g.sc60.37' => 'cpa', 'CsaV3_6G018520' => 'csa', 'CsaV3_6G036860' => 'csa', 'CSS0001072' => 'camsi', 'CSS0020208' => 'camsi', 'CSS0021253' => 'camsi', 'CSS0022190' => 'camsi', 'CSS0036150' => 'camsi', 'CSS0040442' => 'camsi', 'CSS0042300' => 'camsi', 'CSS0045298' => 'camsi', 'DCAR_012449' => 'dca', 'DCAR_018405' => 'dca', 'DCAR_024573' => 'dca', 'DCAR_030591' => 'dca', 'Dinv16926' => 'din', 'Dinv32963' => 'din', 'Dinv38382' => 'din', 'Dinv38383' => 'din', 'Duzib133G0974' => 'dzi', 'Duzib138G1867' => 'dzi', 'Duzib211G0420' => 'dzi', 'Duzib212G0930' => 'dzi', 'ECA234G1645' => 'eca', 'ECA247G3467' => 'eca', 'ECA248G1703' => 'eca', 'EL10Ac3g06327' => 'bvu', 'EL10Ac7g17204' => 'bvu', 'Eucgr.A00855' => 'egr', 'Eucgr.A00858' => 'egr', 'Eucgr.H01520' => 'egr', 'Eucgr.H03604' => 'egr', 'Eucgr.L03465' => 'egr', 'Eucgr.L03466' => 'egr', 'FAN01G0988' => 'fan', 'FAN02G3892' => 'fan', 'FAN05G3381' => 'fan', 'FAN07G0967' => 'fan', 'FAN07G1493' => 'fan', 'FAN08G3125' => 'fan', 'FAN09G0402' => 'fan', 'FAN12G2594' => 'fan', 'FAN12G3879' => 'fan', 'FAN14G1546' => 'fan', 'FAN15G3626' => 'fan', 'FAN17G0588' => 'fan', 'FAN17G0609' => 'fan', 'FAN18G2817' => 'fan', 'FAN19G1305' => 'fan', 'FAN20G1787' => 'fan', 'FAN22G0073' => 'fan', 'FAN22G0352' => 'fan', 'FAN22G0368' => 'fan', 'FAN22G2273' => 'fan', 'FAN24G1998' => 'fan', 'FAN27G1317' => 'fan', 'FvH4_2g23980' => 'fve', 'FvH4_4g14380' => 'fve', 'FvH4_4g14390' => 'fve', 'FvH4_6g09250' => 'fve', 'Glyma.03G151100' => 'gma', 'Glyma.04G122550' => 'gma', 'Glyma.05G001600' => 'gma', 'Glyma.09G270766' => 'gma', 'Glyma.09G270832' => 'gma', 'Glyma.13G209800' => 'gma', 'Glyma.15G102800' => 'gma', 'Glyma.18G218900' => 'gma', 'Glyma.19G001500' => 'gma', 'Glyma.19G153600' => 'gma', 'Gohir.A02G028600' => 'ghi', 'Gohir.A08G045000' => 'ghi', 'Gohir.A11G120500' => 'ghi', 'Gohir.A12G006200' => 'ghi', 'Gohir.A12G006250' => 'ghi', 'Gohir.D02G036300' => 'ghi', 'Gohir.D08G054700' => 'ghi', 'Gohir.D11G125600' => 'ghi', 'Gohir.D12G005700' => 'ghi', 'Gorai.004G055200' => 'gra', 'Gorai.005G040400' => 'gra', 'Gorai.007G134500' => 'gra', 'Gorai.008G005500' => 'gra', 'GSVIVG01011094001' => 'vvi', 'GSVIVG01017879001' => 'vvi', 'GSVIVG01025988001' => 'vvi', 'GSVIVG01029847001' => 'vvi', 'HanXRQChr10g0282901' => 'han', 'HanXRQChr10g0310371' => 'han', 'HanXRQChr10g0315041' => 'han', 'HanXRQChr11g0327651' => 'han', 'HanXRQChr12g0359391' => 'han', 'Haze_00972' => 'cav', 'Haze_00973' => 'cav', 'Haze_00974' => 'cav', 'Haze_04747' => 'cav', 'Haze_04749' => 'cav', 'Haze_04750' => 'cav', 'Haze_21217' => 'cav', 'Hma1.2p1_1037F.1_g250680' => 'hma', 'Hma1.2p1_1644F.1_g295320' => 'hma', 'HPP92_011322' => 'vpl', 'HPP92_011323' => 'vpl', 'HPP92_011324' => 'vpl', 'HPP92_011325' => 'vpl', 'HPP92_011326' => 'vpl', 'Hund12205' => 'sun', 'Hund17957' => 'sun', 'Lalb_Chr06g0176771' => 'lal', 'Lalb_Chr18g0056021' => 'lal', 'Lalb_Chr18g0056031' => 'lal', 'Lalb_Chr18g0056041' => 'lal', 'Lalb_Chr20g0107751' => 'lal', 'Lalb_Chr20g0118371' => 'lal', 'Lj1g0010239' => 'lja', 'Lj1g0017101' => 'lja', 'Lj2A1178G40' => 'lonja', 'Lj2A54G84' => 'lonja', 'Lj2g0015248' => 'lja', 'Lj3A761T51' => 'lonja', 'Lj6g0018116' => 'lja', 'Lsat_1_v5_gn_4_136040' => 'lsa', 'Lsat_1_v5_gn_5_187461' => 'lsa', 'Lsat_1_v5_gn_5_77001' => 'lsa', 'Lsat_1_v5_gn_9_4461' => 'lsa', 'Manes.01G210100' => 'mes', 'Manes.03G185600' => 'mes', 'Manes.05G073300' => 'mes', 'Manes.09G120300' => 'mes', 'Manes.15G022100' => 'mes', 'Mapoly0096s0053' => 'mpo', 'MBI03_g14058_MAGBIO' => 'mbi', 'MBI03_g33876_MAGBIO' => 'mbi', 'MBI03_g36854_MAGBIO' => 'mbi', 'MBI17_g11997_MAGBIO' => 'mbi', 'MD03G1269000' => 'mdo', 'MD04G1179600' => 'mdo', 'MD11G1289800' => 'mdo', 'MD12G1194700' => 'mdo', 'MD13G1182100' => 'mdo', 'MD13G1182200' => 'mdo', 'MD16G1182600' => 'mdo', 'Medtr2g021400' => 'mtr', 'Medtr2g021470' => 'mtr', 'Medtr2g105810' => 'mtr', 'Medtr3g033580' => 'mtr', 'Medtr6g007970' => 'mtr', 'Medtr7g056330' => 'mtr', 'Medtr7g074290' => 'mtr', 'Medtr7g074380' => 'mtr', 'Medtr7g094550' => 'mtr', 'Medtr8g069995' => 'mtr', 'MELO3C014345.2' => 'cme', 'MELO3C021395.2' => 'cme', 'Migut.D00262' => 'egut', 'Migut.G00257' => 'egut', 'MSTRG.21575' => 'ama', 'MSTRG.3985' => 'ama', 'Nitab4.5_0000295g0140' => 'nta', 'Nitab4.5_0000732g0140' => 'nta', 'Nitab4.5_0003162g0020' => 'nta', 'Nitab4.5_0006180g0090' => 'nta', 'Nitab4.5_0006390g0010' => 'nta', 'Nitab4.5_0007392g0040' => 'nta', 'Nn1g02140' => 'nnu', 'Nn4g26168' => 'nnu', 'Nn5g26754' => 'nnu', 'Oeu001433.1' => 'oeu', 'Oeu010299.2' => 'oeu', 'Oeu011171.1' => 'oeu', 'Oeu037675.1' => 'oeu', 'Oeu038359.1' => 'oeu', 'Oeu063834.1' => 'oeu', 'Oeu063835.1' => 'oeu', 'Os05g0312000' => 'osa', 'Os07g0211101' => 'osa', 'Os07g0211200' => 'osa', 'Os07g0681500' => 'osa', 'Peaxi162Scf00095g01015' => 'pax', 'Peaxi162Scf00104g00329' => 'pax', 'Peaxi162Scf00161g00137' => 'pax', 'PGR004G1665' => 'pgr', 'PGR031G2937' => 'pgr', 'PGR119G2145' => 'pgr', 'PGSC0003DMG400004351' => 'stu', 'PGSC0003DMG400014625' => 'stu', 'PGSC0003DMG401000943' => 'stu', 'Phvul.001G148600' => 'pvu', 'Phvul.004G001700' => 'pvu', 'Phvul.006G154900' => 'pvu', 'Phvul.008G078200' => 'pvu', 'Phvul.011G136500' => 'pvu', 'Potri.002G215600' => 'ptr', 'Potri.008G201600' => 'ptr', 'Potri.014G138400' => 'ptr', 'Potri.016G142500' => 'ptr', 'Pp3c16_10580' => 'ppa', 'Pp3c5_25280' => 'ppa', 'Prupe.1G150000' => 'ppe', 'Prupe.1G150100' => 'ppe', 'Prupe.6G299600' => 'ppe', 'Prupe.8G245000' => 'ppe', 'Psat0s4927g0040' => 'psa', 'Psat1g052080' => 'psa', 'Psat1g183800' => 'psa', 'Psat3g113840' => 'psa', 'Psat3g126120' => 'psa', 'Psat3g126160' => 'psa', 'Psat3g158760' => 'psa', 'Psat3g158840' => 'psa', 'PSO170G2858' => 'pso', 'PSO339G0606' => 'pso', 'PSO384G4709' => 'pso', 'PSO407G0334' => 'pso', 'QL04p040276' => 'qlo', 'QL06p005458' => 'qlo', 'QL06p005472' => 'qlo', 'QL07p030546' => 'qlo', 'QL07p031519' => 'qlo', 'QL09p050949' => 'qlo', 'QL09p050966' => 'qlo', 'QL09p051067' => 'qlo', 'QL12p022706' => 'qlo', 'RcHm_v2.0_Chr2g0119601' => 'rch', 'RcHm_v2.0_Chr3g0459591' => 'rch', 'RcHm_v2.0_Chr4g0418521' => 'rch', 'RcHm_v2.0_Chr4g0418531' => 'rch', 'RcHm_v2.0_Chr4g0418541' => 'rch', 'RcHm_v2.0_Chr6g0291641' => 'rch', 'Rhsim01G0086300' => 'rsi', 'Rhsim01G0276300' => 'rsi', 'Rhsim01G0276500' => 'rsi', 'Rhsim04G0207700' => 'rsi', 'Rhsim05G0234500' => 'rsi', 'Rhsim13G0022400' => 'rsi', 'Sabra02G0167900' => 'sbr', 'Sabra04G0158500' => 'sbr', 'Sabra08G0159800' => 'sbr', 'Sabra10G0011500' => 'sbr', 'Sabra14G0104400' => 'sbr', 'SalBow2G2440' => 'sbo', 'SalBow4G2265' => 'sbo', 'Sc02g0000060' => 'sci', 'Sc05g0005020' => 'sci', 'Sc13g0003890' => 'sci', 'Sed0014865' => 'sed', 'Sed0017224' => 'sed', 'Sed0026391' => 'sed', 'SEGI_00063' => 'sgi', 'SEGI_10967' => 'sgi', 'SEGI_17510' => 'sgi', 'SEGI_24396' => 'sgi', 'SEGI_39719' => 'sgi', 'SEGI_41392' => 'sgi', 'SGA_v2.0_scaffold11G05794' => 'sas', 'SGA_v2.0_scaffold142G35607' => 'sas', 'SGA_v2.0_scaffold1G00447' => 'sas', 'SHI15388' => 'shi', 'SHI15394' => 'shi', 'SHI15396' => 'shi', 'SHI15399' => 'shi', 'SMO343G0151' => 'smo', 'SMO367G1118' => 'smo', 'Solyc01g080200.3' => 'sly', 'Solyc06g008960.3' => 'sly', 'Solyc09g064780.3' => 'sly', 'Sopen01g031980' => 'spe', 'Sopen06g003710' => 'spe', 'Sopen09g026460' => 'spe', 'Sp3g21240' => 'spa', 'Sp4g30030' => 'spa', 'TAR365G0022' => 'tar', 'TAR365G1023' => 'tar', 'TAR365G1253' => 'tar', 'TAR623G0078' => 'tar', 'TAR623G1721' => 'tar', 'TAR633G0959' => 'tar', 'THA.LOC104802225' => 'tha', 'THA.LOC104804769' => 'tha', 'THA.LOC104808660' => 'tha', 'THA.LOC104812792' => 'tha', 'Thecc.01G284000' => 'tca', 'Thecc.04G220600' => 'tca', 'Thecc.05G268900' => 'tca', 'Thecc.08G171100' => 'tca', 'Thhalv10001284m.g' => 'esa', 'Thhalv10019912m.g' => 'esa', 'TPR.G14189' => 'tpr', 'TPR.G18110' => 'tpr', 'TPR.G18130' => 'tpr', 'TPR.G18131' => 'tpr', 'TPR.G18140' => 'tpr', 'TPR.G24282' => 'tpr', 'TPR.G25221' => 'tpr', 'TPR.G29267' => 'tpr', 'TPR.G35315' => 'tpr', 'TPR.G36173' => 'tpr', 'TWI09G0794' => 'twi', 'TWI59G1348' => 'twi', 'TWI74G0430' => 'twi', 'unitig_26.g8940' => 'ugi', 'unitig_749.g13744' => 'ugi', 'unitig_749.g13745' => 'ugi', 'vmacro08269' => 'vma', 'vmacro14937' => 'vma', 'vmacro20401' => 'vma', 'VMungo0464G1349' => 'vmu', 'VMungo0540G0289' => 'vmu', 'VMungo1215G1590' => 'vmu', 'VMungo1309G0221' => 'vmu', 'VMungo1309G2815' => 'vmu', 'VMungo1383G0239' => 'vmu', 'VMungo1383G2910' => 'vmu', 'Zm00001eb095270' => 'zma', 'Zm00001eb095280' => 'zma', 'Zm00001eb111630' => 'zma', 'Zm00001eb237080' => 'zma', 'Zm00001eb273740' => 'zma', 'Zm00001eb285040' => 'zma', 'Zm00001eb330790' => 'zma', 'Zm00001eb337380' => 'zma' ) $gf_id = 'HOM05D001484' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001484' ) $data_identifier = 'HOM05D001484' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 2, 'aly' => (int) 2, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 22, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 7, 'hma' => (int) 2, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 7, 'mtr' => (int) 10, 'cme' => (int) 2, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 4, 'ppa' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 4, 'qlo' => (int) 9, 'rch' => (int) 6, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 10, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 7, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb337380' $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' => 'HOM05D001484', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p31500' => 'bna', 'A05p00020' => 'bna', 'A07p08820' => 'bna', 'Aa31LG4G3300' => 'aar', 'Aa31LG8G10030' => 'aar', 'Actinidia00731' => 'ach', 'Actinidia11473' => 'ach', 'Actinidia23469' => 'ach', 'Actinidia24318' => 'ach', 'Actinidia40196' => 'ach', 'Actinidia40197' => 'ach', 'Actinidia40198' => 'ach', 'Ah.08g212990' => 'amhyb', 'Ah.15g091720' => 'amhyb', 'AL3G38260' => 'aly', 'AL4G47710' => 'aly', 'Aqoxy2G00671' => 'aox', 'Aqoxy2G03236' => 'aox', 'arahy.Tifrunner.gnm1.ann1.05IDCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KR684' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATY3SJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK6QJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6APGL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IDT7Z9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM073U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ0R87' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LE7RV4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT4QRX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V5ENPK' => 'arhy', 'AT2G48110' => 'ath', 'AT3G23590' => 'ath', 'ATR0626G186' => 'atr', 'ATR1127G141' => 'atr', 'Atru.chr4.2583' => 'acertr', 'Atru.chr5.1358' => 'acertr', 'Atru.chr5.1359' => 'acertr', 'Atru.chr8.46' => 'acertr', 'AUR62002640' => 'cqu', 'AUR62030055' => 'cqu', 'AUR62033713' => 'cqu', 'AUR62033714' => 'cqu', 'AUR62036795' => 'cqu', 'AUR62039891' => 'cqu', 'BcaB02g08737' => 'bca', 'BcaB04g20441' => 'bca', 'BcaB06g26509' => 'bca', 'BcaB06g26510' => 'bca', 'BcaB06g26511' => 'bca', 'BcaB06g26512' => 'bca', 'BcaB06g26513' => 'bca', 'BcaC02g12564' => 'bca', 'BcaC02g12565' => 'bca', 'BcaC02g12794' => 'bca', 'BcaC02g12795' => 'bca', 'BcaC02g12796' => 'bca', 'BcaC06g35541' => 'bca', 'BNapus_Darmor_BZH_scaffold_188p00080' => 'bna', 'BNapus_Darmor_BZH_scaffold_188p00090' => 'bna', 'BolC1t03972H' => 'bol', 'BolC1t03973H' => 'bol', 'BolC4t21680H' => 'bol', 'BolC7t41863H' => 'bol', 'BolSC55t61227H' => 'bol', 'BolSC55t61228H' => 'bol', 'BraA01t03278Z' => 'bra', 'BraA05t18998Z' => 'bra', 'BraA07t28673Z' => 'bra', 'C01p40150' => 'bna', 'C05p12370' => 'bna', 'C07p13680' => 'bna', 'CAN.G1006.16' => 'can', 'CAN.G1006.17' => 'can', 'CAN.G1170.2' => 'can', 'CAN.G962.7' => 'can', 'CANSAT25G2179' => 'cansat', 'CANSAT78G1573' => 'cansat', 'CARHR099510' => 'chi', 'CARHR143510' => 'chi', 'Carub.0003s2380' => 'cru', 'Carub.0004s3082' => 'cru', 'Ca_00614_v3' => 'car', 'Ca_07801_v3' => 'car', 'Ca_08567_v3' => 'car', 'Ca_09571_v3' => 'car', 'CBR_g19290' => 'cbr', 'Cc01_g19770' => 'ccan', 'Cc03_g03030' => 'ccan', 'CDE07G0968' => 'cde', 'CDE09G1441' => 'cde', 'Cfa006103' => 'cfa', 'Cfa015573' => 'cfa', 'Cfa016988' => 'cfa', 'Ciclev10006738m.g' => 'ccl', 'Ciclev10010920m.g' => 'ccl', 'Ciclev10018517m.g' => 'ccl', 'CiPaw.01G159200' => 'cil', 'CiPaw.02G091000' => 'cil', 'CiPaw.02G091100' => 'cil', 'CiPaw.08G103100' => 'cil', 'CiPaw.09G224900' => 'cil', 'ClCG06G005740' => 'cla', 'ClCG07G000090' => 'cla', 'ClCG07G000100' => 'cla', 'COL.COLO4_09143' => 'col', 'COL.COLO4_25124' => 'col', 'Cpa.g.sc16.34' => 'cpa', 'Cpa.g.sc3504.1' => 'cpa', 'Cpa.g.sc60.37' => 'cpa', 'CsaV3_6G018520' => 'csa', 'CsaV3_6G036860' => 'csa', 'CSS0001072' => 'camsi', 'CSS0020208' => 'camsi', 'CSS0021253' => 'camsi', 'CSS0022190' => 'camsi', 'CSS0036150' => 'camsi', 'CSS0040442' => 'camsi', 'CSS0042300' => 'camsi', 'CSS0045298' => 'camsi', 'DCAR_012449' => 'dca', 'DCAR_018405' => 'dca', 'DCAR_024573' => 'dca', 'DCAR_030591' => 'dca', 'Dinv16926' => 'din', 'Dinv32963' => 'din', 'Dinv38382' => 'din', 'Dinv38383' => 'din', 'Duzib133G0974' => 'dzi', 'Duzib138G1867' => 'dzi', 'Duzib211G0420' => 'dzi', 'Duzib212G0930' => 'dzi', 'ECA234G1645' => 'eca', 'ECA247G3467' => 'eca', 'ECA248G1703' => 'eca', 'EL10Ac3g06327' => 'bvu', 'EL10Ac7g17204' => 'bvu', 'Eucgr.A00855' => 'egr', 'Eucgr.A00858' => 'egr', 'Eucgr.H01520' => 'egr', 'Eucgr.H03604' => 'egr', 'Eucgr.L03465' => 'egr', 'Eucgr.L03466' => 'egr', 'FAN01G0988' => 'fan', 'FAN02G3892' => 'fan', 'FAN05G3381' => 'fan', 'FAN07G0967' => 'fan', 'FAN07G1493' => 'fan', 'FAN08G3125' => 'fan', 'FAN09G0402' => 'fan', 'FAN12G2594' => 'fan', 'FAN12G3879' => 'fan', 'FAN14G1546' => 'fan', 'FAN15G3626' => 'fan', 'FAN17G0588' => 'fan', 'FAN17G0609' => 'fan', 'FAN18G2817' => 'fan', 'FAN19G1305' => 'fan', 'FAN20G1787' => 'fan', 'FAN22G0073' => 'fan', 'FAN22G0352' => 'fan', 'FAN22G0368' => 'fan', 'FAN22G2273' => 'fan', 'FAN24G1998' => 'fan', 'FAN27G1317' => 'fan', 'FvH4_2g23980' => 'fve', 'FvH4_4g14380' => 'fve', 'FvH4_4g14390' => 'fve', 'FvH4_6g09250' => 'fve', 'Glyma.03G151100' => 'gma', 'Glyma.04G122550' => 'gma', 'Glyma.05G001600' => 'gma', 'Glyma.09G270766' => 'gma', 'Glyma.09G270832' => 'gma', 'Glyma.13G209800' => 'gma', 'Glyma.15G102800' => 'gma', 'Glyma.18G218900' => 'gma', 'Glyma.19G001500' => 'gma', 'Glyma.19G153600' => 'gma', 'Gohir.A02G028600' => 'ghi', 'Gohir.A08G045000' => 'ghi', 'Gohir.A11G120500' => 'ghi', 'Gohir.A12G006200' => 'ghi', 'Gohir.A12G006250' => 'ghi', 'Gohir.D02G036300' => 'ghi', 'Gohir.D08G054700' => 'ghi', 'Gohir.D11G125600' => 'ghi', 'Gohir.D12G005700' => 'ghi', 'Gorai.004G055200' => 'gra', 'Gorai.005G040400' => 'gra', 'Gorai.007G134500' => 'gra', 'Gorai.008G005500' => 'gra', 'GSVIVG01011094001' => 'vvi', 'GSVIVG01017879001' => 'vvi', 'GSVIVG01025988001' => 'vvi', 'GSVIVG01029847001' => 'vvi', 'HanXRQChr10g0282901' => 'han', 'HanXRQChr10g0310371' => 'han', 'HanXRQChr10g0315041' => 'han', 'HanXRQChr11g0327651' => 'han', 'HanXRQChr12g0359391' => 'han', 'Haze_00972' => 'cav', 'Haze_00973' => 'cav', 'Haze_00974' => 'cav', 'Haze_04747' => 'cav', 'Haze_04749' => 'cav', 'Haze_04750' => 'cav', 'Haze_21217' => 'cav', 'Hma1.2p1_1037F.1_g250680' => 'hma', 'Hma1.2p1_1644F.1_g295320' => 'hma', 'HPP92_011322' => 'vpl', 'HPP92_011323' => 'vpl', 'HPP92_011324' => 'vpl', 'HPP92_011325' => 'vpl', 'HPP92_011326' => 'vpl', 'Hund12205' => 'sun', 'Hund17957' => 'sun', 'Lalb_Chr06g0176771' => 'lal', 'Lalb_Chr18g0056021' => 'lal', 'Lalb_Chr18g0056031' => 'lal', 'Lalb_Chr18g0056041' => 'lal', 'Lalb_Chr20g0107751' => 'lal', 'Lalb_Chr20g0118371' => 'lal', 'Lj1g0010239' => 'lja', 'Lj1g0017101' => 'lja', 'Lj2A1178G40' => 'lonja', 'Lj2A54G84' => 'lonja', 'Lj2g0015248' => 'lja', 'Lj3A761T51' => 'lonja', 'Lj6g0018116' => 'lja', 'Lsat_1_v5_gn_4_136040' => 'lsa', 'Lsat_1_v5_gn_5_187461' => 'lsa', 'Lsat_1_v5_gn_5_77001' => 'lsa', 'Lsat_1_v5_gn_9_4461' => 'lsa', 'Manes.01G210100' => 'mes', 'Manes.03G185600' => 'mes', 'Manes.05G073300' => 'mes', 'Manes.09G120300' => 'mes', 'Manes.15G022100' => 'mes', 'Mapoly0096s0053' => 'mpo', 'MBI03_g14058_MAGBIO' => 'mbi', 'MBI03_g33876_MAGBIO' => 'mbi', 'MBI03_g36854_MAGBIO' => 'mbi', 'MBI17_g11997_MAGBIO' => 'mbi', 'MD03G1269000' => 'mdo', 'MD04G1179600' => 'mdo', 'MD11G1289800' => 'mdo', 'MD12G1194700' => 'mdo', 'MD13G1182100' => 'mdo', 'MD13G1182200' => 'mdo', 'MD16G1182600' => 'mdo', 'Medtr2g021400' => 'mtr', 'Medtr2g021470' => 'mtr', 'Medtr2g105810' => 'mtr', 'Medtr3g033580' => 'mtr', 'Medtr6g007970' => 'mtr', 'Medtr7g056330' => 'mtr', 'Medtr7g074290' => 'mtr', 'Medtr7g074380' => 'mtr', 'Medtr7g094550' => 'mtr', 'Medtr8g069995' => 'mtr', 'MELO3C014345.2' => 'cme', 'MELO3C021395.2' => 'cme', 'Migut.D00262' => 'egut', 'Migut.G00257' => 'egut', 'MSTRG.21575' => 'ama', 'MSTRG.3985' => 'ama', 'Nitab4.5_0000295g0140' => 'nta', 'Nitab4.5_0000732g0140' => 'nta', 'Nitab4.5_0003162g0020' => 'nta', 'Nitab4.5_0006180g0090' => 'nta', 'Nitab4.5_0006390g0010' => 'nta', 'Nitab4.5_0007392g0040' => 'nta', 'Nn1g02140' => 'nnu', 'Nn4g26168' => 'nnu', 'Nn5g26754' => 'nnu', 'Oeu001433.1' => 'oeu', 'Oeu010299.2' => 'oeu', 'Oeu011171.1' => 'oeu', 'Oeu037675.1' => 'oeu', 'Oeu038359.1' => 'oeu', 'Oeu063834.1' => 'oeu', 'Oeu063835.1' => 'oeu', 'Os05g0312000' => 'osa', 'Os07g0211101' => 'osa', 'Os07g0211200' => 'osa', 'Os07g0681500' => 'osa', 'Peaxi162Scf00095g01015' => 'pax', 'Peaxi162Scf00104g00329' => 'pax', 'Peaxi162Scf00161g00137' => 'pax', 'PGR004G1665' => 'pgr', 'PGR031G2937' => 'pgr', 'PGR119G2145' => 'pgr', 'PGSC0003DMG400004351' => 'stu', 'PGSC0003DMG400014625' => 'stu', 'PGSC0003DMG401000943' => 'stu', 'Phvul.001G148600' => 'pvu', 'Phvul.004G001700' => 'pvu', 'Phvul.006G154900' => 'pvu', 'Phvul.008G078200' => 'pvu', 'Phvul.011G136500' => 'pvu', 'Potri.002G215600' => 'ptr', 'Potri.008G201600' => 'ptr', 'Potri.014G138400' => 'ptr', 'Potri.016G142500' => 'ptr', 'Pp3c16_10580' => 'ppa', 'Pp3c5_25280' => 'ppa', 'Prupe.1G150000' => 'ppe', 'Prupe.1G150100' => 'ppe', 'Prupe.6G299600' => 'ppe', 'Prupe.8G245000' => 'ppe', 'Psat0s4927g0040' => 'psa', 'Psat1g052080' => 'psa', 'Psat1g183800' => 'psa', 'Psat3g113840' => 'psa', 'Psat3g126120' => 'psa', 'Psat3g126160' => 'psa', 'Psat3g158760' => 'psa', 'Psat3g158840' => 'psa', 'PSO170G2858' => 'pso', 'PSO339G0606' => 'pso', 'PSO384G4709' => 'pso', 'PSO407G0334' => 'pso', 'QL04p040276' => 'qlo', 'QL06p005458' => 'qlo', 'QL06p005472' => 'qlo', 'QL07p030546' => 'qlo', 'QL07p031519' => 'qlo', 'QL09p050949' => 'qlo', 'QL09p050966' => 'qlo', 'QL09p051067' => 'qlo', 'QL12p022706' => 'qlo', 'RcHm_v2.0_Chr2g0119601' => 'rch', 'RcHm_v2.0_Chr3g0459591' => 'rch', 'RcHm_v2.0_Chr4g0418521' => 'rch', 'RcHm_v2.0_Chr4g0418531' => 'rch', 'RcHm_v2.0_Chr4g0418541' => 'rch', 'RcHm_v2.0_Chr6g0291641' => 'rch', 'Rhsim01G0086300' => 'rsi', 'Rhsim01G0276300' => 'rsi', 'Rhsim01G0276500' => 'rsi', 'Rhsim04G0207700' => 'rsi', 'Rhsim05G0234500' => 'rsi', 'Rhsim13G0022400' => 'rsi', 'Sabra02G0167900' => 'sbr', 'Sabra04G0158500' => 'sbr', 'Sabra08G0159800' => 'sbr', 'Sabra10G0011500' => 'sbr', 'Sabra14G0104400' => 'sbr', 'SalBow2G2440' => 'sbo', 'SalBow4G2265' => 'sbo', 'Sc02g0000060' => 'sci', 'Sc05g0005020' => 'sci', 'Sc13g0003890' => 'sci', 'Sed0014865' => 'sed', 'Sed0017224' => 'sed', 'Sed0026391' => 'sed', 'SEGI_00063' => 'sgi', 'SEGI_10967' => 'sgi', 'SEGI_17510' => 'sgi', 'SEGI_24396' => 'sgi', 'SEGI_39719' => 'sgi', 'SEGI_41392' => 'sgi', 'SGA_v2.0_scaffold11G05794' => 'sas', 'SGA_v2.0_scaffold142G35607' => 'sas', 'SGA_v2.0_scaffold1G00447' => 'sas', 'SHI15388' => 'shi', 'SHI15394' => 'shi', 'SHI15396' => 'shi', 'SHI15399' => 'shi', 'SMO343G0151' => 'smo', 'SMO367G1118' => 'smo', 'Solyc01g080200.3' => 'sly', 'Solyc06g008960.3' => 'sly', 'Solyc09g064780.3' => 'sly', 'Sopen01g031980' => 'spe', 'Sopen06g003710' => 'spe', 'Sopen09g026460' => 'spe', 'Sp3g21240' => 'spa', 'Sp4g30030' => 'spa', 'TAR365G0022' => 'tar', 'TAR365G1023' => 'tar', 'TAR365G1253' => 'tar', 'TAR623G0078' => 'tar', 'TAR623G1721' => 'tar', 'TAR633G0959' => 'tar', 'THA.LOC104802225' => 'tha', 'THA.LOC104804769' => 'tha', 'THA.LOC104808660' => 'tha', 'THA.LOC104812792' => 'tha', 'Thecc.01G284000' => 'tca', 'Thecc.04G220600' => 'tca', 'Thecc.05G268900' => 'tca', 'Thecc.08G171100' => 'tca', 'Thhalv10001284m.g' => 'esa', 'Thhalv10019912m.g' => 'esa', 'TPR.G14189' => 'tpr', 'TPR.G18110' => 'tpr', 'TPR.G18130' => 'tpr', 'TPR.G18131' => 'tpr', 'TPR.G18140' => 'tpr', 'TPR.G24282' => 'tpr', 'TPR.G25221' => 'tpr', 'TPR.G29267' => 'tpr', 'TPR.G35315' => 'tpr', 'TPR.G36173' => 'tpr', 'TWI09G0794' => 'twi', 'TWI59G1348' => 'twi', 'TWI74G0430' => 'twi', 'unitig_26.g8940' => 'ugi', 'unitig_749.g13744' => 'ugi', 'unitig_749.g13745' => 'ugi', 'vmacro08269' => 'vma', 'vmacro14937' => 'vma', 'vmacro20401' => 'vma', 'VMungo0464G1349' => 'vmu', 'VMungo0540G0289' => 'vmu', 'VMungo1215G1590' => 'vmu', 'VMungo1309G0221' => 'vmu', 'VMungo1309G2815' => 'vmu', 'VMungo1383G0239' => 'vmu', 'VMungo1383G2910' => 'vmu', 'Zm00001eb095270' => 'zma', 'Zm00001eb095280' => 'zma', 'Zm00001eb111630' => 'zma', 'Zm00001eb237080' => 'zma', 'Zm00001eb273740' => 'zma', 'Zm00001eb285040' => 'zma', 'Zm00001eb330790' => 'zma', 'Zm00001eb337380' => 'zma' ), 'gf_id' => 'HOM05D001484', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001484' ), 'data_identifier' => 'HOM05D001484', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001484', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p31500' => 'bna', 'A05p00020' => 'bna', 'A07p08820' => 'bna', 'Aa31LG4G3300' => 'aar', 'Aa31LG8G10030' => 'aar', 'Actinidia00731' => 'ach', 'Actinidia11473' => 'ach', 'Actinidia23469' => 'ach', 'Actinidia24318' => 'ach', 'Actinidia40196' => 'ach', 'Actinidia40197' => 'ach', 'Actinidia40198' => 'ach', 'Ah.08g212990' => 'amhyb', 'Ah.15g091720' => 'amhyb', 'AL3G38260' => 'aly', 'AL4G47710' => 'aly', 'Aqoxy2G00671' => 'aox', 'Aqoxy2G03236' => 'aox', 'arahy.Tifrunner.gnm1.ann1.05IDCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KR684' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATY3SJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK6QJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6APGL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IDT7Z9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM073U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ0R87' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LE7RV4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT4QRX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V5ENPK' => 'arhy', 'AT2G48110' => 'ath', 'AT3G23590' => 'ath', 'ATR0626G186' => 'atr', 'ATR1127G141' => 'atr', 'Atru.chr4.2583' => 'acertr', 'Atru.chr5.1358' => 'acertr', 'Atru.chr5.1359' => 'acertr', 'Atru.chr8.46' => 'acertr', 'AUR62002640' => 'cqu', 'AUR62030055' => 'cqu', 'AUR62033713' => 'cqu', 'AUR62033714' => 'cqu', 'AUR62036795' => 'cqu', 'AUR62039891' => 'cqu', 'BcaB02g08737' => 'bca', 'BcaB04g20441' => 'bca', 'BcaB06g26509' => 'bca', 'BcaB06g26510' => 'bca', 'BcaB06g26511' => 'bca', 'BcaB06g26512' => 'bca', 'BcaB06g26513' => 'bca', 'BcaC02g12564' => 'bca', 'BcaC02g12565' => 'bca', 'BcaC02g12794' => 'bca', 'BcaC02g12795' => 'bca', 'BcaC02g12796' => 'bca', 'BcaC06g35541' => 'bca', 'BNapus_Darmor_BZH_scaffold_188p00080' => 'bna', 'BNapus_Darmor_BZH_scaffold_188p00090' => 'bna', 'BolC1t03972H' => 'bol', 'BolC1t03973H' => 'bol', 'BolC4t21680H' => 'bol', 'BolC7t41863H' => 'bol', 'BolSC55t61227H' => 'bol', 'BolSC55t61228H' => 'bol', 'BraA01t03278Z' => 'bra', 'BraA05t18998Z' => 'bra', 'BraA07t28673Z' => 'bra', 'C01p40150' => 'bna', 'C05p12370' => 'bna', 'C07p13680' => 'bna', 'CAN.G1006.16' => 'can', 'CAN.G1006.17' => 'can', 'CAN.G1170.2' => 'can', 'CAN.G962.7' => 'can', 'CANSAT25G2179' => 'cansat', 'CANSAT78G1573' => 'cansat', 'CARHR099510' => 'chi', 'CARHR143510' => 'chi', 'Carub.0003s2380' => 'cru', 'Carub.0004s3082' => 'cru', 'Ca_00614_v3' => 'car', 'Ca_07801_v3' => 'car', 'Ca_08567_v3' => 'car', 'Ca_09571_v3' => 'car', 'CBR_g19290' => 'cbr', 'Cc01_g19770' => 'ccan', 'Cc03_g03030' => 'ccan', 'CDE07G0968' => 'cde', 'CDE09G1441' => 'cde', 'Cfa006103' => 'cfa', 'Cfa015573' => 'cfa', 'Cfa016988' => 'cfa', 'Ciclev10006738m.g' => 'ccl', 'Ciclev10010920m.g' => 'ccl', 'Ciclev10018517m.g' => 'ccl', 'CiPaw.01G159200' => 'cil', 'CiPaw.02G091000' => 'cil', 'CiPaw.02G091100' => 'cil', 'CiPaw.08G103100' => 'cil', 'CiPaw.09G224900' => 'cil', 'ClCG06G005740' => 'cla', 'ClCG07G000090' => 'cla', 'ClCG07G000100' => 'cla', 'COL.COLO4_09143' => 'col', 'COL.COLO4_25124' => 'col', 'Cpa.g.sc16.34' => 'cpa', 'Cpa.g.sc3504.1' => 'cpa', 'Cpa.g.sc60.37' => 'cpa', 'CsaV3_6G018520' => 'csa', 'CsaV3_6G036860' => 'csa', 'CSS0001072' => 'camsi', 'CSS0020208' => 'camsi', 'CSS0021253' => 'camsi', 'CSS0022190' => 'camsi', 'CSS0036150' => 'camsi', 'CSS0040442' => 'camsi', 'CSS0042300' => 'camsi', 'CSS0045298' => 'camsi', 'DCAR_012449' => 'dca', 'DCAR_018405' => 'dca', 'DCAR_024573' => 'dca', 'DCAR_030591' => 'dca', 'Dinv16926' => 'din', 'Dinv32963' => 'din', 'Dinv38382' => 'din', 'Dinv38383' => 'din', 'Duzib133G0974' => 'dzi', 'Duzib138G1867' => 'dzi', 'Duzib211G0420' => 'dzi', 'Duzib212G0930' => 'dzi', 'ECA234G1645' => 'eca', 'ECA247G3467' => 'eca', 'ECA248G1703' => 'eca', 'EL10Ac3g06327' => 'bvu', 'EL10Ac7g17204' => 'bvu', 'Eucgr.A00855' => 'egr', 'Eucgr.A00858' => 'egr', 'Eucgr.H01520' => 'egr', 'Eucgr.H03604' => 'egr', 'Eucgr.L03465' => 'egr', 'Eucgr.L03466' => 'egr', 'FAN01G0988' => 'fan', 'FAN02G3892' => 'fan', 'FAN05G3381' => 'fan', 'FAN07G0967' => 'fan', 'FAN07G1493' => 'fan', 'FAN08G3125' => 'fan', 'FAN09G0402' => 'fan', 'FAN12G2594' => 'fan', 'FAN12G3879' => 'fan', 'FAN14G1546' => 'fan', 'FAN15G3626' => 'fan', 'FAN17G0588' => 'fan', 'FAN17G0609' => 'fan', 'FAN18G2817' => 'fan', 'FAN19G1305' => 'fan', 'FAN20G1787' => 'fan', 'FAN22G0073' => 'fan', 'FAN22G0352' => 'fan', 'FAN22G0368' => 'fan', 'FAN22G2273' => 'fan', 'FAN24G1998' => 'fan', 'FAN27G1317' => 'fan', 'FvH4_2g23980' => 'fve', 'FvH4_4g14380' => 'fve', 'FvH4_4g14390' => 'fve', 'FvH4_6g09250' => 'fve', 'Glyma.03G151100' => 'gma', 'Glyma.04G122550' => 'gma', 'Glyma.05G001600' => 'gma', 'Glyma.09G270766' => 'gma', 'Glyma.09G270832' => 'gma', 'Glyma.13G209800' => 'gma', 'Glyma.15G102800' => 'gma', 'Glyma.18G218900' => 'gma', 'Glyma.19G001500' => 'gma', 'Glyma.19G153600' => 'gma', 'Gohir.A02G028600' => 'ghi', 'Gohir.A08G045000' => 'ghi', 'Gohir.A11G120500' => 'ghi', 'Gohir.A12G006200' => 'ghi', 'Gohir.A12G006250' => 'ghi', 'Gohir.D02G036300' => 'ghi', 'Gohir.D08G054700' => 'ghi', 'Gohir.D11G125600' => 'ghi', 'Gohir.D12G005700' => 'ghi', 'Gorai.004G055200' => 'gra', 'Gorai.005G040400' => 'gra', 'Gorai.007G134500' => 'gra', 'Gorai.008G005500' => 'gra', 'GSVIVG01011094001' => 'vvi', 'GSVIVG01017879001' => 'vvi', 'GSVIVG01025988001' => 'vvi', 'GSVIVG01029847001' => 'vvi', 'HanXRQChr10g0282901' => 'han', 'HanXRQChr10g0310371' => 'han', 'HanXRQChr10g0315041' => 'han', 'HanXRQChr11g0327651' => 'han', 'HanXRQChr12g0359391' => 'han', 'Haze_00972' => 'cav', 'Haze_00973' => 'cav', 'Haze_00974' => 'cav', 'Haze_04747' => 'cav', 'Haze_04749' => 'cav', 'Haze_04750' => 'cav', 'Haze_21217' => 'cav', 'Hma1.2p1_1037F.1_g250680' => 'hma', 'Hma1.2p1_1644F.1_g295320' => 'hma', 'HPP92_011322' => 'vpl', 'HPP92_011323' => 'vpl', 'HPP92_011324' => 'vpl', 'HPP92_011325' => 'vpl', 'HPP92_011326' => 'vpl', 'Hund12205' => 'sun', 'Hund17957' => 'sun', 'Lalb_Chr06g0176771' => 'lal', 'Lalb_Chr18g0056021' => 'lal', 'Lalb_Chr18g0056031' => 'lal', 'Lalb_Chr18g0056041' => 'lal', 'Lalb_Chr20g0107751' => 'lal', 'Lalb_Chr20g0118371' => 'lal', 'Lj1g0010239' => 'lja', 'Lj1g0017101' => 'lja', 'Lj2A1178G40' => 'lonja', 'Lj2A54G84' => 'lonja', 'Lj2g0015248' => 'lja', 'Lj3A761T51' => 'lonja', 'Lj6g0018116' => 'lja', 'Lsat_1_v5_gn_4_136040' => 'lsa', 'Lsat_1_v5_gn_5_187461' => 'lsa', 'Lsat_1_v5_gn_5_77001' => 'lsa', 'Lsat_1_v5_gn_9_4461' => 'lsa', 'Manes.01G210100' => 'mes', 'Manes.03G185600' => 'mes', 'Manes.05G073300' => 'mes', 'Manes.09G120300' => 'mes', 'Manes.15G022100' => 'mes', 'Mapoly0096s0053' => 'mpo', 'MBI03_g14058_MAGBIO' => 'mbi', 'MBI03_g33876_MAGBIO' => 'mbi', 'MBI03_g36854_MAGBIO' => 'mbi', 'MBI17_g11997_MAGBIO' => 'mbi', 'MD03G1269000' => 'mdo', 'MD04G1179600' => 'mdo', 'MD11G1289800' => 'mdo', 'MD12G1194700' => 'mdo', 'MD13G1182100' => 'mdo', 'MD13G1182200' => 'mdo', 'MD16G1182600' => 'mdo', 'Medtr2g021400' => 'mtr', 'Medtr2g021470' => 'mtr', 'Medtr2g105810' => 'mtr', 'Medtr3g033580' => 'mtr', 'Medtr6g007970' => 'mtr', 'Medtr7g056330' => 'mtr', 'Medtr7g074290' => 'mtr', 'Medtr7g074380' => 'mtr', 'Medtr7g094550' => 'mtr', 'Medtr8g069995' => 'mtr', 'MELO3C014345.2' => 'cme', 'MELO3C021395.2' => 'cme', 'Migut.D00262' => 'egut', 'Migut.G00257' => 'egut', 'MSTRG.21575' => 'ama', 'MSTRG.3985' => 'ama', 'Nitab4.5_0000295g0140' => 'nta', 'Nitab4.5_0000732g0140' => 'nta', 'Nitab4.5_0003162g0020' => 'nta', 'Nitab4.5_0006180g0090' => 'nta', 'Nitab4.5_0006390g0010' => 'nta', 'Nitab4.5_0007392g0040' => 'nta', 'Nn1g02140' => 'nnu', 'Nn4g26168' => 'nnu', 'Nn5g26754' => 'nnu', 'Oeu001433.1' => 'oeu', 'Oeu010299.2' => 'oeu', 'Oeu011171.1' => 'oeu', 'Oeu037675.1' => 'oeu', 'Oeu038359.1' => 'oeu', 'Oeu063834.1' => 'oeu', 'Oeu063835.1' => 'oeu', 'Os05g0312000' => 'osa', 'Os07g0211101' => 'osa', 'Os07g0211200' => 'osa', 'Os07g0681500' => 'osa', 'Peaxi162Scf00095g01015' => 'pax', 'Peaxi162Scf00104g00329' => 'pax', 'Peaxi162Scf00161g00137' => 'pax', 'PGR004G1665' => 'pgr', 'PGR031G2937' => 'pgr', 'PGR119G2145' => 'pgr', 'PGSC0003DMG400004351' => 'stu', 'PGSC0003DMG400014625' => 'stu', 'PGSC0003DMG401000943' => 'stu', 'Phvul.001G148600' => 'pvu', 'Phvul.004G001700' => 'pvu', 'Phvul.006G154900' => 'pvu', 'Phvul.008G078200' => 'pvu', 'Phvul.011G136500' => 'pvu', 'Potri.002G215600' => 'ptr', 'Potri.008G201600' => 'ptr', 'Potri.014G138400' => 'ptr', 'Potri.016G142500' => 'ptr', 'Pp3c16_10580' => 'ppa', 'Pp3c5_25280' => 'ppa', 'Prupe.1G150000' => 'ppe', 'Prupe.1G150100' => 'ppe', 'Prupe.6G299600' => 'ppe', 'Prupe.8G245000' => 'ppe', 'Psat0s4927g0040' => 'psa', 'Psat1g052080' => 'psa', 'Psat1g183800' => 'psa', 'Psat3g113840' => 'psa', 'Psat3g126120' => 'psa', 'Psat3g126160' => 'psa', 'Psat3g158760' => 'psa', 'Psat3g158840' => 'psa', 'PSO170G2858' => 'pso', 'PSO339G0606' => 'pso', 'PSO384G4709' => 'pso', 'PSO407G0334' => 'pso', 'QL04p040276' => 'qlo', 'QL06p005458' => 'qlo', 'QL06p005472' => 'qlo', 'QL07p030546' => 'qlo', 'QL07p031519' => 'qlo', 'QL09p050949' => 'qlo', 'QL09p050966' => 'qlo', 'QL09p051067' => 'qlo', 'QL12p022706' => 'qlo', 'RcHm_v2.0_Chr2g0119601' => 'rch', 'RcHm_v2.0_Chr3g0459591' => 'rch', 'RcHm_v2.0_Chr4g0418521' => 'rch', 'RcHm_v2.0_Chr4g0418531' => 'rch', 'RcHm_v2.0_Chr4g0418541' => 'rch', 'RcHm_v2.0_Chr6g0291641' => 'rch', 'Rhsim01G0086300' => 'rsi', 'Rhsim01G0276300' => 'rsi', 'Rhsim01G0276500' => 'rsi', 'Rhsim04G0207700' => 'rsi', 'Rhsim05G0234500' => 'rsi', 'Rhsim13G0022400' => 'rsi', 'Sabra02G0167900' => 'sbr', 'Sabra04G0158500' => 'sbr', 'Sabra08G0159800' => 'sbr', 'Sabra10G0011500' => 'sbr', 'Sabra14G0104400' => 'sbr', 'SalBow2G2440' => 'sbo', 'SalBow4G2265' => 'sbo', 'Sc02g0000060' => 'sci', 'Sc05g0005020' => 'sci', 'Sc13g0003890' => 'sci', 'Sed0014865' => 'sed', 'Sed0017224' => 'sed', 'Sed0026391' => 'sed', 'SEGI_00063' => 'sgi', 'SEGI_10967' => 'sgi', 'SEGI_17510' => 'sgi', 'SEGI_24396' => 'sgi', 'SEGI_39719' => 'sgi', 'SEGI_41392' => 'sgi', 'SGA_v2.0_scaffold11G05794' => 'sas', 'SGA_v2.0_scaffold142G35607' => 'sas', 'SGA_v2.0_scaffold1G00447' => 'sas', 'SHI15388' => 'shi', 'SHI15394' => 'shi', 'SHI15396' => 'shi', 'SHI15399' => 'shi', 'SMO343G0151' => 'smo', 'SMO367G1118' => 'smo', 'Solyc01g080200.3' => 'sly', 'Solyc06g008960.3' => 'sly', 'Solyc09g064780.3' => 'sly', 'Sopen01g031980' => 'spe', 'Sopen06g003710' => 'spe', 'Sopen09g026460' => 'spe', 'Sp3g21240' => 'spa', 'Sp4g30030' => 'spa', 'TAR365G0022' => 'tar', 'TAR365G1023' => 'tar', 'TAR365G1253' => 'tar', 'TAR623G0078' => 'tar', 'TAR623G1721' => 'tar', 'TAR633G0959' => 'tar', 'THA.LOC104802225' => 'tha', 'THA.LOC104804769' => 'tha', 'THA.LOC104808660' => 'tha', 'THA.LOC104812792' => 'tha', 'Thecc.01G284000' => 'tca', 'Thecc.04G220600' => 'tca', 'Thecc.05G268900' => 'tca', 'Thecc.08G171100' => 'tca', 'Thhalv10001284m.g' => 'esa', 'Thhalv10019912m.g' => 'esa', 'TPR.G14189' => 'tpr', 'TPR.G18110' => 'tpr', 'TPR.G18130' => 'tpr', 'TPR.G18131' => 'tpr', 'TPR.G18140' => 'tpr', 'TPR.G24282' => 'tpr', 'TPR.G25221' => 'tpr', 'TPR.G29267' => 'tpr', 'TPR.G35315' => 'tpr', 'TPR.G36173' => 'tpr', 'TWI09G0794' => 'twi', 'TWI59G1348' => 'twi', 'TWI74G0430' => 'twi', 'unitig_26.g8940' => 'ugi', 'unitig_749.g13744' => 'ugi', 'unitig_749.g13745' => 'ugi', 'vmacro08269' => 'vma', 'vmacro14937' => 'vma', 'vmacro20401' => 'vma', 'VMungo0464G1349' => 'vmu', 'VMungo0540G0289' => 'vmu', 'VMungo1215G1590' => 'vmu', 'VMungo1309G0221' => 'vmu', 'VMungo1309G2815' => 'vmu', 'VMungo1383G0239' => 'vmu', 'VMungo1383G2910' => 'vmu', 'Zm00001eb095270' => 'zma', 'Zm00001eb095280' => 'zma', 'Zm00001eb111630' => 'zma', 'Zm00001eb237080' => 'zma', 'Zm00001eb273740' => 'zma', 'Zm00001eb285040' => 'zma', 'Zm00001eb330790' => 'zma', 'Zm00001eb337380' => 'zma' ) $gf_id = 'HOM05D001484' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001484' ) $data_identifier = 'HOM05D001484' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 2, 'aly' => (int) 2, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 22, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 7, 'hma' => (int) 2, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 7, 'mtr' => (int) 10, 'cme' => (int) 2, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 4, 'ppa' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 4, 'qlo' => (int) 9, 'rch' => (int) 6, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 10, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 7, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb337380' $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' => 'HOM05D001484', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p31500' => 'bna', 'A05p00020' => 'bna', 'A07p08820' => 'bna', 'Aa31LG4G3300' => 'aar', 'Aa31LG8G10030' => 'aar', 'Actinidia00731' => 'ach', 'Actinidia11473' => 'ach', 'Actinidia23469' => 'ach', 'Actinidia24318' => 'ach', 'Actinidia40196' => 'ach', 'Actinidia40197' => 'ach', 'Actinidia40198' => 'ach', 'Ah.08g212990' => 'amhyb', 'Ah.15g091720' => 'amhyb', 'AL3G38260' => 'aly', 'AL4G47710' => 'aly', 'Aqoxy2G00671' => 'aox', 'Aqoxy2G03236' => 'aox', 'arahy.Tifrunner.gnm1.ann1.05IDCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KR684' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATY3SJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK6QJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6APGL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IDT7Z9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM073U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ0R87' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LE7RV4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT4QRX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V5ENPK' => 'arhy', 'AT2G48110' => 'ath', 'AT3G23590' => 'ath', 'ATR0626G186' => 'atr', 'ATR1127G141' => 'atr', 'Atru.chr4.2583' => 'acertr', 'Atru.chr5.1358' => 'acertr', 'Atru.chr5.1359' => 'acertr', 'Atru.chr8.46' => 'acertr', 'AUR62002640' => 'cqu', 'AUR62030055' => 'cqu', 'AUR62033713' => 'cqu', 'AUR62033714' => 'cqu', 'AUR62036795' => 'cqu', 'AUR62039891' => 'cqu', 'BcaB02g08737' => 'bca', 'BcaB04g20441' => 'bca', 'BcaB06g26509' => 'bca', 'BcaB06g26510' => 'bca', 'BcaB06g26511' => 'bca', 'BcaB06g26512' => 'bca', 'BcaB06g26513' => 'bca', 'BcaC02g12564' => 'bca', 'BcaC02g12565' => 'bca', 'BcaC02g12794' => 'bca', 'BcaC02g12795' => 'bca', 'BcaC02g12796' => 'bca', 'BcaC06g35541' => 'bca', 'BNapus_Darmor_BZH_scaffold_188p00080' => 'bna', 'BNapus_Darmor_BZH_scaffold_188p00090' => 'bna', 'BolC1t03972H' => 'bol', 'BolC1t03973H' => 'bol', 'BolC4t21680H' => 'bol', 'BolC7t41863H' => 'bol', 'BolSC55t61227H' => 'bol', 'BolSC55t61228H' => 'bol', 'BraA01t03278Z' => 'bra', 'BraA05t18998Z' => 'bra', 'BraA07t28673Z' => 'bra', 'C01p40150' => 'bna', 'C05p12370' => 'bna', 'C07p13680' => 'bna', 'CAN.G1006.16' => 'can', 'CAN.G1006.17' => 'can', 'CAN.G1170.2' => 'can', 'CAN.G962.7' => 'can', 'CANSAT25G2179' => 'cansat', 'CANSAT78G1573' => 'cansat', 'CARHR099510' => 'chi', 'CARHR143510' => 'chi', 'Carub.0003s2380' => 'cru', 'Carub.0004s3082' => 'cru', 'Ca_00614_v3' => 'car', 'Ca_07801_v3' => 'car', 'Ca_08567_v3' => 'car', 'Ca_09571_v3' => 'car', 'CBR_g19290' => 'cbr', 'Cc01_g19770' => 'ccan', 'Cc03_g03030' => 'ccan', 'CDE07G0968' => 'cde', 'CDE09G1441' => 'cde', 'Cfa006103' => 'cfa', 'Cfa015573' => 'cfa', 'Cfa016988' => 'cfa', 'Ciclev10006738m.g' => 'ccl', 'Ciclev10010920m.g' => 'ccl', 'Ciclev10018517m.g' => 'ccl', 'CiPaw.01G159200' => 'cil', 'CiPaw.02G091000' => 'cil', 'CiPaw.02G091100' => 'cil', 'CiPaw.08G103100' => 'cil', 'CiPaw.09G224900' => 'cil', 'ClCG06G005740' => 'cla', 'ClCG07G000090' => 'cla', 'ClCG07G000100' => 'cla', 'COL.COLO4_09143' => 'col', 'COL.COLO4_25124' => 'col', 'Cpa.g.sc16.34' => 'cpa', 'Cpa.g.sc3504.1' => 'cpa', 'Cpa.g.sc60.37' => 'cpa', 'CsaV3_6G018520' => 'csa', 'CsaV3_6G036860' => 'csa', 'CSS0001072' => 'camsi', 'CSS0020208' => 'camsi', 'CSS0021253' => 'camsi', 'CSS0022190' => 'camsi', 'CSS0036150' => 'camsi', 'CSS0040442' => 'camsi', 'CSS0042300' => 'camsi', 'CSS0045298' => 'camsi', 'DCAR_012449' => 'dca', 'DCAR_018405' => 'dca', 'DCAR_024573' => 'dca', 'DCAR_030591' => 'dca', 'Dinv16926' => 'din', 'Dinv32963' => 'din', 'Dinv38382' => 'din', 'Dinv38383' => 'din', 'Duzib133G0974' => 'dzi', 'Duzib138G1867' => 'dzi', 'Duzib211G0420' => 'dzi', 'Duzib212G0930' => 'dzi', 'ECA234G1645' => 'eca', 'ECA247G3467' => 'eca', 'ECA248G1703' => 'eca', 'EL10Ac3g06327' => 'bvu', 'EL10Ac7g17204' => 'bvu', 'Eucgr.A00855' => 'egr', 'Eucgr.A00858' => 'egr', 'Eucgr.H01520' => 'egr', 'Eucgr.H03604' => 'egr', 'Eucgr.L03465' => 'egr', 'Eucgr.L03466' => 'egr', 'FAN01G0988' => 'fan', 'FAN02G3892' => 'fan', 'FAN05G3381' => 'fan', 'FAN07G0967' => 'fan', 'FAN07G1493' => 'fan', 'FAN08G3125' => 'fan', 'FAN09G0402' => 'fan', 'FAN12G2594' => 'fan', 'FAN12G3879' => 'fan', 'FAN14G1546' => 'fan', 'FAN15G3626' => 'fan', 'FAN17G0588' => 'fan', 'FAN17G0609' => 'fan', 'FAN18G2817' => 'fan', 'FAN19G1305' => 'fan', 'FAN20G1787' => 'fan', 'FAN22G0073' => 'fan', 'FAN22G0352' => 'fan', 'FAN22G0368' => 'fan', 'FAN22G2273' => 'fan', 'FAN24G1998' => 'fan', 'FAN27G1317' => 'fan', 'FvH4_2g23980' => 'fve', 'FvH4_4g14380' => 'fve', 'FvH4_4g14390' => 'fve', 'FvH4_6g09250' => 'fve', 'Glyma.03G151100' => 'gma', 'Glyma.04G122550' => 'gma', 'Glyma.05G001600' => 'gma', 'Glyma.09G270766' => 'gma', 'Glyma.09G270832' => 'gma', 'Glyma.13G209800' => 'gma', 'Glyma.15G102800' => 'gma', 'Glyma.18G218900' => 'gma', 'Glyma.19G001500' => 'gma', 'Glyma.19G153600' => 'gma', 'Gohir.A02G028600' => 'ghi', 'Gohir.A08G045000' => 'ghi', 'Gohir.A11G120500' => 'ghi', 'Gohir.A12G006200' => 'ghi', 'Gohir.A12G006250' => 'ghi', 'Gohir.D02G036300' => 'ghi', 'Gohir.D08G054700' => 'ghi', 'Gohir.D11G125600' => 'ghi', 'Gohir.D12G005700' => 'ghi', 'Gorai.004G055200' => 'gra', 'Gorai.005G040400' => 'gra', 'Gorai.007G134500' => 'gra', 'Gorai.008G005500' => 'gra', 'GSVIVG01011094001' => 'vvi', 'GSVIVG01017879001' => 'vvi', 'GSVIVG01025988001' => 'vvi', 'GSVIVG01029847001' => 'vvi', 'HanXRQChr10g0282901' => 'han', 'HanXRQChr10g0310371' => 'han', 'HanXRQChr10g0315041' => 'han', 'HanXRQChr11g0327651' => 'han', 'HanXRQChr12g0359391' => 'han', 'Haze_00972' => 'cav', 'Haze_00973' => 'cav', 'Haze_00974' => 'cav', 'Haze_04747' => 'cav', 'Haze_04749' => 'cav', 'Haze_04750' => 'cav', 'Haze_21217' => 'cav', 'Hma1.2p1_1037F.1_g250680' => 'hma', 'Hma1.2p1_1644F.1_g295320' => 'hma', 'HPP92_011322' => 'vpl', 'HPP92_011323' => 'vpl', 'HPP92_011324' => 'vpl', 'HPP92_011325' => 'vpl', 'HPP92_011326' => 'vpl', 'Hund12205' => 'sun', 'Hund17957' => 'sun', 'Lalb_Chr06g0176771' => 'lal', 'Lalb_Chr18g0056021' => 'lal', 'Lalb_Chr18g0056031' => 'lal', 'Lalb_Chr18g0056041' => 'lal', 'Lalb_Chr20g0107751' => 'lal', 'Lalb_Chr20g0118371' => 'lal', 'Lj1g0010239' => 'lja', 'Lj1g0017101' => 'lja', 'Lj2A1178G40' => 'lonja', 'Lj2A54G84' => 'lonja', 'Lj2g0015248' => 'lja', 'Lj3A761T51' => 'lonja', 'Lj6g0018116' => 'lja', 'Lsat_1_v5_gn_4_136040' => 'lsa', 'Lsat_1_v5_gn_5_187461' => 'lsa', 'Lsat_1_v5_gn_5_77001' => 'lsa', 'Lsat_1_v5_gn_9_4461' => 'lsa', 'Manes.01G210100' => 'mes', 'Manes.03G185600' => 'mes', 'Manes.05G073300' => 'mes', 'Manes.09G120300' => 'mes', 'Manes.15G022100' => 'mes', 'Mapoly0096s0053' => 'mpo', 'MBI03_g14058_MAGBIO' => 'mbi', 'MBI03_g33876_MAGBIO' => 'mbi', 'MBI03_g36854_MAGBIO' => 'mbi', 'MBI17_g11997_MAGBIO' => 'mbi', 'MD03G1269000' => 'mdo', 'MD04G1179600' => 'mdo', 'MD11G1289800' => 'mdo', 'MD12G1194700' => 'mdo', 'MD13G1182100' => 'mdo', 'MD13G1182200' => 'mdo', 'MD16G1182600' => 'mdo', 'Medtr2g021400' => 'mtr', 'Medtr2g021470' => 'mtr', 'Medtr2g105810' => 'mtr', 'Medtr3g033580' => 'mtr', 'Medtr6g007970' => 'mtr', 'Medtr7g056330' => 'mtr', 'Medtr7g074290' => 'mtr', 'Medtr7g074380' => 'mtr', 'Medtr7g094550' => 'mtr', 'Medtr8g069995' => 'mtr', 'MELO3C014345.2' => 'cme', 'MELO3C021395.2' => 'cme', 'Migut.D00262' => 'egut', 'Migut.G00257' => 'egut', 'MSTRG.21575' => 'ama', 'MSTRG.3985' => 'ama', 'Nitab4.5_0000295g0140' => 'nta', 'Nitab4.5_0000732g0140' => 'nta', 'Nitab4.5_0003162g0020' => 'nta', 'Nitab4.5_0006180g0090' => 'nta', 'Nitab4.5_0006390g0010' => 'nta', 'Nitab4.5_0007392g0040' => 'nta', 'Nn1g02140' => 'nnu', 'Nn4g26168' => 'nnu', 'Nn5g26754' => 'nnu', 'Oeu001433.1' => 'oeu', 'Oeu010299.2' => 'oeu', 'Oeu011171.1' => 'oeu', 'Oeu037675.1' => 'oeu', 'Oeu038359.1' => 'oeu', 'Oeu063834.1' => 'oeu', 'Oeu063835.1' => 'oeu', 'Os05g0312000' => 'osa', 'Os07g0211101' => 'osa', 'Os07g0211200' => 'osa', 'Os07g0681500' => 'osa', 'Peaxi162Scf00095g01015' => 'pax', 'Peaxi162Scf00104g00329' => 'pax', 'Peaxi162Scf00161g00137' => 'pax', 'PGR004G1665' => 'pgr', 'PGR031G2937' => 'pgr', 'PGR119G2145' => 'pgr', 'PGSC0003DMG400004351' => 'stu', 'PGSC0003DMG400014625' => 'stu', 'PGSC0003DMG401000943' => 'stu', 'Phvul.001G148600' => 'pvu', 'Phvul.004G001700' => 'pvu', 'Phvul.006G154900' => 'pvu', 'Phvul.008G078200' => 'pvu', 'Phvul.011G136500' => 'pvu', 'Potri.002G215600' => 'ptr', 'Potri.008G201600' => 'ptr', 'Potri.014G138400' => 'ptr', 'Potri.016G142500' => 'ptr', 'Pp3c16_10580' => 'ppa', 'Pp3c5_25280' => 'ppa', 'Prupe.1G150000' => 'ppe', 'Prupe.1G150100' => 'ppe', 'Prupe.6G299600' => 'ppe', 'Prupe.8G245000' => 'ppe', 'Psat0s4927g0040' => 'psa', 'Psat1g052080' => 'psa', 'Psat1g183800' => 'psa', 'Psat3g113840' => 'psa', 'Psat3g126120' => 'psa', 'Psat3g126160' => 'psa', 'Psat3g158760' => 'psa', 'Psat3g158840' => 'psa', 'PSO170G2858' => 'pso', 'PSO339G0606' => 'pso', 'PSO384G4709' => 'pso', 'PSO407G0334' => 'pso', 'QL04p040276' => 'qlo', 'QL06p005458' => 'qlo', 'QL06p005472' => 'qlo', 'QL07p030546' => 'qlo', 'QL07p031519' => 'qlo', 'QL09p050949' => 'qlo', 'QL09p050966' => 'qlo', 'QL09p051067' => 'qlo', 'QL12p022706' => 'qlo', 'RcHm_v2.0_Chr2g0119601' => 'rch', 'RcHm_v2.0_Chr3g0459591' => 'rch', 'RcHm_v2.0_Chr4g0418521' => 'rch', 'RcHm_v2.0_Chr4g0418531' => 'rch', 'RcHm_v2.0_Chr4g0418541' => 'rch', 'RcHm_v2.0_Chr6g0291641' => 'rch', 'Rhsim01G0086300' => 'rsi', 'Rhsim01G0276300' => 'rsi', 'Rhsim01G0276500' => 'rsi', 'Rhsim04G0207700' => 'rsi', 'Rhsim05G0234500' => 'rsi', 'Rhsim13G0022400' => 'rsi', 'Sabra02G0167900' => 'sbr', 'Sabra04G0158500' => 'sbr', 'Sabra08G0159800' => 'sbr', 'Sabra10G0011500' => 'sbr', 'Sabra14G0104400' => 'sbr', 'SalBow2G2440' => 'sbo', 'SalBow4G2265' => 'sbo', 'Sc02g0000060' => 'sci', 'Sc05g0005020' => 'sci', 'Sc13g0003890' => 'sci', 'Sed0014865' => 'sed', 'Sed0017224' => 'sed', 'Sed0026391' => 'sed', 'SEGI_00063' => 'sgi', 'SEGI_10967' => 'sgi', 'SEGI_17510' => 'sgi', 'SEGI_24396' => 'sgi', 'SEGI_39719' => 'sgi', 'SEGI_41392' => 'sgi', 'SGA_v2.0_scaffold11G05794' => 'sas', 'SGA_v2.0_scaffold142G35607' => 'sas', 'SGA_v2.0_scaffold1G00447' => 'sas', 'SHI15388' => 'shi', 'SHI15394' => 'shi', 'SHI15396' => 'shi', 'SHI15399' => 'shi', 'SMO343G0151' => 'smo', 'SMO367G1118' => 'smo', 'Solyc01g080200.3' => 'sly', 'Solyc06g008960.3' => 'sly', 'Solyc09g064780.3' => 'sly', 'Sopen01g031980' => 'spe', 'Sopen06g003710' => 'spe', 'Sopen09g026460' => 'spe', 'Sp3g21240' => 'spa', 'Sp4g30030' => 'spa', 'TAR365G0022' => 'tar', 'TAR365G1023' => 'tar', 'TAR365G1253' => 'tar', 'TAR623G0078' => 'tar', 'TAR623G1721' => 'tar', 'TAR633G0959' => 'tar', 'THA.LOC104802225' => 'tha', 'THA.LOC104804769' => 'tha', 'THA.LOC104808660' => 'tha', 'THA.LOC104812792' => 'tha', 'Thecc.01G284000' => 'tca', 'Thecc.04G220600' => 'tca', 'Thecc.05G268900' => 'tca', 'Thecc.08G171100' => 'tca', 'Thhalv10001284m.g' => 'esa', 'Thhalv10019912m.g' => 'esa', 'TPR.G14189' => 'tpr', 'TPR.G18110' => 'tpr', 'TPR.G18130' => 'tpr', 'TPR.G18131' => 'tpr', 'TPR.G18140' => 'tpr', 'TPR.G24282' => 'tpr', 'TPR.G25221' => 'tpr', 'TPR.G29267' => 'tpr', 'TPR.G35315' => 'tpr', 'TPR.G36173' => 'tpr', 'TWI09G0794' => 'twi', 'TWI59G1348' => 'twi', 'TWI74G0430' => 'twi', 'unitig_26.g8940' => 'ugi', 'unitig_749.g13744' => 'ugi', 'unitig_749.g13745' => 'ugi', 'vmacro08269' => 'vma', 'vmacro14937' => 'vma', 'vmacro20401' => 'vma', 'VMungo0464G1349' => 'vmu', 'VMungo0540G0289' => 'vmu', 'VMungo1215G1590' => 'vmu', 'VMungo1309G0221' => 'vmu', 'VMungo1309G2815' => 'vmu', 'VMungo1383G0239' => 'vmu', 'VMungo1383G2910' => 'vmu', 'Zm00001eb095270' => 'zma', 'Zm00001eb095280' => 'zma', 'Zm00001eb111630' => 'zma', 'Zm00001eb237080' => 'zma', 'Zm00001eb273740' => 'zma', 'Zm00001eb285040' => 'zma', 'Zm00001eb330790' => 'zma', 'Zm00001eb337380' => 'zma' ), 'gf_id' => 'HOM05D001484', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001484' ), 'data_identifier' => 'HOM05D001484', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001484', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p31500' => 'bna', 'A05p00020' => 'bna', 'A07p08820' => 'bna', 'Aa31LG4G3300' => 'aar', 'Aa31LG8G10030' => 'aar', 'Actinidia00731' => 'ach', 'Actinidia11473' => 'ach', 'Actinidia23469' => 'ach', 'Actinidia24318' => 'ach', 'Actinidia40196' => 'ach', 'Actinidia40197' => 'ach', 'Actinidia40198' => 'ach', 'Ah.08g212990' => 'amhyb', 'Ah.15g091720' => 'amhyb', 'AL3G38260' => 'aly', 'AL4G47710' => 'aly', 'Aqoxy2G00671' => 'aox', 'Aqoxy2G03236' => 'aox', 'arahy.Tifrunner.gnm1.ann1.05IDCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KR684' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATY3SJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK6QJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6APGL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IDT7Z9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM073U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ0R87' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LE7RV4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT4QRX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V5ENPK' => 'arhy', 'AT2G48110' => 'ath', 'AT3G23590' => 'ath', 'ATR0626G186' => 'atr', 'ATR1127G141' => 'atr', 'Atru.chr4.2583' => 'acertr', 'Atru.chr5.1358' => 'acertr', 'Atru.chr5.1359' => 'acertr', 'Atru.chr8.46' => 'acertr', 'AUR62002640' => 'cqu', 'AUR62030055' => 'cqu', 'AUR62033713' => 'cqu', 'AUR62033714' => 'cqu', 'AUR62036795' => 'cqu', 'AUR62039891' => 'cqu', 'BcaB02g08737' => 'bca', 'BcaB04g20441' => 'bca', 'BcaB06g26509' => 'bca', 'BcaB06g26510' => 'bca', 'BcaB06g26511' => 'bca', 'BcaB06g26512' => 'bca', 'BcaB06g26513' => 'bca', 'BcaC02g12564' => 'bca', 'BcaC02g12565' => 'bca', 'BcaC02g12794' => 'bca', 'BcaC02g12795' => 'bca', 'BcaC02g12796' => 'bca', 'BcaC06g35541' => 'bca', 'BNapus_Darmor_BZH_scaffold_188p00080' => 'bna', 'BNapus_Darmor_BZH_scaffold_188p00090' => 'bna', 'BolC1t03972H' => 'bol', 'BolC1t03973H' => 'bol', 'BolC4t21680H' => 'bol', 'BolC7t41863H' => 'bol', 'BolSC55t61227H' => 'bol', 'BolSC55t61228H' => 'bol', 'BraA01t03278Z' => 'bra', 'BraA05t18998Z' => 'bra', 'BraA07t28673Z' => 'bra', 'C01p40150' => 'bna', 'C05p12370' => 'bna', 'C07p13680' => 'bna', 'CAN.G1006.16' => 'can', 'CAN.G1006.17' => 'can', 'CAN.G1170.2' => 'can', 'CAN.G962.7' => 'can', 'CANSAT25G2179' => 'cansat', 'CANSAT78G1573' => 'cansat', 'CARHR099510' => 'chi', 'CARHR143510' => 'chi', 'Carub.0003s2380' => 'cru', 'Carub.0004s3082' => 'cru', 'Ca_00614_v3' => 'car', 'Ca_07801_v3' => 'car', 'Ca_08567_v3' => 'car', 'Ca_09571_v3' => 'car', 'CBR_g19290' => 'cbr', 'Cc01_g19770' => 'ccan', 'Cc03_g03030' => 'ccan', 'CDE07G0968' => 'cde', 'CDE09G1441' => 'cde', 'Cfa006103' => 'cfa', 'Cfa015573' => 'cfa', 'Cfa016988' => 'cfa', 'Ciclev10006738m.g' => 'ccl', 'Ciclev10010920m.g' => 'ccl', 'Ciclev10018517m.g' => 'ccl', 'CiPaw.01G159200' => 'cil', 'CiPaw.02G091000' => 'cil', 'CiPaw.02G091100' => 'cil', 'CiPaw.08G103100' => 'cil', 'CiPaw.09G224900' => 'cil', 'ClCG06G005740' => 'cla', 'ClCG07G000090' => 'cla', 'ClCG07G000100' => 'cla', 'COL.COLO4_09143' => 'col', 'COL.COLO4_25124' => 'col', 'Cpa.g.sc16.34' => 'cpa', 'Cpa.g.sc3504.1' => 'cpa', 'Cpa.g.sc60.37' => 'cpa', 'CsaV3_6G018520' => 'csa', 'CsaV3_6G036860' => 'csa', 'CSS0001072' => 'camsi', 'CSS0020208' => 'camsi', 'CSS0021253' => 'camsi', 'CSS0022190' => 'camsi', 'CSS0036150' => 'camsi', 'CSS0040442' => 'camsi', 'CSS0042300' => 'camsi', 'CSS0045298' => 'camsi', 'DCAR_012449' => 'dca', 'DCAR_018405' => 'dca', 'DCAR_024573' => 'dca', 'DCAR_030591' => 'dca', 'Dinv16926' => 'din', 'Dinv32963' => 'din', 'Dinv38382' => 'din', 'Dinv38383' => 'din', 'Duzib133G0974' => 'dzi', 'Duzib138G1867' => 'dzi', 'Duzib211G0420' => 'dzi', 'Duzib212G0930' => 'dzi', 'ECA234G1645' => 'eca', 'ECA247G3467' => 'eca', 'ECA248G1703' => 'eca', 'EL10Ac3g06327' => 'bvu', 'EL10Ac7g17204' => 'bvu', 'Eucgr.A00855' => 'egr', 'Eucgr.A00858' => 'egr', 'Eucgr.H01520' => 'egr', 'Eucgr.H03604' => 'egr', 'Eucgr.L03465' => 'egr', 'Eucgr.L03466' => 'egr', 'FAN01G0988' => 'fan', 'FAN02G3892' => 'fan', 'FAN05G3381' => 'fan', 'FAN07G0967' => 'fan', 'FAN07G1493' => 'fan', 'FAN08G3125' => 'fan', 'FAN09G0402' => 'fan', 'FAN12G2594' => 'fan', 'FAN12G3879' => 'fan', 'FAN14G1546' => 'fan', 'FAN15G3626' => 'fan', 'FAN17G0588' => 'fan', 'FAN17G0609' => 'fan', 'FAN18G2817' => 'fan', 'FAN19G1305' => 'fan', 'FAN20G1787' => 'fan', 'FAN22G0073' => 'fan', 'FAN22G0352' => 'fan', 'FAN22G0368' => 'fan', 'FAN22G2273' => 'fan', 'FAN24G1998' => 'fan', 'FAN27G1317' => 'fan', 'FvH4_2g23980' => 'fve', 'FvH4_4g14380' => 'fve', 'FvH4_4g14390' => 'fve', 'FvH4_6g09250' => 'fve', 'Glyma.03G151100' => 'gma', 'Glyma.04G122550' => 'gma', 'Glyma.05G001600' => 'gma', 'Glyma.09G270766' => 'gma', 'Glyma.09G270832' => 'gma', 'Glyma.13G209800' => 'gma', 'Glyma.15G102800' => 'gma', 'Glyma.18G218900' => 'gma', 'Glyma.19G001500' => 'gma', 'Glyma.19G153600' => 'gma', 'Gohir.A02G028600' => 'ghi', 'Gohir.A08G045000' => 'ghi', 'Gohir.A11G120500' => 'ghi', 'Gohir.A12G006200' => 'ghi', 'Gohir.A12G006250' => 'ghi', 'Gohir.D02G036300' => 'ghi', 'Gohir.D08G054700' => 'ghi', 'Gohir.D11G125600' => 'ghi', 'Gohir.D12G005700' => 'ghi', 'Gorai.004G055200' => 'gra', 'Gorai.005G040400' => 'gra', 'Gorai.007G134500' => 'gra', 'Gorai.008G005500' => 'gra', 'GSVIVG01011094001' => 'vvi', 'GSVIVG01017879001' => 'vvi', 'GSVIVG01025988001' => 'vvi', 'GSVIVG01029847001' => 'vvi', 'HanXRQChr10g0282901' => 'han', 'HanXRQChr10g0310371' => 'han', 'HanXRQChr10g0315041' => 'han', 'HanXRQChr11g0327651' => 'han', 'HanXRQChr12g0359391' => 'han', 'Haze_00972' => 'cav', 'Haze_00973' => 'cav', 'Haze_00974' => 'cav', 'Haze_04747' => 'cav', 'Haze_04749' => 'cav', 'Haze_04750' => 'cav', 'Haze_21217' => 'cav', 'Hma1.2p1_1037F.1_g250680' => 'hma', 'Hma1.2p1_1644F.1_g295320' => 'hma', 'HPP92_011322' => 'vpl', 'HPP92_011323' => 'vpl', 'HPP92_011324' => 'vpl', 'HPP92_011325' => 'vpl', 'HPP92_011326' => 'vpl', 'Hund12205' => 'sun', 'Hund17957' => 'sun', 'Lalb_Chr06g0176771' => 'lal', 'Lalb_Chr18g0056021' => 'lal', 'Lalb_Chr18g0056031' => 'lal', 'Lalb_Chr18g0056041' => 'lal', 'Lalb_Chr20g0107751' => 'lal', 'Lalb_Chr20g0118371' => 'lal', 'Lj1g0010239' => 'lja', 'Lj1g0017101' => 'lja', 'Lj2A1178G40' => 'lonja', 'Lj2A54G84' => 'lonja', 'Lj2g0015248' => 'lja', 'Lj3A761T51' => 'lonja', 'Lj6g0018116' => 'lja', 'Lsat_1_v5_gn_4_136040' => 'lsa', 'Lsat_1_v5_gn_5_187461' => 'lsa', 'Lsat_1_v5_gn_5_77001' => 'lsa', 'Lsat_1_v5_gn_9_4461' => 'lsa', 'Manes.01G210100' => 'mes', 'Manes.03G185600' => 'mes', 'Manes.05G073300' => 'mes', 'Manes.09G120300' => 'mes', 'Manes.15G022100' => 'mes', 'Mapoly0096s0053' => 'mpo', 'MBI03_g14058_MAGBIO' => 'mbi', 'MBI03_g33876_MAGBIO' => 'mbi', 'MBI03_g36854_MAGBIO' => 'mbi', 'MBI17_g11997_MAGBIO' => 'mbi', 'MD03G1269000' => 'mdo', 'MD04G1179600' => 'mdo', 'MD11G1289800' => 'mdo', 'MD12G1194700' => 'mdo', 'MD13G1182100' => 'mdo', 'MD13G1182200' => 'mdo', 'MD16G1182600' => 'mdo', 'Medtr2g021400' => 'mtr', 'Medtr2g021470' => 'mtr', 'Medtr2g105810' => 'mtr', 'Medtr3g033580' => 'mtr', 'Medtr6g007970' => 'mtr', 'Medtr7g056330' => 'mtr', 'Medtr7g074290' => 'mtr', 'Medtr7g074380' => 'mtr', 'Medtr7g094550' => 'mtr', 'Medtr8g069995' => 'mtr', 'MELO3C014345.2' => 'cme', 'MELO3C021395.2' => 'cme', 'Migut.D00262' => 'egut', 'Migut.G00257' => 'egut', 'MSTRG.21575' => 'ama', 'MSTRG.3985' => 'ama', 'Nitab4.5_0000295g0140' => 'nta', 'Nitab4.5_0000732g0140' => 'nta', 'Nitab4.5_0003162g0020' => 'nta', 'Nitab4.5_0006180g0090' => 'nta', 'Nitab4.5_0006390g0010' => 'nta', 'Nitab4.5_0007392g0040' => 'nta', 'Nn1g02140' => 'nnu', 'Nn4g26168' => 'nnu', 'Nn5g26754' => 'nnu', 'Oeu001433.1' => 'oeu', 'Oeu010299.2' => 'oeu', 'Oeu011171.1' => 'oeu', 'Oeu037675.1' => 'oeu', 'Oeu038359.1' => 'oeu', 'Oeu063834.1' => 'oeu', 'Oeu063835.1' => 'oeu', 'Os05g0312000' => 'osa', 'Os07g0211101' => 'osa', 'Os07g0211200' => 'osa', 'Os07g0681500' => 'osa', 'Peaxi162Scf00095g01015' => 'pax', 'Peaxi162Scf00104g00329' => 'pax', 'Peaxi162Scf00161g00137' => 'pax', 'PGR004G1665' => 'pgr', 'PGR031G2937' => 'pgr', 'PGR119G2145' => 'pgr', 'PGSC0003DMG400004351' => 'stu', 'PGSC0003DMG400014625' => 'stu', 'PGSC0003DMG401000943' => 'stu', 'Phvul.001G148600' => 'pvu', 'Phvul.004G001700' => 'pvu', 'Phvul.006G154900' => 'pvu', 'Phvul.008G078200' => 'pvu', 'Phvul.011G136500' => 'pvu', 'Potri.002G215600' => 'ptr', 'Potri.008G201600' => 'ptr', 'Potri.014G138400' => 'ptr', 'Potri.016G142500' => 'ptr', 'Pp3c16_10580' => 'ppa', 'Pp3c5_25280' => 'ppa', 'Prupe.1G150000' => 'ppe', 'Prupe.1G150100' => 'ppe', 'Prupe.6G299600' => 'ppe', 'Prupe.8G245000' => 'ppe', 'Psat0s4927g0040' => 'psa', 'Psat1g052080' => 'psa', 'Psat1g183800' => 'psa', 'Psat3g113840' => 'psa', 'Psat3g126120' => 'psa', 'Psat3g126160' => 'psa', 'Psat3g158760' => 'psa', 'Psat3g158840' => 'psa', 'PSO170G2858' => 'pso', 'PSO339G0606' => 'pso', 'PSO384G4709' => 'pso', 'PSO407G0334' => 'pso', 'QL04p040276' => 'qlo', 'QL06p005458' => 'qlo', 'QL06p005472' => 'qlo', 'QL07p030546' => 'qlo', 'QL07p031519' => 'qlo', 'QL09p050949' => 'qlo', 'QL09p050966' => 'qlo', 'QL09p051067' => 'qlo', 'QL12p022706' => 'qlo', 'RcHm_v2.0_Chr2g0119601' => 'rch', 'RcHm_v2.0_Chr3g0459591' => 'rch', 'RcHm_v2.0_Chr4g0418521' => 'rch', 'RcHm_v2.0_Chr4g0418531' => 'rch', 'RcHm_v2.0_Chr4g0418541' => 'rch', 'RcHm_v2.0_Chr6g0291641' => 'rch', 'Rhsim01G0086300' => 'rsi', 'Rhsim01G0276300' => 'rsi', 'Rhsim01G0276500' => 'rsi', 'Rhsim04G0207700' => 'rsi', 'Rhsim05G0234500' => 'rsi', 'Rhsim13G0022400' => 'rsi', 'Sabra02G0167900' => 'sbr', 'Sabra04G0158500' => 'sbr', 'Sabra08G0159800' => 'sbr', 'Sabra10G0011500' => 'sbr', 'Sabra14G0104400' => 'sbr', 'SalBow2G2440' => 'sbo', 'SalBow4G2265' => 'sbo', 'Sc02g0000060' => 'sci', 'Sc05g0005020' => 'sci', 'Sc13g0003890' => 'sci', 'Sed0014865' => 'sed', 'Sed0017224' => 'sed', 'Sed0026391' => 'sed', 'SEGI_00063' => 'sgi', 'SEGI_10967' => 'sgi', 'SEGI_17510' => 'sgi', 'SEGI_24396' => 'sgi', 'SEGI_39719' => 'sgi', 'SEGI_41392' => 'sgi', 'SGA_v2.0_scaffold11G05794' => 'sas', 'SGA_v2.0_scaffold142G35607' => 'sas', 'SGA_v2.0_scaffold1G00447' => 'sas', 'SHI15388' => 'shi', 'SHI15394' => 'shi', 'SHI15396' => 'shi', 'SHI15399' => 'shi', 'SMO343G0151' => 'smo', 'SMO367G1118' => 'smo', 'Solyc01g080200.3' => 'sly', 'Solyc06g008960.3' => 'sly', 'Solyc09g064780.3' => 'sly', 'Sopen01g031980' => 'spe', 'Sopen06g003710' => 'spe', 'Sopen09g026460' => 'spe', 'Sp3g21240' => 'spa', 'Sp4g30030' => 'spa', 'TAR365G0022' => 'tar', 'TAR365G1023' => 'tar', 'TAR365G1253' => 'tar', 'TAR623G0078' => 'tar', 'TAR623G1721' => 'tar', 'TAR633G0959' => 'tar', 'THA.LOC104802225' => 'tha', 'THA.LOC104804769' => 'tha', 'THA.LOC104808660' => 'tha', 'THA.LOC104812792' => 'tha', 'Thecc.01G284000' => 'tca', 'Thecc.04G220600' => 'tca', 'Thecc.05G268900' => 'tca', 'Thecc.08G171100' => 'tca', 'Thhalv10001284m.g' => 'esa', 'Thhalv10019912m.g' => 'esa', 'TPR.G14189' => 'tpr', 'TPR.G18110' => 'tpr', 'TPR.G18130' => 'tpr', 'TPR.G18131' => 'tpr', 'TPR.G18140' => 'tpr', 'TPR.G24282' => 'tpr', 'TPR.G25221' => 'tpr', 'TPR.G29267' => 'tpr', 'TPR.G35315' => 'tpr', 'TPR.G36173' => 'tpr', 'TWI09G0794' => 'twi', 'TWI59G1348' => 'twi', 'TWI74G0430' => 'twi', 'unitig_26.g8940' => 'ugi', 'unitig_749.g13744' => 'ugi', 'unitig_749.g13745' => 'ugi', 'vmacro08269' => 'vma', 'vmacro14937' => 'vma', 'vmacro20401' => 'vma', 'VMungo0464G1349' => 'vmu', 'VMungo0540G0289' => 'vmu', 'VMungo1215G1590' => 'vmu', 'VMungo1309G0221' => 'vmu', 'VMungo1309G2815' => 'vmu', 'VMungo1383G0239' => 'vmu', 'VMungo1383G2910' => 'vmu', 'Zm00001eb095270' => 'zma', 'Zm00001eb095280' => 'zma', 'Zm00001eb111630' => 'zma', 'Zm00001eb237080' => 'zma', 'Zm00001eb273740' => 'zma', 'Zm00001eb285040' => 'zma', 'Zm00001eb330790' => 'zma', 'Zm00001eb337380' => 'zma' ) $gf_id = 'HOM05D001484' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001484' ) $data_identifier = 'HOM05D001484' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 2, 'aly' => (int) 2, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 22, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 7, 'hma' => (int) 2, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 7, 'mtr' => (int) 10, 'cme' => (int) 2, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 4, 'ppa' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 4, 'qlo' => (int) 9, 'rch' => (int) 6, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 10, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 7, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb337380' $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' => 'HOM05D001484', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p31500' => 'bna', 'A05p00020' => 'bna', 'A07p08820' => 'bna', 'Aa31LG4G3300' => 'aar', 'Aa31LG8G10030' => 'aar', 'Actinidia00731' => 'ach', 'Actinidia11473' => 'ach', 'Actinidia23469' => 'ach', 'Actinidia24318' => 'ach', 'Actinidia40196' => 'ach', 'Actinidia40197' => 'ach', 'Actinidia40198' => 'ach', 'Ah.08g212990' => 'amhyb', 'Ah.15g091720' => 'amhyb', 'AL3G38260' => 'aly', 'AL4G47710' => 'aly', 'Aqoxy2G00671' => 'aox', 'Aqoxy2G03236' => 'aox', 'arahy.Tifrunner.gnm1.ann1.05IDCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KR684' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATY3SJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK6QJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6APGL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IDT7Z9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM073U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ0R87' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LE7RV4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT4QRX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V5ENPK' => 'arhy', 'AT2G48110' => 'ath', 'AT3G23590' => 'ath', 'ATR0626G186' => 'atr', 'ATR1127G141' => 'atr', 'Atru.chr4.2583' => 'acertr', 'Atru.chr5.1358' => 'acertr', 'Atru.chr5.1359' => 'acertr', 'Atru.chr8.46' => 'acertr', 'AUR62002640' => 'cqu', 'AUR62030055' => 'cqu', 'AUR62033713' => 'cqu', 'AUR62033714' => 'cqu', 'AUR62036795' => 'cqu', 'AUR62039891' => 'cqu', 'BcaB02g08737' => 'bca', 'BcaB04g20441' => 'bca', 'BcaB06g26509' => 'bca', 'BcaB06g26510' => 'bca', 'BcaB06g26511' => 'bca', 'BcaB06g26512' => 'bca', 'BcaB06g26513' => 'bca', 'BcaC02g12564' => 'bca', 'BcaC02g12565' => 'bca', 'BcaC02g12794' => 'bca', 'BcaC02g12795' => 'bca', 'BcaC02g12796' => 'bca', 'BcaC06g35541' => 'bca', 'BNapus_Darmor_BZH_scaffold_188p00080' => 'bna', 'BNapus_Darmor_BZH_scaffold_188p00090' => 'bna', 'BolC1t03972H' => 'bol', 'BolC1t03973H' => 'bol', 'BolC4t21680H' => 'bol', 'BolC7t41863H' => 'bol', 'BolSC55t61227H' => 'bol', 'BolSC55t61228H' => 'bol', 'BraA01t03278Z' => 'bra', 'BraA05t18998Z' => 'bra', 'BraA07t28673Z' => 'bra', 'C01p40150' => 'bna', 'C05p12370' => 'bna', 'C07p13680' => 'bna', 'CAN.G1006.16' => 'can', 'CAN.G1006.17' => 'can', 'CAN.G1170.2' => 'can', 'CAN.G962.7' => 'can', 'CANSAT25G2179' => 'cansat', 'CANSAT78G1573' => 'cansat', 'CARHR099510' => 'chi', 'CARHR143510' => 'chi', 'Carub.0003s2380' => 'cru', 'Carub.0004s3082' => 'cru', 'Ca_00614_v3' => 'car', 'Ca_07801_v3' => 'car', 'Ca_08567_v3' => 'car', 'Ca_09571_v3' => 'car', 'CBR_g19290' => 'cbr', 'Cc01_g19770' => 'ccan', 'Cc03_g03030' => 'ccan', 'CDE07G0968' => 'cde', 'CDE09G1441' => 'cde', 'Cfa006103' => 'cfa', 'Cfa015573' => 'cfa', 'Cfa016988' => 'cfa', 'Ciclev10006738m.g' => 'ccl', 'Ciclev10010920m.g' => 'ccl', 'Ciclev10018517m.g' => 'ccl', 'CiPaw.01G159200' => 'cil', 'CiPaw.02G091000' => 'cil', 'CiPaw.02G091100' => 'cil', 'CiPaw.08G103100' => 'cil', 'CiPaw.09G224900' => 'cil', 'ClCG06G005740' => 'cla', 'ClCG07G000090' => 'cla', 'ClCG07G000100' => 'cla', 'COL.COLO4_09143' => 'col', 'COL.COLO4_25124' => 'col', 'Cpa.g.sc16.34' => 'cpa', 'Cpa.g.sc3504.1' => 'cpa', 'Cpa.g.sc60.37' => 'cpa', 'CsaV3_6G018520' => 'csa', 'CsaV3_6G036860' => 'csa', 'CSS0001072' => 'camsi', 'CSS0020208' => 'camsi', 'CSS0021253' => 'camsi', 'CSS0022190' => 'camsi', 'CSS0036150' => 'camsi', 'CSS0040442' => 'camsi', 'CSS0042300' => 'camsi', 'CSS0045298' => 'camsi', 'DCAR_012449' => 'dca', 'DCAR_018405' => 'dca', 'DCAR_024573' => 'dca', 'DCAR_030591' => 'dca', 'Dinv16926' => 'din', 'Dinv32963' => 'din', 'Dinv38382' => 'din', 'Dinv38383' => 'din', 'Duzib133G0974' => 'dzi', 'Duzib138G1867' => 'dzi', 'Duzib211G0420' => 'dzi', 'Duzib212G0930' => 'dzi', 'ECA234G1645' => 'eca', 'ECA247G3467' => 'eca', 'ECA248G1703' => 'eca', 'EL10Ac3g06327' => 'bvu', 'EL10Ac7g17204' => 'bvu', 'Eucgr.A00855' => 'egr', 'Eucgr.A00858' => 'egr', 'Eucgr.H01520' => 'egr', 'Eucgr.H03604' => 'egr', 'Eucgr.L03465' => 'egr', 'Eucgr.L03466' => 'egr', 'FAN01G0988' => 'fan', 'FAN02G3892' => 'fan', 'FAN05G3381' => 'fan', 'FAN07G0967' => 'fan', 'FAN07G1493' => 'fan', 'FAN08G3125' => 'fan', 'FAN09G0402' => 'fan', 'FAN12G2594' => 'fan', 'FAN12G3879' => 'fan', 'FAN14G1546' => 'fan', 'FAN15G3626' => 'fan', 'FAN17G0588' => 'fan', 'FAN17G0609' => 'fan', 'FAN18G2817' => 'fan', 'FAN19G1305' => 'fan', 'FAN20G1787' => 'fan', 'FAN22G0073' => 'fan', 'FAN22G0352' => 'fan', 'FAN22G0368' => 'fan', 'FAN22G2273' => 'fan', 'FAN24G1998' => 'fan', 'FAN27G1317' => 'fan', 'FvH4_2g23980' => 'fve', 'FvH4_4g14380' => 'fve', 'FvH4_4g14390' => 'fve', 'FvH4_6g09250' => 'fve', 'Glyma.03G151100' => 'gma', 'Glyma.04G122550' => 'gma', 'Glyma.05G001600' => 'gma', 'Glyma.09G270766' => 'gma', 'Glyma.09G270832' => 'gma', 'Glyma.13G209800' => 'gma', 'Glyma.15G102800' => 'gma', 'Glyma.18G218900' => 'gma', 'Glyma.19G001500' => 'gma', 'Glyma.19G153600' => 'gma', 'Gohir.A02G028600' => 'ghi', 'Gohir.A08G045000' => 'ghi', 'Gohir.A11G120500' => 'ghi', 'Gohir.A12G006200' => 'ghi', 'Gohir.A12G006250' => 'ghi', 'Gohir.D02G036300' => 'ghi', 'Gohir.D08G054700' => 'ghi', 'Gohir.D11G125600' => 'ghi', 'Gohir.D12G005700' => 'ghi', 'Gorai.004G055200' => 'gra', 'Gorai.005G040400' => 'gra', 'Gorai.007G134500' => 'gra', 'Gorai.008G005500' => 'gra', 'GSVIVG01011094001' => 'vvi', 'GSVIVG01017879001' => 'vvi', 'GSVIVG01025988001' => 'vvi', 'GSVIVG01029847001' => 'vvi', 'HanXRQChr10g0282901' => 'han', 'HanXRQChr10g0310371' => 'han', 'HanXRQChr10g0315041' => 'han', 'HanXRQChr11g0327651' => 'han', 'HanXRQChr12g0359391' => 'han', 'Haze_00972' => 'cav', 'Haze_00973' => 'cav', 'Haze_00974' => 'cav', 'Haze_04747' => 'cav', 'Haze_04749' => 'cav', 'Haze_04750' => 'cav', 'Haze_21217' => 'cav', 'Hma1.2p1_1037F.1_g250680' => 'hma', 'Hma1.2p1_1644F.1_g295320' => 'hma', 'HPP92_011322' => 'vpl', 'HPP92_011323' => 'vpl', 'HPP92_011324' => 'vpl', 'HPP92_011325' => 'vpl', 'HPP92_011326' => 'vpl', 'Hund12205' => 'sun', 'Hund17957' => 'sun', 'Lalb_Chr06g0176771' => 'lal', 'Lalb_Chr18g0056021' => 'lal', 'Lalb_Chr18g0056031' => 'lal', 'Lalb_Chr18g0056041' => 'lal', 'Lalb_Chr20g0107751' => 'lal', 'Lalb_Chr20g0118371' => 'lal', 'Lj1g0010239' => 'lja', 'Lj1g0017101' => 'lja', 'Lj2A1178G40' => 'lonja', 'Lj2A54G84' => 'lonja', 'Lj2g0015248' => 'lja', 'Lj3A761T51' => 'lonja', 'Lj6g0018116' => 'lja', 'Lsat_1_v5_gn_4_136040' => 'lsa', 'Lsat_1_v5_gn_5_187461' => 'lsa', 'Lsat_1_v5_gn_5_77001' => 'lsa', 'Lsat_1_v5_gn_9_4461' => 'lsa', 'Manes.01G210100' => 'mes', 'Manes.03G185600' => 'mes', 'Manes.05G073300' => 'mes', 'Manes.09G120300' => 'mes', 'Manes.15G022100' => 'mes', 'Mapoly0096s0053' => 'mpo', 'MBI03_g14058_MAGBIO' => 'mbi', 'MBI03_g33876_MAGBIO' => 'mbi', 'MBI03_g36854_MAGBIO' => 'mbi', 'MBI17_g11997_MAGBIO' => 'mbi', 'MD03G1269000' => 'mdo', 'MD04G1179600' => 'mdo', 'MD11G1289800' => 'mdo', 'MD12G1194700' => 'mdo', 'MD13G1182100' => 'mdo', 'MD13G1182200' => 'mdo', 'MD16G1182600' => 'mdo', 'Medtr2g021400' => 'mtr', 'Medtr2g021470' => 'mtr', 'Medtr2g105810' => 'mtr', 'Medtr3g033580' => 'mtr', 'Medtr6g007970' => 'mtr', 'Medtr7g056330' => 'mtr', 'Medtr7g074290' => 'mtr', 'Medtr7g074380' => 'mtr', 'Medtr7g094550' => 'mtr', 'Medtr8g069995' => 'mtr', 'MELO3C014345.2' => 'cme', 'MELO3C021395.2' => 'cme', 'Migut.D00262' => 'egut', 'Migut.G00257' => 'egut', 'MSTRG.21575' => 'ama', 'MSTRG.3985' => 'ama', 'Nitab4.5_0000295g0140' => 'nta', 'Nitab4.5_0000732g0140' => 'nta', 'Nitab4.5_0003162g0020' => 'nta', 'Nitab4.5_0006180g0090' => 'nta', 'Nitab4.5_0006390g0010' => 'nta', 'Nitab4.5_0007392g0040' => 'nta', 'Nn1g02140' => 'nnu', 'Nn4g26168' => 'nnu', 'Nn5g26754' => 'nnu', 'Oeu001433.1' => 'oeu', 'Oeu010299.2' => 'oeu', 'Oeu011171.1' => 'oeu', 'Oeu037675.1' => 'oeu', 'Oeu038359.1' => 'oeu', 'Oeu063834.1' => 'oeu', 'Oeu063835.1' => 'oeu', 'Os05g0312000' => 'osa', 'Os07g0211101' => 'osa', 'Os07g0211200' => 'osa', 'Os07g0681500' => 'osa', 'Peaxi162Scf00095g01015' => 'pax', 'Peaxi162Scf00104g00329' => 'pax', 'Peaxi162Scf00161g00137' => 'pax', 'PGR004G1665' => 'pgr', 'PGR031G2937' => 'pgr', 'PGR119G2145' => 'pgr', 'PGSC0003DMG400004351' => 'stu', 'PGSC0003DMG400014625' => 'stu', 'PGSC0003DMG401000943' => 'stu', 'Phvul.001G148600' => 'pvu', 'Phvul.004G001700' => 'pvu', 'Phvul.006G154900' => 'pvu', 'Phvul.008G078200' => 'pvu', 'Phvul.011G136500' => 'pvu', 'Potri.002G215600' => 'ptr', 'Potri.008G201600' => 'ptr', 'Potri.014G138400' => 'ptr', 'Potri.016G142500' => 'ptr', 'Pp3c16_10580' => 'ppa', 'Pp3c5_25280' => 'ppa', 'Prupe.1G150000' => 'ppe', 'Prupe.1G150100' => 'ppe', 'Prupe.6G299600' => 'ppe', 'Prupe.8G245000' => 'ppe', 'Psat0s4927g0040' => 'psa', 'Psat1g052080' => 'psa', 'Psat1g183800' => 'psa', 'Psat3g113840' => 'psa', 'Psat3g126120' => 'psa', 'Psat3g126160' => 'psa', 'Psat3g158760' => 'psa', 'Psat3g158840' => 'psa', 'PSO170G2858' => 'pso', 'PSO339G0606' => 'pso', 'PSO384G4709' => 'pso', 'PSO407G0334' => 'pso', 'QL04p040276' => 'qlo', 'QL06p005458' => 'qlo', 'QL06p005472' => 'qlo', 'QL07p030546' => 'qlo', 'QL07p031519' => 'qlo', 'QL09p050949' => 'qlo', 'QL09p050966' => 'qlo', 'QL09p051067' => 'qlo', 'QL12p022706' => 'qlo', 'RcHm_v2.0_Chr2g0119601' => 'rch', 'RcHm_v2.0_Chr3g0459591' => 'rch', 'RcHm_v2.0_Chr4g0418521' => 'rch', 'RcHm_v2.0_Chr4g0418531' => 'rch', 'RcHm_v2.0_Chr4g0418541' => 'rch', 'RcHm_v2.0_Chr6g0291641' => 'rch', 'Rhsim01G0086300' => 'rsi', 'Rhsim01G0276300' => 'rsi', 'Rhsim01G0276500' => 'rsi', 'Rhsim04G0207700' => 'rsi', 'Rhsim05G0234500' => 'rsi', 'Rhsim13G0022400' => 'rsi', 'Sabra02G0167900' => 'sbr', 'Sabra04G0158500' => 'sbr', 'Sabra08G0159800' => 'sbr', 'Sabra10G0011500' => 'sbr', 'Sabra14G0104400' => 'sbr', 'SalBow2G2440' => 'sbo', 'SalBow4G2265' => 'sbo', 'Sc02g0000060' => 'sci', 'Sc05g0005020' => 'sci', 'Sc13g0003890' => 'sci', 'Sed0014865' => 'sed', 'Sed0017224' => 'sed', 'Sed0026391' => 'sed', 'SEGI_00063' => 'sgi', 'SEGI_10967' => 'sgi', 'SEGI_17510' => 'sgi', 'SEGI_24396' => 'sgi', 'SEGI_39719' => 'sgi', 'SEGI_41392' => 'sgi', 'SGA_v2.0_scaffold11G05794' => 'sas', 'SGA_v2.0_scaffold142G35607' => 'sas', 'SGA_v2.0_scaffold1G00447' => 'sas', 'SHI15388' => 'shi', 'SHI15394' => 'shi', 'SHI15396' => 'shi', 'SHI15399' => 'shi', 'SMO343G0151' => 'smo', 'SMO367G1118' => 'smo', 'Solyc01g080200.3' => 'sly', 'Solyc06g008960.3' => 'sly', 'Solyc09g064780.3' => 'sly', 'Sopen01g031980' => 'spe', 'Sopen06g003710' => 'spe', 'Sopen09g026460' => 'spe', 'Sp3g21240' => 'spa', 'Sp4g30030' => 'spa', 'TAR365G0022' => 'tar', 'TAR365G1023' => 'tar', 'TAR365G1253' => 'tar', 'TAR623G0078' => 'tar', 'TAR623G1721' => 'tar', 'TAR633G0959' => 'tar', 'THA.LOC104802225' => 'tha', 'THA.LOC104804769' => 'tha', 'THA.LOC104808660' => 'tha', 'THA.LOC104812792' => 'tha', 'Thecc.01G284000' => 'tca', 'Thecc.04G220600' => 'tca', 'Thecc.05G268900' => 'tca', 'Thecc.08G171100' => 'tca', 'Thhalv10001284m.g' => 'esa', 'Thhalv10019912m.g' => 'esa', 'TPR.G14189' => 'tpr', 'TPR.G18110' => 'tpr', 'TPR.G18130' => 'tpr', 'TPR.G18131' => 'tpr', 'TPR.G18140' => 'tpr', 'TPR.G24282' => 'tpr', 'TPR.G25221' => 'tpr', 'TPR.G29267' => 'tpr', 'TPR.G35315' => 'tpr', 'TPR.G36173' => 'tpr', 'TWI09G0794' => 'twi', 'TWI59G1348' => 'twi', 'TWI74G0430' => 'twi', 'unitig_26.g8940' => 'ugi', 'unitig_749.g13744' => 'ugi', 'unitig_749.g13745' => 'ugi', 'vmacro08269' => 'vma', 'vmacro14937' => 'vma', 'vmacro20401' => 'vma', 'VMungo0464G1349' => 'vmu', 'VMungo0540G0289' => 'vmu', 'VMungo1215G1590' => 'vmu', 'VMungo1309G0221' => 'vmu', 'VMungo1309G2815' => 'vmu', 'VMungo1383G0239' => 'vmu', 'VMungo1383G2910' => 'vmu', 'Zm00001eb095270' => 'zma', 'Zm00001eb095280' => 'zma', 'Zm00001eb111630' => 'zma', 'Zm00001eb237080' => 'zma', 'Zm00001eb273740' => 'zma', 'Zm00001eb285040' => 'zma', 'Zm00001eb330790' => 'zma', 'Zm00001eb337380' => 'zma' ), 'gf_id' => 'HOM05D001484', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001484' ), 'data_identifier' => 'HOM05D001484', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001484', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p31500' => 'bna', 'A05p00020' => 'bna', 'A07p08820' => 'bna', 'Aa31LG4G3300' => 'aar', 'Aa31LG8G10030' => 'aar', 'Actinidia00731' => 'ach', 'Actinidia11473' => 'ach', 'Actinidia23469' => 'ach', 'Actinidia24318' => 'ach', 'Actinidia40196' => 'ach', 'Actinidia40197' => 'ach', 'Actinidia40198' => 'ach', 'Ah.08g212990' => 'amhyb', 'Ah.15g091720' => 'amhyb', 'AL3G38260' => 'aly', 'AL4G47710' => 'aly', 'Aqoxy2G00671' => 'aox', 'Aqoxy2G03236' => 'aox', 'arahy.Tifrunner.gnm1.ann1.05IDCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KR684' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATY3SJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK6QJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6APGL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IDT7Z9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM073U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ0R87' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LE7RV4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT4QRX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V5ENPK' => 'arhy', 'AT2G48110' => 'ath', 'AT3G23590' => 'ath', 'ATR0626G186' => 'atr', 'ATR1127G141' => 'atr', 'Atru.chr4.2583' => 'acertr', 'Atru.chr5.1358' => 'acertr', 'Atru.chr5.1359' => 'acertr', 'Atru.chr8.46' => 'acertr', 'AUR62002640' => 'cqu', 'AUR62030055' => 'cqu', 'AUR62033713' => 'cqu', 'AUR62033714' => 'cqu', 'AUR62036795' => 'cqu', 'AUR62039891' => 'cqu', 'BcaB02g08737' => 'bca', 'BcaB04g20441' => 'bca', 'BcaB06g26509' => 'bca', 'BcaB06g26510' => 'bca', 'BcaB06g26511' => 'bca', 'BcaB06g26512' => 'bca', 'BcaB06g26513' => 'bca', 'BcaC02g12564' => 'bca', 'BcaC02g12565' => 'bca', 'BcaC02g12794' => 'bca', 'BcaC02g12795' => 'bca', 'BcaC02g12796' => 'bca', 'BcaC06g35541' => 'bca', 'BNapus_Darmor_BZH_scaffold_188p00080' => 'bna', 'BNapus_Darmor_BZH_scaffold_188p00090' => 'bna', 'BolC1t03972H' => 'bol', 'BolC1t03973H' => 'bol', 'BolC4t21680H' => 'bol', 'BolC7t41863H' => 'bol', 'BolSC55t61227H' => 'bol', 'BolSC55t61228H' => 'bol', 'BraA01t03278Z' => 'bra', 'BraA05t18998Z' => 'bra', 'BraA07t28673Z' => 'bra', 'C01p40150' => 'bna', 'C05p12370' => 'bna', 'C07p13680' => 'bna', 'CAN.G1006.16' => 'can', 'CAN.G1006.17' => 'can', 'CAN.G1170.2' => 'can', 'CAN.G962.7' => 'can', 'CANSAT25G2179' => 'cansat', 'CANSAT78G1573' => 'cansat', 'CARHR099510' => 'chi', 'CARHR143510' => 'chi', 'Carub.0003s2380' => 'cru', 'Carub.0004s3082' => 'cru', 'Ca_00614_v3' => 'car', 'Ca_07801_v3' => 'car', 'Ca_08567_v3' => 'car', 'Ca_09571_v3' => 'car', 'CBR_g19290' => 'cbr', 'Cc01_g19770' => 'ccan', 'Cc03_g03030' => 'ccan', 'CDE07G0968' => 'cde', 'CDE09G1441' => 'cde', 'Cfa006103' => 'cfa', 'Cfa015573' => 'cfa', 'Cfa016988' => 'cfa', 'Ciclev10006738m.g' => 'ccl', 'Ciclev10010920m.g' => 'ccl', 'Ciclev10018517m.g' => 'ccl', 'CiPaw.01G159200' => 'cil', 'CiPaw.02G091000' => 'cil', 'CiPaw.02G091100' => 'cil', 'CiPaw.08G103100' => 'cil', 'CiPaw.09G224900' => 'cil', 'ClCG06G005740' => 'cla', 'ClCG07G000090' => 'cla', 'ClCG07G000100' => 'cla', 'COL.COLO4_09143' => 'col', 'COL.COLO4_25124' => 'col', 'Cpa.g.sc16.34' => 'cpa', 'Cpa.g.sc3504.1' => 'cpa', 'Cpa.g.sc60.37' => 'cpa', 'CsaV3_6G018520' => 'csa', 'CsaV3_6G036860' => 'csa', 'CSS0001072' => 'camsi', 'CSS0020208' => 'camsi', 'CSS0021253' => 'camsi', 'CSS0022190' => 'camsi', 'CSS0036150' => 'camsi', 'CSS0040442' => 'camsi', 'CSS0042300' => 'camsi', 'CSS0045298' => 'camsi', 'DCAR_012449' => 'dca', 'DCAR_018405' => 'dca', 'DCAR_024573' => 'dca', 'DCAR_030591' => 'dca', 'Dinv16926' => 'din', 'Dinv32963' => 'din', 'Dinv38382' => 'din', 'Dinv38383' => 'din', 'Duzib133G0974' => 'dzi', 'Duzib138G1867' => 'dzi', 'Duzib211G0420' => 'dzi', 'Duzib212G0930' => 'dzi', 'ECA234G1645' => 'eca', 'ECA247G3467' => 'eca', 'ECA248G1703' => 'eca', 'EL10Ac3g06327' => 'bvu', 'EL10Ac7g17204' => 'bvu', 'Eucgr.A00855' => 'egr', 'Eucgr.A00858' => 'egr', 'Eucgr.H01520' => 'egr', 'Eucgr.H03604' => 'egr', 'Eucgr.L03465' => 'egr', 'Eucgr.L03466' => 'egr', 'FAN01G0988' => 'fan', 'FAN02G3892' => 'fan', 'FAN05G3381' => 'fan', 'FAN07G0967' => 'fan', 'FAN07G1493' => 'fan', 'FAN08G3125' => 'fan', 'FAN09G0402' => 'fan', 'FAN12G2594' => 'fan', 'FAN12G3879' => 'fan', 'FAN14G1546' => 'fan', 'FAN15G3626' => 'fan', 'FAN17G0588' => 'fan', 'FAN17G0609' => 'fan', 'FAN18G2817' => 'fan', 'FAN19G1305' => 'fan', 'FAN20G1787' => 'fan', 'FAN22G0073' => 'fan', 'FAN22G0352' => 'fan', 'FAN22G0368' => 'fan', 'FAN22G2273' => 'fan', 'FAN24G1998' => 'fan', 'FAN27G1317' => 'fan', 'FvH4_2g23980' => 'fve', 'FvH4_4g14380' => 'fve', 'FvH4_4g14390' => 'fve', 'FvH4_6g09250' => 'fve', 'Glyma.03G151100' => 'gma', 'Glyma.04G122550' => 'gma', 'Glyma.05G001600' => 'gma', 'Glyma.09G270766' => 'gma', 'Glyma.09G270832' => 'gma', 'Glyma.13G209800' => 'gma', 'Glyma.15G102800' => 'gma', 'Glyma.18G218900' => 'gma', 'Glyma.19G001500' => 'gma', 'Glyma.19G153600' => 'gma', 'Gohir.A02G028600' => 'ghi', 'Gohir.A08G045000' => 'ghi', 'Gohir.A11G120500' => 'ghi', 'Gohir.A12G006200' => 'ghi', 'Gohir.A12G006250' => 'ghi', 'Gohir.D02G036300' => 'ghi', 'Gohir.D08G054700' => 'ghi', 'Gohir.D11G125600' => 'ghi', 'Gohir.D12G005700' => 'ghi', 'Gorai.004G055200' => 'gra', 'Gorai.005G040400' => 'gra', 'Gorai.007G134500' => 'gra', 'Gorai.008G005500' => 'gra', 'GSVIVG01011094001' => 'vvi', 'GSVIVG01017879001' => 'vvi', 'GSVIVG01025988001' => 'vvi', 'GSVIVG01029847001' => 'vvi', 'HanXRQChr10g0282901' => 'han', 'HanXRQChr10g0310371' => 'han', 'HanXRQChr10g0315041' => 'han', 'HanXRQChr11g0327651' => 'han', 'HanXRQChr12g0359391' => 'han', 'Haze_00972' => 'cav', 'Haze_00973' => 'cav', 'Haze_00974' => 'cav', 'Haze_04747' => 'cav', 'Haze_04749' => 'cav', 'Haze_04750' => 'cav', 'Haze_21217' => 'cav', 'Hma1.2p1_1037F.1_g250680' => 'hma', 'Hma1.2p1_1644F.1_g295320' => 'hma', 'HPP92_011322' => 'vpl', 'HPP92_011323' => 'vpl', 'HPP92_011324' => 'vpl', 'HPP92_011325' => 'vpl', 'HPP92_011326' => 'vpl', 'Hund12205' => 'sun', 'Hund17957' => 'sun', 'Lalb_Chr06g0176771' => 'lal', 'Lalb_Chr18g0056021' => 'lal', 'Lalb_Chr18g0056031' => 'lal', 'Lalb_Chr18g0056041' => 'lal', 'Lalb_Chr20g0107751' => 'lal', 'Lalb_Chr20g0118371' => 'lal', 'Lj1g0010239' => 'lja', 'Lj1g0017101' => 'lja', 'Lj2A1178G40' => 'lonja', 'Lj2A54G84' => 'lonja', 'Lj2g0015248' => 'lja', 'Lj3A761T51' => 'lonja', 'Lj6g0018116' => 'lja', 'Lsat_1_v5_gn_4_136040' => 'lsa', 'Lsat_1_v5_gn_5_187461' => 'lsa', 'Lsat_1_v5_gn_5_77001' => 'lsa', 'Lsat_1_v5_gn_9_4461' => 'lsa', 'Manes.01G210100' => 'mes', 'Manes.03G185600' => 'mes', 'Manes.05G073300' => 'mes', 'Manes.09G120300' => 'mes', 'Manes.15G022100' => 'mes', 'Mapoly0096s0053' => 'mpo', 'MBI03_g14058_MAGBIO' => 'mbi', 'MBI03_g33876_MAGBIO' => 'mbi', 'MBI03_g36854_MAGBIO' => 'mbi', 'MBI17_g11997_MAGBIO' => 'mbi', 'MD03G1269000' => 'mdo', 'MD04G1179600' => 'mdo', 'MD11G1289800' => 'mdo', 'MD12G1194700' => 'mdo', 'MD13G1182100' => 'mdo', 'MD13G1182200' => 'mdo', 'MD16G1182600' => 'mdo', 'Medtr2g021400' => 'mtr', 'Medtr2g021470' => 'mtr', 'Medtr2g105810' => 'mtr', 'Medtr3g033580' => 'mtr', 'Medtr6g007970' => 'mtr', 'Medtr7g056330' => 'mtr', 'Medtr7g074290' => 'mtr', 'Medtr7g074380' => 'mtr', 'Medtr7g094550' => 'mtr', 'Medtr8g069995' => 'mtr', 'MELO3C014345.2' => 'cme', 'MELO3C021395.2' => 'cme', 'Migut.D00262' => 'egut', 'Migut.G00257' => 'egut', 'MSTRG.21575' => 'ama', 'MSTRG.3985' => 'ama', 'Nitab4.5_0000295g0140' => 'nta', 'Nitab4.5_0000732g0140' => 'nta', 'Nitab4.5_0003162g0020' => 'nta', 'Nitab4.5_0006180g0090' => 'nta', 'Nitab4.5_0006390g0010' => 'nta', 'Nitab4.5_0007392g0040' => 'nta', 'Nn1g02140' => 'nnu', 'Nn4g26168' => 'nnu', 'Nn5g26754' => 'nnu', 'Oeu001433.1' => 'oeu', 'Oeu010299.2' => 'oeu', 'Oeu011171.1' => 'oeu', 'Oeu037675.1' => 'oeu', 'Oeu038359.1' => 'oeu', 'Oeu063834.1' => 'oeu', 'Oeu063835.1' => 'oeu', 'Os05g0312000' => 'osa', 'Os07g0211101' => 'osa', 'Os07g0211200' => 'osa', 'Os07g0681500' => 'osa', 'Peaxi162Scf00095g01015' => 'pax', 'Peaxi162Scf00104g00329' => 'pax', 'Peaxi162Scf00161g00137' => 'pax', 'PGR004G1665' => 'pgr', 'PGR031G2937' => 'pgr', 'PGR119G2145' => 'pgr', 'PGSC0003DMG400004351' => 'stu', 'PGSC0003DMG400014625' => 'stu', 'PGSC0003DMG401000943' => 'stu', 'Phvul.001G148600' => 'pvu', 'Phvul.004G001700' => 'pvu', 'Phvul.006G154900' => 'pvu', 'Phvul.008G078200' => 'pvu', 'Phvul.011G136500' => 'pvu', 'Potri.002G215600' => 'ptr', 'Potri.008G201600' => 'ptr', 'Potri.014G138400' => 'ptr', 'Potri.016G142500' => 'ptr', 'Pp3c16_10580' => 'ppa', 'Pp3c5_25280' => 'ppa', 'Prupe.1G150000' => 'ppe', 'Prupe.1G150100' => 'ppe', 'Prupe.6G299600' => 'ppe', 'Prupe.8G245000' => 'ppe', 'Psat0s4927g0040' => 'psa', 'Psat1g052080' => 'psa', 'Psat1g183800' => 'psa', 'Psat3g113840' => 'psa', 'Psat3g126120' => 'psa', 'Psat3g126160' => 'psa', 'Psat3g158760' => 'psa', 'Psat3g158840' => 'psa', 'PSO170G2858' => 'pso', 'PSO339G0606' => 'pso', 'PSO384G4709' => 'pso', 'PSO407G0334' => 'pso', 'QL04p040276' => 'qlo', 'QL06p005458' => 'qlo', 'QL06p005472' => 'qlo', 'QL07p030546' => 'qlo', 'QL07p031519' => 'qlo', 'QL09p050949' => 'qlo', 'QL09p050966' => 'qlo', 'QL09p051067' => 'qlo', 'QL12p022706' => 'qlo', 'RcHm_v2.0_Chr2g0119601' => 'rch', 'RcHm_v2.0_Chr3g0459591' => 'rch', 'RcHm_v2.0_Chr4g0418521' => 'rch', 'RcHm_v2.0_Chr4g0418531' => 'rch', 'RcHm_v2.0_Chr4g0418541' => 'rch', 'RcHm_v2.0_Chr6g0291641' => 'rch', 'Rhsim01G0086300' => 'rsi', 'Rhsim01G0276300' => 'rsi', 'Rhsim01G0276500' => 'rsi', 'Rhsim04G0207700' => 'rsi', 'Rhsim05G0234500' => 'rsi', 'Rhsim13G0022400' => 'rsi', 'Sabra02G0167900' => 'sbr', 'Sabra04G0158500' => 'sbr', 'Sabra08G0159800' => 'sbr', 'Sabra10G0011500' => 'sbr', 'Sabra14G0104400' => 'sbr', 'SalBow2G2440' => 'sbo', 'SalBow4G2265' => 'sbo', 'Sc02g0000060' => 'sci', 'Sc05g0005020' => 'sci', 'Sc13g0003890' => 'sci', 'Sed0014865' => 'sed', 'Sed0017224' => 'sed', 'Sed0026391' => 'sed', 'SEGI_00063' => 'sgi', 'SEGI_10967' => 'sgi', 'SEGI_17510' => 'sgi', 'SEGI_24396' => 'sgi', 'SEGI_39719' => 'sgi', 'SEGI_41392' => 'sgi', 'SGA_v2.0_scaffold11G05794' => 'sas', 'SGA_v2.0_scaffold142G35607' => 'sas', 'SGA_v2.0_scaffold1G00447' => 'sas', 'SHI15388' => 'shi', 'SHI15394' => 'shi', 'SHI15396' => 'shi', 'SHI15399' => 'shi', 'SMO343G0151' => 'smo', 'SMO367G1118' => 'smo', 'Solyc01g080200.3' => 'sly', 'Solyc06g008960.3' => 'sly', 'Solyc09g064780.3' => 'sly', 'Sopen01g031980' => 'spe', 'Sopen06g003710' => 'spe', 'Sopen09g026460' => 'spe', 'Sp3g21240' => 'spa', 'Sp4g30030' => 'spa', 'TAR365G0022' => 'tar', 'TAR365G1023' => 'tar', 'TAR365G1253' => 'tar', 'TAR623G0078' => 'tar', 'TAR623G1721' => 'tar', 'TAR633G0959' => 'tar', 'THA.LOC104802225' => 'tha', 'THA.LOC104804769' => 'tha', 'THA.LOC104808660' => 'tha', 'THA.LOC104812792' => 'tha', 'Thecc.01G284000' => 'tca', 'Thecc.04G220600' => 'tca', 'Thecc.05G268900' => 'tca', 'Thecc.08G171100' => 'tca', 'Thhalv10001284m.g' => 'esa', 'Thhalv10019912m.g' => 'esa', 'TPR.G14189' => 'tpr', 'TPR.G18110' => 'tpr', 'TPR.G18130' => 'tpr', 'TPR.G18131' => 'tpr', 'TPR.G18140' => 'tpr', 'TPR.G24282' => 'tpr', 'TPR.G25221' => 'tpr', 'TPR.G29267' => 'tpr', 'TPR.G35315' => 'tpr', 'TPR.G36173' => 'tpr', 'TWI09G0794' => 'twi', 'TWI59G1348' => 'twi', 'TWI74G0430' => 'twi', 'unitig_26.g8940' => 'ugi', 'unitig_749.g13744' => 'ugi', 'unitig_749.g13745' => 'ugi', 'vmacro08269' => 'vma', 'vmacro14937' => 'vma', 'vmacro20401' => 'vma', 'VMungo0464G1349' => 'vmu', 'VMungo0540G0289' => 'vmu', 'VMungo1215G1590' => 'vmu', 'VMungo1309G0221' => 'vmu', 'VMungo1309G2815' => 'vmu', 'VMungo1383G0239' => 'vmu', 'VMungo1383G2910' => 'vmu', 'Zm00001eb095270' => 'zma', 'Zm00001eb095280' => 'zma', 'Zm00001eb111630' => 'zma', 'Zm00001eb237080' => 'zma', 'Zm00001eb273740' => 'zma', 'Zm00001eb285040' => 'zma', 'Zm00001eb330790' => 'zma', 'Zm00001eb337380' => 'zma' ) $gf_id = 'HOM05D001484' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001484' ) $data_identifier = 'HOM05D001484' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 2, 'aly' => (int) 2, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 22, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 7, 'hma' => (int) 2, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 7, 'mtr' => (int) 10, 'cme' => (int) 2, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 4, 'ppa' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 4, 'qlo' => (int) 9, 'rch' => (int) 6, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 10, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 7, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb337380' $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' => 'HOM05D001484', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p31500' => 'bna', 'A05p00020' => 'bna', 'A07p08820' => 'bna', 'Aa31LG4G3300' => 'aar', 'Aa31LG8G10030' => 'aar', 'Actinidia00731' => 'ach', 'Actinidia11473' => 'ach', 'Actinidia23469' => 'ach', 'Actinidia24318' => 'ach', 'Actinidia40196' => 'ach', 'Actinidia40197' => 'ach', 'Actinidia40198' => 'ach', 'Ah.08g212990' => 'amhyb', 'Ah.15g091720' => 'amhyb', 'AL3G38260' => 'aly', 'AL4G47710' => 'aly', 'Aqoxy2G00671' => 'aox', 'Aqoxy2G03236' => 'aox', 'arahy.Tifrunner.gnm1.ann1.05IDCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KR684' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATY3SJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK6QJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6APGL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IDT7Z9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM073U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ0R87' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LE7RV4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT4QRX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V5ENPK' => 'arhy', 'AT2G48110' => 'ath', 'AT3G23590' => 'ath', 'ATR0626G186' => 'atr', 'ATR1127G141' => 'atr', 'Atru.chr4.2583' => 'acertr', 'Atru.chr5.1358' => 'acertr', 'Atru.chr5.1359' => 'acertr', 'Atru.chr8.46' => 'acertr', 'AUR62002640' => 'cqu', 'AUR62030055' => 'cqu', 'AUR62033713' => 'cqu', 'AUR62033714' => 'cqu', 'AUR62036795' => 'cqu', 'AUR62039891' => 'cqu', 'BcaB02g08737' => 'bca', 'BcaB04g20441' => 'bca', 'BcaB06g26509' => 'bca', 'BcaB06g26510' => 'bca', 'BcaB06g26511' => 'bca', 'BcaB06g26512' => 'bca', 'BcaB06g26513' => 'bca', 'BcaC02g12564' => 'bca', 'BcaC02g12565' => 'bca', 'BcaC02g12794' => 'bca', 'BcaC02g12795' => 'bca', 'BcaC02g12796' => 'bca', 'BcaC06g35541' => 'bca', 'BNapus_Darmor_BZH_scaffold_188p00080' => 'bna', 'BNapus_Darmor_BZH_scaffold_188p00090' => 'bna', 'BolC1t03972H' => 'bol', 'BolC1t03973H' => 'bol', 'BolC4t21680H' => 'bol', 'BolC7t41863H' => 'bol', 'BolSC55t61227H' => 'bol', 'BolSC55t61228H' => 'bol', 'BraA01t03278Z' => 'bra', 'BraA05t18998Z' => 'bra', 'BraA07t28673Z' => 'bra', 'C01p40150' => 'bna', 'C05p12370' => 'bna', 'C07p13680' => 'bna', 'CAN.G1006.16' => 'can', 'CAN.G1006.17' => 'can', 'CAN.G1170.2' => 'can', 'CAN.G962.7' => 'can', 'CANSAT25G2179' => 'cansat', 'CANSAT78G1573' => 'cansat', 'CARHR099510' => 'chi', 'CARHR143510' => 'chi', 'Carub.0003s2380' => 'cru', 'Carub.0004s3082' => 'cru', 'Ca_00614_v3' => 'car', 'Ca_07801_v3' => 'car', 'Ca_08567_v3' => 'car', 'Ca_09571_v3' => 'car', 'CBR_g19290' => 'cbr', 'Cc01_g19770' => 'ccan', 'Cc03_g03030' => 'ccan', 'CDE07G0968' => 'cde', 'CDE09G1441' => 'cde', 'Cfa006103' => 'cfa', 'Cfa015573' => 'cfa', 'Cfa016988' => 'cfa', 'Ciclev10006738m.g' => 'ccl', 'Ciclev10010920m.g' => 'ccl', 'Ciclev10018517m.g' => 'ccl', 'CiPaw.01G159200' => 'cil', 'CiPaw.02G091000' => 'cil', 'CiPaw.02G091100' => 'cil', 'CiPaw.08G103100' => 'cil', 'CiPaw.09G224900' => 'cil', 'ClCG06G005740' => 'cla', 'ClCG07G000090' => 'cla', 'ClCG07G000100' => 'cla', 'COL.COLO4_09143' => 'col', 'COL.COLO4_25124' => 'col', 'Cpa.g.sc16.34' => 'cpa', 'Cpa.g.sc3504.1' => 'cpa', 'Cpa.g.sc60.37' => 'cpa', 'CsaV3_6G018520' => 'csa', 'CsaV3_6G036860' => 'csa', 'CSS0001072' => 'camsi', 'CSS0020208' => 'camsi', 'CSS0021253' => 'camsi', 'CSS0022190' => 'camsi', 'CSS0036150' => 'camsi', 'CSS0040442' => 'camsi', 'CSS0042300' => 'camsi', 'CSS0045298' => 'camsi', 'DCAR_012449' => 'dca', 'DCAR_018405' => 'dca', 'DCAR_024573' => 'dca', 'DCAR_030591' => 'dca', 'Dinv16926' => 'din', 'Dinv32963' => 'din', 'Dinv38382' => 'din', 'Dinv38383' => 'din', 'Duzib133G0974' => 'dzi', 'Duzib138G1867' => 'dzi', 'Duzib211G0420' => 'dzi', 'Duzib212G0930' => 'dzi', 'ECA234G1645' => 'eca', 'ECA247G3467' => 'eca', 'ECA248G1703' => 'eca', 'EL10Ac3g06327' => 'bvu', 'EL10Ac7g17204' => 'bvu', 'Eucgr.A00855' => 'egr', 'Eucgr.A00858' => 'egr', 'Eucgr.H01520' => 'egr', 'Eucgr.H03604' => 'egr', 'Eucgr.L03465' => 'egr', 'Eucgr.L03466' => 'egr', 'FAN01G0988' => 'fan', 'FAN02G3892' => 'fan', 'FAN05G3381' => 'fan', 'FAN07G0967' => 'fan', 'FAN07G1493' => 'fan', 'FAN08G3125' => 'fan', 'FAN09G0402' => 'fan', 'FAN12G2594' => 'fan', 'FAN12G3879' => 'fan', 'FAN14G1546' => 'fan', 'FAN15G3626' => 'fan', 'FAN17G0588' => 'fan', 'FAN17G0609' => 'fan', 'FAN18G2817' => 'fan', 'FAN19G1305' => 'fan', 'FAN20G1787' => 'fan', 'FAN22G0073' => 'fan', 'FAN22G0352' => 'fan', 'FAN22G0368' => 'fan', 'FAN22G2273' => 'fan', 'FAN24G1998' => 'fan', 'FAN27G1317' => 'fan', 'FvH4_2g23980' => 'fve', 'FvH4_4g14380' => 'fve', 'FvH4_4g14390' => 'fve', 'FvH4_6g09250' => 'fve', 'Glyma.03G151100' => 'gma', 'Glyma.04G122550' => 'gma', 'Glyma.05G001600' => 'gma', 'Glyma.09G270766' => 'gma', 'Glyma.09G270832' => 'gma', 'Glyma.13G209800' => 'gma', 'Glyma.15G102800' => 'gma', 'Glyma.18G218900' => 'gma', 'Glyma.19G001500' => 'gma', 'Glyma.19G153600' => 'gma', 'Gohir.A02G028600' => 'ghi', 'Gohir.A08G045000' => 'ghi', 'Gohir.A11G120500' => 'ghi', 'Gohir.A12G006200' => 'ghi', 'Gohir.A12G006250' => 'ghi', 'Gohir.D02G036300' => 'ghi', 'Gohir.D08G054700' => 'ghi', 'Gohir.D11G125600' => 'ghi', 'Gohir.D12G005700' => 'ghi', 'Gorai.004G055200' => 'gra', 'Gorai.005G040400' => 'gra', 'Gorai.007G134500' => 'gra', 'Gorai.008G005500' => 'gra', 'GSVIVG01011094001' => 'vvi', 'GSVIVG01017879001' => 'vvi', 'GSVIVG01025988001' => 'vvi', 'GSVIVG01029847001' => 'vvi', 'HanXRQChr10g0282901' => 'han', 'HanXRQChr10g0310371' => 'han', 'HanXRQChr10g0315041' => 'han', 'HanXRQChr11g0327651' => 'han', 'HanXRQChr12g0359391' => 'han', 'Haze_00972' => 'cav', 'Haze_00973' => 'cav', 'Haze_00974' => 'cav', 'Haze_04747' => 'cav', 'Haze_04749' => 'cav', 'Haze_04750' => 'cav', 'Haze_21217' => 'cav', 'Hma1.2p1_1037F.1_g250680' => 'hma', 'Hma1.2p1_1644F.1_g295320' => 'hma', 'HPP92_011322' => 'vpl', 'HPP92_011323' => 'vpl', 'HPP92_011324' => 'vpl', 'HPP92_011325' => 'vpl', 'HPP92_011326' => 'vpl', 'Hund12205' => 'sun', 'Hund17957' => 'sun', 'Lalb_Chr06g0176771' => 'lal', 'Lalb_Chr18g0056021' => 'lal', 'Lalb_Chr18g0056031' => 'lal', 'Lalb_Chr18g0056041' => 'lal', 'Lalb_Chr20g0107751' => 'lal', 'Lalb_Chr20g0118371' => 'lal', 'Lj1g0010239' => 'lja', 'Lj1g0017101' => 'lja', 'Lj2A1178G40' => 'lonja', 'Lj2A54G84' => 'lonja', 'Lj2g0015248' => 'lja', 'Lj3A761T51' => 'lonja', 'Lj6g0018116' => 'lja', 'Lsat_1_v5_gn_4_136040' => 'lsa', 'Lsat_1_v5_gn_5_187461' => 'lsa', 'Lsat_1_v5_gn_5_77001' => 'lsa', 'Lsat_1_v5_gn_9_4461' => 'lsa', 'Manes.01G210100' => 'mes', 'Manes.03G185600' => 'mes', 'Manes.05G073300' => 'mes', 'Manes.09G120300' => 'mes', 'Manes.15G022100' => 'mes', 'Mapoly0096s0053' => 'mpo', 'MBI03_g14058_MAGBIO' => 'mbi', 'MBI03_g33876_MAGBIO' => 'mbi', 'MBI03_g36854_MAGBIO' => 'mbi', 'MBI17_g11997_MAGBIO' => 'mbi', 'MD03G1269000' => 'mdo', 'MD04G1179600' => 'mdo', 'MD11G1289800' => 'mdo', 'MD12G1194700' => 'mdo', 'MD13G1182100' => 'mdo', 'MD13G1182200' => 'mdo', 'MD16G1182600' => 'mdo', 'Medtr2g021400' => 'mtr', 'Medtr2g021470' => 'mtr', 'Medtr2g105810' => 'mtr', 'Medtr3g033580' => 'mtr', 'Medtr6g007970' => 'mtr', 'Medtr7g056330' => 'mtr', 'Medtr7g074290' => 'mtr', 'Medtr7g074380' => 'mtr', 'Medtr7g094550' => 'mtr', 'Medtr8g069995' => 'mtr', 'MELO3C014345.2' => 'cme', 'MELO3C021395.2' => 'cme', 'Migut.D00262' => 'egut', 'Migut.G00257' => 'egut', 'MSTRG.21575' => 'ama', 'MSTRG.3985' => 'ama', 'Nitab4.5_0000295g0140' => 'nta', 'Nitab4.5_0000732g0140' => 'nta', 'Nitab4.5_0003162g0020' => 'nta', 'Nitab4.5_0006180g0090' => 'nta', 'Nitab4.5_0006390g0010' => 'nta', 'Nitab4.5_0007392g0040' => 'nta', 'Nn1g02140' => 'nnu', 'Nn4g26168' => 'nnu', 'Nn5g26754' => 'nnu', 'Oeu001433.1' => 'oeu', 'Oeu010299.2' => 'oeu', 'Oeu011171.1' => 'oeu', 'Oeu037675.1' => 'oeu', 'Oeu038359.1' => 'oeu', 'Oeu063834.1' => 'oeu', 'Oeu063835.1' => 'oeu', 'Os05g0312000' => 'osa', 'Os07g0211101' => 'osa', 'Os07g0211200' => 'osa', 'Os07g0681500' => 'osa', 'Peaxi162Scf00095g01015' => 'pax', 'Peaxi162Scf00104g00329' => 'pax', 'Peaxi162Scf00161g00137' => 'pax', 'PGR004G1665' => 'pgr', 'PGR031G2937' => 'pgr', 'PGR119G2145' => 'pgr', 'PGSC0003DMG400004351' => 'stu', 'PGSC0003DMG400014625' => 'stu', 'PGSC0003DMG401000943' => 'stu', 'Phvul.001G148600' => 'pvu', 'Phvul.004G001700' => 'pvu', 'Phvul.006G154900' => 'pvu', 'Phvul.008G078200' => 'pvu', 'Phvul.011G136500' => 'pvu', 'Potri.002G215600' => 'ptr', 'Potri.008G201600' => 'ptr', 'Potri.014G138400' => 'ptr', 'Potri.016G142500' => 'ptr', 'Pp3c16_10580' => 'ppa', 'Pp3c5_25280' => 'ppa', 'Prupe.1G150000' => 'ppe', 'Prupe.1G150100' => 'ppe', 'Prupe.6G299600' => 'ppe', 'Prupe.8G245000' => 'ppe', 'Psat0s4927g0040' => 'psa', 'Psat1g052080' => 'psa', 'Psat1g183800' => 'psa', 'Psat3g113840' => 'psa', 'Psat3g126120' => 'psa', 'Psat3g126160' => 'psa', 'Psat3g158760' => 'psa', 'Psat3g158840' => 'psa', 'PSO170G2858' => 'pso', 'PSO339G0606' => 'pso', 'PSO384G4709' => 'pso', 'PSO407G0334' => 'pso', 'QL04p040276' => 'qlo', 'QL06p005458' => 'qlo', 'QL06p005472' => 'qlo', 'QL07p030546' => 'qlo', 'QL07p031519' => 'qlo', 'QL09p050949' => 'qlo', 'QL09p050966' => 'qlo', 'QL09p051067' => 'qlo', 'QL12p022706' => 'qlo', 'RcHm_v2.0_Chr2g0119601' => 'rch', 'RcHm_v2.0_Chr3g0459591' => 'rch', 'RcHm_v2.0_Chr4g0418521' => 'rch', 'RcHm_v2.0_Chr4g0418531' => 'rch', 'RcHm_v2.0_Chr4g0418541' => 'rch', 'RcHm_v2.0_Chr6g0291641' => 'rch', 'Rhsim01G0086300' => 'rsi', 'Rhsim01G0276300' => 'rsi', 'Rhsim01G0276500' => 'rsi', 'Rhsim04G0207700' => 'rsi', 'Rhsim05G0234500' => 'rsi', 'Rhsim13G0022400' => 'rsi', 'Sabra02G0167900' => 'sbr', 'Sabra04G0158500' => 'sbr', 'Sabra08G0159800' => 'sbr', 'Sabra10G0011500' => 'sbr', 'Sabra14G0104400' => 'sbr', 'SalBow2G2440' => 'sbo', 'SalBow4G2265' => 'sbo', 'Sc02g0000060' => 'sci', 'Sc05g0005020' => 'sci', 'Sc13g0003890' => 'sci', 'Sed0014865' => 'sed', 'Sed0017224' => 'sed', 'Sed0026391' => 'sed', 'SEGI_00063' => 'sgi', 'SEGI_10967' => 'sgi', 'SEGI_17510' => 'sgi', 'SEGI_24396' => 'sgi', 'SEGI_39719' => 'sgi', 'SEGI_41392' => 'sgi', 'SGA_v2.0_scaffold11G05794' => 'sas', 'SGA_v2.0_scaffold142G35607' => 'sas', 'SGA_v2.0_scaffold1G00447' => 'sas', 'SHI15388' => 'shi', 'SHI15394' => 'shi', 'SHI15396' => 'shi', 'SHI15399' => 'shi', 'SMO343G0151' => 'smo', 'SMO367G1118' => 'smo', 'Solyc01g080200.3' => 'sly', 'Solyc06g008960.3' => 'sly', 'Solyc09g064780.3' => 'sly', 'Sopen01g031980' => 'spe', 'Sopen06g003710' => 'spe', 'Sopen09g026460' => 'spe', 'Sp3g21240' => 'spa', 'Sp4g30030' => 'spa', 'TAR365G0022' => 'tar', 'TAR365G1023' => 'tar', 'TAR365G1253' => 'tar', 'TAR623G0078' => 'tar', 'TAR623G1721' => 'tar', 'TAR633G0959' => 'tar', 'THA.LOC104802225' => 'tha', 'THA.LOC104804769' => 'tha', 'THA.LOC104808660' => 'tha', 'THA.LOC104812792' => 'tha', 'Thecc.01G284000' => 'tca', 'Thecc.04G220600' => 'tca', 'Thecc.05G268900' => 'tca', 'Thecc.08G171100' => 'tca', 'Thhalv10001284m.g' => 'esa', 'Thhalv10019912m.g' => 'esa', 'TPR.G14189' => 'tpr', 'TPR.G18110' => 'tpr', 'TPR.G18130' => 'tpr', 'TPR.G18131' => 'tpr', 'TPR.G18140' => 'tpr', 'TPR.G24282' => 'tpr', 'TPR.G25221' => 'tpr', 'TPR.G29267' => 'tpr', 'TPR.G35315' => 'tpr', 'TPR.G36173' => 'tpr', 'TWI09G0794' => 'twi', 'TWI59G1348' => 'twi', 'TWI74G0430' => 'twi', 'unitig_26.g8940' => 'ugi', 'unitig_749.g13744' => 'ugi', 'unitig_749.g13745' => 'ugi', 'vmacro08269' => 'vma', 'vmacro14937' => 'vma', 'vmacro20401' => 'vma', 'VMungo0464G1349' => 'vmu', 'VMungo0540G0289' => 'vmu', 'VMungo1215G1590' => 'vmu', 'VMungo1309G0221' => 'vmu', 'VMungo1309G2815' => 'vmu', 'VMungo1383G0239' => 'vmu', 'VMungo1383G2910' => 'vmu', 'Zm00001eb095270' => 'zma', 'Zm00001eb095280' => 'zma', 'Zm00001eb111630' => 'zma', 'Zm00001eb237080' => 'zma', 'Zm00001eb273740' => 'zma', 'Zm00001eb285040' => 'zma', 'Zm00001eb330790' => 'zma', 'Zm00001eb337380' => 'zma' ), 'gf_id' => 'HOM05D001484', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001484' ), 'data_identifier' => 'HOM05D001484', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001484', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p31500' => 'bna', 'A05p00020' => 'bna', 'A07p08820' => 'bna', 'Aa31LG4G3300' => 'aar', 'Aa31LG8G10030' => 'aar', 'Actinidia00731' => 'ach', 'Actinidia11473' => 'ach', 'Actinidia23469' => 'ach', 'Actinidia24318' => 'ach', 'Actinidia40196' => 'ach', 'Actinidia40197' => 'ach', 'Actinidia40198' => 'ach', 'Ah.08g212990' => 'amhyb', 'Ah.15g091720' => 'amhyb', 'AL3G38260' => 'aly', 'AL4G47710' => 'aly', 'Aqoxy2G00671' => 'aox', 'Aqoxy2G03236' => 'aox', 'arahy.Tifrunner.gnm1.ann1.05IDCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KR684' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATY3SJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK6QJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6APGL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IDT7Z9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM073U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ0R87' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LE7RV4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT4QRX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V5ENPK' => 'arhy', 'AT2G48110' => 'ath', 'AT3G23590' => 'ath', 'ATR0626G186' => 'atr', 'ATR1127G141' => 'atr', 'Atru.chr4.2583' => 'acertr', 'Atru.chr5.1358' => 'acertr', 'Atru.chr5.1359' => 'acertr', 'Atru.chr8.46' => 'acertr', 'AUR62002640' => 'cqu', 'AUR62030055' => 'cqu', 'AUR62033713' => 'cqu', 'AUR62033714' => 'cqu', 'AUR62036795' => 'cqu', 'AUR62039891' => 'cqu', 'BcaB02g08737' => 'bca', 'BcaB04g20441' => 'bca', 'BcaB06g26509' => 'bca', 'BcaB06g26510' => 'bca', 'BcaB06g26511' => 'bca', 'BcaB06g26512' => 'bca', 'BcaB06g26513' => 'bca', 'BcaC02g12564' => 'bca', 'BcaC02g12565' => 'bca', 'BcaC02g12794' => 'bca', 'BcaC02g12795' => 'bca', 'BcaC02g12796' => 'bca', 'BcaC06g35541' => 'bca', 'BNapus_Darmor_BZH_scaffold_188p00080' => 'bna', 'BNapus_Darmor_BZH_scaffold_188p00090' => 'bna', 'BolC1t03972H' => 'bol', 'BolC1t03973H' => 'bol', 'BolC4t21680H' => 'bol', 'BolC7t41863H' => 'bol', 'BolSC55t61227H' => 'bol', 'BolSC55t61228H' => 'bol', 'BraA01t03278Z' => 'bra', 'BraA05t18998Z' => 'bra', 'BraA07t28673Z' => 'bra', 'C01p40150' => 'bna', 'C05p12370' => 'bna', 'C07p13680' => 'bna', 'CAN.G1006.16' => 'can', 'CAN.G1006.17' => 'can', 'CAN.G1170.2' => 'can', 'CAN.G962.7' => 'can', 'CANSAT25G2179' => 'cansat', 'CANSAT78G1573' => 'cansat', 'CARHR099510' => 'chi', 'CARHR143510' => 'chi', 'Carub.0003s2380' => 'cru', 'Carub.0004s3082' => 'cru', 'Ca_00614_v3' => 'car', 'Ca_07801_v3' => 'car', 'Ca_08567_v3' => 'car', 'Ca_09571_v3' => 'car', 'CBR_g19290' => 'cbr', 'Cc01_g19770' => 'ccan', 'Cc03_g03030' => 'ccan', 'CDE07G0968' => 'cde', 'CDE09G1441' => 'cde', 'Cfa006103' => 'cfa', 'Cfa015573' => 'cfa', 'Cfa016988' => 'cfa', 'Ciclev10006738m.g' => 'ccl', 'Ciclev10010920m.g' => 'ccl', 'Ciclev10018517m.g' => 'ccl', 'CiPaw.01G159200' => 'cil', 'CiPaw.02G091000' => 'cil', 'CiPaw.02G091100' => 'cil', 'CiPaw.08G103100' => 'cil', 'CiPaw.09G224900' => 'cil', 'ClCG06G005740' => 'cla', 'ClCG07G000090' => 'cla', 'ClCG07G000100' => 'cla', 'COL.COLO4_09143' => 'col', 'COL.COLO4_25124' => 'col', 'Cpa.g.sc16.34' => 'cpa', 'Cpa.g.sc3504.1' => 'cpa', 'Cpa.g.sc60.37' => 'cpa', 'CsaV3_6G018520' => 'csa', 'CsaV3_6G036860' => 'csa', 'CSS0001072' => 'camsi', 'CSS0020208' => 'camsi', 'CSS0021253' => 'camsi', 'CSS0022190' => 'camsi', 'CSS0036150' => 'camsi', 'CSS0040442' => 'camsi', 'CSS0042300' => 'camsi', 'CSS0045298' => 'camsi', 'DCAR_012449' => 'dca', 'DCAR_018405' => 'dca', 'DCAR_024573' => 'dca', 'DCAR_030591' => 'dca', 'Dinv16926' => 'din', 'Dinv32963' => 'din', 'Dinv38382' => 'din', 'Dinv38383' => 'din', 'Duzib133G0974' => 'dzi', 'Duzib138G1867' => 'dzi', 'Duzib211G0420' => 'dzi', 'Duzib212G0930' => 'dzi', 'ECA234G1645' => 'eca', 'ECA247G3467' => 'eca', 'ECA248G1703' => 'eca', 'EL10Ac3g06327' => 'bvu', 'EL10Ac7g17204' => 'bvu', 'Eucgr.A00855' => 'egr', 'Eucgr.A00858' => 'egr', 'Eucgr.H01520' => 'egr', 'Eucgr.H03604' => 'egr', 'Eucgr.L03465' => 'egr', 'Eucgr.L03466' => 'egr', 'FAN01G0988' => 'fan', 'FAN02G3892' => 'fan', 'FAN05G3381' => 'fan', 'FAN07G0967' => 'fan', 'FAN07G1493' => 'fan', 'FAN08G3125' => 'fan', 'FAN09G0402' => 'fan', 'FAN12G2594' => 'fan', 'FAN12G3879' => 'fan', 'FAN14G1546' => 'fan', 'FAN15G3626' => 'fan', 'FAN17G0588' => 'fan', 'FAN17G0609' => 'fan', 'FAN18G2817' => 'fan', 'FAN19G1305' => 'fan', 'FAN20G1787' => 'fan', 'FAN22G0073' => 'fan', 'FAN22G0352' => 'fan', 'FAN22G0368' => 'fan', 'FAN22G2273' => 'fan', 'FAN24G1998' => 'fan', 'FAN27G1317' => 'fan', 'FvH4_2g23980' => 'fve', 'FvH4_4g14380' => 'fve', 'FvH4_4g14390' => 'fve', 'FvH4_6g09250' => 'fve', 'Glyma.03G151100' => 'gma', 'Glyma.04G122550' => 'gma', 'Glyma.05G001600' => 'gma', 'Glyma.09G270766' => 'gma', 'Glyma.09G270832' => 'gma', 'Glyma.13G209800' => 'gma', 'Glyma.15G102800' => 'gma', 'Glyma.18G218900' => 'gma', 'Glyma.19G001500' => 'gma', 'Glyma.19G153600' => 'gma', 'Gohir.A02G028600' => 'ghi', 'Gohir.A08G045000' => 'ghi', 'Gohir.A11G120500' => 'ghi', 'Gohir.A12G006200' => 'ghi', 'Gohir.A12G006250' => 'ghi', 'Gohir.D02G036300' => 'ghi', 'Gohir.D08G054700' => 'ghi', 'Gohir.D11G125600' => 'ghi', 'Gohir.D12G005700' => 'ghi', 'Gorai.004G055200' => 'gra', 'Gorai.005G040400' => 'gra', 'Gorai.007G134500' => 'gra', 'Gorai.008G005500' => 'gra', 'GSVIVG01011094001' => 'vvi', 'GSVIVG01017879001' => 'vvi', 'GSVIVG01025988001' => 'vvi', 'GSVIVG01029847001' => 'vvi', 'HanXRQChr10g0282901' => 'han', 'HanXRQChr10g0310371' => 'han', 'HanXRQChr10g0315041' => 'han', 'HanXRQChr11g0327651' => 'han', 'HanXRQChr12g0359391' => 'han', 'Haze_00972' => 'cav', 'Haze_00973' => 'cav', 'Haze_00974' => 'cav', 'Haze_04747' => 'cav', 'Haze_04749' => 'cav', 'Haze_04750' => 'cav', 'Haze_21217' => 'cav', 'Hma1.2p1_1037F.1_g250680' => 'hma', 'Hma1.2p1_1644F.1_g295320' => 'hma', 'HPP92_011322' => 'vpl', 'HPP92_011323' => 'vpl', 'HPP92_011324' => 'vpl', 'HPP92_011325' => 'vpl', 'HPP92_011326' => 'vpl', 'Hund12205' => 'sun', 'Hund17957' => 'sun', 'Lalb_Chr06g0176771' => 'lal', 'Lalb_Chr18g0056021' => 'lal', 'Lalb_Chr18g0056031' => 'lal', 'Lalb_Chr18g0056041' => 'lal', 'Lalb_Chr20g0107751' => 'lal', 'Lalb_Chr20g0118371' => 'lal', 'Lj1g0010239' => 'lja', 'Lj1g0017101' => 'lja', 'Lj2A1178G40' => 'lonja', 'Lj2A54G84' => 'lonja', 'Lj2g0015248' => 'lja', 'Lj3A761T51' => 'lonja', 'Lj6g0018116' => 'lja', 'Lsat_1_v5_gn_4_136040' => 'lsa', 'Lsat_1_v5_gn_5_187461' => 'lsa', 'Lsat_1_v5_gn_5_77001' => 'lsa', 'Lsat_1_v5_gn_9_4461' => 'lsa', 'Manes.01G210100' => 'mes', 'Manes.03G185600' => 'mes', 'Manes.05G073300' => 'mes', 'Manes.09G120300' => 'mes', 'Manes.15G022100' => 'mes', 'Mapoly0096s0053' => 'mpo', 'MBI03_g14058_MAGBIO' => 'mbi', 'MBI03_g33876_MAGBIO' => 'mbi', 'MBI03_g36854_MAGBIO' => 'mbi', 'MBI17_g11997_MAGBIO' => 'mbi', 'MD03G1269000' => 'mdo', 'MD04G1179600' => 'mdo', 'MD11G1289800' => 'mdo', 'MD12G1194700' => 'mdo', 'MD13G1182100' => 'mdo', 'MD13G1182200' => 'mdo', 'MD16G1182600' => 'mdo', 'Medtr2g021400' => 'mtr', 'Medtr2g021470' => 'mtr', 'Medtr2g105810' => 'mtr', 'Medtr3g033580' => 'mtr', 'Medtr6g007970' => 'mtr', 'Medtr7g056330' => 'mtr', 'Medtr7g074290' => 'mtr', 'Medtr7g074380' => 'mtr', 'Medtr7g094550' => 'mtr', 'Medtr8g069995' => 'mtr', 'MELO3C014345.2' => 'cme', 'MELO3C021395.2' => 'cme', 'Migut.D00262' => 'egut', 'Migut.G00257' => 'egut', 'MSTRG.21575' => 'ama', 'MSTRG.3985' => 'ama', 'Nitab4.5_0000295g0140' => 'nta', 'Nitab4.5_0000732g0140' => 'nta', 'Nitab4.5_0003162g0020' => 'nta', 'Nitab4.5_0006180g0090' => 'nta', 'Nitab4.5_0006390g0010' => 'nta', 'Nitab4.5_0007392g0040' => 'nta', 'Nn1g02140' => 'nnu', 'Nn4g26168' => 'nnu', 'Nn5g26754' => 'nnu', 'Oeu001433.1' => 'oeu', 'Oeu010299.2' => 'oeu', 'Oeu011171.1' => 'oeu', 'Oeu037675.1' => 'oeu', 'Oeu038359.1' => 'oeu', 'Oeu063834.1' => 'oeu', 'Oeu063835.1' => 'oeu', 'Os05g0312000' => 'osa', 'Os07g0211101' => 'osa', 'Os07g0211200' => 'osa', 'Os07g0681500' => 'osa', 'Peaxi162Scf00095g01015' => 'pax', 'Peaxi162Scf00104g00329' => 'pax', 'Peaxi162Scf00161g00137' => 'pax', 'PGR004G1665' => 'pgr', 'PGR031G2937' => 'pgr', 'PGR119G2145' => 'pgr', 'PGSC0003DMG400004351' => 'stu', 'PGSC0003DMG400014625' => 'stu', 'PGSC0003DMG401000943' => 'stu', 'Phvul.001G148600' => 'pvu', 'Phvul.004G001700' => 'pvu', 'Phvul.006G154900' => 'pvu', 'Phvul.008G078200' => 'pvu', 'Phvul.011G136500' => 'pvu', 'Potri.002G215600' => 'ptr', 'Potri.008G201600' => 'ptr', 'Potri.014G138400' => 'ptr', 'Potri.016G142500' => 'ptr', 'Pp3c16_10580' => 'ppa', 'Pp3c5_25280' => 'ppa', 'Prupe.1G150000' => 'ppe', 'Prupe.1G150100' => 'ppe', 'Prupe.6G299600' => 'ppe', 'Prupe.8G245000' => 'ppe', 'Psat0s4927g0040' => 'psa', 'Psat1g052080' => 'psa', 'Psat1g183800' => 'psa', 'Psat3g113840' => 'psa', 'Psat3g126120' => 'psa', 'Psat3g126160' => 'psa', 'Psat3g158760' => 'psa', 'Psat3g158840' => 'psa', 'PSO170G2858' => 'pso', 'PSO339G0606' => 'pso', 'PSO384G4709' => 'pso', 'PSO407G0334' => 'pso', 'QL04p040276' => 'qlo', 'QL06p005458' => 'qlo', 'QL06p005472' => 'qlo', 'QL07p030546' => 'qlo', 'QL07p031519' => 'qlo', 'QL09p050949' => 'qlo', 'QL09p050966' => 'qlo', 'QL09p051067' => 'qlo', 'QL12p022706' => 'qlo', 'RcHm_v2.0_Chr2g0119601' => 'rch', 'RcHm_v2.0_Chr3g0459591' => 'rch', 'RcHm_v2.0_Chr4g0418521' => 'rch', 'RcHm_v2.0_Chr4g0418531' => 'rch', 'RcHm_v2.0_Chr4g0418541' => 'rch', 'RcHm_v2.0_Chr6g0291641' => 'rch', 'Rhsim01G0086300' => 'rsi', 'Rhsim01G0276300' => 'rsi', 'Rhsim01G0276500' => 'rsi', 'Rhsim04G0207700' => 'rsi', 'Rhsim05G0234500' => 'rsi', 'Rhsim13G0022400' => 'rsi', 'Sabra02G0167900' => 'sbr', 'Sabra04G0158500' => 'sbr', 'Sabra08G0159800' => 'sbr', 'Sabra10G0011500' => 'sbr', 'Sabra14G0104400' => 'sbr', 'SalBow2G2440' => 'sbo', 'SalBow4G2265' => 'sbo', 'Sc02g0000060' => 'sci', 'Sc05g0005020' => 'sci', 'Sc13g0003890' => 'sci', 'Sed0014865' => 'sed', 'Sed0017224' => 'sed', 'Sed0026391' => 'sed', 'SEGI_00063' => 'sgi', 'SEGI_10967' => 'sgi', 'SEGI_17510' => 'sgi', 'SEGI_24396' => 'sgi', 'SEGI_39719' => 'sgi', 'SEGI_41392' => 'sgi', 'SGA_v2.0_scaffold11G05794' => 'sas', 'SGA_v2.0_scaffold142G35607' => 'sas', 'SGA_v2.0_scaffold1G00447' => 'sas', 'SHI15388' => 'shi', 'SHI15394' => 'shi', 'SHI15396' => 'shi', 'SHI15399' => 'shi', 'SMO343G0151' => 'smo', 'SMO367G1118' => 'smo', 'Solyc01g080200.3' => 'sly', 'Solyc06g008960.3' => 'sly', 'Solyc09g064780.3' => 'sly', 'Sopen01g031980' => 'spe', 'Sopen06g003710' => 'spe', 'Sopen09g026460' => 'spe', 'Sp3g21240' => 'spa', 'Sp4g30030' => 'spa', 'TAR365G0022' => 'tar', 'TAR365G1023' => 'tar', 'TAR365G1253' => 'tar', 'TAR623G0078' => 'tar', 'TAR623G1721' => 'tar', 'TAR633G0959' => 'tar', 'THA.LOC104802225' => 'tha', 'THA.LOC104804769' => 'tha', 'THA.LOC104808660' => 'tha', 'THA.LOC104812792' => 'tha', 'Thecc.01G284000' => 'tca', 'Thecc.04G220600' => 'tca', 'Thecc.05G268900' => 'tca', 'Thecc.08G171100' => 'tca', 'Thhalv10001284m.g' => 'esa', 'Thhalv10019912m.g' => 'esa', 'TPR.G14189' => 'tpr', 'TPR.G18110' => 'tpr', 'TPR.G18130' => 'tpr', 'TPR.G18131' => 'tpr', 'TPR.G18140' => 'tpr', 'TPR.G24282' => 'tpr', 'TPR.G25221' => 'tpr', 'TPR.G29267' => 'tpr', 'TPR.G35315' => 'tpr', 'TPR.G36173' => 'tpr', 'TWI09G0794' => 'twi', 'TWI59G1348' => 'twi', 'TWI74G0430' => 'twi', 'unitig_26.g8940' => 'ugi', 'unitig_749.g13744' => 'ugi', 'unitig_749.g13745' => 'ugi', 'vmacro08269' => 'vma', 'vmacro14937' => 'vma', 'vmacro20401' => 'vma', 'VMungo0464G1349' => 'vmu', 'VMungo0540G0289' => 'vmu', 'VMungo1215G1590' => 'vmu', 'VMungo1309G0221' => 'vmu', 'VMungo1309G2815' => 'vmu', 'VMungo1383G0239' => 'vmu', 'VMungo1383G2910' => 'vmu', 'Zm00001eb095270' => 'zma', 'Zm00001eb095280' => 'zma', 'Zm00001eb111630' => 'zma', 'Zm00001eb237080' => 'zma', 'Zm00001eb273740' => 'zma', 'Zm00001eb285040' => 'zma', 'Zm00001eb330790' => 'zma', 'Zm00001eb337380' => 'zma' ) $gf_id = 'HOM05D001484' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001484' ) $data_identifier = 'HOM05D001484' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 2, 'aly' => (int) 2, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 22, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 7, 'hma' => (int) 2, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 7, 'mtr' => (int) 10, 'cme' => (int) 2, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 4, 'ppa' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 4, 'qlo' => (int) 9, 'rch' => (int) 6, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 10, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 7, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb337380' $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' => 'HOM05D001484', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p31500' => 'bna', 'A05p00020' => 'bna', 'A07p08820' => 'bna', 'Aa31LG4G3300' => 'aar', 'Aa31LG8G10030' => 'aar', 'Actinidia00731' => 'ach', 'Actinidia11473' => 'ach', 'Actinidia23469' => 'ach', 'Actinidia24318' => 'ach', 'Actinidia40196' => 'ach', 'Actinidia40197' => 'ach', 'Actinidia40198' => 'ach', 'Ah.08g212990' => 'amhyb', 'Ah.15g091720' => 'amhyb', 'AL3G38260' => 'aly', 'AL4G47710' => 'aly', 'Aqoxy2G00671' => 'aox', 'Aqoxy2G03236' => 'aox', 'arahy.Tifrunner.gnm1.ann1.05IDCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KR684' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATY3SJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK6QJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6APGL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IDT7Z9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM073U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ0R87' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LE7RV4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT4QRX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V5ENPK' => 'arhy', 'AT2G48110' => 'ath', 'AT3G23590' => 'ath', 'ATR0626G186' => 'atr', 'ATR1127G141' => 'atr', 'Atru.chr4.2583' => 'acertr', 'Atru.chr5.1358' => 'acertr', 'Atru.chr5.1359' => 'acertr', 'Atru.chr8.46' => 'acertr', 'AUR62002640' => 'cqu', 'AUR62030055' => 'cqu', 'AUR62033713' => 'cqu', 'AUR62033714' => 'cqu', 'AUR62036795' => 'cqu', 'AUR62039891' => 'cqu', 'BcaB02g08737' => 'bca', 'BcaB04g20441' => 'bca', 'BcaB06g26509' => 'bca', 'BcaB06g26510' => 'bca', 'BcaB06g26511' => 'bca', 'BcaB06g26512' => 'bca', 'BcaB06g26513' => 'bca', 'BcaC02g12564' => 'bca', 'BcaC02g12565' => 'bca', 'BcaC02g12794' => 'bca', 'BcaC02g12795' => 'bca', 'BcaC02g12796' => 'bca', 'BcaC06g35541' => 'bca', 'BNapus_Darmor_BZH_scaffold_188p00080' => 'bna', 'BNapus_Darmor_BZH_scaffold_188p00090' => 'bna', 'BolC1t03972H' => 'bol', 'BolC1t03973H' => 'bol', 'BolC4t21680H' => 'bol', 'BolC7t41863H' => 'bol', 'BolSC55t61227H' => 'bol', 'BolSC55t61228H' => 'bol', 'BraA01t03278Z' => 'bra', 'BraA05t18998Z' => 'bra', 'BraA07t28673Z' => 'bra', 'C01p40150' => 'bna', 'C05p12370' => 'bna', 'C07p13680' => 'bna', 'CAN.G1006.16' => 'can', 'CAN.G1006.17' => 'can', 'CAN.G1170.2' => 'can', 'CAN.G962.7' => 'can', 'CANSAT25G2179' => 'cansat', 'CANSAT78G1573' => 'cansat', 'CARHR099510' => 'chi', 'CARHR143510' => 'chi', 'Carub.0003s2380' => 'cru', 'Carub.0004s3082' => 'cru', 'Ca_00614_v3' => 'car', 'Ca_07801_v3' => 'car', 'Ca_08567_v3' => 'car', 'Ca_09571_v3' => 'car', 'CBR_g19290' => 'cbr', 'Cc01_g19770' => 'ccan', 'Cc03_g03030' => 'ccan', 'CDE07G0968' => 'cde', 'CDE09G1441' => 'cde', 'Cfa006103' => 'cfa', 'Cfa015573' => 'cfa', 'Cfa016988' => 'cfa', 'Ciclev10006738m.g' => 'ccl', 'Ciclev10010920m.g' => 'ccl', 'Ciclev10018517m.g' => 'ccl', 'CiPaw.01G159200' => 'cil', 'CiPaw.02G091000' => 'cil', 'CiPaw.02G091100' => 'cil', 'CiPaw.08G103100' => 'cil', 'CiPaw.09G224900' => 'cil', 'ClCG06G005740' => 'cla', 'ClCG07G000090' => 'cla', 'ClCG07G000100' => 'cla', 'COL.COLO4_09143' => 'col', 'COL.COLO4_25124' => 'col', 'Cpa.g.sc16.34' => 'cpa', 'Cpa.g.sc3504.1' => 'cpa', 'Cpa.g.sc60.37' => 'cpa', 'CsaV3_6G018520' => 'csa', 'CsaV3_6G036860' => 'csa', 'CSS0001072' => 'camsi', 'CSS0020208' => 'camsi', 'CSS0021253' => 'camsi', 'CSS0022190' => 'camsi', 'CSS0036150' => 'camsi', 'CSS0040442' => 'camsi', 'CSS0042300' => 'camsi', 'CSS0045298' => 'camsi', 'DCAR_012449' => 'dca', 'DCAR_018405' => 'dca', 'DCAR_024573' => 'dca', 'DCAR_030591' => 'dca', 'Dinv16926' => 'din', 'Dinv32963' => 'din', 'Dinv38382' => 'din', 'Dinv38383' => 'din', 'Duzib133G0974' => 'dzi', 'Duzib138G1867' => 'dzi', 'Duzib211G0420' => 'dzi', 'Duzib212G0930' => 'dzi', 'ECA234G1645' => 'eca', 'ECA247G3467' => 'eca', 'ECA248G1703' => 'eca', 'EL10Ac3g06327' => 'bvu', 'EL10Ac7g17204' => 'bvu', 'Eucgr.A00855' => 'egr', 'Eucgr.A00858' => 'egr', 'Eucgr.H01520' => 'egr', 'Eucgr.H03604' => 'egr', 'Eucgr.L03465' => 'egr', 'Eucgr.L03466' => 'egr', 'FAN01G0988' => 'fan', 'FAN02G3892' => 'fan', 'FAN05G3381' => 'fan', 'FAN07G0967' => 'fan', 'FAN07G1493' => 'fan', 'FAN08G3125' => 'fan', 'FAN09G0402' => 'fan', 'FAN12G2594' => 'fan', 'FAN12G3879' => 'fan', 'FAN14G1546' => 'fan', 'FAN15G3626' => 'fan', 'FAN17G0588' => 'fan', 'FAN17G0609' => 'fan', 'FAN18G2817' => 'fan', 'FAN19G1305' => 'fan', 'FAN20G1787' => 'fan', 'FAN22G0073' => 'fan', 'FAN22G0352' => 'fan', 'FAN22G0368' => 'fan', 'FAN22G2273' => 'fan', 'FAN24G1998' => 'fan', 'FAN27G1317' => 'fan', 'FvH4_2g23980' => 'fve', 'FvH4_4g14380' => 'fve', 'FvH4_4g14390' => 'fve', 'FvH4_6g09250' => 'fve', 'Glyma.03G151100' => 'gma', 'Glyma.04G122550' => 'gma', 'Glyma.05G001600' => 'gma', 'Glyma.09G270766' => 'gma', 'Glyma.09G270832' => 'gma', 'Glyma.13G209800' => 'gma', 'Glyma.15G102800' => 'gma', 'Glyma.18G218900' => 'gma', 'Glyma.19G001500' => 'gma', 'Glyma.19G153600' => 'gma', 'Gohir.A02G028600' => 'ghi', 'Gohir.A08G045000' => 'ghi', 'Gohir.A11G120500' => 'ghi', 'Gohir.A12G006200' => 'ghi', 'Gohir.A12G006250' => 'ghi', 'Gohir.D02G036300' => 'ghi', 'Gohir.D08G054700' => 'ghi', 'Gohir.D11G125600' => 'ghi', 'Gohir.D12G005700' => 'ghi', 'Gorai.004G055200' => 'gra', 'Gorai.005G040400' => 'gra', 'Gorai.007G134500' => 'gra', 'Gorai.008G005500' => 'gra', 'GSVIVG01011094001' => 'vvi', 'GSVIVG01017879001' => 'vvi', 'GSVIVG01025988001' => 'vvi', 'GSVIVG01029847001' => 'vvi', 'HanXRQChr10g0282901' => 'han', 'HanXRQChr10g0310371' => 'han', 'HanXRQChr10g0315041' => 'han', 'HanXRQChr11g0327651' => 'han', 'HanXRQChr12g0359391' => 'han', 'Haze_00972' => 'cav', 'Haze_00973' => 'cav', 'Haze_00974' => 'cav', 'Haze_04747' => 'cav', 'Haze_04749' => 'cav', 'Haze_04750' => 'cav', 'Haze_21217' => 'cav', 'Hma1.2p1_1037F.1_g250680' => 'hma', 'Hma1.2p1_1644F.1_g295320' => 'hma', 'HPP92_011322' => 'vpl', 'HPP92_011323' => 'vpl', 'HPP92_011324' => 'vpl', 'HPP92_011325' => 'vpl', 'HPP92_011326' => 'vpl', 'Hund12205' => 'sun', 'Hund17957' => 'sun', 'Lalb_Chr06g0176771' => 'lal', 'Lalb_Chr18g0056021' => 'lal', 'Lalb_Chr18g0056031' => 'lal', 'Lalb_Chr18g0056041' => 'lal', 'Lalb_Chr20g0107751' => 'lal', 'Lalb_Chr20g0118371' => 'lal', 'Lj1g0010239' => 'lja', 'Lj1g0017101' => 'lja', 'Lj2A1178G40' => 'lonja', 'Lj2A54G84' => 'lonja', 'Lj2g0015248' => 'lja', 'Lj3A761T51' => 'lonja', 'Lj6g0018116' => 'lja', 'Lsat_1_v5_gn_4_136040' => 'lsa', 'Lsat_1_v5_gn_5_187461' => 'lsa', 'Lsat_1_v5_gn_5_77001' => 'lsa', 'Lsat_1_v5_gn_9_4461' => 'lsa', 'Manes.01G210100' => 'mes', 'Manes.03G185600' => 'mes', 'Manes.05G073300' => 'mes', 'Manes.09G120300' => 'mes', 'Manes.15G022100' => 'mes', 'Mapoly0096s0053' => 'mpo', 'MBI03_g14058_MAGBIO' => 'mbi', 'MBI03_g33876_MAGBIO' => 'mbi', 'MBI03_g36854_MAGBIO' => 'mbi', 'MBI17_g11997_MAGBIO' => 'mbi', 'MD03G1269000' => 'mdo', 'MD04G1179600' => 'mdo', 'MD11G1289800' => 'mdo', 'MD12G1194700' => 'mdo', 'MD13G1182100' => 'mdo', 'MD13G1182200' => 'mdo', 'MD16G1182600' => 'mdo', 'Medtr2g021400' => 'mtr', 'Medtr2g021470' => 'mtr', 'Medtr2g105810' => 'mtr', 'Medtr3g033580' => 'mtr', 'Medtr6g007970' => 'mtr', 'Medtr7g056330' => 'mtr', 'Medtr7g074290' => 'mtr', 'Medtr7g074380' => 'mtr', 'Medtr7g094550' => 'mtr', 'Medtr8g069995' => 'mtr', 'MELO3C014345.2' => 'cme', 'MELO3C021395.2' => 'cme', 'Migut.D00262' => 'egut', 'Migut.G00257' => 'egut', 'MSTRG.21575' => 'ama', 'MSTRG.3985' => 'ama', 'Nitab4.5_0000295g0140' => 'nta', 'Nitab4.5_0000732g0140' => 'nta', 'Nitab4.5_0003162g0020' => 'nta', 'Nitab4.5_0006180g0090' => 'nta', 'Nitab4.5_0006390g0010' => 'nta', 'Nitab4.5_0007392g0040' => 'nta', 'Nn1g02140' => 'nnu', 'Nn4g26168' => 'nnu', 'Nn5g26754' => 'nnu', 'Oeu001433.1' => 'oeu', 'Oeu010299.2' => 'oeu', 'Oeu011171.1' => 'oeu', 'Oeu037675.1' => 'oeu', 'Oeu038359.1' => 'oeu', 'Oeu063834.1' => 'oeu', 'Oeu063835.1' => 'oeu', 'Os05g0312000' => 'osa', 'Os07g0211101' => 'osa', 'Os07g0211200' => 'osa', 'Os07g0681500' => 'osa', 'Peaxi162Scf00095g01015' => 'pax', 'Peaxi162Scf00104g00329' => 'pax', 'Peaxi162Scf00161g00137' => 'pax', 'PGR004G1665' => 'pgr', 'PGR031G2937' => 'pgr', 'PGR119G2145' => 'pgr', 'PGSC0003DMG400004351' => 'stu', 'PGSC0003DMG400014625' => 'stu', 'PGSC0003DMG401000943' => 'stu', 'Phvul.001G148600' => 'pvu', 'Phvul.004G001700' => 'pvu', 'Phvul.006G154900' => 'pvu', 'Phvul.008G078200' => 'pvu', 'Phvul.011G136500' => 'pvu', 'Potri.002G215600' => 'ptr', 'Potri.008G201600' => 'ptr', 'Potri.014G138400' => 'ptr', 'Potri.016G142500' => 'ptr', 'Pp3c16_10580' => 'ppa', 'Pp3c5_25280' => 'ppa', 'Prupe.1G150000' => 'ppe', 'Prupe.1G150100' => 'ppe', 'Prupe.6G299600' => 'ppe', 'Prupe.8G245000' => 'ppe', 'Psat0s4927g0040' => 'psa', 'Psat1g052080' => 'psa', 'Psat1g183800' => 'psa', 'Psat3g113840' => 'psa', 'Psat3g126120' => 'psa', 'Psat3g126160' => 'psa', 'Psat3g158760' => 'psa', 'Psat3g158840' => 'psa', 'PSO170G2858' => 'pso', 'PSO339G0606' => 'pso', 'PSO384G4709' => 'pso', 'PSO407G0334' => 'pso', 'QL04p040276' => 'qlo', 'QL06p005458' => 'qlo', 'QL06p005472' => 'qlo', 'QL07p030546' => 'qlo', 'QL07p031519' => 'qlo', 'QL09p050949' => 'qlo', 'QL09p050966' => 'qlo', 'QL09p051067' => 'qlo', 'QL12p022706' => 'qlo', 'RcHm_v2.0_Chr2g0119601' => 'rch', 'RcHm_v2.0_Chr3g0459591' => 'rch', 'RcHm_v2.0_Chr4g0418521' => 'rch', 'RcHm_v2.0_Chr4g0418531' => 'rch', 'RcHm_v2.0_Chr4g0418541' => 'rch', 'RcHm_v2.0_Chr6g0291641' => 'rch', 'Rhsim01G0086300' => 'rsi', 'Rhsim01G0276300' => 'rsi', 'Rhsim01G0276500' => 'rsi', 'Rhsim04G0207700' => 'rsi', 'Rhsim05G0234500' => 'rsi', 'Rhsim13G0022400' => 'rsi', 'Sabra02G0167900' => 'sbr', 'Sabra04G0158500' => 'sbr', 'Sabra08G0159800' => 'sbr', 'Sabra10G0011500' => 'sbr', 'Sabra14G0104400' => 'sbr', 'SalBow2G2440' => 'sbo', 'SalBow4G2265' => 'sbo', 'Sc02g0000060' => 'sci', 'Sc05g0005020' => 'sci', 'Sc13g0003890' => 'sci', 'Sed0014865' => 'sed', 'Sed0017224' => 'sed', 'Sed0026391' => 'sed', 'SEGI_00063' => 'sgi', 'SEGI_10967' => 'sgi', 'SEGI_17510' => 'sgi', 'SEGI_24396' => 'sgi', 'SEGI_39719' => 'sgi', 'SEGI_41392' => 'sgi', 'SGA_v2.0_scaffold11G05794' => 'sas', 'SGA_v2.0_scaffold142G35607' => 'sas', 'SGA_v2.0_scaffold1G00447' => 'sas', 'SHI15388' => 'shi', 'SHI15394' => 'shi', 'SHI15396' => 'shi', 'SHI15399' => 'shi', 'SMO343G0151' => 'smo', 'SMO367G1118' => 'smo', 'Solyc01g080200.3' => 'sly', 'Solyc06g008960.3' => 'sly', 'Solyc09g064780.3' => 'sly', 'Sopen01g031980' => 'spe', 'Sopen06g003710' => 'spe', 'Sopen09g026460' => 'spe', 'Sp3g21240' => 'spa', 'Sp4g30030' => 'spa', 'TAR365G0022' => 'tar', 'TAR365G1023' => 'tar', 'TAR365G1253' => 'tar', 'TAR623G0078' => 'tar', 'TAR623G1721' => 'tar', 'TAR633G0959' => 'tar', 'THA.LOC104802225' => 'tha', 'THA.LOC104804769' => 'tha', 'THA.LOC104808660' => 'tha', 'THA.LOC104812792' => 'tha', 'Thecc.01G284000' => 'tca', 'Thecc.04G220600' => 'tca', 'Thecc.05G268900' => 'tca', 'Thecc.08G171100' => 'tca', 'Thhalv10001284m.g' => 'esa', 'Thhalv10019912m.g' => 'esa', 'TPR.G14189' => 'tpr', 'TPR.G18110' => 'tpr', 'TPR.G18130' => 'tpr', 'TPR.G18131' => 'tpr', 'TPR.G18140' => 'tpr', 'TPR.G24282' => 'tpr', 'TPR.G25221' => 'tpr', 'TPR.G29267' => 'tpr', 'TPR.G35315' => 'tpr', 'TPR.G36173' => 'tpr', 'TWI09G0794' => 'twi', 'TWI59G1348' => 'twi', 'TWI74G0430' => 'twi', 'unitig_26.g8940' => 'ugi', 'unitig_749.g13744' => 'ugi', 'unitig_749.g13745' => 'ugi', 'vmacro08269' => 'vma', 'vmacro14937' => 'vma', 'vmacro20401' => 'vma', 'VMungo0464G1349' => 'vmu', 'VMungo0540G0289' => 'vmu', 'VMungo1215G1590' => 'vmu', 'VMungo1309G0221' => 'vmu', 'VMungo1309G2815' => 'vmu', 'VMungo1383G0239' => 'vmu', 'VMungo1383G2910' => 'vmu', 'Zm00001eb095270' => 'zma', 'Zm00001eb095280' => 'zma', 'Zm00001eb111630' => 'zma', 'Zm00001eb237080' => 'zma', 'Zm00001eb273740' => 'zma', 'Zm00001eb285040' => 'zma', 'Zm00001eb330790' => 'zma', 'Zm00001eb337380' => 'zma' ), 'gf_id' => 'HOM05D001484', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001484' ), 'data_identifier' => 'HOM05D001484', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001484', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p31500' => 'bna', 'A05p00020' => 'bna', 'A07p08820' => 'bna', 'Aa31LG4G3300' => 'aar', 'Aa31LG8G10030' => 'aar', 'Actinidia00731' => 'ach', 'Actinidia11473' => 'ach', 'Actinidia23469' => 'ach', 'Actinidia24318' => 'ach', 'Actinidia40196' => 'ach', 'Actinidia40197' => 'ach', 'Actinidia40198' => 'ach', 'Ah.08g212990' => 'amhyb', 'Ah.15g091720' => 'amhyb', 'AL3G38260' => 'aly', 'AL4G47710' => 'aly', 'Aqoxy2G00671' => 'aox', 'Aqoxy2G03236' => 'aox', 'arahy.Tifrunner.gnm1.ann1.05IDCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KR684' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATY3SJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK6QJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6APGL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IDT7Z9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM073U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ0R87' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LE7RV4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT4QRX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V5ENPK' => 'arhy', 'AT2G48110' => 'ath', 'AT3G23590' => 'ath', 'ATR0626G186' => 'atr', 'ATR1127G141' => 'atr', 'Atru.chr4.2583' => 'acertr', 'Atru.chr5.1358' => 'acertr', 'Atru.chr5.1359' => 'acertr', 'Atru.chr8.46' => 'acertr', 'AUR62002640' => 'cqu', 'AUR62030055' => 'cqu', 'AUR62033713' => 'cqu', 'AUR62033714' => 'cqu', 'AUR62036795' => 'cqu', 'AUR62039891' => 'cqu', 'BcaB02g08737' => 'bca', 'BcaB04g20441' => 'bca', 'BcaB06g26509' => 'bca', 'BcaB06g26510' => 'bca', 'BcaB06g26511' => 'bca', 'BcaB06g26512' => 'bca', 'BcaB06g26513' => 'bca', 'BcaC02g12564' => 'bca', 'BcaC02g12565' => 'bca', 'BcaC02g12794' => 'bca', 'BcaC02g12795' => 'bca', 'BcaC02g12796' => 'bca', 'BcaC06g35541' => 'bca', 'BNapus_Darmor_BZH_scaffold_188p00080' => 'bna', 'BNapus_Darmor_BZH_scaffold_188p00090' => 'bna', 'BolC1t03972H' => 'bol', 'BolC1t03973H' => 'bol', 'BolC4t21680H' => 'bol', 'BolC7t41863H' => 'bol', 'BolSC55t61227H' => 'bol', 'BolSC55t61228H' => 'bol', 'BraA01t03278Z' => 'bra', 'BraA05t18998Z' => 'bra', 'BraA07t28673Z' => 'bra', 'C01p40150' => 'bna', 'C05p12370' => 'bna', 'C07p13680' => 'bna', 'CAN.G1006.16' => 'can', 'CAN.G1006.17' => 'can', 'CAN.G1170.2' => 'can', 'CAN.G962.7' => 'can', 'CANSAT25G2179' => 'cansat', 'CANSAT78G1573' => 'cansat', 'CARHR099510' => 'chi', 'CARHR143510' => 'chi', 'Carub.0003s2380' => 'cru', 'Carub.0004s3082' => 'cru', 'Ca_00614_v3' => 'car', 'Ca_07801_v3' => 'car', 'Ca_08567_v3' => 'car', 'Ca_09571_v3' => 'car', 'CBR_g19290' => 'cbr', 'Cc01_g19770' => 'ccan', 'Cc03_g03030' => 'ccan', 'CDE07G0968' => 'cde', 'CDE09G1441' => 'cde', 'Cfa006103' => 'cfa', 'Cfa015573' => 'cfa', 'Cfa016988' => 'cfa', 'Ciclev10006738m.g' => 'ccl', 'Ciclev10010920m.g' => 'ccl', 'Ciclev10018517m.g' => 'ccl', 'CiPaw.01G159200' => 'cil', 'CiPaw.02G091000' => 'cil', 'CiPaw.02G091100' => 'cil', 'CiPaw.08G103100' => 'cil', 'CiPaw.09G224900' => 'cil', 'ClCG06G005740' => 'cla', 'ClCG07G000090' => 'cla', 'ClCG07G000100' => 'cla', 'COL.COLO4_09143' => 'col', 'COL.COLO4_25124' => 'col', 'Cpa.g.sc16.34' => 'cpa', 'Cpa.g.sc3504.1' => 'cpa', 'Cpa.g.sc60.37' => 'cpa', 'CsaV3_6G018520' => 'csa', 'CsaV3_6G036860' => 'csa', 'CSS0001072' => 'camsi', 'CSS0020208' => 'camsi', 'CSS0021253' => 'camsi', 'CSS0022190' => 'camsi', 'CSS0036150' => 'camsi', 'CSS0040442' => 'camsi', 'CSS0042300' => 'camsi', 'CSS0045298' => 'camsi', 'DCAR_012449' => 'dca', 'DCAR_018405' => 'dca', 'DCAR_024573' => 'dca', 'DCAR_030591' => 'dca', 'Dinv16926' => 'din', 'Dinv32963' => 'din', 'Dinv38382' => 'din', 'Dinv38383' => 'din', 'Duzib133G0974' => 'dzi', 'Duzib138G1867' => 'dzi', 'Duzib211G0420' => 'dzi', 'Duzib212G0930' => 'dzi', 'ECA234G1645' => 'eca', 'ECA247G3467' => 'eca', 'ECA248G1703' => 'eca', 'EL10Ac3g06327' => 'bvu', 'EL10Ac7g17204' => 'bvu', 'Eucgr.A00855' => 'egr', 'Eucgr.A00858' => 'egr', 'Eucgr.H01520' => 'egr', 'Eucgr.H03604' => 'egr', 'Eucgr.L03465' => 'egr', 'Eucgr.L03466' => 'egr', 'FAN01G0988' => 'fan', 'FAN02G3892' => 'fan', 'FAN05G3381' => 'fan', 'FAN07G0967' => 'fan', 'FAN07G1493' => 'fan', 'FAN08G3125' => 'fan', 'FAN09G0402' => 'fan', 'FAN12G2594' => 'fan', 'FAN12G3879' => 'fan', 'FAN14G1546' => 'fan', 'FAN15G3626' => 'fan', 'FAN17G0588' => 'fan', 'FAN17G0609' => 'fan', 'FAN18G2817' => 'fan', 'FAN19G1305' => 'fan', 'FAN20G1787' => 'fan', 'FAN22G0073' => 'fan', 'FAN22G0352' => 'fan', 'FAN22G0368' => 'fan', 'FAN22G2273' => 'fan', 'FAN24G1998' => 'fan', 'FAN27G1317' => 'fan', 'FvH4_2g23980' => 'fve', 'FvH4_4g14380' => 'fve', 'FvH4_4g14390' => 'fve', 'FvH4_6g09250' => 'fve', 'Glyma.03G151100' => 'gma', 'Glyma.04G122550' => 'gma', 'Glyma.05G001600' => 'gma', 'Glyma.09G270766' => 'gma', 'Glyma.09G270832' => 'gma', 'Glyma.13G209800' => 'gma', 'Glyma.15G102800' => 'gma', 'Glyma.18G218900' => 'gma', 'Glyma.19G001500' => 'gma', 'Glyma.19G153600' => 'gma', 'Gohir.A02G028600' => 'ghi', 'Gohir.A08G045000' => 'ghi', 'Gohir.A11G120500' => 'ghi', 'Gohir.A12G006200' => 'ghi', 'Gohir.A12G006250' => 'ghi', 'Gohir.D02G036300' => 'ghi', 'Gohir.D08G054700' => 'ghi', 'Gohir.D11G125600' => 'ghi', 'Gohir.D12G005700' => 'ghi', 'Gorai.004G055200' => 'gra', 'Gorai.005G040400' => 'gra', 'Gorai.007G134500' => 'gra', 'Gorai.008G005500' => 'gra', 'GSVIVG01011094001' => 'vvi', 'GSVIVG01017879001' => 'vvi', 'GSVIVG01025988001' => 'vvi', 'GSVIVG01029847001' => 'vvi', 'HanXRQChr10g0282901' => 'han', 'HanXRQChr10g0310371' => 'han', 'HanXRQChr10g0315041' => 'han', 'HanXRQChr11g0327651' => 'han', 'HanXRQChr12g0359391' => 'han', 'Haze_00972' => 'cav', 'Haze_00973' => 'cav', 'Haze_00974' => 'cav', 'Haze_04747' => 'cav', 'Haze_04749' => 'cav', 'Haze_04750' => 'cav', 'Haze_21217' => 'cav', 'Hma1.2p1_1037F.1_g250680' => 'hma', 'Hma1.2p1_1644F.1_g295320' => 'hma', 'HPP92_011322' => 'vpl', 'HPP92_011323' => 'vpl', 'HPP92_011324' => 'vpl', 'HPP92_011325' => 'vpl', 'HPP92_011326' => 'vpl', 'Hund12205' => 'sun', 'Hund17957' => 'sun', 'Lalb_Chr06g0176771' => 'lal', 'Lalb_Chr18g0056021' => 'lal', 'Lalb_Chr18g0056031' => 'lal', 'Lalb_Chr18g0056041' => 'lal', 'Lalb_Chr20g0107751' => 'lal', 'Lalb_Chr20g0118371' => 'lal', 'Lj1g0010239' => 'lja', 'Lj1g0017101' => 'lja', 'Lj2A1178G40' => 'lonja', 'Lj2A54G84' => 'lonja', 'Lj2g0015248' => 'lja', 'Lj3A761T51' => 'lonja', 'Lj6g0018116' => 'lja', 'Lsat_1_v5_gn_4_136040' => 'lsa', 'Lsat_1_v5_gn_5_187461' => 'lsa', 'Lsat_1_v5_gn_5_77001' => 'lsa', 'Lsat_1_v5_gn_9_4461' => 'lsa', 'Manes.01G210100' => 'mes', 'Manes.03G185600' => 'mes', 'Manes.05G073300' => 'mes', 'Manes.09G120300' => 'mes', 'Manes.15G022100' => 'mes', 'Mapoly0096s0053' => 'mpo', 'MBI03_g14058_MAGBIO' => 'mbi', 'MBI03_g33876_MAGBIO' => 'mbi', 'MBI03_g36854_MAGBIO' => 'mbi', 'MBI17_g11997_MAGBIO' => 'mbi', 'MD03G1269000' => 'mdo', 'MD04G1179600' => 'mdo', 'MD11G1289800' => 'mdo', 'MD12G1194700' => 'mdo', 'MD13G1182100' => 'mdo', 'MD13G1182200' => 'mdo', 'MD16G1182600' => 'mdo', 'Medtr2g021400' => 'mtr', 'Medtr2g021470' => 'mtr', 'Medtr2g105810' => 'mtr', 'Medtr3g033580' => 'mtr', 'Medtr6g007970' => 'mtr', 'Medtr7g056330' => 'mtr', 'Medtr7g074290' => 'mtr', 'Medtr7g074380' => 'mtr', 'Medtr7g094550' => 'mtr', 'Medtr8g069995' => 'mtr', 'MELO3C014345.2' => 'cme', 'MELO3C021395.2' => 'cme', 'Migut.D00262' => 'egut', 'Migut.G00257' => 'egut', 'MSTRG.21575' => 'ama', 'MSTRG.3985' => 'ama', 'Nitab4.5_0000295g0140' => 'nta', 'Nitab4.5_0000732g0140' => 'nta', 'Nitab4.5_0003162g0020' => 'nta', 'Nitab4.5_0006180g0090' => 'nta', 'Nitab4.5_0006390g0010' => 'nta', 'Nitab4.5_0007392g0040' => 'nta', 'Nn1g02140' => 'nnu', 'Nn4g26168' => 'nnu', 'Nn5g26754' => 'nnu', 'Oeu001433.1' => 'oeu', 'Oeu010299.2' => 'oeu', 'Oeu011171.1' => 'oeu', 'Oeu037675.1' => 'oeu', 'Oeu038359.1' => 'oeu', 'Oeu063834.1' => 'oeu', 'Oeu063835.1' => 'oeu', 'Os05g0312000' => 'osa', 'Os07g0211101' => 'osa', 'Os07g0211200' => 'osa', 'Os07g0681500' => 'osa', 'Peaxi162Scf00095g01015' => 'pax', 'Peaxi162Scf00104g00329' => 'pax', 'Peaxi162Scf00161g00137' => 'pax', 'PGR004G1665' => 'pgr', 'PGR031G2937' => 'pgr', 'PGR119G2145' => 'pgr', 'PGSC0003DMG400004351' => 'stu', 'PGSC0003DMG400014625' => 'stu', 'PGSC0003DMG401000943' => 'stu', 'Phvul.001G148600' => 'pvu', 'Phvul.004G001700' => 'pvu', 'Phvul.006G154900' => 'pvu', 'Phvul.008G078200' => 'pvu', 'Phvul.011G136500' => 'pvu', 'Potri.002G215600' => 'ptr', 'Potri.008G201600' => 'ptr', 'Potri.014G138400' => 'ptr', 'Potri.016G142500' => 'ptr', 'Pp3c16_10580' => 'ppa', 'Pp3c5_25280' => 'ppa', 'Prupe.1G150000' => 'ppe', 'Prupe.1G150100' => 'ppe', 'Prupe.6G299600' => 'ppe', 'Prupe.8G245000' => 'ppe', 'Psat0s4927g0040' => 'psa', 'Psat1g052080' => 'psa', 'Psat1g183800' => 'psa', 'Psat3g113840' => 'psa', 'Psat3g126120' => 'psa', 'Psat3g126160' => 'psa', 'Psat3g158760' => 'psa', 'Psat3g158840' => 'psa', 'PSO170G2858' => 'pso', 'PSO339G0606' => 'pso', 'PSO384G4709' => 'pso', 'PSO407G0334' => 'pso', 'QL04p040276' => 'qlo', 'QL06p005458' => 'qlo', 'QL06p005472' => 'qlo', 'QL07p030546' => 'qlo', 'QL07p031519' => 'qlo', 'QL09p050949' => 'qlo', 'QL09p050966' => 'qlo', 'QL09p051067' => 'qlo', 'QL12p022706' => 'qlo', 'RcHm_v2.0_Chr2g0119601' => 'rch', 'RcHm_v2.0_Chr3g0459591' => 'rch', 'RcHm_v2.0_Chr4g0418521' => 'rch', 'RcHm_v2.0_Chr4g0418531' => 'rch', 'RcHm_v2.0_Chr4g0418541' => 'rch', 'RcHm_v2.0_Chr6g0291641' => 'rch', 'Rhsim01G0086300' => 'rsi', 'Rhsim01G0276300' => 'rsi', 'Rhsim01G0276500' => 'rsi', 'Rhsim04G0207700' => 'rsi', 'Rhsim05G0234500' => 'rsi', 'Rhsim13G0022400' => 'rsi', 'Sabra02G0167900' => 'sbr', 'Sabra04G0158500' => 'sbr', 'Sabra08G0159800' => 'sbr', 'Sabra10G0011500' => 'sbr', 'Sabra14G0104400' => 'sbr', 'SalBow2G2440' => 'sbo', 'SalBow4G2265' => 'sbo', 'Sc02g0000060' => 'sci', 'Sc05g0005020' => 'sci', 'Sc13g0003890' => 'sci', 'Sed0014865' => 'sed', 'Sed0017224' => 'sed', 'Sed0026391' => 'sed', 'SEGI_00063' => 'sgi', 'SEGI_10967' => 'sgi', 'SEGI_17510' => 'sgi', 'SEGI_24396' => 'sgi', 'SEGI_39719' => 'sgi', 'SEGI_41392' => 'sgi', 'SGA_v2.0_scaffold11G05794' => 'sas', 'SGA_v2.0_scaffold142G35607' => 'sas', 'SGA_v2.0_scaffold1G00447' => 'sas', 'SHI15388' => 'shi', 'SHI15394' => 'shi', 'SHI15396' => 'shi', 'SHI15399' => 'shi', 'SMO343G0151' => 'smo', 'SMO367G1118' => 'smo', 'Solyc01g080200.3' => 'sly', 'Solyc06g008960.3' => 'sly', 'Solyc09g064780.3' => 'sly', 'Sopen01g031980' => 'spe', 'Sopen06g003710' => 'spe', 'Sopen09g026460' => 'spe', 'Sp3g21240' => 'spa', 'Sp4g30030' => 'spa', 'TAR365G0022' => 'tar', 'TAR365G1023' => 'tar', 'TAR365G1253' => 'tar', 'TAR623G0078' => 'tar', 'TAR623G1721' => 'tar', 'TAR633G0959' => 'tar', 'THA.LOC104802225' => 'tha', 'THA.LOC104804769' => 'tha', 'THA.LOC104808660' => 'tha', 'THA.LOC104812792' => 'tha', 'Thecc.01G284000' => 'tca', 'Thecc.04G220600' => 'tca', 'Thecc.05G268900' => 'tca', 'Thecc.08G171100' => 'tca', 'Thhalv10001284m.g' => 'esa', 'Thhalv10019912m.g' => 'esa', 'TPR.G14189' => 'tpr', 'TPR.G18110' => 'tpr', 'TPR.G18130' => 'tpr', 'TPR.G18131' => 'tpr', 'TPR.G18140' => 'tpr', 'TPR.G24282' => 'tpr', 'TPR.G25221' => 'tpr', 'TPR.G29267' => 'tpr', 'TPR.G35315' => 'tpr', 'TPR.G36173' => 'tpr', 'TWI09G0794' => 'twi', 'TWI59G1348' => 'twi', 'TWI74G0430' => 'twi', 'unitig_26.g8940' => 'ugi', 'unitig_749.g13744' => 'ugi', 'unitig_749.g13745' => 'ugi', 'vmacro08269' => 'vma', 'vmacro14937' => 'vma', 'vmacro20401' => 'vma', 'VMungo0464G1349' => 'vmu', 'VMungo0540G0289' => 'vmu', 'VMungo1215G1590' => 'vmu', 'VMungo1309G0221' => 'vmu', 'VMungo1309G2815' => 'vmu', 'VMungo1383G0239' => 'vmu', 'VMungo1383G2910' => 'vmu', 'Zm00001eb095270' => 'zma', 'Zm00001eb095280' => 'zma', 'Zm00001eb111630' => 'zma', 'Zm00001eb237080' => 'zma', 'Zm00001eb273740' => 'zma', 'Zm00001eb285040' => 'zma', 'Zm00001eb330790' => 'zma', 'Zm00001eb337380' => 'zma' ) $gf_id = 'HOM05D001484' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001484' ) $data_identifier = 'HOM05D001484' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 2, 'aly' => (int) 2, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 22, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 7, 'hma' => (int) 2, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 7, 'mtr' => (int) 10, 'cme' => (int) 2, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 4, 'ppa' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 4, 'qlo' => (int) 9, 'rch' => (int) 6, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 10, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 7, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb337380' $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' => 'HOM05D001484', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p31500' => 'bna', 'A05p00020' => 'bna', 'A07p08820' => 'bna', 'Aa31LG4G3300' => 'aar', 'Aa31LG8G10030' => 'aar', 'Actinidia00731' => 'ach', 'Actinidia11473' => 'ach', 'Actinidia23469' => 'ach', 'Actinidia24318' => 'ach', 'Actinidia40196' => 'ach', 'Actinidia40197' => 'ach', 'Actinidia40198' => 'ach', 'Ah.08g212990' => 'amhyb', 'Ah.15g091720' => 'amhyb', 'AL3G38260' => 'aly', 'AL4G47710' => 'aly', 'Aqoxy2G00671' => 'aox', 'Aqoxy2G03236' => 'aox', 'arahy.Tifrunner.gnm1.ann1.05IDCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KR684' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATY3SJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK6QJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6APGL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IDT7Z9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM073U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ0R87' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LE7RV4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT4QRX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V5ENPK' => 'arhy', 'AT2G48110' => 'ath', 'AT3G23590' => 'ath', 'ATR0626G186' => 'atr', 'ATR1127G141' => 'atr', 'Atru.chr4.2583' => 'acertr', 'Atru.chr5.1358' => 'acertr', 'Atru.chr5.1359' => 'acertr', 'Atru.chr8.46' => 'acertr', 'AUR62002640' => 'cqu', 'AUR62030055' => 'cqu', 'AUR62033713' => 'cqu', 'AUR62033714' => 'cqu', 'AUR62036795' => 'cqu', 'AUR62039891' => 'cqu', 'BcaB02g08737' => 'bca', 'BcaB04g20441' => 'bca', 'BcaB06g26509' => 'bca', 'BcaB06g26510' => 'bca', 'BcaB06g26511' => 'bca', 'BcaB06g26512' => 'bca', 'BcaB06g26513' => 'bca', 'BcaC02g12564' => 'bca', 'BcaC02g12565' => 'bca', 'BcaC02g12794' => 'bca', 'BcaC02g12795' => 'bca', 'BcaC02g12796' => 'bca', 'BcaC06g35541' => 'bca', 'BNapus_Darmor_BZH_scaffold_188p00080' => 'bna', 'BNapus_Darmor_BZH_scaffold_188p00090' => 'bna', 'BolC1t03972H' => 'bol', 'BolC1t03973H' => 'bol', 'BolC4t21680H' => 'bol', 'BolC7t41863H' => 'bol', 'BolSC55t61227H' => 'bol', 'BolSC55t61228H' => 'bol', 'BraA01t03278Z' => 'bra', 'BraA05t18998Z' => 'bra', 'BraA07t28673Z' => 'bra', 'C01p40150' => 'bna', 'C05p12370' => 'bna', 'C07p13680' => 'bna', 'CAN.G1006.16' => 'can', 'CAN.G1006.17' => 'can', 'CAN.G1170.2' => 'can', 'CAN.G962.7' => 'can', 'CANSAT25G2179' => 'cansat', 'CANSAT78G1573' => 'cansat', 'CARHR099510' => 'chi', 'CARHR143510' => 'chi', 'Carub.0003s2380' => 'cru', 'Carub.0004s3082' => 'cru', 'Ca_00614_v3' => 'car', 'Ca_07801_v3' => 'car', 'Ca_08567_v3' => 'car', 'Ca_09571_v3' => 'car', 'CBR_g19290' => 'cbr', 'Cc01_g19770' => 'ccan', 'Cc03_g03030' => 'ccan', 'CDE07G0968' => 'cde', 'CDE09G1441' => 'cde', 'Cfa006103' => 'cfa', 'Cfa015573' => 'cfa', 'Cfa016988' => 'cfa', 'Ciclev10006738m.g' => 'ccl', 'Ciclev10010920m.g' => 'ccl', 'Ciclev10018517m.g' => 'ccl', 'CiPaw.01G159200' => 'cil', 'CiPaw.02G091000' => 'cil', 'CiPaw.02G091100' => 'cil', 'CiPaw.08G103100' => 'cil', 'CiPaw.09G224900' => 'cil', 'ClCG06G005740' => 'cla', 'ClCG07G000090' => 'cla', 'ClCG07G000100' => 'cla', 'COL.COLO4_09143' => 'col', 'COL.COLO4_25124' => 'col', 'Cpa.g.sc16.34' => 'cpa', 'Cpa.g.sc3504.1' => 'cpa', 'Cpa.g.sc60.37' => 'cpa', 'CsaV3_6G018520' => 'csa', 'CsaV3_6G036860' => 'csa', 'CSS0001072' => 'camsi', 'CSS0020208' => 'camsi', 'CSS0021253' => 'camsi', 'CSS0022190' => 'camsi', 'CSS0036150' => 'camsi', 'CSS0040442' => 'camsi', 'CSS0042300' => 'camsi', 'CSS0045298' => 'camsi', 'DCAR_012449' => 'dca', 'DCAR_018405' => 'dca', 'DCAR_024573' => 'dca', 'DCAR_030591' => 'dca', 'Dinv16926' => 'din', 'Dinv32963' => 'din', 'Dinv38382' => 'din', 'Dinv38383' => 'din', 'Duzib133G0974' => 'dzi', 'Duzib138G1867' => 'dzi', 'Duzib211G0420' => 'dzi', 'Duzib212G0930' => 'dzi', 'ECA234G1645' => 'eca', 'ECA247G3467' => 'eca', 'ECA248G1703' => 'eca', 'EL10Ac3g06327' => 'bvu', 'EL10Ac7g17204' => 'bvu', 'Eucgr.A00855' => 'egr', 'Eucgr.A00858' => 'egr', 'Eucgr.H01520' => 'egr', 'Eucgr.H03604' => 'egr', 'Eucgr.L03465' => 'egr', 'Eucgr.L03466' => 'egr', 'FAN01G0988' => 'fan', 'FAN02G3892' => 'fan', 'FAN05G3381' => 'fan', 'FAN07G0967' => 'fan', 'FAN07G1493' => 'fan', 'FAN08G3125' => 'fan', 'FAN09G0402' => 'fan', 'FAN12G2594' => 'fan', 'FAN12G3879' => 'fan', 'FAN14G1546' => 'fan', 'FAN15G3626' => 'fan', 'FAN17G0588' => 'fan', 'FAN17G0609' => 'fan', 'FAN18G2817' => 'fan', 'FAN19G1305' => 'fan', 'FAN20G1787' => 'fan', 'FAN22G0073' => 'fan', 'FAN22G0352' => 'fan', 'FAN22G0368' => 'fan', 'FAN22G2273' => 'fan', 'FAN24G1998' => 'fan', 'FAN27G1317' => 'fan', 'FvH4_2g23980' => 'fve', 'FvH4_4g14380' => 'fve', 'FvH4_4g14390' => 'fve', 'FvH4_6g09250' => 'fve', 'Glyma.03G151100' => 'gma', 'Glyma.04G122550' => 'gma', 'Glyma.05G001600' => 'gma', 'Glyma.09G270766' => 'gma', 'Glyma.09G270832' => 'gma', 'Glyma.13G209800' => 'gma', 'Glyma.15G102800' => 'gma', 'Glyma.18G218900' => 'gma', 'Glyma.19G001500' => 'gma', 'Glyma.19G153600' => 'gma', 'Gohir.A02G028600' => 'ghi', 'Gohir.A08G045000' => 'ghi', 'Gohir.A11G120500' => 'ghi', 'Gohir.A12G006200' => 'ghi', 'Gohir.A12G006250' => 'ghi', 'Gohir.D02G036300' => 'ghi', 'Gohir.D08G054700' => 'ghi', 'Gohir.D11G125600' => 'ghi', 'Gohir.D12G005700' => 'ghi', 'Gorai.004G055200' => 'gra', 'Gorai.005G040400' => 'gra', 'Gorai.007G134500' => 'gra', 'Gorai.008G005500' => 'gra', 'GSVIVG01011094001' => 'vvi', 'GSVIVG01017879001' => 'vvi', 'GSVIVG01025988001' => 'vvi', 'GSVIVG01029847001' => 'vvi', 'HanXRQChr10g0282901' => 'han', 'HanXRQChr10g0310371' => 'han', 'HanXRQChr10g0315041' => 'han', 'HanXRQChr11g0327651' => 'han', 'HanXRQChr12g0359391' => 'han', 'Haze_00972' => 'cav', 'Haze_00973' => 'cav', 'Haze_00974' => 'cav', 'Haze_04747' => 'cav', 'Haze_04749' => 'cav', 'Haze_04750' => 'cav', 'Haze_21217' => 'cav', 'Hma1.2p1_1037F.1_g250680' => 'hma', 'Hma1.2p1_1644F.1_g295320' => 'hma', 'HPP92_011322' => 'vpl', 'HPP92_011323' => 'vpl', 'HPP92_011324' => 'vpl', 'HPP92_011325' => 'vpl', 'HPP92_011326' => 'vpl', 'Hund12205' => 'sun', 'Hund17957' => 'sun', 'Lalb_Chr06g0176771' => 'lal', 'Lalb_Chr18g0056021' => 'lal', 'Lalb_Chr18g0056031' => 'lal', 'Lalb_Chr18g0056041' => 'lal', 'Lalb_Chr20g0107751' => 'lal', 'Lalb_Chr20g0118371' => 'lal', 'Lj1g0010239' => 'lja', 'Lj1g0017101' => 'lja', 'Lj2A1178G40' => 'lonja', 'Lj2A54G84' => 'lonja', 'Lj2g0015248' => 'lja', 'Lj3A761T51' => 'lonja', 'Lj6g0018116' => 'lja', 'Lsat_1_v5_gn_4_136040' => 'lsa', 'Lsat_1_v5_gn_5_187461' => 'lsa', 'Lsat_1_v5_gn_5_77001' => 'lsa', 'Lsat_1_v5_gn_9_4461' => 'lsa', 'Manes.01G210100' => 'mes', 'Manes.03G185600' => 'mes', 'Manes.05G073300' => 'mes', 'Manes.09G120300' => 'mes', 'Manes.15G022100' => 'mes', 'Mapoly0096s0053' => 'mpo', 'MBI03_g14058_MAGBIO' => 'mbi', 'MBI03_g33876_MAGBIO' => 'mbi', 'MBI03_g36854_MAGBIO' => 'mbi', 'MBI17_g11997_MAGBIO' => 'mbi', 'MD03G1269000' => 'mdo', 'MD04G1179600' => 'mdo', 'MD11G1289800' => 'mdo', 'MD12G1194700' => 'mdo', 'MD13G1182100' => 'mdo', 'MD13G1182200' => 'mdo', 'MD16G1182600' => 'mdo', 'Medtr2g021400' => 'mtr', 'Medtr2g021470' => 'mtr', 'Medtr2g105810' => 'mtr', 'Medtr3g033580' => 'mtr', 'Medtr6g007970' => 'mtr', 'Medtr7g056330' => 'mtr', 'Medtr7g074290' => 'mtr', 'Medtr7g074380' => 'mtr', 'Medtr7g094550' => 'mtr', 'Medtr8g069995' => 'mtr', 'MELO3C014345.2' => 'cme', 'MELO3C021395.2' => 'cme', 'Migut.D00262' => 'egut', 'Migut.G00257' => 'egut', 'MSTRG.21575' => 'ama', 'MSTRG.3985' => 'ama', 'Nitab4.5_0000295g0140' => 'nta', 'Nitab4.5_0000732g0140' => 'nta', 'Nitab4.5_0003162g0020' => 'nta', 'Nitab4.5_0006180g0090' => 'nta', 'Nitab4.5_0006390g0010' => 'nta', 'Nitab4.5_0007392g0040' => 'nta', 'Nn1g02140' => 'nnu', 'Nn4g26168' => 'nnu', 'Nn5g26754' => 'nnu', 'Oeu001433.1' => 'oeu', 'Oeu010299.2' => 'oeu', 'Oeu011171.1' => 'oeu', 'Oeu037675.1' => 'oeu', 'Oeu038359.1' => 'oeu', 'Oeu063834.1' => 'oeu', 'Oeu063835.1' => 'oeu', 'Os05g0312000' => 'osa', 'Os07g0211101' => 'osa', 'Os07g0211200' => 'osa', 'Os07g0681500' => 'osa', 'Peaxi162Scf00095g01015' => 'pax', 'Peaxi162Scf00104g00329' => 'pax', 'Peaxi162Scf00161g00137' => 'pax', 'PGR004G1665' => 'pgr', 'PGR031G2937' => 'pgr', 'PGR119G2145' => 'pgr', 'PGSC0003DMG400004351' => 'stu', 'PGSC0003DMG400014625' => 'stu', 'PGSC0003DMG401000943' => 'stu', 'Phvul.001G148600' => 'pvu', 'Phvul.004G001700' => 'pvu', 'Phvul.006G154900' => 'pvu', 'Phvul.008G078200' => 'pvu', 'Phvul.011G136500' => 'pvu', 'Potri.002G215600' => 'ptr', 'Potri.008G201600' => 'ptr', 'Potri.014G138400' => 'ptr', 'Potri.016G142500' => 'ptr', 'Pp3c16_10580' => 'ppa', 'Pp3c5_25280' => 'ppa', 'Prupe.1G150000' => 'ppe', 'Prupe.1G150100' => 'ppe', 'Prupe.6G299600' => 'ppe', 'Prupe.8G245000' => 'ppe', 'Psat0s4927g0040' => 'psa', 'Psat1g052080' => 'psa', 'Psat1g183800' => 'psa', 'Psat3g113840' => 'psa', 'Psat3g126120' => 'psa', 'Psat3g126160' => 'psa', 'Psat3g158760' => 'psa', 'Psat3g158840' => 'psa', 'PSO170G2858' => 'pso', 'PSO339G0606' => 'pso', 'PSO384G4709' => 'pso', 'PSO407G0334' => 'pso', 'QL04p040276' => 'qlo', 'QL06p005458' => 'qlo', 'QL06p005472' => 'qlo', 'QL07p030546' => 'qlo', 'QL07p031519' => 'qlo', 'QL09p050949' => 'qlo', 'QL09p050966' => 'qlo', 'QL09p051067' => 'qlo', 'QL12p022706' => 'qlo', 'RcHm_v2.0_Chr2g0119601' => 'rch', 'RcHm_v2.0_Chr3g0459591' => 'rch', 'RcHm_v2.0_Chr4g0418521' => 'rch', 'RcHm_v2.0_Chr4g0418531' => 'rch', 'RcHm_v2.0_Chr4g0418541' => 'rch', 'RcHm_v2.0_Chr6g0291641' => 'rch', 'Rhsim01G0086300' => 'rsi', 'Rhsim01G0276300' => 'rsi', 'Rhsim01G0276500' => 'rsi', 'Rhsim04G0207700' => 'rsi', 'Rhsim05G0234500' => 'rsi', 'Rhsim13G0022400' => 'rsi', 'Sabra02G0167900' => 'sbr', 'Sabra04G0158500' => 'sbr', 'Sabra08G0159800' => 'sbr', 'Sabra10G0011500' => 'sbr', 'Sabra14G0104400' => 'sbr', 'SalBow2G2440' => 'sbo', 'SalBow4G2265' => 'sbo', 'Sc02g0000060' => 'sci', 'Sc05g0005020' => 'sci', 'Sc13g0003890' => 'sci', 'Sed0014865' => 'sed', 'Sed0017224' => 'sed', 'Sed0026391' => 'sed', 'SEGI_00063' => 'sgi', 'SEGI_10967' => 'sgi', 'SEGI_17510' => 'sgi', 'SEGI_24396' => 'sgi', 'SEGI_39719' => 'sgi', 'SEGI_41392' => 'sgi', 'SGA_v2.0_scaffold11G05794' => 'sas', 'SGA_v2.0_scaffold142G35607' => 'sas', 'SGA_v2.0_scaffold1G00447' => 'sas', 'SHI15388' => 'shi', 'SHI15394' => 'shi', 'SHI15396' => 'shi', 'SHI15399' => 'shi', 'SMO343G0151' => 'smo', 'SMO367G1118' => 'smo', 'Solyc01g080200.3' => 'sly', 'Solyc06g008960.3' => 'sly', 'Solyc09g064780.3' => 'sly', 'Sopen01g031980' => 'spe', 'Sopen06g003710' => 'spe', 'Sopen09g026460' => 'spe', 'Sp3g21240' => 'spa', 'Sp4g30030' => 'spa', 'TAR365G0022' => 'tar', 'TAR365G1023' => 'tar', 'TAR365G1253' => 'tar', 'TAR623G0078' => 'tar', 'TAR623G1721' => 'tar', 'TAR633G0959' => 'tar', 'THA.LOC104802225' => 'tha', 'THA.LOC104804769' => 'tha', 'THA.LOC104808660' => 'tha', 'THA.LOC104812792' => 'tha', 'Thecc.01G284000' => 'tca', 'Thecc.04G220600' => 'tca', 'Thecc.05G268900' => 'tca', 'Thecc.08G171100' => 'tca', 'Thhalv10001284m.g' => 'esa', 'Thhalv10019912m.g' => 'esa', 'TPR.G14189' => 'tpr', 'TPR.G18110' => 'tpr', 'TPR.G18130' => 'tpr', 'TPR.G18131' => 'tpr', 'TPR.G18140' => 'tpr', 'TPR.G24282' => 'tpr', 'TPR.G25221' => 'tpr', 'TPR.G29267' => 'tpr', 'TPR.G35315' => 'tpr', 'TPR.G36173' => 'tpr', 'TWI09G0794' => 'twi', 'TWI59G1348' => 'twi', 'TWI74G0430' => 'twi', 'unitig_26.g8940' => 'ugi', 'unitig_749.g13744' => 'ugi', 'unitig_749.g13745' => 'ugi', 'vmacro08269' => 'vma', 'vmacro14937' => 'vma', 'vmacro20401' => 'vma', 'VMungo0464G1349' => 'vmu', 'VMungo0540G0289' => 'vmu', 'VMungo1215G1590' => 'vmu', 'VMungo1309G0221' => 'vmu', 'VMungo1309G2815' => 'vmu', 'VMungo1383G0239' => 'vmu', 'VMungo1383G2910' => 'vmu', 'Zm00001eb095270' => 'zma', 'Zm00001eb095280' => 'zma', 'Zm00001eb111630' => 'zma', 'Zm00001eb237080' => 'zma', 'Zm00001eb273740' => 'zma', 'Zm00001eb285040' => 'zma', 'Zm00001eb330790' => 'zma', 'Zm00001eb337380' => 'zma' ), 'gf_id' => 'HOM05D001484', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001484' ), 'data_identifier' => 'HOM05D001484', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001484', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p31500' => 'bna', 'A05p00020' => 'bna', 'A07p08820' => 'bna', 'Aa31LG4G3300' => 'aar', 'Aa31LG8G10030' => 'aar', 'Actinidia00731' => 'ach', 'Actinidia11473' => 'ach', 'Actinidia23469' => 'ach', 'Actinidia24318' => 'ach', 'Actinidia40196' => 'ach', 'Actinidia40197' => 'ach', 'Actinidia40198' => 'ach', 'Ah.08g212990' => 'amhyb', 'Ah.15g091720' => 'amhyb', 'AL3G38260' => 'aly', 'AL4G47710' => 'aly', 'Aqoxy2G00671' => 'aox', 'Aqoxy2G03236' => 'aox', 'arahy.Tifrunner.gnm1.ann1.05IDCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KR684' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATY3SJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK6QJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6APGL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IDT7Z9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM073U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ0R87' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LE7RV4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT4QRX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V5ENPK' => 'arhy', 'AT2G48110' => 'ath', 'AT3G23590' => 'ath', 'ATR0626G186' => 'atr', 'ATR1127G141' => 'atr', 'Atru.chr4.2583' => 'acertr', 'Atru.chr5.1358' => 'acertr', 'Atru.chr5.1359' => 'acertr', 'Atru.chr8.46' => 'acertr', 'AUR62002640' => 'cqu', 'AUR62030055' => 'cqu', 'AUR62033713' => 'cqu', 'AUR62033714' => 'cqu', 'AUR62036795' => 'cqu', 'AUR62039891' => 'cqu', 'BcaB02g08737' => 'bca', 'BcaB04g20441' => 'bca', 'BcaB06g26509' => 'bca', 'BcaB06g26510' => 'bca', 'BcaB06g26511' => 'bca', 'BcaB06g26512' => 'bca', 'BcaB06g26513' => 'bca', 'BcaC02g12564' => 'bca', 'BcaC02g12565' => 'bca', 'BcaC02g12794' => 'bca', 'BcaC02g12795' => 'bca', 'BcaC02g12796' => 'bca', 'BcaC06g35541' => 'bca', 'BNapus_Darmor_BZH_scaffold_188p00080' => 'bna', 'BNapus_Darmor_BZH_scaffold_188p00090' => 'bna', 'BolC1t03972H' => 'bol', 'BolC1t03973H' => 'bol', 'BolC4t21680H' => 'bol', 'BolC7t41863H' => 'bol', 'BolSC55t61227H' => 'bol', 'BolSC55t61228H' => 'bol', 'BraA01t03278Z' => 'bra', 'BraA05t18998Z' => 'bra', 'BraA07t28673Z' => 'bra', 'C01p40150' => 'bna', 'C05p12370' => 'bna', 'C07p13680' => 'bna', 'CAN.G1006.16' => 'can', 'CAN.G1006.17' => 'can', 'CAN.G1170.2' => 'can', 'CAN.G962.7' => 'can', 'CANSAT25G2179' => 'cansat', 'CANSAT78G1573' => 'cansat', 'CARHR099510' => 'chi', 'CARHR143510' => 'chi', 'Carub.0003s2380' => 'cru', 'Carub.0004s3082' => 'cru', 'Ca_00614_v3' => 'car', 'Ca_07801_v3' => 'car', 'Ca_08567_v3' => 'car', 'Ca_09571_v3' => 'car', 'CBR_g19290' => 'cbr', 'Cc01_g19770' => 'ccan', 'Cc03_g03030' => 'ccan', 'CDE07G0968' => 'cde', 'CDE09G1441' => 'cde', 'Cfa006103' => 'cfa', 'Cfa015573' => 'cfa', 'Cfa016988' => 'cfa', 'Ciclev10006738m.g' => 'ccl', 'Ciclev10010920m.g' => 'ccl', 'Ciclev10018517m.g' => 'ccl', 'CiPaw.01G159200' => 'cil', 'CiPaw.02G091000' => 'cil', 'CiPaw.02G091100' => 'cil', 'CiPaw.08G103100' => 'cil', 'CiPaw.09G224900' => 'cil', 'ClCG06G005740' => 'cla', 'ClCG07G000090' => 'cla', 'ClCG07G000100' => 'cla', 'COL.COLO4_09143' => 'col', 'COL.COLO4_25124' => 'col', 'Cpa.g.sc16.34' => 'cpa', 'Cpa.g.sc3504.1' => 'cpa', 'Cpa.g.sc60.37' => 'cpa', 'CsaV3_6G018520' => 'csa', 'CsaV3_6G036860' => 'csa', 'CSS0001072' => 'camsi', 'CSS0020208' => 'camsi', 'CSS0021253' => 'camsi', 'CSS0022190' => 'camsi', 'CSS0036150' => 'camsi', 'CSS0040442' => 'camsi', 'CSS0042300' => 'camsi', 'CSS0045298' => 'camsi', 'DCAR_012449' => 'dca', 'DCAR_018405' => 'dca', 'DCAR_024573' => 'dca', 'DCAR_030591' => 'dca', 'Dinv16926' => 'din', 'Dinv32963' => 'din', 'Dinv38382' => 'din', 'Dinv38383' => 'din', 'Duzib133G0974' => 'dzi', 'Duzib138G1867' => 'dzi', 'Duzib211G0420' => 'dzi', 'Duzib212G0930' => 'dzi', 'ECA234G1645' => 'eca', 'ECA247G3467' => 'eca', 'ECA248G1703' => 'eca', 'EL10Ac3g06327' => 'bvu', 'EL10Ac7g17204' => 'bvu', 'Eucgr.A00855' => 'egr', 'Eucgr.A00858' => 'egr', 'Eucgr.H01520' => 'egr', 'Eucgr.H03604' => 'egr', 'Eucgr.L03465' => 'egr', 'Eucgr.L03466' => 'egr', 'FAN01G0988' => 'fan', 'FAN02G3892' => 'fan', 'FAN05G3381' => 'fan', 'FAN07G0967' => 'fan', 'FAN07G1493' => 'fan', 'FAN08G3125' => 'fan', 'FAN09G0402' => 'fan', 'FAN12G2594' => 'fan', 'FAN12G3879' => 'fan', 'FAN14G1546' => 'fan', 'FAN15G3626' => 'fan', 'FAN17G0588' => 'fan', 'FAN17G0609' => 'fan', 'FAN18G2817' => 'fan', 'FAN19G1305' => 'fan', 'FAN20G1787' => 'fan', 'FAN22G0073' => 'fan', 'FAN22G0352' => 'fan', 'FAN22G0368' => 'fan', 'FAN22G2273' => 'fan', 'FAN24G1998' => 'fan', 'FAN27G1317' => 'fan', 'FvH4_2g23980' => 'fve', 'FvH4_4g14380' => 'fve', 'FvH4_4g14390' => 'fve', 'FvH4_6g09250' => 'fve', 'Glyma.03G151100' => 'gma', 'Glyma.04G122550' => 'gma', 'Glyma.05G001600' => 'gma', 'Glyma.09G270766' => 'gma', 'Glyma.09G270832' => 'gma', 'Glyma.13G209800' => 'gma', 'Glyma.15G102800' => 'gma', 'Glyma.18G218900' => 'gma', 'Glyma.19G001500' => 'gma', 'Glyma.19G153600' => 'gma', 'Gohir.A02G028600' => 'ghi', 'Gohir.A08G045000' => 'ghi', 'Gohir.A11G120500' => 'ghi', 'Gohir.A12G006200' => 'ghi', 'Gohir.A12G006250' => 'ghi', 'Gohir.D02G036300' => 'ghi', 'Gohir.D08G054700' => 'ghi', 'Gohir.D11G125600' => 'ghi', 'Gohir.D12G005700' => 'ghi', 'Gorai.004G055200' => 'gra', 'Gorai.005G040400' => 'gra', 'Gorai.007G134500' => 'gra', 'Gorai.008G005500' => 'gra', 'GSVIVG01011094001' => 'vvi', 'GSVIVG01017879001' => 'vvi', 'GSVIVG01025988001' => 'vvi', 'GSVIVG01029847001' => 'vvi', 'HanXRQChr10g0282901' => 'han', 'HanXRQChr10g0310371' => 'han', 'HanXRQChr10g0315041' => 'han', 'HanXRQChr11g0327651' => 'han', 'HanXRQChr12g0359391' => 'han', 'Haze_00972' => 'cav', 'Haze_00973' => 'cav', 'Haze_00974' => 'cav', 'Haze_04747' => 'cav', 'Haze_04749' => 'cav', 'Haze_04750' => 'cav', 'Haze_21217' => 'cav', 'Hma1.2p1_1037F.1_g250680' => 'hma', 'Hma1.2p1_1644F.1_g295320' => 'hma', 'HPP92_011322' => 'vpl', 'HPP92_011323' => 'vpl', 'HPP92_011324' => 'vpl', 'HPP92_011325' => 'vpl', 'HPP92_011326' => 'vpl', 'Hund12205' => 'sun', 'Hund17957' => 'sun', 'Lalb_Chr06g0176771' => 'lal', 'Lalb_Chr18g0056021' => 'lal', 'Lalb_Chr18g0056031' => 'lal', 'Lalb_Chr18g0056041' => 'lal', 'Lalb_Chr20g0107751' => 'lal', 'Lalb_Chr20g0118371' => 'lal', 'Lj1g0010239' => 'lja', 'Lj1g0017101' => 'lja', 'Lj2A1178G40' => 'lonja', 'Lj2A54G84' => 'lonja', 'Lj2g0015248' => 'lja', 'Lj3A761T51' => 'lonja', 'Lj6g0018116' => 'lja', 'Lsat_1_v5_gn_4_136040' => 'lsa', 'Lsat_1_v5_gn_5_187461' => 'lsa', 'Lsat_1_v5_gn_5_77001' => 'lsa', 'Lsat_1_v5_gn_9_4461' => 'lsa', 'Manes.01G210100' => 'mes', 'Manes.03G185600' => 'mes', 'Manes.05G073300' => 'mes', 'Manes.09G120300' => 'mes', 'Manes.15G022100' => 'mes', 'Mapoly0096s0053' => 'mpo', 'MBI03_g14058_MAGBIO' => 'mbi', 'MBI03_g33876_MAGBIO' => 'mbi', 'MBI03_g36854_MAGBIO' => 'mbi', 'MBI17_g11997_MAGBIO' => 'mbi', 'MD03G1269000' => 'mdo', 'MD04G1179600' => 'mdo', 'MD11G1289800' => 'mdo', 'MD12G1194700' => 'mdo', 'MD13G1182100' => 'mdo', 'MD13G1182200' => 'mdo', 'MD16G1182600' => 'mdo', 'Medtr2g021400' => 'mtr', 'Medtr2g021470' => 'mtr', 'Medtr2g105810' => 'mtr', 'Medtr3g033580' => 'mtr', 'Medtr6g007970' => 'mtr', 'Medtr7g056330' => 'mtr', 'Medtr7g074290' => 'mtr', 'Medtr7g074380' => 'mtr', 'Medtr7g094550' => 'mtr', 'Medtr8g069995' => 'mtr', 'MELO3C014345.2' => 'cme', 'MELO3C021395.2' => 'cme', 'Migut.D00262' => 'egut', 'Migut.G00257' => 'egut', 'MSTRG.21575' => 'ama', 'MSTRG.3985' => 'ama', 'Nitab4.5_0000295g0140' => 'nta', 'Nitab4.5_0000732g0140' => 'nta', 'Nitab4.5_0003162g0020' => 'nta', 'Nitab4.5_0006180g0090' => 'nta', 'Nitab4.5_0006390g0010' => 'nta', 'Nitab4.5_0007392g0040' => 'nta', 'Nn1g02140' => 'nnu', 'Nn4g26168' => 'nnu', 'Nn5g26754' => 'nnu', 'Oeu001433.1' => 'oeu', 'Oeu010299.2' => 'oeu', 'Oeu011171.1' => 'oeu', 'Oeu037675.1' => 'oeu', 'Oeu038359.1' => 'oeu', 'Oeu063834.1' => 'oeu', 'Oeu063835.1' => 'oeu', 'Os05g0312000' => 'osa', 'Os07g0211101' => 'osa', 'Os07g0211200' => 'osa', 'Os07g0681500' => 'osa', 'Peaxi162Scf00095g01015' => 'pax', 'Peaxi162Scf00104g00329' => 'pax', 'Peaxi162Scf00161g00137' => 'pax', 'PGR004G1665' => 'pgr', 'PGR031G2937' => 'pgr', 'PGR119G2145' => 'pgr', 'PGSC0003DMG400004351' => 'stu', 'PGSC0003DMG400014625' => 'stu', 'PGSC0003DMG401000943' => 'stu', 'Phvul.001G148600' => 'pvu', 'Phvul.004G001700' => 'pvu', 'Phvul.006G154900' => 'pvu', 'Phvul.008G078200' => 'pvu', 'Phvul.011G136500' => 'pvu', 'Potri.002G215600' => 'ptr', 'Potri.008G201600' => 'ptr', 'Potri.014G138400' => 'ptr', 'Potri.016G142500' => 'ptr', 'Pp3c16_10580' => 'ppa', 'Pp3c5_25280' => 'ppa', 'Prupe.1G150000' => 'ppe', 'Prupe.1G150100' => 'ppe', 'Prupe.6G299600' => 'ppe', 'Prupe.8G245000' => 'ppe', 'Psat0s4927g0040' => 'psa', 'Psat1g052080' => 'psa', 'Psat1g183800' => 'psa', 'Psat3g113840' => 'psa', 'Psat3g126120' => 'psa', 'Psat3g126160' => 'psa', 'Psat3g158760' => 'psa', 'Psat3g158840' => 'psa', 'PSO170G2858' => 'pso', 'PSO339G0606' => 'pso', 'PSO384G4709' => 'pso', 'PSO407G0334' => 'pso', 'QL04p040276' => 'qlo', 'QL06p005458' => 'qlo', 'QL06p005472' => 'qlo', 'QL07p030546' => 'qlo', 'QL07p031519' => 'qlo', 'QL09p050949' => 'qlo', 'QL09p050966' => 'qlo', 'QL09p051067' => 'qlo', 'QL12p022706' => 'qlo', 'RcHm_v2.0_Chr2g0119601' => 'rch', 'RcHm_v2.0_Chr3g0459591' => 'rch', 'RcHm_v2.0_Chr4g0418521' => 'rch', 'RcHm_v2.0_Chr4g0418531' => 'rch', 'RcHm_v2.0_Chr4g0418541' => 'rch', 'RcHm_v2.0_Chr6g0291641' => 'rch', 'Rhsim01G0086300' => 'rsi', 'Rhsim01G0276300' => 'rsi', 'Rhsim01G0276500' => 'rsi', 'Rhsim04G0207700' => 'rsi', 'Rhsim05G0234500' => 'rsi', 'Rhsim13G0022400' => 'rsi', 'Sabra02G0167900' => 'sbr', 'Sabra04G0158500' => 'sbr', 'Sabra08G0159800' => 'sbr', 'Sabra10G0011500' => 'sbr', 'Sabra14G0104400' => 'sbr', 'SalBow2G2440' => 'sbo', 'SalBow4G2265' => 'sbo', 'Sc02g0000060' => 'sci', 'Sc05g0005020' => 'sci', 'Sc13g0003890' => 'sci', 'Sed0014865' => 'sed', 'Sed0017224' => 'sed', 'Sed0026391' => 'sed', 'SEGI_00063' => 'sgi', 'SEGI_10967' => 'sgi', 'SEGI_17510' => 'sgi', 'SEGI_24396' => 'sgi', 'SEGI_39719' => 'sgi', 'SEGI_41392' => 'sgi', 'SGA_v2.0_scaffold11G05794' => 'sas', 'SGA_v2.0_scaffold142G35607' => 'sas', 'SGA_v2.0_scaffold1G00447' => 'sas', 'SHI15388' => 'shi', 'SHI15394' => 'shi', 'SHI15396' => 'shi', 'SHI15399' => 'shi', 'SMO343G0151' => 'smo', 'SMO367G1118' => 'smo', 'Solyc01g080200.3' => 'sly', 'Solyc06g008960.3' => 'sly', 'Solyc09g064780.3' => 'sly', 'Sopen01g031980' => 'spe', 'Sopen06g003710' => 'spe', 'Sopen09g026460' => 'spe', 'Sp3g21240' => 'spa', 'Sp4g30030' => 'spa', 'TAR365G0022' => 'tar', 'TAR365G1023' => 'tar', 'TAR365G1253' => 'tar', 'TAR623G0078' => 'tar', 'TAR623G1721' => 'tar', 'TAR633G0959' => 'tar', 'THA.LOC104802225' => 'tha', 'THA.LOC104804769' => 'tha', 'THA.LOC104808660' => 'tha', 'THA.LOC104812792' => 'tha', 'Thecc.01G284000' => 'tca', 'Thecc.04G220600' => 'tca', 'Thecc.05G268900' => 'tca', 'Thecc.08G171100' => 'tca', 'Thhalv10001284m.g' => 'esa', 'Thhalv10019912m.g' => 'esa', 'TPR.G14189' => 'tpr', 'TPR.G18110' => 'tpr', 'TPR.G18130' => 'tpr', 'TPR.G18131' => 'tpr', 'TPR.G18140' => 'tpr', 'TPR.G24282' => 'tpr', 'TPR.G25221' => 'tpr', 'TPR.G29267' => 'tpr', 'TPR.G35315' => 'tpr', 'TPR.G36173' => 'tpr', 'TWI09G0794' => 'twi', 'TWI59G1348' => 'twi', 'TWI74G0430' => 'twi', 'unitig_26.g8940' => 'ugi', 'unitig_749.g13744' => 'ugi', 'unitig_749.g13745' => 'ugi', 'vmacro08269' => 'vma', 'vmacro14937' => 'vma', 'vmacro20401' => 'vma', 'VMungo0464G1349' => 'vmu', 'VMungo0540G0289' => 'vmu', 'VMungo1215G1590' => 'vmu', 'VMungo1309G0221' => 'vmu', 'VMungo1309G2815' => 'vmu', 'VMungo1383G0239' => 'vmu', 'VMungo1383G2910' => 'vmu', 'Zm00001eb095270' => 'zma', 'Zm00001eb095280' => 'zma', 'Zm00001eb111630' => 'zma', 'Zm00001eb237080' => 'zma', 'Zm00001eb273740' => 'zma', 'Zm00001eb285040' => 'zma', 'Zm00001eb330790' => 'zma', 'Zm00001eb337380' => 'zma' ) $gf_id = 'HOM05D001484' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001484' ) $data_identifier = 'HOM05D001484' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 2, 'aly' => (int) 2, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 22, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 7, 'hma' => (int) 2, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 7, 'mtr' => (int) 10, 'cme' => (int) 2, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 4, 'ppa' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 4, 'qlo' => (int) 9, 'rch' => (int) 6, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 10, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 7, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb337380' $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' => 'HOM05D001484', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p31500' => 'bna', 'A05p00020' => 'bna', 'A07p08820' => 'bna', 'Aa31LG4G3300' => 'aar', 'Aa31LG8G10030' => 'aar', 'Actinidia00731' => 'ach', 'Actinidia11473' => 'ach', 'Actinidia23469' => 'ach', 'Actinidia24318' => 'ach', 'Actinidia40196' => 'ach', 'Actinidia40197' => 'ach', 'Actinidia40198' => 'ach', 'Ah.08g212990' => 'amhyb', 'Ah.15g091720' => 'amhyb', 'AL3G38260' => 'aly', 'AL4G47710' => 'aly', 'Aqoxy2G00671' => 'aox', 'Aqoxy2G03236' => 'aox', 'arahy.Tifrunner.gnm1.ann1.05IDCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KR684' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATY3SJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK6QJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6APGL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IDT7Z9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM073U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ0R87' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LE7RV4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT4QRX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V5ENPK' => 'arhy', 'AT2G48110' => 'ath', 'AT3G23590' => 'ath', 'ATR0626G186' => 'atr', 'ATR1127G141' => 'atr', 'Atru.chr4.2583' => 'acertr', 'Atru.chr5.1358' => 'acertr', 'Atru.chr5.1359' => 'acertr', 'Atru.chr8.46' => 'acertr', 'AUR62002640' => 'cqu', 'AUR62030055' => 'cqu', 'AUR62033713' => 'cqu', 'AUR62033714' => 'cqu', 'AUR62036795' => 'cqu', 'AUR62039891' => 'cqu', 'BcaB02g08737' => 'bca', 'BcaB04g20441' => 'bca', 'BcaB06g26509' => 'bca', 'BcaB06g26510' => 'bca', 'BcaB06g26511' => 'bca', 'BcaB06g26512' => 'bca', 'BcaB06g26513' => 'bca', 'BcaC02g12564' => 'bca', 'BcaC02g12565' => 'bca', 'BcaC02g12794' => 'bca', 'BcaC02g12795' => 'bca', 'BcaC02g12796' => 'bca', 'BcaC06g35541' => 'bca', 'BNapus_Darmor_BZH_scaffold_188p00080' => 'bna', 'BNapus_Darmor_BZH_scaffold_188p00090' => 'bna', 'BolC1t03972H' => 'bol', 'BolC1t03973H' => 'bol', 'BolC4t21680H' => 'bol', 'BolC7t41863H' => 'bol', 'BolSC55t61227H' => 'bol', 'BolSC55t61228H' => 'bol', 'BraA01t03278Z' => 'bra', 'BraA05t18998Z' => 'bra', 'BraA07t28673Z' => 'bra', 'C01p40150' => 'bna', 'C05p12370' => 'bna', 'C07p13680' => 'bna', 'CAN.G1006.16' => 'can', 'CAN.G1006.17' => 'can', 'CAN.G1170.2' => 'can', 'CAN.G962.7' => 'can', 'CANSAT25G2179' => 'cansat', 'CANSAT78G1573' => 'cansat', 'CARHR099510' => 'chi', 'CARHR143510' => 'chi', 'Carub.0003s2380' => 'cru', 'Carub.0004s3082' => 'cru', 'Ca_00614_v3' => 'car', 'Ca_07801_v3' => 'car', 'Ca_08567_v3' => 'car', 'Ca_09571_v3' => 'car', 'CBR_g19290' => 'cbr', 'Cc01_g19770' => 'ccan', 'Cc03_g03030' => 'ccan', 'CDE07G0968' => 'cde', 'CDE09G1441' => 'cde', 'Cfa006103' => 'cfa', 'Cfa015573' => 'cfa', 'Cfa016988' => 'cfa', 'Ciclev10006738m.g' => 'ccl', 'Ciclev10010920m.g' => 'ccl', 'Ciclev10018517m.g' => 'ccl', 'CiPaw.01G159200' => 'cil', 'CiPaw.02G091000' => 'cil', 'CiPaw.02G091100' => 'cil', 'CiPaw.08G103100' => 'cil', 'CiPaw.09G224900' => 'cil', 'ClCG06G005740' => 'cla', 'ClCG07G000090' => 'cla', 'ClCG07G000100' => 'cla', 'COL.COLO4_09143' => 'col', 'COL.COLO4_25124' => 'col', 'Cpa.g.sc16.34' => 'cpa', 'Cpa.g.sc3504.1' => 'cpa', 'Cpa.g.sc60.37' => 'cpa', 'CsaV3_6G018520' => 'csa', 'CsaV3_6G036860' => 'csa', 'CSS0001072' => 'camsi', 'CSS0020208' => 'camsi', 'CSS0021253' => 'camsi', 'CSS0022190' => 'camsi', 'CSS0036150' => 'camsi', 'CSS0040442' => 'camsi', 'CSS0042300' => 'camsi', 'CSS0045298' => 'camsi', 'DCAR_012449' => 'dca', 'DCAR_018405' => 'dca', 'DCAR_024573' => 'dca', 'DCAR_030591' => 'dca', 'Dinv16926' => 'din', 'Dinv32963' => 'din', 'Dinv38382' => 'din', 'Dinv38383' => 'din', 'Duzib133G0974' => 'dzi', 'Duzib138G1867' => 'dzi', 'Duzib211G0420' => 'dzi', 'Duzib212G0930' => 'dzi', 'ECA234G1645' => 'eca', 'ECA247G3467' => 'eca', 'ECA248G1703' => 'eca', 'EL10Ac3g06327' => 'bvu', 'EL10Ac7g17204' => 'bvu', 'Eucgr.A00855' => 'egr', 'Eucgr.A00858' => 'egr', 'Eucgr.H01520' => 'egr', 'Eucgr.H03604' => 'egr', 'Eucgr.L03465' => 'egr', 'Eucgr.L03466' => 'egr', 'FAN01G0988' => 'fan', 'FAN02G3892' => 'fan', 'FAN05G3381' => 'fan', 'FAN07G0967' => 'fan', 'FAN07G1493' => 'fan', 'FAN08G3125' => 'fan', 'FAN09G0402' => 'fan', 'FAN12G2594' => 'fan', 'FAN12G3879' => 'fan', 'FAN14G1546' => 'fan', 'FAN15G3626' => 'fan', 'FAN17G0588' => 'fan', 'FAN17G0609' => 'fan', 'FAN18G2817' => 'fan', 'FAN19G1305' => 'fan', 'FAN20G1787' => 'fan', 'FAN22G0073' => 'fan', 'FAN22G0352' => 'fan', 'FAN22G0368' => 'fan', 'FAN22G2273' => 'fan', 'FAN24G1998' => 'fan', 'FAN27G1317' => 'fan', 'FvH4_2g23980' => 'fve', 'FvH4_4g14380' => 'fve', 'FvH4_4g14390' => 'fve', 'FvH4_6g09250' => 'fve', 'Glyma.03G151100' => 'gma', 'Glyma.04G122550' => 'gma', 'Glyma.05G001600' => 'gma', 'Glyma.09G270766' => 'gma', 'Glyma.09G270832' => 'gma', 'Glyma.13G209800' => 'gma', 'Glyma.15G102800' => 'gma', 'Glyma.18G218900' => 'gma', 'Glyma.19G001500' => 'gma', 'Glyma.19G153600' => 'gma', 'Gohir.A02G028600' => 'ghi', 'Gohir.A08G045000' => 'ghi', 'Gohir.A11G120500' => 'ghi', 'Gohir.A12G006200' => 'ghi', 'Gohir.A12G006250' => 'ghi', 'Gohir.D02G036300' => 'ghi', 'Gohir.D08G054700' => 'ghi', 'Gohir.D11G125600' => 'ghi', 'Gohir.D12G005700' => 'ghi', 'Gorai.004G055200' => 'gra', 'Gorai.005G040400' => 'gra', 'Gorai.007G134500' => 'gra', 'Gorai.008G005500' => 'gra', 'GSVIVG01011094001' => 'vvi', 'GSVIVG01017879001' => 'vvi', 'GSVIVG01025988001' => 'vvi', 'GSVIVG01029847001' => 'vvi', 'HanXRQChr10g0282901' => 'han', 'HanXRQChr10g0310371' => 'han', 'HanXRQChr10g0315041' => 'han', 'HanXRQChr11g0327651' => 'han', 'HanXRQChr12g0359391' => 'han', 'Haze_00972' => 'cav', 'Haze_00973' => 'cav', 'Haze_00974' => 'cav', 'Haze_04747' => 'cav', 'Haze_04749' => 'cav', 'Haze_04750' => 'cav', 'Haze_21217' => 'cav', 'Hma1.2p1_1037F.1_g250680' => 'hma', 'Hma1.2p1_1644F.1_g295320' => 'hma', 'HPP92_011322' => 'vpl', 'HPP92_011323' => 'vpl', 'HPP92_011324' => 'vpl', 'HPP92_011325' => 'vpl', 'HPP92_011326' => 'vpl', 'Hund12205' => 'sun', 'Hund17957' => 'sun', 'Lalb_Chr06g0176771' => 'lal', 'Lalb_Chr18g0056021' => 'lal', 'Lalb_Chr18g0056031' => 'lal', 'Lalb_Chr18g0056041' => 'lal', 'Lalb_Chr20g0107751' => 'lal', 'Lalb_Chr20g0118371' => 'lal', 'Lj1g0010239' => 'lja', 'Lj1g0017101' => 'lja', 'Lj2A1178G40' => 'lonja', 'Lj2A54G84' => 'lonja', 'Lj2g0015248' => 'lja', 'Lj3A761T51' => 'lonja', 'Lj6g0018116' => 'lja', 'Lsat_1_v5_gn_4_136040' => 'lsa', 'Lsat_1_v5_gn_5_187461' => 'lsa', 'Lsat_1_v5_gn_5_77001' => 'lsa', 'Lsat_1_v5_gn_9_4461' => 'lsa', 'Manes.01G210100' => 'mes', 'Manes.03G185600' => 'mes', 'Manes.05G073300' => 'mes', 'Manes.09G120300' => 'mes', 'Manes.15G022100' => 'mes', 'Mapoly0096s0053' => 'mpo', 'MBI03_g14058_MAGBIO' => 'mbi', 'MBI03_g33876_MAGBIO' => 'mbi', 'MBI03_g36854_MAGBIO' => 'mbi', 'MBI17_g11997_MAGBIO' => 'mbi', 'MD03G1269000' => 'mdo', 'MD04G1179600' => 'mdo', 'MD11G1289800' => 'mdo', 'MD12G1194700' => 'mdo', 'MD13G1182100' => 'mdo', 'MD13G1182200' => 'mdo', 'MD16G1182600' => 'mdo', 'Medtr2g021400' => 'mtr', 'Medtr2g021470' => 'mtr', 'Medtr2g105810' => 'mtr', 'Medtr3g033580' => 'mtr', 'Medtr6g007970' => 'mtr', 'Medtr7g056330' => 'mtr', 'Medtr7g074290' => 'mtr', 'Medtr7g074380' => 'mtr', 'Medtr7g094550' => 'mtr', 'Medtr8g069995' => 'mtr', 'MELO3C014345.2' => 'cme', 'MELO3C021395.2' => 'cme', 'Migut.D00262' => 'egut', 'Migut.G00257' => 'egut', 'MSTRG.21575' => 'ama', 'MSTRG.3985' => 'ama', 'Nitab4.5_0000295g0140' => 'nta', 'Nitab4.5_0000732g0140' => 'nta', 'Nitab4.5_0003162g0020' => 'nta', 'Nitab4.5_0006180g0090' => 'nta', 'Nitab4.5_0006390g0010' => 'nta', 'Nitab4.5_0007392g0040' => 'nta', 'Nn1g02140' => 'nnu', 'Nn4g26168' => 'nnu', 'Nn5g26754' => 'nnu', 'Oeu001433.1' => 'oeu', 'Oeu010299.2' => 'oeu', 'Oeu011171.1' => 'oeu', 'Oeu037675.1' => 'oeu', 'Oeu038359.1' => 'oeu', 'Oeu063834.1' => 'oeu', 'Oeu063835.1' => 'oeu', 'Os05g0312000' => 'osa', 'Os07g0211101' => 'osa', 'Os07g0211200' => 'osa', 'Os07g0681500' => 'osa', 'Peaxi162Scf00095g01015' => 'pax', 'Peaxi162Scf00104g00329' => 'pax', 'Peaxi162Scf00161g00137' => 'pax', 'PGR004G1665' => 'pgr', 'PGR031G2937' => 'pgr', 'PGR119G2145' => 'pgr', 'PGSC0003DMG400004351' => 'stu', 'PGSC0003DMG400014625' => 'stu', 'PGSC0003DMG401000943' => 'stu', 'Phvul.001G148600' => 'pvu', 'Phvul.004G001700' => 'pvu', 'Phvul.006G154900' => 'pvu', 'Phvul.008G078200' => 'pvu', 'Phvul.011G136500' => 'pvu', 'Potri.002G215600' => 'ptr', 'Potri.008G201600' => 'ptr', 'Potri.014G138400' => 'ptr', 'Potri.016G142500' => 'ptr', 'Pp3c16_10580' => 'ppa', 'Pp3c5_25280' => 'ppa', 'Prupe.1G150000' => 'ppe', 'Prupe.1G150100' => 'ppe', 'Prupe.6G299600' => 'ppe', 'Prupe.8G245000' => 'ppe', 'Psat0s4927g0040' => 'psa', 'Psat1g052080' => 'psa', 'Psat1g183800' => 'psa', 'Psat3g113840' => 'psa', 'Psat3g126120' => 'psa', 'Psat3g126160' => 'psa', 'Psat3g158760' => 'psa', 'Psat3g158840' => 'psa', 'PSO170G2858' => 'pso', 'PSO339G0606' => 'pso', 'PSO384G4709' => 'pso', 'PSO407G0334' => 'pso', 'QL04p040276' => 'qlo', 'QL06p005458' => 'qlo', 'QL06p005472' => 'qlo', 'QL07p030546' => 'qlo', 'QL07p031519' => 'qlo', 'QL09p050949' => 'qlo', 'QL09p050966' => 'qlo', 'QL09p051067' => 'qlo', 'QL12p022706' => 'qlo', 'RcHm_v2.0_Chr2g0119601' => 'rch', 'RcHm_v2.0_Chr3g0459591' => 'rch', 'RcHm_v2.0_Chr4g0418521' => 'rch', 'RcHm_v2.0_Chr4g0418531' => 'rch', 'RcHm_v2.0_Chr4g0418541' => 'rch', 'RcHm_v2.0_Chr6g0291641' => 'rch', 'Rhsim01G0086300' => 'rsi', 'Rhsim01G0276300' => 'rsi', 'Rhsim01G0276500' => 'rsi', 'Rhsim04G0207700' => 'rsi', 'Rhsim05G0234500' => 'rsi', 'Rhsim13G0022400' => 'rsi', 'Sabra02G0167900' => 'sbr', 'Sabra04G0158500' => 'sbr', 'Sabra08G0159800' => 'sbr', 'Sabra10G0011500' => 'sbr', 'Sabra14G0104400' => 'sbr', 'SalBow2G2440' => 'sbo', 'SalBow4G2265' => 'sbo', 'Sc02g0000060' => 'sci', 'Sc05g0005020' => 'sci', 'Sc13g0003890' => 'sci', 'Sed0014865' => 'sed', 'Sed0017224' => 'sed', 'Sed0026391' => 'sed', 'SEGI_00063' => 'sgi', 'SEGI_10967' => 'sgi', 'SEGI_17510' => 'sgi', 'SEGI_24396' => 'sgi', 'SEGI_39719' => 'sgi', 'SEGI_41392' => 'sgi', 'SGA_v2.0_scaffold11G05794' => 'sas', 'SGA_v2.0_scaffold142G35607' => 'sas', 'SGA_v2.0_scaffold1G00447' => 'sas', 'SHI15388' => 'shi', 'SHI15394' => 'shi', 'SHI15396' => 'shi', 'SHI15399' => 'shi', 'SMO343G0151' => 'smo', 'SMO367G1118' => 'smo', 'Solyc01g080200.3' => 'sly', 'Solyc06g008960.3' => 'sly', 'Solyc09g064780.3' => 'sly', 'Sopen01g031980' => 'spe', 'Sopen06g003710' => 'spe', 'Sopen09g026460' => 'spe', 'Sp3g21240' => 'spa', 'Sp4g30030' => 'spa', 'TAR365G0022' => 'tar', 'TAR365G1023' => 'tar', 'TAR365G1253' => 'tar', 'TAR623G0078' => 'tar', 'TAR623G1721' => 'tar', 'TAR633G0959' => 'tar', 'THA.LOC104802225' => 'tha', 'THA.LOC104804769' => 'tha', 'THA.LOC104808660' => 'tha', 'THA.LOC104812792' => 'tha', 'Thecc.01G284000' => 'tca', 'Thecc.04G220600' => 'tca', 'Thecc.05G268900' => 'tca', 'Thecc.08G171100' => 'tca', 'Thhalv10001284m.g' => 'esa', 'Thhalv10019912m.g' => 'esa', 'TPR.G14189' => 'tpr', 'TPR.G18110' => 'tpr', 'TPR.G18130' => 'tpr', 'TPR.G18131' => 'tpr', 'TPR.G18140' => 'tpr', 'TPR.G24282' => 'tpr', 'TPR.G25221' => 'tpr', 'TPR.G29267' => 'tpr', 'TPR.G35315' => 'tpr', 'TPR.G36173' => 'tpr', 'TWI09G0794' => 'twi', 'TWI59G1348' => 'twi', 'TWI74G0430' => 'twi', 'unitig_26.g8940' => 'ugi', 'unitig_749.g13744' => 'ugi', 'unitig_749.g13745' => 'ugi', 'vmacro08269' => 'vma', 'vmacro14937' => 'vma', 'vmacro20401' => 'vma', 'VMungo0464G1349' => 'vmu', 'VMungo0540G0289' => 'vmu', 'VMungo1215G1590' => 'vmu', 'VMungo1309G0221' => 'vmu', 'VMungo1309G2815' => 'vmu', 'VMungo1383G0239' => 'vmu', 'VMungo1383G2910' => 'vmu', 'Zm00001eb095270' => 'zma', 'Zm00001eb095280' => 'zma', 'Zm00001eb111630' => 'zma', 'Zm00001eb237080' => 'zma', 'Zm00001eb273740' => 'zma', 'Zm00001eb285040' => 'zma', 'Zm00001eb330790' => 'zma', 'Zm00001eb337380' => 'zma' ), 'gf_id' => 'HOM05D001484', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001484' ), 'data_identifier' => 'HOM05D001484', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001484', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p31500' => 'bna', 'A05p00020' => 'bna', 'A07p08820' => 'bna', 'Aa31LG4G3300' => 'aar', 'Aa31LG8G10030' => 'aar', 'Actinidia00731' => 'ach', 'Actinidia11473' => 'ach', 'Actinidia23469' => 'ach', 'Actinidia24318' => 'ach', 'Actinidia40196' => 'ach', 'Actinidia40197' => 'ach', 'Actinidia40198' => 'ach', 'Ah.08g212990' => 'amhyb', 'Ah.15g091720' => 'amhyb', 'AL3G38260' => 'aly', 'AL4G47710' => 'aly', 'Aqoxy2G00671' => 'aox', 'Aqoxy2G03236' => 'aox', 'arahy.Tifrunner.gnm1.ann1.05IDCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KR684' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATY3SJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK6QJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6APGL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IDT7Z9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM073U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ0R87' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LE7RV4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT4QRX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V5ENPK' => 'arhy', 'AT2G48110' => 'ath', 'AT3G23590' => 'ath', 'ATR0626G186' => 'atr', 'ATR1127G141' => 'atr', 'Atru.chr4.2583' => 'acertr', 'Atru.chr5.1358' => 'acertr', 'Atru.chr5.1359' => 'acertr', 'Atru.chr8.46' => 'acertr', 'AUR62002640' => 'cqu', 'AUR62030055' => 'cqu', 'AUR62033713' => 'cqu', 'AUR62033714' => 'cqu', 'AUR62036795' => 'cqu', 'AUR62039891' => 'cqu', 'BcaB02g08737' => 'bca', 'BcaB04g20441' => 'bca', 'BcaB06g26509' => 'bca', 'BcaB06g26510' => 'bca', 'BcaB06g26511' => 'bca', 'BcaB06g26512' => 'bca', 'BcaB06g26513' => 'bca', 'BcaC02g12564' => 'bca', 'BcaC02g12565' => 'bca', 'BcaC02g12794' => 'bca', 'BcaC02g12795' => 'bca', 'BcaC02g12796' => 'bca', 'BcaC06g35541' => 'bca', 'BNapus_Darmor_BZH_scaffold_188p00080' => 'bna', 'BNapus_Darmor_BZH_scaffold_188p00090' => 'bna', 'BolC1t03972H' => 'bol', 'BolC1t03973H' => 'bol', 'BolC4t21680H' => 'bol', 'BolC7t41863H' => 'bol', 'BolSC55t61227H' => 'bol', 'BolSC55t61228H' => 'bol', 'BraA01t03278Z' => 'bra', 'BraA05t18998Z' => 'bra', 'BraA07t28673Z' => 'bra', 'C01p40150' => 'bna', 'C05p12370' => 'bna', 'C07p13680' => 'bna', 'CAN.G1006.16' => 'can', 'CAN.G1006.17' => 'can', 'CAN.G1170.2' => 'can', 'CAN.G962.7' => 'can', 'CANSAT25G2179' => 'cansat', 'CANSAT78G1573' => 'cansat', 'CARHR099510' => 'chi', 'CARHR143510' => 'chi', 'Carub.0003s2380' => 'cru', 'Carub.0004s3082' => 'cru', 'Ca_00614_v3' => 'car', 'Ca_07801_v3' => 'car', 'Ca_08567_v3' => 'car', 'Ca_09571_v3' => 'car', 'CBR_g19290' => 'cbr', 'Cc01_g19770' => 'ccan', 'Cc03_g03030' => 'ccan', 'CDE07G0968' => 'cde', 'CDE09G1441' => 'cde', 'Cfa006103' => 'cfa', 'Cfa015573' => 'cfa', 'Cfa016988' => 'cfa', 'Ciclev10006738m.g' => 'ccl', 'Ciclev10010920m.g' => 'ccl', 'Ciclev10018517m.g' => 'ccl', 'CiPaw.01G159200' => 'cil', 'CiPaw.02G091000' => 'cil', 'CiPaw.02G091100' => 'cil', 'CiPaw.08G103100' => 'cil', 'CiPaw.09G224900' => 'cil', 'ClCG06G005740' => 'cla', 'ClCG07G000090' => 'cla', 'ClCG07G000100' => 'cla', 'COL.COLO4_09143' => 'col', 'COL.COLO4_25124' => 'col', 'Cpa.g.sc16.34' => 'cpa', 'Cpa.g.sc3504.1' => 'cpa', 'Cpa.g.sc60.37' => 'cpa', 'CsaV3_6G018520' => 'csa', 'CsaV3_6G036860' => 'csa', 'CSS0001072' => 'camsi', 'CSS0020208' => 'camsi', 'CSS0021253' => 'camsi', 'CSS0022190' => 'camsi', 'CSS0036150' => 'camsi', 'CSS0040442' => 'camsi', 'CSS0042300' => 'camsi', 'CSS0045298' => 'camsi', 'DCAR_012449' => 'dca', 'DCAR_018405' => 'dca', 'DCAR_024573' => 'dca', 'DCAR_030591' => 'dca', 'Dinv16926' => 'din', 'Dinv32963' => 'din', 'Dinv38382' => 'din', 'Dinv38383' => 'din', 'Duzib133G0974' => 'dzi', 'Duzib138G1867' => 'dzi', 'Duzib211G0420' => 'dzi', 'Duzib212G0930' => 'dzi', 'ECA234G1645' => 'eca', 'ECA247G3467' => 'eca', 'ECA248G1703' => 'eca', 'EL10Ac3g06327' => 'bvu', 'EL10Ac7g17204' => 'bvu', 'Eucgr.A00855' => 'egr', 'Eucgr.A00858' => 'egr', 'Eucgr.H01520' => 'egr', 'Eucgr.H03604' => 'egr', 'Eucgr.L03465' => 'egr', 'Eucgr.L03466' => 'egr', 'FAN01G0988' => 'fan', 'FAN02G3892' => 'fan', 'FAN05G3381' => 'fan', 'FAN07G0967' => 'fan', 'FAN07G1493' => 'fan', 'FAN08G3125' => 'fan', 'FAN09G0402' => 'fan', 'FAN12G2594' => 'fan', 'FAN12G3879' => 'fan', 'FAN14G1546' => 'fan', 'FAN15G3626' => 'fan', 'FAN17G0588' => 'fan', 'FAN17G0609' => 'fan', 'FAN18G2817' => 'fan', 'FAN19G1305' => 'fan', 'FAN20G1787' => 'fan', 'FAN22G0073' => 'fan', 'FAN22G0352' => 'fan', 'FAN22G0368' => 'fan', 'FAN22G2273' => 'fan', 'FAN24G1998' => 'fan', 'FAN27G1317' => 'fan', 'FvH4_2g23980' => 'fve', 'FvH4_4g14380' => 'fve', 'FvH4_4g14390' => 'fve', 'FvH4_6g09250' => 'fve', 'Glyma.03G151100' => 'gma', 'Glyma.04G122550' => 'gma', 'Glyma.05G001600' => 'gma', 'Glyma.09G270766' => 'gma', 'Glyma.09G270832' => 'gma', 'Glyma.13G209800' => 'gma', 'Glyma.15G102800' => 'gma', 'Glyma.18G218900' => 'gma', 'Glyma.19G001500' => 'gma', 'Glyma.19G153600' => 'gma', 'Gohir.A02G028600' => 'ghi', 'Gohir.A08G045000' => 'ghi', 'Gohir.A11G120500' => 'ghi', 'Gohir.A12G006200' => 'ghi', 'Gohir.A12G006250' => 'ghi', 'Gohir.D02G036300' => 'ghi', 'Gohir.D08G054700' => 'ghi', 'Gohir.D11G125600' => 'ghi', 'Gohir.D12G005700' => 'ghi', 'Gorai.004G055200' => 'gra', 'Gorai.005G040400' => 'gra', 'Gorai.007G134500' => 'gra', 'Gorai.008G005500' => 'gra', 'GSVIVG01011094001' => 'vvi', 'GSVIVG01017879001' => 'vvi', 'GSVIVG01025988001' => 'vvi', 'GSVIVG01029847001' => 'vvi', 'HanXRQChr10g0282901' => 'han', 'HanXRQChr10g0310371' => 'han', 'HanXRQChr10g0315041' => 'han', 'HanXRQChr11g0327651' => 'han', 'HanXRQChr12g0359391' => 'han', 'Haze_00972' => 'cav', 'Haze_00973' => 'cav', 'Haze_00974' => 'cav', 'Haze_04747' => 'cav', 'Haze_04749' => 'cav', 'Haze_04750' => 'cav', 'Haze_21217' => 'cav', 'Hma1.2p1_1037F.1_g250680' => 'hma', 'Hma1.2p1_1644F.1_g295320' => 'hma', 'HPP92_011322' => 'vpl', 'HPP92_011323' => 'vpl', 'HPP92_011324' => 'vpl', 'HPP92_011325' => 'vpl', 'HPP92_011326' => 'vpl', 'Hund12205' => 'sun', 'Hund17957' => 'sun', 'Lalb_Chr06g0176771' => 'lal', 'Lalb_Chr18g0056021' => 'lal', 'Lalb_Chr18g0056031' => 'lal', 'Lalb_Chr18g0056041' => 'lal', 'Lalb_Chr20g0107751' => 'lal', 'Lalb_Chr20g0118371' => 'lal', 'Lj1g0010239' => 'lja', 'Lj1g0017101' => 'lja', 'Lj2A1178G40' => 'lonja', 'Lj2A54G84' => 'lonja', 'Lj2g0015248' => 'lja', 'Lj3A761T51' => 'lonja', 'Lj6g0018116' => 'lja', 'Lsat_1_v5_gn_4_136040' => 'lsa', 'Lsat_1_v5_gn_5_187461' => 'lsa', 'Lsat_1_v5_gn_5_77001' => 'lsa', 'Lsat_1_v5_gn_9_4461' => 'lsa', 'Manes.01G210100' => 'mes', 'Manes.03G185600' => 'mes', 'Manes.05G073300' => 'mes', 'Manes.09G120300' => 'mes', 'Manes.15G022100' => 'mes', 'Mapoly0096s0053' => 'mpo', 'MBI03_g14058_MAGBIO' => 'mbi', 'MBI03_g33876_MAGBIO' => 'mbi', 'MBI03_g36854_MAGBIO' => 'mbi', 'MBI17_g11997_MAGBIO' => 'mbi', 'MD03G1269000' => 'mdo', 'MD04G1179600' => 'mdo', 'MD11G1289800' => 'mdo', 'MD12G1194700' => 'mdo', 'MD13G1182100' => 'mdo', 'MD13G1182200' => 'mdo', 'MD16G1182600' => 'mdo', 'Medtr2g021400' => 'mtr', 'Medtr2g021470' => 'mtr', 'Medtr2g105810' => 'mtr', 'Medtr3g033580' => 'mtr', 'Medtr6g007970' => 'mtr', 'Medtr7g056330' => 'mtr', 'Medtr7g074290' => 'mtr', 'Medtr7g074380' => 'mtr', 'Medtr7g094550' => 'mtr', 'Medtr8g069995' => 'mtr', 'MELO3C014345.2' => 'cme', 'MELO3C021395.2' => 'cme', 'Migut.D00262' => 'egut', 'Migut.G00257' => 'egut', 'MSTRG.21575' => 'ama', 'MSTRG.3985' => 'ama', 'Nitab4.5_0000295g0140' => 'nta', 'Nitab4.5_0000732g0140' => 'nta', 'Nitab4.5_0003162g0020' => 'nta', 'Nitab4.5_0006180g0090' => 'nta', 'Nitab4.5_0006390g0010' => 'nta', 'Nitab4.5_0007392g0040' => 'nta', 'Nn1g02140' => 'nnu', 'Nn4g26168' => 'nnu', 'Nn5g26754' => 'nnu', 'Oeu001433.1' => 'oeu', 'Oeu010299.2' => 'oeu', 'Oeu011171.1' => 'oeu', 'Oeu037675.1' => 'oeu', 'Oeu038359.1' => 'oeu', 'Oeu063834.1' => 'oeu', 'Oeu063835.1' => 'oeu', 'Os05g0312000' => 'osa', 'Os07g0211101' => 'osa', 'Os07g0211200' => 'osa', 'Os07g0681500' => 'osa', 'Peaxi162Scf00095g01015' => 'pax', 'Peaxi162Scf00104g00329' => 'pax', 'Peaxi162Scf00161g00137' => 'pax', 'PGR004G1665' => 'pgr', 'PGR031G2937' => 'pgr', 'PGR119G2145' => 'pgr', 'PGSC0003DMG400004351' => 'stu', 'PGSC0003DMG400014625' => 'stu', 'PGSC0003DMG401000943' => 'stu', 'Phvul.001G148600' => 'pvu', 'Phvul.004G001700' => 'pvu', 'Phvul.006G154900' => 'pvu', 'Phvul.008G078200' => 'pvu', 'Phvul.011G136500' => 'pvu', 'Potri.002G215600' => 'ptr', 'Potri.008G201600' => 'ptr', 'Potri.014G138400' => 'ptr', 'Potri.016G142500' => 'ptr', 'Pp3c16_10580' => 'ppa', 'Pp3c5_25280' => 'ppa', 'Prupe.1G150000' => 'ppe', 'Prupe.1G150100' => 'ppe', 'Prupe.6G299600' => 'ppe', 'Prupe.8G245000' => 'ppe', 'Psat0s4927g0040' => 'psa', 'Psat1g052080' => 'psa', 'Psat1g183800' => 'psa', 'Psat3g113840' => 'psa', 'Psat3g126120' => 'psa', 'Psat3g126160' => 'psa', 'Psat3g158760' => 'psa', 'Psat3g158840' => 'psa', 'PSO170G2858' => 'pso', 'PSO339G0606' => 'pso', 'PSO384G4709' => 'pso', 'PSO407G0334' => 'pso', 'QL04p040276' => 'qlo', 'QL06p005458' => 'qlo', 'QL06p005472' => 'qlo', 'QL07p030546' => 'qlo', 'QL07p031519' => 'qlo', 'QL09p050949' => 'qlo', 'QL09p050966' => 'qlo', 'QL09p051067' => 'qlo', 'QL12p022706' => 'qlo', 'RcHm_v2.0_Chr2g0119601' => 'rch', 'RcHm_v2.0_Chr3g0459591' => 'rch', 'RcHm_v2.0_Chr4g0418521' => 'rch', 'RcHm_v2.0_Chr4g0418531' => 'rch', 'RcHm_v2.0_Chr4g0418541' => 'rch', 'RcHm_v2.0_Chr6g0291641' => 'rch', 'Rhsim01G0086300' => 'rsi', 'Rhsim01G0276300' => 'rsi', 'Rhsim01G0276500' => 'rsi', 'Rhsim04G0207700' => 'rsi', 'Rhsim05G0234500' => 'rsi', 'Rhsim13G0022400' => 'rsi', 'Sabra02G0167900' => 'sbr', 'Sabra04G0158500' => 'sbr', 'Sabra08G0159800' => 'sbr', 'Sabra10G0011500' => 'sbr', 'Sabra14G0104400' => 'sbr', 'SalBow2G2440' => 'sbo', 'SalBow4G2265' => 'sbo', 'Sc02g0000060' => 'sci', 'Sc05g0005020' => 'sci', 'Sc13g0003890' => 'sci', 'Sed0014865' => 'sed', 'Sed0017224' => 'sed', 'Sed0026391' => 'sed', 'SEGI_00063' => 'sgi', 'SEGI_10967' => 'sgi', 'SEGI_17510' => 'sgi', 'SEGI_24396' => 'sgi', 'SEGI_39719' => 'sgi', 'SEGI_41392' => 'sgi', 'SGA_v2.0_scaffold11G05794' => 'sas', 'SGA_v2.0_scaffold142G35607' => 'sas', 'SGA_v2.0_scaffold1G00447' => 'sas', 'SHI15388' => 'shi', 'SHI15394' => 'shi', 'SHI15396' => 'shi', 'SHI15399' => 'shi', 'SMO343G0151' => 'smo', 'SMO367G1118' => 'smo', 'Solyc01g080200.3' => 'sly', 'Solyc06g008960.3' => 'sly', 'Solyc09g064780.3' => 'sly', 'Sopen01g031980' => 'spe', 'Sopen06g003710' => 'spe', 'Sopen09g026460' => 'spe', 'Sp3g21240' => 'spa', 'Sp4g30030' => 'spa', 'TAR365G0022' => 'tar', 'TAR365G1023' => 'tar', 'TAR365G1253' => 'tar', 'TAR623G0078' => 'tar', 'TAR623G1721' => 'tar', 'TAR633G0959' => 'tar', 'THA.LOC104802225' => 'tha', 'THA.LOC104804769' => 'tha', 'THA.LOC104808660' => 'tha', 'THA.LOC104812792' => 'tha', 'Thecc.01G284000' => 'tca', 'Thecc.04G220600' => 'tca', 'Thecc.05G268900' => 'tca', 'Thecc.08G171100' => 'tca', 'Thhalv10001284m.g' => 'esa', 'Thhalv10019912m.g' => 'esa', 'TPR.G14189' => 'tpr', 'TPR.G18110' => 'tpr', 'TPR.G18130' => 'tpr', 'TPR.G18131' => 'tpr', 'TPR.G18140' => 'tpr', 'TPR.G24282' => 'tpr', 'TPR.G25221' => 'tpr', 'TPR.G29267' => 'tpr', 'TPR.G35315' => 'tpr', 'TPR.G36173' => 'tpr', 'TWI09G0794' => 'twi', 'TWI59G1348' => 'twi', 'TWI74G0430' => 'twi', 'unitig_26.g8940' => 'ugi', 'unitig_749.g13744' => 'ugi', 'unitig_749.g13745' => 'ugi', 'vmacro08269' => 'vma', 'vmacro14937' => 'vma', 'vmacro20401' => 'vma', 'VMungo0464G1349' => 'vmu', 'VMungo0540G0289' => 'vmu', 'VMungo1215G1590' => 'vmu', 'VMungo1309G0221' => 'vmu', 'VMungo1309G2815' => 'vmu', 'VMungo1383G0239' => 'vmu', 'VMungo1383G2910' => 'vmu', 'Zm00001eb095270' => 'zma', 'Zm00001eb095280' => 'zma', 'Zm00001eb111630' => 'zma', 'Zm00001eb237080' => 'zma', 'Zm00001eb273740' => 'zma', 'Zm00001eb285040' => 'zma', 'Zm00001eb330790' => 'zma', 'Zm00001eb337380' => 'zma' ) $gf_id = 'HOM05D001484' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001484' ) $data_identifier = 'HOM05D001484' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 2, 'aly' => (int) 2, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 22, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 7, 'hma' => (int) 2, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 7, 'mtr' => (int) 10, 'cme' => (int) 2, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 4, 'ppa' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 4, 'qlo' => (int) 9, 'rch' => (int) 6, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 10, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 7, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb337380' $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' => 'HOM05D001484', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p31500' => 'bna', 'A05p00020' => 'bna', 'A07p08820' => 'bna', 'Aa31LG4G3300' => 'aar', 'Aa31LG8G10030' => 'aar', 'Actinidia00731' => 'ach', 'Actinidia11473' => 'ach', 'Actinidia23469' => 'ach', 'Actinidia24318' => 'ach', 'Actinidia40196' => 'ach', 'Actinidia40197' => 'ach', 'Actinidia40198' => 'ach', 'Ah.08g212990' => 'amhyb', 'Ah.15g091720' => 'amhyb', 'AL3G38260' => 'aly', 'AL4G47710' => 'aly', 'Aqoxy2G00671' => 'aox', 'Aqoxy2G03236' => 'aox', 'arahy.Tifrunner.gnm1.ann1.05IDCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KR684' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATY3SJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK6QJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6APGL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IDT7Z9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM073U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ0R87' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LE7RV4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT4QRX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V5ENPK' => 'arhy', 'AT2G48110' => 'ath', 'AT3G23590' => 'ath', 'ATR0626G186' => 'atr', 'ATR1127G141' => 'atr', 'Atru.chr4.2583' => 'acertr', 'Atru.chr5.1358' => 'acertr', 'Atru.chr5.1359' => 'acertr', 'Atru.chr8.46' => 'acertr', 'AUR62002640' => 'cqu', 'AUR62030055' => 'cqu', 'AUR62033713' => 'cqu', 'AUR62033714' => 'cqu', 'AUR62036795' => 'cqu', 'AUR62039891' => 'cqu', 'BcaB02g08737' => 'bca', 'BcaB04g20441' => 'bca', 'BcaB06g26509' => 'bca', 'BcaB06g26510' => 'bca', 'BcaB06g26511' => 'bca', 'BcaB06g26512' => 'bca', 'BcaB06g26513' => 'bca', 'BcaC02g12564' => 'bca', 'BcaC02g12565' => 'bca', 'BcaC02g12794' => 'bca', 'BcaC02g12795' => 'bca', 'BcaC02g12796' => 'bca', 'BcaC06g35541' => 'bca', 'BNapus_Darmor_BZH_scaffold_188p00080' => 'bna', 'BNapus_Darmor_BZH_scaffold_188p00090' => 'bna', 'BolC1t03972H' => 'bol', 'BolC1t03973H' => 'bol', 'BolC4t21680H' => 'bol', 'BolC7t41863H' => 'bol', 'BolSC55t61227H' => 'bol', 'BolSC55t61228H' => 'bol', 'BraA01t03278Z' => 'bra', 'BraA05t18998Z' => 'bra', 'BraA07t28673Z' => 'bra', 'C01p40150' => 'bna', 'C05p12370' => 'bna', 'C07p13680' => 'bna', 'CAN.G1006.16' => 'can', 'CAN.G1006.17' => 'can', 'CAN.G1170.2' => 'can', 'CAN.G962.7' => 'can', 'CANSAT25G2179' => 'cansat', 'CANSAT78G1573' => 'cansat', 'CARHR099510' => 'chi', 'CARHR143510' => 'chi', 'Carub.0003s2380' => 'cru', 'Carub.0004s3082' => 'cru', 'Ca_00614_v3' => 'car', 'Ca_07801_v3' => 'car', 'Ca_08567_v3' => 'car', 'Ca_09571_v3' => 'car', 'CBR_g19290' => 'cbr', 'Cc01_g19770' => 'ccan', 'Cc03_g03030' => 'ccan', 'CDE07G0968' => 'cde', 'CDE09G1441' => 'cde', 'Cfa006103' => 'cfa', 'Cfa015573' => 'cfa', 'Cfa016988' => 'cfa', 'Ciclev10006738m.g' => 'ccl', 'Ciclev10010920m.g' => 'ccl', 'Ciclev10018517m.g' => 'ccl', 'CiPaw.01G159200' => 'cil', 'CiPaw.02G091000' => 'cil', 'CiPaw.02G091100' => 'cil', 'CiPaw.08G103100' => 'cil', 'CiPaw.09G224900' => 'cil', 'ClCG06G005740' => 'cla', 'ClCG07G000090' => 'cla', 'ClCG07G000100' => 'cla', 'COL.COLO4_09143' => 'col', 'COL.COLO4_25124' => 'col', 'Cpa.g.sc16.34' => 'cpa', 'Cpa.g.sc3504.1' => 'cpa', 'Cpa.g.sc60.37' => 'cpa', 'CsaV3_6G018520' => 'csa', 'CsaV3_6G036860' => 'csa', 'CSS0001072' => 'camsi', 'CSS0020208' => 'camsi', 'CSS0021253' => 'camsi', 'CSS0022190' => 'camsi', 'CSS0036150' => 'camsi', 'CSS0040442' => 'camsi', 'CSS0042300' => 'camsi', 'CSS0045298' => 'camsi', 'DCAR_012449' => 'dca', 'DCAR_018405' => 'dca', 'DCAR_024573' => 'dca', 'DCAR_030591' => 'dca', 'Dinv16926' => 'din', 'Dinv32963' => 'din', 'Dinv38382' => 'din', 'Dinv38383' => 'din', 'Duzib133G0974' => 'dzi', 'Duzib138G1867' => 'dzi', 'Duzib211G0420' => 'dzi', 'Duzib212G0930' => 'dzi', 'ECA234G1645' => 'eca', 'ECA247G3467' => 'eca', 'ECA248G1703' => 'eca', 'EL10Ac3g06327' => 'bvu', 'EL10Ac7g17204' => 'bvu', 'Eucgr.A00855' => 'egr', 'Eucgr.A00858' => 'egr', 'Eucgr.H01520' => 'egr', 'Eucgr.H03604' => 'egr', 'Eucgr.L03465' => 'egr', 'Eucgr.L03466' => 'egr', 'FAN01G0988' => 'fan', 'FAN02G3892' => 'fan', 'FAN05G3381' => 'fan', 'FAN07G0967' => 'fan', 'FAN07G1493' => 'fan', 'FAN08G3125' => 'fan', 'FAN09G0402' => 'fan', 'FAN12G2594' => 'fan', 'FAN12G3879' => 'fan', 'FAN14G1546' => 'fan', 'FAN15G3626' => 'fan', 'FAN17G0588' => 'fan', 'FAN17G0609' => 'fan', 'FAN18G2817' => 'fan', 'FAN19G1305' => 'fan', 'FAN20G1787' => 'fan', 'FAN22G0073' => 'fan', 'FAN22G0352' => 'fan', 'FAN22G0368' => 'fan', 'FAN22G2273' => 'fan', 'FAN24G1998' => 'fan', 'FAN27G1317' => 'fan', 'FvH4_2g23980' => 'fve', 'FvH4_4g14380' => 'fve', 'FvH4_4g14390' => 'fve', 'FvH4_6g09250' => 'fve', 'Glyma.03G151100' => 'gma', 'Glyma.04G122550' => 'gma', 'Glyma.05G001600' => 'gma', 'Glyma.09G270766' => 'gma', 'Glyma.09G270832' => 'gma', 'Glyma.13G209800' => 'gma', 'Glyma.15G102800' => 'gma', 'Glyma.18G218900' => 'gma', 'Glyma.19G001500' => 'gma', 'Glyma.19G153600' => 'gma', 'Gohir.A02G028600' => 'ghi', 'Gohir.A08G045000' => 'ghi', 'Gohir.A11G120500' => 'ghi', 'Gohir.A12G006200' => 'ghi', 'Gohir.A12G006250' => 'ghi', 'Gohir.D02G036300' => 'ghi', 'Gohir.D08G054700' => 'ghi', 'Gohir.D11G125600' => 'ghi', 'Gohir.D12G005700' => 'ghi', 'Gorai.004G055200' => 'gra', 'Gorai.005G040400' => 'gra', 'Gorai.007G134500' => 'gra', 'Gorai.008G005500' => 'gra', 'GSVIVG01011094001' => 'vvi', 'GSVIVG01017879001' => 'vvi', 'GSVIVG01025988001' => 'vvi', 'GSVIVG01029847001' => 'vvi', 'HanXRQChr10g0282901' => 'han', 'HanXRQChr10g0310371' => 'han', 'HanXRQChr10g0315041' => 'han', 'HanXRQChr11g0327651' => 'han', 'HanXRQChr12g0359391' => 'han', 'Haze_00972' => 'cav', 'Haze_00973' => 'cav', 'Haze_00974' => 'cav', 'Haze_04747' => 'cav', 'Haze_04749' => 'cav', 'Haze_04750' => 'cav', 'Haze_21217' => 'cav', 'Hma1.2p1_1037F.1_g250680' => 'hma', 'Hma1.2p1_1644F.1_g295320' => 'hma', 'HPP92_011322' => 'vpl', 'HPP92_011323' => 'vpl', 'HPP92_011324' => 'vpl', 'HPP92_011325' => 'vpl', 'HPP92_011326' => 'vpl', 'Hund12205' => 'sun', 'Hund17957' => 'sun', 'Lalb_Chr06g0176771' => 'lal', 'Lalb_Chr18g0056021' => 'lal', 'Lalb_Chr18g0056031' => 'lal', 'Lalb_Chr18g0056041' => 'lal', 'Lalb_Chr20g0107751' => 'lal', 'Lalb_Chr20g0118371' => 'lal', 'Lj1g0010239' => 'lja', 'Lj1g0017101' => 'lja', 'Lj2A1178G40' => 'lonja', 'Lj2A54G84' => 'lonja', 'Lj2g0015248' => 'lja', 'Lj3A761T51' => 'lonja', 'Lj6g0018116' => 'lja', 'Lsat_1_v5_gn_4_136040' => 'lsa', 'Lsat_1_v5_gn_5_187461' => 'lsa', 'Lsat_1_v5_gn_5_77001' => 'lsa', 'Lsat_1_v5_gn_9_4461' => 'lsa', 'Manes.01G210100' => 'mes', 'Manes.03G185600' => 'mes', 'Manes.05G073300' => 'mes', 'Manes.09G120300' => 'mes', 'Manes.15G022100' => 'mes', 'Mapoly0096s0053' => 'mpo', 'MBI03_g14058_MAGBIO' => 'mbi', 'MBI03_g33876_MAGBIO' => 'mbi', 'MBI03_g36854_MAGBIO' => 'mbi', 'MBI17_g11997_MAGBIO' => 'mbi', 'MD03G1269000' => 'mdo', 'MD04G1179600' => 'mdo', 'MD11G1289800' => 'mdo', 'MD12G1194700' => 'mdo', 'MD13G1182100' => 'mdo', 'MD13G1182200' => 'mdo', 'MD16G1182600' => 'mdo', 'Medtr2g021400' => 'mtr', 'Medtr2g021470' => 'mtr', 'Medtr2g105810' => 'mtr', 'Medtr3g033580' => 'mtr', 'Medtr6g007970' => 'mtr', 'Medtr7g056330' => 'mtr', 'Medtr7g074290' => 'mtr', 'Medtr7g074380' => 'mtr', 'Medtr7g094550' => 'mtr', 'Medtr8g069995' => 'mtr', 'MELO3C014345.2' => 'cme', 'MELO3C021395.2' => 'cme', 'Migut.D00262' => 'egut', 'Migut.G00257' => 'egut', 'MSTRG.21575' => 'ama', 'MSTRG.3985' => 'ama', 'Nitab4.5_0000295g0140' => 'nta', 'Nitab4.5_0000732g0140' => 'nta', 'Nitab4.5_0003162g0020' => 'nta', 'Nitab4.5_0006180g0090' => 'nta', 'Nitab4.5_0006390g0010' => 'nta', 'Nitab4.5_0007392g0040' => 'nta', 'Nn1g02140' => 'nnu', 'Nn4g26168' => 'nnu', 'Nn5g26754' => 'nnu', 'Oeu001433.1' => 'oeu', 'Oeu010299.2' => 'oeu', 'Oeu011171.1' => 'oeu', 'Oeu037675.1' => 'oeu', 'Oeu038359.1' => 'oeu', 'Oeu063834.1' => 'oeu', 'Oeu063835.1' => 'oeu', 'Os05g0312000' => 'osa', 'Os07g0211101' => 'osa', 'Os07g0211200' => 'osa', 'Os07g0681500' => 'osa', 'Peaxi162Scf00095g01015' => 'pax', 'Peaxi162Scf00104g00329' => 'pax', 'Peaxi162Scf00161g00137' => 'pax', 'PGR004G1665' => 'pgr', 'PGR031G2937' => 'pgr', 'PGR119G2145' => 'pgr', 'PGSC0003DMG400004351' => 'stu', 'PGSC0003DMG400014625' => 'stu', 'PGSC0003DMG401000943' => 'stu', 'Phvul.001G148600' => 'pvu', 'Phvul.004G001700' => 'pvu', 'Phvul.006G154900' => 'pvu', 'Phvul.008G078200' => 'pvu', 'Phvul.011G136500' => 'pvu', 'Potri.002G215600' => 'ptr', 'Potri.008G201600' => 'ptr', 'Potri.014G138400' => 'ptr', 'Potri.016G142500' => 'ptr', 'Pp3c16_10580' => 'ppa', 'Pp3c5_25280' => 'ppa', 'Prupe.1G150000' => 'ppe', 'Prupe.1G150100' => 'ppe', 'Prupe.6G299600' => 'ppe', 'Prupe.8G245000' => 'ppe', 'Psat0s4927g0040' => 'psa', 'Psat1g052080' => 'psa', 'Psat1g183800' => 'psa', 'Psat3g113840' => 'psa', 'Psat3g126120' => 'psa', 'Psat3g126160' => 'psa', 'Psat3g158760' => 'psa', 'Psat3g158840' => 'psa', 'PSO170G2858' => 'pso', 'PSO339G0606' => 'pso', 'PSO384G4709' => 'pso', 'PSO407G0334' => 'pso', 'QL04p040276' => 'qlo', 'QL06p005458' => 'qlo', 'QL06p005472' => 'qlo', 'QL07p030546' => 'qlo', 'QL07p031519' => 'qlo', 'QL09p050949' => 'qlo', 'QL09p050966' => 'qlo', 'QL09p051067' => 'qlo', 'QL12p022706' => 'qlo', 'RcHm_v2.0_Chr2g0119601' => 'rch', 'RcHm_v2.0_Chr3g0459591' => 'rch', 'RcHm_v2.0_Chr4g0418521' => 'rch', 'RcHm_v2.0_Chr4g0418531' => 'rch', 'RcHm_v2.0_Chr4g0418541' => 'rch', 'RcHm_v2.0_Chr6g0291641' => 'rch', 'Rhsim01G0086300' => 'rsi', 'Rhsim01G0276300' => 'rsi', 'Rhsim01G0276500' => 'rsi', 'Rhsim04G0207700' => 'rsi', 'Rhsim05G0234500' => 'rsi', 'Rhsim13G0022400' => 'rsi', 'Sabra02G0167900' => 'sbr', 'Sabra04G0158500' => 'sbr', 'Sabra08G0159800' => 'sbr', 'Sabra10G0011500' => 'sbr', 'Sabra14G0104400' => 'sbr', 'SalBow2G2440' => 'sbo', 'SalBow4G2265' => 'sbo', 'Sc02g0000060' => 'sci', 'Sc05g0005020' => 'sci', 'Sc13g0003890' => 'sci', 'Sed0014865' => 'sed', 'Sed0017224' => 'sed', 'Sed0026391' => 'sed', 'SEGI_00063' => 'sgi', 'SEGI_10967' => 'sgi', 'SEGI_17510' => 'sgi', 'SEGI_24396' => 'sgi', 'SEGI_39719' => 'sgi', 'SEGI_41392' => 'sgi', 'SGA_v2.0_scaffold11G05794' => 'sas', 'SGA_v2.0_scaffold142G35607' => 'sas', 'SGA_v2.0_scaffold1G00447' => 'sas', 'SHI15388' => 'shi', 'SHI15394' => 'shi', 'SHI15396' => 'shi', 'SHI15399' => 'shi', 'SMO343G0151' => 'smo', 'SMO367G1118' => 'smo', 'Solyc01g080200.3' => 'sly', 'Solyc06g008960.3' => 'sly', 'Solyc09g064780.3' => 'sly', 'Sopen01g031980' => 'spe', 'Sopen06g003710' => 'spe', 'Sopen09g026460' => 'spe', 'Sp3g21240' => 'spa', 'Sp4g30030' => 'spa', 'TAR365G0022' => 'tar', 'TAR365G1023' => 'tar', 'TAR365G1253' => 'tar', 'TAR623G0078' => 'tar', 'TAR623G1721' => 'tar', 'TAR633G0959' => 'tar', 'THA.LOC104802225' => 'tha', 'THA.LOC104804769' => 'tha', 'THA.LOC104808660' => 'tha', 'THA.LOC104812792' => 'tha', 'Thecc.01G284000' => 'tca', 'Thecc.04G220600' => 'tca', 'Thecc.05G268900' => 'tca', 'Thecc.08G171100' => 'tca', 'Thhalv10001284m.g' => 'esa', 'Thhalv10019912m.g' => 'esa', 'TPR.G14189' => 'tpr', 'TPR.G18110' => 'tpr', 'TPR.G18130' => 'tpr', 'TPR.G18131' => 'tpr', 'TPR.G18140' => 'tpr', 'TPR.G24282' => 'tpr', 'TPR.G25221' => 'tpr', 'TPR.G29267' => 'tpr', 'TPR.G35315' => 'tpr', 'TPR.G36173' => 'tpr', 'TWI09G0794' => 'twi', 'TWI59G1348' => 'twi', 'TWI74G0430' => 'twi', 'unitig_26.g8940' => 'ugi', 'unitig_749.g13744' => 'ugi', 'unitig_749.g13745' => 'ugi', 'vmacro08269' => 'vma', 'vmacro14937' => 'vma', 'vmacro20401' => 'vma', 'VMungo0464G1349' => 'vmu', 'VMungo0540G0289' => 'vmu', 'VMungo1215G1590' => 'vmu', 'VMungo1309G0221' => 'vmu', 'VMungo1309G2815' => 'vmu', 'VMungo1383G0239' => 'vmu', 'VMungo1383G2910' => 'vmu', 'Zm00001eb095270' => 'zma', 'Zm00001eb095280' => 'zma', 'Zm00001eb111630' => 'zma', 'Zm00001eb237080' => 'zma', 'Zm00001eb273740' => 'zma', 'Zm00001eb285040' => 'zma', 'Zm00001eb330790' => 'zma', 'Zm00001eb337380' => 'zma' ), 'gf_id' => 'HOM05D001484', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001484' ), 'data_identifier' => 'HOM05D001484', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001484', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p31500' => 'bna', 'A05p00020' => 'bna', 'A07p08820' => 'bna', 'Aa31LG4G3300' => 'aar', 'Aa31LG8G10030' => 'aar', 'Actinidia00731' => 'ach', 'Actinidia11473' => 'ach', 'Actinidia23469' => 'ach', 'Actinidia24318' => 'ach', 'Actinidia40196' => 'ach', 'Actinidia40197' => 'ach', 'Actinidia40198' => 'ach', 'Ah.08g212990' => 'amhyb', 'Ah.15g091720' => 'amhyb', 'AL3G38260' => 'aly', 'AL4G47710' => 'aly', 'Aqoxy2G00671' => 'aox', 'Aqoxy2G03236' => 'aox', 'arahy.Tifrunner.gnm1.ann1.05IDCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KR684' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATY3SJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK6QJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6APGL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IDT7Z9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM073U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ0R87' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LE7RV4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT4QRX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V5ENPK' => 'arhy', 'AT2G48110' => 'ath', 'AT3G23590' => 'ath', 'ATR0626G186' => 'atr', 'ATR1127G141' => 'atr', 'Atru.chr4.2583' => 'acertr', 'Atru.chr5.1358' => 'acertr', 'Atru.chr5.1359' => 'acertr', 'Atru.chr8.46' => 'acertr', 'AUR62002640' => 'cqu', 'AUR62030055' => 'cqu', 'AUR62033713' => 'cqu', 'AUR62033714' => 'cqu', 'AUR62036795' => 'cqu', 'AUR62039891' => 'cqu', 'BcaB02g08737' => 'bca', 'BcaB04g20441' => 'bca', 'BcaB06g26509' => 'bca', 'BcaB06g26510' => 'bca', 'BcaB06g26511' => 'bca', 'BcaB06g26512' => 'bca', 'BcaB06g26513' => 'bca', 'BcaC02g12564' => 'bca', 'BcaC02g12565' => 'bca', 'BcaC02g12794' => 'bca', 'BcaC02g12795' => 'bca', 'BcaC02g12796' => 'bca', 'BcaC06g35541' => 'bca', 'BNapus_Darmor_BZH_scaffold_188p00080' => 'bna', 'BNapus_Darmor_BZH_scaffold_188p00090' => 'bna', 'BolC1t03972H' => 'bol', 'BolC1t03973H' => 'bol', 'BolC4t21680H' => 'bol', 'BolC7t41863H' => 'bol', 'BolSC55t61227H' => 'bol', 'BolSC55t61228H' => 'bol', 'BraA01t03278Z' => 'bra', 'BraA05t18998Z' => 'bra', 'BraA07t28673Z' => 'bra', 'C01p40150' => 'bna', 'C05p12370' => 'bna', 'C07p13680' => 'bna', 'CAN.G1006.16' => 'can', 'CAN.G1006.17' => 'can', 'CAN.G1170.2' => 'can', 'CAN.G962.7' => 'can', 'CANSAT25G2179' => 'cansat', 'CANSAT78G1573' => 'cansat', 'CARHR099510' => 'chi', 'CARHR143510' => 'chi', 'Carub.0003s2380' => 'cru', 'Carub.0004s3082' => 'cru', 'Ca_00614_v3' => 'car', 'Ca_07801_v3' => 'car', 'Ca_08567_v3' => 'car', 'Ca_09571_v3' => 'car', 'CBR_g19290' => 'cbr', 'Cc01_g19770' => 'ccan', 'Cc03_g03030' => 'ccan', 'CDE07G0968' => 'cde', 'CDE09G1441' => 'cde', 'Cfa006103' => 'cfa', 'Cfa015573' => 'cfa', 'Cfa016988' => 'cfa', 'Ciclev10006738m.g' => 'ccl', 'Ciclev10010920m.g' => 'ccl', 'Ciclev10018517m.g' => 'ccl', 'CiPaw.01G159200' => 'cil', 'CiPaw.02G091000' => 'cil', 'CiPaw.02G091100' => 'cil', 'CiPaw.08G103100' => 'cil', 'CiPaw.09G224900' => 'cil', 'ClCG06G005740' => 'cla', 'ClCG07G000090' => 'cla', 'ClCG07G000100' => 'cla', 'COL.COLO4_09143' => 'col', 'COL.COLO4_25124' => 'col', 'Cpa.g.sc16.34' => 'cpa', 'Cpa.g.sc3504.1' => 'cpa', 'Cpa.g.sc60.37' => 'cpa', 'CsaV3_6G018520' => 'csa', 'CsaV3_6G036860' => 'csa', 'CSS0001072' => 'camsi', 'CSS0020208' => 'camsi', 'CSS0021253' => 'camsi', 'CSS0022190' => 'camsi', 'CSS0036150' => 'camsi', 'CSS0040442' => 'camsi', 'CSS0042300' => 'camsi', 'CSS0045298' => 'camsi', 'DCAR_012449' => 'dca', 'DCAR_018405' => 'dca', 'DCAR_024573' => 'dca', 'DCAR_030591' => 'dca', 'Dinv16926' => 'din', 'Dinv32963' => 'din', 'Dinv38382' => 'din', 'Dinv38383' => 'din', 'Duzib133G0974' => 'dzi', 'Duzib138G1867' => 'dzi', 'Duzib211G0420' => 'dzi', 'Duzib212G0930' => 'dzi', 'ECA234G1645' => 'eca', 'ECA247G3467' => 'eca', 'ECA248G1703' => 'eca', 'EL10Ac3g06327' => 'bvu', 'EL10Ac7g17204' => 'bvu', 'Eucgr.A00855' => 'egr', 'Eucgr.A00858' => 'egr', 'Eucgr.H01520' => 'egr', 'Eucgr.H03604' => 'egr', 'Eucgr.L03465' => 'egr', 'Eucgr.L03466' => 'egr', 'FAN01G0988' => 'fan', 'FAN02G3892' => 'fan', 'FAN05G3381' => 'fan', 'FAN07G0967' => 'fan', 'FAN07G1493' => 'fan', 'FAN08G3125' => 'fan', 'FAN09G0402' => 'fan', 'FAN12G2594' => 'fan', 'FAN12G3879' => 'fan', 'FAN14G1546' => 'fan', 'FAN15G3626' => 'fan', 'FAN17G0588' => 'fan', 'FAN17G0609' => 'fan', 'FAN18G2817' => 'fan', 'FAN19G1305' => 'fan', 'FAN20G1787' => 'fan', 'FAN22G0073' => 'fan', 'FAN22G0352' => 'fan', 'FAN22G0368' => 'fan', 'FAN22G2273' => 'fan', 'FAN24G1998' => 'fan', 'FAN27G1317' => 'fan', 'FvH4_2g23980' => 'fve', 'FvH4_4g14380' => 'fve', 'FvH4_4g14390' => 'fve', 'FvH4_6g09250' => 'fve', 'Glyma.03G151100' => 'gma', 'Glyma.04G122550' => 'gma', 'Glyma.05G001600' => 'gma', 'Glyma.09G270766' => 'gma', 'Glyma.09G270832' => 'gma', 'Glyma.13G209800' => 'gma', 'Glyma.15G102800' => 'gma', 'Glyma.18G218900' => 'gma', 'Glyma.19G001500' => 'gma', 'Glyma.19G153600' => 'gma', 'Gohir.A02G028600' => 'ghi', 'Gohir.A08G045000' => 'ghi', 'Gohir.A11G120500' => 'ghi', 'Gohir.A12G006200' => 'ghi', 'Gohir.A12G006250' => 'ghi', 'Gohir.D02G036300' => 'ghi', 'Gohir.D08G054700' => 'ghi', 'Gohir.D11G125600' => 'ghi', 'Gohir.D12G005700' => 'ghi', 'Gorai.004G055200' => 'gra', 'Gorai.005G040400' => 'gra', 'Gorai.007G134500' => 'gra', 'Gorai.008G005500' => 'gra', 'GSVIVG01011094001' => 'vvi', 'GSVIVG01017879001' => 'vvi', 'GSVIVG01025988001' => 'vvi', 'GSVIVG01029847001' => 'vvi', 'HanXRQChr10g0282901' => 'han', 'HanXRQChr10g0310371' => 'han', 'HanXRQChr10g0315041' => 'han', 'HanXRQChr11g0327651' => 'han', 'HanXRQChr12g0359391' => 'han', 'Haze_00972' => 'cav', 'Haze_00973' => 'cav', 'Haze_00974' => 'cav', 'Haze_04747' => 'cav', 'Haze_04749' => 'cav', 'Haze_04750' => 'cav', 'Haze_21217' => 'cav', 'Hma1.2p1_1037F.1_g250680' => 'hma', 'Hma1.2p1_1644F.1_g295320' => 'hma', 'HPP92_011322' => 'vpl', 'HPP92_011323' => 'vpl', 'HPP92_011324' => 'vpl', 'HPP92_011325' => 'vpl', 'HPP92_011326' => 'vpl', 'Hund12205' => 'sun', 'Hund17957' => 'sun', 'Lalb_Chr06g0176771' => 'lal', 'Lalb_Chr18g0056021' => 'lal', 'Lalb_Chr18g0056031' => 'lal', 'Lalb_Chr18g0056041' => 'lal', 'Lalb_Chr20g0107751' => 'lal', 'Lalb_Chr20g0118371' => 'lal', 'Lj1g0010239' => 'lja', 'Lj1g0017101' => 'lja', 'Lj2A1178G40' => 'lonja', 'Lj2A54G84' => 'lonja', 'Lj2g0015248' => 'lja', 'Lj3A761T51' => 'lonja', 'Lj6g0018116' => 'lja', 'Lsat_1_v5_gn_4_136040' => 'lsa', 'Lsat_1_v5_gn_5_187461' => 'lsa', 'Lsat_1_v5_gn_5_77001' => 'lsa', 'Lsat_1_v5_gn_9_4461' => 'lsa', 'Manes.01G210100' => 'mes', 'Manes.03G185600' => 'mes', 'Manes.05G073300' => 'mes', 'Manes.09G120300' => 'mes', 'Manes.15G022100' => 'mes', 'Mapoly0096s0053' => 'mpo', 'MBI03_g14058_MAGBIO' => 'mbi', 'MBI03_g33876_MAGBIO' => 'mbi', 'MBI03_g36854_MAGBIO' => 'mbi', 'MBI17_g11997_MAGBIO' => 'mbi', 'MD03G1269000' => 'mdo', 'MD04G1179600' => 'mdo', 'MD11G1289800' => 'mdo', 'MD12G1194700' => 'mdo', 'MD13G1182100' => 'mdo', 'MD13G1182200' => 'mdo', 'MD16G1182600' => 'mdo', 'Medtr2g021400' => 'mtr', 'Medtr2g021470' => 'mtr', 'Medtr2g105810' => 'mtr', 'Medtr3g033580' => 'mtr', 'Medtr6g007970' => 'mtr', 'Medtr7g056330' => 'mtr', 'Medtr7g074290' => 'mtr', 'Medtr7g074380' => 'mtr', 'Medtr7g094550' => 'mtr', 'Medtr8g069995' => 'mtr', 'MELO3C014345.2' => 'cme', 'MELO3C021395.2' => 'cme', 'Migut.D00262' => 'egut', 'Migut.G00257' => 'egut', 'MSTRG.21575' => 'ama', 'MSTRG.3985' => 'ama', 'Nitab4.5_0000295g0140' => 'nta', 'Nitab4.5_0000732g0140' => 'nta', 'Nitab4.5_0003162g0020' => 'nta', 'Nitab4.5_0006180g0090' => 'nta', 'Nitab4.5_0006390g0010' => 'nta', 'Nitab4.5_0007392g0040' => 'nta', 'Nn1g02140' => 'nnu', 'Nn4g26168' => 'nnu', 'Nn5g26754' => 'nnu', 'Oeu001433.1' => 'oeu', 'Oeu010299.2' => 'oeu', 'Oeu011171.1' => 'oeu', 'Oeu037675.1' => 'oeu', 'Oeu038359.1' => 'oeu', 'Oeu063834.1' => 'oeu', 'Oeu063835.1' => 'oeu', 'Os05g0312000' => 'osa', 'Os07g0211101' => 'osa', 'Os07g0211200' => 'osa', 'Os07g0681500' => 'osa', 'Peaxi162Scf00095g01015' => 'pax', 'Peaxi162Scf00104g00329' => 'pax', 'Peaxi162Scf00161g00137' => 'pax', 'PGR004G1665' => 'pgr', 'PGR031G2937' => 'pgr', 'PGR119G2145' => 'pgr', 'PGSC0003DMG400004351' => 'stu', 'PGSC0003DMG400014625' => 'stu', 'PGSC0003DMG401000943' => 'stu', 'Phvul.001G148600' => 'pvu', 'Phvul.004G001700' => 'pvu', 'Phvul.006G154900' => 'pvu', 'Phvul.008G078200' => 'pvu', 'Phvul.011G136500' => 'pvu', 'Potri.002G215600' => 'ptr', 'Potri.008G201600' => 'ptr', 'Potri.014G138400' => 'ptr', 'Potri.016G142500' => 'ptr', 'Pp3c16_10580' => 'ppa', 'Pp3c5_25280' => 'ppa', 'Prupe.1G150000' => 'ppe', 'Prupe.1G150100' => 'ppe', 'Prupe.6G299600' => 'ppe', 'Prupe.8G245000' => 'ppe', 'Psat0s4927g0040' => 'psa', 'Psat1g052080' => 'psa', 'Psat1g183800' => 'psa', 'Psat3g113840' => 'psa', 'Psat3g126120' => 'psa', 'Psat3g126160' => 'psa', 'Psat3g158760' => 'psa', 'Psat3g158840' => 'psa', 'PSO170G2858' => 'pso', 'PSO339G0606' => 'pso', 'PSO384G4709' => 'pso', 'PSO407G0334' => 'pso', 'QL04p040276' => 'qlo', 'QL06p005458' => 'qlo', 'QL06p005472' => 'qlo', 'QL07p030546' => 'qlo', 'QL07p031519' => 'qlo', 'QL09p050949' => 'qlo', 'QL09p050966' => 'qlo', 'QL09p051067' => 'qlo', 'QL12p022706' => 'qlo', 'RcHm_v2.0_Chr2g0119601' => 'rch', 'RcHm_v2.0_Chr3g0459591' => 'rch', 'RcHm_v2.0_Chr4g0418521' => 'rch', 'RcHm_v2.0_Chr4g0418531' => 'rch', 'RcHm_v2.0_Chr4g0418541' => 'rch', 'RcHm_v2.0_Chr6g0291641' => 'rch', 'Rhsim01G0086300' => 'rsi', 'Rhsim01G0276300' => 'rsi', 'Rhsim01G0276500' => 'rsi', 'Rhsim04G0207700' => 'rsi', 'Rhsim05G0234500' => 'rsi', 'Rhsim13G0022400' => 'rsi', 'Sabra02G0167900' => 'sbr', 'Sabra04G0158500' => 'sbr', 'Sabra08G0159800' => 'sbr', 'Sabra10G0011500' => 'sbr', 'Sabra14G0104400' => 'sbr', 'SalBow2G2440' => 'sbo', 'SalBow4G2265' => 'sbo', 'Sc02g0000060' => 'sci', 'Sc05g0005020' => 'sci', 'Sc13g0003890' => 'sci', 'Sed0014865' => 'sed', 'Sed0017224' => 'sed', 'Sed0026391' => 'sed', 'SEGI_00063' => 'sgi', 'SEGI_10967' => 'sgi', 'SEGI_17510' => 'sgi', 'SEGI_24396' => 'sgi', 'SEGI_39719' => 'sgi', 'SEGI_41392' => 'sgi', 'SGA_v2.0_scaffold11G05794' => 'sas', 'SGA_v2.0_scaffold142G35607' => 'sas', 'SGA_v2.0_scaffold1G00447' => 'sas', 'SHI15388' => 'shi', 'SHI15394' => 'shi', 'SHI15396' => 'shi', 'SHI15399' => 'shi', 'SMO343G0151' => 'smo', 'SMO367G1118' => 'smo', 'Solyc01g080200.3' => 'sly', 'Solyc06g008960.3' => 'sly', 'Solyc09g064780.3' => 'sly', 'Sopen01g031980' => 'spe', 'Sopen06g003710' => 'spe', 'Sopen09g026460' => 'spe', 'Sp3g21240' => 'spa', 'Sp4g30030' => 'spa', 'TAR365G0022' => 'tar', 'TAR365G1023' => 'tar', 'TAR365G1253' => 'tar', 'TAR623G0078' => 'tar', 'TAR623G1721' => 'tar', 'TAR633G0959' => 'tar', 'THA.LOC104802225' => 'tha', 'THA.LOC104804769' => 'tha', 'THA.LOC104808660' => 'tha', 'THA.LOC104812792' => 'tha', 'Thecc.01G284000' => 'tca', 'Thecc.04G220600' => 'tca', 'Thecc.05G268900' => 'tca', 'Thecc.08G171100' => 'tca', 'Thhalv10001284m.g' => 'esa', 'Thhalv10019912m.g' => 'esa', 'TPR.G14189' => 'tpr', 'TPR.G18110' => 'tpr', 'TPR.G18130' => 'tpr', 'TPR.G18131' => 'tpr', 'TPR.G18140' => 'tpr', 'TPR.G24282' => 'tpr', 'TPR.G25221' => 'tpr', 'TPR.G29267' => 'tpr', 'TPR.G35315' => 'tpr', 'TPR.G36173' => 'tpr', 'TWI09G0794' => 'twi', 'TWI59G1348' => 'twi', 'TWI74G0430' => 'twi', 'unitig_26.g8940' => 'ugi', 'unitig_749.g13744' => 'ugi', 'unitig_749.g13745' => 'ugi', 'vmacro08269' => 'vma', 'vmacro14937' => 'vma', 'vmacro20401' => 'vma', 'VMungo0464G1349' => 'vmu', 'VMungo0540G0289' => 'vmu', 'VMungo1215G1590' => 'vmu', 'VMungo1309G0221' => 'vmu', 'VMungo1309G2815' => 'vmu', 'VMungo1383G0239' => 'vmu', 'VMungo1383G2910' => 'vmu', 'Zm00001eb095270' => 'zma', 'Zm00001eb095280' => 'zma', 'Zm00001eb111630' => 'zma', 'Zm00001eb237080' => 'zma', 'Zm00001eb273740' => 'zma', 'Zm00001eb285040' => 'zma', 'Zm00001eb330790' => 'zma', 'Zm00001eb337380' => 'zma' ) $gf_id = 'HOM05D001484' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001484' ) $data_identifier = 'HOM05D001484' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 2, 'aly' => (int) 2, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 22, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 7, 'hma' => (int) 2, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 7, 'mtr' => (int) 10, 'cme' => (int) 2, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 4, 'ppa' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 4, 'qlo' => (int) 9, 'rch' => (int) 6, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 10, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 7, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb337380' $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' => 'HOM05D001484', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p31500' => 'bna', 'A05p00020' => 'bna', 'A07p08820' => 'bna', 'Aa31LG4G3300' => 'aar', 'Aa31LG8G10030' => 'aar', 'Actinidia00731' => 'ach', 'Actinidia11473' => 'ach', 'Actinidia23469' => 'ach', 'Actinidia24318' => 'ach', 'Actinidia40196' => 'ach', 'Actinidia40197' => 'ach', 'Actinidia40198' => 'ach', 'Ah.08g212990' => 'amhyb', 'Ah.15g091720' => 'amhyb', 'AL3G38260' => 'aly', 'AL4G47710' => 'aly', 'Aqoxy2G00671' => 'aox', 'Aqoxy2G03236' => 'aox', 'arahy.Tifrunner.gnm1.ann1.05IDCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KR684' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATY3SJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK6QJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6APGL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IDT7Z9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM073U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ0R87' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LE7RV4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT4QRX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V5ENPK' => 'arhy', 'AT2G48110' => 'ath', 'AT3G23590' => 'ath', 'ATR0626G186' => 'atr', 'ATR1127G141' => 'atr', 'Atru.chr4.2583' => 'acertr', 'Atru.chr5.1358' => 'acertr', 'Atru.chr5.1359' => 'acertr', 'Atru.chr8.46' => 'acertr', 'AUR62002640' => 'cqu', 'AUR62030055' => 'cqu', 'AUR62033713' => 'cqu', 'AUR62033714' => 'cqu', 'AUR62036795' => 'cqu', 'AUR62039891' => 'cqu', 'BcaB02g08737' => 'bca', 'BcaB04g20441' => 'bca', 'BcaB06g26509' => 'bca', 'BcaB06g26510' => 'bca', 'BcaB06g26511' => 'bca', 'BcaB06g26512' => 'bca', 'BcaB06g26513' => 'bca', 'BcaC02g12564' => 'bca', 'BcaC02g12565' => 'bca', 'BcaC02g12794' => 'bca', 'BcaC02g12795' => 'bca', 'BcaC02g12796' => 'bca', 'BcaC06g35541' => 'bca', 'BNapus_Darmor_BZH_scaffold_188p00080' => 'bna', 'BNapus_Darmor_BZH_scaffold_188p00090' => 'bna', 'BolC1t03972H' => 'bol', 'BolC1t03973H' => 'bol', 'BolC4t21680H' => 'bol', 'BolC7t41863H' => 'bol', 'BolSC55t61227H' => 'bol', 'BolSC55t61228H' => 'bol', 'BraA01t03278Z' => 'bra', 'BraA05t18998Z' => 'bra', 'BraA07t28673Z' => 'bra', 'C01p40150' => 'bna', 'C05p12370' => 'bna', 'C07p13680' => 'bna', 'CAN.G1006.16' => 'can', 'CAN.G1006.17' => 'can', 'CAN.G1170.2' => 'can', 'CAN.G962.7' => 'can', 'CANSAT25G2179' => 'cansat', 'CANSAT78G1573' => 'cansat', 'CARHR099510' => 'chi', 'CARHR143510' => 'chi', 'Carub.0003s2380' => 'cru', 'Carub.0004s3082' => 'cru', 'Ca_00614_v3' => 'car', 'Ca_07801_v3' => 'car', 'Ca_08567_v3' => 'car', 'Ca_09571_v3' => 'car', 'CBR_g19290' => 'cbr', 'Cc01_g19770' => 'ccan', 'Cc03_g03030' => 'ccan', 'CDE07G0968' => 'cde', 'CDE09G1441' => 'cde', 'Cfa006103' => 'cfa', 'Cfa015573' => 'cfa', 'Cfa016988' => 'cfa', 'Ciclev10006738m.g' => 'ccl', 'Ciclev10010920m.g' => 'ccl', 'Ciclev10018517m.g' => 'ccl', 'CiPaw.01G159200' => 'cil', 'CiPaw.02G091000' => 'cil', 'CiPaw.02G091100' => 'cil', 'CiPaw.08G103100' => 'cil', 'CiPaw.09G224900' => 'cil', 'ClCG06G005740' => 'cla', 'ClCG07G000090' => 'cla', 'ClCG07G000100' => 'cla', 'COL.COLO4_09143' => 'col', 'COL.COLO4_25124' => 'col', 'Cpa.g.sc16.34' => 'cpa', 'Cpa.g.sc3504.1' => 'cpa', 'Cpa.g.sc60.37' => 'cpa', 'CsaV3_6G018520' => 'csa', 'CsaV3_6G036860' => 'csa', 'CSS0001072' => 'camsi', 'CSS0020208' => 'camsi', 'CSS0021253' => 'camsi', 'CSS0022190' => 'camsi', 'CSS0036150' => 'camsi', 'CSS0040442' => 'camsi', 'CSS0042300' => 'camsi', 'CSS0045298' => 'camsi', 'DCAR_012449' => 'dca', 'DCAR_018405' => 'dca', 'DCAR_024573' => 'dca', 'DCAR_030591' => 'dca', 'Dinv16926' => 'din', 'Dinv32963' => 'din', 'Dinv38382' => 'din', 'Dinv38383' => 'din', 'Duzib133G0974' => 'dzi', 'Duzib138G1867' => 'dzi', 'Duzib211G0420' => 'dzi', 'Duzib212G0930' => 'dzi', 'ECA234G1645' => 'eca', 'ECA247G3467' => 'eca', 'ECA248G1703' => 'eca', 'EL10Ac3g06327' => 'bvu', 'EL10Ac7g17204' => 'bvu', 'Eucgr.A00855' => 'egr', 'Eucgr.A00858' => 'egr', 'Eucgr.H01520' => 'egr', 'Eucgr.H03604' => 'egr', 'Eucgr.L03465' => 'egr', 'Eucgr.L03466' => 'egr', 'FAN01G0988' => 'fan', 'FAN02G3892' => 'fan', 'FAN05G3381' => 'fan', 'FAN07G0967' => 'fan', 'FAN07G1493' => 'fan', 'FAN08G3125' => 'fan', 'FAN09G0402' => 'fan', 'FAN12G2594' => 'fan', 'FAN12G3879' => 'fan', 'FAN14G1546' => 'fan', 'FAN15G3626' => 'fan', 'FAN17G0588' => 'fan', 'FAN17G0609' => 'fan', 'FAN18G2817' => 'fan', 'FAN19G1305' => 'fan', 'FAN20G1787' => 'fan', 'FAN22G0073' => 'fan', 'FAN22G0352' => 'fan', 'FAN22G0368' => 'fan', 'FAN22G2273' => 'fan', 'FAN24G1998' => 'fan', 'FAN27G1317' => 'fan', 'FvH4_2g23980' => 'fve', 'FvH4_4g14380' => 'fve', 'FvH4_4g14390' => 'fve', 'FvH4_6g09250' => 'fve', 'Glyma.03G151100' => 'gma', 'Glyma.04G122550' => 'gma', 'Glyma.05G001600' => 'gma', 'Glyma.09G270766' => 'gma', 'Glyma.09G270832' => 'gma', 'Glyma.13G209800' => 'gma', 'Glyma.15G102800' => 'gma', 'Glyma.18G218900' => 'gma', 'Glyma.19G001500' => 'gma', 'Glyma.19G153600' => 'gma', 'Gohir.A02G028600' => 'ghi', 'Gohir.A08G045000' => 'ghi', 'Gohir.A11G120500' => 'ghi', 'Gohir.A12G006200' => 'ghi', 'Gohir.A12G006250' => 'ghi', 'Gohir.D02G036300' => 'ghi', 'Gohir.D08G054700' => 'ghi', 'Gohir.D11G125600' => 'ghi', 'Gohir.D12G005700' => 'ghi', 'Gorai.004G055200' => 'gra', 'Gorai.005G040400' => 'gra', 'Gorai.007G134500' => 'gra', 'Gorai.008G005500' => 'gra', 'GSVIVG01011094001' => 'vvi', 'GSVIVG01017879001' => 'vvi', 'GSVIVG01025988001' => 'vvi', 'GSVIVG01029847001' => 'vvi', 'HanXRQChr10g0282901' => 'han', 'HanXRQChr10g0310371' => 'han', 'HanXRQChr10g0315041' => 'han', 'HanXRQChr11g0327651' => 'han', 'HanXRQChr12g0359391' => 'han', 'Haze_00972' => 'cav', 'Haze_00973' => 'cav', 'Haze_00974' => 'cav', 'Haze_04747' => 'cav', 'Haze_04749' => 'cav', 'Haze_04750' => 'cav', 'Haze_21217' => 'cav', 'Hma1.2p1_1037F.1_g250680' => 'hma', 'Hma1.2p1_1644F.1_g295320' => 'hma', 'HPP92_011322' => 'vpl', 'HPP92_011323' => 'vpl', 'HPP92_011324' => 'vpl', 'HPP92_011325' => 'vpl', 'HPP92_011326' => 'vpl', 'Hund12205' => 'sun', 'Hund17957' => 'sun', 'Lalb_Chr06g0176771' => 'lal', 'Lalb_Chr18g0056021' => 'lal', 'Lalb_Chr18g0056031' => 'lal', 'Lalb_Chr18g0056041' => 'lal', 'Lalb_Chr20g0107751' => 'lal', 'Lalb_Chr20g0118371' => 'lal', 'Lj1g0010239' => 'lja', 'Lj1g0017101' => 'lja', 'Lj2A1178G40' => 'lonja', 'Lj2A54G84' => 'lonja', 'Lj2g0015248' => 'lja', 'Lj3A761T51' => 'lonja', 'Lj6g0018116' => 'lja', 'Lsat_1_v5_gn_4_136040' => 'lsa', 'Lsat_1_v5_gn_5_187461' => 'lsa', 'Lsat_1_v5_gn_5_77001' => 'lsa', 'Lsat_1_v5_gn_9_4461' => 'lsa', 'Manes.01G210100' => 'mes', 'Manes.03G185600' => 'mes', 'Manes.05G073300' => 'mes', 'Manes.09G120300' => 'mes', 'Manes.15G022100' => 'mes', 'Mapoly0096s0053' => 'mpo', 'MBI03_g14058_MAGBIO' => 'mbi', 'MBI03_g33876_MAGBIO' => 'mbi', 'MBI03_g36854_MAGBIO' => 'mbi', 'MBI17_g11997_MAGBIO' => 'mbi', 'MD03G1269000' => 'mdo', 'MD04G1179600' => 'mdo', 'MD11G1289800' => 'mdo', 'MD12G1194700' => 'mdo', 'MD13G1182100' => 'mdo', 'MD13G1182200' => 'mdo', 'MD16G1182600' => 'mdo', 'Medtr2g021400' => 'mtr', 'Medtr2g021470' => 'mtr', 'Medtr2g105810' => 'mtr', 'Medtr3g033580' => 'mtr', 'Medtr6g007970' => 'mtr', 'Medtr7g056330' => 'mtr', 'Medtr7g074290' => 'mtr', 'Medtr7g074380' => 'mtr', 'Medtr7g094550' => 'mtr', 'Medtr8g069995' => 'mtr', 'MELO3C014345.2' => 'cme', 'MELO3C021395.2' => 'cme', 'Migut.D00262' => 'egut', 'Migut.G00257' => 'egut', 'MSTRG.21575' => 'ama', 'MSTRG.3985' => 'ama', 'Nitab4.5_0000295g0140' => 'nta', 'Nitab4.5_0000732g0140' => 'nta', 'Nitab4.5_0003162g0020' => 'nta', 'Nitab4.5_0006180g0090' => 'nta', 'Nitab4.5_0006390g0010' => 'nta', 'Nitab4.5_0007392g0040' => 'nta', 'Nn1g02140' => 'nnu', 'Nn4g26168' => 'nnu', 'Nn5g26754' => 'nnu', 'Oeu001433.1' => 'oeu', 'Oeu010299.2' => 'oeu', 'Oeu011171.1' => 'oeu', 'Oeu037675.1' => 'oeu', 'Oeu038359.1' => 'oeu', 'Oeu063834.1' => 'oeu', 'Oeu063835.1' => 'oeu', 'Os05g0312000' => 'osa', 'Os07g0211101' => 'osa', 'Os07g0211200' => 'osa', 'Os07g0681500' => 'osa', 'Peaxi162Scf00095g01015' => 'pax', 'Peaxi162Scf00104g00329' => 'pax', 'Peaxi162Scf00161g00137' => 'pax', 'PGR004G1665' => 'pgr', 'PGR031G2937' => 'pgr', 'PGR119G2145' => 'pgr', 'PGSC0003DMG400004351' => 'stu', 'PGSC0003DMG400014625' => 'stu', 'PGSC0003DMG401000943' => 'stu', 'Phvul.001G148600' => 'pvu', 'Phvul.004G001700' => 'pvu', 'Phvul.006G154900' => 'pvu', 'Phvul.008G078200' => 'pvu', 'Phvul.011G136500' => 'pvu', 'Potri.002G215600' => 'ptr', 'Potri.008G201600' => 'ptr', 'Potri.014G138400' => 'ptr', 'Potri.016G142500' => 'ptr', 'Pp3c16_10580' => 'ppa', 'Pp3c5_25280' => 'ppa', 'Prupe.1G150000' => 'ppe', 'Prupe.1G150100' => 'ppe', 'Prupe.6G299600' => 'ppe', 'Prupe.8G245000' => 'ppe', 'Psat0s4927g0040' => 'psa', 'Psat1g052080' => 'psa', 'Psat1g183800' => 'psa', 'Psat3g113840' => 'psa', 'Psat3g126120' => 'psa', 'Psat3g126160' => 'psa', 'Psat3g158760' => 'psa', 'Psat3g158840' => 'psa', 'PSO170G2858' => 'pso', 'PSO339G0606' => 'pso', 'PSO384G4709' => 'pso', 'PSO407G0334' => 'pso', 'QL04p040276' => 'qlo', 'QL06p005458' => 'qlo', 'QL06p005472' => 'qlo', 'QL07p030546' => 'qlo', 'QL07p031519' => 'qlo', 'QL09p050949' => 'qlo', 'QL09p050966' => 'qlo', 'QL09p051067' => 'qlo', 'QL12p022706' => 'qlo', 'RcHm_v2.0_Chr2g0119601' => 'rch', 'RcHm_v2.0_Chr3g0459591' => 'rch', 'RcHm_v2.0_Chr4g0418521' => 'rch', 'RcHm_v2.0_Chr4g0418531' => 'rch', 'RcHm_v2.0_Chr4g0418541' => 'rch', 'RcHm_v2.0_Chr6g0291641' => 'rch', 'Rhsim01G0086300' => 'rsi', 'Rhsim01G0276300' => 'rsi', 'Rhsim01G0276500' => 'rsi', 'Rhsim04G0207700' => 'rsi', 'Rhsim05G0234500' => 'rsi', 'Rhsim13G0022400' => 'rsi', 'Sabra02G0167900' => 'sbr', 'Sabra04G0158500' => 'sbr', 'Sabra08G0159800' => 'sbr', 'Sabra10G0011500' => 'sbr', 'Sabra14G0104400' => 'sbr', 'SalBow2G2440' => 'sbo', 'SalBow4G2265' => 'sbo', 'Sc02g0000060' => 'sci', 'Sc05g0005020' => 'sci', 'Sc13g0003890' => 'sci', 'Sed0014865' => 'sed', 'Sed0017224' => 'sed', 'Sed0026391' => 'sed', 'SEGI_00063' => 'sgi', 'SEGI_10967' => 'sgi', 'SEGI_17510' => 'sgi', 'SEGI_24396' => 'sgi', 'SEGI_39719' => 'sgi', 'SEGI_41392' => 'sgi', 'SGA_v2.0_scaffold11G05794' => 'sas', 'SGA_v2.0_scaffold142G35607' => 'sas', 'SGA_v2.0_scaffold1G00447' => 'sas', 'SHI15388' => 'shi', 'SHI15394' => 'shi', 'SHI15396' => 'shi', 'SHI15399' => 'shi', 'SMO343G0151' => 'smo', 'SMO367G1118' => 'smo', 'Solyc01g080200.3' => 'sly', 'Solyc06g008960.3' => 'sly', 'Solyc09g064780.3' => 'sly', 'Sopen01g031980' => 'spe', 'Sopen06g003710' => 'spe', 'Sopen09g026460' => 'spe', 'Sp3g21240' => 'spa', 'Sp4g30030' => 'spa', 'TAR365G0022' => 'tar', 'TAR365G1023' => 'tar', 'TAR365G1253' => 'tar', 'TAR623G0078' => 'tar', 'TAR623G1721' => 'tar', 'TAR633G0959' => 'tar', 'THA.LOC104802225' => 'tha', 'THA.LOC104804769' => 'tha', 'THA.LOC104808660' => 'tha', 'THA.LOC104812792' => 'tha', 'Thecc.01G284000' => 'tca', 'Thecc.04G220600' => 'tca', 'Thecc.05G268900' => 'tca', 'Thecc.08G171100' => 'tca', 'Thhalv10001284m.g' => 'esa', 'Thhalv10019912m.g' => 'esa', 'TPR.G14189' => 'tpr', 'TPR.G18110' => 'tpr', 'TPR.G18130' => 'tpr', 'TPR.G18131' => 'tpr', 'TPR.G18140' => 'tpr', 'TPR.G24282' => 'tpr', 'TPR.G25221' => 'tpr', 'TPR.G29267' => 'tpr', 'TPR.G35315' => 'tpr', 'TPR.G36173' => 'tpr', 'TWI09G0794' => 'twi', 'TWI59G1348' => 'twi', 'TWI74G0430' => 'twi', 'unitig_26.g8940' => 'ugi', 'unitig_749.g13744' => 'ugi', 'unitig_749.g13745' => 'ugi', 'vmacro08269' => 'vma', 'vmacro14937' => 'vma', 'vmacro20401' => 'vma', 'VMungo0464G1349' => 'vmu', 'VMungo0540G0289' => 'vmu', 'VMungo1215G1590' => 'vmu', 'VMungo1309G0221' => 'vmu', 'VMungo1309G2815' => 'vmu', 'VMungo1383G0239' => 'vmu', 'VMungo1383G2910' => 'vmu', 'Zm00001eb095270' => 'zma', 'Zm00001eb095280' => 'zma', 'Zm00001eb111630' => 'zma', 'Zm00001eb237080' => 'zma', 'Zm00001eb273740' => 'zma', 'Zm00001eb285040' => 'zma', 'Zm00001eb330790' => 'zma', 'Zm00001eb337380' => 'zma' ), 'gf_id' => 'HOM05D001484', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001484' ), 'data_identifier' => 'HOM05D001484', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001484', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p31500' => 'bna', 'A05p00020' => 'bna', 'A07p08820' => 'bna', 'Aa31LG4G3300' => 'aar', 'Aa31LG8G10030' => 'aar', 'Actinidia00731' => 'ach', 'Actinidia11473' => 'ach', 'Actinidia23469' => 'ach', 'Actinidia24318' => 'ach', 'Actinidia40196' => 'ach', 'Actinidia40197' => 'ach', 'Actinidia40198' => 'ach', 'Ah.08g212990' => 'amhyb', 'Ah.15g091720' => 'amhyb', 'AL3G38260' => 'aly', 'AL4G47710' => 'aly', 'Aqoxy2G00671' => 'aox', 'Aqoxy2G03236' => 'aox', 'arahy.Tifrunner.gnm1.ann1.05IDCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KR684' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATY3SJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK6QJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6APGL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IDT7Z9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM073U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ0R87' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LE7RV4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT4QRX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V5ENPK' => 'arhy', 'AT2G48110' => 'ath', 'AT3G23590' => 'ath', 'ATR0626G186' => 'atr', 'ATR1127G141' => 'atr', 'Atru.chr4.2583' => 'acertr', 'Atru.chr5.1358' => 'acertr', 'Atru.chr5.1359' => 'acertr', 'Atru.chr8.46' => 'acertr', 'AUR62002640' => 'cqu', 'AUR62030055' => 'cqu', 'AUR62033713' => 'cqu', 'AUR62033714' => 'cqu', 'AUR62036795' => 'cqu', 'AUR62039891' => 'cqu', 'BcaB02g08737' => 'bca', 'BcaB04g20441' => 'bca', 'BcaB06g26509' => 'bca', 'BcaB06g26510' => 'bca', 'BcaB06g26511' => 'bca', 'BcaB06g26512' => 'bca', 'BcaB06g26513' => 'bca', 'BcaC02g12564' => 'bca', 'BcaC02g12565' => 'bca', 'BcaC02g12794' => 'bca', 'BcaC02g12795' => 'bca', 'BcaC02g12796' => 'bca', 'BcaC06g35541' => 'bca', 'BNapus_Darmor_BZH_scaffold_188p00080' => 'bna', 'BNapus_Darmor_BZH_scaffold_188p00090' => 'bna', 'BolC1t03972H' => 'bol', 'BolC1t03973H' => 'bol', 'BolC4t21680H' => 'bol', 'BolC7t41863H' => 'bol', 'BolSC55t61227H' => 'bol', 'BolSC55t61228H' => 'bol', 'BraA01t03278Z' => 'bra', 'BraA05t18998Z' => 'bra', 'BraA07t28673Z' => 'bra', 'C01p40150' => 'bna', 'C05p12370' => 'bna', 'C07p13680' => 'bna', 'CAN.G1006.16' => 'can', 'CAN.G1006.17' => 'can', 'CAN.G1170.2' => 'can', 'CAN.G962.7' => 'can', 'CANSAT25G2179' => 'cansat', 'CANSAT78G1573' => 'cansat', 'CARHR099510' => 'chi', 'CARHR143510' => 'chi', 'Carub.0003s2380' => 'cru', 'Carub.0004s3082' => 'cru', 'Ca_00614_v3' => 'car', 'Ca_07801_v3' => 'car', 'Ca_08567_v3' => 'car', 'Ca_09571_v3' => 'car', 'CBR_g19290' => 'cbr', 'Cc01_g19770' => 'ccan', 'Cc03_g03030' => 'ccan', 'CDE07G0968' => 'cde', 'CDE09G1441' => 'cde', 'Cfa006103' => 'cfa', 'Cfa015573' => 'cfa', 'Cfa016988' => 'cfa', 'Ciclev10006738m.g' => 'ccl', 'Ciclev10010920m.g' => 'ccl', 'Ciclev10018517m.g' => 'ccl', 'CiPaw.01G159200' => 'cil', 'CiPaw.02G091000' => 'cil', 'CiPaw.02G091100' => 'cil', 'CiPaw.08G103100' => 'cil', 'CiPaw.09G224900' => 'cil', 'ClCG06G005740' => 'cla', 'ClCG07G000090' => 'cla', 'ClCG07G000100' => 'cla', 'COL.COLO4_09143' => 'col', 'COL.COLO4_25124' => 'col', 'Cpa.g.sc16.34' => 'cpa', 'Cpa.g.sc3504.1' => 'cpa', 'Cpa.g.sc60.37' => 'cpa', 'CsaV3_6G018520' => 'csa', 'CsaV3_6G036860' => 'csa', 'CSS0001072' => 'camsi', 'CSS0020208' => 'camsi', 'CSS0021253' => 'camsi', 'CSS0022190' => 'camsi', 'CSS0036150' => 'camsi', 'CSS0040442' => 'camsi', 'CSS0042300' => 'camsi', 'CSS0045298' => 'camsi', 'DCAR_012449' => 'dca', 'DCAR_018405' => 'dca', 'DCAR_024573' => 'dca', 'DCAR_030591' => 'dca', 'Dinv16926' => 'din', 'Dinv32963' => 'din', 'Dinv38382' => 'din', 'Dinv38383' => 'din', 'Duzib133G0974' => 'dzi', 'Duzib138G1867' => 'dzi', 'Duzib211G0420' => 'dzi', 'Duzib212G0930' => 'dzi', 'ECA234G1645' => 'eca', 'ECA247G3467' => 'eca', 'ECA248G1703' => 'eca', 'EL10Ac3g06327' => 'bvu', 'EL10Ac7g17204' => 'bvu', 'Eucgr.A00855' => 'egr', 'Eucgr.A00858' => 'egr', 'Eucgr.H01520' => 'egr', 'Eucgr.H03604' => 'egr', 'Eucgr.L03465' => 'egr', 'Eucgr.L03466' => 'egr', 'FAN01G0988' => 'fan', 'FAN02G3892' => 'fan', 'FAN05G3381' => 'fan', 'FAN07G0967' => 'fan', 'FAN07G1493' => 'fan', 'FAN08G3125' => 'fan', 'FAN09G0402' => 'fan', 'FAN12G2594' => 'fan', 'FAN12G3879' => 'fan', 'FAN14G1546' => 'fan', 'FAN15G3626' => 'fan', 'FAN17G0588' => 'fan', 'FAN17G0609' => 'fan', 'FAN18G2817' => 'fan', 'FAN19G1305' => 'fan', 'FAN20G1787' => 'fan', 'FAN22G0073' => 'fan', 'FAN22G0352' => 'fan', 'FAN22G0368' => 'fan', 'FAN22G2273' => 'fan', 'FAN24G1998' => 'fan', 'FAN27G1317' => 'fan', 'FvH4_2g23980' => 'fve', 'FvH4_4g14380' => 'fve', 'FvH4_4g14390' => 'fve', 'FvH4_6g09250' => 'fve', 'Glyma.03G151100' => 'gma', 'Glyma.04G122550' => 'gma', 'Glyma.05G001600' => 'gma', 'Glyma.09G270766' => 'gma', 'Glyma.09G270832' => 'gma', 'Glyma.13G209800' => 'gma', 'Glyma.15G102800' => 'gma', 'Glyma.18G218900' => 'gma', 'Glyma.19G001500' => 'gma', 'Glyma.19G153600' => 'gma', 'Gohir.A02G028600' => 'ghi', 'Gohir.A08G045000' => 'ghi', 'Gohir.A11G120500' => 'ghi', 'Gohir.A12G006200' => 'ghi', 'Gohir.A12G006250' => 'ghi', 'Gohir.D02G036300' => 'ghi', 'Gohir.D08G054700' => 'ghi', 'Gohir.D11G125600' => 'ghi', 'Gohir.D12G005700' => 'ghi', 'Gorai.004G055200' => 'gra', 'Gorai.005G040400' => 'gra', 'Gorai.007G134500' => 'gra', 'Gorai.008G005500' => 'gra', 'GSVIVG01011094001' => 'vvi', 'GSVIVG01017879001' => 'vvi', 'GSVIVG01025988001' => 'vvi', 'GSVIVG01029847001' => 'vvi', 'HanXRQChr10g0282901' => 'han', 'HanXRQChr10g0310371' => 'han', 'HanXRQChr10g0315041' => 'han', 'HanXRQChr11g0327651' => 'han', 'HanXRQChr12g0359391' => 'han', 'Haze_00972' => 'cav', 'Haze_00973' => 'cav', 'Haze_00974' => 'cav', 'Haze_04747' => 'cav', 'Haze_04749' => 'cav', 'Haze_04750' => 'cav', 'Haze_21217' => 'cav', 'Hma1.2p1_1037F.1_g250680' => 'hma', 'Hma1.2p1_1644F.1_g295320' => 'hma', 'HPP92_011322' => 'vpl', 'HPP92_011323' => 'vpl', 'HPP92_011324' => 'vpl', 'HPP92_011325' => 'vpl', 'HPP92_011326' => 'vpl', 'Hund12205' => 'sun', 'Hund17957' => 'sun', 'Lalb_Chr06g0176771' => 'lal', 'Lalb_Chr18g0056021' => 'lal', 'Lalb_Chr18g0056031' => 'lal', 'Lalb_Chr18g0056041' => 'lal', 'Lalb_Chr20g0107751' => 'lal', 'Lalb_Chr20g0118371' => 'lal', 'Lj1g0010239' => 'lja', 'Lj1g0017101' => 'lja', 'Lj2A1178G40' => 'lonja', 'Lj2A54G84' => 'lonja', 'Lj2g0015248' => 'lja', 'Lj3A761T51' => 'lonja', 'Lj6g0018116' => 'lja', 'Lsat_1_v5_gn_4_136040' => 'lsa', 'Lsat_1_v5_gn_5_187461' => 'lsa', 'Lsat_1_v5_gn_5_77001' => 'lsa', 'Lsat_1_v5_gn_9_4461' => 'lsa', 'Manes.01G210100' => 'mes', 'Manes.03G185600' => 'mes', 'Manes.05G073300' => 'mes', 'Manes.09G120300' => 'mes', 'Manes.15G022100' => 'mes', 'Mapoly0096s0053' => 'mpo', 'MBI03_g14058_MAGBIO' => 'mbi', 'MBI03_g33876_MAGBIO' => 'mbi', 'MBI03_g36854_MAGBIO' => 'mbi', 'MBI17_g11997_MAGBIO' => 'mbi', 'MD03G1269000' => 'mdo', 'MD04G1179600' => 'mdo', 'MD11G1289800' => 'mdo', 'MD12G1194700' => 'mdo', 'MD13G1182100' => 'mdo', 'MD13G1182200' => 'mdo', 'MD16G1182600' => 'mdo', 'Medtr2g021400' => 'mtr', 'Medtr2g021470' => 'mtr', 'Medtr2g105810' => 'mtr', 'Medtr3g033580' => 'mtr', 'Medtr6g007970' => 'mtr', 'Medtr7g056330' => 'mtr', 'Medtr7g074290' => 'mtr', 'Medtr7g074380' => 'mtr', 'Medtr7g094550' => 'mtr', 'Medtr8g069995' => 'mtr', 'MELO3C014345.2' => 'cme', 'MELO3C021395.2' => 'cme', 'Migut.D00262' => 'egut', 'Migut.G00257' => 'egut', 'MSTRG.21575' => 'ama', 'MSTRG.3985' => 'ama', 'Nitab4.5_0000295g0140' => 'nta', 'Nitab4.5_0000732g0140' => 'nta', 'Nitab4.5_0003162g0020' => 'nta', 'Nitab4.5_0006180g0090' => 'nta', 'Nitab4.5_0006390g0010' => 'nta', 'Nitab4.5_0007392g0040' => 'nta', 'Nn1g02140' => 'nnu', 'Nn4g26168' => 'nnu', 'Nn5g26754' => 'nnu', 'Oeu001433.1' => 'oeu', 'Oeu010299.2' => 'oeu', 'Oeu011171.1' => 'oeu', 'Oeu037675.1' => 'oeu', 'Oeu038359.1' => 'oeu', 'Oeu063834.1' => 'oeu', 'Oeu063835.1' => 'oeu', 'Os05g0312000' => 'osa', 'Os07g0211101' => 'osa', 'Os07g0211200' => 'osa', 'Os07g0681500' => 'osa', 'Peaxi162Scf00095g01015' => 'pax', 'Peaxi162Scf00104g00329' => 'pax', 'Peaxi162Scf00161g00137' => 'pax', 'PGR004G1665' => 'pgr', 'PGR031G2937' => 'pgr', 'PGR119G2145' => 'pgr', 'PGSC0003DMG400004351' => 'stu', 'PGSC0003DMG400014625' => 'stu', 'PGSC0003DMG401000943' => 'stu', 'Phvul.001G148600' => 'pvu', 'Phvul.004G001700' => 'pvu', 'Phvul.006G154900' => 'pvu', 'Phvul.008G078200' => 'pvu', 'Phvul.011G136500' => 'pvu', 'Potri.002G215600' => 'ptr', 'Potri.008G201600' => 'ptr', 'Potri.014G138400' => 'ptr', 'Potri.016G142500' => 'ptr', 'Pp3c16_10580' => 'ppa', 'Pp3c5_25280' => 'ppa', 'Prupe.1G150000' => 'ppe', 'Prupe.1G150100' => 'ppe', 'Prupe.6G299600' => 'ppe', 'Prupe.8G245000' => 'ppe', 'Psat0s4927g0040' => 'psa', 'Psat1g052080' => 'psa', 'Psat1g183800' => 'psa', 'Psat3g113840' => 'psa', 'Psat3g126120' => 'psa', 'Psat3g126160' => 'psa', 'Psat3g158760' => 'psa', 'Psat3g158840' => 'psa', 'PSO170G2858' => 'pso', 'PSO339G0606' => 'pso', 'PSO384G4709' => 'pso', 'PSO407G0334' => 'pso', 'QL04p040276' => 'qlo', 'QL06p005458' => 'qlo', 'QL06p005472' => 'qlo', 'QL07p030546' => 'qlo', 'QL07p031519' => 'qlo', 'QL09p050949' => 'qlo', 'QL09p050966' => 'qlo', 'QL09p051067' => 'qlo', 'QL12p022706' => 'qlo', 'RcHm_v2.0_Chr2g0119601' => 'rch', 'RcHm_v2.0_Chr3g0459591' => 'rch', 'RcHm_v2.0_Chr4g0418521' => 'rch', 'RcHm_v2.0_Chr4g0418531' => 'rch', 'RcHm_v2.0_Chr4g0418541' => 'rch', 'RcHm_v2.0_Chr6g0291641' => 'rch', 'Rhsim01G0086300' => 'rsi', 'Rhsim01G0276300' => 'rsi', 'Rhsim01G0276500' => 'rsi', 'Rhsim04G0207700' => 'rsi', 'Rhsim05G0234500' => 'rsi', 'Rhsim13G0022400' => 'rsi', 'Sabra02G0167900' => 'sbr', 'Sabra04G0158500' => 'sbr', 'Sabra08G0159800' => 'sbr', 'Sabra10G0011500' => 'sbr', 'Sabra14G0104400' => 'sbr', 'SalBow2G2440' => 'sbo', 'SalBow4G2265' => 'sbo', 'Sc02g0000060' => 'sci', 'Sc05g0005020' => 'sci', 'Sc13g0003890' => 'sci', 'Sed0014865' => 'sed', 'Sed0017224' => 'sed', 'Sed0026391' => 'sed', 'SEGI_00063' => 'sgi', 'SEGI_10967' => 'sgi', 'SEGI_17510' => 'sgi', 'SEGI_24396' => 'sgi', 'SEGI_39719' => 'sgi', 'SEGI_41392' => 'sgi', 'SGA_v2.0_scaffold11G05794' => 'sas', 'SGA_v2.0_scaffold142G35607' => 'sas', 'SGA_v2.0_scaffold1G00447' => 'sas', 'SHI15388' => 'shi', 'SHI15394' => 'shi', 'SHI15396' => 'shi', 'SHI15399' => 'shi', 'SMO343G0151' => 'smo', 'SMO367G1118' => 'smo', 'Solyc01g080200.3' => 'sly', 'Solyc06g008960.3' => 'sly', 'Solyc09g064780.3' => 'sly', 'Sopen01g031980' => 'spe', 'Sopen06g003710' => 'spe', 'Sopen09g026460' => 'spe', 'Sp3g21240' => 'spa', 'Sp4g30030' => 'spa', 'TAR365G0022' => 'tar', 'TAR365G1023' => 'tar', 'TAR365G1253' => 'tar', 'TAR623G0078' => 'tar', 'TAR623G1721' => 'tar', 'TAR633G0959' => 'tar', 'THA.LOC104802225' => 'tha', 'THA.LOC104804769' => 'tha', 'THA.LOC104808660' => 'tha', 'THA.LOC104812792' => 'tha', 'Thecc.01G284000' => 'tca', 'Thecc.04G220600' => 'tca', 'Thecc.05G268900' => 'tca', 'Thecc.08G171100' => 'tca', 'Thhalv10001284m.g' => 'esa', 'Thhalv10019912m.g' => 'esa', 'TPR.G14189' => 'tpr', 'TPR.G18110' => 'tpr', 'TPR.G18130' => 'tpr', 'TPR.G18131' => 'tpr', 'TPR.G18140' => 'tpr', 'TPR.G24282' => 'tpr', 'TPR.G25221' => 'tpr', 'TPR.G29267' => 'tpr', 'TPR.G35315' => 'tpr', 'TPR.G36173' => 'tpr', 'TWI09G0794' => 'twi', 'TWI59G1348' => 'twi', 'TWI74G0430' => 'twi', 'unitig_26.g8940' => 'ugi', 'unitig_749.g13744' => 'ugi', 'unitig_749.g13745' => 'ugi', 'vmacro08269' => 'vma', 'vmacro14937' => 'vma', 'vmacro20401' => 'vma', 'VMungo0464G1349' => 'vmu', 'VMungo0540G0289' => 'vmu', 'VMungo1215G1590' => 'vmu', 'VMungo1309G0221' => 'vmu', 'VMungo1309G2815' => 'vmu', 'VMungo1383G0239' => 'vmu', 'VMungo1383G2910' => 'vmu', 'Zm00001eb095270' => 'zma', 'Zm00001eb095280' => 'zma', 'Zm00001eb111630' => 'zma', 'Zm00001eb237080' => 'zma', 'Zm00001eb273740' => 'zma', 'Zm00001eb285040' => 'zma', 'Zm00001eb330790' => 'zma', 'Zm00001eb337380' => 'zma' ) $gf_id = 'HOM05D001484' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001484' ) $data_identifier = 'HOM05D001484' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 2, 'aly' => (int) 2, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 22, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 7, 'hma' => (int) 2, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 7, 'mtr' => (int) 10, 'cme' => (int) 2, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 4, 'ppa' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 4, 'qlo' => (int) 9, 'rch' => (int) 6, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 10, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 7, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb337380' $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' => 'HOM05D001484', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p31500' => 'bna', 'A05p00020' => 'bna', 'A07p08820' => 'bna', 'Aa31LG4G3300' => 'aar', 'Aa31LG8G10030' => 'aar', 'Actinidia00731' => 'ach', 'Actinidia11473' => 'ach', 'Actinidia23469' => 'ach', 'Actinidia24318' => 'ach', 'Actinidia40196' => 'ach', 'Actinidia40197' => 'ach', 'Actinidia40198' => 'ach', 'Ah.08g212990' => 'amhyb', 'Ah.15g091720' => 'amhyb', 'AL3G38260' => 'aly', 'AL4G47710' => 'aly', 'Aqoxy2G00671' => 'aox', 'Aqoxy2G03236' => 'aox', 'arahy.Tifrunner.gnm1.ann1.05IDCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KR684' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATY3SJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK6QJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6APGL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IDT7Z9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM073U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ0R87' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LE7RV4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT4QRX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V5ENPK' => 'arhy', 'AT2G48110' => 'ath', 'AT3G23590' => 'ath', 'ATR0626G186' => 'atr', 'ATR1127G141' => 'atr', 'Atru.chr4.2583' => 'acertr', 'Atru.chr5.1358' => 'acertr', 'Atru.chr5.1359' => 'acertr', 'Atru.chr8.46' => 'acertr', 'AUR62002640' => 'cqu', 'AUR62030055' => 'cqu', 'AUR62033713' => 'cqu', 'AUR62033714' => 'cqu', 'AUR62036795' => 'cqu', 'AUR62039891' => 'cqu', 'BcaB02g08737' => 'bca', 'BcaB04g20441' => 'bca', 'BcaB06g26509' => 'bca', 'BcaB06g26510' => 'bca', 'BcaB06g26511' => 'bca', 'BcaB06g26512' => 'bca', 'BcaB06g26513' => 'bca', 'BcaC02g12564' => 'bca', 'BcaC02g12565' => 'bca', 'BcaC02g12794' => 'bca', 'BcaC02g12795' => 'bca', 'BcaC02g12796' => 'bca', 'BcaC06g35541' => 'bca', 'BNapus_Darmor_BZH_scaffold_188p00080' => 'bna', 'BNapus_Darmor_BZH_scaffold_188p00090' => 'bna', 'BolC1t03972H' => 'bol', 'BolC1t03973H' => 'bol', 'BolC4t21680H' => 'bol', 'BolC7t41863H' => 'bol', 'BolSC55t61227H' => 'bol', 'BolSC55t61228H' => 'bol', 'BraA01t03278Z' => 'bra', 'BraA05t18998Z' => 'bra', 'BraA07t28673Z' => 'bra', 'C01p40150' => 'bna', 'C05p12370' => 'bna', 'C07p13680' => 'bna', 'CAN.G1006.16' => 'can', 'CAN.G1006.17' => 'can', 'CAN.G1170.2' => 'can', 'CAN.G962.7' => 'can', 'CANSAT25G2179' => 'cansat', 'CANSAT78G1573' => 'cansat', 'CARHR099510' => 'chi', 'CARHR143510' => 'chi', 'Carub.0003s2380' => 'cru', 'Carub.0004s3082' => 'cru', 'Ca_00614_v3' => 'car', 'Ca_07801_v3' => 'car', 'Ca_08567_v3' => 'car', 'Ca_09571_v3' => 'car', 'CBR_g19290' => 'cbr', 'Cc01_g19770' => 'ccan', 'Cc03_g03030' => 'ccan', 'CDE07G0968' => 'cde', 'CDE09G1441' => 'cde', 'Cfa006103' => 'cfa', 'Cfa015573' => 'cfa', 'Cfa016988' => 'cfa', 'Ciclev10006738m.g' => 'ccl', 'Ciclev10010920m.g' => 'ccl', 'Ciclev10018517m.g' => 'ccl', 'CiPaw.01G159200' => 'cil', 'CiPaw.02G091000' => 'cil', 'CiPaw.02G091100' => 'cil', 'CiPaw.08G103100' => 'cil', 'CiPaw.09G224900' => 'cil', 'ClCG06G005740' => 'cla', 'ClCG07G000090' => 'cla', 'ClCG07G000100' => 'cla', 'COL.COLO4_09143' => 'col', 'COL.COLO4_25124' => 'col', 'Cpa.g.sc16.34' => 'cpa', 'Cpa.g.sc3504.1' => 'cpa', 'Cpa.g.sc60.37' => 'cpa', 'CsaV3_6G018520' => 'csa', 'CsaV3_6G036860' => 'csa', 'CSS0001072' => 'camsi', 'CSS0020208' => 'camsi', 'CSS0021253' => 'camsi', 'CSS0022190' => 'camsi', 'CSS0036150' => 'camsi', 'CSS0040442' => 'camsi', 'CSS0042300' => 'camsi', 'CSS0045298' => 'camsi', 'DCAR_012449' => 'dca', 'DCAR_018405' => 'dca', 'DCAR_024573' => 'dca', 'DCAR_030591' => 'dca', 'Dinv16926' => 'din', 'Dinv32963' => 'din', 'Dinv38382' => 'din', 'Dinv38383' => 'din', 'Duzib133G0974' => 'dzi', 'Duzib138G1867' => 'dzi', 'Duzib211G0420' => 'dzi', 'Duzib212G0930' => 'dzi', 'ECA234G1645' => 'eca', 'ECA247G3467' => 'eca', 'ECA248G1703' => 'eca', 'EL10Ac3g06327' => 'bvu', 'EL10Ac7g17204' => 'bvu', 'Eucgr.A00855' => 'egr', 'Eucgr.A00858' => 'egr', 'Eucgr.H01520' => 'egr', 'Eucgr.H03604' => 'egr', 'Eucgr.L03465' => 'egr', 'Eucgr.L03466' => 'egr', 'FAN01G0988' => 'fan', 'FAN02G3892' => 'fan', 'FAN05G3381' => 'fan', 'FAN07G0967' => 'fan', 'FAN07G1493' => 'fan', 'FAN08G3125' => 'fan', 'FAN09G0402' => 'fan', 'FAN12G2594' => 'fan', 'FAN12G3879' => 'fan', 'FAN14G1546' => 'fan', 'FAN15G3626' => 'fan', 'FAN17G0588' => 'fan', 'FAN17G0609' => 'fan', 'FAN18G2817' => 'fan', 'FAN19G1305' => 'fan', 'FAN20G1787' => 'fan', 'FAN22G0073' => 'fan', 'FAN22G0352' => 'fan', 'FAN22G0368' => 'fan', 'FAN22G2273' => 'fan', 'FAN24G1998' => 'fan', 'FAN27G1317' => 'fan', 'FvH4_2g23980' => 'fve', 'FvH4_4g14380' => 'fve', 'FvH4_4g14390' => 'fve', 'FvH4_6g09250' => 'fve', 'Glyma.03G151100' => 'gma', 'Glyma.04G122550' => 'gma', 'Glyma.05G001600' => 'gma', 'Glyma.09G270766' => 'gma', 'Glyma.09G270832' => 'gma', 'Glyma.13G209800' => 'gma', 'Glyma.15G102800' => 'gma', 'Glyma.18G218900' => 'gma', 'Glyma.19G001500' => 'gma', 'Glyma.19G153600' => 'gma', 'Gohir.A02G028600' => 'ghi', 'Gohir.A08G045000' => 'ghi', 'Gohir.A11G120500' => 'ghi', 'Gohir.A12G006200' => 'ghi', 'Gohir.A12G006250' => 'ghi', 'Gohir.D02G036300' => 'ghi', 'Gohir.D08G054700' => 'ghi', 'Gohir.D11G125600' => 'ghi', 'Gohir.D12G005700' => 'ghi', 'Gorai.004G055200' => 'gra', 'Gorai.005G040400' => 'gra', 'Gorai.007G134500' => 'gra', 'Gorai.008G005500' => 'gra', 'GSVIVG01011094001' => 'vvi', 'GSVIVG01017879001' => 'vvi', 'GSVIVG01025988001' => 'vvi', 'GSVIVG01029847001' => 'vvi', 'HanXRQChr10g0282901' => 'han', 'HanXRQChr10g0310371' => 'han', 'HanXRQChr10g0315041' => 'han', 'HanXRQChr11g0327651' => 'han', 'HanXRQChr12g0359391' => 'han', 'Haze_00972' => 'cav', 'Haze_00973' => 'cav', 'Haze_00974' => 'cav', 'Haze_04747' => 'cav', 'Haze_04749' => 'cav', 'Haze_04750' => 'cav', 'Haze_21217' => 'cav', 'Hma1.2p1_1037F.1_g250680' => 'hma', 'Hma1.2p1_1644F.1_g295320' => 'hma', 'HPP92_011322' => 'vpl', 'HPP92_011323' => 'vpl', 'HPP92_011324' => 'vpl', 'HPP92_011325' => 'vpl', 'HPP92_011326' => 'vpl', 'Hund12205' => 'sun', 'Hund17957' => 'sun', 'Lalb_Chr06g0176771' => 'lal', 'Lalb_Chr18g0056021' => 'lal', 'Lalb_Chr18g0056031' => 'lal', 'Lalb_Chr18g0056041' => 'lal', 'Lalb_Chr20g0107751' => 'lal', 'Lalb_Chr20g0118371' => 'lal', 'Lj1g0010239' => 'lja', 'Lj1g0017101' => 'lja', 'Lj2A1178G40' => 'lonja', 'Lj2A54G84' => 'lonja', 'Lj2g0015248' => 'lja', 'Lj3A761T51' => 'lonja', 'Lj6g0018116' => 'lja', 'Lsat_1_v5_gn_4_136040' => 'lsa', 'Lsat_1_v5_gn_5_187461' => 'lsa', 'Lsat_1_v5_gn_5_77001' => 'lsa', 'Lsat_1_v5_gn_9_4461' => 'lsa', 'Manes.01G210100' => 'mes', 'Manes.03G185600' => 'mes', 'Manes.05G073300' => 'mes', 'Manes.09G120300' => 'mes', 'Manes.15G022100' => 'mes', 'Mapoly0096s0053' => 'mpo', 'MBI03_g14058_MAGBIO' => 'mbi', 'MBI03_g33876_MAGBIO' => 'mbi', 'MBI03_g36854_MAGBIO' => 'mbi', 'MBI17_g11997_MAGBIO' => 'mbi', 'MD03G1269000' => 'mdo', 'MD04G1179600' => 'mdo', 'MD11G1289800' => 'mdo', 'MD12G1194700' => 'mdo', 'MD13G1182100' => 'mdo', 'MD13G1182200' => 'mdo', 'MD16G1182600' => 'mdo', 'Medtr2g021400' => 'mtr', 'Medtr2g021470' => 'mtr', 'Medtr2g105810' => 'mtr', 'Medtr3g033580' => 'mtr', 'Medtr6g007970' => 'mtr', 'Medtr7g056330' => 'mtr', 'Medtr7g074290' => 'mtr', 'Medtr7g074380' => 'mtr', 'Medtr7g094550' => 'mtr', 'Medtr8g069995' => 'mtr', 'MELO3C014345.2' => 'cme', 'MELO3C021395.2' => 'cme', 'Migut.D00262' => 'egut', 'Migut.G00257' => 'egut', 'MSTRG.21575' => 'ama', 'MSTRG.3985' => 'ama', 'Nitab4.5_0000295g0140' => 'nta', 'Nitab4.5_0000732g0140' => 'nta', 'Nitab4.5_0003162g0020' => 'nta', 'Nitab4.5_0006180g0090' => 'nta', 'Nitab4.5_0006390g0010' => 'nta', 'Nitab4.5_0007392g0040' => 'nta', 'Nn1g02140' => 'nnu', 'Nn4g26168' => 'nnu', 'Nn5g26754' => 'nnu', 'Oeu001433.1' => 'oeu', 'Oeu010299.2' => 'oeu', 'Oeu011171.1' => 'oeu', 'Oeu037675.1' => 'oeu', 'Oeu038359.1' => 'oeu', 'Oeu063834.1' => 'oeu', 'Oeu063835.1' => 'oeu', 'Os05g0312000' => 'osa', 'Os07g0211101' => 'osa', 'Os07g0211200' => 'osa', 'Os07g0681500' => 'osa', 'Peaxi162Scf00095g01015' => 'pax', 'Peaxi162Scf00104g00329' => 'pax', 'Peaxi162Scf00161g00137' => 'pax', 'PGR004G1665' => 'pgr', 'PGR031G2937' => 'pgr', 'PGR119G2145' => 'pgr', 'PGSC0003DMG400004351' => 'stu', 'PGSC0003DMG400014625' => 'stu', 'PGSC0003DMG401000943' => 'stu', 'Phvul.001G148600' => 'pvu', 'Phvul.004G001700' => 'pvu', 'Phvul.006G154900' => 'pvu', 'Phvul.008G078200' => 'pvu', 'Phvul.011G136500' => 'pvu', 'Potri.002G215600' => 'ptr', 'Potri.008G201600' => 'ptr', 'Potri.014G138400' => 'ptr', 'Potri.016G142500' => 'ptr', 'Pp3c16_10580' => 'ppa', 'Pp3c5_25280' => 'ppa', 'Prupe.1G150000' => 'ppe', 'Prupe.1G150100' => 'ppe', 'Prupe.6G299600' => 'ppe', 'Prupe.8G245000' => 'ppe', 'Psat0s4927g0040' => 'psa', 'Psat1g052080' => 'psa', 'Psat1g183800' => 'psa', 'Psat3g113840' => 'psa', 'Psat3g126120' => 'psa', 'Psat3g126160' => 'psa', 'Psat3g158760' => 'psa', 'Psat3g158840' => 'psa', 'PSO170G2858' => 'pso', 'PSO339G0606' => 'pso', 'PSO384G4709' => 'pso', 'PSO407G0334' => 'pso', 'QL04p040276' => 'qlo', 'QL06p005458' => 'qlo', 'QL06p005472' => 'qlo', 'QL07p030546' => 'qlo', 'QL07p031519' => 'qlo', 'QL09p050949' => 'qlo', 'QL09p050966' => 'qlo', 'QL09p051067' => 'qlo', 'QL12p022706' => 'qlo', 'RcHm_v2.0_Chr2g0119601' => 'rch', 'RcHm_v2.0_Chr3g0459591' => 'rch', 'RcHm_v2.0_Chr4g0418521' => 'rch', 'RcHm_v2.0_Chr4g0418531' => 'rch', 'RcHm_v2.0_Chr4g0418541' => 'rch', 'RcHm_v2.0_Chr6g0291641' => 'rch', 'Rhsim01G0086300' => 'rsi', 'Rhsim01G0276300' => 'rsi', 'Rhsim01G0276500' => 'rsi', 'Rhsim04G0207700' => 'rsi', 'Rhsim05G0234500' => 'rsi', 'Rhsim13G0022400' => 'rsi', 'Sabra02G0167900' => 'sbr', 'Sabra04G0158500' => 'sbr', 'Sabra08G0159800' => 'sbr', 'Sabra10G0011500' => 'sbr', 'Sabra14G0104400' => 'sbr', 'SalBow2G2440' => 'sbo', 'SalBow4G2265' => 'sbo', 'Sc02g0000060' => 'sci', 'Sc05g0005020' => 'sci', 'Sc13g0003890' => 'sci', 'Sed0014865' => 'sed', 'Sed0017224' => 'sed', 'Sed0026391' => 'sed', 'SEGI_00063' => 'sgi', 'SEGI_10967' => 'sgi', 'SEGI_17510' => 'sgi', 'SEGI_24396' => 'sgi', 'SEGI_39719' => 'sgi', 'SEGI_41392' => 'sgi', 'SGA_v2.0_scaffold11G05794' => 'sas', 'SGA_v2.0_scaffold142G35607' => 'sas', 'SGA_v2.0_scaffold1G00447' => 'sas', 'SHI15388' => 'shi', 'SHI15394' => 'shi', 'SHI15396' => 'shi', 'SHI15399' => 'shi', 'SMO343G0151' => 'smo', 'SMO367G1118' => 'smo', 'Solyc01g080200.3' => 'sly', 'Solyc06g008960.3' => 'sly', 'Solyc09g064780.3' => 'sly', 'Sopen01g031980' => 'spe', 'Sopen06g003710' => 'spe', 'Sopen09g026460' => 'spe', 'Sp3g21240' => 'spa', 'Sp4g30030' => 'spa', 'TAR365G0022' => 'tar', 'TAR365G1023' => 'tar', 'TAR365G1253' => 'tar', 'TAR623G0078' => 'tar', 'TAR623G1721' => 'tar', 'TAR633G0959' => 'tar', 'THA.LOC104802225' => 'tha', 'THA.LOC104804769' => 'tha', 'THA.LOC104808660' => 'tha', 'THA.LOC104812792' => 'tha', 'Thecc.01G284000' => 'tca', 'Thecc.04G220600' => 'tca', 'Thecc.05G268900' => 'tca', 'Thecc.08G171100' => 'tca', 'Thhalv10001284m.g' => 'esa', 'Thhalv10019912m.g' => 'esa', 'TPR.G14189' => 'tpr', 'TPR.G18110' => 'tpr', 'TPR.G18130' => 'tpr', 'TPR.G18131' => 'tpr', 'TPR.G18140' => 'tpr', 'TPR.G24282' => 'tpr', 'TPR.G25221' => 'tpr', 'TPR.G29267' => 'tpr', 'TPR.G35315' => 'tpr', 'TPR.G36173' => 'tpr', 'TWI09G0794' => 'twi', 'TWI59G1348' => 'twi', 'TWI74G0430' => 'twi', 'unitig_26.g8940' => 'ugi', 'unitig_749.g13744' => 'ugi', 'unitig_749.g13745' => 'ugi', 'vmacro08269' => 'vma', 'vmacro14937' => 'vma', 'vmacro20401' => 'vma', 'VMungo0464G1349' => 'vmu', 'VMungo0540G0289' => 'vmu', 'VMungo1215G1590' => 'vmu', 'VMungo1309G0221' => 'vmu', 'VMungo1309G2815' => 'vmu', 'VMungo1383G0239' => 'vmu', 'VMungo1383G2910' => 'vmu', 'Zm00001eb095270' => 'zma', 'Zm00001eb095280' => 'zma', 'Zm00001eb111630' => 'zma', 'Zm00001eb237080' => 'zma', 'Zm00001eb273740' => 'zma', 'Zm00001eb285040' => 'zma', 'Zm00001eb330790' => 'zma', 'Zm00001eb337380' => 'zma' ), 'gf_id' => 'HOM05D001484', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001484' ), 'data_identifier' => 'HOM05D001484', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001484', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p31500' => 'bna', 'A05p00020' => 'bna', 'A07p08820' => 'bna', 'Aa31LG4G3300' => 'aar', 'Aa31LG8G10030' => 'aar', 'Actinidia00731' => 'ach', 'Actinidia11473' => 'ach', 'Actinidia23469' => 'ach', 'Actinidia24318' => 'ach', 'Actinidia40196' => 'ach', 'Actinidia40197' => 'ach', 'Actinidia40198' => 'ach', 'Ah.08g212990' => 'amhyb', 'Ah.15g091720' => 'amhyb', 'AL3G38260' => 'aly', 'AL4G47710' => 'aly', 'Aqoxy2G00671' => 'aox', 'Aqoxy2G03236' => 'aox', 'arahy.Tifrunner.gnm1.ann1.05IDCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KR684' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATY3SJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK6QJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6APGL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IDT7Z9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM073U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ0R87' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LE7RV4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT4QRX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V5ENPK' => 'arhy', 'AT2G48110' => 'ath', 'AT3G23590' => 'ath', 'ATR0626G186' => 'atr', 'ATR1127G141' => 'atr', 'Atru.chr4.2583' => 'acertr', 'Atru.chr5.1358' => 'acertr', 'Atru.chr5.1359' => 'acertr', 'Atru.chr8.46' => 'acertr', 'AUR62002640' => 'cqu', 'AUR62030055' => 'cqu', 'AUR62033713' => 'cqu', 'AUR62033714' => 'cqu', 'AUR62036795' => 'cqu', 'AUR62039891' => 'cqu', 'BcaB02g08737' => 'bca', 'BcaB04g20441' => 'bca', 'BcaB06g26509' => 'bca', 'BcaB06g26510' => 'bca', 'BcaB06g26511' => 'bca', 'BcaB06g26512' => 'bca', 'BcaB06g26513' => 'bca', 'BcaC02g12564' => 'bca', 'BcaC02g12565' => 'bca', 'BcaC02g12794' => 'bca', 'BcaC02g12795' => 'bca', 'BcaC02g12796' => 'bca', 'BcaC06g35541' => 'bca', 'BNapus_Darmor_BZH_scaffold_188p00080' => 'bna', 'BNapus_Darmor_BZH_scaffold_188p00090' => 'bna', 'BolC1t03972H' => 'bol', 'BolC1t03973H' => 'bol', 'BolC4t21680H' => 'bol', 'BolC7t41863H' => 'bol', 'BolSC55t61227H' => 'bol', 'BolSC55t61228H' => 'bol', 'BraA01t03278Z' => 'bra', 'BraA05t18998Z' => 'bra', 'BraA07t28673Z' => 'bra', 'C01p40150' => 'bna', 'C05p12370' => 'bna', 'C07p13680' => 'bna', 'CAN.G1006.16' => 'can', 'CAN.G1006.17' => 'can', 'CAN.G1170.2' => 'can', 'CAN.G962.7' => 'can', 'CANSAT25G2179' => 'cansat', 'CANSAT78G1573' => 'cansat', 'CARHR099510' => 'chi', 'CARHR143510' => 'chi', 'Carub.0003s2380' => 'cru', 'Carub.0004s3082' => 'cru', 'Ca_00614_v3' => 'car', 'Ca_07801_v3' => 'car', 'Ca_08567_v3' => 'car', 'Ca_09571_v3' => 'car', 'CBR_g19290' => 'cbr', 'Cc01_g19770' => 'ccan', 'Cc03_g03030' => 'ccan', 'CDE07G0968' => 'cde', 'CDE09G1441' => 'cde', 'Cfa006103' => 'cfa', 'Cfa015573' => 'cfa', 'Cfa016988' => 'cfa', 'Ciclev10006738m.g' => 'ccl', 'Ciclev10010920m.g' => 'ccl', 'Ciclev10018517m.g' => 'ccl', 'CiPaw.01G159200' => 'cil', 'CiPaw.02G091000' => 'cil', 'CiPaw.02G091100' => 'cil', 'CiPaw.08G103100' => 'cil', 'CiPaw.09G224900' => 'cil', 'ClCG06G005740' => 'cla', 'ClCG07G000090' => 'cla', 'ClCG07G000100' => 'cla', 'COL.COLO4_09143' => 'col', 'COL.COLO4_25124' => 'col', 'Cpa.g.sc16.34' => 'cpa', 'Cpa.g.sc3504.1' => 'cpa', 'Cpa.g.sc60.37' => 'cpa', 'CsaV3_6G018520' => 'csa', 'CsaV3_6G036860' => 'csa', 'CSS0001072' => 'camsi', 'CSS0020208' => 'camsi', 'CSS0021253' => 'camsi', 'CSS0022190' => 'camsi', 'CSS0036150' => 'camsi', 'CSS0040442' => 'camsi', 'CSS0042300' => 'camsi', 'CSS0045298' => 'camsi', 'DCAR_012449' => 'dca', 'DCAR_018405' => 'dca', 'DCAR_024573' => 'dca', 'DCAR_030591' => 'dca', 'Dinv16926' => 'din', 'Dinv32963' => 'din', 'Dinv38382' => 'din', 'Dinv38383' => 'din', 'Duzib133G0974' => 'dzi', 'Duzib138G1867' => 'dzi', 'Duzib211G0420' => 'dzi', 'Duzib212G0930' => 'dzi', 'ECA234G1645' => 'eca', 'ECA247G3467' => 'eca', 'ECA248G1703' => 'eca', 'EL10Ac3g06327' => 'bvu', 'EL10Ac7g17204' => 'bvu', 'Eucgr.A00855' => 'egr', 'Eucgr.A00858' => 'egr', 'Eucgr.H01520' => 'egr', 'Eucgr.H03604' => 'egr', 'Eucgr.L03465' => 'egr', 'Eucgr.L03466' => 'egr', 'FAN01G0988' => 'fan', 'FAN02G3892' => 'fan', 'FAN05G3381' => 'fan', 'FAN07G0967' => 'fan', 'FAN07G1493' => 'fan', 'FAN08G3125' => 'fan', 'FAN09G0402' => 'fan', 'FAN12G2594' => 'fan', 'FAN12G3879' => 'fan', 'FAN14G1546' => 'fan', 'FAN15G3626' => 'fan', 'FAN17G0588' => 'fan', 'FAN17G0609' => 'fan', 'FAN18G2817' => 'fan', 'FAN19G1305' => 'fan', 'FAN20G1787' => 'fan', 'FAN22G0073' => 'fan', 'FAN22G0352' => 'fan', 'FAN22G0368' => 'fan', 'FAN22G2273' => 'fan', 'FAN24G1998' => 'fan', 'FAN27G1317' => 'fan', 'FvH4_2g23980' => 'fve', 'FvH4_4g14380' => 'fve', 'FvH4_4g14390' => 'fve', 'FvH4_6g09250' => 'fve', 'Glyma.03G151100' => 'gma', 'Glyma.04G122550' => 'gma', 'Glyma.05G001600' => 'gma', 'Glyma.09G270766' => 'gma', 'Glyma.09G270832' => 'gma', 'Glyma.13G209800' => 'gma', 'Glyma.15G102800' => 'gma', 'Glyma.18G218900' => 'gma', 'Glyma.19G001500' => 'gma', 'Glyma.19G153600' => 'gma', 'Gohir.A02G028600' => 'ghi', 'Gohir.A08G045000' => 'ghi', 'Gohir.A11G120500' => 'ghi', 'Gohir.A12G006200' => 'ghi', 'Gohir.A12G006250' => 'ghi', 'Gohir.D02G036300' => 'ghi', 'Gohir.D08G054700' => 'ghi', 'Gohir.D11G125600' => 'ghi', 'Gohir.D12G005700' => 'ghi', 'Gorai.004G055200' => 'gra', 'Gorai.005G040400' => 'gra', 'Gorai.007G134500' => 'gra', 'Gorai.008G005500' => 'gra', 'GSVIVG01011094001' => 'vvi', 'GSVIVG01017879001' => 'vvi', 'GSVIVG01025988001' => 'vvi', 'GSVIVG01029847001' => 'vvi', 'HanXRQChr10g0282901' => 'han', 'HanXRQChr10g0310371' => 'han', 'HanXRQChr10g0315041' => 'han', 'HanXRQChr11g0327651' => 'han', 'HanXRQChr12g0359391' => 'han', 'Haze_00972' => 'cav', 'Haze_00973' => 'cav', 'Haze_00974' => 'cav', 'Haze_04747' => 'cav', 'Haze_04749' => 'cav', 'Haze_04750' => 'cav', 'Haze_21217' => 'cav', 'Hma1.2p1_1037F.1_g250680' => 'hma', 'Hma1.2p1_1644F.1_g295320' => 'hma', 'HPP92_011322' => 'vpl', 'HPP92_011323' => 'vpl', 'HPP92_011324' => 'vpl', 'HPP92_011325' => 'vpl', 'HPP92_011326' => 'vpl', 'Hund12205' => 'sun', 'Hund17957' => 'sun', 'Lalb_Chr06g0176771' => 'lal', 'Lalb_Chr18g0056021' => 'lal', 'Lalb_Chr18g0056031' => 'lal', 'Lalb_Chr18g0056041' => 'lal', 'Lalb_Chr20g0107751' => 'lal', 'Lalb_Chr20g0118371' => 'lal', 'Lj1g0010239' => 'lja', 'Lj1g0017101' => 'lja', 'Lj2A1178G40' => 'lonja', 'Lj2A54G84' => 'lonja', 'Lj2g0015248' => 'lja', 'Lj3A761T51' => 'lonja', 'Lj6g0018116' => 'lja', 'Lsat_1_v5_gn_4_136040' => 'lsa', 'Lsat_1_v5_gn_5_187461' => 'lsa', 'Lsat_1_v5_gn_5_77001' => 'lsa', 'Lsat_1_v5_gn_9_4461' => 'lsa', 'Manes.01G210100' => 'mes', 'Manes.03G185600' => 'mes', 'Manes.05G073300' => 'mes', 'Manes.09G120300' => 'mes', 'Manes.15G022100' => 'mes', 'Mapoly0096s0053' => 'mpo', 'MBI03_g14058_MAGBIO' => 'mbi', 'MBI03_g33876_MAGBIO' => 'mbi', 'MBI03_g36854_MAGBIO' => 'mbi', 'MBI17_g11997_MAGBIO' => 'mbi', 'MD03G1269000' => 'mdo', 'MD04G1179600' => 'mdo', 'MD11G1289800' => 'mdo', 'MD12G1194700' => 'mdo', 'MD13G1182100' => 'mdo', 'MD13G1182200' => 'mdo', 'MD16G1182600' => 'mdo', 'Medtr2g021400' => 'mtr', 'Medtr2g021470' => 'mtr', 'Medtr2g105810' => 'mtr', 'Medtr3g033580' => 'mtr', 'Medtr6g007970' => 'mtr', 'Medtr7g056330' => 'mtr', 'Medtr7g074290' => 'mtr', 'Medtr7g074380' => 'mtr', 'Medtr7g094550' => 'mtr', 'Medtr8g069995' => 'mtr', 'MELO3C014345.2' => 'cme', 'MELO3C021395.2' => 'cme', 'Migut.D00262' => 'egut', 'Migut.G00257' => 'egut', 'MSTRG.21575' => 'ama', 'MSTRG.3985' => 'ama', 'Nitab4.5_0000295g0140' => 'nta', 'Nitab4.5_0000732g0140' => 'nta', 'Nitab4.5_0003162g0020' => 'nta', 'Nitab4.5_0006180g0090' => 'nta', 'Nitab4.5_0006390g0010' => 'nta', 'Nitab4.5_0007392g0040' => 'nta', 'Nn1g02140' => 'nnu', 'Nn4g26168' => 'nnu', 'Nn5g26754' => 'nnu', 'Oeu001433.1' => 'oeu', 'Oeu010299.2' => 'oeu', 'Oeu011171.1' => 'oeu', 'Oeu037675.1' => 'oeu', 'Oeu038359.1' => 'oeu', 'Oeu063834.1' => 'oeu', 'Oeu063835.1' => 'oeu', 'Os05g0312000' => 'osa', 'Os07g0211101' => 'osa', 'Os07g0211200' => 'osa', 'Os07g0681500' => 'osa', 'Peaxi162Scf00095g01015' => 'pax', 'Peaxi162Scf00104g00329' => 'pax', 'Peaxi162Scf00161g00137' => 'pax', 'PGR004G1665' => 'pgr', 'PGR031G2937' => 'pgr', 'PGR119G2145' => 'pgr', 'PGSC0003DMG400004351' => 'stu', 'PGSC0003DMG400014625' => 'stu', 'PGSC0003DMG401000943' => 'stu', 'Phvul.001G148600' => 'pvu', 'Phvul.004G001700' => 'pvu', 'Phvul.006G154900' => 'pvu', 'Phvul.008G078200' => 'pvu', 'Phvul.011G136500' => 'pvu', 'Potri.002G215600' => 'ptr', 'Potri.008G201600' => 'ptr', 'Potri.014G138400' => 'ptr', 'Potri.016G142500' => 'ptr', 'Pp3c16_10580' => 'ppa', 'Pp3c5_25280' => 'ppa', 'Prupe.1G150000' => 'ppe', 'Prupe.1G150100' => 'ppe', 'Prupe.6G299600' => 'ppe', 'Prupe.8G245000' => 'ppe', 'Psat0s4927g0040' => 'psa', 'Psat1g052080' => 'psa', 'Psat1g183800' => 'psa', 'Psat3g113840' => 'psa', 'Psat3g126120' => 'psa', 'Psat3g126160' => 'psa', 'Psat3g158760' => 'psa', 'Psat3g158840' => 'psa', 'PSO170G2858' => 'pso', 'PSO339G0606' => 'pso', 'PSO384G4709' => 'pso', 'PSO407G0334' => 'pso', 'QL04p040276' => 'qlo', 'QL06p005458' => 'qlo', 'QL06p005472' => 'qlo', 'QL07p030546' => 'qlo', 'QL07p031519' => 'qlo', 'QL09p050949' => 'qlo', 'QL09p050966' => 'qlo', 'QL09p051067' => 'qlo', 'QL12p022706' => 'qlo', 'RcHm_v2.0_Chr2g0119601' => 'rch', 'RcHm_v2.0_Chr3g0459591' => 'rch', 'RcHm_v2.0_Chr4g0418521' => 'rch', 'RcHm_v2.0_Chr4g0418531' => 'rch', 'RcHm_v2.0_Chr4g0418541' => 'rch', 'RcHm_v2.0_Chr6g0291641' => 'rch', 'Rhsim01G0086300' => 'rsi', 'Rhsim01G0276300' => 'rsi', 'Rhsim01G0276500' => 'rsi', 'Rhsim04G0207700' => 'rsi', 'Rhsim05G0234500' => 'rsi', 'Rhsim13G0022400' => 'rsi', 'Sabra02G0167900' => 'sbr', 'Sabra04G0158500' => 'sbr', 'Sabra08G0159800' => 'sbr', 'Sabra10G0011500' => 'sbr', 'Sabra14G0104400' => 'sbr', 'SalBow2G2440' => 'sbo', 'SalBow4G2265' => 'sbo', 'Sc02g0000060' => 'sci', 'Sc05g0005020' => 'sci', 'Sc13g0003890' => 'sci', 'Sed0014865' => 'sed', 'Sed0017224' => 'sed', 'Sed0026391' => 'sed', 'SEGI_00063' => 'sgi', 'SEGI_10967' => 'sgi', 'SEGI_17510' => 'sgi', 'SEGI_24396' => 'sgi', 'SEGI_39719' => 'sgi', 'SEGI_41392' => 'sgi', 'SGA_v2.0_scaffold11G05794' => 'sas', 'SGA_v2.0_scaffold142G35607' => 'sas', 'SGA_v2.0_scaffold1G00447' => 'sas', 'SHI15388' => 'shi', 'SHI15394' => 'shi', 'SHI15396' => 'shi', 'SHI15399' => 'shi', 'SMO343G0151' => 'smo', 'SMO367G1118' => 'smo', 'Solyc01g080200.3' => 'sly', 'Solyc06g008960.3' => 'sly', 'Solyc09g064780.3' => 'sly', 'Sopen01g031980' => 'spe', 'Sopen06g003710' => 'spe', 'Sopen09g026460' => 'spe', 'Sp3g21240' => 'spa', 'Sp4g30030' => 'spa', 'TAR365G0022' => 'tar', 'TAR365G1023' => 'tar', 'TAR365G1253' => 'tar', 'TAR623G0078' => 'tar', 'TAR623G1721' => 'tar', 'TAR633G0959' => 'tar', 'THA.LOC104802225' => 'tha', 'THA.LOC104804769' => 'tha', 'THA.LOC104808660' => 'tha', 'THA.LOC104812792' => 'tha', 'Thecc.01G284000' => 'tca', 'Thecc.04G220600' => 'tca', 'Thecc.05G268900' => 'tca', 'Thecc.08G171100' => 'tca', 'Thhalv10001284m.g' => 'esa', 'Thhalv10019912m.g' => 'esa', 'TPR.G14189' => 'tpr', 'TPR.G18110' => 'tpr', 'TPR.G18130' => 'tpr', 'TPR.G18131' => 'tpr', 'TPR.G18140' => 'tpr', 'TPR.G24282' => 'tpr', 'TPR.G25221' => 'tpr', 'TPR.G29267' => 'tpr', 'TPR.G35315' => 'tpr', 'TPR.G36173' => 'tpr', 'TWI09G0794' => 'twi', 'TWI59G1348' => 'twi', 'TWI74G0430' => 'twi', 'unitig_26.g8940' => 'ugi', 'unitig_749.g13744' => 'ugi', 'unitig_749.g13745' => 'ugi', 'vmacro08269' => 'vma', 'vmacro14937' => 'vma', 'vmacro20401' => 'vma', 'VMungo0464G1349' => 'vmu', 'VMungo0540G0289' => 'vmu', 'VMungo1215G1590' => 'vmu', 'VMungo1309G0221' => 'vmu', 'VMungo1309G2815' => 'vmu', 'VMungo1383G0239' => 'vmu', 'VMungo1383G2910' => 'vmu', 'Zm00001eb095270' => 'zma', 'Zm00001eb095280' => 'zma', 'Zm00001eb111630' => 'zma', 'Zm00001eb237080' => 'zma', 'Zm00001eb273740' => 'zma', 'Zm00001eb285040' => 'zma', 'Zm00001eb330790' => 'zma', 'Zm00001eb337380' => 'zma' ) $gf_id = 'HOM05D001484' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001484' ) $data_identifier = 'HOM05D001484' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 2, 'aly' => (int) 2, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 22, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 7, 'hma' => (int) 2, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 7, 'mtr' => (int) 10, 'cme' => (int) 2, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 4, 'ppa' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 4, 'qlo' => (int) 9, 'rch' => (int) 6, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 10, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 7, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb337380' $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' => 'HOM05D001484', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p31500' => 'bna', 'A05p00020' => 'bna', 'A07p08820' => 'bna', 'Aa31LG4G3300' => 'aar', 'Aa31LG8G10030' => 'aar', 'Actinidia00731' => 'ach', 'Actinidia11473' => 'ach', 'Actinidia23469' => 'ach', 'Actinidia24318' => 'ach', 'Actinidia40196' => 'ach', 'Actinidia40197' => 'ach', 'Actinidia40198' => 'ach', 'Ah.08g212990' => 'amhyb', 'Ah.15g091720' => 'amhyb', 'AL3G38260' => 'aly', 'AL4G47710' => 'aly', 'Aqoxy2G00671' => 'aox', 'Aqoxy2G03236' => 'aox', 'arahy.Tifrunner.gnm1.ann1.05IDCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KR684' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATY3SJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK6QJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6APGL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IDT7Z9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM073U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ0R87' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LE7RV4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT4QRX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V5ENPK' => 'arhy', 'AT2G48110' => 'ath', 'AT3G23590' => 'ath', 'ATR0626G186' => 'atr', 'ATR1127G141' => 'atr', 'Atru.chr4.2583' => 'acertr', 'Atru.chr5.1358' => 'acertr', 'Atru.chr5.1359' => 'acertr', 'Atru.chr8.46' => 'acertr', 'AUR62002640' => 'cqu', 'AUR62030055' => 'cqu', 'AUR62033713' => 'cqu', 'AUR62033714' => 'cqu', 'AUR62036795' => 'cqu', 'AUR62039891' => 'cqu', 'BcaB02g08737' => 'bca', 'BcaB04g20441' => 'bca', 'BcaB06g26509' => 'bca', 'BcaB06g26510' => 'bca', 'BcaB06g26511' => 'bca', 'BcaB06g26512' => 'bca', 'BcaB06g26513' => 'bca', 'BcaC02g12564' => 'bca', 'BcaC02g12565' => 'bca', 'BcaC02g12794' => 'bca', 'BcaC02g12795' => 'bca', 'BcaC02g12796' => 'bca', 'BcaC06g35541' => 'bca', 'BNapus_Darmor_BZH_scaffold_188p00080' => 'bna', 'BNapus_Darmor_BZH_scaffold_188p00090' => 'bna', 'BolC1t03972H' => 'bol', 'BolC1t03973H' => 'bol', 'BolC4t21680H' => 'bol', 'BolC7t41863H' => 'bol', 'BolSC55t61227H' => 'bol', 'BolSC55t61228H' => 'bol', 'BraA01t03278Z' => 'bra', 'BraA05t18998Z' => 'bra', 'BraA07t28673Z' => 'bra', 'C01p40150' => 'bna', 'C05p12370' => 'bna', 'C07p13680' => 'bna', 'CAN.G1006.16' => 'can', 'CAN.G1006.17' => 'can', 'CAN.G1170.2' => 'can', 'CAN.G962.7' => 'can', 'CANSAT25G2179' => 'cansat', 'CANSAT78G1573' => 'cansat', 'CARHR099510' => 'chi', 'CARHR143510' => 'chi', 'Carub.0003s2380' => 'cru', 'Carub.0004s3082' => 'cru', 'Ca_00614_v3' => 'car', 'Ca_07801_v3' => 'car', 'Ca_08567_v3' => 'car', 'Ca_09571_v3' => 'car', 'CBR_g19290' => 'cbr', 'Cc01_g19770' => 'ccan', 'Cc03_g03030' => 'ccan', 'CDE07G0968' => 'cde', 'CDE09G1441' => 'cde', 'Cfa006103' => 'cfa', 'Cfa015573' => 'cfa', 'Cfa016988' => 'cfa', 'Ciclev10006738m.g' => 'ccl', 'Ciclev10010920m.g' => 'ccl', 'Ciclev10018517m.g' => 'ccl', 'CiPaw.01G159200' => 'cil', 'CiPaw.02G091000' => 'cil', 'CiPaw.02G091100' => 'cil', 'CiPaw.08G103100' => 'cil', 'CiPaw.09G224900' => 'cil', 'ClCG06G005740' => 'cla', 'ClCG07G000090' => 'cla', 'ClCG07G000100' => 'cla', 'COL.COLO4_09143' => 'col', 'COL.COLO4_25124' => 'col', 'Cpa.g.sc16.34' => 'cpa', 'Cpa.g.sc3504.1' => 'cpa', 'Cpa.g.sc60.37' => 'cpa', 'CsaV3_6G018520' => 'csa', 'CsaV3_6G036860' => 'csa', 'CSS0001072' => 'camsi', 'CSS0020208' => 'camsi', 'CSS0021253' => 'camsi', 'CSS0022190' => 'camsi', 'CSS0036150' => 'camsi', 'CSS0040442' => 'camsi', 'CSS0042300' => 'camsi', 'CSS0045298' => 'camsi', 'DCAR_012449' => 'dca', 'DCAR_018405' => 'dca', 'DCAR_024573' => 'dca', 'DCAR_030591' => 'dca', 'Dinv16926' => 'din', 'Dinv32963' => 'din', 'Dinv38382' => 'din', 'Dinv38383' => 'din', 'Duzib133G0974' => 'dzi', 'Duzib138G1867' => 'dzi', 'Duzib211G0420' => 'dzi', 'Duzib212G0930' => 'dzi', 'ECA234G1645' => 'eca', 'ECA247G3467' => 'eca', 'ECA248G1703' => 'eca', 'EL10Ac3g06327' => 'bvu', 'EL10Ac7g17204' => 'bvu', 'Eucgr.A00855' => 'egr', 'Eucgr.A00858' => 'egr', 'Eucgr.H01520' => 'egr', 'Eucgr.H03604' => 'egr', 'Eucgr.L03465' => 'egr', 'Eucgr.L03466' => 'egr', 'FAN01G0988' => 'fan', 'FAN02G3892' => 'fan', 'FAN05G3381' => 'fan', 'FAN07G0967' => 'fan', 'FAN07G1493' => 'fan', 'FAN08G3125' => 'fan', 'FAN09G0402' => 'fan', 'FAN12G2594' => 'fan', 'FAN12G3879' => 'fan', 'FAN14G1546' => 'fan', 'FAN15G3626' => 'fan', 'FAN17G0588' => 'fan', 'FAN17G0609' => 'fan', 'FAN18G2817' => 'fan', 'FAN19G1305' => 'fan', 'FAN20G1787' => 'fan', 'FAN22G0073' => 'fan', 'FAN22G0352' => 'fan', 'FAN22G0368' => 'fan', 'FAN22G2273' => 'fan', 'FAN24G1998' => 'fan', 'FAN27G1317' => 'fan', 'FvH4_2g23980' => 'fve', 'FvH4_4g14380' => 'fve', 'FvH4_4g14390' => 'fve', 'FvH4_6g09250' => 'fve', 'Glyma.03G151100' => 'gma', 'Glyma.04G122550' => 'gma', 'Glyma.05G001600' => 'gma', 'Glyma.09G270766' => 'gma', 'Glyma.09G270832' => 'gma', 'Glyma.13G209800' => 'gma', 'Glyma.15G102800' => 'gma', 'Glyma.18G218900' => 'gma', 'Glyma.19G001500' => 'gma', 'Glyma.19G153600' => 'gma', 'Gohir.A02G028600' => 'ghi', 'Gohir.A08G045000' => 'ghi', 'Gohir.A11G120500' => 'ghi', 'Gohir.A12G006200' => 'ghi', 'Gohir.A12G006250' => 'ghi', 'Gohir.D02G036300' => 'ghi', 'Gohir.D08G054700' => 'ghi', 'Gohir.D11G125600' => 'ghi', 'Gohir.D12G005700' => 'ghi', 'Gorai.004G055200' => 'gra', 'Gorai.005G040400' => 'gra', 'Gorai.007G134500' => 'gra', 'Gorai.008G005500' => 'gra', 'GSVIVG01011094001' => 'vvi', 'GSVIVG01017879001' => 'vvi', 'GSVIVG01025988001' => 'vvi', 'GSVIVG01029847001' => 'vvi', 'HanXRQChr10g0282901' => 'han', 'HanXRQChr10g0310371' => 'han', 'HanXRQChr10g0315041' => 'han', 'HanXRQChr11g0327651' => 'han', 'HanXRQChr12g0359391' => 'han', 'Haze_00972' => 'cav', 'Haze_00973' => 'cav', 'Haze_00974' => 'cav', 'Haze_04747' => 'cav', 'Haze_04749' => 'cav', 'Haze_04750' => 'cav', 'Haze_21217' => 'cav', 'Hma1.2p1_1037F.1_g250680' => 'hma', 'Hma1.2p1_1644F.1_g295320' => 'hma', 'HPP92_011322' => 'vpl', 'HPP92_011323' => 'vpl', 'HPP92_011324' => 'vpl', 'HPP92_011325' => 'vpl', 'HPP92_011326' => 'vpl', 'Hund12205' => 'sun', 'Hund17957' => 'sun', 'Lalb_Chr06g0176771' => 'lal', 'Lalb_Chr18g0056021' => 'lal', 'Lalb_Chr18g0056031' => 'lal', 'Lalb_Chr18g0056041' => 'lal', 'Lalb_Chr20g0107751' => 'lal', 'Lalb_Chr20g0118371' => 'lal', 'Lj1g0010239' => 'lja', 'Lj1g0017101' => 'lja', 'Lj2A1178G40' => 'lonja', 'Lj2A54G84' => 'lonja', 'Lj2g0015248' => 'lja', 'Lj3A761T51' => 'lonja', 'Lj6g0018116' => 'lja', 'Lsat_1_v5_gn_4_136040' => 'lsa', 'Lsat_1_v5_gn_5_187461' => 'lsa', 'Lsat_1_v5_gn_5_77001' => 'lsa', 'Lsat_1_v5_gn_9_4461' => 'lsa', 'Manes.01G210100' => 'mes', 'Manes.03G185600' => 'mes', 'Manes.05G073300' => 'mes', 'Manes.09G120300' => 'mes', 'Manes.15G022100' => 'mes', 'Mapoly0096s0053' => 'mpo', 'MBI03_g14058_MAGBIO' => 'mbi', 'MBI03_g33876_MAGBIO' => 'mbi', 'MBI03_g36854_MAGBIO' => 'mbi', 'MBI17_g11997_MAGBIO' => 'mbi', 'MD03G1269000' => 'mdo', 'MD04G1179600' => 'mdo', 'MD11G1289800' => 'mdo', 'MD12G1194700' => 'mdo', 'MD13G1182100' => 'mdo', 'MD13G1182200' => 'mdo', 'MD16G1182600' => 'mdo', 'Medtr2g021400' => 'mtr', 'Medtr2g021470' => 'mtr', 'Medtr2g105810' => 'mtr', 'Medtr3g033580' => 'mtr', 'Medtr6g007970' => 'mtr', 'Medtr7g056330' => 'mtr', 'Medtr7g074290' => 'mtr', 'Medtr7g074380' => 'mtr', 'Medtr7g094550' => 'mtr', 'Medtr8g069995' => 'mtr', 'MELO3C014345.2' => 'cme', 'MELO3C021395.2' => 'cme', 'Migut.D00262' => 'egut', 'Migut.G00257' => 'egut', 'MSTRG.21575' => 'ama', 'MSTRG.3985' => 'ama', 'Nitab4.5_0000295g0140' => 'nta', 'Nitab4.5_0000732g0140' => 'nta', 'Nitab4.5_0003162g0020' => 'nta', 'Nitab4.5_0006180g0090' => 'nta', 'Nitab4.5_0006390g0010' => 'nta', 'Nitab4.5_0007392g0040' => 'nta', 'Nn1g02140' => 'nnu', 'Nn4g26168' => 'nnu', 'Nn5g26754' => 'nnu', 'Oeu001433.1' => 'oeu', 'Oeu010299.2' => 'oeu', 'Oeu011171.1' => 'oeu', 'Oeu037675.1' => 'oeu', 'Oeu038359.1' => 'oeu', 'Oeu063834.1' => 'oeu', 'Oeu063835.1' => 'oeu', 'Os05g0312000' => 'osa', 'Os07g0211101' => 'osa', 'Os07g0211200' => 'osa', 'Os07g0681500' => 'osa', 'Peaxi162Scf00095g01015' => 'pax', 'Peaxi162Scf00104g00329' => 'pax', 'Peaxi162Scf00161g00137' => 'pax', 'PGR004G1665' => 'pgr', 'PGR031G2937' => 'pgr', 'PGR119G2145' => 'pgr', 'PGSC0003DMG400004351' => 'stu', 'PGSC0003DMG400014625' => 'stu', 'PGSC0003DMG401000943' => 'stu', 'Phvul.001G148600' => 'pvu', 'Phvul.004G001700' => 'pvu', 'Phvul.006G154900' => 'pvu', 'Phvul.008G078200' => 'pvu', 'Phvul.011G136500' => 'pvu', 'Potri.002G215600' => 'ptr', 'Potri.008G201600' => 'ptr', 'Potri.014G138400' => 'ptr', 'Potri.016G142500' => 'ptr', 'Pp3c16_10580' => 'ppa', 'Pp3c5_25280' => 'ppa', 'Prupe.1G150000' => 'ppe', 'Prupe.1G150100' => 'ppe', 'Prupe.6G299600' => 'ppe', 'Prupe.8G245000' => 'ppe', 'Psat0s4927g0040' => 'psa', 'Psat1g052080' => 'psa', 'Psat1g183800' => 'psa', 'Psat3g113840' => 'psa', 'Psat3g126120' => 'psa', 'Psat3g126160' => 'psa', 'Psat3g158760' => 'psa', 'Psat3g158840' => 'psa', 'PSO170G2858' => 'pso', 'PSO339G0606' => 'pso', 'PSO384G4709' => 'pso', 'PSO407G0334' => 'pso', 'QL04p040276' => 'qlo', 'QL06p005458' => 'qlo', 'QL06p005472' => 'qlo', 'QL07p030546' => 'qlo', 'QL07p031519' => 'qlo', 'QL09p050949' => 'qlo', 'QL09p050966' => 'qlo', 'QL09p051067' => 'qlo', 'QL12p022706' => 'qlo', 'RcHm_v2.0_Chr2g0119601' => 'rch', 'RcHm_v2.0_Chr3g0459591' => 'rch', 'RcHm_v2.0_Chr4g0418521' => 'rch', 'RcHm_v2.0_Chr4g0418531' => 'rch', 'RcHm_v2.0_Chr4g0418541' => 'rch', 'RcHm_v2.0_Chr6g0291641' => 'rch', 'Rhsim01G0086300' => 'rsi', 'Rhsim01G0276300' => 'rsi', 'Rhsim01G0276500' => 'rsi', 'Rhsim04G0207700' => 'rsi', 'Rhsim05G0234500' => 'rsi', 'Rhsim13G0022400' => 'rsi', 'Sabra02G0167900' => 'sbr', 'Sabra04G0158500' => 'sbr', 'Sabra08G0159800' => 'sbr', 'Sabra10G0011500' => 'sbr', 'Sabra14G0104400' => 'sbr', 'SalBow2G2440' => 'sbo', 'SalBow4G2265' => 'sbo', 'Sc02g0000060' => 'sci', 'Sc05g0005020' => 'sci', 'Sc13g0003890' => 'sci', 'Sed0014865' => 'sed', 'Sed0017224' => 'sed', 'Sed0026391' => 'sed', 'SEGI_00063' => 'sgi', 'SEGI_10967' => 'sgi', 'SEGI_17510' => 'sgi', 'SEGI_24396' => 'sgi', 'SEGI_39719' => 'sgi', 'SEGI_41392' => 'sgi', 'SGA_v2.0_scaffold11G05794' => 'sas', 'SGA_v2.0_scaffold142G35607' => 'sas', 'SGA_v2.0_scaffold1G00447' => 'sas', 'SHI15388' => 'shi', 'SHI15394' => 'shi', 'SHI15396' => 'shi', 'SHI15399' => 'shi', 'SMO343G0151' => 'smo', 'SMO367G1118' => 'smo', 'Solyc01g080200.3' => 'sly', 'Solyc06g008960.3' => 'sly', 'Solyc09g064780.3' => 'sly', 'Sopen01g031980' => 'spe', 'Sopen06g003710' => 'spe', 'Sopen09g026460' => 'spe', 'Sp3g21240' => 'spa', 'Sp4g30030' => 'spa', 'TAR365G0022' => 'tar', 'TAR365G1023' => 'tar', 'TAR365G1253' => 'tar', 'TAR623G0078' => 'tar', 'TAR623G1721' => 'tar', 'TAR633G0959' => 'tar', 'THA.LOC104802225' => 'tha', 'THA.LOC104804769' => 'tha', 'THA.LOC104808660' => 'tha', 'THA.LOC104812792' => 'tha', 'Thecc.01G284000' => 'tca', 'Thecc.04G220600' => 'tca', 'Thecc.05G268900' => 'tca', 'Thecc.08G171100' => 'tca', 'Thhalv10001284m.g' => 'esa', 'Thhalv10019912m.g' => 'esa', 'TPR.G14189' => 'tpr', 'TPR.G18110' => 'tpr', 'TPR.G18130' => 'tpr', 'TPR.G18131' => 'tpr', 'TPR.G18140' => 'tpr', 'TPR.G24282' => 'tpr', 'TPR.G25221' => 'tpr', 'TPR.G29267' => 'tpr', 'TPR.G35315' => 'tpr', 'TPR.G36173' => 'tpr', 'TWI09G0794' => 'twi', 'TWI59G1348' => 'twi', 'TWI74G0430' => 'twi', 'unitig_26.g8940' => 'ugi', 'unitig_749.g13744' => 'ugi', 'unitig_749.g13745' => 'ugi', 'vmacro08269' => 'vma', 'vmacro14937' => 'vma', 'vmacro20401' => 'vma', 'VMungo0464G1349' => 'vmu', 'VMungo0540G0289' => 'vmu', 'VMungo1215G1590' => 'vmu', 'VMungo1309G0221' => 'vmu', 'VMungo1309G2815' => 'vmu', 'VMungo1383G0239' => 'vmu', 'VMungo1383G2910' => 'vmu', 'Zm00001eb095270' => 'zma', 'Zm00001eb095280' => 'zma', 'Zm00001eb111630' => 'zma', 'Zm00001eb237080' => 'zma', 'Zm00001eb273740' => 'zma', 'Zm00001eb285040' => 'zma', 'Zm00001eb330790' => 'zma', 'Zm00001eb337380' => 'zma' ), 'gf_id' => 'HOM05D001484', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001484' ), 'data_identifier' => 'HOM05D001484', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001484', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p31500' => 'bna', 'A05p00020' => 'bna', 'A07p08820' => 'bna', 'Aa31LG4G3300' => 'aar', 'Aa31LG8G10030' => 'aar', 'Actinidia00731' => 'ach', 'Actinidia11473' => 'ach', 'Actinidia23469' => 'ach', 'Actinidia24318' => 'ach', 'Actinidia40196' => 'ach', 'Actinidia40197' => 'ach', 'Actinidia40198' => 'ach', 'Ah.08g212990' => 'amhyb', 'Ah.15g091720' => 'amhyb', 'AL3G38260' => 'aly', 'AL4G47710' => 'aly', 'Aqoxy2G00671' => 'aox', 'Aqoxy2G03236' => 'aox', 'arahy.Tifrunner.gnm1.ann1.05IDCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KR684' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATY3SJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK6QJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6APGL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IDT7Z9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM073U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ0R87' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LE7RV4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT4QRX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V5ENPK' => 'arhy', 'AT2G48110' => 'ath', 'AT3G23590' => 'ath', 'ATR0626G186' => 'atr', 'ATR1127G141' => 'atr', 'Atru.chr4.2583' => 'acertr', 'Atru.chr5.1358' => 'acertr', 'Atru.chr5.1359' => 'acertr', 'Atru.chr8.46' => 'acertr', 'AUR62002640' => 'cqu', 'AUR62030055' => 'cqu', 'AUR62033713' => 'cqu', 'AUR62033714' => 'cqu', 'AUR62036795' => 'cqu', 'AUR62039891' => 'cqu', 'BcaB02g08737' => 'bca', 'BcaB04g20441' => 'bca', 'BcaB06g26509' => 'bca', 'BcaB06g26510' => 'bca', 'BcaB06g26511' => 'bca', 'BcaB06g26512' => 'bca', 'BcaB06g26513' => 'bca', 'BcaC02g12564' => 'bca', 'BcaC02g12565' => 'bca', 'BcaC02g12794' => 'bca', 'BcaC02g12795' => 'bca', 'BcaC02g12796' => 'bca', 'BcaC06g35541' => 'bca', 'BNapus_Darmor_BZH_scaffold_188p00080' => 'bna', 'BNapus_Darmor_BZH_scaffold_188p00090' => 'bna', 'BolC1t03972H' => 'bol', 'BolC1t03973H' => 'bol', 'BolC4t21680H' => 'bol', 'BolC7t41863H' => 'bol', 'BolSC55t61227H' => 'bol', 'BolSC55t61228H' => 'bol', 'BraA01t03278Z' => 'bra', 'BraA05t18998Z' => 'bra', 'BraA07t28673Z' => 'bra', 'C01p40150' => 'bna', 'C05p12370' => 'bna', 'C07p13680' => 'bna', 'CAN.G1006.16' => 'can', 'CAN.G1006.17' => 'can', 'CAN.G1170.2' => 'can', 'CAN.G962.7' => 'can', 'CANSAT25G2179' => 'cansat', 'CANSAT78G1573' => 'cansat', 'CARHR099510' => 'chi', 'CARHR143510' => 'chi', 'Carub.0003s2380' => 'cru', 'Carub.0004s3082' => 'cru', 'Ca_00614_v3' => 'car', 'Ca_07801_v3' => 'car', 'Ca_08567_v3' => 'car', 'Ca_09571_v3' => 'car', 'CBR_g19290' => 'cbr', 'Cc01_g19770' => 'ccan', 'Cc03_g03030' => 'ccan', 'CDE07G0968' => 'cde', 'CDE09G1441' => 'cde', 'Cfa006103' => 'cfa', 'Cfa015573' => 'cfa', 'Cfa016988' => 'cfa', 'Ciclev10006738m.g' => 'ccl', 'Ciclev10010920m.g' => 'ccl', 'Ciclev10018517m.g' => 'ccl', 'CiPaw.01G159200' => 'cil', 'CiPaw.02G091000' => 'cil', 'CiPaw.02G091100' => 'cil', 'CiPaw.08G103100' => 'cil', 'CiPaw.09G224900' => 'cil', 'ClCG06G005740' => 'cla', 'ClCG07G000090' => 'cla', 'ClCG07G000100' => 'cla', 'COL.COLO4_09143' => 'col', 'COL.COLO4_25124' => 'col', 'Cpa.g.sc16.34' => 'cpa', 'Cpa.g.sc3504.1' => 'cpa', 'Cpa.g.sc60.37' => 'cpa', 'CsaV3_6G018520' => 'csa', 'CsaV3_6G036860' => 'csa', 'CSS0001072' => 'camsi', 'CSS0020208' => 'camsi', 'CSS0021253' => 'camsi', 'CSS0022190' => 'camsi', 'CSS0036150' => 'camsi', 'CSS0040442' => 'camsi', 'CSS0042300' => 'camsi', 'CSS0045298' => 'camsi', 'DCAR_012449' => 'dca', 'DCAR_018405' => 'dca', 'DCAR_024573' => 'dca', 'DCAR_030591' => 'dca', 'Dinv16926' => 'din', 'Dinv32963' => 'din', 'Dinv38382' => 'din', 'Dinv38383' => 'din', 'Duzib133G0974' => 'dzi', 'Duzib138G1867' => 'dzi', 'Duzib211G0420' => 'dzi', 'Duzib212G0930' => 'dzi', 'ECA234G1645' => 'eca', 'ECA247G3467' => 'eca', 'ECA248G1703' => 'eca', 'EL10Ac3g06327' => 'bvu', 'EL10Ac7g17204' => 'bvu', 'Eucgr.A00855' => 'egr', 'Eucgr.A00858' => 'egr', 'Eucgr.H01520' => 'egr', 'Eucgr.H03604' => 'egr', 'Eucgr.L03465' => 'egr', 'Eucgr.L03466' => 'egr', 'FAN01G0988' => 'fan', 'FAN02G3892' => 'fan', 'FAN05G3381' => 'fan', 'FAN07G0967' => 'fan', 'FAN07G1493' => 'fan', 'FAN08G3125' => 'fan', 'FAN09G0402' => 'fan', 'FAN12G2594' => 'fan', 'FAN12G3879' => 'fan', 'FAN14G1546' => 'fan', 'FAN15G3626' => 'fan', 'FAN17G0588' => 'fan', 'FAN17G0609' => 'fan', 'FAN18G2817' => 'fan', 'FAN19G1305' => 'fan', 'FAN20G1787' => 'fan', 'FAN22G0073' => 'fan', 'FAN22G0352' => 'fan', 'FAN22G0368' => 'fan', 'FAN22G2273' => 'fan', 'FAN24G1998' => 'fan', 'FAN27G1317' => 'fan', 'FvH4_2g23980' => 'fve', 'FvH4_4g14380' => 'fve', 'FvH4_4g14390' => 'fve', 'FvH4_6g09250' => 'fve', 'Glyma.03G151100' => 'gma', 'Glyma.04G122550' => 'gma', 'Glyma.05G001600' => 'gma', 'Glyma.09G270766' => 'gma', 'Glyma.09G270832' => 'gma', 'Glyma.13G209800' => 'gma', 'Glyma.15G102800' => 'gma', 'Glyma.18G218900' => 'gma', 'Glyma.19G001500' => 'gma', 'Glyma.19G153600' => 'gma', 'Gohir.A02G028600' => 'ghi', 'Gohir.A08G045000' => 'ghi', 'Gohir.A11G120500' => 'ghi', 'Gohir.A12G006200' => 'ghi', 'Gohir.A12G006250' => 'ghi', 'Gohir.D02G036300' => 'ghi', 'Gohir.D08G054700' => 'ghi', 'Gohir.D11G125600' => 'ghi', 'Gohir.D12G005700' => 'ghi', 'Gorai.004G055200' => 'gra', 'Gorai.005G040400' => 'gra', 'Gorai.007G134500' => 'gra', 'Gorai.008G005500' => 'gra', 'GSVIVG01011094001' => 'vvi', 'GSVIVG01017879001' => 'vvi', 'GSVIVG01025988001' => 'vvi', 'GSVIVG01029847001' => 'vvi', 'HanXRQChr10g0282901' => 'han', 'HanXRQChr10g0310371' => 'han', 'HanXRQChr10g0315041' => 'han', 'HanXRQChr11g0327651' => 'han', 'HanXRQChr12g0359391' => 'han', 'Haze_00972' => 'cav', 'Haze_00973' => 'cav', 'Haze_00974' => 'cav', 'Haze_04747' => 'cav', 'Haze_04749' => 'cav', 'Haze_04750' => 'cav', 'Haze_21217' => 'cav', 'Hma1.2p1_1037F.1_g250680' => 'hma', 'Hma1.2p1_1644F.1_g295320' => 'hma', 'HPP92_011322' => 'vpl', 'HPP92_011323' => 'vpl', 'HPP92_011324' => 'vpl', 'HPP92_011325' => 'vpl', 'HPP92_011326' => 'vpl', 'Hund12205' => 'sun', 'Hund17957' => 'sun', 'Lalb_Chr06g0176771' => 'lal', 'Lalb_Chr18g0056021' => 'lal', 'Lalb_Chr18g0056031' => 'lal', 'Lalb_Chr18g0056041' => 'lal', 'Lalb_Chr20g0107751' => 'lal', 'Lalb_Chr20g0118371' => 'lal', 'Lj1g0010239' => 'lja', 'Lj1g0017101' => 'lja', 'Lj2A1178G40' => 'lonja', 'Lj2A54G84' => 'lonja', 'Lj2g0015248' => 'lja', 'Lj3A761T51' => 'lonja', 'Lj6g0018116' => 'lja', 'Lsat_1_v5_gn_4_136040' => 'lsa', 'Lsat_1_v5_gn_5_187461' => 'lsa', 'Lsat_1_v5_gn_5_77001' => 'lsa', 'Lsat_1_v5_gn_9_4461' => 'lsa', 'Manes.01G210100' => 'mes', 'Manes.03G185600' => 'mes', 'Manes.05G073300' => 'mes', 'Manes.09G120300' => 'mes', 'Manes.15G022100' => 'mes', 'Mapoly0096s0053' => 'mpo', 'MBI03_g14058_MAGBIO' => 'mbi', 'MBI03_g33876_MAGBIO' => 'mbi', 'MBI03_g36854_MAGBIO' => 'mbi', 'MBI17_g11997_MAGBIO' => 'mbi', 'MD03G1269000' => 'mdo', 'MD04G1179600' => 'mdo', 'MD11G1289800' => 'mdo', 'MD12G1194700' => 'mdo', 'MD13G1182100' => 'mdo', 'MD13G1182200' => 'mdo', 'MD16G1182600' => 'mdo', 'Medtr2g021400' => 'mtr', 'Medtr2g021470' => 'mtr', 'Medtr2g105810' => 'mtr', 'Medtr3g033580' => 'mtr', 'Medtr6g007970' => 'mtr', 'Medtr7g056330' => 'mtr', 'Medtr7g074290' => 'mtr', 'Medtr7g074380' => 'mtr', 'Medtr7g094550' => 'mtr', 'Medtr8g069995' => 'mtr', 'MELO3C014345.2' => 'cme', 'MELO3C021395.2' => 'cme', 'Migut.D00262' => 'egut', 'Migut.G00257' => 'egut', 'MSTRG.21575' => 'ama', 'MSTRG.3985' => 'ama', 'Nitab4.5_0000295g0140' => 'nta', 'Nitab4.5_0000732g0140' => 'nta', 'Nitab4.5_0003162g0020' => 'nta', 'Nitab4.5_0006180g0090' => 'nta', 'Nitab4.5_0006390g0010' => 'nta', 'Nitab4.5_0007392g0040' => 'nta', 'Nn1g02140' => 'nnu', 'Nn4g26168' => 'nnu', 'Nn5g26754' => 'nnu', 'Oeu001433.1' => 'oeu', 'Oeu010299.2' => 'oeu', 'Oeu011171.1' => 'oeu', 'Oeu037675.1' => 'oeu', 'Oeu038359.1' => 'oeu', 'Oeu063834.1' => 'oeu', 'Oeu063835.1' => 'oeu', 'Os05g0312000' => 'osa', 'Os07g0211101' => 'osa', 'Os07g0211200' => 'osa', 'Os07g0681500' => 'osa', 'Peaxi162Scf00095g01015' => 'pax', 'Peaxi162Scf00104g00329' => 'pax', 'Peaxi162Scf00161g00137' => 'pax', 'PGR004G1665' => 'pgr', 'PGR031G2937' => 'pgr', 'PGR119G2145' => 'pgr', 'PGSC0003DMG400004351' => 'stu', 'PGSC0003DMG400014625' => 'stu', 'PGSC0003DMG401000943' => 'stu', 'Phvul.001G148600' => 'pvu', 'Phvul.004G001700' => 'pvu', 'Phvul.006G154900' => 'pvu', 'Phvul.008G078200' => 'pvu', 'Phvul.011G136500' => 'pvu', 'Potri.002G215600' => 'ptr', 'Potri.008G201600' => 'ptr', 'Potri.014G138400' => 'ptr', 'Potri.016G142500' => 'ptr', 'Pp3c16_10580' => 'ppa', 'Pp3c5_25280' => 'ppa', 'Prupe.1G150000' => 'ppe', 'Prupe.1G150100' => 'ppe', 'Prupe.6G299600' => 'ppe', 'Prupe.8G245000' => 'ppe', 'Psat0s4927g0040' => 'psa', 'Psat1g052080' => 'psa', 'Psat1g183800' => 'psa', 'Psat3g113840' => 'psa', 'Psat3g126120' => 'psa', 'Psat3g126160' => 'psa', 'Psat3g158760' => 'psa', 'Psat3g158840' => 'psa', 'PSO170G2858' => 'pso', 'PSO339G0606' => 'pso', 'PSO384G4709' => 'pso', 'PSO407G0334' => 'pso', 'QL04p040276' => 'qlo', 'QL06p005458' => 'qlo', 'QL06p005472' => 'qlo', 'QL07p030546' => 'qlo', 'QL07p031519' => 'qlo', 'QL09p050949' => 'qlo', 'QL09p050966' => 'qlo', 'QL09p051067' => 'qlo', 'QL12p022706' => 'qlo', 'RcHm_v2.0_Chr2g0119601' => 'rch', 'RcHm_v2.0_Chr3g0459591' => 'rch', 'RcHm_v2.0_Chr4g0418521' => 'rch', 'RcHm_v2.0_Chr4g0418531' => 'rch', 'RcHm_v2.0_Chr4g0418541' => 'rch', 'RcHm_v2.0_Chr6g0291641' => 'rch', 'Rhsim01G0086300' => 'rsi', 'Rhsim01G0276300' => 'rsi', 'Rhsim01G0276500' => 'rsi', 'Rhsim04G0207700' => 'rsi', 'Rhsim05G0234500' => 'rsi', 'Rhsim13G0022400' => 'rsi', 'Sabra02G0167900' => 'sbr', 'Sabra04G0158500' => 'sbr', 'Sabra08G0159800' => 'sbr', 'Sabra10G0011500' => 'sbr', 'Sabra14G0104400' => 'sbr', 'SalBow2G2440' => 'sbo', 'SalBow4G2265' => 'sbo', 'Sc02g0000060' => 'sci', 'Sc05g0005020' => 'sci', 'Sc13g0003890' => 'sci', 'Sed0014865' => 'sed', 'Sed0017224' => 'sed', 'Sed0026391' => 'sed', 'SEGI_00063' => 'sgi', 'SEGI_10967' => 'sgi', 'SEGI_17510' => 'sgi', 'SEGI_24396' => 'sgi', 'SEGI_39719' => 'sgi', 'SEGI_41392' => 'sgi', 'SGA_v2.0_scaffold11G05794' => 'sas', 'SGA_v2.0_scaffold142G35607' => 'sas', 'SGA_v2.0_scaffold1G00447' => 'sas', 'SHI15388' => 'shi', 'SHI15394' => 'shi', 'SHI15396' => 'shi', 'SHI15399' => 'shi', 'SMO343G0151' => 'smo', 'SMO367G1118' => 'smo', 'Solyc01g080200.3' => 'sly', 'Solyc06g008960.3' => 'sly', 'Solyc09g064780.3' => 'sly', 'Sopen01g031980' => 'spe', 'Sopen06g003710' => 'spe', 'Sopen09g026460' => 'spe', 'Sp3g21240' => 'spa', 'Sp4g30030' => 'spa', 'TAR365G0022' => 'tar', 'TAR365G1023' => 'tar', 'TAR365G1253' => 'tar', 'TAR623G0078' => 'tar', 'TAR623G1721' => 'tar', 'TAR633G0959' => 'tar', 'THA.LOC104802225' => 'tha', 'THA.LOC104804769' => 'tha', 'THA.LOC104808660' => 'tha', 'THA.LOC104812792' => 'tha', 'Thecc.01G284000' => 'tca', 'Thecc.04G220600' => 'tca', 'Thecc.05G268900' => 'tca', 'Thecc.08G171100' => 'tca', 'Thhalv10001284m.g' => 'esa', 'Thhalv10019912m.g' => 'esa', 'TPR.G14189' => 'tpr', 'TPR.G18110' => 'tpr', 'TPR.G18130' => 'tpr', 'TPR.G18131' => 'tpr', 'TPR.G18140' => 'tpr', 'TPR.G24282' => 'tpr', 'TPR.G25221' => 'tpr', 'TPR.G29267' => 'tpr', 'TPR.G35315' => 'tpr', 'TPR.G36173' => 'tpr', 'TWI09G0794' => 'twi', 'TWI59G1348' => 'twi', 'TWI74G0430' => 'twi', 'unitig_26.g8940' => 'ugi', 'unitig_749.g13744' => 'ugi', 'unitig_749.g13745' => 'ugi', 'vmacro08269' => 'vma', 'vmacro14937' => 'vma', 'vmacro20401' => 'vma', 'VMungo0464G1349' => 'vmu', 'VMungo0540G0289' => 'vmu', 'VMungo1215G1590' => 'vmu', 'VMungo1309G0221' => 'vmu', 'VMungo1309G2815' => 'vmu', 'VMungo1383G0239' => 'vmu', 'VMungo1383G2910' => 'vmu', 'Zm00001eb095270' => 'zma', 'Zm00001eb095280' => 'zma', 'Zm00001eb111630' => 'zma', 'Zm00001eb237080' => 'zma', 'Zm00001eb273740' => 'zma', 'Zm00001eb285040' => 'zma', 'Zm00001eb330790' => 'zma', 'Zm00001eb337380' => 'zma' ) $gf_id = 'HOM05D001484' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001484' ) $data_identifier = 'HOM05D001484' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 2, 'aly' => (int) 2, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 22, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 7, 'hma' => (int) 2, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 7, 'mtr' => (int) 10, 'cme' => (int) 2, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 4, 'ppa' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 4, 'qlo' => (int) 9, 'rch' => (int) 6, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 10, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 7, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb337380' $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' => 'HOM05D001484', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p31500' => 'bna', 'A05p00020' => 'bna', 'A07p08820' => 'bna', 'Aa31LG4G3300' => 'aar', 'Aa31LG8G10030' => 'aar', 'Actinidia00731' => 'ach', 'Actinidia11473' => 'ach', 'Actinidia23469' => 'ach', 'Actinidia24318' => 'ach', 'Actinidia40196' => 'ach', 'Actinidia40197' => 'ach', 'Actinidia40198' => 'ach', 'Ah.08g212990' => 'amhyb', 'Ah.15g091720' => 'amhyb', 'AL3G38260' => 'aly', 'AL4G47710' => 'aly', 'Aqoxy2G00671' => 'aox', 'Aqoxy2G03236' => 'aox', 'arahy.Tifrunner.gnm1.ann1.05IDCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KR684' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATY3SJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK6QJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6APGL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IDT7Z9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM073U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ0R87' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LE7RV4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT4QRX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V5ENPK' => 'arhy', 'AT2G48110' => 'ath', 'AT3G23590' => 'ath', 'ATR0626G186' => 'atr', 'ATR1127G141' => 'atr', 'Atru.chr4.2583' => 'acertr', 'Atru.chr5.1358' => 'acertr', 'Atru.chr5.1359' => 'acertr', 'Atru.chr8.46' => 'acertr', 'AUR62002640' => 'cqu', 'AUR62030055' => 'cqu', 'AUR62033713' => 'cqu', 'AUR62033714' => 'cqu', 'AUR62036795' => 'cqu', 'AUR62039891' => 'cqu', 'BcaB02g08737' => 'bca', 'BcaB04g20441' => 'bca', 'BcaB06g26509' => 'bca', 'BcaB06g26510' => 'bca', 'BcaB06g26511' => 'bca', 'BcaB06g26512' => 'bca', 'BcaB06g26513' => 'bca', 'BcaC02g12564' => 'bca', 'BcaC02g12565' => 'bca', 'BcaC02g12794' => 'bca', 'BcaC02g12795' => 'bca', 'BcaC02g12796' => 'bca', 'BcaC06g35541' => 'bca', 'BNapus_Darmor_BZH_scaffold_188p00080' => 'bna', 'BNapus_Darmor_BZH_scaffold_188p00090' => 'bna', 'BolC1t03972H' => 'bol', 'BolC1t03973H' => 'bol', 'BolC4t21680H' => 'bol', 'BolC7t41863H' => 'bol', 'BolSC55t61227H' => 'bol', 'BolSC55t61228H' => 'bol', 'BraA01t03278Z' => 'bra', 'BraA05t18998Z' => 'bra', 'BraA07t28673Z' => 'bra', 'C01p40150' => 'bna', 'C05p12370' => 'bna', 'C07p13680' => 'bna', 'CAN.G1006.16' => 'can', 'CAN.G1006.17' => 'can', 'CAN.G1170.2' => 'can', 'CAN.G962.7' => 'can', 'CANSAT25G2179' => 'cansat', 'CANSAT78G1573' => 'cansat', 'CARHR099510' => 'chi', 'CARHR143510' => 'chi', 'Carub.0003s2380' => 'cru', 'Carub.0004s3082' => 'cru', 'Ca_00614_v3' => 'car', 'Ca_07801_v3' => 'car', 'Ca_08567_v3' => 'car', 'Ca_09571_v3' => 'car', 'CBR_g19290' => 'cbr', 'Cc01_g19770' => 'ccan', 'Cc03_g03030' => 'ccan', 'CDE07G0968' => 'cde', 'CDE09G1441' => 'cde', 'Cfa006103' => 'cfa', 'Cfa015573' => 'cfa', 'Cfa016988' => 'cfa', 'Ciclev10006738m.g' => 'ccl', 'Ciclev10010920m.g' => 'ccl', 'Ciclev10018517m.g' => 'ccl', 'CiPaw.01G159200' => 'cil', 'CiPaw.02G091000' => 'cil', 'CiPaw.02G091100' => 'cil', 'CiPaw.08G103100' => 'cil', 'CiPaw.09G224900' => 'cil', 'ClCG06G005740' => 'cla', 'ClCG07G000090' => 'cla', 'ClCG07G000100' => 'cla', 'COL.COLO4_09143' => 'col', 'COL.COLO4_25124' => 'col', 'Cpa.g.sc16.34' => 'cpa', 'Cpa.g.sc3504.1' => 'cpa', 'Cpa.g.sc60.37' => 'cpa', 'CsaV3_6G018520' => 'csa', 'CsaV3_6G036860' => 'csa', 'CSS0001072' => 'camsi', 'CSS0020208' => 'camsi', 'CSS0021253' => 'camsi', 'CSS0022190' => 'camsi', 'CSS0036150' => 'camsi', 'CSS0040442' => 'camsi', 'CSS0042300' => 'camsi', 'CSS0045298' => 'camsi', 'DCAR_012449' => 'dca', 'DCAR_018405' => 'dca', 'DCAR_024573' => 'dca', 'DCAR_030591' => 'dca', 'Dinv16926' => 'din', 'Dinv32963' => 'din', 'Dinv38382' => 'din', 'Dinv38383' => 'din', 'Duzib133G0974' => 'dzi', 'Duzib138G1867' => 'dzi', 'Duzib211G0420' => 'dzi', 'Duzib212G0930' => 'dzi', 'ECA234G1645' => 'eca', 'ECA247G3467' => 'eca', 'ECA248G1703' => 'eca', 'EL10Ac3g06327' => 'bvu', 'EL10Ac7g17204' => 'bvu', 'Eucgr.A00855' => 'egr', 'Eucgr.A00858' => 'egr', 'Eucgr.H01520' => 'egr', 'Eucgr.H03604' => 'egr', 'Eucgr.L03465' => 'egr', 'Eucgr.L03466' => 'egr', 'FAN01G0988' => 'fan', 'FAN02G3892' => 'fan', 'FAN05G3381' => 'fan', 'FAN07G0967' => 'fan', 'FAN07G1493' => 'fan', 'FAN08G3125' => 'fan', 'FAN09G0402' => 'fan', 'FAN12G2594' => 'fan', 'FAN12G3879' => 'fan', 'FAN14G1546' => 'fan', 'FAN15G3626' => 'fan', 'FAN17G0588' => 'fan', 'FAN17G0609' => 'fan', 'FAN18G2817' => 'fan', 'FAN19G1305' => 'fan', 'FAN20G1787' => 'fan', 'FAN22G0073' => 'fan', 'FAN22G0352' => 'fan', 'FAN22G0368' => 'fan', 'FAN22G2273' => 'fan', 'FAN24G1998' => 'fan', 'FAN27G1317' => 'fan', 'FvH4_2g23980' => 'fve', 'FvH4_4g14380' => 'fve', 'FvH4_4g14390' => 'fve', 'FvH4_6g09250' => 'fve', 'Glyma.03G151100' => 'gma', 'Glyma.04G122550' => 'gma', 'Glyma.05G001600' => 'gma', 'Glyma.09G270766' => 'gma', 'Glyma.09G270832' => 'gma', 'Glyma.13G209800' => 'gma', 'Glyma.15G102800' => 'gma', 'Glyma.18G218900' => 'gma', 'Glyma.19G001500' => 'gma', 'Glyma.19G153600' => 'gma', 'Gohir.A02G028600' => 'ghi', 'Gohir.A08G045000' => 'ghi', 'Gohir.A11G120500' => 'ghi', 'Gohir.A12G006200' => 'ghi', 'Gohir.A12G006250' => 'ghi', 'Gohir.D02G036300' => 'ghi', 'Gohir.D08G054700' => 'ghi', 'Gohir.D11G125600' => 'ghi', 'Gohir.D12G005700' => 'ghi', 'Gorai.004G055200' => 'gra', 'Gorai.005G040400' => 'gra', 'Gorai.007G134500' => 'gra', 'Gorai.008G005500' => 'gra', 'GSVIVG01011094001' => 'vvi', 'GSVIVG01017879001' => 'vvi', 'GSVIVG01025988001' => 'vvi', 'GSVIVG01029847001' => 'vvi', 'HanXRQChr10g0282901' => 'han', 'HanXRQChr10g0310371' => 'han', 'HanXRQChr10g0315041' => 'han', 'HanXRQChr11g0327651' => 'han', 'HanXRQChr12g0359391' => 'han', 'Haze_00972' => 'cav', 'Haze_00973' => 'cav', 'Haze_00974' => 'cav', 'Haze_04747' => 'cav', 'Haze_04749' => 'cav', 'Haze_04750' => 'cav', 'Haze_21217' => 'cav', 'Hma1.2p1_1037F.1_g250680' => 'hma', 'Hma1.2p1_1644F.1_g295320' => 'hma', 'HPP92_011322' => 'vpl', 'HPP92_011323' => 'vpl', 'HPP92_011324' => 'vpl', 'HPP92_011325' => 'vpl', 'HPP92_011326' => 'vpl', 'Hund12205' => 'sun', 'Hund17957' => 'sun', 'Lalb_Chr06g0176771' => 'lal', 'Lalb_Chr18g0056021' => 'lal', 'Lalb_Chr18g0056031' => 'lal', 'Lalb_Chr18g0056041' => 'lal', 'Lalb_Chr20g0107751' => 'lal', 'Lalb_Chr20g0118371' => 'lal', 'Lj1g0010239' => 'lja', 'Lj1g0017101' => 'lja', 'Lj2A1178G40' => 'lonja', 'Lj2A54G84' => 'lonja', 'Lj2g0015248' => 'lja', 'Lj3A761T51' => 'lonja', 'Lj6g0018116' => 'lja', 'Lsat_1_v5_gn_4_136040' => 'lsa', 'Lsat_1_v5_gn_5_187461' => 'lsa', 'Lsat_1_v5_gn_5_77001' => 'lsa', 'Lsat_1_v5_gn_9_4461' => 'lsa', 'Manes.01G210100' => 'mes', 'Manes.03G185600' => 'mes', 'Manes.05G073300' => 'mes', 'Manes.09G120300' => 'mes', 'Manes.15G022100' => 'mes', 'Mapoly0096s0053' => 'mpo', 'MBI03_g14058_MAGBIO' => 'mbi', 'MBI03_g33876_MAGBIO' => 'mbi', 'MBI03_g36854_MAGBIO' => 'mbi', 'MBI17_g11997_MAGBIO' => 'mbi', 'MD03G1269000' => 'mdo', 'MD04G1179600' => 'mdo', 'MD11G1289800' => 'mdo', 'MD12G1194700' => 'mdo', 'MD13G1182100' => 'mdo', 'MD13G1182200' => 'mdo', 'MD16G1182600' => 'mdo', 'Medtr2g021400' => 'mtr', 'Medtr2g021470' => 'mtr', 'Medtr2g105810' => 'mtr', 'Medtr3g033580' => 'mtr', 'Medtr6g007970' => 'mtr', 'Medtr7g056330' => 'mtr', 'Medtr7g074290' => 'mtr', 'Medtr7g074380' => 'mtr', 'Medtr7g094550' => 'mtr', 'Medtr8g069995' => 'mtr', 'MELO3C014345.2' => 'cme', 'MELO3C021395.2' => 'cme', 'Migut.D00262' => 'egut', 'Migut.G00257' => 'egut', 'MSTRG.21575' => 'ama', 'MSTRG.3985' => 'ama', 'Nitab4.5_0000295g0140' => 'nta', 'Nitab4.5_0000732g0140' => 'nta', 'Nitab4.5_0003162g0020' => 'nta', 'Nitab4.5_0006180g0090' => 'nta', 'Nitab4.5_0006390g0010' => 'nta', 'Nitab4.5_0007392g0040' => 'nta', 'Nn1g02140' => 'nnu', 'Nn4g26168' => 'nnu', 'Nn5g26754' => 'nnu', 'Oeu001433.1' => 'oeu', 'Oeu010299.2' => 'oeu', 'Oeu011171.1' => 'oeu', 'Oeu037675.1' => 'oeu', 'Oeu038359.1' => 'oeu', 'Oeu063834.1' => 'oeu', 'Oeu063835.1' => 'oeu', 'Os05g0312000' => 'osa', 'Os07g0211101' => 'osa', 'Os07g0211200' => 'osa', 'Os07g0681500' => 'osa', 'Peaxi162Scf00095g01015' => 'pax', 'Peaxi162Scf00104g00329' => 'pax', 'Peaxi162Scf00161g00137' => 'pax', 'PGR004G1665' => 'pgr', 'PGR031G2937' => 'pgr', 'PGR119G2145' => 'pgr', 'PGSC0003DMG400004351' => 'stu', 'PGSC0003DMG400014625' => 'stu', 'PGSC0003DMG401000943' => 'stu', 'Phvul.001G148600' => 'pvu', 'Phvul.004G001700' => 'pvu', 'Phvul.006G154900' => 'pvu', 'Phvul.008G078200' => 'pvu', 'Phvul.011G136500' => 'pvu', 'Potri.002G215600' => 'ptr', 'Potri.008G201600' => 'ptr', 'Potri.014G138400' => 'ptr', 'Potri.016G142500' => 'ptr', 'Pp3c16_10580' => 'ppa', 'Pp3c5_25280' => 'ppa', 'Prupe.1G150000' => 'ppe', 'Prupe.1G150100' => 'ppe', 'Prupe.6G299600' => 'ppe', 'Prupe.8G245000' => 'ppe', 'Psat0s4927g0040' => 'psa', 'Psat1g052080' => 'psa', 'Psat1g183800' => 'psa', 'Psat3g113840' => 'psa', 'Psat3g126120' => 'psa', 'Psat3g126160' => 'psa', 'Psat3g158760' => 'psa', 'Psat3g158840' => 'psa', 'PSO170G2858' => 'pso', 'PSO339G0606' => 'pso', 'PSO384G4709' => 'pso', 'PSO407G0334' => 'pso', 'QL04p040276' => 'qlo', 'QL06p005458' => 'qlo', 'QL06p005472' => 'qlo', 'QL07p030546' => 'qlo', 'QL07p031519' => 'qlo', 'QL09p050949' => 'qlo', 'QL09p050966' => 'qlo', 'QL09p051067' => 'qlo', 'QL12p022706' => 'qlo', 'RcHm_v2.0_Chr2g0119601' => 'rch', 'RcHm_v2.0_Chr3g0459591' => 'rch', 'RcHm_v2.0_Chr4g0418521' => 'rch', 'RcHm_v2.0_Chr4g0418531' => 'rch', 'RcHm_v2.0_Chr4g0418541' => 'rch', 'RcHm_v2.0_Chr6g0291641' => 'rch', 'Rhsim01G0086300' => 'rsi', 'Rhsim01G0276300' => 'rsi', 'Rhsim01G0276500' => 'rsi', 'Rhsim04G0207700' => 'rsi', 'Rhsim05G0234500' => 'rsi', 'Rhsim13G0022400' => 'rsi', 'Sabra02G0167900' => 'sbr', 'Sabra04G0158500' => 'sbr', 'Sabra08G0159800' => 'sbr', 'Sabra10G0011500' => 'sbr', 'Sabra14G0104400' => 'sbr', 'SalBow2G2440' => 'sbo', 'SalBow4G2265' => 'sbo', 'Sc02g0000060' => 'sci', 'Sc05g0005020' => 'sci', 'Sc13g0003890' => 'sci', 'Sed0014865' => 'sed', 'Sed0017224' => 'sed', 'Sed0026391' => 'sed', 'SEGI_00063' => 'sgi', 'SEGI_10967' => 'sgi', 'SEGI_17510' => 'sgi', 'SEGI_24396' => 'sgi', 'SEGI_39719' => 'sgi', 'SEGI_41392' => 'sgi', 'SGA_v2.0_scaffold11G05794' => 'sas', 'SGA_v2.0_scaffold142G35607' => 'sas', 'SGA_v2.0_scaffold1G00447' => 'sas', 'SHI15388' => 'shi', 'SHI15394' => 'shi', 'SHI15396' => 'shi', 'SHI15399' => 'shi', 'SMO343G0151' => 'smo', 'SMO367G1118' => 'smo', 'Solyc01g080200.3' => 'sly', 'Solyc06g008960.3' => 'sly', 'Solyc09g064780.3' => 'sly', 'Sopen01g031980' => 'spe', 'Sopen06g003710' => 'spe', 'Sopen09g026460' => 'spe', 'Sp3g21240' => 'spa', 'Sp4g30030' => 'spa', 'TAR365G0022' => 'tar', 'TAR365G1023' => 'tar', 'TAR365G1253' => 'tar', 'TAR623G0078' => 'tar', 'TAR623G1721' => 'tar', 'TAR633G0959' => 'tar', 'THA.LOC104802225' => 'tha', 'THA.LOC104804769' => 'tha', 'THA.LOC104808660' => 'tha', 'THA.LOC104812792' => 'tha', 'Thecc.01G284000' => 'tca', 'Thecc.04G220600' => 'tca', 'Thecc.05G268900' => 'tca', 'Thecc.08G171100' => 'tca', 'Thhalv10001284m.g' => 'esa', 'Thhalv10019912m.g' => 'esa', 'TPR.G14189' => 'tpr', 'TPR.G18110' => 'tpr', 'TPR.G18130' => 'tpr', 'TPR.G18131' => 'tpr', 'TPR.G18140' => 'tpr', 'TPR.G24282' => 'tpr', 'TPR.G25221' => 'tpr', 'TPR.G29267' => 'tpr', 'TPR.G35315' => 'tpr', 'TPR.G36173' => 'tpr', 'TWI09G0794' => 'twi', 'TWI59G1348' => 'twi', 'TWI74G0430' => 'twi', 'unitig_26.g8940' => 'ugi', 'unitig_749.g13744' => 'ugi', 'unitig_749.g13745' => 'ugi', 'vmacro08269' => 'vma', 'vmacro14937' => 'vma', 'vmacro20401' => 'vma', 'VMungo0464G1349' => 'vmu', 'VMungo0540G0289' => 'vmu', 'VMungo1215G1590' => 'vmu', 'VMungo1309G0221' => 'vmu', 'VMungo1309G2815' => 'vmu', 'VMungo1383G0239' => 'vmu', 'VMungo1383G2910' => 'vmu', 'Zm00001eb095270' => 'zma', 'Zm00001eb095280' => 'zma', 'Zm00001eb111630' => 'zma', 'Zm00001eb237080' => 'zma', 'Zm00001eb273740' => 'zma', 'Zm00001eb285040' => 'zma', 'Zm00001eb330790' => 'zma', 'Zm00001eb337380' => 'zma' ), 'gf_id' => 'HOM05D001484', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001484' ), 'data_identifier' => 'HOM05D001484', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001484', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p31500' => 'bna', 'A05p00020' => 'bna', 'A07p08820' => 'bna', 'Aa31LG4G3300' => 'aar', 'Aa31LG8G10030' => 'aar', 'Actinidia00731' => 'ach', 'Actinidia11473' => 'ach', 'Actinidia23469' => 'ach', 'Actinidia24318' => 'ach', 'Actinidia40196' => 'ach', 'Actinidia40197' => 'ach', 'Actinidia40198' => 'ach', 'Ah.08g212990' => 'amhyb', 'Ah.15g091720' => 'amhyb', 'AL3G38260' => 'aly', 'AL4G47710' => 'aly', 'Aqoxy2G00671' => 'aox', 'Aqoxy2G03236' => 'aox', 'arahy.Tifrunner.gnm1.ann1.05IDCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KR684' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATY3SJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK6QJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6APGL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IDT7Z9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM073U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ0R87' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LE7RV4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT4QRX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V5ENPK' => 'arhy', 'AT2G48110' => 'ath', 'AT3G23590' => 'ath', 'ATR0626G186' => 'atr', 'ATR1127G141' => 'atr', 'Atru.chr4.2583' => 'acertr', 'Atru.chr5.1358' => 'acertr', 'Atru.chr5.1359' => 'acertr', 'Atru.chr8.46' => 'acertr', 'AUR62002640' => 'cqu', 'AUR62030055' => 'cqu', 'AUR62033713' => 'cqu', 'AUR62033714' => 'cqu', 'AUR62036795' => 'cqu', 'AUR62039891' => 'cqu', 'BcaB02g08737' => 'bca', 'BcaB04g20441' => 'bca', 'BcaB06g26509' => 'bca', 'BcaB06g26510' => 'bca', 'BcaB06g26511' => 'bca', 'BcaB06g26512' => 'bca', 'BcaB06g26513' => 'bca', 'BcaC02g12564' => 'bca', 'BcaC02g12565' => 'bca', 'BcaC02g12794' => 'bca', 'BcaC02g12795' => 'bca', 'BcaC02g12796' => 'bca', 'BcaC06g35541' => 'bca', 'BNapus_Darmor_BZH_scaffold_188p00080' => 'bna', 'BNapus_Darmor_BZH_scaffold_188p00090' => 'bna', 'BolC1t03972H' => 'bol', 'BolC1t03973H' => 'bol', 'BolC4t21680H' => 'bol', 'BolC7t41863H' => 'bol', 'BolSC55t61227H' => 'bol', 'BolSC55t61228H' => 'bol', 'BraA01t03278Z' => 'bra', 'BraA05t18998Z' => 'bra', 'BraA07t28673Z' => 'bra', 'C01p40150' => 'bna', 'C05p12370' => 'bna', 'C07p13680' => 'bna', 'CAN.G1006.16' => 'can', 'CAN.G1006.17' => 'can', 'CAN.G1170.2' => 'can', 'CAN.G962.7' => 'can', 'CANSAT25G2179' => 'cansat', 'CANSAT78G1573' => 'cansat', 'CARHR099510' => 'chi', 'CARHR143510' => 'chi', 'Carub.0003s2380' => 'cru', 'Carub.0004s3082' => 'cru', 'Ca_00614_v3' => 'car', 'Ca_07801_v3' => 'car', 'Ca_08567_v3' => 'car', 'Ca_09571_v3' => 'car', 'CBR_g19290' => 'cbr', 'Cc01_g19770' => 'ccan', 'Cc03_g03030' => 'ccan', 'CDE07G0968' => 'cde', 'CDE09G1441' => 'cde', 'Cfa006103' => 'cfa', 'Cfa015573' => 'cfa', 'Cfa016988' => 'cfa', 'Ciclev10006738m.g' => 'ccl', 'Ciclev10010920m.g' => 'ccl', 'Ciclev10018517m.g' => 'ccl', 'CiPaw.01G159200' => 'cil', 'CiPaw.02G091000' => 'cil', 'CiPaw.02G091100' => 'cil', 'CiPaw.08G103100' => 'cil', 'CiPaw.09G224900' => 'cil', 'ClCG06G005740' => 'cla', 'ClCG07G000090' => 'cla', 'ClCG07G000100' => 'cla', 'COL.COLO4_09143' => 'col', 'COL.COLO4_25124' => 'col', 'Cpa.g.sc16.34' => 'cpa', 'Cpa.g.sc3504.1' => 'cpa', 'Cpa.g.sc60.37' => 'cpa', 'CsaV3_6G018520' => 'csa', 'CsaV3_6G036860' => 'csa', 'CSS0001072' => 'camsi', 'CSS0020208' => 'camsi', 'CSS0021253' => 'camsi', 'CSS0022190' => 'camsi', 'CSS0036150' => 'camsi', 'CSS0040442' => 'camsi', 'CSS0042300' => 'camsi', 'CSS0045298' => 'camsi', 'DCAR_012449' => 'dca', 'DCAR_018405' => 'dca', 'DCAR_024573' => 'dca', 'DCAR_030591' => 'dca', 'Dinv16926' => 'din', 'Dinv32963' => 'din', 'Dinv38382' => 'din', 'Dinv38383' => 'din', 'Duzib133G0974' => 'dzi', 'Duzib138G1867' => 'dzi', 'Duzib211G0420' => 'dzi', 'Duzib212G0930' => 'dzi', 'ECA234G1645' => 'eca', 'ECA247G3467' => 'eca', 'ECA248G1703' => 'eca', 'EL10Ac3g06327' => 'bvu', 'EL10Ac7g17204' => 'bvu', 'Eucgr.A00855' => 'egr', 'Eucgr.A00858' => 'egr', 'Eucgr.H01520' => 'egr', 'Eucgr.H03604' => 'egr', 'Eucgr.L03465' => 'egr', 'Eucgr.L03466' => 'egr', 'FAN01G0988' => 'fan', 'FAN02G3892' => 'fan', 'FAN05G3381' => 'fan', 'FAN07G0967' => 'fan', 'FAN07G1493' => 'fan', 'FAN08G3125' => 'fan', 'FAN09G0402' => 'fan', 'FAN12G2594' => 'fan', 'FAN12G3879' => 'fan', 'FAN14G1546' => 'fan', 'FAN15G3626' => 'fan', 'FAN17G0588' => 'fan', 'FAN17G0609' => 'fan', 'FAN18G2817' => 'fan', 'FAN19G1305' => 'fan', 'FAN20G1787' => 'fan', 'FAN22G0073' => 'fan', 'FAN22G0352' => 'fan', 'FAN22G0368' => 'fan', 'FAN22G2273' => 'fan', 'FAN24G1998' => 'fan', 'FAN27G1317' => 'fan', 'FvH4_2g23980' => 'fve', 'FvH4_4g14380' => 'fve', 'FvH4_4g14390' => 'fve', 'FvH4_6g09250' => 'fve', 'Glyma.03G151100' => 'gma', 'Glyma.04G122550' => 'gma', 'Glyma.05G001600' => 'gma', 'Glyma.09G270766' => 'gma', 'Glyma.09G270832' => 'gma', 'Glyma.13G209800' => 'gma', 'Glyma.15G102800' => 'gma', 'Glyma.18G218900' => 'gma', 'Glyma.19G001500' => 'gma', 'Glyma.19G153600' => 'gma', 'Gohir.A02G028600' => 'ghi', 'Gohir.A08G045000' => 'ghi', 'Gohir.A11G120500' => 'ghi', 'Gohir.A12G006200' => 'ghi', 'Gohir.A12G006250' => 'ghi', 'Gohir.D02G036300' => 'ghi', 'Gohir.D08G054700' => 'ghi', 'Gohir.D11G125600' => 'ghi', 'Gohir.D12G005700' => 'ghi', 'Gorai.004G055200' => 'gra', 'Gorai.005G040400' => 'gra', 'Gorai.007G134500' => 'gra', 'Gorai.008G005500' => 'gra', 'GSVIVG01011094001' => 'vvi', 'GSVIVG01017879001' => 'vvi', 'GSVIVG01025988001' => 'vvi', 'GSVIVG01029847001' => 'vvi', 'HanXRQChr10g0282901' => 'han', 'HanXRQChr10g0310371' => 'han', 'HanXRQChr10g0315041' => 'han', 'HanXRQChr11g0327651' => 'han', 'HanXRQChr12g0359391' => 'han', 'Haze_00972' => 'cav', 'Haze_00973' => 'cav', 'Haze_00974' => 'cav', 'Haze_04747' => 'cav', 'Haze_04749' => 'cav', 'Haze_04750' => 'cav', 'Haze_21217' => 'cav', 'Hma1.2p1_1037F.1_g250680' => 'hma', 'Hma1.2p1_1644F.1_g295320' => 'hma', 'HPP92_011322' => 'vpl', 'HPP92_011323' => 'vpl', 'HPP92_011324' => 'vpl', 'HPP92_011325' => 'vpl', 'HPP92_011326' => 'vpl', 'Hund12205' => 'sun', 'Hund17957' => 'sun', 'Lalb_Chr06g0176771' => 'lal', 'Lalb_Chr18g0056021' => 'lal', 'Lalb_Chr18g0056031' => 'lal', 'Lalb_Chr18g0056041' => 'lal', 'Lalb_Chr20g0107751' => 'lal', 'Lalb_Chr20g0118371' => 'lal', 'Lj1g0010239' => 'lja', 'Lj1g0017101' => 'lja', 'Lj2A1178G40' => 'lonja', 'Lj2A54G84' => 'lonja', 'Lj2g0015248' => 'lja', 'Lj3A761T51' => 'lonja', 'Lj6g0018116' => 'lja', 'Lsat_1_v5_gn_4_136040' => 'lsa', 'Lsat_1_v5_gn_5_187461' => 'lsa', 'Lsat_1_v5_gn_5_77001' => 'lsa', 'Lsat_1_v5_gn_9_4461' => 'lsa', 'Manes.01G210100' => 'mes', 'Manes.03G185600' => 'mes', 'Manes.05G073300' => 'mes', 'Manes.09G120300' => 'mes', 'Manes.15G022100' => 'mes', 'Mapoly0096s0053' => 'mpo', 'MBI03_g14058_MAGBIO' => 'mbi', 'MBI03_g33876_MAGBIO' => 'mbi', 'MBI03_g36854_MAGBIO' => 'mbi', 'MBI17_g11997_MAGBIO' => 'mbi', 'MD03G1269000' => 'mdo', 'MD04G1179600' => 'mdo', 'MD11G1289800' => 'mdo', 'MD12G1194700' => 'mdo', 'MD13G1182100' => 'mdo', 'MD13G1182200' => 'mdo', 'MD16G1182600' => 'mdo', 'Medtr2g021400' => 'mtr', 'Medtr2g021470' => 'mtr', 'Medtr2g105810' => 'mtr', 'Medtr3g033580' => 'mtr', 'Medtr6g007970' => 'mtr', 'Medtr7g056330' => 'mtr', 'Medtr7g074290' => 'mtr', 'Medtr7g074380' => 'mtr', 'Medtr7g094550' => 'mtr', 'Medtr8g069995' => 'mtr', 'MELO3C014345.2' => 'cme', 'MELO3C021395.2' => 'cme', 'Migut.D00262' => 'egut', 'Migut.G00257' => 'egut', 'MSTRG.21575' => 'ama', 'MSTRG.3985' => 'ama', 'Nitab4.5_0000295g0140' => 'nta', 'Nitab4.5_0000732g0140' => 'nta', 'Nitab4.5_0003162g0020' => 'nta', 'Nitab4.5_0006180g0090' => 'nta', 'Nitab4.5_0006390g0010' => 'nta', 'Nitab4.5_0007392g0040' => 'nta', 'Nn1g02140' => 'nnu', 'Nn4g26168' => 'nnu', 'Nn5g26754' => 'nnu', 'Oeu001433.1' => 'oeu', 'Oeu010299.2' => 'oeu', 'Oeu011171.1' => 'oeu', 'Oeu037675.1' => 'oeu', 'Oeu038359.1' => 'oeu', 'Oeu063834.1' => 'oeu', 'Oeu063835.1' => 'oeu', 'Os05g0312000' => 'osa', 'Os07g0211101' => 'osa', 'Os07g0211200' => 'osa', 'Os07g0681500' => 'osa', 'Peaxi162Scf00095g01015' => 'pax', 'Peaxi162Scf00104g00329' => 'pax', 'Peaxi162Scf00161g00137' => 'pax', 'PGR004G1665' => 'pgr', 'PGR031G2937' => 'pgr', 'PGR119G2145' => 'pgr', 'PGSC0003DMG400004351' => 'stu', 'PGSC0003DMG400014625' => 'stu', 'PGSC0003DMG401000943' => 'stu', 'Phvul.001G148600' => 'pvu', 'Phvul.004G001700' => 'pvu', 'Phvul.006G154900' => 'pvu', 'Phvul.008G078200' => 'pvu', 'Phvul.011G136500' => 'pvu', 'Potri.002G215600' => 'ptr', 'Potri.008G201600' => 'ptr', 'Potri.014G138400' => 'ptr', 'Potri.016G142500' => 'ptr', 'Pp3c16_10580' => 'ppa', 'Pp3c5_25280' => 'ppa', 'Prupe.1G150000' => 'ppe', 'Prupe.1G150100' => 'ppe', 'Prupe.6G299600' => 'ppe', 'Prupe.8G245000' => 'ppe', 'Psat0s4927g0040' => 'psa', 'Psat1g052080' => 'psa', 'Psat1g183800' => 'psa', 'Psat3g113840' => 'psa', 'Psat3g126120' => 'psa', 'Psat3g126160' => 'psa', 'Psat3g158760' => 'psa', 'Psat3g158840' => 'psa', 'PSO170G2858' => 'pso', 'PSO339G0606' => 'pso', 'PSO384G4709' => 'pso', 'PSO407G0334' => 'pso', 'QL04p040276' => 'qlo', 'QL06p005458' => 'qlo', 'QL06p005472' => 'qlo', 'QL07p030546' => 'qlo', 'QL07p031519' => 'qlo', 'QL09p050949' => 'qlo', 'QL09p050966' => 'qlo', 'QL09p051067' => 'qlo', 'QL12p022706' => 'qlo', 'RcHm_v2.0_Chr2g0119601' => 'rch', 'RcHm_v2.0_Chr3g0459591' => 'rch', 'RcHm_v2.0_Chr4g0418521' => 'rch', 'RcHm_v2.0_Chr4g0418531' => 'rch', 'RcHm_v2.0_Chr4g0418541' => 'rch', 'RcHm_v2.0_Chr6g0291641' => 'rch', 'Rhsim01G0086300' => 'rsi', 'Rhsim01G0276300' => 'rsi', 'Rhsim01G0276500' => 'rsi', 'Rhsim04G0207700' => 'rsi', 'Rhsim05G0234500' => 'rsi', 'Rhsim13G0022400' => 'rsi', 'Sabra02G0167900' => 'sbr', 'Sabra04G0158500' => 'sbr', 'Sabra08G0159800' => 'sbr', 'Sabra10G0011500' => 'sbr', 'Sabra14G0104400' => 'sbr', 'SalBow2G2440' => 'sbo', 'SalBow4G2265' => 'sbo', 'Sc02g0000060' => 'sci', 'Sc05g0005020' => 'sci', 'Sc13g0003890' => 'sci', 'Sed0014865' => 'sed', 'Sed0017224' => 'sed', 'Sed0026391' => 'sed', 'SEGI_00063' => 'sgi', 'SEGI_10967' => 'sgi', 'SEGI_17510' => 'sgi', 'SEGI_24396' => 'sgi', 'SEGI_39719' => 'sgi', 'SEGI_41392' => 'sgi', 'SGA_v2.0_scaffold11G05794' => 'sas', 'SGA_v2.0_scaffold142G35607' => 'sas', 'SGA_v2.0_scaffold1G00447' => 'sas', 'SHI15388' => 'shi', 'SHI15394' => 'shi', 'SHI15396' => 'shi', 'SHI15399' => 'shi', 'SMO343G0151' => 'smo', 'SMO367G1118' => 'smo', 'Solyc01g080200.3' => 'sly', 'Solyc06g008960.3' => 'sly', 'Solyc09g064780.3' => 'sly', 'Sopen01g031980' => 'spe', 'Sopen06g003710' => 'spe', 'Sopen09g026460' => 'spe', 'Sp3g21240' => 'spa', 'Sp4g30030' => 'spa', 'TAR365G0022' => 'tar', 'TAR365G1023' => 'tar', 'TAR365G1253' => 'tar', 'TAR623G0078' => 'tar', 'TAR623G1721' => 'tar', 'TAR633G0959' => 'tar', 'THA.LOC104802225' => 'tha', 'THA.LOC104804769' => 'tha', 'THA.LOC104808660' => 'tha', 'THA.LOC104812792' => 'tha', 'Thecc.01G284000' => 'tca', 'Thecc.04G220600' => 'tca', 'Thecc.05G268900' => 'tca', 'Thecc.08G171100' => 'tca', 'Thhalv10001284m.g' => 'esa', 'Thhalv10019912m.g' => 'esa', 'TPR.G14189' => 'tpr', 'TPR.G18110' => 'tpr', 'TPR.G18130' => 'tpr', 'TPR.G18131' => 'tpr', 'TPR.G18140' => 'tpr', 'TPR.G24282' => 'tpr', 'TPR.G25221' => 'tpr', 'TPR.G29267' => 'tpr', 'TPR.G35315' => 'tpr', 'TPR.G36173' => 'tpr', 'TWI09G0794' => 'twi', 'TWI59G1348' => 'twi', 'TWI74G0430' => 'twi', 'unitig_26.g8940' => 'ugi', 'unitig_749.g13744' => 'ugi', 'unitig_749.g13745' => 'ugi', 'vmacro08269' => 'vma', 'vmacro14937' => 'vma', 'vmacro20401' => 'vma', 'VMungo0464G1349' => 'vmu', 'VMungo0540G0289' => 'vmu', 'VMungo1215G1590' => 'vmu', 'VMungo1309G0221' => 'vmu', 'VMungo1309G2815' => 'vmu', 'VMungo1383G0239' => 'vmu', 'VMungo1383G2910' => 'vmu', 'Zm00001eb095270' => 'zma', 'Zm00001eb095280' => 'zma', 'Zm00001eb111630' => 'zma', 'Zm00001eb237080' => 'zma', 'Zm00001eb273740' => 'zma', 'Zm00001eb285040' => 'zma', 'Zm00001eb330790' => 'zma', 'Zm00001eb337380' => 'zma' ) $gf_id = 'HOM05D001484' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001484' ) $data_identifier = 'HOM05D001484' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 2, 'aly' => (int) 2, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 22, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 7, 'hma' => (int) 2, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 7, 'mtr' => (int) 10, 'cme' => (int) 2, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 4, 'ppa' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 4, 'qlo' => (int) 9, 'rch' => (int) 6, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 10, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 7, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb337380' $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' => 'HOM05D001484', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p31500' => 'bna', 'A05p00020' => 'bna', 'A07p08820' => 'bna', 'Aa31LG4G3300' => 'aar', 'Aa31LG8G10030' => 'aar', 'Actinidia00731' => 'ach', 'Actinidia11473' => 'ach', 'Actinidia23469' => 'ach', 'Actinidia24318' => 'ach', 'Actinidia40196' => 'ach', 'Actinidia40197' => 'ach', 'Actinidia40198' => 'ach', 'Ah.08g212990' => 'amhyb', 'Ah.15g091720' => 'amhyb', 'AL3G38260' => 'aly', 'AL4G47710' => 'aly', 'Aqoxy2G00671' => 'aox', 'Aqoxy2G03236' => 'aox', 'arahy.Tifrunner.gnm1.ann1.05IDCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KR684' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATY3SJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK6QJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6APGL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IDT7Z9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM073U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ0R87' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LE7RV4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT4QRX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V5ENPK' => 'arhy', 'AT2G48110' => 'ath', 'AT3G23590' => 'ath', 'ATR0626G186' => 'atr', 'ATR1127G141' => 'atr', 'Atru.chr4.2583' => 'acertr', 'Atru.chr5.1358' => 'acertr', 'Atru.chr5.1359' => 'acertr', 'Atru.chr8.46' => 'acertr', 'AUR62002640' => 'cqu', 'AUR62030055' => 'cqu', 'AUR62033713' => 'cqu', 'AUR62033714' => 'cqu', 'AUR62036795' => 'cqu', 'AUR62039891' => 'cqu', 'BcaB02g08737' => 'bca', 'BcaB04g20441' => 'bca', 'BcaB06g26509' => 'bca', 'BcaB06g26510' => 'bca', 'BcaB06g26511' => 'bca', 'BcaB06g26512' => 'bca', 'BcaB06g26513' => 'bca', 'BcaC02g12564' => 'bca', 'BcaC02g12565' => 'bca', 'BcaC02g12794' => 'bca', 'BcaC02g12795' => 'bca', 'BcaC02g12796' => 'bca', 'BcaC06g35541' => 'bca', 'BNapus_Darmor_BZH_scaffold_188p00080' => 'bna', 'BNapus_Darmor_BZH_scaffold_188p00090' => 'bna', 'BolC1t03972H' => 'bol', 'BolC1t03973H' => 'bol', 'BolC4t21680H' => 'bol', 'BolC7t41863H' => 'bol', 'BolSC55t61227H' => 'bol', 'BolSC55t61228H' => 'bol', 'BraA01t03278Z' => 'bra', 'BraA05t18998Z' => 'bra', 'BraA07t28673Z' => 'bra', 'C01p40150' => 'bna', 'C05p12370' => 'bna', 'C07p13680' => 'bna', 'CAN.G1006.16' => 'can', 'CAN.G1006.17' => 'can', 'CAN.G1170.2' => 'can', 'CAN.G962.7' => 'can', 'CANSAT25G2179' => 'cansat', 'CANSAT78G1573' => 'cansat', 'CARHR099510' => 'chi', 'CARHR143510' => 'chi', 'Carub.0003s2380' => 'cru', 'Carub.0004s3082' => 'cru', 'Ca_00614_v3' => 'car', 'Ca_07801_v3' => 'car', 'Ca_08567_v3' => 'car', 'Ca_09571_v3' => 'car', 'CBR_g19290' => 'cbr', 'Cc01_g19770' => 'ccan', 'Cc03_g03030' => 'ccan', 'CDE07G0968' => 'cde', 'CDE09G1441' => 'cde', 'Cfa006103' => 'cfa', 'Cfa015573' => 'cfa', 'Cfa016988' => 'cfa', 'Ciclev10006738m.g' => 'ccl', 'Ciclev10010920m.g' => 'ccl', 'Ciclev10018517m.g' => 'ccl', 'CiPaw.01G159200' => 'cil', 'CiPaw.02G091000' => 'cil', 'CiPaw.02G091100' => 'cil', 'CiPaw.08G103100' => 'cil', 'CiPaw.09G224900' => 'cil', 'ClCG06G005740' => 'cla', 'ClCG07G000090' => 'cla', 'ClCG07G000100' => 'cla', 'COL.COLO4_09143' => 'col', 'COL.COLO4_25124' => 'col', 'Cpa.g.sc16.34' => 'cpa', 'Cpa.g.sc3504.1' => 'cpa', 'Cpa.g.sc60.37' => 'cpa', 'CsaV3_6G018520' => 'csa', 'CsaV3_6G036860' => 'csa', 'CSS0001072' => 'camsi', 'CSS0020208' => 'camsi', 'CSS0021253' => 'camsi', 'CSS0022190' => 'camsi', 'CSS0036150' => 'camsi', 'CSS0040442' => 'camsi', 'CSS0042300' => 'camsi', 'CSS0045298' => 'camsi', 'DCAR_012449' => 'dca', 'DCAR_018405' => 'dca', 'DCAR_024573' => 'dca', 'DCAR_030591' => 'dca', 'Dinv16926' => 'din', 'Dinv32963' => 'din', 'Dinv38382' => 'din', 'Dinv38383' => 'din', 'Duzib133G0974' => 'dzi', 'Duzib138G1867' => 'dzi', 'Duzib211G0420' => 'dzi', 'Duzib212G0930' => 'dzi', 'ECA234G1645' => 'eca', 'ECA247G3467' => 'eca', 'ECA248G1703' => 'eca', 'EL10Ac3g06327' => 'bvu', 'EL10Ac7g17204' => 'bvu', 'Eucgr.A00855' => 'egr', 'Eucgr.A00858' => 'egr', 'Eucgr.H01520' => 'egr', 'Eucgr.H03604' => 'egr', 'Eucgr.L03465' => 'egr', 'Eucgr.L03466' => 'egr', 'FAN01G0988' => 'fan', 'FAN02G3892' => 'fan', 'FAN05G3381' => 'fan', 'FAN07G0967' => 'fan', 'FAN07G1493' => 'fan', 'FAN08G3125' => 'fan', 'FAN09G0402' => 'fan', 'FAN12G2594' => 'fan', 'FAN12G3879' => 'fan', 'FAN14G1546' => 'fan', 'FAN15G3626' => 'fan', 'FAN17G0588' => 'fan', 'FAN17G0609' => 'fan', 'FAN18G2817' => 'fan', 'FAN19G1305' => 'fan', 'FAN20G1787' => 'fan', 'FAN22G0073' => 'fan', 'FAN22G0352' => 'fan', 'FAN22G0368' => 'fan', 'FAN22G2273' => 'fan', 'FAN24G1998' => 'fan', 'FAN27G1317' => 'fan', 'FvH4_2g23980' => 'fve', 'FvH4_4g14380' => 'fve', 'FvH4_4g14390' => 'fve', 'FvH4_6g09250' => 'fve', 'Glyma.03G151100' => 'gma', 'Glyma.04G122550' => 'gma', 'Glyma.05G001600' => 'gma', 'Glyma.09G270766' => 'gma', 'Glyma.09G270832' => 'gma', 'Glyma.13G209800' => 'gma', 'Glyma.15G102800' => 'gma', 'Glyma.18G218900' => 'gma', 'Glyma.19G001500' => 'gma', 'Glyma.19G153600' => 'gma', 'Gohir.A02G028600' => 'ghi', 'Gohir.A08G045000' => 'ghi', 'Gohir.A11G120500' => 'ghi', 'Gohir.A12G006200' => 'ghi', 'Gohir.A12G006250' => 'ghi', 'Gohir.D02G036300' => 'ghi', 'Gohir.D08G054700' => 'ghi', 'Gohir.D11G125600' => 'ghi', 'Gohir.D12G005700' => 'ghi', 'Gorai.004G055200' => 'gra', 'Gorai.005G040400' => 'gra', 'Gorai.007G134500' => 'gra', 'Gorai.008G005500' => 'gra', 'GSVIVG01011094001' => 'vvi', 'GSVIVG01017879001' => 'vvi', 'GSVIVG01025988001' => 'vvi', 'GSVIVG01029847001' => 'vvi', 'HanXRQChr10g0282901' => 'han', 'HanXRQChr10g0310371' => 'han', 'HanXRQChr10g0315041' => 'han', 'HanXRQChr11g0327651' => 'han', 'HanXRQChr12g0359391' => 'han', 'Haze_00972' => 'cav', 'Haze_00973' => 'cav', 'Haze_00974' => 'cav', 'Haze_04747' => 'cav', 'Haze_04749' => 'cav', 'Haze_04750' => 'cav', 'Haze_21217' => 'cav', 'Hma1.2p1_1037F.1_g250680' => 'hma', 'Hma1.2p1_1644F.1_g295320' => 'hma', 'HPP92_011322' => 'vpl', 'HPP92_011323' => 'vpl', 'HPP92_011324' => 'vpl', 'HPP92_011325' => 'vpl', 'HPP92_011326' => 'vpl', 'Hund12205' => 'sun', 'Hund17957' => 'sun', 'Lalb_Chr06g0176771' => 'lal', 'Lalb_Chr18g0056021' => 'lal', 'Lalb_Chr18g0056031' => 'lal', 'Lalb_Chr18g0056041' => 'lal', 'Lalb_Chr20g0107751' => 'lal', 'Lalb_Chr20g0118371' => 'lal', 'Lj1g0010239' => 'lja', 'Lj1g0017101' => 'lja', 'Lj2A1178G40' => 'lonja', 'Lj2A54G84' => 'lonja', 'Lj2g0015248' => 'lja', 'Lj3A761T51' => 'lonja', 'Lj6g0018116' => 'lja', 'Lsat_1_v5_gn_4_136040' => 'lsa', 'Lsat_1_v5_gn_5_187461' => 'lsa', 'Lsat_1_v5_gn_5_77001' => 'lsa', 'Lsat_1_v5_gn_9_4461' => 'lsa', 'Manes.01G210100' => 'mes', 'Manes.03G185600' => 'mes', 'Manes.05G073300' => 'mes', 'Manes.09G120300' => 'mes', 'Manes.15G022100' => 'mes', 'Mapoly0096s0053' => 'mpo', 'MBI03_g14058_MAGBIO' => 'mbi', 'MBI03_g33876_MAGBIO' => 'mbi', 'MBI03_g36854_MAGBIO' => 'mbi', 'MBI17_g11997_MAGBIO' => 'mbi', 'MD03G1269000' => 'mdo', 'MD04G1179600' => 'mdo', 'MD11G1289800' => 'mdo', 'MD12G1194700' => 'mdo', 'MD13G1182100' => 'mdo', 'MD13G1182200' => 'mdo', 'MD16G1182600' => 'mdo', 'Medtr2g021400' => 'mtr', 'Medtr2g021470' => 'mtr', 'Medtr2g105810' => 'mtr', 'Medtr3g033580' => 'mtr', 'Medtr6g007970' => 'mtr', 'Medtr7g056330' => 'mtr', 'Medtr7g074290' => 'mtr', 'Medtr7g074380' => 'mtr', 'Medtr7g094550' => 'mtr', 'Medtr8g069995' => 'mtr', 'MELO3C014345.2' => 'cme', 'MELO3C021395.2' => 'cme', 'Migut.D00262' => 'egut', 'Migut.G00257' => 'egut', 'MSTRG.21575' => 'ama', 'MSTRG.3985' => 'ama', 'Nitab4.5_0000295g0140' => 'nta', 'Nitab4.5_0000732g0140' => 'nta', 'Nitab4.5_0003162g0020' => 'nta', 'Nitab4.5_0006180g0090' => 'nta', 'Nitab4.5_0006390g0010' => 'nta', 'Nitab4.5_0007392g0040' => 'nta', 'Nn1g02140' => 'nnu', 'Nn4g26168' => 'nnu', 'Nn5g26754' => 'nnu', 'Oeu001433.1' => 'oeu', 'Oeu010299.2' => 'oeu', 'Oeu011171.1' => 'oeu', 'Oeu037675.1' => 'oeu', 'Oeu038359.1' => 'oeu', 'Oeu063834.1' => 'oeu', 'Oeu063835.1' => 'oeu', 'Os05g0312000' => 'osa', 'Os07g0211101' => 'osa', 'Os07g0211200' => 'osa', 'Os07g0681500' => 'osa', 'Peaxi162Scf00095g01015' => 'pax', 'Peaxi162Scf00104g00329' => 'pax', 'Peaxi162Scf00161g00137' => 'pax', 'PGR004G1665' => 'pgr', 'PGR031G2937' => 'pgr', 'PGR119G2145' => 'pgr', 'PGSC0003DMG400004351' => 'stu', 'PGSC0003DMG400014625' => 'stu', 'PGSC0003DMG401000943' => 'stu', 'Phvul.001G148600' => 'pvu', 'Phvul.004G001700' => 'pvu', 'Phvul.006G154900' => 'pvu', 'Phvul.008G078200' => 'pvu', 'Phvul.011G136500' => 'pvu', 'Potri.002G215600' => 'ptr', 'Potri.008G201600' => 'ptr', 'Potri.014G138400' => 'ptr', 'Potri.016G142500' => 'ptr', 'Pp3c16_10580' => 'ppa', 'Pp3c5_25280' => 'ppa', 'Prupe.1G150000' => 'ppe', 'Prupe.1G150100' => 'ppe', 'Prupe.6G299600' => 'ppe', 'Prupe.8G245000' => 'ppe', 'Psat0s4927g0040' => 'psa', 'Psat1g052080' => 'psa', 'Psat1g183800' => 'psa', 'Psat3g113840' => 'psa', 'Psat3g126120' => 'psa', 'Psat3g126160' => 'psa', 'Psat3g158760' => 'psa', 'Psat3g158840' => 'psa', 'PSO170G2858' => 'pso', 'PSO339G0606' => 'pso', 'PSO384G4709' => 'pso', 'PSO407G0334' => 'pso', 'QL04p040276' => 'qlo', 'QL06p005458' => 'qlo', 'QL06p005472' => 'qlo', 'QL07p030546' => 'qlo', 'QL07p031519' => 'qlo', 'QL09p050949' => 'qlo', 'QL09p050966' => 'qlo', 'QL09p051067' => 'qlo', 'QL12p022706' => 'qlo', 'RcHm_v2.0_Chr2g0119601' => 'rch', 'RcHm_v2.0_Chr3g0459591' => 'rch', 'RcHm_v2.0_Chr4g0418521' => 'rch', 'RcHm_v2.0_Chr4g0418531' => 'rch', 'RcHm_v2.0_Chr4g0418541' => 'rch', 'RcHm_v2.0_Chr6g0291641' => 'rch', 'Rhsim01G0086300' => 'rsi', 'Rhsim01G0276300' => 'rsi', 'Rhsim01G0276500' => 'rsi', 'Rhsim04G0207700' => 'rsi', 'Rhsim05G0234500' => 'rsi', 'Rhsim13G0022400' => 'rsi', 'Sabra02G0167900' => 'sbr', 'Sabra04G0158500' => 'sbr', 'Sabra08G0159800' => 'sbr', 'Sabra10G0011500' => 'sbr', 'Sabra14G0104400' => 'sbr', 'SalBow2G2440' => 'sbo', 'SalBow4G2265' => 'sbo', 'Sc02g0000060' => 'sci', 'Sc05g0005020' => 'sci', 'Sc13g0003890' => 'sci', 'Sed0014865' => 'sed', 'Sed0017224' => 'sed', 'Sed0026391' => 'sed', 'SEGI_00063' => 'sgi', 'SEGI_10967' => 'sgi', 'SEGI_17510' => 'sgi', 'SEGI_24396' => 'sgi', 'SEGI_39719' => 'sgi', 'SEGI_41392' => 'sgi', 'SGA_v2.0_scaffold11G05794' => 'sas', 'SGA_v2.0_scaffold142G35607' => 'sas', 'SGA_v2.0_scaffold1G00447' => 'sas', 'SHI15388' => 'shi', 'SHI15394' => 'shi', 'SHI15396' => 'shi', 'SHI15399' => 'shi', 'SMO343G0151' => 'smo', 'SMO367G1118' => 'smo', 'Solyc01g080200.3' => 'sly', 'Solyc06g008960.3' => 'sly', 'Solyc09g064780.3' => 'sly', 'Sopen01g031980' => 'spe', 'Sopen06g003710' => 'spe', 'Sopen09g026460' => 'spe', 'Sp3g21240' => 'spa', 'Sp4g30030' => 'spa', 'TAR365G0022' => 'tar', 'TAR365G1023' => 'tar', 'TAR365G1253' => 'tar', 'TAR623G0078' => 'tar', 'TAR623G1721' => 'tar', 'TAR633G0959' => 'tar', 'THA.LOC104802225' => 'tha', 'THA.LOC104804769' => 'tha', 'THA.LOC104808660' => 'tha', 'THA.LOC104812792' => 'tha', 'Thecc.01G284000' => 'tca', 'Thecc.04G220600' => 'tca', 'Thecc.05G268900' => 'tca', 'Thecc.08G171100' => 'tca', 'Thhalv10001284m.g' => 'esa', 'Thhalv10019912m.g' => 'esa', 'TPR.G14189' => 'tpr', 'TPR.G18110' => 'tpr', 'TPR.G18130' => 'tpr', 'TPR.G18131' => 'tpr', 'TPR.G18140' => 'tpr', 'TPR.G24282' => 'tpr', 'TPR.G25221' => 'tpr', 'TPR.G29267' => 'tpr', 'TPR.G35315' => 'tpr', 'TPR.G36173' => 'tpr', 'TWI09G0794' => 'twi', 'TWI59G1348' => 'twi', 'TWI74G0430' => 'twi', 'unitig_26.g8940' => 'ugi', 'unitig_749.g13744' => 'ugi', 'unitig_749.g13745' => 'ugi', 'vmacro08269' => 'vma', 'vmacro14937' => 'vma', 'vmacro20401' => 'vma', 'VMungo0464G1349' => 'vmu', 'VMungo0540G0289' => 'vmu', 'VMungo1215G1590' => 'vmu', 'VMungo1309G0221' => 'vmu', 'VMungo1309G2815' => 'vmu', 'VMungo1383G0239' => 'vmu', 'VMungo1383G2910' => 'vmu', 'Zm00001eb095270' => 'zma', 'Zm00001eb095280' => 'zma', 'Zm00001eb111630' => 'zma', 'Zm00001eb237080' => 'zma', 'Zm00001eb273740' => 'zma', 'Zm00001eb285040' => 'zma', 'Zm00001eb330790' => 'zma', 'Zm00001eb337380' => 'zma' ), 'gf_id' => 'HOM05D001484', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001484' ), 'data_identifier' => 'HOM05D001484', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001484', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p31500' => 'bna', 'A05p00020' => 'bna', 'A07p08820' => 'bna', 'Aa31LG4G3300' => 'aar', 'Aa31LG8G10030' => 'aar', 'Actinidia00731' => 'ach', 'Actinidia11473' => 'ach', 'Actinidia23469' => 'ach', 'Actinidia24318' => 'ach', 'Actinidia40196' => 'ach', 'Actinidia40197' => 'ach', 'Actinidia40198' => 'ach', 'Ah.08g212990' => 'amhyb', 'Ah.15g091720' => 'amhyb', 'AL3G38260' => 'aly', 'AL4G47710' => 'aly', 'Aqoxy2G00671' => 'aox', 'Aqoxy2G03236' => 'aox', 'arahy.Tifrunner.gnm1.ann1.05IDCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KR684' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATY3SJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK6QJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6APGL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IDT7Z9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM073U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ0R87' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LE7RV4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT4QRX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V5ENPK' => 'arhy', 'AT2G48110' => 'ath', 'AT3G23590' => 'ath', 'ATR0626G186' => 'atr', 'ATR1127G141' => 'atr', 'Atru.chr4.2583' => 'acertr', 'Atru.chr5.1358' => 'acertr', 'Atru.chr5.1359' => 'acertr', 'Atru.chr8.46' => 'acertr', 'AUR62002640' => 'cqu', 'AUR62030055' => 'cqu', 'AUR62033713' => 'cqu', 'AUR62033714' => 'cqu', 'AUR62036795' => 'cqu', 'AUR62039891' => 'cqu', 'BcaB02g08737' => 'bca', 'BcaB04g20441' => 'bca', 'BcaB06g26509' => 'bca', 'BcaB06g26510' => 'bca', 'BcaB06g26511' => 'bca', 'BcaB06g26512' => 'bca', 'BcaB06g26513' => 'bca', 'BcaC02g12564' => 'bca', 'BcaC02g12565' => 'bca', 'BcaC02g12794' => 'bca', 'BcaC02g12795' => 'bca', 'BcaC02g12796' => 'bca', 'BcaC06g35541' => 'bca', 'BNapus_Darmor_BZH_scaffold_188p00080' => 'bna', 'BNapus_Darmor_BZH_scaffold_188p00090' => 'bna', 'BolC1t03972H' => 'bol', 'BolC1t03973H' => 'bol', 'BolC4t21680H' => 'bol', 'BolC7t41863H' => 'bol', 'BolSC55t61227H' => 'bol', 'BolSC55t61228H' => 'bol', 'BraA01t03278Z' => 'bra', 'BraA05t18998Z' => 'bra', 'BraA07t28673Z' => 'bra', 'C01p40150' => 'bna', 'C05p12370' => 'bna', 'C07p13680' => 'bna', 'CAN.G1006.16' => 'can', 'CAN.G1006.17' => 'can', 'CAN.G1170.2' => 'can', 'CAN.G962.7' => 'can', 'CANSAT25G2179' => 'cansat', 'CANSAT78G1573' => 'cansat', 'CARHR099510' => 'chi', 'CARHR143510' => 'chi', 'Carub.0003s2380' => 'cru', 'Carub.0004s3082' => 'cru', 'Ca_00614_v3' => 'car', 'Ca_07801_v3' => 'car', 'Ca_08567_v3' => 'car', 'Ca_09571_v3' => 'car', 'CBR_g19290' => 'cbr', 'Cc01_g19770' => 'ccan', 'Cc03_g03030' => 'ccan', 'CDE07G0968' => 'cde', 'CDE09G1441' => 'cde', 'Cfa006103' => 'cfa', 'Cfa015573' => 'cfa', 'Cfa016988' => 'cfa', 'Ciclev10006738m.g' => 'ccl', 'Ciclev10010920m.g' => 'ccl', 'Ciclev10018517m.g' => 'ccl', 'CiPaw.01G159200' => 'cil', 'CiPaw.02G091000' => 'cil', 'CiPaw.02G091100' => 'cil', 'CiPaw.08G103100' => 'cil', 'CiPaw.09G224900' => 'cil', 'ClCG06G005740' => 'cla', 'ClCG07G000090' => 'cla', 'ClCG07G000100' => 'cla', 'COL.COLO4_09143' => 'col', 'COL.COLO4_25124' => 'col', 'Cpa.g.sc16.34' => 'cpa', 'Cpa.g.sc3504.1' => 'cpa', 'Cpa.g.sc60.37' => 'cpa', 'CsaV3_6G018520' => 'csa', 'CsaV3_6G036860' => 'csa', 'CSS0001072' => 'camsi', 'CSS0020208' => 'camsi', 'CSS0021253' => 'camsi', 'CSS0022190' => 'camsi', 'CSS0036150' => 'camsi', 'CSS0040442' => 'camsi', 'CSS0042300' => 'camsi', 'CSS0045298' => 'camsi', 'DCAR_012449' => 'dca', 'DCAR_018405' => 'dca', 'DCAR_024573' => 'dca', 'DCAR_030591' => 'dca', 'Dinv16926' => 'din', 'Dinv32963' => 'din', 'Dinv38382' => 'din', 'Dinv38383' => 'din', 'Duzib133G0974' => 'dzi', 'Duzib138G1867' => 'dzi', 'Duzib211G0420' => 'dzi', 'Duzib212G0930' => 'dzi', 'ECA234G1645' => 'eca', 'ECA247G3467' => 'eca', 'ECA248G1703' => 'eca', 'EL10Ac3g06327' => 'bvu', 'EL10Ac7g17204' => 'bvu', 'Eucgr.A00855' => 'egr', 'Eucgr.A00858' => 'egr', 'Eucgr.H01520' => 'egr', 'Eucgr.H03604' => 'egr', 'Eucgr.L03465' => 'egr', 'Eucgr.L03466' => 'egr', 'FAN01G0988' => 'fan', 'FAN02G3892' => 'fan', 'FAN05G3381' => 'fan', 'FAN07G0967' => 'fan', 'FAN07G1493' => 'fan', 'FAN08G3125' => 'fan', 'FAN09G0402' => 'fan', 'FAN12G2594' => 'fan', 'FAN12G3879' => 'fan', 'FAN14G1546' => 'fan', 'FAN15G3626' => 'fan', 'FAN17G0588' => 'fan', 'FAN17G0609' => 'fan', 'FAN18G2817' => 'fan', 'FAN19G1305' => 'fan', 'FAN20G1787' => 'fan', 'FAN22G0073' => 'fan', 'FAN22G0352' => 'fan', 'FAN22G0368' => 'fan', 'FAN22G2273' => 'fan', 'FAN24G1998' => 'fan', 'FAN27G1317' => 'fan', 'FvH4_2g23980' => 'fve', 'FvH4_4g14380' => 'fve', 'FvH4_4g14390' => 'fve', 'FvH4_6g09250' => 'fve', 'Glyma.03G151100' => 'gma', 'Glyma.04G122550' => 'gma', 'Glyma.05G001600' => 'gma', 'Glyma.09G270766' => 'gma', 'Glyma.09G270832' => 'gma', 'Glyma.13G209800' => 'gma', 'Glyma.15G102800' => 'gma', 'Glyma.18G218900' => 'gma', 'Glyma.19G001500' => 'gma', 'Glyma.19G153600' => 'gma', 'Gohir.A02G028600' => 'ghi', 'Gohir.A08G045000' => 'ghi', 'Gohir.A11G120500' => 'ghi', 'Gohir.A12G006200' => 'ghi', 'Gohir.A12G006250' => 'ghi', 'Gohir.D02G036300' => 'ghi', 'Gohir.D08G054700' => 'ghi', 'Gohir.D11G125600' => 'ghi', 'Gohir.D12G005700' => 'ghi', 'Gorai.004G055200' => 'gra', 'Gorai.005G040400' => 'gra', 'Gorai.007G134500' => 'gra', 'Gorai.008G005500' => 'gra', 'GSVIVG01011094001' => 'vvi', 'GSVIVG01017879001' => 'vvi', 'GSVIVG01025988001' => 'vvi', 'GSVIVG01029847001' => 'vvi', 'HanXRQChr10g0282901' => 'han', 'HanXRQChr10g0310371' => 'han', 'HanXRQChr10g0315041' => 'han', 'HanXRQChr11g0327651' => 'han', 'HanXRQChr12g0359391' => 'han', 'Haze_00972' => 'cav', 'Haze_00973' => 'cav', 'Haze_00974' => 'cav', 'Haze_04747' => 'cav', 'Haze_04749' => 'cav', 'Haze_04750' => 'cav', 'Haze_21217' => 'cav', 'Hma1.2p1_1037F.1_g250680' => 'hma', 'Hma1.2p1_1644F.1_g295320' => 'hma', 'HPP92_011322' => 'vpl', 'HPP92_011323' => 'vpl', 'HPP92_011324' => 'vpl', 'HPP92_011325' => 'vpl', 'HPP92_011326' => 'vpl', 'Hund12205' => 'sun', 'Hund17957' => 'sun', 'Lalb_Chr06g0176771' => 'lal', 'Lalb_Chr18g0056021' => 'lal', 'Lalb_Chr18g0056031' => 'lal', 'Lalb_Chr18g0056041' => 'lal', 'Lalb_Chr20g0107751' => 'lal', 'Lalb_Chr20g0118371' => 'lal', 'Lj1g0010239' => 'lja', 'Lj1g0017101' => 'lja', 'Lj2A1178G40' => 'lonja', 'Lj2A54G84' => 'lonja', 'Lj2g0015248' => 'lja', 'Lj3A761T51' => 'lonja', 'Lj6g0018116' => 'lja', 'Lsat_1_v5_gn_4_136040' => 'lsa', 'Lsat_1_v5_gn_5_187461' => 'lsa', 'Lsat_1_v5_gn_5_77001' => 'lsa', 'Lsat_1_v5_gn_9_4461' => 'lsa', 'Manes.01G210100' => 'mes', 'Manes.03G185600' => 'mes', 'Manes.05G073300' => 'mes', 'Manes.09G120300' => 'mes', 'Manes.15G022100' => 'mes', 'Mapoly0096s0053' => 'mpo', 'MBI03_g14058_MAGBIO' => 'mbi', 'MBI03_g33876_MAGBIO' => 'mbi', 'MBI03_g36854_MAGBIO' => 'mbi', 'MBI17_g11997_MAGBIO' => 'mbi', 'MD03G1269000' => 'mdo', 'MD04G1179600' => 'mdo', 'MD11G1289800' => 'mdo', 'MD12G1194700' => 'mdo', 'MD13G1182100' => 'mdo', 'MD13G1182200' => 'mdo', 'MD16G1182600' => 'mdo', 'Medtr2g021400' => 'mtr', 'Medtr2g021470' => 'mtr', 'Medtr2g105810' => 'mtr', 'Medtr3g033580' => 'mtr', 'Medtr6g007970' => 'mtr', 'Medtr7g056330' => 'mtr', 'Medtr7g074290' => 'mtr', 'Medtr7g074380' => 'mtr', 'Medtr7g094550' => 'mtr', 'Medtr8g069995' => 'mtr', 'MELO3C014345.2' => 'cme', 'MELO3C021395.2' => 'cme', 'Migut.D00262' => 'egut', 'Migut.G00257' => 'egut', 'MSTRG.21575' => 'ama', 'MSTRG.3985' => 'ama', 'Nitab4.5_0000295g0140' => 'nta', 'Nitab4.5_0000732g0140' => 'nta', 'Nitab4.5_0003162g0020' => 'nta', 'Nitab4.5_0006180g0090' => 'nta', 'Nitab4.5_0006390g0010' => 'nta', 'Nitab4.5_0007392g0040' => 'nta', 'Nn1g02140' => 'nnu', 'Nn4g26168' => 'nnu', 'Nn5g26754' => 'nnu', 'Oeu001433.1' => 'oeu', 'Oeu010299.2' => 'oeu', 'Oeu011171.1' => 'oeu', 'Oeu037675.1' => 'oeu', 'Oeu038359.1' => 'oeu', 'Oeu063834.1' => 'oeu', 'Oeu063835.1' => 'oeu', 'Os05g0312000' => 'osa', 'Os07g0211101' => 'osa', 'Os07g0211200' => 'osa', 'Os07g0681500' => 'osa', 'Peaxi162Scf00095g01015' => 'pax', 'Peaxi162Scf00104g00329' => 'pax', 'Peaxi162Scf00161g00137' => 'pax', 'PGR004G1665' => 'pgr', 'PGR031G2937' => 'pgr', 'PGR119G2145' => 'pgr', 'PGSC0003DMG400004351' => 'stu', 'PGSC0003DMG400014625' => 'stu', 'PGSC0003DMG401000943' => 'stu', 'Phvul.001G148600' => 'pvu', 'Phvul.004G001700' => 'pvu', 'Phvul.006G154900' => 'pvu', 'Phvul.008G078200' => 'pvu', 'Phvul.011G136500' => 'pvu', 'Potri.002G215600' => 'ptr', 'Potri.008G201600' => 'ptr', 'Potri.014G138400' => 'ptr', 'Potri.016G142500' => 'ptr', 'Pp3c16_10580' => 'ppa', 'Pp3c5_25280' => 'ppa', 'Prupe.1G150000' => 'ppe', 'Prupe.1G150100' => 'ppe', 'Prupe.6G299600' => 'ppe', 'Prupe.8G245000' => 'ppe', 'Psat0s4927g0040' => 'psa', 'Psat1g052080' => 'psa', 'Psat1g183800' => 'psa', 'Psat3g113840' => 'psa', 'Psat3g126120' => 'psa', 'Psat3g126160' => 'psa', 'Psat3g158760' => 'psa', 'Psat3g158840' => 'psa', 'PSO170G2858' => 'pso', 'PSO339G0606' => 'pso', 'PSO384G4709' => 'pso', 'PSO407G0334' => 'pso', 'QL04p040276' => 'qlo', 'QL06p005458' => 'qlo', 'QL06p005472' => 'qlo', 'QL07p030546' => 'qlo', 'QL07p031519' => 'qlo', 'QL09p050949' => 'qlo', 'QL09p050966' => 'qlo', 'QL09p051067' => 'qlo', 'QL12p022706' => 'qlo', 'RcHm_v2.0_Chr2g0119601' => 'rch', 'RcHm_v2.0_Chr3g0459591' => 'rch', 'RcHm_v2.0_Chr4g0418521' => 'rch', 'RcHm_v2.0_Chr4g0418531' => 'rch', 'RcHm_v2.0_Chr4g0418541' => 'rch', 'RcHm_v2.0_Chr6g0291641' => 'rch', 'Rhsim01G0086300' => 'rsi', 'Rhsim01G0276300' => 'rsi', 'Rhsim01G0276500' => 'rsi', 'Rhsim04G0207700' => 'rsi', 'Rhsim05G0234500' => 'rsi', 'Rhsim13G0022400' => 'rsi', 'Sabra02G0167900' => 'sbr', 'Sabra04G0158500' => 'sbr', 'Sabra08G0159800' => 'sbr', 'Sabra10G0011500' => 'sbr', 'Sabra14G0104400' => 'sbr', 'SalBow2G2440' => 'sbo', 'SalBow4G2265' => 'sbo', 'Sc02g0000060' => 'sci', 'Sc05g0005020' => 'sci', 'Sc13g0003890' => 'sci', 'Sed0014865' => 'sed', 'Sed0017224' => 'sed', 'Sed0026391' => 'sed', 'SEGI_00063' => 'sgi', 'SEGI_10967' => 'sgi', 'SEGI_17510' => 'sgi', 'SEGI_24396' => 'sgi', 'SEGI_39719' => 'sgi', 'SEGI_41392' => 'sgi', 'SGA_v2.0_scaffold11G05794' => 'sas', 'SGA_v2.0_scaffold142G35607' => 'sas', 'SGA_v2.0_scaffold1G00447' => 'sas', 'SHI15388' => 'shi', 'SHI15394' => 'shi', 'SHI15396' => 'shi', 'SHI15399' => 'shi', 'SMO343G0151' => 'smo', 'SMO367G1118' => 'smo', 'Solyc01g080200.3' => 'sly', 'Solyc06g008960.3' => 'sly', 'Solyc09g064780.3' => 'sly', 'Sopen01g031980' => 'spe', 'Sopen06g003710' => 'spe', 'Sopen09g026460' => 'spe', 'Sp3g21240' => 'spa', 'Sp4g30030' => 'spa', 'TAR365G0022' => 'tar', 'TAR365G1023' => 'tar', 'TAR365G1253' => 'tar', 'TAR623G0078' => 'tar', 'TAR623G1721' => 'tar', 'TAR633G0959' => 'tar', 'THA.LOC104802225' => 'tha', 'THA.LOC104804769' => 'tha', 'THA.LOC104808660' => 'tha', 'THA.LOC104812792' => 'tha', 'Thecc.01G284000' => 'tca', 'Thecc.04G220600' => 'tca', 'Thecc.05G268900' => 'tca', 'Thecc.08G171100' => 'tca', 'Thhalv10001284m.g' => 'esa', 'Thhalv10019912m.g' => 'esa', 'TPR.G14189' => 'tpr', 'TPR.G18110' => 'tpr', 'TPR.G18130' => 'tpr', 'TPR.G18131' => 'tpr', 'TPR.G18140' => 'tpr', 'TPR.G24282' => 'tpr', 'TPR.G25221' => 'tpr', 'TPR.G29267' => 'tpr', 'TPR.G35315' => 'tpr', 'TPR.G36173' => 'tpr', 'TWI09G0794' => 'twi', 'TWI59G1348' => 'twi', 'TWI74G0430' => 'twi', 'unitig_26.g8940' => 'ugi', 'unitig_749.g13744' => 'ugi', 'unitig_749.g13745' => 'ugi', 'vmacro08269' => 'vma', 'vmacro14937' => 'vma', 'vmacro20401' => 'vma', 'VMungo0464G1349' => 'vmu', 'VMungo0540G0289' => 'vmu', 'VMungo1215G1590' => 'vmu', 'VMungo1309G0221' => 'vmu', 'VMungo1309G2815' => 'vmu', 'VMungo1383G0239' => 'vmu', 'VMungo1383G2910' => 'vmu', 'Zm00001eb095270' => 'zma', 'Zm00001eb095280' => 'zma', 'Zm00001eb111630' => 'zma', 'Zm00001eb237080' => 'zma', 'Zm00001eb273740' => 'zma', 'Zm00001eb285040' => 'zma', 'Zm00001eb330790' => 'zma', 'Zm00001eb337380' => 'zma' ) $gf_id = 'HOM05D001484' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001484' ) $data_identifier = 'HOM05D001484' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 2, 'aly' => (int) 2, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 22, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 7, 'hma' => (int) 2, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 7, 'mtr' => (int) 10, 'cme' => (int) 2, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 4, 'ppa' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 4, 'qlo' => (int) 9, 'rch' => (int) 6, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 10, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 7, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb337380' $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' => 'HOM05D001484', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p31500' => 'bna', 'A05p00020' => 'bna', 'A07p08820' => 'bna', 'Aa31LG4G3300' => 'aar', 'Aa31LG8G10030' => 'aar', 'Actinidia00731' => 'ach', 'Actinidia11473' => 'ach', 'Actinidia23469' => 'ach', 'Actinidia24318' => 'ach', 'Actinidia40196' => 'ach', 'Actinidia40197' => 'ach', 'Actinidia40198' => 'ach', 'Ah.08g212990' => 'amhyb', 'Ah.15g091720' => 'amhyb', 'AL3G38260' => 'aly', 'AL4G47710' => 'aly', 'Aqoxy2G00671' => 'aox', 'Aqoxy2G03236' => 'aox', 'arahy.Tifrunner.gnm1.ann1.05IDCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KR684' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATY3SJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK6QJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6APGL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IDT7Z9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM073U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ0R87' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LE7RV4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT4QRX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V5ENPK' => 'arhy', 'AT2G48110' => 'ath', 'AT3G23590' => 'ath', 'ATR0626G186' => 'atr', 'ATR1127G141' => 'atr', 'Atru.chr4.2583' => 'acertr', 'Atru.chr5.1358' => 'acertr', 'Atru.chr5.1359' => 'acertr', 'Atru.chr8.46' => 'acertr', 'AUR62002640' => 'cqu', 'AUR62030055' => 'cqu', 'AUR62033713' => 'cqu', 'AUR62033714' => 'cqu', 'AUR62036795' => 'cqu', 'AUR62039891' => 'cqu', 'BcaB02g08737' => 'bca', 'BcaB04g20441' => 'bca', 'BcaB06g26509' => 'bca', 'BcaB06g26510' => 'bca', 'BcaB06g26511' => 'bca', 'BcaB06g26512' => 'bca', 'BcaB06g26513' => 'bca', 'BcaC02g12564' => 'bca', 'BcaC02g12565' => 'bca', 'BcaC02g12794' => 'bca', 'BcaC02g12795' => 'bca', 'BcaC02g12796' => 'bca', 'BcaC06g35541' => 'bca', 'BNapus_Darmor_BZH_scaffold_188p00080' => 'bna', 'BNapus_Darmor_BZH_scaffold_188p00090' => 'bna', 'BolC1t03972H' => 'bol', 'BolC1t03973H' => 'bol', 'BolC4t21680H' => 'bol', 'BolC7t41863H' => 'bol', 'BolSC55t61227H' => 'bol', 'BolSC55t61228H' => 'bol', 'BraA01t03278Z' => 'bra', 'BraA05t18998Z' => 'bra', 'BraA07t28673Z' => 'bra', 'C01p40150' => 'bna', 'C05p12370' => 'bna', 'C07p13680' => 'bna', 'CAN.G1006.16' => 'can', 'CAN.G1006.17' => 'can', 'CAN.G1170.2' => 'can', 'CAN.G962.7' => 'can', 'CANSAT25G2179' => 'cansat', 'CANSAT78G1573' => 'cansat', 'CARHR099510' => 'chi', 'CARHR143510' => 'chi', 'Carub.0003s2380' => 'cru', 'Carub.0004s3082' => 'cru', 'Ca_00614_v3' => 'car', 'Ca_07801_v3' => 'car', 'Ca_08567_v3' => 'car', 'Ca_09571_v3' => 'car', 'CBR_g19290' => 'cbr', 'Cc01_g19770' => 'ccan', 'Cc03_g03030' => 'ccan', 'CDE07G0968' => 'cde', 'CDE09G1441' => 'cde', 'Cfa006103' => 'cfa', 'Cfa015573' => 'cfa', 'Cfa016988' => 'cfa', 'Ciclev10006738m.g' => 'ccl', 'Ciclev10010920m.g' => 'ccl', 'Ciclev10018517m.g' => 'ccl', 'CiPaw.01G159200' => 'cil', 'CiPaw.02G091000' => 'cil', 'CiPaw.02G091100' => 'cil', 'CiPaw.08G103100' => 'cil', 'CiPaw.09G224900' => 'cil', 'ClCG06G005740' => 'cla', 'ClCG07G000090' => 'cla', 'ClCG07G000100' => 'cla', 'COL.COLO4_09143' => 'col', 'COL.COLO4_25124' => 'col', 'Cpa.g.sc16.34' => 'cpa', 'Cpa.g.sc3504.1' => 'cpa', 'Cpa.g.sc60.37' => 'cpa', 'CsaV3_6G018520' => 'csa', 'CsaV3_6G036860' => 'csa', 'CSS0001072' => 'camsi', 'CSS0020208' => 'camsi', 'CSS0021253' => 'camsi', 'CSS0022190' => 'camsi', 'CSS0036150' => 'camsi', 'CSS0040442' => 'camsi', 'CSS0042300' => 'camsi', 'CSS0045298' => 'camsi', 'DCAR_012449' => 'dca', 'DCAR_018405' => 'dca', 'DCAR_024573' => 'dca', 'DCAR_030591' => 'dca', 'Dinv16926' => 'din', 'Dinv32963' => 'din', 'Dinv38382' => 'din', 'Dinv38383' => 'din', 'Duzib133G0974' => 'dzi', 'Duzib138G1867' => 'dzi', 'Duzib211G0420' => 'dzi', 'Duzib212G0930' => 'dzi', 'ECA234G1645' => 'eca', 'ECA247G3467' => 'eca', 'ECA248G1703' => 'eca', 'EL10Ac3g06327' => 'bvu', 'EL10Ac7g17204' => 'bvu', 'Eucgr.A00855' => 'egr', 'Eucgr.A00858' => 'egr', 'Eucgr.H01520' => 'egr', 'Eucgr.H03604' => 'egr', 'Eucgr.L03465' => 'egr', 'Eucgr.L03466' => 'egr', 'FAN01G0988' => 'fan', 'FAN02G3892' => 'fan', 'FAN05G3381' => 'fan', 'FAN07G0967' => 'fan', 'FAN07G1493' => 'fan', 'FAN08G3125' => 'fan', 'FAN09G0402' => 'fan', 'FAN12G2594' => 'fan', 'FAN12G3879' => 'fan', 'FAN14G1546' => 'fan', 'FAN15G3626' => 'fan', 'FAN17G0588' => 'fan', 'FAN17G0609' => 'fan', 'FAN18G2817' => 'fan', 'FAN19G1305' => 'fan', 'FAN20G1787' => 'fan', 'FAN22G0073' => 'fan', 'FAN22G0352' => 'fan', 'FAN22G0368' => 'fan', 'FAN22G2273' => 'fan', 'FAN24G1998' => 'fan', 'FAN27G1317' => 'fan', 'FvH4_2g23980' => 'fve', 'FvH4_4g14380' => 'fve', 'FvH4_4g14390' => 'fve', 'FvH4_6g09250' => 'fve', 'Glyma.03G151100' => 'gma', 'Glyma.04G122550' => 'gma', 'Glyma.05G001600' => 'gma', 'Glyma.09G270766' => 'gma', 'Glyma.09G270832' => 'gma', 'Glyma.13G209800' => 'gma', 'Glyma.15G102800' => 'gma', 'Glyma.18G218900' => 'gma', 'Glyma.19G001500' => 'gma', 'Glyma.19G153600' => 'gma', 'Gohir.A02G028600' => 'ghi', 'Gohir.A08G045000' => 'ghi', 'Gohir.A11G120500' => 'ghi', 'Gohir.A12G006200' => 'ghi', 'Gohir.A12G006250' => 'ghi', 'Gohir.D02G036300' => 'ghi', 'Gohir.D08G054700' => 'ghi', 'Gohir.D11G125600' => 'ghi', 'Gohir.D12G005700' => 'ghi', 'Gorai.004G055200' => 'gra', 'Gorai.005G040400' => 'gra', 'Gorai.007G134500' => 'gra', 'Gorai.008G005500' => 'gra', 'GSVIVG01011094001' => 'vvi', 'GSVIVG01017879001' => 'vvi', 'GSVIVG01025988001' => 'vvi', 'GSVIVG01029847001' => 'vvi', 'HanXRQChr10g0282901' => 'han', 'HanXRQChr10g0310371' => 'han', 'HanXRQChr10g0315041' => 'han', 'HanXRQChr11g0327651' => 'han', 'HanXRQChr12g0359391' => 'han', 'Haze_00972' => 'cav', 'Haze_00973' => 'cav', 'Haze_00974' => 'cav', 'Haze_04747' => 'cav', 'Haze_04749' => 'cav', 'Haze_04750' => 'cav', 'Haze_21217' => 'cav', 'Hma1.2p1_1037F.1_g250680' => 'hma', 'Hma1.2p1_1644F.1_g295320' => 'hma', 'HPP92_011322' => 'vpl', 'HPP92_011323' => 'vpl', 'HPP92_011324' => 'vpl', 'HPP92_011325' => 'vpl', 'HPP92_011326' => 'vpl', 'Hund12205' => 'sun', 'Hund17957' => 'sun', 'Lalb_Chr06g0176771' => 'lal', 'Lalb_Chr18g0056021' => 'lal', 'Lalb_Chr18g0056031' => 'lal', 'Lalb_Chr18g0056041' => 'lal', 'Lalb_Chr20g0107751' => 'lal', 'Lalb_Chr20g0118371' => 'lal', 'Lj1g0010239' => 'lja', 'Lj1g0017101' => 'lja', 'Lj2A1178G40' => 'lonja', 'Lj2A54G84' => 'lonja', 'Lj2g0015248' => 'lja', 'Lj3A761T51' => 'lonja', 'Lj6g0018116' => 'lja', 'Lsat_1_v5_gn_4_136040' => 'lsa', 'Lsat_1_v5_gn_5_187461' => 'lsa', 'Lsat_1_v5_gn_5_77001' => 'lsa', 'Lsat_1_v5_gn_9_4461' => 'lsa', 'Manes.01G210100' => 'mes', 'Manes.03G185600' => 'mes', 'Manes.05G073300' => 'mes', 'Manes.09G120300' => 'mes', 'Manes.15G022100' => 'mes', 'Mapoly0096s0053' => 'mpo', 'MBI03_g14058_MAGBIO' => 'mbi', 'MBI03_g33876_MAGBIO' => 'mbi', 'MBI03_g36854_MAGBIO' => 'mbi', 'MBI17_g11997_MAGBIO' => 'mbi', 'MD03G1269000' => 'mdo', 'MD04G1179600' => 'mdo', 'MD11G1289800' => 'mdo', 'MD12G1194700' => 'mdo', 'MD13G1182100' => 'mdo', 'MD13G1182200' => 'mdo', 'MD16G1182600' => 'mdo', 'Medtr2g021400' => 'mtr', 'Medtr2g021470' => 'mtr', 'Medtr2g105810' => 'mtr', 'Medtr3g033580' => 'mtr', 'Medtr6g007970' => 'mtr', 'Medtr7g056330' => 'mtr', 'Medtr7g074290' => 'mtr', 'Medtr7g074380' => 'mtr', 'Medtr7g094550' => 'mtr', 'Medtr8g069995' => 'mtr', 'MELO3C014345.2' => 'cme', 'MELO3C021395.2' => 'cme', 'Migut.D00262' => 'egut', 'Migut.G00257' => 'egut', 'MSTRG.21575' => 'ama', 'MSTRG.3985' => 'ama', 'Nitab4.5_0000295g0140' => 'nta', 'Nitab4.5_0000732g0140' => 'nta', 'Nitab4.5_0003162g0020' => 'nta', 'Nitab4.5_0006180g0090' => 'nta', 'Nitab4.5_0006390g0010' => 'nta', 'Nitab4.5_0007392g0040' => 'nta', 'Nn1g02140' => 'nnu', 'Nn4g26168' => 'nnu', 'Nn5g26754' => 'nnu', 'Oeu001433.1' => 'oeu', 'Oeu010299.2' => 'oeu', 'Oeu011171.1' => 'oeu', 'Oeu037675.1' => 'oeu', 'Oeu038359.1' => 'oeu', 'Oeu063834.1' => 'oeu', 'Oeu063835.1' => 'oeu', 'Os05g0312000' => 'osa', 'Os07g0211101' => 'osa', 'Os07g0211200' => 'osa', 'Os07g0681500' => 'osa', 'Peaxi162Scf00095g01015' => 'pax', 'Peaxi162Scf00104g00329' => 'pax', 'Peaxi162Scf00161g00137' => 'pax', 'PGR004G1665' => 'pgr', 'PGR031G2937' => 'pgr', 'PGR119G2145' => 'pgr', 'PGSC0003DMG400004351' => 'stu', 'PGSC0003DMG400014625' => 'stu', 'PGSC0003DMG401000943' => 'stu', 'Phvul.001G148600' => 'pvu', 'Phvul.004G001700' => 'pvu', 'Phvul.006G154900' => 'pvu', 'Phvul.008G078200' => 'pvu', 'Phvul.011G136500' => 'pvu', 'Potri.002G215600' => 'ptr', 'Potri.008G201600' => 'ptr', 'Potri.014G138400' => 'ptr', 'Potri.016G142500' => 'ptr', 'Pp3c16_10580' => 'ppa', 'Pp3c5_25280' => 'ppa', 'Prupe.1G150000' => 'ppe', 'Prupe.1G150100' => 'ppe', 'Prupe.6G299600' => 'ppe', 'Prupe.8G245000' => 'ppe', 'Psat0s4927g0040' => 'psa', 'Psat1g052080' => 'psa', 'Psat1g183800' => 'psa', 'Psat3g113840' => 'psa', 'Psat3g126120' => 'psa', 'Psat3g126160' => 'psa', 'Psat3g158760' => 'psa', 'Psat3g158840' => 'psa', 'PSO170G2858' => 'pso', 'PSO339G0606' => 'pso', 'PSO384G4709' => 'pso', 'PSO407G0334' => 'pso', 'QL04p040276' => 'qlo', 'QL06p005458' => 'qlo', 'QL06p005472' => 'qlo', 'QL07p030546' => 'qlo', 'QL07p031519' => 'qlo', 'QL09p050949' => 'qlo', 'QL09p050966' => 'qlo', 'QL09p051067' => 'qlo', 'QL12p022706' => 'qlo', 'RcHm_v2.0_Chr2g0119601' => 'rch', 'RcHm_v2.0_Chr3g0459591' => 'rch', 'RcHm_v2.0_Chr4g0418521' => 'rch', 'RcHm_v2.0_Chr4g0418531' => 'rch', 'RcHm_v2.0_Chr4g0418541' => 'rch', 'RcHm_v2.0_Chr6g0291641' => 'rch', 'Rhsim01G0086300' => 'rsi', 'Rhsim01G0276300' => 'rsi', 'Rhsim01G0276500' => 'rsi', 'Rhsim04G0207700' => 'rsi', 'Rhsim05G0234500' => 'rsi', 'Rhsim13G0022400' => 'rsi', 'Sabra02G0167900' => 'sbr', 'Sabra04G0158500' => 'sbr', 'Sabra08G0159800' => 'sbr', 'Sabra10G0011500' => 'sbr', 'Sabra14G0104400' => 'sbr', 'SalBow2G2440' => 'sbo', 'SalBow4G2265' => 'sbo', 'Sc02g0000060' => 'sci', 'Sc05g0005020' => 'sci', 'Sc13g0003890' => 'sci', 'Sed0014865' => 'sed', 'Sed0017224' => 'sed', 'Sed0026391' => 'sed', 'SEGI_00063' => 'sgi', 'SEGI_10967' => 'sgi', 'SEGI_17510' => 'sgi', 'SEGI_24396' => 'sgi', 'SEGI_39719' => 'sgi', 'SEGI_41392' => 'sgi', 'SGA_v2.0_scaffold11G05794' => 'sas', 'SGA_v2.0_scaffold142G35607' => 'sas', 'SGA_v2.0_scaffold1G00447' => 'sas', 'SHI15388' => 'shi', 'SHI15394' => 'shi', 'SHI15396' => 'shi', 'SHI15399' => 'shi', 'SMO343G0151' => 'smo', 'SMO367G1118' => 'smo', 'Solyc01g080200.3' => 'sly', 'Solyc06g008960.3' => 'sly', 'Solyc09g064780.3' => 'sly', 'Sopen01g031980' => 'spe', 'Sopen06g003710' => 'spe', 'Sopen09g026460' => 'spe', 'Sp3g21240' => 'spa', 'Sp4g30030' => 'spa', 'TAR365G0022' => 'tar', 'TAR365G1023' => 'tar', 'TAR365G1253' => 'tar', 'TAR623G0078' => 'tar', 'TAR623G1721' => 'tar', 'TAR633G0959' => 'tar', 'THA.LOC104802225' => 'tha', 'THA.LOC104804769' => 'tha', 'THA.LOC104808660' => 'tha', 'THA.LOC104812792' => 'tha', 'Thecc.01G284000' => 'tca', 'Thecc.04G220600' => 'tca', 'Thecc.05G268900' => 'tca', 'Thecc.08G171100' => 'tca', 'Thhalv10001284m.g' => 'esa', 'Thhalv10019912m.g' => 'esa', 'TPR.G14189' => 'tpr', 'TPR.G18110' => 'tpr', 'TPR.G18130' => 'tpr', 'TPR.G18131' => 'tpr', 'TPR.G18140' => 'tpr', 'TPR.G24282' => 'tpr', 'TPR.G25221' => 'tpr', 'TPR.G29267' => 'tpr', 'TPR.G35315' => 'tpr', 'TPR.G36173' => 'tpr', 'TWI09G0794' => 'twi', 'TWI59G1348' => 'twi', 'TWI74G0430' => 'twi', 'unitig_26.g8940' => 'ugi', 'unitig_749.g13744' => 'ugi', 'unitig_749.g13745' => 'ugi', 'vmacro08269' => 'vma', 'vmacro14937' => 'vma', 'vmacro20401' => 'vma', 'VMungo0464G1349' => 'vmu', 'VMungo0540G0289' => 'vmu', 'VMungo1215G1590' => 'vmu', 'VMungo1309G0221' => 'vmu', 'VMungo1309G2815' => 'vmu', 'VMungo1383G0239' => 'vmu', 'VMungo1383G2910' => 'vmu', 'Zm00001eb095270' => 'zma', 'Zm00001eb095280' => 'zma', 'Zm00001eb111630' => 'zma', 'Zm00001eb237080' => 'zma', 'Zm00001eb273740' => 'zma', 'Zm00001eb285040' => 'zma', 'Zm00001eb330790' => 'zma', 'Zm00001eb337380' => 'zma' ), 'gf_id' => 'HOM05D001484', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001484' ), 'data_identifier' => 'HOM05D001484', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001484', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p31500' => 'bna', 'A05p00020' => 'bna', 'A07p08820' => 'bna', 'Aa31LG4G3300' => 'aar', 'Aa31LG8G10030' => 'aar', 'Actinidia00731' => 'ach', 'Actinidia11473' => 'ach', 'Actinidia23469' => 'ach', 'Actinidia24318' => 'ach', 'Actinidia40196' => 'ach', 'Actinidia40197' => 'ach', 'Actinidia40198' => 'ach', 'Ah.08g212990' => 'amhyb', 'Ah.15g091720' => 'amhyb', 'AL3G38260' => 'aly', 'AL4G47710' => 'aly', 'Aqoxy2G00671' => 'aox', 'Aqoxy2G03236' => 'aox', 'arahy.Tifrunner.gnm1.ann1.05IDCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KR684' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATY3SJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK6QJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6APGL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IDT7Z9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM073U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ0R87' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LE7RV4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT4QRX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V5ENPK' => 'arhy', 'AT2G48110' => 'ath', 'AT3G23590' => 'ath', 'ATR0626G186' => 'atr', 'ATR1127G141' => 'atr', 'Atru.chr4.2583' => 'acertr', 'Atru.chr5.1358' => 'acertr', 'Atru.chr5.1359' => 'acertr', 'Atru.chr8.46' => 'acertr', 'AUR62002640' => 'cqu', 'AUR62030055' => 'cqu', 'AUR62033713' => 'cqu', 'AUR62033714' => 'cqu', 'AUR62036795' => 'cqu', 'AUR62039891' => 'cqu', 'BcaB02g08737' => 'bca', 'BcaB04g20441' => 'bca', 'BcaB06g26509' => 'bca', 'BcaB06g26510' => 'bca', 'BcaB06g26511' => 'bca', 'BcaB06g26512' => 'bca', 'BcaB06g26513' => 'bca', 'BcaC02g12564' => 'bca', 'BcaC02g12565' => 'bca', 'BcaC02g12794' => 'bca', 'BcaC02g12795' => 'bca', 'BcaC02g12796' => 'bca', 'BcaC06g35541' => 'bca', 'BNapus_Darmor_BZH_scaffold_188p00080' => 'bna', 'BNapus_Darmor_BZH_scaffold_188p00090' => 'bna', 'BolC1t03972H' => 'bol', 'BolC1t03973H' => 'bol', 'BolC4t21680H' => 'bol', 'BolC7t41863H' => 'bol', 'BolSC55t61227H' => 'bol', 'BolSC55t61228H' => 'bol', 'BraA01t03278Z' => 'bra', 'BraA05t18998Z' => 'bra', 'BraA07t28673Z' => 'bra', 'C01p40150' => 'bna', 'C05p12370' => 'bna', 'C07p13680' => 'bna', 'CAN.G1006.16' => 'can', 'CAN.G1006.17' => 'can', 'CAN.G1170.2' => 'can', 'CAN.G962.7' => 'can', 'CANSAT25G2179' => 'cansat', 'CANSAT78G1573' => 'cansat', 'CARHR099510' => 'chi', 'CARHR143510' => 'chi', 'Carub.0003s2380' => 'cru', 'Carub.0004s3082' => 'cru', 'Ca_00614_v3' => 'car', 'Ca_07801_v3' => 'car', 'Ca_08567_v3' => 'car', 'Ca_09571_v3' => 'car', 'CBR_g19290' => 'cbr', 'Cc01_g19770' => 'ccan', 'Cc03_g03030' => 'ccan', 'CDE07G0968' => 'cde', 'CDE09G1441' => 'cde', 'Cfa006103' => 'cfa', 'Cfa015573' => 'cfa', 'Cfa016988' => 'cfa', 'Ciclev10006738m.g' => 'ccl', 'Ciclev10010920m.g' => 'ccl', 'Ciclev10018517m.g' => 'ccl', 'CiPaw.01G159200' => 'cil', 'CiPaw.02G091000' => 'cil', 'CiPaw.02G091100' => 'cil', 'CiPaw.08G103100' => 'cil', 'CiPaw.09G224900' => 'cil', 'ClCG06G005740' => 'cla', 'ClCG07G000090' => 'cla', 'ClCG07G000100' => 'cla', 'COL.COLO4_09143' => 'col', 'COL.COLO4_25124' => 'col', 'Cpa.g.sc16.34' => 'cpa', 'Cpa.g.sc3504.1' => 'cpa', 'Cpa.g.sc60.37' => 'cpa', 'CsaV3_6G018520' => 'csa', 'CsaV3_6G036860' => 'csa', 'CSS0001072' => 'camsi', 'CSS0020208' => 'camsi', 'CSS0021253' => 'camsi', 'CSS0022190' => 'camsi', 'CSS0036150' => 'camsi', 'CSS0040442' => 'camsi', 'CSS0042300' => 'camsi', 'CSS0045298' => 'camsi', 'DCAR_012449' => 'dca', 'DCAR_018405' => 'dca', 'DCAR_024573' => 'dca', 'DCAR_030591' => 'dca', 'Dinv16926' => 'din', 'Dinv32963' => 'din', 'Dinv38382' => 'din', 'Dinv38383' => 'din', 'Duzib133G0974' => 'dzi', 'Duzib138G1867' => 'dzi', 'Duzib211G0420' => 'dzi', 'Duzib212G0930' => 'dzi', 'ECA234G1645' => 'eca', 'ECA247G3467' => 'eca', 'ECA248G1703' => 'eca', 'EL10Ac3g06327' => 'bvu', 'EL10Ac7g17204' => 'bvu', 'Eucgr.A00855' => 'egr', 'Eucgr.A00858' => 'egr', 'Eucgr.H01520' => 'egr', 'Eucgr.H03604' => 'egr', 'Eucgr.L03465' => 'egr', 'Eucgr.L03466' => 'egr', 'FAN01G0988' => 'fan', 'FAN02G3892' => 'fan', 'FAN05G3381' => 'fan', 'FAN07G0967' => 'fan', 'FAN07G1493' => 'fan', 'FAN08G3125' => 'fan', 'FAN09G0402' => 'fan', 'FAN12G2594' => 'fan', 'FAN12G3879' => 'fan', 'FAN14G1546' => 'fan', 'FAN15G3626' => 'fan', 'FAN17G0588' => 'fan', 'FAN17G0609' => 'fan', 'FAN18G2817' => 'fan', 'FAN19G1305' => 'fan', 'FAN20G1787' => 'fan', 'FAN22G0073' => 'fan', 'FAN22G0352' => 'fan', 'FAN22G0368' => 'fan', 'FAN22G2273' => 'fan', 'FAN24G1998' => 'fan', 'FAN27G1317' => 'fan', 'FvH4_2g23980' => 'fve', 'FvH4_4g14380' => 'fve', 'FvH4_4g14390' => 'fve', 'FvH4_6g09250' => 'fve', 'Glyma.03G151100' => 'gma', 'Glyma.04G122550' => 'gma', 'Glyma.05G001600' => 'gma', 'Glyma.09G270766' => 'gma', 'Glyma.09G270832' => 'gma', 'Glyma.13G209800' => 'gma', 'Glyma.15G102800' => 'gma', 'Glyma.18G218900' => 'gma', 'Glyma.19G001500' => 'gma', 'Glyma.19G153600' => 'gma', 'Gohir.A02G028600' => 'ghi', 'Gohir.A08G045000' => 'ghi', 'Gohir.A11G120500' => 'ghi', 'Gohir.A12G006200' => 'ghi', 'Gohir.A12G006250' => 'ghi', 'Gohir.D02G036300' => 'ghi', 'Gohir.D08G054700' => 'ghi', 'Gohir.D11G125600' => 'ghi', 'Gohir.D12G005700' => 'ghi', 'Gorai.004G055200' => 'gra', 'Gorai.005G040400' => 'gra', 'Gorai.007G134500' => 'gra', 'Gorai.008G005500' => 'gra', 'GSVIVG01011094001' => 'vvi', 'GSVIVG01017879001' => 'vvi', 'GSVIVG01025988001' => 'vvi', 'GSVIVG01029847001' => 'vvi', 'HanXRQChr10g0282901' => 'han', 'HanXRQChr10g0310371' => 'han', 'HanXRQChr10g0315041' => 'han', 'HanXRQChr11g0327651' => 'han', 'HanXRQChr12g0359391' => 'han', 'Haze_00972' => 'cav', 'Haze_00973' => 'cav', 'Haze_00974' => 'cav', 'Haze_04747' => 'cav', 'Haze_04749' => 'cav', 'Haze_04750' => 'cav', 'Haze_21217' => 'cav', 'Hma1.2p1_1037F.1_g250680' => 'hma', 'Hma1.2p1_1644F.1_g295320' => 'hma', 'HPP92_011322' => 'vpl', 'HPP92_011323' => 'vpl', 'HPP92_011324' => 'vpl', 'HPP92_011325' => 'vpl', 'HPP92_011326' => 'vpl', 'Hund12205' => 'sun', 'Hund17957' => 'sun', 'Lalb_Chr06g0176771' => 'lal', 'Lalb_Chr18g0056021' => 'lal', 'Lalb_Chr18g0056031' => 'lal', 'Lalb_Chr18g0056041' => 'lal', 'Lalb_Chr20g0107751' => 'lal', 'Lalb_Chr20g0118371' => 'lal', 'Lj1g0010239' => 'lja', 'Lj1g0017101' => 'lja', 'Lj2A1178G40' => 'lonja', 'Lj2A54G84' => 'lonja', 'Lj2g0015248' => 'lja', 'Lj3A761T51' => 'lonja', 'Lj6g0018116' => 'lja', 'Lsat_1_v5_gn_4_136040' => 'lsa', 'Lsat_1_v5_gn_5_187461' => 'lsa', 'Lsat_1_v5_gn_5_77001' => 'lsa', 'Lsat_1_v5_gn_9_4461' => 'lsa', 'Manes.01G210100' => 'mes', 'Manes.03G185600' => 'mes', 'Manes.05G073300' => 'mes', 'Manes.09G120300' => 'mes', 'Manes.15G022100' => 'mes', 'Mapoly0096s0053' => 'mpo', 'MBI03_g14058_MAGBIO' => 'mbi', 'MBI03_g33876_MAGBIO' => 'mbi', 'MBI03_g36854_MAGBIO' => 'mbi', 'MBI17_g11997_MAGBIO' => 'mbi', 'MD03G1269000' => 'mdo', 'MD04G1179600' => 'mdo', 'MD11G1289800' => 'mdo', 'MD12G1194700' => 'mdo', 'MD13G1182100' => 'mdo', 'MD13G1182200' => 'mdo', 'MD16G1182600' => 'mdo', 'Medtr2g021400' => 'mtr', 'Medtr2g021470' => 'mtr', 'Medtr2g105810' => 'mtr', 'Medtr3g033580' => 'mtr', 'Medtr6g007970' => 'mtr', 'Medtr7g056330' => 'mtr', 'Medtr7g074290' => 'mtr', 'Medtr7g074380' => 'mtr', 'Medtr7g094550' => 'mtr', 'Medtr8g069995' => 'mtr', 'MELO3C014345.2' => 'cme', 'MELO3C021395.2' => 'cme', 'Migut.D00262' => 'egut', 'Migut.G00257' => 'egut', 'MSTRG.21575' => 'ama', 'MSTRG.3985' => 'ama', 'Nitab4.5_0000295g0140' => 'nta', 'Nitab4.5_0000732g0140' => 'nta', 'Nitab4.5_0003162g0020' => 'nta', 'Nitab4.5_0006180g0090' => 'nta', 'Nitab4.5_0006390g0010' => 'nta', 'Nitab4.5_0007392g0040' => 'nta', 'Nn1g02140' => 'nnu', 'Nn4g26168' => 'nnu', 'Nn5g26754' => 'nnu', 'Oeu001433.1' => 'oeu', 'Oeu010299.2' => 'oeu', 'Oeu011171.1' => 'oeu', 'Oeu037675.1' => 'oeu', 'Oeu038359.1' => 'oeu', 'Oeu063834.1' => 'oeu', 'Oeu063835.1' => 'oeu', 'Os05g0312000' => 'osa', 'Os07g0211101' => 'osa', 'Os07g0211200' => 'osa', 'Os07g0681500' => 'osa', 'Peaxi162Scf00095g01015' => 'pax', 'Peaxi162Scf00104g00329' => 'pax', 'Peaxi162Scf00161g00137' => 'pax', 'PGR004G1665' => 'pgr', 'PGR031G2937' => 'pgr', 'PGR119G2145' => 'pgr', 'PGSC0003DMG400004351' => 'stu', 'PGSC0003DMG400014625' => 'stu', 'PGSC0003DMG401000943' => 'stu', 'Phvul.001G148600' => 'pvu', 'Phvul.004G001700' => 'pvu', 'Phvul.006G154900' => 'pvu', 'Phvul.008G078200' => 'pvu', 'Phvul.011G136500' => 'pvu', 'Potri.002G215600' => 'ptr', 'Potri.008G201600' => 'ptr', 'Potri.014G138400' => 'ptr', 'Potri.016G142500' => 'ptr', 'Pp3c16_10580' => 'ppa', 'Pp3c5_25280' => 'ppa', 'Prupe.1G150000' => 'ppe', 'Prupe.1G150100' => 'ppe', 'Prupe.6G299600' => 'ppe', 'Prupe.8G245000' => 'ppe', 'Psat0s4927g0040' => 'psa', 'Psat1g052080' => 'psa', 'Psat1g183800' => 'psa', 'Psat3g113840' => 'psa', 'Psat3g126120' => 'psa', 'Psat3g126160' => 'psa', 'Psat3g158760' => 'psa', 'Psat3g158840' => 'psa', 'PSO170G2858' => 'pso', 'PSO339G0606' => 'pso', 'PSO384G4709' => 'pso', 'PSO407G0334' => 'pso', 'QL04p040276' => 'qlo', 'QL06p005458' => 'qlo', 'QL06p005472' => 'qlo', 'QL07p030546' => 'qlo', 'QL07p031519' => 'qlo', 'QL09p050949' => 'qlo', 'QL09p050966' => 'qlo', 'QL09p051067' => 'qlo', 'QL12p022706' => 'qlo', 'RcHm_v2.0_Chr2g0119601' => 'rch', 'RcHm_v2.0_Chr3g0459591' => 'rch', 'RcHm_v2.0_Chr4g0418521' => 'rch', 'RcHm_v2.0_Chr4g0418531' => 'rch', 'RcHm_v2.0_Chr4g0418541' => 'rch', 'RcHm_v2.0_Chr6g0291641' => 'rch', 'Rhsim01G0086300' => 'rsi', 'Rhsim01G0276300' => 'rsi', 'Rhsim01G0276500' => 'rsi', 'Rhsim04G0207700' => 'rsi', 'Rhsim05G0234500' => 'rsi', 'Rhsim13G0022400' => 'rsi', 'Sabra02G0167900' => 'sbr', 'Sabra04G0158500' => 'sbr', 'Sabra08G0159800' => 'sbr', 'Sabra10G0011500' => 'sbr', 'Sabra14G0104400' => 'sbr', 'SalBow2G2440' => 'sbo', 'SalBow4G2265' => 'sbo', 'Sc02g0000060' => 'sci', 'Sc05g0005020' => 'sci', 'Sc13g0003890' => 'sci', 'Sed0014865' => 'sed', 'Sed0017224' => 'sed', 'Sed0026391' => 'sed', 'SEGI_00063' => 'sgi', 'SEGI_10967' => 'sgi', 'SEGI_17510' => 'sgi', 'SEGI_24396' => 'sgi', 'SEGI_39719' => 'sgi', 'SEGI_41392' => 'sgi', 'SGA_v2.0_scaffold11G05794' => 'sas', 'SGA_v2.0_scaffold142G35607' => 'sas', 'SGA_v2.0_scaffold1G00447' => 'sas', 'SHI15388' => 'shi', 'SHI15394' => 'shi', 'SHI15396' => 'shi', 'SHI15399' => 'shi', 'SMO343G0151' => 'smo', 'SMO367G1118' => 'smo', 'Solyc01g080200.3' => 'sly', 'Solyc06g008960.3' => 'sly', 'Solyc09g064780.3' => 'sly', 'Sopen01g031980' => 'spe', 'Sopen06g003710' => 'spe', 'Sopen09g026460' => 'spe', 'Sp3g21240' => 'spa', 'Sp4g30030' => 'spa', 'TAR365G0022' => 'tar', 'TAR365G1023' => 'tar', 'TAR365G1253' => 'tar', 'TAR623G0078' => 'tar', 'TAR623G1721' => 'tar', 'TAR633G0959' => 'tar', 'THA.LOC104802225' => 'tha', 'THA.LOC104804769' => 'tha', 'THA.LOC104808660' => 'tha', 'THA.LOC104812792' => 'tha', 'Thecc.01G284000' => 'tca', 'Thecc.04G220600' => 'tca', 'Thecc.05G268900' => 'tca', 'Thecc.08G171100' => 'tca', 'Thhalv10001284m.g' => 'esa', 'Thhalv10019912m.g' => 'esa', 'TPR.G14189' => 'tpr', 'TPR.G18110' => 'tpr', 'TPR.G18130' => 'tpr', 'TPR.G18131' => 'tpr', 'TPR.G18140' => 'tpr', 'TPR.G24282' => 'tpr', 'TPR.G25221' => 'tpr', 'TPR.G29267' => 'tpr', 'TPR.G35315' => 'tpr', 'TPR.G36173' => 'tpr', 'TWI09G0794' => 'twi', 'TWI59G1348' => 'twi', 'TWI74G0430' => 'twi', 'unitig_26.g8940' => 'ugi', 'unitig_749.g13744' => 'ugi', 'unitig_749.g13745' => 'ugi', 'vmacro08269' => 'vma', 'vmacro14937' => 'vma', 'vmacro20401' => 'vma', 'VMungo0464G1349' => 'vmu', 'VMungo0540G0289' => 'vmu', 'VMungo1215G1590' => 'vmu', 'VMungo1309G0221' => 'vmu', 'VMungo1309G2815' => 'vmu', 'VMungo1383G0239' => 'vmu', 'VMungo1383G2910' => 'vmu', 'Zm00001eb095270' => 'zma', 'Zm00001eb095280' => 'zma', 'Zm00001eb111630' => 'zma', 'Zm00001eb237080' => 'zma', 'Zm00001eb273740' => 'zma', 'Zm00001eb285040' => 'zma', 'Zm00001eb330790' => 'zma', 'Zm00001eb337380' => 'zma' ) $gf_id = 'HOM05D001484' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001484' ) $data_identifier = 'HOM05D001484' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 2, 'aly' => (int) 2, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 22, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 7, 'hma' => (int) 2, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 7, 'mtr' => (int) 10, 'cme' => (int) 2, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 4, 'ppa' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 4, 'qlo' => (int) 9, 'rch' => (int) 6, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 10, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 7, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb337380' $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' => 'HOM05D001484', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p31500' => 'bna', 'A05p00020' => 'bna', 'A07p08820' => 'bna', 'Aa31LG4G3300' => 'aar', 'Aa31LG8G10030' => 'aar', 'Actinidia00731' => 'ach', 'Actinidia11473' => 'ach', 'Actinidia23469' => 'ach', 'Actinidia24318' => 'ach', 'Actinidia40196' => 'ach', 'Actinidia40197' => 'ach', 'Actinidia40198' => 'ach', 'Ah.08g212990' => 'amhyb', 'Ah.15g091720' => 'amhyb', 'AL3G38260' => 'aly', 'AL4G47710' => 'aly', 'Aqoxy2G00671' => 'aox', 'Aqoxy2G03236' => 'aox', 'arahy.Tifrunner.gnm1.ann1.05IDCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KR684' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATY3SJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK6QJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6APGL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IDT7Z9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM073U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ0R87' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LE7RV4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT4QRX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V5ENPK' => 'arhy', 'AT2G48110' => 'ath', 'AT3G23590' => 'ath', 'ATR0626G186' => 'atr', 'ATR1127G141' => 'atr', 'Atru.chr4.2583' => 'acertr', 'Atru.chr5.1358' => 'acertr', 'Atru.chr5.1359' => 'acertr', 'Atru.chr8.46' => 'acertr', 'AUR62002640' => 'cqu', 'AUR62030055' => 'cqu', 'AUR62033713' => 'cqu', 'AUR62033714' => 'cqu', 'AUR62036795' => 'cqu', 'AUR62039891' => 'cqu', 'BcaB02g08737' => 'bca', 'BcaB04g20441' => 'bca', 'BcaB06g26509' => 'bca', 'BcaB06g26510' => 'bca', 'BcaB06g26511' => 'bca', 'BcaB06g26512' => 'bca', 'BcaB06g26513' => 'bca', 'BcaC02g12564' => 'bca', 'BcaC02g12565' => 'bca', 'BcaC02g12794' => 'bca', 'BcaC02g12795' => 'bca', 'BcaC02g12796' => 'bca', 'BcaC06g35541' => 'bca', 'BNapus_Darmor_BZH_scaffold_188p00080' => 'bna', 'BNapus_Darmor_BZH_scaffold_188p00090' => 'bna', 'BolC1t03972H' => 'bol', 'BolC1t03973H' => 'bol', 'BolC4t21680H' => 'bol', 'BolC7t41863H' => 'bol', 'BolSC55t61227H' => 'bol', 'BolSC55t61228H' => 'bol', 'BraA01t03278Z' => 'bra', 'BraA05t18998Z' => 'bra', 'BraA07t28673Z' => 'bra', 'C01p40150' => 'bna', 'C05p12370' => 'bna', 'C07p13680' => 'bna', 'CAN.G1006.16' => 'can', 'CAN.G1006.17' => 'can', 'CAN.G1170.2' => 'can', 'CAN.G962.7' => 'can', 'CANSAT25G2179' => 'cansat', 'CANSAT78G1573' => 'cansat', 'CARHR099510' => 'chi', 'CARHR143510' => 'chi', 'Carub.0003s2380' => 'cru', 'Carub.0004s3082' => 'cru', 'Ca_00614_v3' => 'car', 'Ca_07801_v3' => 'car', 'Ca_08567_v3' => 'car', 'Ca_09571_v3' => 'car', 'CBR_g19290' => 'cbr', 'Cc01_g19770' => 'ccan', 'Cc03_g03030' => 'ccan', 'CDE07G0968' => 'cde', 'CDE09G1441' => 'cde', 'Cfa006103' => 'cfa', 'Cfa015573' => 'cfa', 'Cfa016988' => 'cfa', 'Ciclev10006738m.g' => 'ccl', 'Ciclev10010920m.g' => 'ccl', 'Ciclev10018517m.g' => 'ccl', 'CiPaw.01G159200' => 'cil', 'CiPaw.02G091000' => 'cil', 'CiPaw.02G091100' => 'cil', 'CiPaw.08G103100' => 'cil', 'CiPaw.09G224900' => 'cil', 'ClCG06G005740' => 'cla', 'ClCG07G000090' => 'cla', 'ClCG07G000100' => 'cla', 'COL.COLO4_09143' => 'col', 'COL.COLO4_25124' => 'col', 'Cpa.g.sc16.34' => 'cpa', 'Cpa.g.sc3504.1' => 'cpa', 'Cpa.g.sc60.37' => 'cpa', 'CsaV3_6G018520' => 'csa', 'CsaV3_6G036860' => 'csa', 'CSS0001072' => 'camsi', 'CSS0020208' => 'camsi', 'CSS0021253' => 'camsi', 'CSS0022190' => 'camsi', 'CSS0036150' => 'camsi', 'CSS0040442' => 'camsi', 'CSS0042300' => 'camsi', 'CSS0045298' => 'camsi', 'DCAR_012449' => 'dca', 'DCAR_018405' => 'dca', 'DCAR_024573' => 'dca', 'DCAR_030591' => 'dca', 'Dinv16926' => 'din', 'Dinv32963' => 'din', 'Dinv38382' => 'din', 'Dinv38383' => 'din', 'Duzib133G0974' => 'dzi', 'Duzib138G1867' => 'dzi', 'Duzib211G0420' => 'dzi', 'Duzib212G0930' => 'dzi', 'ECA234G1645' => 'eca', 'ECA247G3467' => 'eca', 'ECA248G1703' => 'eca', 'EL10Ac3g06327' => 'bvu', 'EL10Ac7g17204' => 'bvu', 'Eucgr.A00855' => 'egr', 'Eucgr.A00858' => 'egr', 'Eucgr.H01520' => 'egr', 'Eucgr.H03604' => 'egr', 'Eucgr.L03465' => 'egr', 'Eucgr.L03466' => 'egr', 'FAN01G0988' => 'fan', 'FAN02G3892' => 'fan', 'FAN05G3381' => 'fan', 'FAN07G0967' => 'fan', 'FAN07G1493' => 'fan', 'FAN08G3125' => 'fan', 'FAN09G0402' => 'fan', 'FAN12G2594' => 'fan', 'FAN12G3879' => 'fan', 'FAN14G1546' => 'fan', 'FAN15G3626' => 'fan', 'FAN17G0588' => 'fan', 'FAN17G0609' => 'fan', 'FAN18G2817' => 'fan', 'FAN19G1305' => 'fan', 'FAN20G1787' => 'fan', 'FAN22G0073' => 'fan', 'FAN22G0352' => 'fan', 'FAN22G0368' => 'fan', 'FAN22G2273' => 'fan', 'FAN24G1998' => 'fan', 'FAN27G1317' => 'fan', 'FvH4_2g23980' => 'fve', 'FvH4_4g14380' => 'fve', 'FvH4_4g14390' => 'fve', 'FvH4_6g09250' => 'fve', 'Glyma.03G151100' => 'gma', 'Glyma.04G122550' => 'gma', 'Glyma.05G001600' => 'gma', 'Glyma.09G270766' => 'gma', 'Glyma.09G270832' => 'gma', 'Glyma.13G209800' => 'gma', 'Glyma.15G102800' => 'gma', 'Glyma.18G218900' => 'gma', 'Glyma.19G001500' => 'gma', 'Glyma.19G153600' => 'gma', 'Gohir.A02G028600' => 'ghi', 'Gohir.A08G045000' => 'ghi', 'Gohir.A11G120500' => 'ghi', 'Gohir.A12G006200' => 'ghi', 'Gohir.A12G006250' => 'ghi', 'Gohir.D02G036300' => 'ghi', 'Gohir.D08G054700' => 'ghi', 'Gohir.D11G125600' => 'ghi', 'Gohir.D12G005700' => 'ghi', 'Gorai.004G055200' => 'gra', 'Gorai.005G040400' => 'gra', 'Gorai.007G134500' => 'gra', 'Gorai.008G005500' => 'gra', 'GSVIVG01011094001' => 'vvi', 'GSVIVG01017879001' => 'vvi', 'GSVIVG01025988001' => 'vvi', 'GSVIVG01029847001' => 'vvi', 'HanXRQChr10g0282901' => 'han', 'HanXRQChr10g0310371' => 'han', 'HanXRQChr10g0315041' => 'han', 'HanXRQChr11g0327651' => 'han', 'HanXRQChr12g0359391' => 'han', 'Haze_00972' => 'cav', 'Haze_00973' => 'cav', 'Haze_00974' => 'cav', 'Haze_04747' => 'cav', 'Haze_04749' => 'cav', 'Haze_04750' => 'cav', 'Haze_21217' => 'cav', 'Hma1.2p1_1037F.1_g250680' => 'hma', 'Hma1.2p1_1644F.1_g295320' => 'hma', 'HPP92_011322' => 'vpl', 'HPP92_011323' => 'vpl', 'HPP92_011324' => 'vpl', 'HPP92_011325' => 'vpl', 'HPP92_011326' => 'vpl', 'Hund12205' => 'sun', 'Hund17957' => 'sun', 'Lalb_Chr06g0176771' => 'lal', 'Lalb_Chr18g0056021' => 'lal', 'Lalb_Chr18g0056031' => 'lal', 'Lalb_Chr18g0056041' => 'lal', 'Lalb_Chr20g0107751' => 'lal', 'Lalb_Chr20g0118371' => 'lal', 'Lj1g0010239' => 'lja', 'Lj1g0017101' => 'lja', 'Lj2A1178G40' => 'lonja', 'Lj2A54G84' => 'lonja', 'Lj2g0015248' => 'lja', 'Lj3A761T51' => 'lonja', 'Lj6g0018116' => 'lja', 'Lsat_1_v5_gn_4_136040' => 'lsa', 'Lsat_1_v5_gn_5_187461' => 'lsa', 'Lsat_1_v5_gn_5_77001' => 'lsa', 'Lsat_1_v5_gn_9_4461' => 'lsa', 'Manes.01G210100' => 'mes', 'Manes.03G185600' => 'mes', 'Manes.05G073300' => 'mes', 'Manes.09G120300' => 'mes', 'Manes.15G022100' => 'mes', 'Mapoly0096s0053' => 'mpo', 'MBI03_g14058_MAGBIO' => 'mbi', 'MBI03_g33876_MAGBIO' => 'mbi', 'MBI03_g36854_MAGBIO' => 'mbi', 'MBI17_g11997_MAGBIO' => 'mbi', 'MD03G1269000' => 'mdo', 'MD04G1179600' => 'mdo', 'MD11G1289800' => 'mdo', 'MD12G1194700' => 'mdo', 'MD13G1182100' => 'mdo', 'MD13G1182200' => 'mdo', 'MD16G1182600' => 'mdo', 'Medtr2g021400' => 'mtr', 'Medtr2g021470' => 'mtr', 'Medtr2g105810' => 'mtr', 'Medtr3g033580' => 'mtr', 'Medtr6g007970' => 'mtr', 'Medtr7g056330' => 'mtr', 'Medtr7g074290' => 'mtr', 'Medtr7g074380' => 'mtr', 'Medtr7g094550' => 'mtr', 'Medtr8g069995' => 'mtr', 'MELO3C014345.2' => 'cme', 'MELO3C021395.2' => 'cme', 'Migut.D00262' => 'egut', 'Migut.G00257' => 'egut', 'MSTRG.21575' => 'ama', 'MSTRG.3985' => 'ama', 'Nitab4.5_0000295g0140' => 'nta', 'Nitab4.5_0000732g0140' => 'nta', 'Nitab4.5_0003162g0020' => 'nta', 'Nitab4.5_0006180g0090' => 'nta', 'Nitab4.5_0006390g0010' => 'nta', 'Nitab4.5_0007392g0040' => 'nta', 'Nn1g02140' => 'nnu', 'Nn4g26168' => 'nnu', 'Nn5g26754' => 'nnu', 'Oeu001433.1' => 'oeu', 'Oeu010299.2' => 'oeu', 'Oeu011171.1' => 'oeu', 'Oeu037675.1' => 'oeu', 'Oeu038359.1' => 'oeu', 'Oeu063834.1' => 'oeu', 'Oeu063835.1' => 'oeu', 'Os05g0312000' => 'osa', 'Os07g0211101' => 'osa', 'Os07g0211200' => 'osa', 'Os07g0681500' => 'osa', 'Peaxi162Scf00095g01015' => 'pax', 'Peaxi162Scf00104g00329' => 'pax', 'Peaxi162Scf00161g00137' => 'pax', 'PGR004G1665' => 'pgr', 'PGR031G2937' => 'pgr', 'PGR119G2145' => 'pgr', 'PGSC0003DMG400004351' => 'stu', 'PGSC0003DMG400014625' => 'stu', 'PGSC0003DMG401000943' => 'stu', 'Phvul.001G148600' => 'pvu', 'Phvul.004G001700' => 'pvu', 'Phvul.006G154900' => 'pvu', 'Phvul.008G078200' => 'pvu', 'Phvul.011G136500' => 'pvu', 'Potri.002G215600' => 'ptr', 'Potri.008G201600' => 'ptr', 'Potri.014G138400' => 'ptr', 'Potri.016G142500' => 'ptr', 'Pp3c16_10580' => 'ppa', 'Pp3c5_25280' => 'ppa', 'Prupe.1G150000' => 'ppe', 'Prupe.1G150100' => 'ppe', 'Prupe.6G299600' => 'ppe', 'Prupe.8G245000' => 'ppe', 'Psat0s4927g0040' => 'psa', 'Psat1g052080' => 'psa', 'Psat1g183800' => 'psa', 'Psat3g113840' => 'psa', 'Psat3g126120' => 'psa', 'Psat3g126160' => 'psa', 'Psat3g158760' => 'psa', 'Psat3g158840' => 'psa', 'PSO170G2858' => 'pso', 'PSO339G0606' => 'pso', 'PSO384G4709' => 'pso', 'PSO407G0334' => 'pso', 'QL04p040276' => 'qlo', 'QL06p005458' => 'qlo', 'QL06p005472' => 'qlo', 'QL07p030546' => 'qlo', 'QL07p031519' => 'qlo', 'QL09p050949' => 'qlo', 'QL09p050966' => 'qlo', 'QL09p051067' => 'qlo', 'QL12p022706' => 'qlo', 'RcHm_v2.0_Chr2g0119601' => 'rch', 'RcHm_v2.0_Chr3g0459591' => 'rch', 'RcHm_v2.0_Chr4g0418521' => 'rch', 'RcHm_v2.0_Chr4g0418531' => 'rch', 'RcHm_v2.0_Chr4g0418541' => 'rch', 'RcHm_v2.0_Chr6g0291641' => 'rch', 'Rhsim01G0086300' => 'rsi', 'Rhsim01G0276300' => 'rsi', 'Rhsim01G0276500' => 'rsi', 'Rhsim04G0207700' => 'rsi', 'Rhsim05G0234500' => 'rsi', 'Rhsim13G0022400' => 'rsi', 'Sabra02G0167900' => 'sbr', 'Sabra04G0158500' => 'sbr', 'Sabra08G0159800' => 'sbr', 'Sabra10G0011500' => 'sbr', 'Sabra14G0104400' => 'sbr', 'SalBow2G2440' => 'sbo', 'SalBow4G2265' => 'sbo', 'Sc02g0000060' => 'sci', 'Sc05g0005020' => 'sci', 'Sc13g0003890' => 'sci', 'Sed0014865' => 'sed', 'Sed0017224' => 'sed', 'Sed0026391' => 'sed', 'SEGI_00063' => 'sgi', 'SEGI_10967' => 'sgi', 'SEGI_17510' => 'sgi', 'SEGI_24396' => 'sgi', 'SEGI_39719' => 'sgi', 'SEGI_41392' => 'sgi', 'SGA_v2.0_scaffold11G05794' => 'sas', 'SGA_v2.0_scaffold142G35607' => 'sas', 'SGA_v2.0_scaffold1G00447' => 'sas', 'SHI15388' => 'shi', 'SHI15394' => 'shi', 'SHI15396' => 'shi', 'SHI15399' => 'shi', 'SMO343G0151' => 'smo', 'SMO367G1118' => 'smo', 'Solyc01g080200.3' => 'sly', 'Solyc06g008960.3' => 'sly', 'Solyc09g064780.3' => 'sly', 'Sopen01g031980' => 'spe', 'Sopen06g003710' => 'spe', 'Sopen09g026460' => 'spe', 'Sp3g21240' => 'spa', 'Sp4g30030' => 'spa', 'TAR365G0022' => 'tar', 'TAR365G1023' => 'tar', 'TAR365G1253' => 'tar', 'TAR623G0078' => 'tar', 'TAR623G1721' => 'tar', 'TAR633G0959' => 'tar', 'THA.LOC104802225' => 'tha', 'THA.LOC104804769' => 'tha', 'THA.LOC104808660' => 'tha', 'THA.LOC104812792' => 'tha', 'Thecc.01G284000' => 'tca', 'Thecc.04G220600' => 'tca', 'Thecc.05G268900' => 'tca', 'Thecc.08G171100' => 'tca', 'Thhalv10001284m.g' => 'esa', 'Thhalv10019912m.g' => 'esa', 'TPR.G14189' => 'tpr', 'TPR.G18110' => 'tpr', 'TPR.G18130' => 'tpr', 'TPR.G18131' => 'tpr', 'TPR.G18140' => 'tpr', 'TPR.G24282' => 'tpr', 'TPR.G25221' => 'tpr', 'TPR.G29267' => 'tpr', 'TPR.G35315' => 'tpr', 'TPR.G36173' => 'tpr', 'TWI09G0794' => 'twi', 'TWI59G1348' => 'twi', 'TWI74G0430' => 'twi', 'unitig_26.g8940' => 'ugi', 'unitig_749.g13744' => 'ugi', 'unitig_749.g13745' => 'ugi', 'vmacro08269' => 'vma', 'vmacro14937' => 'vma', 'vmacro20401' => 'vma', 'VMungo0464G1349' => 'vmu', 'VMungo0540G0289' => 'vmu', 'VMungo1215G1590' => 'vmu', 'VMungo1309G0221' => 'vmu', 'VMungo1309G2815' => 'vmu', 'VMungo1383G0239' => 'vmu', 'VMungo1383G2910' => 'vmu', 'Zm00001eb095270' => 'zma', 'Zm00001eb095280' => 'zma', 'Zm00001eb111630' => 'zma', 'Zm00001eb237080' => 'zma', 'Zm00001eb273740' => 'zma', 'Zm00001eb285040' => 'zma', 'Zm00001eb330790' => 'zma', 'Zm00001eb337380' => 'zma' ), 'gf_id' => 'HOM05D001484', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001484' ), 'data_identifier' => 'HOM05D001484', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001484', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p31500' => 'bna', 'A05p00020' => 'bna', 'A07p08820' => 'bna', 'Aa31LG4G3300' => 'aar', 'Aa31LG8G10030' => 'aar', 'Actinidia00731' => 'ach', 'Actinidia11473' => 'ach', 'Actinidia23469' => 'ach', 'Actinidia24318' => 'ach', 'Actinidia40196' => 'ach', 'Actinidia40197' => 'ach', 'Actinidia40198' => 'ach', 'Ah.08g212990' => 'amhyb', 'Ah.15g091720' => 'amhyb', 'AL3G38260' => 'aly', 'AL4G47710' => 'aly', 'Aqoxy2G00671' => 'aox', 'Aqoxy2G03236' => 'aox', 'arahy.Tifrunner.gnm1.ann1.05IDCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KR684' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATY3SJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK6QJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6APGL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IDT7Z9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM073U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ0R87' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LE7RV4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT4QRX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V5ENPK' => 'arhy', 'AT2G48110' => 'ath', 'AT3G23590' => 'ath', 'ATR0626G186' => 'atr', 'ATR1127G141' => 'atr', 'Atru.chr4.2583' => 'acertr', 'Atru.chr5.1358' => 'acertr', 'Atru.chr5.1359' => 'acertr', 'Atru.chr8.46' => 'acertr', 'AUR62002640' => 'cqu', 'AUR62030055' => 'cqu', 'AUR62033713' => 'cqu', 'AUR62033714' => 'cqu', 'AUR62036795' => 'cqu', 'AUR62039891' => 'cqu', 'BcaB02g08737' => 'bca', 'BcaB04g20441' => 'bca', 'BcaB06g26509' => 'bca', 'BcaB06g26510' => 'bca', 'BcaB06g26511' => 'bca', 'BcaB06g26512' => 'bca', 'BcaB06g26513' => 'bca', 'BcaC02g12564' => 'bca', 'BcaC02g12565' => 'bca', 'BcaC02g12794' => 'bca', 'BcaC02g12795' => 'bca', 'BcaC02g12796' => 'bca', 'BcaC06g35541' => 'bca', 'BNapus_Darmor_BZH_scaffold_188p00080' => 'bna', 'BNapus_Darmor_BZH_scaffold_188p00090' => 'bna', 'BolC1t03972H' => 'bol', 'BolC1t03973H' => 'bol', 'BolC4t21680H' => 'bol', 'BolC7t41863H' => 'bol', 'BolSC55t61227H' => 'bol', 'BolSC55t61228H' => 'bol', 'BraA01t03278Z' => 'bra', 'BraA05t18998Z' => 'bra', 'BraA07t28673Z' => 'bra', 'C01p40150' => 'bna', 'C05p12370' => 'bna', 'C07p13680' => 'bna', 'CAN.G1006.16' => 'can', 'CAN.G1006.17' => 'can', 'CAN.G1170.2' => 'can', 'CAN.G962.7' => 'can', 'CANSAT25G2179' => 'cansat', 'CANSAT78G1573' => 'cansat', 'CARHR099510' => 'chi', 'CARHR143510' => 'chi', 'Carub.0003s2380' => 'cru', 'Carub.0004s3082' => 'cru', 'Ca_00614_v3' => 'car', 'Ca_07801_v3' => 'car', 'Ca_08567_v3' => 'car', 'Ca_09571_v3' => 'car', 'CBR_g19290' => 'cbr', 'Cc01_g19770' => 'ccan', 'Cc03_g03030' => 'ccan', 'CDE07G0968' => 'cde', 'CDE09G1441' => 'cde', 'Cfa006103' => 'cfa', 'Cfa015573' => 'cfa', 'Cfa016988' => 'cfa', 'Ciclev10006738m.g' => 'ccl', 'Ciclev10010920m.g' => 'ccl', 'Ciclev10018517m.g' => 'ccl', 'CiPaw.01G159200' => 'cil', 'CiPaw.02G091000' => 'cil', 'CiPaw.02G091100' => 'cil', 'CiPaw.08G103100' => 'cil', 'CiPaw.09G224900' => 'cil', 'ClCG06G005740' => 'cla', 'ClCG07G000090' => 'cla', 'ClCG07G000100' => 'cla', 'COL.COLO4_09143' => 'col', 'COL.COLO4_25124' => 'col', 'Cpa.g.sc16.34' => 'cpa', 'Cpa.g.sc3504.1' => 'cpa', 'Cpa.g.sc60.37' => 'cpa', 'CsaV3_6G018520' => 'csa', 'CsaV3_6G036860' => 'csa', 'CSS0001072' => 'camsi', 'CSS0020208' => 'camsi', 'CSS0021253' => 'camsi', 'CSS0022190' => 'camsi', 'CSS0036150' => 'camsi', 'CSS0040442' => 'camsi', 'CSS0042300' => 'camsi', 'CSS0045298' => 'camsi', 'DCAR_012449' => 'dca', 'DCAR_018405' => 'dca', 'DCAR_024573' => 'dca', 'DCAR_030591' => 'dca', 'Dinv16926' => 'din', 'Dinv32963' => 'din', 'Dinv38382' => 'din', 'Dinv38383' => 'din', 'Duzib133G0974' => 'dzi', 'Duzib138G1867' => 'dzi', 'Duzib211G0420' => 'dzi', 'Duzib212G0930' => 'dzi', 'ECA234G1645' => 'eca', 'ECA247G3467' => 'eca', 'ECA248G1703' => 'eca', 'EL10Ac3g06327' => 'bvu', 'EL10Ac7g17204' => 'bvu', 'Eucgr.A00855' => 'egr', 'Eucgr.A00858' => 'egr', 'Eucgr.H01520' => 'egr', 'Eucgr.H03604' => 'egr', 'Eucgr.L03465' => 'egr', 'Eucgr.L03466' => 'egr', 'FAN01G0988' => 'fan', 'FAN02G3892' => 'fan', 'FAN05G3381' => 'fan', 'FAN07G0967' => 'fan', 'FAN07G1493' => 'fan', 'FAN08G3125' => 'fan', 'FAN09G0402' => 'fan', 'FAN12G2594' => 'fan', 'FAN12G3879' => 'fan', 'FAN14G1546' => 'fan', 'FAN15G3626' => 'fan', 'FAN17G0588' => 'fan', 'FAN17G0609' => 'fan', 'FAN18G2817' => 'fan', 'FAN19G1305' => 'fan', 'FAN20G1787' => 'fan', 'FAN22G0073' => 'fan', 'FAN22G0352' => 'fan', 'FAN22G0368' => 'fan', 'FAN22G2273' => 'fan', 'FAN24G1998' => 'fan', 'FAN27G1317' => 'fan', 'FvH4_2g23980' => 'fve', 'FvH4_4g14380' => 'fve', 'FvH4_4g14390' => 'fve', 'FvH4_6g09250' => 'fve', 'Glyma.03G151100' => 'gma', 'Glyma.04G122550' => 'gma', 'Glyma.05G001600' => 'gma', 'Glyma.09G270766' => 'gma', 'Glyma.09G270832' => 'gma', 'Glyma.13G209800' => 'gma', 'Glyma.15G102800' => 'gma', 'Glyma.18G218900' => 'gma', 'Glyma.19G001500' => 'gma', 'Glyma.19G153600' => 'gma', 'Gohir.A02G028600' => 'ghi', 'Gohir.A08G045000' => 'ghi', 'Gohir.A11G120500' => 'ghi', 'Gohir.A12G006200' => 'ghi', 'Gohir.A12G006250' => 'ghi', 'Gohir.D02G036300' => 'ghi', 'Gohir.D08G054700' => 'ghi', 'Gohir.D11G125600' => 'ghi', 'Gohir.D12G005700' => 'ghi', 'Gorai.004G055200' => 'gra', 'Gorai.005G040400' => 'gra', 'Gorai.007G134500' => 'gra', 'Gorai.008G005500' => 'gra', 'GSVIVG01011094001' => 'vvi', 'GSVIVG01017879001' => 'vvi', 'GSVIVG01025988001' => 'vvi', 'GSVIVG01029847001' => 'vvi', 'HanXRQChr10g0282901' => 'han', 'HanXRQChr10g0310371' => 'han', 'HanXRQChr10g0315041' => 'han', 'HanXRQChr11g0327651' => 'han', 'HanXRQChr12g0359391' => 'han', 'Haze_00972' => 'cav', 'Haze_00973' => 'cav', 'Haze_00974' => 'cav', 'Haze_04747' => 'cav', 'Haze_04749' => 'cav', 'Haze_04750' => 'cav', 'Haze_21217' => 'cav', 'Hma1.2p1_1037F.1_g250680' => 'hma', 'Hma1.2p1_1644F.1_g295320' => 'hma', 'HPP92_011322' => 'vpl', 'HPP92_011323' => 'vpl', 'HPP92_011324' => 'vpl', 'HPP92_011325' => 'vpl', 'HPP92_011326' => 'vpl', 'Hund12205' => 'sun', 'Hund17957' => 'sun', 'Lalb_Chr06g0176771' => 'lal', 'Lalb_Chr18g0056021' => 'lal', 'Lalb_Chr18g0056031' => 'lal', 'Lalb_Chr18g0056041' => 'lal', 'Lalb_Chr20g0107751' => 'lal', 'Lalb_Chr20g0118371' => 'lal', 'Lj1g0010239' => 'lja', 'Lj1g0017101' => 'lja', 'Lj2A1178G40' => 'lonja', 'Lj2A54G84' => 'lonja', 'Lj2g0015248' => 'lja', 'Lj3A761T51' => 'lonja', 'Lj6g0018116' => 'lja', 'Lsat_1_v5_gn_4_136040' => 'lsa', 'Lsat_1_v5_gn_5_187461' => 'lsa', 'Lsat_1_v5_gn_5_77001' => 'lsa', 'Lsat_1_v5_gn_9_4461' => 'lsa', 'Manes.01G210100' => 'mes', 'Manes.03G185600' => 'mes', 'Manes.05G073300' => 'mes', 'Manes.09G120300' => 'mes', 'Manes.15G022100' => 'mes', 'Mapoly0096s0053' => 'mpo', 'MBI03_g14058_MAGBIO' => 'mbi', 'MBI03_g33876_MAGBIO' => 'mbi', 'MBI03_g36854_MAGBIO' => 'mbi', 'MBI17_g11997_MAGBIO' => 'mbi', 'MD03G1269000' => 'mdo', 'MD04G1179600' => 'mdo', 'MD11G1289800' => 'mdo', 'MD12G1194700' => 'mdo', 'MD13G1182100' => 'mdo', 'MD13G1182200' => 'mdo', 'MD16G1182600' => 'mdo', 'Medtr2g021400' => 'mtr', 'Medtr2g021470' => 'mtr', 'Medtr2g105810' => 'mtr', 'Medtr3g033580' => 'mtr', 'Medtr6g007970' => 'mtr', 'Medtr7g056330' => 'mtr', 'Medtr7g074290' => 'mtr', 'Medtr7g074380' => 'mtr', 'Medtr7g094550' => 'mtr', 'Medtr8g069995' => 'mtr', 'MELO3C014345.2' => 'cme', 'MELO3C021395.2' => 'cme', 'Migut.D00262' => 'egut', 'Migut.G00257' => 'egut', 'MSTRG.21575' => 'ama', 'MSTRG.3985' => 'ama', 'Nitab4.5_0000295g0140' => 'nta', 'Nitab4.5_0000732g0140' => 'nta', 'Nitab4.5_0003162g0020' => 'nta', 'Nitab4.5_0006180g0090' => 'nta', 'Nitab4.5_0006390g0010' => 'nta', 'Nitab4.5_0007392g0040' => 'nta', 'Nn1g02140' => 'nnu', 'Nn4g26168' => 'nnu', 'Nn5g26754' => 'nnu', 'Oeu001433.1' => 'oeu', 'Oeu010299.2' => 'oeu', 'Oeu011171.1' => 'oeu', 'Oeu037675.1' => 'oeu', 'Oeu038359.1' => 'oeu', 'Oeu063834.1' => 'oeu', 'Oeu063835.1' => 'oeu', 'Os05g0312000' => 'osa', 'Os07g0211101' => 'osa', 'Os07g0211200' => 'osa', 'Os07g0681500' => 'osa', 'Peaxi162Scf00095g01015' => 'pax', 'Peaxi162Scf00104g00329' => 'pax', 'Peaxi162Scf00161g00137' => 'pax', 'PGR004G1665' => 'pgr', 'PGR031G2937' => 'pgr', 'PGR119G2145' => 'pgr', 'PGSC0003DMG400004351' => 'stu', 'PGSC0003DMG400014625' => 'stu', 'PGSC0003DMG401000943' => 'stu', 'Phvul.001G148600' => 'pvu', 'Phvul.004G001700' => 'pvu', 'Phvul.006G154900' => 'pvu', 'Phvul.008G078200' => 'pvu', 'Phvul.011G136500' => 'pvu', 'Potri.002G215600' => 'ptr', 'Potri.008G201600' => 'ptr', 'Potri.014G138400' => 'ptr', 'Potri.016G142500' => 'ptr', 'Pp3c16_10580' => 'ppa', 'Pp3c5_25280' => 'ppa', 'Prupe.1G150000' => 'ppe', 'Prupe.1G150100' => 'ppe', 'Prupe.6G299600' => 'ppe', 'Prupe.8G245000' => 'ppe', 'Psat0s4927g0040' => 'psa', 'Psat1g052080' => 'psa', 'Psat1g183800' => 'psa', 'Psat3g113840' => 'psa', 'Psat3g126120' => 'psa', 'Psat3g126160' => 'psa', 'Psat3g158760' => 'psa', 'Psat3g158840' => 'psa', 'PSO170G2858' => 'pso', 'PSO339G0606' => 'pso', 'PSO384G4709' => 'pso', 'PSO407G0334' => 'pso', 'QL04p040276' => 'qlo', 'QL06p005458' => 'qlo', 'QL06p005472' => 'qlo', 'QL07p030546' => 'qlo', 'QL07p031519' => 'qlo', 'QL09p050949' => 'qlo', 'QL09p050966' => 'qlo', 'QL09p051067' => 'qlo', 'QL12p022706' => 'qlo', 'RcHm_v2.0_Chr2g0119601' => 'rch', 'RcHm_v2.0_Chr3g0459591' => 'rch', 'RcHm_v2.0_Chr4g0418521' => 'rch', 'RcHm_v2.0_Chr4g0418531' => 'rch', 'RcHm_v2.0_Chr4g0418541' => 'rch', 'RcHm_v2.0_Chr6g0291641' => 'rch', 'Rhsim01G0086300' => 'rsi', 'Rhsim01G0276300' => 'rsi', 'Rhsim01G0276500' => 'rsi', 'Rhsim04G0207700' => 'rsi', 'Rhsim05G0234500' => 'rsi', 'Rhsim13G0022400' => 'rsi', 'Sabra02G0167900' => 'sbr', 'Sabra04G0158500' => 'sbr', 'Sabra08G0159800' => 'sbr', 'Sabra10G0011500' => 'sbr', 'Sabra14G0104400' => 'sbr', 'SalBow2G2440' => 'sbo', 'SalBow4G2265' => 'sbo', 'Sc02g0000060' => 'sci', 'Sc05g0005020' => 'sci', 'Sc13g0003890' => 'sci', 'Sed0014865' => 'sed', 'Sed0017224' => 'sed', 'Sed0026391' => 'sed', 'SEGI_00063' => 'sgi', 'SEGI_10967' => 'sgi', 'SEGI_17510' => 'sgi', 'SEGI_24396' => 'sgi', 'SEGI_39719' => 'sgi', 'SEGI_41392' => 'sgi', 'SGA_v2.0_scaffold11G05794' => 'sas', 'SGA_v2.0_scaffold142G35607' => 'sas', 'SGA_v2.0_scaffold1G00447' => 'sas', 'SHI15388' => 'shi', 'SHI15394' => 'shi', 'SHI15396' => 'shi', 'SHI15399' => 'shi', 'SMO343G0151' => 'smo', 'SMO367G1118' => 'smo', 'Solyc01g080200.3' => 'sly', 'Solyc06g008960.3' => 'sly', 'Solyc09g064780.3' => 'sly', 'Sopen01g031980' => 'spe', 'Sopen06g003710' => 'spe', 'Sopen09g026460' => 'spe', 'Sp3g21240' => 'spa', 'Sp4g30030' => 'spa', 'TAR365G0022' => 'tar', 'TAR365G1023' => 'tar', 'TAR365G1253' => 'tar', 'TAR623G0078' => 'tar', 'TAR623G1721' => 'tar', 'TAR633G0959' => 'tar', 'THA.LOC104802225' => 'tha', 'THA.LOC104804769' => 'tha', 'THA.LOC104808660' => 'tha', 'THA.LOC104812792' => 'tha', 'Thecc.01G284000' => 'tca', 'Thecc.04G220600' => 'tca', 'Thecc.05G268900' => 'tca', 'Thecc.08G171100' => 'tca', 'Thhalv10001284m.g' => 'esa', 'Thhalv10019912m.g' => 'esa', 'TPR.G14189' => 'tpr', 'TPR.G18110' => 'tpr', 'TPR.G18130' => 'tpr', 'TPR.G18131' => 'tpr', 'TPR.G18140' => 'tpr', 'TPR.G24282' => 'tpr', 'TPR.G25221' => 'tpr', 'TPR.G29267' => 'tpr', 'TPR.G35315' => 'tpr', 'TPR.G36173' => 'tpr', 'TWI09G0794' => 'twi', 'TWI59G1348' => 'twi', 'TWI74G0430' => 'twi', 'unitig_26.g8940' => 'ugi', 'unitig_749.g13744' => 'ugi', 'unitig_749.g13745' => 'ugi', 'vmacro08269' => 'vma', 'vmacro14937' => 'vma', 'vmacro20401' => 'vma', 'VMungo0464G1349' => 'vmu', 'VMungo0540G0289' => 'vmu', 'VMungo1215G1590' => 'vmu', 'VMungo1309G0221' => 'vmu', 'VMungo1309G2815' => 'vmu', 'VMungo1383G0239' => 'vmu', 'VMungo1383G2910' => 'vmu', 'Zm00001eb095270' => 'zma', 'Zm00001eb095280' => 'zma', 'Zm00001eb111630' => 'zma', 'Zm00001eb237080' => 'zma', 'Zm00001eb273740' => 'zma', 'Zm00001eb285040' => 'zma', 'Zm00001eb330790' => 'zma', 'Zm00001eb337380' => 'zma' ) $gf_id = 'HOM05D001484' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001484' ) $data_identifier = 'HOM05D001484' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 2, 'aly' => (int) 2, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 22, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 7, 'hma' => (int) 2, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 7, 'mtr' => (int) 10, 'cme' => (int) 2, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 4, 'ppa' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 4, 'qlo' => (int) 9, 'rch' => (int) 6, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 10, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 7, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb337380' $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' => 'HOM05D001484', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p31500' => 'bna', 'A05p00020' => 'bna', 'A07p08820' => 'bna', 'Aa31LG4G3300' => 'aar', 'Aa31LG8G10030' => 'aar', 'Actinidia00731' => 'ach', 'Actinidia11473' => 'ach', 'Actinidia23469' => 'ach', 'Actinidia24318' => 'ach', 'Actinidia40196' => 'ach', 'Actinidia40197' => 'ach', 'Actinidia40198' => 'ach', 'Ah.08g212990' => 'amhyb', 'Ah.15g091720' => 'amhyb', 'AL3G38260' => 'aly', 'AL4G47710' => 'aly', 'Aqoxy2G00671' => 'aox', 'Aqoxy2G03236' => 'aox', 'arahy.Tifrunner.gnm1.ann1.05IDCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KR684' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATY3SJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK6QJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6APGL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IDT7Z9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM073U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ0R87' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LE7RV4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT4QRX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V5ENPK' => 'arhy', 'AT2G48110' => 'ath', 'AT3G23590' => 'ath', 'ATR0626G186' => 'atr', 'ATR1127G141' => 'atr', 'Atru.chr4.2583' => 'acertr', 'Atru.chr5.1358' => 'acertr', 'Atru.chr5.1359' => 'acertr', 'Atru.chr8.46' => 'acertr', 'AUR62002640' => 'cqu', 'AUR62030055' => 'cqu', 'AUR62033713' => 'cqu', 'AUR62033714' => 'cqu', 'AUR62036795' => 'cqu', 'AUR62039891' => 'cqu', 'BcaB02g08737' => 'bca', 'BcaB04g20441' => 'bca', 'BcaB06g26509' => 'bca', 'BcaB06g26510' => 'bca', 'BcaB06g26511' => 'bca', 'BcaB06g26512' => 'bca', 'BcaB06g26513' => 'bca', 'BcaC02g12564' => 'bca', 'BcaC02g12565' => 'bca', 'BcaC02g12794' => 'bca', 'BcaC02g12795' => 'bca', 'BcaC02g12796' => 'bca', 'BcaC06g35541' => 'bca', 'BNapus_Darmor_BZH_scaffold_188p00080' => 'bna', 'BNapus_Darmor_BZH_scaffold_188p00090' => 'bna', 'BolC1t03972H' => 'bol', 'BolC1t03973H' => 'bol', 'BolC4t21680H' => 'bol', 'BolC7t41863H' => 'bol', 'BolSC55t61227H' => 'bol', 'BolSC55t61228H' => 'bol', 'BraA01t03278Z' => 'bra', 'BraA05t18998Z' => 'bra', 'BraA07t28673Z' => 'bra', 'C01p40150' => 'bna', 'C05p12370' => 'bna', 'C07p13680' => 'bna', 'CAN.G1006.16' => 'can', 'CAN.G1006.17' => 'can', 'CAN.G1170.2' => 'can', 'CAN.G962.7' => 'can', 'CANSAT25G2179' => 'cansat', 'CANSAT78G1573' => 'cansat', 'CARHR099510' => 'chi', 'CARHR143510' => 'chi', 'Carub.0003s2380' => 'cru', 'Carub.0004s3082' => 'cru', 'Ca_00614_v3' => 'car', 'Ca_07801_v3' => 'car', 'Ca_08567_v3' => 'car', 'Ca_09571_v3' => 'car', 'CBR_g19290' => 'cbr', 'Cc01_g19770' => 'ccan', 'Cc03_g03030' => 'ccan', 'CDE07G0968' => 'cde', 'CDE09G1441' => 'cde', 'Cfa006103' => 'cfa', 'Cfa015573' => 'cfa', 'Cfa016988' => 'cfa', 'Ciclev10006738m.g' => 'ccl', 'Ciclev10010920m.g' => 'ccl', 'Ciclev10018517m.g' => 'ccl', 'CiPaw.01G159200' => 'cil', 'CiPaw.02G091000' => 'cil', 'CiPaw.02G091100' => 'cil', 'CiPaw.08G103100' => 'cil', 'CiPaw.09G224900' => 'cil', 'ClCG06G005740' => 'cla', 'ClCG07G000090' => 'cla', 'ClCG07G000100' => 'cla', 'COL.COLO4_09143' => 'col', 'COL.COLO4_25124' => 'col', 'Cpa.g.sc16.34' => 'cpa', 'Cpa.g.sc3504.1' => 'cpa', 'Cpa.g.sc60.37' => 'cpa', 'CsaV3_6G018520' => 'csa', 'CsaV3_6G036860' => 'csa', 'CSS0001072' => 'camsi', 'CSS0020208' => 'camsi', 'CSS0021253' => 'camsi', 'CSS0022190' => 'camsi', 'CSS0036150' => 'camsi', 'CSS0040442' => 'camsi', 'CSS0042300' => 'camsi', 'CSS0045298' => 'camsi', 'DCAR_012449' => 'dca', 'DCAR_018405' => 'dca', 'DCAR_024573' => 'dca', 'DCAR_030591' => 'dca', 'Dinv16926' => 'din', 'Dinv32963' => 'din', 'Dinv38382' => 'din', 'Dinv38383' => 'din', 'Duzib133G0974' => 'dzi', 'Duzib138G1867' => 'dzi', 'Duzib211G0420' => 'dzi', 'Duzib212G0930' => 'dzi', 'ECA234G1645' => 'eca', 'ECA247G3467' => 'eca', 'ECA248G1703' => 'eca', 'EL10Ac3g06327' => 'bvu', 'EL10Ac7g17204' => 'bvu', 'Eucgr.A00855' => 'egr', 'Eucgr.A00858' => 'egr', 'Eucgr.H01520' => 'egr', 'Eucgr.H03604' => 'egr', 'Eucgr.L03465' => 'egr', 'Eucgr.L03466' => 'egr', 'FAN01G0988' => 'fan', 'FAN02G3892' => 'fan', 'FAN05G3381' => 'fan', 'FAN07G0967' => 'fan', 'FAN07G1493' => 'fan', 'FAN08G3125' => 'fan', 'FAN09G0402' => 'fan', 'FAN12G2594' => 'fan', 'FAN12G3879' => 'fan', 'FAN14G1546' => 'fan', 'FAN15G3626' => 'fan', 'FAN17G0588' => 'fan', 'FAN17G0609' => 'fan', 'FAN18G2817' => 'fan', 'FAN19G1305' => 'fan', 'FAN20G1787' => 'fan', 'FAN22G0073' => 'fan', 'FAN22G0352' => 'fan', 'FAN22G0368' => 'fan', 'FAN22G2273' => 'fan', 'FAN24G1998' => 'fan', 'FAN27G1317' => 'fan', 'FvH4_2g23980' => 'fve', 'FvH4_4g14380' => 'fve', 'FvH4_4g14390' => 'fve', 'FvH4_6g09250' => 'fve', 'Glyma.03G151100' => 'gma', 'Glyma.04G122550' => 'gma', 'Glyma.05G001600' => 'gma', 'Glyma.09G270766' => 'gma', 'Glyma.09G270832' => 'gma', 'Glyma.13G209800' => 'gma', 'Glyma.15G102800' => 'gma', 'Glyma.18G218900' => 'gma', 'Glyma.19G001500' => 'gma', 'Glyma.19G153600' => 'gma', 'Gohir.A02G028600' => 'ghi', 'Gohir.A08G045000' => 'ghi', 'Gohir.A11G120500' => 'ghi', 'Gohir.A12G006200' => 'ghi', 'Gohir.A12G006250' => 'ghi', 'Gohir.D02G036300' => 'ghi', 'Gohir.D08G054700' => 'ghi', 'Gohir.D11G125600' => 'ghi', 'Gohir.D12G005700' => 'ghi', 'Gorai.004G055200' => 'gra', 'Gorai.005G040400' => 'gra', 'Gorai.007G134500' => 'gra', 'Gorai.008G005500' => 'gra', 'GSVIVG01011094001' => 'vvi', 'GSVIVG01017879001' => 'vvi', 'GSVIVG01025988001' => 'vvi', 'GSVIVG01029847001' => 'vvi', 'HanXRQChr10g0282901' => 'han', 'HanXRQChr10g0310371' => 'han', 'HanXRQChr10g0315041' => 'han', 'HanXRQChr11g0327651' => 'han', 'HanXRQChr12g0359391' => 'han', 'Haze_00972' => 'cav', 'Haze_00973' => 'cav', 'Haze_00974' => 'cav', 'Haze_04747' => 'cav', 'Haze_04749' => 'cav', 'Haze_04750' => 'cav', 'Haze_21217' => 'cav', 'Hma1.2p1_1037F.1_g250680' => 'hma', 'Hma1.2p1_1644F.1_g295320' => 'hma', 'HPP92_011322' => 'vpl', 'HPP92_011323' => 'vpl', 'HPP92_011324' => 'vpl', 'HPP92_011325' => 'vpl', 'HPP92_011326' => 'vpl', 'Hund12205' => 'sun', 'Hund17957' => 'sun', 'Lalb_Chr06g0176771' => 'lal', 'Lalb_Chr18g0056021' => 'lal', 'Lalb_Chr18g0056031' => 'lal', 'Lalb_Chr18g0056041' => 'lal', 'Lalb_Chr20g0107751' => 'lal', 'Lalb_Chr20g0118371' => 'lal', 'Lj1g0010239' => 'lja', 'Lj1g0017101' => 'lja', 'Lj2A1178G40' => 'lonja', 'Lj2A54G84' => 'lonja', 'Lj2g0015248' => 'lja', 'Lj3A761T51' => 'lonja', 'Lj6g0018116' => 'lja', 'Lsat_1_v5_gn_4_136040' => 'lsa', 'Lsat_1_v5_gn_5_187461' => 'lsa', 'Lsat_1_v5_gn_5_77001' => 'lsa', 'Lsat_1_v5_gn_9_4461' => 'lsa', 'Manes.01G210100' => 'mes', 'Manes.03G185600' => 'mes', 'Manes.05G073300' => 'mes', 'Manes.09G120300' => 'mes', 'Manes.15G022100' => 'mes', 'Mapoly0096s0053' => 'mpo', 'MBI03_g14058_MAGBIO' => 'mbi', 'MBI03_g33876_MAGBIO' => 'mbi', 'MBI03_g36854_MAGBIO' => 'mbi', 'MBI17_g11997_MAGBIO' => 'mbi', 'MD03G1269000' => 'mdo', 'MD04G1179600' => 'mdo', 'MD11G1289800' => 'mdo', 'MD12G1194700' => 'mdo', 'MD13G1182100' => 'mdo', 'MD13G1182200' => 'mdo', 'MD16G1182600' => 'mdo', 'Medtr2g021400' => 'mtr', 'Medtr2g021470' => 'mtr', 'Medtr2g105810' => 'mtr', 'Medtr3g033580' => 'mtr', 'Medtr6g007970' => 'mtr', 'Medtr7g056330' => 'mtr', 'Medtr7g074290' => 'mtr', 'Medtr7g074380' => 'mtr', 'Medtr7g094550' => 'mtr', 'Medtr8g069995' => 'mtr', 'MELO3C014345.2' => 'cme', 'MELO3C021395.2' => 'cme', 'Migut.D00262' => 'egut', 'Migut.G00257' => 'egut', 'MSTRG.21575' => 'ama', 'MSTRG.3985' => 'ama', 'Nitab4.5_0000295g0140' => 'nta', 'Nitab4.5_0000732g0140' => 'nta', 'Nitab4.5_0003162g0020' => 'nta', 'Nitab4.5_0006180g0090' => 'nta', 'Nitab4.5_0006390g0010' => 'nta', 'Nitab4.5_0007392g0040' => 'nta', 'Nn1g02140' => 'nnu', 'Nn4g26168' => 'nnu', 'Nn5g26754' => 'nnu', 'Oeu001433.1' => 'oeu', 'Oeu010299.2' => 'oeu', 'Oeu011171.1' => 'oeu', 'Oeu037675.1' => 'oeu', 'Oeu038359.1' => 'oeu', 'Oeu063834.1' => 'oeu', 'Oeu063835.1' => 'oeu', 'Os05g0312000' => 'osa', 'Os07g0211101' => 'osa', 'Os07g0211200' => 'osa', 'Os07g0681500' => 'osa', 'Peaxi162Scf00095g01015' => 'pax', 'Peaxi162Scf00104g00329' => 'pax', 'Peaxi162Scf00161g00137' => 'pax', 'PGR004G1665' => 'pgr', 'PGR031G2937' => 'pgr', 'PGR119G2145' => 'pgr', 'PGSC0003DMG400004351' => 'stu', 'PGSC0003DMG400014625' => 'stu', 'PGSC0003DMG401000943' => 'stu', 'Phvul.001G148600' => 'pvu', 'Phvul.004G001700' => 'pvu', 'Phvul.006G154900' => 'pvu', 'Phvul.008G078200' => 'pvu', 'Phvul.011G136500' => 'pvu', 'Potri.002G215600' => 'ptr', 'Potri.008G201600' => 'ptr', 'Potri.014G138400' => 'ptr', 'Potri.016G142500' => 'ptr', 'Pp3c16_10580' => 'ppa', 'Pp3c5_25280' => 'ppa', 'Prupe.1G150000' => 'ppe', 'Prupe.1G150100' => 'ppe', 'Prupe.6G299600' => 'ppe', 'Prupe.8G245000' => 'ppe', 'Psat0s4927g0040' => 'psa', 'Psat1g052080' => 'psa', 'Psat1g183800' => 'psa', 'Psat3g113840' => 'psa', 'Psat3g126120' => 'psa', 'Psat3g126160' => 'psa', 'Psat3g158760' => 'psa', 'Psat3g158840' => 'psa', 'PSO170G2858' => 'pso', 'PSO339G0606' => 'pso', 'PSO384G4709' => 'pso', 'PSO407G0334' => 'pso', 'QL04p040276' => 'qlo', 'QL06p005458' => 'qlo', 'QL06p005472' => 'qlo', 'QL07p030546' => 'qlo', 'QL07p031519' => 'qlo', 'QL09p050949' => 'qlo', 'QL09p050966' => 'qlo', 'QL09p051067' => 'qlo', 'QL12p022706' => 'qlo', 'RcHm_v2.0_Chr2g0119601' => 'rch', 'RcHm_v2.0_Chr3g0459591' => 'rch', 'RcHm_v2.0_Chr4g0418521' => 'rch', 'RcHm_v2.0_Chr4g0418531' => 'rch', 'RcHm_v2.0_Chr4g0418541' => 'rch', 'RcHm_v2.0_Chr6g0291641' => 'rch', 'Rhsim01G0086300' => 'rsi', 'Rhsim01G0276300' => 'rsi', 'Rhsim01G0276500' => 'rsi', 'Rhsim04G0207700' => 'rsi', 'Rhsim05G0234500' => 'rsi', 'Rhsim13G0022400' => 'rsi', 'Sabra02G0167900' => 'sbr', 'Sabra04G0158500' => 'sbr', 'Sabra08G0159800' => 'sbr', 'Sabra10G0011500' => 'sbr', 'Sabra14G0104400' => 'sbr', 'SalBow2G2440' => 'sbo', 'SalBow4G2265' => 'sbo', 'Sc02g0000060' => 'sci', 'Sc05g0005020' => 'sci', 'Sc13g0003890' => 'sci', 'Sed0014865' => 'sed', 'Sed0017224' => 'sed', 'Sed0026391' => 'sed', 'SEGI_00063' => 'sgi', 'SEGI_10967' => 'sgi', 'SEGI_17510' => 'sgi', 'SEGI_24396' => 'sgi', 'SEGI_39719' => 'sgi', 'SEGI_41392' => 'sgi', 'SGA_v2.0_scaffold11G05794' => 'sas', 'SGA_v2.0_scaffold142G35607' => 'sas', 'SGA_v2.0_scaffold1G00447' => 'sas', 'SHI15388' => 'shi', 'SHI15394' => 'shi', 'SHI15396' => 'shi', 'SHI15399' => 'shi', 'SMO343G0151' => 'smo', 'SMO367G1118' => 'smo', 'Solyc01g080200.3' => 'sly', 'Solyc06g008960.3' => 'sly', 'Solyc09g064780.3' => 'sly', 'Sopen01g031980' => 'spe', 'Sopen06g003710' => 'spe', 'Sopen09g026460' => 'spe', 'Sp3g21240' => 'spa', 'Sp4g30030' => 'spa', 'TAR365G0022' => 'tar', 'TAR365G1023' => 'tar', 'TAR365G1253' => 'tar', 'TAR623G0078' => 'tar', 'TAR623G1721' => 'tar', 'TAR633G0959' => 'tar', 'THA.LOC104802225' => 'tha', 'THA.LOC104804769' => 'tha', 'THA.LOC104808660' => 'tha', 'THA.LOC104812792' => 'tha', 'Thecc.01G284000' => 'tca', 'Thecc.04G220600' => 'tca', 'Thecc.05G268900' => 'tca', 'Thecc.08G171100' => 'tca', 'Thhalv10001284m.g' => 'esa', 'Thhalv10019912m.g' => 'esa', 'TPR.G14189' => 'tpr', 'TPR.G18110' => 'tpr', 'TPR.G18130' => 'tpr', 'TPR.G18131' => 'tpr', 'TPR.G18140' => 'tpr', 'TPR.G24282' => 'tpr', 'TPR.G25221' => 'tpr', 'TPR.G29267' => 'tpr', 'TPR.G35315' => 'tpr', 'TPR.G36173' => 'tpr', 'TWI09G0794' => 'twi', 'TWI59G1348' => 'twi', 'TWI74G0430' => 'twi', 'unitig_26.g8940' => 'ugi', 'unitig_749.g13744' => 'ugi', 'unitig_749.g13745' => 'ugi', 'vmacro08269' => 'vma', 'vmacro14937' => 'vma', 'vmacro20401' => 'vma', 'VMungo0464G1349' => 'vmu', 'VMungo0540G0289' => 'vmu', 'VMungo1215G1590' => 'vmu', 'VMungo1309G0221' => 'vmu', 'VMungo1309G2815' => 'vmu', 'VMungo1383G0239' => 'vmu', 'VMungo1383G2910' => 'vmu', 'Zm00001eb095270' => 'zma', 'Zm00001eb095280' => 'zma', 'Zm00001eb111630' => 'zma', 'Zm00001eb237080' => 'zma', 'Zm00001eb273740' => 'zma', 'Zm00001eb285040' => 'zma', 'Zm00001eb330790' => 'zma', 'Zm00001eb337380' => 'zma' ), 'gf_id' => 'HOM05D001484', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001484' ), 'data_identifier' => 'HOM05D001484', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001484', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p31500' => 'bna', 'A05p00020' => 'bna', 'A07p08820' => 'bna', 'Aa31LG4G3300' => 'aar', 'Aa31LG8G10030' => 'aar', 'Actinidia00731' => 'ach', 'Actinidia11473' => 'ach', 'Actinidia23469' => 'ach', 'Actinidia24318' => 'ach', 'Actinidia40196' => 'ach', 'Actinidia40197' => 'ach', 'Actinidia40198' => 'ach', 'Ah.08g212990' => 'amhyb', 'Ah.15g091720' => 'amhyb', 'AL3G38260' => 'aly', 'AL4G47710' => 'aly', 'Aqoxy2G00671' => 'aox', 'Aqoxy2G03236' => 'aox', 'arahy.Tifrunner.gnm1.ann1.05IDCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KR684' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATY3SJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK6QJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6APGL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IDT7Z9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM073U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ0R87' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LE7RV4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT4QRX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V5ENPK' => 'arhy', 'AT2G48110' => 'ath', 'AT3G23590' => 'ath', 'ATR0626G186' => 'atr', 'ATR1127G141' => 'atr', 'Atru.chr4.2583' => 'acertr', 'Atru.chr5.1358' => 'acertr', 'Atru.chr5.1359' => 'acertr', 'Atru.chr8.46' => 'acertr', 'AUR62002640' => 'cqu', 'AUR62030055' => 'cqu', 'AUR62033713' => 'cqu', 'AUR62033714' => 'cqu', 'AUR62036795' => 'cqu', 'AUR62039891' => 'cqu', 'BcaB02g08737' => 'bca', 'BcaB04g20441' => 'bca', 'BcaB06g26509' => 'bca', 'BcaB06g26510' => 'bca', 'BcaB06g26511' => 'bca', 'BcaB06g26512' => 'bca', 'BcaB06g26513' => 'bca', 'BcaC02g12564' => 'bca', 'BcaC02g12565' => 'bca', 'BcaC02g12794' => 'bca', 'BcaC02g12795' => 'bca', 'BcaC02g12796' => 'bca', 'BcaC06g35541' => 'bca', 'BNapus_Darmor_BZH_scaffold_188p00080' => 'bna', 'BNapus_Darmor_BZH_scaffold_188p00090' => 'bna', 'BolC1t03972H' => 'bol', 'BolC1t03973H' => 'bol', 'BolC4t21680H' => 'bol', 'BolC7t41863H' => 'bol', 'BolSC55t61227H' => 'bol', 'BolSC55t61228H' => 'bol', 'BraA01t03278Z' => 'bra', 'BraA05t18998Z' => 'bra', 'BraA07t28673Z' => 'bra', 'C01p40150' => 'bna', 'C05p12370' => 'bna', 'C07p13680' => 'bna', 'CAN.G1006.16' => 'can', 'CAN.G1006.17' => 'can', 'CAN.G1170.2' => 'can', 'CAN.G962.7' => 'can', 'CANSAT25G2179' => 'cansat', 'CANSAT78G1573' => 'cansat', 'CARHR099510' => 'chi', 'CARHR143510' => 'chi', 'Carub.0003s2380' => 'cru', 'Carub.0004s3082' => 'cru', 'Ca_00614_v3' => 'car', 'Ca_07801_v3' => 'car', 'Ca_08567_v3' => 'car', 'Ca_09571_v3' => 'car', 'CBR_g19290' => 'cbr', 'Cc01_g19770' => 'ccan', 'Cc03_g03030' => 'ccan', 'CDE07G0968' => 'cde', 'CDE09G1441' => 'cde', 'Cfa006103' => 'cfa', 'Cfa015573' => 'cfa', 'Cfa016988' => 'cfa', 'Ciclev10006738m.g' => 'ccl', 'Ciclev10010920m.g' => 'ccl', 'Ciclev10018517m.g' => 'ccl', 'CiPaw.01G159200' => 'cil', 'CiPaw.02G091000' => 'cil', 'CiPaw.02G091100' => 'cil', 'CiPaw.08G103100' => 'cil', 'CiPaw.09G224900' => 'cil', 'ClCG06G005740' => 'cla', 'ClCG07G000090' => 'cla', 'ClCG07G000100' => 'cla', 'COL.COLO4_09143' => 'col', 'COL.COLO4_25124' => 'col', 'Cpa.g.sc16.34' => 'cpa', 'Cpa.g.sc3504.1' => 'cpa', 'Cpa.g.sc60.37' => 'cpa', 'CsaV3_6G018520' => 'csa', 'CsaV3_6G036860' => 'csa', 'CSS0001072' => 'camsi', 'CSS0020208' => 'camsi', 'CSS0021253' => 'camsi', 'CSS0022190' => 'camsi', 'CSS0036150' => 'camsi', 'CSS0040442' => 'camsi', 'CSS0042300' => 'camsi', 'CSS0045298' => 'camsi', 'DCAR_012449' => 'dca', 'DCAR_018405' => 'dca', 'DCAR_024573' => 'dca', 'DCAR_030591' => 'dca', 'Dinv16926' => 'din', 'Dinv32963' => 'din', 'Dinv38382' => 'din', 'Dinv38383' => 'din', 'Duzib133G0974' => 'dzi', 'Duzib138G1867' => 'dzi', 'Duzib211G0420' => 'dzi', 'Duzib212G0930' => 'dzi', 'ECA234G1645' => 'eca', 'ECA247G3467' => 'eca', 'ECA248G1703' => 'eca', 'EL10Ac3g06327' => 'bvu', 'EL10Ac7g17204' => 'bvu', 'Eucgr.A00855' => 'egr', 'Eucgr.A00858' => 'egr', 'Eucgr.H01520' => 'egr', 'Eucgr.H03604' => 'egr', 'Eucgr.L03465' => 'egr', 'Eucgr.L03466' => 'egr', 'FAN01G0988' => 'fan', 'FAN02G3892' => 'fan', 'FAN05G3381' => 'fan', 'FAN07G0967' => 'fan', 'FAN07G1493' => 'fan', 'FAN08G3125' => 'fan', 'FAN09G0402' => 'fan', 'FAN12G2594' => 'fan', 'FAN12G3879' => 'fan', 'FAN14G1546' => 'fan', 'FAN15G3626' => 'fan', 'FAN17G0588' => 'fan', 'FAN17G0609' => 'fan', 'FAN18G2817' => 'fan', 'FAN19G1305' => 'fan', 'FAN20G1787' => 'fan', 'FAN22G0073' => 'fan', 'FAN22G0352' => 'fan', 'FAN22G0368' => 'fan', 'FAN22G2273' => 'fan', 'FAN24G1998' => 'fan', 'FAN27G1317' => 'fan', 'FvH4_2g23980' => 'fve', 'FvH4_4g14380' => 'fve', 'FvH4_4g14390' => 'fve', 'FvH4_6g09250' => 'fve', 'Glyma.03G151100' => 'gma', 'Glyma.04G122550' => 'gma', 'Glyma.05G001600' => 'gma', 'Glyma.09G270766' => 'gma', 'Glyma.09G270832' => 'gma', 'Glyma.13G209800' => 'gma', 'Glyma.15G102800' => 'gma', 'Glyma.18G218900' => 'gma', 'Glyma.19G001500' => 'gma', 'Glyma.19G153600' => 'gma', 'Gohir.A02G028600' => 'ghi', 'Gohir.A08G045000' => 'ghi', 'Gohir.A11G120500' => 'ghi', 'Gohir.A12G006200' => 'ghi', 'Gohir.A12G006250' => 'ghi', 'Gohir.D02G036300' => 'ghi', 'Gohir.D08G054700' => 'ghi', 'Gohir.D11G125600' => 'ghi', 'Gohir.D12G005700' => 'ghi', 'Gorai.004G055200' => 'gra', 'Gorai.005G040400' => 'gra', 'Gorai.007G134500' => 'gra', 'Gorai.008G005500' => 'gra', 'GSVIVG01011094001' => 'vvi', 'GSVIVG01017879001' => 'vvi', 'GSVIVG01025988001' => 'vvi', 'GSVIVG01029847001' => 'vvi', 'HanXRQChr10g0282901' => 'han', 'HanXRQChr10g0310371' => 'han', 'HanXRQChr10g0315041' => 'han', 'HanXRQChr11g0327651' => 'han', 'HanXRQChr12g0359391' => 'han', 'Haze_00972' => 'cav', 'Haze_00973' => 'cav', 'Haze_00974' => 'cav', 'Haze_04747' => 'cav', 'Haze_04749' => 'cav', 'Haze_04750' => 'cav', 'Haze_21217' => 'cav', 'Hma1.2p1_1037F.1_g250680' => 'hma', 'Hma1.2p1_1644F.1_g295320' => 'hma', 'HPP92_011322' => 'vpl', 'HPP92_011323' => 'vpl', 'HPP92_011324' => 'vpl', 'HPP92_011325' => 'vpl', 'HPP92_011326' => 'vpl', 'Hund12205' => 'sun', 'Hund17957' => 'sun', 'Lalb_Chr06g0176771' => 'lal', 'Lalb_Chr18g0056021' => 'lal', 'Lalb_Chr18g0056031' => 'lal', 'Lalb_Chr18g0056041' => 'lal', 'Lalb_Chr20g0107751' => 'lal', 'Lalb_Chr20g0118371' => 'lal', 'Lj1g0010239' => 'lja', 'Lj1g0017101' => 'lja', 'Lj2A1178G40' => 'lonja', 'Lj2A54G84' => 'lonja', 'Lj2g0015248' => 'lja', 'Lj3A761T51' => 'lonja', 'Lj6g0018116' => 'lja', 'Lsat_1_v5_gn_4_136040' => 'lsa', 'Lsat_1_v5_gn_5_187461' => 'lsa', 'Lsat_1_v5_gn_5_77001' => 'lsa', 'Lsat_1_v5_gn_9_4461' => 'lsa', 'Manes.01G210100' => 'mes', 'Manes.03G185600' => 'mes', 'Manes.05G073300' => 'mes', 'Manes.09G120300' => 'mes', 'Manes.15G022100' => 'mes', 'Mapoly0096s0053' => 'mpo', 'MBI03_g14058_MAGBIO' => 'mbi', 'MBI03_g33876_MAGBIO' => 'mbi', 'MBI03_g36854_MAGBIO' => 'mbi', 'MBI17_g11997_MAGBIO' => 'mbi', 'MD03G1269000' => 'mdo', 'MD04G1179600' => 'mdo', 'MD11G1289800' => 'mdo', 'MD12G1194700' => 'mdo', 'MD13G1182100' => 'mdo', 'MD13G1182200' => 'mdo', 'MD16G1182600' => 'mdo', 'Medtr2g021400' => 'mtr', 'Medtr2g021470' => 'mtr', 'Medtr2g105810' => 'mtr', 'Medtr3g033580' => 'mtr', 'Medtr6g007970' => 'mtr', 'Medtr7g056330' => 'mtr', 'Medtr7g074290' => 'mtr', 'Medtr7g074380' => 'mtr', 'Medtr7g094550' => 'mtr', 'Medtr8g069995' => 'mtr', 'MELO3C014345.2' => 'cme', 'MELO3C021395.2' => 'cme', 'Migut.D00262' => 'egut', 'Migut.G00257' => 'egut', 'MSTRG.21575' => 'ama', 'MSTRG.3985' => 'ama', 'Nitab4.5_0000295g0140' => 'nta', 'Nitab4.5_0000732g0140' => 'nta', 'Nitab4.5_0003162g0020' => 'nta', 'Nitab4.5_0006180g0090' => 'nta', 'Nitab4.5_0006390g0010' => 'nta', 'Nitab4.5_0007392g0040' => 'nta', 'Nn1g02140' => 'nnu', 'Nn4g26168' => 'nnu', 'Nn5g26754' => 'nnu', 'Oeu001433.1' => 'oeu', 'Oeu010299.2' => 'oeu', 'Oeu011171.1' => 'oeu', 'Oeu037675.1' => 'oeu', 'Oeu038359.1' => 'oeu', 'Oeu063834.1' => 'oeu', 'Oeu063835.1' => 'oeu', 'Os05g0312000' => 'osa', 'Os07g0211101' => 'osa', 'Os07g0211200' => 'osa', 'Os07g0681500' => 'osa', 'Peaxi162Scf00095g01015' => 'pax', 'Peaxi162Scf00104g00329' => 'pax', 'Peaxi162Scf00161g00137' => 'pax', 'PGR004G1665' => 'pgr', 'PGR031G2937' => 'pgr', 'PGR119G2145' => 'pgr', 'PGSC0003DMG400004351' => 'stu', 'PGSC0003DMG400014625' => 'stu', 'PGSC0003DMG401000943' => 'stu', 'Phvul.001G148600' => 'pvu', 'Phvul.004G001700' => 'pvu', 'Phvul.006G154900' => 'pvu', 'Phvul.008G078200' => 'pvu', 'Phvul.011G136500' => 'pvu', 'Potri.002G215600' => 'ptr', 'Potri.008G201600' => 'ptr', 'Potri.014G138400' => 'ptr', 'Potri.016G142500' => 'ptr', 'Pp3c16_10580' => 'ppa', 'Pp3c5_25280' => 'ppa', 'Prupe.1G150000' => 'ppe', 'Prupe.1G150100' => 'ppe', 'Prupe.6G299600' => 'ppe', 'Prupe.8G245000' => 'ppe', 'Psat0s4927g0040' => 'psa', 'Psat1g052080' => 'psa', 'Psat1g183800' => 'psa', 'Psat3g113840' => 'psa', 'Psat3g126120' => 'psa', 'Psat3g126160' => 'psa', 'Psat3g158760' => 'psa', 'Psat3g158840' => 'psa', 'PSO170G2858' => 'pso', 'PSO339G0606' => 'pso', 'PSO384G4709' => 'pso', 'PSO407G0334' => 'pso', 'QL04p040276' => 'qlo', 'QL06p005458' => 'qlo', 'QL06p005472' => 'qlo', 'QL07p030546' => 'qlo', 'QL07p031519' => 'qlo', 'QL09p050949' => 'qlo', 'QL09p050966' => 'qlo', 'QL09p051067' => 'qlo', 'QL12p022706' => 'qlo', 'RcHm_v2.0_Chr2g0119601' => 'rch', 'RcHm_v2.0_Chr3g0459591' => 'rch', 'RcHm_v2.0_Chr4g0418521' => 'rch', 'RcHm_v2.0_Chr4g0418531' => 'rch', 'RcHm_v2.0_Chr4g0418541' => 'rch', 'RcHm_v2.0_Chr6g0291641' => 'rch', 'Rhsim01G0086300' => 'rsi', 'Rhsim01G0276300' => 'rsi', 'Rhsim01G0276500' => 'rsi', 'Rhsim04G0207700' => 'rsi', 'Rhsim05G0234500' => 'rsi', 'Rhsim13G0022400' => 'rsi', 'Sabra02G0167900' => 'sbr', 'Sabra04G0158500' => 'sbr', 'Sabra08G0159800' => 'sbr', 'Sabra10G0011500' => 'sbr', 'Sabra14G0104400' => 'sbr', 'SalBow2G2440' => 'sbo', 'SalBow4G2265' => 'sbo', 'Sc02g0000060' => 'sci', 'Sc05g0005020' => 'sci', 'Sc13g0003890' => 'sci', 'Sed0014865' => 'sed', 'Sed0017224' => 'sed', 'Sed0026391' => 'sed', 'SEGI_00063' => 'sgi', 'SEGI_10967' => 'sgi', 'SEGI_17510' => 'sgi', 'SEGI_24396' => 'sgi', 'SEGI_39719' => 'sgi', 'SEGI_41392' => 'sgi', 'SGA_v2.0_scaffold11G05794' => 'sas', 'SGA_v2.0_scaffold142G35607' => 'sas', 'SGA_v2.0_scaffold1G00447' => 'sas', 'SHI15388' => 'shi', 'SHI15394' => 'shi', 'SHI15396' => 'shi', 'SHI15399' => 'shi', 'SMO343G0151' => 'smo', 'SMO367G1118' => 'smo', 'Solyc01g080200.3' => 'sly', 'Solyc06g008960.3' => 'sly', 'Solyc09g064780.3' => 'sly', 'Sopen01g031980' => 'spe', 'Sopen06g003710' => 'spe', 'Sopen09g026460' => 'spe', 'Sp3g21240' => 'spa', 'Sp4g30030' => 'spa', 'TAR365G0022' => 'tar', 'TAR365G1023' => 'tar', 'TAR365G1253' => 'tar', 'TAR623G0078' => 'tar', 'TAR623G1721' => 'tar', 'TAR633G0959' => 'tar', 'THA.LOC104802225' => 'tha', 'THA.LOC104804769' => 'tha', 'THA.LOC104808660' => 'tha', 'THA.LOC104812792' => 'tha', 'Thecc.01G284000' => 'tca', 'Thecc.04G220600' => 'tca', 'Thecc.05G268900' => 'tca', 'Thecc.08G171100' => 'tca', 'Thhalv10001284m.g' => 'esa', 'Thhalv10019912m.g' => 'esa', 'TPR.G14189' => 'tpr', 'TPR.G18110' => 'tpr', 'TPR.G18130' => 'tpr', 'TPR.G18131' => 'tpr', 'TPR.G18140' => 'tpr', 'TPR.G24282' => 'tpr', 'TPR.G25221' => 'tpr', 'TPR.G29267' => 'tpr', 'TPR.G35315' => 'tpr', 'TPR.G36173' => 'tpr', 'TWI09G0794' => 'twi', 'TWI59G1348' => 'twi', 'TWI74G0430' => 'twi', 'unitig_26.g8940' => 'ugi', 'unitig_749.g13744' => 'ugi', 'unitig_749.g13745' => 'ugi', 'vmacro08269' => 'vma', 'vmacro14937' => 'vma', 'vmacro20401' => 'vma', 'VMungo0464G1349' => 'vmu', 'VMungo0540G0289' => 'vmu', 'VMungo1215G1590' => 'vmu', 'VMungo1309G0221' => 'vmu', 'VMungo1309G2815' => 'vmu', 'VMungo1383G0239' => 'vmu', 'VMungo1383G2910' => 'vmu', 'Zm00001eb095270' => 'zma', 'Zm00001eb095280' => 'zma', 'Zm00001eb111630' => 'zma', 'Zm00001eb237080' => 'zma', 'Zm00001eb273740' => 'zma', 'Zm00001eb285040' => 'zma', 'Zm00001eb330790' => 'zma', 'Zm00001eb337380' => 'zma' ) $gf_id = 'HOM05D001484' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001484' ) $data_identifier = 'HOM05D001484' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 2, 'aly' => (int) 2, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 22, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 7, 'hma' => (int) 2, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 7, 'mtr' => (int) 10, 'cme' => (int) 2, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 4, 'ppa' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 4, 'qlo' => (int) 9, 'rch' => (int) 6, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 10, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 7, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb337380' $species_info = array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ) $local_species = 'ppe' $disabled = '' $selected = '' $num_hits = (int) 0include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001484', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p31500' => 'bna', 'A05p00020' => 'bna', 'A07p08820' => 'bna', 'Aa31LG4G3300' => 'aar', 'Aa31LG8G10030' => 'aar', 'Actinidia00731' => 'ach', 'Actinidia11473' => 'ach', 'Actinidia23469' => 'ach', 'Actinidia24318' => 'ach', 'Actinidia40196' => 'ach', 'Actinidia40197' => 'ach', 'Actinidia40198' => 'ach', 'Ah.08g212990' => 'amhyb', 'Ah.15g091720' => 'amhyb', 'AL3G38260' => 'aly', 'AL4G47710' => 'aly', 'Aqoxy2G00671' => 'aox', 'Aqoxy2G03236' => 'aox', 'arahy.Tifrunner.gnm1.ann1.05IDCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KR684' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATY3SJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK6QJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6APGL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IDT7Z9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM073U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ0R87' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LE7RV4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT4QRX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V5ENPK' => 'arhy', 'AT2G48110' => 'ath', 'AT3G23590' => 'ath', 'ATR0626G186' => 'atr', 'ATR1127G141' => 'atr', 'Atru.chr4.2583' => 'acertr', 'Atru.chr5.1358' => 'acertr', 'Atru.chr5.1359' => 'acertr', 'Atru.chr8.46' => 'acertr', 'AUR62002640' => 'cqu', 'AUR62030055' => 'cqu', 'AUR62033713' => 'cqu', 'AUR62033714' => 'cqu', 'AUR62036795' => 'cqu', 'AUR62039891' => 'cqu', 'BcaB02g08737' => 'bca', 'BcaB04g20441' => 'bca', 'BcaB06g26509' => 'bca', 'BcaB06g26510' => 'bca', 'BcaB06g26511' => 'bca', 'BcaB06g26512' => 'bca', 'BcaB06g26513' => 'bca', 'BcaC02g12564' => 'bca', 'BcaC02g12565' => 'bca', 'BcaC02g12794' => 'bca', 'BcaC02g12795' => 'bca', 'BcaC02g12796' => 'bca', 'BcaC06g35541' => 'bca', 'BNapus_Darmor_BZH_scaffold_188p00080' => 'bna', 'BNapus_Darmor_BZH_scaffold_188p00090' => 'bna', 'BolC1t03972H' => 'bol', 'BolC1t03973H' => 'bol', 'BolC4t21680H' => 'bol', 'BolC7t41863H' => 'bol', 'BolSC55t61227H' => 'bol', 'BolSC55t61228H' => 'bol', 'BraA01t03278Z' => 'bra', 'BraA05t18998Z' => 'bra', 'BraA07t28673Z' => 'bra', 'C01p40150' => 'bna', 'C05p12370' => 'bna', 'C07p13680' => 'bna', 'CAN.G1006.16' => 'can', 'CAN.G1006.17' => 'can', 'CAN.G1170.2' => 'can', 'CAN.G962.7' => 'can', 'CANSAT25G2179' => 'cansat', 'CANSAT78G1573' => 'cansat', 'CARHR099510' => 'chi', 'CARHR143510' => 'chi', 'Carub.0003s2380' => 'cru', 'Carub.0004s3082' => 'cru', 'Ca_00614_v3' => 'car', 'Ca_07801_v3' => 'car', 'Ca_08567_v3' => 'car', 'Ca_09571_v3' => 'car', 'CBR_g19290' => 'cbr', 'Cc01_g19770' => 'ccan', 'Cc03_g03030' => 'ccan', 'CDE07G0968' => 'cde', 'CDE09G1441' => 'cde', 'Cfa006103' => 'cfa', 'Cfa015573' => 'cfa', 'Cfa016988' => 'cfa', 'Ciclev10006738m.g' => 'ccl', 'Ciclev10010920m.g' => 'ccl', 'Ciclev10018517m.g' => 'ccl', 'CiPaw.01G159200' => 'cil', 'CiPaw.02G091000' => 'cil', 'CiPaw.02G091100' => 'cil', 'CiPaw.08G103100' => 'cil', 'CiPaw.09G224900' => 'cil', 'ClCG06G005740' => 'cla', 'ClCG07G000090' => 'cla', 'ClCG07G000100' => 'cla', 'COL.COLO4_09143' => 'col', 'COL.COLO4_25124' => 'col', 'Cpa.g.sc16.34' => 'cpa', 'Cpa.g.sc3504.1' => 'cpa', 'Cpa.g.sc60.37' => 'cpa', 'CsaV3_6G018520' => 'csa', 'CsaV3_6G036860' => 'csa', 'CSS0001072' => 'camsi', 'CSS0020208' => 'camsi', 'CSS0021253' => 'camsi', 'CSS0022190' => 'camsi', 'CSS0036150' => 'camsi', 'CSS0040442' => 'camsi', 'CSS0042300' => 'camsi', 'CSS0045298' => 'camsi', 'DCAR_012449' => 'dca', 'DCAR_018405' => 'dca', 'DCAR_024573' => 'dca', 'DCAR_030591' => 'dca', 'Dinv16926' => 'din', 'Dinv32963' => 'din', 'Dinv38382' => 'din', 'Dinv38383' => 'din', 'Duzib133G0974' => 'dzi', 'Duzib138G1867' => 'dzi', 'Duzib211G0420' => 'dzi', 'Duzib212G0930' => 'dzi', 'ECA234G1645' => 'eca', 'ECA247G3467' => 'eca', 'ECA248G1703' => 'eca', 'EL10Ac3g06327' => 'bvu', 'EL10Ac7g17204' => 'bvu', 'Eucgr.A00855' => 'egr', 'Eucgr.A00858' => 'egr', 'Eucgr.H01520' => 'egr', 'Eucgr.H03604' => 'egr', 'Eucgr.L03465' => 'egr', 'Eucgr.L03466' => 'egr', 'FAN01G0988' => 'fan', 'FAN02G3892' => 'fan', 'FAN05G3381' => 'fan', 'FAN07G0967' => 'fan', 'FAN07G1493' => 'fan', 'FAN08G3125' => 'fan', 'FAN09G0402' => 'fan', 'FAN12G2594' => 'fan', 'FAN12G3879' => 'fan', 'FAN14G1546' => 'fan', 'FAN15G3626' => 'fan', 'FAN17G0588' => 'fan', 'FAN17G0609' => 'fan', 'FAN18G2817' => 'fan', 'FAN19G1305' => 'fan', 'FAN20G1787' => 'fan', 'FAN22G0073' => 'fan', 'FAN22G0352' => 'fan', 'FAN22G0368' => 'fan', 'FAN22G2273' => 'fan', 'FAN24G1998' => 'fan', 'FAN27G1317' => 'fan', 'FvH4_2g23980' => 'fve', 'FvH4_4g14380' => 'fve', 'FvH4_4g14390' => 'fve', 'FvH4_6g09250' => 'fve', 'Glyma.03G151100' => 'gma', 'Glyma.04G122550' => 'gma', 'Glyma.05G001600' => 'gma', 'Glyma.09G270766' => 'gma', 'Glyma.09G270832' => 'gma', 'Glyma.13G209800' => 'gma', 'Glyma.15G102800' => 'gma', 'Glyma.18G218900' => 'gma', 'Glyma.19G001500' => 'gma', 'Glyma.19G153600' => 'gma', 'Gohir.A02G028600' => 'ghi', 'Gohir.A08G045000' => 'ghi', 'Gohir.A11G120500' => 'ghi', 'Gohir.A12G006200' => 'ghi', 'Gohir.A12G006250' => 'ghi', 'Gohir.D02G036300' => 'ghi', 'Gohir.D08G054700' => 'ghi', 'Gohir.D11G125600' => 'ghi', 'Gohir.D12G005700' => 'ghi', 'Gorai.004G055200' => 'gra', 'Gorai.005G040400' => 'gra', 'Gorai.007G134500' => 'gra', 'Gorai.008G005500' => 'gra', 'GSVIVG01011094001' => 'vvi', 'GSVIVG01017879001' => 'vvi', 'GSVIVG01025988001' => 'vvi', 'GSVIVG01029847001' => 'vvi', 'HanXRQChr10g0282901' => 'han', 'HanXRQChr10g0310371' => 'han', 'HanXRQChr10g0315041' => 'han', 'HanXRQChr11g0327651' => 'han', 'HanXRQChr12g0359391' => 'han', 'Haze_00972' => 'cav', 'Haze_00973' => 'cav', 'Haze_00974' => 'cav', 'Haze_04747' => 'cav', 'Haze_04749' => 'cav', 'Haze_04750' => 'cav', 'Haze_21217' => 'cav', 'Hma1.2p1_1037F.1_g250680' => 'hma', 'Hma1.2p1_1644F.1_g295320' => 'hma', 'HPP92_011322' => 'vpl', 'HPP92_011323' => 'vpl', 'HPP92_011324' => 'vpl', 'HPP92_011325' => 'vpl', 'HPP92_011326' => 'vpl', 'Hund12205' => 'sun', 'Hund17957' => 'sun', 'Lalb_Chr06g0176771' => 'lal', 'Lalb_Chr18g0056021' => 'lal', 'Lalb_Chr18g0056031' => 'lal', 'Lalb_Chr18g0056041' => 'lal', 'Lalb_Chr20g0107751' => 'lal', 'Lalb_Chr20g0118371' => 'lal', 'Lj1g0010239' => 'lja', 'Lj1g0017101' => 'lja', 'Lj2A1178G40' => 'lonja', 'Lj2A54G84' => 'lonja', 'Lj2g0015248' => 'lja', 'Lj3A761T51' => 'lonja', 'Lj6g0018116' => 'lja', 'Lsat_1_v5_gn_4_136040' => 'lsa', 'Lsat_1_v5_gn_5_187461' => 'lsa', 'Lsat_1_v5_gn_5_77001' => 'lsa', 'Lsat_1_v5_gn_9_4461' => 'lsa', 'Manes.01G210100' => 'mes', 'Manes.03G185600' => 'mes', 'Manes.05G073300' => 'mes', 'Manes.09G120300' => 'mes', 'Manes.15G022100' => 'mes', 'Mapoly0096s0053' => 'mpo', 'MBI03_g14058_MAGBIO' => 'mbi', 'MBI03_g33876_MAGBIO' => 'mbi', 'MBI03_g36854_MAGBIO' => 'mbi', 'MBI17_g11997_MAGBIO' => 'mbi', 'MD03G1269000' => 'mdo', 'MD04G1179600' => 'mdo', 'MD11G1289800' => 'mdo', 'MD12G1194700' => 'mdo', 'MD13G1182100' => 'mdo', 'MD13G1182200' => 'mdo', 'MD16G1182600' => 'mdo', 'Medtr2g021400' => 'mtr', 'Medtr2g021470' => 'mtr', 'Medtr2g105810' => 'mtr', 'Medtr3g033580' => 'mtr', 'Medtr6g007970' => 'mtr', 'Medtr7g056330' => 'mtr', 'Medtr7g074290' => 'mtr', 'Medtr7g074380' => 'mtr', 'Medtr7g094550' => 'mtr', 'Medtr8g069995' => 'mtr', 'MELO3C014345.2' => 'cme', 'MELO3C021395.2' => 'cme', 'Migut.D00262' => 'egut', 'Migut.G00257' => 'egut', 'MSTRG.21575' => 'ama', 'MSTRG.3985' => 'ama', 'Nitab4.5_0000295g0140' => 'nta', 'Nitab4.5_0000732g0140' => 'nta', 'Nitab4.5_0003162g0020' => 'nta', 'Nitab4.5_0006180g0090' => 'nta', 'Nitab4.5_0006390g0010' => 'nta', 'Nitab4.5_0007392g0040' => 'nta', 'Nn1g02140' => 'nnu', 'Nn4g26168' => 'nnu', 'Nn5g26754' => 'nnu', 'Oeu001433.1' => 'oeu', 'Oeu010299.2' => 'oeu', 'Oeu011171.1' => 'oeu', 'Oeu037675.1' => 'oeu', 'Oeu038359.1' => 'oeu', 'Oeu063834.1' => 'oeu', 'Oeu063835.1' => 'oeu', 'Os05g0312000' => 'osa', 'Os07g0211101' => 'osa', 'Os07g0211200' => 'osa', 'Os07g0681500' => 'osa', 'Peaxi162Scf00095g01015' => 'pax', 'Peaxi162Scf00104g00329' => 'pax', 'Peaxi162Scf00161g00137' => 'pax', 'PGR004G1665' => 'pgr', 'PGR031G2937' => 'pgr', 'PGR119G2145' => 'pgr', 'PGSC0003DMG400004351' => 'stu', 'PGSC0003DMG400014625' => 'stu', 'PGSC0003DMG401000943' => 'stu', 'Phvul.001G148600' => 'pvu', 'Phvul.004G001700' => 'pvu', 'Phvul.006G154900' => 'pvu', 'Phvul.008G078200' => 'pvu', 'Phvul.011G136500' => 'pvu', 'Potri.002G215600' => 'ptr', 'Potri.008G201600' => 'ptr', 'Potri.014G138400' => 'ptr', 'Potri.016G142500' => 'ptr', 'Pp3c16_10580' => 'ppa', 'Pp3c5_25280' => 'ppa', 'Prupe.1G150000' => 'ppe', 'Prupe.1G150100' => 'ppe', 'Prupe.6G299600' => 'ppe', 'Prupe.8G245000' => 'ppe', 'Psat0s4927g0040' => 'psa', 'Psat1g052080' => 'psa', 'Psat1g183800' => 'psa', 'Psat3g113840' => 'psa', 'Psat3g126120' => 'psa', 'Psat3g126160' => 'psa', 'Psat3g158760' => 'psa', 'Psat3g158840' => 'psa', 'PSO170G2858' => 'pso', 'PSO339G0606' => 'pso', 'PSO384G4709' => 'pso', 'PSO407G0334' => 'pso', 'QL04p040276' => 'qlo', 'QL06p005458' => 'qlo', 'QL06p005472' => 'qlo', 'QL07p030546' => 'qlo', 'QL07p031519' => 'qlo', 'QL09p050949' => 'qlo', 'QL09p050966' => 'qlo', 'QL09p051067' => 'qlo', 'QL12p022706' => 'qlo', 'RcHm_v2.0_Chr2g0119601' => 'rch', 'RcHm_v2.0_Chr3g0459591' => 'rch', 'RcHm_v2.0_Chr4g0418521' => 'rch', 'RcHm_v2.0_Chr4g0418531' => 'rch', 'RcHm_v2.0_Chr4g0418541' => 'rch', 'RcHm_v2.0_Chr6g0291641' => 'rch', 'Rhsim01G0086300' => 'rsi', 'Rhsim01G0276300' => 'rsi', 'Rhsim01G0276500' => 'rsi', 'Rhsim04G0207700' => 'rsi', 'Rhsim05G0234500' => 'rsi', 'Rhsim13G0022400' => 'rsi', 'Sabra02G0167900' => 'sbr', 'Sabra04G0158500' => 'sbr', 'Sabra08G0159800' => 'sbr', 'Sabra10G0011500' => 'sbr', 'Sabra14G0104400' => 'sbr', 'SalBow2G2440' => 'sbo', 'SalBow4G2265' => 'sbo', 'Sc02g0000060' => 'sci', 'Sc05g0005020' => 'sci', 'Sc13g0003890' => 'sci', 'Sed0014865' => 'sed', 'Sed0017224' => 'sed', 'Sed0026391' => 'sed', 'SEGI_00063' => 'sgi', 'SEGI_10967' => 'sgi', 'SEGI_17510' => 'sgi', 'SEGI_24396' => 'sgi', 'SEGI_39719' => 'sgi', 'SEGI_41392' => 'sgi', 'SGA_v2.0_scaffold11G05794' => 'sas', 'SGA_v2.0_scaffold142G35607' => 'sas', 'SGA_v2.0_scaffold1G00447' => 'sas', 'SHI15388' => 'shi', 'SHI15394' => 'shi', 'SHI15396' => 'shi', 'SHI15399' => 'shi', 'SMO343G0151' => 'smo', 'SMO367G1118' => 'smo', 'Solyc01g080200.3' => 'sly', 'Solyc06g008960.3' => 'sly', 'Solyc09g064780.3' => 'sly', 'Sopen01g031980' => 'spe', 'Sopen06g003710' => 'spe', 'Sopen09g026460' => 'spe', 'Sp3g21240' => 'spa', 'Sp4g30030' => 'spa', 'TAR365G0022' => 'tar', 'TAR365G1023' => 'tar', 'TAR365G1253' => 'tar', 'TAR623G0078' => 'tar', 'TAR623G1721' => 'tar', 'TAR633G0959' => 'tar', 'THA.LOC104802225' => 'tha', 'THA.LOC104804769' => 'tha', 'THA.LOC104808660' => 'tha', 'THA.LOC104812792' => 'tha', 'Thecc.01G284000' => 'tca', 'Thecc.04G220600' => 'tca', 'Thecc.05G268900' => 'tca', 'Thecc.08G171100' => 'tca', 'Thhalv10001284m.g' => 'esa', 'Thhalv10019912m.g' => 'esa', 'TPR.G14189' => 'tpr', 'TPR.G18110' => 'tpr', 'TPR.G18130' => 'tpr', 'TPR.G18131' => 'tpr', 'TPR.G18140' => 'tpr', 'TPR.G24282' => 'tpr', 'TPR.G25221' => 'tpr', 'TPR.G29267' => 'tpr', 'TPR.G35315' => 'tpr', 'TPR.G36173' => 'tpr', 'TWI09G0794' => 'twi', 'TWI59G1348' => 'twi', 'TWI74G0430' => 'twi', 'unitig_26.g8940' => 'ugi', 'unitig_749.g13744' => 'ugi', 'unitig_749.g13745' => 'ugi', 'vmacro08269' => 'vma', 'vmacro14937' => 'vma', 'vmacro20401' => 'vma', 'VMungo0464G1349' => 'vmu', 'VMungo0540G0289' => 'vmu', 'VMungo1215G1590' => 'vmu', 'VMungo1309G0221' => 'vmu', 'VMungo1309G2815' => 'vmu', 'VMungo1383G0239' => 'vmu', 'VMungo1383G2910' => 'vmu', 'Zm00001eb095270' => 'zma', 'Zm00001eb095280' => 'zma', 'Zm00001eb111630' => 'zma', 'Zm00001eb237080' => 'zma', 'Zm00001eb273740' => 'zma', 'Zm00001eb285040' => 'zma', 'Zm00001eb330790' => 'zma', 'Zm00001eb337380' => 'zma' ), 'gf_id' => 'HOM05D001484', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001484' ), 'data_identifier' => 'HOM05D001484', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001484', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p31500' => 'bna', 'A05p00020' => 'bna', 'A07p08820' => 'bna', 'Aa31LG4G3300' => 'aar', 'Aa31LG8G10030' => 'aar', 'Actinidia00731' => 'ach', 'Actinidia11473' => 'ach', 'Actinidia23469' => 'ach', 'Actinidia24318' => 'ach', 'Actinidia40196' => 'ach', 'Actinidia40197' => 'ach', 'Actinidia40198' => 'ach', 'Ah.08g212990' => 'amhyb', 'Ah.15g091720' => 'amhyb', 'AL3G38260' => 'aly', 'AL4G47710' => 'aly', 'Aqoxy2G00671' => 'aox', 'Aqoxy2G03236' => 'aox', 'arahy.Tifrunner.gnm1.ann1.05IDCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KR684' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATY3SJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK6QJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6APGL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IDT7Z9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM073U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ0R87' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LE7RV4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT4QRX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V5ENPK' => 'arhy', 'AT2G48110' => 'ath', 'AT3G23590' => 'ath', 'ATR0626G186' => 'atr', 'ATR1127G141' => 'atr', 'Atru.chr4.2583' => 'acertr', 'Atru.chr5.1358' => 'acertr', 'Atru.chr5.1359' => 'acertr', 'Atru.chr8.46' => 'acertr', 'AUR62002640' => 'cqu', 'AUR62030055' => 'cqu', 'AUR62033713' => 'cqu', 'AUR62033714' => 'cqu', 'AUR62036795' => 'cqu', 'AUR62039891' => 'cqu', 'BcaB02g08737' => 'bca', 'BcaB04g20441' => 'bca', 'BcaB06g26509' => 'bca', 'BcaB06g26510' => 'bca', 'BcaB06g26511' => 'bca', 'BcaB06g26512' => 'bca', 'BcaB06g26513' => 'bca', 'BcaC02g12564' => 'bca', 'BcaC02g12565' => 'bca', 'BcaC02g12794' => 'bca', 'BcaC02g12795' => 'bca', 'BcaC02g12796' => 'bca', 'BcaC06g35541' => 'bca', 'BNapus_Darmor_BZH_scaffold_188p00080' => 'bna', 'BNapus_Darmor_BZH_scaffold_188p00090' => 'bna', 'BolC1t03972H' => 'bol', 'BolC1t03973H' => 'bol', 'BolC4t21680H' => 'bol', 'BolC7t41863H' => 'bol', 'BolSC55t61227H' => 'bol', 'BolSC55t61228H' => 'bol', 'BraA01t03278Z' => 'bra', 'BraA05t18998Z' => 'bra', 'BraA07t28673Z' => 'bra', 'C01p40150' => 'bna', 'C05p12370' => 'bna', 'C07p13680' => 'bna', 'CAN.G1006.16' => 'can', 'CAN.G1006.17' => 'can', 'CAN.G1170.2' => 'can', 'CAN.G962.7' => 'can', 'CANSAT25G2179' => 'cansat', 'CANSAT78G1573' => 'cansat', 'CARHR099510' => 'chi', 'CARHR143510' => 'chi', 'Carub.0003s2380' => 'cru', 'Carub.0004s3082' => 'cru', 'Ca_00614_v3' => 'car', 'Ca_07801_v3' => 'car', 'Ca_08567_v3' => 'car', 'Ca_09571_v3' => 'car', 'CBR_g19290' => 'cbr', 'Cc01_g19770' => 'ccan', 'Cc03_g03030' => 'ccan', 'CDE07G0968' => 'cde', 'CDE09G1441' => 'cde', 'Cfa006103' => 'cfa', 'Cfa015573' => 'cfa', 'Cfa016988' => 'cfa', 'Ciclev10006738m.g' => 'ccl', 'Ciclev10010920m.g' => 'ccl', 'Ciclev10018517m.g' => 'ccl', 'CiPaw.01G159200' => 'cil', 'CiPaw.02G091000' => 'cil', 'CiPaw.02G091100' => 'cil', 'CiPaw.08G103100' => 'cil', 'CiPaw.09G224900' => 'cil', 'ClCG06G005740' => 'cla', 'ClCG07G000090' => 'cla', 'ClCG07G000100' => 'cla', 'COL.COLO4_09143' => 'col', 'COL.COLO4_25124' => 'col', 'Cpa.g.sc16.34' => 'cpa', 'Cpa.g.sc3504.1' => 'cpa', 'Cpa.g.sc60.37' => 'cpa', 'CsaV3_6G018520' => 'csa', 'CsaV3_6G036860' => 'csa', 'CSS0001072' => 'camsi', 'CSS0020208' => 'camsi', 'CSS0021253' => 'camsi', 'CSS0022190' => 'camsi', 'CSS0036150' => 'camsi', 'CSS0040442' => 'camsi', 'CSS0042300' => 'camsi', 'CSS0045298' => 'camsi', 'DCAR_012449' => 'dca', 'DCAR_018405' => 'dca', 'DCAR_024573' => 'dca', 'DCAR_030591' => 'dca', 'Dinv16926' => 'din', 'Dinv32963' => 'din', 'Dinv38382' => 'din', 'Dinv38383' => 'din', 'Duzib133G0974' => 'dzi', 'Duzib138G1867' => 'dzi', 'Duzib211G0420' => 'dzi', 'Duzib212G0930' => 'dzi', 'ECA234G1645' => 'eca', 'ECA247G3467' => 'eca', 'ECA248G1703' => 'eca', 'EL10Ac3g06327' => 'bvu', 'EL10Ac7g17204' => 'bvu', 'Eucgr.A00855' => 'egr', 'Eucgr.A00858' => 'egr', 'Eucgr.H01520' => 'egr', 'Eucgr.H03604' => 'egr', 'Eucgr.L03465' => 'egr', 'Eucgr.L03466' => 'egr', 'FAN01G0988' => 'fan', 'FAN02G3892' => 'fan', 'FAN05G3381' => 'fan', 'FAN07G0967' => 'fan', 'FAN07G1493' => 'fan', 'FAN08G3125' => 'fan', 'FAN09G0402' => 'fan', 'FAN12G2594' => 'fan', 'FAN12G3879' => 'fan', 'FAN14G1546' => 'fan', 'FAN15G3626' => 'fan', 'FAN17G0588' => 'fan', 'FAN17G0609' => 'fan', 'FAN18G2817' => 'fan', 'FAN19G1305' => 'fan', 'FAN20G1787' => 'fan', 'FAN22G0073' => 'fan', 'FAN22G0352' => 'fan', 'FAN22G0368' => 'fan', 'FAN22G2273' => 'fan', 'FAN24G1998' => 'fan', 'FAN27G1317' => 'fan', 'FvH4_2g23980' => 'fve', 'FvH4_4g14380' => 'fve', 'FvH4_4g14390' => 'fve', 'FvH4_6g09250' => 'fve', 'Glyma.03G151100' => 'gma', 'Glyma.04G122550' => 'gma', 'Glyma.05G001600' => 'gma', 'Glyma.09G270766' => 'gma', 'Glyma.09G270832' => 'gma', 'Glyma.13G209800' => 'gma', 'Glyma.15G102800' => 'gma', 'Glyma.18G218900' => 'gma', 'Glyma.19G001500' => 'gma', 'Glyma.19G153600' => 'gma', 'Gohir.A02G028600' => 'ghi', 'Gohir.A08G045000' => 'ghi', 'Gohir.A11G120500' => 'ghi', 'Gohir.A12G006200' => 'ghi', 'Gohir.A12G006250' => 'ghi', 'Gohir.D02G036300' => 'ghi', 'Gohir.D08G054700' => 'ghi', 'Gohir.D11G125600' => 'ghi', 'Gohir.D12G005700' => 'ghi', 'Gorai.004G055200' => 'gra', 'Gorai.005G040400' => 'gra', 'Gorai.007G134500' => 'gra', 'Gorai.008G005500' => 'gra', 'GSVIVG01011094001' => 'vvi', 'GSVIVG01017879001' => 'vvi', 'GSVIVG01025988001' => 'vvi', 'GSVIVG01029847001' => 'vvi', 'HanXRQChr10g0282901' => 'han', 'HanXRQChr10g0310371' => 'han', 'HanXRQChr10g0315041' => 'han', 'HanXRQChr11g0327651' => 'han', 'HanXRQChr12g0359391' => 'han', 'Haze_00972' => 'cav', 'Haze_00973' => 'cav', 'Haze_00974' => 'cav', 'Haze_04747' => 'cav', 'Haze_04749' => 'cav', 'Haze_04750' => 'cav', 'Haze_21217' => 'cav', 'Hma1.2p1_1037F.1_g250680' => 'hma', 'Hma1.2p1_1644F.1_g295320' => 'hma', 'HPP92_011322' => 'vpl', 'HPP92_011323' => 'vpl', 'HPP92_011324' => 'vpl', 'HPP92_011325' => 'vpl', 'HPP92_011326' => 'vpl', 'Hund12205' => 'sun', 'Hund17957' => 'sun', 'Lalb_Chr06g0176771' => 'lal', 'Lalb_Chr18g0056021' => 'lal', 'Lalb_Chr18g0056031' => 'lal', 'Lalb_Chr18g0056041' => 'lal', 'Lalb_Chr20g0107751' => 'lal', 'Lalb_Chr20g0118371' => 'lal', 'Lj1g0010239' => 'lja', 'Lj1g0017101' => 'lja', 'Lj2A1178G40' => 'lonja', 'Lj2A54G84' => 'lonja', 'Lj2g0015248' => 'lja', 'Lj3A761T51' => 'lonja', 'Lj6g0018116' => 'lja', 'Lsat_1_v5_gn_4_136040' => 'lsa', 'Lsat_1_v5_gn_5_187461' => 'lsa', 'Lsat_1_v5_gn_5_77001' => 'lsa', 'Lsat_1_v5_gn_9_4461' => 'lsa', 'Manes.01G210100' => 'mes', 'Manes.03G185600' => 'mes', 'Manes.05G073300' => 'mes', 'Manes.09G120300' => 'mes', 'Manes.15G022100' => 'mes', 'Mapoly0096s0053' => 'mpo', 'MBI03_g14058_MAGBIO' => 'mbi', 'MBI03_g33876_MAGBIO' => 'mbi', 'MBI03_g36854_MAGBIO' => 'mbi', 'MBI17_g11997_MAGBIO' => 'mbi', 'MD03G1269000' => 'mdo', 'MD04G1179600' => 'mdo', 'MD11G1289800' => 'mdo', 'MD12G1194700' => 'mdo', 'MD13G1182100' => 'mdo', 'MD13G1182200' => 'mdo', 'MD16G1182600' => 'mdo', 'Medtr2g021400' => 'mtr', 'Medtr2g021470' => 'mtr', 'Medtr2g105810' => 'mtr', 'Medtr3g033580' => 'mtr', 'Medtr6g007970' => 'mtr', 'Medtr7g056330' => 'mtr', 'Medtr7g074290' => 'mtr', 'Medtr7g074380' => 'mtr', 'Medtr7g094550' => 'mtr', 'Medtr8g069995' => 'mtr', 'MELO3C014345.2' => 'cme', 'MELO3C021395.2' => 'cme', 'Migut.D00262' => 'egut', 'Migut.G00257' => 'egut', 'MSTRG.21575' => 'ama', 'MSTRG.3985' => 'ama', 'Nitab4.5_0000295g0140' => 'nta', 'Nitab4.5_0000732g0140' => 'nta', 'Nitab4.5_0003162g0020' => 'nta', 'Nitab4.5_0006180g0090' => 'nta', 'Nitab4.5_0006390g0010' => 'nta', 'Nitab4.5_0007392g0040' => 'nta', 'Nn1g02140' => 'nnu', 'Nn4g26168' => 'nnu', 'Nn5g26754' => 'nnu', 'Oeu001433.1' => 'oeu', 'Oeu010299.2' => 'oeu', 'Oeu011171.1' => 'oeu', 'Oeu037675.1' => 'oeu', 'Oeu038359.1' => 'oeu', 'Oeu063834.1' => 'oeu', 'Oeu063835.1' => 'oeu', 'Os05g0312000' => 'osa', 'Os07g0211101' => 'osa', 'Os07g0211200' => 'osa', 'Os07g0681500' => 'osa', 'Peaxi162Scf00095g01015' => 'pax', 'Peaxi162Scf00104g00329' => 'pax', 'Peaxi162Scf00161g00137' => 'pax', 'PGR004G1665' => 'pgr', 'PGR031G2937' => 'pgr', 'PGR119G2145' => 'pgr', 'PGSC0003DMG400004351' => 'stu', 'PGSC0003DMG400014625' => 'stu', 'PGSC0003DMG401000943' => 'stu', 'Phvul.001G148600' => 'pvu', 'Phvul.004G001700' => 'pvu', 'Phvul.006G154900' => 'pvu', 'Phvul.008G078200' => 'pvu', 'Phvul.011G136500' => 'pvu', 'Potri.002G215600' => 'ptr', 'Potri.008G201600' => 'ptr', 'Potri.014G138400' => 'ptr', 'Potri.016G142500' => 'ptr', 'Pp3c16_10580' => 'ppa', 'Pp3c5_25280' => 'ppa', 'Prupe.1G150000' => 'ppe', 'Prupe.1G150100' => 'ppe', 'Prupe.6G299600' => 'ppe', 'Prupe.8G245000' => 'ppe', 'Psat0s4927g0040' => 'psa', 'Psat1g052080' => 'psa', 'Psat1g183800' => 'psa', 'Psat3g113840' => 'psa', 'Psat3g126120' => 'psa', 'Psat3g126160' => 'psa', 'Psat3g158760' => 'psa', 'Psat3g158840' => 'psa', 'PSO170G2858' => 'pso', 'PSO339G0606' => 'pso', 'PSO384G4709' => 'pso', 'PSO407G0334' => 'pso', 'QL04p040276' => 'qlo', 'QL06p005458' => 'qlo', 'QL06p005472' => 'qlo', 'QL07p030546' => 'qlo', 'QL07p031519' => 'qlo', 'QL09p050949' => 'qlo', 'QL09p050966' => 'qlo', 'QL09p051067' => 'qlo', 'QL12p022706' => 'qlo', 'RcHm_v2.0_Chr2g0119601' => 'rch', 'RcHm_v2.0_Chr3g0459591' => 'rch', 'RcHm_v2.0_Chr4g0418521' => 'rch', 'RcHm_v2.0_Chr4g0418531' => 'rch', 'RcHm_v2.0_Chr4g0418541' => 'rch', 'RcHm_v2.0_Chr6g0291641' => 'rch', 'Rhsim01G0086300' => 'rsi', 'Rhsim01G0276300' => 'rsi', 'Rhsim01G0276500' => 'rsi', 'Rhsim04G0207700' => 'rsi', 'Rhsim05G0234500' => 'rsi', 'Rhsim13G0022400' => 'rsi', 'Sabra02G0167900' => 'sbr', 'Sabra04G0158500' => 'sbr', 'Sabra08G0159800' => 'sbr', 'Sabra10G0011500' => 'sbr', 'Sabra14G0104400' => 'sbr', 'SalBow2G2440' => 'sbo', 'SalBow4G2265' => 'sbo', 'Sc02g0000060' => 'sci', 'Sc05g0005020' => 'sci', 'Sc13g0003890' => 'sci', 'Sed0014865' => 'sed', 'Sed0017224' => 'sed', 'Sed0026391' => 'sed', 'SEGI_00063' => 'sgi', 'SEGI_10967' => 'sgi', 'SEGI_17510' => 'sgi', 'SEGI_24396' => 'sgi', 'SEGI_39719' => 'sgi', 'SEGI_41392' => 'sgi', 'SGA_v2.0_scaffold11G05794' => 'sas', 'SGA_v2.0_scaffold142G35607' => 'sas', 'SGA_v2.0_scaffold1G00447' => 'sas', 'SHI15388' => 'shi', 'SHI15394' => 'shi', 'SHI15396' => 'shi', 'SHI15399' => 'shi', 'SMO343G0151' => 'smo', 'SMO367G1118' => 'smo', 'Solyc01g080200.3' => 'sly', 'Solyc06g008960.3' => 'sly', 'Solyc09g064780.3' => 'sly', 'Sopen01g031980' => 'spe', 'Sopen06g003710' => 'spe', 'Sopen09g026460' => 'spe', 'Sp3g21240' => 'spa', 'Sp4g30030' => 'spa', 'TAR365G0022' => 'tar', 'TAR365G1023' => 'tar', 'TAR365G1253' => 'tar', 'TAR623G0078' => 'tar', 'TAR623G1721' => 'tar', 'TAR633G0959' => 'tar', 'THA.LOC104802225' => 'tha', 'THA.LOC104804769' => 'tha', 'THA.LOC104808660' => 'tha', 'THA.LOC104812792' => 'tha', 'Thecc.01G284000' => 'tca', 'Thecc.04G220600' => 'tca', 'Thecc.05G268900' => 'tca', 'Thecc.08G171100' => 'tca', 'Thhalv10001284m.g' => 'esa', 'Thhalv10019912m.g' => 'esa', 'TPR.G14189' => 'tpr', 'TPR.G18110' => 'tpr', 'TPR.G18130' => 'tpr', 'TPR.G18131' => 'tpr', 'TPR.G18140' => 'tpr', 'TPR.G24282' => 'tpr', 'TPR.G25221' => 'tpr', 'TPR.G29267' => 'tpr', 'TPR.G35315' => 'tpr', 'TPR.G36173' => 'tpr', 'TWI09G0794' => 'twi', 'TWI59G1348' => 'twi', 'TWI74G0430' => 'twi', 'unitig_26.g8940' => 'ugi', 'unitig_749.g13744' => 'ugi', 'unitig_749.g13745' => 'ugi', 'vmacro08269' => 'vma', 'vmacro14937' => 'vma', 'vmacro20401' => 'vma', 'VMungo0464G1349' => 'vmu', 'VMungo0540G0289' => 'vmu', 'VMungo1215G1590' => 'vmu', 'VMungo1309G0221' => 'vmu', 'VMungo1309G2815' => 'vmu', 'VMungo1383G0239' => 'vmu', 'VMungo1383G2910' => 'vmu', 'Zm00001eb095270' => 'zma', 'Zm00001eb095280' => 'zma', 'Zm00001eb111630' => 'zma', 'Zm00001eb237080' => 'zma', 'Zm00001eb273740' => 'zma', 'Zm00001eb285040' => 'zma', 'Zm00001eb330790' => 'zma', 'Zm00001eb337380' => 'zma' ) $gf_id = 'HOM05D001484' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001484' ) $data_identifier = 'HOM05D001484' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 2, 'aly' => (int) 2, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 22, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 7, 'hma' => (int) 2, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 7, 'mtr' => (int) 10, 'cme' => (int) 2, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 4, 'ppa' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 4, 'qlo' => (int) 9, 'rch' => (int) 6, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 10, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 7, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb337380' $species_info = array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ) $local_species = 'ppe' $disabled = '' $selected = '' $num_hits = (int) 0
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001484', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p31500' => 'bna', 'A05p00020' => 'bna', 'A07p08820' => 'bna', 'Aa31LG4G3300' => 'aar', 'Aa31LG8G10030' => 'aar', 'Actinidia00731' => 'ach', 'Actinidia11473' => 'ach', 'Actinidia23469' => 'ach', 'Actinidia24318' => 'ach', 'Actinidia40196' => 'ach', 'Actinidia40197' => 'ach', 'Actinidia40198' => 'ach', 'Ah.08g212990' => 'amhyb', 'Ah.15g091720' => 'amhyb', 'AL3G38260' => 'aly', 'AL4G47710' => 'aly', 'Aqoxy2G00671' => 'aox', 'Aqoxy2G03236' => 'aox', 'arahy.Tifrunner.gnm1.ann1.05IDCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KR684' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATY3SJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK6QJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6APGL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IDT7Z9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM073U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ0R87' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LE7RV4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT4QRX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V5ENPK' => 'arhy', 'AT2G48110' => 'ath', 'AT3G23590' => 'ath', 'ATR0626G186' => 'atr', 'ATR1127G141' => 'atr', 'Atru.chr4.2583' => 'acertr', 'Atru.chr5.1358' => 'acertr', 'Atru.chr5.1359' => 'acertr', 'Atru.chr8.46' => 'acertr', 'AUR62002640' => 'cqu', 'AUR62030055' => 'cqu', 'AUR62033713' => 'cqu', 'AUR62033714' => 'cqu', 'AUR62036795' => 'cqu', 'AUR62039891' => 'cqu', 'BcaB02g08737' => 'bca', 'BcaB04g20441' => 'bca', 'BcaB06g26509' => 'bca', 'BcaB06g26510' => 'bca', 'BcaB06g26511' => 'bca', 'BcaB06g26512' => 'bca', 'BcaB06g26513' => 'bca', 'BcaC02g12564' => 'bca', 'BcaC02g12565' => 'bca', 'BcaC02g12794' => 'bca', 'BcaC02g12795' => 'bca', 'BcaC02g12796' => 'bca', 'BcaC06g35541' => 'bca', 'BNapus_Darmor_BZH_scaffold_188p00080' => 'bna', 'BNapus_Darmor_BZH_scaffold_188p00090' => 'bna', 'BolC1t03972H' => 'bol', 'BolC1t03973H' => 'bol', 'BolC4t21680H' => 'bol', 'BolC7t41863H' => 'bol', 'BolSC55t61227H' => 'bol', 'BolSC55t61228H' => 'bol', 'BraA01t03278Z' => 'bra', 'BraA05t18998Z' => 'bra', 'BraA07t28673Z' => 'bra', 'C01p40150' => 'bna', 'C05p12370' => 'bna', 'C07p13680' => 'bna', 'CAN.G1006.16' => 'can', 'CAN.G1006.17' => 'can', 'CAN.G1170.2' => 'can', 'CAN.G962.7' => 'can', 'CANSAT25G2179' => 'cansat', 'CANSAT78G1573' => 'cansat', 'CARHR099510' => 'chi', 'CARHR143510' => 'chi', 'Carub.0003s2380' => 'cru', 'Carub.0004s3082' => 'cru', 'Ca_00614_v3' => 'car', 'Ca_07801_v3' => 'car', 'Ca_08567_v3' => 'car', 'Ca_09571_v3' => 'car', 'CBR_g19290' => 'cbr', 'Cc01_g19770' => 'ccan', 'Cc03_g03030' => 'ccan', 'CDE07G0968' => 'cde', 'CDE09G1441' => 'cde', 'Cfa006103' => 'cfa', 'Cfa015573' => 'cfa', 'Cfa016988' => 'cfa', 'Ciclev10006738m.g' => 'ccl', 'Ciclev10010920m.g' => 'ccl', 'Ciclev10018517m.g' => 'ccl', 'CiPaw.01G159200' => 'cil', 'CiPaw.02G091000' => 'cil', 'CiPaw.02G091100' => 'cil', 'CiPaw.08G103100' => 'cil', 'CiPaw.09G224900' => 'cil', 'ClCG06G005740' => 'cla', 'ClCG07G000090' => 'cla', 'ClCG07G000100' => 'cla', 'COL.COLO4_09143' => 'col', 'COL.COLO4_25124' => 'col', 'Cpa.g.sc16.34' => 'cpa', 'Cpa.g.sc3504.1' => 'cpa', 'Cpa.g.sc60.37' => 'cpa', 'CsaV3_6G018520' => 'csa', 'CsaV3_6G036860' => 'csa', 'CSS0001072' => 'camsi', 'CSS0020208' => 'camsi', 'CSS0021253' => 'camsi', 'CSS0022190' => 'camsi', 'CSS0036150' => 'camsi', 'CSS0040442' => 'camsi', 'CSS0042300' => 'camsi', 'CSS0045298' => 'camsi', 'DCAR_012449' => 'dca', 'DCAR_018405' => 'dca', 'DCAR_024573' => 'dca', 'DCAR_030591' => 'dca', 'Dinv16926' => 'din', 'Dinv32963' => 'din', 'Dinv38382' => 'din', 'Dinv38383' => 'din', 'Duzib133G0974' => 'dzi', 'Duzib138G1867' => 'dzi', 'Duzib211G0420' => 'dzi', 'Duzib212G0930' => 'dzi', 'ECA234G1645' => 'eca', 'ECA247G3467' => 'eca', 'ECA248G1703' => 'eca', 'EL10Ac3g06327' => 'bvu', 'EL10Ac7g17204' => 'bvu', 'Eucgr.A00855' => 'egr', 'Eucgr.A00858' => 'egr', 'Eucgr.H01520' => 'egr', 'Eucgr.H03604' => 'egr', 'Eucgr.L03465' => 'egr', 'Eucgr.L03466' => 'egr', 'FAN01G0988' => 'fan', 'FAN02G3892' => 'fan', 'FAN05G3381' => 'fan', 'FAN07G0967' => 'fan', 'FAN07G1493' => 'fan', 'FAN08G3125' => 'fan', 'FAN09G0402' => 'fan', 'FAN12G2594' => 'fan', 'FAN12G3879' => 'fan', 'FAN14G1546' => 'fan', 'FAN15G3626' => 'fan', 'FAN17G0588' => 'fan', 'FAN17G0609' => 'fan', 'FAN18G2817' => 'fan', 'FAN19G1305' => 'fan', 'FAN20G1787' => 'fan', 'FAN22G0073' => 'fan', 'FAN22G0352' => 'fan', 'FAN22G0368' => 'fan', 'FAN22G2273' => 'fan', 'FAN24G1998' => 'fan', 'FAN27G1317' => 'fan', 'FvH4_2g23980' => 'fve', 'FvH4_4g14380' => 'fve', 'FvH4_4g14390' => 'fve', 'FvH4_6g09250' => 'fve', 'Glyma.03G151100' => 'gma', 'Glyma.04G122550' => 'gma', 'Glyma.05G001600' => 'gma', 'Glyma.09G270766' => 'gma', 'Glyma.09G270832' => 'gma', 'Glyma.13G209800' => 'gma', 'Glyma.15G102800' => 'gma', 'Glyma.18G218900' => 'gma', 'Glyma.19G001500' => 'gma', 'Glyma.19G153600' => 'gma', 'Gohir.A02G028600' => 'ghi', 'Gohir.A08G045000' => 'ghi', 'Gohir.A11G120500' => 'ghi', 'Gohir.A12G006200' => 'ghi', 'Gohir.A12G006250' => 'ghi', 'Gohir.D02G036300' => 'ghi', 'Gohir.D08G054700' => 'ghi', 'Gohir.D11G125600' => 'ghi', 'Gohir.D12G005700' => 'ghi', 'Gorai.004G055200' => 'gra', 'Gorai.005G040400' => 'gra', 'Gorai.007G134500' => 'gra', 'Gorai.008G005500' => 'gra', 'GSVIVG01011094001' => 'vvi', 'GSVIVG01017879001' => 'vvi', 'GSVIVG01025988001' => 'vvi', 'GSVIVG01029847001' => 'vvi', 'HanXRQChr10g0282901' => 'han', 'HanXRQChr10g0310371' => 'han', 'HanXRQChr10g0315041' => 'han', 'HanXRQChr11g0327651' => 'han', 'HanXRQChr12g0359391' => 'han', 'Haze_00972' => 'cav', 'Haze_00973' => 'cav', 'Haze_00974' => 'cav', 'Haze_04747' => 'cav', 'Haze_04749' => 'cav', 'Haze_04750' => 'cav', 'Haze_21217' => 'cav', 'Hma1.2p1_1037F.1_g250680' => 'hma', 'Hma1.2p1_1644F.1_g295320' => 'hma', 'HPP92_011322' => 'vpl', 'HPP92_011323' => 'vpl', 'HPP92_011324' => 'vpl', 'HPP92_011325' => 'vpl', 'HPP92_011326' => 'vpl', 'Hund12205' => 'sun', 'Hund17957' => 'sun', 'Lalb_Chr06g0176771' => 'lal', 'Lalb_Chr18g0056021' => 'lal', 'Lalb_Chr18g0056031' => 'lal', 'Lalb_Chr18g0056041' => 'lal', 'Lalb_Chr20g0107751' => 'lal', 'Lalb_Chr20g0118371' => 'lal', 'Lj1g0010239' => 'lja', 'Lj1g0017101' => 'lja', 'Lj2A1178G40' => 'lonja', 'Lj2A54G84' => 'lonja', 'Lj2g0015248' => 'lja', 'Lj3A761T51' => 'lonja', 'Lj6g0018116' => 'lja', 'Lsat_1_v5_gn_4_136040' => 'lsa', 'Lsat_1_v5_gn_5_187461' => 'lsa', 'Lsat_1_v5_gn_5_77001' => 'lsa', 'Lsat_1_v5_gn_9_4461' => 'lsa', 'Manes.01G210100' => 'mes', 'Manes.03G185600' => 'mes', 'Manes.05G073300' => 'mes', 'Manes.09G120300' => 'mes', 'Manes.15G022100' => 'mes', 'Mapoly0096s0053' => 'mpo', 'MBI03_g14058_MAGBIO' => 'mbi', 'MBI03_g33876_MAGBIO' => 'mbi', 'MBI03_g36854_MAGBIO' => 'mbi', 'MBI17_g11997_MAGBIO' => 'mbi', 'MD03G1269000' => 'mdo', 'MD04G1179600' => 'mdo', 'MD11G1289800' => 'mdo', 'MD12G1194700' => 'mdo', 'MD13G1182100' => 'mdo', 'MD13G1182200' => 'mdo', 'MD16G1182600' => 'mdo', 'Medtr2g021400' => 'mtr', 'Medtr2g021470' => 'mtr', 'Medtr2g105810' => 'mtr', 'Medtr3g033580' => 'mtr', 'Medtr6g007970' => 'mtr', 'Medtr7g056330' => 'mtr', 'Medtr7g074290' => 'mtr', 'Medtr7g074380' => 'mtr', 'Medtr7g094550' => 'mtr', 'Medtr8g069995' => 'mtr', 'MELO3C014345.2' => 'cme', 'MELO3C021395.2' => 'cme', 'Migut.D00262' => 'egut', 'Migut.G00257' => 'egut', 'MSTRG.21575' => 'ama', 'MSTRG.3985' => 'ama', 'Nitab4.5_0000295g0140' => 'nta', 'Nitab4.5_0000732g0140' => 'nta', 'Nitab4.5_0003162g0020' => 'nta', 'Nitab4.5_0006180g0090' => 'nta', 'Nitab4.5_0006390g0010' => 'nta', 'Nitab4.5_0007392g0040' => 'nta', 'Nn1g02140' => 'nnu', 'Nn4g26168' => 'nnu', 'Nn5g26754' => 'nnu', 'Oeu001433.1' => 'oeu', 'Oeu010299.2' => 'oeu', 'Oeu011171.1' => 'oeu', 'Oeu037675.1' => 'oeu', 'Oeu038359.1' => 'oeu', 'Oeu063834.1' => 'oeu', 'Oeu063835.1' => 'oeu', 'Os05g0312000' => 'osa', 'Os07g0211101' => 'osa', 'Os07g0211200' => 'osa', 'Os07g0681500' => 'osa', 'Peaxi162Scf00095g01015' => 'pax', 'Peaxi162Scf00104g00329' => 'pax', 'Peaxi162Scf00161g00137' => 'pax', 'PGR004G1665' => 'pgr', 'PGR031G2937' => 'pgr', 'PGR119G2145' => 'pgr', 'PGSC0003DMG400004351' => 'stu', 'PGSC0003DMG400014625' => 'stu', 'PGSC0003DMG401000943' => 'stu', 'Phvul.001G148600' => 'pvu', 'Phvul.004G001700' => 'pvu', 'Phvul.006G154900' => 'pvu', 'Phvul.008G078200' => 'pvu', 'Phvul.011G136500' => 'pvu', 'Potri.002G215600' => 'ptr', 'Potri.008G201600' => 'ptr', 'Potri.014G138400' => 'ptr', 'Potri.016G142500' => 'ptr', 'Pp3c16_10580' => 'ppa', 'Pp3c5_25280' => 'ppa', 'Prupe.1G150000' => 'ppe', 'Prupe.1G150100' => 'ppe', 'Prupe.6G299600' => 'ppe', 'Prupe.8G245000' => 'ppe', 'Psat0s4927g0040' => 'psa', 'Psat1g052080' => 'psa', 'Psat1g183800' => 'psa', 'Psat3g113840' => 'psa', 'Psat3g126120' => 'psa', 'Psat3g126160' => 'psa', 'Psat3g158760' => 'psa', 'Psat3g158840' => 'psa', 'PSO170G2858' => 'pso', 'PSO339G0606' => 'pso', 'PSO384G4709' => 'pso', 'PSO407G0334' => 'pso', 'QL04p040276' => 'qlo', 'QL06p005458' => 'qlo', 'QL06p005472' => 'qlo', 'QL07p030546' => 'qlo', 'QL07p031519' => 'qlo', 'QL09p050949' => 'qlo', 'QL09p050966' => 'qlo', 'QL09p051067' => 'qlo', 'QL12p022706' => 'qlo', 'RcHm_v2.0_Chr2g0119601' => 'rch', 'RcHm_v2.0_Chr3g0459591' => 'rch', 'RcHm_v2.0_Chr4g0418521' => 'rch', 'RcHm_v2.0_Chr4g0418531' => 'rch', 'RcHm_v2.0_Chr4g0418541' => 'rch', 'RcHm_v2.0_Chr6g0291641' => 'rch', 'Rhsim01G0086300' => 'rsi', 'Rhsim01G0276300' => 'rsi', 'Rhsim01G0276500' => 'rsi', 'Rhsim04G0207700' => 'rsi', 'Rhsim05G0234500' => 'rsi', 'Rhsim13G0022400' => 'rsi', 'Sabra02G0167900' => 'sbr', 'Sabra04G0158500' => 'sbr', 'Sabra08G0159800' => 'sbr', 'Sabra10G0011500' => 'sbr', 'Sabra14G0104400' => 'sbr', 'SalBow2G2440' => 'sbo', 'SalBow4G2265' => 'sbo', 'Sc02g0000060' => 'sci', 'Sc05g0005020' => 'sci', 'Sc13g0003890' => 'sci', 'Sed0014865' => 'sed', 'Sed0017224' => 'sed', 'Sed0026391' => 'sed', 'SEGI_00063' => 'sgi', 'SEGI_10967' => 'sgi', 'SEGI_17510' => 'sgi', 'SEGI_24396' => 'sgi', 'SEGI_39719' => 'sgi', 'SEGI_41392' => 'sgi', 'SGA_v2.0_scaffold11G05794' => 'sas', 'SGA_v2.0_scaffold142G35607' => 'sas', 'SGA_v2.0_scaffold1G00447' => 'sas', 'SHI15388' => 'shi', 'SHI15394' => 'shi', 'SHI15396' => 'shi', 'SHI15399' => 'shi', 'SMO343G0151' => 'smo', 'SMO367G1118' => 'smo', 'Solyc01g080200.3' => 'sly', 'Solyc06g008960.3' => 'sly', 'Solyc09g064780.3' => 'sly', 'Sopen01g031980' => 'spe', 'Sopen06g003710' => 'spe', 'Sopen09g026460' => 'spe', 'Sp3g21240' => 'spa', 'Sp4g30030' => 'spa', 'TAR365G0022' => 'tar', 'TAR365G1023' => 'tar', 'TAR365G1253' => 'tar', 'TAR623G0078' => 'tar', 'TAR623G1721' => 'tar', 'TAR633G0959' => 'tar', 'THA.LOC104802225' => 'tha', 'THA.LOC104804769' => 'tha', 'THA.LOC104808660' => 'tha', 'THA.LOC104812792' => 'tha', 'Thecc.01G284000' => 'tca', 'Thecc.04G220600' => 'tca', 'Thecc.05G268900' => 'tca', 'Thecc.08G171100' => 'tca', 'Thhalv10001284m.g' => 'esa', 'Thhalv10019912m.g' => 'esa', 'TPR.G14189' => 'tpr', 'TPR.G18110' => 'tpr', 'TPR.G18130' => 'tpr', 'TPR.G18131' => 'tpr', 'TPR.G18140' => 'tpr', 'TPR.G24282' => 'tpr', 'TPR.G25221' => 'tpr', 'TPR.G29267' => 'tpr', 'TPR.G35315' => 'tpr', 'TPR.G36173' => 'tpr', 'TWI09G0794' => 'twi', 'TWI59G1348' => 'twi', 'TWI74G0430' => 'twi', 'unitig_26.g8940' => 'ugi', 'unitig_749.g13744' => 'ugi', 'unitig_749.g13745' => 'ugi', 'vmacro08269' => 'vma', 'vmacro14937' => 'vma', 'vmacro20401' => 'vma', 'VMungo0464G1349' => 'vmu', 'VMungo0540G0289' => 'vmu', 'VMungo1215G1590' => 'vmu', 'VMungo1309G0221' => 'vmu', 'VMungo1309G2815' => 'vmu', 'VMungo1383G0239' => 'vmu', 'VMungo1383G2910' => 'vmu', 'Zm00001eb095270' => 'zma', 'Zm00001eb095280' => 'zma', 'Zm00001eb111630' => 'zma', 'Zm00001eb237080' => 'zma', 'Zm00001eb273740' => 'zma', 'Zm00001eb285040' => 'zma', 'Zm00001eb330790' => 'zma', 'Zm00001eb337380' => 'zma' ), 'gf_id' => 'HOM05D001484', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001484' ), 'data_identifier' => 'HOM05D001484', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001484', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p31500' => 'bna', 'A05p00020' => 'bna', 'A07p08820' => 'bna', 'Aa31LG4G3300' => 'aar', 'Aa31LG8G10030' => 'aar', 'Actinidia00731' => 'ach', 'Actinidia11473' => 'ach', 'Actinidia23469' => 'ach', 'Actinidia24318' => 'ach', 'Actinidia40196' => 'ach', 'Actinidia40197' => 'ach', 'Actinidia40198' => 'ach', 'Ah.08g212990' => 'amhyb', 'Ah.15g091720' => 'amhyb', 'AL3G38260' => 'aly', 'AL4G47710' => 'aly', 'Aqoxy2G00671' => 'aox', 'Aqoxy2G03236' => 'aox', 'arahy.Tifrunner.gnm1.ann1.05IDCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KR684' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATY3SJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK6QJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6APGL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IDT7Z9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM073U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ0R87' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LE7RV4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT4QRX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V5ENPK' => 'arhy', 'AT2G48110' => 'ath', 'AT3G23590' => 'ath', 'ATR0626G186' => 'atr', 'ATR1127G141' => 'atr', 'Atru.chr4.2583' => 'acertr', 'Atru.chr5.1358' => 'acertr', 'Atru.chr5.1359' => 'acertr', 'Atru.chr8.46' => 'acertr', 'AUR62002640' => 'cqu', 'AUR62030055' => 'cqu', 'AUR62033713' => 'cqu', 'AUR62033714' => 'cqu', 'AUR62036795' => 'cqu', 'AUR62039891' => 'cqu', 'BcaB02g08737' => 'bca', 'BcaB04g20441' => 'bca', 'BcaB06g26509' => 'bca', 'BcaB06g26510' => 'bca', 'BcaB06g26511' => 'bca', 'BcaB06g26512' => 'bca', 'BcaB06g26513' => 'bca', 'BcaC02g12564' => 'bca', 'BcaC02g12565' => 'bca', 'BcaC02g12794' => 'bca', 'BcaC02g12795' => 'bca', 'BcaC02g12796' => 'bca', 'BcaC06g35541' => 'bca', 'BNapus_Darmor_BZH_scaffold_188p00080' => 'bna', 'BNapus_Darmor_BZH_scaffold_188p00090' => 'bna', 'BolC1t03972H' => 'bol', 'BolC1t03973H' => 'bol', 'BolC4t21680H' => 'bol', 'BolC7t41863H' => 'bol', 'BolSC55t61227H' => 'bol', 'BolSC55t61228H' => 'bol', 'BraA01t03278Z' => 'bra', 'BraA05t18998Z' => 'bra', 'BraA07t28673Z' => 'bra', 'C01p40150' => 'bna', 'C05p12370' => 'bna', 'C07p13680' => 'bna', 'CAN.G1006.16' => 'can', 'CAN.G1006.17' => 'can', 'CAN.G1170.2' => 'can', 'CAN.G962.7' => 'can', 'CANSAT25G2179' => 'cansat', 'CANSAT78G1573' => 'cansat', 'CARHR099510' => 'chi', 'CARHR143510' => 'chi', 'Carub.0003s2380' => 'cru', 'Carub.0004s3082' => 'cru', 'Ca_00614_v3' => 'car', 'Ca_07801_v3' => 'car', 'Ca_08567_v3' => 'car', 'Ca_09571_v3' => 'car', 'CBR_g19290' => 'cbr', 'Cc01_g19770' => 'ccan', 'Cc03_g03030' => 'ccan', 'CDE07G0968' => 'cde', 'CDE09G1441' => 'cde', 'Cfa006103' => 'cfa', 'Cfa015573' => 'cfa', 'Cfa016988' => 'cfa', 'Ciclev10006738m.g' => 'ccl', 'Ciclev10010920m.g' => 'ccl', 'Ciclev10018517m.g' => 'ccl', 'CiPaw.01G159200' => 'cil', 'CiPaw.02G091000' => 'cil', 'CiPaw.02G091100' => 'cil', 'CiPaw.08G103100' => 'cil', 'CiPaw.09G224900' => 'cil', 'ClCG06G005740' => 'cla', 'ClCG07G000090' => 'cla', 'ClCG07G000100' => 'cla', 'COL.COLO4_09143' => 'col', 'COL.COLO4_25124' => 'col', 'Cpa.g.sc16.34' => 'cpa', 'Cpa.g.sc3504.1' => 'cpa', 'Cpa.g.sc60.37' => 'cpa', 'CsaV3_6G018520' => 'csa', 'CsaV3_6G036860' => 'csa', 'CSS0001072' => 'camsi', 'CSS0020208' => 'camsi', 'CSS0021253' => 'camsi', 'CSS0022190' => 'camsi', 'CSS0036150' => 'camsi', 'CSS0040442' => 'camsi', 'CSS0042300' => 'camsi', 'CSS0045298' => 'camsi', 'DCAR_012449' => 'dca', 'DCAR_018405' => 'dca', 'DCAR_024573' => 'dca', 'DCAR_030591' => 'dca', 'Dinv16926' => 'din', 'Dinv32963' => 'din', 'Dinv38382' => 'din', 'Dinv38383' => 'din', 'Duzib133G0974' => 'dzi', 'Duzib138G1867' => 'dzi', 'Duzib211G0420' => 'dzi', 'Duzib212G0930' => 'dzi', 'ECA234G1645' => 'eca', 'ECA247G3467' => 'eca', 'ECA248G1703' => 'eca', 'EL10Ac3g06327' => 'bvu', 'EL10Ac7g17204' => 'bvu', 'Eucgr.A00855' => 'egr', 'Eucgr.A00858' => 'egr', 'Eucgr.H01520' => 'egr', 'Eucgr.H03604' => 'egr', 'Eucgr.L03465' => 'egr', 'Eucgr.L03466' => 'egr', 'FAN01G0988' => 'fan', 'FAN02G3892' => 'fan', 'FAN05G3381' => 'fan', 'FAN07G0967' => 'fan', 'FAN07G1493' => 'fan', 'FAN08G3125' => 'fan', 'FAN09G0402' => 'fan', 'FAN12G2594' => 'fan', 'FAN12G3879' => 'fan', 'FAN14G1546' => 'fan', 'FAN15G3626' => 'fan', 'FAN17G0588' => 'fan', 'FAN17G0609' => 'fan', 'FAN18G2817' => 'fan', 'FAN19G1305' => 'fan', 'FAN20G1787' => 'fan', 'FAN22G0073' => 'fan', 'FAN22G0352' => 'fan', 'FAN22G0368' => 'fan', 'FAN22G2273' => 'fan', 'FAN24G1998' => 'fan', 'FAN27G1317' => 'fan', 'FvH4_2g23980' => 'fve', 'FvH4_4g14380' => 'fve', 'FvH4_4g14390' => 'fve', 'FvH4_6g09250' => 'fve', 'Glyma.03G151100' => 'gma', 'Glyma.04G122550' => 'gma', 'Glyma.05G001600' => 'gma', 'Glyma.09G270766' => 'gma', 'Glyma.09G270832' => 'gma', 'Glyma.13G209800' => 'gma', 'Glyma.15G102800' => 'gma', 'Glyma.18G218900' => 'gma', 'Glyma.19G001500' => 'gma', 'Glyma.19G153600' => 'gma', 'Gohir.A02G028600' => 'ghi', 'Gohir.A08G045000' => 'ghi', 'Gohir.A11G120500' => 'ghi', 'Gohir.A12G006200' => 'ghi', 'Gohir.A12G006250' => 'ghi', 'Gohir.D02G036300' => 'ghi', 'Gohir.D08G054700' => 'ghi', 'Gohir.D11G125600' => 'ghi', 'Gohir.D12G005700' => 'ghi', 'Gorai.004G055200' => 'gra', 'Gorai.005G040400' => 'gra', 'Gorai.007G134500' => 'gra', 'Gorai.008G005500' => 'gra', 'GSVIVG01011094001' => 'vvi', 'GSVIVG01017879001' => 'vvi', 'GSVIVG01025988001' => 'vvi', 'GSVIVG01029847001' => 'vvi', 'HanXRQChr10g0282901' => 'han', 'HanXRQChr10g0310371' => 'han', 'HanXRQChr10g0315041' => 'han', 'HanXRQChr11g0327651' => 'han', 'HanXRQChr12g0359391' => 'han', 'Haze_00972' => 'cav', 'Haze_00973' => 'cav', 'Haze_00974' => 'cav', 'Haze_04747' => 'cav', 'Haze_04749' => 'cav', 'Haze_04750' => 'cav', 'Haze_21217' => 'cav', 'Hma1.2p1_1037F.1_g250680' => 'hma', 'Hma1.2p1_1644F.1_g295320' => 'hma', 'HPP92_011322' => 'vpl', 'HPP92_011323' => 'vpl', 'HPP92_011324' => 'vpl', 'HPP92_011325' => 'vpl', 'HPP92_011326' => 'vpl', 'Hund12205' => 'sun', 'Hund17957' => 'sun', 'Lalb_Chr06g0176771' => 'lal', 'Lalb_Chr18g0056021' => 'lal', 'Lalb_Chr18g0056031' => 'lal', 'Lalb_Chr18g0056041' => 'lal', 'Lalb_Chr20g0107751' => 'lal', 'Lalb_Chr20g0118371' => 'lal', 'Lj1g0010239' => 'lja', 'Lj1g0017101' => 'lja', 'Lj2A1178G40' => 'lonja', 'Lj2A54G84' => 'lonja', 'Lj2g0015248' => 'lja', 'Lj3A761T51' => 'lonja', 'Lj6g0018116' => 'lja', 'Lsat_1_v5_gn_4_136040' => 'lsa', 'Lsat_1_v5_gn_5_187461' => 'lsa', 'Lsat_1_v5_gn_5_77001' => 'lsa', 'Lsat_1_v5_gn_9_4461' => 'lsa', 'Manes.01G210100' => 'mes', 'Manes.03G185600' => 'mes', 'Manes.05G073300' => 'mes', 'Manes.09G120300' => 'mes', 'Manes.15G022100' => 'mes', 'Mapoly0096s0053' => 'mpo', 'MBI03_g14058_MAGBIO' => 'mbi', 'MBI03_g33876_MAGBIO' => 'mbi', 'MBI03_g36854_MAGBIO' => 'mbi', 'MBI17_g11997_MAGBIO' => 'mbi', 'MD03G1269000' => 'mdo', 'MD04G1179600' => 'mdo', 'MD11G1289800' => 'mdo', 'MD12G1194700' => 'mdo', 'MD13G1182100' => 'mdo', 'MD13G1182200' => 'mdo', 'MD16G1182600' => 'mdo', 'Medtr2g021400' => 'mtr', 'Medtr2g021470' => 'mtr', 'Medtr2g105810' => 'mtr', 'Medtr3g033580' => 'mtr', 'Medtr6g007970' => 'mtr', 'Medtr7g056330' => 'mtr', 'Medtr7g074290' => 'mtr', 'Medtr7g074380' => 'mtr', 'Medtr7g094550' => 'mtr', 'Medtr8g069995' => 'mtr', 'MELO3C014345.2' => 'cme', 'MELO3C021395.2' => 'cme', 'Migut.D00262' => 'egut', 'Migut.G00257' => 'egut', 'MSTRG.21575' => 'ama', 'MSTRG.3985' => 'ama', 'Nitab4.5_0000295g0140' => 'nta', 'Nitab4.5_0000732g0140' => 'nta', 'Nitab4.5_0003162g0020' => 'nta', 'Nitab4.5_0006180g0090' => 'nta', 'Nitab4.5_0006390g0010' => 'nta', 'Nitab4.5_0007392g0040' => 'nta', 'Nn1g02140' => 'nnu', 'Nn4g26168' => 'nnu', 'Nn5g26754' => 'nnu', 'Oeu001433.1' => 'oeu', 'Oeu010299.2' => 'oeu', 'Oeu011171.1' => 'oeu', 'Oeu037675.1' => 'oeu', 'Oeu038359.1' => 'oeu', 'Oeu063834.1' => 'oeu', 'Oeu063835.1' => 'oeu', 'Os05g0312000' => 'osa', 'Os07g0211101' => 'osa', 'Os07g0211200' => 'osa', 'Os07g0681500' => 'osa', 'Peaxi162Scf00095g01015' => 'pax', 'Peaxi162Scf00104g00329' => 'pax', 'Peaxi162Scf00161g00137' => 'pax', 'PGR004G1665' => 'pgr', 'PGR031G2937' => 'pgr', 'PGR119G2145' => 'pgr', 'PGSC0003DMG400004351' => 'stu', 'PGSC0003DMG400014625' => 'stu', 'PGSC0003DMG401000943' => 'stu', 'Phvul.001G148600' => 'pvu', 'Phvul.004G001700' => 'pvu', 'Phvul.006G154900' => 'pvu', 'Phvul.008G078200' => 'pvu', 'Phvul.011G136500' => 'pvu', 'Potri.002G215600' => 'ptr', 'Potri.008G201600' => 'ptr', 'Potri.014G138400' => 'ptr', 'Potri.016G142500' => 'ptr', 'Pp3c16_10580' => 'ppa', 'Pp3c5_25280' => 'ppa', 'Prupe.1G150000' => 'ppe', 'Prupe.1G150100' => 'ppe', 'Prupe.6G299600' => 'ppe', 'Prupe.8G245000' => 'ppe', 'Psat0s4927g0040' => 'psa', 'Psat1g052080' => 'psa', 'Psat1g183800' => 'psa', 'Psat3g113840' => 'psa', 'Psat3g126120' => 'psa', 'Psat3g126160' => 'psa', 'Psat3g158760' => 'psa', 'Psat3g158840' => 'psa', 'PSO170G2858' => 'pso', 'PSO339G0606' => 'pso', 'PSO384G4709' => 'pso', 'PSO407G0334' => 'pso', 'QL04p040276' => 'qlo', 'QL06p005458' => 'qlo', 'QL06p005472' => 'qlo', 'QL07p030546' => 'qlo', 'QL07p031519' => 'qlo', 'QL09p050949' => 'qlo', 'QL09p050966' => 'qlo', 'QL09p051067' => 'qlo', 'QL12p022706' => 'qlo', 'RcHm_v2.0_Chr2g0119601' => 'rch', 'RcHm_v2.0_Chr3g0459591' => 'rch', 'RcHm_v2.0_Chr4g0418521' => 'rch', 'RcHm_v2.0_Chr4g0418531' => 'rch', 'RcHm_v2.0_Chr4g0418541' => 'rch', 'RcHm_v2.0_Chr6g0291641' => 'rch', 'Rhsim01G0086300' => 'rsi', 'Rhsim01G0276300' => 'rsi', 'Rhsim01G0276500' => 'rsi', 'Rhsim04G0207700' => 'rsi', 'Rhsim05G0234500' => 'rsi', 'Rhsim13G0022400' => 'rsi', 'Sabra02G0167900' => 'sbr', 'Sabra04G0158500' => 'sbr', 'Sabra08G0159800' => 'sbr', 'Sabra10G0011500' => 'sbr', 'Sabra14G0104400' => 'sbr', 'SalBow2G2440' => 'sbo', 'SalBow4G2265' => 'sbo', 'Sc02g0000060' => 'sci', 'Sc05g0005020' => 'sci', 'Sc13g0003890' => 'sci', 'Sed0014865' => 'sed', 'Sed0017224' => 'sed', 'Sed0026391' => 'sed', 'SEGI_00063' => 'sgi', 'SEGI_10967' => 'sgi', 'SEGI_17510' => 'sgi', 'SEGI_24396' => 'sgi', 'SEGI_39719' => 'sgi', 'SEGI_41392' => 'sgi', 'SGA_v2.0_scaffold11G05794' => 'sas', 'SGA_v2.0_scaffold142G35607' => 'sas', 'SGA_v2.0_scaffold1G00447' => 'sas', 'SHI15388' => 'shi', 'SHI15394' => 'shi', 'SHI15396' => 'shi', 'SHI15399' => 'shi', 'SMO343G0151' => 'smo', 'SMO367G1118' => 'smo', 'Solyc01g080200.3' => 'sly', 'Solyc06g008960.3' => 'sly', 'Solyc09g064780.3' => 'sly', 'Sopen01g031980' => 'spe', 'Sopen06g003710' => 'spe', 'Sopen09g026460' => 'spe', 'Sp3g21240' => 'spa', 'Sp4g30030' => 'spa', 'TAR365G0022' => 'tar', 'TAR365G1023' => 'tar', 'TAR365G1253' => 'tar', 'TAR623G0078' => 'tar', 'TAR623G1721' => 'tar', 'TAR633G0959' => 'tar', 'THA.LOC104802225' => 'tha', 'THA.LOC104804769' => 'tha', 'THA.LOC104808660' => 'tha', 'THA.LOC104812792' => 'tha', 'Thecc.01G284000' => 'tca', 'Thecc.04G220600' => 'tca', 'Thecc.05G268900' => 'tca', 'Thecc.08G171100' => 'tca', 'Thhalv10001284m.g' => 'esa', 'Thhalv10019912m.g' => 'esa', 'TPR.G14189' => 'tpr', 'TPR.G18110' => 'tpr', 'TPR.G18130' => 'tpr', 'TPR.G18131' => 'tpr', 'TPR.G18140' => 'tpr', 'TPR.G24282' => 'tpr', 'TPR.G25221' => 'tpr', 'TPR.G29267' => 'tpr', 'TPR.G35315' => 'tpr', 'TPR.G36173' => 'tpr', 'TWI09G0794' => 'twi', 'TWI59G1348' => 'twi', 'TWI74G0430' => 'twi', 'unitig_26.g8940' => 'ugi', 'unitig_749.g13744' => 'ugi', 'unitig_749.g13745' => 'ugi', 'vmacro08269' => 'vma', 'vmacro14937' => 'vma', 'vmacro20401' => 'vma', 'VMungo0464G1349' => 'vmu', 'VMungo0540G0289' => 'vmu', 'VMungo1215G1590' => 'vmu', 'VMungo1309G0221' => 'vmu', 'VMungo1309G2815' => 'vmu', 'VMungo1383G0239' => 'vmu', 'VMungo1383G2910' => 'vmu', 'Zm00001eb095270' => 'zma', 'Zm00001eb095280' => 'zma', 'Zm00001eb111630' => 'zma', 'Zm00001eb237080' => 'zma', 'Zm00001eb273740' => 'zma', 'Zm00001eb285040' => 'zma', 'Zm00001eb330790' => 'zma', 'Zm00001eb337380' => 'zma' ) $gf_id = 'HOM05D001484' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001484' ) $data_identifier = 'HOM05D001484' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 2, 'aly' => (int) 2, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 22, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 7, 'hma' => (int) 2, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 7, 'mtr' => (int) 10, 'cme' => (int) 2, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 4, 'ppa' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 4, 'qlo' => (int) 9, 'rch' => (int) 6, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 10, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 7, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb337380' $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' => 'HOM05D001484', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p31500' => 'bna', 'A05p00020' => 'bna', 'A07p08820' => 'bna', 'Aa31LG4G3300' => 'aar', 'Aa31LG8G10030' => 'aar', 'Actinidia00731' => 'ach', 'Actinidia11473' => 'ach', 'Actinidia23469' => 'ach', 'Actinidia24318' => 'ach', 'Actinidia40196' => 'ach', 'Actinidia40197' => 'ach', 'Actinidia40198' => 'ach', 'Ah.08g212990' => 'amhyb', 'Ah.15g091720' => 'amhyb', 'AL3G38260' => 'aly', 'AL4G47710' => 'aly', 'Aqoxy2G00671' => 'aox', 'Aqoxy2G03236' => 'aox', 'arahy.Tifrunner.gnm1.ann1.05IDCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KR684' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATY3SJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK6QJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6APGL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IDT7Z9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM073U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ0R87' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LE7RV4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT4QRX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V5ENPK' => 'arhy', 'AT2G48110' => 'ath', 'AT3G23590' => 'ath', 'ATR0626G186' => 'atr', 'ATR1127G141' => 'atr', 'Atru.chr4.2583' => 'acertr', 'Atru.chr5.1358' => 'acertr', 'Atru.chr5.1359' => 'acertr', 'Atru.chr8.46' => 'acertr', 'AUR62002640' => 'cqu', 'AUR62030055' => 'cqu', 'AUR62033713' => 'cqu', 'AUR62033714' => 'cqu', 'AUR62036795' => 'cqu', 'AUR62039891' => 'cqu', 'BcaB02g08737' => 'bca', 'BcaB04g20441' => 'bca', 'BcaB06g26509' => 'bca', 'BcaB06g26510' => 'bca', 'BcaB06g26511' => 'bca', 'BcaB06g26512' => 'bca', 'BcaB06g26513' => 'bca', 'BcaC02g12564' => 'bca', 'BcaC02g12565' => 'bca', 'BcaC02g12794' => 'bca', 'BcaC02g12795' => 'bca', 'BcaC02g12796' => 'bca', 'BcaC06g35541' => 'bca', 'BNapus_Darmor_BZH_scaffold_188p00080' => 'bna', 'BNapus_Darmor_BZH_scaffold_188p00090' => 'bna', 'BolC1t03972H' => 'bol', 'BolC1t03973H' => 'bol', 'BolC4t21680H' => 'bol', 'BolC7t41863H' => 'bol', 'BolSC55t61227H' => 'bol', 'BolSC55t61228H' => 'bol', 'BraA01t03278Z' => 'bra', 'BraA05t18998Z' => 'bra', 'BraA07t28673Z' => 'bra', 'C01p40150' => 'bna', 'C05p12370' => 'bna', 'C07p13680' => 'bna', 'CAN.G1006.16' => 'can', 'CAN.G1006.17' => 'can', 'CAN.G1170.2' => 'can', 'CAN.G962.7' => 'can', 'CANSAT25G2179' => 'cansat', 'CANSAT78G1573' => 'cansat', 'CARHR099510' => 'chi', 'CARHR143510' => 'chi', 'Carub.0003s2380' => 'cru', 'Carub.0004s3082' => 'cru', 'Ca_00614_v3' => 'car', 'Ca_07801_v3' => 'car', 'Ca_08567_v3' => 'car', 'Ca_09571_v3' => 'car', 'CBR_g19290' => 'cbr', 'Cc01_g19770' => 'ccan', 'Cc03_g03030' => 'ccan', 'CDE07G0968' => 'cde', 'CDE09G1441' => 'cde', 'Cfa006103' => 'cfa', 'Cfa015573' => 'cfa', 'Cfa016988' => 'cfa', 'Ciclev10006738m.g' => 'ccl', 'Ciclev10010920m.g' => 'ccl', 'Ciclev10018517m.g' => 'ccl', 'CiPaw.01G159200' => 'cil', 'CiPaw.02G091000' => 'cil', 'CiPaw.02G091100' => 'cil', 'CiPaw.08G103100' => 'cil', 'CiPaw.09G224900' => 'cil', 'ClCG06G005740' => 'cla', 'ClCG07G000090' => 'cla', 'ClCG07G000100' => 'cla', 'COL.COLO4_09143' => 'col', 'COL.COLO4_25124' => 'col', 'Cpa.g.sc16.34' => 'cpa', 'Cpa.g.sc3504.1' => 'cpa', 'Cpa.g.sc60.37' => 'cpa', 'CsaV3_6G018520' => 'csa', 'CsaV3_6G036860' => 'csa', 'CSS0001072' => 'camsi', 'CSS0020208' => 'camsi', 'CSS0021253' => 'camsi', 'CSS0022190' => 'camsi', 'CSS0036150' => 'camsi', 'CSS0040442' => 'camsi', 'CSS0042300' => 'camsi', 'CSS0045298' => 'camsi', 'DCAR_012449' => 'dca', 'DCAR_018405' => 'dca', 'DCAR_024573' => 'dca', 'DCAR_030591' => 'dca', 'Dinv16926' => 'din', 'Dinv32963' => 'din', 'Dinv38382' => 'din', 'Dinv38383' => 'din', 'Duzib133G0974' => 'dzi', 'Duzib138G1867' => 'dzi', 'Duzib211G0420' => 'dzi', 'Duzib212G0930' => 'dzi', 'ECA234G1645' => 'eca', 'ECA247G3467' => 'eca', 'ECA248G1703' => 'eca', 'EL10Ac3g06327' => 'bvu', 'EL10Ac7g17204' => 'bvu', 'Eucgr.A00855' => 'egr', 'Eucgr.A00858' => 'egr', 'Eucgr.H01520' => 'egr', 'Eucgr.H03604' => 'egr', 'Eucgr.L03465' => 'egr', 'Eucgr.L03466' => 'egr', 'FAN01G0988' => 'fan', 'FAN02G3892' => 'fan', 'FAN05G3381' => 'fan', 'FAN07G0967' => 'fan', 'FAN07G1493' => 'fan', 'FAN08G3125' => 'fan', 'FAN09G0402' => 'fan', 'FAN12G2594' => 'fan', 'FAN12G3879' => 'fan', 'FAN14G1546' => 'fan', 'FAN15G3626' => 'fan', 'FAN17G0588' => 'fan', 'FAN17G0609' => 'fan', 'FAN18G2817' => 'fan', 'FAN19G1305' => 'fan', 'FAN20G1787' => 'fan', 'FAN22G0073' => 'fan', 'FAN22G0352' => 'fan', 'FAN22G0368' => 'fan', 'FAN22G2273' => 'fan', 'FAN24G1998' => 'fan', 'FAN27G1317' => 'fan', 'FvH4_2g23980' => 'fve', 'FvH4_4g14380' => 'fve', 'FvH4_4g14390' => 'fve', 'FvH4_6g09250' => 'fve', 'Glyma.03G151100' => 'gma', 'Glyma.04G122550' => 'gma', 'Glyma.05G001600' => 'gma', 'Glyma.09G270766' => 'gma', 'Glyma.09G270832' => 'gma', 'Glyma.13G209800' => 'gma', 'Glyma.15G102800' => 'gma', 'Glyma.18G218900' => 'gma', 'Glyma.19G001500' => 'gma', 'Glyma.19G153600' => 'gma', 'Gohir.A02G028600' => 'ghi', 'Gohir.A08G045000' => 'ghi', 'Gohir.A11G120500' => 'ghi', 'Gohir.A12G006200' => 'ghi', 'Gohir.A12G006250' => 'ghi', 'Gohir.D02G036300' => 'ghi', 'Gohir.D08G054700' => 'ghi', 'Gohir.D11G125600' => 'ghi', 'Gohir.D12G005700' => 'ghi', 'Gorai.004G055200' => 'gra', 'Gorai.005G040400' => 'gra', 'Gorai.007G134500' => 'gra', 'Gorai.008G005500' => 'gra', 'GSVIVG01011094001' => 'vvi', 'GSVIVG01017879001' => 'vvi', 'GSVIVG01025988001' => 'vvi', 'GSVIVG01029847001' => 'vvi', 'HanXRQChr10g0282901' => 'han', 'HanXRQChr10g0310371' => 'han', 'HanXRQChr10g0315041' => 'han', 'HanXRQChr11g0327651' => 'han', 'HanXRQChr12g0359391' => 'han', 'Haze_00972' => 'cav', 'Haze_00973' => 'cav', 'Haze_00974' => 'cav', 'Haze_04747' => 'cav', 'Haze_04749' => 'cav', 'Haze_04750' => 'cav', 'Haze_21217' => 'cav', 'Hma1.2p1_1037F.1_g250680' => 'hma', 'Hma1.2p1_1644F.1_g295320' => 'hma', 'HPP92_011322' => 'vpl', 'HPP92_011323' => 'vpl', 'HPP92_011324' => 'vpl', 'HPP92_011325' => 'vpl', 'HPP92_011326' => 'vpl', 'Hund12205' => 'sun', 'Hund17957' => 'sun', 'Lalb_Chr06g0176771' => 'lal', 'Lalb_Chr18g0056021' => 'lal', 'Lalb_Chr18g0056031' => 'lal', 'Lalb_Chr18g0056041' => 'lal', 'Lalb_Chr20g0107751' => 'lal', 'Lalb_Chr20g0118371' => 'lal', 'Lj1g0010239' => 'lja', 'Lj1g0017101' => 'lja', 'Lj2A1178G40' => 'lonja', 'Lj2A54G84' => 'lonja', 'Lj2g0015248' => 'lja', 'Lj3A761T51' => 'lonja', 'Lj6g0018116' => 'lja', 'Lsat_1_v5_gn_4_136040' => 'lsa', 'Lsat_1_v5_gn_5_187461' => 'lsa', 'Lsat_1_v5_gn_5_77001' => 'lsa', 'Lsat_1_v5_gn_9_4461' => 'lsa', 'Manes.01G210100' => 'mes', 'Manes.03G185600' => 'mes', 'Manes.05G073300' => 'mes', 'Manes.09G120300' => 'mes', 'Manes.15G022100' => 'mes', 'Mapoly0096s0053' => 'mpo', 'MBI03_g14058_MAGBIO' => 'mbi', 'MBI03_g33876_MAGBIO' => 'mbi', 'MBI03_g36854_MAGBIO' => 'mbi', 'MBI17_g11997_MAGBIO' => 'mbi', 'MD03G1269000' => 'mdo', 'MD04G1179600' => 'mdo', 'MD11G1289800' => 'mdo', 'MD12G1194700' => 'mdo', 'MD13G1182100' => 'mdo', 'MD13G1182200' => 'mdo', 'MD16G1182600' => 'mdo', 'Medtr2g021400' => 'mtr', 'Medtr2g021470' => 'mtr', 'Medtr2g105810' => 'mtr', 'Medtr3g033580' => 'mtr', 'Medtr6g007970' => 'mtr', 'Medtr7g056330' => 'mtr', 'Medtr7g074290' => 'mtr', 'Medtr7g074380' => 'mtr', 'Medtr7g094550' => 'mtr', 'Medtr8g069995' => 'mtr', 'MELO3C014345.2' => 'cme', 'MELO3C021395.2' => 'cme', 'Migut.D00262' => 'egut', 'Migut.G00257' => 'egut', 'MSTRG.21575' => 'ama', 'MSTRG.3985' => 'ama', 'Nitab4.5_0000295g0140' => 'nta', 'Nitab4.5_0000732g0140' => 'nta', 'Nitab4.5_0003162g0020' => 'nta', 'Nitab4.5_0006180g0090' => 'nta', 'Nitab4.5_0006390g0010' => 'nta', 'Nitab4.5_0007392g0040' => 'nta', 'Nn1g02140' => 'nnu', 'Nn4g26168' => 'nnu', 'Nn5g26754' => 'nnu', 'Oeu001433.1' => 'oeu', 'Oeu010299.2' => 'oeu', 'Oeu011171.1' => 'oeu', 'Oeu037675.1' => 'oeu', 'Oeu038359.1' => 'oeu', 'Oeu063834.1' => 'oeu', 'Oeu063835.1' => 'oeu', 'Os05g0312000' => 'osa', 'Os07g0211101' => 'osa', 'Os07g0211200' => 'osa', 'Os07g0681500' => 'osa', 'Peaxi162Scf00095g01015' => 'pax', 'Peaxi162Scf00104g00329' => 'pax', 'Peaxi162Scf00161g00137' => 'pax', 'PGR004G1665' => 'pgr', 'PGR031G2937' => 'pgr', 'PGR119G2145' => 'pgr', 'PGSC0003DMG400004351' => 'stu', 'PGSC0003DMG400014625' => 'stu', 'PGSC0003DMG401000943' => 'stu', 'Phvul.001G148600' => 'pvu', 'Phvul.004G001700' => 'pvu', 'Phvul.006G154900' => 'pvu', 'Phvul.008G078200' => 'pvu', 'Phvul.011G136500' => 'pvu', 'Potri.002G215600' => 'ptr', 'Potri.008G201600' => 'ptr', 'Potri.014G138400' => 'ptr', 'Potri.016G142500' => 'ptr', 'Pp3c16_10580' => 'ppa', 'Pp3c5_25280' => 'ppa', 'Prupe.1G150000' => 'ppe', 'Prupe.1G150100' => 'ppe', 'Prupe.6G299600' => 'ppe', 'Prupe.8G245000' => 'ppe', 'Psat0s4927g0040' => 'psa', 'Psat1g052080' => 'psa', 'Psat1g183800' => 'psa', 'Psat3g113840' => 'psa', 'Psat3g126120' => 'psa', 'Psat3g126160' => 'psa', 'Psat3g158760' => 'psa', 'Psat3g158840' => 'psa', 'PSO170G2858' => 'pso', 'PSO339G0606' => 'pso', 'PSO384G4709' => 'pso', 'PSO407G0334' => 'pso', 'QL04p040276' => 'qlo', 'QL06p005458' => 'qlo', 'QL06p005472' => 'qlo', 'QL07p030546' => 'qlo', 'QL07p031519' => 'qlo', 'QL09p050949' => 'qlo', 'QL09p050966' => 'qlo', 'QL09p051067' => 'qlo', 'QL12p022706' => 'qlo', 'RcHm_v2.0_Chr2g0119601' => 'rch', 'RcHm_v2.0_Chr3g0459591' => 'rch', 'RcHm_v2.0_Chr4g0418521' => 'rch', 'RcHm_v2.0_Chr4g0418531' => 'rch', 'RcHm_v2.0_Chr4g0418541' => 'rch', 'RcHm_v2.0_Chr6g0291641' => 'rch', 'Rhsim01G0086300' => 'rsi', 'Rhsim01G0276300' => 'rsi', 'Rhsim01G0276500' => 'rsi', 'Rhsim04G0207700' => 'rsi', 'Rhsim05G0234500' => 'rsi', 'Rhsim13G0022400' => 'rsi', 'Sabra02G0167900' => 'sbr', 'Sabra04G0158500' => 'sbr', 'Sabra08G0159800' => 'sbr', 'Sabra10G0011500' => 'sbr', 'Sabra14G0104400' => 'sbr', 'SalBow2G2440' => 'sbo', 'SalBow4G2265' => 'sbo', 'Sc02g0000060' => 'sci', 'Sc05g0005020' => 'sci', 'Sc13g0003890' => 'sci', 'Sed0014865' => 'sed', 'Sed0017224' => 'sed', 'Sed0026391' => 'sed', 'SEGI_00063' => 'sgi', 'SEGI_10967' => 'sgi', 'SEGI_17510' => 'sgi', 'SEGI_24396' => 'sgi', 'SEGI_39719' => 'sgi', 'SEGI_41392' => 'sgi', 'SGA_v2.0_scaffold11G05794' => 'sas', 'SGA_v2.0_scaffold142G35607' => 'sas', 'SGA_v2.0_scaffold1G00447' => 'sas', 'SHI15388' => 'shi', 'SHI15394' => 'shi', 'SHI15396' => 'shi', 'SHI15399' => 'shi', 'SMO343G0151' => 'smo', 'SMO367G1118' => 'smo', 'Solyc01g080200.3' => 'sly', 'Solyc06g008960.3' => 'sly', 'Solyc09g064780.3' => 'sly', 'Sopen01g031980' => 'spe', 'Sopen06g003710' => 'spe', 'Sopen09g026460' => 'spe', 'Sp3g21240' => 'spa', 'Sp4g30030' => 'spa', 'TAR365G0022' => 'tar', 'TAR365G1023' => 'tar', 'TAR365G1253' => 'tar', 'TAR623G0078' => 'tar', 'TAR623G1721' => 'tar', 'TAR633G0959' => 'tar', 'THA.LOC104802225' => 'tha', 'THA.LOC104804769' => 'tha', 'THA.LOC104808660' => 'tha', 'THA.LOC104812792' => 'tha', 'Thecc.01G284000' => 'tca', 'Thecc.04G220600' => 'tca', 'Thecc.05G268900' => 'tca', 'Thecc.08G171100' => 'tca', 'Thhalv10001284m.g' => 'esa', 'Thhalv10019912m.g' => 'esa', 'TPR.G14189' => 'tpr', 'TPR.G18110' => 'tpr', 'TPR.G18130' => 'tpr', 'TPR.G18131' => 'tpr', 'TPR.G18140' => 'tpr', 'TPR.G24282' => 'tpr', 'TPR.G25221' => 'tpr', 'TPR.G29267' => 'tpr', 'TPR.G35315' => 'tpr', 'TPR.G36173' => 'tpr', 'TWI09G0794' => 'twi', 'TWI59G1348' => 'twi', 'TWI74G0430' => 'twi', 'unitig_26.g8940' => 'ugi', 'unitig_749.g13744' => 'ugi', 'unitig_749.g13745' => 'ugi', 'vmacro08269' => 'vma', 'vmacro14937' => 'vma', 'vmacro20401' => 'vma', 'VMungo0464G1349' => 'vmu', 'VMungo0540G0289' => 'vmu', 'VMungo1215G1590' => 'vmu', 'VMungo1309G0221' => 'vmu', 'VMungo1309G2815' => 'vmu', 'VMungo1383G0239' => 'vmu', 'VMungo1383G2910' => 'vmu', 'Zm00001eb095270' => 'zma', 'Zm00001eb095280' => 'zma', 'Zm00001eb111630' => 'zma', 'Zm00001eb237080' => 'zma', 'Zm00001eb273740' => 'zma', 'Zm00001eb285040' => 'zma', 'Zm00001eb330790' => 'zma', 'Zm00001eb337380' => 'zma' ), 'gf_id' => 'HOM05D001484', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001484' ), 'data_identifier' => 'HOM05D001484', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001484', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p31500' => 'bna', 'A05p00020' => 'bna', 'A07p08820' => 'bna', 'Aa31LG4G3300' => 'aar', 'Aa31LG8G10030' => 'aar', 'Actinidia00731' => 'ach', 'Actinidia11473' => 'ach', 'Actinidia23469' => 'ach', 'Actinidia24318' => 'ach', 'Actinidia40196' => 'ach', 'Actinidia40197' => 'ach', 'Actinidia40198' => 'ach', 'Ah.08g212990' => 'amhyb', 'Ah.15g091720' => 'amhyb', 'AL3G38260' => 'aly', 'AL4G47710' => 'aly', 'Aqoxy2G00671' => 'aox', 'Aqoxy2G03236' => 'aox', 'arahy.Tifrunner.gnm1.ann1.05IDCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KR684' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATY3SJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK6QJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6APGL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IDT7Z9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM073U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ0R87' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LE7RV4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT4QRX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V5ENPK' => 'arhy', 'AT2G48110' => 'ath', 'AT3G23590' => 'ath', 'ATR0626G186' => 'atr', 'ATR1127G141' => 'atr', 'Atru.chr4.2583' => 'acertr', 'Atru.chr5.1358' => 'acertr', 'Atru.chr5.1359' => 'acertr', 'Atru.chr8.46' => 'acertr', 'AUR62002640' => 'cqu', 'AUR62030055' => 'cqu', 'AUR62033713' => 'cqu', 'AUR62033714' => 'cqu', 'AUR62036795' => 'cqu', 'AUR62039891' => 'cqu', 'BcaB02g08737' => 'bca', 'BcaB04g20441' => 'bca', 'BcaB06g26509' => 'bca', 'BcaB06g26510' => 'bca', 'BcaB06g26511' => 'bca', 'BcaB06g26512' => 'bca', 'BcaB06g26513' => 'bca', 'BcaC02g12564' => 'bca', 'BcaC02g12565' => 'bca', 'BcaC02g12794' => 'bca', 'BcaC02g12795' => 'bca', 'BcaC02g12796' => 'bca', 'BcaC06g35541' => 'bca', 'BNapus_Darmor_BZH_scaffold_188p00080' => 'bna', 'BNapus_Darmor_BZH_scaffold_188p00090' => 'bna', 'BolC1t03972H' => 'bol', 'BolC1t03973H' => 'bol', 'BolC4t21680H' => 'bol', 'BolC7t41863H' => 'bol', 'BolSC55t61227H' => 'bol', 'BolSC55t61228H' => 'bol', 'BraA01t03278Z' => 'bra', 'BraA05t18998Z' => 'bra', 'BraA07t28673Z' => 'bra', 'C01p40150' => 'bna', 'C05p12370' => 'bna', 'C07p13680' => 'bna', 'CAN.G1006.16' => 'can', 'CAN.G1006.17' => 'can', 'CAN.G1170.2' => 'can', 'CAN.G962.7' => 'can', 'CANSAT25G2179' => 'cansat', 'CANSAT78G1573' => 'cansat', 'CARHR099510' => 'chi', 'CARHR143510' => 'chi', 'Carub.0003s2380' => 'cru', 'Carub.0004s3082' => 'cru', 'Ca_00614_v3' => 'car', 'Ca_07801_v3' => 'car', 'Ca_08567_v3' => 'car', 'Ca_09571_v3' => 'car', 'CBR_g19290' => 'cbr', 'Cc01_g19770' => 'ccan', 'Cc03_g03030' => 'ccan', 'CDE07G0968' => 'cde', 'CDE09G1441' => 'cde', 'Cfa006103' => 'cfa', 'Cfa015573' => 'cfa', 'Cfa016988' => 'cfa', 'Ciclev10006738m.g' => 'ccl', 'Ciclev10010920m.g' => 'ccl', 'Ciclev10018517m.g' => 'ccl', 'CiPaw.01G159200' => 'cil', 'CiPaw.02G091000' => 'cil', 'CiPaw.02G091100' => 'cil', 'CiPaw.08G103100' => 'cil', 'CiPaw.09G224900' => 'cil', 'ClCG06G005740' => 'cla', 'ClCG07G000090' => 'cla', 'ClCG07G000100' => 'cla', 'COL.COLO4_09143' => 'col', 'COL.COLO4_25124' => 'col', 'Cpa.g.sc16.34' => 'cpa', 'Cpa.g.sc3504.1' => 'cpa', 'Cpa.g.sc60.37' => 'cpa', 'CsaV3_6G018520' => 'csa', 'CsaV3_6G036860' => 'csa', 'CSS0001072' => 'camsi', 'CSS0020208' => 'camsi', 'CSS0021253' => 'camsi', 'CSS0022190' => 'camsi', 'CSS0036150' => 'camsi', 'CSS0040442' => 'camsi', 'CSS0042300' => 'camsi', 'CSS0045298' => 'camsi', 'DCAR_012449' => 'dca', 'DCAR_018405' => 'dca', 'DCAR_024573' => 'dca', 'DCAR_030591' => 'dca', 'Dinv16926' => 'din', 'Dinv32963' => 'din', 'Dinv38382' => 'din', 'Dinv38383' => 'din', 'Duzib133G0974' => 'dzi', 'Duzib138G1867' => 'dzi', 'Duzib211G0420' => 'dzi', 'Duzib212G0930' => 'dzi', 'ECA234G1645' => 'eca', 'ECA247G3467' => 'eca', 'ECA248G1703' => 'eca', 'EL10Ac3g06327' => 'bvu', 'EL10Ac7g17204' => 'bvu', 'Eucgr.A00855' => 'egr', 'Eucgr.A00858' => 'egr', 'Eucgr.H01520' => 'egr', 'Eucgr.H03604' => 'egr', 'Eucgr.L03465' => 'egr', 'Eucgr.L03466' => 'egr', 'FAN01G0988' => 'fan', 'FAN02G3892' => 'fan', 'FAN05G3381' => 'fan', 'FAN07G0967' => 'fan', 'FAN07G1493' => 'fan', 'FAN08G3125' => 'fan', 'FAN09G0402' => 'fan', 'FAN12G2594' => 'fan', 'FAN12G3879' => 'fan', 'FAN14G1546' => 'fan', 'FAN15G3626' => 'fan', 'FAN17G0588' => 'fan', 'FAN17G0609' => 'fan', 'FAN18G2817' => 'fan', 'FAN19G1305' => 'fan', 'FAN20G1787' => 'fan', 'FAN22G0073' => 'fan', 'FAN22G0352' => 'fan', 'FAN22G0368' => 'fan', 'FAN22G2273' => 'fan', 'FAN24G1998' => 'fan', 'FAN27G1317' => 'fan', 'FvH4_2g23980' => 'fve', 'FvH4_4g14380' => 'fve', 'FvH4_4g14390' => 'fve', 'FvH4_6g09250' => 'fve', 'Glyma.03G151100' => 'gma', 'Glyma.04G122550' => 'gma', 'Glyma.05G001600' => 'gma', 'Glyma.09G270766' => 'gma', 'Glyma.09G270832' => 'gma', 'Glyma.13G209800' => 'gma', 'Glyma.15G102800' => 'gma', 'Glyma.18G218900' => 'gma', 'Glyma.19G001500' => 'gma', 'Glyma.19G153600' => 'gma', 'Gohir.A02G028600' => 'ghi', 'Gohir.A08G045000' => 'ghi', 'Gohir.A11G120500' => 'ghi', 'Gohir.A12G006200' => 'ghi', 'Gohir.A12G006250' => 'ghi', 'Gohir.D02G036300' => 'ghi', 'Gohir.D08G054700' => 'ghi', 'Gohir.D11G125600' => 'ghi', 'Gohir.D12G005700' => 'ghi', 'Gorai.004G055200' => 'gra', 'Gorai.005G040400' => 'gra', 'Gorai.007G134500' => 'gra', 'Gorai.008G005500' => 'gra', 'GSVIVG01011094001' => 'vvi', 'GSVIVG01017879001' => 'vvi', 'GSVIVG01025988001' => 'vvi', 'GSVIVG01029847001' => 'vvi', 'HanXRQChr10g0282901' => 'han', 'HanXRQChr10g0310371' => 'han', 'HanXRQChr10g0315041' => 'han', 'HanXRQChr11g0327651' => 'han', 'HanXRQChr12g0359391' => 'han', 'Haze_00972' => 'cav', 'Haze_00973' => 'cav', 'Haze_00974' => 'cav', 'Haze_04747' => 'cav', 'Haze_04749' => 'cav', 'Haze_04750' => 'cav', 'Haze_21217' => 'cav', 'Hma1.2p1_1037F.1_g250680' => 'hma', 'Hma1.2p1_1644F.1_g295320' => 'hma', 'HPP92_011322' => 'vpl', 'HPP92_011323' => 'vpl', 'HPP92_011324' => 'vpl', 'HPP92_011325' => 'vpl', 'HPP92_011326' => 'vpl', 'Hund12205' => 'sun', 'Hund17957' => 'sun', 'Lalb_Chr06g0176771' => 'lal', 'Lalb_Chr18g0056021' => 'lal', 'Lalb_Chr18g0056031' => 'lal', 'Lalb_Chr18g0056041' => 'lal', 'Lalb_Chr20g0107751' => 'lal', 'Lalb_Chr20g0118371' => 'lal', 'Lj1g0010239' => 'lja', 'Lj1g0017101' => 'lja', 'Lj2A1178G40' => 'lonja', 'Lj2A54G84' => 'lonja', 'Lj2g0015248' => 'lja', 'Lj3A761T51' => 'lonja', 'Lj6g0018116' => 'lja', 'Lsat_1_v5_gn_4_136040' => 'lsa', 'Lsat_1_v5_gn_5_187461' => 'lsa', 'Lsat_1_v5_gn_5_77001' => 'lsa', 'Lsat_1_v5_gn_9_4461' => 'lsa', 'Manes.01G210100' => 'mes', 'Manes.03G185600' => 'mes', 'Manes.05G073300' => 'mes', 'Manes.09G120300' => 'mes', 'Manes.15G022100' => 'mes', 'Mapoly0096s0053' => 'mpo', 'MBI03_g14058_MAGBIO' => 'mbi', 'MBI03_g33876_MAGBIO' => 'mbi', 'MBI03_g36854_MAGBIO' => 'mbi', 'MBI17_g11997_MAGBIO' => 'mbi', 'MD03G1269000' => 'mdo', 'MD04G1179600' => 'mdo', 'MD11G1289800' => 'mdo', 'MD12G1194700' => 'mdo', 'MD13G1182100' => 'mdo', 'MD13G1182200' => 'mdo', 'MD16G1182600' => 'mdo', 'Medtr2g021400' => 'mtr', 'Medtr2g021470' => 'mtr', 'Medtr2g105810' => 'mtr', 'Medtr3g033580' => 'mtr', 'Medtr6g007970' => 'mtr', 'Medtr7g056330' => 'mtr', 'Medtr7g074290' => 'mtr', 'Medtr7g074380' => 'mtr', 'Medtr7g094550' => 'mtr', 'Medtr8g069995' => 'mtr', 'MELO3C014345.2' => 'cme', 'MELO3C021395.2' => 'cme', 'Migut.D00262' => 'egut', 'Migut.G00257' => 'egut', 'MSTRG.21575' => 'ama', 'MSTRG.3985' => 'ama', 'Nitab4.5_0000295g0140' => 'nta', 'Nitab4.5_0000732g0140' => 'nta', 'Nitab4.5_0003162g0020' => 'nta', 'Nitab4.5_0006180g0090' => 'nta', 'Nitab4.5_0006390g0010' => 'nta', 'Nitab4.5_0007392g0040' => 'nta', 'Nn1g02140' => 'nnu', 'Nn4g26168' => 'nnu', 'Nn5g26754' => 'nnu', 'Oeu001433.1' => 'oeu', 'Oeu010299.2' => 'oeu', 'Oeu011171.1' => 'oeu', 'Oeu037675.1' => 'oeu', 'Oeu038359.1' => 'oeu', 'Oeu063834.1' => 'oeu', 'Oeu063835.1' => 'oeu', 'Os05g0312000' => 'osa', 'Os07g0211101' => 'osa', 'Os07g0211200' => 'osa', 'Os07g0681500' => 'osa', 'Peaxi162Scf00095g01015' => 'pax', 'Peaxi162Scf00104g00329' => 'pax', 'Peaxi162Scf00161g00137' => 'pax', 'PGR004G1665' => 'pgr', 'PGR031G2937' => 'pgr', 'PGR119G2145' => 'pgr', 'PGSC0003DMG400004351' => 'stu', 'PGSC0003DMG400014625' => 'stu', 'PGSC0003DMG401000943' => 'stu', 'Phvul.001G148600' => 'pvu', 'Phvul.004G001700' => 'pvu', 'Phvul.006G154900' => 'pvu', 'Phvul.008G078200' => 'pvu', 'Phvul.011G136500' => 'pvu', 'Potri.002G215600' => 'ptr', 'Potri.008G201600' => 'ptr', 'Potri.014G138400' => 'ptr', 'Potri.016G142500' => 'ptr', 'Pp3c16_10580' => 'ppa', 'Pp3c5_25280' => 'ppa', 'Prupe.1G150000' => 'ppe', 'Prupe.1G150100' => 'ppe', 'Prupe.6G299600' => 'ppe', 'Prupe.8G245000' => 'ppe', 'Psat0s4927g0040' => 'psa', 'Psat1g052080' => 'psa', 'Psat1g183800' => 'psa', 'Psat3g113840' => 'psa', 'Psat3g126120' => 'psa', 'Psat3g126160' => 'psa', 'Psat3g158760' => 'psa', 'Psat3g158840' => 'psa', 'PSO170G2858' => 'pso', 'PSO339G0606' => 'pso', 'PSO384G4709' => 'pso', 'PSO407G0334' => 'pso', 'QL04p040276' => 'qlo', 'QL06p005458' => 'qlo', 'QL06p005472' => 'qlo', 'QL07p030546' => 'qlo', 'QL07p031519' => 'qlo', 'QL09p050949' => 'qlo', 'QL09p050966' => 'qlo', 'QL09p051067' => 'qlo', 'QL12p022706' => 'qlo', 'RcHm_v2.0_Chr2g0119601' => 'rch', 'RcHm_v2.0_Chr3g0459591' => 'rch', 'RcHm_v2.0_Chr4g0418521' => 'rch', 'RcHm_v2.0_Chr4g0418531' => 'rch', 'RcHm_v2.0_Chr4g0418541' => 'rch', 'RcHm_v2.0_Chr6g0291641' => 'rch', 'Rhsim01G0086300' => 'rsi', 'Rhsim01G0276300' => 'rsi', 'Rhsim01G0276500' => 'rsi', 'Rhsim04G0207700' => 'rsi', 'Rhsim05G0234500' => 'rsi', 'Rhsim13G0022400' => 'rsi', 'Sabra02G0167900' => 'sbr', 'Sabra04G0158500' => 'sbr', 'Sabra08G0159800' => 'sbr', 'Sabra10G0011500' => 'sbr', 'Sabra14G0104400' => 'sbr', 'SalBow2G2440' => 'sbo', 'SalBow4G2265' => 'sbo', 'Sc02g0000060' => 'sci', 'Sc05g0005020' => 'sci', 'Sc13g0003890' => 'sci', 'Sed0014865' => 'sed', 'Sed0017224' => 'sed', 'Sed0026391' => 'sed', 'SEGI_00063' => 'sgi', 'SEGI_10967' => 'sgi', 'SEGI_17510' => 'sgi', 'SEGI_24396' => 'sgi', 'SEGI_39719' => 'sgi', 'SEGI_41392' => 'sgi', 'SGA_v2.0_scaffold11G05794' => 'sas', 'SGA_v2.0_scaffold142G35607' => 'sas', 'SGA_v2.0_scaffold1G00447' => 'sas', 'SHI15388' => 'shi', 'SHI15394' => 'shi', 'SHI15396' => 'shi', 'SHI15399' => 'shi', 'SMO343G0151' => 'smo', 'SMO367G1118' => 'smo', 'Solyc01g080200.3' => 'sly', 'Solyc06g008960.3' => 'sly', 'Solyc09g064780.3' => 'sly', 'Sopen01g031980' => 'spe', 'Sopen06g003710' => 'spe', 'Sopen09g026460' => 'spe', 'Sp3g21240' => 'spa', 'Sp4g30030' => 'spa', 'TAR365G0022' => 'tar', 'TAR365G1023' => 'tar', 'TAR365G1253' => 'tar', 'TAR623G0078' => 'tar', 'TAR623G1721' => 'tar', 'TAR633G0959' => 'tar', 'THA.LOC104802225' => 'tha', 'THA.LOC104804769' => 'tha', 'THA.LOC104808660' => 'tha', 'THA.LOC104812792' => 'tha', 'Thecc.01G284000' => 'tca', 'Thecc.04G220600' => 'tca', 'Thecc.05G268900' => 'tca', 'Thecc.08G171100' => 'tca', 'Thhalv10001284m.g' => 'esa', 'Thhalv10019912m.g' => 'esa', 'TPR.G14189' => 'tpr', 'TPR.G18110' => 'tpr', 'TPR.G18130' => 'tpr', 'TPR.G18131' => 'tpr', 'TPR.G18140' => 'tpr', 'TPR.G24282' => 'tpr', 'TPR.G25221' => 'tpr', 'TPR.G29267' => 'tpr', 'TPR.G35315' => 'tpr', 'TPR.G36173' => 'tpr', 'TWI09G0794' => 'twi', 'TWI59G1348' => 'twi', 'TWI74G0430' => 'twi', 'unitig_26.g8940' => 'ugi', 'unitig_749.g13744' => 'ugi', 'unitig_749.g13745' => 'ugi', 'vmacro08269' => 'vma', 'vmacro14937' => 'vma', 'vmacro20401' => 'vma', 'VMungo0464G1349' => 'vmu', 'VMungo0540G0289' => 'vmu', 'VMungo1215G1590' => 'vmu', 'VMungo1309G0221' => 'vmu', 'VMungo1309G2815' => 'vmu', 'VMungo1383G0239' => 'vmu', 'VMungo1383G2910' => 'vmu', 'Zm00001eb095270' => 'zma', 'Zm00001eb095280' => 'zma', 'Zm00001eb111630' => 'zma', 'Zm00001eb237080' => 'zma', 'Zm00001eb273740' => 'zma', 'Zm00001eb285040' => 'zma', 'Zm00001eb330790' => 'zma', 'Zm00001eb337380' => 'zma' ) $gf_id = 'HOM05D001484' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001484' ) $data_identifier = 'HOM05D001484' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 2, 'aly' => (int) 2, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 22, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 7, 'hma' => (int) 2, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 7, 'mtr' => (int) 10, 'cme' => (int) 2, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 4, 'ppa' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 4, 'qlo' => (int) 9, 'rch' => (int) 6, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 10, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 7, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb337380' $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' => 'HOM05D001484', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p31500' => 'bna', 'A05p00020' => 'bna', 'A07p08820' => 'bna', 'Aa31LG4G3300' => 'aar', 'Aa31LG8G10030' => 'aar', 'Actinidia00731' => 'ach', 'Actinidia11473' => 'ach', 'Actinidia23469' => 'ach', 'Actinidia24318' => 'ach', 'Actinidia40196' => 'ach', 'Actinidia40197' => 'ach', 'Actinidia40198' => 'ach', 'Ah.08g212990' => 'amhyb', 'Ah.15g091720' => 'amhyb', 'AL3G38260' => 'aly', 'AL4G47710' => 'aly', 'Aqoxy2G00671' => 'aox', 'Aqoxy2G03236' => 'aox', 'arahy.Tifrunner.gnm1.ann1.05IDCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KR684' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATY3SJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK6QJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6APGL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IDT7Z9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM073U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ0R87' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LE7RV4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT4QRX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V5ENPK' => 'arhy', 'AT2G48110' => 'ath', 'AT3G23590' => 'ath', 'ATR0626G186' => 'atr', 'ATR1127G141' => 'atr', 'Atru.chr4.2583' => 'acertr', 'Atru.chr5.1358' => 'acertr', 'Atru.chr5.1359' => 'acertr', 'Atru.chr8.46' => 'acertr', 'AUR62002640' => 'cqu', 'AUR62030055' => 'cqu', 'AUR62033713' => 'cqu', 'AUR62033714' => 'cqu', 'AUR62036795' => 'cqu', 'AUR62039891' => 'cqu', 'BcaB02g08737' => 'bca', 'BcaB04g20441' => 'bca', 'BcaB06g26509' => 'bca', 'BcaB06g26510' => 'bca', 'BcaB06g26511' => 'bca', 'BcaB06g26512' => 'bca', 'BcaB06g26513' => 'bca', 'BcaC02g12564' => 'bca', 'BcaC02g12565' => 'bca', 'BcaC02g12794' => 'bca', 'BcaC02g12795' => 'bca', 'BcaC02g12796' => 'bca', 'BcaC06g35541' => 'bca', 'BNapus_Darmor_BZH_scaffold_188p00080' => 'bna', 'BNapus_Darmor_BZH_scaffold_188p00090' => 'bna', 'BolC1t03972H' => 'bol', 'BolC1t03973H' => 'bol', 'BolC4t21680H' => 'bol', 'BolC7t41863H' => 'bol', 'BolSC55t61227H' => 'bol', 'BolSC55t61228H' => 'bol', 'BraA01t03278Z' => 'bra', 'BraA05t18998Z' => 'bra', 'BraA07t28673Z' => 'bra', 'C01p40150' => 'bna', 'C05p12370' => 'bna', 'C07p13680' => 'bna', 'CAN.G1006.16' => 'can', 'CAN.G1006.17' => 'can', 'CAN.G1170.2' => 'can', 'CAN.G962.7' => 'can', 'CANSAT25G2179' => 'cansat', 'CANSAT78G1573' => 'cansat', 'CARHR099510' => 'chi', 'CARHR143510' => 'chi', 'Carub.0003s2380' => 'cru', 'Carub.0004s3082' => 'cru', 'Ca_00614_v3' => 'car', 'Ca_07801_v3' => 'car', 'Ca_08567_v3' => 'car', 'Ca_09571_v3' => 'car', 'CBR_g19290' => 'cbr', 'Cc01_g19770' => 'ccan', 'Cc03_g03030' => 'ccan', 'CDE07G0968' => 'cde', 'CDE09G1441' => 'cde', 'Cfa006103' => 'cfa', 'Cfa015573' => 'cfa', 'Cfa016988' => 'cfa', 'Ciclev10006738m.g' => 'ccl', 'Ciclev10010920m.g' => 'ccl', 'Ciclev10018517m.g' => 'ccl', 'CiPaw.01G159200' => 'cil', 'CiPaw.02G091000' => 'cil', 'CiPaw.02G091100' => 'cil', 'CiPaw.08G103100' => 'cil', 'CiPaw.09G224900' => 'cil', 'ClCG06G005740' => 'cla', 'ClCG07G000090' => 'cla', 'ClCG07G000100' => 'cla', 'COL.COLO4_09143' => 'col', 'COL.COLO4_25124' => 'col', 'Cpa.g.sc16.34' => 'cpa', 'Cpa.g.sc3504.1' => 'cpa', 'Cpa.g.sc60.37' => 'cpa', 'CsaV3_6G018520' => 'csa', 'CsaV3_6G036860' => 'csa', 'CSS0001072' => 'camsi', 'CSS0020208' => 'camsi', 'CSS0021253' => 'camsi', 'CSS0022190' => 'camsi', 'CSS0036150' => 'camsi', 'CSS0040442' => 'camsi', 'CSS0042300' => 'camsi', 'CSS0045298' => 'camsi', 'DCAR_012449' => 'dca', 'DCAR_018405' => 'dca', 'DCAR_024573' => 'dca', 'DCAR_030591' => 'dca', 'Dinv16926' => 'din', 'Dinv32963' => 'din', 'Dinv38382' => 'din', 'Dinv38383' => 'din', 'Duzib133G0974' => 'dzi', 'Duzib138G1867' => 'dzi', 'Duzib211G0420' => 'dzi', 'Duzib212G0930' => 'dzi', 'ECA234G1645' => 'eca', 'ECA247G3467' => 'eca', 'ECA248G1703' => 'eca', 'EL10Ac3g06327' => 'bvu', 'EL10Ac7g17204' => 'bvu', 'Eucgr.A00855' => 'egr', 'Eucgr.A00858' => 'egr', 'Eucgr.H01520' => 'egr', 'Eucgr.H03604' => 'egr', 'Eucgr.L03465' => 'egr', 'Eucgr.L03466' => 'egr', 'FAN01G0988' => 'fan', 'FAN02G3892' => 'fan', 'FAN05G3381' => 'fan', 'FAN07G0967' => 'fan', 'FAN07G1493' => 'fan', 'FAN08G3125' => 'fan', 'FAN09G0402' => 'fan', 'FAN12G2594' => 'fan', 'FAN12G3879' => 'fan', 'FAN14G1546' => 'fan', 'FAN15G3626' => 'fan', 'FAN17G0588' => 'fan', 'FAN17G0609' => 'fan', 'FAN18G2817' => 'fan', 'FAN19G1305' => 'fan', 'FAN20G1787' => 'fan', 'FAN22G0073' => 'fan', 'FAN22G0352' => 'fan', 'FAN22G0368' => 'fan', 'FAN22G2273' => 'fan', 'FAN24G1998' => 'fan', 'FAN27G1317' => 'fan', 'FvH4_2g23980' => 'fve', 'FvH4_4g14380' => 'fve', 'FvH4_4g14390' => 'fve', 'FvH4_6g09250' => 'fve', 'Glyma.03G151100' => 'gma', 'Glyma.04G122550' => 'gma', 'Glyma.05G001600' => 'gma', 'Glyma.09G270766' => 'gma', 'Glyma.09G270832' => 'gma', 'Glyma.13G209800' => 'gma', 'Glyma.15G102800' => 'gma', 'Glyma.18G218900' => 'gma', 'Glyma.19G001500' => 'gma', 'Glyma.19G153600' => 'gma', 'Gohir.A02G028600' => 'ghi', 'Gohir.A08G045000' => 'ghi', 'Gohir.A11G120500' => 'ghi', 'Gohir.A12G006200' => 'ghi', 'Gohir.A12G006250' => 'ghi', 'Gohir.D02G036300' => 'ghi', 'Gohir.D08G054700' => 'ghi', 'Gohir.D11G125600' => 'ghi', 'Gohir.D12G005700' => 'ghi', 'Gorai.004G055200' => 'gra', 'Gorai.005G040400' => 'gra', 'Gorai.007G134500' => 'gra', 'Gorai.008G005500' => 'gra', 'GSVIVG01011094001' => 'vvi', 'GSVIVG01017879001' => 'vvi', 'GSVIVG01025988001' => 'vvi', 'GSVIVG01029847001' => 'vvi', 'HanXRQChr10g0282901' => 'han', 'HanXRQChr10g0310371' => 'han', 'HanXRQChr10g0315041' => 'han', 'HanXRQChr11g0327651' => 'han', 'HanXRQChr12g0359391' => 'han', 'Haze_00972' => 'cav', 'Haze_00973' => 'cav', 'Haze_00974' => 'cav', 'Haze_04747' => 'cav', 'Haze_04749' => 'cav', 'Haze_04750' => 'cav', 'Haze_21217' => 'cav', 'Hma1.2p1_1037F.1_g250680' => 'hma', 'Hma1.2p1_1644F.1_g295320' => 'hma', 'HPP92_011322' => 'vpl', 'HPP92_011323' => 'vpl', 'HPP92_011324' => 'vpl', 'HPP92_011325' => 'vpl', 'HPP92_011326' => 'vpl', 'Hund12205' => 'sun', 'Hund17957' => 'sun', 'Lalb_Chr06g0176771' => 'lal', 'Lalb_Chr18g0056021' => 'lal', 'Lalb_Chr18g0056031' => 'lal', 'Lalb_Chr18g0056041' => 'lal', 'Lalb_Chr20g0107751' => 'lal', 'Lalb_Chr20g0118371' => 'lal', 'Lj1g0010239' => 'lja', 'Lj1g0017101' => 'lja', 'Lj2A1178G40' => 'lonja', 'Lj2A54G84' => 'lonja', 'Lj2g0015248' => 'lja', 'Lj3A761T51' => 'lonja', 'Lj6g0018116' => 'lja', 'Lsat_1_v5_gn_4_136040' => 'lsa', 'Lsat_1_v5_gn_5_187461' => 'lsa', 'Lsat_1_v5_gn_5_77001' => 'lsa', 'Lsat_1_v5_gn_9_4461' => 'lsa', 'Manes.01G210100' => 'mes', 'Manes.03G185600' => 'mes', 'Manes.05G073300' => 'mes', 'Manes.09G120300' => 'mes', 'Manes.15G022100' => 'mes', 'Mapoly0096s0053' => 'mpo', 'MBI03_g14058_MAGBIO' => 'mbi', 'MBI03_g33876_MAGBIO' => 'mbi', 'MBI03_g36854_MAGBIO' => 'mbi', 'MBI17_g11997_MAGBIO' => 'mbi', 'MD03G1269000' => 'mdo', 'MD04G1179600' => 'mdo', 'MD11G1289800' => 'mdo', 'MD12G1194700' => 'mdo', 'MD13G1182100' => 'mdo', 'MD13G1182200' => 'mdo', 'MD16G1182600' => 'mdo', 'Medtr2g021400' => 'mtr', 'Medtr2g021470' => 'mtr', 'Medtr2g105810' => 'mtr', 'Medtr3g033580' => 'mtr', 'Medtr6g007970' => 'mtr', 'Medtr7g056330' => 'mtr', 'Medtr7g074290' => 'mtr', 'Medtr7g074380' => 'mtr', 'Medtr7g094550' => 'mtr', 'Medtr8g069995' => 'mtr', 'MELO3C014345.2' => 'cme', 'MELO3C021395.2' => 'cme', 'Migut.D00262' => 'egut', 'Migut.G00257' => 'egut', 'MSTRG.21575' => 'ama', 'MSTRG.3985' => 'ama', 'Nitab4.5_0000295g0140' => 'nta', 'Nitab4.5_0000732g0140' => 'nta', 'Nitab4.5_0003162g0020' => 'nta', 'Nitab4.5_0006180g0090' => 'nta', 'Nitab4.5_0006390g0010' => 'nta', 'Nitab4.5_0007392g0040' => 'nta', 'Nn1g02140' => 'nnu', 'Nn4g26168' => 'nnu', 'Nn5g26754' => 'nnu', 'Oeu001433.1' => 'oeu', 'Oeu010299.2' => 'oeu', 'Oeu011171.1' => 'oeu', 'Oeu037675.1' => 'oeu', 'Oeu038359.1' => 'oeu', 'Oeu063834.1' => 'oeu', 'Oeu063835.1' => 'oeu', 'Os05g0312000' => 'osa', 'Os07g0211101' => 'osa', 'Os07g0211200' => 'osa', 'Os07g0681500' => 'osa', 'Peaxi162Scf00095g01015' => 'pax', 'Peaxi162Scf00104g00329' => 'pax', 'Peaxi162Scf00161g00137' => 'pax', 'PGR004G1665' => 'pgr', 'PGR031G2937' => 'pgr', 'PGR119G2145' => 'pgr', 'PGSC0003DMG400004351' => 'stu', 'PGSC0003DMG400014625' => 'stu', 'PGSC0003DMG401000943' => 'stu', 'Phvul.001G148600' => 'pvu', 'Phvul.004G001700' => 'pvu', 'Phvul.006G154900' => 'pvu', 'Phvul.008G078200' => 'pvu', 'Phvul.011G136500' => 'pvu', 'Potri.002G215600' => 'ptr', 'Potri.008G201600' => 'ptr', 'Potri.014G138400' => 'ptr', 'Potri.016G142500' => 'ptr', 'Pp3c16_10580' => 'ppa', 'Pp3c5_25280' => 'ppa', 'Prupe.1G150000' => 'ppe', 'Prupe.1G150100' => 'ppe', 'Prupe.6G299600' => 'ppe', 'Prupe.8G245000' => 'ppe', 'Psat0s4927g0040' => 'psa', 'Psat1g052080' => 'psa', 'Psat1g183800' => 'psa', 'Psat3g113840' => 'psa', 'Psat3g126120' => 'psa', 'Psat3g126160' => 'psa', 'Psat3g158760' => 'psa', 'Psat3g158840' => 'psa', 'PSO170G2858' => 'pso', 'PSO339G0606' => 'pso', 'PSO384G4709' => 'pso', 'PSO407G0334' => 'pso', 'QL04p040276' => 'qlo', 'QL06p005458' => 'qlo', 'QL06p005472' => 'qlo', 'QL07p030546' => 'qlo', 'QL07p031519' => 'qlo', 'QL09p050949' => 'qlo', 'QL09p050966' => 'qlo', 'QL09p051067' => 'qlo', 'QL12p022706' => 'qlo', 'RcHm_v2.0_Chr2g0119601' => 'rch', 'RcHm_v2.0_Chr3g0459591' => 'rch', 'RcHm_v2.0_Chr4g0418521' => 'rch', 'RcHm_v2.0_Chr4g0418531' => 'rch', 'RcHm_v2.0_Chr4g0418541' => 'rch', 'RcHm_v2.0_Chr6g0291641' => 'rch', 'Rhsim01G0086300' => 'rsi', 'Rhsim01G0276300' => 'rsi', 'Rhsim01G0276500' => 'rsi', 'Rhsim04G0207700' => 'rsi', 'Rhsim05G0234500' => 'rsi', 'Rhsim13G0022400' => 'rsi', 'Sabra02G0167900' => 'sbr', 'Sabra04G0158500' => 'sbr', 'Sabra08G0159800' => 'sbr', 'Sabra10G0011500' => 'sbr', 'Sabra14G0104400' => 'sbr', 'SalBow2G2440' => 'sbo', 'SalBow4G2265' => 'sbo', 'Sc02g0000060' => 'sci', 'Sc05g0005020' => 'sci', 'Sc13g0003890' => 'sci', 'Sed0014865' => 'sed', 'Sed0017224' => 'sed', 'Sed0026391' => 'sed', 'SEGI_00063' => 'sgi', 'SEGI_10967' => 'sgi', 'SEGI_17510' => 'sgi', 'SEGI_24396' => 'sgi', 'SEGI_39719' => 'sgi', 'SEGI_41392' => 'sgi', 'SGA_v2.0_scaffold11G05794' => 'sas', 'SGA_v2.0_scaffold142G35607' => 'sas', 'SGA_v2.0_scaffold1G00447' => 'sas', 'SHI15388' => 'shi', 'SHI15394' => 'shi', 'SHI15396' => 'shi', 'SHI15399' => 'shi', 'SMO343G0151' => 'smo', 'SMO367G1118' => 'smo', 'Solyc01g080200.3' => 'sly', 'Solyc06g008960.3' => 'sly', 'Solyc09g064780.3' => 'sly', 'Sopen01g031980' => 'spe', 'Sopen06g003710' => 'spe', 'Sopen09g026460' => 'spe', 'Sp3g21240' => 'spa', 'Sp4g30030' => 'spa', 'TAR365G0022' => 'tar', 'TAR365G1023' => 'tar', 'TAR365G1253' => 'tar', 'TAR623G0078' => 'tar', 'TAR623G1721' => 'tar', 'TAR633G0959' => 'tar', 'THA.LOC104802225' => 'tha', 'THA.LOC104804769' => 'tha', 'THA.LOC104808660' => 'tha', 'THA.LOC104812792' => 'tha', 'Thecc.01G284000' => 'tca', 'Thecc.04G220600' => 'tca', 'Thecc.05G268900' => 'tca', 'Thecc.08G171100' => 'tca', 'Thhalv10001284m.g' => 'esa', 'Thhalv10019912m.g' => 'esa', 'TPR.G14189' => 'tpr', 'TPR.G18110' => 'tpr', 'TPR.G18130' => 'tpr', 'TPR.G18131' => 'tpr', 'TPR.G18140' => 'tpr', 'TPR.G24282' => 'tpr', 'TPR.G25221' => 'tpr', 'TPR.G29267' => 'tpr', 'TPR.G35315' => 'tpr', 'TPR.G36173' => 'tpr', 'TWI09G0794' => 'twi', 'TWI59G1348' => 'twi', 'TWI74G0430' => 'twi', 'unitig_26.g8940' => 'ugi', 'unitig_749.g13744' => 'ugi', 'unitig_749.g13745' => 'ugi', 'vmacro08269' => 'vma', 'vmacro14937' => 'vma', 'vmacro20401' => 'vma', 'VMungo0464G1349' => 'vmu', 'VMungo0540G0289' => 'vmu', 'VMungo1215G1590' => 'vmu', 'VMungo1309G0221' => 'vmu', 'VMungo1309G2815' => 'vmu', 'VMungo1383G0239' => 'vmu', 'VMungo1383G2910' => 'vmu', 'Zm00001eb095270' => 'zma', 'Zm00001eb095280' => 'zma', 'Zm00001eb111630' => 'zma', 'Zm00001eb237080' => 'zma', 'Zm00001eb273740' => 'zma', 'Zm00001eb285040' => 'zma', 'Zm00001eb330790' => 'zma', 'Zm00001eb337380' => 'zma' ), 'gf_id' => 'HOM05D001484', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001484' ), 'data_identifier' => 'HOM05D001484', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001484', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p31500' => 'bna', 'A05p00020' => 'bna', 'A07p08820' => 'bna', 'Aa31LG4G3300' => 'aar', 'Aa31LG8G10030' => 'aar', 'Actinidia00731' => 'ach', 'Actinidia11473' => 'ach', 'Actinidia23469' => 'ach', 'Actinidia24318' => 'ach', 'Actinidia40196' => 'ach', 'Actinidia40197' => 'ach', 'Actinidia40198' => 'ach', 'Ah.08g212990' => 'amhyb', 'Ah.15g091720' => 'amhyb', 'AL3G38260' => 'aly', 'AL4G47710' => 'aly', 'Aqoxy2G00671' => 'aox', 'Aqoxy2G03236' => 'aox', 'arahy.Tifrunner.gnm1.ann1.05IDCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KR684' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATY3SJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK6QJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6APGL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IDT7Z9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM073U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ0R87' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LE7RV4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT4QRX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V5ENPK' => 'arhy', 'AT2G48110' => 'ath', 'AT3G23590' => 'ath', 'ATR0626G186' => 'atr', 'ATR1127G141' => 'atr', 'Atru.chr4.2583' => 'acertr', 'Atru.chr5.1358' => 'acertr', 'Atru.chr5.1359' => 'acertr', 'Atru.chr8.46' => 'acertr', 'AUR62002640' => 'cqu', 'AUR62030055' => 'cqu', 'AUR62033713' => 'cqu', 'AUR62033714' => 'cqu', 'AUR62036795' => 'cqu', 'AUR62039891' => 'cqu', 'BcaB02g08737' => 'bca', 'BcaB04g20441' => 'bca', 'BcaB06g26509' => 'bca', 'BcaB06g26510' => 'bca', 'BcaB06g26511' => 'bca', 'BcaB06g26512' => 'bca', 'BcaB06g26513' => 'bca', 'BcaC02g12564' => 'bca', 'BcaC02g12565' => 'bca', 'BcaC02g12794' => 'bca', 'BcaC02g12795' => 'bca', 'BcaC02g12796' => 'bca', 'BcaC06g35541' => 'bca', 'BNapus_Darmor_BZH_scaffold_188p00080' => 'bna', 'BNapus_Darmor_BZH_scaffold_188p00090' => 'bna', 'BolC1t03972H' => 'bol', 'BolC1t03973H' => 'bol', 'BolC4t21680H' => 'bol', 'BolC7t41863H' => 'bol', 'BolSC55t61227H' => 'bol', 'BolSC55t61228H' => 'bol', 'BraA01t03278Z' => 'bra', 'BraA05t18998Z' => 'bra', 'BraA07t28673Z' => 'bra', 'C01p40150' => 'bna', 'C05p12370' => 'bna', 'C07p13680' => 'bna', 'CAN.G1006.16' => 'can', 'CAN.G1006.17' => 'can', 'CAN.G1170.2' => 'can', 'CAN.G962.7' => 'can', 'CANSAT25G2179' => 'cansat', 'CANSAT78G1573' => 'cansat', 'CARHR099510' => 'chi', 'CARHR143510' => 'chi', 'Carub.0003s2380' => 'cru', 'Carub.0004s3082' => 'cru', 'Ca_00614_v3' => 'car', 'Ca_07801_v3' => 'car', 'Ca_08567_v3' => 'car', 'Ca_09571_v3' => 'car', 'CBR_g19290' => 'cbr', 'Cc01_g19770' => 'ccan', 'Cc03_g03030' => 'ccan', 'CDE07G0968' => 'cde', 'CDE09G1441' => 'cde', 'Cfa006103' => 'cfa', 'Cfa015573' => 'cfa', 'Cfa016988' => 'cfa', 'Ciclev10006738m.g' => 'ccl', 'Ciclev10010920m.g' => 'ccl', 'Ciclev10018517m.g' => 'ccl', 'CiPaw.01G159200' => 'cil', 'CiPaw.02G091000' => 'cil', 'CiPaw.02G091100' => 'cil', 'CiPaw.08G103100' => 'cil', 'CiPaw.09G224900' => 'cil', 'ClCG06G005740' => 'cla', 'ClCG07G000090' => 'cla', 'ClCG07G000100' => 'cla', 'COL.COLO4_09143' => 'col', 'COL.COLO4_25124' => 'col', 'Cpa.g.sc16.34' => 'cpa', 'Cpa.g.sc3504.1' => 'cpa', 'Cpa.g.sc60.37' => 'cpa', 'CsaV3_6G018520' => 'csa', 'CsaV3_6G036860' => 'csa', 'CSS0001072' => 'camsi', 'CSS0020208' => 'camsi', 'CSS0021253' => 'camsi', 'CSS0022190' => 'camsi', 'CSS0036150' => 'camsi', 'CSS0040442' => 'camsi', 'CSS0042300' => 'camsi', 'CSS0045298' => 'camsi', 'DCAR_012449' => 'dca', 'DCAR_018405' => 'dca', 'DCAR_024573' => 'dca', 'DCAR_030591' => 'dca', 'Dinv16926' => 'din', 'Dinv32963' => 'din', 'Dinv38382' => 'din', 'Dinv38383' => 'din', 'Duzib133G0974' => 'dzi', 'Duzib138G1867' => 'dzi', 'Duzib211G0420' => 'dzi', 'Duzib212G0930' => 'dzi', 'ECA234G1645' => 'eca', 'ECA247G3467' => 'eca', 'ECA248G1703' => 'eca', 'EL10Ac3g06327' => 'bvu', 'EL10Ac7g17204' => 'bvu', 'Eucgr.A00855' => 'egr', 'Eucgr.A00858' => 'egr', 'Eucgr.H01520' => 'egr', 'Eucgr.H03604' => 'egr', 'Eucgr.L03465' => 'egr', 'Eucgr.L03466' => 'egr', 'FAN01G0988' => 'fan', 'FAN02G3892' => 'fan', 'FAN05G3381' => 'fan', 'FAN07G0967' => 'fan', 'FAN07G1493' => 'fan', 'FAN08G3125' => 'fan', 'FAN09G0402' => 'fan', 'FAN12G2594' => 'fan', 'FAN12G3879' => 'fan', 'FAN14G1546' => 'fan', 'FAN15G3626' => 'fan', 'FAN17G0588' => 'fan', 'FAN17G0609' => 'fan', 'FAN18G2817' => 'fan', 'FAN19G1305' => 'fan', 'FAN20G1787' => 'fan', 'FAN22G0073' => 'fan', 'FAN22G0352' => 'fan', 'FAN22G0368' => 'fan', 'FAN22G2273' => 'fan', 'FAN24G1998' => 'fan', 'FAN27G1317' => 'fan', 'FvH4_2g23980' => 'fve', 'FvH4_4g14380' => 'fve', 'FvH4_4g14390' => 'fve', 'FvH4_6g09250' => 'fve', 'Glyma.03G151100' => 'gma', 'Glyma.04G122550' => 'gma', 'Glyma.05G001600' => 'gma', 'Glyma.09G270766' => 'gma', 'Glyma.09G270832' => 'gma', 'Glyma.13G209800' => 'gma', 'Glyma.15G102800' => 'gma', 'Glyma.18G218900' => 'gma', 'Glyma.19G001500' => 'gma', 'Glyma.19G153600' => 'gma', 'Gohir.A02G028600' => 'ghi', 'Gohir.A08G045000' => 'ghi', 'Gohir.A11G120500' => 'ghi', 'Gohir.A12G006200' => 'ghi', 'Gohir.A12G006250' => 'ghi', 'Gohir.D02G036300' => 'ghi', 'Gohir.D08G054700' => 'ghi', 'Gohir.D11G125600' => 'ghi', 'Gohir.D12G005700' => 'ghi', 'Gorai.004G055200' => 'gra', 'Gorai.005G040400' => 'gra', 'Gorai.007G134500' => 'gra', 'Gorai.008G005500' => 'gra', 'GSVIVG01011094001' => 'vvi', 'GSVIVG01017879001' => 'vvi', 'GSVIVG01025988001' => 'vvi', 'GSVIVG01029847001' => 'vvi', 'HanXRQChr10g0282901' => 'han', 'HanXRQChr10g0310371' => 'han', 'HanXRQChr10g0315041' => 'han', 'HanXRQChr11g0327651' => 'han', 'HanXRQChr12g0359391' => 'han', 'Haze_00972' => 'cav', 'Haze_00973' => 'cav', 'Haze_00974' => 'cav', 'Haze_04747' => 'cav', 'Haze_04749' => 'cav', 'Haze_04750' => 'cav', 'Haze_21217' => 'cav', 'Hma1.2p1_1037F.1_g250680' => 'hma', 'Hma1.2p1_1644F.1_g295320' => 'hma', 'HPP92_011322' => 'vpl', 'HPP92_011323' => 'vpl', 'HPP92_011324' => 'vpl', 'HPP92_011325' => 'vpl', 'HPP92_011326' => 'vpl', 'Hund12205' => 'sun', 'Hund17957' => 'sun', 'Lalb_Chr06g0176771' => 'lal', 'Lalb_Chr18g0056021' => 'lal', 'Lalb_Chr18g0056031' => 'lal', 'Lalb_Chr18g0056041' => 'lal', 'Lalb_Chr20g0107751' => 'lal', 'Lalb_Chr20g0118371' => 'lal', 'Lj1g0010239' => 'lja', 'Lj1g0017101' => 'lja', 'Lj2A1178G40' => 'lonja', 'Lj2A54G84' => 'lonja', 'Lj2g0015248' => 'lja', 'Lj3A761T51' => 'lonja', 'Lj6g0018116' => 'lja', 'Lsat_1_v5_gn_4_136040' => 'lsa', 'Lsat_1_v5_gn_5_187461' => 'lsa', 'Lsat_1_v5_gn_5_77001' => 'lsa', 'Lsat_1_v5_gn_9_4461' => 'lsa', 'Manes.01G210100' => 'mes', 'Manes.03G185600' => 'mes', 'Manes.05G073300' => 'mes', 'Manes.09G120300' => 'mes', 'Manes.15G022100' => 'mes', 'Mapoly0096s0053' => 'mpo', 'MBI03_g14058_MAGBIO' => 'mbi', 'MBI03_g33876_MAGBIO' => 'mbi', 'MBI03_g36854_MAGBIO' => 'mbi', 'MBI17_g11997_MAGBIO' => 'mbi', 'MD03G1269000' => 'mdo', 'MD04G1179600' => 'mdo', 'MD11G1289800' => 'mdo', 'MD12G1194700' => 'mdo', 'MD13G1182100' => 'mdo', 'MD13G1182200' => 'mdo', 'MD16G1182600' => 'mdo', 'Medtr2g021400' => 'mtr', 'Medtr2g021470' => 'mtr', 'Medtr2g105810' => 'mtr', 'Medtr3g033580' => 'mtr', 'Medtr6g007970' => 'mtr', 'Medtr7g056330' => 'mtr', 'Medtr7g074290' => 'mtr', 'Medtr7g074380' => 'mtr', 'Medtr7g094550' => 'mtr', 'Medtr8g069995' => 'mtr', 'MELO3C014345.2' => 'cme', 'MELO3C021395.2' => 'cme', 'Migut.D00262' => 'egut', 'Migut.G00257' => 'egut', 'MSTRG.21575' => 'ama', 'MSTRG.3985' => 'ama', 'Nitab4.5_0000295g0140' => 'nta', 'Nitab4.5_0000732g0140' => 'nta', 'Nitab4.5_0003162g0020' => 'nta', 'Nitab4.5_0006180g0090' => 'nta', 'Nitab4.5_0006390g0010' => 'nta', 'Nitab4.5_0007392g0040' => 'nta', 'Nn1g02140' => 'nnu', 'Nn4g26168' => 'nnu', 'Nn5g26754' => 'nnu', 'Oeu001433.1' => 'oeu', 'Oeu010299.2' => 'oeu', 'Oeu011171.1' => 'oeu', 'Oeu037675.1' => 'oeu', 'Oeu038359.1' => 'oeu', 'Oeu063834.1' => 'oeu', 'Oeu063835.1' => 'oeu', 'Os05g0312000' => 'osa', 'Os07g0211101' => 'osa', 'Os07g0211200' => 'osa', 'Os07g0681500' => 'osa', 'Peaxi162Scf00095g01015' => 'pax', 'Peaxi162Scf00104g00329' => 'pax', 'Peaxi162Scf00161g00137' => 'pax', 'PGR004G1665' => 'pgr', 'PGR031G2937' => 'pgr', 'PGR119G2145' => 'pgr', 'PGSC0003DMG400004351' => 'stu', 'PGSC0003DMG400014625' => 'stu', 'PGSC0003DMG401000943' => 'stu', 'Phvul.001G148600' => 'pvu', 'Phvul.004G001700' => 'pvu', 'Phvul.006G154900' => 'pvu', 'Phvul.008G078200' => 'pvu', 'Phvul.011G136500' => 'pvu', 'Potri.002G215600' => 'ptr', 'Potri.008G201600' => 'ptr', 'Potri.014G138400' => 'ptr', 'Potri.016G142500' => 'ptr', 'Pp3c16_10580' => 'ppa', 'Pp3c5_25280' => 'ppa', 'Prupe.1G150000' => 'ppe', 'Prupe.1G150100' => 'ppe', 'Prupe.6G299600' => 'ppe', 'Prupe.8G245000' => 'ppe', 'Psat0s4927g0040' => 'psa', 'Psat1g052080' => 'psa', 'Psat1g183800' => 'psa', 'Psat3g113840' => 'psa', 'Psat3g126120' => 'psa', 'Psat3g126160' => 'psa', 'Psat3g158760' => 'psa', 'Psat3g158840' => 'psa', 'PSO170G2858' => 'pso', 'PSO339G0606' => 'pso', 'PSO384G4709' => 'pso', 'PSO407G0334' => 'pso', 'QL04p040276' => 'qlo', 'QL06p005458' => 'qlo', 'QL06p005472' => 'qlo', 'QL07p030546' => 'qlo', 'QL07p031519' => 'qlo', 'QL09p050949' => 'qlo', 'QL09p050966' => 'qlo', 'QL09p051067' => 'qlo', 'QL12p022706' => 'qlo', 'RcHm_v2.0_Chr2g0119601' => 'rch', 'RcHm_v2.0_Chr3g0459591' => 'rch', 'RcHm_v2.0_Chr4g0418521' => 'rch', 'RcHm_v2.0_Chr4g0418531' => 'rch', 'RcHm_v2.0_Chr4g0418541' => 'rch', 'RcHm_v2.0_Chr6g0291641' => 'rch', 'Rhsim01G0086300' => 'rsi', 'Rhsim01G0276300' => 'rsi', 'Rhsim01G0276500' => 'rsi', 'Rhsim04G0207700' => 'rsi', 'Rhsim05G0234500' => 'rsi', 'Rhsim13G0022400' => 'rsi', 'Sabra02G0167900' => 'sbr', 'Sabra04G0158500' => 'sbr', 'Sabra08G0159800' => 'sbr', 'Sabra10G0011500' => 'sbr', 'Sabra14G0104400' => 'sbr', 'SalBow2G2440' => 'sbo', 'SalBow4G2265' => 'sbo', 'Sc02g0000060' => 'sci', 'Sc05g0005020' => 'sci', 'Sc13g0003890' => 'sci', 'Sed0014865' => 'sed', 'Sed0017224' => 'sed', 'Sed0026391' => 'sed', 'SEGI_00063' => 'sgi', 'SEGI_10967' => 'sgi', 'SEGI_17510' => 'sgi', 'SEGI_24396' => 'sgi', 'SEGI_39719' => 'sgi', 'SEGI_41392' => 'sgi', 'SGA_v2.0_scaffold11G05794' => 'sas', 'SGA_v2.0_scaffold142G35607' => 'sas', 'SGA_v2.0_scaffold1G00447' => 'sas', 'SHI15388' => 'shi', 'SHI15394' => 'shi', 'SHI15396' => 'shi', 'SHI15399' => 'shi', 'SMO343G0151' => 'smo', 'SMO367G1118' => 'smo', 'Solyc01g080200.3' => 'sly', 'Solyc06g008960.3' => 'sly', 'Solyc09g064780.3' => 'sly', 'Sopen01g031980' => 'spe', 'Sopen06g003710' => 'spe', 'Sopen09g026460' => 'spe', 'Sp3g21240' => 'spa', 'Sp4g30030' => 'spa', 'TAR365G0022' => 'tar', 'TAR365G1023' => 'tar', 'TAR365G1253' => 'tar', 'TAR623G0078' => 'tar', 'TAR623G1721' => 'tar', 'TAR633G0959' => 'tar', 'THA.LOC104802225' => 'tha', 'THA.LOC104804769' => 'tha', 'THA.LOC104808660' => 'tha', 'THA.LOC104812792' => 'tha', 'Thecc.01G284000' => 'tca', 'Thecc.04G220600' => 'tca', 'Thecc.05G268900' => 'tca', 'Thecc.08G171100' => 'tca', 'Thhalv10001284m.g' => 'esa', 'Thhalv10019912m.g' => 'esa', 'TPR.G14189' => 'tpr', 'TPR.G18110' => 'tpr', 'TPR.G18130' => 'tpr', 'TPR.G18131' => 'tpr', 'TPR.G18140' => 'tpr', 'TPR.G24282' => 'tpr', 'TPR.G25221' => 'tpr', 'TPR.G29267' => 'tpr', 'TPR.G35315' => 'tpr', 'TPR.G36173' => 'tpr', 'TWI09G0794' => 'twi', 'TWI59G1348' => 'twi', 'TWI74G0430' => 'twi', 'unitig_26.g8940' => 'ugi', 'unitig_749.g13744' => 'ugi', 'unitig_749.g13745' => 'ugi', 'vmacro08269' => 'vma', 'vmacro14937' => 'vma', 'vmacro20401' => 'vma', 'VMungo0464G1349' => 'vmu', 'VMungo0540G0289' => 'vmu', 'VMungo1215G1590' => 'vmu', 'VMungo1309G0221' => 'vmu', 'VMungo1309G2815' => 'vmu', 'VMungo1383G0239' => 'vmu', 'VMungo1383G2910' => 'vmu', 'Zm00001eb095270' => 'zma', 'Zm00001eb095280' => 'zma', 'Zm00001eb111630' => 'zma', 'Zm00001eb237080' => 'zma', 'Zm00001eb273740' => 'zma', 'Zm00001eb285040' => 'zma', 'Zm00001eb330790' => 'zma', 'Zm00001eb337380' => 'zma' ) $gf_id = 'HOM05D001484' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001484' ) $data_identifier = 'HOM05D001484' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 2, 'aly' => (int) 2, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 22, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 7, 'hma' => (int) 2, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 7, 'mtr' => (int) 10, 'cme' => (int) 2, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 4, 'ppa' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 4, 'qlo' => (int) 9, 'rch' => (int) 6, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 10, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 7, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb337380' $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' => 'HOM05D001484', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p31500' => 'bna', 'A05p00020' => 'bna', 'A07p08820' => 'bna', 'Aa31LG4G3300' => 'aar', 'Aa31LG8G10030' => 'aar', 'Actinidia00731' => 'ach', 'Actinidia11473' => 'ach', 'Actinidia23469' => 'ach', 'Actinidia24318' => 'ach', 'Actinidia40196' => 'ach', 'Actinidia40197' => 'ach', 'Actinidia40198' => 'ach', 'Ah.08g212990' => 'amhyb', 'Ah.15g091720' => 'amhyb', 'AL3G38260' => 'aly', 'AL4G47710' => 'aly', 'Aqoxy2G00671' => 'aox', 'Aqoxy2G03236' => 'aox', 'arahy.Tifrunner.gnm1.ann1.05IDCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KR684' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATY3SJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK6QJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6APGL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IDT7Z9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM073U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ0R87' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LE7RV4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT4QRX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V5ENPK' => 'arhy', 'AT2G48110' => 'ath', 'AT3G23590' => 'ath', 'ATR0626G186' => 'atr', 'ATR1127G141' => 'atr', 'Atru.chr4.2583' => 'acertr', 'Atru.chr5.1358' => 'acertr', 'Atru.chr5.1359' => 'acertr', 'Atru.chr8.46' => 'acertr', 'AUR62002640' => 'cqu', 'AUR62030055' => 'cqu', 'AUR62033713' => 'cqu', 'AUR62033714' => 'cqu', 'AUR62036795' => 'cqu', 'AUR62039891' => 'cqu', 'BcaB02g08737' => 'bca', 'BcaB04g20441' => 'bca', 'BcaB06g26509' => 'bca', 'BcaB06g26510' => 'bca', 'BcaB06g26511' => 'bca', 'BcaB06g26512' => 'bca', 'BcaB06g26513' => 'bca', 'BcaC02g12564' => 'bca', 'BcaC02g12565' => 'bca', 'BcaC02g12794' => 'bca', 'BcaC02g12795' => 'bca', 'BcaC02g12796' => 'bca', 'BcaC06g35541' => 'bca', 'BNapus_Darmor_BZH_scaffold_188p00080' => 'bna', 'BNapus_Darmor_BZH_scaffold_188p00090' => 'bna', 'BolC1t03972H' => 'bol', 'BolC1t03973H' => 'bol', 'BolC4t21680H' => 'bol', 'BolC7t41863H' => 'bol', 'BolSC55t61227H' => 'bol', 'BolSC55t61228H' => 'bol', 'BraA01t03278Z' => 'bra', 'BraA05t18998Z' => 'bra', 'BraA07t28673Z' => 'bra', 'C01p40150' => 'bna', 'C05p12370' => 'bna', 'C07p13680' => 'bna', 'CAN.G1006.16' => 'can', 'CAN.G1006.17' => 'can', 'CAN.G1170.2' => 'can', 'CAN.G962.7' => 'can', 'CANSAT25G2179' => 'cansat', 'CANSAT78G1573' => 'cansat', 'CARHR099510' => 'chi', 'CARHR143510' => 'chi', 'Carub.0003s2380' => 'cru', 'Carub.0004s3082' => 'cru', 'Ca_00614_v3' => 'car', 'Ca_07801_v3' => 'car', 'Ca_08567_v3' => 'car', 'Ca_09571_v3' => 'car', 'CBR_g19290' => 'cbr', 'Cc01_g19770' => 'ccan', 'Cc03_g03030' => 'ccan', 'CDE07G0968' => 'cde', 'CDE09G1441' => 'cde', 'Cfa006103' => 'cfa', 'Cfa015573' => 'cfa', 'Cfa016988' => 'cfa', 'Ciclev10006738m.g' => 'ccl', 'Ciclev10010920m.g' => 'ccl', 'Ciclev10018517m.g' => 'ccl', 'CiPaw.01G159200' => 'cil', 'CiPaw.02G091000' => 'cil', 'CiPaw.02G091100' => 'cil', 'CiPaw.08G103100' => 'cil', 'CiPaw.09G224900' => 'cil', 'ClCG06G005740' => 'cla', 'ClCG07G000090' => 'cla', 'ClCG07G000100' => 'cla', 'COL.COLO4_09143' => 'col', 'COL.COLO4_25124' => 'col', 'Cpa.g.sc16.34' => 'cpa', 'Cpa.g.sc3504.1' => 'cpa', 'Cpa.g.sc60.37' => 'cpa', 'CsaV3_6G018520' => 'csa', 'CsaV3_6G036860' => 'csa', 'CSS0001072' => 'camsi', 'CSS0020208' => 'camsi', 'CSS0021253' => 'camsi', 'CSS0022190' => 'camsi', 'CSS0036150' => 'camsi', 'CSS0040442' => 'camsi', 'CSS0042300' => 'camsi', 'CSS0045298' => 'camsi', 'DCAR_012449' => 'dca', 'DCAR_018405' => 'dca', 'DCAR_024573' => 'dca', 'DCAR_030591' => 'dca', 'Dinv16926' => 'din', 'Dinv32963' => 'din', 'Dinv38382' => 'din', 'Dinv38383' => 'din', 'Duzib133G0974' => 'dzi', 'Duzib138G1867' => 'dzi', 'Duzib211G0420' => 'dzi', 'Duzib212G0930' => 'dzi', 'ECA234G1645' => 'eca', 'ECA247G3467' => 'eca', 'ECA248G1703' => 'eca', 'EL10Ac3g06327' => 'bvu', 'EL10Ac7g17204' => 'bvu', 'Eucgr.A00855' => 'egr', 'Eucgr.A00858' => 'egr', 'Eucgr.H01520' => 'egr', 'Eucgr.H03604' => 'egr', 'Eucgr.L03465' => 'egr', 'Eucgr.L03466' => 'egr', 'FAN01G0988' => 'fan', 'FAN02G3892' => 'fan', 'FAN05G3381' => 'fan', 'FAN07G0967' => 'fan', 'FAN07G1493' => 'fan', 'FAN08G3125' => 'fan', 'FAN09G0402' => 'fan', 'FAN12G2594' => 'fan', 'FAN12G3879' => 'fan', 'FAN14G1546' => 'fan', 'FAN15G3626' => 'fan', 'FAN17G0588' => 'fan', 'FAN17G0609' => 'fan', 'FAN18G2817' => 'fan', 'FAN19G1305' => 'fan', 'FAN20G1787' => 'fan', 'FAN22G0073' => 'fan', 'FAN22G0352' => 'fan', 'FAN22G0368' => 'fan', 'FAN22G2273' => 'fan', 'FAN24G1998' => 'fan', 'FAN27G1317' => 'fan', 'FvH4_2g23980' => 'fve', 'FvH4_4g14380' => 'fve', 'FvH4_4g14390' => 'fve', 'FvH4_6g09250' => 'fve', 'Glyma.03G151100' => 'gma', 'Glyma.04G122550' => 'gma', 'Glyma.05G001600' => 'gma', 'Glyma.09G270766' => 'gma', 'Glyma.09G270832' => 'gma', 'Glyma.13G209800' => 'gma', 'Glyma.15G102800' => 'gma', 'Glyma.18G218900' => 'gma', 'Glyma.19G001500' => 'gma', 'Glyma.19G153600' => 'gma', 'Gohir.A02G028600' => 'ghi', 'Gohir.A08G045000' => 'ghi', 'Gohir.A11G120500' => 'ghi', 'Gohir.A12G006200' => 'ghi', 'Gohir.A12G006250' => 'ghi', 'Gohir.D02G036300' => 'ghi', 'Gohir.D08G054700' => 'ghi', 'Gohir.D11G125600' => 'ghi', 'Gohir.D12G005700' => 'ghi', 'Gorai.004G055200' => 'gra', 'Gorai.005G040400' => 'gra', 'Gorai.007G134500' => 'gra', 'Gorai.008G005500' => 'gra', 'GSVIVG01011094001' => 'vvi', 'GSVIVG01017879001' => 'vvi', 'GSVIVG01025988001' => 'vvi', 'GSVIVG01029847001' => 'vvi', 'HanXRQChr10g0282901' => 'han', 'HanXRQChr10g0310371' => 'han', 'HanXRQChr10g0315041' => 'han', 'HanXRQChr11g0327651' => 'han', 'HanXRQChr12g0359391' => 'han', 'Haze_00972' => 'cav', 'Haze_00973' => 'cav', 'Haze_00974' => 'cav', 'Haze_04747' => 'cav', 'Haze_04749' => 'cav', 'Haze_04750' => 'cav', 'Haze_21217' => 'cav', 'Hma1.2p1_1037F.1_g250680' => 'hma', 'Hma1.2p1_1644F.1_g295320' => 'hma', 'HPP92_011322' => 'vpl', 'HPP92_011323' => 'vpl', 'HPP92_011324' => 'vpl', 'HPP92_011325' => 'vpl', 'HPP92_011326' => 'vpl', 'Hund12205' => 'sun', 'Hund17957' => 'sun', 'Lalb_Chr06g0176771' => 'lal', 'Lalb_Chr18g0056021' => 'lal', 'Lalb_Chr18g0056031' => 'lal', 'Lalb_Chr18g0056041' => 'lal', 'Lalb_Chr20g0107751' => 'lal', 'Lalb_Chr20g0118371' => 'lal', 'Lj1g0010239' => 'lja', 'Lj1g0017101' => 'lja', 'Lj2A1178G40' => 'lonja', 'Lj2A54G84' => 'lonja', 'Lj2g0015248' => 'lja', 'Lj3A761T51' => 'lonja', 'Lj6g0018116' => 'lja', 'Lsat_1_v5_gn_4_136040' => 'lsa', 'Lsat_1_v5_gn_5_187461' => 'lsa', 'Lsat_1_v5_gn_5_77001' => 'lsa', 'Lsat_1_v5_gn_9_4461' => 'lsa', 'Manes.01G210100' => 'mes', 'Manes.03G185600' => 'mes', 'Manes.05G073300' => 'mes', 'Manes.09G120300' => 'mes', 'Manes.15G022100' => 'mes', 'Mapoly0096s0053' => 'mpo', 'MBI03_g14058_MAGBIO' => 'mbi', 'MBI03_g33876_MAGBIO' => 'mbi', 'MBI03_g36854_MAGBIO' => 'mbi', 'MBI17_g11997_MAGBIO' => 'mbi', 'MD03G1269000' => 'mdo', 'MD04G1179600' => 'mdo', 'MD11G1289800' => 'mdo', 'MD12G1194700' => 'mdo', 'MD13G1182100' => 'mdo', 'MD13G1182200' => 'mdo', 'MD16G1182600' => 'mdo', 'Medtr2g021400' => 'mtr', 'Medtr2g021470' => 'mtr', 'Medtr2g105810' => 'mtr', 'Medtr3g033580' => 'mtr', 'Medtr6g007970' => 'mtr', 'Medtr7g056330' => 'mtr', 'Medtr7g074290' => 'mtr', 'Medtr7g074380' => 'mtr', 'Medtr7g094550' => 'mtr', 'Medtr8g069995' => 'mtr', 'MELO3C014345.2' => 'cme', 'MELO3C021395.2' => 'cme', 'Migut.D00262' => 'egut', 'Migut.G00257' => 'egut', 'MSTRG.21575' => 'ama', 'MSTRG.3985' => 'ama', 'Nitab4.5_0000295g0140' => 'nta', 'Nitab4.5_0000732g0140' => 'nta', 'Nitab4.5_0003162g0020' => 'nta', 'Nitab4.5_0006180g0090' => 'nta', 'Nitab4.5_0006390g0010' => 'nta', 'Nitab4.5_0007392g0040' => 'nta', 'Nn1g02140' => 'nnu', 'Nn4g26168' => 'nnu', 'Nn5g26754' => 'nnu', 'Oeu001433.1' => 'oeu', 'Oeu010299.2' => 'oeu', 'Oeu011171.1' => 'oeu', 'Oeu037675.1' => 'oeu', 'Oeu038359.1' => 'oeu', 'Oeu063834.1' => 'oeu', 'Oeu063835.1' => 'oeu', 'Os05g0312000' => 'osa', 'Os07g0211101' => 'osa', 'Os07g0211200' => 'osa', 'Os07g0681500' => 'osa', 'Peaxi162Scf00095g01015' => 'pax', 'Peaxi162Scf00104g00329' => 'pax', 'Peaxi162Scf00161g00137' => 'pax', 'PGR004G1665' => 'pgr', 'PGR031G2937' => 'pgr', 'PGR119G2145' => 'pgr', 'PGSC0003DMG400004351' => 'stu', 'PGSC0003DMG400014625' => 'stu', 'PGSC0003DMG401000943' => 'stu', 'Phvul.001G148600' => 'pvu', 'Phvul.004G001700' => 'pvu', 'Phvul.006G154900' => 'pvu', 'Phvul.008G078200' => 'pvu', 'Phvul.011G136500' => 'pvu', 'Potri.002G215600' => 'ptr', 'Potri.008G201600' => 'ptr', 'Potri.014G138400' => 'ptr', 'Potri.016G142500' => 'ptr', 'Pp3c16_10580' => 'ppa', 'Pp3c5_25280' => 'ppa', 'Prupe.1G150000' => 'ppe', 'Prupe.1G150100' => 'ppe', 'Prupe.6G299600' => 'ppe', 'Prupe.8G245000' => 'ppe', 'Psat0s4927g0040' => 'psa', 'Psat1g052080' => 'psa', 'Psat1g183800' => 'psa', 'Psat3g113840' => 'psa', 'Psat3g126120' => 'psa', 'Psat3g126160' => 'psa', 'Psat3g158760' => 'psa', 'Psat3g158840' => 'psa', 'PSO170G2858' => 'pso', 'PSO339G0606' => 'pso', 'PSO384G4709' => 'pso', 'PSO407G0334' => 'pso', 'QL04p040276' => 'qlo', 'QL06p005458' => 'qlo', 'QL06p005472' => 'qlo', 'QL07p030546' => 'qlo', 'QL07p031519' => 'qlo', 'QL09p050949' => 'qlo', 'QL09p050966' => 'qlo', 'QL09p051067' => 'qlo', 'QL12p022706' => 'qlo', 'RcHm_v2.0_Chr2g0119601' => 'rch', 'RcHm_v2.0_Chr3g0459591' => 'rch', 'RcHm_v2.0_Chr4g0418521' => 'rch', 'RcHm_v2.0_Chr4g0418531' => 'rch', 'RcHm_v2.0_Chr4g0418541' => 'rch', 'RcHm_v2.0_Chr6g0291641' => 'rch', 'Rhsim01G0086300' => 'rsi', 'Rhsim01G0276300' => 'rsi', 'Rhsim01G0276500' => 'rsi', 'Rhsim04G0207700' => 'rsi', 'Rhsim05G0234500' => 'rsi', 'Rhsim13G0022400' => 'rsi', 'Sabra02G0167900' => 'sbr', 'Sabra04G0158500' => 'sbr', 'Sabra08G0159800' => 'sbr', 'Sabra10G0011500' => 'sbr', 'Sabra14G0104400' => 'sbr', 'SalBow2G2440' => 'sbo', 'SalBow4G2265' => 'sbo', 'Sc02g0000060' => 'sci', 'Sc05g0005020' => 'sci', 'Sc13g0003890' => 'sci', 'Sed0014865' => 'sed', 'Sed0017224' => 'sed', 'Sed0026391' => 'sed', 'SEGI_00063' => 'sgi', 'SEGI_10967' => 'sgi', 'SEGI_17510' => 'sgi', 'SEGI_24396' => 'sgi', 'SEGI_39719' => 'sgi', 'SEGI_41392' => 'sgi', 'SGA_v2.0_scaffold11G05794' => 'sas', 'SGA_v2.0_scaffold142G35607' => 'sas', 'SGA_v2.0_scaffold1G00447' => 'sas', 'SHI15388' => 'shi', 'SHI15394' => 'shi', 'SHI15396' => 'shi', 'SHI15399' => 'shi', 'SMO343G0151' => 'smo', 'SMO367G1118' => 'smo', 'Solyc01g080200.3' => 'sly', 'Solyc06g008960.3' => 'sly', 'Solyc09g064780.3' => 'sly', 'Sopen01g031980' => 'spe', 'Sopen06g003710' => 'spe', 'Sopen09g026460' => 'spe', 'Sp3g21240' => 'spa', 'Sp4g30030' => 'spa', 'TAR365G0022' => 'tar', 'TAR365G1023' => 'tar', 'TAR365G1253' => 'tar', 'TAR623G0078' => 'tar', 'TAR623G1721' => 'tar', 'TAR633G0959' => 'tar', 'THA.LOC104802225' => 'tha', 'THA.LOC104804769' => 'tha', 'THA.LOC104808660' => 'tha', 'THA.LOC104812792' => 'tha', 'Thecc.01G284000' => 'tca', 'Thecc.04G220600' => 'tca', 'Thecc.05G268900' => 'tca', 'Thecc.08G171100' => 'tca', 'Thhalv10001284m.g' => 'esa', 'Thhalv10019912m.g' => 'esa', 'TPR.G14189' => 'tpr', 'TPR.G18110' => 'tpr', 'TPR.G18130' => 'tpr', 'TPR.G18131' => 'tpr', 'TPR.G18140' => 'tpr', 'TPR.G24282' => 'tpr', 'TPR.G25221' => 'tpr', 'TPR.G29267' => 'tpr', 'TPR.G35315' => 'tpr', 'TPR.G36173' => 'tpr', 'TWI09G0794' => 'twi', 'TWI59G1348' => 'twi', 'TWI74G0430' => 'twi', 'unitig_26.g8940' => 'ugi', 'unitig_749.g13744' => 'ugi', 'unitig_749.g13745' => 'ugi', 'vmacro08269' => 'vma', 'vmacro14937' => 'vma', 'vmacro20401' => 'vma', 'VMungo0464G1349' => 'vmu', 'VMungo0540G0289' => 'vmu', 'VMungo1215G1590' => 'vmu', 'VMungo1309G0221' => 'vmu', 'VMungo1309G2815' => 'vmu', 'VMungo1383G0239' => 'vmu', 'VMungo1383G2910' => 'vmu', 'Zm00001eb095270' => 'zma', 'Zm00001eb095280' => 'zma', 'Zm00001eb111630' => 'zma', 'Zm00001eb237080' => 'zma', 'Zm00001eb273740' => 'zma', 'Zm00001eb285040' => 'zma', 'Zm00001eb330790' => 'zma', 'Zm00001eb337380' => 'zma' ), 'gf_id' => 'HOM05D001484', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001484' ), 'data_identifier' => 'HOM05D001484', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001484', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p31500' => 'bna', 'A05p00020' => 'bna', 'A07p08820' => 'bna', 'Aa31LG4G3300' => 'aar', 'Aa31LG8G10030' => 'aar', 'Actinidia00731' => 'ach', 'Actinidia11473' => 'ach', 'Actinidia23469' => 'ach', 'Actinidia24318' => 'ach', 'Actinidia40196' => 'ach', 'Actinidia40197' => 'ach', 'Actinidia40198' => 'ach', 'Ah.08g212990' => 'amhyb', 'Ah.15g091720' => 'amhyb', 'AL3G38260' => 'aly', 'AL4G47710' => 'aly', 'Aqoxy2G00671' => 'aox', 'Aqoxy2G03236' => 'aox', 'arahy.Tifrunner.gnm1.ann1.05IDCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KR684' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATY3SJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK6QJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6APGL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IDT7Z9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM073U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ0R87' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LE7RV4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT4QRX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V5ENPK' => 'arhy', 'AT2G48110' => 'ath', 'AT3G23590' => 'ath', 'ATR0626G186' => 'atr', 'ATR1127G141' => 'atr', 'Atru.chr4.2583' => 'acertr', 'Atru.chr5.1358' => 'acertr', 'Atru.chr5.1359' => 'acertr', 'Atru.chr8.46' => 'acertr', 'AUR62002640' => 'cqu', 'AUR62030055' => 'cqu', 'AUR62033713' => 'cqu', 'AUR62033714' => 'cqu', 'AUR62036795' => 'cqu', 'AUR62039891' => 'cqu', 'BcaB02g08737' => 'bca', 'BcaB04g20441' => 'bca', 'BcaB06g26509' => 'bca', 'BcaB06g26510' => 'bca', 'BcaB06g26511' => 'bca', 'BcaB06g26512' => 'bca', 'BcaB06g26513' => 'bca', 'BcaC02g12564' => 'bca', 'BcaC02g12565' => 'bca', 'BcaC02g12794' => 'bca', 'BcaC02g12795' => 'bca', 'BcaC02g12796' => 'bca', 'BcaC06g35541' => 'bca', 'BNapus_Darmor_BZH_scaffold_188p00080' => 'bna', 'BNapus_Darmor_BZH_scaffold_188p00090' => 'bna', 'BolC1t03972H' => 'bol', 'BolC1t03973H' => 'bol', 'BolC4t21680H' => 'bol', 'BolC7t41863H' => 'bol', 'BolSC55t61227H' => 'bol', 'BolSC55t61228H' => 'bol', 'BraA01t03278Z' => 'bra', 'BraA05t18998Z' => 'bra', 'BraA07t28673Z' => 'bra', 'C01p40150' => 'bna', 'C05p12370' => 'bna', 'C07p13680' => 'bna', 'CAN.G1006.16' => 'can', 'CAN.G1006.17' => 'can', 'CAN.G1170.2' => 'can', 'CAN.G962.7' => 'can', 'CANSAT25G2179' => 'cansat', 'CANSAT78G1573' => 'cansat', 'CARHR099510' => 'chi', 'CARHR143510' => 'chi', 'Carub.0003s2380' => 'cru', 'Carub.0004s3082' => 'cru', 'Ca_00614_v3' => 'car', 'Ca_07801_v3' => 'car', 'Ca_08567_v3' => 'car', 'Ca_09571_v3' => 'car', 'CBR_g19290' => 'cbr', 'Cc01_g19770' => 'ccan', 'Cc03_g03030' => 'ccan', 'CDE07G0968' => 'cde', 'CDE09G1441' => 'cde', 'Cfa006103' => 'cfa', 'Cfa015573' => 'cfa', 'Cfa016988' => 'cfa', 'Ciclev10006738m.g' => 'ccl', 'Ciclev10010920m.g' => 'ccl', 'Ciclev10018517m.g' => 'ccl', 'CiPaw.01G159200' => 'cil', 'CiPaw.02G091000' => 'cil', 'CiPaw.02G091100' => 'cil', 'CiPaw.08G103100' => 'cil', 'CiPaw.09G224900' => 'cil', 'ClCG06G005740' => 'cla', 'ClCG07G000090' => 'cla', 'ClCG07G000100' => 'cla', 'COL.COLO4_09143' => 'col', 'COL.COLO4_25124' => 'col', 'Cpa.g.sc16.34' => 'cpa', 'Cpa.g.sc3504.1' => 'cpa', 'Cpa.g.sc60.37' => 'cpa', 'CsaV3_6G018520' => 'csa', 'CsaV3_6G036860' => 'csa', 'CSS0001072' => 'camsi', 'CSS0020208' => 'camsi', 'CSS0021253' => 'camsi', 'CSS0022190' => 'camsi', 'CSS0036150' => 'camsi', 'CSS0040442' => 'camsi', 'CSS0042300' => 'camsi', 'CSS0045298' => 'camsi', 'DCAR_012449' => 'dca', 'DCAR_018405' => 'dca', 'DCAR_024573' => 'dca', 'DCAR_030591' => 'dca', 'Dinv16926' => 'din', 'Dinv32963' => 'din', 'Dinv38382' => 'din', 'Dinv38383' => 'din', 'Duzib133G0974' => 'dzi', 'Duzib138G1867' => 'dzi', 'Duzib211G0420' => 'dzi', 'Duzib212G0930' => 'dzi', 'ECA234G1645' => 'eca', 'ECA247G3467' => 'eca', 'ECA248G1703' => 'eca', 'EL10Ac3g06327' => 'bvu', 'EL10Ac7g17204' => 'bvu', 'Eucgr.A00855' => 'egr', 'Eucgr.A00858' => 'egr', 'Eucgr.H01520' => 'egr', 'Eucgr.H03604' => 'egr', 'Eucgr.L03465' => 'egr', 'Eucgr.L03466' => 'egr', 'FAN01G0988' => 'fan', 'FAN02G3892' => 'fan', 'FAN05G3381' => 'fan', 'FAN07G0967' => 'fan', 'FAN07G1493' => 'fan', 'FAN08G3125' => 'fan', 'FAN09G0402' => 'fan', 'FAN12G2594' => 'fan', 'FAN12G3879' => 'fan', 'FAN14G1546' => 'fan', 'FAN15G3626' => 'fan', 'FAN17G0588' => 'fan', 'FAN17G0609' => 'fan', 'FAN18G2817' => 'fan', 'FAN19G1305' => 'fan', 'FAN20G1787' => 'fan', 'FAN22G0073' => 'fan', 'FAN22G0352' => 'fan', 'FAN22G0368' => 'fan', 'FAN22G2273' => 'fan', 'FAN24G1998' => 'fan', 'FAN27G1317' => 'fan', 'FvH4_2g23980' => 'fve', 'FvH4_4g14380' => 'fve', 'FvH4_4g14390' => 'fve', 'FvH4_6g09250' => 'fve', 'Glyma.03G151100' => 'gma', 'Glyma.04G122550' => 'gma', 'Glyma.05G001600' => 'gma', 'Glyma.09G270766' => 'gma', 'Glyma.09G270832' => 'gma', 'Glyma.13G209800' => 'gma', 'Glyma.15G102800' => 'gma', 'Glyma.18G218900' => 'gma', 'Glyma.19G001500' => 'gma', 'Glyma.19G153600' => 'gma', 'Gohir.A02G028600' => 'ghi', 'Gohir.A08G045000' => 'ghi', 'Gohir.A11G120500' => 'ghi', 'Gohir.A12G006200' => 'ghi', 'Gohir.A12G006250' => 'ghi', 'Gohir.D02G036300' => 'ghi', 'Gohir.D08G054700' => 'ghi', 'Gohir.D11G125600' => 'ghi', 'Gohir.D12G005700' => 'ghi', 'Gorai.004G055200' => 'gra', 'Gorai.005G040400' => 'gra', 'Gorai.007G134500' => 'gra', 'Gorai.008G005500' => 'gra', 'GSVIVG01011094001' => 'vvi', 'GSVIVG01017879001' => 'vvi', 'GSVIVG01025988001' => 'vvi', 'GSVIVG01029847001' => 'vvi', 'HanXRQChr10g0282901' => 'han', 'HanXRQChr10g0310371' => 'han', 'HanXRQChr10g0315041' => 'han', 'HanXRQChr11g0327651' => 'han', 'HanXRQChr12g0359391' => 'han', 'Haze_00972' => 'cav', 'Haze_00973' => 'cav', 'Haze_00974' => 'cav', 'Haze_04747' => 'cav', 'Haze_04749' => 'cav', 'Haze_04750' => 'cav', 'Haze_21217' => 'cav', 'Hma1.2p1_1037F.1_g250680' => 'hma', 'Hma1.2p1_1644F.1_g295320' => 'hma', 'HPP92_011322' => 'vpl', 'HPP92_011323' => 'vpl', 'HPP92_011324' => 'vpl', 'HPP92_011325' => 'vpl', 'HPP92_011326' => 'vpl', 'Hund12205' => 'sun', 'Hund17957' => 'sun', 'Lalb_Chr06g0176771' => 'lal', 'Lalb_Chr18g0056021' => 'lal', 'Lalb_Chr18g0056031' => 'lal', 'Lalb_Chr18g0056041' => 'lal', 'Lalb_Chr20g0107751' => 'lal', 'Lalb_Chr20g0118371' => 'lal', 'Lj1g0010239' => 'lja', 'Lj1g0017101' => 'lja', 'Lj2A1178G40' => 'lonja', 'Lj2A54G84' => 'lonja', 'Lj2g0015248' => 'lja', 'Lj3A761T51' => 'lonja', 'Lj6g0018116' => 'lja', 'Lsat_1_v5_gn_4_136040' => 'lsa', 'Lsat_1_v5_gn_5_187461' => 'lsa', 'Lsat_1_v5_gn_5_77001' => 'lsa', 'Lsat_1_v5_gn_9_4461' => 'lsa', 'Manes.01G210100' => 'mes', 'Manes.03G185600' => 'mes', 'Manes.05G073300' => 'mes', 'Manes.09G120300' => 'mes', 'Manes.15G022100' => 'mes', 'Mapoly0096s0053' => 'mpo', 'MBI03_g14058_MAGBIO' => 'mbi', 'MBI03_g33876_MAGBIO' => 'mbi', 'MBI03_g36854_MAGBIO' => 'mbi', 'MBI17_g11997_MAGBIO' => 'mbi', 'MD03G1269000' => 'mdo', 'MD04G1179600' => 'mdo', 'MD11G1289800' => 'mdo', 'MD12G1194700' => 'mdo', 'MD13G1182100' => 'mdo', 'MD13G1182200' => 'mdo', 'MD16G1182600' => 'mdo', 'Medtr2g021400' => 'mtr', 'Medtr2g021470' => 'mtr', 'Medtr2g105810' => 'mtr', 'Medtr3g033580' => 'mtr', 'Medtr6g007970' => 'mtr', 'Medtr7g056330' => 'mtr', 'Medtr7g074290' => 'mtr', 'Medtr7g074380' => 'mtr', 'Medtr7g094550' => 'mtr', 'Medtr8g069995' => 'mtr', 'MELO3C014345.2' => 'cme', 'MELO3C021395.2' => 'cme', 'Migut.D00262' => 'egut', 'Migut.G00257' => 'egut', 'MSTRG.21575' => 'ama', 'MSTRG.3985' => 'ama', 'Nitab4.5_0000295g0140' => 'nta', 'Nitab4.5_0000732g0140' => 'nta', 'Nitab4.5_0003162g0020' => 'nta', 'Nitab4.5_0006180g0090' => 'nta', 'Nitab4.5_0006390g0010' => 'nta', 'Nitab4.5_0007392g0040' => 'nta', 'Nn1g02140' => 'nnu', 'Nn4g26168' => 'nnu', 'Nn5g26754' => 'nnu', 'Oeu001433.1' => 'oeu', 'Oeu010299.2' => 'oeu', 'Oeu011171.1' => 'oeu', 'Oeu037675.1' => 'oeu', 'Oeu038359.1' => 'oeu', 'Oeu063834.1' => 'oeu', 'Oeu063835.1' => 'oeu', 'Os05g0312000' => 'osa', 'Os07g0211101' => 'osa', 'Os07g0211200' => 'osa', 'Os07g0681500' => 'osa', 'Peaxi162Scf00095g01015' => 'pax', 'Peaxi162Scf00104g00329' => 'pax', 'Peaxi162Scf00161g00137' => 'pax', 'PGR004G1665' => 'pgr', 'PGR031G2937' => 'pgr', 'PGR119G2145' => 'pgr', 'PGSC0003DMG400004351' => 'stu', 'PGSC0003DMG400014625' => 'stu', 'PGSC0003DMG401000943' => 'stu', 'Phvul.001G148600' => 'pvu', 'Phvul.004G001700' => 'pvu', 'Phvul.006G154900' => 'pvu', 'Phvul.008G078200' => 'pvu', 'Phvul.011G136500' => 'pvu', 'Potri.002G215600' => 'ptr', 'Potri.008G201600' => 'ptr', 'Potri.014G138400' => 'ptr', 'Potri.016G142500' => 'ptr', 'Pp3c16_10580' => 'ppa', 'Pp3c5_25280' => 'ppa', 'Prupe.1G150000' => 'ppe', 'Prupe.1G150100' => 'ppe', 'Prupe.6G299600' => 'ppe', 'Prupe.8G245000' => 'ppe', 'Psat0s4927g0040' => 'psa', 'Psat1g052080' => 'psa', 'Psat1g183800' => 'psa', 'Psat3g113840' => 'psa', 'Psat3g126120' => 'psa', 'Psat3g126160' => 'psa', 'Psat3g158760' => 'psa', 'Psat3g158840' => 'psa', 'PSO170G2858' => 'pso', 'PSO339G0606' => 'pso', 'PSO384G4709' => 'pso', 'PSO407G0334' => 'pso', 'QL04p040276' => 'qlo', 'QL06p005458' => 'qlo', 'QL06p005472' => 'qlo', 'QL07p030546' => 'qlo', 'QL07p031519' => 'qlo', 'QL09p050949' => 'qlo', 'QL09p050966' => 'qlo', 'QL09p051067' => 'qlo', 'QL12p022706' => 'qlo', 'RcHm_v2.0_Chr2g0119601' => 'rch', 'RcHm_v2.0_Chr3g0459591' => 'rch', 'RcHm_v2.0_Chr4g0418521' => 'rch', 'RcHm_v2.0_Chr4g0418531' => 'rch', 'RcHm_v2.0_Chr4g0418541' => 'rch', 'RcHm_v2.0_Chr6g0291641' => 'rch', 'Rhsim01G0086300' => 'rsi', 'Rhsim01G0276300' => 'rsi', 'Rhsim01G0276500' => 'rsi', 'Rhsim04G0207700' => 'rsi', 'Rhsim05G0234500' => 'rsi', 'Rhsim13G0022400' => 'rsi', 'Sabra02G0167900' => 'sbr', 'Sabra04G0158500' => 'sbr', 'Sabra08G0159800' => 'sbr', 'Sabra10G0011500' => 'sbr', 'Sabra14G0104400' => 'sbr', 'SalBow2G2440' => 'sbo', 'SalBow4G2265' => 'sbo', 'Sc02g0000060' => 'sci', 'Sc05g0005020' => 'sci', 'Sc13g0003890' => 'sci', 'Sed0014865' => 'sed', 'Sed0017224' => 'sed', 'Sed0026391' => 'sed', 'SEGI_00063' => 'sgi', 'SEGI_10967' => 'sgi', 'SEGI_17510' => 'sgi', 'SEGI_24396' => 'sgi', 'SEGI_39719' => 'sgi', 'SEGI_41392' => 'sgi', 'SGA_v2.0_scaffold11G05794' => 'sas', 'SGA_v2.0_scaffold142G35607' => 'sas', 'SGA_v2.0_scaffold1G00447' => 'sas', 'SHI15388' => 'shi', 'SHI15394' => 'shi', 'SHI15396' => 'shi', 'SHI15399' => 'shi', 'SMO343G0151' => 'smo', 'SMO367G1118' => 'smo', 'Solyc01g080200.3' => 'sly', 'Solyc06g008960.3' => 'sly', 'Solyc09g064780.3' => 'sly', 'Sopen01g031980' => 'spe', 'Sopen06g003710' => 'spe', 'Sopen09g026460' => 'spe', 'Sp3g21240' => 'spa', 'Sp4g30030' => 'spa', 'TAR365G0022' => 'tar', 'TAR365G1023' => 'tar', 'TAR365G1253' => 'tar', 'TAR623G0078' => 'tar', 'TAR623G1721' => 'tar', 'TAR633G0959' => 'tar', 'THA.LOC104802225' => 'tha', 'THA.LOC104804769' => 'tha', 'THA.LOC104808660' => 'tha', 'THA.LOC104812792' => 'tha', 'Thecc.01G284000' => 'tca', 'Thecc.04G220600' => 'tca', 'Thecc.05G268900' => 'tca', 'Thecc.08G171100' => 'tca', 'Thhalv10001284m.g' => 'esa', 'Thhalv10019912m.g' => 'esa', 'TPR.G14189' => 'tpr', 'TPR.G18110' => 'tpr', 'TPR.G18130' => 'tpr', 'TPR.G18131' => 'tpr', 'TPR.G18140' => 'tpr', 'TPR.G24282' => 'tpr', 'TPR.G25221' => 'tpr', 'TPR.G29267' => 'tpr', 'TPR.G35315' => 'tpr', 'TPR.G36173' => 'tpr', 'TWI09G0794' => 'twi', 'TWI59G1348' => 'twi', 'TWI74G0430' => 'twi', 'unitig_26.g8940' => 'ugi', 'unitig_749.g13744' => 'ugi', 'unitig_749.g13745' => 'ugi', 'vmacro08269' => 'vma', 'vmacro14937' => 'vma', 'vmacro20401' => 'vma', 'VMungo0464G1349' => 'vmu', 'VMungo0540G0289' => 'vmu', 'VMungo1215G1590' => 'vmu', 'VMungo1309G0221' => 'vmu', 'VMungo1309G2815' => 'vmu', 'VMungo1383G0239' => 'vmu', 'VMungo1383G2910' => 'vmu', 'Zm00001eb095270' => 'zma', 'Zm00001eb095280' => 'zma', 'Zm00001eb111630' => 'zma', 'Zm00001eb237080' => 'zma', 'Zm00001eb273740' => 'zma', 'Zm00001eb285040' => 'zma', 'Zm00001eb330790' => 'zma', 'Zm00001eb337380' => 'zma' ) $gf_id = 'HOM05D001484' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001484' ) $data_identifier = 'HOM05D001484' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 2, 'aly' => (int) 2, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 22, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 7, 'hma' => (int) 2, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 7, 'mtr' => (int) 10, 'cme' => (int) 2, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 4, 'ppa' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 4, 'qlo' => (int) 9, 'rch' => (int) 6, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 10, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 7, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb337380' $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' => 'HOM05D001484', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p31500' => 'bna', 'A05p00020' => 'bna', 'A07p08820' => 'bna', 'Aa31LG4G3300' => 'aar', 'Aa31LG8G10030' => 'aar', 'Actinidia00731' => 'ach', 'Actinidia11473' => 'ach', 'Actinidia23469' => 'ach', 'Actinidia24318' => 'ach', 'Actinidia40196' => 'ach', 'Actinidia40197' => 'ach', 'Actinidia40198' => 'ach', 'Ah.08g212990' => 'amhyb', 'Ah.15g091720' => 'amhyb', 'AL3G38260' => 'aly', 'AL4G47710' => 'aly', 'Aqoxy2G00671' => 'aox', 'Aqoxy2G03236' => 'aox', 'arahy.Tifrunner.gnm1.ann1.05IDCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KR684' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATY3SJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK6QJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6APGL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IDT7Z9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM073U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ0R87' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LE7RV4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT4QRX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V5ENPK' => 'arhy', 'AT2G48110' => 'ath', 'AT3G23590' => 'ath', 'ATR0626G186' => 'atr', 'ATR1127G141' => 'atr', 'Atru.chr4.2583' => 'acertr', 'Atru.chr5.1358' => 'acertr', 'Atru.chr5.1359' => 'acertr', 'Atru.chr8.46' => 'acertr', 'AUR62002640' => 'cqu', 'AUR62030055' => 'cqu', 'AUR62033713' => 'cqu', 'AUR62033714' => 'cqu', 'AUR62036795' => 'cqu', 'AUR62039891' => 'cqu', 'BcaB02g08737' => 'bca', 'BcaB04g20441' => 'bca', 'BcaB06g26509' => 'bca', 'BcaB06g26510' => 'bca', 'BcaB06g26511' => 'bca', 'BcaB06g26512' => 'bca', 'BcaB06g26513' => 'bca', 'BcaC02g12564' => 'bca', 'BcaC02g12565' => 'bca', 'BcaC02g12794' => 'bca', 'BcaC02g12795' => 'bca', 'BcaC02g12796' => 'bca', 'BcaC06g35541' => 'bca', 'BNapus_Darmor_BZH_scaffold_188p00080' => 'bna', 'BNapus_Darmor_BZH_scaffold_188p00090' => 'bna', 'BolC1t03972H' => 'bol', 'BolC1t03973H' => 'bol', 'BolC4t21680H' => 'bol', 'BolC7t41863H' => 'bol', 'BolSC55t61227H' => 'bol', 'BolSC55t61228H' => 'bol', 'BraA01t03278Z' => 'bra', 'BraA05t18998Z' => 'bra', 'BraA07t28673Z' => 'bra', 'C01p40150' => 'bna', 'C05p12370' => 'bna', 'C07p13680' => 'bna', 'CAN.G1006.16' => 'can', 'CAN.G1006.17' => 'can', 'CAN.G1170.2' => 'can', 'CAN.G962.7' => 'can', 'CANSAT25G2179' => 'cansat', 'CANSAT78G1573' => 'cansat', 'CARHR099510' => 'chi', 'CARHR143510' => 'chi', 'Carub.0003s2380' => 'cru', 'Carub.0004s3082' => 'cru', 'Ca_00614_v3' => 'car', 'Ca_07801_v3' => 'car', 'Ca_08567_v3' => 'car', 'Ca_09571_v3' => 'car', 'CBR_g19290' => 'cbr', 'Cc01_g19770' => 'ccan', 'Cc03_g03030' => 'ccan', 'CDE07G0968' => 'cde', 'CDE09G1441' => 'cde', 'Cfa006103' => 'cfa', 'Cfa015573' => 'cfa', 'Cfa016988' => 'cfa', 'Ciclev10006738m.g' => 'ccl', 'Ciclev10010920m.g' => 'ccl', 'Ciclev10018517m.g' => 'ccl', 'CiPaw.01G159200' => 'cil', 'CiPaw.02G091000' => 'cil', 'CiPaw.02G091100' => 'cil', 'CiPaw.08G103100' => 'cil', 'CiPaw.09G224900' => 'cil', 'ClCG06G005740' => 'cla', 'ClCG07G000090' => 'cla', 'ClCG07G000100' => 'cla', 'COL.COLO4_09143' => 'col', 'COL.COLO4_25124' => 'col', 'Cpa.g.sc16.34' => 'cpa', 'Cpa.g.sc3504.1' => 'cpa', 'Cpa.g.sc60.37' => 'cpa', 'CsaV3_6G018520' => 'csa', 'CsaV3_6G036860' => 'csa', 'CSS0001072' => 'camsi', 'CSS0020208' => 'camsi', 'CSS0021253' => 'camsi', 'CSS0022190' => 'camsi', 'CSS0036150' => 'camsi', 'CSS0040442' => 'camsi', 'CSS0042300' => 'camsi', 'CSS0045298' => 'camsi', 'DCAR_012449' => 'dca', 'DCAR_018405' => 'dca', 'DCAR_024573' => 'dca', 'DCAR_030591' => 'dca', 'Dinv16926' => 'din', 'Dinv32963' => 'din', 'Dinv38382' => 'din', 'Dinv38383' => 'din', 'Duzib133G0974' => 'dzi', 'Duzib138G1867' => 'dzi', 'Duzib211G0420' => 'dzi', 'Duzib212G0930' => 'dzi', 'ECA234G1645' => 'eca', 'ECA247G3467' => 'eca', 'ECA248G1703' => 'eca', 'EL10Ac3g06327' => 'bvu', 'EL10Ac7g17204' => 'bvu', 'Eucgr.A00855' => 'egr', 'Eucgr.A00858' => 'egr', 'Eucgr.H01520' => 'egr', 'Eucgr.H03604' => 'egr', 'Eucgr.L03465' => 'egr', 'Eucgr.L03466' => 'egr', 'FAN01G0988' => 'fan', 'FAN02G3892' => 'fan', 'FAN05G3381' => 'fan', 'FAN07G0967' => 'fan', 'FAN07G1493' => 'fan', 'FAN08G3125' => 'fan', 'FAN09G0402' => 'fan', 'FAN12G2594' => 'fan', 'FAN12G3879' => 'fan', 'FAN14G1546' => 'fan', 'FAN15G3626' => 'fan', 'FAN17G0588' => 'fan', 'FAN17G0609' => 'fan', 'FAN18G2817' => 'fan', 'FAN19G1305' => 'fan', 'FAN20G1787' => 'fan', 'FAN22G0073' => 'fan', 'FAN22G0352' => 'fan', 'FAN22G0368' => 'fan', 'FAN22G2273' => 'fan', 'FAN24G1998' => 'fan', 'FAN27G1317' => 'fan', 'FvH4_2g23980' => 'fve', 'FvH4_4g14380' => 'fve', 'FvH4_4g14390' => 'fve', 'FvH4_6g09250' => 'fve', 'Glyma.03G151100' => 'gma', 'Glyma.04G122550' => 'gma', 'Glyma.05G001600' => 'gma', 'Glyma.09G270766' => 'gma', 'Glyma.09G270832' => 'gma', 'Glyma.13G209800' => 'gma', 'Glyma.15G102800' => 'gma', 'Glyma.18G218900' => 'gma', 'Glyma.19G001500' => 'gma', 'Glyma.19G153600' => 'gma', 'Gohir.A02G028600' => 'ghi', 'Gohir.A08G045000' => 'ghi', 'Gohir.A11G120500' => 'ghi', 'Gohir.A12G006200' => 'ghi', 'Gohir.A12G006250' => 'ghi', 'Gohir.D02G036300' => 'ghi', 'Gohir.D08G054700' => 'ghi', 'Gohir.D11G125600' => 'ghi', 'Gohir.D12G005700' => 'ghi', 'Gorai.004G055200' => 'gra', 'Gorai.005G040400' => 'gra', 'Gorai.007G134500' => 'gra', 'Gorai.008G005500' => 'gra', 'GSVIVG01011094001' => 'vvi', 'GSVIVG01017879001' => 'vvi', 'GSVIVG01025988001' => 'vvi', 'GSVIVG01029847001' => 'vvi', 'HanXRQChr10g0282901' => 'han', 'HanXRQChr10g0310371' => 'han', 'HanXRQChr10g0315041' => 'han', 'HanXRQChr11g0327651' => 'han', 'HanXRQChr12g0359391' => 'han', 'Haze_00972' => 'cav', 'Haze_00973' => 'cav', 'Haze_00974' => 'cav', 'Haze_04747' => 'cav', 'Haze_04749' => 'cav', 'Haze_04750' => 'cav', 'Haze_21217' => 'cav', 'Hma1.2p1_1037F.1_g250680' => 'hma', 'Hma1.2p1_1644F.1_g295320' => 'hma', 'HPP92_011322' => 'vpl', 'HPP92_011323' => 'vpl', 'HPP92_011324' => 'vpl', 'HPP92_011325' => 'vpl', 'HPP92_011326' => 'vpl', 'Hund12205' => 'sun', 'Hund17957' => 'sun', 'Lalb_Chr06g0176771' => 'lal', 'Lalb_Chr18g0056021' => 'lal', 'Lalb_Chr18g0056031' => 'lal', 'Lalb_Chr18g0056041' => 'lal', 'Lalb_Chr20g0107751' => 'lal', 'Lalb_Chr20g0118371' => 'lal', 'Lj1g0010239' => 'lja', 'Lj1g0017101' => 'lja', 'Lj2A1178G40' => 'lonja', 'Lj2A54G84' => 'lonja', 'Lj2g0015248' => 'lja', 'Lj3A761T51' => 'lonja', 'Lj6g0018116' => 'lja', 'Lsat_1_v5_gn_4_136040' => 'lsa', 'Lsat_1_v5_gn_5_187461' => 'lsa', 'Lsat_1_v5_gn_5_77001' => 'lsa', 'Lsat_1_v5_gn_9_4461' => 'lsa', 'Manes.01G210100' => 'mes', 'Manes.03G185600' => 'mes', 'Manes.05G073300' => 'mes', 'Manes.09G120300' => 'mes', 'Manes.15G022100' => 'mes', 'Mapoly0096s0053' => 'mpo', 'MBI03_g14058_MAGBIO' => 'mbi', 'MBI03_g33876_MAGBIO' => 'mbi', 'MBI03_g36854_MAGBIO' => 'mbi', 'MBI17_g11997_MAGBIO' => 'mbi', 'MD03G1269000' => 'mdo', 'MD04G1179600' => 'mdo', 'MD11G1289800' => 'mdo', 'MD12G1194700' => 'mdo', 'MD13G1182100' => 'mdo', 'MD13G1182200' => 'mdo', 'MD16G1182600' => 'mdo', 'Medtr2g021400' => 'mtr', 'Medtr2g021470' => 'mtr', 'Medtr2g105810' => 'mtr', 'Medtr3g033580' => 'mtr', 'Medtr6g007970' => 'mtr', 'Medtr7g056330' => 'mtr', 'Medtr7g074290' => 'mtr', 'Medtr7g074380' => 'mtr', 'Medtr7g094550' => 'mtr', 'Medtr8g069995' => 'mtr', 'MELO3C014345.2' => 'cme', 'MELO3C021395.2' => 'cme', 'Migut.D00262' => 'egut', 'Migut.G00257' => 'egut', 'MSTRG.21575' => 'ama', 'MSTRG.3985' => 'ama', 'Nitab4.5_0000295g0140' => 'nta', 'Nitab4.5_0000732g0140' => 'nta', 'Nitab4.5_0003162g0020' => 'nta', 'Nitab4.5_0006180g0090' => 'nta', 'Nitab4.5_0006390g0010' => 'nta', 'Nitab4.5_0007392g0040' => 'nta', 'Nn1g02140' => 'nnu', 'Nn4g26168' => 'nnu', 'Nn5g26754' => 'nnu', 'Oeu001433.1' => 'oeu', 'Oeu010299.2' => 'oeu', 'Oeu011171.1' => 'oeu', 'Oeu037675.1' => 'oeu', 'Oeu038359.1' => 'oeu', 'Oeu063834.1' => 'oeu', 'Oeu063835.1' => 'oeu', 'Os05g0312000' => 'osa', 'Os07g0211101' => 'osa', 'Os07g0211200' => 'osa', 'Os07g0681500' => 'osa', 'Peaxi162Scf00095g01015' => 'pax', 'Peaxi162Scf00104g00329' => 'pax', 'Peaxi162Scf00161g00137' => 'pax', 'PGR004G1665' => 'pgr', 'PGR031G2937' => 'pgr', 'PGR119G2145' => 'pgr', 'PGSC0003DMG400004351' => 'stu', 'PGSC0003DMG400014625' => 'stu', 'PGSC0003DMG401000943' => 'stu', 'Phvul.001G148600' => 'pvu', 'Phvul.004G001700' => 'pvu', 'Phvul.006G154900' => 'pvu', 'Phvul.008G078200' => 'pvu', 'Phvul.011G136500' => 'pvu', 'Potri.002G215600' => 'ptr', 'Potri.008G201600' => 'ptr', 'Potri.014G138400' => 'ptr', 'Potri.016G142500' => 'ptr', 'Pp3c16_10580' => 'ppa', 'Pp3c5_25280' => 'ppa', 'Prupe.1G150000' => 'ppe', 'Prupe.1G150100' => 'ppe', 'Prupe.6G299600' => 'ppe', 'Prupe.8G245000' => 'ppe', 'Psat0s4927g0040' => 'psa', 'Psat1g052080' => 'psa', 'Psat1g183800' => 'psa', 'Psat3g113840' => 'psa', 'Psat3g126120' => 'psa', 'Psat3g126160' => 'psa', 'Psat3g158760' => 'psa', 'Psat3g158840' => 'psa', 'PSO170G2858' => 'pso', 'PSO339G0606' => 'pso', 'PSO384G4709' => 'pso', 'PSO407G0334' => 'pso', 'QL04p040276' => 'qlo', 'QL06p005458' => 'qlo', 'QL06p005472' => 'qlo', 'QL07p030546' => 'qlo', 'QL07p031519' => 'qlo', 'QL09p050949' => 'qlo', 'QL09p050966' => 'qlo', 'QL09p051067' => 'qlo', 'QL12p022706' => 'qlo', 'RcHm_v2.0_Chr2g0119601' => 'rch', 'RcHm_v2.0_Chr3g0459591' => 'rch', 'RcHm_v2.0_Chr4g0418521' => 'rch', 'RcHm_v2.0_Chr4g0418531' => 'rch', 'RcHm_v2.0_Chr4g0418541' => 'rch', 'RcHm_v2.0_Chr6g0291641' => 'rch', 'Rhsim01G0086300' => 'rsi', 'Rhsim01G0276300' => 'rsi', 'Rhsim01G0276500' => 'rsi', 'Rhsim04G0207700' => 'rsi', 'Rhsim05G0234500' => 'rsi', 'Rhsim13G0022400' => 'rsi', 'Sabra02G0167900' => 'sbr', 'Sabra04G0158500' => 'sbr', 'Sabra08G0159800' => 'sbr', 'Sabra10G0011500' => 'sbr', 'Sabra14G0104400' => 'sbr', 'SalBow2G2440' => 'sbo', 'SalBow4G2265' => 'sbo', 'Sc02g0000060' => 'sci', 'Sc05g0005020' => 'sci', 'Sc13g0003890' => 'sci', 'Sed0014865' => 'sed', 'Sed0017224' => 'sed', 'Sed0026391' => 'sed', 'SEGI_00063' => 'sgi', 'SEGI_10967' => 'sgi', 'SEGI_17510' => 'sgi', 'SEGI_24396' => 'sgi', 'SEGI_39719' => 'sgi', 'SEGI_41392' => 'sgi', 'SGA_v2.0_scaffold11G05794' => 'sas', 'SGA_v2.0_scaffold142G35607' => 'sas', 'SGA_v2.0_scaffold1G00447' => 'sas', 'SHI15388' => 'shi', 'SHI15394' => 'shi', 'SHI15396' => 'shi', 'SHI15399' => 'shi', 'SMO343G0151' => 'smo', 'SMO367G1118' => 'smo', 'Solyc01g080200.3' => 'sly', 'Solyc06g008960.3' => 'sly', 'Solyc09g064780.3' => 'sly', 'Sopen01g031980' => 'spe', 'Sopen06g003710' => 'spe', 'Sopen09g026460' => 'spe', 'Sp3g21240' => 'spa', 'Sp4g30030' => 'spa', 'TAR365G0022' => 'tar', 'TAR365G1023' => 'tar', 'TAR365G1253' => 'tar', 'TAR623G0078' => 'tar', 'TAR623G1721' => 'tar', 'TAR633G0959' => 'tar', 'THA.LOC104802225' => 'tha', 'THA.LOC104804769' => 'tha', 'THA.LOC104808660' => 'tha', 'THA.LOC104812792' => 'tha', 'Thecc.01G284000' => 'tca', 'Thecc.04G220600' => 'tca', 'Thecc.05G268900' => 'tca', 'Thecc.08G171100' => 'tca', 'Thhalv10001284m.g' => 'esa', 'Thhalv10019912m.g' => 'esa', 'TPR.G14189' => 'tpr', 'TPR.G18110' => 'tpr', 'TPR.G18130' => 'tpr', 'TPR.G18131' => 'tpr', 'TPR.G18140' => 'tpr', 'TPR.G24282' => 'tpr', 'TPR.G25221' => 'tpr', 'TPR.G29267' => 'tpr', 'TPR.G35315' => 'tpr', 'TPR.G36173' => 'tpr', 'TWI09G0794' => 'twi', 'TWI59G1348' => 'twi', 'TWI74G0430' => 'twi', 'unitig_26.g8940' => 'ugi', 'unitig_749.g13744' => 'ugi', 'unitig_749.g13745' => 'ugi', 'vmacro08269' => 'vma', 'vmacro14937' => 'vma', 'vmacro20401' => 'vma', 'VMungo0464G1349' => 'vmu', 'VMungo0540G0289' => 'vmu', 'VMungo1215G1590' => 'vmu', 'VMungo1309G0221' => 'vmu', 'VMungo1309G2815' => 'vmu', 'VMungo1383G0239' => 'vmu', 'VMungo1383G2910' => 'vmu', 'Zm00001eb095270' => 'zma', 'Zm00001eb095280' => 'zma', 'Zm00001eb111630' => 'zma', 'Zm00001eb237080' => 'zma', 'Zm00001eb273740' => 'zma', 'Zm00001eb285040' => 'zma', 'Zm00001eb330790' => 'zma', 'Zm00001eb337380' => 'zma' ), 'gf_id' => 'HOM05D001484', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001484' ), 'data_identifier' => 'HOM05D001484', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001484', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p31500' => 'bna', 'A05p00020' => 'bna', 'A07p08820' => 'bna', 'Aa31LG4G3300' => 'aar', 'Aa31LG8G10030' => 'aar', 'Actinidia00731' => 'ach', 'Actinidia11473' => 'ach', 'Actinidia23469' => 'ach', 'Actinidia24318' => 'ach', 'Actinidia40196' => 'ach', 'Actinidia40197' => 'ach', 'Actinidia40198' => 'ach', 'Ah.08g212990' => 'amhyb', 'Ah.15g091720' => 'amhyb', 'AL3G38260' => 'aly', 'AL4G47710' => 'aly', 'Aqoxy2G00671' => 'aox', 'Aqoxy2G03236' => 'aox', 'arahy.Tifrunner.gnm1.ann1.05IDCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KR684' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATY3SJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK6QJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6APGL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IDT7Z9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM073U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ0R87' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LE7RV4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT4QRX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V5ENPK' => 'arhy', 'AT2G48110' => 'ath', 'AT3G23590' => 'ath', 'ATR0626G186' => 'atr', 'ATR1127G141' => 'atr', 'Atru.chr4.2583' => 'acertr', 'Atru.chr5.1358' => 'acertr', 'Atru.chr5.1359' => 'acertr', 'Atru.chr8.46' => 'acertr', 'AUR62002640' => 'cqu', 'AUR62030055' => 'cqu', 'AUR62033713' => 'cqu', 'AUR62033714' => 'cqu', 'AUR62036795' => 'cqu', 'AUR62039891' => 'cqu', 'BcaB02g08737' => 'bca', 'BcaB04g20441' => 'bca', 'BcaB06g26509' => 'bca', 'BcaB06g26510' => 'bca', 'BcaB06g26511' => 'bca', 'BcaB06g26512' => 'bca', 'BcaB06g26513' => 'bca', 'BcaC02g12564' => 'bca', 'BcaC02g12565' => 'bca', 'BcaC02g12794' => 'bca', 'BcaC02g12795' => 'bca', 'BcaC02g12796' => 'bca', 'BcaC06g35541' => 'bca', 'BNapus_Darmor_BZH_scaffold_188p00080' => 'bna', 'BNapus_Darmor_BZH_scaffold_188p00090' => 'bna', 'BolC1t03972H' => 'bol', 'BolC1t03973H' => 'bol', 'BolC4t21680H' => 'bol', 'BolC7t41863H' => 'bol', 'BolSC55t61227H' => 'bol', 'BolSC55t61228H' => 'bol', 'BraA01t03278Z' => 'bra', 'BraA05t18998Z' => 'bra', 'BraA07t28673Z' => 'bra', 'C01p40150' => 'bna', 'C05p12370' => 'bna', 'C07p13680' => 'bna', 'CAN.G1006.16' => 'can', 'CAN.G1006.17' => 'can', 'CAN.G1170.2' => 'can', 'CAN.G962.7' => 'can', 'CANSAT25G2179' => 'cansat', 'CANSAT78G1573' => 'cansat', 'CARHR099510' => 'chi', 'CARHR143510' => 'chi', 'Carub.0003s2380' => 'cru', 'Carub.0004s3082' => 'cru', 'Ca_00614_v3' => 'car', 'Ca_07801_v3' => 'car', 'Ca_08567_v3' => 'car', 'Ca_09571_v3' => 'car', 'CBR_g19290' => 'cbr', 'Cc01_g19770' => 'ccan', 'Cc03_g03030' => 'ccan', 'CDE07G0968' => 'cde', 'CDE09G1441' => 'cde', 'Cfa006103' => 'cfa', 'Cfa015573' => 'cfa', 'Cfa016988' => 'cfa', 'Ciclev10006738m.g' => 'ccl', 'Ciclev10010920m.g' => 'ccl', 'Ciclev10018517m.g' => 'ccl', 'CiPaw.01G159200' => 'cil', 'CiPaw.02G091000' => 'cil', 'CiPaw.02G091100' => 'cil', 'CiPaw.08G103100' => 'cil', 'CiPaw.09G224900' => 'cil', 'ClCG06G005740' => 'cla', 'ClCG07G000090' => 'cla', 'ClCG07G000100' => 'cla', 'COL.COLO4_09143' => 'col', 'COL.COLO4_25124' => 'col', 'Cpa.g.sc16.34' => 'cpa', 'Cpa.g.sc3504.1' => 'cpa', 'Cpa.g.sc60.37' => 'cpa', 'CsaV3_6G018520' => 'csa', 'CsaV3_6G036860' => 'csa', 'CSS0001072' => 'camsi', 'CSS0020208' => 'camsi', 'CSS0021253' => 'camsi', 'CSS0022190' => 'camsi', 'CSS0036150' => 'camsi', 'CSS0040442' => 'camsi', 'CSS0042300' => 'camsi', 'CSS0045298' => 'camsi', 'DCAR_012449' => 'dca', 'DCAR_018405' => 'dca', 'DCAR_024573' => 'dca', 'DCAR_030591' => 'dca', 'Dinv16926' => 'din', 'Dinv32963' => 'din', 'Dinv38382' => 'din', 'Dinv38383' => 'din', 'Duzib133G0974' => 'dzi', 'Duzib138G1867' => 'dzi', 'Duzib211G0420' => 'dzi', 'Duzib212G0930' => 'dzi', 'ECA234G1645' => 'eca', 'ECA247G3467' => 'eca', 'ECA248G1703' => 'eca', 'EL10Ac3g06327' => 'bvu', 'EL10Ac7g17204' => 'bvu', 'Eucgr.A00855' => 'egr', 'Eucgr.A00858' => 'egr', 'Eucgr.H01520' => 'egr', 'Eucgr.H03604' => 'egr', 'Eucgr.L03465' => 'egr', 'Eucgr.L03466' => 'egr', 'FAN01G0988' => 'fan', 'FAN02G3892' => 'fan', 'FAN05G3381' => 'fan', 'FAN07G0967' => 'fan', 'FAN07G1493' => 'fan', 'FAN08G3125' => 'fan', 'FAN09G0402' => 'fan', 'FAN12G2594' => 'fan', 'FAN12G3879' => 'fan', 'FAN14G1546' => 'fan', 'FAN15G3626' => 'fan', 'FAN17G0588' => 'fan', 'FAN17G0609' => 'fan', 'FAN18G2817' => 'fan', 'FAN19G1305' => 'fan', 'FAN20G1787' => 'fan', 'FAN22G0073' => 'fan', 'FAN22G0352' => 'fan', 'FAN22G0368' => 'fan', 'FAN22G2273' => 'fan', 'FAN24G1998' => 'fan', 'FAN27G1317' => 'fan', 'FvH4_2g23980' => 'fve', 'FvH4_4g14380' => 'fve', 'FvH4_4g14390' => 'fve', 'FvH4_6g09250' => 'fve', 'Glyma.03G151100' => 'gma', 'Glyma.04G122550' => 'gma', 'Glyma.05G001600' => 'gma', 'Glyma.09G270766' => 'gma', 'Glyma.09G270832' => 'gma', 'Glyma.13G209800' => 'gma', 'Glyma.15G102800' => 'gma', 'Glyma.18G218900' => 'gma', 'Glyma.19G001500' => 'gma', 'Glyma.19G153600' => 'gma', 'Gohir.A02G028600' => 'ghi', 'Gohir.A08G045000' => 'ghi', 'Gohir.A11G120500' => 'ghi', 'Gohir.A12G006200' => 'ghi', 'Gohir.A12G006250' => 'ghi', 'Gohir.D02G036300' => 'ghi', 'Gohir.D08G054700' => 'ghi', 'Gohir.D11G125600' => 'ghi', 'Gohir.D12G005700' => 'ghi', 'Gorai.004G055200' => 'gra', 'Gorai.005G040400' => 'gra', 'Gorai.007G134500' => 'gra', 'Gorai.008G005500' => 'gra', 'GSVIVG01011094001' => 'vvi', 'GSVIVG01017879001' => 'vvi', 'GSVIVG01025988001' => 'vvi', 'GSVIVG01029847001' => 'vvi', 'HanXRQChr10g0282901' => 'han', 'HanXRQChr10g0310371' => 'han', 'HanXRQChr10g0315041' => 'han', 'HanXRQChr11g0327651' => 'han', 'HanXRQChr12g0359391' => 'han', 'Haze_00972' => 'cav', 'Haze_00973' => 'cav', 'Haze_00974' => 'cav', 'Haze_04747' => 'cav', 'Haze_04749' => 'cav', 'Haze_04750' => 'cav', 'Haze_21217' => 'cav', 'Hma1.2p1_1037F.1_g250680' => 'hma', 'Hma1.2p1_1644F.1_g295320' => 'hma', 'HPP92_011322' => 'vpl', 'HPP92_011323' => 'vpl', 'HPP92_011324' => 'vpl', 'HPP92_011325' => 'vpl', 'HPP92_011326' => 'vpl', 'Hund12205' => 'sun', 'Hund17957' => 'sun', 'Lalb_Chr06g0176771' => 'lal', 'Lalb_Chr18g0056021' => 'lal', 'Lalb_Chr18g0056031' => 'lal', 'Lalb_Chr18g0056041' => 'lal', 'Lalb_Chr20g0107751' => 'lal', 'Lalb_Chr20g0118371' => 'lal', 'Lj1g0010239' => 'lja', 'Lj1g0017101' => 'lja', 'Lj2A1178G40' => 'lonja', 'Lj2A54G84' => 'lonja', 'Lj2g0015248' => 'lja', 'Lj3A761T51' => 'lonja', 'Lj6g0018116' => 'lja', 'Lsat_1_v5_gn_4_136040' => 'lsa', 'Lsat_1_v5_gn_5_187461' => 'lsa', 'Lsat_1_v5_gn_5_77001' => 'lsa', 'Lsat_1_v5_gn_9_4461' => 'lsa', 'Manes.01G210100' => 'mes', 'Manes.03G185600' => 'mes', 'Manes.05G073300' => 'mes', 'Manes.09G120300' => 'mes', 'Manes.15G022100' => 'mes', 'Mapoly0096s0053' => 'mpo', 'MBI03_g14058_MAGBIO' => 'mbi', 'MBI03_g33876_MAGBIO' => 'mbi', 'MBI03_g36854_MAGBIO' => 'mbi', 'MBI17_g11997_MAGBIO' => 'mbi', 'MD03G1269000' => 'mdo', 'MD04G1179600' => 'mdo', 'MD11G1289800' => 'mdo', 'MD12G1194700' => 'mdo', 'MD13G1182100' => 'mdo', 'MD13G1182200' => 'mdo', 'MD16G1182600' => 'mdo', 'Medtr2g021400' => 'mtr', 'Medtr2g021470' => 'mtr', 'Medtr2g105810' => 'mtr', 'Medtr3g033580' => 'mtr', 'Medtr6g007970' => 'mtr', 'Medtr7g056330' => 'mtr', 'Medtr7g074290' => 'mtr', 'Medtr7g074380' => 'mtr', 'Medtr7g094550' => 'mtr', 'Medtr8g069995' => 'mtr', 'MELO3C014345.2' => 'cme', 'MELO3C021395.2' => 'cme', 'Migut.D00262' => 'egut', 'Migut.G00257' => 'egut', 'MSTRG.21575' => 'ama', 'MSTRG.3985' => 'ama', 'Nitab4.5_0000295g0140' => 'nta', 'Nitab4.5_0000732g0140' => 'nta', 'Nitab4.5_0003162g0020' => 'nta', 'Nitab4.5_0006180g0090' => 'nta', 'Nitab4.5_0006390g0010' => 'nta', 'Nitab4.5_0007392g0040' => 'nta', 'Nn1g02140' => 'nnu', 'Nn4g26168' => 'nnu', 'Nn5g26754' => 'nnu', 'Oeu001433.1' => 'oeu', 'Oeu010299.2' => 'oeu', 'Oeu011171.1' => 'oeu', 'Oeu037675.1' => 'oeu', 'Oeu038359.1' => 'oeu', 'Oeu063834.1' => 'oeu', 'Oeu063835.1' => 'oeu', 'Os05g0312000' => 'osa', 'Os07g0211101' => 'osa', 'Os07g0211200' => 'osa', 'Os07g0681500' => 'osa', 'Peaxi162Scf00095g01015' => 'pax', 'Peaxi162Scf00104g00329' => 'pax', 'Peaxi162Scf00161g00137' => 'pax', 'PGR004G1665' => 'pgr', 'PGR031G2937' => 'pgr', 'PGR119G2145' => 'pgr', 'PGSC0003DMG400004351' => 'stu', 'PGSC0003DMG400014625' => 'stu', 'PGSC0003DMG401000943' => 'stu', 'Phvul.001G148600' => 'pvu', 'Phvul.004G001700' => 'pvu', 'Phvul.006G154900' => 'pvu', 'Phvul.008G078200' => 'pvu', 'Phvul.011G136500' => 'pvu', 'Potri.002G215600' => 'ptr', 'Potri.008G201600' => 'ptr', 'Potri.014G138400' => 'ptr', 'Potri.016G142500' => 'ptr', 'Pp3c16_10580' => 'ppa', 'Pp3c5_25280' => 'ppa', 'Prupe.1G150000' => 'ppe', 'Prupe.1G150100' => 'ppe', 'Prupe.6G299600' => 'ppe', 'Prupe.8G245000' => 'ppe', 'Psat0s4927g0040' => 'psa', 'Psat1g052080' => 'psa', 'Psat1g183800' => 'psa', 'Psat3g113840' => 'psa', 'Psat3g126120' => 'psa', 'Psat3g126160' => 'psa', 'Psat3g158760' => 'psa', 'Psat3g158840' => 'psa', 'PSO170G2858' => 'pso', 'PSO339G0606' => 'pso', 'PSO384G4709' => 'pso', 'PSO407G0334' => 'pso', 'QL04p040276' => 'qlo', 'QL06p005458' => 'qlo', 'QL06p005472' => 'qlo', 'QL07p030546' => 'qlo', 'QL07p031519' => 'qlo', 'QL09p050949' => 'qlo', 'QL09p050966' => 'qlo', 'QL09p051067' => 'qlo', 'QL12p022706' => 'qlo', 'RcHm_v2.0_Chr2g0119601' => 'rch', 'RcHm_v2.0_Chr3g0459591' => 'rch', 'RcHm_v2.0_Chr4g0418521' => 'rch', 'RcHm_v2.0_Chr4g0418531' => 'rch', 'RcHm_v2.0_Chr4g0418541' => 'rch', 'RcHm_v2.0_Chr6g0291641' => 'rch', 'Rhsim01G0086300' => 'rsi', 'Rhsim01G0276300' => 'rsi', 'Rhsim01G0276500' => 'rsi', 'Rhsim04G0207700' => 'rsi', 'Rhsim05G0234500' => 'rsi', 'Rhsim13G0022400' => 'rsi', 'Sabra02G0167900' => 'sbr', 'Sabra04G0158500' => 'sbr', 'Sabra08G0159800' => 'sbr', 'Sabra10G0011500' => 'sbr', 'Sabra14G0104400' => 'sbr', 'SalBow2G2440' => 'sbo', 'SalBow4G2265' => 'sbo', 'Sc02g0000060' => 'sci', 'Sc05g0005020' => 'sci', 'Sc13g0003890' => 'sci', 'Sed0014865' => 'sed', 'Sed0017224' => 'sed', 'Sed0026391' => 'sed', 'SEGI_00063' => 'sgi', 'SEGI_10967' => 'sgi', 'SEGI_17510' => 'sgi', 'SEGI_24396' => 'sgi', 'SEGI_39719' => 'sgi', 'SEGI_41392' => 'sgi', 'SGA_v2.0_scaffold11G05794' => 'sas', 'SGA_v2.0_scaffold142G35607' => 'sas', 'SGA_v2.0_scaffold1G00447' => 'sas', 'SHI15388' => 'shi', 'SHI15394' => 'shi', 'SHI15396' => 'shi', 'SHI15399' => 'shi', 'SMO343G0151' => 'smo', 'SMO367G1118' => 'smo', 'Solyc01g080200.3' => 'sly', 'Solyc06g008960.3' => 'sly', 'Solyc09g064780.3' => 'sly', 'Sopen01g031980' => 'spe', 'Sopen06g003710' => 'spe', 'Sopen09g026460' => 'spe', 'Sp3g21240' => 'spa', 'Sp4g30030' => 'spa', 'TAR365G0022' => 'tar', 'TAR365G1023' => 'tar', 'TAR365G1253' => 'tar', 'TAR623G0078' => 'tar', 'TAR623G1721' => 'tar', 'TAR633G0959' => 'tar', 'THA.LOC104802225' => 'tha', 'THA.LOC104804769' => 'tha', 'THA.LOC104808660' => 'tha', 'THA.LOC104812792' => 'tha', 'Thecc.01G284000' => 'tca', 'Thecc.04G220600' => 'tca', 'Thecc.05G268900' => 'tca', 'Thecc.08G171100' => 'tca', 'Thhalv10001284m.g' => 'esa', 'Thhalv10019912m.g' => 'esa', 'TPR.G14189' => 'tpr', 'TPR.G18110' => 'tpr', 'TPR.G18130' => 'tpr', 'TPR.G18131' => 'tpr', 'TPR.G18140' => 'tpr', 'TPR.G24282' => 'tpr', 'TPR.G25221' => 'tpr', 'TPR.G29267' => 'tpr', 'TPR.G35315' => 'tpr', 'TPR.G36173' => 'tpr', 'TWI09G0794' => 'twi', 'TWI59G1348' => 'twi', 'TWI74G0430' => 'twi', 'unitig_26.g8940' => 'ugi', 'unitig_749.g13744' => 'ugi', 'unitig_749.g13745' => 'ugi', 'vmacro08269' => 'vma', 'vmacro14937' => 'vma', 'vmacro20401' => 'vma', 'VMungo0464G1349' => 'vmu', 'VMungo0540G0289' => 'vmu', 'VMungo1215G1590' => 'vmu', 'VMungo1309G0221' => 'vmu', 'VMungo1309G2815' => 'vmu', 'VMungo1383G0239' => 'vmu', 'VMungo1383G2910' => 'vmu', 'Zm00001eb095270' => 'zma', 'Zm00001eb095280' => 'zma', 'Zm00001eb111630' => 'zma', 'Zm00001eb237080' => 'zma', 'Zm00001eb273740' => 'zma', 'Zm00001eb285040' => 'zma', 'Zm00001eb330790' => 'zma', 'Zm00001eb337380' => 'zma' ) $gf_id = 'HOM05D001484' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001484' ) $data_identifier = 'HOM05D001484' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 2, 'aly' => (int) 2, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 22, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 7, 'hma' => (int) 2, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 7, 'mtr' => (int) 10, 'cme' => (int) 2, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 4, 'ppa' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 4, 'qlo' => (int) 9, 'rch' => (int) 6, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 10, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 7, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb337380' $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' => 'HOM05D001484', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p31500' => 'bna', 'A05p00020' => 'bna', 'A07p08820' => 'bna', 'Aa31LG4G3300' => 'aar', 'Aa31LG8G10030' => 'aar', 'Actinidia00731' => 'ach', 'Actinidia11473' => 'ach', 'Actinidia23469' => 'ach', 'Actinidia24318' => 'ach', 'Actinidia40196' => 'ach', 'Actinidia40197' => 'ach', 'Actinidia40198' => 'ach', 'Ah.08g212990' => 'amhyb', 'Ah.15g091720' => 'amhyb', 'AL3G38260' => 'aly', 'AL4G47710' => 'aly', 'Aqoxy2G00671' => 'aox', 'Aqoxy2G03236' => 'aox', 'arahy.Tifrunner.gnm1.ann1.05IDCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KR684' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATY3SJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK6QJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6APGL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IDT7Z9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM073U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ0R87' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LE7RV4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT4QRX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V5ENPK' => 'arhy', 'AT2G48110' => 'ath', 'AT3G23590' => 'ath', 'ATR0626G186' => 'atr', 'ATR1127G141' => 'atr', 'Atru.chr4.2583' => 'acertr', 'Atru.chr5.1358' => 'acertr', 'Atru.chr5.1359' => 'acertr', 'Atru.chr8.46' => 'acertr', 'AUR62002640' => 'cqu', 'AUR62030055' => 'cqu', 'AUR62033713' => 'cqu', 'AUR62033714' => 'cqu', 'AUR62036795' => 'cqu', 'AUR62039891' => 'cqu', 'BcaB02g08737' => 'bca', 'BcaB04g20441' => 'bca', 'BcaB06g26509' => 'bca', 'BcaB06g26510' => 'bca', 'BcaB06g26511' => 'bca', 'BcaB06g26512' => 'bca', 'BcaB06g26513' => 'bca', 'BcaC02g12564' => 'bca', 'BcaC02g12565' => 'bca', 'BcaC02g12794' => 'bca', 'BcaC02g12795' => 'bca', 'BcaC02g12796' => 'bca', 'BcaC06g35541' => 'bca', 'BNapus_Darmor_BZH_scaffold_188p00080' => 'bna', 'BNapus_Darmor_BZH_scaffold_188p00090' => 'bna', 'BolC1t03972H' => 'bol', 'BolC1t03973H' => 'bol', 'BolC4t21680H' => 'bol', 'BolC7t41863H' => 'bol', 'BolSC55t61227H' => 'bol', 'BolSC55t61228H' => 'bol', 'BraA01t03278Z' => 'bra', 'BraA05t18998Z' => 'bra', 'BraA07t28673Z' => 'bra', 'C01p40150' => 'bna', 'C05p12370' => 'bna', 'C07p13680' => 'bna', 'CAN.G1006.16' => 'can', 'CAN.G1006.17' => 'can', 'CAN.G1170.2' => 'can', 'CAN.G962.7' => 'can', 'CANSAT25G2179' => 'cansat', 'CANSAT78G1573' => 'cansat', 'CARHR099510' => 'chi', 'CARHR143510' => 'chi', 'Carub.0003s2380' => 'cru', 'Carub.0004s3082' => 'cru', 'Ca_00614_v3' => 'car', 'Ca_07801_v3' => 'car', 'Ca_08567_v3' => 'car', 'Ca_09571_v3' => 'car', 'CBR_g19290' => 'cbr', 'Cc01_g19770' => 'ccan', 'Cc03_g03030' => 'ccan', 'CDE07G0968' => 'cde', 'CDE09G1441' => 'cde', 'Cfa006103' => 'cfa', 'Cfa015573' => 'cfa', 'Cfa016988' => 'cfa', 'Ciclev10006738m.g' => 'ccl', 'Ciclev10010920m.g' => 'ccl', 'Ciclev10018517m.g' => 'ccl', 'CiPaw.01G159200' => 'cil', 'CiPaw.02G091000' => 'cil', 'CiPaw.02G091100' => 'cil', 'CiPaw.08G103100' => 'cil', 'CiPaw.09G224900' => 'cil', 'ClCG06G005740' => 'cla', 'ClCG07G000090' => 'cla', 'ClCG07G000100' => 'cla', 'COL.COLO4_09143' => 'col', 'COL.COLO4_25124' => 'col', 'Cpa.g.sc16.34' => 'cpa', 'Cpa.g.sc3504.1' => 'cpa', 'Cpa.g.sc60.37' => 'cpa', 'CsaV3_6G018520' => 'csa', 'CsaV3_6G036860' => 'csa', 'CSS0001072' => 'camsi', 'CSS0020208' => 'camsi', 'CSS0021253' => 'camsi', 'CSS0022190' => 'camsi', 'CSS0036150' => 'camsi', 'CSS0040442' => 'camsi', 'CSS0042300' => 'camsi', 'CSS0045298' => 'camsi', 'DCAR_012449' => 'dca', 'DCAR_018405' => 'dca', 'DCAR_024573' => 'dca', 'DCAR_030591' => 'dca', 'Dinv16926' => 'din', 'Dinv32963' => 'din', 'Dinv38382' => 'din', 'Dinv38383' => 'din', 'Duzib133G0974' => 'dzi', 'Duzib138G1867' => 'dzi', 'Duzib211G0420' => 'dzi', 'Duzib212G0930' => 'dzi', 'ECA234G1645' => 'eca', 'ECA247G3467' => 'eca', 'ECA248G1703' => 'eca', 'EL10Ac3g06327' => 'bvu', 'EL10Ac7g17204' => 'bvu', 'Eucgr.A00855' => 'egr', 'Eucgr.A00858' => 'egr', 'Eucgr.H01520' => 'egr', 'Eucgr.H03604' => 'egr', 'Eucgr.L03465' => 'egr', 'Eucgr.L03466' => 'egr', 'FAN01G0988' => 'fan', 'FAN02G3892' => 'fan', 'FAN05G3381' => 'fan', 'FAN07G0967' => 'fan', 'FAN07G1493' => 'fan', 'FAN08G3125' => 'fan', 'FAN09G0402' => 'fan', 'FAN12G2594' => 'fan', 'FAN12G3879' => 'fan', 'FAN14G1546' => 'fan', 'FAN15G3626' => 'fan', 'FAN17G0588' => 'fan', 'FAN17G0609' => 'fan', 'FAN18G2817' => 'fan', 'FAN19G1305' => 'fan', 'FAN20G1787' => 'fan', 'FAN22G0073' => 'fan', 'FAN22G0352' => 'fan', 'FAN22G0368' => 'fan', 'FAN22G2273' => 'fan', 'FAN24G1998' => 'fan', 'FAN27G1317' => 'fan', 'FvH4_2g23980' => 'fve', 'FvH4_4g14380' => 'fve', 'FvH4_4g14390' => 'fve', 'FvH4_6g09250' => 'fve', 'Glyma.03G151100' => 'gma', 'Glyma.04G122550' => 'gma', 'Glyma.05G001600' => 'gma', 'Glyma.09G270766' => 'gma', 'Glyma.09G270832' => 'gma', 'Glyma.13G209800' => 'gma', 'Glyma.15G102800' => 'gma', 'Glyma.18G218900' => 'gma', 'Glyma.19G001500' => 'gma', 'Glyma.19G153600' => 'gma', 'Gohir.A02G028600' => 'ghi', 'Gohir.A08G045000' => 'ghi', 'Gohir.A11G120500' => 'ghi', 'Gohir.A12G006200' => 'ghi', 'Gohir.A12G006250' => 'ghi', 'Gohir.D02G036300' => 'ghi', 'Gohir.D08G054700' => 'ghi', 'Gohir.D11G125600' => 'ghi', 'Gohir.D12G005700' => 'ghi', 'Gorai.004G055200' => 'gra', 'Gorai.005G040400' => 'gra', 'Gorai.007G134500' => 'gra', 'Gorai.008G005500' => 'gra', 'GSVIVG01011094001' => 'vvi', 'GSVIVG01017879001' => 'vvi', 'GSVIVG01025988001' => 'vvi', 'GSVIVG01029847001' => 'vvi', 'HanXRQChr10g0282901' => 'han', 'HanXRQChr10g0310371' => 'han', 'HanXRQChr10g0315041' => 'han', 'HanXRQChr11g0327651' => 'han', 'HanXRQChr12g0359391' => 'han', 'Haze_00972' => 'cav', 'Haze_00973' => 'cav', 'Haze_00974' => 'cav', 'Haze_04747' => 'cav', 'Haze_04749' => 'cav', 'Haze_04750' => 'cav', 'Haze_21217' => 'cav', 'Hma1.2p1_1037F.1_g250680' => 'hma', 'Hma1.2p1_1644F.1_g295320' => 'hma', 'HPP92_011322' => 'vpl', 'HPP92_011323' => 'vpl', 'HPP92_011324' => 'vpl', 'HPP92_011325' => 'vpl', 'HPP92_011326' => 'vpl', 'Hund12205' => 'sun', 'Hund17957' => 'sun', 'Lalb_Chr06g0176771' => 'lal', 'Lalb_Chr18g0056021' => 'lal', 'Lalb_Chr18g0056031' => 'lal', 'Lalb_Chr18g0056041' => 'lal', 'Lalb_Chr20g0107751' => 'lal', 'Lalb_Chr20g0118371' => 'lal', 'Lj1g0010239' => 'lja', 'Lj1g0017101' => 'lja', 'Lj2A1178G40' => 'lonja', 'Lj2A54G84' => 'lonja', 'Lj2g0015248' => 'lja', 'Lj3A761T51' => 'lonja', 'Lj6g0018116' => 'lja', 'Lsat_1_v5_gn_4_136040' => 'lsa', 'Lsat_1_v5_gn_5_187461' => 'lsa', 'Lsat_1_v5_gn_5_77001' => 'lsa', 'Lsat_1_v5_gn_9_4461' => 'lsa', 'Manes.01G210100' => 'mes', 'Manes.03G185600' => 'mes', 'Manes.05G073300' => 'mes', 'Manes.09G120300' => 'mes', 'Manes.15G022100' => 'mes', 'Mapoly0096s0053' => 'mpo', 'MBI03_g14058_MAGBIO' => 'mbi', 'MBI03_g33876_MAGBIO' => 'mbi', 'MBI03_g36854_MAGBIO' => 'mbi', 'MBI17_g11997_MAGBIO' => 'mbi', 'MD03G1269000' => 'mdo', 'MD04G1179600' => 'mdo', 'MD11G1289800' => 'mdo', 'MD12G1194700' => 'mdo', 'MD13G1182100' => 'mdo', 'MD13G1182200' => 'mdo', 'MD16G1182600' => 'mdo', 'Medtr2g021400' => 'mtr', 'Medtr2g021470' => 'mtr', 'Medtr2g105810' => 'mtr', 'Medtr3g033580' => 'mtr', 'Medtr6g007970' => 'mtr', 'Medtr7g056330' => 'mtr', 'Medtr7g074290' => 'mtr', 'Medtr7g074380' => 'mtr', 'Medtr7g094550' => 'mtr', 'Medtr8g069995' => 'mtr', 'MELO3C014345.2' => 'cme', 'MELO3C021395.2' => 'cme', 'Migut.D00262' => 'egut', 'Migut.G00257' => 'egut', 'MSTRG.21575' => 'ama', 'MSTRG.3985' => 'ama', 'Nitab4.5_0000295g0140' => 'nta', 'Nitab4.5_0000732g0140' => 'nta', 'Nitab4.5_0003162g0020' => 'nta', 'Nitab4.5_0006180g0090' => 'nta', 'Nitab4.5_0006390g0010' => 'nta', 'Nitab4.5_0007392g0040' => 'nta', 'Nn1g02140' => 'nnu', 'Nn4g26168' => 'nnu', 'Nn5g26754' => 'nnu', 'Oeu001433.1' => 'oeu', 'Oeu010299.2' => 'oeu', 'Oeu011171.1' => 'oeu', 'Oeu037675.1' => 'oeu', 'Oeu038359.1' => 'oeu', 'Oeu063834.1' => 'oeu', 'Oeu063835.1' => 'oeu', 'Os05g0312000' => 'osa', 'Os07g0211101' => 'osa', 'Os07g0211200' => 'osa', 'Os07g0681500' => 'osa', 'Peaxi162Scf00095g01015' => 'pax', 'Peaxi162Scf00104g00329' => 'pax', 'Peaxi162Scf00161g00137' => 'pax', 'PGR004G1665' => 'pgr', 'PGR031G2937' => 'pgr', 'PGR119G2145' => 'pgr', 'PGSC0003DMG400004351' => 'stu', 'PGSC0003DMG400014625' => 'stu', 'PGSC0003DMG401000943' => 'stu', 'Phvul.001G148600' => 'pvu', 'Phvul.004G001700' => 'pvu', 'Phvul.006G154900' => 'pvu', 'Phvul.008G078200' => 'pvu', 'Phvul.011G136500' => 'pvu', 'Potri.002G215600' => 'ptr', 'Potri.008G201600' => 'ptr', 'Potri.014G138400' => 'ptr', 'Potri.016G142500' => 'ptr', 'Pp3c16_10580' => 'ppa', 'Pp3c5_25280' => 'ppa', 'Prupe.1G150000' => 'ppe', 'Prupe.1G150100' => 'ppe', 'Prupe.6G299600' => 'ppe', 'Prupe.8G245000' => 'ppe', 'Psat0s4927g0040' => 'psa', 'Psat1g052080' => 'psa', 'Psat1g183800' => 'psa', 'Psat3g113840' => 'psa', 'Psat3g126120' => 'psa', 'Psat3g126160' => 'psa', 'Psat3g158760' => 'psa', 'Psat3g158840' => 'psa', 'PSO170G2858' => 'pso', 'PSO339G0606' => 'pso', 'PSO384G4709' => 'pso', 'PSO407G0334' => 'pso', 'QL04p040276' => 'qlo', 'QL06p005458' => 'qlo', 'QL06p005472' => 'qlo', 'QL07p030546' => 'qlo', 'QL07p031519' => 'qlo', 'QL09p050949' => 'qlo', 'QL09p050966' => 'qlo', 'QL09p051067' => 'qlo', 'QL12p022706' => 'qlo', 'RcHm_v2.0_Chr2g0119601' => 'rch', 'RcHm_v2.0_Chr3g0459591' => 'rch', 'RcHm_v2.0_Chr4g0418521' => 'rch', 'RcHm_v2.0_Chr4g0418531' => 'rch', 'RcHm_v2.0_Chr4g0418541' => 'rch', 'RcHm_v2.0_Chr6g0291641' => 'rch', 'Rhsim01G0086300' => 'rsi', 'Rhsim01G0276300' => 'rsi', 'Rhsim01G0276500' => 'rsi', 'Rhsim04G0207700' => 'rsi', 'Rhsim05G0234500' => 'rsi', 'Rhsim13G0022400' => 'rsi', 'Sabra02G0167900' => 'sbr', 'Sabra04G0158500' => 'sbr', 'Sabra08G0159800' => 'sbr', 'Sabra10G0011500' => 'sbr', 'Sabra14G0104400' => 'sbr', 'SalBow2G2440' => 'sbo', 'SalBow4G2265' => 'sbo', 'Sc02g0000060' => 'sci', 'Sc05g0005020' => 'sci', 'Sc13g0003890' => 'sci', 'Sed0014865' => 'sed', 'Sed0017224' => 'sed', 'Sed0026391' => 'sed', 'SEGI_00063' => 'sgi', 'SEGI_10967' => 'sgi', 'SEGI_17510' => 'sgi', 'SEGI_24396' => 'sgi', 'SEGI_39719' => 'sgi', 'SEGI_41392' => 'sgi', 'SGA_v2.0_scaffold11G05794' => 'sas', 'SGA_v2.0_scaffold142G35607' => 'sas', 'SGA_v2.0_scaffold1G00447' => 'sas', 'SHI15388' => 'shi', 'SHI15394' => 'shi', 'SHI15396' => 'shi', 'SHI15399' => 'shi', 'SMO343G0151' => 'smo', 'SMO367G1118' => 'smo', 'Solyc01g080200.3' => 'sly', 'Solyc06g008960.3' => 'sly', 'Solyc09g064780.3' => 'sly', 'Sopen01g031980' => 'spe', 'Sopen06g003710' => 'spe', 'Sopen09g026460' => 'spe', 'Sp3g21240' => 'spa', 'Sp4g30030' => 'spa', 'TAR365G0022' => 'tar', 'TAR365G1023' => 'tar', 'TAR365G1253' => 'tar', 'TAR623G0078' => 'tar', 'TAR623G1721' => 'tar', 'TAR633G0959' => 'tar', 'THA.LOC104802225' => 'tha', 'THA.LOC104804769' => 'tha', 'THA.LOC104808660' => 'tha', 'THA.LOC104812792' => 'tha', 'Thecc.01G284000' => 'tca', 'Thecc.04G220600' => 'tca', 'Thecc.05G268900' => 'tca', 'Thecc.08G171100' => 'tca', 'Thhalv10001284m.g' => 'esa', 'Thhalv10019912m.g' => 'esa', 'TPR.G14189' => 'tpr', 'TPR.G18110' => 'tpr', 'TPR.G18130' => 'tpr', 'TPR.G18131' => 'tpr', 'TPR.G18140' => 'tpr', 'TPR.G24282' => 'tpr', 'TPR.G25221' => 'tpr', 'TPR.G29267' => 'tpr', 'TPR.G35315' => 'tpr', 'TPR.G36173' => 'tpr', 'TWI09G0794' => 'twi', 'TWI59G1348' => 'twi', 'TWI74G0430' => 'twi', 'unitig_26.g8940' => 'ugi', 'unitig_749.g13744' => 'ugi', 'unitig_749.g13745' => 'ugi', 'vmacro08269' => 'vma', 'vmacro14937' => 'vma', 'vmacro20401' => 'vma', 'VMungo0464G1349' => 'vmu', 'VMungo0540G0289' => 'vmu', 'VMungo1215G1590' => 'vmu', 'VMungo1309G0221' => 'vmu', 'VMungo1309G2815' => 'vmu', 'VMungo1383G0239' => 'vmu', 'VMungo1383G2910' => 'vmu', 'Zm00001eb095270' => 'zma', 'Zm00001eb095280' => 'zma', 'Zm00001eb111630' => 'zma', 'Zm00001eb237080' => 'zma', 'Zm00001eb273740' => 'zma', 'Zm00001eb285040' => 'zma', 'Zm00001eb330790' => 'zma', 'Zm00001eb337380' => 'zma' ), 'gf_id' => 'HOM05D001484', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001484' ), 'data_identifier' => 'HOM05D001484', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001484', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p31500' => 'bna', 'A05p00020' => 'bna', 'A07p08820' => 'bna', 'Aa31LG4G3300' => 'aar', 'Aa31LG8G10030' => 'aar', 'Actinidia00731' => 'ach', 'Actinidia11473' => 'ach', 'Actinidia23469' => 'ach', 'Actinidia24318' => 'ach', 'Actinidia40196' => 'ach', 'Actinidia40197' => 'ach', 'Actinidia40198' => 'ach', 'Ah.08g212990' => 'amhyb', 'Ah.15g091720' => 'amhyb', 'AL3G38260' => 'aly', 'AL4G47710' => 'aly', 'Aqoxy2G00671' => 'aox', 'Aqoxy2G03236' => 'aox', 'arahy.Tifrunner.gnm1.ann1.05IDCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KR684' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATY3SJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK6QJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6APGL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IDT7Z9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM073U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ0R87' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LE7RV4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT4QRX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V5ENPK' => 'arhy', 'AT2G48110' => 'ath', 'AT3G23590' => 'ath', 'ATR0626G186' => 'atr', 'ATR1127G141' => 'atr', 'Atru.chr4.2583' => 'acertr', 'Atru.chr5.1358' => 'acertr', 'Atru.chr5.1359' => 'acertr', 'Atru.chr8.46' => 'acertr', 'AUR62002640' => 'cqu', 'AUR62030055' => 'cqu', 'AUR62033713' => 'cqu', 'AUR62033714' => 'cqu', 'AUR62036795' => 'cqu', 'AUR62039891' => 'cqu', 'BcaB02g08737' => 'bca', 'BcaB04g20441' => 'bca', 'BcaB06g26509' => 'bca', 'BcaB06g26510' => 'bca', 'BcaB06g26511' => 'bca', 'BcaB06g26512' => 'bca', 'BcaB06g26513' => 'bca', 'BcaC02g12564' => 'bca', 'BcaC02g12565' => 'bca', 'BcaC02g12794' => 'bca', 'BcaC02g12795' => 'bca', 'BcaC02g12796' => 'bca', 'BcaC06g35541' => 'bca', 'BNapus_Darmor_BZH_scaffold_188p00080' => 'bna', 'BNapus_Darmor_BZH_scaffold_188p00090' => 'bna', 'BolC1t03972H' => 'bol', 'BolC1t03973H' => 'bol', 'BolC4t21680H' => 'bol', 'BolC7t41863H' => 'bol', 'BolSC55t61227H' => 'bol', 'BolSC55t61228H' => 'bol', 'BraA01t03278Z' => 'bra', 'BraA05t18998Z' => 'bra', 'BraA07t28673Z' => 'bra', 'C01p40150' => 'bna', 'C05p12370' => 'bna', 'C07p13680' => 'bna', 'CAN.G1006.16' => 'can', 'CAN.G1006.17' => 'can', 'CAN.G1170.2' => 'can', 'CAN.G962.7' => 'can', 'CANSAT25G2179' => 'cansat', 'CANSAT78G1573' => 'cansat', 'CARHR099510' => 'chi', 'CARHR143510' => 'chi', 'Carub.0003s2380' => 'cru', 'Carub.0004s3082' => 'cru', 'Ca_00614_v3' => 'car', 'Ca_07801_v3' => 'car', 'Ca_08567_v3' => 'car', 'Ca_09571_v3' => 'car', 'CBR_g19290' => 'cbr', 'Cc01_g19770' => 'ccan', 'Cc03_g03030' => 'ccan', 'CDE07G0968' => 'cde', 'CDE09G1441' => 'cde', 'Cfa006103' => 'cfa', 'Cfa015573' => 'cfa', 'Cfa016988' => 'cfa', 'Ciclev10006738m.g' => 'ccl', 'Ciclev10010920m.g' => 'ccl', 'Ciclev10018517m.g' => 'ccl', 'CiPaw.01G159200' => 'cil', 'CiPaw.02G091000' => 'cil', 'CiPaw.02G091100' => 'cil', 'CiPaw.08G103100' => 'cil', 'CiPaw.09G224900' => 'cil', 'ClCG06G005740' => 'cla', 'ClCG07G000090' => 'cla', 'ClCG07G000100' => 'cla', 'COL.COLO4_09143' => 'col', 'COL.COLO4_25124' => 'col', 'Cpa.g.sc16.34' => 'cpa', 'Cpa.g.sc3504.1' => 'cpa', 'Cpa.g.sc60.37' => 'cpa', 'CsaV3_6G018520' => 'csa', 'CsaV3_6G036860' => 'csa', 'CSS0001072' => 'camsi', 'CSS0020208' => 'camsi', 'CSS0021253' => 'camsi', 'CSS0022190' => 'camsi', 'CSS0036150' => 'camsi', 'CSS0040442' => 'camsi', 'CSS0042300' => 'camsi', 'CSS0045298' => 'camsi', 'DCAR_012449' => 'dca', 'DCAR_018405' => 'dca', 'DCAR_024573' => 'dca', 'DCAR_030591' => 'dca', 'Dinv16926' => 'din', 'Dinv32963' => 'din', 'Dinv38382' => 'din', 'Dinv38383' => 'din', 'Duzib133G0974' => 'dzi', 'Duzib138G1867' => 'dzi', 'Duzib211G0420' => 'dzi', 'Duzib212G0930' => 'dzi', 'ECA234G1645' => 'eca', 'ECA247G3467' => 'eca', 'ECA248G1703' => 'eca', 'EL10Ac3g06327' => 'bvu', 'EL10Ac7g17204' => 'bvu', 'Eucgr.A00855' => 'egr', 'Eucgr.A00858' => 'egr', 'Eucgr.H01520' => 'egr', 'Eucgr.H03604' => 'egr', 'Eucgr.L03465' => 'egr', 'Eucgr.L03466' => 'egr', 'FAN01G0988' => 'fan', 'FAN02G3892' => 'fan', 'FAN05G3381' => 'fan', 'FAN07G0967' => 'fan', 'FAN07G1493' => 'fan', 'FAN08G3125' => 'fan', 'FAN09G0402' => 'fan', 'FAN12G2594' => 'fan', 'FAN12G3879' => 'fan', 'FAN14G1546' => 'fan', 'FAN15G3626' => 'fan', 'FAN17G0588' => 'fan', 'FAN17G0609' => 'fan', 'FAN18G2817' => 'fan', 'FAN19G1305' => 'fan', 'FAN20G1787' => 'fan', 'FAN22G0073' => 'fan', 'FAN22G0352' => 'fan', 'FAN22G0368' => 'fan', 'FAN22G2273' => 'fan', 'FAN24G1998' => 'fan', 'FAN27G1317' => 'fan', 'FvH4_2g23980' => 'fve', 'FvH4_4g14380' => 'fve', 'FvH4_4g14390' => 'fve', 'FvH4_6g09250' => 'fve', 'Glyma.03G151100' => 'gma', 'Glyma.04G122550' => 'gma', 'Glyma.05G001600' => 'gma', 'Glyma.09G270766' => 'gma', 'Glyma.09G270832' => 'gma', 'Glyma.13G209800' => 'gma', 'Glyma.15G102800' => 'gma', 'Glyma.18G218900' => 'gma', 'Glyma.19G001500' => 'gma', 'Glyma.19G153600' => 'gma', 'Gohir.A02G028600' => 'ghi', 'Gohir.A08G045000' => 'ghi', 'Gohir.A11G120500' => 'ghi', 'Gohir.A12G006200' => 'ghi', 'Gohir.A12G006250' => 'ghi', 'Gohir.D02G036300' => 'ghi', 'Gohir.D08G054700' => 'ghi', 'Gohir.D11G125600' => 'ghi', 'Gohir.D12G005700' => 'ghi', 'Gorai.004G055200' => 'gra', 'Gorai.005G040400' => 'gra', 'Gorai.007G134500' => 'gra', 'Gorai.008G005500' => 'gra', 'GSVIVG01011094001' => 'vvi', 'GSVIVG01017879001' => 'vvi', 'GSVIVG01025988001' => 'vvi', 'GSVIVG01029847001' => 'vvi', 'HanXRQChr10g0282901' => 'han', 'HanXRQChr10g0310371' => 'han', 'HanXRQChr10g0315041' => 'han', 'HanXRQChr11g0327651' => 'han', 'HanXRQChr12g0359391' => 'han', 'Haze_00972' => 'cav', 'Haze_00973' => 'cav', 'Haze_00974' => 'cav', 'Haze_04747' => 'cav', 'Haze_04749' => 'cav', 'Haze_04750' => 'cav', 'Haze_21217' => 'cav', 'Hma1.2p1_1037F.1_g250680' => 'hma', 'Hma1.2p1_1644F.1_g295320' => 'hma', 'HPP92_011322' => 'vpl', 'HPP92_011323' => 'vpl', 'HPP92_011324' => 'vpl', 'HPP92_011325' => 'vpl', 'HPP92_011326' => 'vpl', 'Hund12205' => 'sun', 'Hund17957' => 'sun', 'Lalb_Chr06g0176771' => 'lal', 'Lalb_Chr18g0056021' => 'lal', 'Lalb_Chr18g0056031' => 'lal', 'Lalb_Chr18g0056041' => 'lal', 'Lalb_Chr20g0107751' => 'lal', 'Lalb_Chr20g0118371' => 'lal', 'Lj1g0010239' => 'lja', 'Lj1g0017101' => 'lja', 'Lj2A1178G40' => 'lonja', 'Lj2A54G84' => 'lonja', 'Lj2g0015248' => 'lja', 'Lj3A761T51' => 'lonja', 'Lj6g0018116' => 'lja', 'Lsat_1_v5_gn_4_136040' => 'lsa', 'Lsat_1_v5_gn_5_187461' => 'lsa', 'Lsat_1_v5_gn_5_77001' => 'lsa', 'Lsat_1_v5_gn_9_4461' => 'lsa', 'Manes.01G210100' => 'mes', 'Manes.03G185600' => 'mes', 'Manes.05G073300' => 'mes', 'Manes.09G120300' => 'mes', 'Manes.15G022100' => 'mes', 'Mapoly0096s0053' => 'mpo', 'MBI03_g14058_MAGBIO' => 'mbi', 'MBI03_g33876_MAGBIO' => 'mbi', 'MBI03_g36854_MAGBIO' => 'mbi', 'MBI17_g11997_MAGBIO' => 'mbi', 'MD03G1269000' => 'mdo', 'MD04G1179600' => 'mdo', 'MD11G1289800' => 'mdo', 'MD12G1194700' => 'mdo', 'MD13G1182100' => 'mdo', 'MD13G1182200' => 'mdo', 'MD16G1182600' => 'mdo', 'Medtr2g021400' => 'mtr', 'Medtr2g021470' => 'mtr', 'Medtr2g105810' => 'mtr', 'Medtr3g033580' => 'mtr', 'Medtr6g007970' => 'mtr', 'Medtr7g056330' => 'mtr', 'Medtr7g074290' => 'mtr', 'Medtr7g074380' => 'mtr', 'Medtr7g094550' => 'mtr', 'Medtr8g069995' => 'mtr', 'MELO3C014345.2' => 'cme', 'MELO3C021395.2' => 'cme', 'Migut.D00262' => 'egut', 'Migut.G00257' => 'egut', 'MSTRG.21575' => 'ama', 'MSTRG.3985' => 'ama', 'Nitab4.5_0000295g0140' => 'nta', 'Nitab4.5_0000732g0140' => 'nta', 'Nitab4.5_0003162g0020' => 'nta', 'Nitab4.5_0006180g0090' => 'nta', 'Nitab4.5_0006390g0010' => 'nta', 'Nitab4.5_0007392g0040' => 'nta', 'Nn1g02140' => 'nnu', 'Nn4g26168' => 'nnu', 'Nn5g26754' => 'nnu', 'Oeu001433.1' => 'oeu', 'Oeu010299.2' => 'oeu', 'Oeu011171.1' => 'oeu', 'Oeu037675.1' => 'oeu', 'Oeu038359.1' => 'oeu', 'Oeu063834.1' => 'oeu', 'Oeu063835.1' => 'oeu', 'Os05g0312000' => 'osa', 'Os07g0211101' => 'osa', 'Os07g0211200' => 'osa', 'Os07g0681500' => 'osa', 'Peaxi162Scf00095g01015' => 'pax', 'Peaxi162Scf00104g00329' => 'pax', 'Peaxi162Scf00161g00137' => 'pax', 'PGR004G1665' => 'pgr', 'PGR031G2937' => 'pgr', 'PGR119G2145' => 'pgr', 'PGSC0003DMG400004351' => 'stu', 'PGSC0003DMG400014625' => 'stu', 'PGSC0003DMG401000943' => 'stu', 'Phvul.001G148600' => 'pvu', 'Phvul.004G001700' => 'pvu', 'Phvul.006G154900' => 'pvu', 'Phvul.008G078200' => 'pvu', 'Phvul.011G136500' => 'pvu', 'Potri.002G215600' => 'ptr', 'Potri.008G201600' => 'ptr', 'Potri.014G138400' => 'ptr', 'Potri.016G142500' => 'ptr', 'Pp3c16_10580' => 'ppa', 'Pp3c5_25280' => 'ppa', 'Prupe.1G150000' => 'ppe', 'Prupe.1G150100' => 'ppe', 'Prupe.6G299600' => 'ppe', 'Prupe.8G245000' => 'ppe', 'Psat0s4927g0040' => 'psa', 'Psat1g052080' => 'psa', 'Psat1g183800' => 'psa', 'Psat3g113840' => 'psa', 'Psat3g126120' => 'psa', 'Psat3g126160' => 'psa', 'Psat3g158760' => 'psa', 'Psat3g158840' => 'psa', 'PSO170G2858' => 'pso', 'PSO339G0606' => 'pso', 'PSO384G4709' => 'pso', 'PSO407G0334' => 'pso', 'QL04p040276' => 'qlo', 'QL06p005458' => 'qlo', 'QL06p005472' => 'qlo', 'QL07p030546' => 'qlo', 'QL07p031519' => 'qlo', 'QL09p050949' => 'qlo', 'QL09p050966' => 'qlo', 'QL09p051067' => 'qlo', 'QL12p022706' => 'qlo', 'RcHm_v2.0_Chr2g0119601' => 'rch', 'RcHm_v2.0_Chr3g0459591' => 'rch', 'RcHm_v2.0_Chr4g0418521' => 'rch', 'RcHm_v2.0_Chr4g0418531' => 'rch', 'RcHm_v2.0_Chr4g0418541' => 'rch', 'RcHm_v2.0_Chr6g0291641' => 'rch', 'Rhsim01G0086300' => 'rsi', 'Rhsim01G0276300' => 'rsi', 'Rhsim01G0276500' => 'rsi', 'Rhsim04G0207700' => 'rsi', 'Rhsim05G0234500' => 'rsi', 'Rhsim13G0022400' => 'rsi', 'Sabra02G0167900' => 'sbr', 'Sabra04G0158500' => 'sbr', 'Sabra08G0159800' => 'sbr', 'Sabra10G0011500' => 'sbr', 'Sabra14G0104400' => 'sbr', 'SalBow2G2440' => 'sbo', 'SalBow4G2265' => 'sbo', 'Sc02g0000060' => 'sci', 'Sc05g0005020' => 'sci', 'Sc13g0003890' => 'sci', 'Sed0014865' => 'sed', 'Sed0017224' => 'sed', 'Sed0026391' => 'sed', 'SEGI_00063' => 'sgi', 'SEGI_10967' => 'sgi', 'SEGI_17510' => 'sgi', 'SEGI_24396' => 'sgi', 'SEGI_39719' => 'sgi', 'SEGI_41392' => 'sgi', 'SGA_v2.0_scaffold11G05794' => 'sas', 'SGA_v2.0_scaffold142G35607' => 'sas', 'SGA_v2.0_scaffold1G00447' => 'sas', 'SHI15388' => 'shi', 'SHI15394' => 'shi', 'SHI15396' => 'shi', 'SHI15399' => 'shi', 'SMO343G0151' => 'smo', 'SMO367G1118' => 'smo', 'Solyc01g080200.3' => 'sly', 'Solyc06g008960.3' => 'sly', 'Solyc09g064780.3' => 'sly', 'Sopen01g031980' => 'spe', 'Sopen06g003710' => 'spe', 'Sopen09g026460' => 'spe', 'Sp3g21240' => 'spa', 'Sp4g30030' => 'spa', 'TAR365G0022' => 'tar', 'TAR365G1023' => 'tar', 'TAR365G1253' => 'tar', 'TAR623G0078' => 'tar', 'TAR623G1721' => 'tar', 'TAR633G0959' => 'tar', 'THA.LOC104802225' => 'tha', 'THA.LOC104804769' => 'tha', 'THA.LOC104808660' => 'tha', 'THA.LOC104812792' => 'tha', 'Thecc.01G284000' => 'tca', 'Thecc.04G220600' => 'tca', 'Thecc.05G268900' => 'tca', 'Thecc.08G171100' => 'tca', 'Thhalv10001284m.g' => 'esa', 'Thhalv10019912m.g' => 'esa', 'TPR.G14189' => 'tpr', 'TPR.G18110' => 'tpr', 'TPR.G18130' => 'tpr', 'TPR.G18131' => 'tpr', 'TPR.G18140' => 'tpr', 'TPR.G24282' => 'tpr', 'TPR.G25221' => 'tpr', 'TPR.G29267' => 'tpr', 'TPR.G35315' => 'tpr', 'TPR.G36173' => 'tpr', 'TWI09G0794' => 'twi', 'TWI59G1348' => 'twi', 'TWI74G0430' => 'twi', 'unitig_26.g8940' => 'ugi', 'unitig_749.g13744' => 'ugi', 'unitig_749.g13745' => 'ugi', 'vmacro08269' => 'vma', 'vmacro14937' => 'vma', 'vmacro20401' => 'vma', 'VMungo0464G1349' => 'vmu', 'VMungo0540G0289' => 'vmu', 'VMungo1215G1590' => 'vmu', 'VMungo1309G0221' => 'vmu', 'VMungo1309G2815' => 'vmu', 'VMungo1383G0239' => 'vmu', 'VMungo1383G2910' => 'vmu', 'Zm00001eb095270' => 'zma', 'Zm00001eb095280' => 'zma', 'Zm00001eb111630' => 'zma', 'Zm00001eb237080' => 'zma', 'Zm00001eb273740' => 'zma', 'Zm00001eb285040' => 'zma', 'Zm00001eb330790' => 'zma', 'Zm00001eb337380' => 'zma' ) $gf_id = 'HOM05D001484' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001484' ) $data_identifier = 'HOM05D001484' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 2, 'aly' => (int) 2, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 22, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 7, 'hma' => (int) 2, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 7, 'mtr' => (int) 10, 'cme' => (int) 2, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 4, 'ppa' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 4, 'qlo' => (int) 9, 'rch' => (int) 6, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 10, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 7, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb337380' $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' => 'HOM05D001484', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p31500' => 'bna', 'A05p00020' => 'bna', 'A07p08820' => 'bna', 'Aa31LG4G3300' => 'aar', 'Aa31LG8G10030' => 'aar', 'Actinidia00731' => 'ach', 'Actinidia11473' => 'ach', 'Actinidia23469' => 'ach', 'Actinidia24318' => 'ach', 'Actinidia40196' => 'ach', 'Actinidia40197' => 'ach', 'Actinidia40198' => 'ach', 'Ah.08g212990' => 'amhyb', 'Ah.15g091720' => 'amhyb', 'AL3G38260' => 'aly', 'AL4G47710' => 'aly', 'Aqoxy2G00671' => 'aox', 'Aqoxy2G03236' => 'aox', 'arahy.Tifrunner.gnm1.ann1.05IDCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KR684' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATY3SJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK6QJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6APGL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IDT7Z9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM073U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ0R87' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LE7RV4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT4QRX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V5ENPK' => 'arhy', 'AT2G48110' => 'ath', 'AT3G23590' => 'ath', 'ATR0626G186' => 'atr', 'ATR1127G141' => 'atr', 'Atru.chr4.2583' => 'acertr', 'Atru.chr5.1358' => 'acertr', 'Atru.chr5.1359' => 'acertr', 'Atru.chr8.46' => 'acertr', 'AUR62002640' => 'cqu', 'AUR62030055' => 'cqu', 'AUR62033713' => 'cqu', 'AUR62033714' => 'cqu', 'AUR62036795' => 'cqu', 'AUR62039891' => 'cqu', 'BcaB02g08737' => 'bca', 'BcaB04g20441' => 'bca', 'BcaB06g26509' => 'bca', 'BcaB06g26510' => 'bca', 'BcaB06g26511' => 'bca', 'BcaB06g26512' => 'bca', 'BcaB06g26513' => 'bca', 'BcaC02g12564' => 'bca', 'BcaC02g12565' => 'bca', 'BcaC02g12794' => 'bca', 'BcaC02g12795' => 'bca', 'BcaC02g12796' => 'bca', 'BcaC06g35541' => 'bca', 'BNapus_Darmor_BZH_scaffold_188p00080' => 'bna', 'BNapus_Darmor_BZH_scaffold_188p00090' => 'bna', 'BolC1t03972H' => 'bol', 'BolC1t03973H' => 'bol', 'BolC4t21680H' => 'bol', 'BolC7t41863H' => 'bol', 'BolSC55t61227H' => 'bol', 'BolSC55t61228H' => 'bol', 'BraA01t03278Z' => 'bra', 'BraA05t18998Z' => 'bra', 'BraA07t28673Z' => 'bra', 'C01p40150' => 'bna', 'C05p12370' => 'bna', 'C07p13680' => 'bna', 'CAN.G1006.16' => 'can', 'CAN.G1006.17' => 'can', 'CAN.G1170.2' => 'can', 'CAN.G962.7' => 'can', 'CANSAT25G2179' => 'cansat', 'CANSAT78G1573' => 'cansat', 'CARHR099510' => 'chi', 'CARHR143510' => 'chi', 'Carub.0003s2380' => 'cru', 'Carub.0004s3082' => 'cru', 'Ca_00614_v3' => 'car', 'Ca_07801_v3' => 'car', 'Ca_08567_v3' => 'car', 'Ca_09571_v3' => 'car', 'CBR_g19290' => 'cbr', 'Cc01_g19770' => 'ccan', 'Cc03_g03030' => 'ccan', 'CDE07G0968' => 'cde', 'CDE09G1441' => 'cde', 'Cfa006103' => 'cfa', 'Cfa015573' => 'cfa', 'Cfa016988' => 'cfa', 'Ciclev10006738m.g' => 'ccl', 'Ciclev10010920m.g' => 'ccl', 'Ciclev10018517m.g' => 'ccl', 'CiPaw.01G159200' => 'cil', 'CiPaw.02G091000' => 'cil', 'CiPaw.02G091100' => 'cil', 'CiPaw.08G103100' => 'cil', 'CiPaw.09G224900' => 'cil', 'ClCG06G005740' => 'cla', 'ClCG07G000090' => 'cla', 'ClCG07G000100' => 'cla', 'COL.COLO4_09143' => 'col', 'COL.COLO4_25124' => 'col', 'Cpa.g.sc16.34' => 'cpa', 'Cpa.g.sc3504.1' => 'cpa', 'Cpa.g.sc60.37' => 'cpa', 'CsaV3_6G018520' => 'csa', 'CsaV3_6G036860' => 'csa', 'CSS0001072' => 'camsi', 'CSS0020208' => 'camsi', 'CSS0021253' => 'camsi', 'CSS0022190' => 'camsi', 'CSS0036150' => 'camsi', 'CSS0040442' => 'camsi', 'CSS0042300' => 'camsi', 'CSS0045298' => 'camsi', 'DCAR_012449' => 'dca', 'DCAR_018405' => 'dca', 'DCAR_024573' => 'dca', 'DCAR_030591' => 'dca', 'Dinv16926' => 'din', 'Dinv32963' => 'din', 'Dinv38382' => 'din', 'Dinv38383' => 'din', 'Duzib133G0974' => 'dzi', 'Duzib138G1867' => 'dzi', 'Duzib211G0420' => 'dzi', 'Duzib212G0930' => 'dzi', 'ECA234G1645' => 'eca', 'ECA247G3467' => 'eca', 'ECA248G1703' => 'eca', 'EL10Ac3g06327' => 'bvu', 'EL10Ac7g17204' => 'bvu', 'Eucgr.A00855' => 'egr', 'Eucgr.A00858' => 'egr', 'Eucgr.H01520' => 'egr', 'Eucgr.H03604' => 'egr', 'Eucgr.L03465' => 'egr', 'Eucgr.L03466' => 'egr', 'FAN01G0988' => 'fan', 'FAN02G3892' => 'fan', 'FAN05G3381' => 'fan', 'FAN07G0967' => 'fan', 'FAN07G1493' => 'fan', 'FAN08G3125' => 'fan', 'FAN09G0402' => 'fan', 'FAN12G2594' => 'fan', 'FAN12G3879' => 'fan', 'FAN14G1546' => 'fan', 'FAN15G3626' => 'fan', 'FAN17G0588' => 'fan', 'FAN17G0609' => 'fan', 'FAN18G2817' => 'fan', 'FAN19G1305' => 'fan', 'FAN20G1787' => 'fan', 'FAN22G0073' => 'fan', 'FAN22G0352' => 'fan', 'FAN22G0368' => 'fan', 'FAN22G2273' => 'fan', 'FAN24G1998' => 'fan', 'FAN27G1317' => 'fan', 'FvH4_2g23980' => 'fve', 'FvH4_4g14380' => 'fve', 'FvH4_4g14390' => 'fve', 'FvH4_6g09250' => 'fve', 'Glyma.03G151100' => 'gma', 'Glyma.04G122550' => 'gma', 'Glyma.05G001600' => 'gma', 'Glyma.09G270766' => 'gma', 'Glyma.09G270832' => 'gma', 'Glyma.13G209800' => 'gma', 'Glyma.15G102800' => 'gma', 'Glyma.18G218900' => 'gma', 'Glyma.19G001500' => 'gma', 'Glyma.19G153600' => 'gma', 'Gohir.A02G028600' => 'ghi', 'Gohir.A08G045000' => 'ghi', 'Gohir.A11G120500' => 'ghi', 'Gohir.A12G006200' => 'ghi', 'Gohir.A12G006250' => 'ghi', 'Gohir.D02G036300' => 'ghi', 'Gohir.D08G054700' => 'ghi', 'Gohir.D11G125600' => 'ghi', 'Gohir.D12G005700' => 'ghi', 'Gorai.004G055200' => 'gra', 'Gorai.005G040400' => 'gra', 'Gorai.007G134500' => 'gra', 'Gorai.008G005500' => 'gra', 'GSVIVG01011094001' => 'vvi', 'GSVIVG01017879001' => 'vvi', 'GSVIVG01025988001' => 'vvi', 'GSVIVG01029847001' => 'vvi', 'HanXRQChr10g0282901' => 'han', 'HanXRQChr10g0310371' => 'han', 'HanXRQChr10g0315041' => 'han', 'HanXRQChr11g0327651' => 'han', 'HanXRQChr12g0359391' => 'han', 'Haze_00972' => 'cav', 'Haze_00973' => 'cav', 'Haze_00974' => 'cav', 'Haze_04747' => 'cav', 'Haze_04749' => 'cav', 'Haze_04750' => 'cav', 'Haze_21217' => 'cav', 'Hma1.2p1_1037F.1_g250680' => 'hma', 'Hma1.2p1_1644F.1_g295320' => 'hma', 'HPP92_011322' => 'vpl', 'HPP92_011323' => 'vpl', 'HPP92_011324' => 'vpl', 'HPP92_011325' => 'vpl', 'HPP92_011326' => 'vpl', 'Hund12205' => 'sun', 'Hund17957' => 'sun', 'Lalb_Chr06g0176771' => 'lal', 'Lalb_Chr18g0056021' => 'lal', 'Lalb_Chr18g0056031' => 'lal', 'Lalb_Chr18g0056041' => 'lal', 'Lalb_Chr20g0107751' => 'lal', 'Lalb_Chr20g0118371' => 'lal', 'Lj1g0010239' => 'lja', 'Lj1g0017101' => 'lja', 'Lj2A1178G40' => 'lonja', 'Lj2A54G84' => 'lonja', 'Lj2g0015248' => 'lja', 'Lj3A761T51' => 'lonja', 'Lj6g0018116' => 'lja', 'Lsat_1_v5_gn_4_136040' => 'lsa', 'Lsat_1_v5_gn_5_187461' => 'lsa', 'Lsat_1_v5_gn_5_77001' => 'lsa', 'Lsat_1_v5_gn_9_4461' => 'lsa', 'Manes.01G210100' => 'mes', 'Manes.03G185600' => 'mes', 'Manes.05G073300' => 'mes', 'Manes.09G120300' => 'mes', 'Manes.15G022100' => 'mes', 'Mapoly0096s0053' => 'mpo', 'MBI03_g14058_MAGBIO' => 'mbi', 'MBI03_g33876_MAGBIO' => 'mbi', 'MBI03_g36854_MAGBIO' => 'mbi', 'MBI17_g11997_MAGBIO' => 'mbi', 'MD03G1269000' => 'mdo', 'MD04G1179600' => 'mdo', 'MD11G1289800' => 'mdo', 'MD12G1194700' => 'mdo', 'MD13G1182100' => 'mdo', 'MD13G1182200' => 'mdo', 'MD16G1182600' => 'mdo', 'Medtr2g021400' => 'mtr', 'Medtr2g021470' => 'mtr', 'Medtr2g105810' => 'mtr', 'Medtr3g033580' => 'mtr', 'Medtr6g007970' => 'mtr', 'Medtr7g056330' => 'mtr', 'Medtr7g074290' => 'mtr', 'Medtr7g074380' => 'mtr', 'Medtr7g094550' => 'mtr', 'Medtr8g069995' => 'mtr', 'MELO3C014345.2' => 'cme', 'MELO3C021395.2' => 'cme', 'Migut.D00262' => 'egut', 'Migut.G00257' => 'egut', 'MSTRG.21575' => 'ama', 'MSTRG.3985' => 'ama', 'Nitab4.5_0000295g0140' => 'nta', 'Nitab4.5_0000732g0140' => 'nta', 'Nitab4.5_0003162g0020' => 'nta', 'Nitab4.5_0006180g0090' => 'nta', 'Nitab4.5_0006390g0010' => 'nta', 'Nitab4.5_0007392g0040' => 'nta', 'Nn1g02140' => 'nnu', 'Nn4g26168' => 'nnu', 'Nn5g26754' => 'nnu', 'Oeu001433.1' => 'oeu', 'Oeu010299.2' => 'oeu', 'Oeu011171.1' => 'oeu', 'Oeu037675.1' => 'oeu', 'Oeu038359.1' => 'oeu', 'Oeu063834.1' => 'oeu', 'Oeu063835.1' => 'oeu', 'Os05g0312000' => 'osa', 'Os07g0211101' => 'osa', 'Os07g0211200' => 'osa', 'Os07g0681500' => 'osa', 'Peaxi162Scf00095g01015' => 'pax', 'Peaxi162Scf00104g00329' => 'pax', 'Peaxi162Scf00161g00137' => 'pax', 'PGR004G1665' => 'pgr', 'PGR031G2937' => 'pgr', 'PGR119G2145' => 'pgr', 'PGSC0003DMG400004351' => 'stu', 'PGSC0003DMG400014625' => 'stu', 'PGSC0003DMG401000943' => 'stu', 'Phvul.001G148600' => 'pvu', 'Phvul.004G001700' => 'pvu', 'Phvul.006G154900' => 'pvu', 'Phvul.008G078200' => 'pvu', 'Phvul.011G136500' => 'pvu', 'Potri.002G215600' => 'ptr', 'Potri.008G201600' => 'ptr', 'Potri.014G138400' => 'ptr', 'Potri.016G142500' => 'ptr', 'Pp3c16_10580' => 'ppa', 'Pp3c5_25280' => 'ppa', 'Prupe.1G150000' => 'ppe', 'Prupe.1G150100' => 'ppe', 'Prupe.6G299600' => 'ppe', 'Prupe.8G245000' => 'ppe', 'Psat0s4927g0040' => 'psa', 'Psat1g052080' => 'psa', 'Psat1g183800' => 'psa', 'Psat3g113840' => 'psa', 'Psat3g126120' => 'psa', 'Psat3g126160' => 'psa', 'Psat3g158760' => 'psa', 'Psat3g158840' => 'psa', 'PSO170G2858' => 'pso', 'PSO339G0606' => 'pso', 'PSO384G4709' => 'pso', 'PSO407G0334' => 'pso', 'QL04p040276' => 'qlo', 'QL06p005458' => 'qlo', 'QL06p005472' => 'qlo', 'QL07p030546' => 'qlo', 'QL07p031519' => 'qlo', 'QL09p050949' => 'qlo', 'QL09p050966' => 'qlo', 'QL09p051067' => 'qlo', 'QL12p022706' => 'qlo', 'RcHm_v2.0_Chr2g0119601' => 'rch', 'RcHm_v2.0_Chr3g0459591' => 'rch', 'RcHm_v2.0_Chr4g0418521' => 'rch', 'RcHm_v2.0_Chr4g0418531' => 'rch', 'RcHm_v2.0_Chr4g0418541' => 'rch', 'RcHm_v2.0_Chr6g0291641' => 'rch', 'Rhsim01G0086300' => 'rsi', 'Rhsim01G0276300' => 'rsi', 'Rhsim01G0276500' => 'rsi', 'Rhsim04G0207700' => 'rsi', 'Rhsim05G0234500' => 'rsi', 'Rhsim13G0022400' => 'rsi', 'Sabra02G0167900' => 'sbr', 'Sabra04G0158500' => 'sbr', 'Sabra08G0159800' => 'sbr', 'Sabra10G0011500' => 'sbr', 'Sabra14G0104400' => 'sbr', 'SalBow2G2440' => 'sbo', 'SalBow4G2265' => 'sbo', 'Sc02g0000060' => 'sci', 'Sc05g0005020' => 'sci', 'Sc13g0003890' => 'sci', 'Sed0014865' => 'sed', 'Sed0017224' => 'sed', 'Sed0026391' => 'sed', 'SEGI_00063' => 'sgi', 'SEGI_10967' => 'sgi', 'SEGI_17510' => 'sgi', 'SEGI_24396' => 'sgi', 'SEGI_39719' => 'sgi', 'SEGI_41392' => 'sgi', 'SGA_v2.0_scaffold11G05794' => 'sas', 'SGA_v2.0_scaffold142G35607' => 'sas', 'SGA_v2.0_scaffold1G00447' => 'sas', 'SHI15388' => 'shi', 'SHI15394' => 'shi', 'SHI15396' => 'shi', 'SHI15399' => 'shi', 'SMO343G0151' => 'smo', 'SMO367G1118' => 'smo', 'Solyc01g080200.3' => 'sly', 'Solyc06g008960.3' => 'sly', 'Solyc09g064780.3' => 'sly', 'Sopen01g031980' => 'spe', 'Sopen06g003710' => 'spe', 'Sopen09g026460' => 'spe', 'Sp3g21240' => 'spa', 'Sp4g30030' => 'spa', 'TAR365G0022' => 'tar', 'TAR365G1023' => 'tar', 'TAR365G1253' => 'tar', 'TAR623G0078' => 'tar', 'TAR623G1721' => 'tar', 'TAR633G0959' => 'tar', 'THA.LOC104802225' => 'tha', 'THA.LOC104804769' => 'tha', 'THA.LOC104808660' => 'tha', 'THA.LOC104812792' => 'tha', 'Thecc.01G284000' => 'tca', 'Thecc.04G220600' => 'tca', 'Thecc.05G268900' => 'tca', 'Thecc.08G171100' => 'tca', 'Thhalv10001284m.g' => 'esa', 'Thhalv10019912m.g' => 'esa', 'TPR.G14189' => 'tpr', 'TPR.G18110' => 'tpr', 'TPR.G18130' => 'tpr', 'TPR.G18131' => 'tpr', 'TPR.G18140' => 'tpr', 'TPR.G24282' => 'tpr', 'TPR.G25221' => 'tpr', 'TPR.G29267' => 'tpr', 'TPR.G35315' => 'tpr', 'TPR.G36173' => 'tpr', 'TWI09G0794' => 'twi', 'TWI59G1348' => 'twi', 'TWI74G0430' => 'twi', 'unitig_26.g8940' => 'ugi', 'unitig_749.g13744' => 'ugi', 'unitig_749.g13745' => 'ugi', 'vmacro08269' => 'vma', 'vmacro14937' => 'vma', 'vmacro20401' => 'vma', 'VMungo0464G1349' => 'vmu', 'VMungo0540G0289' => 'vmu', 'VMungo1215G1590' => 'vmu', 'VMungo1309G0221' => 'vmu', 'VMungo1309G2815' => 'vmu', 'VMungo1383G0239' => 'vmu', 'VMungo1383G2910' => 'vmu', 'Zm00001eb095270' => 'zma', 'Zm00001eb095280' => 'zma', 'Zm00001eb111630' => 'zma', 'Zm00001eb237080' => 'zma', 'Zm00001eb273740' => 'zma', 'Zm00001eb285040' => 'zma', 'Zm00001eb330790' => 'zma', 'Zm00001eb337380' => 'zma' ), 'gf_id' => 'HOM05D001484', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001484' ), 'data_identifier' => 'HOM05D001484', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001484', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p31500' => 'bna', 'A05p00020' => 'bna', 'A07p08820' => 'bna', 'Aa31LG4G3300' => 'aar', 'Aa31LG8G10030' => 'aar', 'Actinidia00731' => 'ach', 'Actinidia11473' => 'ach', 'Actinidia23469' => 'ach', 'Actinidia24318' => 'ach', 'Actinidia40196' => 'ach', 'Actinidia40197' => 'ach', 'Actinidia40198' => 'ach', 'Ah.08g212990' => 'amhyb', 'Ah.15g091720' => 'amhyb', 'AL3G38260' => 'aly', 'AL4G47710' => 'aly', 'Aqoxy2G00671' => 'aox', 'Aqoxy2G03236' => 'aox', 'arahy.Tifrunner.gnm1.ann1.05IDCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KR684' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATY3SJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK6QJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6APGL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IDT7Z9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM073U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ0R87' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LE7RV4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT4QRX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V5ENPK' => 'arhy', 'AT2G48110' => 'ath', 'AT3G23590' => 'ath', 'ATR0626G186' => 'atr', 'ATR1127G141' => 'atr', 'Atru.chr4.2583' => 'acertr', 'Atru.chr5.1358' => 'acertr', 'Atru.chr5.1359' => 'acertr', 'Atru.chr8.46' => 'acertr', 'AUR62002640' => 'cqu', 'AUR62030055' => 'cqu', 'AUR62033713' => 'cqu', 'AUR62033714' => 'cqu', 'AUR62036795' => 'cqu', 'AUR62039891' => 'cqu', 'BcaB02g08737' => 'bca', 'BcaB04g20441' => 'bca', 'BcaB06g26509' => 'bca', 'BcaB06g26510' => 'bca', 'BcaB06g26511' => 'bca', 'BcaB06g26512' => 'bca', 'BcaB06g26513' => 'bca', 'BcaC02g12564' => 'bca', 'BcaC02g12565' => 'bca', 'BcaC02g12794' => 'bca', 'BcaC02g12795' => 'bca', 'BcaC02g12796' => 'bca', 'BcaC06g35541' => 'bca', 'BNapus_Darmor_BZH_scaffold_188p00080' => 'bna', 'BNapus_Darmor_BZH_scaffold_188p00090' => 'bna', 'BolC1t03972H' => 'bol', 'BolC1t03973H' => 'bol', 'BolC4t21680H' => 'bol', 'BolC7t41863H' => 'bol', 'BolSC55t61227H' => 'bol', 'BolSC55t61228H' => 'bol', 'BraA01t03278Z' => 'bra', 'BraA05t18998Z' => 'bra', 'BraA07t28673Z' => 'bra', 'C01p40150' => 'bna', 'C05p12370' => 'bna', 'C07p13680' => 'bna', 'CAN.G1006.16' => 'can', 'CAN.G1006.17' => 'can', 'CAN.G1170.2' => 'can', 'CAN.G962.7' => 'can', 'CANSAT25G2179' => 'cansat', 'CANSAT78G1573' => 'cansat', 'CARHR099510' => 'chi', 'CARHR143510' => 'chi', 'Carub.0003s2380' => 'cru', 'Carub.0004s3082' => 'cru', 'Ca_00614_v3' => 'car', 'Ca_07801_v3' => 'car', 'Ca_08567_v3' => 'car', 'Ca_09571_v3' => 'car', 'CBR_g19290' => 'cbr', 'Cc01_g19770' => 'ccan', 'Cc03_g03030' => 'ccan', 'CDE07G0968' => 'cde', 'CDE09G1441' => 'cde', 'Cfa006103' => 'cfa', 'Cfa015573' => 'cfa', 'Cfa016988' => 'cfa', 'Ciclev10006738m.g' => 'ccl', 'Ciclev10010920m.g' => 'ccl', 'Ciclev10018517m.g' => 'ccl', 'CiPaw.01G159200' => 'cil', 'CiPaw.02G091000' => 'cil', 'CiPaw.02G091100' => 'cil', 'CiPaw.08G103100' => 'cil', 'CiPaw.09G224900' => 'cil', 'ClCG06G005740' => 'cla', 'ClCG07G000090' => 'cla', 'ClCG07G000100' => 'cla', 'COL.COLO4_09143' => 'col', 'COL.COLO4_25124' => 'col', 'Cpa.g.sc16.34' => 'cpa', 'Cpa.g.sc3504.1' => 'cpa', 'Cpa.g.sc60.37' => 'cpa', 'CsaV3_6G018520' => 'csa', 'CsaV3_6G036860' => 'csa', 'CSS0001072' => 'camsi', 'CSS0020208' => 'camsi', 'CSS0021253' => 'camsi', 'CSS0022190' => 'camsi', 'CSS0036150' => 'camsi', 'CSS0040442' => 'camsi', 'CSS0042300' => 'camsi', 'CSS0045298' => 'camsi', 'DCAR_012449' => 'dca', 'DCAR_018405' => 'dca', 'DCAR_024573' => 'dca', 'DCAR_030591' => 'dca', 'Dinv16926' => 'din', 'Dinv32963' => 'din', 'Dinv38382' => 'din', 'Dinv38383' => 'din', 'Duzib133G0974' => 'dzi', 'Duzib138G1867' => 'dzi', 'Duzib211G0420' => 'dzi', 'Duzib212G0930' => 'dzi', 'ECA234G1645' => 'eca', 'ECA247G3467' => 'eca', 'ECA248G1703' => 'eca', 'EL10Ac3g06327' => 'bvu', 'EL10Ac7g17204' => 'bvu', 'Eucgr.A00855' => 'egr', 'Eucgr.A00858' => 'egr', 'Eucgr.H01520' => 'egr', 'Eucgr.H03604' => 'egr', 'Eucgr.L03465' => 'egr', 'Eucgr.L03466' => 'egr', 'FAN01G0988' => 'fan', 'FAN02G3892' => 'fan', 'FAN05G3381' => 'fan', 'FAN07G0967' => 'fan', 'FAN07G1493' => 'fan', 'FAN08G3125' => 'fan', 'FAN09G0402' => 'fan', 'FAN12G2594' => 'fan', 'FAN12G3879' => 'fan', 'FAN14G1546' => 'fan', 'FAN15G3626' => 'fan', 'FAN17G0588' => 'fan', 'FAN17G0609' => 'fan', 'FAN18G2817' => 'fan', 'FAN19G1305' => 'fan', 'FAN20G1787' => 'fan', 'FAN22G0073' => 'fan', 'FAN22G0352' => 'fan', 'FAN22G0368' => 'fan', 'FAN22G2273' => 'fan', 'FAN24G1998' => 'fan', 'FAN27G1317' => 'fan', 'FvH4_2g23980' => 'fve', 'FvH4_4g14380' => 'fve', 'FvH4_4g14390' => 'fve', 'FvH4_6g09250' => 'fve', 'Glyma.03G151100' => 'gma', 'Glyma.04G122550' => 'gma', 'Glyma.05G001600' => 'gma', 'Glyma.09G270766' => 'gma', 'Glyma.09G270832' => 'gma', 'Glyma.13G209800' => 'gma', 'Glyma.15G102800' => 'gma', 'Glyma.18G218900' => 'gma', 'Glyma.19G001500' => 'gma', 'Glyma.19G153600' => 'gma', 'Gohir.A02G028600' => 'ghi', 'Gohir.A08G045000' => 'ghi', 'Gohir.A11G120500' => 'ghi', 'Gohir.A12G006200' => 'ghi', 'Gohir.A12G006250' => 'ghi', 'Gohir.D02G036300' => 'ghi', 'Gohir.D08G054700' => 'ghi', 'Gohir.D11G125600' => 'ghi', 'Gohir.D12G005700' => 'ghi', 'Gorai.004G055200' => 'gra', 'Gorai.005G040400' => 'gra', 'Gorai.007G134500' => 'gra', 'Gorai.008G005500' => 'gra', 'GSVIVG01011094001' => 'vvi', 'GSVIVG01017879001' => 'vvi', 'GSVIVG01025988001' => 'vvi', 'GSVIVG01029847001' => 'vvi', 'HanXRQChr10g0282901' => 'han', 'HanXRQChr10g0310371' => 'han', 'HanXRQChr10g0315041' => 'han', 'HanXRQChr11g0327651' => 'han', 'HanXRQChr12g0359391' => 'han', 'Haze_00972' => 'cav', 'Haze_00973' => 'cav', 'Haze_00974' => 'cav', 'Haze_04747' => 'cav', 'Haze_04749' => 'cav', 'Haze_04750' => 'cav', 'Haze_21217' => 'cav', 'Hma1.2p1_1037F.1_g250680' => 'hma', 'Hma1.2p1_1644F.1_g295320' => 'hma', 'HPP92_011322' => 'vpl', 'HPP92_011323' => 'vpl', 'HPP92_011324' => 'vpl', 'HPP92_011325' => 'vpl', 'HPP92_011326' => 'vpl', 'Hund12205' => 'sun', 'Hund17957' => 'sun', 'Lalb_Chr06g0176771' => 'lal', 'Lalb_Chr18g0056021' => 'lal', 'Lalb_Chr18g0056031' => 'lal', 'Lalb_Chr18g0056041' => 'lal', 'Lalb_Chr20g0107751' => 'lal', 'Lalb_Chr20g0118371' => 'lal', 'Lj1g0010239' => 'lja', 'Lj1g0017101' => 'lja', 'Lj2A1178G40' => 'lonja', 'Lj2A54G84' => 'lonja', 'Lj2g0015248' => 'lja', 'Lj3A761T51' => 'lonja', 'Lj6g0018116' => 'lja', 'Lsat_1_v5_gn_4_136040' => 'lsa', 'Lsat_1_v5_gn_5_187461' => 'lsa', 'Lsat_1_v5_gn_5_77001' => 'lsa', 'Lsat_1_v5_gn_9_4461' => 'lsa', 'Manes.01G210100' => 'mes', 'Manes.03G185600' => 'mes', 'Manes.05G073300' => 'mes', 'Manes.09G120300' => 'mes', 'Manes.15G022100' => 'mes', 'Mapoly0096s0053' => 'mpo', 'MBI03_g14058_MAGBIO' => 'mbi', 'MBI03_g33876_MAGBIO' => 'mbi', 'MBI03_g36854_MAGBIO' => 'mbi', 'MBI17_g11997_MAGBIO' => 'mbi', 'MD03G1269000' => 'mdo', 'MD04G1179600' => 'mdo', 'MD11G1289800' => 'mdo', 'MD12G1194700' => 'mdo', 'MD13G1182100' => 'mdo', 'MD13G1182200' => 'mdo', 'MD16G1182600' => 'mdo', 'Medtr2g021400' => 'mtr', 'Medtr2g021470' => 'mtr', 'Medtr2g105810' => 'mtr', 'Medtr3g033580' => 'mtr', 'Medtr6g007970' => 'mtr', 'Medtr7g056330' => 'mtr', 'Medtr7g074290' => 'mtr', 'Medtr7g074380' => 'mtr', 'Medtr7g094550' => 'mtr', 'Medtr8g069995' => 'mtr', 'MELO3C014345.2' => 'cme', 'MELO3C021395.2' => 'cme', 'Migut.D00262' => 'egut', 'Migut.G00257' => 'egut', 'MSTRG.21575' => 'ama', 'MSTRG.3985' => 'ama', 'Nitab4.5_0000295g0140' => 'nta', 'Nitab4.5_0000732g0140' => 'nta', 'Nitab4.5_0003162g0020' => 'nta', 'Nitab4.5_0006180g0090' => 'nta', 'Nitab4.5_0006390g0010' => 'nta', 'Nitab4.5_0007392g0040' => 'nta', 'Nn1g02140' => 'nnu', 'Nn4g26168' => 'nnu', 'Nn5g26754' => 'nnu', 'Oeu001433.1' => 'oeu', 'Oeu010299.2' => 'oeu', 'Oeu011171.1' => 'oeu', 'Oeu037675.1' => 'oeu', 'Oeu038359.1' => 'oeu', 'Oeu063834.1' => 'oeu', 'Oeu063835.1' => 'oeu', 'Os05g0312000' => 'osa', 'Os07g0211101' => 'osa', 'Os07g0211200' => 'osa', 'Os07g0681500' => 'osa', 'Peaxi162Scf00095g01015' => 'pax', 'Peaxi162Scf00104g00329' => 'pax', 'Peaxi162Scf00161g00137' => 'pax', 'PGR004G1665' => 'pgr', 'PGR031G2937' => 'pgr', 'PGR119G2145' => 'pgr', 'PGSC0003DMG400004351' => 'stu', 'PGSC0003DMG400014625' => 'stu', 'PGSC0003DMG401000943' => 'stu', 'Phvul.001G148600' => 'pvu', 'Phvul.004G001700' => 'pvu', 'Phvul.006G154900' => 'pvu', 'Phvul.008G078200' => 'pvu', 'Phvul.011G136500' => 'pvu', 'Potri.002G215600' => 'ptr', 'Potri.008G201600' => 'ptr', 'Potri.014G138400' => 'ptr', 'Potri.016G142500' => 'ptr', 'Pp3c16_10580' => 'ppa', 'Pp3c5_25280' => 'ppa', 'Prupe.1G150000' => 'ppe', 'Prupe.1G150100' => 'ppe', 'Prupe.6G299600' => 'ppe', 'Prupe.8G245000' => 'ppe', 'Psat0s4927g0040' => 'psa', 'Psat1g052080' => 'psa', 'Psat1g183800' => 'psa', 'Psat3g113840' => 'psa', 'Psat3g126120' => 'psa', 'Psat3g126160' => 'psa', 'Psat3g158760' => 'psa', 'Psat3g158840' => 'psa', 'PSO170G2858' => 'pso', 'PSO339G0606' => 'pso', 'PSO384G4709' => 'pso', 'PSO407G0334' => 'pso', 'QL04p040276' => 'qlo', 'QL06p005458' => 'qlo', 'QL06p005472' => 'qlo', 'QL07p030546' => 'qlo', 'QL07p031519' => 'qlo', 'QL09p050949' => 'qlo', 'QL09p050966' => 'qlo', 'QL09p051067' => 'qlo', 'QL12p022706' => 'qlo', 'RcHm_v2.0_Chr2g0119601' => 'rch', 'RcHm_v2.0_Chr3g0459591' => 'rch', 'RcHm_v2.0_Chr4g0418521' => 'rch', 'RcHm_v2.0_Chr4g0418531' => 'rch', 'RcHm_v2.0_Chr4g0418541' => 'rch', 'RcHm_v2.0_Chr6g0291641' => 'rch', 'Rhsim01G0086300' => 'rsi', 'Rhsim01G0276300' => 'rsi', 'Rhsim01G0276500' => 'rsi', 'Rhsim04G0207700' => 'rsi', 'Rhsim05G0234500' => 'rsi', 'Rhsim13G0022400' => 'rsi', 'Sabra02G0167900' => 'sbr', 'Sabra04G0158500' => 'sbr', 'Sabra08G0159800' => 'sbr', 'Sabra10G0011500' => 'sbr', 'Sabra14G0104400' => 'sbr', 'SalBow2G2440' => 'sbo', 'SalBow4G2265' => 'sbo', 'Sc02g0000060' => 'sci', 'Sc05g0005020' => 'sci', 'Sc13g0003890' => 'sci', 'Sed0014865' => 'sed', 'Sed0017224' => 'sed', 'Sed0026391' => 'sed', 'SEGI_00063' => 'sgi', 'SEGI_10967' => 'sgi', 'SEGI_17510' => 'sgi', 'SEGI_24396' => 'sgi', 'SEGI_39719' => 'sgi', 'SEGI_41392' => 'sgi', 'SGA_v2.0_scaffold11G05794' => 'sas', 'SGA_v2.0_scaffold142G35607' => 'sas', 'SGA_v2.0_scaffold1G00447' => 'sas', 'SHI15388' => 'shi', 'SHI15394' => 'shi', 'SHI15396' => 'shi', 'SHI15399' => 'shi', 'SMO343G0151' => 'smo', 'SMO367G1118' => 'smo', 'Solyc01g080200.3' => 'sly', 'Solyc06g008960.3' => 'sly', 'Solyc09g064780.3' => 'sly', 'Sopen01g031980' => 'spe', 'Sopen06g003710' => 'spe', 'Sopen09g026460' => 'spe', 'Sp3g21240' => 'spa', 'Sp4g30030' => 'spa', 'TAR365G0022' => 'tar', 'TAR365G1023' => 'tar', 'TAR365G1253' => 'tar', 'TAR623G0078' => 'tar', 'TAR623G1721' => 'tar', 'TAR633G0959' => 'tar', 'THA.LOC104802225' => 'tha', 'THA.LOC104804769' => 'tha', 'THA.LOC104808660' => 'tha', 'THA.LOC104812792' => 'tha', 'Thecc.01G284000' => 'tca', 'Thecc.04G220600' => 'tca', 'Thecc.05G268900' => 'tca', 'Thecc.08G171100' => 'tca', 'Thhalv10001284m.g' => 'esa', 'Thhalv10019912m.g' => 'esa', 'TPR.G14189' => 'tpr', 'TPR.G18110' => 'tpr', 'TPR.G18130' => 'tpr', 'TPR.G18131' => 'tpr', 'TPR.G18140' => 'tpr', 'TPR.G24282' => 'tpr', 'TPR.G25221' => 'tpr', 'TPR.G29267' => 'tpr', 'TPR.G35315' => 'tpr', 'TPR.G36173' => 'tpr', 'TWI09G0794' => 'twi', 'TWI59G1348' => 'twi', 'TWI74G0430' => 'twi', 'unitig_26.g8940' => 'ugi', 'unitig_749.g13744' => 'ugi', 'unitig_749.g13745' => 'ugi', 'vmacro08269' => 'vma', 'vmacro14937' => 'vma', 'vmacro20401' => 'vma', 'VMungo0464G1349' => 'vmu', 'VMungo0540G0289' => 'vmu', 'VMungo1215G1590' => 'vmu', 'VMungo1309G0221' => 'vmu', 'VMungo1309G2815' => 'vmu', 'VMungo1383G0239' => 'vmu', 'VMungo1383G2910' => 'vmu', 'Zm00001eb095270' => 'zma', 'Zm00001eb095280' => 'zma', 'Zm00001eb111630' => 'zma', 'Zm00001eb237080' => 'zma', 'Zm00001eb273740' => 'zma', 'Zm00001eb285040' => 'zma', 'Zm00001eb330790' => 'zma', 'Zm00001eb337380' => 'zma' ) $gf_id = 'HOM05D001484' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001484' ) $data_identifier = 'HOM05D001484' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 2, 'aly' => (int) 2, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 22, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 7, 'hma' => (int) 2, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 7, 'mtr' => (int) 10, 'cme' => (int) 2, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 4, 'ppa' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 4, 'qlo' => (int) 9, 'rch' => (int) 6, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 10, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 7, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb337380' $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' => 'HOM05D001484', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p31500' => 'bna', 'A05p00020' => 'bna', 'A07p08820' => 'bna', 'Aa31LG4G3300' => 'aar', 'Aa31LG8G10030' => 'aar', 'Actinidia00731' => 'ach', 'Actinidia11473' => 'ach', 'Actinidia23469' => 'ach', 'Actinidia24318' => 'ach', 'Actinidia40196' => 'ach', 'Actinidia40197' => 'ach', 'Actinidia40198' => 'ach', 'Ah.08g212990' => 'amhyb', 'Ah.15g091720' => 'amhyb', 'AL3G38260' => 'aly', 'AL4G47710' => 'aly', 'Aqoxy2G00671' => 'aox', 'Aqoxy2G03236' => 'aox', 'arahy.Tifrunner.gnm1.ann1.05IDCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KR684' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATY3SJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK6QJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6APGL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IDT7Z9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM073U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ0R87' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LE7RV4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT4QRX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V5ENPK' => 'arhy', 'AT2G48110' => 'ath', 'AT3G23590' => 'ath', 'ATR0626G186' => 'atr', 'ATR1127G141' => 'atr', 'Atru.chr4.2583' => 'acertr', 'Atru.chr5.1358' => 'acertr', 'Atru.chr5.1359' => 'acertr', 'Atru.chr8.46' => 'acertr', 'AUR62002640' => 'cqu', 'AUR62030055' => 'cqu', 'AUR62033713' => 'cqu', 'AUR62033714' => 'cqu', 'AUR62036795' => 'cqu', 'AUR62039891' => 'cqu', 'BcaB02g08737' => 'bca', 'BcaB04g20441' => 'bca', 'BcaB06g26509' => 'bca', 'BcaB06g26510' => 'bca', 'BcaB06g26511' => 'bca', 'BcaB06g26512' => 'bca', 'BcaB06g26513' => 'bca', 'BcaC02g12564' => 'bca', 'BcaC02g12565' => 'bca', 'BcaC02g12794' => 'bca', 'BcaC02g12795' => 'bca', 'BcaC02g12796' => 'bca', 'BcaC06g35541' => 'bca', 'BNapus_Darmor_BZH_scaffold_188p00080' => 'bna', 'BNapus_Darmor_BZH_scaffold_188p00090' => 'bna', 'BolC1t03972H' => 'bol', 'BolC1t03973H' => 'bol', 'BolC4t21680H' => 'bol', 'BolC7t41863H' => 'bol', 'BolSC55t61227H' => 'bol', 'BolSC55t61228H' => 'bol', 'BraA01t03278Z' => 'bra', 'BraA05t18998Z' => 'bra', 'BraA07t28673Z' => 'bra', 'C01p40150' => 'bna', 'C05p12370' => 'bna', 'C07p13680' => 'bna', 'CAN.G1006.16' => 'can', 'CAN.G1006.17' => 'can', 'CAN.G1170.2' => 'can', 'CAN.G962.7' => 'can', 'CANSAT25G2179' => 'cansat', 'CANSAT78G1573' => 'cansat', 'CARHR099510' => 'chi', 'CARHR143510' => 'chi', 'Carub.0003s2380' => 'cru', 'Carub.0004s3082' => 'cru', 'Ca_00614_v3' => 'car', 'Ca_07801_v3' => 'car', 'Ca_08567_v3' => 'car', 'Ca_09571_v3' => 'car', 'CBR_g19290' => 'cbr', 'Cc01_g19770' => 'ccan', 'Cc03_g03030' => 'ccan', 'CDE07G0968' => 'cde', 'CDE09G1441' => 'cde', 'Cfa006103' => 'cfa', 'Cfa015573' => 'cfa', 'Cfa016988' => 'cfa', 'Ciclev10006738m.g' => 'ccl', 'Ciclev10010920m.g' => 'ccl', 'Ciclev10018517m.g' => 'ccl', 'CiPaw.01G159200' => 'cil', 'CiPaw.02G091000' => 'cil', 'CiPaw.02G091100' => 'cil', 'CiPaw.08G103100' => 'cil', 'CiPaw.09G224900' => 'cil', 'ClCG06G005740' => 'cla', 'ClCG07G000090' => 'cla', 'ClCG07G000100' => 'cla', 'COL.COLO4_09143' => 'col', 'COL.COLO4_25124' => 'col', 'Cpa.g.sc16.34' => 'cpa', 'Cpa.g.sc3504.1' => 'cpa', 'Cpa.g.sc60.37' => 'cpa', 'CsaV3_6G018520' => 'csa', 'CsaV3_6G036860' => 'csa', 'CSS0001072' => 'camsi', 'CSS0020208' => 'camsi', 'CSS0021253' => 'camsi', 'CSS0022190' => 'camsi', 'CSS0036150' => 'camsi', 'CSS0040442' => 'camsi', 'CSS0042300' => 'camsi', 'CSS0045298' => 'camsi', 'DCAR_012449' => 'dca', 'DCAR_018405' => 'dca', 'DCAR_024573' => 'dca', 'DCAR_030591' => 'dca', 'Dinv16926' => 'din', 'Dinv32963' => 'din', 'Dinv38382' => 'din', 'Dinv38383' => 'din', 'Duzib133G0974' => 'dzi', 'Duzib138G1867' => 'dzi', 'Duzib211G0420' => 'dzi', 'Duzib212G0930' => 'dzi', 'ECA234G1645' => 'eca', 'ECA247G3467' => 'eca', 'ECA248G1703' => 'eca', 'EL10Ac3g06327' => 'bvu', 'EL10Ac7g17204' => 'bvu', 'Eucgr.A00855' => 'egr', 'Eucgr.A00858' => 'egr', 'Eucgr.H01520' => 'egr', 'Eucgr.H03604' => 'egr', 'Eucgr.L03465' => 'egr', 'Eucgr.L03466' => 'egr', 'FAN01G0988' => 'fan', 'FAN02G3892' => 'fan', 'FAN05G3381' => 'fan', 'FAN07G0967' => 'fan', 'FAN07G1493' => 'fan', 'FAN08G3125' => 'fan', 'FAN09G0402' => 'fan', 'FAN12G2594' => 'fan', 'FAN12G3879' => 'fan', 'FAN14G1546' => 'fan', 'FAN15G3626' => 'fan', 'FAN17G0588' => 'fan', 'FAN17G0609' => 'fan', 'FAN18G2817' => 'fan', 'FAN19G1305' => 'fan', 'FAN20G1787' => 'fan', 'FAN22G0073' => 'fan', 'FAN22G0352' => 'fan', 'FAN22G0368' => 'fan', 'FAN22G2273' => 'fan', 'FAN24G1998' => 'fan', 'FAN27G1317' => 'fan', 'FvH4_2g23980' => 'fve', 'FvH4_4g14380' => 'fve', 'FvH4_4g14390' => 'fve', 'FvH4_6g09250' => 'fve', 'Glyma.03G151100' => 'gma', 'Glyma.04G122550' => 'gma', 'Glyma.05G001600' => 'gma', 'Glyma.09G270766' => 'gma', 'Glyma.09G270832' => 'gma', 'Glyma.13G209800' => 'gma', 'Glyma.15G102800' => 'gma', 'Glyma.18G218900' => 'gma', 'Glyma.19G001500' => 'gma', 'Glyma.19G153600' => 'gma', 'Gohir.A02G028600' => 'ghi', 'Gohir.A08G045000' => 'ghi', 'Gohir.A11G120500' => 'ghi', 'Gohir.A12G006200' => 'ghi', 'Gohir.A12G006250' => 'ghi', 'Gohir.D02G036300' => 'ghi', 'Gohir.D08G054700' => 'ghi', 'Gohir.D11G125600' => 'ghi', 'Gohir.D12G005700' => 'ghi', 'Gorai.004G055200' => 'gra', 'Gorai.005G040400' => 'gra', 'Gorai.007G134500' => 'gra', 'Gorai.008G005500' => 'gra', 'GSVIVG01011094001' => 'vvi', 'GSVIVG01017879001' => 'vvi', 'GSVIVG01025988001' => 'vvi', 'GSVIVG01029847001' => 'vvi', 'HanXRQChr10g0282901' => 'han', 'HanXRQChr10g0310371' => 'han', 'HanXRQChr10g0315041' => 'han', 'HanXRQChr11g0327651' => 'han', 'HanXRQChr12g0359391' => 'han', 'Haze_00972' => 'cav', 'Haze_00973' => 'cav', 'Haze_00974' => 'cav', 'Haze_04747' => 'cav', 'Haze_04749' => 'cav', 'Haze_04750' => 'cav', 'Haze_21217' => 'cav', 'Hma1.2p1_1037F.1_g250680' => 'hma', 'Hma1.2p1_1644F.1_g295320' => 'hma', 'HPP92_011322' => 'vpl', 'HPP92_011323' => 'vpl', 'HPP92_011324' => 'vpl', 'HPP92_011325' => 'vpl', 'HPP92_011326' => 'vpl', 'Hund12205' => 'sun', 'Hund17957' => 'sun', 'Lalb_Chr06g0176771' => 'lal', 'Lalb_Chr18g0056021' => 'lal', 'Lalb_Chr18g0056031' => 'lal', 'Lalb_Chr18g0056041' => 'lal', 'Lalb_Chr20g0107751' => 'lal', 'Lalb_Chr20g0118371' => 'lal', 'Lj1g0010239' => 'lja', 'Lj1g0017101' => 'lja', 'Lj2A1178G40' => 'lonja', 'Lj2A54G84' => 'lonja', 'Lj2g0015248' => 'lja', 'Lj3A761T51' => 'lonja', 'Lj6g0018116' => 'lja', 'Lsat_1_v5_gn_4_136040' => 'lsa', 'Lsat_1_v5_gn_5_187461' => 'lsa', 'Lsat_1_v5_gn_5_77001' => 'lsa', 'Lsat_1_v5_gn_9_4461' => 'lsa', 'Manes.01G210100' => 'mes', 'Manes.03G185600' => 'mes', 'Manes.05G073300' => 'mes', 'Manes.09G120300' => 'mes', 'Manes.15G022100' => 'mes', 'Mapoly0096s0053' => 'mpo', 'MBI03_g14058_MAGBIO' => 'mbi', 'MBI03_g33876_MAGBIO' => 'mbi', 'MBI03_g36854_MAGBIO' => 'mbi', 'MBI17_g11997_MAGBIO' => 'mbi', 'MD03G1269000' => 'mdo', 'MD04G1179600' => 'mdo', 'MD11G1289800' => 'mdo', 'MD12G1194700' => 'mdo', 'MD13G1182100' => 'mdo', 'MD13G1182200' => 'mdo', 'MD16G1182600' => 'mdo', 'Medtr2g021400' => 'mtr', 'Medtr2g021470' => 'mtr', 'Medtr2g105810' => 'mtr', 'Medtr3g033580' => 'mtr', 'Medtr6g007970' => 'mtr', 'Medtr7g056330' => 'mtr', 'Medtr7g074290' => 'mtr', 'Medtr7g074380' => 'mtr', 'Medtr7g094550' => 'mtr', 'Medtr8g069995' => 'mtr', 'MELO3C014345.2' => 'cme', 'MELO3C021395.2' => 'cme', 'Migut.D00262' => 'egut', 'Migut.G00257' => 'egut', 'MSTRG.21575' => 'ama', 'MSTRG.3985' => 'ama', 'Nitab4.5_0000295g0140' => 'nta', 'Nitab4.5_0000732g0140' => 'nta', 'Nitab4.5_0003162g0020' => 'nta', 'Nitab4.5_0006180g0090' => 'nta', 'Nitab4.5_0006390g0010' => 'nta', 'Nitab4.5_0007392g0040' => 'nta', 'Nn1g02140' => 'nnu', 'Nn4g26168' => 'nnu', 'Nn5g26754' => 'nnu', 'Oeu001433.1' => 'oeu', 'Oeu010299.2' => 'oeu', 'Oeu011171.1' => 'oeu', 'Oeu037675.1' => 'oeu', 'Oeu038359.1' => 'oeu', 'Oeu063834.1' => 'oeu', 'Oeu063835.1' => 'oeu', 'Os05g0312000' => 'osa', 'Os07g0211101' => 'osa', 'Os07g0211200' => 'osa', 'Os07g0681500' => 'osa', 'Peaxi162Scf00095g01015' => 'pax', 'Peaxi162Scf00104g00329' => 'pax', 'Peaxi162Scf00161g00137' => 'pax', 'PGR004G1665' => 'pgr', 'PGR031G2937' => 'pgr', 'PGR119G2145' => 'pgr', 'PGSC0003DMG400004351' => 'stu', 'PGSC0003DMG400014625' => 'stu', 'PGSC0003DMG401000943' => 'stu', 'Phvul.001G148600' => 'pvu', 'Phvul.004G001700' => 'pvu', 'Phvul.006G154900' => 'pvu', 'Phvul.008G078200' => 'pvu', 'Phvul.011G136500' => 'pvu', 'Potri.002G215600' => 'ptr', 'Potri.008G201600' => 'ptr', 'Potri.014G138400' => 'ptr', 'Potri.016G142500' => 'ptr', 'Pp3c16_10580' => 'ppa', 'Pp3c5_25280' => 'ppa', 'Prupe.1G150000' => 'ppe', 'Prupe.1G150100' => 'ppe', 'Prupe.6G299600' => 'ppe', 'Prupe.8G245000' => 'ppe', 'Psat0s4927g0040' => 'psa', 'Psat1g052080' => 'psa', 'Psat1g183800' => 'psa', 'Psat3g113840' => 'psa', 'Psat3g126120' => 'psa', 'Psat3g126160' => 'psa', 'Psat3g158760' => 'psa', 'Psat3g158840' => 'psa', 'PSO170G2858' => 'pso', 'PSO339G0606' => 'pso', 'PSO384G4709' => 'pso', 'PSO407G0334' => 'pso', 'QL04p040276' => 'qlo', 'QL06p005458' => 'qlo', 'QL06p005472' => 'qlo', 'QL07p030546' => 'qlo', 'QL07p031519' => 'qlo', 'QL09p050949' => 'qlo', 'QL09p050966' => 'qlo', 'QL09p051067' => 'qlo', 'QL12p022706' => 'qlo', 'RcHm_v2.0_Chr2g0119601' => 'rch', 'RcHm_v2.0_Chr3g0459591' => 'rch', 'RcHm_v2.0_Chr4g0418521' => 'rch', 'RcHm_v2.0_Chr4g0418531' => 'rch', 'RcHm_v2.0_Chr4g0418541' => 'rch', 'RcHm_v2.0_Chr6g0291641' => 'rch', 'Rhsim01G0086300' => 'rsi', 'Rhsim01G0276300' => 'rsi', 'Rhsim01G0276500' => 'rsi', 'Rhsim04G0207700' => 'rsi', 'Rhsim05G0234500' => 'rsi', 'Rhsim13G0022400' => 'rsi', 'Sabra02G0167900' => 'sbr', 'Sabra04G0158500' => 'sbr', 'Sabra08G0159800' => 'sbr', 'Sabra10G0011500' => 'sbr', 'Sabra14G0104400' => 'sbr', 'SalBow2G2440' => 'sbo', 'SalBow4G2265' => 'sbo', 'Sc02g0000060' => 'sci', 'Sc05g0005020' => 'sci', 'Sc13g0003890' => 'sci', 'Sed0014865' => 'sed', 'Sed0017224' => 'sed', 'Sed0026391' => 'sed', 'SEGI_00063' => 'sgi', 'SEGI_10967' => 'sgi', 'SEGI_17510' => 'sgi', 'SEGI_24396' => 'sgi', 'SEGI_39719' => 'sgi', 'SEGI_41392' => 'sgi', 'SGA_v2.0_scaffold11G05794' => 'sas', 'SGA_v2.0_scaffold142G35607' => 'sas', 'SGA_v2.0_scaffold1G00447' => 'sas', 'SHI15388' => 'shi', 'SHI15394' => 'shi', 'SHI15396' => 'shi', 'SHI15399' => 'shi', 'SMO343G0151' => 'smo', 'SMO367G1118' => 'smo', 'Solyc01g080200.3' => 'sly', 'Solyc06g008960.3' => 'sly', 'Solyc09g064780.3' => 'sly', 'Sopen01g031980' => 'spe', 'Sopen06g003710' => 'spe', 'Sopen09g026460' => 'spe', 'Sp3g21240' => 'spa', 'Sp4g30030' => 'spa', 'TAR365G0022' => 'tar', 'TAR365G1023' => 'tar', 'TAR365G1253' => 'tar', 'TAR623G0078' => 'tar', 'TAR623G1721' => 'tar', 'TAR633G0959' => 'tar', 'THA.LOC104802225' => 'tha', 'THA.LOC104804769' => 'tha', 'THA.LOC104808660' => 'tha', 'THA.LOC104812792' => 'tha', 'Thecc.01G284000' => 'tca', 'Thecc.04G220600' => 'tca', 'Thecc.05G268900' => 'tca', 'Thecc.08G171100' => 'tca', 'Thhalv10001284m.g' => 'esa', 'Thhalv10019912m.g' => 'esa', 'TPR.G14189' => 'tpr', 'TPR.G18110' => 'tpr', 'TPR.G18130' => 'tpr', 'TPR.G18131' => 'tpr', 'TPR.G18140' => 'tpr', 'TPR.G24282' => 'tpr', 'TPR.G25221' => 'tpr', 'TPR.G29267' => 'tpr', 'TPR.G35315' => 'tpr', 'TPR.G36173' => 'tpr', 'TWI09G0794' => 'twi', 'TWI59G1348' => 'twi', 'TWI74G0430' => 'twi', 'unitig_26.g8940' => 'ugi', 'unitig_749.g13744' => 'ugi', 'unitig_749.g13745' => 'ugi', 'vmacro08269' => 'vma', 'vmacro14937' => 'vma', 'vmacro20401' => 'vma', 'VMungo0464G1349' => 'vmu', 'VMungo0540G0289' => 'vmu', 'VMungo1215G1590' => 'vmu', 'VMungo1309G0221' => 'vmu', 'VMungo1309G2815' => 'vmu', 'VMungo1383G0239' => 'vmu', 'VMungo1383G2910' => 'vmu', 'Zm00001eb095270' => 'zma', 'Zm00001eb095280' => 'zma', 'Zm00001eb111630' => 'zma', 'Zm00001eb237080' => 'zma', 'Zm00001eb273740' => 'zma', 'Zm00001eb285040' => 'zma', 'Zm00001eb330790' => 'zma', 'Zm00001eb337380' => 'zma' ), 'gf_id' => 'HOM05D001484', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001484' ), 'data_identifier' => 'HOM05D001484', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001484', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p31500' => 'bna', 'A05p00020' => 'bna', 'A07p08820' => 'bna', 'Aa31LG4G3300' => 'aar', 'Aa31LG8G10030' => 'aar', 'Actinidia00731' => 'ach', 'Actinidia11473' => 'ach', 'Actinidia23469' => 'ach', 'Actinidia24318' => 'ach', 'Actinidia40196' => 'ach', 'Actinidia40197' => 'ach', 'Actinidia40198' => 'ach', 'Ah.08g212990' => 'amhyb', 'Ah.15g091720' => 'amhyb', 'AL3G38260' => 'aly', 'AL4G47710' => 'aly', 'Aqoxy2G00671' => 'aox', 'Aqoxy2G03236' => 'aox', 'arahy.Tifrunner.gnm1.ann1.05IDCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KR684' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATY3SJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK6QJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6APGL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IDT7Z9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM073U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ0R87' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LE7RV4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT4QRX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V5ENPK' => 'arhy', 'AT2G48110' => 'ath', 'AT3G23590' => 'ath', 'ATR0626G186' => 'atr', 'ATR1127G141' => 'atr', 'Atru.chr4.2583' => 'acertr', 'Atru.chr5.1358' => 'acertr', 'Atru.chr5.1359' => 'acertr', 'Atru.chr8.46' => 'acertr', 'AUR62002640' => 'cqu', 'AUR62030055' => 'cqu', 'AUR62033713' => 'cqu', 'AUR62033714' => 'cqu', 'AUR62036795' => 'cqu', 'AUR62039891' => 'cqu', 'BcaB02g08737' => 'bca', 'BcaB04g20441' => 'bca', 'BcaB06g26509' => 'bca', 'BcaB06g26510' => 'bca', 'BcaB06g26511' => 'bca', 'BcaB06g26512' => 'bca', 'BcaB06g26513' => 'bca', 'BcaC02g12564' => 'bca', 'BcaC02g12565' => 'bca', 'BcaC02g12794' => 'bca', 'BcaC02g12795' => 'bca', 'BcaC02g12796' => 'bca', 'BcaC06g35541' => 'bca', 'BNapus_Darmor_BZH_scaffold_188p00080' => 'bna', 'BNapus_Darmor_BZH_scaffold_188p00090' => 'bna', 'BolC1t03972H' => 'bol', 'BolC1t03973H' => 'bol', 'BolC4t21680H' => 'bol', 'BolC7t41863H' => 'bol', 'BolSC55t61227H' => 'bol', 'BolSC55t61228H' => 'bol', 'BraA01t03278Z' => 'bra', 'BraA05t18998Z' => 'bra', 'BraA07t28673Z' => 'bra', 'C01p40150' => 'bna', 'C05p12370' => 'bna', 'C07p13680' => 'bna', 'CAN.G1006.16' => 'can', 'CAN.G1006.17' => 'can', 'CAN.G1170.2' => 'can', 'CAN.G962.7' => 'can', 'CANSAT25G2179' => 'cansat', 'CANSAT78G1573' => 'cansat', 'CARHR099510' => 'chi', 'CARHR143510' => 'chi', 'Carub.0003s2380' => 'cru', 'Carub.0004s3082' => 'cru', 'Ca_00614_v3' => 'car', 'Ca_07801_v3' => 'car', 'Ca_08567_v3' => 'car', 'Ca_09571_v3' => 'car', 'CBR_g19290' => 'cbr', 'Cc01_g19770' => 'ccan', 'Cc03_g03030' => 'ccan', 'CDE07G0968' => 'cde', 'CDE09G1441' => 'cde', 'Cfa006103' => 'cfa', 'Cfa015573' => 'cfa', 'Cfa016988' => 'cfa', 'Ciclev10006738m.g' => 'ccl', 'Ciclev10010920m.g' => 'ccl', 'Ciclev10018517m.g' => 'ccl', 'CiPaw.01G159200' => 'cil', 'CiPaw.02G091000' => 'cil', 'CiPaw.02G091100' => 'cil', 'CiPaw.08G103100' => 'cil', 'CiPaw.09G224900' => 'cil', 'ClCG06G005740' => 'cla', 'ClCG07G000090' => 'cla', 'ClCG07G000100' => 'cla', 'COL.COLO4_09143' => 'col', 'COL.COLO4_25124' => 'col', 'Cpa.g.sc16.34' => 'cpa', 'Cpa.g.sc3504.1' => 'cpa', 'Cpa.g.sc60.37' => 'cpa', 'CsaV3_6G018520' => 'csa', 'CsaV3_6G036860' => 'csa', 'CSS0001072' => 'camsi', 'CSS0020208' => 'camsi', 'CSS0021253' => 'camsi', 'CSS0022190' => 'camsi', 'CSS0036150' => 'camsi', 'CSS0040442' => 'camsi', 'CSS0042300' => 'camsi', 'CSS0045298' => 'camsi', 'DCAR_012449' => 'dca', 'DCAR_018405' => 'dca', 'DCAR_024573' => 'dca', 'DCAR_030591' => 'dca', 'Dinv16926' => 'din', 'Dinv32963' => 'din', 'Dinv38382' => 'din', 'Dinv38383' => 'din', 'Duzib133G0974' => 'dzi', 'Duzib138G1867' => 'dzi', 'Duzib211G0420' => 'dzi', 'Duzib212G0930' => 'dzi', 'ECA234G1645' => 'eca', 'ECA247G3467' => 'eca', 'ECA248G1703' => 'eca', 'EL10Ac3g06327' => 'bvu', 'EL10Ac7g17204' => 'bvu', 'Eucgr.A00855' => 'egr', 'Eucgr.A00858' => 'egr', 'Eucgr.H01520' => 'egr', 'Eucgr.H03604' => 'egr', 'Eucgr.L03465' => 'egr', 'Eucgr.L03466' => 'egr', 'FAN01G0988' => 'fan', 'FAN02G3892' => 'fan', 'FAN05G3381' => 'fan', 'FAN07G0967' => 'fan', 'FAN07G1493' => 'fan', 'FAN08G3125' => 'fan', 'FAN09G0402' => 'fan', 'FAN12G2594' => 'fan', 'FAN12G3879' => 'fan', 'FAN14G1546' => 'fan', 'FAN15G3626' => 'fan', 'FAN17G0588' => 'fan', 'FAN17G0609' => 'fan', 'FAN18G2817' => 'fan', 'FAN19G1305' => 'fan', 'FAN20G1787' => 'fan', 'FAN22G0073' => 'fan', 'FAN22G0352' => 'fan', 'FAN22G0368' => 'fan', 'FAN22G2273' => 'fan', 'FAN24G1998' => 'fan', 'FAN27G1317' => 'fan', 'FvH4_2g23980' => 'fve', 'FvH4_4g14380' => 'fve', 'FvH4_4g14390' => 'fve', 'FvH4_6g09250' => 'fve', 'Glyma.03G151100' => 'gma', 'Glyma.04G122550' => 'gma', 'Glyma.05G001600' => 'gma', 'Glyma.09G270766' => 'gma', 'Glyma.09G270832' => 'gma', 'Glyma.13G209800' => 'gma', 'Glyma.15G102800' => 'gma', 'Glyma.18G218900' => 'gma', 'Glyma.19G001500' => 'gma', 'Glyma.19G153600' => 'gma', 'Gohir.A02G028600' => 'ghi', 'Gohir.A08G045000' => 'ghi', 'Gohir.A11G120500' => 'ghi', 'Gohir.A12G006200' => 'ghi', 'Gohir.A12G006250' => 'ghi', 'Gohir.D02G036300' => 'ghi', 'Gohir.D08G054700' => 'ghi', 'Gohir.D11G125600' => 'ghi', 'Gohir.D12G005700' => 'ghi', 'Gorai.004G055200' => 'gra', 'Gorai.005G040400' => 'gra', 'Gorai.007G134500' => 'gra', 'Gorai.008G005500' => 'gra', 'GSVIVG01011094001' => 'vvi', 'GSVIVG01017879001' => 'vvi', 'GSVIVG01025988001' => 'vvi', 'GSVIVG01029847001' => 'vvi', 'HanXRQChr10g0282901' => 'han', 'HanXRQChr10g0310371' => 'han', 'HanXRQChr10g0315041' => 'han', 'HanXRQChr11g0327651' => 'han', 'HanXRQChr12g0359391' => 'han', 'Haze_00972' => 'cav', 'Haze_00973' => 'cav', 'Haze_00974' => 'cav', 'Haze_04747' => 'cav', 'Haze_04749' => 'cav', 'Haze_04750' => 'cav', 'Haze_21217' => 'cav', 'Hma1.2p1_1037F.1_g250680' => 'hma', 'Hma1.2p1_1644F.1_g295320' => 'hma', 'HPP92_011322' => 'vpl', 'HPP92_011323' => 'vpl', 'HPP92_011324' => 'vpl', 'HPP92_011325' => 'vpl', 'HPP92_011326' => 'vpl', 'Hund12205' => 'sun', 'Hund17957' => 'sun', 'Lalb_Chr06g0176771' => 'lal', 'Lalb_Chr18g0056021' => 'lal', 'Lalb_Chr18g0056031' => 'lal', 'Lalb_Chr18g0056041' => 'lal', 'Lalb_Chr20g0107751' => 'lal', 'Lalb_Chr20g0118371' => 'lal', 'Lj1g0010239' => 'lja', 'Lj1g0017101' => 'lja', 'Lj2A1178G40' => 'lonja', 'Lj2A54G84' => 'lonja', 'Lj2g0015248' => 'lja', 'Lj3A761T51' => 'lonja', 'Lj6g0018116' => 'lja', 'Lsat_1_v5_gn_4_136040' => 'lsa', 'Lsat_1_v5_gn_5_187461' => 'lsa', 'Lsat_1_v5_gn_5_77001' => 'lsa', 'Lsat_1_v5_gn_9_4461' => 'lsa', 'Manes.01G210100' => 'mes', 'Manes.03G185600' => 'mes', 'Manes.05G073300' => 'mes', 'Manes.09G120300' => 'mes', 'Manes.15G022100' => 'mes', 'Mapoly0096s0053' => 'mpo', 'MBI03_g14058_MAGBIO' => 'mbi', 'MBI03_g33876_MAGBIO' => 'mbi', 'MBI03_g36854_MAGBIO' => 'mbi', 'MBI17_g11997_MAGBIO' => 'mbi', 'MD03G1269000' => 'mdo', 'MD04G1179600' => 'mdo', 'MD11G1289800' => 'mdo', 'MD12G1194700' => 'mdo', 'MD13G1182100' => 'mdo', 'MD13G1182200' => 'mdo', 'MD16G1182600' => 'mdo', 'Medtr2g021400' => 'mtr', 'Medtr2g021470' => 'mtr', 'Medtr2g105810' => 'mtr', 'Medtr3g033580' => 'mtr', 'Medtr6g007970' => 'mtr', 'Medtr7g056330' => 'mtr', 'Medtr7g074290' => 'mtr', 'Medtr7g074380' => 'mtr', 'Medtr7g094550' => 'mtr', 'Medtr8g069995' => 'mtr', 'MELO3C014345.2' => 'cme', 'MELO3C021395.2' => 'cme', 'Migut.D00262' => 'egut', 'Migut.G00257' => 'egut', 'MSTRG.21575' => 'ama', 'MSTRG.3985' => 'ama', 'Nitab4.5_0000295g0140' => 'nta', 'Nitab4.5_0000732g0140' => 'nta', 'Nitab4.5_0003162g0020' => 'nta', 'Nitab4.5_0006180g0090' => 'nta', 'Nitab4.5_0006390g0010' => 'nta', 'Nitab4.5_0007392g0040' => 'nta', 'Nn1g02140' => 'nnu', 'Nn4g26168' => 'nnu', 'Nn5g26754' => 'nnu', 'Oeu001433.1' => 'oeu', 'Oeu010299.2' => 'oeu', 'Oeu011171.1' => 'oeu', 'Oeu037675.1' => 'oeu', 'Oeu038359.1' => 'oeu', 'Oeu063834.1' => 'oeu', 'Oeu063835.1' => 'oeu', 'Os05g0312000' => 'osa', 'Os07g0211101' => 'osa', 'Os07g0211200' => 'osa', 'Os07g0681500' => 'osa', 'Peaxi162Scf00095g01015' => 'pax', 'Peaxi162Scf00104g00329' => 'pax', 'Peaxi162Scf00161g00137' => 'pax', 'PGR004G1665' => 'pgr', 'PGR031G2937' => 'pgr', 'PGR119G2145' => 'pgr', 'PGSC0003DMG400004351' => 'stu', 'PGSC0003DMG400014625' => 'stu', 'PGSC0003DMG401000943' => 'stu', 'Phvul.001G148600' => 'pvu', 'Phvul.004G001700' => 'pvu', 'Phvul.006G154900' => 'pvu', 'Phvul.008G078200' => 'pvu', 'Phvul.011G136500' => 'pvu', 'Potri.002G215600' => 'ptr', 'Potri.008G201600' => 'ptr', 'Potri.014G138400' => 'ptr', 'Potri.016G142500' => 'ptr', 'Pp3c16_10580' => 'ppa', 'Pp3c5_25280' => 'ppa', 'Prupe.1G150000' => 'ppe', 'Prupe.1G150100' => 'ppe', 'Prupe.6G299600' => 'ppe', 'Prupe.8G245000' => 'ppe', 'Psat0s4927g0040' => 'psa', 'Psat1g052080' => 'psa', 'Psat1g183800' => 'psa', 'Psat3g113840' => 'psa', 'Psat3g126120' => 'psa', 'Psat3g126160' => 'psa', 'Psat3g158760' => 'psa', 'Psat3g158840' => 'psa', 'PSO170G2858' => 'pso', 'PSO339G0606' => 'pso', 'PSO384G4709' => 'pso', 'PSO407G0334' => 'pso', 'QL04p040276' => 'qlo', 'QL06p005458' => 'qlo', 'QL06p005472' => 'qlo', 'QL07p030546' => 'qlo', 'QL07p031519' => 'qlo', 'QL09p050949' => 'qlo', 'QL09p050966' => 'qlo', 'QL09p051067' => 'qlo', 'QL12p022706' => 'qlo', 'RcHm_v2.0_Chr2g0119601' => 'rch', 'RcHm_v2.0_Chr3g0459591' => 'rch', 'RcHm_v2.0_Chr4g0418521' => 'rch', 'RcHm_v2.0_Chr4g0418531' => 'rch', 'RcHm_v2.0_Chr4g0418541' => 'rch', 'RcHm_v2.0_Chr6g0291641' => 'rch', 'Rhsim01G0086300' => 'rsi', 'Rhsim01G0276300' => 'rsi', 'Rhsim01G0276500' => 'rsi', 'Rhsim04G0207700' => 'rsi', 'Rhsim05G0234500' => 'rsi', 'Rhsim13G0022400' => 'rsi', 'Sabra02G0167900' => 'sbr', 'Sabra04G0158500' => 'sbr', 'Sabra08G0159800' => 'sbr', 'Sabra10G0011500' => 'sbr', 'Sabra14G0104400' => 'sbr', 'SalBow2G2440' => 'sbo', 'SalBow4G2265' => 'sbo', 'Sc02g0000060' => 'sci', 'Sc05g0005020' => 'sci', 'Sc13g0003890' => 'sci', 'Sed0014865' => 'sed', 'Sed0017224' => 'sed', 'Sed0026391' => 'sed', 'SEGI_00063' => 'sgi', 'SEGI_10967' => 'sgi', 'SEGI_17510' => 'sgi', 'SEGI_24396' => 'sgi', 'SEGI_39719' => 'sgi', 'SEGI_41392' => 'sgi', 'SGA_v2.0_scaffold11G05794' => 'sas', 'SGA_v2.0_scaffold142G35607' => 'sas', 'SGA_v2.0_scaffold1G00447' => 'sas', 'SHI15388' => 'shi', 'SHI15394' => 'shi', 'SHI15396' => 'shi', 'SHI15399' => 'shi', 'SMO343G0151' => 'smo', 'SMO367G1118' => 'smo', 'Solyc01g080200.3' => 'sly', 'Solyc06g008960.3' => 'sly', 'Solyc09g064780.3' => 'sly', 'Sopen01g031980' => 'spe', 'Sopen06g003710' => 'spe', 'Sopen09g026460' => 'spe', 'Sp3g21240' => 'spa', 'Sp4g30030' => 'spa', 'TAR365G0022' => 'tar', 'TAR365G1023' => 'tar', 'TAR365G1253' => 'tar', 'TAR623G0078' => 'tar', 'TAR623G1721' => 'tar', 'TAR633G0959' => 'tar', 'THA.LOC104802225' => 'tha', 'THA.LOC104804769' => 'tha', 'THA.LOC104808660' => 'tha', 'THA.LOC104812792' => 'tha', 'Thecc.01G284000' => 'tca', 'Thecc.04G220600' => 'tca', 'Thecc.05G268900' => 'tca', 'Thecc.08G171100' => 'tca', 'Thhalv10001284m.g' => 'esa', 'Thhalv10019912m.g' => 'esa', 'TPR.G14189' => 'tpr', 'TPR.G18110' => 'tpr', 'TPR.G18130' => 'tpr', 'TPR.G18131' => 'tpr', 'TPR.G18140' => 'tpr', 'TPR.G24282' => 'tpr', 'TPR.G25221' => 'tpr', 'TPR.G29267' => 'tpr', 'TPR.G35315' => 'tpr', 'TPR.G36173' => 'tpr', 'TWI09G0794' => 'twi', 'TWI59G1348' => 'twi', 'TWI74G0430' => 'twi', 'unitig_26.g8940' => 'ugi', 'unitig_749.g13744' => 'ugi', 'unitig_749.g13745' => 'ugi', 'vmacro08269' => 'vma', 'vmacro14937' => 'vma', 'vmacro20401' => 'vma', 'VMungo0464G1349' => 'vmu', 'VMungo0540G0289' => 'vmu', 'VMungo1215G1590' => 'vmu', 'VMungo1309G0221' => 'vmu', 'VMungo1309G2815' => 'vmu', 'VMungo1383G0239' => 'vmu', 'VMungo1383G2910' => 'vmu', 'Zm00001eb095270' => 'zma', 'Zm00001eb095280' => 'zma', 'Zm00001eb111630' => 'zma', 'Zm00001eb237080' => 'zma', 'Zm00001eb273740' => 'zma', 'Zm00001eb285040' => 'zma', 'Zm00001eb330790' => 'zma', 'Zm00001eb337380' => 'zma' ) $gf_id = 'HOM05D001484' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001484' ) $data_identifier = 'HOM05D001484' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 2, 'aly' => (int) 2, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 22, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 7, 'hma' => (int) 2, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 7, 'mtr' => (int) 10, 'cme' => (int) 2, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 4, 'ppa' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 4, 'qlo' => (int) 9, 'rch' => (int) 6, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 10, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 7, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb337380' $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' => 'HOM05D001484', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p31500' => 'bna', 'A05p00020' => 'bna', 'A07p08820' => 'bna', 'Aa31LG4G3300' => 'aar', 'Aa31LG8G10030' => 'aar', 'Actinidia00731' => 'ach', 'Actinidia11473' => 'ach', 'Actinidia23469' => 'ach', 'Actinidia24318' => 'ach', 'Actinidia40196' => 'ach', 'Actinidia40197' => 'ach', 'Actinidia40198' => 'ach', 'Ah.08g212990' => 'amhyb', 'Ah.15g091720' => 'amhyb', 'AL3G38260' => 'aly', 'AL4G47710' => 'aly', 'Aqoxy2G00671' => 'aox', 'Aqoxy2G03236' => 'aox', 'arahy.Tifrunner.gnm1.ann1.05IDCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KR684' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATY3SJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK6QJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6APGL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IDT7Z9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM073U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ0R87' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LE7RV4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT4QRX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V5ENPK' => 'arhy', 'AT2G48110' => 'ath', 'AT3G23590' => 'ath', 'ATR0626G186' => 'atr', 'ATR1127G141' => 'atr', 'Atru.chr4.2583' => 'acertr', 'Atru.chr5.1358' => 'acertr', 'Atru.chr5.1359' => 'acertr', 'Atru.chr8.46' => 'acertr', 'AUR62002640' => 'cqu', 'AUR62030055' => 'cqu', 'AUR62033713' => 'cqu', 'AUR62033714' => 'cqu', 'AUR62036795' => 'cqu', 'AUR62039891' => 'cqu', 'BcaB02g08737' => 'bca', 'BcaB04g20441' => 'bca', 'BcaB06g26509' => 'bca', 'BcaB06g26510' => 'bca', 'BcaB06g26511' => 'bca', 'BcaB06g26512' => 'bca', 'BcaB06g26513' => 'bca', 'BcaC02g12564' => 'bca', 'BcaC02g12565' => 'bca', 'BcaC02g12794' => 'bca', 'BcaC02g12795' => 'bca', 'BcaC02g12796' => 'bca', 'BcaC06g35541' => 'bca', 'BNapus_Darmor_BZH_scaffold_188p00080' => 'bna', 'BNapus_Darmor_BZH_scaffold_188p00090' => 'bna', 'BolC1t03972H' => 'bol', 'BolC1t03973H' => 'bol', 'BolC4t21680H' => 'bol', 'BolC7t41863H' => 'bol', 'BolSC55t61227H' => 'bol', 'BolSC55t61228H' => 'bol', 'BraA01t03278Z' => 'bra', 'BraA05t18998Z' => 'bra', 'BraA07t28673Z' => 'bra', 'C01p40150' => 'bna', 'C05p12370' => 'bna', 'C07p13680' => 'bna', 'CAN.G1006.16' => 'can', 'CAN.G1006.17' => 'can', 'CAN.G1170.2' => 'can', 'CAN.G962.7' => 'can', 'CANSAT25G2179' => 'cansat', 'CANSAT78G1573' => 'cansat', 'CARHR099510' => 'chi', 'CARHR143510' => 'chi', 'Carub.0003s2380' => 'cru', 'Carub.0004s3082' => 'cru', 'Ca_00614_v3' => 'car', 'Ca_07801_v3' => 'car', 'Ca_08567_v3' => 'car', 'Ca_09571_v3' => 'car', 'CBR_g19290' => 'cbr', 'Cc01_g19770' => 'ccan', 'Cc03_g03030' => 'ccan', 'CDE07G0968' => 'cde', 'CDE09G1441' => 'cde', 'Cfa006103' => 'cfa', 'Cfa015573' => 'cfa', 'Cfa016988' => 'cfa', 'Ciclev10006738m.g' => 'ccl', 'Ciclev10010920m.g' => 'ccl', 'Ciclev10018517m.g' => 'ccl', 'CiPaw.01G159200' => 'cil', 'CiPaw.02G091000' => 'cil', 'CiPaw.02G091100' => 'cil', 'CiPaw.08G103100' => 'cil', 'CiPaw.09G224900' => 'cil', 'ClCG06G005740' => 'cla', 'ClCG07G000090' => 'cla', 'ClCG07G000100' => 'cla', 'COL.COLO4_09143' => 'col', 'COL.COLO4_25124' => 'col', 'Cpa.g.sc16.34' => 'cpa', 'Cpa.g.sc3504.1' => 'cpa', 'Cpa.g.sc60.37' => 'cpa', 'CsaV3_6G018520' => 'csa', 'CsaV3_6G036860' => 'csa', 'CSS0001072' => 'camsi', 'CSS0020208' => 'camsi', 'CSS0021253' => 'camsi', 'CSS0022190' => 'camsi', 'CSS0036150' => 'camsi', 'CSS0040442' => 'camsi', 'CSS0042300' => 'camsi', 'CSS0045298' => 'camsi', 'DCAR_012449' => 'dca', 'DCAR_018405' => 'dca', 'DCAR_024573' => 'dca', 'DCAR_030591' => 'dca', 'Dinv16926' => 'din', 'Dinv32963' => 'din', 'Dinv38382' => 'din', 'Dinv38383' => 'din', 'Duzib133G0974' => 'dzi', 'Duzib138G1867' => 'dzi', 'Duzib211G0420' => 'dzi', 'Duzib212G0930' => 'dzi', 'ECA234G1645' => 'eca', 'ECA247G3467' => 'eca', 'ECA248G1703' => 'eca', 'EL10Ac3g06327' => 'bvu', 'EL10Ac7g17204' => 'bvu', 'Eucgr.A00855' => 'egr', 'Eucgr.A00858' => 'egr', 'Eucgr.H01520' => 'egr', 'Eucgr.H03604' => 'egr', 'Eucgr.L03465' => 'egr', 'Eucgr.L03466' => 'egr', 'FAN01G0988' => 'fan', 'FAN02G3892' => 'fan', 'FAN05G3381' => 'fan', 'FAN07G0967' => 'fan', 'FAN07G1493' => 'fan', 'FAN08G3125' => 'fan', 'FAN09G0402' => 'fan', 'FAN12G2594' => 'fan', 'FAN12G3879' => 'fan', 'FAN14G1546' => 'fan', 'FAN15G3626' => 'fan', 'FAN17G0588' => 'fan', 'FAN17G0609' => 'fan', 'FAN18G2817' => 'fan', 'FAN19G1305' => 'fan', 'FAN20G1787' => 'fan', 'FAN22G0073' => 'fan', 'FAN22G0352' => 'fan', 'FAN22G0368' => 'fan', 'FAN22G2273' => 'fan', 'FAN24G1998' => 'fan', 'FAN27G1317' => 'fan', 'FvH4_2g23980' => 'fve', 'FvH4_4g14380' => 'fve', 'FvH4_4g14390' => 'fve', 'FvH4_6g09250' => 'fve', 'Glyma.03G151100' => 'gma', 'Glyma.04G122550' => 'gma', 'Glyma.05G001600' => 'gma', 'Glyma.09G270766' => 'gma', 'Glyma.09G270832' => 'gma', 'Glyma.13G209800' => 'gma', 'Glyma.15G102800' => 'gma', 'Glyma.18G218900' => 'gma', 'Glyma.19G001500' => 'gma', 'Glyma.19G153600' => 'gma', 'Gohir.A02G028600' => 'ghi', 'Gohir.A08G045000' => 'ghi', 'Gohir.A11G120500' => 'ghi', 'Gohir.A12G006200' => 'ghi', 'Gohir.A12G006250' => 'ghi', 'Gohir.D02G036300' => 'ghi', 'Gohir.D08G054700' => 'ghi', 'Gohir.D11G125600' => 'ghi', 'Gohir.D12G005700' => 'ghi', 'Gorai.004G055200' => 'gra', 'Gorai.005G040400' => 'gra', 'Gorai.007G134500' => 'gra', 'Gorai.008G005500' => 'gra', 'GSVIVG01011094001' => 'vvi', 'GSVIVG01017879001' => 'vvi', 'GSVIVG01025988001' => 'vvi', 'GSVIVG01029847001' => 'vvi', 'HanXRQChr10g0282901' => 'han', 'HanXRQChr10g0310371' => 'han', 'HanXRQChr10g0315041' => 'han', 'HanXRQChr11g0327651' => 'han', 'HanXRQChr12g0359391' => 'han', 'Haze_00972' => 'cav', 'Haze_00973' => 'cav', 'Haze_00974' => 'cav', 'Haze_04747' => 'cav', 'Haze_04749' => 'cav', 'Haze_04750' => 'cav', 'Haze_21217' => 'cav', 'Hma1.2p1_1037F.1_g250680' => 'hma', 'Hma1.2p1_1644F.1_g295320' => 'hma', 'HPP92_011322' => 'vpl', 'HPP92_011323' => 'vpl', 'HPP92_011324' => 'vpl', 'HPP92_011325' => 'vpl', 'HPP92_011326' => 'vpl', 'Hund12205' => 'sun', 'Hund17957' => 'sun', 'Lalb_Chr06g0176771' => 'lal', 'Lalb_Chr18g0056021' => 'lal', 'Lalb_Chr18g0056031' => 'lal', 'Lalb_Chr18g0056041' => 'lal', 'Lalb_Chr20g0107751' => 'lal', 'Lalb_Chr20g0118371' => 'lal', 'Lj1g0010239' => 'lja', 'Lj1g0017101' => 'lja', 'Lj2A1178G40' => 'lonja', 'Lj2A54G84' => 'lonja', 'Lj2g0015248' => 'lja', 'Lj3A761T51' => 'lonja', 'Lj6g0018116' => 'lja', 'Lsat_1_v5_gn_4_136040' => 'lsa', 'Lsat_1_v5_gn_5_187461' => 'lsa', 'Lsat_1_v5_gn_5_77001' => 'lsa', 'Lsat_1_v5_gn_9_4461' => 'lsa', 'Manes.01G210100' => 'mes', 'Manes.03G185600' => 'mes', 'Manes.05G073300' => 'mes', 'Manes.09G120300' => 'mes', 'Manes.15G022100' => 'mes', 'Mapoly0096s0053' => 'mpo', 'MBI03_g14058_MAGBIO' => 'mbi', 'MBI03_g33876_MAGBIO' => 'mbi', 'MBI03_g36854_MAGBIO' => 'mbi', 'MBI17_g11997_MAGBIO' => 'mbi', 'MD03G1269000' => 'mdo', 'MD04G1179600' => 'mdo', 'MD11G1289800' => 'mdo', 'MD12G1194700' => 'mdo', 'MD13G1182100' => 'mdo', 'MD13G1182200' => 'mdo', 'MD16G1182600' => 'mdo', 'Medtr2g021400' => 'mtr', 'Medtr2g021470' => 'mtr', 'Medtr2g105810' => 'mtr', 'Medtr3g033580' => 'mtr', 'Medtr6g007970' => 'mtr', 'Medtr7g056330' => 'mtr', 'Medtr7g074290' => 'mtr', 'Medtr7g074380' => 'mtr', 'Medtr7g094550' => 'mtr', 'Medtr8g069995' => 'mtr', 'MELO3C014345.2' => 'cme', 'MELO3C021395.2' => 'cme', 'Migut.D00262' => 'egut', 'Migut.G00257' => 'egut', 'MSTRG.21575' => 'ama', 'MSTRG.3985' => 'ama', 'Nitab4.5_0000295g0140' => 'nta', 'Nitab4.5_0000732g0140' => 'nta', 'Nitab4.5_0003162g0020' => 'nta', 'Nitab4.5_0006180g0090' => 'nta', 'Nitab4.5_0006390g0010' => 'nta', 'Nitab4.5_0007392g0040' => 'nta', 'Nn1g02140' => 'nnu', 'Nn4g26168' => 'nnu', 'Nn5g26754' => 'nnu', 'Oeu001433.1' => 'oeu', 'Oeu010299.2' => 'oeu', 'Oeu011171.1' => 'oeu', 'Oeu037675.1' => 'oeu', 'Oeu038359.1' => 'oeu', 'Oeu063834.1' => 'oeu', 'Oeu063835.1' => 'oeu', 'Os05g0312000' => 'osa', 'Os07g0211101' => 'osa', 'Os07g0211200' => 'osa', 'Os07g0681500' => 'osa', 'Peaxi162Scf00095g01015' => 'pax', 'Peaxi162Scf00104g00329' => 'pax', 'Peaxi162Scf00161g00137' => 'pax', 'PGR004G1665' => 'pgr', 'PGR031G2937' => 'pgr', 'PGR119G2145' => 'pgr', 'PGSC0003DMG400004351' => 'stu', 'PGSC0003DMG400014625' => 'stu', 'PGSC0003DMG401000943' => 'stu', 'Phvul.001G148600' => 'pvu', 'Phvul.004G001700' => 'pvu', 'Phvul.006G154900' => 'pvu', 'Phvul.008G078200' => 'pvu', 'Phvul.011G136500' => 'pvu', 'Potri.002G215600' => 'ptr', 'Potri.008G201600' => 'ptr', 'Potri.014G138400' => 'ptr', 'Potri.016G142500' => 'ptr', 'Pp3c16_10580' => 'ppa', 'Pp3c5_25280' => 'ppa', 'Prupe.1G150000' => 'ppe', 'Prupe.1G150100' => 'ppe', 'Prupe.6G299600' => 'ppe', 'Prupe.8G245000' => 'ppe', 'Psat0s4927g0040' => 'psa', 'Psat1g052080' => 'psa', 'Psat1g183800' => 'psa', 'Psat3g113840' => 'psa', 'Psat3g126120' => 'psa', 'Psat3g126160' => 'psa', 'Psat3g158760' => 'psa', 'Psat3g158840' => 'psa', 'PSO170G2858' => 'pso', 'PSO339G0606' => 'pso', 'PSO384G4709' => 'pso', 'PSO407G0334' => 'pso', 'QL04p040276' => 'qlo', 'QL06p005458' => 'qlo', 'QL06p005472' => 'qlo', 'QL07p030546' => 'qlo', 'QL07p031519' => 'qlo', 'QL09p050949' => 'qlo', 'QL09p050966' => 'qlo', 'QL09p051067' => 'qlo', 'QL12p022706' => 'qlo', 'RcHm_v2.0_Chr2g0119601' => 'rch', 'RcHm_v2.0_Chr3g0459591' => 'rch', 'RcHm_v2.0_Chr4g0418521' => 'rch', 'RcHm_v2.0_Chr4g0418531' => 'rch', 'RcHm_v2.0_Chr4g0418541' => 'rch', 'RcHm_v2.0_Chr6g0291641' => 'rch', 'Rhsim01G0086300' => 'rsi', 'Rhsim01G0276300' => 'rsi', 'Rhsim01G0276500' => 'rsi', 'Rhsim04G0207700' => 'rsi', 'Rhsim05G0234500' => 'rsi', 'Rhsim13G0022400' => 'rsi', 'Sabra02G0167900' => 'sbr', 'Sabra04G0158500' => 'sbr', 'Sabra08G0159800' => 'sbr', 'Sabra10G0011500' => 'sbr', 'Sabra14G0104400' => 'sbr', 'SalBow2G2440' => 'sbo', 'SalBow4G2265' => 'sbo', 'Sc02g0000060' => 'sci', 'Sc05g0005020' => 'sci', 'Sc13g0003890' => 'sci', 'Sed0014865' => 'sed', 'Sed0017224' => 'sed', 'Sed0026391' => 'sed', 'SEGI_00063' => 'sgi', 'SEGI_10967' => 'sgi', 'SEGI_17510' => 'sgi', 'SEGI_24396' => 'sgi', 'SEGI_39719' => 'sgi', 'SEGI_41392' => 'sgi', 'SGA_v2.0_scaffold11G05794' => 'sas', 'SGA_v2.0_scaffold142G35607' => 'sas', 'SGA_v2.0_scaffold1G00447' => 'sas', 'SHI15388' => 'shi', 'SHI15394' => 'shi', 'SHI15396' => 'shi', 'SHI15399' => 'shi', 'SMO343G0151' => 'smo', 'SMO367G1118' => 'smo', 'Solyc01g080200.3' => 'sly', 'Solyc06g008960.3' => 'sly', 'Solyc09g064780.3' => 'sly', 'Sopen01g031980' => 'spe', 'Sopen06g003710' => 'spe', 'Sopen09g026460' => 'spe', 'Sp3g21240' => 'spa', 'Sp4g30030' => 'spa', 'TAR365G0022' => 'tar', 'TAR365G1023' => 'tar', 'TAR365G1253' => 'tar', 'TAR623G0078' => 'tar', 'TAR623G1721' => 'tar', 'TAR633G0959' => 'tar', 'THA.LOC104802225' => 'tha', 'THA.LOC104804769' => 'tha', 'THA.LOC104808660' => 'tha', 'THA.LOC104812792' => 'tha', 'Thecc.01G284000' => 'tca', 'Thecc.04G220600' => 'tca', 'Thecc.05G268900' => 'tca', 'Thecc.08G171100' => 'tca', 'Thhalv10001284m.g' => 'esa', 'Thhalv10019912m.g' => 'esa', 'TPR.G14189' => 'tpr', 'TPR.G18110' => 'tpr', 'TPR.G18130' => 'tpr', 'TPR.G18131' => 'tpr', 'TPR.G18140' => 'tpr', 'TPR.G24282' => 'tpr', 'TPR.G25221' => 'tpr', 'TPR.G29267' => 'tpr', 'TPR.G35315' => 'tpr', 'TPR.G36173' => 'tpr', 'TWI09G0794' => 'twi', 'TWI59G1348' => 'twi', 'TWI74G0430' => 'twi', 'unitig_26.g8940' => 'ugi', 'unitig_749.g13744' => 'ugi', 'unitig_749.g13745' => 'ugi', 'vmacro08269' => 'vma', 'vmacro14937' => 'vma', 'vmacro20401' => 'vma', 'VMungo0464G1349' => 'vmu', 'VMungo0540G0289' => 'vmu', 'VMungo1215G1590' => 'vmu', 'VMungo1309G0221' => 'vmu', 'VMungo1309G2815' => 'vmu', 'VMungo1383G0239' => 'vmu', 'VMungo1383G2910' => 'vmu', 'Zm00001eb095270' => 'zma', 'Zm00001eb095280' => 'zma', 'Zm00001eb111630' => 'zma', 'Zm00001eb237080' => 'zma', 'Zm00001eb273740' => 'zma', 'Zm00001eb285040' => 'zma', 'Zm00001eb330790' => 'zma', 'Zm00001eb337380' => 'zma' ), 'gf_id' => 'HOM05D001484', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001484' ), 'data_identifier' => 'HOM05D001484', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001484', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p31500' => 'bna', 'A05p00020' => 'bna', 'A07p08820' => 'bna', 'Aa31LG4G3300' => 'aar', 'Aa31LG8G10030' => 'aar', 'Actinidia00731' => 'ach', 'Actinidia11473' => 'ach', 'Actinidia23469' => 'ach', 'Actinidia24318' => 'ach', 'Actinidia40196' => 'ach', 'Actinidia40197' => 'ach', 'Actinidia40198' => 'ach', 'Ah.08g212990' => 'amhyb', 'Ah.15g091720' => 'amhyb', 'AL3G38260' => 'aly', 'AL4G47710' => 'aly', 'Aqoxy2G00671' => 'aox', 'Aqoxy2G03236' => 'aox', 'arahy.Tifrunner.gnm1.ann1.05IDCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KR684' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATY3SJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK6QJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6APGL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IDT7Z9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM073U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ0R87' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LE7RV4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT4QRX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V5ENPK' => 'arhy', 'AT2G48110' => 'ath', 'AT3G23590' => 'ath', 'ATR0626G186' => 'atr', 'ATR1127G141' => 'atr', 'Atru.chr4.2583' => 'acertr', 'Atru.chr5.1358' => 'acertr', 'Atru.chr5.1359' => 'acertr', 'Atru.chr8.46' => 'acertr', 'AUR62002640' => 'cqu', 'AUR62030055' => 'cqu', 'AUR62033713' => 'cqu', 'AUR62033714' => 'cqu', 'AUR62036795' => 'cqu', 'AUR62039891' => 'cqu', 'BcaB02g08737' => 'bca', 'BcaB04g20441' => 'bca', 'BcaB06g26509' => 'bca', 'BcaB06g26510' => 'bca', 'BcaB06g26511' => 'bca', 'BcaB06g26512' => 'bca', 'BcaB06g26513' => 'bca', 'BcaC02g12564' => 'bca', 'BcaC02g12565' => 'bca', 'BcaC02g12794' => 'bca', 'BcaC02g12795' => 'bca', 'BcaC02g12796' => 'bca', 'BcaC06g35541' => 'bca', 'BNapus_Darmor_BZH_scaffold_188p00080' => 'bna', 'BNapus_Darmor_BZH_scaffold_188p00090' => 'bna', 'BolC1t03972H' => 'bol', 'BolC1t03973H' => 'bol', 'BolC4t21680H' => 'bol', 'BolC7t41863H' => 'bol', 'BolSC55t61227H' => 'bol', 'BolSC55t61228H' => 'bol', 'BraA01t03278Z' => 'bra', 'BraA05t18998Z' => 'bra', 'BraA07t28673Z' => 'bra', 'C01p40150' => 'bna', 'C05p12370' => 'bna', 'C07p13680' => 'bna', 'CAN.G1006.16' => 'can', 'CAN.G1006.17' => 'can', 'CAN.G1170.2' => 'can', 'CAN.G962.7' => 'can', 'CANSAT25G2179' => 'cansat', 'CANSAT78G1573' => 'cansat', 'CARHR099510' => 'chi', 'CARHR143510' => 'chi', 'Carub.0003s2380' => 'cru', 'Carub.0004s3082' => 'cru', 'Ca_00614_v3' => 'car', 'Ca_07801_v3' => 'car', 'Ca_08567_v3' => 'car', 'Ca_09571_v3' => 'car', 'CBR_g19290' => 'cbr', 'Cc01_g19770' => 'ccan', 'Cc03_g03030' => 'ccan', 'CDE07G0968' => 'cde', 'CDE09G1441' => 'cde', 'Cfa006103' => 'cfa', 'Cfa015573' => 'cfa', 'Cfa016988' => 'cfa', 'Ciclev10006738m.g' => 'ccl', 'Ciclev10010920m.g' => 'ccl', 'Ciclev10018517m.g' => 'ccl', 'CiPaw.01G159200' => 'cil', 'CiPaw.02G091000' => 'cil', 'CiPaw.02G091100' => 'cil', 'CiPaw.08G103100' => 'cil', 'CiPaw.09G224900' => 'cil', 'ClCG06G005740' => 'cla', 'ClCG07G000090' => 'cla', 'ClCG07G000100' => 'cla', 'COL.COLO4_09143' => 'col', 'COL.COLO4_25124' => 'col', 'Cpa.g.sc16.34' => 'cpa', 'Cpa.g.sc3504.1' => 'cpa', 'Cpa.g.sc60.37' => 'cpa', 'CsaV3_6G018520' => 'csa', 'CsaV3_6G036860' => 'csa', 'CSS0001072' => 'camsi', 'CSS0020208' => 'camsi', 'CSS0021253' => 'camsi', 'CSS0022190' => 'camsi', 'CSS0036150' => 'camsi', 'CSS0040442' => 'camsi', 'CSS0042300' => 'camsi', 'CSS0045298' => 'camsi', 'DCAR_012449' => 'dca', 'DCAR_018405' => 'dca', 'DCAR_024573' => 'dca', 'DCAR_030591' => 'dca', 'Dinv16926' => 'din', 'Dinv32963' => 'din', 'Dinv38382' => 'din', 'Dinv38383' => 'din', 'Duzib133G0974' => 'dzi', 'Duzib138G1867' => 'dzi', 'Duzib211G0420' => 'dzi', 'Duzib212G0930' => 'dzi', 'ECA234G1645' => 'eca', 'ECA247G3467' => 'eca', 'ECA248G1703' => 'eca', 'EL10Ac3g06327' => 'bvu', 'EL10Ac7g17204' => 'bvu', 'Eucgr.A00855' => 'egr', 'Eucgr.A00858' => 'egr', 'Eucgr.H01520' => 'egr', 'Eucgr.H03604' => 'egr', 'Eucgr.L03465' => 'egr', 'Eucgr.L03466' => 'egr', 'FAN01G0988' => 'fan', 'FAN02G3892' => 'fan', 'FAN05G3381' => 'fan', 'FAN07G0967' => 'fan', 'FAN07G1493' => 'fan', 'FAN08G3125' => 'fan', 'FAN09G0402' => 'fan', 'FAN12G2594' => 'fan', 'FAN12G3879' => 'fan', 'FAN14G1546' => 'fan', 'FAN15G3626' => 'fan', 'FAN17G0588' => 'fan', 'FAN17G0609' => 'fan', 'FAN18G2817' => 'fan', 'FAN19G1305' => 'fan', 'FAN20G1787' => 'fan', 'FAN22G0073' => 'fan', 'FAN22G0352' => 'fan', 'FAN22G0368' => 'fan', 'FAN22G2273' => 'fan', 'FAN24G1998' => 'fan', 'FAN27G1317' => 'fan', 'FvH4_2g23980' => 'fve', 'FvH4_4g14380' => 'fve', 'FvH4_4g14390' => 'fve', 'FvH4_6g09250' => 'fve', 'Glyma.03G151100' => 'gma', 'Glyma.04G122550' => 'gma', 'Glyma.05G001600' => 'gma', 'Glyma.09G270766' => 'gma', 'Glyma.09G270832' => 'gma', 'Glyma.13G209800' => 'gma', 'Glyma.15G102800' => 'gma', 'Glyma.18G218900' => 'gma', 'Glyma.19G001500' => 'gma', 'Glyma.19G153600' => 'gma', 'Gohir.A02G028600' => 'ghi', 'Gohir.A08G045000' => 'ghi', 'Gohir.A11G120500' => 'ghi', 'Gohir.A12G006200' => 'ghi', 'Gohir.A12G006250' => 'ghi', 'Gohir.D02G036300' => 'ghi', 'Gohir.D08G054700' => 'ghi', 'Gohir.D11G125600' => 'ghi', 'Gohir.D12G005700' => 'ghi', 'Gorai.004G055200' => 'gra', 'Gorai.005G040400' => 'gra', 'Gorai.007G134500' => 'gra', 'Gorai.008G005500' => 'gra', 'GSVIVG01011094001' => 'vvi', 'GSVIVG01017879001' => 'vvi', 'GSVIVG01025988001' => 'vvi', 'GSVIVG01029847001' => 'vvi', 'HanXRQChr10g0282901' => 'han', 'HanXRQChr10g0310371' => 'han', 'HanXRQChr10g0315041' => 'han', 'HanXRQChr11g0327651' => 'han', 'HanXRQChr12g0359391' => 'han', 'Haze_00972' => 'cav', 'Haze_00973' => 'cav', 'Haze_00974' => 'cav', 'Haze_04747' => 'cav', 'Haze_04749' => 'cav', 'Haze_04750' => 'cav', 'Haze_21217' => 'cav', 'Hma1.2p1_1037F.1_g250680' => 'hma', 'Hma1.2p1_1644F.1_g295320' => 'hma', 'HPP92_011322' => 'vpl', 'HPP92_011323' => 'vpl', 'HPP92_011324' => 'vpl', 'HPP92_011325' => 'vpl', 'HPP92_011326' => 'vpl', 'Hund12205' => 'sun', 'Hund17957' => 'sun', 'Lalb_Chr06g0176771' => 'lal', 'Lalb_Chr18g0056021' => 'lal', 'Lalb_Chr18g0056031' => 'lal', 'Lalb_Chr18g0056041' => 'lal', 'Lalb_Chr20g0107751' => 'lal', 'Lalb_Chr20g0118371' => 'lal', 'Lj1g0010239' => 'lja', 'Lj1g0017101' => 'lja', 'Lj2A1178G40' => 'lonja', 'Lj2A54G84' => 'lonja', 'Lj2g0015248' => 'lja', 'Lj3A761T51' => 'lonja', 'Lj6g0018116' => 'lja', 'Lsat_1_v5_gn_4_136040' => 'lsa', 'Lsat_1_v5_gn_5_187461' => 'lsa', 'Lsat_1_v5_gn_5_77001' => 'lsa', 'Lsat_1_v5_gn_9_4461' => 'lsa', 'Manes.01G210100' => 'mes', 'Manes.03G185600' => 'mes', 'Manes.05G073300' => 'mes', 'Manes.09G120300' => 'mes', 'Manes.15G022100' => 'mes', 'Mapoly0096s0053' => 'mpo', 'MBI03_g14058_MAGBIO' => 'mbi', 'MBI03_g33876_MAGBIO' => 'mbi', 'MBI03_g36854_MAGBIO' => 'mbi', 'MBI17_g11997_MAGBIO' => 'mbi', 'MD03G1269000' => 'mdo', 'MD04G1179600' => 'mdo', 'MD11G1289800' => 'mdo', 'MD12G1194700' => 'mdo', 'MD13G1182100' => 'mdo', 'MD13G1182200' => 'mdo', 'MD16G1182600' => 'mdo', 'Medtr2g021400' => 'mtr', 'Medtr2g021470' => 'mtr', 'Medtr2g105810' => 'mtr', 'Medtr3g033580' => 'mtr', 'Medtr6g007970' => 'mtr', 'Medtr7g056330' => 'mtr', 'Medtr7g074290' => 'mtr', 'Medtr7g074380' => 'mtr', 'Medtr7g094550' => 'mtr', 'Medtr8g069995' => 'mtr', 'MELO3C014345.2' => 'cme', 'MELO3C021395.2' => 'cme', 'Migut.D00262' => 'egut', 'Migut.G00257' => 'egut', 'MSTRG.21575' => 'ama', 'MSTRG.3985' => 'ama', 'Nitab4.5_0000295g0140' => 'nta', 'Nitab4.5_0000732g0140' => 'nta', 'Nitab4.5_0003162g0020' => 'nta', 'Nitab4.5_0006180g0090' => 'nta', 'Nitab4.5_0006390g0010' => 'nta', 'Nitab4.5_0007392g0040' => 'nta', 'Nn1g02140' => 'nnu', 'Nn4g26168' => 'nnu', 'Nn5g26754' => 'nnu', 'Oeu001433.1' => 'oeu', 'Oeu010299.2' => 'oeu', 'Oeu011171.1' => 'oeu', 'Oeu037675.1' => 'oeu', 'Oeu038359.1' => 'oeu', 'Oeu063834.1' => 'oeu', 'Oeu063835.1' => 'oeu', 'Os05g0312000' => 'osa', 'Os07g0211101' => 'osa', 'Os07g0211200' => 'osa', 'Os07g0681500' => 'osa', 'Peaxi162Scf00095g01015' => 'pax', 'Peaxi162Scf00104g00329' => 'pax', 'Peaxi162Scf00161g00137' => 'pax', 'PGR004G1665' => 'pgr', 'PGR031G2937' => 'pgr', 'PGR119G2145' => 'pgr', 'PGSC0003DMG400004351' => 'stu', 'PGSC0003DMG400014625' => 'stu', 'PGSC0003DMG401000943' => 'stu', 'Phvul.001G148600' => 'pvu', 'Phvul.004G001700' => 'pvu', 'Phvul.006G154900' => 'pvu', 'Phvul.008G078200' => 'pvu', 'Phvul.011G136500' => 'pvu', 'Potri.002G215600' => 'ptr', 'Potri.008G201600' => 'ptr', 'Potri.014G138400' => 'ptr', 'Potri.016G142500' => 'ptr', 'Pp3c16_10580' => 'ppa', 'Pp3c5_25280' => 'ppa', 'Prupe.1G150000' => 'ppe', 'Prupe.1G150100' => 'ppe', 'Prupe.6G299600' => 'ppe', 'Prupe.8G245000' => 'ppe', 'Psat0s4927g0040' => 'psa', 'Psat1g052080' => 'psa', 'Psat1g183800' => 'psa', 'Psat3g113840' => 'psa', 'Psat3g126120' => 'psa', 'Psat3g126160' => 'psa', 'Psat3g158760' => 'psa', 'Psat3g158840' => 'psa', 'PSO170G2858' => 'pso', 'PSO339G0606' => 'pso', 'PSO384G4709' => 'pso', 'PSO407G0334' => 'pso', 'QL04p040276' => 'qlo', 'QL06p005458' => 'qlo', 'QL06p005472' => 'qlo', 'QL07p030546' => 'qlo', 'QL07p031519' => 'qlo', 'QL09p050949' => 'qlo', 'QL09p050966' => 'qlo', 'QL09p051067' => 'qlo', 'QL12p022706' => 'qlo', 'RcHm_v2.0_Chr2g0119601' => 'rch', 'RcHm_v2.0_Chr3g0459591' => 'rch', 'RcHm_v2.0_Chr4g0418521' => 'rch', 'RcHm_v2.0_Chr4g0418531' => 'rch', 'RcHm_v2.0_Chr4g0418541' => 'rch', 'RcHm_v2.0_Chr6g0291641' => 'rch', 'Rhsim01G0086300' => 'rsi', 'Rhsim01G0276300' => 'rsi', 'Rhsim01G0276500' => 'rsi', 'Rhsim04G0207700' => 'rsi', 'Rhsim05G0234500' => 'rsi', 'Rhsim13G0022400' => 'rsi', 'Sabra02G0167900' => 'sbr', 'Sabra04G0158500' => 'sbr', 'Sabra08G0159800' => 'sbr', 'Sabra10G0011500' => 'sbr', 'Sabra14G0104400' => 'sbr', 'SalBow2G2440' => 'sbo', 'SalBow4G2265' => 'sbo', 'Sc02g0000060' => 'sci', 'Sc05g0005020' => 'sci', 'Sc13g0003890' => 'sci', 'Sed0014865' => 'sed', 'Sed0017224' => 'sed', 'Sed0026391' => 'sed', 'SEGI_00063' => 'sgi', 'SEGI_10967' => 'sgi', 'SEGI_17510' => 'sgi', 'SEGI_24396' => 'sgi', 'SEGI_39719' => 'sgi', 'SEGI_41392' => 'sgi', 'SGA_v2.0_scaffold11G05794' => 'sas', 'SGA_v2.0_scaffold142G35607' => 'sas', 'SGA_v2.0_scaffold1G00447' => 'sas', 'SHI15388' => 'shi', 'SHI15394' => 'shi', 'SHI15396' => 'shi', 'SHI15399' => 'shi', 'SMO343G0151' => 'smo', 'SMO367G1118' => 'smo', 'Solyc01g080200.3' => 'sly', 'Solyc06g008960.3' => 'sly', 'Solyc09g064780.3' => 'sly', 'Sopen01g031980' => 'spe', 'Sopen06g003710' => 'spe', 'Sopen09g026460' => 'spe', 'Sp3g21240' => 'spa', 'Sp4g30030' => 'spa', 'TAR365G0022' => 'tar', 'TAR365G1023' => 'tar', 'TAR365G1253' => 'tar', 'TAR623G0078' => 'tar', 'TAR623G1721' => 'tar', 'TAR633G0959' => 'tar', 'THA.LOC104802225' => 'tha', 'THA.LOC104804769' => 'tha', 'THA.LOC104808660' => 'tha', 'THA.LOC104812792' => 'tha', 'Thecc.01G284000' => 'tca', 'Thecc.04G220600' => 'tca', 'Thecc.05G268900' => 'tca', 'Thecc.08G171100' => 'tca', 'Thhalv10001284m.g' => 'esa', 'Thhalv10019912m.g' => 'esa', 'TPR.G14189' => 'tpr', 'TPR.G18110' => 'tpr', 'TPR.G18130' => 'tpr', 'TPR.G18131' => 'tpr', 'TPR.G18140' => 'tpr', 'TPR.G24282' => 'tpr', 'TPR.G25221' => 'tpr', 'TPR.G29267' => 'tpr', 'TPR.G35315' => 'tpr', 'TPR.G36173' => 'tpr', 'TWI09G0794' => 'twi', 'TWI59G1348' => 'twi', 'TWI74G0430' => 'twi', 'unitig_26.g8940' => 'ugi', 'unitig_749.g13744' => 'ugi', 'unitig_749.g13745' => 'ugi', 'vmacro08269' => 'vma', 'vmacro14937' => 'vma', 'vmacro20401' => 'vma', 'VMungo0464G1349' => 'vmu', 'VMungo0540G0289' => 'vmu', 'VMungo1215G1590' => 'vmu', 'VMungo1309G0221' => 'vmu', 'VMungo1309G2815' => 'vmu', 'VMungo1383G0239' => 'vmu', 'VMungo1383G2910' => 'vmu', 'Zm00001eb095270' => 'zma', 'Zm00001eb095280' => 'zma', 'Zm00001eb111630' => 'zma', 'Zm00001eb237080' => 'zma', 'Zm00001eb273740' => 'zma', 'Zm00001eb285040' => 'zma', 'Zm00001eb330790' => 'zma', 'Zm00001eb337380' => 'zma' ) $gf_id = 'HOM05D001484' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001484' ) $data_identifier = 'HOM05D001484' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 2, 'aly' => (int) 2, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 22, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 7, 'hma' => (int) 2, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 7, 'mtr' => (int) 10, 'cme' => (int) 2, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 4, 'ppa' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 4, 'qlo' => (int) 9, 'rch' => (int) 6, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 10, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 7, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb337380' $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' => 'HOM05D001484', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p31500' => 'bna', 'A05p00020' => 'bna', 'A07p08820' => 'bna', 'Aa31LG4G3300' => 'aar', 'Aa31LG8G10030' => 'aar', 'Actinidia00731' => 'ach', 'Actinidia11473' => 'ach', 'Actinidia23469' => 'ach', 'Actinidia24318' => 'ach', 'Actinidia40196' => 'ach', 'Actinidia40197' => 'ach', 'Actinidia40198' => 'ach', 'Ah.08g212990' => 'amhyb', 'Ah.15g091720' => 'amhyb', 'AL3G38260' => 'aly', 'AL4G47710' => 'aly', 'Aqoxy2G00671' => 'aox', 'Aqoxy2G03236' => 'aox', 'arahy.Tifrunner.gnm1.ann1.05IDCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KR684' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATY3SJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK6QJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6APGL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IDT7Z9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM073U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ0R87' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LE7RV4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT4QRX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V5ENPK' => 'arhy', 'AT2G48110' => 'ath', 'AT3G23590' => 'ath', 'ATR0626G186' => 'atr', 'ATR1127G141' => 'atr', 'Atru.chr4.2583' => 'acertr', 'Atru.chr5.1358' => 'acertr', 'Atru.chr5.1359' => 'acertr', 'Atru.chr8.46' => 'acertr', 'AUR62002640' => 'cqu', 'AUR62030055' => 'cqu', 'AUR62033713' => 'cqu', 'AUR62033714' => 'cqu', 'AUR62036795' => 'cqu', 'AUR62039891' => 'cqu', 'BcaB02g08737' => 'bca', 'BcaB04g20441' => 'bca', 'BcaB06g26509' => 'bca', 'BcaB06g26510' => 'bca', 'BcaB06g26511' => 'bca', 'BcaB06g26512' => 'bca', 'BcaB06g26513' => 'bca', 'BcaC02g12564' => 'bca', 'BcaC02g12565' => 'bca', 'BcaC02g12794' => 'bca', 'BcaC02g12795' => 'bca', 'BcaC02g12796' => 'bca', 'BcaC06g35541' => 'bca', 'BNapus_Darmor_BZH_scaffold_188p00080' => 'bna', 'BNapus_Darmor_BZH_scaffold_188p00090' => 'bna', 'BolC1t03972H' => 'bol', 'BolC1t03973H' => 'bol', 'BolC4t21680H' => 'bol', 'BolC7t41863H' => 'bol', 'BolSC55t61227H' => 'bol', 'BolSC55t61228H' => 'bol', 'BraA01t03278Z' => 'bra', 'BraA05t18998Z' => 'bra', 'BraA07t28673Z' => 'bra', 'C01p40150' => 'bna', 'C05p12370' => 'bna', 'C07p13680' => 'bna', 'CAN.G1006.16' => 'can', 'CAN.G1006.17' => 'can', 'CAN.G1170.2' => 'can', 'CAN.G962.7' => 'can', 'CANSAT25G2179' => 'cansat', 'CANSAT78G1573' => 'cansat', 'CARHR099510' => 'chi', 'CARHR143510' => 'chi', 'Carub.0003s2380' => 'cru', 'Carub.0004s3082' => 'cru', 'Ca_00614_v3' => 'car', 'Ca_07801_v3' => 'car', 'Ca_08567_v3' => 'car', 'Ca_09571_v3' => 'car', 'CBR_g19290' => 'cbr', 'Cc01_g19770' => 'ccan', 'Cc03_g03030' => 'ccan', 'CDE07G0968' => 'cde', 'CDE09G1441' => 'cde', 'Cfa006103' => 'cfa', 'Cfa015573' => 'cfa', 'Cfa016988' => 'cfa', 'Ciclev10006738m.g' => 'ccl', 'Ciclev10010920m.g' => 'ccl', 'Ciclev10018517m.g' => 'ccl', 'CiPaw.01G159200' => 'cil', 'CiPaw.02G091000' => 'cil', 'CiPaw.02G091100' => 'cil', 'CiPaw.08G103100' => 'cil', 'CiPaw.09G224900' => 'cil', 'ClCG06G005740' => 'cla', 'ClCG07G000090' => 'cla', 'ClCG07G000100' => 'cla', 'COL.COLO4_09143' => 'col', 'COL.COLO4_25124' => 'col', 'Cpa.g.sc16.34' => 'cpa', 'Cpa.g.sc3504.1' => 'cpa', 'Cpa.g.sc60.37' => 'cpa', 'CsaV3_6G018520' => 'csa', 'CsaV3_6G036860' => 'csa', 'CSS0001072' => 'camsi', 'CSS0020208' => 'camsi', 'CSS0021253' => 'camsi', 'CSS0022190' => 'camsi', 'CSS0036150' => 'camsi', 'CSS0040442' => 'camsi', 'CSS0042300' => 'camsi', 'CSS0045298' => 'camsi', 'DCAR_012449' => 'dca', 'DCAR_018405' => 'dca', 'DCAR_024573' => 'dca', 'DCAR_030591' => 'dca', 'Dinv16926' => 'din', 'Dinv32963' => 'din', 'Dinv38382' => 'din', 'Dinv38383' => 'din', 'Duzib133G0974' => 'dzi', 'Duzib138G1867' => 'dzi', 'Duzib211G0420' => 'dzi', 'Duzib212G0930' => 'dzi', 'ECA234G1645' => 'eca', 'ECA247G3467' => 'eca', 'ECA248G1703' => 'eca', 'EL10Ac3g06327' => 'bvu', 'EL10Ac7g17204' => 'bvu', 'Eucgr.A00855' => 'egr', 'Eucgr.A00858' => 'egr', 'Eucgr.H01520' => 'egr', 'Eucgr.H03604' => 'egr', 'Eucgr.L03465' => 'egr', 'Eucgr.L03466' => 'egr', 'FAN01G0988' => 'fan', 'FAN02G3892' => 'fan', 'FAN05G3381' => 'fan', 'FAN07G0967' => 'fan', 'FAN07G1493' => 'fan', 'FAN08G3125' => 'fan', 'FAN09G0402' => 'fan', 'FAN12G2594' => 'fan', 'FAN12G3879' => 'fan', 'FAN14G1546' => 'fan', 'FAN15G3626' => 'fan', 'FAN17G0588' => 'fan', 'FAN17G0609' => 'fan', 'FAN18G2817' => 'fan', 'FAN19G1305' => 'fan', 'FAN20G1787' => 'fan', 'FAN22G0073' => 'fan', 'FAN22G0352' => 'fan', 'FAN22G0368' => 'fan', 'FAN22G2273' => 'fan', 'FAN24G1998' => 'fan', 'FAN27G1317' => 'fan', 'FvH4_2g23980' => 'fve', 'FvH4_4g14380' => 'fve', 'FvH4_4g14390' => 'fve', 'FvH4_6g09250' => 'fve', 'Glyma.03G151100' => 'gma', 'Glyma.04G122550' => 'gma', 'Glyma.05G001600' => 'gma', 'Glyma.09G270766' => 'gma', 'Glyma.09G270832' => 'gma', 'Glyma.13G209800' => 'gma', 'Glyma.15G102800' => 'gma', 'Glyma.18G218900' => 'gma', 'Glyma.19G001500' => 'gma', 'Glyma.19G153600' => 'gma', 'Gohir.A02G028600' => 'ghi', 'Gohir.A08G045000' => 'ghi', 'Gohir.A11G120500' => 'ghi', 'Gohir.A12G006200' => 'ghi', 'Gohir.A12G006250' => 'ghi', 'Gohir.D02G036300' => 'ghi', 'Gohir.D08G054700' => 'ghi', 'Gohir.D11G125600' => 'ghi', 'Gohir.D12G005700' => 'ghi', 'Gorai.004G055200' => 'gra', 'Gorai.005G040400' => 'gra', 'Gorai.007G134500' => 'gra', 'Gorai.008G005500' => 'gra', 'GSVIVG01011094001' => 'vvi', 'GSVIVG01017879001' => 'vvi', 'GSVIVG01025988001' => 'vvi', 'GSVIVG01029847001' => 'vvi', 'HanXRQChr10g0282901' => 'han', 'HanXRQChr10g0310371' => 'han', 'HanXRQChr10g0315041' => 'han', 'HanXRQChr11g0327651' => 'han', 'HanXRQChr12g0359391' => 'han', 'Haze_00972' => 'cav', 'Haze_00973' => 'cav', 'Haze_00974' => 'cav', 'Haze_04747' => 'cav', 'Haze_04749' => 'cav', 'Haze_04750' => 'cav', 'Haze_21217' => 'cav', 'Hma1.2p1_1037F.1_g250680' => 'hma', 'Hma1.2p1_1644F.1_g295320' => 'hma', 'HPP92_011322' => 'vpl', 'HPP92_011323' => 'vpl', 'HPP92_011324' => 'vpl', 'HPP92_011325' => 'vpl', 'HPP92_011326' => 'vpl', 'Hund12205' => 'sun', 'Hund17957' => 'sun', 'Lalb_Chr06g0176771' => 'lal', 'Lalb_Chr18g0056021' => 'lal', 'Lalb_Chr18g0056031' => 'lal', 'Lalb_Chr18g0056041' => 'lal', 'Lalb_Chr20g0107751' => 'lal', 'Lalb_Chr20g0118371' => 'lal', 'Lj1g0010239' => 'lja', 'Lj1g0017101' => 'lja', 'Lj2A1178G40' => 'lonja', 'Lj2A54G84' => 'lonja', 'Lj2g0015248' => 'lja', 'Lj3A761T51' => 'lonja', 'Lj6g0018116' => 'lja', 'Lsat_1_v5_gn_4_136040' => 'lsa', 'Lsat_1_v5_gn_5_187461' => 'lsa', 'Lsat_1_v5_gn_5_77001' => 'lsa', 'Lsat_1_v5_gn_9_4461' => 'lsa', 'Manes.01G210100' => 'mes', 'Manes.03G185600' => 'mes', 'Manes.05G073300' => 'mes', 'Manes.09G120300' => 'mes', 'Manes.15G022100' => 'mes', 'Mapoly0096s0053' => 'mpo', 'MBI03_g14058_MAGBIO' => 'mbi', 'MBI03_g33876_MAGBIO' => 'mbi', 'MBI03_g36854_MAGBIO' => 'mbi', 'MBI17_g11997_MAGBIO' => 'mbi', 'MD03G1269000' => 'mdo', 'MD04G1179600' => 'mdo', 'MD11G1289800' => 'mdo', 'MD12G1194700' => 'mdo', 'MD13G1182100' => 'mdo', 'MD13G1182200' => 'mdo', 'MD16G1182600' => 'mdo', 'Medtr2g021400' => 'mtr', 'Medtr2g021470' => 'mtr', 'Medtr2g105810' => 'mtr', 'Medtr3g033580' => 'mtr', 'Medtr6g007970' => 'mtr', 'Medtr7g056330' => 'mtr', 'Medtr7g074290' => 'mtr', 'Medtr7g074380' => 'mtr', 'Medtr7g094550' => 'mtr', 'Medtr8g069995' => 'mtr', 'MELO3C014345.2' => 'cme', 'MELO3C021395.2' => 'cme', 'Migut.D00262' => 'egut', 'Migut.G00257' => 'egut', 'MSTRG.21575' => 'ama', 'MSTRG.3985' => 'ama', 'Nitab4.5_0000295g0140' => 'nta', 'Nitab4.5_0000732g0140' => 'nta', 'Nitab4.5_0003162g0020' => 'nta', 'Nitab4.5_0006180g0090' => 'nta', 'Nitab4.5_0006390g0010' => 'nta', 'Nitab4.5_0007392g0040' => 'nta', 'Nn1g02140' => 'nnu', 'Nn4g26168' => 'nnu', 'Nn5g26754' => 'nnu', 'Oeu001433.1' => 'oeu', 'Oeu010299.2' => 'oeu', 'Oeu011171.1' => 'oeu', 'Oeu037675.1' => 'oeu', 'Oeu038359.1' => 'oeu', 'Oeu063834.1' => 'oeu', 'Oeu063835.1' => 'oeu', 'Os05g0312000' => 'osa', 'Os07g0211101' => 'osa', 'Os07g0211200' => 'osa', 'Os07g0681500' => 'osa', 'Peaxi162Scf00095g01015' => 'pax', 'Peaxi162Scf00104g00329' => 'pax', 'Peaxi162Scf00161g00137' => 'pax', 'PGR004G1665' => 'pgr', 'PGR031G2937' => 'pgr', 'PGR119G2145' => 'pgr', 'PGSC0003DMG400004351' => 'stu', 'PGSC0003DMG400014625' => 'stu', 'PGSC0003DMG401000943' => 'stu', 'Phvul.001G148600' => 'pvu', 'Phvul.004G001700' => 'pvu', 'Phvul.006G154900' => 'pvu', 'Phvul.008G078200' => 'pvu', 'Phvul.011G136500' => 'pvu', 'Potri.002G215600' => 'ptr', 'Potri.008G201600' => 'ptr', 'Potri.014G138400' => 'ptr', 'Potri.016G142500' => 'ptr', 'Pp3c16_10580' => 'ppa', 'Pp3c5_25280' => 'ppa', 'Prupe.1G150000' => 'ppe', 'Prupe.1G150100' => 'ppe', 'Prupe.6G299600' => 'ppe', 'Prupe.8G245000' => 'ppe', 'Psat0s4927g0040' => 'psa', 'Psat1g052080' => 'psa', 'Psat1g183800' => 'psa', 'Psat3g113840' => 'psa', 'Psat3g126120' => 'psa', 'Psat3g126160' => 'psa', 'Psat3g158760' => 'psa', 'Psat3g158840' => 'psa', 'PSO170G2858' => 'pso', 'PSO339G0606' => 'pso', 'PSO384G4709' => 'pso', 'PSO407G0334' => 'pso', 'QL04p040276' => 'qlo', 'QL06p005458' => 'qlo', 'QL06p005472' => 'qlo', 'QL07p030546' => 'qlo', 'QL07p031519' => 'qlo', 'QL09p050949' => 'qlo', 'QL09p050966' => 'qlo', 'QL09p051067' => 'qlo', 'QL12p022706' => 'qlo', 'RcHm_v2.0_Chr2g0119601' => 'rch', 'RcHm_v2.0_Chr3g0459591' => 'rch', 'RcHm_v2.0_Chr4g0418521' => 'rch', 'RcHm_v2.0_Chr4g0418531' => 'rch', 'RcHm_v2.0_Chr4g0418541' => 'rch', 'RcHm_v2.0_Chr6g0291641' => 'rch', 'Rhsim01G0086300' => 'rsi', 'Rhsim01G0276300' => 'rsi', 'Rhsim01G0276500' => 'rsi', 'Rhsim04G0207700' => 'rsi', 'Rhsim05G0234500' => 'rsi', 'Rhsim13G0022400' => 'rsi', 'Sabra02G0167900' => 'sbr', 'Sabra04G0158500' => 'sbr', 'Sabra08G0159800' => 'sbr', 'Sabra10G0011500' => 'sbr', 'Sabra14G0104400' => 'sbr', 'SalBow2G2440' => 'sbo', 'SalBow4G2265' => 'sbo', 'Sc02g0000060' => 'sci', 'Sc05g0005020' => 'sci', 'Sc13g0003890' => 'sci', 'Sed0014865' => 'sed', 'Sed0017224' => 'sed', 'Sed0026391' => 'sed', 'SEGI_00063' => 'sgi', 'SEGI_10967' => 'sgi', 'SEGI_17510' => 'sgi', 'SEGI_24396' => 'sgi', 'SEGI_39719' => 'sgi', 'SEGI_41392' => 'sgi', 'SGA_v2.0_scaffold11G05794' => 'sas', 'SGA_v2.0_scaffold142G35607' => 'sas', 'SGA_v2.0_scaffold1G00447' => 'sas', 'SHI15388' => 'shi', 'SHI15394' => 'shi', 'SHI15396' => 'shi', 'SHI15399' => 'shi', 'SMO343G0151' => 'smo', 'SMO367G1118' => 'smo', 'Solyc01g080200.3' => 'sly', 'Solyc06g008960.3' => 'sly', 'Solyc09g064780.3' => 'sly', 'Sopen01g031980' => 'spe', 'Sopen06g003710' => 'spe', 'Sopen09g026460' => 'spe', 'Sp3g21240' => 'spa', 'Sp4g30030' => 'spa', 'TAR365G0022' => 'tar', 'TAR365G1023' => 'tar', 'TAR365G1253' => 'tar', 'TAR623G0078' => 'tar', 'TAR623G1721' => 'tar', 'TAR633G0959' => 'tar', 'THA.LOC104802225' => 'tha', 'THA.LOC104804769' => 'tha', 'THA.LOC104808660' => 'tha', 'THA.LOC104812792' => 'tha', 'Thecc.01G284000' => 'tca', 'Thecc.04G220600' => 'tca', 'Thecc.05G268900' => 'tca', 'Thecc.08G171100' => 'tca', 'Thhalv10001284m.g' => 'esa', 'Thhalv10019912m.g' => 'esa', 'TPR.G14189' => 'tpr', 'TPR.G18110' => 'tpr', 'TPR.G18130' => 'tpr', 'TPR.G18131' => 'tpr', 'TPR.G18140' => 'tpr', 'TPR.G24282' => 'tpr', 'TPR.G25221' => 'tpr', 'TPR.G29267' => 'tpr', 'TPR.G35315' => 'tpr', 'TPR.G36173' => 'tpr', 'TWI09G0794' => 'twi', 'TWI59G1348' => 'twi', 'TWI74G0430' => 'twi', 'unitig_26.g8940' => 'ugi', 'unitig_749.g13744' => 'ugi', 'unitig_749.g13745' => 'ugi', 'vmacro08269' => 'vma', 'vmacro14937' => 'vma', 'vmacro20401' => 'vma', 'VMungo0464G1349' => 'vmu', 'VMungo0540G0289' => 'vmu', 'VMungo1215G1590' => 'vmu', 'VMungo1309G0221' => 'vmu', 'VMungo1309G2815' => 'vmu', 'VMungo1383G0239' => 'vmu', 'VMungo1383G2910' => 'vmu', 'Zm00001eb095270' => 'zma', 'Zm00001eb095280' => 'zma', 'Zm00001eb111630' => 'zma', 'Zm00001eb237080' => 'zma', 'Zm00001eb273740' => 'zma', 'Zm00001eb285040' => 'zma', 'Zm00001eb330790' => 'zma', 'Zm00001eb337380' => 'zma' ), 'gf_id' => 'HOM05D001484', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001484' ), 'data_identifier' => 'HOM05D001484', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001484', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p31500' => 'bna', 'A05p00020' => 'bna', 'A07p08820' => 'bna', 'Aa31LG4G3300' => 'aar', 'Aa31LG8G10030' => 'aar', 'Actinidia00731' => 'ach', 'Actinidia11473' => 'ach', 'Actinidia23469' => 'ach', 'Actinidia24318' => 'ach', 'Actinidia40196' => 'ach', 'Actinidia40197' => 'ach', 'Actinidia40198' => 'ach', 'Ah.08g212990' => 'amhyb', 'Ah.15g091720' => 'amhyb', 'AL3G38260' => 'aly', 'AL4G47710' => 'aly', 'Aqoxy2G00671' => 'aox', 'Aqoxy2G03236' => 'aox', 'arahy.Tifrunner.gnm1.ann1.05IDCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KR684' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATY3SJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK6QJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6APGL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IDT7Z9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM073U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ0R87' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LE7RV4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT4QRX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V5ENPK' => 'arhy', 'AT2G48110' => 'ath', 'AT3G23590' => 'ath', 'ATR0626G186' => 'atr', 'ATR1127G141' => 'atr', 'Atru.chr4.2583' => 'acertr', 'Atru.chr5.1358' => 'acertr', 'Atru.chr5.1359' => 'acertr', 'Atru.chr8.46' => 'acertr', 'AUR62002640' => 'cqu', 'AUR62030055' => 'cqu', 'AUR62033713' => 'cqu', 'AUR62033714' => 'cqu', 'AUR62036795' => 'cqu', 'AUR62039891' => 'cqu', 'BcaB02g08737' => 'bca', 'BcaB04g20441' => 'bca', 'BcaB06g26509' => 'bca', 'BcaB06g26510' => 'bca', 'BcaB06g26511' => 'bca', 'BcaB06g26512' => 'bca', 'BcaB06g26513' => 'bca', 'BcaC02g12564' => 'bca', 'BcaC02g12565' => 'bca', 'BcaC02g12794' => 'bca', 'BcaC02g12795' => 'bca', 'BcaC02g12796' => 'bca', 'BcaC06g35541' => 'bca', 'BNapus_Darmor_BZH_scaffold_188p00080' => 'bna', 'BNapus_Darmor_BZH_scaffold_188p00090' => 'bna', 'BolC1t03972H' => 'bol', 'BolC1t03973H' => 'bol', 'BolC4t21680H' => 'bol', 'BolC7t41863H' => 'bol', 'BolSC55t61227H' => 'bol', 'BolSC55t61228H' => 'bol', 'BraA01t03278Z' => 'bra', 'BraA05t18998Z' => 'bra', 'BraA07t28673Z' => 'bra', 'C01p40150' => 'bna', 'C05p12370' => 'bna', 'C07p13680' => 'bna', 'CAN.G1006.16' => 'can', 'CAN.G1006.17' => 'can', 'CAN.G1170.2' => 'can', 'CAN.G962.7' => 'can', 'CANSAT25G2179' => 'cansat', 'CANSAT78G1573' => 'cansat', 'CARHR099510' => 'chi', 'CARHR143510' => 'chi', 'Carub.0003s2380' => 'cru', 'Carub.0004s3082' => 'cru', 'Ca_00614_v3' => 'car', 'Ca_07801_v3' => 'car', 'Ca_08567_v3' => 'car', 'Ca_09571_v3' => 'car', 'CBR_g19290' => 'cbr', 'Cc01_g19770' => 'ccan', 'Cc03_g03030' => 'ccan', 'CDE07G0968' => 'cde', 'CDE09G1441' => 'cde', 'Cfa006103' => 'cfa', 'Cfa015573' => 'cfa', 'Cfa016988' => 'cfa', 'Ciclev10006738m.g' => 'ccl', 'Ciclev10010920m.g' => 'ccl', 'Ciclev10018517m.g' => 'ccl', 'CiPaw.01G159200' => 'cil', 'CiPaw.02G091000' => 'cil', 'CiPaw.02G091100' => 'cil', 'CiPaw.08G103100' => 'cil', 'CiPaw.09G224900' => 'cil', 'ClCG06G005740' => 'cla', 'ClCG07G000090' => 'cla', 'ClCG07G000100' => 'cla', 'COL.COLO4_09143' => 'col', 'COL.COLO4_25124' => 'col', 'Cpa.g.sc16.34' => 'cpa', 'Cpa.g.sc3504.1' => 'cpa', 'Cpa.g.sc60.37' => 'cpa', 'CsaV3_6G018520' => 'csa', 'CsaV3_6G036860' => 'csa', 'CSS0001072' => 'camsi', 'CSS0020208' => 'camsi', 'CSS0021253' => 'camsi', 'CSS0022190' => 'camsi', 'CSS0036150' => 'camsi', 'CSS0040442' => 'camsi', 'CSS0042300' => 'camsi', 'CSS0045298' => 'camsi', 'DCAR_012449' => 'dca', 'DCAR_018405' => 'dca', 'DCAR_024573' => 'dca', 'DCAR_030591' => 'dca', 'Dinv16926' => 'din', 'Dinv32963' => 'din', 'Dinv38382' => 'din', 'Dinv38383' => 'din', 'Duzib133G0974' => 'dzi', 'Duzib138G1867' => 'dzi', 'Duzib211G0420' => 'dzi', 'Duzib212G0930' => 'dzi', 'ECA234G1645' => 'eca', 'ECA247G3467' => 'eca', 'ECA248G1703' => 'eca', 'EL10Ac3g06327' => 'bvu', 'EL10Ac7g17204' => 'bvu', 'Eucgr.A00855' => 'egr', 'Eucgr.A00858' => 'egr', 'Eucgr.H01520' => 'egr', 'Eucgr.H03604' => 'egr', 'Eucgr.L03465' => 'egr', 'Eucgr.L03466' => 'egr', 'FAN01G0988' => 'fan', 'FAN02G3892' => 'fan', 'FAN05G3381' => 'fan', 'FAN07G0967' => 'fan', 'FAN07G1493' => 'fan', 'FAN08G3125' => 'fan', 'FAN09G0402' => 'fan', 'FAN12G2594' => 'fan', 'FAN12G3879' => 'fan', 'FAN14G1546' => 'fan', 'FAN15G3626' => 'fan', 'FAN17G0588' => 'fan', 'FAN17G0609' => 'fan', 'FAN18G2817' => 'fan', 'FAN19G1305' => 'fan', 'FAN20G1787' => 'fan', 'FAN22G0073' => 'fan', 'FAN22G0352' => 'fan', 'FAN22G0368' => 'fan', 'FAN22G2273' => 'fan', 'FAN24G1998' => 'fan', 'FAN27G1317' => 'fan', 'FvH4_2g23980' => 'fve', 'FvH4_4g14380' => 'fve', 'FvH4_4g14390' => 'fve', 'FvH4_6g09250' => 'fve', 'Glyma.03G151100' => 'gma', 'Glyma.04G122550' => 'gma', 'Glyma.05G001600' => 'gma', 'Glyma.09G270766' => 'gma', 'Glyma.09G270832' => 'gma', 'Glyma.13G209800' => 'gma', 'Glyma.15G102800' => 'gma', 'Glyma.18G218900' => 'gma', 'Glyma.19G001500' => 'gma', 'Glyma.19G153600' => 'gma', 'Gohir.A02G028600' => 'ghi', 'Gohir.A08G045000' => 'ghi', 'Gohir.A11G120500' => 'ghi', 'Gohir.A12G006200' => 'ghi', 'Gohir.A12G006250' => 'ghi', 'Gohir.D02G036300' => 'ghi', 'Gohir.D08G054700' => 'ghi', 'Gohir.D11G125600' => 'ghi', 'Gohir.D12G005700' => 'ghi', 'Gorai.004G055200' => 'gra', 'Gorai.005G040400' => 'gra', 'Gorai.007G134500' => 'gra', 'Gorai.008G005500' => 'gra', 'GSVIVG01011094001' => 'vvi', 'GSVIVG01017879001' => 'vvi', 'GSVIVG01025988001' => 'vvi', 'GSVIVG01029847001' => 'vvi', 'HanXRQChr10g0282901' => 'han', 'HanXRQChr10g0310371' => 'han', 'HanXRQChr10g0315041' => 'han', 'HanXRQChr11g0327651' => 'han', 'HanXRQChr12g0359391' => 'han', 'Haze_00972' => 'cav', 'Haze_00973' => 'cav', 'Haze_00974' => 'cav', 'Haze_04747' => 'cav', 'Haze_04749' => 'cav', 'Haze_04750' => 'cav', 'Haze_21217' => 'cav', 'Hma1.2p1_1037F.1_g250680' => 'hma', 'Hma1.2p1_1644F.1_g295320' => 'hma', 'HPP92_011322' => 'vpl', 'HPP92_011323' => 'vpl', 'HPP92_011324' => 'vpl', 'HPP92_011325' => 'vpl', 'HPP92_011326' => 'vpl', 'Hund12205' => 'sun', 'Hund17957' => 'sun', 'Lalb_Chr06g0176771' => 'lal', 'Lalb_Chr18g0056021' => 'lal', 'Lalb_Chr18g0056031' => 'lal', 'Lalb_Chr18g0056041' => 'lal', 'Lalb_Chr20g0107751' => 'lal', 'Lalb_Chr20g0118371' => 'lal', 'Lj1g0010239' => 'lja', 'Lj1g0017101' => 'lja', 'Lj2A1178G40' => 'lonja', 'Lj2A54G84' => 'lonja', 'Lj2g0015248' => 'lja', 'Lj3A761T51' => 'lonja', 'Lj6g0018116' => 'lja', 'Lsat_1_v5_gn_4_136040' => 'lsa', 'Lsat_1_v5_gn_5_187461' => 'lsa', 'Lsat_1_v5_gn_5_77001' => 'lsa', 'Lsat_1_v5_gn_9_4461' => 'lsa', 'Manes.01G210100' => 'mes', 'Manes.03G185600' => 'mes', 'Manes.05G073300' => 'mes', 'Manes.09G120300' => 'mes', 'Manes.15G022100' => 'mes', 'Mapoly0096s0053' => 'mpo', 'MBI03_g14058_MAGBIO' => 'mbi', 'MBI03_g33876_MAGBIO' => 'mbi', 'MBI03_g36854_MAGBIO' => 'mbi', 'MBI17_g11997_MAGBIO' => 'mbi', 'MD03G1269000' => 'mdo', 'MD04G1179600' => 'mdo', 'MD11G1289800' => 'mdo', 'MD12G1194700' => 'mdo', 'MD13G1182100' => 'mdo', 'MD13G1182200' => 'mdo', 'MD16G1182600' => 'mdo', 'Medtr2g021400' => 'mtr', 'Medtr2g021470' => 'mtr', 'Medtr2g105810' => 'mtr', 'Medtr3g033580' => 'mtr', 'Medtr6g007970' => 'mtr', 'Medtr7g056330' => 'mtr', 'Medtr7g074290' => 'mtr', 'Medtr7g074380' => 'mtr', 'Medtr7g094550' => 'mtr', 'Medtr8g069995' => 'mtr', 'MELO3C014345.2' => 'cme', 'MELO3C021395.2' => 'cme', 'Migut.D00262' => 'egut', 'Migut.G00257' => 'egut', 'MSTRG.21575' => 'ama', 'MSTRG.3985' => 'ama', 'Nitab4.5_0000295g0140' => 'nta', 'Nitab4.5_0000732g0140' => 'nta', 'Nitab4.5_0003162g0020' => 'nta', 'Nitab4.5_0006180g0090' => 'nta', 'Nitab4.5_0006390g0010' => 'nta', 'Nitab4.5_0007392g0040' => 'nta', 'Nn1g02140' => 'nnu', 'Nn4g26168' => 'nnu', 'Nn5g26754' => 'nnu', 'Oeu001433.1' => 'oeu', 'Oeu010299.2' => 'oeu', 'Oeu011171.1' => 'oeu', 'Oeu037675.1' => 'oeu', 'Oeu038359.1' => 'oeu', 'Oeu063834.1' => 'oeu', 'Oeu063835.1' => 'oeu', 'Os05g0312000' => 'osa', 'Os07g0211101' => 'osa', 'Os07g0211200' => 'osa', 'Os07g0681500' => 'osa', 'Peaxi162Scf00095g01015' => 'pax', 'Peaxi162Scf00104g00329' => 'pax', 'Peaxi162Scf00161g00137' => 'pax', 'PGR004G1665' => 'pgr', 'PGR031G2937' => 'pgr', 'PGR119G2145' => 'pgr', 'PGSC0003DMG400004351' => 'stu', 'PGSC0003DMG400014625' => 'stu', 'PGSC0003DMG401000943' => 'stu', 'Phvul.001G148600' => 'pvu', 'Phvul.004G001700' => 'pvu', 'Phvul.006G154900' => 'pvu', 'Phvul.008G078200' => 'pvu', 'Phvul.011G136500' => 'pvu', 'Potri.002G215600' => 'ptr', 'Potri.008G201600' => 'ptr', 'Potri.014G138400' => 'ptr', 'Potri.016G142500' => 'ptr', 'Pp3c16_10580' => 'ppa', 'Pp3c5_25280' => 'ppa', 'Prupe.1G150000' => 'ppe', 'Prupe.1G150100' => 'ppe', 'Prupe.6G299600' => 'ppe', 'Prupe.8G245000' => 'ppe', 'Psat0s4927g0040' => 'psa', 'Psat1g052080' => 'psa', 'Psat1g183800' => 'psa', 'Psat3g113840' => 'psa', 'Psat3g126120' => 'psa', 'Psat3g126160' => 'psa', 'Psat3g158760' => 'psa', 'Psat3g158840' => 'psa', 'PSO170G2858' => 'pso', 'PSO339G0606' => 'pso', 'PSO384G4709' => 'pso', 'PSO407G0334' => 'pso', 'QL04p040276' => 'qlo', 'QL06p005458' => 'qlo', 'QL06p005472' => 'qlo', 'QL07p030546' => 'qlo', 'QL07p031519' => 'qlo', 'QL09p050949' => 'qlo', 'QL09p050966' => 'qlo', 'QL09p051067' => 'qlo', 'QL12p022706' => 'qlo', 'RcHm_v2.0_Chr2g0119601' => 'rch', 'RcHm_v2.0_Chr3g0459591' => 'rch', 'RcHm_v2.0_Chr4g0418521' => 'rch', 'RcHm_v2.0_Chr4g0418531' => 'rch', 'RcHm_v2.0_Chr4g0418541' => 'rch', 'RcHm_v2.0_Chr6g0291641' => 'rch', 'Rhsim01G0086300' => 'rsi', 'Rhsim01G0276300' => 'rsi', 'Rhsim01G0276500' => 'rsi', 'Rhsim04G0207700' => 'rsi', 'Rhsim05G0234500' => 'rsi', 'Rhsim13G0022400' => 'rsi', 'Sabra02G0167900' => 'sbr', 'Sabra04G0158500' => 'sbr', 'Sabra08G0159800' => 'sbr', 'Sabra10G0011500' => 'sbr', 'Sabra14G0104400' => 'sbr', 'SalBow2G2440' => 'sbo', 'SalBow4G2265' => 'sbo', 'Sc02g0000060' => 'sci', 'Sc05g0005020' => 'sci', 'Sc13g0003890' => 'sci', 'Sed0014865' => 'sed', 'Sed0017224' => 'sed', 'Sed0026391' => 'sed', 'SEGI_00063' => 'sgi', 'SEGI_10967' => 'sgi', 'SEGI_17510' => 'sgi', 'SEGI_24396' => 'sgi', 'SEGI_39719' => 'sgi', 'SEGI_41392' => 'sgi', 'SGA_v2.0_scaffold11G05794' => 'sas', 'SGA_v2.0_scaffold142G35607' => 'sas', 'SGA_v2.0_scaffold1G00447' => 'sas', 'SHI15388' => 'shi', 'SHI15394' => 'shi', 'SHI15396' => 'shi', 'SHI15399' => 'shi', 'SMO343G0151' => 'smo', 'SMO367G1118' => 'smo', 'Solyc01g080200.3' => 'sly', 'Solyc06g008960.3' => 'sly', 'Solyc09g064780.3' => 'sly', 'Sopen01g031980' => 'spe', 'Sopen06g003710' => 'spe', 'Sopen09g026460' => 'spe', 'Sp3g21240' => 'spa', 'Sp4g30030' => 'spa', 'TAR365G0022' => 'tar', 'TAR365G1023' => 'tar', 'TAR365G1253' => 'tar', 'TAR623G0078' => 'tar', 'TAR623G1721' => 'tar', 'TAR633G0959' => 'tar', 'THA.LOC104802225' => 'tha', 'THA.LOC104804769' => 'tha', 'THA.LOC104808660' => 'tha', 'THA.LOC104812792' => 'tha', 'Thecc.01G284000' => 'tca', 'Thecc.04G220600' => 'tca', 'Thecc.05G268900' => 'tca', 'Thecc.08G171100' => 'tca', 'Thhalv10001284m.g' => 'esa', 'Thhalv10019912m.g' => 'esa', 'TPR.G14189' => 'tpr', 'TPR.G18110' => 'tpr', 'TPR.G18130' => 'tpr', 'TPR.G18131' => 'tpr', 'TPR.G18140' => 'tpr', 'TPR.G24282' => 'tpr', 'TPR.G25221' => 'tpr', 'TPR.G29267' => 'tpr', 'TPR.G35315' => 'tpr', 'TPR.G36173' => 'tpr', 'TWI09G0794' => 'twi', 'TWI59G1348' => 'twi', 'TWI74G0430' => 'twi', 'unitig_26.g8940' => 'ugi', 'unitig_749.g13744' => 'ugi', 'unitig_749.g13745' => 'ugi', 'vmacro08269' => 'vma', 'vmacro14937' => 'vma', 'vmacro20401' => 'vma', 'VMungo0464G1349' => 'vmu', 'VMungo0540G0289' => 'vmu', 'VMungo1215G1590' => 'vmu', 'VMungo1309G0221' => 'vmu', 'VMungo1309G2815' => 'vmu', 'VMungo1383G0239' => 'vmu', 'VMungo1383G2910' => 'vmu', 'Zm00001eb095270' => 'zma', 'Zm00001eb095280' => 'zma', 'Zm00001eb111630' => 'zma', 'Zm00001eb237080' => 'zma', 'Zm00001eb273740' => 'zma', 'Zm00001eb285040' => 'zma', 'Zm00001eb330790' => 'zma', 'Zm00001eb337380' => 'zma' ) $gf_id = 'HOM05D001484' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001484' ) $data_identifier = 'HOM05D001484' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 2, 'aly' => (int) 2, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 22, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 7, 'hma' => (int) 2, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 7, 'mtr' => (int) 10, 'cme' => (int) 2, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 4, 'ppa' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 4, 'qlo' => (int) 9, 'rch' => (int) 6, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 10, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 7, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb337380' $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' => 'HOM05D001484', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p31500' => 'bna', 'A05p00020' => 'bna', 'A07p08820' => 'bna', 'Aa31LG4G3300' => 'aar', 'Aa31LG8G10030' => 'aar', 'Actinidia00731' => 'ach', 'Actinidia11473' => 'ach', 'Actinidia23469' => 'ach', 'Actinidia24318' => 'ach', 'Actinidia40196' => 'ach', 'Actinidia40197' => 'ach', 'Actinidia40198' => 'ach', 'Ah.08g212990' => 'amhyb', 'Ah.15g091720' => 'amhyb', 'AL3G38260' => 'aly', 'AL4G47710' => 'aly', 'Aqoxy2G00671' => 'aox', 'Aqoxy2G03236' => 'aox', 'arahy.Tifrunner.gnm1.ann1.05IDCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KR684' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATY3SJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK6QJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6APGL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IDT7Z9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM073U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ0R87' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LE7RV4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT4QRX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V5ENPK' => 'arhy', 'AT2G48110' => 'ath', 'AT3G23590' => 'ath', 'ATR0626G186' => 'atr', 'ATR1127G141' => 'atr', 'Atru.chr4.2583' => 'acertr', 'Atru.chr5.1358' => 'acertr', 'Atru.chr5.1359' => 'acertr', 'Atru.chr8.46' => 'acertr', 'AUR62002640' => 'cqu', 'AUR62030055' => 'cqu', 'AUR62033713' => 'cqu', 'AUR62033714' => 'cqu', 'AUR62036795' => 'cqu', 'AUR62039891' => 'cqu', 'BcaB02g08737' => 'bca', 'BcaB04g20441' => 'bca', 'BcaB06g26509' => 'bca', 'BcaB06g26510' => 'bca', 'BcaB06g26511' => 'bca', 'BcaB06g26512' => 'bca', 'BcaB06g26513' => 'bca', 'BcaC02g12564' => 'bca', 'BcaC02g12565' => 'bca', 'BcaC02g12794' => 'bca', 'BcaC02g12795' => 'bca', 'BcaC02g12796' => 'bca', 'BcaC06g35541' => 'bca', 'BNapus_Darmor_BZH_scaffold_188p00080' => 'bna', 'BNapus_Darmor_BZH_scaffold_188p00090' => 'bna', 'BolC1t03972H' => 'bol', 'BolC1t03973H' => 'bol', 'BolC4t21680H' => 'bol', 'BolC7t41863H' => 'bol', 'BolSC55t61227H' => 'bol', 'BolSC55t61228H' => 'bol', 'BraA01t03278Z' => 'bra', 'BraA05t18998Z' => 'bra', 'BraA07t28673Z' => 'bra', 'C01p40150' => 'bna', 'C05p12370' => 'bna', 'C07p13680' => 'bna', 'CAN.G1006.16' => 'can', 'CAN.G1006.17' => 'can', 'CAN.G1170.2' => 'can', 'CAN.G962.7' => 'can', 'CANSAT25G2179' => 'cansat', 'CANSAT78G1573' => 'cansat', 'CARHR099510' => 'chi', 'CARHR143510' => 'chi', 'Carub.0003s2380' => 'cru', 'Carub.0004s3082' => 'cru', 'Ca_00614_v3' => 'car', 'Ca_07801_v3' => 'car', 'Ca_08567_v3' => 'car', 'Ca_09571_v3' => 'car', 'CBR_g19290' => 'cbr', 'Cc01_g19770' => 'ccan', 'Cc03_g03030' => 'ccan', 'CDE07G0968' => 'cde', 'CDE09G1441' => 'cde', 'Cfa006103' => 'cfa', 'Cfa015573' => 'cfa', 'Cfa016988' => 'cfa', 'Ciclev10006738m.g' => 'ccl', 'Ciclev10010920m.g' => 'ccl', 'Ciclev10018517m.g' => 'ccl', 'CiPaw.01G159200' => 'cil', 'CiPaw.02G091000' => 'cil', 'CiPaw.02G091100' => 'cil', 'CiPaw.08G103100' => 'cil', 'CiPaw.09G224900' => 'cil', 'ClCG06G005740' => 'cla', 'ClCG07G000090' => 'cla', 'ClCG07G000100' => 'cla', 'COL.COLO4_09143' => 'col', 'COL.COLO4_25124' => 'col', 'Cpa.g.sc16.34' => 'cpa', 'Cpa.g.sc3504.1' => 'cpa', 'Cpa.g.sc60.37' => 'cpa', 'CsaV3_6G018520' => 'csa', 'CsaV3_6G036860' => 'csa', 'CSS0001072' => 'camsi', 'CSS0020208' => 'camsi', 'CSS0021253' => 'camsi', 'CSS0022190' => 'camsi', 'CSS0036150' => 'camsi', 'CSS0040442' => 'camsi', 'CSS0042300' => 'camsi', 'CSS0045298' => 'camsi', 'DCAR_012449' => 'dca', 'DCAR_018405' => 'dca', 'DCAR_024573' => 'dca', 'DCAR_030591' => 'dca', 'Dinv16926' => 'din', 'Dinv32963' => 'din', 'Dinv38382' => 'din', 'Dinv38383' => 'din', 'Duzib133G0974' => 'dzi', 'Duzib138G1867' => 'dzi', 'Duzib211G0420' => 'dzi', 'Duzib212G0930' => 'dzi', 'ECA234G1645' => 'eca', 'ECA247G3467' => 'eca', 'ECA248G1703' => 'eca', 'EL10Ac3g06327' => 'bvu', 'EL10Ac7g17204' => 'bvu', 'Eucgr.A00855' => 'egr', 'Eucgr.A00858' => 'egr', 'Eucgr.H01520' => 'egr', 'Eucgr.H03604' => 'egr', 'Eucgr.L03465' => 'egr', 'Eucgr.L03466' => 'egr', 'FAN01G0988' => 'fan', 'FAN02G3892' => 'fan', 'FAN05G3381' => 'fan', 'FAN07G0967' => 'fan', 'FAN07G1493' => 'fan', 'FAN08G3125' => 'fan', 'FAN09G0402' => 'fan', 'FAN12G2594' => 'fan', 'FAN12G3879' => 'fan', 'FAN14G1546' => 'fan', 'FAN15G3626' => 'fan', 'FAN17G0588' => 'fan', 'FAN17G0609' => 'fan', 'FAN18G2817' => 'fan', 'FAN19G1305' => 'fan', 'FAN20G1787' => 'fan', 'FAN22G0073' => 'fan', 'FAN22G0352' => 'fan', 'FAN22G0368' => 'fan', 'FAN22G2273' => 'fan', 'FAN24G1998' => 'fan', 'FAN27G1317' => 'fan', 'FvH4_2g23980' => 'fve', 'FvH4_4g14380' => 'fve', 'FvH4_4g14390' => 'fve', 'FvH4_6g09250' => 'fve', 'Glyma.03G151100' => 'gma', 'Glyma.04G122550' => 'gma', 'Glyma.05G001600' => 'gma', 'Glyma.09G270766' => 'gma', 'Glyma.09G270832' => 'gma', 'Glyma.13G209800' => 'gma', 'Glyma.15G102800' => 'gma', 'Glyma.18G218900' => 'gma', 'Glyma.19G001500' => 'gma', 'Glyma.19G153600' => 'gma', 'Gohir.A02G028600' => 'ghi', 'Gohir.A08G045000' => 'ghi', 'Gohir.A11G120500' => 'ghi', 'Gohir.A12G006200' => 'ghi', 'Gohir.A12G006250' => 'ghi', 'Gohir.D02G036300' => 'ghi', 'Gohir.D08G054700' => 'ghi', 'Gohir.D11G125600' => 'ghi', 'Gohir.D12G005700' => 'ghi', 'Gorai.004G055200' => 'gra', 'Gorai.005G040400' => 'gra', 'Gorai.007G134500' => 'gra', 'Gorai.008G005500' => 'gra', 'GSVIVG01011094001' => 'vvi', 'GSVIVG01017879001' => 'vvi', 'GSVIVG01025988001' => 'vvi', 'GSVIVG01029847001' => 'vvi', 'HanXRQChr10g0282901' => 'han', 'HanXRQChr10g0310371' => 'han', 'HanXRQChr10g0315041' => 'han', 'HanXRQChr11g0327651' => 'han', 'HanXRQChr12g0359391' => 'han', 'Haze_00972' => 'cav', 'Haze_00973' => 'cav', 'Haze_00974' => 'cav', 'Haze_04747' => 'cav', 'Haze_04749' => 'cav', 'Haze_04750' => 'cav', 'Haze_21217' => 'cav', 'Hma1.2p1_1037F.1_g250680' => 'hma', 'Hma1.2p1_1644F.1_g295320' => 'hma', 'HPP92_011322' => 'vpl', 'HPP92_011323' => 'vpl', 'HPP92_011324' => 'vpl', 'HPP92_011325' => 'vpl', 'HPP92_011326' => 'vpl', 'Hund12205' => 'sun', 'Hund17957' => 'sun', 'Lalb_Chr06g0176771' => 'lal', 'Lalb_Chr18g0056021' => 'lal', 'Lalb_Chr18g0056031' => 'lal', 'Lalb_Chr18g0056041' => 'lal', 'Lalb_Chr20g0107751' => 'lal', 'Lalb_Chr20g0118371' => 'lal', 'Lj1g0010239' => 'lja', 'Lj1g0017101' => 'lja', 'Lj2A1178G40' => 'lonja', 'Lj2A54G84' => 'lonja', 'Lj2g0015248' => 'lja', 'Lj3A761T51' => 'lonja', 'Lj6g0018116' => 'lja', 'Lsat_1_v5_gn_4_136040' => 'lsa', 'Lsat_1_v5_gn_5_187461' => 'lsa', 'Lsat_1_v5_gn_5_77001' => 'lsa', 'Lsat_1_v5_gn_9_4461' => 'lsa', 'Manes.01G210100' => 'mes', 'Manes.03G185600' => 'mes', 'Manes.05G073300' => 'mes', 'Manes.09G120300' => 'mes', 'Manes.15G022100' => 'mes', 'Mapoly0096s0053' => 'mpo', 'MBI03_g14058_MAGBIO' => 'mbi', 'MBI03_g33876_MAGBIO' => 'mbi', 'MBI03_g36854_MAGBIO' => 'mbi', 'MBI17_g11997_MAGBIO' => 'mbi', 'MD03G1269000' => 'mdo', 'MD04G1179600' => 'mdo', 'MD11G1289800' => 'mdo', 'MD12G1194700' => 'mdo', 'MD13G1182100' => 'mdo', 'MD13G1182200' => 'mdo', 'MD16G1182600' => 'mdo', 'Medtr2g021400' => 'mtr', 'Medtr2g021470' => 'mtr', 'Medtr2g105810' => 'mtr', 'Medtr3g033580' => 'mtr', 'Medtr6g007970' => 'mtr', 'Medtr7g056330' => 'mtr', 'Medtr7g074290' => 'mtr', 'Medtr7g074380' => 'mtr', 'Medtr7g094550' => 'mtr', 'Medtr8g069995' => 'mtr', 'MELO3C014345.2' => 'cme', 'MELO3C021395.2' => 'cme', 'Migut.D00262' => 'egut', 'Migut.G00257' => 'egut', 'MSTRG.21575' => 'ama', 'MSTRG.3985' => 'ama', 'Nitab4.5_0000295g0140' => 'nta', 'Nitab4.5_0000732g0140' => 'nta', 'Nitab4.5_0003162g0020' => 'nta', 'Nitab4.5_0006180g0090' => 'nta', 'Nitab4.5_0006390g0010' => 'nta', 'Nitab4.5_0007392g0040' => 'nta', 'Nn1g02140' => 'nnu', 'Nn4g26168' => 'nnu', 'Nn5g26754' => 'nnu', 'Oeu001433.1' => 'oeu', 'Oeu010299.2' => 'oeu', 'Oeu011171.1' => 'oeu', 'Oeu037675.1' => 'oeu', 'Oeu038359.1' => 'oeu', 'Oeu063834.1' => 'oeu', 'Oeu063835.1' => 'oeu', 'Os05g0312000' => 'osa', 'Os07g0211101' => 'osa', 'Os07g0211200' => 'osa', 'Os07g0681500' => 'osa', 'Peaxi162Scf00095g01015' => 'pax', 'Peaxi162Scf00104g00329' => 'pax', 'Peaxi162Scf00161g00137' => 'pax', 'PGR004G1665' => 'pgr', 'PGR031G2937' => 'pgr', 'PGR119G2145' => 'pgr', 'PGSC0003DMG400004351' => 'stu', 'PGSC0003DMG400014625' => 'stu', 'PGSC0003DMG401000943' => 'stu', 'Phvul.001G148600' => 'pvu', 'Phvul.004G001700' => 'pvu', 'Phvul.006G154900' => 'pvu', 'Phvul.008G078200' => 'pvu', 'Phvul.011G136500' => 'pvu', 'Potri.002G215600' => 'ptr', 'Potri.008G201600' => 'ptr', 'Potri.014G138400' => 'ptr', 'Potri.016G142500' => 'ptr', 'Pp3c16_10580' => 'ppa', 'Pp3c5_25280' => 'ppa', 'Prupe.1G150000' => 'ppe', 'Prupe.1G150100' => 'ppe', 'Prupe.6G299600' => 'ppe', 'Prupe.8G245000' => 'ppe', 'Psat0s4927g0040' => 'psa', 'Psat1g052080' => 'psa', 'Psat1g183800' => 'psa', 'Psat3g113840' => 'psa', 'Psat3g126120' => 'psa', 'Psat3g126160' => 'psa', 'Psat3g158760' => 'psa', 'Psat3g158840' => 'psa', 'PSO170G2858' => 'pso', 'PSO339G0606' => 'pso', 'PSO384G4709' => 'pso', 'PSO407G0334' => 'pso', 'QL04p040276' => 'qlo', 'QL06p005458' => 'qlo', 'QL06p005472' => 'qlo', 'QL07p030546' => 'qlo', 'QL07p031519' => 'qlo', 'QL09p050949' => 'qlo', 'QL09p050966' => 'qlo', 'QL09p051067' => 'qlo', 'QL12p022706' => 'qlo', 'RcHm_v2.0_Chr2g0119601' => 'rch', 'RcHm_v2.0_Chr3g0459591' => 'rch', 'RcHm_v2.0_Chr4g0418521' => 'rch', 'RcHm_v2.0_Chr4g0418531' => 'rch', 'RcHm_v2.0_Chr4g0418541' => 'rch', 'RcHm_v2.0_Chr6g0291641' => 'rch', 'Rhsim01G0086300' => 'rsi', 'Rhsim01G0276300' => 'rsi', 'Rhsim01G0276500' => 'rsi', 'Rhsim04G0207700' => 'rsi', 'Rhsim05G0234500' => 'rsi', 'Rhsim13G0022400' => 'rsi', 'Sabra02G0167900' => 'sbr', 'Sabra04G0158500' => 'sbr', 'Sabra08G0159800' => 'sbr', 'Sabra10G0011500' => 'sbr', 'Sabra14G0104400' => 'sbr', 'SalBow2G2440' => 'sbo', 'SalBow4G2265' => 'sbo', 'Sc02g0000060' => 'sci', 'Sc05g0005020' => 'sci', 'Sc13g0003890' => 'sci', 'Sed0014865' => 'sed', 'Sed0017224' => 'sed', 'Sed0026391' => 'sed', 'SEGI_00063' => 'sgi', 'SEGI_10967' => 'sgi', 'SEGI_17510' => 'sgi', 'SEGI_24396' => 'sgi', 'SEGI_39719' => 'sgi', 'SEGI_41392' => 'sgi', 'SGA_v2.0_scaffold11G05794' => 'sas', 'SGA_v2.0_scaffold142G35607' => 'sas', 'SGA_v2.0_scaffold1G00447' => 'sas', 'SHI15388' => 'shi', 'SHI15394' => 'shi', 'SHI15396' => 'shi', 'SHI15399' => 'shi', 'SMO343G0151' => 'smo', 'SMO367G1118' => 'smo', 'Solyc01g080200.3' => 'sly', 'Solyc06g008960.3' => 'sly', 'Solyc09g064780.3' => 'sly', 'Sopen01g031980' => 'spe', 'Sopen06g003710' => 'spe', 'Sopen09g026460' => 'spe', 'Sp3g21240' => 'spa', 'Sp4g30030' => 'spa', 'TAR365G0022' => 'tar', 'TAR365G1023' => 'tar', 'TAR365G1253' => 'tar', 'TAR623G0078' => 'tar', 'TAR623G1721' => 'tar', 'TAR633G0959' => 'tar', 'THA.LOC104802225' => 'tha', 'THA.LOC104804769' => 'tha', 'THA.LOC104808660' => 'tha', 'THA.LOC104812792' => 'tha', 'Thecc.01G284000' => 'tca', 'Thecc.04G220600' => 'tca', 'Thecc.05G268900' => 'tca', 'Thecc.08G171100' => 'tca', 'Thhalv10001284m.g' => 'esa', 'Thhalv10019912m.g' => 'esa', 'TPR.G14189' => 'tpr', 'TPR.G18110' => 'tpr', 'TPR.G18130' => 'tpr', 'TPR.G18131' => 'tpr', 'TPR.G18140' => 'tpr', 'TPR.G24282' => 'tpr', 'TPR.G25221' => 'tpr', 'TPR.G29267' => 'tpr', 'TPR.G35315' => 'tpr', 'TPR.G36173' => 'tpr', 'TWI09G0794' => 'twi', 'TWI59G1348' => 'twi', 'TWI74G0430' => 'twi', 'unitig_26.g8940' => 'ugi', 'unitig_749.g13744' => 'ugi', 'unitig_749.g13745' => 'ugi', 'vmacro08269' => 'vma', 'vmacro14937' => 'vma', 'vmacro20401' => 'vma', 'VMungo0464G1349' => 'vmu', 'VMungo0540G0289' => 'vmu', 'VMungo1215G1590' => 'vmu', 'VMungo1309G0221' => 'vmu', 'VMungo1309G2815' => 'vmu', 'VMungo1383G0239' => 'vmu', 'VMungo1383G2910' => 'vmu', 'Zm00001eb095270' => 'zma', 'Zm00001eb095280' => 'zma', 'Zm00001eb111630' => 'zma', 'Zm00001eb237080' => 'zma', 'Zm00001eb273740' => 'zma', 'Zm00001eb285040' => 'zma', 'Zm00001eb330790' => 'zma', 'Zm00001eb337380' => 'zma' ), 'gf_id' => 'HOM05D001484', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001484' ), 'data_identifier' => 'HOM05D001484', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001484', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p31500' => 'bna', 'A05p00020' => 'bna', 'A07p08820' => 'bna', 'Aa31LG4G3300' => 'aar', 'Aa31LG8G10030' => 'aar', 'Actinidia00731' => 'ach', 'Actinidia11473' => 'ach', 'Actinidia23469' => 'ach', 'Actinidia24318' => 'ach', 'Actinidia40196' => 'ach', 'Actinidia40197' => 'ach', 'Actinidia40198' => 'ach', 'Ah.08g212990' => 'amhyb', 'Ah.15g091720' => 'amhyb', 'AL3G38260' => 'aly', 'AL4G47710' => 'aly', 'Aqoxy2G00671' => 'aox', 'Aqoxy2G03236' => 'aox', 'arahy.Tifrunner.gnm1.ann1.05IDCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KR684' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATY3SJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK6QJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6APGL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IDT7Z9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM073U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ0R87' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LE7RV4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT4QRX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V5ENPK' => 'arhy', 'AT2G48110' => 'ath', 'AT3G23590' => 'ath', 'ATR0626G186' => 'atr', 'ATR1127G141' => 'atr', 'Atru.chr4.2583' => 'acertr', 'Atru.chr5.1358' => 'acertr', 'Atru.chr5.1359' => 'acertr', 'Atru.chr8.46' => 'acertr', 'AUR62002640' => 'cqu', 'AUR62030055' => 'cqu', 'AUR62033713' => 'cqu', 'AUR62033714' => 'cqu', 'AUR62036795' => 'cqu', 'AUR62039891' => 'cqu', 'BcaB02g08737' => 'bca', 'BcaB04g20441' => 'bca', 'BcaB06g26509' => 'bca', 'BcaB06g26510' => 'bca', 'BcaB06g26511' => 'bca', 'BcaB06g26512' => 'bca', 'BcaB06g26513' => 'bca', 'BcaC02g12564' => 'bca', 'BcaC02g12565' => 'bca', 'BcaC02g12794' => 'bca', 'BcaC02g12795' => 'bca', 'BcaC02g12796' => 'bca', 'BcaC06g35541' => 'bca', 'BNapus_Darmor_BZH_scaffold_188p00080' => 'bna', 'BNapus_Darmor_BZH_scaffold_188p00090' => 'bna', 'BolC1t03972H' => 'bol', 'BolC1t03973H' => 'bol', 'BolC4t21680H' => 'bol', 'BolC7t41863H' => 'bol', 'BolSC55t61227H' => 'bol', 'BolSC55t61228H' => 'bol', 'BraA01t03278Z' => 'bra', 'BraA05t18998Z' => 'bra', 'BraA07t28673Z' => 'bra', 'C01p40150' => 'bna', 'C05p12370' => 'bna', 'C07p13680' => 'bna', 'CAN.G1006.16' => 'can', 'CAN.G1006.17' => 'can', 'CAN.G1170.2' => 'can', 'CAN.G962.7' => 'can', 'CANSAT25G2179' => 'cansat', 'CANSAT78G1573' => 'cansat', 'CARHR099510' => 'chi', 'CARHR143510' => 'chi', 'Carub.0003s2380' => 'cru', 'Carub.0004s3082' => 'cru', 'Ca_00614_v3' => 'car', 'Ca_07801_v3' => 'car', 'Ca_08567_v3' => 'car', 'Ca_09571_v3' => 'car', 'CBR_g19290' => 'cbr', 'Cc01_g19770' => 'ccan', 'Cc03_g03030' => 'ccan', 'CDE07G0968' => 'cde', 'CDE09G1441' => 'cde', 'Cfa006103' => 'cfa', 'Cfa015573' => 'cfa', 'Cfa016988' => 'cfa', 'Ciclev10006738m.g' => 'ccl', 'Ciclev10010920m.g' => 'ccl', 'Ciclev10018517m.g' => 'ccl', 'CiPaw.01G159200' => 'cil', 'CiPaw.02G091000' => 'cil', 'CiPaw.02G091100' => 'cil', 'CiPaw.08G103100' => 'cil', 'CiPaw.09G224900' => 'cil', 'ClCG06G005740' => 'cla', 'ClCG07G000090' => 'cla', 'ClCG07G000100' => 'cla', 'COL.COLO4_09143' => 'col', 'COL.COLO4_25124' => 'col', 'Cpa.g.sc16.34' => 'cpa', 'Cpa.g.sc3504.1' => 'cpa', 'Cpa.g.sc60.37' => 'cpa', 'CsaV3_6G018520' => 'csa', 'CsaV3_6G036860' => 'csa', 'CSS0001072' => 'camsi', 'CSS0020208' => 'camsi', 'CSS0021253' => 'camsi', 'CSS0022190' => 'camsi', 'CSS0036150' => 'camsi', 'CSS0040442' => 'camsi', 'CSS0042300' => 'camsi', 'CSS0045298' => 'camsi', 'DCAR_012449' => 'dca', 'DCAR_018405' => 'dca', 'DCAR_024573' => 'dca', 'DCAR_030591' => 'dca', 'Dinv16926' => 'din', 'Dinv32963' => 'din', 'Dinv38382' => 'din', 'Dinv38383' => 'din', 'Duzib133G0974' => 'dzi', 'Duzib138G1867' => 'dzi', 'Duzib211G0420' => 'dzi', 'Duzib212G0930' => 'dzi', 'ECA234G1645' => 'eca', 'ECA247G3467' => 'eca', 'ECA248G1703' => 'eca', 'EL10Ac3g06327' => 'bvu', 'EL10Ac7g17204' => 'bvu', 'Eucgr.A00855' => 'egr', 'Eucgr.A00858' => 'egr', 'Eucgr.H01520' => 'egr', 'Eucgr.H03604' => 'egr', 'Eucgr.L03465' => 'egr', 'Eucgr.L03466' => 'egr', 'FAN01G0988' => 'fan', 'FAN02G3892' => 'fan', 'FAN05G3381' => 'fan', 'FAN07G0967' => 'fan', 'FAN07G1493' => 'fan', 'FAN08G3125' => 'fan', 'FAN09G0402' => 'fan', 'FAN12G2594' => 'fan', 'FAN12G3879' => 'fan', 'FAN14G1546' => 'fan', 'FAN15G3626' => 'fan', 'FAN17G0588' => 'fan', 'FAN17G0609' => 'fan', 'FAN18G2817' => 'fan', 'FAN19G1305' => 'fan', 'FAN20G1787' => 'fan', 'FAN22G0073' => 'fan', 'FAN22G0352' => 'fan', 'FAN22G0368' => 'fan', 'FAN22G2273' => 'fan', 'FAN24G1998' => 'fan', 'FAN27G1317' => 'fan', 'FvH4_2g23980' => 'fve', 'FvH4_4g14380' => 'fve', 'FvH4_4g14390' => 'fve', 'FvH4_6g09250' => 'fve', 'Glyma.03G151100' => 'gma', 'Glyma.04G122550' => 'gma', 'Glyma.05G001600' => 'gma', 'Glyma.09G270766' => 'gma', 'Glyma.09G270832' => 'gma', 'Glyma.13G209800' => 'gma', 'Glyma.15G102800' => 'gma', 'Glyma.18G218900' => 'gma', 'Glyma.19G001500' => 'gma', 'Glyma.19G153600' => 'gma', 'Gohir.A02G028600' => 'ghi', 'Gohir.A08G045000' => 'ghi', 'Gohir.A11G120500' => 'ghi', 'Gohir.A12G006200' => 'ghi', 'Gohir.A12G006250' => 'ghi', 'Gohir.D02G036300' => 'ghi', 'Gohir.D08G054700' => 'ghi', 'Gohir.D11G125600' => 'ghi', 'Gohir.D12G005700' => 'ghi', 'Gorai.004G055200' => 'gra', 'Gorai.005G040400' => 'gra', 'Gorai.007G134500' => 'gra', 'Gorai.008G005500' => 'gra', 'GSVIVG01011094001' => 'vvi', 'GSVIVG01017879001' => 'vvi', 'GSVIVG01025988001' => 'vvi', 'GSVIVG01029847001' => 'vvi', 'HanXRQChr10g0282901' => 'han', 'HanXRQChr10g0310371' => 'han', 'HanXRQChr10g0315041' => 'han', 'HanXRQChr11g0327651' => 'han', 'HanXRQChr12g0359391' => 'han', 'Haze_00972' => 'cav', 'Haze_00973' => 'cav', 'Haze_00974' => 'cav', 'Haze_04747' => 'cav', 'Haze_04749' => 'cav', 'Haze_04750' => 'cav', 'Haze_21217' => 'cav', 'Hma1.2p1_1037F.1_g250680' => 'hma', 'Hma1.2p1_1644F.1_g295320' => 'hma', 'HPP92_011322' => 'vpl', 'HPP92_011323' => 'vpl', 'HPP92_011324' => 'vpl', 'HPP92_011325' => 'vpl', 'HPP92_011326' => 'vpl', 'Hund12205' => 'sun', 'Hund17957' => 'sun', 'Lalb_Chr06g0176771' => 'lal', 'Lalb_Chr18g0056021' => 'lal', 'Lalb_Chr18g0056031' => 'lal', 'Lalb_Chr18g0056041' => 'lal', 'Lalb_Chr20g0107751' => 'lal', 'Lalb_Chr20g0118371' => 'lal', 'Lj1g0010239' => 'lja', 'Lj1g0017101' => 'lja', 'Lj2A1178G40' => 'lonja', 'Lj2A54G84' => 'lonja', 'Lj2g0015248' => 'lja', 'Lj3A761T51' => 'lonja', 'Lj6g0018116' => 'lja', 'Lsat_1_v5_gn_4_136040' => 'lsa', 'Lsat_1_v5_gn_5_187461' => 'lsa', 'Lsat_1_v5_gn_5_77001' => 'lsa', 'Lsat_1_v5_gn_9_4461' => 'lsa', 'Manes.01G210100' => 'mes', 'Manes.03G185600' => 'mes', 'Manes.05G073300' => 'mes', 'Manes.09G120300' => 'mes', 'Manes.15G022100' => 'mes', 'Mapoly0096s0053' => 'mpo', 'MBI03_g14058_MAGBIO' => 'mbi', 'MBI03_g33876_MAGBIO' => 'mbi', 'MBI03_g36854_MAGBIO' => 'mbi', 'MBI17_g11997_MAGBIO' => 'mbi', 'MD03G1269000' => 'mdo', 'MD04G1179600' => 'mdo', 'MD11G1289800' => 'mdo', 'MD12G1194700' => 'mdo', 'MD13G1182100' => 'mdo', 'MD13G1182200' => 'mdo', 'MD16G1182600' => 'mdo', 'Medtr2g021400' => 'mtr', 'Medtr2g021470' => 'mtr', 'Medtr2g105810' => 'mtr', 'Medtr3g033580' => 'mtr', 'Medtr6g007970' => 'mtr', 'Medtr7g056330' => 'mtr', 'Medtr7g074290' => 'mtr', 'Medtr7g074380' => 'mtr', 'Medtr7g094550' => 'mtr', 'Medtr8g069995' => 'mtr', 'MELO3C014345.2' => 'cme', 'MELO3C021395.2' => 'cme', 'Migut.D00262' => 'egut', 'Migut.G00257' => 'egut', 'MSTRG.21575' => 'ama', 'MSTRG.3985' => 'ama', 'Nitab4.5_0000295g0140' => 'nta', 'Nitab4.5_0000732g0140' => 'nta', 'Nitab4.5_0003162g0020' => 'nta', 'Nitab4.5_0006180g0090' => 'nta', 'Nitab4.5_0006390g0010' => 'nta', 'Nitab4.5_0007392g0040' => 'nta', 'Nn1g02140' => 'nnu', 'Nn4g26168' => 'nnu', 'Nn5g26754' => 'nnu', 'Oeu001433.1' => 'oeu', 'Oeu010299.2' => 'oeu', 'Oeu011171.1' => 'oeu', 'Oeu037675.1' => 'oeu', 'Oeu038359.1' => 'oeu', 'Oeu063834.1' => 'oeu', 'Oeu063835.1' => 'oeu', 'Os05g0312000' => 'osa', 'Os07g0211101' => 'osa', 'Os07g0211200' => 'osa', 'Os07g0681500' => 'osa', 'Peaxi162Scf00095g01015' => 'pax', 'Peaxi162Scf00104g00329' => 'pax', 'Peaxi162Scf00161g00137' => 'pax', 'PGR004G1665' => 'pgr', 'PGR031G2937' => 'pgr', 'PGR119G2145' => 'pgr', 'PGSC0003DMG400004351' => 'stu', 'PGSC0003DMG400014625' => 'stu', 'PGSC0003DMG401000943' => 'stu', 'Phvul.001G148600' => 'pvu', 'Phvul.004G001700' => 'pvu', 'Phvul.006G154900' => 'pvu', 'Phvul.008G078200' => 'pvu', 'Phvul.011G136500' => 'pvu', 'Potri.002G215600' => 'ptr', 'Potri.008G201600' => 'ptr', 'Potri.014G138400' => 'ptr', 'Potri.016G142500' => 'ptr', 'Pp3c16_10580' => 'ppa', 'Pp3c5_25280' => 'ppa', 'Prupe.1G150000' => 'ppe', 'Prupe.1G150100' => 'ppe', 'Prupe.6G299600' => 'ppe', 'Prupe.8G245000' => 'ppe', 'Psat0s4927g0040' => 'psa', 'Psat1g052080' => 'psa', 'Psat1g183800' => 'psa', 'Psat3g113840' => 'psa', 'Psat3g126120' => 'psa', 'Psat3g126160' => 'psa', 'Psat3g158760' => 'psa', 'Psat3g158840' => 'psa', 'PSO170G2858' => 'pso', 'PSO339G0606' => 'pso', 'PSO384G4709' => 'pso', 'PSO407G0334' => 'pso', 'QL04p040276' => 'qlo', 'QL06p005458' => 'qlo', 'QL06p005472' => 'qlo', 'QL07p030546' => 'qlo', 'QL07p031519' => 'qlo', 'QL09p050949' => 'qlo', 'QL09p050966' => 'qlo', 'QL09p051067' => 'qlo', 'QL12p022706' => 'qlo', 'RcHm_v2.0_Chr2g0119601' => 'rch', 'RcHm_v2.0_Chr3g0459591' => 'rch', 'RcHm_v2.0_Chr4g0418521' => 'rch', 'RcHm_v2.0_Chr4g0418531' => 'rch', 'RcHm_v2.0_Chr4g0418541' => 'rch', 'RcHm_v2.0_Chr6g0291641' => 'rch', 'Rhsim01G0086300' => 'rsi', 'Rhsim01G0276300' => 'rsi', 'Rhsim01G0276500' => 'rsi', 'Rhsim04G0207700' => 'rsi', 'Rhsim05G0234500' => 'rsi', 'Rhsim13G0022400' => 'rsi', 'Sabra02G0167900' => 'sbr', 'Sabra04G0158500' => 'sbr', 'Sabra08G0159800' => 'sbr', 'Sabra10G0011500' => 'sbr', 'Sabra14G0104400' => 'sbr', 'SalBow2G2440' => 'sbo', 'SalBow4G2265' => 'sbo', 'Sc02g0000060' => 'sci', 'Sc05g0005020' => 'sci', 'Sc13g0003890' => 'sci', 'Sed0014865' => 'sed', 'Sed0017224' => 'sed', 'Sed0026391' => 'sed', 'SEGI_00063' => 'sgi', 'SEGI_10967' => 'sgi', 'SEGI_17510' => 'sgi', 'SEGI_24396' => 'sgi', 'SEGI_39719' => 'sgi', 'SEGI_41392' => 'sgi', 'SGA_v2.0_scaffold11G05794' => 'sas', 'SGA_v2.0_scaffold142G35607' => 'sas', 'SGA_v2.0_scaffold1G00447' => 'sas', 'SHI15388' => 'shi', 'SHI15394' => 'shi', 'SHI15396' => 'shi', 'SHI15399' => 'shi', 'SMO343G0151' => 'smo', 'SMO367G1118' => 'smo', 'Solyc01g080200.3' => 'sly', 'Solyc06g008960.3' => 'sly', 'Solyc09g064780.3' => 'sly', 'Sopen01g031980' => 'spe', 'Sopen06g003710' => 'spe', 'Sopen09g026460' => 'spe', 'Sp3g21240' => 'spa', 'Sp4g30030' => 'spa', 'TAR365G0022' => 'tar', 'TAR365G1023' => 'tar', 'TAR365G1253' => 'tar', 'TAR623G0078' => 'tar', 'TAR623G1721' => 'tar', 'TAR633G0959' => 'tar', 'THA.LOC104802225' => 'tha', 'THA.LOC104804769' => 'tha', 'THA.LOC104808660' => 'tha', 'THA.LOC104812792' => 'tha', 'Thecc.01G284000' => 'tca', 'Thecc.04G220600' => 'tca', 'Thecc.05G268900' => 'tca', 'Thecc.08G171100' => 'tca', 'Thhalv10001284m.g' => 'esa', 'Thhalv10019912m.g' => 'esa', 'TPR.G14189' => 'tpr', 'TPR.G18110' => 'tpr', 'TPR.G18130' => 'tpr', 'TPR.G18131' => 'tpr', 'TPR.G18140' => 'tpr', 'TPR.G24282' => 'tpr', 'TPR.G25221' => 'tpr', 'TPR.G29267' => 'tpr', 'TPR.G35315' => 'tpr', 'TPR.G36173' => 'tpr', 'TWI09G0794' => 'twi', 'TWI59G1348' => 'twi', 'TWI74G0430' => 'twi', 'unitig_26.g8940' => 'ugi', 'unitig_749.g13744' => 'ugi', 'unitig_749.g13745' => 'ugi', 'vmacro08269' => 'vma', 'vmacro14937' => 'vma', 'vmacro20401' => 'vma', 'VMungo0464G1349' => 'vmu', 'VMungo0540G0289' => 'vmu', 'VMungo1215G1590' => 'vmu', 'VMungo1309G0221' => 'vmu', 'VMungo1309G2815' => 'vmu', 'VMungo1383G0239' => 'vmu', 'VMungo1383G2910' => 'vmu', 'Zm00001eb095270' => 'zma', 'Zm00001eb095280' => 'zma', 'Zm00001eb111630' => 'zma', 'Zm00001eb237080' => 'zma', 'Zm00001eb273740' => 'zma', 'Zm00001eb285040' => 'zma', 'Zm00001eb330790' => 'zma', 'Zm00001eb337380' => 'zma' ) $gf_id = 'HOM05D001484' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001484' ) $data_identifier = 'HOM05D001484' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 2, 'aly' => (int) 2, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 22, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 7, 'hma' => (int) 2, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 7, 'mtr' => (int) 10, 'cme' => (int) 2, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 4, 'ppa' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 4, 'qlo' => (int) 9, 'rch' => (int) 6, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 10, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 7, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb337380' $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' => 'HOM05D001484', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p31500' => 'bna', 'A05p00020' => 'bna', 'A07p08820' => 'bna', 'Aa31LG4G3300' => 'aar', 'Aa31LG8G10030' => 'aar', 'Actinidia00731' => 'ach', 'Actinidia11473' => 'ach', 'Actinidia23469' => 'ach', 'Actinidia24318' => 'ach', 'Actinidia40196' => 'ach', 'Actinidia40197' => 'ach', 'Actinidia40198' => 'ach', 'Ah.08g212990' => 'amhyb', 'Ah.15g091720' => 'amhyb', 'AL3G38260' => 'aly', 'AL4G47710' => 'aly', 'Aqoxy2G00671' => 'aox', 'Aqoxy2G03236' => 'aox', 'arahy.Tifrunner.gnm1.ann1.05IDCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KR684' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATY3SJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK6QJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6APGL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IDT7Z9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM073U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ0R87' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LE7RV4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT4QRX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V5ENPK' => 'arhy', 'AT2G48110' => 'ath', 'AT3G23590' => 'ath', 'ATR0626G186' => 'atr', 'ATR1127G141' => 'atr', 'Atru.chr4.2583' => 'acertr', 'Atru.chr5.1358' => 'acertr', 'Atru.chr5.1359' => 'acertr', 'Atru.chr8.46' => 'acertr', 'AUR62002640' => 'cqu', 'AUR62030055' => 'cqu', 'AUR62033713' => 'cqu', 'AUR62033714' => 'cqu', 'AUR62036795' => 'cqu', 'AUR62039891' => 'cqu', 'BcaB02g08737' => 'bca', 'BcaB04g20441' => 'bca', 'BcaB06g26509' => 'bca', 'BcaB06g26510' => 'bca', 'BcaB06g26511' => 'bca', 'BcaB06g26512' => 'bca', 'BcaB06g26513' => 'bca', 'BcaC02g12564' => 'bca', 'BcaC02g12565' => 'bca', 'BcaC02g12794' => 'bca', 'BcaC02g12795' => 'bca', 'BcaC02g12796' => 'bca', 'BcaC06g35541' => 'bca', 'BNapus_Darmor_BZH_scaffold_188p00080' => 'bna', 'BNapus_Darmor_BZH_scaffold_188p00090' => 'bna', 'BolC1t03972H' => 'bol', 'BolC1t03973H' => 'bol', 'BolC4t21680H' => 'bol', 'BolC7t41863H' => 'bol', 'BolSC55t61227H' => 'bol', 'BolSC55t61228H' => 'bol', 'BraA01t03278Z' => 'bra', 'BraA05t18998Z' => 'bra', 'BraA07t28673Z' => 'bra', 'C01p40150' => 'bna', 'C05p12370' => 'bna', 'C07p13680' => 'bna', 'CAN.G1006.16' => 'can', 'CAN.G1006.17' => 'can', 'CAN.G1170.2' => 'can', 'CAN.G962.7' => 'can', 'CANSAT25G2179' => 'cansat', 'CANSAT78G1573' => 'cansat', 'CARHR099510' => 'chi', 'CARHR143510' => 'chi', 'Carub.0003s2380' => 'cru', 'Carub.0004s3082' => 'cru', 'Ca_00614_v3' => 'car', 'Ca_07801_v3' => 'car', 'Ca_08567_v3' => 'car', 'Ca_09571_v3' => 'car', 'CBR_g19290' => 'cbr', 'Cc01_g19770' => 'ccan', 'Cc03_g03030' => 'ccan', 'CDE07G0968' => 'cde', 'CDE09G1441' => 'cde', 'Cfa006103' => 'cfa', 'Cfa015573' => 'cfa', 'Cfa016988' => 'cfa', 'Ciclev10006738m.g' => 'ccl', 'Ciclev10010920m.g' => 'ccl', 'Ciclev10018517m.g' => 'ccl', 'CiPaw.01G159200' => 'cil', 'CiPaw.02G091000' => 'cil', 'CiPaw.02G091100' => 'cil', 'CiPaw.08G103100' => 'cil', 'CiPaw.09G224900' => 'cil', 'ClCG06G005740' => 'cla', 'ClCG07G000090' => 'cla', 'ClCG07G000100' => 'cla', 'COL.COLO4_09143' => 'col', 'COL.COLO4_25124' => 'col', 'Cpa.g.sc16.34' => 'cpa', 'Cpa.g.sc3504.1' => 'cpa', 'Cpa.g.sc60.37' => 'cpa', 'CsaV3_6G018520' => 'csa', 'CsaV3_6G036860' => 'csa', 'CSS0001072' => 'camsi', 'CSS0020208' => 'camsi', 'CSS0021253' => 'camsi', 'CSS0022190' => 'camsi', 'CSS0036150' => 'camsi', 'CSS0040442' => 'camsi', 'CSS0042300' => 'camsi', 'CSS0045298' => 'camsi', 'DCAR_012449' => 'dca', 'DCAR_018405' => 'dca', 'DCAR_024573' => 'dca', 'DCAR_030591' => 'dca', 'Dinv16926' => 'din', 'Dinv32963' => 'din', 'Dinv38382' => 'din', 'Dinv38383' => 'din', 'Duzib133G0974' => 'dzi', 'Duzib138G1867' => 'dzi', 'Duzib211G0420' => 'dzi', 'Duzib212G0930' => 'dzi', 'ECA234G1645' => 'eca', 'ECA247G3467' => 'eca', 'ECA248G1703' => 'eca', 'EL10Ac3g06327' => 'bvu', 'EL10Ac7g17204' => 'bvu', 'Eucgr.A00855' => 'egr', 'Eucgr.A00858' => 'egr', 'Eucgr.H01520' => 'egr', 'Eucgr.H03604' => 'egr', 'Eucgr.L03465' => 'egr', 'Eucgr.L03466' => 'egr', 'FAN01G0988' => 'fan', 'FAN02G3892' => 'fan', 'FAN05G3381' => 'fan', 'FAN07G0967' => 'fan', 'FAN07G1493' => 'fan', 'FAN08G3125' => 'fan', 'FAN09G0402' => 'fan', 'FAN12G2594' => 'fan', 'FAN12G3879' => 'fan', 'FAN14G1546' => 'fan', 'FAN15G3626' => 'fan', 'FAN17G0588' => 'fan', 'FAN17G0609' => 'fan', 'FAN18G2817' => 'fan', 'FAN19G1305' => 'fan', 'FAN20G1787' => 'fan', 'FAN22G0073' => 'fan', 'FAN22G0352' => 'fan', 'FAN22G0368' => 'fan', 'FAN22G2273' => 'fan', 'FAN24G1998' => 'fan', 'FAN27G1317' => 'fan', 'FvH4_2g23980' => 'fve', 'FvH4_4g14380' => 'fve', 'FvH4_4g14390' => 'fve', 'FvH4_6g09250' => 'fve', 'Glyma.03G151100' => 'gma', 'Glyma.04G122550' => 'gma', 'Glyma.05G001600' => 'gma', 'Glyma.09G270766' => 'gma', 'Glyma.09G270832' => 'gma', 'Glyma.13G209800' => 'gma', 'Glyma.15G102800' => 'gma', 'Glyma.18G218900' => 'gma', 'Glyma.19G001500' => 'gma', 'Glyma.19G153600' => 'gma', 'Gohir.A02G028600' => 'ghi', 'Gohir.A08G045000' => 'ghi', 'Gohir.A11G120500' => 'ghi', 'Gohir.A12G006200' => 'ghi', 'Gohir.A12G006250' => 'ghi', 'Gohir.D02G036300' => 'ghi', 'Gohir.D08G054700' => 'ghi', 'Gohir.D11G125600' => 'ghi', 'Gohir.D12G005700' => 'ghi', 'Gorai.004G055200' => 'gra', 'Gorai.005G040400' => 'gra', 'Gorai.007G134500' => 'gra', 'Gorai.008G005500' => 'gra', 'GSVIVG01011094001' => 'vvi', 'GSVIVG01017879001' => 'vvi', 'GSVIVG01025988001' => 'vvi', 'GSVIVG01029847001' => 'vvi', 'HanXRQChr10g0282901' => 'han', 'HanXRQChr10g0310371' => 'han', 'HanXRQChr10g0315041' => 'han', 'HanXRQChr11g0327651' => 'han', 'HanXRQChr12g0359391' => 'han', 'Haze_00972' => 'cav', 'Haze_00973' => 'cav', 'Haze_00974' => 'cav', 'Haze_04747' => 'cav', 'Haze_04749' => 'cav', 'Haze_04750' => 'cav', 'Haze_21217' => 'cav', 'Hma1.2p1_1037F.1_g250680' => 'hma', 'Hma1.2p1_1644F.1_g295320' => 'hma', 'HPP92_011322' => 'vpl', 'HPP92_011323' => 'vpl', 'HPP92_011324' => 'vpl', 'HPP92_011325' => 'vpl', 'HPP92_011326' => 'vpl', 'Hund12205' => 'sun', 'Hund17957' => 'sun', 'Lalb_Chr06g0176771' => 'lal', 'Lalb_Chr18g0056021' => 'lal', 'Lalb_Chr18g0056031' => 'lal', 'Lalb_Chr18g0056041' => 'lal', 'Lalb_Chr20g0107751' => 'lal', 'Lalb_Chr20g0118371' => 'lal', 'Lj1g0010239' => 'lja', 'Lj1g0017101' => 'lja', 'Lj2A1178G40' => 'lonja', 'Lj2A54G84' => 'lonja', 'Lj2g0015248' => 'lja', 'Lj3A761T51' => 'lonja', 'Lj6g0018116' => 'lja', 'Lsat_1_v5_gn_4_136040' => 'lsa', 'Lsat_1_v5_gn_5_187461' => 'lsa', 'Lsat_1_v5_gn_5_77001' => 'lsa', 'Lsat_1_v5_gn_9_4461' => 'lsa', 'Manes.01G210100' => 'mes', 'Manes.03G185600' => 'mes', 'Manes.05G073300' => 'mes', 'Manes.09G120300' => 'mes', 'Manes.15G022100' => 'mes', 'Mapoly0096s0053' => 'mpo', 'MBI03_g14058_MAGBIO' => 'mbi', 'MBI03_g33876_MAGBIO' => 'mbi', 'MBI03_g36854_MAGBIO' => 'mbi', 'MBI17_g11997_MAGBIO' => 'mbi', 'MD03G1269000' => 'mdo', 'MD04G1179600' => 'mdo', 'MD11G1289800' => 'mdo', 'MD12G1194700' => 'mdo', 'MD13G1182100' => 'mdo', 'MD13G1182200' => 'mdo', 'MD16G1182600' => 'mdo', 'Medtr2g021400' => 'mtr', 'Medtr2g021470' => 'mtr', 'Medtr2g105810' => 'mtr', 'Medtr3g033580' => 'mtr', 'Medtr6g007970' => 'mtr', 'Medtr7g056330' => 'mtr', 'Medtr7g074290' => 'mtr', 'Medtr7g074380' => 'mtr', 'Medtr7g094550' => 'mtr', 'Medtr8g069995' => 'mtr', 'MELO3C014345.2' => 'cme', 'MELO3C021395.2' => 'cme', 'Migut.D00262' => 'egut', 'Migut.G00257' => 'egut', 'MSTRG.21575' => 'ama', 'MSTRG.3985' => 'ama', 'Nitab4.5_0000295g0140' => 'nta', 'Nitab4.5_0000732g0140' => 'nta', 'Nitab4.5_0003162g0020' => 'nta', 'Nitab4.5_0006180g0090' => 'nta', 'Nitab4.5_0006390g0010' => 'nta', 'Nitab4.5_0007392g0040' => 'nta', 'Nn1g02140' => 'nnu', 'Nn4g26168' => 'nnu', 'Nn5g26754' => 'nnu', 'Oeu001433.1' => 'oeu', 'Oeu010299.2' => 'oeu', 'Oeu011171.1' => 'oeu', 'Oeu037675.1' => 'oeu', 'Oeu038359.1' => 'oeu', 'Oeu063834.1' => 'oeu', 'Oeu063835.1' => 'oeu', 'Os05g0312000' => 'osa', 'Os07g0211101' => 'osa', 'Os07g0211200' => 'osa', 'Os07g0681500' => 'osa', 'Peaxi162Scf00095g01015' => 'pax', 'Peaxi162Scf00104g00329' => 'pax', 'Peaxi162Scf00161g00137' => 'pax', 'PGR004G1665' => 'pgr', 'PGR031G2937' => 'pgr', 'PGR119G2145' => 'pgr', 'PGSC0003DMG400004351' => 'stu', 'PGSC0003DMG400014625' => 'stu', 'PGSC0003DMG401000943' => 'stu', 'Phvul.001G148600' => 'pvu', 'Phvul.004G001700' => 'pvu', 'Phvul.006G154900' => 'pvu', 'Phvul.008G078200' => 'pvu', 'Phvul.011G136500' => 'pvu', 'Potri.002G215600' => 'ptr', 'Potri.008G201600' => 'ptr', 'Potri.014G138400' => 'ptr', 'Potri.016G142500' => 'ptr', 'Pp3c16_10580' => 'ppa', 'Pp3c5_25280' => 'ppa', 'Prupe.1G150000' => 'ppe', 'Prupe.1G150100' => 'ppe', 'Prupe.6G299600' => 'ppe', 'Prupe.8G245000' => 'ppe', 'Psat0s4927g0040' => 'psa', 'Psat1g052080' => 'psa', 'Psat1g183800' => 'psa', 'Psat3g113840' => 'psa', 'Psat3g126120' => 'psa', 'Psat3g126160' => 'psa', 'Psat3g158760' => 'psa', 'Psat3g158840' => 'psa', 'PSO170G2858' => 'pso', 'PSO339G0606' => 'pso', 'PSO384G4709' => 'pso', 'PSO407G0334' => 'pso', 'QL04p040276' => 'qlo', 'QL06p005458' => 'qlo', 'QL06p005472' => 'qlo', 'QL07p030546' => 'qlo', 'QL07p031519' => 'qlo', 'QL09p050949' => 'qlo', 'QL09p050966' => 'qlo', 'QL09p051067' => 'qlo', 'QL12p022706' => 'qlo', 'RcHm_v2.0_Chr2g0119601' => 'rch', 'RcHm_v2.0_Chr3g0459591' => 'rch', 'RcHm_v2.0_Chr4g0418521' => 'rch', 'RcHm_v2.0_Chr4g0418531' => 'rch', 'RcHm_v2.0_Chr4g0418541' => 'rch', 'RcHm_v2.0_Chr6g0291641' => 'rch', 'Rhsim01G0086300' => 'rsi', 'Rhsim01G0276300' => 'rsi', 'Rhsim01G0276500' => 'rsi', 'Rhsim04G0207700' => 'rsi', 'Rhsim05G0234500' => 'rsi', 'Rhsim13G0022400' => 'rsi', 'Sabra02G0167900' => 'sbr', 'Sabra04G0158500' => 'sbr', 'Sabra08G0159800' => 'sbr', 'Sabra10G0011500' => 'sbr', 'Sabra14G0104400' => 'sbr', 'SalBow2G2440' => 'sbo', 'SalBow4G2265' => 'sbo', 'Sc02g0000060' => 'sci', 'Sc05g0005020' => 'sci', 'Sc13g0003890' => 'sci', 'Sed0014865' => 'sed', 'Sed0017224' => 'sed', 'Sed0026391' => 'sed', 'SEGI_00063' => 'sgi', 'SEGI_10967' => 'sgi', 'SEGI_17510' => 'sgi', 'SEGI_24396' => 'sgi', 'SEGI_39719' => 'sgi', 'SEGI_41392' => 'sgi', 'SGA_v2.0_scaffold11G05794' => 'sas', 'SGA_v2.0_scaffold142G35607' => 'sas', 'SGA_v2.0_scaffold1G00447' => 'sas', 'SHI15388' => 'shi', 'SHI15394' => 'shi', 'SHI15396' => 'shi', 'SHI15399' => 'shi', 'SMO343G0151' => 'smo', 'SMO367G1118' => 'smo', 'Solyc01g080200.3' => 'sly', 'Solyc06g008960.3' => 'sly', 'Solyc09g064780.3' => 'sly', 'Sopen01g031980' => 'spe', 'Sopen06g003710' => 'spe', 'Sopen09g026460' => 'spe', 'Sp3g21240' => 'spa', 'Sp4g30030' => 'spa', 'TAR365G0022' => 'tar', 'TAR365G1023' => 'tar', 'TAR365G1253' => 'tar', 'TAR623G0078' => 'tar', 'TAR623G1721' => 'tar', 'TAR633G0959' => 'tar', 'THA.LOC104802225' => 'tha', 'THA.LOC104804769' => 'tha', 'THA.LOC104808660' => 'tha', 'THA.LOC104812792' => 'tha', 'Thecc.01G284000' => 'tca', 'Thecc.04G220600' => 'tca', 'Thecc.05G268900' => 'tca', 'Thecc.08G171100' => 'tca', 'Thhalv10001284m.g' => 'esa', 'Thhalv10019912m.g' => 'esa', 'TPR.G14189' => 'tpr', 'TPR.G18110' => 'tpr', 'TPR.G18130' => 'tpr', 'TPR.G18131' => 'tpr', 'TPR.G18140' => 'tpr', 'TPR.G24282' => 'tpr', 'TPR.G25221' => 'tpr', 'TPR.G29267' => 'tpr', 'TPR.G35315' => 'tpr', 'TPR.G36173' => 'tpr', 'TWI09G0794' => 'twi', 'TWI59G1348' => 'twi', 'TWI74G0430' => 'twi', 'unitig_26.g8940' => 'ugi', 'unitig_749.g13744' => 'ugi', 'unitig_749.g13745' => 'ugi', 'vmacro08269' => 'vma', 'vmacro14937' => 'vma', 'vmacro20401' => 'vma', 'VMungo0464G1349' => 'vmu', 'VMungo0540G0289' => 'vmu', 'VMungo1215G1590' => 'vmu', 'VMungo1309G0221' => 'vmu', 'VMungo1309G2815' => 'vmu', 'VMungo1383G0239' => 'vmu', 'VMungo1383G2910' => 'vmu', 'Zm00001eb095270' => 'zma', 'Zm00001eb095280' => 'zma', 'Zm00001eb111630' => 'zma', 'Zm00001eb237080' => 'zma', 'Zm00001eb273740' => 'zma', 'Zm00001eb285040' => 'zma', 'Zm00001eb330790' => 'zma', 'Zm00001eb337380' => 'zma' ), 'gf_id' => 'HOM05D001484', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001484' ), 'data_identifier' => 'HOM05D001484', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001484', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p31500' => 'bna', 'A05p00020' => 'bna', 'A07p08820' => 'bna', 'Aa31LG4G3300' => 'aar', 'Aa31LG8G10030' => 'aar', 'Actinidia00731' => 'ach', 'Actinidia11473' => 'ach', 'Actinidia23469' => 'ach', 'Actinidia24318' => 'ach', 'Actinidia40196' => 'ach', 'Actinidia40197' => 'ach', 'Actinidia40198' => 'ach', 'Ah.08g212990' => 'amhyb', 'Ah.15g091720' => 'amhyb', 'AL3G38260' => 'aly', 'AL4G47710' => 'aly', 'Aqoxy2G00671' => 'aox', 'Aqoxy2G03236' => 'aox', 'arahy.Tifrunner.gnm1.ann1.05IDCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KR684' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATY3SJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK6QJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6APGL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IDT7Z9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM073U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ0R87' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LE7RV4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT4QRX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V5ENPK' => 'arhy', 'AT2G48110' => 'ath', 'AT3G23590' => 'ath', 'ATR0626G186' => 'atr', 'ATR1127G141' => 'atr', 'Atru.chr4.2583' => 'acertr', 'Atru.chr5.1358' => 'acertr', 'Atru.chr5.1359' => 'acertr', 'Atru.chr8.46' => 'acertr', 'AUR62002640' => 'cqu', 'AUR62030055' => 'cqu', 'AUR62033713' => 'cqu', 'AUR62033714' => 'cqu', 'AUR62036795' => 'cqu', 'AUR62039891' => 'cqu', 'BcaB02g08737' => 'bca', 'BcaB04g20441' => 'bca', 'BcaB06g26509' => 'bca', 'BcaB06g26510' => 'bca', 'BcaB06g26511' => 'bca', 'BcaB06g26512' => 'bca', 'BcaB06g26513' => 'bca', 'BcaC02g12564' => 'bca', 'BcaC02g12565' => 'bca', 'BcaC02g12794' => 'bca', 'BcaC02g12795' => 'bca', 'BcaC02g12796' => 'bca', 'BcaC06g35541' => 'bca', 'BNapus_Darmor_BZH_scaffold_188p00080' => 'bna', 'BNapus_Darmor_BZH_scaffold_188p00090' => 'bna', 'BolC1t03972H' => 'bol', 'BolC1t03973H' => 'bol', 'BolC4t21680H' => 'bol', 'BolC7t41863H' => 'bol', 'BolSC55t61227H' => 'bol', 'BolSC55t61228H' => 'bol', 'BraA01t03278Z' => 'bra', 'BraA05t18998Z' => 'bra', 'BraA07t28673Z' => 'bra', 'C01p40150' => 'bna', 'C05p12370' => 'bna', 'C07p13680' => 'bna', 'CAN.G1006.16' => 'can', 'CAN.G1006.17' => 'can', 'CAN.G1170.2' => 'can', 'CAN.G962.7' => 'can', 'CANSAT25G2179' => 'cansat', 'CANSAT78G1573' => 'cansat', 'CARHR099510' => 'chi', 'CARHR143510' => 'chi', 'Carub.0003s2380' => 'cru', 'Carub.0004s3082' => 'cru', 'Ca_00614_v3' => 'car', 'Ca_07801_v3' => 'car', 'Ca_08567_v3' => 'car', 'Ca_09571_v3' => 'car', 'CBR_g19290' => 'cbr', 'Cc01_g19770' => 'ccan', 'Cc03_g03030' => 'ccan', 'CDE07G0968' => 'cde', 'CDE09G1441' => 'cde', 'Cfa006103' => 'cfa', 'Cfa015573' => 'cfa', 'Cfa016988' => 'cfa', 'Ciclev10006738m.g' => 'ccl', 'Ciclev10010920m.g' => 'ccl', 'Ciclev10018517m.g' => 'ccl', 'CiPaw.01G159200' => 'cil', 'CiPaw.02G091000' => 'cil', 'CiPaw.02G091100' => 'cil', 'CiPaw.08G103100' => 'cil', 'CiPaw.09G224900' => 'cil', 'ClCG06G005740' => 'cla', 'ClCG07G000090' => 'cla', 'ClCG07G000100' => 'cla', 'COL.COLO4_09143' => 'col', 'COL.COLO4_25124' => 'col', 'Cpa.g.sc16.34' => 'cpa', 'Cpa.g.sc3504.1' => 'cpa', 'Cpa.g.sc60.37' => 'cpa', 'CsaV3_6G018520' => 'csa', 'CsaV3_6G036860' => 'csa', 'CSS0001072' => 'camsi', 'CSS0020208' => 'camsi', 'CSS0021253' => 'camsi', 'CSS0022190' => 'camsi', 'CSS0036150' => 'camsi', 'CSS0040442' => 'camsi', 'CSS0042300' => 'camsi', 'CSS0045298' => 'camsi', 'DCAR_012449' => 'dca', 'DCAR_018405' => 'dca', 'DCAR_024573' => 'dca', 'DCAR_030591' => 'dca', 'Dinv16926' => 'din', 'Dinv32963' => 'din', 'Dinv38382' => 'din', 'Dinv38383' => 'din', 'Duzib133G0974' => 'dzi', 'Duzib138G1867' => 'dzi', 'Duzib211G0420' => 'dzi', 'Duzib212G0930' => 'dzi', 'ECA234G1645' => 'eca', 'ECA247G3467' => 'eca', 'ECA248G1703' => 'eca', 'EL10Ac3g06327' => 'bvu', 'EL10Ac7g17204' => 'bvu', 'Eucgr.A00855' => 'egr', 'Eucgr.A00858' => 'egr', 'Eucgr.H01520' => 'egr', 'Eucgr.H03604' => 'egr', 'Eucgr.L03465' => 'egr', 'Eucgr.L03466' => 'egr', 'FAN01G0988' => 'fan', 'FAN02G3892' => 'fan', 'FAN05G3381' => 'fan', 'FAN07G0967' => 'fan', 'FAN07G1493' => 'fan', 'FAN08G3125' => 'fan', 'FAN09G0402' => 'fan', 'FAN12G2594' => 'fan', 'FAN12G3879' => 'fan', 'FAN14G1546' => 'fan', 'FAN15G3626' => 'fan', 'FAN17G0588' => 'fan', 'FAN17G0609' => 'fan', 'FAN18G2817' => 'fan', 'FAN19G1305' => 'fan', 'FAN20G1787' => 'fan', 'FAN22G0073' => 'fan', 'FAN22G0352' => 'fan', 'FAN22G0368' => 'fan', 'FAN22G2273' => 'fan', 'FAN24G1998' => 'fan', 'FAN27G1317' => 'fan', 'FvH4_2g23980' => 'fve', 'FvH4_4g14380' => 'fve', 'FvH4_4g14390' => 'fve', 'FvH4_6g09250' => 'fve', 'Glyma.03G151100' => 'gma', 'Glyma.04G122550' => 'gma', 'Glyma.05G001600' => 'gma', 'Glyma.09G270766' => 'gma', 'Glyma.09G270832' => 'gma', 'Glyma.13G209800' => 'gma', 'Glyma.15G102800' => 'gma', 'Glyma.18G218900' => 'gma', 'Glyma.19G001500' => 'gma', 'Glyma.19G153600' => 'gma', 'Gohir.A02G028600' => 'ghi', 'Gohir.A08G045000' => 'ghi', 'Gohir.A11G120500' => 'ghi', 'Gohir.A12G006200' => 'ghi', 'Gohir.A12G006250' => 'ghi', 'Gohir.D02G036300' => 'ghi', 'Gohir.D08G054700' => 'ghi', 'Gohir.D11G125600' => 'ghi', 'Gohir.D12G005700' => 'ghi', 'Gorai.004G055200' => 'gra', 'Gorai.005G040400' => 'gra', 'Gorai.007G134500' => 'gra', 'Gorai.008G005500' => 'gra', 'GSVIVG01011094001' => 'vvi', 'GSVIVG01017879001' => 'vvi', 'GSVIVG01025988001' => 'vvi', 'GSVIVG01029847001' => 'vvi', 'HanXRQChr10g0282901' => 'han', 'HanXRQChr10g0310371' => 'han', 'HanXRQChr10g0315041' => 'han', 'HanXRQChr11g0327651' => 'han', 'HanXRQChr12g0359391' => 'han', 'Haze_00972' => 'cav', 'Haze_00973' => 'cav', 'Haze_00974' => 'cav', 'Haze_04747' => 'cav', 'Haze_04749' => 'cav', 'Haze_04750' => 'cav', 'Haze_21217' => 'cav', 'Hma1.2p1_1037F.1_g250680' => 'hma', 'Hma1.2p1_1644F.1_g295320' => 'hma', 'HPP92_011322' => 'vpl', 'HPP92_011323' => 'vpl', 'HPP92_011324' => 'vpl', 'HPP92_011325' => 'vpl', 'HPP92_011326' => 'vpl', 'Hund12205' => 'sun', 'Hund17957' => 'sun', 'Lalb_Chr06g0176771' => 'lal', 'Lalb_Chr18g0056021' => 'lal', 'Lalb_Chr18g0056031' => 'lal', 'Lalb_Chr18g0056041' => 'lal', 'Lalb_Chr20g0107751' => 'lal', 'Lalb_Chr20g0118371' => 'lal', 'Lj1g0010239' => 'lja', 'Lj1g0017101' => 'lja', 'Lj2A1178G40' => 'lonja', 'Lj2A54G84' => 'lonja', 'Lj2g0015248' => 'lja', 'Lj3A761T51' => 'lonja', 'Lj6g0018116' => 'lja', 'Lsat_1_v5_gn_4_136040' => 'lsa', 'Lsat_1_v5_gn_5_187461' => 'lsa', 'Lsat_1_v5_gn_5_77001' => 'lsa', 'Lsat_1_v5_gn_9_4461' => 'lsa', 'Manes.01G210100' => 'mes', 'Manes.03G185600' => 'mes', 'Manes.05G073300' => 'mes', 'Manes.09G120300' => 'mes', 'Manes.15G022100' => 'mes', 'Mapoly0096s0053' => 'mpo', 'MBI03_g14058_MAGBIO' => 'mbi', 'MBI03_g33876_MAGBIO' => 'mbi', 'MBI03_g36854_MAGBIO' => 'mbi', 'MBI17_g11997_MAGBIO' => 'mbi', 'MD03G1269000' => 'mdo', 'MD04G1179600' => 'mdo', 'MD11G1289800' => 'mdo', 'MD12G1194700' => 'mdo', 'MD13G1182100' => 'mdo', 'MD13G1182200' => 'mdo', 'MD16G1182600' => 'mdo', 'Medtr2g021400' => 'mtr', 'Medtr2g021470' => 'mtr', 'Medtr2g105810' => 'mtr', 'Medtr3g033580' => 'mtr', 'Medtr6g007970' => 'mtr', 'Medtr7g056330' => 'mtr', 'Medtr7g074290' => 'mtr', 'Medtr7g074380' => 'mtr', 'Medtr7g094550' => 'mtr', 'Medtr8g069995' => 'mtr', 'MELO3C014345.2' => 'cme', 'MELO3C021395.2' => 'cme', 'Migut.D00262' => 'egut', 'Migut.G00257' => 'egut', 'MSTRG.21575' => 'ama', 'MSTRG.3985' => 'ama', 'Nitab4.5_0000295g0140' => 'nta', 'Nitab4.5_0000732g0140' => 'nta', 'Nitab4.5_0003162g0020' => 'nta', 'Nitab4.5_0006180g0090' => 'nta', 'Nitab4.5_0006390g0010' => 'nta', 'Nitab4.5_0007392g0040' => 'nta', 'Nn1g02140' => 'nnu', 'Nn4g26168' => 'nnu', 'Nn5g26754' => 'nnu', 'Oeu001433.1' => 'oeu', 'Oeu010299.2' => 'oeu', 'Oeu011171.1' => 'oeu', 'Oeu037675.1' => 'oeu', 'Oeu038359.1' => 'oeu', 'Oeu063834.1' => 'oeu', 'Oeu063835.1' => 'oeu', 'Os05g0312000' => 'osa', 'Os07g0211101' => 'osa', 'Os07g0211200' => 'osa', 'Os07g0681500' => 'osa', 'Peaxi162Scf00095g01015' => 'pax', 'Peaxi162Scf00104g00329' => 'pax', 'Peaxi162Scf00161g00137' => 'pax', 'PGR004G1665' => 'pgr', 'PGR031G2937' => 'pgr', 'PGR119G2145' => 'pgr', 'PGSC0003DMG400004351' => 'stu', 'PGSC0003DMG400014625' => 'stu', 'PGSC0003DMG401000943' => 'stu', 'Phvul.001G148600' => 'pvu', 'Phvul.004G001700' => 'pvu', 'Phvul.006G154900' => 'pvu', 'Phvul.008G078200' => 'pvu', 'Phvul.011G136500' => 'pvu', 'Potri.002G215600' => 'ptr', 'Potri.008G201600' => 'ptr', 'Potri.014G138400' => 'ptr', 'Potri.016G142500' => 'ptr', 'Pp3c16_10580' => 'ppa', 'Pp3c5_25280' => 'ppa', 'Prupe.1G150000' => 'ppe', 'Prupe.1G150100' => 'ppe', 'Prupe.6G299600' => 'ppe', 'Prupe.8G245000' => 'ppe', 'Psat0s4927g0040' => 'psa', 'Psat1g052080' => 'psa', 'Psat1g183800' => 'psa', 'Psat3g113840' => 'psa', 'Psat3g126120' => 'psa', 'Psat3g126160' => 'psa', 'Psat3g158760' => 'psa', 'Psat3g158840' => 'psa', 'PSO170G2858' => 'pso', 'PSO339G0606' => 'pso', 'PSO384G4709' => 'pso', 'PSO407G0334' => 'pso', 'QL04p040276' => 'qlo', 'QL06p005458' => 'qlo', 'QL06p005472' => 'qlo', 'QL07p030546' => 'qlo', 'QL07p031519' => 'qlo', 'QL09p050949' => 'qlo', 'QL09p050966' => 'qlo', 'QL09p051067' => 'qlo', 'QL12p022706' => 'qlo', 'RcHm_v2.0_Chr2g0119601' => 'rch', 'RcHm_v2.0_Chr3g0459591' => 'rch', 'RcHm_v2.0_Chr4g0418521' => 'rch', 'RcHm_v2.0_Chr4g0418531' => 'rch', 'RcHm_v2.0_Chr4g0418541' => 'rch', 'RcHm_v2.0_Chr6g0291641' => 'rch', 'Rhsim01G0086300' => 'rsi', 'Rhsim01G0276300' => 'rsi', 'Rhsim01G0276500' => 'rsi', 'Rhsim04G0207700' => 'rsi', 'Rhsim05G0234500' => 'rsi', 'Rhsim13G0022400' => 'rsi', 'Sabra02G0167900' => 'sbr', 'Sabra04G0158500' => 'sbr', 'Sabra08G0159800' => 'sbr', 'Sabra10G0011500' => 'sbr', 'Sabra14G0104400' => 'sbr', 'SalBow2G2440' => 'sbo', 'SalBow4G2265' => 'sbo', 'Sc02g0000060' => 'sci', 'Sc05g0005020' => 'sci', 'Sc13g0003890' => 'sci', 'Sed0014865' => 'sed', 'Sed0017224' => 'sed', 'Sed0026391' => 'sed', 'SEGI_00063' => 'sgi', 'SEGI_10967' => 'sgi', 'SEGI_17510' => 'sgi', 'SEGI_24396' => 'sgi', 'SEGI_39719' => 'sgi', 'SEGI_41392' => 'sgi', 'SGA_v2.0_scaffold11G05794' => 'sas', 'SGA_v2.0_scaffold142G35607' => 'sas', 'SGA_v2.0_scaffold1G00447' => 'sas', 'SHI15388' => 'shi', 'SHI15394' => 'shi', 'SHI15396' => 'shi', 'SHI15399' => 'shi', 'SMO343G0151' => 'smo', 'SMO367G1118' => 'smo', 'Solyc01g080200.3' => 'sly', 'Solyc06g008960.3' => 'sly', 'Solyc09g064780.3' => 'sly', 'Sopen01g031980' => 'spe', 'Sopen06g003710' => 'spe', 'Sopen09g026460' => 'spe', 'Sp3g21240' => 'spa', 'Sp4g30030' => 'spa', 'TAR365G0022' => 'tar', 'TAR365G1023' => 'tar', 'TAR365G1253' => 'tar', 'TAR623G0078' => 'tar', 'TAR623G1721' => 'tar', 'TAR633G0959' => 'tar', 'THA.LOC104802225' => 'tha', 'THA.LOC104804769' => 'tha', 'THA.LOC104808660' => 'tha', 'THA.LOC104812792' => 'tha', 'Thecc.01G284000' => 'tca', 'Thecc.04G220600' => 'tca', 'Thecc.05G268900' => 'tca', 'Thecc.08G171100' => 'tca', 'Thhalv10001284m.g' => 'esa', 'Thhalv10019912m.g' => 'esa', 'TPR.G14189' => 'tpr', 'TPR.G18110' => 'tpr', 'TPR.G18130' => 'tpr', 'TPR.G18131' => 'tpr', 'TPR.G18140' => 'tpr', 'TPR.G24282' => 'tpr', 'TPR.G25221' => 'tpr', 'TPR.G29267' => 'tpr', 'TPR.G35315' => 'tpr', 'TPR.G36173' => 'tpr', 'TWI09G0794' => 'twi', 'TWI59G1348' => 'twi', 'TWI74G0430' => 'twi', 'unitig_26.g8940' => 'ugi', 'unitig_749.g13744' => 'ugi', 'unitig_749.g13745' => 'ugi', 'vmacro08269' => 'vma', 'vmacro14937' => 'vma', 'vmacro20401' => 'vma', 'VMungo0464G1349' => 'vmu', 'VMungo0540G0289' => 'vmu', 'VMungo1215G1590' => 'vmu', 'VMungo1309G0221' => 'vmu', 'VMungo1309G2815' => 'vmu', 'VMungo1383G0239' => 'vmu', 'VMungo1383G2910' => 'vmu', 'Zm00001eb095270' => 'zma', 'Zm00001eb095280' => 'zma', 'Zm00001eb111630' => 'zma', 'Zm00001eb237080' => 'zma', 'Zm00001eb273740' => 'zma', 'Zm00001eb285040' => 'zma', 'Zm00001eb330790' => 'zma', 'Zm00001eb337380' => 'zma' ) $gf_id = 'HOM05D001484' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001484' ) $data_identifier = 'HOM05D001484' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 2, 'aly' => (int) 2, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 22, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 7, 'hma' => (int) 2, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 7, 'mtr' => (int) 10, 'cme' => (int) 2, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 4, 'ppa' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 4, 'qlo' => (int) 9, 'rch' => (int) 6, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 10, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 7, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb337380' $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' => 'HOM05D001484', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p31500' => 'bna', 'A05p00020' => 'bna', 'A07p08820' => 'bna', 'Aa31LG4G3300' => 'aar', 'Aa31LG8G10030' => 'aar', 'Actinidia00731' => 'ach', 'Actinidia11473' => 'ach', 'Actinidia23469' => 'ach', 'Actinidia24318' => 'ach', 'Actinidia40196' => 'ach', 'Actinidia40197' => 'ach', 'Actinidia40198' => 'ach', 'Ah.08g212990' => 'amhyb', 'Ah.15g091720' => 'amhyb', 'AL3G38260' => 'aly', 'AL4G47710' => 'aly', 'Aqoxy2G00671' => 'aox', 'Aqoxy2G03236' => 'aox', 'arahy.Tifrunner.gnm1.ann1.05IDCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KR684' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATY3SJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK6QJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6APGL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IDT7Z9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM073U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ0R87' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LE7RV4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT4QRX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V5ENPK' => 'arhy', 'AT2G48110' => 'ath', 'AT3G23590' => 'ath', 'ATR0626G186' => 'atr', 'ATR1127G141' => 'atr', 'Atru.chr4.2583' => 'acertr', 'Atru.chr5.1358' => 'acertr', 'Atru.chr5.1359' => 'acertr', 'Atru.chr8.46' => 'acertr', 'AUR62002640' => 'cqu', 'AUR62030055' => 'cqu', 'AUR62033713' => 'cqu', 'AUR62033714' => 'cqu', 'AUR62036795' => 'cqu', 'AUR62039891' => 'cqu', 'BcaB02g08737' => 'bca', 'BcaB04g20441' => 'bca', 'BcaB06g26509' => 'bca', 'BcaB06g26510' => 'bca', 'BcaB06g26511' => 'bca', 'BcaB06g26512' => 'bca', 'BcaB06g26513' => 'bca', 'BcaC02g12564' => 'bca', 'BcaC02g12565' => 'bca', 'BcaC02g12794' => 'bca', 'BcaC02g12795' => 'bca', 'BcaC02g12796' => 'bca', 'BcaC06g35541' => 'bca', 'BNapus_Darmor_BZH_scaffold_188p00080' => 'bna', 'BNapus_Darmor_BZH_scaffold_188p00090' => 'bna', 'BolC1t03972H' => 'bol', 'BolC1t03973H' => 'bol', 'BolC4t21680H' => 'bol', 'BolC7t41863H' => 'bol', 'BolSC55t61227H' => 'bol', 'BolSC55t61228H' => 'bol', 'BraA01t03278Z' => 'bra', 'BraA05t18998Z' => 'bra', 'BraA07t28673Z' => 'bra', 'C01p40150' => 'bna', 'C05p12370' => 'bna', 'C07p13680' => 'bna', 'CAN.G1006.16' => 'can', 'CAN.G1006.17' => 'can', 'CAN.G1170.2' => 'can', 'CAN.G962.7' => 'can', 'CANSAT25G2179' => 'cansat', 'CANSAT78G1573' => 'cansat', 'CARHR099510' => 'chi', 'CARHR143510' => 'chi', 'Carub.0003s2380' => 'cru', 'Carub.0004s3082' => 'cru', 'Ca_00614_v3' => 'car', 'Ca_07801_v3' => 'car', 'Ca_08567_v3' => 'car', 'Ca_09571_v3' => 'car', 'CBR_g19290' => 'cbr', 'Cc01_g19770' => 'ccan', 'Cc03_g03030' => 'ccan', 'CDE07G0968' => 'cde', 'CDE09G1441' => 'cde', 'Cfa006103' => 'cfa', 'Cfa015573' => 'cfa', 'Cfa016988' => 'cfa', 'Ciclev10006738m.g' => 'ccl', 'Ciclev10010920m.g' => 'ccl', 'Ciclev10018517m.g' => 'ccl', 'CiPaw.01G159200' => 'cil', 'CiPaw.02G091000' => 'cil', 'CiPaw.02G091100' => 'cil', 'CiPaw.08G103100' => 'cil', 'CiPaw.09G224900' => 'cil', 'ClCG06G005740' => 'cla', 'ClCG07G000090' => 'cla', 'ClCG07G000100' => 'cla', 'COL.COLO4_09143' => 'col', 'COL.COLO4_25124' => 'col', 'Cpa.g.sc16.34' => 'cpa', 'Cpa.g.sc3504.1' => 'cpa', 'Cpa.g.sc60.37' => 'cpa', 'CsaV3_6G018520' => 'csa', 'CsaV3_6G036860' => 'csa', 'CSS0001072' => 'camsi', 'CSS0020208' => 'camsi', 'CSS0021253' => 'camsi', 'CSS0022190' => 'camsi', 'CSS0036150' => 'camsi', 'CSS0040442' => 'camsi', 'CSS0042300' => 'camsi', 'CSS0045298' => 'camsi', 'DCAR_012449' => 'dca', 'DCAR_018405' => 'dca', 'DCAR_024573' => 'dca', 'DCAR_030591' => 'dca', 'Dinv16926' => 'din', 'Dinv32963' => 'din', 'Dinv38382' => 'din', 'Dinv38383' => 'din', 'Duzib133G0974' => 'dzi', 'Duzib138G1867' => 'dzi', 'Duzib211G0420' => 'dzi', 'Duzib212G0930' => 'dzi', 'ECA234G1645' => 'eca', 'ECA247G3467' => 'eca', 'ECA248G1703' => 'eca', 'EL10Ac3g06327' => 'bvu', 'EL10Ac7g17204' => 'bvu', 'Eucgr.A00855' => 'egr', 'Eucgr.A00858' => 'egr', 'Eucgr.H01520' => 'egr', 'Eucgr.H03604' => 'egr', 'Eucgr.L03465' => 'egr', 'Eucgr.L03466' => 'egr', 'FAN01G0988' => 'fan', 'FAN02G3892' => 'fan', 'FAN05G3381' => 'fan', 'FAN07G0967' => 'fan', 'FAN07G1493' => 'fan', 'FAN08G3125' => 'fan', 'FAN09G0402' => 'fan', 'FAN12G2594' => 'fan', 'FAN12G3879' => 'fan', 'FAN14G1546' => 'fan', 'FAN15G3626' => 'fan', 'FAN17G0588' => 'fan', 'FAN17G0609' => 'fan', 'FAN18G2817' => 'fan', 'FAN19G1305' => 'fan', 'FAN20G1787' => 'fan', 'FAN22G0073' => 'fan', 'FAN22G0352' => 'fan', 'FAN22G0368' => 'fan', 'FAN22G2273' => 'fan', 'FAN24G1998' => 'fan', 'FAN27G1317' => 'fan', 'FvH4_2g23980' => 'fve', 'FvH4_4g14380' => 'fve', 'FvH4_4g14390' => 'fve', 'FvH4_6g09250' => 'fve', 'Glyma.03G151100' => 'gma', 'Glyma.04G122550' => 'gma', 'Glyma.05G001600' => 'gma', 'Glyma.09G270766' => 'gma', 'Glyma.09G270832' => 'gma', 'Glyma.13G209800' => 'gma', 'Glyma.15G102800' => 'gma', 'Glyma.18G218900' => 'gma', 'Glyma.19G001500' => 'gma', 'Glyma.19G153600' => 'gma', 'Gohir.A02G028600' => 'ghi', 'Gohir.A08G045000' => 'ghi', 'Gohir.A11G120500' => 'ghi', 'Gohir.A12G006200' => 'ghi', 'Gohir.A12G006250' => 'ghi', 'Gohir.D02G036300' => 'ghi', 'Gohir.D08G054700' => 'ghi', 'Gohir.D11G125600' => 'ghi', 'Gohir.D12G005700' => 'ghi', 'Gorai.004G055200' => 'gra', 'Gorai.005G040400' => 'gra', 'Gorai.007G134500' => 'gra', 'Gorai.008G005500' => 'gra', 'GSVIVG01011094001' => 'vvi', 'GSVIVG01017879001' => 'vvi', 'GSVIVG01025988001' => 'vvi', 'GSVIVG01029847001' => 'vvi', 'HanXRQChr10g0282901' => 'han', 'HanXRQChr10g0310371' => 'han', 'HanXRQChr10g0315041' => 'han', 'HanXRQChr11g0327651' => 'han', 'HanXRQChr12g0359391' => 'han', 'Haze_00972' => 'cav', 'Haze_00973' => 'cav', 'Haze_00974' => 'cav', 'Haze_04747' => 'cav', 'Haze_04749' => 'cav', 'Haze_04750' => 'cav', 'Haze_21217' => 'cav', 'Hma1.2p1_1037F.1_g250680' => 'hma', 'Hma1.2p1_1644F.1_g295320' => 'hma', 'HPP92_011322' => 'vpl', 'HPP92_011323' => 'vpl', 'HPP92_011324' => 'vpl', 'HPP92_011325' => 'vpl', 'HPP92_011326' => 'vpl', 'Hund12205' => 'sun', 'Hund17957' => 'sun', 'Lalb_Chr06g0176771' => 'lal', 'Lalb_Chr18g0056021' => 'lal', 'Lalb_Chr18g0056031' => 'lal', 'Lalb_Chr18g0056041' => 'lal', 'Lalb_Chr20g0107751' => 'lal', 'Lalb_Chr20g0118371' => 'lal', 'Lj1g0010239' => 'lja', 'Lj1g0017101' => 'lja', 'Lj2A1178G40' => 'lonja', 'Lj2A54G84' => 'lonja', 'Lj2g0015248' => 'lja', 'Lj3A761T51' => 'lonja', 'Lj6g0018116' => 'lja', 'Lsat_1_v5_gn_4_136040' => 'lsa', 'Lsat_1_v5_gn_5_187461' => 'lsa', 'Lsat_1_v5_gn_5_77001' => 'lsa', 'Lsat_1_v5_gn_9_4461' => 'lsa', 'Manes.01G210100' => 'mes', 'Manes.03G185600' => 'mes', 'Manes.05G073300' => 'mes', 'Manes.09G120300' => 'mes', 'Manes.15G022100' => 'mes', 'Mapoly0096s0053' => 'mpo', 'MBI03_g14058_MAGBIO' => 'mbi', 'MBI03_g33876_MAGBIO' => 'mbi', 'MBI03_g36854_MAGBIO' => 'mbi', 'MBI17_g11997_MAGBIO' => 'mbi', 'MD03G1269000' => 'mdo', 'MD04G1179600' => 'mdo', 'MD11G1289800' => 'mdo', 'MD12G1194700' => 'mdo', 'MD13G1182100' => 'mdo', 'MD13G1182200' => 'mdo', 'MD16G1182600' => 'mdo', 'Medtr2g021400' => 'mtr', 'Medtr2g021470' => 'mtr', 'Medtr2g105810' => 'mtr', 'Medtr3g033580' => 'mtr', 'Medtr6g007970' => 'mtr', 'Medtr7g056330' => 'mtr', 'Medtr7g074290' => 'mtr', 'Medtr7g074380' => 'mtr', 'Medtr7g094550' => 'mtr', 'Medtr8g069995' => 'mtr', 'MELO3C014345.2' => 'cme', 'MELO3C021395.2' => 'cme', 'Migut.D00262' => 'egut', 'Migut.G00257' => 'egut', 'MSTRG.21575' => 'ama', 'MSTRG.3985' => 'ama', 'Nitab4.5_0000295g0140' => 'nta', 'Nitab4.5_0000732g0140' => 'nta', 'Nitab4.5_0003162g0020' => 'nta', 'Nitab4.5_0006180g0090' => 'nta', 'Nitab4.5_0006390g0010' => 'nta', 'Nitab4.5_0007392g0040' => 'nta', 'Nn1g02140' => 'nnu', 'Nn4g26168' => 'nnu', 'Nn5g26754' => 'nnu', 'Oeu001433.1' => 'oeu', 'Oeu010299.2' => 'oeu', 'Oeu011171.1' => 'oeu', 'Oeu037675.1' => 'oeu', 'Oeu038359.1' => 'oeu', 'Oeu063834.1' => 'oeu', 'Oeu063835.1' => 'oeu', 'Os05g0312000' => 'osa', 'Os07g0211101' => 'osa', 'Os07g0211200' => 'osa', 'Os07g0681500' => 'osa', 'Peaxi162Scf00095g01015' => 'pax', 'Peaxi162Scf00104g00329' => 'pax', 'Peaxi162Scf00161g00137' => 'pax', 'PGR004G1665' => 'pgr', 'PGR031G2937' => 'pgr', 'PGR119G2145' => 'pgr', 'PGSC0003DMG400004351' => 'stu', 'PGSC0003DMG400014625' => 'stu', 'PGSC0003DMG401000943' => 'stu', 'Phvul.001G148600' => 'pvu', 'Phvul.004G001700' => 'pvu', 'Phvul.006G154900' => 'pvu', 'Phvul.008G078200' => 'pvu', 'Phvul.011G136500' => 'pvu', 'Potri.002G215600' => 'ptr', 'Potri.008G201600' => 'ptr', 'Potri.014G138400' => 'ptr', 'Potri.016G142500' => 'ptr', 'Pp3c16_10580' => 'ppa', 'Pp3c5_25280' => 'ppa', 'Prupe.1G150000' => 'ppe', 'Prupe.1G150100' => 'ppe', 'Prupe.6G299600' => 'ppe', 'Prupe.8G245000' => 'ppe', 'Psat0s4927g0040' => 'psa', 'Psat1g052080' => 'psa', 'Psat1g183800' => 'psa', 'Psat3g113840' => 'psa', 'Psat3g126120' => 'psa', 'Psat3g126160' => 'psa', 'Psat3g158760' => 'psa', 'Psat3g158840' => 'psa', 'PSO170G2858' => 'pso', 'PSO339G0606' => 'pso', 'PSO384G4709' => 'pso', 'PSO407G0334' => 'pso', 'QL04p040276' => 'qlo', 'QL06p005458' => 'qlo', 'QL06p005472' => 'qlo', 'QL07p030546' => 'qlo', 'QL07p031519' => 'qlo', 'QL09p050949' => 'qlo', 'QL09p050966' => 'qlo', 'QL09p051067' => 'qlo', 'QL12p022706' => 'qlo', 'RcHm_v2.0_Chr2g0119601' => 'rch', 'RcHm_v2.0_Chr3g0459591' => 'rch', 'RcHm_v2.0_Chr4g0418521' => 'rch', 'RcHm_v2.0_Chr4g0418531' => 'rch', 'RcHm_v2.0_Chr4g0418541' => 'rch', 'RcHm_v2.0_Chr6g0291641' => 'rch', 'Rhsim01G0086300' => 'rsi', 'Rhsim01G0276300' => 'rsi', 'Rhsim01G0276500' => 'rsi', 'Rhsim04G0207700' => 'rsi', 'Rhsim05G0234500' => 'rsi', 'Rhsim13G0022400' => 'rsi', 'Sabra02G0167900' => 'sbr', 'Sabra04G0158500' => 'sbr', 'Sabra08G0159800' => 'sbr', 'Sabra10G0011500' => 'sbr', 'Sabra14G0104400' => 'sbr', 'SalBow2G2440' => 'sbo', 'SalBow4G2265' => 'sbo', 'Sc02g0000060' => 'sci', 'Sc05g0005020' => 'sci', 'Sc13g0003890' => 'sci', 'Sed0014865' => 'sed', 'Sed0017224' => 'sed', 'Sed0026391' => 'sed', 'SEGI_00063' => 'sgi', 'SEGI_10967' => 'sgi', 'SEGI_17510' => 'sgi', 'SEGI_24396' => 'sgi', 'SEGI_39719' => 'sgi', 'SEGI_41392' => 'sgi', 'SGA_v2.0_scaffold11G05794' => 'sas', 'SGA_v2.0_scaffold142G35607' => 'sas', 'SGA_v2.0_scaffold1G00447' => 'sas', 'SHI15388' => 'shi', 'SHI15394' => 'shi', 'SHI15396' => 'shi', 'SHI15399' => 'shi', 'SMO343G0151' => 'smo', 'SMO367G1118' => 'smo', 'Solyc01g080200.3' => 'sly', 'Solyc06g008960.3' => 'sly', 'Solyc09g064780.3' => 'sly', 'Sopen01g031980' => 'spe', 'Sopen06g003710' => 'spe', 'Sopen09g026460' => 'spe', 'Sp3g21240' => 'spa', 'Sp4g30030' => 'spa', 'TAR365G0022' => 'tar', 'TAR365G1023' => 'tar', 'TAR365G1253' => 'tar', 'TAR623G0078' => 'tar', 'TAR623G1721' => 'tar', 'TAR633G0959' => 'tar', 'THA.LOC104802225' => 'tha', 'THA.LOC104804769' => 'tha', 'THA.LOC104808660' => 'tha', 'THA.LOC104812792' => 'tha', 'Thecc.01G284000' => 'tca', 'Thecc.04G220600' => 'tca', 'Thecc.05G268900' => 'tca', 'Thecc.08G171100' => 'tca', 'Thhalv10001284m.g' => 'esa', 'Thhalv10019912m.g' => 'esa', 'TPR.G14189' => 'tpr', 'TPR.G18110' => 'tpr', 'TPR.G18130' => 'tpr', 'TPR.G18131' => 'tpr', 'TPR.G18140' => 'tpr', 'TPR.G24282' => 'tpr', 'TPR.G25221' => 'tpr', 'TPR.G29267' => 'tpr', 'TPR.G35315' => 'tpr', 'TPR.G36173' => 'tpr', 'TWI09G0794' => 'twi', 'TWI59G1348' => 'twi', 'TWI74G0430' => 'twi', 'unitig_26.g8940' => 'ugi', 'unitig_749.g13744' => 'ugi', 'unitig_749.g13745' => 'ugi', 'vmacro08269' => 'vma', 'vmacro14937' => 'vma', 'vmacro20401' => 'vma', 'VMungo0464G1349' => 'vmu', 'VMungo0540G0289' => 'vmu', 'VMungo1215G1590' => 'vmu', 'VMungo1309G0221' => 'vmu', 'VMungo1309G2815' => 'vmu', 'VMungo1383G0239' => 'vmu', 'VMungo1383G2910' => 'vmu', 'Zm00001eb095270' => 'zma', 'Zm00001eb095280' => 'zma', 'Zm00001eb111630' => 'zma', 'Zm00001eb237080' => 'zma', 'Zm00001eb273740' => 'zma', 'Zm00001eb285040' => 'zma', 'Zm00001eb330790' => 'zma', 'Zm00001eb337380' => 'zma' ), 'gf_id' => 'HOM05D001484', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001484' ), 'data_identifier' => 'HOM05D001484', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001484', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p31500' => 'bna', 'A05p00020' => 'bna', 'A07p08820' => 'bna', 'Aa31LG4G3300' => 'aar', 'Aa31LG8G10030' => 'aar', 'Actinidia00731' => 'ach', 'Actinidia11473' => 'ach', 'Actinidia23469' => 'ach', 'Actinidia24318' => 'ach', 'Actinidia40196' => 'ach', 'Actinidia40197' => 'ach', 'Actinidia40198' => 'ach', 'Ah.08g212990' => 'amhyb', 'Ah.15g091720' => 'amhyb', 'AL3G38260' => 'aly', 'AL4G47710' => 'aly', 'Aqoxy2G00671' => 'aox', 'Aqoxy2G03236' => 'aox', 'arahy.Tifrunner.gnm1.ann1.05IDCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KR684' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATY3SJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK6QJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6APGL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IDT7Z9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM073U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ0R87' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LE7RV4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT4QRX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V5ENPK' => 'arhy', 'AT2G48110' => 'ath', 'AT3G23590' => 'ath', 'ATR0626G186' => 'atr', 'ATR1127G141' => 'atr', 'Atru.chr4.2583' => 'acertr', 'Atru.chr5.1358' => 'acertr', 'Atru.chr5.1359' => 'acertr', 'Atru.chr8.46' => 'acertr', 'AUR62002640' => 'cqu', 'AUR62030055' => 'cqu', 'AUR62033713' => 'cqu', 'AUR62033714' => 'cqu', 'AUR62036795' => 'cqu', 'AUR62039891' => 'cqu', 'BcaB02g08737' => 'bca', 'BcaB04g20441' => 'bca', 'BcaB06g26509' => 'bca', 'BcaB06g26510' => 'bca', 'BcaB06g26511' => 'bca', 'BcaB06g26512' => 'bca', 'BcaB06g26513' => 'bca', 'BcaC02g12564' => 'bca', 'BcaC02g12565' => 'bca', 'BcaC02g12794' => 'bca', 'BcaC02g12795' => 'bca', 'BcaC02g12796' => 'bca', 'BcaC06g35541' => 'bca', 'BNapus_Darmor_BZH_scaffold_188p00080' => 'bna', 'BNapus_Darmor_BZH_scaffold_188p00090' => 'bna', 'BolC1t03972H' => 'bol', 'BolC1t03973H' => 'bol', 'BolC4t21680H' => 'bol', 'BolC7t41863H' => 'bol', 'BolSC55t61227H' => 'bol', 'BolSC55t61228H' => 'bol', 'BraA01t03278Z' => 'bra', 'BraA05t18998Z' => 'bra', 'BraA07t28673Z' => 'bra', 'C01p40150' => 'bna', 'C05p12370' => 'bna', 'C07p13680' => 'bna', 'CAN.G1006.16' => 'can', 'CAN.G1006.17' => 'can', 'CAN.G1170.2' => 'can', 'CAN.G962.7' => 'can', 'CANSAT25G2179' => 'cansat', 'CANSAT78G1573' => 'cansat', 'CARHR099510' => 'chi', 'CARHR143510' => 'chi', 'Carub.0003s2380' => 'cru', 'Carub.0004s3082' => 'cru', 'Ca_00614_v3' => 'car', 'Ca_07801_v3' => 'car', 'Ca_08567_v3' => 'car', 'Ca_09571_v3' => 'car', 'CBR_g19290' => 'cbr', 'Cc01_g19770' => 'ccan', 'Cc03_g03030' => 'ccan', 'CDE07G0968' => 'cde', 'CDE09G1441' => 'cde', 'Cfa006103' => 'cfa', 'Cfa015573' => 'cfa', 'Cfa016988' => 'cfa', 'Ciclev10006738m.g' => 'ccl', 'Ciclev10010920m.g' => 'ccl', 'Ciclev10018517m.g' => 'ccl', 'CiPaw.01G159200' => 'cil', 'CiPaw.02G091000' => 'cil', 'CiPaw.02G091100' => 'cil', 'CiPaw.08G103100' => 'cil', 'CiPaw.09G224900' => 'cil', 'ClCG06G005740' => 'cla', 'ClCG07G000090' => 'cla', 'ClCG07G000100' => 'cla', 'COL.COLO4_09143' => 'col', 'COL.COLO4_25124' => 'col', 'Cpa.g.sc16.34' => 'cpa', 'Cpa.g.sc3504.1' => 'cpa', 'Cpa.g.sc60.37' => 'cpa', 'CsaV3_6G018520' => 'csa', 'CsaV3_6G036860' => 'csa', 'CSS0001072' => 'camsi', 'CSS0020208' => 'camsi', 'CSS0021253' => 'camsi', 'CSS0022190' => 'camsi', 'CSS0036150' => 'camsi', 'CSS0040442' => 'camsi', 'CSS0042300' => 'camsi', 'CSS0045298' => 'camsi', 'DCAR_012449' => 'dca', 'DCAR_018405' => 'dca', 'DCAR_024573' => 'dca', 'DCAR_030591' => 'dca', 'Dinv16926' => 'din', 'Dinv32963' => 'din', 'Dinv38382' => 'din', 'Dinv38383' => 'din', 'Duzib133G0974' => 'dzi', 'Duzib138G1867' => 'dzi', 'Duzib211G0420' => 'dzi', 'Duzib212G0930' => 'dzi', 'ECA234G1645' => 'eca', 'ECA247G3467' => 'eca', 'ECA248G1703' => 'eca', 'EL10Ac3g06327' => 'bvu', 'EL10Ac7g17204' => 'bvu', 'Eucgr.A00855' => 'egr', 'Eucgr.A00858' => 'egr', 'Eucgr.H01520' => 'egr', 'Eucgr.H03604' => 'egr', 'Eucgr.L03465' => 'egr', 'Eucgr.L03466' => 'egr', 'FAN01G0988' => 'fan', 'FAN02G3892' => 'fan', 'FAN05G3381' => 'fan', 'FAN07G0967' => 'fan', 'FAN07G1493' => 'fan', 'FAN08G3125' => 'fan', 'FAN09G0402' => 'fan', 'FAN12G2594' => 'fan', 'FAN12G3879' => 'fan', 'FAN14G1546' => 'fan', 'FAN15G3626' => 'fan', 'FAN17G0588' => 'fan', 'FAN17G0609' => 'fan', 'FAN18G2817' => 'fan', 'FAN19G1305' => 'fan', 'FAN20G1787' => 'fan', 'FAN22G0073' => 'fan', 'FAN22G0352' => 'fan', 'FAN22G0368' => 'fan', 'FAN22G2273' => 'fan', 'FAN24G1998' => 'fan', 'FAN27G1317' => 'fan', 'FvH4_2g23980' => 'fve', 'FvH4_4g14380' => 'fve', 'FvH4_4g14390' => 'fve', 'FvH4_6g09250' => 'fve', 'Glyma.03G151100' => 'gma', 'Glyma.04G122550' => 'gma', 'Glyma.05G001600' => 'gma', 'Glyma.09G270766' => 'gma', 'Glyma.09G270832' => 'gma', 'Glyma.13G209800' => 'gma', 'Glyma.15G102800' => 'gma', 'Glyma.18G218900' => 'gma', 'Glyma.19G001500' => 'gma', 'Glyma.19G153600' => 'gma', 'Gohir.A02G028600' => 'ghi', 'Gohir.A08G045000' => 'ghi', 'Gohir.A11G120500' => 'ghi', 'Gohir.A12G006200' => 'ghi', 'Gohir.A12G006250' => 'ghi', 'Gohir.D02G036300' => 'ghi', 'Gohir.D08G054700' => 'ghi', 'Gohir.D11G125600' => 'ghi', 'Gohir.D12G005700' => 'ghi', 'Gorai.004G055200' => 'gra', 'Gorai.005G040400' => 'gra', 'Gorai.007G134500' => 'gra', 'Gorai.008G005500' => 'gra', 'GSVIVG01011094001' => 'vvi', 'GSVIVG01017879001' => 'vvi', 'GSVIVG01025988001' => 'vvi', 'GSVIVG01029847001' => 'vvi', 'HanXRQChr10g0282901' => 'han', 'HanXRQChr10g0310371' => 'han', 'HanXRQChr10g0315041' => 'han', 'HanXRQChr11g0327651' => 'han', 'HanXRQChr12g0359391' => 'han', 'Haze_00972' => 'cav', 'Haze_00973' => 'cav', 'Haze_00974' => 'cav', 'Haze_04747' => 'cav', 'Haze_04749' => 'cav', 'Haze_04750' => 'cav', 'Haze_21217' => 'cav', 'Hma1.2p1_1037F.1_g250680' => 'hma', 'Hma1.2p1_1644F.1_g295320' => 'hma', 'HPP92_011322' => 'vpl', 'HPP92_011323' => 'vpl', 'HPP92_011324' => 'vpl', 'HPP92_011325' => 'vpl', 'HPP92_011326' => 'vpl', 'Hund12205' => 'sun', 'Hund17957' => 'sun', 'Lalb_Chr06g0176771' => 'lal', 'Lalb_Chr18g0056021' => 'lal', 'Lalb_Chr18g0056031' => 'lal', 'Lalb_Chr18g0056041' => 'lal', 'Lalb_Chr20g0107751' => 'lal', 'Lalb_Chr20g0118371' => 'lal', 'Lj1g0010239' => 'lja', 'Lj1g0017101' => 'lja', 'Lj2A1178G40' => 'lonja', 'Lj2A54G84' => 'lonja', 'Lj2g0015248' => 'lja', 'Lj3A761T51' => 'lonja', 'Lj6g0018116' => 'lja', 'Lsat_1_v5_gn_4_136040' => 'lsa', 'Lsat_1_v5_gn_5_187461' => 'lsa', 'Lsat_1_v5_gn_5_77001' => 'lsa', 'Lsat_1_v5_gn_9_4461' => 'lsa', 'Manes.01G210100' => 'mes', 'Manes.03G185600' => 'mes', 'Manes.05G073300' => 'mes', 'Manes.09G120300' => 'mes', 'Manes.15G022100' => 'mes', 'Mapoly0096s0053' => 'mpo', 'MBI03_g14058_MAGBIO' => 'mbi', 'MBI03_g33876_MAGBIO' => 'mbi', 'MBI03_g36854_MAGBIO' => 'mbi', 'MBI17_g11997_MAGBIO' => 'mbi', 'MD03G1269000' => 'mdo', 'MD04G1179600' => 'mdo', 'MD11G1289800' => 'mdo', 'MD12G1194700' => 'mdo', 'MD13G1182100' => 'mdo', 'MD13G1182200' => 'mdo', 'MD16G1182600' => 'mdo', 'Medtr2g021400' => 'mtr', 'Medtr2g021470' => 'mtr', 'Medtr2g105810' => 'mtr', 'Medtr3g033580' => 'mtr', 'Medtr6g007970' => 'mtr', 'Medtr7g056330' => 'mtr', 'Medtr7g074290' => 'mtr', 'Medtr7g074380' => 'mtr', 'Medtr7g094550' => 'mtr', 'Medtr8g069995' => 'mtr', 'MELO3C014345.2' => 'cme', 'MELO3C021395.2' => 'cme', 'Migut.D00262' => 'egut', 'Migut.G00257' => 'egut', 'MSTRG.21575' => 'ama', 'MSTRG.3985' => 'ama', 'Nitab4.5_0000295g0140' => 'nta', 'Nitab4.5_0000732g0140' => 'nta', 'Nitab4.5_0003162g0020' => 'nta', 'Nitab4.5_0006180g0090' => 'nta', 'Nitab4.5_0006390g0010' => 'nta', 'Nitab4.5_0007392g0040' => 'nta', 'Nn1g02140' => 'nnu', 'Nn4g26168' => 'nnu', 'Nn5g26754' => 'nnu', 'Oeu001433.1' => 'oeu', 'Oeu010299.2' => 'oeu', 'Oeu011171.1' => 'oeu', 'Oeu037675.1' => 'oeu', 'Oeu038359.1' => 'oeu', 'Oeu063834.1' => 'oeu', 'Oeu063835.1' => 'oeu', 'Os05g0312000' => 'osa', 'Os07g0211101' => 'osa', 'Os07g0211200' => 'osa', 'Os07g0681500' => 'osa', 'Peaxi162Scf00095g01015' => 'pax', 'Peaxi162Scf00104g00329' => 'pax', 'Peaxi162Scf00161g00137' => 'pax', 'PGR004G1665' => 'pgr', 'PGR031G2937' => 'pgr', 'PGR119G2145' => 'pgr', 'PGSC0003DMG400004351' => 'stu', 'PGSC0003DMG400014625' => 'stu', 'PGSC0003DMG401000943' => 'stu', 'Phvul.001G148600' => 'pvu', 'Phvul.004G001700' => 'pvu', 'Phvul.006G154900' => 'pvu', 'Phvul.008G078200' => 'pvu', 'Phvul.011G136500' => 'pvu', 'Potri.002G215600' => 'ptr', 'Potri.008G201600' => 'ptr', 'Potri.014G138400' => 'ptr', 'Potri.016G142500' => 'ptr', 'Pp3c16_10580' => 'ppa', 'Pp3c5_25280' => 'ppa', 'Prupe.1G150000' => 'ppe', 'Prupe.1G150100' => 'ppe', 'Prupe.6G299600' => 'ppe', 'Prupe.8G245000' => 'ppe', 'Psat0s4927g0040' => 'psa', 'Psat1g052080' => 'psa', 'Psat1g183800' => 'psa', 'Psat3g113840' => 'psa', 'Psat3g126120' => 'psa', 'Psat3g126160' => 'psa', 'Psat3g158760' => 'psa', 'Psat3g158840' => 'psa', 'PSO170G2858' => 'pso', 'PSO339G0606' => 'pso', 'PSO384G4709' => 'pso', 'PSO407G0334' => 'pso', 'QL04p040276' => 'qlo', 'QL06p005458' => 'qlo', 'QL06p005472' => 'qlo', 'QL07p030546' => 'qlo', 'QL07p031519' => 'qlo', 'QL09p050949' => 'qlo', 'QL09p050966' => 'qlo', 'QL09p051067' => 'qlo', 'QL12p022706' => 'qlo', 'RcHm_v2.0_Chr2g0119601' => 'rch', 'RcHm_v2.0_Chr3g0459591' => 'rch', 'RcHm_v2.0_Chr4g0418521' => 'rch', 'RcHm_v2.0_Chr4g0418531' => 'rch', 'RcHm_v2.0_Chr4g0418541' => 'rch', 'RcHm_v2.0_Chr6g0291641' => 'rch', 'Rhsim01G0086300' => 'rsi', 'Rhsim01G0276300' => 'rsi', 'Rhsim01G0276500' => 'rsi', 'Rhsim04G0207700' => 'rsi', 'Rhsim05G0234500' => 'rsi', 'Rhsim13G0022400' => 'rsi', 'Sabra02G0167900' => 'sbr', 'Sabra04G0158500' => 'sbr', 'Sabra08G0159800' => 'sbr', 'Sabra10G0011500' => 'sbr', 'Sabra14G0104400' => 'sbr', 'SalBow2G2440' => 'sbo', 'SalBow4G2265' => 'sbo', 'Sc02g0000060' => 'sci', 'Sc05g0005020' => 'sci', 'Sc13g0003890' => 'sci', 'Sed0014865' => 'sed', 'Sed0017224' => 'sed', 'Sed0026391' => 'sed', 'SEGI_00063' => 'sgi', 'SEGI_10967' => 'sgi', 'SEGI_17510' => 'sgi', 'SEGI_24396' => 'sgi', 'SEGI_39719' => 'sgi', 'SEGI_41392' => 'sgi', 'SGA_v2.0_scaffold11G05794' => 'sas', 'SGA_v2.0_scaffold142G35607' => 'sas', 'SGA_v2.0_scaffold1G00447' => 'sas', 'SHI15388' => 'shi', 'SHI15394' => 'shi', 'SHI15396' => 'shi', 'SHI15399' => 'shi', 'SMO343G0151' => 'smo', 'SMO367G1118' => 'smo', 'Solyc01g080200.3' => 'sly', 'Solyc06g008960.3' => 'sly', 'Solyc09g064780.3' => 'sly', 'Sopen01g031980' => 'spe', 'Sopen06g003710' => 'spe', 'Sopen09g026460' => 'spe', 'Sp3g21240' => 'spa', 'Sp4g30030' => 'spa', 'TAR365G0022' => 'tar', 'TAR365G1023' => 'tar', 'TAR365G1253' => 'tar', 'TAR623G0078' => 'tar', 'TAR623G1721' => 'tar', 'TAR633G0959' => 'tar', 'THA.LOC104802225' => 'tha', 'THA.LOC104804769' => 'tha', 'THA.LOC104808660' => 'tha', 'THA.LOC104812792' => 'tha', 'Thecc.01G284000' => 'tca', 'Thecc.04G220600' => 'tca', 'Thecc.05G268900' => 'tca', 'Thecc.08G171100' => 'tca', 'Thhalv10001284m.g' => 'esa', 'Thhalv10019912m.g' => 'esa', 'TPR.G14189' => 'tpr', 'TPR.G18110' => 'tpr', 'TPR.G18130' => 'tpr', 'TPR.G18131' => 'tpr', 'TPR.G18140' => 'tpr', 'TPR.G24282' => 'tpr', 'TPR.G25221' => 'tpr', 'TPR.G29267' => 'tpr', 'TPR.G35315' => 'tpr', 'TPR.G36173' => 'tpr', 'TWI09G0794' => 'twi', 'TWI59G1348' => 'twi', 'TWI74G0430' => 'twi', 'unitig_26.g8940' => 'ugi', 'unitig_749.g13744' => 'ugi', 'unitig_749.g13745' => 'ugi', 'vmacro08269' => 'vma', 'vmacro14937' => 'vma', 'vmacro20401' => 'vma', 'VMungo0464G1349' => 'vmu', 'VMungo0540G0289' => 'vmu', 'VMungo1215G1590' => 'vmu', 'VMungo1309G0221' => 'vmu', 'VMungo1309G2815' => 'vmu', 'VMungo1383G0239' => 'vmu', 'VMungo1383G2910' => 'vmu', 'Zm00001eb095270' => 'zma', 'Zm00001eb095280' => 'zma', 'Zm00001eb111630' => 'zma', 'Zm00001eb237080' => 'zma', 'Zm00001eb273740' => 'zma', 'Zm00001eb285040' => 'zma', 'Zm00001eb330790' => 'zma', 'Zm00001eb337380' => 'zma' ) $gf_id = 'HOM05D001484' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001484' ) $data_identifier = 'HOM05D001484' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 2, 'aly' => (int) 2, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 22, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 7, 'hma' => (int) 2, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 7, 'mtr' => (int) 10, 'cme' => (int) 2, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 4, 'ppa' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 4, 'qlo' => (int) 9, 'rch' => (int) 6, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 10, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 7, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb337380' $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' => 'HOM05D001484', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p31500' => 'bna', 'A05p00020' => 'bna', 'A07p08820' => 'bna', 'Aa31LG4G3300' => 'aar', 'Aa31LG8G10030' => 'aar', 'Actinidia00731' => 'ach', 'Actinidia11473' => 'ach', 'Actinidia23469' => 'ach', 'Actinidia24318' => 'ach', 'Actinidia40196' => 'ach', 'Actinidia40197' => 'ach', 'Actinidia40198' => 'ach', 'Ah.08g212990' => 'amhyb', 'Ah.15g091720' => 'amhyb', 'AL3G38260' => 'aly', 'AL4G47710' => 'aly', 'Aqoxy2G00671' => 'aox', 'Aqoxy2G03236' => 'aox', 'arahy.Tifrunner.gnm1.ann1.05IDCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KR684' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATY3SJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK6QJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6APGL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IDT7Z9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM073U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ0R87' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LE7RV4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT4QRX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V5ENPK' => 'arhy', 'AT2G48110' => 'ath', 'AT3G23590' => 'ath', 'ATR0626G186' => 'atr', 'ATR1127G141' => 'atr', 'Atru.chr4.2583' => 'acertr', 'Atru.chr5.1358' => 'acertr', 'Atru.chr5.1359' => 'acertr', 'Atru.chr8.46' => 'acertr', 'AUR62002640' => 'cqu', 'AUR62030055' => 'cqu', 'AUR62033713' => 'cqu', 'AUR62033714' => 'cqu', 'AUR62036795' => 'cqu', 'AUR62039891' => 'cqu', 'BcaB02g08737' => 'bca', 'BcaB04g20441' => 'bca', 'BcaB06g26509' => 'bca', 'BcaB06g26510' => 'bca', 'BcaB06g26511' => 'bca', 'BcaB06g26512' => 'bca', 'BcaB06g26513' => 'bca', 'BcaC02g12564' => 'bca', 'BcaC02g12565' => 'bca', 'BcaC02g12794' => 'bca', 'BcaC02g12795' => 'bca', 'BcaC02g12796' => 'bca', 'BcaC06g35541' => 'bca', 'BNapus_Darmor_BZH_scaffold_188p00080' => 'bna', 'BNapus_Darmor_BZH_scaffold_188p00090' => 'bna', 'BolC1t03972H' => 'bol', 'BolC1t03973H' => 'bol', 'BolC4t21680H' => 'bol', 'BolC7t41863H' => 'bol', 'BolSC55t61227H' => 'bol', 'BolSC55t61228H' => 'bol', 'BraA01t03278Z' => 'bra', 'BraA05t18998Z' => 'bra', 'BraA07t28673Z' => 'bra', 'C01p40150' => 'bna', 'C05p12370' => 'bna', 'C07p13680' => 'bna', 'CAN.G1006.16' => 'can', 'CAN.G1006.17' => 'can', 'CAN.G1170.2' => 'can', 'CAN.G962.7' => 'can', 'CANSAT25G2179' => 'cansat', 'CANSAT78G1573' => 'cansat', 'CARHR099510' => 'chi', 'CARHR143510' => 'chi', 'Carub.0003s2380' => 'cru', 'Carub.0004s3082' => 'cru', 'Ca_00614_v3' => 'car', 'Ca_07801_v3' => 'car', 'Ca_08567_v3' => 'car', 'Ca_09571_v3' => 'car', 'CBR_g19290' => 'cbr', 'Cc01_g19770' => 'ccan', 'Cc03_g03030' => 'ccan', 'CDE07G0968' => 'cde', 'CDE09G1441' => 'cde', 'Cfa006103' => 'cfa', 'Cfa015573' => 'cfa', 'Cfa016988' => 'cfa', 'Ciclev10006738m.g' => 'ccl', 'Ciclev10010920m.g' => 'ccl', 'Ciclev10018517m.g' => 'ccl', 'CiPaw.01G159200' => 'cil', 'CiPaw.02G091000' => 'cil', 'CiPaw.02G091100' => 'cil', 'CiPaw.08G103100' => 'cil', 'CiPaw.09G224900' => 'cil', 'ClCG06G005740' => 'cla', 'ClCG07G000090' => 'cla', 'ClCG07G000100' => 'cla', 'COL.COLO4_09143' => 'col', 'COL.COLO4_25124' => 'col', 'Cpa.g.sc16.34' => 'cpa', 'Cpa.g.sc3504.1' => 'cpa', 'Cpa.g.sc60.37' => 'cpa', 'CsaV3_6G018520' => 'csa', 'CsaV3_6G036860' => 'csa', 'CSS0001072' => 'camsi', 'CSS0020208' => 'camsi', 'CSS0021253' => 'camsi', 'CSS0022190' => 'camsi', 'CSS0036150' => 'camsi', 'CSS0040442' => 'camsi', 'CSS0042300' => 'camsi', 'CSS0045298' => 'camsi', 'DCAR_012449' => 'dca', 'DCAR_018405' => 'dca', 'DCAR_024573' => 'dca', 'DCAR_030591' => 'dca', 'Dinv16926' => 'din', 'Dinv32963' => 'din', 'Dinv38382' => 'din', 'Dinv38383' => 'din', 'Duzib133G0974' => 'dzi', 'Duzib138G1867' => 'dzi', 'Duzib211G0420' => 'dzi', 'Duzib212G0930' => 'dzi', 'ECA234G1645' => 'eca', 'ECA247G3467' => 'eca', 'ECA248G1703' => 'eca', 'EL10Ac3g06327' => 'bvu', 'EL10Ac7g17204' => 'bvu', 'Eucgr.A00855' => 'egr', 'Eucgr.A00858' => 'egr', 'Eucgr.H01520' => 'egr', 'Eucgr.H03604' => 'egr', 'Eucgr.L03465' => 'egr', 'Eucgr.L03466' => 'egr', 'FAN01G0988' => 'fan', 'FAN02G3892' => 'fan', 'FAN05G3381' => 'fan', 'FAN07G0967' => 'fan', 'FAN07G1493' => 'fan', 'FAN08G3125' => 'fan', 'FAN09G0402' => 'fan', 'FAN12G2594' => 'fan', 'FAN12G3879' => 'fan', 'FAN14G1546' => 'fan', 'FAN15G3626' => 'fan', 'FAN17G0588' => 'fan', 'FAN17G0609' => 'fan', 'FAN18G2817' => 'fan', 'FAN19G1305' => 'fan', 'FAN20G1787' => 'fan', 'FAN22G0073' => 'fan', 'FAN22G0352' => 'fan', 'FAN22G0368' => 'fan', 'FAN22G2273' => 'fan', 'FAN24G1998' => 'fan', 'FAN27G1317' => 'fan', 'FvH4_2g23980' => 'fve', 'FvH4_4g14380' => 'fve', 'FvH4_4g14390' => 'fve', 'FvH4_6g09250' => 'fve', 'Glyma.03G151100' => 'gma', 'Glyma.04G122550' => 'gma', 'Glyma.05G001600' => 'gma', 'Glyma.09G270766' => 'gma', 'Glyma.09G270832' => 'gma', 'Glyma.13G209800' => 'gma', 'Glyma.15G102800' => 'gma', 'Glyma.18G218900' => 'gma', 'Glyma.19G001500' => 'gma', 'Glyma.19G153600' => 'gma', 'Gohir.A02G028600' => 'ghi', 'Gohir.A08G045000' => 'ghi', 'Gohir.A11G120500' => 'ghi', 'Gohir.A12G006200' => 'ghi', 'Gohir.A12G006250' => 'ghi', 'Gohir.D02G036300' => 'ghi', 'Gohir.D08G054700' => 'ghi', 'Gohir.D11G125600' => 'ghi', 'Gohir.D12G005700' => 'ghi', 'Gorai.004G055200' => 'gra', 'Gorai.005G040400' => 'gra', 'Gorai.007G134500' => 'gra', 'Gorai.008G005500' => 'gra', 'GSVIVG01011094001' => 'vvi', 'GSVIVG01017879001' => 'vvi', 'GSVIVG01025988001' => 'vvi', 'GSVIVG01029847001' => 'vvi', 'HanXRQChr10g0282901' => 'han', 'HanXRQChr10g0310371' => 'han', 'HanXRQChr10g0315041' => 'han', 'HanXRQChr11g0327651' => 'han', 'HanXRQChr12g0359391' => 'han', 'Haze_00972' => 'cav', 'Haze_00973' => 'cav', 'Haze_00974' => 'cav', 'Haze_04747' => 'cav', 'Haze_04749' => 'cav', 'Haze_04750' => 'cav', 'Haze_21217' => 'cav', 'Hma1.2p1_1037F.1_g250680' => 'hma', 'Hma1.2p1_1644F.1_g295320' => 'hma', 'HPP92_011322' => 'vpl', 'HPP92_011323' => 'vpl', 'HPP92_011324' => 'vpl', 'HPP92_011325' => 'vpl', 'HPP92_011326' => 'vpl', 'Hund12205' => 'sun', 'Hund17957' => 'sun', 'Lalb_Chr06g0176771' => 'lal', 'Lalb_Chr18g0056021' => 'lal', 'Lalb_Chr18g0056031' => 'lal', 'Lalb_Chr18g0056041' => 'lal', 'Lalb_Chr20g0107751' => 'lal', 'Lalb_Chr20g0118371' => 'lal', 'Lj1g0010239' => 'lja', 'Lj1g0017101' => 'lja', 'Lj2A1178G40' => 'lonja', 'Lj2A54G84' => 'lonja', 'Lj2g0015248' => 'lja', 'Lj3A761T51' => 'lonja', 'Lj6g0018116' => 'lja', 'Lsat_1_v5_gn_4_136040' => 'lsa', 'Lsat_1_v5_gn_5_187461' => 'lsa', 'Lsat_1_v5_gn_5_77001' => 'lsa', 'Lsat_1_v5_gn_9_4461' => 'lsa', 'Manes.01G210100' => 'mes', 'Manes.03G185600' => 'mes', 'Manes.05G073300' => 'mes', 'Manes.09G120300' => 'mes', 'Manes.15G022100' => 'mes', 'Mapoly0096s0053' => 'mpo', 'MBI03_g14058_MAGBIO' => 'mbi', 'MBI03_g33876_MAGBIO' => 'mbi', 'MBI03_g36854_MAGBIO' => 'mbi', 'MBI17_g11997_MAGBIO' => 'mbi', 'MD03G1269000' => 'mdo', 'MD04G1179600' => 'mdo', 'MD11G1289800' => 'mdo', 'MD12G1194700' => 'mdo', 'MD13G1182100' => 'mdo', 'MD13G1182200' => 'mdo', 'MD16G1182600' => 'mdo', 'Medtr2g021400' => 'mtr', 'Medtr2g021470' => 'mtr', 'Medtr2g105810' => 'mtr', 'Medtr3g033580' => 'mtr', 'Medtr6g007970' => 'mtr', 'Medtr7g056330' => 'mtr', 'Medtr7g074290' => 'mtr', 'Medtr7g074380' => 'mtr', 'Medtr7g094550' => 'mtr', 'Medtr8g069995' => 'mtr', 'MELO3C014345.2' => 'cme', 'MELO3C021395.2' => 'cme', 'Migut.D00262' => 'egut', 'Migut.G00257' => 'egut', 'MSTRG.21575' => 'ama', 'MSTRG.3985' => 'ama', 'Nitab4.5_0000295g0140' => 'nta', 'Nitab4.5_0000732g0140' => 'nta', 'Nitab4.5_0003162g0020' => 'nta', 'Nitab4.5_0006180g0090' => 'nta', 'Nitab4.5_0006390g0010' => 'nta', 'Nitab4.5_0007392g0040' => 'nta', 'Nn1g02140' => 'nnu', 'Nn4g26168' => 'nnu', 'Nn5g26754' => 'nnu', 'Oeu001433.1' => 'oeu', 'Oeu010299.2' => 'oeu', 'Oeu011171.1' => 'oeu', 'Oeu037675.1' => 'oeu', 'Oeu038359.1' => 'oeu', 'Oeu063834.1' => 'oeu', 'Oeu063835.1' => 'oeu', 'Os05g0312000' => 'osa', 'Os07g0211101' => 'osa', 'Os07g0211200' => 'osa', 'Os07g0681500' => 'osa', 'Peaxi162Scf00095g01015' => 'pax', 'Peaxi162Scf00104g00329' => 'pax', 'Peaxi162Scf00161g00137' => 'pax', 'PGR004G1665' => 'pgr', 'PGR031G2937' => 'pgr', 'PGR119G2145' => 'pgr', 'PGSC0003DMG400004351' => 'stu', 'PGSC0003DMG400014625' => 'stu', 'PGSC0003DMG401000943' => 'stu', 'Phvul.001G148600' => 'pvu', 'Phvul.004G001700' => 'pvu', 'Phvul.006G154900' => 'pvu', 'Phvul.008G078200' => 'pvu', 'Phvul.011G136500' => 'pvu', 'Potri.002G215600' => 'ptr', 'Potri.008G201600' => 'ptr', 'Potri.014G138400' => 'ptr', 'Potri.016G142500' => 'ptr', 'Pp3c16_10580' => 'ppa', 'Pp3c5_25280' => 'ppa', 'Prupe.1G150000' => 'ppe', 'Prupe.1G150100' => 'ppe', 'Prupe.6G299600' => 'ppe', 'Prupe.8G245000' => 'ppe', 'Psat0s4927g0040' => 'psa', 'Psat1g052080' => 'psa', 'Psat1g183800' => 'psa', 'Psat3g113840' => 'psa', 'Psat3g126120' => 'psa', 'Psat3g126160' => 'psa', 'Psat3g158760' => 'psa', 'Psat3g158840' => 'psa', 'PSO170G2858' => 'pso', 'PSO339G0606' => 'pso', 'PSO384G4709' => 'pso', 'PSO407G0334' => 'pso', 'QL04p040276' => 'qlo', 'QL06p005458' => 'qlo', 'QL06p005472' => 'qlo', 'QL07p030546' => 'qlo', 'QL07p031519' => 'qlo', 'QL09p050949' => 'qlo', 'QL09p050966' => 'qlo', 'QL09p051067' => 'qlo', 'QL12p022706' => 'qlo', 'RcHm_v2.0_Chr2g0119601' => 'rch', 'RcHm_v2.0_Chr3g0459591' => 'rch', 'RcHm_v2.0_Chr4g0418521' => 'rch', 'RcHm_v2.0_Chr4g0418531' => 'rch', 'RcHm_v2.0_Chr4g0418541' => 'rch', 'RcHm_v2.0_Chr6g0291641' => 'rch', 'Rhsim01G0086300' => 'rsi', 'Rhsim01G0276300' => 'rsi', 'Rhsim01G0276500' => 'rsi', 'Rhsim04G0207700' => 'rsi', 'Rhsim05G0234500' => 'rsi', 'Rhsim13G0022400' => 'rsi', 'Sabra02G0167900' => 'sbr', 'Sabra04G0158500' => 'sbr', 'Sabra08G0159800' => 'sbr', 'Sabra10G0011500' => 'sbr', 'Sabra14G0104400' => 'sbr', 'SalBow2G2440' => 'sbo', 'SalBow4G2265' => 'sbo', 'Sc02g0000060' => 'sci', 'Sc05g0005020' => 'sci', 'Sc13g0003890' => 'sci', 'Sed0014865' => 'sed', 'Sed0017224' => 'sed', 'Sed0026391' => 'sed', 'SEGI_00063' => 'sgi', 'SEGI_10967' => 'sgi', 'SEGI_17510' => 'sgi', 'SEGI_24396' => 'sgi', 'SEGI_39719' => 'sgi', 'SEGI_41392' => 'sgi', 'SGA_v2.0_scaffold11G05794' => 'sas', 'SGA_v2.0_scaffold142G35607' => 'sas', 'SGA_v2.0_scaffold1G00447' => 'sas', 'SHI15388' => 'shi', 'SHI15394' => 'shi', 'SHI15396' => 'shi', 'SHI15399' => 'shi', 'SMO343G0151' => 'smo', 'SMO367G1118' => 'smo', 'Solyc01g080200.3' => 'sly', 'Solyc06g008960.3' => 'sly', 'Solyc09g064780.3' => 'sly', 'Sopen01g031980' => 'spe', 'Sopen06g003710' => 'spe', 'Sopen09g026460' => 'spe', 'Sp3g21240' => 'spa', 'Sp4g30030' => 'spa', 'TAR365G0022' => 'tar', 'TAR365G1023' => 'tar', 'TAR365G1253' => 'tar', 'TAR623G0078' => 'tar', 'TAR623G1721' => 'tar', 'TAR633G0959' => 'tar', 'THA.LOC104802225' => 'tha', 'THA.LOC104804769' => 'tha', 'THA.LOC104808660' => 'tha', 'THA.LOC104812792' => 'tha', 'Thecc.01G284000' => 'tca', 'Thecc.04G220600' => 'tca', 'Thecc.05G268900' => 'tca', 'Thecc.08G171100' => 'tca', 'Thhalv10001284m.g' => 'esa', 'Thhalv10019912m.g' => 'esa', 'TPR.G14189' => 'tpr', 'TPR.G18110' => 'tpr', 'TPR.G18130' => 'tpr', 'TPR.G18131' => 'tpr', 'TPR.G18140' => 'tpr', 'TPR.G24282' => 'tpr', 'TPR.G25221' => 'tpr', 'TPR.G29267' => 'tpr', 'TPR.G35315' => 'tpr', 'TPR.G36173' => 'tpr', 'TWI09G0794' => 'twi', 'TWI59G1348' => 'twi', 'TWI74G0430' => 'twi', 'unitig_26.g8940' => 'ugi', 'unitig_749.g13744' => 'ugi', 'unitig_749.g13745' => 'ugi', 'vmacro08269' => 'vma', 'vmacro14937' => 'vma', 'vmacro20401' => 'vma', 'VMungo0464G1349' => 'vmu', 'VMungo0540G0289' => 'vmu', 'VMungo1215G1590' => 'vmu', 'VMungo1309G0221' => 'vmu', 'VMungo1309G2815' => 'vmu', 'VMungo1383G0239' => 'vmu', 'VMungo1383G2910' => 'vmu', 'Zm00001eb095270' => 'zma', 'Zm00001eb095280' => 'zma', 'Zm00001eb111630' => 'zma', 'Zm00001eb237080' => 'zma', 'Zm00001eb273740' => 'zma', 'Zm00001eb285040' => 'zma', 'Zm00001eb330790' => 'zma', 'Zm00001eb337380' => 'zma' ), 'gf_id' => 'HOM05D001484', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001484' ), 'data_identifier' => 'HOM05D001484', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001484', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p31500' => 'bna', 'A05p00020' => 'bna', 'A07p08820' => 'bna', 'Aa31LG4G3300' => 'aar', 'Aa31LG8G10030' => 'aar', 'Actinidia00731' => 'ach', 'Actinidia11473' => 'ach', 'Actinidia23469' => 'ach', 'Actinidia24318' => 'ach', 'Actinidia40196' => 'ach', 'Actinidia40197' => 'ach', 'Actinidia40198' => 'ach', 'Ah.08g212990' => 'amhyb', 'Ah.15g091720' => 'amhyb', 'AL3G38260' => 'aly', 'AL4G47710' => 'aly', 'Aqoxy2G00671' => 'aox', 'Aqoxy2G03236' => 'aox', 'arahy.Tifrunner.gnm1.ann1.05IDCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KR684' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATY3SJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK6QJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6APGL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IDT7Z9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM073U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ0R87' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LE7RV4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT4QRX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V5ENPK' => 'arhy', 'AT2G48110' => 'ath', 'AT3G23590' => 'ath', 'ATR0626G186' => 'atr', 'ATR1127G141' => 'atr', 'Atru.chr4.2583' => 'acertr', 'Atru.chr5.1358' => 'acertr', 'Atru.chr5.1359' => 'acertr', 'Atru.chr8.46' => 'acertr', 'AUR62002640' => 'cqu', 'AUR62030055' => 'cqu', 'AUR62033713' => 'cqu', 'AUR62033714' => 'cqu', 'AUR62036795' => 'cqu', 'AUR62039891' => 'cqu', 'BcaB02g08737' => 'bca', 'BcaB04g20441' => 'bca', 'BcaB06g26509' => 'bca', 'BcaB06g26510' => 'bca', 'BcaB06g26511' => 'bca', 'BcaB06g26512' => 'bca', 'BcaB06g26513' => 'bca', 'BcaC02g12564' => 'bca', 'BcaC02g12565' => 'bca', 'BcaC02g12794' => 'bca', 'BcaC02g12795' => 'bca', 'BcaC02g12796' => 'bca', 'BcaC06g35541' => 'bca', 'BNapus_Darmor_BZH_scaffold_188p00080' => 'bna', 'BNapus_Darmor_BZH_scaffold_188p00090' => 'bna', 'BolC1t03972H' => 'bol', 'BolC1t03973H' => 'bol', 'BolC4t21680H' => 'bol', 'BolC7t41863H' => 'bol', 'BolSC55t61227H' => 'bol', 'BolSC55t61228H' => 'bol', 'BraA01t03278Z' => 'bra', 'BraA05t18998Z' => 'bra', 'BraA07t28673Z' => 'bra', 'C01p40150' => 'bna', 'C05p12370' => 'bna', 'C07p13680' => 'bna', 'CAN.G1006.16' => 'can', 'CAN.G1006.17' => 'can', 'CAN.G1170.2' => 'can', 'CAN.G962.7' => 'can', 'CANSAT25G2179' => 'cansat', 'CANSAT78G1573' => 'cansat', 'CARHR099510' => 'chi', 'CARHR143510' => 'chi', 'Carub.0003s2380' => 'cru', 'Carub.0004s3082' => 'cru', 'Ca_00614_v3' => 'car', 'Ca_07801_v3' => 'car', 'Ca_08567_v3' => 'car', 'Ca_09571_v3' => 'car', 'CBR_g19290' => 'cbr', 'Cc01_g19770' => 'ccan', 'Cc03_g03030' => 'ccan', 'CDE07G0968' => 'cde', 'CDE09G1441' => 'cde', 'Cfa006103' => 'cfa', 'Cfa015573' => 'cfa', 'Cfa016988' => 'cfa', 'Ciclev10006738m.g' => 'ccl', 'Ciclev10010920m.g' => 'ccl', 'Ciclev10018517m.g' => 'ccl', 'CiPaw.01G159200' => 'cil', 'CiPaw.02G091000' => 'cil', 'CiPaw.02G091100' => 'cil', 'CiPaw.08G103100' => 'cil', 'CiPaw.09G224900' => 'cil', 'ClCG06G005740' => 'cla', 'ClCG07G000090' => 'cla', 'ClCG07G000100' => 'cla', 'COL.COLO4_09143' => 'col', 'COL.COLO4_25124' => 'col', 'Cpa.g.sc16.34' => 'cpa', 'Cpa.g.sc3504.1' => 'cpa', 'Cpa.g.sc60.37' => 'cpa', 'CsaV3_6G018520' => 'csa', 'CsaV3_6G036860' => 'csa', 'CSS0001072' => 'camsi', 'CSS0020208' => 'camsi', 'CSS0021253' => 'camsi', 'CSS0022190' => 'camsi', 'CSS0036150' => 'camsi', 'CSS0040442' => 'camsi', 'CSS0042300' => 'camsi', 'CSS0045298' => 'camsi', 'DCAR_012449' => 'dca', 'DCAR_018405' => 'dca', 'DCAR_024573' => 'dca', 'DCAR_030591' => 'dca', 'Dinv16926' => 'din', 'Dinv32963' => 'din', 'Dinv38382' => 'din', 'Dinv38383' => 'din', 'Duzib133G0974' => 'dzi', 'Duzib138G1867' => 'dzi', 'Duzib211G0420' => 'dzi', 'Duzib212G0930' => 'dzi', 'ECA234G1645' => 'eca', 'ECA247G3467' => 'eca', 'ECA248G1703' => 'eca', 'EL10Ac3g06327' => 'bvu', 'EL10Ac7g17204' => 'bvu', 'Eucgr.A00855' => 'egr', 'Eucgr.A00858' => 'egr', 'Eucgr.H01520' => 'egr', 'Eucgr.H03604' => 'egr', 'Eucgr.L03465' => 'egr', 'Eucgr.L03466' => 'egr', 'FAN01G0988' => 'fan', 'FAN02G3892' => 'fan', 'FAN05G3381' => 'fan', 'FAN07G0967' => 'fan', 'FAN07G1493' => 'fan', 'FAN08G3125' => 'fan', 'FAN09G0402' => 'fan', 'FAN12G2594' => 'fan', 'FAN12G3879' => 'fan', 'FAN14G1546' => 'fan', 'FAN15G3626' => 'fan', 'FAN17G0588' => 'fan', 'FAN17G0609' => 'fan', 'FAN18G2817' => 'fan', 'FAN19G1305' => 'fan', 'FAN20G1787' => 'fan', 'FAN22G0073' => 'fan', 'FAN22G0352' => 'fan', 'FAN22G0368' => 'fan', 'FAN22G2273' => 'fan', 'FAN24G1998' => 'fan', 'FAN27G1317' => 'fan', 'FvH4_2g23980' => 'fve', 'FvH4_4g14380' => 'fve', 'FvH4_4g14390' => 'fve', 'FvH4_6g09250' => 'fve', 'Glyma.03G151100' => 'gma', 'Glyma.04G122550' => 'gma', 'Glyma.05G001600' => 'gma', 'Glyma.09G270766' => 'gma', 'Glyma.09G270832' => 'gma', 'Glyma.13G209800' => 'gma', 'Glyma.15G102800' => 'gma', 'Glyma.18G218900' => 'gma', 'Glyma.19G001500' => 'gma', 'Glyma.19G153600' => 'gma', 'Gohir.A02G028600' => 'ghi', 'Gohir.A08G045000' => 'ghi', 'Gohir.A11G120500' => 'ghi', 'Gohir.A12G006200' => 'ghi', 'Gohir.A12G006250' => 'ghi', 'Gohir.D02G036300' => 'ghi', 'Gohir.D08G054700' => 'ghi', 'Gohir.D11G125600' => 'ghi', 'Gohir.D12G005700' => 'ghi', 'Gorai.004G055200' => 'gra', 'Gorai.005G040400' => 'gra', 'Gorai.007G134500' => 'gra', 'Gorai.008G005500' => 'gra', 'GSVIVG01011094001' => 'vvi', 'GSVIVG01017879001' => 'vvi', 'GSVIVG01025988001' => 'vvi', 'GSVIVG01029847001' => 'vvi', 'HanXRQChr10g0282901' => 'han', 'HanXRQChr10g0310371' => 'han', 'HanXRQChr10g0315041' => 'han', 'HanXRQChr11g0327651' => 'han', 'HanXRQChr12g0359391' => 'han', 'Haze_00972' => 'cav', 'Haze_00973' => 'cav', 'Haze_00974' => 'cav', 'Haze_04747' => 'cav', 'Haze_04749' => 'cav', 'Haze_04750' => 'cav', 'Haze_21217' => 'cav', 'Hma1.2p1_1037F.1_g250680' => 'hma', 'Hma1.2p1_1644F.1_g295320' => 'hma', 'HPP92_011322' => 'vpl', 'HPP92_011323' => 'vpl', 'HPP92_011324' => 'vpl', 'HPP92_011325' => 'vpl', 'HPP92_011326' => 'vpl', 'Hund12205' => 'sun', 'Hund17957' => 'sun', 'Lalb_Chr06g0176771' => 'lal', 'Lalb_Chr18g0056021' => 'lal', 'Lalb_Chr18g0056031' => 'lal', 'Lalb_Chr18g0056041' => 'lal', 'Lalb_Chr20g0107751' => 'lal', 'Lalb_Chr20g0118371' => 'lal', 'Lj1g0010239' => 'lja', 'Lj1g0017101' => 'lja', 'Lj2A1178G40' => 'lonja', 'Lj2A54G84' => 'lonja', 'Lj2g0015248' => 'lja', 'Lj3A761T51' => 'lonja', 'Lj6g0018116' => 'lja', 'Lsat_1_v5_gn_4_136040' => 'lsa', 'Lsat_1_v5_gn_5_187461' => 'lsa', 'Lsat_1_v5_gn_5_77001' => 'lsa', 'Lsat_1_v5_gn_9_4461' => 'lsa', 'Manes.01G210100' => 'mes', 'Manes.03G185600' => 'mes', 'Manes.05G073300' => 'mes', 'Manes.09G120300' => 'mes', 'Manes.15G022100' => 'mes', 'Mapoly0096s0053' => 'mpo', 'MBI03_g14058_MAGBIO' => 'mbi', 'MBI03_g33876_MAGBIO' => 'mbi', 'MBI03_g36854_MAGBIO' => 'mbi', 'MBI17_g11997_MAGBIO' => 'mbi', 'MD03G1269000' => 'mdo', 'MD04G1179600' => 'mdo', 'MD11G1289800' => 'mdo', 'MD12G1194700' => 'mdo', 'MD13G1182100' => 'mdo', 'MD13G1182200' => 'mdo', 'MD16G1182600' => 'mdo', 'Medtr2g021400' => 'mtr', 'Medtr2g021470' => 'mtr', 'Medtr2g105810' => 'mtr', 'Medtr3g033580' => 'mtr', 'Medtr6g007970' => 'mtr', 'Medtr7g056330' => 'mtr', 'Medtr7g074290' => 'mtr', 'Medtr7g074380' => 'mtr', 'Medtr7g094550' => 'mtr', 'Medtr8g069995' => 'mtr', 'MELO3C014345.2' => 'cme', 'MELO3C021395.2' => 'cme', 'Migut.D00262' => 'egut', 'Migut.G00257' => 'egut', 'MSTRG.21575' => 'ama', 'MSTRG.3985' => 'ama', 'Nitab4.5_0000295g0140' => 'nta', 'Nitab4.5_0000732g0140' => 'nta', 'Nitab4.5_0003162g0020' => 'nta', 'Nitab4.5_0006180g0090' => 'nta', 'Nitab4.5_0006390g0010' => 'nta', 'Nitab4.5_0007392g0040' => 'nta', 'Nn1g02140' => 'nnu', 'Nn4g26168' => 'nnu', 'Nn5g26754' => 'nnu', 'Oeu001433.1' => 'oeu', 'Oeu010299.2' => 'oeu', 'Oeu011171.1' => 'oeu', 'Oeu037675.1' => 'oeu', 'Oeu038359.1' => 'oeu', 'Oeu063834.1' => 'oeu', 'Oeu063835.1' => 'oeu', 'Os05g0312000' => 'osa', 'Os07g0211101' => 'osa', 'Os07g0211200' => 'osa', 'Os07g0681500' => 'osa', 'Peaxi162Scf00095g01015' => 'pax', 'Peaxi162Scf00104g00329' => 'pax', 'Peaxi162Scf00161g00137' => 'pax', 'PGR004G1665' => 'pgr', 'PGR031G2937' => 'pgr', 'PGR119G2145' => 'pgr', 'PGSC0003DMG400004351' => 'stu', 'PGSC0003DMG400014625' => 'stu', 'PGSC0003DMG401000943' => 'stu', 'Phvul.001G148600' => 'pvu', 'Phvul.004G001700' => 'pvu', 'Phvul.006G154900' => 'pvu', 'Phvul.008G078200' => 'pvu', 'Phvul.011G136500' => 'pvu', 'Potri.002G215600' => 'ptr', 'Potri.008G201600' => 'ptr', 'Potri.014G138400' => 'ptr', 'Potri.016G142500' => 'ptr', 'Pp3c16_10580' => 'ppa', 'Pp3c5_25280' => 'ppa', 'Prupe.1G150000' => 'ppe', 'Prupe.1G150100' => 'ppe', 'Prupe.6G299600' => 'ppe', 'Prupe.8G245000' => 'ppe', 'Psat0s4927g0040' => 'psa', 'Psat1g052080' => 'psa', 'Psat1g183800' => 'psa', 'Psat3g113840' => 'psa', 'Psat3g126120' => 'psa', 'Psat3g126160' => 'psa', 'Psat3g158760' => 'psa', 'Psat3g158840' => 'psa', 'PSO170G2858' => 'pso', 'PSO339G0606' => 'pso', 'PSO384G4709' => 'pso', 'PSO407G0334' => 'pso', 'QL04p040276' => 'qlo', 'QL06p005458' => 'qlo', 'QL06p005472' => 'qlo', 'QL07p030546' => 'qlo', 'QL07p031519' => 'qlo', 'QL09p050949' => 'qlo', 'QL09p050966' => 'qlo', 'QL09p051067' => 'qlo', 'QL12p022706' => 'qlo', 'RcHm_v2.0_Chr2g0119601' => 'rch', 'RcHm_v2.0_Chr3g0459591' => 'rch', 'RcHm_v2.0_Chr4g0418521' => 'rch', 'RcHm_v2.0_Chr4g0418531' => 'rch', 'RcHm_v2.0_Chr4g0418541' => 'rch', 'RcHm_v2.0_Chr6g0291641' => 'rch', 'Rhsim01G0086300' => 'rsi', 'Rhsim01G0276300' => 'rsi', 'Rhsim01G0276500' => 'rsi', 'Rhsim04G0207700' => 'rsi', 'Rhsim05G0234500' => 'rsi', 'Rhsim13G0022400' => 'rsi', 'Sabra02G0167900' => 'sbr', 'Sabra04G0158500' => 'sbr', 'Sabra08G0159800' => 'sbr', 'Sabra10G0011500' => 'sbr', 'Sabra14G0104400' => 'sbr', 'SalBow2G2440' => 'sbo', 'SalBow4G2265' => 'sbo', 'Sc02g0000060' => 'sci', 'Sc05g0005020' => 'sci', 'Sc13g0003890' => 'sci', 'Sed0014865' => 'sed', 'Sed0017224' => 'sed', 'Sed0026391' => 'sed', 'SEGI_00063' => 'sgi', 'SEGI_10967' => 'sgi', 'SEGI_17510' => 'sgi', 'SEGI_24396' => 'sgi', 'SEGI_39719' => 'sgi', 'SEGI_41392' => 'sgi', 'SGA_v2.0_scaffold11G05794' => 'sas', 'SGA_v2.0_scaffold142G35607' => 'sas', 'SGA_v2.0_scaffold1G00447' => 'sas', 'SHI15388' => 'shi', 'SHI15394' => 'shi', 'SHI15396' => 'shi', 'SHI15399' => 'shi', 'SMO343G0151' => 'smo', 'SMO367G1118' => 'smo', 'Solyc01g080200.3' => 'sly', 'Solyc06g008960.3' => 'sly', 'Solyc09g064780.3' => 'sly', 'Sopen01g031980' => 'spe', 'Sopen06g003710' => 'spe', 'Sopen09g026460' => 'spe', 'Sp3g21240' => 'spa', 'Sp4g30030' => 'spa', 'TAR365G0022' => 'tar', 'TAR365G1023' => 'tar', 'TAR365G1253' => 'tar', 'TAR623G0078' => 'tar', 'TAR623G1721' => 'tar', 'TAR633G0959' => 'tar', 'THA.LOC104802225' => 'tha', 'THA.LOC104804769' => 'tha', 'THA.LOC104808660' => 'tha', 'THA.LOC104812792' => 'tha', 'Thecc.01G284000' => 'tca', 'Thecc.04G220600' => 'tca', 'Thecc.05G268900' => 'tca', 'Thecc.08G171100' => 'tca', 'Thhalv10001284m.g' => 'esa', 'Thhalv10019912m.g' => 'esa', 'TPR.G14189' => 'tpr', 'TPR.G18110' => 'tpr', 'TPR.G18130' => 'tpr', 'TPR.G18131' => 'tpr', 'TPR.G18140' => 'tpr', 'TPR.G24282' => 'tpr', 'TPR.G25221' => 'tpr', 'TPR.G29267' => 'tpr', 'TPR.G35315' => 'tpr', 'TPR.G36173' => 'tpr', 'TWI09G0794' => 'twi', 'TWI59G1348' => 'twi', 'TWI74G0430' => 'twi', 'unitig_26.g8940' => 'ugi', 'unitig_749.g13744' => 'ugi', 'unitig_749.g13745' => 'ugi', 'vmacro08269' => 'vma', 'vmacro14937' => 'vma', 'vmacro20401' => 'vma', 'VMungo0464G1349' => 'vmu', 'VMungo0540G0289' => 'vmu', 'VMungo1215G1590' => 'vmu', 'VMungo1309G0221' => 'vmu', 'VMungo1309G2815' => 'vmu', 'VMungo1383G0239' => 'vmu', 'VMungo1383G2910' => 'vmu', 'Zm00001eb095270' => 'zma', 'Zm00001eb095280' => 'zma', 'Zm00001eb111630' => 'zma', 'Zm00001eb237080' => 'zma', 'Zm00001eb273740' => 'zma', 'Zm00001eb285040' => 'zma', 'Zm00001eb330790' => 'zma', 'Zm00001eb337380' => 'zma' ) $gf_id = 'HOM05D001484' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001484' ) $data_identifier = 'HOM05D001484' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 2, 'aly' => (int) 2, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 22, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 7, 'hma' => (int) 2, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 7, 'mtr' => (int) 10, 'cme' => (int) 2, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 4, 'ppa' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 4, 'qlo' => (int) 9, 'rch' => (int) 6, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 10, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 7, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb337380' $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' => 'HOM05D001484', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p31500' => 'bna', 'A05p00020' => 'bna', 'A07p08820' => 'bna', 'Aa31LG4G3300' => 'aar', 'Aa31LG8G10030' => 'aar', 'Actinidia00731' => 'ach', 'Actinidia11473' => 'ach', 'Actinidia23469' => 'ach', 'Actinidia24318' => 'ach', 'Actinidia40196' => 'ach', 'Actinidia40197' => 'ach', 'Actinidia40198' => 'ach', 'Ah.08g212990' => 'amhyb', 'Ah.15g091720' => 'amhyb', 'AL3G38260' => 'aly', 'AL4G47710' => 'aly', 'Aqoxy2G00671' => 'aox', 'Aqoxy2G03236' => 'aox', 'arahy.Tifrunner.gnm1.ann1.05IDCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KR684' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATY3SJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK6QJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6APGL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IDT7Z9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM073U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ0R87' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LE7RV4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT4QRX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V5ENPK' => 'arhy', 'AT2G48110' => 'ath', 'AT3G23590' => 'ath', 'ATR0626G186' => 'atr', 'ATR1127G141' => 'atr', 'Atru.chr4.2583' => 'acertr', 'Atru.chr5.1358' => 'acertr', 'Atru.chr5.1359' => 'acertr', 'Atru.chr8.46' => 'acertr', 'AUR62002640' => 'cqu', 'AUR62030055' => 'cqu', 'AUR62033713' => 'cqu', 'AUR62033714' => 'cqu', 'AUR62036795' => 'cqu', 'AUR62039891' => 'cqu', 'BcaB02g08737' => 'bca', 'BcaB04g20441' => 'bca', 'BcaB06g26509' => 'bca', 'BcaB06g26510' => 'bca', 'BcaB06g26511' => 'bca', 'BcaB06g26512' => 'bca', 'BcaB06g26513' => 'bca', 'BcaC02g12564' => 'bca', 'BcaC02g12565' => 'bca', 'BcaC02g12794' => 'bca', 'BcaC02g12795' => 'bca', 'BcaC02g12796' => 'bca', 'BcaC06g35541' => 'bca', 'BNapus_Darmor_BZH_scaffold_188p00080' => 'bna', 'BNapus_Darmor_BZH_scaffold_188p00090' => 'bna', 'BolC1t03972H' => 'bol', 'BolC1t03973H' => 'bol', 'BolC4t21680H' => 'bol', 'BolC7t41863H' => 'bol', 'BolSC55t61227H' => 'bol', 'BolSC55t61228H' => 'bol', 'BraA01t03278Z' => 'bra', 'BraA05t18998Z' => 'bra', 'BraA07t28673Z' => 'bra', 'C01p40150' => 'bna', 'C05p12370' => 'bna', 'C07p13680' => 'bna', 'CAN.G1006.16' => 'can', 'CAN.G1006.17' => 'can', 'CAN.G1170.2' => 'can', 'CAN.G962.7' => 'can', 'CANSAT25G2179' => 'cansat', 'CANSAT78G1573' => 'cansat', 'CARHR099510' => 'chi', 'CARHR143510' => 'chi', 'Carub.0003s2380' => 'cru', 'Carub.0004s3082' => 'cru', 'Ca_00614_v3' => 'car', 'Ca_07801_v3' => 'car', 'Ca_08567_v3' => 'car', 'Ca_09571_v3' => 'car', 'CBR_g19290' => 'cbr', 'Cc01_g19770' => 'ccan', 'Cc03_g03030' => 'ccan', 'CDE07G0968' => 'cde', 'CDE09G1441' => 'cde', 'Cfa006103' => 'cfa', 'Cfa015573' => 'cfa', 'Cfa016988' => 'cfa', 'Ciclev10006738m.g' => 'ccl', 'Ciclev10010920m.g' => 'ccl', 'Ciclev10018517m.g' => 'ccl', 'CiPaw.01G159200' => 'cil', 'CiPaw.02G091000' => 'cil', 'CiPaw.02G091100' => 'cil', 'CiPaw.08G103100' => 'cil', 'CiPaw.09G224900' => 'cil', 'ClCG06G005740' => 'cla', 'ClCG07G000090' => 'cla', 'ClCG07G000100' => 'cla', 'COL.COLO4_09143' => 'col', 'COL.COLO4_25124' => 'col', 'Cpa.g.sc16.34' => 'cpa', 'Cpa.g.sc3504.1' => 'cpa', 'Cpa.g.sc60.37' => 'cpa', 'CsaV3_6G018520' => 'csa', 'CsaV3_6G036860' => 'csa', 'CSS0001072' => 'camsi', 'CSS0020208' => 'camsi', 'CSS0021253' => 'camsi', 'CSS0022190' => 'camsi', 'CSS0036150' => 'camsi', 'CSS0040442' => 'camsi', 'CSS0042300' => 'camsi', 'CSS0045298' => 'camsi', 'DCAR_012449' => 'dca', 'DCAR_018405' => 'dca', 'DCAR_024573' => 'dca', 'DCAR_030591' => 'dca', 'Dinv16926' => 'din', 'Dinv32963' => 'din', 'Dinv38382' => 'din', 'Dinv38383' => 'din', 'Duzib133G0974' => 'dzi', 'Duzib138G1867' => 'dzi', 'Duzib211G0420' => 'dzi', 'Duzib212G0930' => 'dzi', 'ECA234G1645' => 'eca', 'ECA247G3467' => 'eca', 'ECA248G1703' => 'eca', 'EL10Ac3g06327' => 'bvu', 'EL10Ac7g17204' => 'bvu', 'Eucgr.A00855' => 'egr', 'Eucgr.A00858' => 'egr', 'Eucgr.H01520' => 'egr', 'Eucgr.H03604' => 'egr', 'Eucgr.L03465' => 'egr', 'Eucgr.L03466' => 'egr', 'FAN01G0988' => 'fan', 'FAN02G3892' => 'fan', 'FAN05G3381' => 'fan', 'FAN07G0967' => 'fan', 'FAN07G1493' => 'fan', 'FAN08G3125' => 'fan', 'FAN09G0402' => 'fan', 'FAN12G2594' => 'fan', 'FAN12G3879' => 'fan', 'FAN14G1546' => 'fan', 'FAN15G3626' => 'fan', 'FAN17G0588' => 'fan', 'FAN17G0609' => 'fan', 'FAN18G2817' => 'fan', 'FAN19G1305' => 'fan', 'FAN20G1787' => 'fan', 'FAN22G0073' => 'fan', 'FAN22G0352' => 'fan', 'FAN22G0368' => 'fan', 'FAN22G2273' => 'fan', 'FAN24G1998' => 'fan', 'FAN27G1317' => 'fan', 'FvH4_2g23980' => 'fve', 'FvH4_4g14380' => 'fve', 'FvH4_4g14390' => 'fve', 'FvH4_6g09250' => 'fve', 'Glyma.03G151100' => 'gma', 'Glyma.04G122550' => 'gma', 'Glyma.05G001600' => 'gma', 'Glyma.09G270766' => 'gma', 'Glyma.09G270832' => 'gma', 'Glyma.13G209800' => 'gma', 'Glyma.15G102800' => 'gma', 'Glyma.18G218900' => 'gma', 'Glyma.19G001500' => 'gma', 'Glyma.19G153600' => 'gma', 'Gohir.A02G028600' => 'ghi', 'Gohir.A08G045000' => 'ghi', 'Gohir.A11G120500' => 'ghi', 'Gohir.A12G006200' => 'ghi', 'Gohir.A12G006250' => 'ghi', 'Gohir.D02G036300' => 'ghi', 'Gohir.D08G054700' => 'ghi', 'Gohir.D11G125600' => 'ghi', 'Gohir.D12G005700' => 'ghi', 'Gorai.004G055200' => 'gra', 'Gorai.005G040400' => 'gra', 'Gorai.007G134500' => 'gra', 'Gorai.008G005500' => 'gra', 'GSVIVG01011094001' => 'vvi', 'GSVIVG01017879001' => 'vvi', 'GSVIVG01025988001' => 'vvi', 'GSVIVG01029847001' => 'vvi', 'HanXRQChr10g0282901' => 'han', 'HanXRQChr10g0310371' => 'han', 'HanXRQChr10g0315041' => 'han', 'HanXRQChr11g0327651' => 'han', 'HanXRQChr12g0359391' => 'han', 'Haze_00972' => 'cav', 'Haze_00973' => 'cav', 'Haze_00974' => 'cav', 'Haze_04747' => 'cav', 'Haze_04749' => 'cav', 'Haze_04750' => 'cav', 'Haze_21217' => 'cav', 'Hma1.2p1_1037F.1_g250680' => 'hma', 'Hma1.2p1_1644F.1_g295320' => 'hma', 'HPP92_011322' => 'vpl', 'HPP92_011323' => 'vpl', 'HPP92_011324' => 'vpl', 'HPP92_011325' => 'vpl', 'HPP92_011326' => 'vpl', 'Hund12205' => 'sun', 'Hund17957' => 'sun', 'Lalb_Chr06g0176771' => 'lal', 'Lalb_Chr18g0056021' => 'lal', 'Lalb_Chr18g0056031' => 'lal', 'Lalb_Chr18g0056041' => 'lal', 'Lalb_Chr20g0107751' => 'lal', 'Lalb_Chr20g0118371' => 'lal', 'Lj1g0010239' => 'lja', 'Lj1g0017101' => 'lja', 'Lj2A1178G40' => 'lonja', 'Lj2A54G84' => 'lonja', 'Lj2g0015248' => 'lja', 'Lj3A761T51' => 'lonja', 'Lj6g0018116' => 'lja', 'Lsat_1_v5_gn_4_136040' => 'lsa', 'Lsat_1_v5_gn_5_187461' => 'lsa', 'Lsat_1_v5_gn_5_77001' => 'lsa', 'Lsat_1_v5_gn_9_4461' => 'lsa', 'Manes.01G210100' => 'mes', 'Manes.03G185600' => 'mes', 'Manes.05G073300' => 'mes', 'Manes.09G120300' => 'mes', 'Manes.15G022100' => 'mes', 'Mapoly0096s0053' => 'mpo', 'MBI03_g14058_MAGBIO' => 'mbi', 'MBI03_g33876_MAGBIO' => 'mbi', 'MBI03_g36854_MAGBIO' => 'mbi', 'MBI17_g11997_MAGBIO' => 'mbi', 'MD03G1269000' => 'mdo', 'MD04G1179600' => 'mdo', 'MD11G1289800' => 'mdo', 'MD12G1194700' => 'mdo', 'MD13G1182100' => 'mdo', 'MD13G1182200' => 'mdo', 'MD16G1182600' => 'mdo', 'Medtr2g021400' => 'mtr', 'Medtr2g021470' => 'mtr', 'Medtr2g105810' => 'mtr', 'Medtr3g033580' => 'mtr', 'Medtr6g007970' => 'mtr', 'Medtr7g056330' => 'mtr', 'Medtr7g074290' => 'mtr', 'Medtr7g074380' => 'mtr', 'Medtr7g094550' => 'mtr', 'Medtr8g069995' => 'mtr', 'MELO3C014345.2' => 'cme', 'MELO3C021395.2' => 'cme', 'Migut.D00262' => 'egut', 'Migut.G00257' => 'egut', 'MSTRG.21575' => 'ama', 'MSTRG.3985' => 'ama', 'Nitab4.5_0000295g0140' => 'nta', 'Nitab4.5_0000732g0140' => 'nta', 'Nitab4.5_0003162g0020' => 'nta', 'Nitab4.5_0006180g0090' => 'nta', 'Nitab4.5_0006390g0010' => 'nta', 'Nitab4.5_0007392g0040' => 'nta', 'Nn1g02140' => 'nnu', 'Nn4g26168' => 'nnu', 'Nn5g26754' => 'nnu', 'Oeu001433.1' => 'oeu', 'Oeu010299.2' => 'oeu', 'Oeu011171.1' => 'oeu', 'Oeu037675.1' => 'oeu', 'Oeu038359.1' => 'oeu', 'Oeu063834.1' => 'oeu', 'Oeu063835.1' => 'oeu', 'Os05g0312000' => 'osa', 'Os07g0211101' => 'osa', 'Os07g0211200' => 'osa', 'Os07g0681500' => 'osa', 'Peaxi162Scf00095g01015' => 'pax', 'Peaxi162Scf00104g00329' => 'pax', 'Peaxi162Scf00161g00137' => 'pax', 'PGR004G1665' => 'pgr', 'PGR031G2937' => 'pgr', 'PGR119G2145' => 'pgr', 'PGSC0003DMG400004351' => 'stu', 'PGSC0003DMG400014625' => 'stu', 'PGSC0003DMG401000943' => 'stu', 'Phvul.001G148600' => 'pvu', 'Phvul.004G001700' => 'pvu', 'Phvul.006G154900' => 'pvu', 'Phvul.008G078200' => 'pvu', 'Phvul.011G136500' => 'pvu', 'Potri.002G215600' => 'ptr', 'Potri.008G201600' => 'ptr', 'Potri.014G138400' => 'ptr', 'Potri.016G142500' => 'ptr', 'Pp3c16_10580' => 'ppa', 'Pp3c5_25280' => 'ppa', 'Prupe.1G150000' => 'ppe', 'Prupe.1G150100' => 'ppe', 'Prupe.6G299600' => 'ppe', 'Prupe.8G245000' => 'ppe', 'Psat0s4927g0040' => 'psa', 'Psat1g052080' => 'psa', 'Psat1g183800' => 'psa', 'Psat3g113840' => 'psa', 'Psat3g126120' => 'psa', 'Psat3g126160' => 'psa', 'Psat3g158760' => 'psa', 'Psat3g158840' => 'psa', 'PSO170G2858' => 'pso', 'PSO339G0606' => 'pso', 'PSO384G4709' => 'pso', 'PSO407G0334' => 'pso', 'QL04p040276' => 'qlo', 'QL06p005458' => 'qlo', 'QL06p005472' => 'qlo', 'QL07p030546' => 'qlo', 'QL07p031519' => 'qlo', 'QL09p050949' => 'qlo', 'QL09p050966' => 'qlo', 'QL09p051067' => 'qlo', 'QL12p022706' => 'qlo', 'RcHm_v2.0_Chr2g0119601' => 'rch', 'RcHm_v2.0_Chr3g0459591' => 'rch', 'RcHm_v2.0_Chr4g0418521' => 'rch', 'RcHm_v2.0_Chr4g0418531' => 'rch', 'RcHm_v2.0_Chr4g0418541' => 'rch', 'RcHm_v2.0_Chr6g0291641' => 'rch', 'Rhsim01G0086300' => 'rsi', 'Rhsim01G0276300' => 'rsi', 'Rhsim01G0276500' => 'rsi', 'Rhsim04G0207700' => 'rsi', 'Rhsim05G0234500' => 'rsi', 'Rhsim13G0022400' => 'rsi', 'Sabra02G0167900' => 'sbr', 'Sabra04G0158500' => 'sbr', 'Sabra08G0159800' => 'sbr', 'Sabra10G0011500' => 'sbr', 'Sabra14G0104400' => 'sbr', 'SalBow2G2440' => 'sbo', 'SalBow4G2265' => 'sbo', 'Sc02g0000060' => 'sci', 'Sc05g0005020' => 'sci', 'Sc13g0003890' => 'sci', 'Sed0014865' => 'sed', 'Sed0017224' => 'sed', 'Sed0026391' => 'sed', 'SEGI_00063' => 'sgi', 'SEGI_10967' => 'sgi', 'SEGI_17510' => 'sgi', 'SEGI_24396' => 'sgi', 'SEGI_39719' => 'sgi', 'SEGI_41392' => 'sgi', 'SGA_v2.0_scaffold11G05794' => 'sas', 'SGA_v2.0_scaffold142G35607' => 'sas', 'SGA_v2.0_scaffold1G00447' => 'sas', 'SHI15388' => 'shi', 'SHI15394' => 'shi', 'SHI15396' => 'shi', 'SHI15399' => 'shi', 'SMO343G0151' => 'smo', 'SMO367G1118' => 'smo', 'Solyc01g080200.3' => 'sly', 'Solyc06g008960.3' => 'sly', 'Solyc09g064780.3' => 'sly', 'Sopen01g031980' => 'spe', 'Sopen06g003710' => 'spe', 'Sopen09g026460' => 'spe', 'Sp3g21240' => 'spa', 'Sp4g30030' => 'spa', 'TAR365G0022' => 'tar', 'TAR365G1023' => 'tar', 'TAR365G1253' => 'tar', 'TAR623G0078' => 'tar', 'TAR623G1721' => 'tar', 'TAR633G0959' => 'tar', 'THA.LOC104802225' => 'tha', 'THA.LOC104804769' => 'tha', 'THA.LOC104808660' => 'tha', 'THA.LOC104812792' => 'tha', 'Thecc.01G284000' => 'tca', 'Thecc.04G220600' => 'tca', 'Thecc.05G268900' => 'tca', 'Thecc.08G171100' => 'tca', 'Thhalv10001284m.g' => 'esa', 'Thhalv10019912m.g' => 'esa', 'TPR.G14189' => 'tpr', 'TPR.G18110' => 'tpr', 'TPR.G18130' => 'tpr', 'TPR.G18131' => 'tpr', 'TPR.G18140' => 'tpr', 'TPR.G24282' => 'tpr', 'TPR.G25221' => 'tpr', 'TPR.G29267' => 'tpr', 'TPR.G35315' => 'tpr', 'TPR.G36173' => 'tpr', 'TWI09G0794' => 'twi', 'TWI59G1348' => 'twi', 'TWI74G0430' => 'twi', 'unitig_26.g8940' => 'ugi', 'unitig_749.g13744' => 'ugi', 'unitig_749.g13745' => 'ugi', 'vmacro08269' => 'vma', 'vmacro14937' => 'vma', 'vmacro20401' => 'vma', 'VMungo0464G1349' => 'vmu', 'VMungo0540G0289' => 'vmu', 'VMungo1215G1590' => 'vmu', 'VMungo1309G0221' => 'vmu', 'VMungo1309G2815' => 'vmu', 'VMungo1383G0239' => 'vmu', 'VMungo1383G2910' => 'vmu', 'Zm00001eb095270' => 'zma', 'Zm00001eb095280' => 'zma', 'Zm00001eb111630' => 'zma', 'Zm00001eb237080' => 'zma', 'Zm00001eb273740' => 'zma', 'Zm00001eb285040' => 'zma', 'Zm00001eb330790' => 'zma', 'Zm00001eb337380' => 'zma' ), 'gf_id' => 'HOM05D001484', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001484' ), 'data_identifier' => 'HOM05D001484', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001484', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p31500' => 'bna', 'A05p00020' => 'bna', 'A07p08820' => 'bna', 'Aa31LG4G3300' => 'aar', 'Aa31LG8G10030' => 'aar', 'Actinidia00731' => 'ach', 'Actinidia11473' => 'ach', 'Actinidia23469' => 'ach', 'Actinidia24318' => 'ach', 'Actinidia40196' => 'ach', 'Actinidia40197' => 'ach', 'Actinidia40198' => 'ach', 'Ah.08g212990' => 'amhyb', 'Ah.15g091720' => 'amhyb', 'AL3G38260' => 'aly', 'AL4G47710' => 'aly', 'Aqoxy2G00671' => 'aox', 'Aqoxy2G03236' => 'aox', 'arahy.Tifrunner.gnm1.ann1.05IDCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KR684' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATY3SJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK6QJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6APGL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IDT7Z9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM073U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ0R87' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LE7RV4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT4QRX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V5ENPK' => 'arhy', 'AT2G48110' => 'ath', 'AT3G23590' => 'ath', 'ATR0626G186' => 'atr', 'ATR1127G141' => 'atr', 'Atru.chr4.2583' => 'acertr', 'Atru.chr5.1358' => 'acertr', 'Atru.chr5.1359' => 'acertr', 'Atru.chr8.46' => 'acertr', 'AUR62002640' => 'cqu', 'AUR62030055' => 'cqu', 'AUR62033713' => 'cqu', 'AUR62033714' => 'cqu', 'AUR62036795' => 'cqu', 'AUR62039891' => 'cqu', 'BcaB02g08737' => 'bca', 'BcaB04g20441' => 'bca', 'BcaB06g26509' => 'bca', 'BcaB06g26510' => 'bca', 'BcaB06g26511' => 'bca', 'BcaB06g26512' => 'bca', 'BcaB06g26513' => 'bca', 'BcaC02g12564' => 'bca', 'BcaC02g12565' => 'bca', 'BcaC02g12794' => 'bca', 'BcaC02g12795' => 'bca', 'BcaC02g12796' => 'bca', 'BcaC06g35541' => 'bca', 'BNapus_Darmor_BZH_scaffold_188p00080' => 'bna', 'BNapus_Darmor_BZH_scaffold_188p00090' => 'bna', 'BolC1t03972H' => 'bol', 'BolC1t03973H' => 'bol', 'BolC4t21680H' => 'bol', 'BolC7t41863H' => 'bol', 'BolSC55t61227H' => 'bol', 'BolSC55t61228H' => 'bol', 'BraA01t03278Z' => 'bra', 'BraA05t18998Z' => 'bra', 'BraA07t28673Z' => 'bra', 'C01p40150' => 'bna', 'C05p12370' => 'bna', 'C07p13680' => 'bna', 'CAN.G1006.16' => 'can', 'CAN.G1006.17' => 'can', 'CAN.G1170.2' => 'can', 'CAN.G962.7' => 'can', 'CANSAT25G2179' => 'cansat', 'CANSAT78G1573' => 'cansat', 'CARHR099510' => 'chi', 'CARHR143510' => 'chi', 'Carub.0003s2380' => 'cru', 'Carub.0004s3082' => 'cru', 'Ca_00614_v3' => 'car', 'Ca_07801_v3' => 'car', 'Ca_08567_v3' => 'car', 'Ca_09571_v3' => 'car', 'CBR_g19290' => 'cbr', 'Cc01_g19770' => 'ccan', 'Cc03_g03030' => 'ccan', 'CDE07G0968' => 'cde', 'CDE09G1441' => 'cde', 'Cfa006103' => 'cfa', 'Cfa015573' => 'cfa', 'Cfa016988' => 'cfa', 'Ciclev10006738m.g' => 'ccl', 'Ciclev10010920m.g' => 'ccl', 'Ciclev10018517m.g' => 'ccl', 'CiPaw.01G159200' => 'cil', 'CiPaw.02G091000' => 'cil', 'CiPaw.02G091100' => 'cil', 'CiPaw.08G103100' => 'cil', 'CiPaw.09G224900' => 'cil', 'ClCG06G005740' => 'cla', 'ClCG07G000090' => 'cla', 'ClCG07G000100' => 'cla', 'COL.COLO4_09143' => 'col', 'COL.COLO4_25124' => 'col', 'Cpa.g.sc16.34' => 'cpa', 'Cpa.g.sc3504.1' => 'cpa', 'Cpa.g.sc60.37' => 'cpa', 'CsaV3_6G018520' => 'csa', 'CsaV3_6G036860' => 'csa', 'CSS0001072' => 'camsi', 'CSS0020208' => 'camsi', 'CSS0021253' => 'camsi', 'CSS0022190' => 'camsi', 'CSS0036150' => 'camsi', 'CSS0040442' => 'camsi', 'CSS0042300' => 'camsi', 'CSS0045298' => 'camsi', 'DCAR_012449' => 'dca', 'DCAR_018405' => 'dca', 'DCAR_024573' => 'dca', 'DCAR_030591' => 'dca', 'Dinv16926' => 'din', 'Dinv32963' => 'din', 'Dinv38382' => 'din', 'Dinv38383' => 'din', 'Duzib133G0974' => 'dzi', 'Duzib138G1867' => 'dzi', 'Duzib211G0420' => 'dzi', 'Duzib212G0930' => 'dzi', 'ECA234G1645' => 'eca', 'ECA247G3467' => 'eca', 'ECA248G1703' => 'eca', 'EL10Ac3g06327' => 'bvu', 'EL10Ac7g17204' => 'bvu', 'Eucgr.A00855' => 'egr', 'Eucgr.A00858' => 'egr', 'Eucgr.H01520' => 'egr', 'Eucgr.H03604' => 'egr', 'Eucgr.L03465' => 'egr', 'Eucgr.L03466' => 'egr', 'FAN01G0988' => 'fan', 'FAN02G3892' => 'fan', 'FAN05G3381' => 'fan', 'FAN07G0967' => 'fan', 'FAN07G1493' => 'fan', 'FAN08G3125' => 'fan', 'FAN09G0402' => 'fan', 'FAN12G2594' => 'fan', 'FAN12G3879' => 'fan', 'FAN14G1546' => 'fan', 'FAN15G3626' => 'fan', 'FAN17G0588' => 'fan', 'FAN17G0609' => 'fan', 'FAN18G2817' => 'fan', 'FAN19G1305' => 'fan', 'FAN20G1787' => 'fan', 'FAN22G0073' => 'fan', 'FAN22G0352' => 'fan', 'FAN22G0368' => 'fan', 'FAN22G2273' => 'fan', 'FAN24G1998' => 'fan', 'FAN27G1317' => 'fan', 'FvH4_2g23980' => 'fve', 'FvH4_4g14380' => 'fve', 'FvH4_4g14390' => 'fve', 'FvH4_6g09250' => 'fve', 'Glyma.03G151100' => 'gma', 'Glyma.04G122550' => 'gma', 'Glyma.05G001600' => 'gma', 'Glyma.09G270766' => 'gma', 'Glyma.09G270832' => 'gma', 'Glyma.13G209800' => 'gma', 'Glyma.15G102800' => 'gma', 'Glyma.18G218900' => 'gma', 'Glyma.19G001500' => 'gma', 'Glyma.19G153600' => 'gma', 'Gohir.A02G028600' => 'ghi', 'Gohir.A08G045000' => 'ghi', 'Gohir.A11G120500' => 'ghi', 'Gohir.A12G006200' => 'ghi', 'Gohir.A12G006250' => 'ghi', 'Gohir.D02G036300' => 'ghi', 'Gohir.D08G054700' => 'ghi', 'Gohir.D11G125600' => 'ghi', 'Gohir.D12G005700' => 'ghi', 'Gorai.004G055200' => 'gra', 'Gorai.005G040400' => 'gra', 'Gorai.007G134500' => 'gra', 'Gorai.008G005500' => 'gra', 'GSVIVG01011094001' => 'vvi', 'GSVIVG01017879001' => 'vvi', 'GSVIVG01025988001' => 'vvi', 'GSVIVG01029847001' => 'vvi', 'HanXRQChr10g0282901' => 'han', 'HanXRQChr10g0310371' => 'han', 'HanXRQChr10g0315041' => 'han', 'HanXRQChr11g0327651' => 'han', 'HanXRQChr12g0359391' => 'han', 'Haze_00972' => 'cav', 'Haze_00973' => 'cav', 'Haze_00974' => 'cav', 'Haze_04747' => 'cav', 'Haze_04749' => 'cav', 'Haze_04750' => 'cav', 'Haze_21217' => 'cav', 'Hma1.2p1_1037F.1_g250680' => 'hma', 'Hma1.2p1_1644F.1_g295320' => 'hma', 'HPP92_011322' => 'vpl', 'HPP92_011323' => 'vpl', 'HPP92_011324' => 'vpl', 'HPP92_011325' => 'vpl', 'HPP92_011326' => 'vpl', 'Hund12205' => 'sun', 'Hund17957' => 'sun', 'Lalb_Chr06g0176771' => 'lal', 'Lalb_Chr18g0056021' => 'lal', 'Lalb_Chr18g0056031' => 'lal', 'Lalb_Chr18g0056041' => 'lal', 'Lalb_Chr20g0107751' => 'lal', 'Lalb_Chr20g0118371' => 'lal', 'Lj1g0010239' => 'lja', 'Lj1g0017101' => 'lja', 'Lj2A1178G40' => 'lonja', 'Lj2A54G84' => 'lonja', 'Lj2g0015248' => 'lja', 'Lj3A761T51' => 'lonja', 'Lj6g0018116' => 'lja', 'Lsat_1_v5_gn_4_136040' => 'lsa', 'Lsat_1_v5_gn_5_187461' => 'lsa', 'Lsat_1_v5_gn_5_77001' => 'lsa', 'Lsat_1_v5_gn_9_4461' => 'lsa', 'Manes.01G210100' => 'mes', 'Manes.03G185600' => 'mes', 'Manes.05G073300' => 'mes', 'Manes.09G120300' => 'mes', 'Manes.15G022100' => 'mes', 'Mapoly0096s0053' => 'mpo', 'MBI03_g14058_MAGBIO' => 'mbi', 'MBI03_g33876_MAGBIO' => 'mbi', 'MBI03_g36854_MAGBIO' => 'mbi', 'MBI17_g11997_MAGBIO' => 'mbi', 'MD03G1269000' => 'mdo', 'MD04G1179600' => 'mdo', 'MD11G1289800' => 'mdo', 'MD12G1194700' => 'mdo', 'MD13G1182100' => 'mdo', 'MD13G1182200' => 'mdo', 'MD16G1182600' => 'mdo', 'Medtr2g021400' => 'mtr', 'Medtr2g021470' => 'mtr', 'Medtr2g105810' => 'mtr', 'Medtr3g033580' => 'mtr', 'Medtr6g007970' => 'mtr', 'Medtr7g056330' => 'mtr', 'Medtr7g074290' => 'mtr', 'Medtr7g074380' => 'mtr', 'Medtr7g094550' => 'mtr', 'Medtr8g069995' => 'mtr', 'MELO3C014345.2' => 'cme', 'MELO3C021395.2' => 'cme', 'Migut.D00262' => 'egut', 'Migut.G00257' => 'egut', 'MSTRG.21575' => 'ama', 'MSTRG.3985' => 'ama', 'Nitab4.5_0000295g0140' => 'nta', 'Nitab4.5_0000732g0140' => 'nta', 'Nitab4.5_0003162g0020' => 'nta', 'Nitab4.5_0006180g0090' => 'nta', 'Nitab4.5_0006390g0010' => 'nta', 'Nitab4.5_0007392g0040' => 'nta', 'Nn1g02140' => 'nnu', 'Nn4g26168' => 'nnu', 'Nn5g26754' => 'nnu', 'Oeu001433.1' => 'oeu', 'Oeu010299.2' => 'oeu', 'Oeu011171.1' => 'oeu', 'Oeu037675.1' => 'oeu', 'Oeu038359.1' => 'oeu', 'Oeu063834.1' => 'oeu', 'Oeu063835.1' => 'oeu', 'Os05g0312000' => 'osa', 'Os07g0211101' => 'osa', 'Os07g0211200' => 'osa', 'Os07g0681500' => 'osa', 'Peaxi162Scf00095g01015' => 'pax', 'Peaxi162Scf00104g00329' => 'pax', 'Peaxi162Scf00161g00137' => 'pax', 'PGR004G1665' => 'pgr', 'PGR031G2937' => 'pgr', 'PGR119G2145' => 'pgr', 'PGSC0003DMG400004351' => 'stu', 'PGSC0003DMG400014625' => 'stu', 'PGSC0003DMG401000943' => 'stu', 'Phvul.001G148600' => 'pvu', 'Phvul.004G001700' => 'pvu', 'Phvul.006G154900' => 'pvu', 'Phvul.008G078200' => 'pvu', 'Phvul.011G136500' => 'pvu', 'Potri.002G215600' => 'ptr', 'Potri.008G201600' => 'ptr', 'Potri.014G138400' => 'ptr', 'Potri.016G142500' => 'ptr', 'Pp3c16_10580' => 'ppa', 'Pp3c5_25280' => 'ppa', 'Prupe.1G150000' => 'ppe', 'Prupe.1G150100' => 'ppe', 'Prupe.6G299600' => 'ppe', 'Prupe.8G245000' => 'ppe', 'Psat0s4927g0040' => 'psa', 'Psat1g052080' => 'psa', 'Psat1g183800' => 'psa', 'Psat3g113840' => 'psa', 'Psat3g126120' => 'psa', 'Psat3g126160' => 'psa', 'Psat3g158760' => 'psa', 'Psat3g158840' => 'psa', 'PSO170G2858' => 'pso', 'PSO339G0606' => 'pso', 'PSO384G4709' => 'pso', 'PSO407G0334' => 'pso', 'QL04p040276' => 'qlo', 'QL06p005458' => 'qlo', 'QL06p005472' => 'qlo', 'QL07p030546' => 'qlo', 'QL07p031519' => 'qlo', 'QL09p050949' => 'qlo', 'QL09p050966' => 'qlo', 'QL09p051067' => 'qlo', 'QL12p022706' => 'qlo', 'RcHm_v2.0_Chr2g0119601' => 'rch', 'RcHm_v2.0_Chr3g0459591' => 'rch', 'RcHm_v2.0_Chr4g0418521' => 'rch', 'RcHm_v2.0_Chr4g0418531' => 'rch', 'RcHm_v2.0_Chr4g0418541' => 'rch', 'RcHm_v2.0_Chr6g0291641' => 'rch', 'Rhsim01G0086300' => 'rsi', 'Rhsim01G0276300' => 'rsi', 'Rhsim01G0276500' => 'rsi', 'Rhsim04G0207700' => 'rsi', 'Rhsim05G0234500' => 'rsi', 'Rhsim13G0022400' => 'rsi', 'Sabra02G0167900' => 'sbr', 'Sabra04G0158500' => 'sbr', 'Sabra08G0159800' => 'sbr', 'Sabra10G0011500' => 'sbr', 'Sabra14G0104400' => 'sbr', 'SalBow2G2440' => 'sbo', 'SalBow4G2265' => 'sbo', 'Sc02g0000060' => 'sci', 'Sc05g0005020' => 'sci', 'Sc13g0003890' => 'sci', 'Sed0014865' => 'sed', 'Sed0017224' => 'sed', 'Sed0026391' => 'sed', 'SEGI_00063' => 'sgi', 'SEGI_10967' => 'sgi', 'SEGI_17510' => 'sgi', 'SEGI_24396' => 'sgi', 'SEGI_39719' => 'sgi', 'SEGI_41392' => 'sgi', 'SGA_v2.0_scaffold11G05794' => 'sas', 'SGA_v2.0_scaffold142G35607' => 'sas', 'SGA_v2.0_scaffold1G00447' => 'sas', 'SHI15388' => 'shi', 'SHI15394' => 'shi', 'SHI15396' => 'shi', 'SHI15399' => 'shi', 'SMO343G0151' => 'smo', 'SMO367G1118' => 'smo', 'Solyc01g080200.3' => 'sly', 'Solyc06g008960.3' => 'sly', 'Solyc09g064780.3' => 'sly', 'Sopen01g031980' => 'spe', 'Sopen06g003710' => 'spe', 'Sopen09g026460' => 'spe', 'Sp3g21240' => 'spa', 'Sp4g30030' => 'spa', 'TAR365G0022' => 'tar', 'TAR365G1023' => 'tar', 'TAR365G1253' => 'tar', 'TAR623G0078' => 'tar', 'TAR623G1721' => 'tar', 'TAR633G0959' => 'tar', 'THA.LOC104802225' => 'tha', 'THA.LOC104804769' => 'tha', 'THA.LOC104808660' => 'tha', 'THA.LOC104812792' => 'tha', 'Thecc.01G284000' => 'tca', 'Thecc.04G220600' => 'tca', 'Thecc.05G268900' => 'tca', 'Thecc.08G171100' => 'tca', 'Thhalv10001284m.g' => 'esa', 'Thhalv10019912m.g' => 'esa', 'TPR.G14189' => 'tpr', 'TPR.G18110' => 'tpr', 'TPR.G18130' => 'tpr', 'TPR.G18131' => 'tpr', 'TPR.G18140' => 'tpr', 'TPR.G24282' => 'tpr', 'TPR.G25221' => 'tpr', 'TPR.G29267' => 'tpr', 'TPR.G35315' => 'tpr', 'TPR.G36173' => 'tpr', 'TWI09G0794' => 'twi', 'TWI59G1348' => 'twi', 'TWI74G0430' => 'twi', 'unitig_26.g8940' => 'ugi', 'unitig_749.g13744' => 'ugi', 'unitig_749.g13745' => 'ugi', 'vmacro08269' => 'vma', 'vmacro14937' => 'vma', 'vmacro20401' => 'vma', 'VMungo0464G1349' => 'vmu', 'VMungo0540G0289' => 'vmu', 'VMungo1215G1590' => 'vmu', 'VMungo1309G0221' => 'vmu', 'VMungo1309G2815' => 'vmu', 'VMungo1383G0239' => 'vmu', 'VMungo1383G2910' => 'vmu', 'Zm00001eb095270' => 'zma', 'Zm00001eb095280' => 'zma', 'Zm00001eb111630' => 'zma', 'Zm00001eb237080' => 'zma', 'Zm00001eb273740' => 'zma', 'Zm00001eb285040' => 'zma', 'Zm00001eb330790' => 'zma', 'Zm00001eb337380' => 'zma' ) $gf_id = 'HOM05D001484' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001484' ) $data_identifier = 'HOM05D001484' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 2, 'aly' => (int) 2, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 22, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 7, 'hma' => (int) 2, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 7, 'mtr' => (int) 10, 'cme' => (int) 2, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 4, 'ppa' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 4, 'qlo' => (int) 9, 'rch' => (int) 6, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 10, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 7, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb337380' $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' => 'HOM05D001484', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p31500' => 'bna', 'A05p00020' => 'bna', 'A07p08820' => 'bna', 'Aa31LG4G3300' => 'aar', 'Aa31LG8G10030' => 'aar', 'Actinidia00731' => 'ach', 'Actinidia11473' => 'ach', 'Actinidia23469' => 'ach', 'Actinidia24318' => 'ach', 'Actinidia40196' => 'ach', 'Actinidia40197' => 'ach', 'Actinidia40198' => 'ach', 'Ah.08g212990' => 'amhyb', 'Ah.15g091720' => 'amhyb', 'AL3G38260' => 'aly', 'AL4G47710' => 'aly', 'Aqoxy2G00671' => 'aox', 'Aqoxy2G03236' => 'aox', 'arahy.Tifrunner.gnm1.ann1.05IDCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KR684' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATY3SJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK6QJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6APGL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IDT7Z9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM073U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ0R87' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LE7RV4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT4QRX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V5ENPK' => 'arhy', 'AT2G48110' => 'ath', 'AT3G23590' => 'ath', 'ATR0626G186' => 'atr', 'ATR1127G141' => 'atr', 'Atru.chr4.2583' => 'acertr', 'Atru.chr5.1358' => 'acertr', 'Atru.chr5.1359' => 'acertr', 'Atru.chr8.46' => 'acertr', 'AUR62002640' => 'cqu', 'AUR62030055' => 'cqu', 'AUR62033713' => 'cqu', 'AUR62033714' => 'cqu', 'AUR62036795' => 'cqu', 'AUR62039891' => 'cqu', 'BcaB02g08737' => 'bca', 'BcaB04g20441' => 'bca', 'BcaB06g26509' => 'bca', 'BcaB06g26510' => 'bca', 'BcaB06g26511' => 'bca', 'BcaB06g26512' => 'bca', 'BcaB06g26513' => 'bca', 'BcaC02g12564' => 'bca', 'BcaC02g12565' => 'bca', 'BcaC02g12794' => 'bca', 'BcaC02g12795' => 'bca', 'BcaC02g12796' => 'bca', 'BcaC06g35541' => 'bca', 'BNapus_Darmor_BZH_scaffold_188p00080' => 'bna', 'BNapus_Darmor_BZH_scaffold_188p00090' => 'bna', 'BolC1t03972H' => 'bol', 'BolC1t03973H' => 'bol', 'BolC4t21680H' => 'bol', 'BolC7t41863H' => 'bol', 'BolSC55t61227H' => 'bol', 'BolSC55t61228H' => 'bol', 'BraA01t03278Z' => 'bra', 'BraA05t18998Z' => 'bra', 'BraA07t28673Z' => 'bra', 'C01p40150' => 'bna', 'C05p12370' => 'bna', 'C07p13680' => 'bna', 'CAN.G1006.16' => 'can', 'CAN.G1006.17' => 'can', 'CAN.G1170.2' => 'can', 'CAN.G962.7' => 'can', 'CANSAT25G2179' => 'cansat', 'CANSAT78G1573' => 'cansat', 'CARHR099510' => 'chi', 'CARHR143510' => 'chi', 'Carub.0003s2380' => 'cru', 'Carub.0004s3082' => 'cru', 'Ca_00614_v3' => 'car', 'Ca_07801_v3' => 'car', 'Ca_08567_v3' => 'car', 'Ca_09571_v3' => 'car', 'CBR_g19290' => 'cbr', 'Cc01_g19770' => 'ccan', 'Cc03_g03030' => 'ccan', 'CDE07G0968' => 'cde', 'CDE09G1441' => 'cde', 'Cfa006103' => 'cfa', 'Cfa015573' => 'cfa', 'Cfa016988' => 'cfa', 'Ciclev10006738m.g' => 'ccl', 'Ciclev10010920m.g' => 'ccl', 'Ciclev10018517m.g' => 'ccl', 'CiPaw.01G159200' => 'cil', 'CiPaw.02G091000' => 'cil', 'CiPaw.02G091100' => 'cil', 'CiPaw.08G103100' => 'cil', 'CiPaw.09G224900' => 'cil', 'ClCG06G005740' => 'cla', 'ClCG07G000090' => 'cla', 'ClCG07G000100' => 'cla', 'COL.COLO4_09143' => 'col', 'COL.COLO4_25124' => 'col', 'Cpa.g.sc16.34' => 'cpa', 'Cpa.g.sc3504.1' => 'cpa', 'Cpa.g.sc60.37' => 'cpa', 'CsaV3_6G018520' => 'csa', 'CsaV3_6G036860' => 'csa', 'CSS0001072' => 'camsi', 'CSS0020208' => 'camsi', 'CSS0021253' => 'camsi', 'CSS0022190' => 'camsi', 'CSS0036150' => 'camsi', 'CSS0040442' => 'camsi', 'CSS0042300' => 'camsi', 'CSS0045298' => 'camsi', 'DCAR_012449' => 'dca', 'DCAR_018405' => 'dca', 'DCAR_024573' => 'dca', 'DCAR_030591' => 'dca', 'Dinv16926' => 'din', 'Dinv32963' => 'din', 'Dinv38382' => 'din', 'Dinv38383' => 'din', 'Duzib133G0974' => 'dzi', 'Duzib138G1867' => 'dzi', 'Duzib211G0420' => 'dzi', 'Duzib212G0930' => 'dzi', 'ECA234G1645' => 'eca', 'ECA247G3467' => 'eca', 'ECA248G1703' => 'eca', 'EL10Ac3g06327' => 'bvu', 'EL10Ac7g17204' => 'bvu', 'Eucgr.A00855' => 'egr', 'Eucgr.A00858' => 'egr', 'Eucgr.H01520' => 'egr', 'Eucgr.H03604' => 'egr', 'Eucgr.L03465' => 'egr', 'Eucgr.L03466' => 'egr', 'FAN01G0988' => 'fan', 'FAN02G3892' => 'fan', 'FAN05G3381' => 'fan', 'FAN07G0967' => 'fan', 'FAN07G1493' => 'fan', 'FAN08G3125' => 'fan', 'FAN09G0402' => 'fan', 'FAN12G2594' => 'fan', 'FAN12G3879' => 'fan', 'FAN14G1546' => 'fan', 'FAN15G3626' => 'fan', 'FAN17G0588' => 'fan', 'FAN17G0609' => 'fan', 'FAN18G2817' => 'fan', 'FAN19G1305' => 'fan', 'FAN20G1787' => 'fan', 'FAN22G0073' => 'fan', 'FAN22G0352' => 'fan', 'FAN22G0368' => 'fan', 'FAN22G2273' => 'fan', 'FAN24G1998' => 'fan', 'FAN27G1317' => 'fan', 'FvH4_2g23980' => 'fve', 'FvH4_4g14380' => 'fve', 'FvH4_4g14390' => 'fve', 'FvH4_6g09250' => 'fve', 'Glyma.03G151100' => 'gma', 'Glyma.04G122550' => 'gma', 'Glyma.05G001600' => 'gma', 'Glyma.09G270766' => 'gma', 'Glyma.09G270832' => 'gma', 'Glyma.13G209800' => 'gma', 'Glyma.15G102800' => 'gma', 'Glyma.18G218900' => 'gma', 'Glyma.19G001500' => 'gma', 'Glyma.19G153600' => 'gma', 'Gohir.A02G028600' => 'ghi', 'Gohir.A08G045000' => 'ghi', 'Gohir.A11G120500' => 'ghi', 'Gohir.A12G006200' => 'ghi', 'Gohir.A12G006250' => 'ghi', 'Gohir.D02G036300' => 'ghi', 'Gohir.D08G054700' => 'ghi', 'Gohir.D11G125600' => 'ghi', 'Gohir.D12G005700' => 'ghi', 'Gorai.004G055200' => 'gra', 'Gorai.005G040400' => 'gra', 'Gorai.007G134500' => 'gra', 'Gorai.008G005500' => 'gra', 'GSVIVG01011094001' => 'vvi', 'GSVIVG01017879001' => 'vvi', 'GSVIVG01025988001' => 'vvi', 'GSVIVG01029847001' => 'vvi', 'HanXRQChr10g0282901' => 'han', 'HanXRQChr10g0310371' => 'han', 'HanXRQChr10g0315041' => 'han', 'HanXRQChr11g0327651' => 'han', 'HanXRQChr12g0359391' => 'han', 'Haze_00972' => 'cav', 'Haze_00973' => 'cav', 'Haze_00974' => 'cav', 'Haze_04747' => 'cav', 'Haze_04749' => 'cav', 'Haze_04750' => 'cav', 'Haze_21217' => 'cav', 'Hma1.2p1_1037F.1_g250680' => 'hma', 'Hma1.2p1_1644F.1_g295320' => 'hma', 'HPP92_011322' => 'vpl', 'HPP92_011323' => 'vpl', 'HPP92_011324' => 'vpl', 'HPP92_011325' => 'vpl', 'HPP92_011326' => 'vpl', 'Hund12205' => 'sun', 'Hund17957' => 'sun', 'Lalb_Chr06g0176771' => 'lal', 'Lalb_Chr18g0056021' => 'lal', 'Lalb_Chr18g0056031' => 'lal', 'Lalb_Chr18g0056041' => 'lal', 'Lalb_Chr20g0107751' => 'lal', 'Lalb_Chr20g0118371' => 'lal', 'Lj1g0010239' => 'lja', 'Lj1g0017101' => 'lja', 'Lj2A1178G40' => 'lonja', 'Lj2A54G84' => 'lonja', 'Lj2g0015248' => 'lja', 'Lj3A761T51' => 'lonja', 'Lj6g0018116' => 'lja', 'Lsat_1_v5_gn_4_136040' => 'lsa', 'Lsat_1_v5_gn_5_187461' => 'lsa', 'Lsat_1_v5_gn_5_77001' => 'lsa', 'Lsat_1_v5_gn_9_4461' => 'lsa', 'Manes.01G210100' => 'mes', 'Manes.03G185600' => 'mes', 'Manes.05G073300' => 'mes', 'Manes.09G120300' => 'mes', 'Manes.15G022100' => 'mes', 'Mapoly0096s0053' => 'mpo', 'MBI03_g14058_MAGBIO' => 'mbi', 'MBI03_g33876_MAGBIO' => 'mbi', 'MBI03_g36854_MAGBIO' => 'mbi', 'MBI17_g11997_MAGBIO' => 'mbi', 'MD03G1269000' => 'mdo', 'MD04G1179600' => 'mdo', 'MD11G1289800' => 'mdo', 'MD12G1194700' => 'mdo', 'MD13G1182100' => 'mdo', 'MD13G1182200' => 'mdo', 'MD16G1182600' => 'mdo', 'Medtr2g021400' => 'mtr', 'Medtr2g021470' => 'mtr', 'Medtr2g105810' => 'mtr', 'Medtr3g033580' => 'mtr', 'Medtr6g007970' => 'mtr', 'Medtr7g056330' => 'mtr', 'Medtr7g074290' => 'mtr', 'Medtr7g074380' => 'mtr', 'Medtr7g094550' => 'mtr', 'Medtr8g069995' => 'mtr', 'MELO3C014345.2' => 'cme', 'MELO3C021395.2' => 'cme', 'Migut.D00262' => 'egut', 'Migut.G00257' => 'egut', 'MSTRG.21575' => 'ama', 'MSTRG.3985' => 'ama', 'Nitab4.5_0000295g0140' => 'nta', 'Nitab4.5_0000732g0140' => 'nta', 'Nitab4.5_0003162g0020' => 'nta', 'Nitab4.5_0006180g0090' => 'nta', 'Nitab4.5_0006390g0010' => 'nta', 'Nitab4.5_0007392g0040' => 'nta', 'Nn1g02140' => 'nnu', 'Nn4g26168' => 'nnu', 'Nn5g26754' => 'nnu', 'Oeu001433.1' => 'oeu', 'Oeu010299.2' => 'oeu', 'Oeu011171.1' => 'oeu', 'Oeu037675.1' => 'oeu', 'Oeu038359.1' => 'oeu', 'Oeu063834.1' => 'oeu', 'Oeu063835.1' => 'oeu', 'Os05g0312000' => 'osa', 'Os07g0211101' => 'osa', 'Os07g0211200' => 'osa', 'Os07g0681500' => 'osa', 'Peaxi162Scf00095g01015' => 'pax', 'Peaxi162Scf00104g00329' => 'pax', 'Peaxi162Scf00161g00137' => 'pax', 'PGR004G1665' => 'pgr', 'PGR031G2937' => 'pgr', 'PGR119G2145' => 'pgr', 'PGSC0003DMG400004351' => 'stu', 'PGSC0003DMG400014625' => 'stu', 'PGSC0003DMG401000943' => 'stu', 'Phvul.001G148600' => 'pvu', 'Phvul.004G001700' => 'pvu', 'Phvul.006G154900' => 'pvu', 'Phvul.008G078200' => 'pvu', 'Phvul.011G136500' => 'pvu', 'Potri.002G215600' => 'ptr', 'Potri.008G201600' => 'ptr', 'Potri.014G138400' => 'ptr', 'Potri.016G142500' => 'ptr', 'Pp3c16_10580' => 'ppa', 'Pp3c5_25280' => 'ppa', 'Prupe.1G150000' => 'ppe', 'Prupe.1G150100' => 'ppe', 'Prupe.6G299600' => 'ppe', 'Prupe.8G245000' => 'ppe', 'Psat0s4927g0040' => 'psa', 'Psat1g052080' => 'psa', 'Psat1g183800' => 'psa', 'Psat3g113840' => 'psa', 'Psat3g126120' => 'psa', 'Psat3g126160' => 'psa', 'Psat3g158760' => 'psa', 'Psat3g158840' => 'psa', 'PSO170G2858' => 'pso', 'PSO339G0606' => 'pso', 'PSO384G4709' => 'pso', 'PSO407G0334' => 'pso', 'QL04p040276' => 'qlo', 'QL06p005458' => 'qlo', 'QL06p005472' => 'qlo', 'QL07p030546' => 'qlo', 'QL07p031519' => 'qlo', 'QL09p050949' => 'qlo', 'QL09p050966' => 'qlo', 'QL09p051067' => 'qlo', 'QL12p022706' => 'qlo', 'RcHm_v2.0_Chr2g0119601' => 'rch', 'RcHm_v2.0_Chr3g0459591' => 'rch', 'RcHm_v2.0_Chr4g0418521' => 'rch', 'RcHm_v2.0_Chr4g0418531' => 'rch', 'RcHm_v2.0_Chr4g0418541' => 'rch', 'RcHm_v2.0_Chr6g0291641' => 'rch', 'Rhsim01G0086300' => 'rsi', 'Rhsim01G0276300' => 'rsi', 'Rhsim01G0276500' => 'rsi', 'Rhsim04G0207700' => 'rsi', 'Rhsim05G0234500' => 'rsi', 'Rhsim13G0022400' => 'rsi', 'Sabra02G0167900' => 'sbr', 'Sabra04G0158500' => 'sbr', 'Sabra08G0159800' => 'sbr', 'Sabra10G0011500' => 'sbr', 'Sabra14G0104400' => 'sbr', 'SalBow2G2440' => 'sbo', 'SalBow4G2265' => 'sbo', 'Sc02g0000060' => 'sci', 'Sc05g0005020' => 'sci', 'Sc13g0003890' => 'sci', 'Sed0014865' => 'sed', 'Sed0017224' => 'sed', 'Sed0026391' => 'sed', 'SEGI_00063' => 'sgi', 'SEGI_10967' => 'sgi', 'SEGI_17510' => 'sgi', 'SEGI_24396' => 'sgi', 'SEGI_39719' => 'sgi', 'SEGI_41392' => 'sgi', 'SGA_v2.0_scaffold11G05794' => 'sas', 'SGA_v2.0_scaffold142G35607' => 'sas', 'SGA_v2.0_scaffold1G00447' => 'sas', 'SHI15388' => 'shi', 'SHI15394' => 'shi', 'SHI15396' => 'shi', 'SHI15399' => 'shi', 'SMO343G0151' => 'smo', 'SMO367G1118' => 'smo', 'Solyc01g080200.3' => 'sly', 'Solyc06g008960.3' => 'sly', 'Solyc09g064780.3' => 'sly', 'Sopen01g031980' => 'spe', 'Sopen06g003710' => 'spe', 'Sopen09g026460' => 'spe', 'Sp3g21240' => 'spa', 'Sp4g30030' => 'spa', 'TAR365G0022' => 'tar', 'TAR365G1023' => 'tar', 'TAR365G1253' => 'tar', 'TAR623G0078' => 'tar', 'TAR623G1721' => 'tar', 'TAR633G0959' => 'tar', 'THA.LOC104802225' => 'tha', 'THA.LOC104804769' => 'tha', 'THA.LOC104808660' => 'tha', 'THA.LOC104812792' => 'tha', 'Thecc.01G284000' => 'tca', 'Thecc.04G220600' => 'tca', 'Thecc.05G268900' => 'tca', 'Thecc.08G171100' => 'tca', 'Thhalv10001284m.g' => 'esa', 'Thhalv10019912m.g' => 'esa', 'TPR.G14189' => 'tpr', 'TPR.G18110' => 'tpr', 'TPR.G18130' => 'tpr', 'TPR.G18131' => 'tpr', 'TPR.G18140' => 'tpr', 'TPR.G24282' => 'tpr', 'TPR.G25221' => 'tpr', 'TPR.G29267' => 'tpr', 'TPR.G35315' => 'tpr', 'TPR.G36173' => 'tpr', 'TWI09G0794' => 'twi', 'TWI59G1348' => 'twi', 'TWI74G0430' => 'twi', 'unitig_26.g8940' => 'ugi', 'unitig_749.g13744' => 'ugi', 'unitig_749.g13745' => 'ugi', 'vmacro08269' => 'vma', 'vmacro14937' => 'vma', 'vmacro20401' => 'vma', 'VMungo0464G1349' => 'vmu', 'VMungo0540G0289' => 'vmu', 'VMungo1215G1590' => 'vmu', 'VMungo1309G0221' => 'vmu', 'VMungo1309G2815' => 'vmu', 'VMungo1383G0239' => 'vmu', 'VMungo1383G2910' => 'vmu', 'Zm00001eb095270' => 'zma', 'Zm00001eb095280' => 'zma', 'Zm00001eb111630' => 'zma', 'Zm00001eb237080' => 'zma', 'Zm00001eb273740' => 'zma', 'Zm00001eb285040' => 'zma', 'Zm00001eb330790' => 'zma', 'Zm00001eb337380' => 'zma' ), 'gf_id' => 'HOM05D001484', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001484' ), 'data_identifier' => 'HOM05D001484', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001484', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p31500' => 'bna', 'A05p00020' => 'bna', 'A07p08820' => 'bna', 'Aa31LG4G3300' => 'aar', 'Aa31LG8G10030' => 'aar', 'Actinidia00731' => 'ach', 'Actinidia11473' => 'ach', 'Actinidia23469' => 'ach', 'Actinidia24318' => 'ach', 'Actinidia40196' => 'ach', 'Actinidia40197' => 'ach', 'Actinidia40198' => 'ach', 'Ah.08g212990' => 'amhyb', 'Ah.15g091720' => 'amhyb', 'AL3G38260' => 'aly', 'AL4G47710' => 'aly', 'Aqoxy2G00671' => 'aox', 'Aqoxy2G03236' => 'aox', 'arahy.Tifrunner.gnm1.ann1.05IDCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KR684' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATY3SJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK6QJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6APGL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IDT7Z9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM073U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ0R87' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LE7RV4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT4QRX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V5ENPK' => 'arhy', 'AT2G48110' => 'ath', 'AT3G23590' => 'ath', 'ATR0626G186' => 'atr', 'ATR1127G141' => 'atr', 'Atru.chr4.2583' => 'acertr', 'Atru.chr5.1358' => 'acertr', 'Atru.chr5.1359' => 'acertr', 'Atru.chr8.46' => 'acertr', 'AUR62002640' => 'cqu', 'AUR62030055' => 'cqu', 'AUR62033713' => 'cqu', 'AUR62033714' => 'cqu', 'AUR62036795' => 'cqu', 'AUR62039891' => 'cqu', 'BcaB02g08737' => 'bca', 'BcaB04g20441' => 'bca', 'BcaB06g26509' => 'bca', 'BcaB06g26510' => 'bca', 'BcaB06g26511' => 'bca', 'BcaB06g26512' => 'bca', 'BcaB06g26513' => 'bca', 'BcaC02g12564' => 'bca', 'BcaC02g12565' => 'bca', 'BcaC02g12794' => 'bca', 'BcaC02g12795' => 'bca', 'BcaC02g12796' => 'bca', 'BcaC06g35541' => 'bca', 'BNapus_Darmor_BZH_scaffold_188p00080' => 'bna', 'BNapus_Darmor_BZH_scaffold_188p00090' => 'bna', 'BolC1t03972H' => 'bol', 'BolC1t03973H' => 'bol', 'BolC4t21680H' => 'bol', 'BolC7t41863H' => 'bol', 'BolSC55t61227H' => 'bol', 'BolSC55t61228H' => 'bol', 'BraA01t03278Z' => 'bra', 'BraA05t18998Z' => 'bra', 'BraA07t28673Z' => 'bra', 'C01p40150' => 'bna', 'C05p12370' => 'bna', 'C07p13680' => 'bna', 'CAN.G1006.16' => 'can', 'CAN.G1006.17' => 'can', 'CAN.G1170.2' => 'can', 'CAN.G962.7' => 'can', 'CANSAT25G2179' => 'cansat', 'CANSAT78G1573' => 'cansat', 'CARHR099510' => 'chi', 'CARHR143510' => 'chi', 'Carub.0003s2380' => 'cru', 'Carub.0004s3082' => 'cru', 'Ca_00614_v3' => 'car', 'Ca_07801_v3' => 'car', 'Ca_08567_v3' => 'car', 'Ca_09571_v3' => 'car', 'CBR_g19290' => 'cbr', 'Cc01_g19770' => 'ccan', 'Cc03_g03030' => 'ccan', 'CDE07G0968' => 'cde', 'CDE09G1441' => 'cde', 'Cfa006103' => 'cfa', 'Cfa015573' => 'cfa', 'Cfa016988' => 'cfa', 'Ciclev10006738m.g' => 'ccl', 'Ciclev10010920m.g' => 'ccl', 'Ciclev10018517m.g' => 'ccl', 'CiPaw.01G159200' => 'cil', 'CiPaw.02G091000' => 'cil', 'CiPaw.02G091100' => 'cil', 'CiPaw.08G103100' => 'cil', 'CiPaw.09G224900' => 'cil', 'ClCG06G005740' => 'cla', 'ClCG07G000090' => 'cla', 'ClCG07G000100' => 'cla', 'COL.COLO4_09143' => 'col', 'COL.COLO4_25124' => 'col', 'Cpa.g.sc16.34' => 'cpa', 'Cpa.g.sc3504.1' => 'cpa', 'Cpa.g.sc60.37' => 'cpa', 'CsaV3_6G018520' => 'csa', 'CsaV3_6G036860' => 'csa', 'CSS0001072' => 'camsi', 'CSS0020208' => 'camsi', 'CSS0021253' => 'camsi', 'CSS0022190' => 'camsi', 'CSS0036150' => 'camsi', 'CSS0040442' => 'camsi', 'CSS0042300' => 'camsi', 'CSS0045298' => 'camsi', 'DCAR_012449' => 'dca', 'DCAR_018405' => 'dca', 'DCAR_024573' => 'dca', 'DCAR_030591' => 'dca', 'Dinv16926' => 'din', 'Dinv32963' => 'din', 'Dinv38382' => 'din', 'Dinv38383' => 'din', 'Duzib133G0974' => 'dzi', 'Duzib138G1867' => 'dzi', 'Duzib211G0420' => 'dzi', 'Duzib212G0930' => 'dzi', 'ECA234G1645' => 'eca', 'ECA247G3467' => 'eca', 'ECA248G1703' => 'eca', 'EL10Ac3g06327' => 'bvu', 'EL10Ac7g17204' => 'bvu', 'Eucgr.A00855' => 'egr', 'Eucgr.A00858' => 'egr', 'Eucgr.H01520' => 'egr', 'Eucgr.H03604' => 'egr', 'Eucgr.L03465' => 'egr', 'Eucgr.L03466' => 'egr', 'FAN01G0988' => 'fan', 'FAN02G3892' => 'fan', 'FAN05G3381' => 'fan', 'FAN07G0967' => 'fan', 'FAN07G1493' => 'fan', 'FAN08G3125' => 'fan', 'FAN09G0402' => 'fan', 'FAN12G2594' => 'fan', 'FAN12G3879' => 'fan', 'FAN14G1546' => 'fan', 'FAN15G3626' => 'fan', 'FAN17G0588' => 'fan', 'FAN17G0609' => 'fan', 'FAN18G2817' => 'fan', 'FAN19G1305' => 'fan', 'FAN20G1787' => 'fan', 'FAN22G0073' => 'fan', 'FAN22G0352' => 'fan', 'FAN22G0368' => 'fan', 'FAN22G2273' => 'fan', 'FAN24G1998' => 'fan', 'FAN27G1317' => 'fan', 'FvH4_2g23980' => 'fve', 'FvH4_4g14380' => 'fve', 'FvH4_4g14390' => 'fve', 'FvH4_6g09250' => 'fve', 'Glyma.03G151100' => 'gma', 'Glyma.04G122550' => 'gma', 'Glyma.05G001600' => 'gma', 'Glyma.09G270766' => 'gma', 'Glyma.09G270832' => 'gma', 'Glyma.13G209800' => 'gma', 'Glyma.15G102800' => 'gma', 'Glyma.18G218900' => 'gma', 'Glyma.19G001500' => 'gma', 'Glyma.19G153600' => 'gma', 'Gohir.A02G028600' => 'ghi', 'Gohir.A08G045000' => 'ghi', 'Gohir.A11G120500' => 'ghi', 'Gohir.A12G006200' => 'ghi', 'Gohir.A12G006250' => 'ghi', 'Gohir.D02G036300' => 'ghi', 'Gohir.D08G054700' => 'ghi', 'Gohir.D11G125600' => 'ghi', 'Gohir.D12G005700' => 'ghi', 'Gorai.004G055200' => 'gra', 'Gorai.005G040400' => 'gra', 'Gorai.007G134500' => 'gra', 'Gorai.008G005500' => 'gra', 'GSVIVG01011094001' => 'vvi', 'GSVIVG01017879001' => 'vvi', 'GSVIVG01025988001' => 'vvi', 'GSVIVG01029847001' => 'vvi', 'HanXRQChr10g0282901' => 'han', 'HanXRQChr10g0310371' => 'han', 'HanXRQChr10g0315041' => 'han', 'HanXRQChr11g0327651' => 'han', 'HanXRQChr12g0359391' => 'han', 'Haze_00972' => 'cav', 'Haze_00973' => 'cav', 'Haze_00974' => 'cav', 'Haze_04747' => 'cav', 'Haze_04749' => 'cav', 'Haze_04750' => 'cav', 'Haze_21217' => 'cav', 'Hma1.2p1_1037F.1_g250680' => 'hma', 'Hma1.2p1_1644F.1_g295320' => 'hma', 'HPP92_011322' => 'vpl', 'HPP92_011323' => 'vpl', 'HPP92_011324' => 'vpl', 'HPP92_011325' => 'vpl', 'HPP92_011326' => 'vpl', 'Hund12205' => 'sun', 'Hund17957' => 'sun', 'Lalb_Chr06g0176771' => 'lal', 'Lalb_Chr18g0056021' => 'lal', 'Lalb_Chr18g0056031' => 'lal', 'Lalb_Chr18g0056041' => 'lal', 'Lalb_Chr20g0107751' => 'lal', 'Lalb_Chr20g0118371' => 'lal', 'Lj1g0010239' => 'lja', 'Lj1g0017101' => 'lja', 'Lj2A1178G40' => 'lonja', 'Lj2A54G84' => 'lonja', 'Lj2g0015248' => 'lja', 'Lj3A761T51' => 'lonja', 'Lj6g0018116' => 'lja', 'Lsat_1_v5_gn_4_136040' => 'lsa', 'Lsat_1_v5_gn_5_187461' => 'lsa', 'Lsat_1_v5_gn_5_77001' => 'lsa', 'Lsat_1_v5_gn_9_4461' => 'lsa', 'Manes.01G210100' => 'mes', 'Manes.03G185600' => 'mes', 'Manes.05G073300' => 'mes', 'Manes.09G120300' => 'mes', 'Manes.15G022100' => 'mes', 'Mapoly0096s0053' => 'mpo', 'MBI03_g14058_MAGBIO' => 'mbi', 'MBI03_g33876_MAGBIO' => 'mbi', 'MBI03_g36854_MAGBIO' => 'mbi', 'MBI17_g11997_MAGBIO' => 'mbi', 'MD03G1269000' => 'mdo', 'MD04G1179600' => 'mdo', 'MD11G1289800' => 'mdo', 'MD12G1194700' => 'mdo', 'MD13G1182100' => 'mdo', 'MD13G1182200' => 'mdo', 'MD16G1182600' => 'mdo', 'Medtr2g021400' => 'mtr', 'Medtr2g021470' => 'mtr', 'Medtr2g105810' => 'mtr', 'Medtr3g033580' => 'mtr', 'Medtr6g007970' => 'mtr', 'Medtr7g056330' => 'mtr', 'Medtr7g074290' => 'mtr', 'Medtr7g074380' => 'mtr', 'Medtr7g094550' => 'mtr', 'Medtr8g069995' => 'mtr', 'MELO3C014345.2' => 'cme', 'MELO3C021395.2' => 'cme', 'Migut.D00262' => 'egut', 'Migut.G00257' => 'egut', 'MSTRG.21575' => 'ama', 'MSTRG.3985' => 'ama', 'Nitab4.5_0000295g0140' => 'nta', 'Nitab4.5_0000732g0140' => 'nta', 'Nitab4.5_0003162g0020' => 'nta', 'Nitab4.5_0006180g0090' => 'nta', 'Nitab4.5_0006390g0010' => 'nta', 'Nitab4.5_0007392g0040' => 'nta', 'Nn1g02140' => 'nnu', 'Nn4g26168' => 'nnu', 'Nn5g26754' => 'nnu', 'Oeu001433.1' => 'oeu', 'Oeu010299.2' => 'oeu', 'Oeu011171.1' => 'oeu', 'Oeu037675.1' => 'oeu', 'Oeu038359.1' => 'oeu', 'Oeu063834.1' => 'oeu', 'Oeu063835.1' => 'oeu', 'Os05g0312000' => 'osa', 'Os07g0211101' => 'osa', 'Os07g0211200' => 'osa', 'Os07g0681500' => 'osa', 'Peaxi162Scf00095g01015' => 'pax', 'Peaxi162Scf00104g00329' => 'pax', 'Peaxi162Scf00161g00137' => 'pax', 'PGR004G1665' => 'pgr', 'PGR031G2937' => 'pgr', 'PGR119G2145' => 'pgr', 'PGSC0003DMG400004351' => 'stu', 'PGSC0003DMG400014625' => 'stu', 'PGSC0003DMG401000943' => 'stu', 'Phvul.001G148600' => 'pvu', 'Phvul.004G001700' => 'pvu', 'Phvul.006G154900' => 'pvu', 'Phvul.008G078200' => 'pvu', 'Phvul.011G136500' => 'pvu', 'Potri.002G215600' => 'ptr', 'Potri.008G201600' => 'ptr', 'Potri.014G138400' => 'ptr', 'Potri.016G142500' => 'ptr', 'Pp3c16_10580' => 'ppa', 'Pp3c5_25280' => 'ppa', 'Prupe.1G150000' => 'ppe', 'Prupe.1G150100' => 'ppe', 'Prupe.6G299600' => 'ppe', 'Prupe.8G245000' => 'ppe', 'Psat0s4927g0040' => 'psa', 'Psat1g052080' => 'psa', 'Psat1g183800' => 'psa', 'Psat3g113840' => 'psa', 'Psat3g126120' => 'psa', 'Psat3g126160' => 'psa', 'Psat3g158760' => 'psa', 'Psat3g158840' => 'psa', 'PSO170G2858' => 'pso', 'PSO339G0606' => 'pso', 'PSO384G4709' => 'pso', 'PSO407G0334' => 'pso', 'QL04p040276' => 'qlo', 'QL06p005458' => 'qlo', 'QL06p005472' => 'qlo', 'QL07p030546' => 'qlo', 'QL07p031519' => 'qlo', 'QL09p050949' => 'qlo', 'QL09p050966' => 'qlo', 'QL09p051067' => 'qlo', 'QL12p022706' => 'qlo', 'RcHm_v2.0_Chr2g0119601' => 'rch', 'RcHm_v2.0_Chr3g0459591' => 'rch', 'RcHm_v2.0_Chr4g0418521' => 'rch', 'RcHm_v2.0_Chr4g0418531' => 'rch', 'RcHm_v2.0_Chr4g0418541' => 'rch', 'RcHm_v2.0_Chr6g0291641' => 'rch', 'Rhsim01G0086300' => 'rsi', 'Rhsim01G0276300' => 'rsi', 'Rhsim01G0276500' => 'rsi', 'Rhsim04G0207700' => 'rsi', 'Rhsim05G0234500' => 'rsi', 'Rhsim13G0022400' => 'rsi', 'Sabra02G0167900' => 'sbr', 'Sabra04G0158500' => 'sbr', 'Sabra08G0159800' => 'sbr', 'Sabra10G0011500' => 'sbr', 'Sabra14G0104400' => 'sbr', 'SalBow2G2440' => 'sbo', 'SalBow4G2265' => 'sbo', 'Sc02g0000060' => 'sci', 'Sc05g0005020' => 'sci', 'Sc13g0003890' => 'sci', 'Sed0014865' => 'sed', 'Sed0017224' => 'sed', 'Sed0026391' => 'sed', 'SEGI_00063' => 'sgi', 'SEGI_10967' => 'sgi', 'SEGI_17510' => 'sgi', 'SEGI_24396' => 'sgi', 'SEGI_39719' => 'sgi', 'SEGI_41392' => 'sgi', 'SGA_v2.0_scaffold11G05794' => 'sas', 'SGA_v2.0_scaffold142G35607' => 'sas', 'SGA_v2.0_scaffold1G00447' => 'sas', 'SHI15388' => 'shi', 'SHI15394' => 'shi', 'SHI15396' => 'shi', 'SHI15399' => 'shi', 'SMO343G0151' => 'smo', 'SMO367G1118' => 'smo', 'Solyc01g080200.3' => 'sly', 'Solyc06g008960.3' => 'sly', 'Solyc09g064780.3' => 'sly', 'Sopen01g031980' => 'spe', 'Sopen06g003710' => 'spe', 'Sopen09g026460' => 'spe', 'Sp3g21240' => 'spa', 'Sp4g30030' => 'spa', 'TAR365G0022' => 'tar', 'TAR365G1023' => 'tar', 'TAR365G1253' => 'tar', 'TAR623G0078' => 'tar', 'TAR623G1721' => 'tar', 'TAR633G0959' => 'tar', 'THA.LOC104802225' => 'tha', 'THA.LOC104804769' => 'tha', 'THA.LOC104808660' => 'tha', 'THA.LOC104812792' => 'tha', 'Thecc.01G284000' => 'tca', 'Thecc.04G220600' => 'tca', 'Thecc.05G268900' => 'tca', 'Thecc.08G171100' => 'tca', 'Thhalv10001284m.g' => 'esa', 'Thhalv10019912m.g' => 'esa', 'TPR.G14189' => 'tpr', 'TPR.G18110' => 'tpr', 'TPR.G18130' => 'tpr', 'TPR.G18131' => 'tpr', 'TPR.G18140' => 'tpr', 'TPR.G24282' => 'tpr', 'TPR.G25221' => 'tpr', 'TPR.G29267' => 'tpr', 'TPR.G35315' => 'tpr', 'TPR.G36173' => 'tpr', 'TWI09G0794' => 'twi', 'TWI59G1348' => 'twi', 'TWI74G0430' => 'twi', 'unitig_26.g8940' => 'ugi', 'unitig_749.g13744' => 'ugi', 'unitig_749.g13745' => 'ugi', 'vmacro08269' => 'vma', 'vmacro14937' => 'vma', 'vmacro20401' => 'vma', 'VMungo0464G1349' => 'vmu', 'VMungo0540G0289' => 'vmu', 'VMungo1215G1590' => 'vmu', 'VMungo1309G0221' => 'vmu', 'VMungo1309G2815' => 'vmu', 'VMungo1383G0239' => 'vmu', 'VMungo1383G2910' => 'vmu', 'Zm00001eb095270' => 'zma', 'Zm00001eb095280' => 'zma', 'Zm00001eb111630' => 'zma', 'Zm00001eb237080' => 'zma', 'Zm00001eb273740' => 'zma', 'Zm00001eb285040' => 'zma', 'Zm00001eb330790' => 'zma', 'Zm00001eb337380' => 'zma' ) $gf_id = 'HOM05D001484' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001484' ) $data_identifier = 'HOM05D001484' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 2, 'aly' => (int) 2, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 22, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 7, 'hma' => (int) 2, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 7, 'mtr' => (int) 10, 'cme' => (int) 2, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 4, 'ppa' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 4, 'qlo' => (int) 9, 'rch' => (int) 6, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 10, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 7, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb337380' $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' => 'HOM05D001484', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p31500' => 'bna', 'A05p00020' => 'bna', 'A07p08820' => 'bna', 'Aa31LG4G3300' => 'aar', 'Aa31LG8G10030' => 'aar', 'Actinidia00731' => 'ach', 'Actinidia11473' => 'ach', 'Actinidia23469' => 'ach', 'Actinidia24318' => 'ach', 'Actinidia40196' => 'ach', 'Actinidia40197' => 'ach', 'Actinidia40198' => 'ach', 'Ah.08g212990' => 'amhyb', 'Ah.15g091720' => 'amhyb', 'AL3G38260' => 'aly', 'AL4G47710' => 'aly', 'Aqoxy2G00671' => 'aox', 'Aqoxy2G03236' => 'aox', 'arahy.Tifrunner.gnm1.ann1.05IDCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KR684' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATY3SJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK6QJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6APGL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IDT7Z9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM073U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ0R87' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LE7RV4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT4QRX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V5ENPK' => 'arhy', 'AT2G48110' => 'ath', 'AT3G23590' => 'ath', 'ATR0626G186' => 'atr', 'ATR1127G141' => 'atr', 'Atru.chr4.2583' => 'acertr', 'Atru.chr5.1358' => 'acertr', 'Atru.chr5.1359' => 'acertr', 'Atru.chr8.46' => 'acertr', 'AUR62002640' => 'cqu', 'AUR62030055' => 'cqu', 'AUR62033713' => 'cqu', 'AUR62033714' => 'cqu', 'AUR62036795' => 'cqu', 'AUR62039891' => 'cqu', 'BcaB02g08737' => 'bca', 'BcaB04g20441' => 'bca', 'BcaB06g26509' => 'bca', 'BcaB06g26510' => 'bca', 'BcaB06g26511' => 'bca', 'BcaB06g26512' => 'bca', 'BcaB06g26513' => 'bca', 'BcaC02g12564' => 'bca', 'BcaC02g12565' => 'bca', 'BcaC02g12794' => 'bca', 'BcaC02g12795' => 'bca', 'BcaC02g12796' => 'bca', 'BcaC06g35541' => 'bca', 'BNapus_Darmor_BZH_scaffold_188p00080' => 'bna', 'BNapus_Darmor_BZH_scaffold_188p00090' => 'bna', 'BolC1t03972H' => 'bol', 'BolC1t03973H' => 'bol', 'BolC4t21680H' => 'bol', 'BolC7t41863H' => 'bol', 'BolSC55t61227H' => 'bol', 'BolSC55t61228H' => 'bol', 'BraA01t03278Z' => 'bra', 'BraA05t18998Z' => 'bra', 'BraA07t28673Z' => 'bra', 'C01p40150' => 'bna', 'C05p12370' => 'bna', 'C07p13680' => 'bna', 'CAN.G1006.16' => 'can', 'CAN.G1006.17' => 'can', 'CAN.G1170.2' => 'can', 'CAN.G962.7' => 'can', 'CANSAT25G2179' => 'cansat', 'CANSAT78G1573' => 'cansat', 'CARHR099510' => 'chi', 'CARHR143510' => 'chi', 'Carub.0003s2380' => 'cru', 'Carub.0004s3082' => 'cru', 'Ca_00614_v3' => 'car', 'Ca_07801_v3' => 'car', 'Ca_08567_v3' => 'car', 'Ca_09571_v3' => 'car', 'CBR_g19290' => 'cbr', 'Cc01_g19770' => 'ccan', 'Cc03_g03030' => 'ccan', 'CDE07G0968' => 'cde', 'CDE09G1441' => 'cde', 'Cfa006103' => 'cfa', 'Cfa015573' => 'cfa', 'Cfa016988' => 'cfa', 'Ciclev10006738m.g' => 'ccl', 'Ciclev10010920m.g' => 'ccl', 'Ciclev10018517m.g' => 'ccl', 'CiPaw.01G159200' => 'cil', 'CiPaw.02G091000' => 'cil', 'CiPaw.02G091100' => 'cil', 'CiPaw.08G103100' => 'cil', 'CiPaw.09G224900' => 'cil', 'ClCG06G005740' => 'cla', 'ClCG07G000090' => 'cla', 'ClCG07G000100' => 'cla', 'COL.COLO4_09143' => 'col', 'COL.COLO4_25124' => 'col', 'Cpa.g.sc16.34' => 'cpa', 'Cpa.g.sc3504.1' => 'cpa', 'Cpa.g.sc60.37' => 'cpa', 'CsaV3_6G018520' => 'csa', 'CsaV3_6G036860' => 'csa', 'CSS0001072' => 'camsi', 'CSS0020208' => 'camsi', 'CSS0021253' => 'camsi', 'CSS0022190' => 'camsi', 'CSS0036150' => 'camsi', 'CSS0040442' => 'camsi', 'CSS0042300' => 'camsi', 'CSS0045298' => 'camsi', 'DCAR_012449' => 'dca', 'DCAR_018405' => 'dca', 'DCAR_024573' => 'dca', 'DCAR_030591' => 'dca', 'Dinv16926' => 'din', 'Dinv32963' => 'din', 'Dinv38382' => 'din', 'Dinv38383' => 'din', 'Duzib133G0974' => 'dzi', 'Duzib138G1867' => 'dzi', 'Duzib211G0420' => 'dzi', 'Duzib212G0930' => 'dzi', 'ECA234G1645' => 'eca', 'ECA247G3467' => 'eca', 'ECA248G1703' => 'eca', 'EL10Ac3g06327' => 'bvu', 'EL10Ac7g17204' => 'bvu', 'Eucgr.A00855' => 'egr', 'Eucgr.A00858' => 'egr', 'Eucgr.H01520' => 'egr', 'Eucgr.H03604' => 'egr', 'Eucgr.L03465' => 'egr', 'Eucgr.L03466' => 'egr', 'FAN01G0988' => 'fan', 'FAN02G3892' => 'fan', 'FAN05G3381' => 'fan', 'FAN07G0967' => 'fan', 'FAN07G1493' => 'fan', 'FAN08G3125' => 'fan', 'FAN09G0402' => 'fan', 'FAN12G2594' => 'fan', 'FAN12G3879' => 'fan', 'FAN14G1546' => 'fan', 'FAN15G3626' => 'fan', 'FAN17G0588' => 'fan', 'FAN17G0609' => 'fan', 'FAN18G2817' => 'fan', 'FAN19G1305' => 'fan', 'FAN20G1787' => 'fan', 'FAN22G0073' => 'fan', 'FAN22G0352' => 'fan', 'FAN22G0368' => 'fan', 'FAN22G2273' => 'fan', 'FAN24G1998' => 'fan', 'FAN27G1317' => 'fan', 'FvH4_2g23980' => 'fve', 'FvH4_4g14380' => 'fve', 'FvH4_4g14390' => 'fve', 'FvH4_6g09250' => 'fve', 'Glyma.03G151100' => 'gma', 'Glyma.04G122550' => 'gma', 'Glyma.05G001600' => 'gma', 'Glyma.09G270766' => 'gma', 'Glyma.09G270832' => 'gma', 'Glyma.13G209800' => 'gma', 'Glyma.15G102800' => 'gma', 'Glyma.18G218900' => 'gma', 'Glyma.19G001500' => 'gma', 'Glyma.19G153600' => 'gma', 'Gohir.A02G028600' => 'ghi', 'Gohir.A08G045000' => 'ghi', 'Gohir.A11G120500' => 'ghi', 'Gohir.A12G006200' => 'ghi', 'Gohir.A12G006250' => 'ghi', 'Gohir.D02G036300' => 'ghi', 'Gohir.D08G054700' => 'ghi', 'Gohir.D11G125600' => 'ghi', 'Gohir.D12G005700' => 'ghi', 'Gorai.004G055200' => 'gra', 'Gorai.005G040400' => 'gra', 'Gorai.007G134500' => 'gra', 'Gorai.008G005500' => 'gra', 'GSVIVG01011094001' => 'vvi', 'GSVIVG01017879001' => 'vvi', 'GSVIVG01025988001' => 'vvi', 'GSVIVG01029847001' => 'vvi', 'HanXRQChr10g0282901' => 'han', 'HanXRQChr10g0310371' => 'han', 'HanXRQChr10g0315041' => 'han', 'HanXRQChr11g0327651' => 'han', 'HanXRQChr12g0359391' => 'han', 'Haze_00972' => 'cav', 'Haze_00973' => 'cav', 'Haze_00974' => 'cav', 'Haze_04747' => 'cav', 'Haze_04749' => 'cav', 'Haze_04750' => 'cav', 'Haze_21217' => 'cav', 'Hma1.2p1_1037F.1_g250680' => 'hma', 'Hma1.2p1_1644F.1_g295320' => 'hma', 'HPP92_011322' => 'vpl', 'HPP92_011323' => 'vpl', 'HPP92_011324' => 'vpl', 'HPP92_011325' => 'vpl', 'HPP92_011326' => 'vpl', 'Hund12205' => 'sun', 'Hund17957' => 'sun', 'Lalb_Chr06g0176771' => 'lal', 'Lalb_Chr18g0056021' => 'lal', 'Lalb_Chr18g0056031' => 'lal', 'Lalb_Chr18g0056041' => 'lal', 'Lalb_Chr20g0107751' => 'lal', 'Lalb_Chr20g0118371' => 'lal', 'Lj1g0010239' => 'lja', 'Lj1g0017101' => 'lja', 'Lj2A1178G40' => 'lonja', 'Lj2A54G84' => 'lonja', 'Lj2g0015248' => 'lja', 'Lj3A761T51' => 'lonja', 'Lj6g0018116' => 'lja', 'Lsat_1_v5_gn_4_136040' => 'lsa', 'Lsat_1_v5_gn_5_187461' => 'lsa', 'Lsat_1_v5_gn_5_77001' => 'lsa', 'Lsat_1_v5_gn_9_4461' => 'lsa', 'Manes.01G210100' => 'mes', 'Manes.03G185600' => 'mes', 'Manes.05G073300' => 'mes', 'Manes.09G120300' => 'mes', 'Manes.15G022100' => 'mes', 'Mapoly0096s0053' => 'mpo', 'MBI03_g14058_MAGBIO' => 'mbi', 'MBI03_g33876_MAGBIO' => 'mbi', 'MBI03_g36854_MAGBIO' => 'mbi', 'MBI17_g11997_MAGBIO' => 'mbi', 'MD03G1269000' => 'mdo', 'MD04G1179600' => 'mdo', 'MD11G1289800' => 'mdo', 'MD12G1194700' => 'mdo', 'MD13G1182100' => 'mdo', 'MD13G1182200' => 'mdo', 'MD16G1182600' => 'mdo', 'Medtr2g021400' => 'mtr', 'Medtr2g021470' => 'mtr', 'Medtr2g105810' => 'mtr', 'Medtr3g033580' => 'mtr', 'Medtr6g007970' => 'mtr', 'Medtr7g056330' => 'mtr', 'Medtr7g074290' => 'mtr', 'Medtr7g074380' => 'mtr', 'Medtr7g094550' => 'mtr', 'Medtr8g069995' => 'mtr', 'MELO3C014345.2' => 'cme', 'MELO3C021395.2' => 'cme', 'Migut.D00262' => 'egut', 'Migut.G00257' => 'egut', 'MSTRG.21575' => 'ama', 'MSTRG.3985' => 'ama', 'Nitab4.5_0000295g0140' => 'nta', 'Nitab4.5_0000732g0140' => 'nta', 'Nitab4.5_0003162g0020' => 'nta', 'Nitab4.5_0006180g0090' => 'nta', 'Nitab4.5_0006390g0010' => 'nta', 'Nitab4.5_0007392g0040' => 'nta', 'Nn1g02140' => 'nnu', 'Nn4g26168' => 'nnu', 'Nn5g26754' => 'nnu', 'Oeu001433.1' => 'oeu', 'Oeu010299.2' => 'oeu', 'Oeu011171.1' => 'oeu', 'Oeu037675.1' => 'oeu', 'Oeu038359.1' => 'oeu', 'Oeu063834.1' => 'oeu', 'Oeu063835.1' => 'oeu', 'Os05g0312000' => 'osa', 'Os07g0211101' => 'osa', 'Os07g0211200' => 'osa', 'Os07g0681500' => 'osa', 'Peaxi162Scf00095g01015' => 'pax', 'Peaxi162Scf00104g00329' => 'pax', 'Peaxi162Scf00161g00137' => 'pax', 'PGR004G1665' => 'pgr', 'PGR031G2937' => 'pgr', 'PGR119G2145' => 'pgr', 'PGSC0003DMG400004351' => 'stu', 'PGSC0003DMG400014625' => 'stu', 'PGSC0003DMG401000943' => 'stu', 'Phvul.001G148600' => 'pvu', 'Phvul.004G001700' => 'pvu', 'Phvul.006G154900' => 'pvu', 'Phvul.008G078200' => 'pvu', 'Phvul.011G136500' => 'pvu', 'Potri.002G215600' => 'ptr', 'Potri.008G201600' => 'ptr', 'Potri.014G138400' => 'ptr', 'Potri.016G142500' => 'ptr', 'Pp3c16_10580' => 'ppa', 'Pp3c5_25280' => 'ppa', 'Prupe.1G150000' => 'ppe', 'Prupe.1G150100' => 'ppe', 'Prupe.6G299600' => 'ppe', 'Prupe.8G245000' => 'ppe', 'Psat0s4927g0040' => 'psa', 'Psat1g052080' => 'psa', 'Psat1g183800' => 'psa', 'Psat3g113840' => 'psa', 'Psat3g126120' => 'psa', 'Psat3g126160' => 'psa', 'Psat3g158760' => 'psa', 'Psat3g158840' => 'psa', 'PSO170G2858' => 'pso', 'PSO339G0606' => 'pso', 'PSO384G4709' => 'pso', 'PSO407G0334' => 'pso', 'QL04p040276' => 'qlo', 'QL06p005458' => 'qlo', 'QL06p005472' => 'qlo', 'QL07p030546' => 'qlo', 'QL07p031519' => 'qlo', 'QL09p050949' => 'qlo', 'QL09p050966' => 'qlo', 'QL09p051067' => 'qlo', 'QL12p022706' => 'qlo', 'RcHm_v2.0_Chr2g0119601' => 'rch', 'RcHm_v2.0_Chr3g0459591' => 'rch', 'RcHm_v2.0_Chr4g0418521' => 'rch', 'RcHm_v2.0_Chr4g0418531' => 'rch', 'RcHm_v2.0_Chr4g0418541' => 'rch', 'RcHm_v2.0_Chr6g0291641' => 'rch', 'Rhsim01G0086300' => 'rsi', 'Rhsim01G0276300' => 'rsi', 'Rhsim01G0276500' => 'rsi', 'Rhsim04G0207700' => 'rsi', 'Rhsim05G0234500' => 'rsi', 'Rhsim13G0022400' => 'rsi', 'Sabra02G0167900' => 'sbr', 'Sabra04G0158500' => 'sbr', 'Sabra08G0159800' => 'sbr', 'Sabra10G0011500' => 'sbr', 'Sabra14G0104400' => 'sbr', 'SalBow2G2440' => 'sbo', 'SalBow4G2265' => 'sbo', 'Sc02g0000060' => 'sci', 'Sc05g0005020' => 'sci', 'Sc13g0003890' => 'sci', 'Sed0014865' => 'sed', 'Sed0017224' => 'sed', 'Sed0026391' => 'sed', 'SEGI_00063' => 'sgi', 'SEGI_10967' => 'sgi', 'SEGI_17510' => 'sgi', 'SEGI_24396' => 'sgi', 'SEGI_39719' => 'sgi', 'SEGI_41392' => 'sgi', 'SGA_v2.0_scaffold11G05794' => 'sas', 'SGA_v2.0_scaffold142G35607' => 'sas', 'SGA_v2.0_scaffold1G00447' => 'sas', 'SHI15388' => 'shi', 'SHI15394' => 'shi', 'SHI15396' => 'shi', 'SHI15399' => 'shi', 'SMO343G0151' => 'smo', 'SMO367G1118' => 'smo', 'Solyc01g080200.3' => 'sly', 'Solyc06g008960.3' => 'sly', 'Solyc09g064780.3' => 'sly', 'Sopen01g031980' => 'spe', 'Sopen06g003710' => 'spe', 'Sopen09g026460' => 'spe', 'Sp3g21240' => 'spa', 'Sp4g30030' => 'spa', 'TAR365G0022' => 'tar', 'TAR365G1023' => 'tar', 'TAR365G1253' => 'tar', 'TAR623G0078' => 'tar', 'TAR623G1721' => 'tar', 'TAR633G0959' => 'tar', 'THA.LOC104802225' => 'tha', 'THA.LOC104804769' => 'tha', 'THA.LOC104808660' => 'tha', 'THA.LOC104812792' => 'tha', 'Thecc.01G284000' => 'tca', 'Thecc.04G220600' => 'tca', 'Thecc.05G268900' => 'tca', 'Thecc.08G171100' => 'tca', 'Thhalv10001284m.g' => 'esa', 'Thhalv10019912m.g' => 'esa', 'TPR.G14189' => 'tpr', 'TPR.G18110' => 'tpr', 'TPR.G18130' => 'tpr', 'TPR.G18131' => 'tpr', 'TPR.G18140' => 'tpr', 'TPR.G24282' => 'tpr', 'TPR.G25221' => 'tpr', 'TPR.G29267' => 'tpr', 'TPR.G35315' => 'tpr', 'TPR.G36173' => 'tpr', 'TWI09G0794' => 'twi', 'TWI59G1348' => 'twi', 'TWI74G0430' => 'twi', 'unitig_26.g8940' => 'ugi', 'unitig_749.g13744' => 'ugi', 'unitig_749.g13745' => 'ugi', 'vmacro08269' => 'vma', 'vmacro14937' => 'vma', 'vmacro20401' => 'vma', 'VMungo0464G1349' => 'vmu', 'VMungo0540G0289' => 'vmu', 'VMungo1215G1590' => 'vmu', 'VMungo1309G0221' => 'vmu', 'VMungo1309G2815' => 'vmu', 'VMungo1383G0239' => 'vmu', 'VMungo1383G2910' => 'vmu', 'Zm00001eb095270' => 'zma', 'Zm00001eb095280' => 'zma', 'Zm00001eb111630' => 'zma', 'Zm00001eb237080' => 'zma', 'Zm00001eb273740' => 'zma', 'Zm00001eb285040' => 'zma', 'Zm00001eb330790' => 'zma', 'Zm00001eb337380' => 'zma' ), 'gf_id' => 'HOM05D001484', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001484' ), 'data_identifier' => 'HOM05D001484', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001484', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p31500' => 'bna', 'A05p00020' => 'bna', 'A07p08820' => 'bna', 'Aa31LG4G3300' => 'aar', 'Aa31LG8G10030' => 'aar', 'Actinidia00731' => 'ach', 'Actinidia11473' => 'ach', 'Actinidia23469' => 'ach', 'Actinidia24318' => 'ach', 'Actinidia40196' => 'ach', 'Actinidia40197' => 'ach', 'Actinidia40198' => 'ach', 'Ah.08g212990' => 'amhyb', 'Ah.15g091720' => 'amhyb', 'AL3G38260' => 'aly', 'AL4G47710' => 'aly', 'Aqoxy2G00671' => 'aox', 'Aqoxy2G03236' => 'aox', 'arahy.Tifrunner.gnm1.ann1.05IDCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KR684' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATY3SJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK6QJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6APGL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IDT7Z9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM073U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ0R87' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LE7RV4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT4QRX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V5ENPK' => 'arhy', 'AT2G48110' => 'ath', 'AT3G23590' => 'ath', 'ATR0626G186' => 'atr', 'ATR1127G141' => 'atr', 'Atru.chr4.2583' => 'acertr', 'Atru.chr5.1358' => 'acertr', 'Atru.chr5.1359' => 'acertr', 'Atru.chr8.46' => 'acertr', 'AUR62002640' => 'cqu', 'AUR62030055' => 'cqu', 'AUR62033713' => 'cqu', 'AUR62033714' => 'cqu', 'AUR62036795' => 'cqu', 'AUR62039891' => 'cqu', 'BcaB02g08737' => 'bca', 'BcaB04g20441' => 'bca', 'BcaB06g26509' => 'bca', 'BcaB06g26510' => 'bca', 'BcaB06g26511' => 'bca', 'BcaB06g26512' => 'bca', 'BcaB06g26513' => 'bca', 'BcaC02g12564' => 'bca', 'BcaC02g12565' => 'bca', 'BcaC02g12794' => 'bca', 'BcaC02g12795' => 'bca', 'BcaC02g12796' => 'bca', 'BcaC06g35541' => 'bca', 'BNapus_Darmor_BZH_scaffold_188p00080' => 'bna', 'BNapus_Darmor_BZH_scaffold_188p00090' => 'bna', 'BolC1t03972H' => 'bol', 'BolC1t03973H' => 'bol', 'BolC4t21680H' => 'bol', 'BolC7t41863H' => 'bol', 'BolSC55t61227H' => 'bol', 'BolSC55t61228H' => 'bol', 'BraA01t03278Z' => 'bra', 'BraA05t18998Z' => 'bra', 'BraA07t28673Z' => 'bra', 'C01p40150' => 'bna', 'C05p12370' => 'bna', 'C07p13680' => 'bna', 'CAN.G1006.16' => 'can', 'CAN.G1006.17' => 'can', 'CAN.G1170.2' => 'can', 'CAN.G962.7' => 'can', 'CANSAT25G2179' => 'cansat', 'CANSAT78G1573' => 'cansat', 'CARHR099510' => 'chi', 'CARHR143510' => 'chi', 'Carub.0003s2380' => 'cru', 'Carub.0004s3082' => 'cru', 'Ca_00614_v3' => 'car', 'Ca_07801_v3' => 'car', 'Ca_08567_v3' => 'car', 'Ca_09571_v3' => 'car', 'CBR_g19290' => 'cbr', 'Cc01_g19770' => 'ccan', 'Cc03_g03030' => 'ccan', 'CDE07G0968' => 'cde', 'CDE09G1441' => 'cde', 'Cfa006103' => 'cfa', 'Cfa015573' => 'cfa', 'Cfa016988' => 'cfa', 'Ciclev10006738m.g' => 'ccl', 'Ciclev10010920m.g' => 'ccl', 'Ciclev10018517m.g' => 'ccl', 'CiPaw.01G159200' => 'cil', 'CiPaw.02G091000' => 'cil', 'CiPaw.02G091100' => 'cil', 'CiPaw.08G103100' => 'cil', 'CiPaw.09G224900' => 'cil', 'ClCG06G005740' => 'cla', 'ClCG07G000090' => 'cla', 'ClCG07G000100' => 'cla', 'COL.COLO4_09143' => 'col', 'COL.COLO4_25124' => 'col', 'Cpa.g.sc16.34' => 'cpa', 'Cpa.g.sc3504.1' => 'cpa', 'Cpa.g.sc60.37' => 'cpa', 'CsaV3_6G018520' => 'csa', 'CsaV3_6G036860' => 'csa', 'CSS0001072' => 'camsi', 'CSS0020208' => 'camsi', 'CSS0021253' => 'camsi', 'CSS0022190' => 'camsi', 'CSS0036150' => 'camsi', 'CSS0040442' => 'camsi', 'CSS0042300' => 'camsi', 'CSS0045298' => 'camsi', 'DCAR_012449' => 'dca', 'DCAR_018405' => 'dca', 'DCAR_024573' => 'dca', 'DCAR_030591' => 'dca', 'Dinv16926' => 'din', 'Dinv32963' => 'din', 'Dinv38382' => 'din', 'Dinv38383' => 'din', 'Duzib133G0974' => 'dzi', 'Duzib138G1867' => 'dzi', 'Duzib211G0420' => 'dzi', 'Duzib212G0930' => 'dzi', 'ECA234G1645' => 'eca', 'ECA247G3467' => 'eca', 'ECA248G1703' => 'eca', 'EL10Ac3g06327' => 'bvu', 'EL10Ac7g17204' => 'bvu', 'Eucgr.A00855' => 'egr', 'Eucgr.A00858' => 'egr', 'Eucgr.H01520' => 'egr', 'Eucgr.H03604' => 'egr', 'Eucgr.L03465' => 'egr', 'Eucgr.L03466' => 'egr', 'FAN01G0988' => 'fan', 'FAN02G3892' => 'fan', 'FAN05G3381' => 'fan', 'FAN07G0967' => 'fan', 'FAN07G1493' => 'fan', 'FAN08G3125' => 'fan', 'FAN09G0402' => 'fan', 'FAN12G2594' => 'fan', 'FAN12G3879' => 'fan', 'FAN14G1546' => 'fan', 'FAN15G3626' => 'fan', 'FAN17G0588' => 'fan', 'FAN17G0609' => 'fan', 'FAN18G2817' => 'fan', 'FAN19G1305' => 'fan', 'FAN20G1787' => 'fan', 'FAN22G0073' => 'fan', 'FAN22G0352' => 'fan', 'FAN22G0368' => 'fan', 'FAN22G2273' => 'fan', 'FAN24G1998' => 'fan', 'FAN27G1317' => 'fan', 'FvH4_2g23980' => 'fve', 'FvH4_4g14380' => 'fve', 'FvH4_4g14390' => 'fve', 'FvH4_6g09250' => 'fve', 'Glyma.03G151100' => 'gma', 'Glyma.04G122550' => 'gma', 'Glyma.05G001600' => 'gma', 'Glyma.09G270766' => 'gma', 'Glyma.09G270832' => 'gma', 'Glyma.13G209800' => 'gma', 'Glyma.15G102800' => 'gma', 'Glyma.18G218900' => 'gma', 'Glyma.19G001500' => 'gma', 'Glyma.19G153600' => 'gma', 'Gohir.A02G028600' => 'ghi', 'Gohir.A08G045000' => 'ghi', 'Gohir.A11G120500' => 'ghi', 'Gohir.A12G006200' => 'ghi', 'Gohir.A12G006250' => 'ghi', 'Gohir.D02G036300' => 'ghi', 'Gohir.D08G054700' => 'ghi', 'Gohir.D11G125600' => 'ghi', 'Gohir.D12G005700' => 'ghi', 'Gorai.004G055200' => 'gra', 'Gorai.005G040400' => 'gra', 'Gorai.007G134500' => 'gra', 'Gorai.008G005500' => 'gra', 'GSVIVG01011094001' => 'vvi', 'GSVIVG01017879001' => 'vvi', 'GSVIVG01025988001' => 'vvi', 'GSVIVG01029847001' => 'vvi', 'HanXRQChr10g0282901' => 'han', 'HanXRQChr10g0310371' => 'han', 'HanXRQChr10g0315041' => 'han', 'HanXRQChr11g0327651' => 'han', 'HanXRQChr12g0359391' => 'han', 'Haze_00972' => 'cav', 'Haze_00973' => 'cav', 'Haze_00974' => 'cav', 'Haze_04747' => 'cav', 'Haze_04749' => 'cav', 'Haze_04750' => 'cav', 'Haze_21217' => 'cav', 'Hma1.2p1_1037F.1_g250680' => 'hma', 'Hma1.2p1_1644F.1_g295320' => 'hma', 'HPP92_011322' => 'vpl', 'HPP92_011323' => 'vpl', 'HPP92_011324' => 'vpl', 'HPP92_011325' => 'vpl', 'HPP92_011326' => 'vpl', 'Hund12205' => 'sun', 'Hund17957' => 'sun', 'Lalb_Chr06g0176771' => 'lal', 'Lalb_Chr18g0056021' => 'lal', 'Lalb_Chr18g0056031' => 'lal', 'Lalb_Chr18g0056041' => 'lal', 'Lalb_Chr20g0107751' => 'lal', 'Lalb_Chr20g0118371' => 'lal', 'Lj1g0010239' => 'lja', 'Lj1g0017101' => 'lja', 'Lj2A1178G40' => 'lonja', 'Lj2A54G84' => 'lonja', 'Lj2g0015248' => 'lja', 'Lj3A761T51' => 'lonja', 'Lj6g0018116' => 'lja', 'Lsat_1_v5_gn_4_136040' => 'lsa', 'Lsat_1_v5_gn_5_187461' => 'lsa', 'Lsat_1_v5_gn_5_77001' => 'lsa', 'Lsat_1_v5_gn_9_4461' => 'lsa', 'Manes.01G210100' => 'mes', 'Manes.03G185600' => 'mes', 'Manes.05G073300' => 'mes', 'Manes.09G120300' => 'mes', 'Manes.15G022100' => 'mes', 'Mapoly0096s0053' => 'mpo', 'MBI03_g14058_MAGBIO' => 'mbi', 'MBI03_g33876_MAGBIO' => 'mbi', 'MBI03_g36854_MAGBIO' => 'mbi', 'MBI17_g11997_MAGBIO' => 'mbi', 'MD03G1269000' => 'mdo', 'MD04G1179600' => 'mdo', 'MD11G1289800' => 'mdo', 'MD12G1194700' => 'mdo', 'MD13G1182100' => 'mdo', 'MD13G1182200' => 'mdo', 'MD16G1182600' => 'mdo', 'Medtr2g021400' => 'mtr', 'Medtr2g021470' => 'mtr', 'Medtr2g105810' => 'mtr', 'Medtr3g033580' => 'mtr', 'Medtr6g007970' => 'mtr', 'Medtr7g056330' => 'mtr', 'Medtr7g074290' => 'mtr', 'Medtr7g074380' => 'mtr', 'Medtr7g094550' => 'mtr', 'Medtr8g069995' => 'mtr', 'MELO3C014345.2' => 'cme', 'MELO3C021395.2' => 'cme', 'Migut.D00262' => 'egut', 'Migut.G00257' => 'egut', 'MSTRG.21575' => 'ama', 'MSTRG.3985' => 'ama', 'Nitab4.5_0000295g0140' => 'nta', 'Nitab4.5_0000732g0140' => 'nta', 'Nitab4.5_0003162g0020' => 'nta', 'Nitab4.5_0006180g0090' => 'nta', 'Nitab4.5_0006390g0010' => 'nta', 'Nitab4.5_0007392g0040' => 'nta', 'Nn1g02140' => 'nnu', 'Nn4g26168' => 'nnu', 'Nn5g26754' => 'nnu', 'Oeu001433.1' => 'oeu', 'Oeu010299.2' => 'oeu', 'Oeu011171.1' => 'oeu', 'Oeu037675.1' => 'oeu', 'Oeu038359.1' => 'oeu', 'Oeu063834.1' => 'oeu', 'Oeu063835.1' => 'oeu', 'Os05g0312000' => 'osa', 'Os07g0211101' => 'osa', 'Os07g0211200' => 'osa', 'Os07g0681500' => 'osa', 'Peaxi162Scf00095g01015' => 'pax', 'Peaxi162Scf00104g00329' => 'pax', 'Peaxi162Scf00161g00137' => 'pax', 'PGR004G1665' => 'pgr', 'PGR031G2937' => 'pgr', 'PGR119G2145' => 'pgr', 'PGSC0003DMG400004351' => 'stu', 'PGSC0003DMG400014625' => 'stu', 'PGSC0003DMG401000943' => 'stu', 'Phvul.001G148600' => 'pvu', 'Phvul.004G001700' => 'pvu', 'Phvul.006G154900' => 'pvu', 'Phvul.008G078200' => 'pvu', 'Phvul.011G136500' => 'pvu', 'Potri.002G215600' => 'ptr', 'Potri.008G201600' => 'ptr', 'Potri.014G138400' => 'ptr', 'Potri.016G142500' => 'ptr', 'Pp3c16_10580' => 'ppa', 'Pp3c5_25280' => 'ppa', 'Prupe.1G150000' => 'ppe', 'Prupe.1G150100' => 'ppe', 'Prupe.6G299600' => 'ppe', 'Prupe.8G245000' => 'ppe', 'Psat0s4927g0040' => 'psa', 'Psat1g052080' => 'psa', 'Psat1g183800' => 'psa', 'Psat3g113840' => 'psa', 'Psat3g126120' => 'psa', 'Psat3g126160' => 'psa', 'Psat3g158760' => 'psa', 'Psat3g158840' => 'psa', 'PSO170G2858' => 'pso', 'PSO339G0606' => 'pso', 'PSO384G4709' => 'pso', 'PSO407G0334' => 'pso', 'QL04p040276' => 'qlo', 'QL06p005458' => 'qlo', 'QL06p005472' => 'qlo', 'QL07p030546' => 'qlo', 'QL07p031519' => 'qlo', 'QL09p050949' => 'qlo', 'QL09p050966' => 'qlo', 'QL09p051067' => 'qlo', 'QL12p022706' => 'qlo', 'RcHm_v2.0_Chr2g0119601' => 'rch', 'RcHm_v2.0_Chr3g0459591' => 'rch', 'RcHm_v2.0_Chr4g0418521' => 'rch', 'RcHm_v2.0_Chr4g0418531' => 'rch', 'RcHm_v2.0_Chr4g0418541' => 'rch', 'RcHm_v2.0_Chr6g0291641' => 'rch', 'Rhsim01G0086300' => 'rsi', 'Rhsim01G0276300' => 'rsi', 'Rhsim01G0276500' => 'rsi', 'Rhsim04G0207700' => 'rsi', 'Rhsim05G0234500' => 'rsi', 'Rhsim13G0022400' => 'rsi', 'Sabra02G0167900' => 'sbr', 'Sabra04G0158500' => 'sbr', 'Sabra08G0159800' => 'sbr', 'Sabra10G0011500' => 'sbr', 'Sabra14G0104400' => 'sbr', 'SalBow2G2440' => 'sbo', 'SalBow4G2265' => 'sbo', 'Sc02g0000060' => 'sci', 'Sc05g0005020' => 'sci', 'Sc13g0003890' => 'sci', 'Sed0014865' => 'sed', 'Sed0017224' => 'sed', 'Sed0026391' => 'sed', 'SEGI_00063' => 'sgi', 'SEGI_10967' => 'sgi', 'SEGI_17510' => 'sgi', 'SEGI_24396' => 'sgi', 'SEGI_39719' => 'sgi', 'SEGI_41392' => 'sgi', 'SGA_v2.0_scaffold11G05794' => 'sas', 'SGA_v2.0_scaffold142G35607' => 'sas', 'SGA_v2.0_scaffold1G00447' => 'sas', 'SHI15388' => 'shi', 'SHI15394' => 'shi', 'SHI15396' => 'shi', 'SHI15399' => 'shi', 'SMO343G0151' => 'smo', 'SMO367G1118' => 'smo', 'Solyc01g080200.3' => 'sly', 'Solyc06g008960.3' => 'sly', 'Solyc09g064780.3' => 'sly', 'Sopen01g031980' => 'spe', 'Sopen06g003710' => 'spe', 'Sopen09g026460' => 'spe', 'Sp3g21240' => 'spa', 'Sp4g30030' => 'spa', 'TAR365G0022' => 'tar', 'TAR365G1023' => 'tar', 'TAR365G1253' => 'tar', 'TAR623G0078' => 'tar', 'TAR623G1721' => 'tar', 'TAR633G0959' => 'tar', 'THA.LOC104802225' => 'tha', 'THA.LOC104804769' => 'tha', 'THA.LOC104808660' => 'tha', 'THA.LOC104812792' => 'tha', 'Thecc.01G284000' => 'tca', 'Thecc.04G220600' => 'tca', 'Thecc.05G268900' => 'tca', 'Thecc.08G171100' => 'tca', 'Thhalv10001284m.g' => 'esa', 'Thhalv10019912m.g' => 'esa', 'TPR.G14189' => 'tpr', 'TPR.G18110' => 'tpr', 'TPR.G18130' => 'tpr', 'TPR.G18131' => 'tpr', 'TPR.G18140' => 'tpr', 'TPR.G24282' => 'tpr', 'TPR.G25221' => 'tpr', 'TPR.G29267' => 'tpr', 'TPR.G35315' => 'tpr', 'TPR.G36173' => 'tpr', 'TWI09G0794' => 'twi', 'TWI59G1348' => 'twi', 'TWI74G0430' => 'twi', 'unitig_26.g8940' => 'ugi', 'unitig_749.g13744' => 'ugi', 'unitig_749.g13745' => 'ugi', 'vmacro08269' => 'vma', 'vmacro14937' => 'vma', 'vmacro20401' => 'vma', 'VMungo0464G1349' => 'vmu', 'VMungo0540G0289' => 'vmu', 'VMungo1215G1590' => 'vmu', 'VMungo1309G0221' => 'vmu', 'VMungo1309G2815' => 'vmu', 'VMungo1383G0239' => 'vmu', 'VMungo1383G2910' => 'vmu', 'Zm00001eb095270' => 'zma', 'Zm00001eb095280' => 'zma', 'Zm00001eb111630' => 'zma', 'Zm00001eb237080' => 'zma', 'Zm00001eb273740' => 'zma', 'Zm00001eb285040' => 'zma', 'Zm00001eb330790' => 'zma', 'Zm00001eb337380' => 'zma' ) $gf_id = 'HOM05D001484' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001484' ) $data_identifier = 'HOM05D001484' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 2, 'aly' => (int) 2, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 22, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 7, 'hma' => (int) 2, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 7, 'mtr' => (int) 10, 'cme' => (int) 2, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 4, 'ppa' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 4, 'qlo' => (int) 9, 'rch' => (int) 6, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 10, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 7, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb337380' $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' => 'HOM05D001484', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p31500' => 'bna', 'A05p00020' => 'bna', 'A07p08820' => 'bna', 'Aa31LG4G3300' => 'aar', 'Aa31LG8G10030' => 'aar', 'Actinidia00731' => 'ach', 'Actinidia11473' => 'ach', 'Actinidia23469' => 'ach', 'Actinidia24318' => 'ach', 'Actinidia40196' => 'ach', 'Actinidia40197' => 'ach', 'Actinidia40198' => 'ach', 'Ah.08g212990' => 'amhyb', 'Ah.15g091720' => 'amhyb', 'AL3G38260' => 'aly', 'AL4G47710' => 'aly', 'Aqoxy2G00671' => 'aox', 'Aqoxy2G03236' => 'aox', 'arahy.Tifrunner.gnm1.ann1.05IDCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KR684' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATY3SJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK6QJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6APGL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IDT7Z9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM073U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ0R87' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LE7RV4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT4QRX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V5ENPK' => 'arhy', 'AT2G48110' => 'ath', 'AT3G23590' => 'ath', 'ATR0626G186' => 'atr', 'ATR1127G141' => 'atr', 'Atru.chr4.2583' => 'acertr', 'Atru.chr5.1358' => 'acertr', 'Atru.chr5.1359' => 'acertr', 'Atru.chr8.46' => 'acertr', 'AUR62002640' => 'cqu', 'AUR62030055' => 'cqu', 'AUR62033713' => 'cqu', 'AUR62033714' => 'cqu', 'AUR62036795' => 'cqu', 'AUR62039891' => 'cqu', 'BcaB02g08737' => 'bca', 'BcaB04g20441' => 'bca', 'BcaB06g26509' => 'bca', 'BcaB06g26510' => 'bca', 'BcaB06g26511' => 'bca', 'BcaB06g26512' => 'bca', 'BcaB06g26513' => 'bca', 'BcaC02g12564' => 'bca', 'BcaC02g12565' => 'bca', 'BcaC02g12794' => 'bca', 'BcaC02g12795' => 'bca', 'BcaC02g12796' => 'bca', 'BcaC06g35541' => 'bca', 'BNapus_Darmor_BZH_scaffold_188p00080' => 'bna', 'BNapus_Darmor_BZH_scaffold_188p00090' => 'bna', 'BolC1t03972H' => 'bol', 'BolC1t03973H' => 'bol', 'BolC4t21680H' => 'bol', 'BolC7t41863H' => 'bol', 'BolSC55t61227H' => 'bol', 'BolSC55t61228H' => 'bol', 'BraA01t03278Z' => 'bra', 'BraA05t18998Z' => 'bra', 'BraA07t28673Z' => 'bra', 'C01p40150' => 'bna', 'C05p12370' => 'bna', 'C07p13680' => 'bna', 'CAN.G1006.16' => 'can', 'CAN.G1006.17' => 'can', 'CAN.G1170.2' => 'can', 'CAN.G962.7' => 'can', 'CANSAT25G2179' => 'cansat', 'CANSAT78G1573' => 'cansat', 'CARHR099510' => 'chi', 'CARHR143510' => 'chi', 'Carub.0003s2380' => 'cru', 'Carub.0004s3082' => 'cru', 'Ca_00614_v3' => 'car', 'Ca_07801_v3' => 'car', 'Ca_08567_v3' => 'car', 'Ca_09571_v3' => 'car', 'CBR_g19290' => 'cbr', 'Cc01_g19770' => 'ccan', 'Cc03_g03030' => 'ccan', 'CDE07G0968' => 'cde', 'CDE09G1441' => 'cde', 'Cfa006103' => 'cfa', 'Cfa015573' => 'cfa', 'Cfa016988' => 'cfa', 'Ciclev10006738m.g' => 'ccl', 'Ciclev10010920m.g' => 'ccl', 'Ciclev10018517m.g' => 'ccl', 'CiPaw.01G159200' => 'cil', 'CiPaw.02G091000' => 'cil', 'CiPaw.02G091100' => 'cil', 'CiPaw.08G103100' => 'cil', 'CiPaw.09G224900' => 'cil', 'ClCG06G005740' => 'cla', 'ClCG07G000090' => 'cla', 'ClCG07G000100' => 'cla', 'COL.COLO4_09143' => 'col', 'COL.COLO4_25124' => 'col', 'Cpa.g.sc16.34' => 'cpa', 'Cpa.g.sc3504.1' => 'cpa', 'Cpa.g.sc60.37' => 'cpa', 'CsaV3_6G018520' => 'csa', 'CsaV3_6G036860' => 'csa', 'CSS0001072' => 'camsi', 'CSS0020208' => 'camsi', 'CSS0021253' => 'camsi', 'CSS0022190' => 'camsi', 'CSS0036150' => 'camsi', 'CSS0040442' => 'camsi', 'CSS0042300' => 'camsi', 'CSS0045298' => 'camsi', 'DCAR_012449' => 'dca', 'DCAR_018405' => 'dca', 'DCAR_024573' => 'dca', 'DCAR_030591' => 'dca', 'Dinv16926' => 'din', 'Dinv32963' => 'din', 'Dinv38382' => 'din', 'Dinv38383' => 'din', 'Duzib133G0974' => 'dzi', 'Duzib138G1867' => 'dzi', 'Duzib211G0420' => 'dzi', 'Duzib212G0930' => 'dzi', 'ECA234G1645' => 'eca', 'ECA247G3467' => 'eca', 'ECA248G1703' => 'eca', 'EL10Ac3g06327' => 'bvu', 'EL10Ac7g17204' => 'bvu', 'Eucgr.A00855' => 'egr', 'Eucgr.A00858' => 'egr', 'Eucgr.H01520' => 'egr', 'Eucgr.H03604' => 'egr', 'Eucgr.L03465' => 'egr', 'Eucgr.L03466' => 'egr', 'FAN01G0988' => 'fan', 'FAN02G3892' => 'fan', 'FAN05G3381' => 'fan', 'FAN07G0967' => 'fan', 'FAN07G1493' => 'fan', 'FAN08G3125' => 'fan', 'FAN09G0402' => 'fan', 'FAN12G2594' => 'fan', 'FAN12G3879' => 'fan', 'FAN14G1546' => 'fan', 'FAN15G3626' => 'fan', 'FAN17G0588' => 'fan', 'FAN17G0609' => 'fan', 'FAN18G2817' => 'fan', 'FAN19G1305' => 'fan', 'FAN20G1787' => 'fan', 'FAN22G0073' => 'fan', 'FAN22G0352' => 'fan', 'FAN22G0368' => 'fan', 'FAN22G2273' => 'fan', 'FAN24G1998' => 'fan', 'FAN27G1317' => 'fan', 'FvH4_2g23980' => 'fve', 'FvH4_4g14380' => 'fve', 'FvH4_4g14390' => 'fve', 'FvH4_6g09250' => 'fve', 'Glyma.03G151100' => 'gma', 'Glyma.04G122550' => 'gma', 'Glyma.05G001600' => 'gma', 'Glyma.09G270766' => 'gma', 'Glyma.09G270832' => 'gma', 'Glyma.13G209800' => 'gma', 'Glyma.15G102800' => 'gma', 'Glyma.18G218900' => 'gma', 'Glyma.19G001500' => 'gma', 'Glyma.19G153600' => 'gma', 'Gohir.A02G028600' => 'ghi', 'Gohir.A08G045000' => 'ghi', 'Gohir.A11G120500' => 'ghi', 'Gohir.A12G006200' => 'ghi', 'Gohir.A12G006250' => 'ghi', 'Gohir.D02G036300' => 'ghi', 'Gohir.D08G054700' => 'ghi', 'Gohir.D11G125600' => 'ghi', 'Gohir.D12G005700' => 'ghi', 'Gorai.004G055200' => 'gra', 'Gorai.005G040400' => 'gra', 'Gorai.007G134500' => 'gra', 'Gorai.008G005500' => 'gra', 'GSVIVG01011094001' => 'vvi', 'GSVIVG01017879001' => 'vvi', 'GSVIVG01025988001' => 'vvi', 'GSVIVG01029847001' => 'vvi', 'HanXRQChr10g0282901' => 'han', 'HanXRQChr10g0310371' => 'han', 'HanXRQChr10g0315041' => 'han', 'HanXRQChr11g0327651' => 'han', 'HanXRQChr12g0359391' => 'han', 'Haze_00972' => 'cav', 'Haze_00973' => 'cav', 'Haze_00974' => 'cav', 'Haze_04747' => 'cav', 'Haze_04749' => 'cav', 'Haze_04750' => 'cav', 'Haze_21217' => 'cav', 'Hma1.2p1_1037F.1_g250680' => 'hma', 'Hma1.2p1_1644F.1_g295320' => 'hma', 'HPP92_011322' => 'vpl', 'HPP92_011323' => 'vpl', 'HPP92_011324' => 'vpl', 'HPP92_011325' => 'vpl', 'HPP92_011326' => 'vpl', 'Hund12205' => 'sun', 'Hund17957' => 'sun', 'Lalb_Chr06g0176771' => 'lal', 'Lalb_Chr18g0056021' => 'lal', 'Lalb_Chr18g0056031' => 'lal', 'Lalb_Chr18g0056041' => 'lal', 'Lalb_Chr20g0107751' => 'lal', 'Lalb_Chr20g0118371' => 'lal', 'Lj1g0010239' => 'lja', 'Lj1g0017101' => 'lja', 'Lj2A1178G40' => 'lonja', 'Lj2A54G84' => 'lonja', 'Lj2g0015248' => 'lja', 'Lj3A761T51' => 'lonja', 'Lj6g0018116' => 'lja', 'Lsat_1_v5_gn_4_136040' => 'lsa', 'Lsat_1_v5_gn_5_187461' => 'lsa', 'Lsat_1_v5_gn_5_77001' => 'lsa', 'Lsat_1_v5_gn_9_4461' => 'lsa', 'Manes.01G210100' => 'mes', 'Manes.03G185600' => 'mes', 'Manes.05G073300' => 'mes', 'Manes.09G120300' => 'mes', 'Manes.15G022100' => 'mes', 'Mapoly0096s0053' => 'mpo', 'MBI03_g14058_MAGBIO' => 'mbi', 'MBI03_g33876_MAGBIO' => 'mbi', 'MBI03_g36854_MAGBIO' => 'mbi', 'MBI17_g11997_MAGBIO' => 'mbi', 'MD03G1269000' => 'mdo', 'MD04G1179600' => 'mdo', 'MD11G1289800' => 'mdo', 'MD12G1194700' => 'mdo', 'MD13G1182100' => 'mdo', 'MD13G1182200' => 'mdo', 'MD16G1182600' => 'mdo', 'Medtr2g021400' => 'mtr', 'Medtr2g021470' => 'mtr', 'Medtr2g105810' => 'mtr', 'Medtr3g033580' => 'mtr', 'Medtr6g007970' => 'mtr', 'Medtr7g056330' => 'mtr', 'Medtr7g074290' => 'mtr', 'Medtr7g074380' => 'mtr', 'Medtr7g094550' => 'mtr', 'Medtr8g069995' => 'mtr', 'MELO3C014345.2' => 'cme', 'MELO3C021395.2' => 'cme', 'Migut.D00262' => 'egut', 'Migut.G00257' => 'egut', 'MSTRG.21575' => 'ama', 'MSTRG.3985' => 'ama', 'Nitab4.5_0000295g0140' => 'nta', 'Nitab4.5_0000732g0140' => 'nta', 'Nitab4.5_0003162g0020' => 'nta', 'Nitab4.5_0006180g0090' => 'nta', 'Nitab4.5_0006390g0010' => 'nta', 'Nitab4.5_0007392g0040' => 'nta', 'Nn1g02140' => 'nnu', 'Nn4g26168' => 'nnu', 'Nn5g26754' => 'nnu', 'Oeu001433.1' => 'oeu', 'Oeu010299.2' => 'oeu', 'Oeu011171.1' => 'oeu', 'Oeu037675.1' => 'oeu', 'Oeu038359.1' => 'oeu', 'Oeu063834.1' => 'oeu', 'Oeu063835.1' => 'oeu', 'Os05g0312000' => 'osa', 'Os07g0211101' => 'osa', 'Os07g0211200' => 'osa', 'Os07g0681500' => 'osa', 'Peaxi162Scf00095g01015' => 'pax', 'Peaxi162Scf00104g00329' => 'pax', 'Peaxi162Scf00161g00137' => 'pax', 'PGR004G1665' => 'pgr', 'PGR031G2937' => 'pgr', 'PGR119G2145' => 'pgr', 'PGSC0003DMG400004351' => 'stu', 'PGSC0003DMG400014625' => 'stu', 'PGSC0003DMG401000943' => 'stu', 'Phvul.001G148600' => 'pvu', 'Phvul.004G001700' => 'pvu', 'Phvul.006G154900' => 'pvu', 'Phvul.008G078200' => 'pvu', 'Phvul.011G136500' => 'pvu', 'Potri.002G215600' => 'ptr', 'Potri.008G201600' => 'ptr', 'Potri.014G138400' => 'ptr', 'Potri.016G142500' => 'ptr', 'Pp3c16_10580' => 'ppa', 'Pp3c5_25280' => 'ppa', 'Prupe.1G150000' => 'ppe', 'Prupe.1G150100' => 'ppe', 'Prupe.6G299600' => 'ppe', 'Prupe.8G245000' => 'ppe', 'Psat0s4927g0040' => 'psa', 'Psat1g052080' => 'psa', 'Psat1g183800' => 'psa', 'Psat3g113840' => 'psa', 'Psat3g126120' => 'psa', 'Psat3g126160' => 'psa', 'Psat3g158760' => 'psa', 'Psat3g158840' => 'psa', 'PSO170G2858' => 'pso', 'PSO339G0606' => 'pso', 'PSO384G4709' => 'pso', 'PSO407G0334' => 'pso', 'QL04p040276' => 'qlo', 'QL06p005458' => 'qlo', 'QL06p005472' => 'qlo', 'QL07p030546' => 'qlo', 'QL07p031519' => 'qlo', 'QL09p050949' => 'qlo', 'QL09p050966' => 'qlo', 'QL09p051067' => 'qlo', 'QL12p022706' => 'qlo', 'RcHm_v2.0_Chr2g0119601' => 'rch', 'RcHm_v2.0_Chr3g0459591' => 'rch', 'RcHm_v2.0_Chr4g0418521' => 'rch', 'RcHm_v2.0_Chr4g0418531' => 'rch', 'RcHm_v2.0_Chr4g0418541' => 'rch', 'RcHm_v2.0_Chr6g0291641' => 'rch', 'Rhsim01G0086300' => 'rsi', 'Rhsim01G0276300' => 'rsi', 'Rhsim01G0276500' => 'rsi', 'Rhsim04G0207700' => 'rsi', 'Rhsim05G0234500' => 'rsi', 'Rhsim13G0022400' => 'rsi', 'Sabra02G0167900' => 'sbr', 'Sabra04G0158500' => 'sbr', 'Sabra08G0159800' => 'sbr', 'Sabra10G0011500' => 'sbr', 'Sabra14G0104400' => 'sbr', 'SalBow2G2440' => 'sbo', 'SalBow4G2265' => 'sbo', 'Sc02g0000060' => 'sci', 'Sc05g0005020' => 'sci', 'Sc13g0003890' => 'sci', 'Sed0014865' => 'sed', 'Sed0017224' => 'sed', 'Sed0026391' => 'sed', 'SEGI_00063' => 'sgi', 'SEGI_10967' => 'sgi', 'SEGI_17510' => 'sgi', 'SEGI_24396' => 'sgi', 'SEGI_39719' => 'sgi', 'SEGI_41392' => 'sgi', 'SGA_v2.0_scaffold11G05794' => 'sas', 'SGA_v2.0_scaffold142G35607' => 'sas', 'SGA_v2.0_scaffold1G00447' => 'sas', 'SHI15388' => 'shi', 'SHI15394' => 'shi', 'SHI15396' => 'shi', 'SHI15399' => 'shi', 'SMO343G0151' => 'smo', 'SMO367G1118' => 'smo', 'Solyc01g080200.3' => 'sly', 'Solyc06g008960.3' => 'sly', 'Solyc09g064780.3' => 'sly', 'Sopen01g031980' => 'spe', 'Sopen06g003710' => 'spe', 'Sopen09g026460' => 'spe', 'Sp3g21240' => 'spa', 'Sp4g30030' => 'spa', 'TAR365G0022' => 'tar', 'TAR365G1023' => 'tar', 'TAR365G1253' => 'tar', 'TAR623G0078' => 'tar', 'TAR623G1721' => 'tar', 'TAR633G0959' => 'tar', 'THA.LOC104802225' => 'tha', 'THA.LOC104804769' => 'tha', 'THA.LOC104808660' => 'tha', 'THA.LOC104812792' => 'tha', 'Thecc.01G284000' => 'tca', 'Thecc.04G220600' => 'tca', 'Thecc.05G268900' => 'tca', 'Thecc.08G171100' => 'tca', 'Thhalv10001284m.g' => 'esa', 'Thhalv10019912m.g' => 'esa', 'TPR.G14189' => 'tpr', 'TPR.G18110' => 'tpr', 'TPR.G18130' => 'tpr', 'TPR.G18131' => 'tpr', 'TPR.G18140' => 'tpr', 'TPR.G24282' => 'tpr', 'TPR.G25221' => 'tpr', 'TPR.G29267' => 'tpr', 'TPR.G35315' => 'tpr', 'TPR.G36173' => 'tpr', 'TWI09G0794' => 'twi', 'TWI59G1348' => 'twi', 'TWI74G0430' => 'twi', 'unitig_26.g8940' => 'ugi', 'unitig_749.g13744' => 'ugi', 'unitig_749.g13745' => 'ugi', 'vmacro08269' => 'vma', 'vmacro14937' => 'vma', 'vmacro20401' => 'vma', 'VMungo0464G1349' => 'vmu', 'VMungo0540G0289' => 'vmu', 'VMungo1215G1590' => 'vmu', 'VMungo1309G0221' => 'vmu', 'VMungo1309G2815' => 'vmu', 'VMungo1383G0239' => 'vmu', 'VMungo1383G2910' => 'vmu', 'Zm00001eb095270' => 'zma', 'Zm00001eb095280' => 'zma', 'Zm00001eb111630' => 'zma', 'Zm00001eb237080' => 'zma', 'Zm00001eb273740' => 'zma', 'Zm00001eb285040' => 'zma', 'Zm00001eb330790' => 'zma', 'Zm00001eb337380' => 'zma' ), 'gf_id' => 'HOM05D001484', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001484' ), 'data_identifier' => 'HOM05D001484', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001484', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p31500' => 'bna', 'A05p00020' => 'bna', 'A07p08820' => 'bna', 'Aa31LG4G3300' => 'aar', 'Aa31LG8G10030' => 'aar', 'Actinidia00731' => 'ach', 'Actinidia11473' => 'ach', 'Actinidia23469' => 'ach', 'Actinidia24318' => 'ach', 'Actinidia40196' => 'ach', 'Actinidia40197' => 'ach', 'Actinidia40198' => 'ach', 'Ah.08g212990' => 'amhyb', 'Ah.15g091720' => 'amhyb', 'AL3G38260' => 'aly', 'AL4G47710' => 'aly', 'Aqoxy2G00671' => 'aox', 'Aqoxy2G03236' => 'aox', 'arahy.Tifrunner.gnm1.ann1.05IDCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KR684' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATY3SJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK6QJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6APGL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IDT7Z9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM073U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ0R87' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LE7RV4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT4QRX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V5ENPK' => 'arhy', 'AT2G48110' => 'ath', 'AT3G23590' => 'ath', 'ATR0626G186' => 'atr', 'ATR1127G141' => 'atr', 'Atru.chr4.2583' => 'acertr', 'Atru.chr5.1358' => 'acertr', 'Atru.chr5.1359' => 'acertr', 'Atru.chr8.46' => 'acertr', 'AUR62002640' => 'cqu', 'AUR62030055' => 'cqu', 'AUR62033713' => 'cqu', 'AUR62033714' => 'cqu', 'AUR62036795' => 'cqu', 'AUR62039891' => 'cqu', 'BcaB02g08737' => 'bca', 'BcaB04g20441' => 'bca', 'BcaB06g26509' => 'bca', 'BcaB06g26510' => 'bca', 'BcaB06g26511' => 'bca', 'BcaB06g26512' => 'bca', 'BcaB06g26513' => 'bca', 'BcaC02g12564' => 'bca', 'BcaC02g12565' => 'bca', 'BcaC02g12794' => 'bca', 'BcaC02g12795' => 'bca', 'BcaC02g12796' => 'bca', 'BcaC06g35541' => 'bca', 'BNapus_Darmor_BZH_scaffold_188p00080' => 'bna', 'BNapus_Darmor_BZH_scaffold_188p00090' => 'bna', 'BolC1t03972H' => 'bol', 'BolC1t03973H' => 'bol', 'BolC4t21680H' => 'bol', 'BolC7t41863H' => 'bol', 'BolSC55t61227H' => 'bol', 'BolSC55t61228H' => 'bol', 'BraA01t03278Z' => 'bra', 'BraA05t18998Z' => 'bra', 'BraA07t28673Z' => 'bra', 'C01p40150' => 'bna', 'C05p12370' => 'bna', 'C07p13680' => 'bna', 'CAN.G1006.16' => 'can', 'CAN.G1006.17' => 'can', 'CAN.G1170.2' => 'can', 'CAN.G962.7' => 'can', 'CANSAT25G2179' => 'cansat', 'CANSAT78G1573' => 'cansat', 'CARHR099510' => 'chi', 'CARHR143510' => 'chi', 'Carub.0003s2380' => 'cru', 'Carub.0004s3082' => 'cru', 'Ca_00614_v3' => 'car', 'Ca_07801_v3' => 'car', 'Ca_08567_v3' => 'car', 'Ca_09571_v3' => 'car', 'CBR_g19290' => 'cbr', 'Cc01_g19770' => 'ccan', 'Cc03_g03030' => 'ccan', 'CDE07G0968' => 'cde', 'CDE09G1441' => 'cde', 'Cfa006103' => 'cfa', 'Cfa015573' => 'cfa', 'Cfa016988' => 'cfa', 'Ciclev10006738m.g' => 'ccl', 'Ciclev10010920m.g' => 'ccl', 'Ciclev10018517m.g' => 'ccl', 'CiPaw.01G159200' => 'cil', 'CiPaw.02G091000' => 'cil', 'CiPaw.02G091100' => 'cil', 'CiPaw.08G103100' => 'cil', 'CiPaw.09G224900' => 'cil', 'ClCG06G005740' => 'cla', 'ClCG07G000090' => 'cla', 'ClCG07G000100' => 'cla', 'COL.COLO4_09143' => 'col', 'COL.COLO4_25124' => 'col', 'Cpa.g.sc16.34' => 'cpa', 'Cpa.g.sc3504.1' => 'cpa', 'Cpa.g.sc60.37' => 'cpa', 'CsaV3_6G018520' => 'csa', 'CsaV3_6G036860' => 'csa', 'CSS0001072' => 'camsi', 'CSS0020208' => 'camsi', 'CSS0021253' => 'camsi', 'CSS0022190' => 'camsi', 'CSS0036150' => 'camsi', 'CSS0040442' => 'camsi', 'CSS0042300' => 'camsi', 'CSS0045298' => 'camsi', 'DCAR_012449' => 'dca', 'DCAR_018405' => 'dca', 'DCAR_024573' => 'dca', 'DCAR_030591' => 'dca', 'Dinv16926' => 'din', 'Dinv32963' => 'din', 'Dinv38382' => 'din', 'Dinv38383' => 'din', 'Duzib133G0974' => 'dzi', 'Duzib138G1867' => 'dzi', 'Duzib211G0420' => 'dzi', 'Duzib212G0930' => 'dzi', 'ECA234G1645' => 'eca', 'ECA247G3467' => 'eca', 'ECA248G1703' => 'eca', 'EL10Ac3g06327' => 'bvu', 'EL10Ac7g17204' => 'bvu', 'Eucgr.A00855' => 'egr', 'Eucgr.A00858' => 'egr', 'Eucgr.H01520' => 'egr', 'Eucgr.H03604' => 'egr', 'Eucgr.L03465' => 'egr', 'Eucgr.L03466' => 'egr', 'FAN01G0988' => 'fan', 'FAN02G3892' => 'fan', 'FAN05G3381' => 'fan', 'FAN07G0967' => 'fan', 'FAN07G1493' => 'fan', 'FAN08G3125' => 'fan', 'FAN09G0402' => 'fan', 'FAN12G2594' => 'fan', 'FAN12G3879' => 'fan', 'FAN14G1546' => 'fan', 'FAN15G3626' => 'fan', 'FAN17G0588' => 'fan', 'FAN17G0609' => 'fan', 'FAN18G2817' => 'fan', 'FAN19G1305' => 'fan', 'FAN20G1787' => 'fan', 'FAN22G0073' => 'fan', 'FAN22G0352' => 'fan', 'FAN22G0368' => 'fan', 'FAN22G2273' => 'fan', 'FAN24G1998' => 'fan', 'FAN27G1317' => 'fan', 'FvH4_2g23980' => 'fve', 'FvH4_4g14380' => 'fve', 'FvH4_4g14390' => 'fve', 'FvH4_6g09250' => 'fve', 'Glyma.03G151100' => 'gma', 'Glyma.04G122550' => 'gma', 'Glyma.05G001600' => 'gma', 'Glyma.09G270766' => 'gma', 'Glyma.09G270832' => 'gma', 'Glyma.13G209800' => 'gma', 'Glyma.15G102800' => 'gma', 'Glyma.18G218900' => 'gma', 'Glyma.19G001500' => 'gma', 'Glyma.19G153600' => 'gma', 'Gohir.A02G028600' => 'ghi', 'Gohir.A08G045000' => 'ghi', 'Gohir.A11G120500' => 'ghi', 'Gohir.A12G006200' => 'ghi', 'Gohir.A12G006250' => 'ghi', 'Gohir.D02G036300' => 'ghi', 'Gohir.D08G054700' => 'ghi', 'Gohir.D11G125600' => 'ghi', 'Gohir.D12G005700' => 'ghi', 'Gorai.004G055200' => 'gra', 'Gorai.005G040400' => 'gra', 'Gorai.007G134500' => 'gra', 'Gorai.008G005500' => 'gra', 'GSVIVG01011094001' => 'vvi', 'GSVIVG01017879001' => 'vvi', 'GSVIVG01025988001' => 'vvi', 'GSVIVG01029847001' => 'vvi', 'HanXRQChr10g0282901' => 'han', 'HanXRQChr10g0310371' => 'han', 'HanXRQChr10g0315041' => 'han', 'HanXRQChr11g0327651' => 'han', 'HanXRQChr12g0359391' => 'han', 'Haze_00972' => 'cav', 'Haze_00973' => 'cav', 'Haze_00974' => 'cav', 'Haze_04747' => 'cav', 'Haze_04749' => 'cav', 'Haze_04750' => 'cav', 'Haze_21217' => 'cav', 'Hma1.2p1_1037F.1_g250680' => 'hma', 'Hma1.2p1_1644F.1_g295320' => 'hma', 'HPP92_011322' => 'vpl', 'HPP92_011323' => 'vpl', 'HPP92_011324' => 'vpl', 'HPP92_011325' => 'vpl', 'HPP92_011326' => 'vpl', 'Hund12205' => 'sun', 'Hund17957' => 'sun', 'Lalb_Chr06g0176771' => 'lal', 'Lalb_Chr18g0056021' => 'lal', 'Lalb_Chr18g0056031' => 'lal', 'Lalb_Chr18g0056041' => 'lal', 'Lalb_Chr20g0107751' => 'lal', 'Lalb_Chr20g0118371' => 'lal', 'Lj1g0010239' => 'lja', 'Lj1g0017101' => 'lja', 'Lj2A1178G40' => 'lonja', 'Lj2A54G84' => 'lonja', 'Lj2g0015248' => 'lja', 'Lj3A761T51' => 'lonja', 'Lj6g0018116' => 'lja', 'Lsat_1_v5_gn_4_136040' => 'lsa', 'Lsat_1_v5_gn_5_187461' => 'lsa', 'Lsat_1_v5_gn_5_77001' => 'lsa', 'Lsat_1_v5_gn_9_4461' => 'lsa', 'Manes.01G210100' => 'mes', 'Manes.03G185600' => 'mes', 'Manes.05G073300' => 'mes', 'Manes.09G120300' => 'mes', 'Manes.15G022100' => 'mes', 'Mapoly0096s0053' => 'mpo', 'MBI03_g14058_MAGBIO' => 'mbi', 'MBI03_g33876_MAGBIO' => 'mbi', 'MBI03_g36854_MAGBIO' => 'mbi', 'MBI17_g11997_MAGBIO' => 'mbi', 'MD03G1269000' => 'mdo', 'MD04G1179600' => 'mdo', 'MD11G1289800' => 'mdo', 'MD12G1194700' => 'mdo', 'MD13G1182100' => 'mdo', 'MD13G1182200' => 'mdo', 'MD16G1182600' => 'mdo', 'Medtr2g021400' => 'mtr', 'Medtr2g021470' => 'mtr', 'Medtr2g105810' => 'mtr', 'Medtr3g033580' => 'mtr', 'Medtr6g007970' => 'mtr', 'Medtr7g056330' => 'mtr', 'Medtr7g074290' => 'mtr', 'Medtr7g074380' => 'mtr', 'Medtr7g094550' => 'mtr', 'Medtr8g069995' => 'mtr', 'MELO3C014345.2' => 'cme', 'MELO3C021395.2' => 'cme', 'Migut.D00262' => 'egut', 'Migut.G00257' => 'egut', 'MSTRG.21575' => 'ama', 'MSTRG.3985' => 'ama', 'Nitab4.5_0000295g0140' => 'nta', 'Nitab4.5_0000732g0140' => 'nta', 'Nitab4.5_0003162g0020' => 'nta', 'Nitab4.5_0006180g0090' => 'nta', 'Nitab4.5_0006390g0010' => 'nta', 'Nitab4.5_0007392g0040' => 'nta', 'Nn1g02140' => 'nnu', 'Nn4g26168' => 'nnu', 'Nn5g26754' => 'nnu', 'Oeu001433.1' => 'oeu', 'Oeu010299.2' => 'oeu', 'Oeu011171.1' => 'oeu', 'Oeu037675.1' => 'oeu', 'Oeu038359.1' => 'oeu', 'Oeu063834.1' => 'oeu', 'Oeu063835.1' => 'oeu', 'Os05g0312000' => 'osa', 'Os07g0211101' => 'osa', 'Os07g0211200' => 'osa', 'Os07g0681500' => 'osa', 'Peaxi162Scf00095g01015' => 'pax', 'Peaxi162Scf00104g00329' => 'pax', 'Peaxi162Scf00161g00137' => 'pax', 'PGR004G1665' => 'pgr', 'PGR031G2937' => 'pgr', 'PGR119G2145' => 'pgr', 'PGSC0003DMG400004351' => 'stu', 'PGSC0003DMG400014625' => 'stu', 'PGSC0003DMG401000943' => 'stu', 'Phvul.001G148600' => 'pvu', 'Phvul.004G001700' => 'pvu', 'Phvul.006G154900' => 'pvu', 'Phvul.008G078200' => 'pvu', 'Phvul.011G136500' => 'pvu', 'Potri.002G215600' => 'ptr', 'Potri.008G201600' => 'ptr', 'Potri.014G138400' => 'ptr', 'Potri.016G142500' => 'ptr', 'Pp3c16_10580' => 'ppa', 'Pp3c5_25280' => 'ppa', 'Prupe.1G150000' => 'ppe', 'Prupe.1G150100' => 'ppe', 'Prupe.6G299600' => 'ppe', 'Prupe.8G245000' => 'ppe', 'Psat0s4927g0040' => 'psa', 'Psat1g052080' => 'psa', 'Psat1g183800' => 'psa', 'Psat3g113840' => 'psa', 'Psat3g126120' => 'psa', 'Psat3g126160' => 'psa', 'Psat3g158760' => 'psa', 'Psat3g158840' => 'psa', 'PSO170G2858' => 'pso', 'PSO339G0606' => 'pso', 'PSO384G4709' => 'pso', 'PSO407G0334' => 'pso', 'QL04p040276' => 'qlo', 'QL06p005458' => 'qlo', 'QL06p005472' => 'qlo', 'QL07p030546' => 'qlo', 'QL07p031519' => 'qlo', 'QL09p050949' => 'qlo', 'QL09p050966' => 'qlo', 'QL09p051067' => 'qlo', 'QL12p022706' => 'qlo', 'RcHm_v2.0_Chr2g0119601' => 'rch', 'RcHm_v2.0_Chr3g0459591' => 'rch', 'RcHm_v2.0_Chr4g0418521' => 'rch', 'RcHm_v2.0_Chr4g0418531' => 'rch', 'RcHm_v2.0_Chr4g0418541' => 'rch', 'RcHm_v2.0_Chr6g0291641' => 'rch', 'Rhsim01G0086300' => 'rsi', 'Rhsim01G0276300' => 'rsi', 'Rhsim01G0276500' => 'rsi', 'Rhsim04G0207700' => 'rsi', 'Rhsim05G0234500' => 'rsi', 'Rhsim13G0022400' => 'rsi', 'Sabra02G0167900' => 'sbr', 'Sabra04G0158500' => 'sbr', 'Sabra08G0159800' => 'sbr', 'Sabra10G0011500' => 'sbr', 'Sabra14G0104400' => 'sbr', 'SalBow2G2440' => 'sbo', 'SalBow4G2265' => 'sbo', 'Sc02g0000060' => 'sci', 'Sc05g0005020' => 'sci', 'Sc13g0003890' => 'sci', 'Sed0014865' => 'sed', 'Sed0017224' => 'sed', 'Sed0026391' => 'sed', 'SEGI_00063' => 'sgi', 'SEGI_10967' => 'sgi', 'SEGI_17510' => 'sgi', 'SEGI_24396' => 'sgi', 'SEGI_39719' => 'sgi', 'SEGI_41392' => 'sgi', 'SGA_v2.0_scaffold11G05794' => 'sas', 'SGA_v2.0_scaffold142G35607' => 'sas', 'SGA_v2.0_scaffold1G00447' => 'sas', 'SHI15388' => 'shi', 'SHI15394' => 'shi', 'SHI15396' => 'shi', 'SHI15399' => 'shi', 'SMO343G0151' => 'smo', 'SMO367G1118' => 'smo', 'Solyc01g080200.3' => 'sly', 'Solyc06g008960.3' => 'sly', 'Solyc09g064780.3' => 'sly', 'Sopen01g031980' => 'spe', 'Sopen06g003710' => 'spe', 'Sopen09g026460' => 'spe', 'Sp3g21240' => 'spa', 'Sp4g30030' => 'spa', 'TAR365G0022' => 'tar', 'TAR365G1023' => 'tar', 'TAR365G1253' => 'tar', 'TAR623G0078' => 'tar', 'TAR623G1721' => 'tar', 'TAR633G0959' => 'tar', 'THA.LOC104802225' => 'tha', 'THA.LOC104804769' => 'tha', 'THA.LOC104808660' => 'tha', 'THA.LOC104812792' => 'tha', 'Thecc.01G284000' => 'tca', 'Thecc.04G220600' => 'tca', 'Thecc.05G268900' => 'tca', 'Thecc.08G171100' => 'tca', 'Thhalv10001284m.g' => 'esa', 'Thhalv10019912m.g' => 'esa', 'TPR.G14189' => 'tpr', 'TPR.G18110' => 'tpr', 'TPR.G18130' => 'tpr', 'TPR.G18131' => 'tpr', 'TPR.G18140' => 'tpr', 'TPR.G24282' => 'tpr', 'TPR.G25221' => 'tpr', 'TPR.G29267' => 'tpr', 'TPR.G35315' => 'tpr', 'TPR.G36173' => 'tpr', 'TWI09G0794' => 'twi', 'TWI59G1348' => 'twi', 'TWI74G0430' => 'twi', 'unitig_26.g8940' => 'ugi', 'unitig_749.g13744' => 'ugi', 'unitig_749.g13745' => 'ugi', 'vmacro08269' => 'vma', 'vmacro14937' => 'vma', 'vmacro20401' => 'vma', 'VMungo0464G1349' => 'vmu', 'VMungo0540G0289' => 'vmu', 'VMungo1215G1590' => 'vmu', 'VMungo1309G0221' => 'vmu', 'VMungo1309G2815' => 'vmu', 'VMungo1383G0239' => 'vmu', 'VMungo1383G2910' => 'vmu', 'Zm00001eb095270' => 'zma', 'Zm00001eb095280' => 'zma', 'Zm00001eb111630' => 'zma', 'Zm00001eb237080' => 'zma', 'Zm00001eb273740' => 'zma', 'Zm00001eb285040' => 'zma', 'Zm00001eb330790' => 'zma', 'Zm00001eb337380' => 'zma' ) $gf_id = 'HOM05D001484' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001484' ) $data_identifier = 'HOM05D001484' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 2, 'aly' => (int) 2, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 22, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 7, 'hma' => (int) 2, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 7, 'mtr' => (int) 10, 'cme' => (int) 2, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 4, 'ppa' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 4, 'qlo' => (int) 9, 'rch' => (int) 6, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 10, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 7, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb337380' $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' => 'HOM05D001484', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p31500' => 'bna', 'A05p00020' => 'bna', 'A07p08820' => 'bna', 'Aa31LG4G3300' => 'aar', 'Aa31LG8G10030' => 'aar', 'Actinidia00731' => 'ach', 'Actinidia11473' => 'ach', 'Actinidia23469' => 'ach', 'Actinidia24318' => 'ach', 'Actinidia40196' => 'ach', 'Actinidia40197' => 'ach', 'Actinidia40198' => 'ach', 'Ah.08g212990' => 'amhyb', 'Ah.15g091720' => 'amhyb', 'AL3G38260' => 'aly', 'AL4G47710' => 'aly', 'Aqoxy2G00671' => 'aox', 'Aqoxy2G03236' => 'aox', 'arahy.Tifrunner.gnm1.ann1.05IDCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KR684' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATY3SJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK6QJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6APGL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IDT7Z9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM073U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ0R87' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LE7RV4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT4QRX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V5ENPK' => 'arhy', 'AT2G48110' => 'ath', 'AT3G23590' => 'ath', 'ATR0626G186' => 'atr', 'ATR1127G141' => 'atr', 'Atru.chr4.2583' => 'acertr', 'Atru.chr5.1358' => 'acertr', 'Atru.chr5.1359' => 'acertr', 'Atru.chr8.46' => 'acertr', 'AUR62002640' => 'cqu', 'AUR62030055' => 'cqu', 'AUR62033713' => 'cqu', 'AUR62033714' => 'cqu', 'AUR62036795' => 'cqu', 'AUR62039891' => 'cqu', 'BcaB02g08737' => 'bca', 'BcaB04g20441' => 'bca', 'BcaB06g26509' => 'bca', 'BcaB06g26510' => 'bca', 'BcaB06g26511' => 'bca', 'BcaB06g26512' => 'bca', 'BcaB06g26513' => 'bca', 'BcaC02g12564' => 'bca', 'BcaC02g12565' => 'bca', 'BcaC02g12794' => 'bca', 'BcaC02g12795' => 'bca', 'BcaC02g12796' => 'bca', 'BcaC06g35541' => 'bca', 'BNapus_Darmor_BZH_scaffold_188p00080' => 'bna', 'BNapus_Darmor_BZH_scaffold_188p00090' => 'bna', 'BolC1t03972H' => 'bol', 'BolC1t03973H' => 'bol', 'BolC4t21680H' => 'bol', 'BolC7t41863H' => 'bol', 'BolSC55t61227H' => 'bol', 'BolSC55t61228H' => 'bol', 'BraA01t03278Z' => 'bra', 'BraA05t18998Z' => 'bra', 'BraA07t28673Z' => 'bra', 'C01p40150' => 'bna', 'C05p12370' => 'bna', 'C07p13680' => 'bna', 'CAN.G1006.16' => 'can', 'CAN.G1006.17' => 'can', 'CAN.G1170.2' => 'can', 'CAN.G962.7' => 'can', 'CANSAT25G2179' => 'cansat', 'CANSAT78G1573' => 'cansat', 'CARHR099510' => 'chi', 'CARHR143510' => 'chi', 'Carub.0003s2380' => 'cru', 'Carub.0004s3082' => 'cru', 'Ca_00614_v3' => 'car', 'Ca_07801_v3' => 'car', 'Ca_08567_v3' => 'car', 'Ca_09571_v3' => 'car', 'CBR_g19290' => 'cbr', 'Cc01_g19770' => 'ccan', 'Cc03_g03030' => 'ccan', 'CDE07G0968' => 'cde', 'CDE09G1441' => 'cde', 'Cfa006103' => 'cfa', 'Cfa015573' => 'cfa', 'Cfa016988' => 'cfa', 'Ciclev10006738m.g' => 'ccl', 'Ciclev10010920m.g' => 'ccl', 'Ciclev10018517m.g' => 'ccl', 'CiPaw.01G159200' => 'cil', 'CiPaw.02G091000' => 'cil', 'CiPaw.02G091100' => 'cil', 'CiPaw.08G103100' => 'cil', 'CiPaw.09G224900' => 'cil', 'ClCG06G005740' => 'cla', 'ClCG07G000090' => 'cla', 'ClCG07G000100' => 'cla', 'COL.COLO4_09143' => 'col', 'COL.COLO4_25124' => 'col', 'Cpa.g.sc16.34' => 'cpa', 'Cpa.g.sc3504.1' => 'cpa', 'Cpa.g.sc60.37' => 'cpa', 'CsaV3_6G018520' => 'csa', 'CsaV3_6G036860' => 'csa', 'CSS0001072' => 'camsi', 'CSS0020208' => 'camsi', 'CSS0021253' => 'camsi', 'CSS0022190' => 'camsi', 'CSS0036150' => 'camsi', 'CSS0040442' => 'camsi', 'CSS0042300' => 'camsi', 'CSS0045298' => 'camsi', 'DCAR_012449' => 'dca', 'DCAR_018405' => 'dca', 'DCAR_024573' => 'dca', 'DCAR_030591' => 'dca', 'Dinv16926' => 'din', 'Dinv32963' => 'din', 'Dinv38382' => 'din', 'Dinv38383' => 'din', 'Duzib133G0974' => 'dzi', 'Duzib138G1867' => 'dzi', 'Duzib211G0420' => 'dzi', 'Duzib212G0930' => 'dzi', 'ECA234G1645' => 'eca', 'ECA247G3467' => 'eca', 'ECA248G1703' => 'eca', 'EL10Ac3g06327' => 'bvu', 'EL10Ac7g17204' => 'bvu', 'Eucgr.A00855' => 'egr', 'Eucgr.A00858' => 'egr', 'Eucgr.H01520' => 'egr', 'Eucgr.H03604' => 'egr', 'Eucgr.L03465' => 'egr', 'Eucgr.L03466' => 'egr', 'FAN01G0988' => 'fan', 'FAN02G3892' => 'fan', 'FAN05G3381' => 'fan', 'FAN07G0967' => 'fan', 'FAN07G1493' => 'fan', 'FAN08G3125' => 'fan', 'FAN09G0402' => 'fan', 'FAN12G2594' => 'fan', 'FAN12G3879' => 'fan', 'FAN14G1546' => 'fan', 'FAN15G3626' => 'fan', 'FAN17G0588' => 'fan', 'FAN17G0609' => 'fan', 'FAN18G2817' => 'fan', 'FAN19G1305' => 'fan', 'FAN20G1787' => 'fan', 'FAN22G0073' => 'fan', 'FAN22G0352' => 'fan', 'FAN22G0368' => 'fan', 'FAN22G2273' => 'fan', 'FAN24G1998' => 'fan', 'FAN27G1317' => 'fan', 'FvH4_2g23980' => 'fve', 'FvH4_4g14380' => 'fve', 'FvH4_4g14390' => 'fve', 'FvH4_6g09250' => 'fve', 'Glyma.03G151100' => 'gma', 'Glyma.04G122550' => 'gma', 'Glyma.05G001600' => 'gma', 'Glyma.09G270766' => 'gma', 'Glyma.09G270832' => 'gma', 'Glyma.13G209800' => 'gma', 'Glyma.15G102800' => 'gma', 'Glyma.18G218900' => 'gma', 'Glyma.19G001500' => 'gma', 'Glyma.19G153600' => 'gma', 'Gohir.A02G028600' => 'ghi', 'Gohir.A08G045000' => 'ghi', 'Gohir.A11G120500' => 'ghi', 'Gohir.A12G006200' => 'ghi', 'Gohir.A12G006250' => 'ghi', 'Gohir.D02G036300' => 'ghi', 'Gohir.D08G054700' => 'ghi', 'Gohir.D11G125600' => 'ghi', 'Gohir.D12G005700' => 'ghi', 'Gorai.004G055200' => 'gra', 'Gorai.005G040400' => 'gra', 'Gorai.007G134500' => 'gra', 'Gorai.008G005500' => 'gra', 'GSVIVG01011094001' => 'vvi', 'GSVIVG01017879001' => 'vvi', 'GSVIVG01025988001' => 'vvi', 'GSVIVG01029847001' => 'vvi', 'HanXRQChr10g0282901' => 'han', 'HanXRQChr10g0310371' => 'han', 'HanXRQChr10g0315041' => 'han', 'HanXRQChr11g0327651' => 'han', 'HanXRQChr12g0359391' => 'han', 'Haze_00972' => 'cav', 'Haze_00973' => 'cav', 'Haze_00974' => 'cav', 'Haze_04747' => 'cav', 'Haze_04749' => 'cav', 'Haze_04750' => 'cav', 'Haze_21217' => 'cav', 'Hma1.2p1_1037F.1_g250680' => 'hma', 'Hma1.2p1_1644F.1_g295320' => 'hma', 'HPP92_011322' => 'vpl', 'HPP92_011323' => 'vpl', 'HPP92_011324' => 'vpl', 'HPP92_011325' => 'vpl', 'HPP92_011326' => 'vpl', 'Hund12205' => 'sun', 'Hund17957' => 'sun', 'Lalb_Chr06g0176771' => 'lal', 'Lalb_Chr18g0056021' => 'lal', 'Lalb_Chr18g0056031' => 'lal', 'Lalb_Chr18g0056041' => 'lal', 'Lalb_Chr20g0107751' => 'lal', 'Lalb_Chr20g0118371' => 'lal', 'Lj1g0010239' => 'lja', 'Lj1g0017101' => 'lja', 'Lj2A1178G40' => 'lonja', 'Lj2A54G84' => 'lonja', 'Lj2g0015248' => 'lja', 'Lj3A761T51' => 'lonja', 'Lj6g0018116' => 'lja', 'Lsat_1_v5_gn_4_136040' => 'lsa', 'Lsat_1_v5_gn_5_187461' => 'lsa', 'Lsat_1_v5_gn_5_77001' => 'lsa', 'Lsat_1_v5_gn_9_4461' => 'lsa', 'Manes.01G210100' => 'mes', 'Manes.03G185600' => 'mes', 'Manes.05G073300' => 'mes', 'Manes.09G120300' => 'mes', 'Manes.15G022100' => 'mes', 'Mapoly0096s0053' => 'mpo', 'MBI03_g14058_MAGBIO' => 'mbi', 'MBI03_g33876_MAGBIO' => 'mbi', 'MBI03_g36854_MAGBIO' => 'mbi', 'MBI17_g11997_MAGBIO' => 'mbi', 'MD03G1269000' => 'mdo', 'MD04G1179600' => 'mdo', 'MD11G1289800' => 'mdo', 'MD12G1194700' => 'mdo', 'MD13G1182100' => 'mdo', 'MD13G1182200' => 'mdo', 'MD16G1182600' => 'mdo', 'Medtr2g021400' => 'mtr', 'Medtr2g021470' => 'mtr', 'Medtr2g105810' => 'mtr', 'Medtr3g033580' => 'mtr', 'Medtr6g007970' => 'mtr', 'Medtr7g056330' => 'mtr', 'Medtr7g074290' => 'mtr', 'Medtr7g074380' => 'mtr', 'Medtr7g094550' => 'mtr', 'Medtr8g069995' => 'mtr', 'MELO3C014345.2' => 'cme', 'MELO3C021395.2' => 'cme', 'Migut.D00262' => 'egut', 'Migut.G00257' => 'egut', 'MSTRG.21575' => 'ama', 'MSTRG.3985' => 'ama', 'Nitab4.5_0000295g0140' => 'nta', 'Nitab4.5_0000732g0140' => 'nta', 'Nitab4.5_0003162g0020' => 'nta', 'Nitab4.5_0006180g0090' => 'nta', 'Nitab4.5_0006390g0010' => 'nta', 'Nitab4.5_0007392g0040' => 'nta', 'Nn1g02140' => 'nnu', 'Nn4g26168' => 'nnu', 'Nn5g26754' => 'nnu', 'Oeu001433.1' => 'oeu', 'Oeu010299.2' => 'oeu', 'Oeu011171.1' => 'oeu', 'Oeu037675.1' => 'oeu', 'Oeu038359.1' => 'oeu', 'Oeu063834.1' => 'oeu', 'Oeu063835.1' => 'oeu', 'Os05g0312000' => 'osa', 'Os07g0211101' => 'osa', 'Os07g0211200' => 'osa', 'Os07g0681500' => 'osa', 'Peaxi162Scf00095g01015' => 'pax', 'Peaxi162Scf00104g00329' => 'pax', 'Peaxi162Scf00161g00137' => 'pax', 'PGR004G1665' => 'pgr', 'PGR031G2937' => 'pgr', 'PGR119G2145' => 'pgr', 'PGSC0003DMG400004351' => 'stu', 'PGSC0003DMG400014625' => 'stu', 'PGSC0003DMG401000943' => 'stu', 'Phvul.001G148600' => 'pvu', 'Phvul.004G001700' => 'pvu', 'Phvul.006G154900' => 'pvu', 'Phvul.008G078200' => 'pvu', 'Phvul.011G136500' => 'pvu', 'Potri.002G215600' => 'ptr', 'Potri.008G201600' => 'ptr', 'Potri.014G138400' => 'ptr', 'Potri.016G142500' => 'ptr', 'Pp3c16_10580' => 'ppa', 'Pp3c5_25280' => 'ppa', 'Prupe.1G150000' => 'ppe', 'Prupe.1G150100' => 'ppe', 'Prupe.6G299600' => 'ppe', 'Prupe.8G245000' => 'ppe', 'Psat0s4927g0040' => 'psa', 'Psat1g052080' => 'psa', 'Psat1g183800' => 'psa', 'Psat3g113840' => 'psa', 'Psat3g126120' => 'psa', 'Psat3g126160' => 'psa', 'Psat3g158760' => 'psa', 'Psat3g158840' => 'psa', 'PSO170G2858' => 'pso', 'PSO339G0606' => 'pso', 'PSO384G4709' => 'pso', 'PSO407G0334' => 'pso', 'QL04p040276' => 'qlo', 'QL06p005458' => 'qlo', 'QL06p005472' => 'qlo', 'QL07p030546' => 'qlo', 'QL07p031519' => 'qlo', 'QL09p050949' => 'qlo', 'QL09p050966' => 'qlo', 'QL09p051067' => 'qlo', 'QL12p022706' => 'qlo', 'RcHm_v2.0_Chr2g0119601' => 'rch', 'RcHm_v2.0_Chr3g0459591' => 'rch', 'RcHm_v2.0_Chr4g0418521' => 'rch', 'RcHm_v2.0_Chr4g0418531' => 'rch', 'RcHm_v2.0_Chr4g0418541' => 'rch', 'RcHm_v2.0_Chr6g0291641' => 'rch', 'Rhsim01G0086300' => 'rsi', 'Rhsim01G0276300' => 'rsi', 'Rhsim01G0276500' => 'rsi', 'Rhsim04G0207700' => 'rsi', 'Rhsim05G0234500' => 'rsi', 'Rhsim13G0022400' => 'rsi', 'Sabra02G0167900' => 'sbr', 'Sabra04G0158500' => 'sbr', 'Sabra08G0159800' => 'sbr', 'Sabra10G0011500' => 'sbr', 'Sabra14G0104400' => 'sbr', 'SalBow2G2440' => 'sbo', 'SalBow4G2265' => 'sbo', 'Sc02g0000060' => 'sci', 'Sc05g0005020' => 'sci', 'Sc13g0003890' => 'sci', 'Sed0014865' => 'sed', 'Sed0017224' => 'sed', 'Sed0026391' => 'sed', 'SEGI_00063' => 'sgi', 'SEGI_10967' => 'sgi', 'SEGI_17510' => 'sgi', 'SEGI_24396' => 'sgi', 'SEGI_39719' => 'sgi', 'SEGI_41392' => 'sgi', 'SGA_v2.0_scaffold11G05794' => 'sas', 'SGA_v2.0_scaffold142G35607' => 'sas', 'SGA_v2.0_scaffold1G00447' => 'sas', 'SHI15388' => 'shi', 'SHI15394' => 'shi', 'SHI15396' => 'shi', 'SHI15399' => 'shi', 'SMO343G0151' => 'smo', 'SMO367G1118' => 'smo', 'Solyc01g080200.3' => 'sly', 'Solyc06g008960.3' => 'sly', 'Solyc09g064780.3' => 'sly', 'Sopen01g031980' => 'spe', 'Sopen06g003710' => 'spe', 'Sopen09g026460' => 'spe', 'Sp3g21240' => 'spa', 'Sp4g30030' => 'spa', 'TAR365G0022' => 'tar', 'TAR365G1023' => 'tar', 'TAR365G1253' => 'tar', 'TAR623G0078' => 'tar', 'TAR623G1721' => 'tar', 'TAR633G0959' => 'tar', 'THA.LOC104802225' => 'tha', 'THA.LOC104804769' => 'tha', 'THA.LOC104808660' => 'tha', 'THA.LOC104812792' => 'tha', 'Thecc.01G284000' => 'tca', 'Thecc.04G220600' => 'tca', 'Thecc.05G268900' => 'tca', 'Thecc.08G171100' => 'tca', 'Thhalv10001284m.g' => 'esa', 'Thhalv10019912m.g' => 'esa', 'TPR.G14189' => 'tpr', 'TPR.G18110' => 'tpr', 'TPR.G18130' => 'tpr', 'TPR.G18131' => 'tpr', 'TPR.G18140' => 'tpr', 'TPR.G24282' => 'tpr', 'TPR.G25221' => 'tpr', 'TPR.G29267' => 'tpr', 'TPR.G35315' => 'tpr', 'TPR.G36173' => 'tpr', 'TWI09G0794' => 'twi', 'TWI59G1348' => 'twi', 'TWI74G0430' => 'twi', 'unitig_26.g8940' => 'ugi', 'unitig_749.g13744' => 'ugi', 'unitig_749.g13745' => 'ugi', 'vmacro08269' => 'vma', 'vmacro14937' => 'vma', 'vmacro20401' => 'vma', 'VMungo0464G1349' => 'vmu', 'VMungo0540G0289' => 'vmu', 'VMungo1215G1590' => 'vmu', 'VMungo1309G0221' => 'vmu', 'VMungo1309G2815' => 'vmu', 'VMungo1383G0239' => 'vmu', 'VMungo1383G2910' => 'vmu', 'Zm00001eb095270' => 'zma', 'Zm00001eb095280' => 'zma', 'Zm00001eb111630' => 'zma', 'Zm00001eb237080' => 'zma', 'Zm00001eb273740' => 'zma', 'Zm00001eb285040' => 'zma', 'Zm00001eb330790' => 'zma', 'Zm00001eb337380' => 'zma' ), 'gf_id' => 'HOM05D001484', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001484' ), 'data_identifier' => 'HOM05D001484', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001484', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p31500' => 'bna', 'A05p00020' => 'bna', 'A07p08820' => 'bna', 'Aa31LG4G3300' => 'aar', 'Aa31LG8G10030' => 'aar', 'Actinidia00731' => 'ach', 'Actinidia11473' => 'ach', 'Actinidia23469' => 'ach', 'Actinidia24318' => 'ach', 'Actinidia40196' => 'ach', 'Actinidia40197' => 'ach', 'Actinidia40198' => 'ach', 'Ah.08g212990' => 'amhyb', 'Ah.15g091720' => 'amhyb', 'AL3G38260' => 'aly', 'AL4G47710' => 'aly', 'Aqoxy2G00671' => 'aox', 'Aqoxy2G03236' => 'aox', 'arahy.Tifrunner.gnm1.ann1.05IDCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KR684' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATY3SJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK6QJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6APGL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IDT7Z9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM073U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ0R87' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LE7RV4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT4QRX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V5ENPK' => 'arhy', 'AT2G48110' => 'ath', 'AT3G23590' => 'ath', 'ATR0626G186' => 'atr', 'ATR1127G141' => 'atr', 'Atru.chr4.2583' => 'acertr', 'Atru.chr5.1358' => 'acertr', 'Atru.chr5.1359' => 'acertr', 'Atru.chr8.46' => 'acertr', 'AUR62002640' => 'cqu', 'AUR62030055' => 'cqu', 'AUR62033713' => 'cqu', 'AUR62033714' => 'cqu', 'AUR62036795' => 'cqu', 'AUR62039891' => 'cqu', 'BcaB02g08737' => 'bca', 'BcaB04g20441' => 'bca', 'BcaB06g26509' => 'bca', 'BcaB06g26510' => 'bca', 'BcaB06g26511' => 'bca', 'BcaB06g26512' => 'bca', 'BcaB06g26513' => 'bca', 'BcaC02g12564' => 'bca', 'BcaC02g12565' => 'bca', 'BcaC02g12794' => 'bca', 'BcaC02g12795' => 'bca', 'BcaC02g12796' => 'bca', 'BcaC06g35541' => 'bca', 'BNapus_Darmor_BZH_scaffold_188p00080' => 'bna', 'BNapus_Darmor_BZH_scaffold_188p00090' => 'bna', 'BolC1t03972H' => 'bol', 'BolC1t03973H' => 'bol', 'BolC4t21680H' => 'bol', 'BolC7t41863H' => 'bol', 'BolSC55t61227H' => 'bol', 'BolSC55t61228H' => 'bol', 'BraA01t03278Z' => 'bra', 'BraA05t18998Z' => 'bra', 'BraA07t28673Z' => 'bra', 'C01p40150' => 'bna', 'C05p12370' => 'bna', 'C07p13680' => 'bna', 'CAN.G1006.16' => 'can', 'CAN.G1006.17' => 'can', 'CAN.G1170.2' => 'can', 'CAN.G962.7' => 'can', 'CANSAT25G2179' => 'cansat', 'CANSAT78G1573' => 'cansat', 'CARHR099510' => 'chi', 'CARHR143510' => 'chi', 'Carub.0003s2380' => 'cru', 'Carub.0004s3082' => 'cru', 'Ca_00614_v3' => 'car', 'Ca_07801_v3' => 'car', 'Ca_08567_v3' => 'car', 'Ca_09571_v3' => 'car', 'CBR_g19290' => 'cbr', 'Cc01_g19770' => 'ccan', 'Cc03_g03030' => 'ccan', 'CDE07G0968' => 'cde', 'CDE09G1441' => 'cde', 'Cfa006103' => 'cfa', 'Cfa015573' => 'cfa', 'Cfa016988' => 'cfa', 'Ciclev10006738m.g' => 'ccl', 'Ciclev10010920m.g' => 'ccl', 'Ciclev10018517m.g' => 'ccl', 'CiPaw.01G159200' => 'cil', 'CiPaw.02G091000' => 'cil', 'CiPaw.02G091100' => 'cil', 'CiPaw.08G103100' => 'cil', 'CiPaw.09G224900' => 'cil', 'ClCG06G005740' => 'cla', 'ClCG07G000090' => 'cla', 'ClCG07G000100' => 'cla', 'COL.COLO4_09143' => 'col', 'COL.COLO4_25124' => 'col', 'Cpa.g.sc16.34' => 'cpa', 'Cpa.g.sc3504.1' => 'cpa', 'Cpa.g.sc60.37' => 'cpa', 'CsaV3_6G018520' => 'csa', 'CsaV3_6G036860' => 'csa', 'CSS0001072' => 'camsi', 'CSS0020208' => 'camsi', 'CSS0021253' => 'camsi', 'CSS0022190' => 'camsi', 'CSS0036150' => 'camsi', 'CSS0040442' => 'camsi', 'CSS0042300' => 'camsi', 'CSS0045298' => 'camsi', 'DCAR_012449' => 'dca', 'DCAR_018405' => 'dca', 'DCAR_024573' => 'dca', 'DCAR_030591' => 'dca', 'Dinv16926' => 'din', 'Dinv32963' => 'din', 'Dinv38382' => 'din', 'Dinv38383' => 'din', 'Duzib133G0974' => 'dzi', 'Duzib138G1867' => 'dzi', 'Duzib211G0420' => 'dzi', 'Duzib212G0930' => 'dzi', 'ECA234G1645' => 'eca', 'ECA247G3467' => 'eca', 'ECA248G1703' => 'eca', 'EL10Ac3g06327' => 'bvu', 'EL10Ac7g17204' => 'bvu', 'Eucgr.A00855' => 'egr', 'Eucgr.A00858' => 'egr', 'Eucgr.H01520' => 'egr', 'Eucgr.H03604' => 'egr', 'Eucgr.L03465' => 'egr', 'Eucgr.L03466' => 'egr', 'FAN01G0988' => 'fan', 'FAN02G3892' => 'fan', 'FAN05G3381' => 'fan', 'FAN07G0967' => 'fan', 'FAN07G1493' => 'fan', 'FAN08G3125' => 'fan', 'FAN09G0402' => 'fan', 'FAN12G2594' => 'fan', 'FAN12G3879' => 'fan', 'FAN14G1546' => 'fan', 'FAN15G3626' => 'fan', 'FAN17G0588' => 'fan', 'FAN17G0609' => 'fan', 'FAN18G2817' => 'fan', 'FAN19G1305' => 'fan', 'FAN20G1787' => 'fan', 'FAN22G0073' => 'fan', 'FAN22G0352' => 'fan', 'FAN22G0368' => 'fan', 'FAN22G2273' => 'fan', 'FAN24G1998' => 'fan', 'FAN27G1317' => 'fan', 'FvH4_2g23980' => 'fve', 'FvH4_4g14380' => 'fve', 'FvH4_4g14390' => 'fve', 'FvH4_6g09250' => 'fve', 'Glyma.03G151100' => 'gma', 'Glyma.04G122550' => 'gma', 'Glyma.05G001600' => 'gma', 'Glyma.09G270766' => 'gma', 'Glyma.09G270832' => 'gma', 'Glyma.13G209800' => 'gma', 'Glyma.15G102800' => 'gma', 'Glyma.18G218900' => 'gma', 'Glyma.19G001500' => 'gma', 'Glyma.19G153600' => 'gma', 'Gohir.A02G028600' => 'ghi', 'Gohir.A08G045000' => 'ghi', 'Gohir.A11G120500' => 'ghi', 'Gohir.A12G006200' => 'ghi', 'Gohir.A12G006250' => 'ghi', 'Gohir.D02G036300' => 'ghi', 'Gohir.D08G054700' => 'ghi', 'Gohir.D11G125600' => 'ghi', 'Gohir.D12G005700' => 'ghi', 'Gorai.004G055200' => 'gra', 'Gorai.005G040400' => 'gra', 'Gorai.007G134500' => 'gra', 'Gorai.008G005500' => 'gra', 'GSVIVG01011094001' => 'vvi', 'GSVIVG01017879001' => 'vvi', 'GSVIVG01025988001' => 'vvi', 'GSVIVG01029847001' => 'vvi', 'HanXRQChr10g0282901' => 'han', 'HanXRQChr10g0310371' => 'han', 'HanXRQChr10g0315041' => 'han', 'HanXRQChr11g0327651' => 'han', 'HanXRQChr12g0359391' => 'han', 'Haze_00972' => 'cav', 'Haze_00973' => 'cav', 'Haze_00974' => 'cav', 'Haze_04747' => 'cav', 'Haze_04749' => 'cav', 'Haze_04750' => 'cav', 'Haze_21217' => 'cav', 'Hma1.2p1_1037F.1_g250680' => 'hma', 'Hma1.2p1_1644F.1_g295320' => 'hma', 'HPP92_011322' => 'vpl', 'HPP92_011323' => 'vpl', 'HPP92_011324' => 'vpl', 'HPP92_011325' => 'vpl', 'HPP92_011326' => 'vpl', 'Hund12205' => 'sun', 'Hund17957' => 'sun', 'Lalb_Chr06g0176771' => 'lal', 'Lalb_Chr18g0056021' => 'lal', 'Lalb_Chr18g0056031' => 'lal', 'Lalb_Chr18g0056041' => 'lal', 'Lalb_Chr20g0107751' => 'lal', 'Lalb_Chr20g0118371' => 'lal', 'Lj1g0010239' => 'lja', 'Lj1g0017101' => 'lja', 'Lj2A1178G40' => 'lonja', 'Lj2A54G84' => 'lonja', 'Lj2g0015248' => 'lja', 'Lj3A761T51' => 'lonja', 'Lj6g0018116' => 'lja', 'Lsat_1_v5_gn_4_136040' => 'lsa', 'Lsat_1_v5_gn_5_187461' => 'lsa', 'Lsat_1_v5_gn_5_77001' => 'lsa', 'Lsat_1_v5_gn_9_4461' => 'lsa', 'Manes.01G210100' => 'mes', 'Manes.03G185600' => 'mes', 'Manes.05G073300' => 'mes', 'Manes.09G120300' => 'mes', 'Manes.15G022100' => 'mes', 'Mapoly0096s0053' => 'mpo', 'MBI03_g14058_MAGBIO' => 'mbi', 'MBI03_g33876_MAGBIO' => 'mbi', 'MBI03_g36854_MAGBIO' => 'mbi', 'MBI17_g11997_MAGBIO' => 'mbi', 'MD03G1269000' => 'mdo', 'MD04G1179600' => 'mdo', 'MD11G1289800' => 'mdo', 'MD12G1194700' => 'mdo', 'MD13G1182100' => 'mdo', 'MD13G1182200' => 'mdo', 'MD16G1182600' => 'mdo', 'Medtr2g021400' => 'mtr', 'Medtr2g021470' => 'mtr', 'Medtr2g105810' => 'mtr', 'Medtr3g033580' => 'mtr', 'Medtr6g007970' => 'mtr', 'Medtr7g056330' => 'mtr', 'Medtr7g074290' => 'mtr', 'Medtr7g074380' => 'mtr', 'Medtr7g094550' => 'mtr', 'Medtr8g069995' => 'mtr', 'MELO3C014345.2' => 'cme', 'MELO3C021395.2' => 'cme', 'Migut.D00262' => 'egut', 'Migut.G00257' => 'egut', 'MSTRG.21575' => 'ama', 'MSTRG.3985' => 'ama', 'Nitab4.5_0000295g0140' => 'nta', 'Nitab4.5_0000732g0140' => 'nta', 'Nitab4.5_0003162g0020' => 'nta', 'Nitab4.5_0006180g0090' => 'nta', 'Nitab4.5_0006390g0010' => 'nta', 'Nitab4.5_0007392g0040' => 'nta', 'Nn1g02140' => 'nnu', 'Nn4g26168' => 'nnu', 'Nn5g26754' => 'nnu', 'Oeu001433.1' => 'oeu', 'Oeu010299.2' => 'oeu', 'Oeu011171.1' => 'oeu', 'Oeu037675.1' => 'oeu', 'Oeu038359.1' => 'oeu', 'Oeu063834.1' => 'oeu', 'Oeu063835.1' => 'oeu', 'Os05g0312000' => 'osa', 'Os07g0211101' => 'osa', 'Os07g0211200' => 'osa', 'Os07g0681500' => 'osa', 'Peaxi162Scf00095g01015' => 'pax', 'Peaxi162Scf00104g00329' => 'pax', 'Peaxi162Scf00161g00137' => 'pax', 'PGR004G1665' => 'pgr', 'PGR031G2937' => 'pgr', 'PGR119G2145' => 'pgr', 'PGSC0003DMG400004351' => 'stu', 'PGSC0003DMG400014625' => 'stu', 'PGSC0003DMG401000943' => 'stu', 'Phvul.001G148600' => 'pvu', 'Phvul.004G001700' => 'pvu', 'Phvul.006G154900' => 'pvu', 'Phvul.008G078200' => 'pvu', 'Phvul.011G136500' => 'pvu', 'Potri.002G215600' => 'ptr', 'Potri.008G201600' => 'ptr', 'Potri.014G138400' => 'ptr', 'Potri.016G142500' => 'ptr', 'Pp3c16_10580' => 'ppa', 'Pp3c5_25280' => 'ppa', 'Prupe.1G150000' => 'ppe', 'Prupe.1G150100' => 'ppe', 'Prupe.6G299600' => 'ppe', 'Prupe.8G245000' => 'ppe', 'Psat0s4927g0040' => 'psa', 'Psat1g052080' => 'psa', 'Psat1g183800' => 'psa', 'Psat3g113840' => 'psa', 'Psat3g126120' => 'psa', 'Psat3g126160' => 'psa', 'Psat3g158760' => 'psa', 'Psat3g158840' => 'psa', 'PSO170G2858' => 'pso', 'PSO339G0606' => 'pso', 'PSO384G4709' => 'pso', 'PSO407G0334' => 'pso', 'QL04p040276' => 'qlo', 'QL06p005458' => 'qlo', 'QL06p005472' => 'qlo', 'QL07p030546' => 'qlo', 'QL07p031519' => 'qlo', 'QL09p050949' => 'qlo', 'QL09p050966' => 'qlo', 'QL09p051067' => 'qlo', 'QL12p022706' => 'qlo', 'RcHm_v2.0_Chr2g0119601' => 'rch', 'RcHm_v2.0_Chr3g0459591' => 'rch', 'RcHm_v2.0_Chr4g0418521' => 'rch', 'RcHm_v2.0_Chr4g0418531' => 'rch', 'RcHm_v2.0_Chr4g0418541' => 'rch', 'RcHm_v2.0_Chr6g0291641' => 'rch', 'Rhsim01G0086300' => 'rsi', 'Rhsim01G0276300' => 'rsi', 'Rhsim01G0276500' => 'rsi', 'Rhsim04G0207700' => 'rsi', 'Rhsim05G0234500' => 'rsi', 'Rhsim13G0022400' => 'rsi', 'Sabra02G0167900' => 'sbr', 'Sabra04G0158500' => 'sbr', 'Sabra08G0159800' => 'sbr', 'Sabra10G0011500' => 'sbr', 'Sabra14G0104400' => 'sbr', 'SalBow2G2440' => 'sbo', 'SalBow4G2265' => 'sbo', 'Sc02g0000060' => 'sci', 'Sc05g0005020' => 'sci', 'Sc13g0003890' => 'sci', 'Sed0014865' => 'sed', 'Sed0017224' => 'sed', 'Sed0026391' => 'sed', 'SEGI_00063' => 'sgi', 'SEGI_10967' => 'sgi', 'SEGI_17510' => 'sgi', 'SEGI_24396' => 'sgi', 'SEGI_39719' => 'sgi', 'SEGI_41392' => 'sgi', 'SGA_v2.0_scaffold11G05794' => 'sas', 'SGA_v2.0_scaffold142G35607' => 'sas', 'SGA_v2.0_scaffold1G00447' => 'sas', 'SHI15388' => 'shi', 'SHI15394' => 'shi', 'SHI15396' => 'shi', 'SHI15399' => 'shi', 'SMO343G0151' => 'smo', 'SMO367G1118' => 'smo', 'Solyc01g080200.3' => 'sly', 'Solyc06g008960.3' => 'sly', 'Solyc09g064780.3' => 'sly', 'Sopen01g031980' => 'spe', 'Sopen06g003710' => 'spe', 'Sopen09g026460' => 'spe', 'Sp3g21240' => 'spa', 'Sp4g30030' => 'spa', 'TAR365G0022' => 'tar', 'TAR365G1023' => 'tar', 'TAR365G1253' => 'tar', 'TAR623G0078' => 'tar', 'TAR623G1721' => 'tar', 'TAR633G0959' => 'tar', 'THA.LOC104802225' => 'tha', 'THA.LOC104804769' => 'tha', 'THA.LOC104808660' => 'tha', 'THA.LOC104812792' => 'tha', 'Thecc.01G284000' => 'tca', 'Thecc.04G220600' => 'tca', 'Thecc.05G268900' => 'tca', 'Thecc.08G171100' => 'tca', 'Thhalv10001284m.g' => 'esa', 'Thhalv10019912m.g' => 'esa', 'TPR.G14189' => 'tpr', 'TPR.G18110' => 'tpr', 'TPR.G18130' => 'tpr', 'TPR.G18131' => 'tpr', 'TPR.G18140' => 'tpr', 'TPR.G24282' => 'tpr', 'TPR.G25221' => 'tpr', 'TPR.G29267' => 'tpr', 'TPR.G35315' => 'tpr', 'TPR.G36173' => 'tpr', 'TWI09G0794' => 'twi', 'TWI59G1348' => 'twi', 'TWI74G0430' => 'twi', 'unitig_26.g8940' => 'ugi', 'unitig_749.g13744' => 'ugi', 'unitig_749.g13745' => 'ugi', 'vmacro08269' => 'vma', 'vmacro14937' => 'vma', 'vmacro20401' => 'vma', 'VMungo0464G1349' => 'vmu', 'VMungo0540G0289' => 'vmu', 'VMungo1215G1590' => 'vmu', 'VMungo1309G0221' => 'vmu', 'VMungo1309G2815' => 'vmu', 'VMungo1383G0239' => 'vmu', 'VMungo1383G2910' => 'vmu', 'Zm00001eb095270' => 'zma', 'Zm00001eb095280' => 'zma', 'Zm00001eb111630' => 'zma', 'Zm00001eb237080' => 'zma', 'Zm00001eb273740' => 'zma', 'Zm00001eb285040' => 'zma', 'Zm00001eb330790' => 'zma', 'Zm00001eb337380' => 'zma' ) $gf_id = 'HOM05D001484' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001484' ) $data_identifier = 'HOM05D001484' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 2, 'aly' => (int) 2, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 22, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 7, 'hma' => (int) 2, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 7, 'mtr' => (int) 10, 'cme' => (int) 2, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 4, 'ppa' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 4, 'qlo' => (int) 9, 'rch' => (int) 6, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 10, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 7, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb337380' $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' => 'HOM05D001484', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p31500' => 'bna', 'A05p00020' => 'bna', 'A07p08820' => 'bna', 'Aa31LG4G3300' => 'aar', 'Aa31LG8G10030' => 'aar', 'Actinidia00731' => 'ach', 'Actinidia11473' => 'ach', 'Actinidia23469' => 'ach', 'Actinidia24318' => 'ach', 'Actinidia40196' => 'ach', 'Actinidia40197' => 'ach', 'Actinidia40198' => 'ach', 'Ah.08g212990' => 'amhyb', 'Ah.15g091720' => 'amhyb', 'AL3G38260' => 'aly', 'AL4G47710' => 'aly', 'Aqoxy2G00671' => 'aox', 'Aqoxy2G03236' => 'aox', 'arahy.Tifrunner.gnm1.ann1.05IDCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KR684' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATY3SJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK6QJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6APGL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IDT7Z9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM073U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ0R87' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LE7RV4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT4QRX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V5ENPK' => 'arhy', 'AT2G48110' => 'ath', 'AT3G23590' => 'ath', 'ATR0626G186' => 'atr', 'ATR1127G141' => 'atr', 'Atru.chr4.2583' => 'acertr', 'Atru.chr5.1358' => 'acertr', 'Atru.chr5.1359' => 'acertr', 'Atru.chr8.46' => 'acertr', 'AUR62002640' => 'cqu', 'AUR62030055' => 'cqu', 'AUR62033713' => 'cqu', 'AUR62033714' => 'cqu', 'AUR62036795' => 'cqu', 'AUR62039891' => 'cqu', 'BcaB02g08737' => 'bca', 'BcaB04g20441' => 'bca', 'BcaB06g26509' => 'bca', 'BcaB06g26510' => 'bca', 'BcaB06g26511' => 'bca', 'BcaB06g26512' => 'bca', 'BcaB06g26513' => 'bca', 'BcaC02g12564' => 'bca', 'BcaC02g12565' => 'bca', 'BcaC02g12794' => 'bca', 'BcaC02g12795' => 'bca', 'BcaC02g12796' => 'bca', 'BcaC06g35541' => 'bca', 'BNapus_Darmor_BZH_scaffold_188p00080' => 'bna', 'BNapus_Darmor_BZH_scaffold_188p00090' => 'bna', 'BolC1t03972H' => 'bol', 'BolC1t03973H' => 'bol', 'BolC4t21680H' => 'bol', 'BolC7t41863H' => 'bol', 'BolSC55t61227H' => 'bol', 'BolSC55t61228H' => 'bol', 'BraA01t03278Z' => 'bra', 'BraA05t18998Z' => 'bra', 'BraA07t28673Z' => 'bra', 'C01p40150' => 'bna', 'C05p12370' => 'bna', 'C07p13680' => 'bna', 'CAN.G1006.16' => 'can', 'CAN.G1006.17' => 'can', 'CAN.G1170.2' => 'can', 'CAN.G962.7' => 'can', 'CANSAT25G2179' => 'cansat', 'CANSAT78G1573' => 'cansat', 'CARHR099510' => 'chi', 'CARHR143510' => 'chi', 'Carub.0003s2380' => 'cru', 'Carub.0004s3082' => 'cru', 'Ca_00614_v3' => 'car', 'Ca_07801_v3' => 'car', 'Ca_08567_v3' => 'car', 'Ca_09571_v3' => 'car', 'CBR_g19290' => 'cbr', 'Cc01_g19770' => 'ccan', 'Cc03_g03030' => 'ccan', 'CDE07G0968' => 'cde', 'CDE09G1441' => 'cde', 'Cfa006103' => 'cfa', 'Cfa015573' => 'cfa', 'Cfa016988' => 'cfa', 'Ciclev10006738m.g' => 'ccl', 'Ciclev10010920m.g' => 'ccl', 'Ciclev10018517m.g' => 'ccl', 'CiPaw.01G159200' => 'cil', 'CiPaw.02G091000' => 'cil', 'CiPaw.02G091100' => 'cil', 'CiPaw.08G103100' => 'cil', 'CiPaw.09G224900' => 'cil', 'ClCG06G005740' => 'cla', 'ClCG07G000090' => 'cla', 'ClCG07G000100' => 'cla', 'COL.COLO4_09143' => 'col', 'COL.COLO4_25124' => 'col', 'Cpa.g.sc16.34' => 'cpa', 'Cpa.g.sc3504.1' => 'cpa', 'Cpa.g.sc60.37' => 'cpa', 'CsaV3_6G018520' => 'csa', 'CsaV3_6G036860' => 'csa', 'CSS0001072' => 'camsi', 'CSS0020208' => 'camsi', 'CSS0021253' => 'camsi', 'CSS0022190' => 'camsi', 'CSS0036150' => 'camsi', 'CSS0040442' => 'camsi', 'CSS0042300' => 'camsi', 'CSS0045298' => 'camsi', 'DCAR_012449' => 'dca', 'DCAR_018405' => 'dca', 'DCAR_024573' => 'dca', 'DCAR_030591' => 'dca', 'Dinv16926' => 'din', 'Dinv32963' => 'din', 'Dinv38382' => 'din', 'Dinv38383' => 'din', 'Duzib133G0974' => 'dzi', 'Duzib138G1867' => 'dzi', 'Duzib211G0420' => 'dzi', 'Duzib212G0930' => 'dzi', 'ECA234G1645' => 'eca', 'ECA247G3467' => 'eca', 'ECA248G1703' => 'eca', 'EL10Ac3g06327' => 'bvu', 'EL10Ac7g17204' => 'bvu', 'Eucgr.A00855' => 'egr', 'Eucgr.A00858' => 'egr', 'Eucgr.H01520' => 'egr', 'Eucgr.H03604' => 'egr', 'Eucgr.L03465' => 'egr', 'Eucgr.L03466' => 'egr', 'FAN01G0988' => 'fan', 'FAN02G3892' => 'fan', 'FAN05G3381' => 'fan', 'FAN07G0967' => 'fan', 'FAN07G1493' => 'fan', 'FAN08G3125' => 'fan', 'FAN09G0402' => 'fan', 'FAN12G2594' => 'fan', 'FAN12G3879' => 'fan', 'FAN14G1546' => 'fan', 'FAN15G3626' => 'fan', 'FAN17G0588' => 'fan', 'FAN17G0609' => 'fan', 'FAN18G2817' => 'fan', 'FAN19G1305' => 'fan', 'FAN20G1787' => 'fan', 'FAN22G0073' => 'fan', 'FAN22G0352' => 'fan', 'FAN22G0368' => 'fan', 'FAN22G2273' => 'fan', 'FAN24G1998' => 'fan', 'FAN27G1317' => 'fan', 'FvH4_2g23980' => 'fve', 'FvH4_4g14380' => 'fve', 'FvH4_4g14390' => 'fve', 'FvH4_6g09250' => 'fve', 'Glyma.03G151100' => 'gma', 'Glyma.04G122550' => 'gma', 'Glyma.05G001600' => 'gma', 'Glyma.09G270766' => 'gma', 'Glyma.09G270832' => 'gma', 'Glyma.13G209800' => 'gma', 'Glyma.15G102800' => 'gma', 'Glyma.18G218900' => 'gma', 'Glyma.19G001500' => 'gma', 'Glyma.19G153600' => 'gma', 'Gohir.A02G028600' => 'ghi', 'Gohir.A08G045000' => 'ghi', 'Gohir.A11G120500' => 'ghi', 'Gohir.A12G006200' => 'ghi', 'Gohir.A12G006250' => 'ghi', 'Gohir.D02G036300' => 'ghi', 'Gohir.D08G054700' => 'ghi', 'Gohir.D11G125600' => 'ghi', 'Gohir.D12G005700' => 'ghi', 'Gorai.004G055200' => 'gra', 'Gorai.005G040400' => 'gra', 'Gorai.007G134500' => 'gra', 'Gorai.008G005500' => 'gra', 'GSVIVG01011094001' => 'vvi', 'GSVIVG01017879001' => 'vvi', 'GSVIVG01025988001' => 'vvi', 'GSVIVG01029847001' => 'vvi', 'HanXRQChr10g0282901' => 'han', 'HanXRQChr10g0310371' => 'han', 'HanXRQChr10g0315041' => 'han', 'HanXRQChr11g0327651' => 'han', 'HanXRQChr12g0359391' => 'han', 'Haze_00972' => 'cav', 'Haze_00973' => 'cav', 'Haze_00974' => 'cav', 'Haze_04747' => 'cav', 'Haze_04749' => 'cav', 'Haze_04750' => 'cav', 'Haze_21217' => 'cav', 'Hma1.2p1_1037F.1_g250680' => 'hma', 'Hma1.2p1_1644F.1_g295320' => 'hma', 'HPP92_011322' => 'vpl', 'HPP92_011323' => 'vpl', 'HPP92_011324' => 'vpl', 'HPP92_011325' => 'vpl', 'HPP92_011326' => 'vpl', 'Hund12205' => 'sun', 'Hund17957' => 'sun', 'Lalb_Chr06g0176771' => 'lal', 'Lalb_Chr18g0056021' => 'lal', 'Lalb_Chr18g0056031' => 'lal', 'Lalb_Chr18g0056041' => 'lal', 'Lalb_Chr20g0107751' => 'lal', 'Lalb_Chr20g0118371' => 'lal', 'Lj1g0010239' => 'lja', 'Lj1g0017101' => 'lja', 'Lj2A1178G40' => 'lonja', 'Lj2A54G84' => 'lonja', 'Lj2g0015248' => 'lja', 'Lj3A761T51' => 'lonja', 'Lj6g0018116' => 'lja', 'Lsat_1_v5_gn_4_136040' => 'lsa', 'Lsat_1_v5_gn_5_187461' => 'lsa', 'Lsat_1_v5_gn_5_77001' => 'lsa', 'Lsat_1_v5_gn_9_4461' => 'lsa', 'Manes.01G210100' => 'mes', 'Manes.03G185600' => 'mes', 'Manes.05G073300' => 'mes', 'Manes.09G120300' => 'mes', 'Manes.15G022100' => 'mes', 'Mapoly0096s0053' => 'mpo', 'MBI03_g14058_MAGBIO' => 'mbi', 'MBI03_g33876_MAGBIO' => 'mbi', 'MBI03_g36854_MAGBIO' => 'mbi', 'MBI17_g11997_MAGBIO' => 'mbi', 'MD03G1269000' => 'mdo', 'MD04G1179600' => 'mdo', 'MD11G1289800' => 'mdo', 'MD12G1194700' => 'mdo', 'MD13G1182100' => 'mdo', 'MD13G1182200' => 'mdo', 'MD16G1182600' => 'mdo', 'Medtr2g021400' => 'mtr', 'Medtr2g021470' => 'mtr', 'Medtr2g105810' => 'mtr', 'Medtr3g033580' => 'mtr', 'Medtr6g007970' => 'mtr', 'Medtr7g056330' => 'mtr', 'Medtr7g074290' => 'mtr', 'Medtr7g074380' => 'mtr', 'Medtr7g094550' => 'mtr', 'Medtr8g069995' => 'mtr', 'MELO3C014345.2' => 'cme', 'MELO3C021395.2' => 'cme', 'Migut.D00262' => 'egut', 'Migut.G00257' => 'egut', 'MSTRG.21575' => 'ama', 'MSTRG.3985' => 'ama', 'Nitab4.5_0000295g0140' => 'nta', 'Nitab4.5_0000732g0140' => 'nta', 'Nitab4.5_0003162g0020' => 'nta', 'Nitab4.5_0006180g0090' => 'nta', 'Nitab4.5_0006390g0010' => 'nta', 'Nitab4.5_0007392g0040' => 'nta', 'Nn1g02140' => 'nnu', 'Nn4g26168' => 'nnu', 'Nn5g26754' => 'nnu', 'Oeu001433.1' => 'oeu', 'Oeu010299.2' => 'oeu', 'Oeu011171.1' => 'oeu', 'Oeu037675.1' => 'oeu', 'Oeu038359.1' => 'oeu', 'Oeu063834.1' => 'oeu', 'Oeu063835.1' => 'oeu', 'Os05g0312000' => 'osa', 'Os07g0211101' => 'osa', 'Os07g0211200' => 'osa', 'Os07g0681500' => 'osa', 'Peaxi162Scf00095g01015' => 'pax', 'Peaxi162Scf00104g00329' => 'pax', 'Peaxi162Scf00161g00137' => 'pax', 'PGR004G1665' => 'pgr', 'PGR031G2937' => 'pgr', 'PGR119G2145' => 'pgr', 'PGSC0003DMG400004351' => 'stu', 'PGSC0003DMG400014625' => 'stu', 'PGSC0003DMG401000943' => 'stu', 'Phvul.001G148600' => 'pvu', 'Phvul.004G001700' => 'pvu', 'Phvul.006G154900' => 'pvu', 'Phvul.008G078200' => 'pvu', 'Phvul.011G136500' => 'pvu', 'Potri.002G215600' => 'ptr', 'Potri.008G201600' => 'ptr', 'Potri.014G138400' => 'ptr', 'Potri.016G142500' => 'ptr', 'Pp3c16_10580' => 'ppa', 'Pp3c5_25280' => 'ppa', 'Prupe.1G150000' => 'ppe', 'Prupe.1G150100' => 'ppe', 'Prupe.6G299600' => 'ppe', 'Prupe.8G245000' => 'ppe', 'Psat0s4927g0040' => 'psa', 'Psat1g052080' => 'psa', 'Psat1g183800' => 'psa', 'Psat3g113840' => 'psa', 'Psat3g126120' => 'psa', 'Psat3g126160' => 'psa', 'Psat3g158760' => 'psa', 'Psat3g158840' => 'psa', 'PSO170G2858' => 'pso', 'PSO339G0606' => 'pso', 'PSO384G4709' => 'pso', 'PSO407G0334' => 'pso', 'QL04p040276' => 'qlo', 'QL06p005458' => 'qlo', 'QL06p005472' => 'qlo', 'QL07p030546' => 'qlo', 'QL07p031519' => 'qlo', 'QL09p050949' => 'qlo', 'QL09p050966' => 'qlo', 'QL09p051067' => 'qlo', 'QL12p022706' => 'qlo', 'RcHm_v2.0_Chr2g0119601' => 'rch', 'RcHm_v2.0_Chr3g0459591' => 'rch', 'RcHm_v2.0_Chr4g0418521' => 'rch', 'RcHm_v2.0_Chr4g0418531' => 'rch', 'RcHm_v2.0_Chr4g0418541' => 'rch', 'RcHm_v2.0_Chr6g0291641' => 'rch', 'Rhsim01G0086300' => 'rsi', 'Rhsim01G0276300' => 'rsi', 'Rhsim01G0276500' => 'rsi', 'Rhsim04G0207700' => 'rsi', 'Rhsim05G0234500' => 'rsi', 'Rhsim13G0022400' => 'rsi', 'Sabra02G0167900' => 'sbr', 'Sabra04G0158500' => 'sbr', 'Sabra08G0159800' => 'sbr', 'Sabra10G0011500' => 'sbr', 'Sabra14G0104400' => 'sbr', 'SalBow2G2440' => 'sbo', 'SalBow4G2265' => 'sbo', 'Sc02g0000060' => 'sci', 'Sc05g0005020' => 'sci', 'Sc13g0003890' => 'sci', 'Sed0014865' => 'sed', 'Sed0017224' => 'sed', 'Sed0026391' => 'sed', 'SEGI_00063' => 'sgi', 'SEGI_10967' => 'sgi', 'SEGI_17510' => 'sgi', 'SEGI_24396' => 'sgi', 'SEGI_39719' => 'sgi', 'SEGI_41392' => 'sgi', 'SGA_v2.0_scaffold11G05794' => 'sas', 'SGA_v2.0_scaffold142G35607' => 'sas', 'SGA_v2.0_scaffold1G00447' => 'sas', 'SHI15388' => 'shi', 'SHI15394' => 'shi', 'SHI15396' => 'shi', 'SHI15399' => 'shi', 'SMO343G0151' => 'smo', 'SMO367G1118' => 'smo', 'Solyc01g080200.3' => 'sly', 'Solyc06g008960.3' => 'sly', 'Solyc09g064780.3' => 'sly', 'Sopen01g031980' => 'spe', 'Sopen06g003710' => 'spe', 'Sopen09g026460' => 'spe', 'Sp3g21240' => 'spa', 'Sp4g30030' => 'spa', 'TAR365G0022' => 'tar', 'TAR365G1023' => 'tar', 'TAR365G1253' => 'tar', 'TAR623G0078' => 'tar', 'TAR623G1721' => 'tar', 'TAR633G0959' => 'tar', 'THA.LOC104802225' => 'tha', 'THA.LOC104804769' => 'tha', 'THA.LOC104808660' => 'tha', 'THA.LOC104812792' => 'tha', 'Thecc.01G284000' => 'tca', 'Thecc.04G220600' => 'tca', 'Thecc.05G268900' => 'tca', 'Thecc.08G171100' => 'tca', 'Thhalv10001284m.g' => 'esa', 'Thhalv10019912m.g' => 'esa', 'TPR.G14189' => 'tpr', 'TPR.G18110' => 'tpr', 'TPR.G18130' => 'tpr', 'TPR.G18131' => 'tpr', 'TPR.G18140' => 'tpr', 'TPR.G24282' => 'tpr', 'TPR.G25221' => 'tpr', 'TPR.G29267' => 'tpr', 'TPR.G35315' => 'tpr', 'TPR.G36173' => 'tpr', 'TWI09G0794' => 'twi', 'TWI59G1348' => 'twi', 'TWI74G0430' => 'twi', 'unitig_26.g8940' => 'ugi', 'unitig_749.g13744' => 'ugi', 'unitig_749.g13745' => 'ugi', 'vmacro08269' => 'vma', 'vmacro14937' => 'vma', 'vmacro20401' => 'vma', 'VMungo0464G1349' => 'vmu', 'VMungo0540G0289' => 'vmu', 'VMungo1215G1590' => 'vmu', 'VMungo1309G0221' => 'vmu', 'VMungo1309G2815' => 'vmu', 'VMungo1383G0239' => 'vmu', 'VMungo1383G2910' => 'vmu', 'Zm00001eb095270' => 'zma', 'Zm00001eb095280' => 'zma', 'Zm00001eb111630' => 'zma', 'Zm00001eb237080' => 'zma', 'Zm00001eb273740' => 'zma', 'Zm00001eb285040' => 'zma', 'Zm00001eb330790' => 'zma', 'Zm00001eb337380' => 'zma' ), 'gf_id' => 'HOM05D001484', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001484' ), 'data_identifier' => 'HOM05D001484', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001484', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p31500' => 'bna', 'A05p00020' => 'bna', 'A07p08820' => 'bna', 'Aa31LG4G3300' => 'aar', 'Aa31LG8G10030' => 'aar', 'Actinidia00731' => 'ach', 'Actinidia11473' => 'ach', 'Actinidia23469' => 'ach', 'Actinidia24318' => 'ach', 'Actinidia40196' => 'ach', 'Actinidia40197' => 'ach', 'Actinidia40198' => 'ach', 'Ah.08g212990' => 'amhyb', 'Ah.15g091720' => 'amhyb', 'AL3G38260' => 'aly', 'AL4G47710' => 'aly', 'Aqoxy2G00671' => 'aox', 'Aqoxy2G03236' => 'aox', 'arahy.Tifrunner.gnm1.ann1.05IDCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KR684' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATY3SJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK6QJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6APGL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IDT7Z9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM073U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ0R87' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LE7RV4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT4QRX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V5ENPK' => 'arhy', 'AT2G48110' => 'ath', 'AT3G23590' => 'ath', 'ATR0626G186' => 'atr', 'ATR1127G141' => 'atr', 'Atru.chr4.2583' => 'acertr', 'Atru.chr5.1358' => 'acertr', 'Atru.chr5.1359' => 'acertr', 'Atru.chr8.46' => 'acertr', 'AUR62002640' => 'cqu', 'AUR62030055' => 'cqu', 'AUR62033713' => 'cqu', 'AUR62033714' => 'cqu', 'AUR62036795' => 'cqu', 'AUR62039891' => 'cqu', 'BcaB02g08737' => 'bca', 'BcaB04g20441' => 'bca', 'BcaB06g26509' => 'bca', 'BcaB06g26510' => 'bca', 'BcaB06g26511' => 'bca', 'BcaB06g26512' => 'bca', 'BcaB06g26513' => 'bca', 'BcaC02g12564' => 'bca', 'BcaC02g12565' => 'bca', 'BcaC02g12794' => 'bca', 'BcaC02g12795' => 'bca', 'BcaC02g12796' => 'bca', 'BcaC06g35541' => 'bca', 'BNapus_Darmor_BZH_scaffold_188p00080' => 'bna', 'BNapus_Darmor_BZH_scaffold_188p00090' => 'bna', 'BolC1t03972H' => 'bol', 'BolC1t03973H' => 'bol', 'BolC4t21680H' => 'bol', 'BolC7t41863H' => 'bol', 'BolSC55t61227H' => 'bol', 'BolSC55t61228H' => 'bol', 'BraA01t03278Z' => 'bra', 'BraA05t18998Z' => 'bra', 'BraA07t28673Z' => 'bra', 'C01p40150' => 'bna', 'C05p12370' => 'bna', 'C07p13680' => 'bna', 'CAN.G1006.16' => 'can', 'CAN.G1006.17' => 'can', 'CAN.G1170.2' => 'can', 'CAN.G962.7' => 'can', 'CANSAT25G2179' => 'cansat', 'CANSAT78G1573' => 'cansat', 'CARHR099510' => 'chi', 'CARHR143510' => 'chi', 'Carub.0003s2380' => 'cru', 'Carub.0004s3082' => 'cru', 'Ca_00614_v3' => 'car', 'Ca_07801_v3' => 'car', 'Ca_08567_v3' => 'car', 'Ca_09571_v3' => 'car', 'CBR_g19290' => 'cbr', 'Cc01_g19770' => 'ccan', 'Cc03_g03030' => 'ccan', 'CDE07G0968' => 'cde', 'CDE09G1441' => 'cde', 'Cfa006103' => 'cfa', 'Cfa015573' => 'cfa', 'Cfa016988' => 'cfa', 'Ciclev10006738m.g' => 'ccl', 'Ciclev10010920m.g' => 'ccl', 'Ciclev10018517m.g' => 'ccl', 'CiPaw.01G159200' => 'cil', 'CiPaw.02G091000' => 'cil', 'CiPaw.02G091100' => 'cil', 'CiPaw.08G103100' => 'cil', 'CiPaw.09G224900' => 'cil', 'ClCG06G005740' => 'cla', 'ClCG07G000090' => 'cla', 'ClCG07G000100' => 'cla', 'COL.COLO4_09143' => 'col', 'COL.COLO4_25124' => 'col', 'Cpa.g.sc16.34' => 'cpa', 'Cpa.g.sc3504.1' => 'cpa', 'Cpa.g.sc60.37' => 'cpa', 'CsaV3_6G018520' => 'csa', 'CsaV3_6G036860' => 'csa', 'CSS0001072' => 'camsi', 'CSS0020208' => 'camsi', 'CSS0021253' => 'camsi', 'CSS0022190' => 'camsi', 'CSS0036150' => 'camsi', 'CSS0040442' => 'camsi', 'CSS0042300' => 'camsi', 'CSS0045298' => 'camsi', 'DCAR_012449' => 'dca', 'DCAR_018405' => 'dca', 'DCAR_024573' => 'dca', 'DCAR_030591' => 'dca', 'Dinv16926' => 'din', 'Dinv32963' => 'din', 'Dinv38382' => 'din', 'Dinv38383' => 'din', 'Duzib133G0974' => 'dzi', 'Duzib138G1867' => 'dzi', 'Duzib211G0420' => 'dzi', 'Duzib212G0930' => 'dzi', 'ECA234G1645' => 'eca', 'ECA247G3467' => 'eca', 'ECA248G1703' => 'eca', 'EL10Ac3g06327' => 'bvu', 'EL10Ac7g17204' => 'bvu', 'Eucgr.A00855' => 'egr', 'Eucgr.A00858' => 'egr', 'Eucgr.H01520' => 'egr', 'Eucgr.H03604' => 'egr', 'Eucgr.L03465' => 'egr', 'Eucgr.L03466' => 'egr', 'FAN01G0988' => 'fan', 'FAN02G3892' => 'fan', 'FAN05G3381' => 'fan', 'FAN07G0967' => 'fan', 'FAN07G1493' => 'fan', 'FAN08G3125' => 'fan', 'FAN09G0402' => 'fan', 'FAN12G2594' => 'fan', 'FAN12G3879' => 'fan', 'FAN14G1546' => 'fan', 'FAN15G3626' => 'fan', 'FAN17G0588' => 'fan', 'FAN17G0609' => 'fan', 'FAN18G2817' => 'fan', 'FAN19G1305' => 'fan', 'FAN20G1787' => 'fan', 'FAN22G0073' => 'fan', 'FAN22G0352' => 'fan', 'FAN22G0368' => 'fan', 'FAN22G2273' => 'fan', 'FAN24G1998' => 'fan', 'FAN27G1317' => 'fan', 'FvH4_2g23980' => 'fve', 'FvH4_4g14380' => 'fve', 'FvH4_4g14390' => 'fve', 'FvH4_6g09250' => 'fve', 'Glyma.03G151100' => 'gma', 'Glyma.04G122550' => 'gma', 'Glyma.05G001600' => 'gma', 'Glyma.09G270766' => 'gma', 'Glyma.09G270832' => 'gma', 'Glyma.13G209800' => 'gma', 'Glyma.15G102800' => 'gma', 'Glyma.18G218900' => 'gma', 'Glyma.19G001500' => 'gma', 'Glyma.19G153600' => 'gma', 'Gohir.A02G028600' => 'ghi', 'Gohir.A08G045000' => 'ghi', 'Gohir.A11G120500' => 'ghi', 'Gohir.A12G006200' => 'ghi', 'Gohir.A12G006250' => 'ghi', 'Gohir.D02G036300' => 'ghi', 'Gohir.D08G054700' => 'ghi', 'Gohir.D11G125600' => 'ghi', 'Gohir.D12G005700' => 'ghi', 'Gorai.004G055200' => 'gra', 'Gorai.005G040400' => 'gra', 'Gorai.007G134500' => 'gra', 'Gorai.008G005500' => 'gra', 'GSVIVG01011094001' => 'vvi', 'GSVIVG01017879001' => 'vvi', 'GSVIVG01025988001' => 'vvi', 'GSVIVG01029847001' => 'vvi', 'HanXRQChr10g0282901' => 'han', 'HanXRQChr10g0310371' => 'han', 'HanXRQChr10g0315041' => 'han', 'HanXRQChr11g0327651' => 'han', 'HanXRQChr12g0359391' => 'han', 'Haze_00972' => 'cav', 'Haze_00973' => 'cav', 'Haze_00974' => 'cav', 'Haze_04747' => 'cav', 'Haze_04749' => 'cav', 'Haze_04750' => 'cav', 'Haze_21217' => 'cav', 'Hma1.2p1_1037F.1_g250680' => 'hma', 'Hma1.2p1_1644F.1_g295320' => 'hma', 'HPP92_011322' => 'vpl', 'HPP92_011323' => 'vpl', 'HPP92_011324' => 'vpl', 'HPP92_011325' => 'vpl', 'HPP92_011326' => 'vpl', 'Hund12205' => 'sun', 'Hund17957' => 'sun', 'Lalb_Chr06g0176771' => 'lal', 'Lalb_Chr18g0056021' => 'lal', 'Lalb_Chr18g0056031' => 'lal', 'Lalb_Chr18g0056041' => 'lal', 'Lalb_Chr20g0107751' => 'lal', 'Lalb_Chr20g0118371' => 'lal', 'Lj1g0010239' => 'lja', 'Lj1g0017101' => 'lja', 'Lj2A1178G40' => 'lonja', 'Lj2A54G84' => 'lonja', 'Lj2g0015248' => 'lja', 'Lj3A761T51' => 'lonja', 'Lj6g0018116' => 'lja', 'Lsat_1_v5_gn_4_136040' => 'lsa', 'Lsat_1_v5_gn_5_187461' => 'lsa', 'Lsat_1_v5_gn_5_77001' => 'lsa', 'Lsat_1_v5_gn_9_4461' => 'lsa', 'Manes.01G210100' => 'mes', 'Manes.03G185600' => 'mes', 'Manes.05G073300' => 'mes', 'Manes.09G120300' => 'mes', 'Manes.15G022100' => 'mes', 'Mapoly0096s0053' => 'mpo', 'MBI03_g14058_MAGBIO' => 'mbi', 'MBI03_g33876_MAGBIO' => 'mbi', 'MBI03_g36854_MAGBIO' => 'mbi', 'MBI17_g11997_MAGBIO' => 'mbi', 'MD03G1269000' => 'mdo', 'MD04G1179600' => 'mdo', 'MD11G1289800' => 'mdo', 'MD12G1194700' => 'mdo', 'MD13G1182100' => 'mdo', 'MD13G1182200' => 'mdo', 'MD16G1182600' => 'mdo', 'Medtr2g021400' => 'mtr', 'Medtr2g021470' => 'mtr', 'Medtr2g105810' => 'mtr', 'Medtr3g033580' => 'mtr', 'Medtr6g007970' => 'mtr', 'Medtr7g056330' => 'mtr', 'Medtr7g074290' => 'mtr', 'Medtr7g074380' => 'mtr', 'Medtr7g094550' => 'mtr', 'Medtr8g069995' => 'mtr', 'MELO3C014345.2' => 'cme', 'MELO3C021395.2' => 'cme', 'Migut.D00262' => 'egut', 'Migut.G00257' => 'egut', 'MSTRG.21575' => 'ama', 'MSTRG.3985' => 'ama', 'Nitab4.5_0000295g0140' => 'nta', 'Nitab4.5_0000732g0140' => 'nta', 'Nitab4.5_0003162g0020' => 'nta', 'Nitab4.5_0006180g0090' => 'nta', 'Nitab4.5_0006390g0010' => 'nta', 'Nitab4.5_0007392g0040' => 'nta', 'Nn1g02140' => 'nnu', 'Nn4g26168' => 'nnu', 'Nn5g26754' => 'nnu', 'Oeu001433.1' => 'oeu', 'Oeu010299.2' => 'oeu', 'Oeu011171.1' => 'oeu', 'Oeu037675.1' => 'oeu', 'Oeu038359.1' => 'oeu', 'Oeu063834.1' => 'oeu', 'Oeu063835.1' => 'oeu', 'Os05g0312000' => 'osa', 'Os07g0211101' => 'osa', 'Os07g0211200' => 'osa', 'Os07g0681500' => 'osa', 'Peaxi162Scf00095g01015' => 'pax', 'Peaxi162Scf00104g00329' => 'pax', 'Peaxi162Scf00161g00137' => 'pax', 'PGR004G1665' => 'pgr', 'PGR031G2937' => 'pgr', 'PGR119G2145' => 'pgr', 'PGSC0003DMG400004351' => 'stu', 'PGSC0003DMG400014625' => 'stu', 'PGSC0003DMG401000943' => 'stu', 'Phvul.001G148600' => 'pvu', 'Phvul.004G001700' => 'pvu', 'Phvul.006G154900' => 'pvu', 'Phvul.008G078200' => 'pvu', 'Phvul.011G136500' => 'pvu', 'Potri.002G215600' => 'ptr', 'Potri.008G201600' => 'ptr', 'Potri.014G138400' => 'ptr', 'Potri.016G142500' => 'ptr', 'Pp3c16_10580' => 'ppa', 'Pp3c5_25280' => 'ppa', 'Prupe.1G150000' => 'ppe', 'Prupe.1G150100' => 'ppe', 'Prupe.6G299600' => 'ppe', 'Prupe.8G245000' => 'ppe', 'Psat0s4927g0040' => 'psa', 'Psat1g052080' => 'psa', 'Psat1g183800' => 'psa', 'Psat3g113840' => 'psa', 'Psat3g126120' => 'psa', 'Psat3g126160' => 'psa', 'Psat3g158760' => 'psa', 'Psat3g158840' => 'psa', 'PSO170G2858' => 'pso', 'PSO339G0606' => 'pso', 'PSO384G4709' => 'pso', 'PSO407G0334' => 'pso', 'QL04p040276' => 'qlo', 'QL06p005458' => 'qlo', 'QL06p005472' => 'qlo', 'QL07p030546' => 'qlo', 'QL07p031519' => 'qlo', 'QL09p050949' => 'qlo', 'QL09p050966' => 'qlo', 'QL09p051067' => 'qlo', 'QL12p022706' => 'qlo', 'RcHm_v2.0_Chr2g0119601' => 'rch', 'RcHm_v2.0_Chr3g0459591' => 'rch', 'RcHm_v2.0_Chr4g0418521' => 'rch', 'RcHm_v2.0_Chr4g0418531' => 'rch', 'RcHm_v2.0_Chr4g0418541' => 'rch', 'RcHm_v2.0_Chr6g0291641' => 'rch', 'Rhsim01G0086300' => 'rsi', 'Rhsim01G0276300' => 'rsi', 'Rhsim01G0276500' => 'rsi', 'Rhsim04G0207700' => 'rsi', 'Rhsim05G0234500' => 'rsi', 'Rhsim13G0022400' => 'rsi', 'Sabra02G0167900' => 'sbr', 'Sabra04G0158500' => 'sbr', 'Sabra08G0159800' => 'sbr', 'Sabra10G0011500' => 'sbr', 'Sabra14G0104400' => 'sbr', 'SalBow2G2440' => 'sbo', 'SalBow4G2265' => 'sbo', 'Sc02g0000060' => 'sci', 'Sc05g0005020' => 'sci', 'Sc13g0003890' => 'sci', 'Sed0014865' => 'sed', 'Sed0017224' => 'sed', 'Sed0026391' => 'sed', 'SEGI_00063' => 'sgi', 'SEGI_10967' => 'sgi', 'SEGI_17510' => 'sgi', 'SEGI_24396' => 'sgi', 'SEGI_39719' => 'sgi', 'SEGI_41392' => 'sgi', 'SGA_v2.0_scaffold11G05794' => 'sas', 'SGA_v2.0_scaffold142G35607' => 'sas', 'SGA_v2.0_scaffold1G00447' => 'sas', 'SHI15388' => 'shi', 'SHI15394' => 'shi', 'SHI15396' => 'shi', 'SHI15399' => 'shi', 'SMO343G0151' => 'smo', 'SMO367G1118' => 'smo', 'Solyc01g080200.3' => 'sly', 'Solyc06g008960.3' => 'sly', 'Solyc09g064780.3' => 'sly', 'Sopen01g031980' => 'spe', 'Sopen06g003710' => 'spe', 'Sopen09g026460' => 'spe', 'Sp3g21240' => 'spa', 'Sp4g30030' => 'spa', 'TAR365G0022' => 'tar', 'TAR365G1023' => 'tar', 'TAR365G1253' => 'tar', 'TAR623G0078' => 'tar', 'TAR623G1721' => 'tar', 'TAR633G0959' => 'tar', 'THA.LOC104802225' => 'tha', 'THA.LOC104804769' => 'tha', 'THA.LOC104808660' => 'tha', 'THA.LOC104812792' => 'tha', 'Thecc.01G284000' => 'tca', 'Thecc.04G220600' => 'tca', 'Thecc.05G268900' => 'tca', 'Thecc.08G171100' => 'tca', 'Thhalv10001284m.g' => 'esa', 'Thhalv10019912m.g' => 'esa', 'TPR.G14189' => 'tpr', 'TPR.G18110' => 'tpr', 'TPR.G18130' => 'tpr', 'TPR.G18131' => 'tpr', 'TPR.G18140' => 'tpr', 'TPR.G24282' => 'tpr', 'TPR.G25221' => 'tpr', 'TPR.G29267' => 'tpr', 'TPR.G35315' => 'tpr', 'TPR.G36173' => 'tpr', 'TWI09G0794' => 'twi', 'TWI59G1348' => 'twi', 'TWI74G0430' => 'twi', 'unitig_26.g8940' => 'ugi', 'unitig_749.g13744' => 'ugi', 'unitig_749.g13745' => 'ugi', 'vmacro08269' => 'vma', 'vmacro14937' => 'vma', 'vmacro20401' => 'vma', 'VMungo0464G1349' => 'vmu', 'VMungo0540G0289' => 'vmu', 'VMungo1215G1590' => 'vmu', 'VMungo1309G0221' => 'vmu', 'VMungo1309G2815' => 'vmu', 'VMungo1383G0239' => 'vmu', 'VMungo1383G2910' => 'vmu', 'Zm00001eb095270' => 'zma', 'Zm00001eb095280' => 'zma', 'Zm00001eb111630' => 'zma', 'Zm00001eb237080' => 'zma', 'Zm00001eb273740' => 'zma', 'Zm00001eb285040' => 'zma', 'Zm00001eb330790' => 'zma', 'Zm00001eb337380' => 'zma' ) $gf_id = 'HOM05D001484' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001484' ) $data_identifier = 'HOM05D001484' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 2, 'aly' => (int) 2, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 22, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 7, 'hma' => (int) 2, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 7, 'mtr' => (int) 10, 'cme' => (int) 2, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 4, 'ppa' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 4, 'qlo' => (int) 9, 'rch' => (int) 6, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 10, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 7, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb337380' $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' => 'HOM05D001484', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p31500' => 'bna', 'A05p00020' => 'bna', 'A07p08820' => 'bna', 'Aa31LG4G3300' => 'aar', 'Aa31LG8G10030' => 'aar', 'Actinidia00731' => 'ach', 'Actinidia11473' => 'ach', 'Actinidia23469' => 'ach', 'Actinidia24318' => 'ach', 'Actinidia40196' => 'ach', 'Actinidia40197' => 'ach', 'Actinidia40198' => 'ach', 'Ah.08g212990' => 'amhyb', 'Ah.15g091720' => 'amhyb', 'AL3G38260' => 'aly', 'AL4G47710' => 'aly', 'Aqoxy2G00671' => 'aox', 'Aqoxy2G03236' => 'aox', 'arahy.Tifrunner.gnm1.ann1.05IDCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KR684' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATY3SJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK6QJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6APGL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IDT7Z9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM073U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ0R87' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LE7RV4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT4QRX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V5ENPK' => 'arhy', 'AT2G48110' => 'ath', 'AT3G23590' => 'ath', 'ATR0626G186' => 'atr', 'ATR1127G141' => 'atr', 'Atru.chr4.2583' => 'acertr', 'Atru.chr5.1358' => 'acertr', 'Atru.chr5.1359' => 'acertr', 'Atru.chr8.46' => 'acertr', 'AUR62002640' => 'cqu', 'AUR62030055' => 'cqu', 'AUR62033713' => 'cqu', 'AUR62033714' => 'cqu', 'AUR62036795' => 'cqu', 'AUR62039891' => 'cqu', 'BcaB02g08737' => 'bca', 'BcaB04g20441' => 'bca', 'BcaB06g26509' => 'bca', 'BcaB06g26510' => 'bca', 'BcaB06g26511' => 'bca', 'BcaB06g26512' => 'bca', 'BcaB06g26513' => 'bca', 'BcaC02g12564' => 'bca', 'BcaC02g12565' => 'bca', 'BcaC02g12794' => 'bca', 'BcaC02g12795' => 'bca', 'BcaC02g12796' => 'bca', 'BcaC06g35541' => 'bca', 'BNapus_Darmor_BZH_scaffold_188p00080' => 'bna', 'BNapus_Darmor_BZH_scaffold_188p00090' => 'bna', 'BolC1t03972H' => 'bol', 'BolC1t03973H' => 'bol', 'BolC4t21680H' => 'bol', 'BolC7t41863H' => 'bol', 'BolSC55t61227H' => 'bol', 'BolSC55t61228H' => 'bol', 'BraA01t03278Z' => 'bra', 'BraA05t18998Z' => 'bra', 'BraA07t28673Z' => 'bra', 'C01p40150' => 'bna', 'C05p12370' => 'bna', 'C07p13680' => 'bna', 'CAN.G1006.16' => 'can', 'CAN.G1006.17' => 'can', 'CAN.G1170.2' => 'can', 'CAN.G962.7' => 'can', 'CANSAT25G2179' => 'cansat', 'CANSAT78G1573' => 'cansat', 'CARHR099510' => 'chi', 'CARHR143510' => 'chi', 'Carub.0003s2380' => 'cru', 'Carub.0004s3082' => 'cru', 'Ca_00614_v3' => 'car', 'Ca_07801_v3' => 'car', 'Ca_08567_v3' => 'car', 'Ca_09571_v3' => 'car', 'CBR_g19290' => 'cbr', 'Cc01_g19770' => 'ccan', 'Cc03_g03030' => 'ccan', 'CDE07G0968' => 'cde', 'CDE09G1441' => 'cde', 'Cfa006103' => 'cfa', 'Cfa015573' => 'cfa', 'Cfa016988' => 'cfa', 'Ciclev10006738m.g' => 'ccl', 'Ciclev10010920m.g' => 'ccl', 'Ciclev10018517m.g' => 'ccl', 'CiPaw.01G159200' => 'cil', 'CiPaw.02G091000' => 'cil', 'CiPaw.02G091100' => 'cil', 'CiPaw.08G103100' => 'cil', 'CiPaw.09G224900' => 'cil', 'ClCG06G005740' => 'cla', 'ClCG07G000090' => 'cla', 'ClCG07G000100' => 'cla', 'COL.COLO4_09143' => 'col', 'COL.COLO4_25124' => 'col', 'Cpa.g.sc16.34' => 'cpa', 'Cpa.g.sc3504.1' => 'cpa', 'Cpa.g.sc60.37' => 'cpa', 'CsaV3_6G018520' => 'csa', 'CsaV3_6G036860' => 'csa', 'CSS0001072' => 'camsi', 'CSS0020208' => 'camsi', 'CSS0021253' => 'camsi', 'CSS0022190' => 'camsi', 'CSS0036150' => 'camsi', 'CSS0040442' => 'camsi', 'CSS0042300' => 'camsi', 'CSS0045298' => 'camsi', 'DCAR_012449' => 'dca', 'DCAR_018405' => 'dca', 'DCAR_024573' => 'dca', 'DCAR_030591' => 'dca', 'Dinv16926' => 'din', 'Dinv32963' => 'din', 'Dinv38382' => 'din', 'Dinv38383' => 'din', 'Duzib133G0974' => 'dzi', 'Duzib138G1867' => 'dzi', 'Duzib211G0420' => 'dzi', 'Duzib212G0930' => 'dzi', 'ECA234G1645' => 'eca', 'ECA247G3467' => 'eca', 'ECA248G1703' => 'eca', 'EL10Ac3g06327' => 'bvu', 'EL10Ac7g17204' => 'bvu', 'Eucgr.A00855' => 'egr', 'Eucgr.A00858' => 'egr', 'Eucgr.H01520' => 'egr', 'Eucgr.H03604' => 'egr', 'Eucgr.L03465' => 'egr', 'Eucgr.L03466' => 'egr', 'FAN01G0988' => 'fan', 'FAN02G3892' => 'fan', 'FAN05G3381' => 'fan', 'FAN07G0967' => 'fan', 'FAN07G1493' => 'fan', 'FAN08G3125' => 'fan', 'FAN09G0402' => 'fan', 'FAN12G2594' => 'fan', 'FAN12G3879' => 'fan', 'FAN14G1546' => 'fan', 'FAN15G3626' => 'fan', 'FAN17G0588' => 'fan', 'FAN17G0609' => 'fan', 'FAN18G2817' => 'fan', 'FAN19G1305' => 'fan', 'FAN20G1787' => 'fan', 'FAN22G0073' => 'fan', 'FAN22G0352' => 'fan', 'FAN22G0368' => 'fan', 'FAN22G2273' => 'fan', 'FAN24G1998' => 'fan', 'FAN27G1317' => 'fan', 'FvH4_2g23980' => 'fve', 'FvH4_4g14380' => 'fve', 'FvH4_4g14390' => 'fve', 'FvH4_6g09250' => 'fve', 'Glyma.03G151100' => 'gma', 'Glyma.04G122550' => 'gma', 'Glyma.05G001600' => 'gma', 'Glyma.09G270766' => 'gma', 'Glyma.09G270832' => 'gma', 'Glyma.13G209800' => 'gma', 'Glyma.15G102800' => 'gma', 'Glyma.18G218900' => 'gma', 'Glyma.19G001500' => 'gma', 'Glyma.19G153600' => 'gma', 'Gohir.A02G028600' => 'ghi', 'Gohir.A08G045000' => 'ghi', 'Gohir.A11G120500' => 'ghi', 'Gohir.A12G006200' => 'ghi', 'Gohir.A12G006250' => 'ghi', 'Gohir.D02G036300' => 'ghi', 'Gohir.D08G054700' => 'ghi', 'Gohir.D11G125600' => 'ghi', 'Gohir.D12G005700' => 'ghi', 'Gorai.004G055200' => 'gra', 'Gorai.005G040400' => 'gra', 'Gorai.007G134500' => 'gra', 'Gorai.008G005500' => 'gra', 'GSVIVG01011094001' => 'vvi', 'GSVIVG01017879001' => 'vvi', 'GSVIVG01025988001' => 'vvi', 'GSVIVG01029847001' => 'vvi', 'HanXRQChr10g0282901' => 'han', 'HanXRQChr10g0310371' => 'han', 'HanXRQChr10g0315041' => 'han', 'HanXRQChr11g0327651' => 'han', 'HanXRQChr12g0359391' => 'han', 'Haze_00972' => 'cav', 'Haze_00973' => 'cav', 'Haze_00974' => 'cav', 'Haze_04747' => 'cav', 'Haze_04749' => 'cav', 'Haze_04750' => 'cav', 'Haze_21217' => 'cav', 'Hma1.2p1_1037F.1_g250680' => 'hma', 'Hma1.2p1_1644F.1_g295320' => 'hma', 'HPP92_011322' => 'vpl', 'HPP92_011323' => 'vpl', 'HPP92_011324' => 'vpl', 'HPP92_011325' => 'vpl', 'HPP92_011326' => 'vpl', 'Hund12205' => 'sun', 'Hund17957' => 'sun', 'Lalb_Chr06g0176771' => 'lal', 'Lalb_Chr18g0056021' => 'lal', 'Lalb_Chr18g0056031' => 'lal', 'Lalb_Chr18g0056041' => 'lal', 'Lalb_Chr20g0107751' => 'lal', 'Lalb_Chr20g0118371' => 'lal', 'Lj1g0010239' => 'lja', 'Lj1g0017101' => 'lja', 'Lj2A1178G40' => 'lonja', 'Lj2A54G84' => 'lonja', 'Lj2g0015248' => 'lja', 'Lj3A761T51' => 'lonja', 'Lj6g0018116' => 'lja', 'Lsat_1_v5_gn_4_136040' => 'lsa', 'Lsat_1_v5_gn_5_187461' => 'lsa', 'Lsat_1_v5_gn_5_77001' => 'lsa', 'Lsat_1_v5_gn_9_4461' => 'lsa', 'Manes.01G210100' => 'mes', 'Manes.03G185600' => 'mes', 'Manes.05G073300' => 'mes', 'Manes.09G120300' => 'mes', 'Manes.15G022100' => 'mes', 'Mapoly0096s0053' => 'mpo', 'MBI03_g14058_MAGBIO' => 'mbi', 'MBI03_g33876_MAGBIO' => 'mbi', 'MBI03_g36854_MAGBIO' => 'mbi', 'MBI17_g11997_MAGBIO' => 'mbi', 'MD03G1269000' => 'mdo', 'MD04G1179600' => 'mdo', 'MD11G1289800' => 'mdo', 'MD12G1194700' => 'mdo', 'MD13G1182100' => 'mdo', 'MD13G1182200' => 'mdo', 'MD16G1182600' => 'mdo', 'Medtr2g021400' => 'mtr', 'Medtr2g021470' => 'mtr', 'Medtr2g105810' => 'mtr', 'Medtr3g033580' => 'mtr', 'Medtr6g007970' => 'mtr', 'Medtr7g056330' => 'mtr', 'Medtr7g074290' => 'mtr', 'Medtr7g074380' => 'mtr', 'Medtr7g094550' => 'mtr', 'Medtr8g069995' => 'mtr', 'MELO3C014345.2' => 'cme', 'MELO3C021395.2' => 'cme', 'Migut.D00262' => 'egut', 'Migut.G00257' => 'egut', 'MSTRG.21575' => 'ama', 'MSTRG.3985' => 'ama', 'Nitab4.5_0000295g0140' => 'nta', 'Nitab4.5_0000732g0140' => 'nta', 'Nitab4.5_0003162g0020' => 'nta', 'Nitab4.5_0006180g0090' => 'nta', 'Nitab4.5_0006390g0010' => 'nta', 'Nitab4.5_0007392g0040' => 'nta', 'Nn1g02140' => 'nnu', 'Nn4g26168' => 'nnu', 'Nn5g26754' => 'nnu', 'Oeu001433.1' => 'oeu', 'Oeu010299.2' => 'oeu', 'Oeu011171.1' => 'oeu', 'Oeu037675.1' => 'oeu', 'Oeu038359.1' => 'oeu', 'Oeu063834.1' => 'oeu', 'Oeu063835.1' => 'oeu', 'Os05g0312000' => 'osa', 'Os07g0211101' => 'osa', 'Os07g0211200' => 'osa', 'Os07g0681500' => 'osa', 'Peaxi162Scf00095g01015' => 'pax', 'Peaxi162Scf00104g00329' => 'pax', 'Peaxi162Scf00161g00137' => 'pax', 'PGR004G1665' => 'pgr', 'PGR031G2937' => 'pgr', 'PGR119G2145' => 'pgr', 'PGSC0003DMG400004351' => 'stu', 'PGSC0003DMG400014625' => 'stu', 'PGSC0003DMG401000943' => 'stu', 'Phvul.001G148600' => 'pvu', 'Phvul.004G001700' => 'pvu', 'Phvul.006G154900' => 'pvu', 'Phvul.008G078200' => 'pvu', 'Phvul.011G136500' => 'pvu', 'Potri.002G215600' => 'ptr', 'Potri.008G201600' => 'ptr', 'Potri.014G138400' => 'ptr', 'Potri.016G142500' => 'ptr', 'Pp3c16_10580' => 'ppa', 'Pp3c5_25280' => 'ppa', 'Prupe.1G150000' => 'ppe', 'Prupe.1G150100' => 'ppe', 'Prupe.6G299600' => 'ppe', 'Prupe.8G245000' => 'ppe', 'Psat0s4927g0040' => 'psa', 'Psat1g052080' => 'psa', 'Psat1g183800' => 'psa', 'Psat3g113840' => 'psa', 'Psat3g126120' => 'psa', 'Psat3g126160' => 'psa', 'Psat3g158760' => 'psa', 'Psat3g158840' => 'psa', 'PSO170G2858' => 'pso', 'PSO339G0606' => 'pso', 'PSO384G4709' => 'pso', 'PSO407G0334' => 'pso', 'QL04p040276' => 'qlo', 'QL06p005458' => 'qlo', 'QL06p005472' => 'qlo', 'QL07p030546' => 'qlo', 'QL07p031519' => 'qlo', 'QL09p050949' => 'qlo', 'QL09p050966' => 'qlo', 'QL09p051067' => 'qlo', 'QL12p022706' => 'qlo', 'RcHm_v2.0_Chr2g0119601' => 'rch', 'RcHm_v2.0_Chr3g0459591' => 'rch', 'RcHm_v2.0_Chr4g0418521' => 'rch', 'RcHm_v2.0_Chr4g0418531' => 'rch', 'RcHm_v2.0_Chr4g0418541' => 'rch', 'RcHm_v2.0_Chr6g0291641' => 'rch', 'Rhsim01G0086300' => 'rsi', 'Rhsim01G0276300' => 'rsi', 'Rhsim01G0276500' => 'rsi', 'Rhsim04G0207700' => 'rsi', 'Rhsim05G0234500' => 'rsi', 'Rhsim13G0022400' => 'rsi', 'Sabra02G0167900' => 'sbr', 'Sabra04G0158500' => 'sbr', 'Sabra08G0159800' => 'sbr', 'Sabra10G0011500' => 'sbr', 'Sabra14G0104400' => 'sbr', 'SalBow2G2440' => 'sbo', 'SalBow4G2265' => 'sbo', 'Sc02g0000060' => 'sci', 'Sc05g0005020' => 'sci', 'Sc13g0003890' => 'sci', 'Sed0014865' => 'sed', 'Sed0017224' => 'sed', 'Sed0026391' => 'sed', 'SEGI_00063' => 'sgi', 'SEGI_10967' => 'sgi', 'SEGI_17510' => 'sgi', 'SEGI_24396' => 'sgi', 'SEGI_39719' => 'sgi', 'SEGI_41392' => 'sgi', 'SGA_v2.0_scaffold11G05794' => 'sas', 'SGA_v2.0_scaffold142G35607' => 'sas', 'SGA_v2.0_scaffold1G00447' => 'sas', 'SHI15388' => 'shi', 'SHI15394' => 'shi', 'SHI15396' => 'shi', 'SHI15399' => 'shi', 'SMO343G0151' => 'smo', 'SMO367G1118' => 'smo', 'Solyc01g080200.3' => 'sly', 'Solyc06g008960.3' => 'sly', 'Solyc09g064780.3' => 'sly', 'Sopen01g031980' => 'spe', 'Sopen06g003710' => 'spe', 'Sopen09g026460' => 'spe', 'Sp3g21240' => 'spa', 'Sp4g30030' => 'spa', 'TAR365G0022' => 'tar', 'TAR365G1023' => 'tar', 'TAR365G1253' => 'tar', 'TAR623G0078' => 'tar', 'TAR623G1721' => 'tar', 'TAR633G0959' => 'tar', 'THA.LOC104802225' => 'tha', 'THA.LOC104804769' => 'tha', 'THA.LOC104808660' => 'tha', 'THA.LOC104812792' => 'tha', 'Thecc.01G284000' => 'tca', 'Thecc.04G220600' => 'tca', 'Thecc.05G268900' => 'tca', 'Thecc.08G171100' => 'tca', 'Thhalv10001284m.g' => 'esa', 'Thhalv10019912m.g' => 'esa', 'TPR.G14189' => 'tpr', 'TPR.G18110' => 'tpr', 'TPR.G18130' => 'tpr', 'TPR.G18131' => 'tpr', 'TPR.G18140' => 'tpr', 'TPR.G24282' => 'tpr', 'TPR.G25221' => 'tpr', 'TPR.G29267' => 'tpr', 'TPR.G35315' => 'tpr', 'TPR.G36173' => 'tpr', 'TWI09G0794' => 'twi', 'TWI59G1348' => 'twi', 'TWI74G0430' => 'twi', 'unitig_26.g8940' => 'ugi', 'unitig_749.g13744' => 'ugi', 'unitig_749.g13745' => 'ugi', 'vmacro08269' => 'vma', 'vmacro14937' => 'vma', 'vmacro20401' => 'vma', 'VMungo0464G1349' => 'vmu', 'VMungo0540G0289' => 'vmu', 'VMungo1215G1590' => 'vmu', 'VMungo1309G0221' => 'vmu', 'VMungo1309G2815' => 'vmu', 'VMungo1383G0239' => 'vmu', 'VMungo1383G2910' => 'vmu', 'Zm00001eb095270' => 'zma', 'Zm00001eb095280' => 'zma', 'Zm00001eb111630' => 'zma', 'Zm00001eb237080' => 'zma', 'Zm00001eb273740' => 'zma', 'Zm00001eb285040' => 'zma', 'Zm00001eb330790' => 'zma', 'Zm00001eb337380' => 'zma' ), 'gf_id' => 'HOM05D001484', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001484' ), 'data_identifier' => 'HOM05D001484', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001484', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p31500' => 'bna', 'A05p00020' => 'bna', 'A07p08820' => 'bna', 'Aa31LG4G3300' => 'aar', 'Aa31LG8G10030' => 'aar', 'Actinidia00731' => 'ach', 'Actinidia11473' => 'ach', 'Actinidia23469' => 'ach', 'Actinidia24318' => 'ach', 'Actinidia40196' => 'ach', 'Actinidia40197' => 'ach', 'Actinidia40198' => 'ach', 'Ah.08g212990' => 'amhyb', 'Ah.15g091720' => 'amhyb', 'AL3G38260' => 'aly', 'AL4G47710' => 'aly', 'Aqoxy2G00671' => 'aox', 'Aqoxy2G03236' => 'aox', 'arahy.Tifrunner.gnm1.ann1.05IDCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KR684' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATY3SJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK6QJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6APGL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IDT7Z9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM073U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ0R87' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LE7RV4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT4QRX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V5ENPK' => 'arhy', 'AT2G48110' => 'ath', 'AT3G23590' => 'ath', 'ATR0626G186' => 'atr', 'ATR1127G141' => 'atr', 'Atru.chr4.2583' => 'acertr', 'Atru.chr5.1358' => 'acertr', 'Atru.chr5.1359' => 'acertr', 'Atru.chr8.46' => 'acertr', 'AUR62002640' => 'cqu', 'AUR62030055' => 'cqu', 'AUR62033713' => 'cqu', 'AUR62033714' => 'cqu', 'AUR62036795' => 'cqu', 'AUR62039891' => 'cqu', 'BcaB02g08737' => 'bca', 'BcaB04g20441' => 'bca', 'BcaB06g26509' => 'bca', 'BcaB06g26510' => 'bca', 'BcaB06g26511' => 'bca', 'BcaB06g26512' => 'bca', 'BcaB06g26513' => 'bca', 'BcaC02g12564' => 'bca', 'BcaC02g12565' => 'bca', 'BcaC02g12794' => 'bca', 'BcaC02g12795' => 'bca', 'BcaC02g12796' => 'bca', 'BcaC06g35541' => 'bca', 'BNapus_Darmor_BZH_scaffold_188p00080' => 'bna', 'BNapus_Darmor_BZH_scaffold_188p00090' => 'bna', 'BolC1t03972H' => 'bol', 'BolC1t03973H' => 'bol', 'BolC4t21680H' => 'bol', 'BolC7t41863H' => 'bol', 'BolSC55t61227H' => 'bol', 'BolSC55t61228H' => 'bol', 'BraA01t03278Z' => 'bra', 'BraA05t18998Z' => 'bra', 'BraA07t28673Z' => 'bra', 'C01p40150' => 'bna', 'C05p12370' => 'bna', 'C07p13680' => 'bna', 'CAN.G1006.16' => 'can', 'CAN.G1006.17' => 'can', 'CAN.G1170.2' => 'can', 'CAN.G962.7' => 'can', 'CANSAT25G2179' => 'cansat', 'CANSAT78G1573' => 'cansat', 'CARHR099510' => 'chi', 'CARHR143510' => 'chi', 'Carub.0003s2380' => 'cru', 'Carub.0004s3082' => 'cru', 'Ca_00614_v3' => 'car', 'Ca_07801_v3' => 'car', 'Ca_08567_v3' => 'car', 'Ca_09571_v3' => 'car', 'CBR_g19290' => 'cbr', 'Cc01_g19770' => 'ccan', 'Cc03_g03030' => 'ccan', 'CDE07G0968' => 'cde', 'CDE09G1441' => 'cde', 'Cfa006103' => 'cfa', 'Cfa015573' => 'cfa', 'Cfa016988' => 'cfa', 'Ciclev10006738m.g' => 'ccl', 'Ciclev10010920m.g' => 'ccl', 'Ciclev10018517m.g' => 'ccl', 'CiPaw.01G159200' => 'cil', 'CiPaw.02G091000' => 'cil', 'CiPaw.02G091100' => 'cil', 'CiPaw.08G103100' => 'cil', 'CiPaw.09G224900' => 'cil', 'ClCG06G005740' => 'cla', 'ClCG07G000090' => 'cla', 'ClCG07G000100' => 'cla', 'COL.COLO4_09143' => 'col', 'COL.COLO4_25124' => 'col', 'Cpa.g.sc16.34' => 'cpa', 'Cpa.g.sc3504.1' => 'cpa', 'Cpa.g.sc60.37' => 'cpa', 'CsaV3_6G018520' => 'csa', 'CsaV3_6G036860' => 'csa', 'CSS0001072' => 'camsi', 'CSS0020208' => 'camsi', 'CSS0021253' => 'camsi', 'CSS0022190' => 'camsi', 'CSS0036150' => 'camsi', 'CSS0040442' => 'camsi', 'CSS0042300' => 'camsi', 'CSS0045298' => 'camsi', 'DCAR_012449' => 'dca', 'DCAR_018405' => 'dca', 'DCAR_024573' => 'dca', 'DCAR_030591' => 'dca', 'Dinv16926' => 'din', 'Dinv32963' => 'din', 'Dinv38382' => 'din', 'Dinv38383' => 'din', 'Duzib133G0974' => 'dzi', 'Duzib138G1867' => 'dzi', 'Duzib211G0420' => 'dzi', 'Duzib212G0930' => 'dzi', 'ECA234G1645' => 'eca', 'ECA247G3467' => 'eca', 'ECA248G1703' => 'eca', 'EL10Ac3g06327' => 'bvu', 'EL10Ac7g17204' => 'bvu', 'Eucgr.A00855' => 'egr', 'Eucgr.A00858' => 'egr', 'Eucgr.H01520' => 'egr', 'Eucgr.H03604' => 'egr', 'Eucgr.L03465' => 'egr', 'Eucgr.L03466' => 'egr', 'FAN01G0988' => 'fan', 'FAN02G3892' => 'fan', 'FAN05G3381' => 'fan', 'FAN07G0967' => 'fan', 'FAN07G1493' => 'fan', 'FAN08G3125' => 'fan', 'FAN09G0402' => 'fan', 'FAN12G2594' => 'fan', 'FAN12G3879' => 'fan', 'FAN14G1546' => 'fan', 'FAN15G3626' => 'fan', 'FAN17G0588' => 'fan', 'FAN17G0609' => 'fan', 'FAN18G2817' => 'fan', 'FAN19G1305' => 'fan', 'FAN20G1787' => 'fan', 'FAN22G0073' => 'fan', 'FAN22G0352' => 'fan', 'FAN22G0368' => 'fan', 'FAN22G2273' => 'fan', 'FAN24G1998' => 'fan', 'FAN27G1317' => 'fan', 'FvH4_2g23980' => 'fve', 'FvH4_4g14380' => 'fve', 'FvH4_4g14390' => 'fve', 'FvH4_6g09250' => 'fve', 'Glyma.03G151100' => 'gma', 'Glyma.04G122550' => 'gma', 'Glyma.05G001600' => 'gma', 'Glyma.09G270766' => 'gma', 'Glyma.09G270832' => 'gma', 'Glyma.13G209800' => 'gma', 'Glyma.15G102800' => 'gma', 'Glyma.18G218900' => 'gma', 'Glyma.19G001500' => 'gma', 'Glyma.19G153600' => 'gma', 'Gohir.A02G028600' => 'ghi', 'Gohir.A08G045000' => 'ghi', 'Gohir.A11G120500' => 'ghi', 'Gohir.A12G006200' => 'ghi', 'Gohir.A12G006250' => 'ghi', 'Gohir.D02G036300' => 'ghi', 'Gohir.D08G054700' => 'ghi', 'Gohir.D11G125600' => 'ghi', 'Gohir.D12G005700' => 'ghi', 'Gorai.004G055200' => 'gra', 'Gorai.005G040400' => 'gra', 'Gorai.007G134500' => 'gra', 'Gorai.008G005500' => 'gra', 'GSVIVG01011094001' => 'vvi', 'GSVIVG01017879001' => 'vvi', 'GSVIVG01025988001' => 'vvi', 'GSVIVG01029847001' => 'vvi', 'HanXRQChr10g0282901' => 'han', 'HanXRQChr10g0310371' => 'han', 'HanXRQChr10g0315041' => 'han', 'HanXRQChr11g0327651' => 'han', 'HanXRQChr12g0359391' => 'han', 'Haze_00972' => 'cav', 'Haze_00973' => 'cav', 'Haze_00974' => 'cav', 'Haze_04747' => 'cav', 'Haze_04749' => 'cav', 'Haze_04750' => 'cav', 'Haze_21217' => 'cav', 'Hma1.2p1_1037F.1_g250680' => 'hma', 'Hma1.2p1_1644F.1_g295320' => 'hma', 'HPP92_011322' => 'vpl', 'HPP92_011323' => 'vpl', 'HPP92_011324' => 'vpl', 'HPP92_011325' => 'vpl', 'HPP92_011326' => 'vpl', 'Hund12205' => 'sun', 'Hund17957' => 'sun', 'Lalb_Chr06g0176771' => 'lal', 'Lalb_Chr18g0056021' => 'lal', 'Lalb_Chr18g0056031' => 'lal', 'Lalb_Chr18g0056041' => 'lal', 'Lalb_Chr20g0107751' => 'lal', 'Lalb_Chr20g0118371' => 'lal', 'Lj1g0010239' => 'lja', 'Lj1g0017101' => 'lja', 'Lj2A1178G40' => 'lonja', 'Lj2A54G84' => 'lonja', 'Lj2g0015248' => 'lja', 'Lj3A761T51' => 'lonja', 'Lj6g0018116' => 'lja', 'Lsat_1_v5_gn_4_136040' => 'lsa', 'Lsat_1_v5_gn_5_187461' => 'lsa', 'Lsat_1_v5_gn_5_77001' => 'lsa', 'Lsat_1_v5_gn_9_4461' => 'lsa', 'Manes.01G210100' => 'mes', 'Manes.03G185600' => 'mes', 'Manes.05G073300' => 'mes', 'Manes.09G120300' => 'mes', 'Manes.15G022100' => 'mes', 'Mapoly0096s0053' => 'mpo', 'MBI03_g14058_MAGBIO' => 'mbi', 'MBI03_g33876_MAGBIO' => 'mbi', 'MBI03_g36854_MAGBIO' => 'mbi', 'MBI17_g11997_MAGBIO' => 'mbi', 'MD03G1269000' => 'mdo', 'MD04G1179600' => 'mdo', 'MD11G1289800' => 'mdo', 'MD12G1194700' => 'mdo', 'MD13G1182100' => 'mdo', 'MD13G1182200' => 'mdo', 'MD16G1182600' => 'mdo', 'Medtr2g021400' => 'mtr', 'Medtr2g021470' => 'mtr', 'Medtr2g105810' => 'mtr', 'Medtr3g033580' => 'mtr', 'Medtr6g007970' => 'mtr', 'Medtr7g056330' => 'mtr', 'Medtr7g074290' => 'mtr', 'Medtr7g074380' => 'mtr', 'Medtr7g094550' => 'mtr', 'Medtr8g069995' => 'mtr', 'MELO3C014345.2' => 'cme', 'MELO3C021395.2' => 'cme', 'Migut.D00262' => 'egut', 'Migut.G00257' => 'egut', 'MSTRG.21575' => 'ama', 'MSTRG.3985' => 'ama', 'Nitab4.5_0000295g0140' => 'nta', 'Nitab4.5_0000732g0140' => 'nta', 'Nitab4.5_0003162g0020' => 'nta', 'Nitab4.5_0006180g0090' => 'nta', 'Nitab4.5_0006390g0010' => 'nta', 'Nitab4.5_0007392g0040' => 'nta', 'Nn1g02140' => 'nnu', 'Nn4g26168' => 'nnu', 'Nn5g26754' => 'nnu', 'Oeu001433.1' => 'oeu', 'Oeu010299.2' => 'oeu', 'Oeu011171.1' => 'oeu', 'Oeu037675.1' => 'oeu', 'Oeu038359.1' => 'oeu', 'Oeu063834.1' => 'oeu', 'Oeu063835.1' => 'oeu', 'Os05g0312000' => 'osa', 'Os07g0211101' => 'osa', 'Os07g0211200' => 'osa', 'Os07g0681500' => 'osa', 'Peaxi162Scf00095g01015' => 'pax', 'Peaxi162Scf00104g00329' => 'pax', 'Peaxi162Scf00161g00137' => 'pax', 'PGR004G1665' => 'pgr', 'PGR031G2937' => 'pgr', 'PGR119G2145' => 'pgr', 'PGSC0003DMG400004351' => 'stu', 'PGSC0003DMG400014625' => 'stu', 'PGSC0003DMG401000943' => 'stu', 'Phvul.001G148600' => 'pvu', 'Phvul.004G001700' => 'pvu', 'Phvul.006G154900' => 'pvu', 'Phvul.008G078200' => 'pvu', 'Phvul.011G136500' => 'pvu', 'Potri.002G215600' => 'ptr', 'Potri.008G201600' => 'ptr', 'Potri.014G138400' => 'ptr', 'Potri.016G142500' => 'ptr', 'Pp3c16_10580' => 'ppa', 'Pp3c5_25280' => 'ppa', 'Prupe.1G150000' => 'ppe', 'Prupe.1G150100' => 'ppe', 'Prupe.6G299600' => 'ppe', 'Prupe.8G245000' => 'ppe', 'Psat0s4927g0040' => 'psa', 'Psat1g052080' => 'psa', 'Psat1g183800' => 'psa', 'Psat3g113840' => 'psa', 'Psat3g126120' => 'psa', 'Psat3g126160' => 'psa', 'Psat3g158760' => 'psa', 'Psat3g158840' => 'psa', 'PSO170G2858' => 'pso', 'PSO339G0606' => 'pso', 'PSO384G4709' => 'pso', 'PSO407G0334' => 'pso', 'QL04p040276' => 'qlo', 'QL06p005458' => 'qlo', 'QL06p005472' => 'qlo', 'QL07p030546' => 'qlo', 'QL07p031519' => 'qlo', 'QL09p050949' => 'qlo', 'QL09p050966' => 'qlo', 'QL09p051067' => 'qlo', 'QL12p022706' => 'qlo', 'RcHm_v2.0_Chr2g0119601' => 'rch', 'RcHm_v2.0_Chr3g0459591' => 'rch', 'RcHm_v2.0_Chr4g0418521' => 'rch', 'RcHm_v2.0_Chr4g0418531' => 'rch', 'RcHm_v2.0_Chr4g0418541' => 'rch', 'RcHm_v2.0_Chr6g0291641' => 'rch', 'Rhsim01G0086300' => 'rsi', 'Rhsim01G0276300' => 'rsi', 'Rhsim01G0276500' => 'rsi', 'Rhsim04G0207700' => 'rsi', 'Rhsim05G0234500' => 'rsi', 'Rhsim13G0022400' => 'rsi', 'Sabra02G0167900' => 'sbr', 'Sabra04G0158500' => 'sbr', 'Sabra08G0159800' => 'sbr', 'Sabra10G0011500' => 'sbr', 'Sabra14G0104400' => 'sbr', 'SalBow2G2440' => 'sbo', 'SalBow4G2265' => 'sbo', 'Sc02g0000060' => 'sci', 'Sc05g0005020' => 'sci', 'Sc13g0003890' => 'sci', 'Sed0014865' => 'sed', 'Sed0017224' => 'sed', 'Sed0026391' => 'sed', 'SEGI_00063' => 'sgi', 'SEGI_10967' => 'sgi', 'SEGI_17510' => 'sgi', 'SEGI_24396' => 'sgi', 'SEGI_39719' => 'sgi', 'SEGI_41392' => 'sgi', 'SGA_v2.0_scaffold11G05794' => 'sas', 'SGA_v2.0_scaffold142G35607' => 'sas', 'SGA_v2.0_scaffold1G00447' => 'sas', 'SHI15388' => 'shi', 'SHI15394' => 'shi', 'SHI15396' => 'shi', 'SHI15399' => 'shi', 'SMO343G0151' => 'smo', 'SMO367G1118' => 'smo', 'Solyc01g080200.3' => 'sly', 'Solyc06g008960.3' => 'sly', 'Solyc09g064780.3' => 'sly', 'Sopen01g031980' => 'spe', 'Sopen06g003710' => 'spe', 'Sopen09g026460' => 'spe', 'Sp3g21240' => 'spa', 'Sp4g30030' => 'spa', 'TAR365G0022' => 'tar', 'TAR365G1023' => 'tar', 'TAR365G1253' => 'tar', 'TAR623G0078' => 'tar', 'TAR623G1721' => 'tar', 'TAR633G0959' => 'tar', 'THA.LOC104802225' => 'tha', 'THA.LOC104804769' => 'tha', 'THA.LOC104808660' => 'tha', 'THA.LOC104812792' => 'tha', 'Thecc.01G284000' => 'tca', 'Thecc.04G220600' => 'tca', 'Thecc.05G268900' => 'tca', 'Thecc.08G171100' => 'tca', 'Thhalv10001284m.g' => 'esa', 'Thhalv10019912m.g' => 'esa', 'TPR.G14189' => 'tpr', 'TPR.G18110' => 'tpr', 'TPR.G18130' => 'tpr', 'TPR.G18131' => 'tpr', 'TPR.G18140' => 'tpr', 'TPR.G24282' => 'tpr', 'TPR.G25221' => 'tpr', 'TPR.G29267' => 'tpr', 'TPR.G35315' => 'tpr', 'TPR.G36173' => 'tpr', 'TWI09G0794' => 'twi', 'TWI59G1348' => 'twi', 'TWI74G0430' => 'twi', 'unitig_26.g8940' => 'ugi', 'unitig_749.g13744' => 'ugi', 'unitig_749.g13745' => 'ugi', 'vmacro08269' => 'vma', 'vmacro14937' => 'vma', 'vmacro20401' => 'vma', 'VMungo0464G1349' => 'vmu', 'VMungo0540G0289' => 'vmu', 'VMungo1215G1590' => 'vmu', 'VMungo1309G0221' => 'vmu', 'VMungo1309G2815' => 'vmu', 'VMungo1383G0239' => 'vmu', 'VMungo1383G2910' => 'vmu', 'Zm00001eb095270' => 'zma', 'Zm00001eb095280' => 'zma', 'Zm00001eb111630' => 'zma', 'Zm00001eb237080' => 'zma', 'Zm00001eb273740' => 'zma', 'Zm00001eb285040' => 'zma', 'Zm00001eb330790' => 'zma', 'Zm00001eb337380' => 'zma' ) $gf_id = 'HOM05D001484' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001484' ) $data_identifier = 'HOM05D001484' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 2, 'aly' => (int) 2, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 22, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 7, 'hma' => (int) 2, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 7, 'mtr' => (int) 10, 'cme' => (int) 2, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 4, 'ppa' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 4, 'qlo' => (int) 9, 'rch' => (int) 6, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 10, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 7, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb337380' $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' => 'HOM05D001484', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p31500' => 'bna', 'A05p00020' => 'bna', 'A07p08820' => 'bna', 'Aa31LG4G3300' => 'aar', 'Aa31LG8G10030' => 'aar', 'Actinidia00731' => 'ach', 'Actinidia11473' => 'ach', 'Actinidia23469' => 'ach', 'Actinidia24318' => 'ach', 'Actinidia40196' => 'ach', 'Actinidia40197' => 'ach', 'Actinidia40198' => 'ach', 'Ah.08g212990' => 'amhyb', 'Ah.15g091720' => 'amhyb', 'AL3G38260' => 'aly', 'AL4G47710' => 'aly', 'Aqoxy2G00671' => 'aox', 'Aqoxy2G03236' => 'aox', 'arahy.Tifrunner.gnm1.ann1.05IDCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KR684' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATY3SJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK6QJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6APGL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IDT7Z9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM073U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ0R87' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LE7RV4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT4QRX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V5ENPK' => 'arhy', 'AT2G48110' => 'ath', 'AT3G23590' => 'ath', 'ATR0626G186' => 'atr', 'ATR1127G141' => 'atr', 'Atru.chr4.2583' => 'acertr', 'Atru.chr5.1358' => 'acertr', 'Atru.chr5.1359' => 'acertr', 'Atru.chr8.46' => 'acertr', 'AUR62002640' => 'cqu', 'AUR62030055' => 'cqu', 'AUR62033713' => 'cqu', 'AUR62033714' => 'cqu', 'AUR62036795' => 'cqu', 'AUR62039891' => 'cqu', 'BcaB02g08737' => 'bca', 'BcaB04g20441' => 'bca', 'BcaB06g26509' => 'bca', 'BcaB06g26510' => 'bca', 'BcaB06g26511' => 'bca', 'BcaB06g26512' => 'bca', 'BcaB06g26513' => 'bca', 'BcaC02g12564' => 'bca', 'BcaC02g12565' => 'bca', 'BcaC02g12794' => 'bca', 'BcaC02g12795' => 'bca', 'BcaC02g12796' => 'bca', 'BcaC06g35541' => 'bca', 'BNapus_Darmor_BZH_scaffold_188p00080' => 'bna', 'BNapus_Darmor_BZH_scaffold_188p00090' => 'bna', 'BolC1t03972H' => 'bol', 'BolC1t03973H' => 'bol', 'BolC4t21680H' => 'bol', 'BolC7t41863H' => 'bol', 'BolSC55t61227H' => 'bol', 'BolSC55t61228H' => 'bol', 'BraA01t03278Z' => 'bra', 'BraA05t18998Z' => 'bra', 'BraA07t28673Z' => 'bra', 'C01p40150' => 'bna', 'C05p12370' => 'bna', 'C07p13680' => 'bna', 'CAN.G1006.16' => 'can', 'CAN.G1006.17' => 'can', 'CAN.G1170.2' => 'can', 'CAN.G962.7' => 'can', 'CANSAT25G2179' => 'cansat', 'CANSAT78G1573' => 'cansat', 'CARHR099510' => 'chi', 'CARHR143510' => 'chi', 'Carub.0003s2380' => 'cru', 'Carub.0004s3082' => 'cru', 'Ca_00614_v3' => 'car', 'Ca_07801_v3' => 'car', 'Ca_08567_v3' => 'car', 'Ca_09571_v3' => 'car', 'CBR_g19290' => 'cbr', 'Cc01_g19770' => 'ccan', 'Cc03_g03030' => 'ccan', 'CDE07G0968' => 'cde', 'CDE09G1441' => 'cde', 'Cfa006103' => 'cfa', 'Cfa015573' => 'cfa', 'Cfa016988' => 'cfa', 'Ciclev10006738m.g' => 'ccl', 'Ciclev10010920m.g' => 'ccl', 'Ciclev10018517m.g' => 'ccl', 'CiPaw.01G159200' => 'cil', 'CiPaw.02G091000' => 'cil', 'CiPaw.02G091100' => 'cil', 'CiPaw.08G103100' => 'cil', 'CiPaw.09G224900' => 'cil', 'ClCG06G005740' => 'cla', 'ClCG07G000090' => 'cla', 'ClCG07G000100' => 'cla', 'COL.COLO4_09143' => 'col', 'COL.COLO4_25124' => 'col', 'Cpa.g.sc16.34' => 'cpa', 'Cpa.g.sc3504.1' => 'cpa', 'Cpa.g.sc60.37' => 'cpa', 'CsaV3_6G018520' => 'csa', 'CsaV3_6G036860' => 'csa', 'CSS0001072' => 'camsi', 'CSS0020208' => 'camsi', 'CSS0021253' => 'camsi', 'CSS0022190' => 'camsi', 'CSS0036150' => 'camsi', 'CSS0040442' => 'camsi', 'CSS0042300' => 'camsi', 'CSS0045298' => 'camsi', 'DCAR_012449' => 'dca', 'DCAR_018405' => 'dca', 'DCAR_024573' => 'dca', 'DCAR_030591' => 'dca', 'Dinv16926' => 'din', 'Dinv32963' => 'din', 'Dinv38382' => 'din', 'Dinv38383' => 'din', 'Duzib133G0974' => 'dzi', 'Duzib138G1867' => 'dzi', 'Duzib211G0420' => 'dzi', 'Duzib212G0930' => 'dzi', 'ECA234G1645' => 'eca', 'ECA247G3467' => 'eca', 'ECA248G1703' => 'eca', 'EL10Ac3g06327' => 'bvu', 'EL10Ac7g17204' => 'bvu', 'Eucgr.A00855' => 'egr', 'Eucgr.A00858' => 'egr', 'Eucgr.H01520' => 'egr', 'Eucgr.H03604' => 'egr', 'Eucgr.L03465' => 'egr', 'Eucgr.L03466' => 'egr', 'FAN01G0988' => 'fan', 'FAN02G3892' => 'fan', 'FAN05G3381' => 'fan', 'FAN07G0967' => 'fan', 'FAN07G1493' => 'fan', 'FAN08G3125' => 'fan', 'FAN09G0402' => 'fan', 'FAN12G2594' => 'fan', 'FAN12G3879' => 'fan', 'FAN14G1546' => 'fan', 'FAN15G3626' => 'fan', 'FAN17G0588' => 'fan', 'FAN17G0609' => 'fan', 'FAN18G2817' => 'fan', 'FAN19G1305' => 'fan', 'FAN20G1787' => 'fan', 'FAN22G0073' => 'fan', 'FAN22G0352' => 'fan', 'FAN22G0368' => 'fan', 'FAN22G2273' => 'fan', 'FAN24G1998' => 'fan', 'FAN27G1317' => 'fan', 'FvH4_2g23980' => 'fve', 'FvH4_4g14380' => 'fve', 'FvH4_4g14390' => 'fve', 'FvH4_6g09250' => 'fve', 'Glyma.03G151100' => 'gma', 'Glyma.04G122550' => 'gma', 'Glyma.05G001600' => 'gma', 'Glyma.09G270766' => 'gma', 'Glyma.09G270832' => 'gma', 'Glyma.13G209800' => 'gma', 'Glyma.15G102800' => 'gma', 'Glyma.18G218900' => 'gma', 'Glyma.19G001500' => 'gma', 'Glyma.19G153600' => 'gma', 'Gohir.A02G028600' => 'ghi', 'Gohir.A08G045000' => 'ghi', 'Gohir.A11G120500' => 'ghi', 'Gohir.A12G006200' => 'ghi', 'Gohir.A12G006250' => 'ghi', 'Gohir.D02G036300' => 'ghi', 'Gohir.D08G054700' => 'ghi', 'Gohir.D11G125600' => 'ghi', 'Gohir.D12G005700' => 'ghi', 'Gorai.004G055200' => 'gra', 'Gorai.005G040400' => 'gra', 'Gorai.007G134500' => 'gra', 'Gorai.008G005500' => 'gra', 'GSVIVG01011094001' => 'vvi', 'GSVIVG01017879001' => 'vvi', 'GSVIVG01025988001' => 'vvi', 'GSVIVG01029847001' => 'vvi', 'HanXRQChr10g0282901' => 'han', 'HanXRQChr10g0310371' => 'han', 'HanXRQChr10g0315041' => 'han', 'HanXRQChr11g0327651' => 'han', 'HanXRQChr12g0359391' => 'han', 'Haze_00972' => 'cav', 'Haze_00973' => 'cav', 'Haze_00974' => 'cav', 'Haze_04747' => 'cav', 'Haze_04749' => 'cav', 'Haze_04750' => 'cav', 'Haze_21217' => 'cav', 'Hma1.2p1_1037F.1_g250680' => 'hma', 'Hma1.2p1_1644F.1_g295320' => 'hma', 'HPP92_011322' => 'vpl', 'HPP92_011323' => 'vpl', 'HPP92_011324' => 'vpl', 'HPP92_011325' => 'vpl', 'HPP92_011326' => 'vpl', 'Hund12205' => 'sun', 'Hund17957' => 'sun', 'Lalb_Chr06g0176771' => 'lal', 'Lalb_Chr18g0056021' => 'lal', 'Lalb_Chr18g0056031' => 'lal', 'Lalb_Chr18g0056041' => 'lal', 'Lalb_Chr20g0107751' => 'lal', 'Lalb_Chr20g0118371' => 'lal', 'Lj1g0010239' => 'lja', 'Lj1g0017101' => 'lja', 'Lj2A1178G40' => 'lonja', 'Lj2A54G84' => 'lonja', 'Lj2g0015248' => 'lja', 'Lj3A761T51' => 'lonja', 'Lj6g0018116' => 'lja', 'Lsat_1_v5_gn_4_136040' => 'lsa', 'Lsat_1_v5_gn_5_187461' => 'lsa', 'Lsat_1_v5_gn_5_77001' => 'lsa', 'Lsat_1_v5_gn_9_4461' => 'lsa', 'Manes.01G210100' => 'mes', 'Manes.03G185600' => 'mes', 'Manes.05G073300' => 'mes', 'Manes.09G120300' => 'mes', 'Manes.15G022100' => 'mes', 'Mapoly0096s0053' => 'mpo', 'MBI03_g14058_MAGBIO' => 'mbi', 'MBI03_g33876_MAGBIO' => 'mbi', 'MBI03_g36854_MAGBIO' => 'mbi', 'MBI17_g11997_MAGBIO' => 'mbi', 'MD03G1269000' => 'mdo', 'MD04G1179600' => 'mdo', 'MD11G1289800' => 'mdo', 'MD12G1194700' => 'mdo', 'MD13G1182100' => 'mdo', 'MD13G1182200' => 'mdo', 'MD16G1182600' => 'mdo', 'Medtr2g021400' => 'mtr', 'Medtr2g021470' => 'mtr', 'Medtr2g105810' => 'mtr', 'Medtr3g033580' => 'mtr', 'Medtr6g007970' => 'mtr', 'Medtr7g056330' => 'mtr', 'Medtr7g074290' => 'mtr', 'Medtr7g074380' => 'mtr', 'Medtr7g094550' => 'mtr', 'Medtr8g069995' => 'mtr', 'MELO3C014345.2' => 'cme', 'MELO3C021395.2' => 'cme', 'Migut.D00262' => 'egut', 'Migut.G00257' => 'egut', 'MSTRG.21575' => 'ama', 'MSTRG.3985' => 'ama', 'Nitab4.5_0000295g0140' => 'nta', 'Nitab4.5_0000732g0140' => 'nta', 'Nitab4.5_0003162g0020' => 'nta', 'Nitab4.5_0006180g0090' => 'nta', 'Nitab4.5_0006390g0010' => 'nta', 'Nitab4.5_0007392g0040' => 'nta', 'Nn1g02140' => 'nnu', 'Nn4g26168' => 'nnu', 'Nn5g26754' => 'nnu', 'Oeu001433.1' => 'oeu', 'Oeu010299.2' => 'oeu', 'Oeu011171.1' => 'oeu', 'Oeu037675.1' => 'oeu', 'Oeu038359.1' => 'oeu', 'Oeu063834.1' => 'oeu', 'Oeu063835.1' => 'oeu', 'Os05g0312000' => 'osa', 'Os07g0211101' => 'osa', 'Os07g0211200' => 'osa', 'Os07g0681500' => 'osa', 'Peaxi162Scf00095g01015' => 'pax', 'Peaxi162Scf00104g00329' => 'pax', 'Peaxi162Scf00161g00137' => 'pax', 'PGR004G1665' => 'pgr', 'PGR031G2937' => 'pgr', 'PGR119G2145' => 'pgr', 'PGSC0003DMG400004351' => 'stu', 'PGSC0003DMG400014625' => 'stu', 'PGSC0003DMG401000943' => 'stu', 'Phvul.001G148600' => 'pvu', 'Phvul.004G001700' => 'pvu', 'Phvul.006G154900' => 'pvu', 'Phvul.008G078200' => 'pvu', 'Phvul.011G136500' => 'pvu', 'Potri.002G215600' => 'ptr', 'Potri.008G201600' => 'ptr', 'Potri.014G138400' => 'ptr', 'Potri.016G142500' => 'ptr', 'Pp3c16_10580' => 'ppa', 'Pp3c5_25280' => 'ppa', 'Prupe.1G150000' => 'ppe', 'Prupe.1G150100' => 'ppe', 'Prupe.6G299600' => 'ppe', 'Prupe.8G245000' => 'ppe', 'Psat0s4927g0040' => 'psa', 'Psat1g052080' => 'psa', 'Psat1g183800' => 'psa', 'Psat3g113840' => 'psa', 'Psat3g126120' => 'psa', 'Psat3g126160' => 'psa', 'Psat3g158760' => 'psa', 'Psat3g158840' => 'psa', 'PSO170G2858' => 'pso', 'PSO339G0606' => 'pso', 'PSO384G4709' => 'pso', 'PSO407G0334' => 'pso', 'QL04p040276' => 'qlo', 'QL06p005458' => 'qlo', 'QL06p005472' => 'qlo', 'QL07p030546' => 'qlo', 'QL07p031519' => 'qlo', 'QL09p050949' => 'qlo', 'QL09p050966' => 'qlo', 'QL09p051067' => 'qlo', 'QL12p022706' => 'qlo', 'RcHm_v2.0_Chr2g0119601' => 'rch', 'RcHm_v2.0_Chr3g0459591' => 'rch', 'RcHm_v2.0_Chr4g0418521' => 'rch', 'RcHm_v2.0_Chr4g0418531' => 'rch', 'RcHm_v2.0_Chr4g0418541' => 'rch', 'RcHm_v2.0_Chr6g0291641' => 'rch', 'Rhsim01G0086300' => 'rsi', 'Rhsim01G0276300' => 'rsi', 'Rhsim01G0276500' => 'rsi', 'Rhsim04G0207700' => 'rsi', 'Rhsim05G0234500' => 'rsi', 'Rhsim13G0022400' => 'rsi', 'Sabra02G0167900' => 'sbr', 'Sabra04G0158500' => 'sbr', 'Sabra08G0159800' => 'sbr', 'Sabra10G0011500' => 'sbr', 'Sabra14G0104400' => 'sbr', 'SalBow2G2440' => 'sbo', 'SalBow4G2265' => 'sbo', 'Sc02g0000060' => 'sci', 'Sc05g0005020' => 'sci', 'Sc13g0003890' => 'sci', 'Sed0014865' => 'sed', 'Sed0017224' => 'sed', 'Sed0026391' => 'sed', 'SEGI_00063' => 'sgi', 'SEGI_10967' => 'sgi', 'SEGI_17510' => 'sgi', 'SEGI_24396' => 'sgi', 'SEGI_39719' => 'sgi', 'SEGI_41392' => 'sgi', 'SGA_v2.0_scaffold11G05794' => 'sas', 'SGA_v2.0_scaffold142G35607' => 'sas', 'SGA_v2.0_scaffold1G00447' => 'sas', 'SHI15388' => 'shi', 'SHI15394' => 'shi', 'SHI15396' => 'shi', 'SHI15399' => 'shi', 'SMO343G0151' => 'smo', 'SMO367G1118' => 'smo', 'Solyc01g080200.3' => 'sly', 'Solyc06g008960.3' => 'sly', 'Solyc09g064780.3' => 'sly', 'Sopen01g031980' => 'spe', 'Sopen06g003710' => 'spe', 'Sopen09g026460' => 'spe', 'Sp3g21240' => 'spa', 'Sp4g30030' => 'spa', 'TAR365G0022' => 'tar', 'TAR365G1023' => 'tar', 'TAR365G1253' => 'tar', 'TAR623G0078' => 'tar', 'TAR623G1721' => 'tar', 'TAR633G0959' => 'tar', 'THA.LOC104802225' => 'tha', 'THA.LOC104804769' => 'tha', 'THA.LOC104808660' => 'tha', 'THA.LOC104812792' => 'tha', 'Thecc.01G284000' => 'tca', 'Thecc.04G220600' => 'tca', 'Thecc.05G268900' => 'tca', 'Thecc.08G171100' => 'tca', 'Thhalv10001284m.g' => 'esa', 'Thhalv10019912m.g' => 'esa', 'TPR.G14189' => 'tpr', 'TPR.G18110' => 'tpr', 'TPR.G18130' => 'tpr', 'TPR.G18131' => 'tpr', 'TPR.G18140' => 'tpr', 'TPR.G24282' => 'tpr', 'TPR.G25221' => 'tpr', 'TPR.G29267' => 'tpr', 'TPR.G35315' => 'tpr', 'TPR.G36173' => 'tpr', 'TWI09G0794' => 'twi', 'TWI59G1348' => 'twi', 'TWI74G0430' => 'twi', 'unitig_26.g8940' => 'ugi', 'unitig_749.g13744' => 'ugi', 'unitig_749.g13745' => 'ugi', 'vmacro08269' => 'vma', 'vmacro14937' => 'vma', 'vmacro20401' => 'vma', 'VMungo0464G1349' => 'vmu', 'VMungo0540G0289' => 'vmu', 'VMungo1215G1590' => 'vmu', 'VMungo1309G0221' => 'vmu', 'VMungo1309G2815' => 'vmu', 'VMungo1383G0239' => 'vmu', 'VMungo1383G2910' => 'vmu', 'Zm00001eb095270' => 'zma', 'Zm00001eb095280' => 'zma', 'Zm00001eb111630' => 'zma', 'Zm00001eb237080' => 'zma', 'Zm00001eb273740' => 'zma', 'Zm00001eb285040' => 'zma', 'Zm00001eb330790' => 'zma', 'Zm00001eb337380' => 'zma' ), 'gf_id' => 'HOM05D001484', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001484' ), 'data_identifier' => 'HOM05D001484', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001484', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p31500' => 'bna', 'A05p00020' => 'bna', 'A07p08820' => 'bna', 'Aa31LG4G3300' => 'aar', 'Aa31LG8G10030' => 'aar', 'Actinidia00731' => 'ach', 'Actinidia11473' => 'ach', 'Actinidia23469' => 'ach', 'Actinidia24318' => 'ach', 'Actinidia40196' => 'ach', 'Actinidia40197' => 'ach', 'Actinidia40198' => 'ach', 'Ah.08g212990' => 'amhyb', 'Ah.15g091720' => 'amhyb', 'AL3G38260' => 'aly', 'AL4G47710' => 'aly', 'Aqoxy2G00671' => 'aox', 'Aqoxy2G03236' => 'aox', 'arahy.Tifrunner.gnm1.ann1.05IDCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KR684' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATY3SJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK6QJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6APGL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IDT7Z9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM073U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ0R87' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LE7RV4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT4QRX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V5ENPK' => 'arhy', 'AT2G48110' => 'ath', 'AT3G23590' => 'ath', 'ATR0626G186' => 'atr', 'ATR1127G141' => 'atr', 'Atru.chr4.2583' => 'acertr', 'Atru.chr5.1358' => 'acertr', 'Atru.chr5.1359' => 'acertr', 'Atru.chr8.46' => 'acertr', 'AUR62002640' => 'cqu', 'AUR62030055' => 'cqu', 'AUR62033713' => 'cqu', 'AUR62033714' => 'cqu', 'AUR62036795' => 'cqu', 'AUR62039891' => 'cqu', 'BcaB02g08737' => 'bca', 'BcaB04g20441' => 'bca', 'BcaB06g26509' => 'bca', 'BcaB06g26510' => 'bca', 'BcaB06g26511' => 'bca', 'BcaB06g26512' => 'bca', 'BcaB06g26513' => 'bca', 'BcaC02g12564' => 'bca', 'BcaC02g12565' => 'bca', 'BcaC02g12794' => 'bca', 'BcaC02g12795' => 'bca', 'BcaC02g12796' => 'bca', 'BcaC06g35541' => 'bca', 'BNapus_Darmor_BZH_scaffold_188p00080' => 'bna', 'BNapus_Darmor_BZH_scaffold_188p00090' => 'bna', 'BolC1t03972H' => 'bol', 'BolC1t03973H' => 'bol', 'BolC4t21680H' => 'bol', 'BolC7t41863H' => 'bol', 'BolSC55t61227H' => 'bol', 'BolSC55t61228H' => 'bol', 'BraA01t03278Z' => 'bra', 'BraA05t18998Z' => 'bra', 'BraA07t28673Z' => 'bra', 'C01p40150' => 'bna', 'C05p12370' => 'bna', 'C07p13680' => 'bna', 'CAN.G1006.16' => 'can', 'CAN.G1006.17' => 'can', 'CAN.G1170.2' => 'can', 'CAN.G962.7' => 'can', 'CANSAT25G2179' => 'cansat', 'CANSAT78G1573' => 'cansat', 'CARHR099510' => 'chi', 'CARHR143510' => 'chi', 'Carub.0003s2380' => 'cru', 'Carub.0004s3082' => 'cru', 'Ca_00614_v3' => 'car', 'Ca_07801_v3' => 'car', 'Ca_08567_v3' => 'car', 'Ca_09571_v3' => 'car', 'CBR_g19290' => 'cbr', 'Cc01_g19770' => 'ccan', 'Cc03_g03030' => 'ccan', 'CDE07G0968' => 'cde', 'CDE09G1441' => 'cde', 'Cfa006103' => 'cfa', 'Cfa015573' => 'cfa', 'Cfa016988' => 'cfa', 'Ciclev10006738m.g' => 'ccl', 'Ciclev10010920m.g' => 'ccl', 'Ciclev10018517m.g' => 'ccl', 'CiPaw.01G159200' => 'cil', 'CiPaw.02G091000' => 'cil', 'CiPaw.02G091100' => 'cil', 'CiPaw.08G103100' => 'cil', 'CiPaw.09G224900' => 'cil', 'ClCG06G005740' => 'cla', 'ClCG07G000090' => 'cla', 'ClCG07G000100' => 'cla', 'COL.COLO4_09143' => 'col', 'COL.COLO4_25124' => 'col', 'Cpa.g.sc16.34' => 'cpa', 'Cpa.g.sc3504.1' => 'cpa', 'Cpa.g.sc60.37' => 'cpa', 'CsaV3_6G018520' => 'csa', 'CsaV3_6G036860' => 'csa', 'CSS0001072' => 'camsi', 'CSS0020208' => 'camsi', 'CSS0021253' => 'camsi', 'CSS0022190' => 'camsi', 'CSS0036150' => 'camsi', 'CSS0040442' => 'camsi', 'CSS0042300' => 'camsi', 'CSS0045298' => 'camsi', 'DCAR_012449' => 'dca', 'DCAR_018405' => 'dca', 'DCAR_024573' => 'dca', 'DCAR_030591' => 'dca', 'Dinv16926' => 'din', 'Dinv32963' => 'din', 'Dinv38382' => 'din', 'Dinv38383' => 'din', 'Duzib133G0974' => 'dzi', 'Duzib138G1867' => 'dzi', 'Duzib211G0420' => 'dzi', 'Duzib212G0930' => 'dzi', 'ECA234G1645' => 'eca', 'ECA247G3467' => 'eca', 'ECA248G1703' => 'eca', 'EL10Ac3g06327' => 'bvu', 'EL10Ac7g17204' => 'bvu', 'Eucgr.A00855' => 'egr', 'Eucgr.A00858' => 'egr', 'Eucgr.H01520' => 'egr', 'Eucgr.H03604' => 'egr', 'Eucgr.L03465' => 'egr', 'Eucgr.L03466' => 'egr', 'FAN01G0988' => 'fan', 'FAN02G3892' => 'fan', 'FAN05G3381' => 'fan', 'FAN07G0967' => 'fan', 'FAN07G1493' => 'fan', 'FAN08G3125' => 'fan', 'FAN09G0402' => 'fan', 'FAN12G2594' => 'fan', 'FAN12G3879' => 'fan', 'FAN14G1546' => 'fan', 'FAN15G3626' => 'fan', 'FAN17G0588' => 'fan', 'FAN17G0609' => 'fan', 'FAN18G2817' => 'fan', 'FAN19G1305' => 'fan', 'FAN20G1787' => 'fan', 'FAN22G0073' => 'fan', 'FAN22G0352' => 'fan', 'FAN22G0368' => 'fan', 'FAN22G2273' => 'fan', 'FAN24G1998' => 'fan', 'FAN27G1317' => 'fan', 'FvH4_2g23980' => 'fve', 'FvH4_4g14380' => 'fve', 'FvH4_4g14390' => 'fve', 'FvH4_6g09250' => 'fve', 'Glyma.03G151100' => 'gma', 'Glyma.04G122550' => 'gma', 'Glyma.05G001600' => 'gma', 'Glyma.09G270766' => 'gma', 'Glyma.09G270832' => 'gma', 'Glyma.13G209800' => 'gma', 'Glyma.15G102800' => 'gma', 'Glyma.18G218900' => 'gma', 'Glyma.19G001500' => 'gma', 'Glyma.19G153600' => 'gma', 'Gohir.A02G028600' => 'ghi', 'Gohir.A08G045000' => 'ghi', 'Gohir.A11G120500' => 'ghi', 'Gohir.A12G006200' => 'ghi', 'Gohir.A12G006250' => 'ghi', 'Gohir.D02G036300' => 'ghi', 'Gohir.D08G054700' => 'ghi', 'Gohir.D11G125600' => 'ghi', 'Gohir.D12G005700' => 'ghi', 'Gorai.004G055200' => 'gra', 'Gorai.005G040400' => 'gra', 'Gorai.007G134500' => 'gra', 'Gorai.008G005500' => 'gra', 'GSVIVG01011094001' => 'vvi', 'GSVIVG01017879001' => 'vvi', 'GSVIVG01025988001' => 'vvi', 'GSVIVG01029847001' => 'vvi', 'HanXRQChr10g0282901' => 'han', 'HanXRQChr10g0310371' => 'han', 'HanXRQChr10g0315041' => 'han', 'HanXRQChr11g0327651' => 'han', 'HanXRQChr12g0359391' => 'han', 'Haze_00972' => 'cav', 'Haze_00973' => 'cav', 'Haze_00974' => 'cav', 'Haze_04747' => 'cav', 'Haze_04749' => 'cav', 'Haze_04750' => 'cav', 'Haze_21217' => 'cav', 'Hma1.2p1_1037F.1_g250680' => 'hma', 'Hma1.2p1_1644F.1_g295320' => 'hma', 'HPP92_011322' => 'vpl', 'HPP92_011323' => 'vpl', 'HPP92_011324' => 'vpl', 'HPP92_011325' => 'vpl', 'HPP92_011326' => 'vpl', 'Hund12205' => 'sun', 'Hund17957' => 'sun', 'Lalb_Chr06g0176771' => 'lal', 'Lalb_Chr18g0056021' => 'lal', 'Lalb_Chr18g0056031' => 'lal', 'Lalb_Chr18g0056041' => 'lal', 'Lalb_Chr20g0107751' => 'lal', 'Lalb_Chr20g0118371' => 'lal', 'Lj1g0010239' => 'lja', 'Lj1g0017101' => 'lja', 'Lj2A1178G40' => 'lonja', 'Lj2A54G84' => 'lonja', 'Lj2g0015248' => 'lja', 'Lj3A761T51' => 'lonja', 'Lj6g0018116' => 'lja', 'Lsat_1_v5_gn_4_136040' => 'lsa', 'Lsat_1_v5_gn_5_187461' => 'lsa', 'Lsat_1_v5_gn_5_77001' => 'lsa', 'Lsat_1_v5_gn_9_4461' => 'lsa', 'Manes.01G210100' => 'mes', 'Manes.03G185600' => 'mes', 'Manes.05G073300' => 'mes', 'Manes.09G120300' => 'mes', 'Manes.15G022100' => 'mes', 'Mapoly0096s0053' => 'mpo', 'MBI03_g14058_MAGBIO' => 'mbi', 'MBI03_g33876_MAGBIO' => 'mbi', 'MBI03_g36854_MAGBIO' => 'mbi', 'MBI17_g11997_MAGBIO' => 'mbi', 'MD03G1269000' => 'mdo', 'MD04G1179600' => 'mdo', 'MD11G1289800' => 'mdo', 'MD12G1194700' => 'mdo', 'MD13G1182100' => 'mdo', 'MD13G1182200' => 'mdo', 'MD16G1182600' => 'mdo', 'Medtr2g021400' => 'mtr', 'Medtr2g021470' => 'mtr', 'Medtr2g105810' => 'mtr', 'Medtr3g033580' => 'mtr', 'Medtr6g007970' => 'mtr', 'Medtr7g056330' => 'mtr', 'Medtr7g074290' => 'mtr', 'Medtr7g074380' => 'mtr', 'Medtr7g094550' => 'mtr', 'Medtr8g069995' => 'mtr', 'MELO3C014345.2' => 'cme', 'MELO3C021395.2' => 'cme', 'Migut.D00262' => 'egut', 'Migut.G00257' => 'egut', 'MSTRG.21575' => 'ama', 'MSTRG.3985' => 'ama', 'Nitab4.5_0000295g0140' => 'nta', 'Nitab4.5_0000732g0140' => 'nta', 'Nitab4.5_0003162g0020' => 'nta', 'Nitab4.5_0006180g0090' => 'nta', 'Nitab4.5_0006390g0010' => 'nta', 'Nitab4.5_0007392g0040' => 'nta', 'Nn1g02140' => 'nnu', 'Nn4g26168' => 'nnu', 'Nn5g26754' => 'nnu', 'Oeu001433.1' => 'oeu', 'Oeu010299.2' => 'oeu', 'Oeu011171.1' => 'oeu', 'Oeu037675.1' => 'oeu', 'Oeu038359.1' => 'oeu', 'Oeu063834.1' => 'oeu', 'Oeu063835.1' => 'oeu', 'Os05g0312000' => 'osa', 'Os07g0211101' => 'osa', 'Os07g0211200' => 'osa', 'Os07g0681500' => 'osa', 'Peaxi162Scf00095g01015' => 'pax', 'Peaxi162Scf00104g00329' => 'pax', 'Peaxi162Scf00161g00137' => 'pax', 'PGR004G1665' => 'pgr', 'PGR031G2937' => 'pgr', 'PGR119G2145' => 'pgr', 'PGSC0003DMG400004351' => 'stu', 'PGSC0003DMG400014625' => 'stu', 'PGSC0003DMG401000943' => 'stu', 'Phvul.001G148600' => 'pvu', 'Phvul.004G001700' => 'pvu', 'Phvul.006G154900' => 'pvu', 'Phvul.008G078200' => 'pvu', 'Phvul.011G136500' => 'pvu', 'Potri.002G215600' => 'ptr', 'Potri.008G201600' => 'ptr', 'Potri.014G138400' => 'ptr', 'Potri.016G142500' => 'ptr', 'Pp3c16_10580' => 'ppa', 'Pp3c5_25280' => 'ppa', 'Prupe.1G150000' => 'ppe', 'Prupe.1G150100' => 'ppe', 'Prupe.6G299600' => 'ppe', 'Prupe.8G245000' => 'ppe', 'Psat0s4927g0040' => 'psa', 'Psat1g052080' => 'psa', 'Psat1g183800' => 'psa', 'Psat3g113840' => 'psa', 'Psat3g126120' => 'psa', 'Psat3g126160' => 'psa', 'Psat3g158760' => 'psa', 'Psat3g158840' => 'psa', 'PSO170G2858' => 'pso', 'PSO339G0606' => 'pso', 'PSO384G4709' => 'pso', 'PSO407G0334' => 'pso', 'QL04p040276' => 'qlo', 'QL06p005458' => 'qlo', 'QL06p005472' => 'qlo', 'QL07p030546' => 'qlo', 'QL07p031519' => 'qlo', 'QL09p050949' => 'qlo', 'QL09p050966' => 'qlo', 'QL09p051067' => 'qlo', 'QL12p022706' => 'qlo', 'RcHm_v2.0_Chr2g0119601' => 'rch', 'RcHm_v2.0_Chr3g0459591' => 'rch', 'RcHm_v2.0_Chr4g0418521' => 'rch', 'RcHm_v2.0_Chr4g0418531' => 'rch', 'RcHm_v2.0_Chr4g0418541' => 'rch', 'RcHm_v2.0_Chr6g0291641' => 'rch', 'Rhsim01G0086300' => 'rsi', 'Rhsim01G0276300' => 'rsi', 'Rhsim01G0276500' => 'rsi', 'Rhsim04G0207700' => 'rsi', 'Rhsim05G0234500' => 'rsi', 'Rhsim13G0022400' => 'rsi', 'Sabra02G0167900' => 'sbr', 'Sabra04G0158500' => 'sbr', 'Sabra08G0159800' => 'sbr', 'Sabra10G0011500' => 'sbr', 'Sabra14G0104400' => 'sbr', 'SalBow2G2440' => 'sbo', 'SalBow4G2265' => 'sbo', 'Sc02g0000060' => 'sci', 'Sc05g0005020' => 'sci', 'Sc13g0003890' => 'sci', 'Sed0014865' => 'sed', 'Sed0017224' => 'sed', 'Sed0026391' => 'sed', 'SEGI_00063' => 'sgi', 'SEGI_10967' => 'sgi', 'SEGI_17510' => 'sgi', 'SEGI_24396' => 'sgi', 'SEGI_39719' => 'sgi', 'SEGI_41392' => 'sgi', 'SGA_v2.0_scaffold11G05794' => 'sas', 'SGA_v2.0_scaffold142G35607' => 'sas', 'SGA_v2.0_scaffold1G00447' => 'sas', 'SHI15388' => 'shi', 'SHI15394' => 'shi', 'SHI15396' => 'shi', 'SHI15399' => 'shi', 'SMO343G0151' => 'smo', 'SMO367G1118' => 'smo', 'Solyc01g080200.3' => 'sly', 'Solyc06g008960.3' => 'sly', 'Solyc09g064780.3' => 'sly', 'Sopen01g031980' => 'spe', 'Sopen06g003710' => 'spe', 'Sopen09g026460' => 'spe', 'Sp3g21240' => 'spa', 'Sp4g30030' => 'spa', 'TAR365G0022' => 'tar', 'TAR365G1023' => 'tar', 'TAR365G1253' => 'tar', 'TAR623G0078' => 'tar', 'TAR623G1721' => 'tar', 'TAR633G0959' => 'tar', 'THA.LOC104802225' => 'tha', 'THA.LOC104804769' => 'tha', 'THA.LOC104808660' => 'tha', 'THA.LOC104812792' => 'tha', 'Thecc.01G284000' => 'tca', 'Thecc.04G220600' => 'tca', 'Thecc.05G268900' => 'tca', 'Thecc.08G171100' => 'tca', 'Thhalv10001284m.g' => 'esa', 'Thhalv10019912m.g' => 'esa', 'TPR.G14189' => 'tpr', 'TPR.G18110' => 'tpr', 'TPR.G18130' => 'tpr', 'TPR.G18131' => 'tpr', 'TPR.G18140' => 'tpr', 'TPR.G24282' => 'tpr', 'TPR.G25221' => 'tpr', 'TPR.G29267' => 'tpr', 'TPR.G35315' => 'tpr', 'TPR.G36173' => 'tpr', 'TWI09G0794' => 'twi', 'TWI59G1348' => 'twi', 'TWI74G0430' => 'twi', 'unitig_26.g8940' => 'ugi', 'unitig_749.g13744' => 'ugi', 'unitig_749.g13745' => 'ugi', 'vmacro08269' => 'vma', 'vmacro14937' => 'vma', 'vmacro20401' => 'vma', 'VMungo0464G1349' => 'vmu', 'VMungo0540G0289' => 'vmu', 'VMungo1215G1590' => 'vmu', 'VMungo1309G0221' => 'vmu', 'VMungo1309G2815' => 'vmu', 'VMungo1383G0239' => 'vmu', 'VMungo1383G2910' => 'vmu', 'Zm00001eb095270' => 'zma', 'Zm00001eb095280' => 'zma', 'Zm00001eb111630' => 'zma', 'Zm00001eb237080' => 'zma', 'Zm00001eb273740' => 'zma', 'Zm00001eb285040' => 'zma', 'Zm00001eb330790' => 'zma', 'Zm00001eb337380' => 'zma' ) $gf_id = 'HOM05D001484' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001484' ) $data_identifier = 'HOM05D001484' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 2, 'aly' => (int) 2, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 22, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 7, 'hma' => (int) 2, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 7, 'mtr' => (int) 10, 'cme' => (int) 2, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 4, 'ppa' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 4, 'qlo' => (int) 9, 'rch' => (int) 6, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 10, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 7, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb337380' $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' => 'HOM05D001484', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p31500' => 'bna', 'A05p00020' => 'bna', 'A07p08820' => 'bna', 'Aa31LG4G3300' => 'aar', 'Aa31LG8G10030' => 'aar', 'Actinidia00731' => 'ach', 'Actinidia11473' => 'ach', 'Actinidia23469' => 'ach', 'Actinidia24318' => 'ach', 'Actinidia40196' => 'ach', 'Actinidia40197' => 'ach', 'Actinidia40198' => 'ach', 'Ah.08g212990' => 'amhyb', 'Ah.15g091720' => 'amhyb', 'AL3G38260' => 'aly', 'AL4G47710' => 'aly', 'Aqoxy2G00671' => 'aox', 'Aqoxy2G03236' => 'aox', 'arahy.Tifrunner.gnm1.ann1.05IDCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KR684' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATY3SJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK6QJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6APGL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IDT7Z9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM073U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ0R87' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LE7RV4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT4QRX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V5ENPK' => 'arhy', 'AT2G48110' => 'ath', 'AT3G23590' => 'ath', 'ATR0626G186' => 'atr', 'ATR1127G141' => 'atr', 'Atru.chr4.2583' => 'acertr', 'Atru.chr5.1358' => 'acertr', 'Atru.chr5.1359' => 'acertr', 'Atru.chr8.46' => 'acertr', 'AUR62002640' => 'cqu', 'AUR62030055' => 'cqu', 'AUR62033713' => 'cqu', 'AUR62033714' => 'cqu', 'AUR62036795' => 'cqu', 'AUR62039891' => 'cqu', 'BcaB02g08737' => 'bca', 'BcaB04g20441' => 'bca', 'BcaB06g26509' => 'bca', 'BcaB06g26510' => 'bca', 'BcaB06g26511' => 'bca', 'BcaB06g26512' => 'bca', 'BcaB06g26513' => 'bca', 'BcaC02g12564' => 'bca', 'BcaC02g12565' => 'bca', 'BcaC02g12794' => 'bca', 'BcaC02g12795' => 'bca', 'BcaC02g12796' => 'bca', 'BcaC06g35541' => 'bca', 'BNapus_Darmor_BZH_scaffold_188p00080' => 'bna', 'BNapus_Darmor_BZH_scaffold_188p00090' => 'bna', 'BolC1t03972H' => 'bol', 'BolC1t03973H' => 'bol', 'BolC4t21680H' => 'bol', 'BolC7t41863H' => 'bol', 'BolSC55t61227H' => 'bol', 'BolSC55t61228H' => 'bol', 'BraA01t03278Z' => 'bra', 'BraA05t18998Z' => 'bra', 'BraA07t28673Z' => 'bra', 'C01p40150' => 'bna', 'C05p12370' => 'bna', 'C07p13680' => 'bna', 'CAN.G1006.16' => 'can', 'CAN.G1006.17' => 'can', 'CAN.G1170.2' => 'can', 'CAN.G962.7' => 'can', 'CANSAT25G2179' => 'cansat', 'CANSAT78G1573' => 'cansat', 'CARHR099510' => 'chi', 'CARHR143510' => 'chi', 'Carub.0003s2380' => 'cru', 'Carub.0004s3082' => 'cru', 'Ca_00614_v3' => 'car', 'Ca_07801_v3' => 'car', 'Ca_08567_v3' => 'car', 'Ca_09571_v3' => 'car', 'CBR_g19290' => 'cbr', 'Cc01_g19770' => 'ccan', 'Cc03_g03030' => 'ccan', 'CDE07G0968' => 'cde', 'CDE09G1441' => 'cde', 'Cfa006103' => 'cfa', 'Cfa015573' => 'cfa', 'Cfa016988' => 'cfa', 'Ciclev10006738m.g' => 'ccl', 'Ciclev10010920m.g' => 'ccl', 'Ciclev10018517m.g' => 'ccl', 'CiPaw.01G159200' => 'cil', 'CiPaw.02G091000' => 'cil', 'CiPaw.02G091100' => 'cil', 'CiPaw.08G103100' => 'cil', 'CiPaw.09G224900' => 'cil', 'ClCG06G005740' => 'cla', 'ClCG07G000090' => 'cla', 'ClCG07G000100' => 'cla', 'COL.COLO4_09143' => 'col', 'COL.COLO4_25124' => 'col', 'Cpa.g.sc16.34' => 'cpa', 'Cpa.g.sc3504.1' => 'cpa', 'Cpa.g.sc60.37' => 'cpa', 'CsaV3_6G018520' => 'csa', 'CsaV3_6G036860' => 'csa', 'CSS0001072' => 'camsi', 'CSS0020208' => 'camsi', 'CSS0021253' => 'camsi', 'CSS0022190' => 'camsi', 'CSS0036150' => 'camsi', 'CSS0040442' => 'camsi', 'CSS0042300' => 'camsi', 'CSS0045298' => 'camsi', 'DCAR_012449' => 'dca', 'DCAR_018405' => 'dca', 'DCAR_024573' => 'dca', 'DCAR_030591' => 'dca', 'Dinv16926' => 'din', 'Dinv32963' => 'din', 'Dinv38382' => 'din', 'Dinv38383' => 'din', 'Duzib133G0974' => 'dzi', 'Duzib138G1867' => 'dzi', 'Duzib211G0420' => 'dzi', 'Duzib212G0930' => 'dzi', 'ECA234G1645' => 'eca', 'ECA247G3467' => 'eca', 'ECA248G1703' => 'eca', 'EL10Ac3g06327' => 'bvu', 'EL10Ac7g17204' => 'bvu', 'Eucgr.A00855' => 'egr', 'Eucgr.A00858' => 'egr', 'Eucgr.H01520' => 'egr', 'Eucgr.H03604' => 'egr', 'Eucgr.L03465' => 'egr', 'Eucgr.L03466' => 'egr', 'FAN01G0988' => 'fan', 'FAN02G3892' => 'fan', 'FAN05G3381' => 'fan', 'FAN07G0967' => 'fan', 'FAN07G1493' => 'fan', 'FAN08G3125' => 'fan', 'FAN09G0402' => 'fan', 'FAN12G2594' => 'fan', 'FAN12G3879' => 'fan', 'FAN14G1546' => 'fan', 'FAN15G3626' => 'fan', 'FAN17G0588' => 'fan', 'FAN17G0609' => 'fan', 'FAN18G2817' => 'fan', 'FAN19G1305' => 'fan', 'FAN20G1787' => 'fan', 'FAN22G0073' => 'fan', 'FAN22G0352' => 'fan', 'FAN22G0368' => 'fan', 'FAN22G2273' => 'fan', 'FAN24G1998' => 'fan', 'FAN27G1317' => 'fan', 'FvH4_2g23980' => 'fve', 'FvH4_4g14380' => 'fve', 'FvH4_4g14390' => 'fve', 'FvH4_6g09250' => 'fve', 'Glyma.03G151100' => 'gma', 'Glyma.04G122550' => 'gma', 'Glyma.05G001600' => 'gma', 'Glyma.09G270766' => 'gma', 'Glyma.09G270832' => 'gma', 'Glyma.13G209800' => 'gma', 'Glyma.15G102800' => 'gma', 'Glyma.18G218900' => 'gma', 'Glyma.19G001500' => 'gma', 'Glyma.19G153600' => 'gma', 'Gohir.A02G028600' => 'ghi', 'Gohir.A08G045000' => 'ghi', 'Gohir.A11G120500' => 'ghi', 'Gohir.A12G006200' => 'ghi', 'Gohir.A12G006250' => 'ghi', 'Gohir.D02G036300' => 'ghi', 'Gohir.D08G054700' => 'ghi', 'Gohir.D11G125600' => 'ghi', 'Gohir.D12G005700' => 'ghi', 'Gorai.004G055200' => 'gra', 'Gorai.005G040400' => 'gra', 'Gorai.007G134500' => 'gra', 'Gorai.008G005500' => 'gra', 'GSVIVG01011094001' => 'vvi', 'GSVIVG01017879001' => 'vvi', 'GSVIVG01025988001' => 'vvi', 'GSVIVG01029847001' => 'vvi', 'HanXRQChr10g0282901' => 'han', 'HanXRQChr10g0310371' => 'han', 'HanXRQChr10g0315041' => 'han', 'HanXRQChr11g0327651' => 'han', 'HanXRQChr12g0359391' => 'han', 'Haze_00972' => 'cav', 'Haze_00973' => 'cav', 'Haze_00974' => 'cav', 'Haze_04747' => 'cav', 'Haze_04749' => 'cav', 'Haze_04750' => 'cav', 'Haze_21217' => 'cav', 'Hma1.2p1_1037F.1_g250680' => 'hma', 'Hma1.2p1_1644F.1_g295320' => 'hma', 'HPP92_011322' => 'vpl', 'HPP92_011323' => 'vpl', 'HPP92_011324' => 'vpl', 'HPP92_011325' => 'vpl', 'HPP92_011326' => 'vpl', 'Hund12205' => 'sun', 'Hund17957' => 'sun', 'Lalb_Chr06g0176771' => 'lal', 'Lalb_Chr18g0056021' => 'lal', 'Lalb_Chr18g0056031' => 'lal', 'Lalb_Chr18g0056041' => 'lal', 'Lalb_Chr20g0107751' => 'lal', 'Lalb_Chr20g0118371' => 'lal', 'Lj1g0010239' => 'lja', 'Lj1g0017101' => 'lja', 'Lj2A1178G40' => 'lonja', 'Lj2A54G84' => 'lonja', 'Lj2g0015248' => 'lja', 'Lj3A761T51' => 'lonja', 'Lj6g0018116' => 'lja', 'Lsat_1_v5_gn_4_136040' => 'lsa', 'Lsat_1_v5_gn_5_187461' => 'lsa', 'Lsat_1_v5_gn_5_77001' => 'lsa', 'Lsat_1_v5_gn_9_4461' => 'lsa', 'Manes.01G210100' => 'mes', 'Manes.03G185600' => 'mes', 'Manes.05G073300' => 'mes', 'Manes.09G120300' => 'mes', 'Manes.15G022100' => 'mes', 'Mapoly0096s0053' => 'mpo', 'MBI03_g14058_MAGBIO' => 'mbi', 'MBI03_g33876_MAGBIO' => 'mbi', 'MBI03_g36854_MAGBIO' => 'mbi', 'MBI17_g11997_MAGBIO' => 'mbi', 'MD03G1269000' => 'mdo', 'MD04G1179600' => 'mdo', 'MD11G1289800' => 'mdo', 'MD12G1194700' => 'mdo', 'MD13G1182100' => 'mdo', 'MD13G1182200' => 'mdo', 'MD16G1182600' => 'mdo', 'Medtr2g021400' => 'mtr', 'Medtr2g021470' => 'mtr', 'Medtr2g105810' => 'mtr', 'Medtr3g033580' => 'mtr', 'Medtr6g007970' => 'mtr', 'Medtr7g056330' => 'mtr', 'Medtr7g074290' => 'mtr', 'Medtr7g074380' => 'mtr', 'Medtr7g094550' => 'mtr', 'Medtr8g069995' => 'mtr', 'MELO3C014345.2' => 'cme', 'MELO3C021395.2' => 'cme', 'Migut.D00262' => 'egut', 'Migut.G00257' => 'egut', 'MSTRG.21575' => 'ama', 'MSTRG.3985' => 'ama', 'Nitab4.5_0000295g0140' => 'nta', 'Nitab4.5_0000732g0140' => 'nta', 'Nitab4.5_0003162g0020' => 'nta', 'Nitab4.5_0006180g0090' => 'nta', 'Nitab4.5_0006390g0010' => 'nta', 'Nitab4.5_0007392g0040' => 'nta', 'Nn1g02140' => 'nnu', 'Nn4g26168' => 'nnu', 'Nn5g26754' => 'nnu', 'Oeu001433.1' => 'oeu', 'Oeu010299.2' => 'oeu', 'Oeu011171.1' => 'oeu', 'Oeu037675.1' => 'oeu', 'Oeu038359.1' => 'oeu', 'Oeu063834.1' => 'oeu', 'Oeu063835.1' => 'oeu', 'Os05g0312000' => 'osa', 'Os07g0211101' => 'osa', 'Os07g0211200' => 'osa', 'Os07g0681500' => 'osa', 'Peaxi162Scf00095g01015' => 'pax', 'Peaxi162Scf00104g00329' => 'pax', 'Peaxi162Scf00161g00137' => 'pax', 'PGR004G1665' => 'pgr', 'PGR031G2937' => 'pgr', 'PGR119G2145' => 'pgr', 'PGSC0003DMG400004351' => 'stu', 'PGSC0003DMG400014625' => 'stu', 'PGSC0003DMG401000943' => 'stu', 'Phvul.001G148600' => 'pvu', 'Phvul.004G001700' => 'pvu', 'Phvul.006G154900' => 'pvu', 'Phvul.008G078200' => 'pvu', 'Phvul.011G136500' => 'pvu', 'Potri.002G215600' => 'ptr', 'Potri.008G201600' => 'ptr', 'Potri.014G138400' => 'ptr', 'Potri.016G142500' => 'ptr', 'Pp3c16_10580' => 'ppa', 'Pp3c5_25280' => 'ppa', 'Prupe.1G150000' => 'ppe', 'Prupe.1G150100' => 'ppe', 'Prupe.6G299600' => 'ppe', 'Prupe.8G245000' => 'ppe', 'Psat0s4927g0040' => 'psa', 'Psat1g052080' => 'psa', 'Psat1g183800' => 'psa', 'Psat3g113840' => 'psa', 'Psat3g126120' => 'psa', 'Psat3g126160' => 'psa', 'Psat3g158760' => 'psa', 'Psat3g158840' => 'psa', 'PSO170G2858' => 'pso', 'PSO339G0606' => 'pso', 'PSO384G4709' => 'pso', 'PSO407G0334' => 'pso', 'QL04p040276' => 'qlo', 'QL06p005458' => 'qlo', 'QL06p005472' => 'qlo', 'QL07p030546' => 'qlo', 'QL07p031519' => 'qlo', 'QL09p050949' => 'qlo', 'QL09p050966' => 'qlo', 'QL09p051067' => 'qlo', 'QL12p022706' => 'qlo', 'RcHm_v2.0_Chr2g0119601' => 'rch', 'RcHm_v2.0_Chr3g0459591' => 'rch', 'RcHm_v2.0_Chr4g0418521' => 'rch', 'RcHm_v2.0_Chr4g0418531' => 'rch', 'RcHm_v2.0_Chr4g0418541' => 'rch', 'RcHm_v2.0_Chr6g0291641' => 'rch', 'Rhsim01G0086300' => 'rsi', 'Rhsim01G0276300' => 'rsi', 'Rhsim01G0276500' => 'rsi', 'Rhsim04G0207700' => 'rsi', 'Rhsim05G0234500' => 'rsi', 'Rhsim13G0022400' => 'rsi', 'Sabra02G0167900' => 'sbr', 'Sabra04G0158500' => 'sbr', 'Sabra08G0159800' => 'sbr', 'Sabra10G0011500' => 'sbr', 'Sabra14G0104400' => 'sbr', 'SalBow2G2440' => 'sbo', 'SalBow4G2265' => 'sbo', 'Sc02g0000060' => 'sci', 'Sc05g0005020' => 'sci', 'Sc13g0003890' => 'sci', 'Sed0014865' => 'sed', 'Sed0017224' => 'sed', 'Sed0026391' => 'sed', 'SEGI_00063' => 'sgi', 'SEGI_10967' => 'sgi', 'SEGI_17510' => 'sgi', 'SEGI_24396' => 'sgi', 'SEGI_39719' => 'sgi', 'SEGI_41392' => 'sgi', 'SGA_v2.0_scaffold11G05794' => 'sas', 'SGA_v2.0_scaffold142G35607' => 'sas', 'SGA_v2.0_scaffold1G00447' => 'sas', 'SHI15388' => 'shi', 'SHI15394' => 'shi', 'SHI15396' => 'shi', 'SHI15399' => 'shi', 'SMO343G0151' => 'smo', 'SMO367G1118' => 'smo', 'Solyc01g080200.3' => 'sly', 'Solyc06g008960.3' => 'sly', 'Solyc09g064780.3' => 'sly', 'Sopen01g031980' => 'spe', 'Sopen06g003710' => 'spe', 'Sopen09g026460' => 'spe', 'Sp3g21240' => 'spa', 'Sp4g30030' => 'spa', 'TAR365G0022' => 'tar', 'TAR365G1023' => 'tar', 'TAR365G1253' => 'tar', 'TAR623G0078' => 'tar', 'TAR623G1721' => 'tar', 'TAR633G0959' => 'tar', 'THA.LOC104802225' => 'tha', 'THA.LOC104804769' => 'tha', 'THA.LOC104808660' => 'tha', 'THA.LOC104812792' => 'tha', 'Thecc.01G284000' => 'tca', 'Thecc.04G220600' => 'tca', 'Thecc.05G268900' => 'tca', 'Thecc.08G171100' => 'tca', 'Thhalv10001284m.g' => 'esa', 'Thhalv10019912m.g' => 'esa', 'TPR.G14189' => 'tpr', 'TPR.G18110' => 'tpr', 'TPR.G18130' => 'tpr', 'TPR.G18131' => 'tpr', 'TPR.G18140' => 'tpr', 'TPR.G24282' => 'tpr', 'TPR.G25221' => 'tpr', 'TPR.G29267' => 'tpr', 'TPR.G35315' => 'tpr', 'TPR.G36173' => 'tpr', 'TWI09G0794' => 'twi', 'TWI59G1348' => 'twi', 'TWI74G0430' => 'twi', 'unitig_26.g8940' => 'ugi', 'unitig_749.g13744' => 'ugi', 'unitig_749.g13745' => 'ugi', 'vmacro08269' => 'vma', 'vmacro14937' => 'vma', 'vmacro20401' => 'vma', 'VMungo0464G1349' => 'vmu', 'VMungo0540G0289' => 'vmu', 'VMungo1215G1590' => 'vmu', 'VMungo1309G0221' => 'vmu', 'VMungo1309G2815' => 'vmu', 'VMungo1383G0239' => 'vmu', 'VMungo1383G2910' => 'vmu', 'Zm00001eb095270' => 'zma', 'Zm00001eb095280' => 'zma', 'Zm00001eb111630' => 'zma', 'Zm00001eb237080' => 'zma', 'Zm00001eb273740' => 'zma', 'Zm00001eb285040' => 'zma', 'Zm00001eb330790' => 'zma', 'Zm00001eb337380' => 'zma' ), 'gf_id' => 'HOM05D001484', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001484' ), 'data_identifier' => 'HOM05D001484', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001484', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p31500' => 'bna', 'A05p00020' => 'bna', 'A07p08820' => 'bna', 'Aa31LG4G3300' => 'aar', 'Aa31LG8G10030' => 'aar', 'Actinidia00731' => 'ach', 'Actinidia11473' => 'ach', 'Actinidia23469' => 'ach', 'Actinidia24318' => 'ach', 'Actinidia40196' => 'ach', 'Actinidia40197' => 'ach', 'Actinidia40198' => 'ach', 'Ah.08g212990' => 'amhyb', 'Ah.15g091720' => 'amhyb', 'AL3G38260' => 'aly', 'AL4G47710' => 'aly', 'Aqoxy2G00671' => 'aox', 'Aqoxy2G03236' => 'aox', 'arahy.Tifrunner.gnm1.ann1.05IDCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KR684' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATY3SJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK6QJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6APGL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IDT7Z9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM073U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ0R87' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LE7RV4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT4QRX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V5ENPK' => 'arhy', 'AT2G48110' => 'ath', 'AT3G23590' => 'ath', 'ATR0626G186' => 'atr', 'ATR1127G141' => 'atr', 'Atru.chr4.2583' => 'acertr', 'Atru.chr5.1358' => 'acertr', 'Atru.chr5.1359' => 'acertr', 'Atru.chr8.46' => 'acertr', 'AUR62002640' => 'cqu', 'AUR62030055' => 'cqu', 'AUR62033713' => 'cqu', 'AUR62033714' => 'cqu', 'AUR62036795' => 'cqu', 'AUR62039891' => 'cqu', 'BcaB02g08737' => 'bca', 'BcaB04g20441' => 'bca', 'BcaB06g26509' => 'bca', 'BcaB06g26510' => 'bca', 'BcaB06g26511' => 'bca', 'BcaB06g26512' => 'bca', 'BcaB06g26513' => 'bca', 'BcaC02g12564' => 'bca', 'BcaC02g12565' => 'bca', 'BcaC02g12794' => 'bca', 'BcaC02g12795' => 'bca', 'BcaC02g12796' => 'bca', 'BcaC06g35541' => 'bca', 'BNapus_Darmor_BZH_scaffold_188p00080' => 'bna', 'BNapus_Darmor_BZH_scaffold_188p00090' => 'bna', 'BolC1t03972H' => 'bol', 'BolC1t03973H' => 'bol', 'BolC4t21680H' => 'bol', 'BolC7t41863H' => 'bol', 'BolSC55t61227H' => 'bol', 'BolSC55t61228H' => 'bol', 'BraA01t03278Z' => 'bra', 'BraA05t18998Z' => 'bra', 'BraA07t28673Z' => 'bra', 'C01p40150' => 'bna', 'C05p12370' => 'bna', 'C07p13680' => 'bna', 'CAN.G1006.16' => 'can', 'CAN.G1006.17' => 'can', 'CAN.G1170.2' => 'can', 'CAN.G962.7' => 'can', 'CANSAT25G2179' => 'cansat', 'CANSAT78G1573' => 'cansat', 'CARHR099510' => 'chi', 'CARHR143510' => 'chi', 'Carub.0003s2380' => 'cru', 'Carub.0004s3082' => 'cru', 'Ca_00614_v3' => 'car', 'Ca_07801_v3' => 'car', 'Ca_08567_v3' => 'car', 'Ca_09571_v3' => 'car', 'CBR_g19290' => 'cbr', 'Cc01_g19770' => 'ccan', 'Cc03_g03030' => 'ccan', 'CDE07G0968' => 'cde', 'CDE09G1441' => 'cde', 'Cfa006103' => 'cfa', 'Cfa015573' => 'cfa', 'Cfa016988' => 'cfa', 'Ciclev10006738m.g' => 'ccl', 'Ciclev10010920m.g' => 'ccl', 'Ciclev10018517m.g' => 'ccl', 'CiPaw.01G159200' => 'cil', 'CiPaw.02G091000' => 'cil', 'CiPaw.02G091100' => 'cil', 'CiPaw.08G103100' => 'cil', 'CiPaw.09G224900' => 'cil', 'ClCG06G005740' => 'cla', 'ClCG07G000090' => 'cla', 'ClCG07G000100' => 'cla', 'COL.COLO4_09143' => 'col', 'COL.COLO4_25124' => 'col', 'Cpa.g.sc16.34' => 'cpa', 'Cpa.g.sc3504.1' => 'cpa', 'Cpa.g.sc60.37' => 'cpa', 'CsaV3_6G018520' => 'csa', 'CsaV3_6G036860' => 'csa', 'CSS0001072' => 'camsi', 'CSS0020208' => 'camsi', 'CSS0021253' => 'camsi', 'CSS0022190' => 'camsi', 'CSS0036150' => 'camsi', 'CSS0040442' => 'camsi', 'CSS0042300' => 'camsi', 'CSS0045298' => 'camsi', 'DCAR_012449' => 'dca', 'DCAR_018405' => 'dca', 'DCAR_024573' => 'dca', 'DCAR_030591' => 'dca', 'Dinv16926' => 'din', 'Dinv32963' => 'din', 'Dinv38382' => 'din', 'Dinv38383' => 'din', 'Duzib133G0974' => 'dzi', 'Duzib138G1867' => 'dzi', 'Duzib211G0420' => 'dzi', 'Duzib212G0930' => 'dzi', 'ECA234G1645' => 'eca', 'ECA247G3467' => 'eca', 'ECA248G1703' => 'eca', 'EL10Ac3g06327' => 'bvu', 'EL10Ac7g17204' => 'bvu', 'Eucgr.A00855' => 'egr', 'Eucgr.A00858' => 'egr', 'Eucgr.H01520' => 'egr', 'Eucgr.H03604' => 'egr', 'Eucgr.L03465' => 'egr', 'Eucgr.L03466' => 'egr', 'FAN01G0988' => 'fan', 'FAN02G3892' => 'fan', 'FAN05G3381' => 'fan', 'FAN07G0967' => 'fan', 'FAN07G1493' => 'fan', 'FAN08G3125' => 'fan', 'FAN09G0402' => 'fan', 'FAN12G2594' => 'fan', 'FAN12G3879' => 'fan', 'FAN14G1546' => 'fan', 'FAN15G3626' => 'fan', 'FAN17G0588' => 'fan', 'FAN17G0609' => 'fan', 'FAN18G2817' => 'fan', 'FAN19G1305' => 'fan', 'FAN20G1787' => 'fan', 'FAN22G0073' => 'fan', 'FAN22G0352' => 'fan', 'FAN22G0368' => 'fan', 'FAN22G2273' => 'fan', 'FAN24G1998' => 'fan', 'FAN27G1317' => 'fan', 'FvH4_2g23980' => 'fve', 'FvH4_4g14380' => 'fve', 'FvH4_4g14390' => 'fve', 'FvH4_6g09250' => 'fve', 'Glyma.03G151100' => 'gma', 'Glyma.04G122550' => 'gma', 'Glyma.05G001600' => 'gma', 'Glyma.09G270766' => 'gma', 'Glyma.09G270832' => 'gma', 'Glyma.13G209800' => 'gma', 'Glyma.15G102800' => 'gma', 'Glyma.18G218900' => 'gma', 'Glyma.19G001500' => 'gma', 'Glyma.19G153600' => 'gma', 'Gohir.A02G028600' => 'ghi', 'Gohir.A08G045000' => 'ghi', 'Gohir.A11G120500' => 'ghi', 'Gohir.A12G006200' => 'ghi', 'Gohir.A12G006250' => 'ghi', 'Gohir.D02G036300' => 'ghi', 'Gohir.D08G054700' => 'ghi', 'Gohir.D11G125600' => 'ghi', 'Gohir.D12G005700' => 'ghi', 'Gorai.004G055200' => 'gra', 'Gorai.005G040400' => 'gra', 'Gorai.007G134500' => 'gra', 'Gorai.008G005500' => 'gra', 'GSVIVG01011094001' => 'vvi', 'GSVIVG01017879001' => 'vvi', 'GSVIVG01025988001' => 'vvi', 'GSVIVG01029847001' => 'vvi', 'HanXRQChr10g0282901' => 'han', 'HanXRQChr10g0310371' => 'han', 'HanXRQChr10g0315041' => 'han', 'HanXRQChr11g0327651' => 'han', 'HanXRQChr12g0359391' => 'han', 'Haze_00972' => 'cav', 'Haze_00973' => 'cav', 'Haze_00974' => 'cav', 'Haze_04747' => 'cav', 'Haze_04749' => 'cav', 'Haze_04750' => 'cav', 'Haze_21217' => 'cav', 'Hma1.2p1_1037F.1_g250680' => 'hma', 'Hma1.2p1_1644F.1_g295320' => 'hma', 'HPP92_011322' => 'vpl', 'HPP92_011323' => 'vpl', 'HPP92_011324' => 'vpl', 'HPP92_011325' => 'vpl', 'HPP92_011326' => 'vpl', 'Hund12205' => 'sun', 'Hund17957' => 'sun', 'Lalb_Chr06g0176771' => 'lal', 'Lalb_Chr18g0056021' => 'lal', 'Lalb_Chr18g0056031' => 'lal', 'Lalb_Chr18g0056041' => 'lal', 'Lalb_Chr20g0107751' => 'lal', 'Lalb_Chr20g0118371' => 'lal', 'Lj1g0010239' => 'lja', 'Lj1g0017101' => 'lja', 'Lj2A1178G40' => 'lonja', 'Lj2A54G84' => 'lonja', 'Lj2g0015248' => 'lja', 'Lj3A761T51' => 'lonja', 'Lj6g0018116' => 'lja', 'Lsat_1_v5_gn_4_136040' => 'lsa', 'Lsat_1_v5_gn_5_187461' => 'lsa', 'Lsat_1_v5_gn_5_77001' => 'lsa', 'Lsat_1_v5_gn_9_4461' => 'lsa', 'Manes.01G210100' => 'mes', 'Manes.03G185600' => 'mes', 'Manes.05G073300' => 'mes', 'Manes.09G120300' => 'mes', 'Manes.15G022100' => 'mes', 'Mapoly0096s0053' => 'mpo', 'MBI03_g14058_MAGBIO' => 'mbi', 'MBI03_g33876_MAGBIO' => 'mbi', 'MBI03_g36854_MAGBIO' => 'mbi', 'MBI17_g11997_MAGBIO' => 'mbi', 'MD03G1269000' => 'mdo', 'MD04G1179600' => 'mdo', 'MD11G1289800' => 'mdo', 'MD12G1194700' => 'mdo', 'MD13G1182100' => 'mdo', 'MD13G1182200' => 'mdo', 'MD16G1182600' => 'mdo', 'Medtr2g021400' => 'mtr', 'Medtr2g021470' => 'mtr', 'Medtr2g105810' => 'mtr', 'Medtr3g033580' => 'mtr', 'Medtr6g007970' => 'mtr', 'Medtr7g056330' => 'mtr', 'Medtr7g074290' => 'mtr', 'Medtr7g074380' => 'mtr', 'Medtr7g094550' => 'mtr', 'Medtr8g069995' => 'mtr', 'MELO3C014345.2' => 'cme', 'MELO3C021395.2' => 'cme', 'Migut.D00262' => 'egut', 'Migut.G00257' => 'egut', 'MSTRG.21575' => 'ama', 'MSTRG.3985' => 'ama', 'Nitab4.5_0000295g0140' => 'nta', 'Nitab4.5_0000732g0140' => 'nta', 'Nitab4.5_0003162g0020' => 'nta', 'Nitab4.5_0006180g0090' => 'nta', 'Nitab4.5_0006390g0010' => 'nta', 'Nitab4.5_0007392g0040' => 'nta', 'Nn1g02140' => 'nnu', 'Nn4g26168' => 'nnu', 'Nn5g26754' => 'nnu', 'Oeu001433.1' => 'oeu', 'Oeu010299.2' => 'oeu', 'Oeu011171.1' => 'oeu', 'Oeu037675.1' => 'oeu', 'Oeu038359.1' => 'oeu', 'Oeu063834.1' => 'oeu', 'Oeu063835.1' => 'oeu', 'Os05g0312000' => 'osa', 'Os07g0211101' => 'osa', 'Os07g0211200' => 'osa', 'Os07g0681500' => 'osa', 'Peaxi162Scf00095g01015' => 'pax', 'Peaxi162Scf00104g00329' => 'pax', 'Peaxi162Scf00161g00137' => 'pax', 'PGR004G1665' => 'pgr', 'PGR031G2937' => 'pgr', 'PGR119G2145' => 'pgr', 'PGSC0003DMG400004351' => 'stu', 'PGSC0003DMG400014625' => 'stu', 'PGSC0003DMG401000943' => 'stu', 'Phvul.001G148600' => 'pvu', 'Phvul.004G001700' => 'pvu', 'Phvul.006G154900' => 'pvu', 'Phvul.008G078200' => 'pvu', 'Phvul.011G136500' => 'pvu', 'Potri.002G215600' => 'ptr', 'Potri.008G201600' => 'ptr', 'Potri.014G138400' => 'ptr', 'Potri.016G142500' => 'ptr', 'Pp3c16_10580' => 'ppa', 'Pp3c5_25280' => 'ppa', 'Prupe.1G150000' => 'ppe', 'Prupe.1G150100' => 'ppe', 'Prupe.6G299600' => 'ppe', 'Prupe.8G245000' => 'ppe', 'Psat0s4927g0040' => 'psa', 'Psat1g052080' => 'psa', 'Psat1g183800' => 'psa', 'Psat3g113840' => 'psa', 'Psat3g126120' => 'psa', 'Psat3g126160' => 'psa', 'Psat3g158760' => 'psa', 'Psat3g158840' => 'psa', 'PSO170G2858' => 'pso', 'PSO339G0606' => 'pso', 'PSO384G4709' => 'pso', 'PSO407G0334' => 'pso', 'QL04p040276' => 'qlo', 'QL06p005458' => 'qlo', 'QL06p005472' => 'qlo', 'QL07p030546' => 'qlo', 'QL07p031519' => 'qlo', 'QL09p050949' => 'qlo', 'QL09p050966' => 'qlo', 'QL09p051067' => 'qlo', 'QL12p022706' => 'qlo', 'RcHm_v2.0_Chr2g0119601' => 'rch', 'RcHm_v2.0_Chr3g0459591' => 'rch', 'RcHm_v2.0_Chr4g0418521' => 'rch', 'RcHm_v2.0_Chr4g0418531' => 'rch', 'RcHm_v2.0_Chr4g0418541' => 'rch', 'RcHm_v2.0_Chr6g0291641' => 'rch', 'Rhsim01G0086300' => 'rsi', 'Rhsim01G0276300' => 'rsi', 'Rhsim01G0276500' => 'rsi', 'Rhsim04G0207700' => 'rsi', 'Rhsim05G0234500' => 'rsi', 'Rhsim13G0022400' => 'rsi', 'Sabra02G0167900' => 'sbr', 'Sabra04G0158500' => 'sbr', 'Sabra08G0159800' => 'sbr', 'Sabra10G0011500' => 'sbr', 'Sabra14G0104400' => 'sbr', 'SalBow2G2440' => 'sbo', 'SalBow4G2265' => 'sbo', 'Sc02g0000060' => 'sci', 'Sc05g0005020' => 'sci', 'Sc13g0003890' => 'sci', 'Sed0014865' => 'sed', 'Sed0017224' => 'sed', 'Sed0026391' => 'sed', 'SEGI_00063' => 'sgi', 'SEGI_10967' => 'sgi', 'SEGI_17510' => 'sgi', 'SEGI_24396' => 'sgi', 'SEGI_39719' => 'sgi', 'SEGI_41392' => 'sgi', 'SGA_v2.0_scaffold11G05794' => 'sas', 'SGA_v2.0_scaffold142G35607' => 'sas', 'SGA_v2.0_scaffold1G00447' => 'sas', 'SHI15388' => 'shi', 'SHI15394' => 'shi', 'SHI15396' => 'shi', 'SHI15399' => 'shi', 'SMO343G0151' => 'smo', 'SMO367G1118' => 'smo', 'Solyc01g080200.3' => 'sly', 'Solyc06g008960.3' => 'sly', 'Solyc09g064780.3' => 'sly', 'Sopen01g031980' => 'spe', 'Sopen06g003710' => 'spe', 'Sopen09g026460' => 'spe', 'Sp3g21240' => 'spa', 'Sp4g30030' => 'spa', 'TAR365G0022' => 'tar', 'TAR365G1023' => 'tar', 'TAR365G1253' => 'tar', 'TAR623G0078' => 'tar', 'TAR623G1721' => 'tar', 'TAR633G0959' => 'tar', 'THA.LOC104802225' => 'tha', 'THA.LOC104804769' => 'tha', 'THA.LOC104808660' => 'tha', 'THA.LOC104812792' => 'tha', 'Thecc.01G284000' => 'tca', 'Thecc.04G220600' => 'tca', 'Thecc.05G268900' => 'tca', 'Thecc.08G171100' => 'tca', 'Thhalv10001284m.g' => 'esa', 'Thhalv10019912m.g' => 'esa', 'TPR.G14189' => 'tpr', 'TPR.G18110' => 'tpr', 'TPR.G18130' => 'tpr', 'TPR.G18131' => 'tpr', 'TPR.G18140' => 'tpr', 'TPR.G24282' => 'tpr', 'TPR.G25221' => 'tpr', 'TPR.G29267' => 'tpr', 'TPR.G35315' => 'tpr', 'TPR.G36173' => 'tpr', 'TWI09G0794' => 'twi', 'TWI59G1348' => 'twi', 'TWI74G0430' => 'twi', 'unitig_26.g8940' => 'ugi', 'unitig_749.g13744' => 'ugi', 'unitig_749.g13745' => 'ugi', 'vmacro08269' => 'vma', 'vmacro14937' => 'vma', 'vmacro20401' => 'vma', 'VMungo0464G1349' => 'vmu', 'VMungo0540G0289' => 'vmu', 'VMungo1215G1590' => 'vmu', 'VMungo1309G0221' => 'vmu', 'VMungo1309G2815' => 'vmu', 'VMungo1383G0239' => 'vmu', 'VMungo1383G2910' => 'vmu', 'Zm00001eb095270' => 'zma', 'Zm00001eb095280' => 'zma', 'Zm00001eb111630' => 'zma', 'Zm00001eb237080' => 'zma', 'Zm00001eb273740' => 'zma', 'Zm00001eb285040' => 'zma', 'Zm00001eb330790' => 'zma', 'Zm00001eb337380' => 'zma' ) $gf_id = 'HOM05D001484' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001484' ) $data_identifier = 'HOM05D001484' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 2, 'aly' => (int) 2, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 22, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 7, 'hma' => (int) 2, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 7, 'mtr' => (int) 10, 'cme' => (int) 2, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 4, 'ppa' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 4, 'qlo' => (int) 9, 'rch' => (int) 6, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 10, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 7, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb337380' $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' => 'HOM05D001484', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p31500' => 'bna', 'A05p00020' => 'bna', 'A07p08820' => 'bna', 'Aa31LG4G3300' => 'aar', 'Aa31LG8G10030' => 'aar', 'Actinidia00731' => 'ach', 'Actinidia11473' => 'ach', 'Actinidia23469' => 'ach', 'Actinidia24318' => 'ach', 'Actinidia40196' => 'ach', 'Actinidia40197' => 'ach', 'Actinidia40198' => 'ach', 'Ah.08g212990' => 'amhyb', 'Ah.15g091720' => 'amhyb', 'AL3G38260' => 'aly', 'AL4G47710' => 'aly', 'Aqoxy2G00671' => 'aox', 'Aqoxy2G03236' => 'aox', 'arahy.Tifrunner.gnm1.ann1.05IDCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KR684' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATY3SJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK6QJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6APGL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IDT7Z9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM073U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ0R87' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LE7RV4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT4QRX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V5ENPK' => 'arhy', 'AT2G48110' => 'ath', 'AT3G23590' => 'ath', 'ATR0626G186' => 'atr', 'ATR1127G141' => 'atr', 'Atru.chr4.2583' => 'acertr', 'Atru.chr5.1358' => 'acertr', 'Atru.chr5.1359' => 'acertr', 'Atru.chr8.46' => 'acertr', 'AUR62002640' => 'cqu', 'AUR62030055' => 'cqu', 'AUR62033713' => 'cqu', 'AUR62033714' => 'cqu', 'AUR62036795' => 'cqu', 'AUR62039891' => 'cqu', 'BcaB02g08737' => 'bca', 'BcaB04g20441' => 'bca', 'BcaB06g26509' => 'bca', 'BcaB06g26510' => 'bca', 'BcaB06g26511' => 'bca', 'BcaB06g26512' => 'bca', 'BcaB06g26513' => 'bca', 'BcaC02g12564' => 'bca', 'BcaC02g12565' => 'bca', 'BcaC02g12794' => 'bca', 'BcaC02g12795' => 'bca', 'BcaC02g12796' => 'bca', 'BcaC06g35541' => 'bca', 'BNapus_Darmor_BZH_scaffold_188p00080' => 'bna', 'BNapus_Darmor_BZH_scaffold_188p00090' => 'bna', 'BolC1t03972H' => 'bol', 'BolC1t03973H' => 'bol', 'BolC4t21680H' => 'bol', 'BolC7t41863H' => 'bol', 'BolSC55t61227H' => 'bol', 'BolSC55t61228H' => 'bol', 'BraA01t03278Z' => 'bra', 'BraA05t18998Z' => 'bra', 'BraA07t28673Z' => 'bra', 'C01p40150' => 'bna', 'C05p12370' => 'bna', 'C07p13680' => 'bna', 'CAN.G1006.16' => 'can', 'CAN.G1006.17' => 'can', 'CAN.G1170.2' => 'can', 'CAN.G962.7' => 'can', 'CANSAT25G2179' => 'cansat', 'CANSAT78G1573' => 'cansat', 'CARHR099510' => 'chi', 'CARHR143510' => 'chi', 'Carub.0003s2380' => 'cru', 'Carub.0004s3082' => 'cru', 'Ca_00614_v3' => 'car', 'Ca_07801_v3' => 'car', 'Ca_08567_v3' => 'car', 'Ca_09571_v3' => 'car', 'CBR_g19290' => 'cbr', 'Cc01_g19770' => 'ccan', 'Cc03_g03030' => 'ccan', 'CDE07G0968' => 'cde', 'CDE09G1441' => 'cde', 'Cfa006103' => 'cfa', 'Cfa015573' => 'cfa', 'Cfa016988' => 'cfa', 'Ciclev10006738m.g' => 'ccl', 'Ciclev10010920m.g' => 'ccl', 'Ciclev10018517m.g' => 'ccl', 'CiPaw.01G159200' => 'cil', 'CiPaw.02G091000' => 'cil', 'CiPaw.02G091100' => 'cil', 'CiPaw.08G103100' => 'cil', 'CiPaw.09G224900' => 'cil', 'ClCG06G005740' => 'cla', 'ClCG07G000090' => 'cla', 'ClCG07G000100' => 'cla', 'COL.COLO4_09143' => 'col', 'COL.COLO4_25124' => 'col', 'Cpa.g.sc16.34' => 'cpa', 'Cpa.g.sc3504.1' => 'cpa', 'Cpa.g.sc60.37' => 'cpa', 'CsaV3_6G018520' => 'csa', 'CsaV3_6G036860' => 'csa', 'CSS0001072' => 'camsi', 'CSS0020208' => 'camsi', 'CSS0021253' => 'camsi', 'CSS0022190' => 'camsi', 'CSS0036150' => 'camsi', 'CSS0040442' => 'camsi', 'CSS0042300' => 'camsi', 'CSS0045298' => 'camsi', 'DCAR_012449' => 'dca', 'DCAR_018405' => 'dca', 'DCAR_024573' => 'dca', 'DCAR_030591' => 'dca', 'Dinv16926' => 'din', 'Dinv32963' => 'din', 'Dinv38382' => 'din', 'Dinv38383' => 'din', 'Duzib133G0974' => 'dzi', 'Duzib138G1867' => 'dzi', 'Duzib211G0420' => 'dzi', 'Duzib212G0930' => 'dzi', 'ECA234G1645' => 'eca', 'ECA247G3467' => 'eca', 'ECA248G1703' => 'eca', 'EL10Ac3g06327' => 'bvu', 'EL10Ac7g17204' => 'bvu', 'Eucgr.A00855' => 'egr', 'Eucgr.A00858' => 'egr', 'Eucgr.H01520' => 'egr', 'Eucgr.H03604' => 'egr', 'Eucgr.L03465' => 'egr', 'Eucgr.L03466' => 'egr', 'FAN01G0988' => 'fan', 'FAN02G3892' => 'fan', 'FAN05G3381' => 'fan', 'FAN07G0967' => 'fan', 'FAN07G1493' => 'fan', 'FAN08G3125' => 'fan', 'FAN09G0402' => 'fan', 'FAN12G2594' => 'fan', 'FAN12G3879' => 'fan', 'FAN14G1546' => 'fan', 'FAN15G3626' => 'fan', 'FAN17G0588' => 'fan', 'FAN17G0609' => 'fan', 'FAN18G2817' => 'fan', 'FAN19G1305' => 'fan', 'FAN20G1787' => 'fan', 'FAN22G0073' => 'fan', 'FAN22G0352' => 'fan', 'FAN22G0368' => 'fan', 'FAN22G2273' => 'fan', 'FAN24G1998' => 'fan', 'FAN27G1317' => 'fan', 'FvH4_2g23980' => 'fve', 'FvH4_4g14380' => 'fve', 'FvH4_4g14390' => 'fve', 'FvH4_6g09250' => 'fve', 'Glyma.03G151100' => 'gma', 'Glyma.04G122550' => 'gma', 'Glyma.05G001600' => 'gma', 'Glyma.09G270766' => 'gma', 'Glyma.09G270832' => 'gma', 'Glyma.13G209800' => 'gma', 'Glyma.15G102800' => 'gma', 'Glyma.18G218900' => 'gma', 'Glyma.19G001500' => 'gma', 'Glyma.19G153600' => 'gma', 'Gohir.A02G028600' => 'ghi', 'Gohir.A08G045000' => 'ghi', 'Gohir.A11G120500' => 'ghi', 'Gohir.A12G006200' => 'ghi', 'Gohir.A12G006250' => 'ghi', 'Gohir.D02G036300' => 'ghi', 'Gohir.D08G054700' => 'ghi', 'Gohir.D11G125600' => 'ghi', 'Gohir.D12G005700' => 'ghi', 'Gorai.004G055200' => 'gra', 'Gorai.005G040400' => 'gra', 'Gorai.007G134500' => 'gra', 'Gorai.008G005500' => 'gra', 'GSVIVG01011094001' => 'vvi', 'GSVIVG01017879001' => 'vvi', 'GSVIVG01025988001' => 'vvi', 'GSVIVG01029847001' => 'vvi', 'HanXRQChr10g0282901' => 'han', 'HanXRQChr10g0310371' => 'han', 'HanXRQChr10g0315041' => 'han', 'HanXRQChr11g0327651' => 'han', 'HanXRQChr12g0359391' => 'han', 'Haze_00972' => 'cav', 'Haze_00973' => 'cav', 'Haze_00974' => 'cav', 'Haze_04747' => 'cav', 'Haze_04749' => 'cav', 'Haze_04750' => 'cav', 'Haze_21217' => 'cav', 'Hma1.2p1_1037F.1_g250680' => 'hma', 'Hma1.2p1_1644F.1_g295320' => 'hma', 'HPP92_011322' => 'vpl', 'HPP92_011323' => 'vpl', 'HPP92_011324' => 'vpl', 'HPP92_011325' => 'vpl', 'HPP92_011326' => 'vpl', 'Hund12205' => 'sun', 'Hund17957' => 'sun', 'Lalb_Chr06g0176771' => 'lal', 'Lalb_Chr18g0056021' => 'lal', 'Lalb_Chr18g0056031' => 'lal', 'Lalb_Chr18g0056041' => 'lal', 'Lalb_Chr20g0107751' => 'lal', 'Lalb_Chr20g0118371' => 'lal', 'Lj1g0010239' => 'lja', 'Lj1g0017101' => 'lja', 'Lj2A1178G40' => 'lonja', 'Lj2A54G84' => 'lonja', 'Lj2g0015248' => 'lja', 'Lj3A761T51' => 'lonja', 'Lj6g0018116' => 'lja', 'Lsat_1_v5_gn_4_136040' => 'lsa', 'Lsat_1_v5_gn_5_187461' => 'lsa', 'Lsat_1_v5_gn_5_77001' => 'lsa', 'Lsat_1_v5_gn_9_4461' => 'lsa', 'Manes.01G210100' => 'mes', 'Manes.03G185600' => 'mes', 'Manes.05G073300' => 'mes', 'Manes.09G120300' => 'mes', 'Manes.15G022100' => 'mes', 'Mapoly0096s0053' => 'mpo', 'MBI03_g14058_MAGBIO' => 'mbi', 'MBI03_g33876_MAGBIO' => 'mbi', 'MBI03_g36854_MAGBIO' => 'mbi', 'MBI17_g11997_MAGBIO' => 'mbi', 'MD03G1269000' => 'mdo', 'MD04G1179600' => 'mdo', 'MD11G1289800' => 'mdo', 'MD12G1194700' => 'mdo', 'MD13G1182100' => 'mdo', 'MD13G1182200' => 'mdo', 'MD16G1182600' => 'mdo', 'Medtr2g021400' => 'mtr', 'Medtr2g021470' => 'mtr', 'Medtr2g105810' => 'mtr', 'Medtr3g033580' => 'mtr', 'Medtr6g007970' => 'mtr', 'Medtr7g056330' => 'mtr', 'Medtr7g074290' => 'mtr', 'Medtr7g074380' => 'mtr', 'Medtr7g094550' => 'mtr', 'Medtr8g069995' => 'mtr', 'MELO3C014345.2' => 'cme', 'MELO3C021395.2' => 'cme', 'Migut.D00262' => 'egut', 'Migut.G00257' => 'egut', 'MSTRG.21575' => 'ama', 'MSTRG.3985' => 'ama', 'Nitab4.5_0000295g0140' => 'nta', 'Nitab4.5_0000732g0140' => 'nta', 'Nitab4.5_0003162g0020' => 'nta', 'Nitab4.5_0006180g0090' => 'nta', 'Nitab4.5_0006390g0010' => 'nta', 'Nitab4.5_0007392g0040' => 'nta', 'Nn1g02140' => 'nnu', 'Nn4g26168' => 'nnu', 'Nn5g26754' => 'nnu', 'Oeu001433.1' => 'oeu', 'Oeu010299.2' => 'oeu', 'Oeu011171.1' => 'oeu', 'Oeu037675.1' => 'oeu', 'Oeu038359.1' => 'oeu', 'Oeu063834.1' => 'oeu', 'Oeu063835.1' => 'oeu', 'Os05g0312000' => 'osa', 'Os07g0211101' => 'osa', 'Os07g0211200' => 'osa', 'Os07g0681500' => 'osa', 'Peaxi162Scf00095g01015' => 'pax', 'Peaxi162Scf00104g00329' => 'pax', 'Peaxi162Scf00161g00137' => 'pax', 'PGR004G1665' => 'pgr', 'PGR031G2937' => 'pgr', 'PGR119G2145' => 'pgr', 'PGSC0003DMG400004351' => 'stu', 'PGSC0003DMG400014625' => 'stu', 'PGSC0003DMG401000943' => 'stu', 'Phvul.001G148600' => 'pvu', 'Phvul.004G001700' => 'pvu', 'Phvul.006G154900' => 'pvu', 'Phvul.008G078200' => 'pvu', 'Phvul.011G136500' => 'pvu', 'Potri.002G215600' => 'ptr', 'Potri.008G201600' => 'ptr', 'Potri.014G138400' => 'ptr', 'Potri.016G142500' => 'ptr', 'Pp3c16_10580' => 'ppa', 'Pp3c5_25280' => 'ppa', 'Prupe.1G150000' => 'ppe', 'Prupe.1G150100' => 'ppe', 'Prupe.6G299600' => 'ppe', 'Prupe.8G245000' => 'ppe', 'Psat0s4927g0040' => 'psa', 'Psat1g052080' => 'psa', 'Psat1g183800' => 'psa', 'Psat3g113840' => 'psa', 'Psat3g126120' => 'psa', 'Psat3g126160' => 'psa', 'Psat3g158760' => 'psa', 'Psat3g158840' => 'psa', 'PSO170G2858' => 'pso', 'PSO339G0606' => 'pso', 'PSO384G4709' => 'pso', 'PSO407G0334' => 'pso', 'QL04p040276' => 'qlo', 'QL06p005458' => 'qlo', 'QL06p005472' => 'qlo', 'QL07p030546' => 'qlo', 'QL07p031519' => 'qlo', 'QL09p050949' => 'qlo', 'QL09p050966' => 'qlo', 'QL09p051067' => 'qlo', 'QL12p022706' => 'qlo', 'RcHm_v2.0_Chr2g0119601' => 'rch', 'RcHm_v2.0_Chr3g0459591' => 'rch', 'RcHm_v2.0_Chr4g0418521' => 'rch', 'RcHm_v2.0_Chr4g0418531' => 'rch', 'RcHm_v2.0_Chr4g0418541' => 'rch', 'RcHm_v2.0_Chr6g0291641' => 'rch', 'Rhsim01G0086300' => 'rsi', 'Rhsim01G0276300' => 'rsi', 'Rhsim01G0276500' => 'rsi', 'Rhsim04G0207700' => 'rsi', 'Rhsim05G0234500' => 'rsi', 'Rhsim13G0022400' => 'rsi', 'Sabra02G0167900' => 'sbr', 'Sabra04G0158500' => 'sbr', 'Sabra08G0159800' => 'sbr', 'Sabra10G0011500' => 'sbr', 'Sabra14G0104400' => 'sbr', 'SalBow2G2440' => 'sbo', 'SalBow4G2265' => 'sbo', 'Sc02g0000060' => 'sci', 'Sc05g0005020' => 'sci', 'Sc13g0003890' => 'sci', 'Sed0014865' => 'sed', 'Sed0017224' => 'sed', 'Sed0026391' => 'sed', 'SEGI_00063' => 'sgi', 'SEGI_10967' => 'sgi', 'SEGI_17510' => 'sgi', 'SEGI_24396' => 'sgi', 'SEGI_39719' => 'sgi', 'SEGI_41392' => 'sgi', 'SGA_v2.0_scaffold11G05794' => 'sas', 'SGA_v2.0_scaffold142G35607' => 'sas', 'SGA_v2.0_scaffold1G00447' => 'sas', 'SHI15388' => 'shi', 'SHI15394' => 'shi', 'SHI15396' => 'shi', 'SHI15399' => 'shi', 'SMO343G0151' => 'smo', 'SMO367G1118' => 'smo', 'Solyc01g080200.3' => 'sly', 'Solyc06g008960.3' => 'sly', 'Solyc09g064780.3' => 'sly', 'Sopen01g031980' => 'spe', 'Sopen06g003710' => 'spe', 'Sopen09g026460' => 'spe', 'Sp3g21240' => 'spa', 'Sp4g30030' => 'spa', 'TAR365G0022' => 'tar', 'TAR365G1023' => 'tar', 'TAR365G1253' => 'tar', 'TAR623G0078' => 'tar', 'TAR623G1721' => 'tar', 'TAR633G0959' => 'tar', 'THA.LOC104802225' => 'tha', 'THA.LOC104804769' => 'tha', 'THA.LOC104808660' => 'tha', 'THA.LOC104812792' => 'tha', 'Thecc.01G284000' => 'tca', 'Thecc.04G220600' => 'tca', 'Thecc.05G268900' => 'tca', 'Thecc.08G171100' => 'tca', 'Thhalv10001284m.g' => 'esa', 'Thhalv10019912m.g' => 'esa', 'TPR.G14189' => 'tpr', 'TPR.G18110' => 'tpr', 'TPR.G18130' => 'tpr', 'TPR.G18131' => 'tpr', 'TPR.G18140' => 'tpr', 'TPR.G24282' => 'tpr', 'TPR.G25221' => 'tpr', 'TPR.G29267' => 'tpr', 'TPR.G35315' => 'tpr', 'TPR.G36173' => 'tpr', 'TWI09G0794' => 'twi', 'TWI59G1348' => 'twi', 'TWI74G0430' => 'twi', 'unitig_26.g8940' => 'ugi', 'unitig_749.g13744' => 'ugi', 'unitig_749.g13745' => 'ugi', 'vmacro08269' => 'vma', 'vmacro14937' => 'vma', 'vmacro20401' => 'vma', 'VMungo0464G1349' => 'vmu', 'VMungo0540G0289' => 'vmu', 'VMungo1215G1590' => 'vmu', 'VMungo1309G0221' => 'vmu', 'VMungo1309G2815' => 'vmu', 'VMungo1383G0239' => 'vmu', 'VMungo1383G2910' => 'vmu', 'Zm00001eb095270' => 'zma', 'Zm00001eb095280' => 'zma', 'Zm00001eb111630' => 'zma', 'Zm00001eb237080' => 'zma', 'Zm00001eb273740' => 'zma', 'Zm00001eb285040' => 'zma', 'Zm00001eb330790' => 'zma', 'Zm00001eb337380' => 'zma' ), 'gf_id' => 'HOM05D001484', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001484' ), 'data_identifier' => 'HOM05D001484', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001484', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p31500' => 'bna', 'A05p00020' => 'bna', 'A07p08820' => 'bna', 'Aa31LG4G3300' => 'aar', 'Aa31LG8G10030' => 'aar', 'Actinidia00731' => 'ach', 'Actinidia11473' => 'ach', 'Actinidia23469' => 'ach', 'Actinidia24318' => 'ach', 'Actinidia40196' => 'ach', 'Actinidia40197' => 'ach', 'Actinidia40198' => 'ach', 'Ah.08g212990' => 'amhyb', 'Ah.15g091720' => 'amhyb', 'AL3G38260' => 'aly', 'AL4G47710' => 'aly', 'Aqoxy2G00671' => 'aox', 'Aqoxy2G03236' => 'aox', 'arahy.Tifrunner.gnm1.ann1.05IDCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KR684' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATY3SJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK6QJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6APGL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IDT7Z9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM073U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ0R87' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LE7RV4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT4QRX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V5ENPK' => 'arhy', 'AT2G48110' => 'ath', 'AT3G23590' => 'ath', 'ATR0626G186' => 'atr', 'ATR1127G141' => 'atr', 'Atru.chr4.2583' => 'acertr', 'Atru.chr5.1358' => 'acertr', 'Atru.chr5.1359' => 'acertr', 'Atru.chr8.46' => 'acertr', 'AUR62002640' => 'cqu', 'AUR62030055' => 'cqu', 'AUR62033713' => 'cqu', 'AUR62033714' => 'cqu', 'AUR62036795' => 'cqu', 'AUR62039891' => 'cqu', 'BcaB02g08737' => 'bca', 'BcaB04g20441' => 'bca', 'BcaB06g26509' => 'bca', 'BcaB06g26510' => 'bca', 'BcaB06g26511' => 'bca', 'BcaB06g26512' => 'bca', 'BcaB06g26513' => 'bca', 'BcaC02g12564' => 'bca', 'BcaC02g12565' => 'bca', 'BcaC02g12794' => 'bca', 'BcaC02g12795' => 'bca', 'BcaC02g12796' => 'bca', 'BcaC06g35541' => 'bca', 'BNapus_Darmor_BZH_scaffold_188p00080' => 'bna', 'BNapus_Darmor_BZH_scaffold_188p00090' => 'bna', 'BolC1t03972H' => 'bol', 'BolC1t03973H' => 'bol', 'BolC4t21680H' => 'bol', 'BolC7t41863H' => 'bol', 'BolSC55t61227H' => 'bol', 'BolSC55t61228H' => 'bol', 'BraA01t03278Z' => 'bra', 'BraA05t18998Z' => 'bra', 'BraA07t28673Z' => 'bra', 'C01p40150' => 'bna', 'C05p12370' => 'bna', 'C07p13680' => 'bna', 'CAN.G1006.16' => 'can', 'CAN.G1006.17' => 'can', 'CAN.G1170.2' => 'can', 'CAN.G962.7' => 'can', 'CANSAT25G2179' => 'cansat', 'CANSAT78G1573' => 'cansat', 'CARHR099510' => 'chi', 'CARHR143510' => 'chi', 'Carub.0003s2380' => 'cru', 'Carub.0004s3082' => 'cru', 'Ca_00614_v3' => 'car', 'Ca_07801_v3' => 'car', 'Ca_08567_v3' => 'car', 'Ca_09571_v3' => 'car', 'CBR_g19290' => 'cbr', 'Cc01_g19770' => 'ccan', 'Cc03_g03030' => 'ccan', 'CDE07G0968' => 'cde', 'CDE09G1441' => 'cde', 'Cfa006103' => 'cfa', 'Cfa015573' => 'cfa', 'Cfa016988' => 'cfa', 'Ciclev10006738m.g' => 'ccl', 'Ciclev10010920m.g' => 'ccl', 'Ciclev10018517m.g' => 'ccl', 'CiPaw.01G159200' => 'cil', 'CiPaw.02G091000' => 'cil', 'CiPaw.02G091100' => 'cil', 'CiPaw.08G103100' => 'cil', 'CiPaw.09G224900' => 'cil', 'ClCG06G005740' => 'cla', 'ClCG07G000090' => 'cla', 'ClCG07G000100' => 'cla', 'COL.COLO4_09143' => 'col', 'COL.COLO4_25124' => 'col', 'Cpa.g.sc16.34' => 'cpa', 'Cpa.g.sc3504.1' => 'cpa', 'Cpa.g.sc60.37' => 'cpa', 'CsaV3_6G018520' => 'csa', 'CsaV3_6G036860' => 'csa', 'CSS0001072' => 'camsi', 'CSS0020208' => 'camsi', 'CSS0021253' => 'camsi', 'CSS0022190' => 'camsi', 'CSS0036150' => 'camsi', 'CSS0040442' => 'camsi', 'CSS0042300' => 'camsi', 'CSS0045298' => 'camsi', 'DCAR_012449' => 'dca', 'DCAR_018405' => 'dca', 'DCAR_024573' => 'dca', 'DCAR_030591' => 'dca', 'Dinv16926' => 'din', 'Dinv32963' => 'din', 'Dinv38382' => 'din', 'Dinv38383' => 'din', 'Duzib133G0974' => 'dzi', 'Duzib138G1867' => 'dzi', 'Duzib211G0420' => 'dzi', 'Duzib212G0930' => 'dzi', 'ECA234G1645' => 'eca', 'ECA247G3467' => 'eca', 'ECA248G1703' => 'eca', 'EL10Ac3g06327' => 'bvu', 'EL10Ac7g17204' => 'bvu', 'Eucgr.A00855' => 'egr', 'Eucgr.A00858' => 'egr', 'Eucgr.H01520' => 'egr', 'Eucgr.H03604' => 'egr', 'Eucgr.L03465' => 'egr', 'Eucgr.L03466' => 'egr', 'FAN01G0988' => 'fan', 'FAN02G3892' => 'fan', 'FAN05G3381' => 'fan', 'FAN07G0967' => 'fan', 'FAN07G1493' => 'fan', 'FAN08G3125' => 'fan', 'FAN09G0402' => 'fan', 'FAN12G2594' => 'fan', 'FAN12G3879' => 'fan', 'FAN14G1546' => 'fan', 'FAN15G3626' => 'fan', 'FAN17G0588' => 'fan', 'FAN17G0609' => 'fan', 'FAN18G2817' => 'fan', 'FAN19G1305' => 'fan', 'FAN20G1787' => 'fan', 'FAN22G0073' => 'fan', 'FAN22G0352' => 'fan', 'FAN22G0368' => 'fan', 'FAN22G2273' => 'fan', 'FAN24G1998' => 'fan', 'FAN27G1317' => 'fan', 'FvH4_2g23980' => 'fve', 'FvH4_4g14380' => 'fve', 'FvH4_4g14390' => 'fve', 'FvH4_6g09250' => 'fve', 'Glyma.03G151100' => 'gma', 'Glyma.04G122550' => 'gma', 'Glyma.05G001600' => 'gma', 'Glyma.09G270766' => 'gma', 'Glyma.09G270832' => 'gma', 'Glyma.13G209800' => 'gma', 'Glyma.15G102800' => 'gma', 'Glyma.18G218900' => 'gma', 'Glyma.19G001500' => 'gma', 'Glyma.19G153600' => 'gma', 'Gohir.A02G028600' => 'ghi', 'Gohir.A08G045000' => 'ghi', 'Gohir.A11G120500' => 'ghi', 'Gohir.A12G006200' => 'ghi', 'Gohir.A12G006250' => 'ghi', 'Gohir.D02G036300' => 'ghi', 'Gohir.D08G054700' => 'ghi', 'Gohir.D11G125600' => 'ghi', 'Gohir.D12G005700' => 'ghi', 'Gorai.004G055200' => 'gra', 'Gorai.005G040400' => 'gra', 'Gorai.007G134500' => 'gra', 'Gorai.008G005500' => 'gra', 'GSVIVG01011094001' => 'vvi', 'GSVIVG01017879001' => 'vvi', 'GSVIVG01025988001' => 'vvi', 'GSVIVG01029847001' => 'vvi', 'HanXRQChr10g0282901' => 'han', 'HanXRQChr10g0310371' => 'han', 'HanXRQChr10g0315041' => 'han', 'HanXRQChr11g0327651' => 'han', 'HanXRQChr12g0359391' => 'han', 'Haze_00972' => 'cav', 'Haze_00973' => 'cav', 'Haze_00974' => 'cav', 'Haze_04747' => 'cav', 'Haze_04749' => 'cav', 'Haze_04750' => 'cav', 'Haze_21217' => 'cav', 'Hma1.2p1_1037F.1_g250680' => 'hma', 'Hma1.2p1_1644F.1_g295320' => 'hma', 'HPP92_011322' => 'vpl', 'HPP92_011323' => 'vpl', 'HPP92_011324' => 'vpl', 'HPP92_011325' => 'vpl', 'HPP92_011326' => 'vpl', 'Hund12205' => 'sun', 'Hund17957' => 'sun', 'Lalb_Chr06g0176771' => 'lal', 'Lalb_Chr18g0056021' => 'lal', 'Lalb_Chr18g0056031' => 'lal', 'Lalb_Chr18g0056041' => 'lal', 'Lalb_Chr20g0107751' => 'lal', 'Lalb_Chr20g0118371' => 'lal', 'Lj1g0010239' => 'lja', 'Lj1g0017101' => 'lja', 'Lj2A1178G40' => 'lonja', 'Lj2A54G84' => 'lonja', 'Lj2g0015248' => 'lja', 'Lj3A761T51' => 'lonja', 'Lj6g0018116' => 'lja', 'Lsat_1_v5_gn_4_136040' => 'lsa', 'Lsat_1_v5_gn_5_187461' => 'lsa', 'Lsat_1_v5_gn_5_77001' => 'lsa', 'Lsat_1_v5_gn_9_4461' => 'lsa', 'Manes.01G210100' => 'mes', 'Manes.03G185600' => 'mes', 'Manes.05G073300' => 'mes', 'Manes.09G120300' => 'mes', 'Manes.15G022100' => 'mes', 'Mapoly0096s0053' => 'mpo', 'MBI03_g14058_MAGBIO' => 'mbi', 'MBI03_g33876_MAGBIO' => 'mbi', 'MBI03_g36854_MAGBIO' => 'mbi', 'MBI17_g11997_MAGBIO' => 'mbi', 'MD03G1269000' => 'mdo', 'MD04G1179600' => 'mdo', 'MD11G1289800' => 'mdo', 'MD12G1194700' => 'mdo', 'MD13G1182100' => 'mdo', 'MD13G1182200' => 'mdo', 'MD16G1182600' => 'mdo', 'Medtr2g021400' => 'mtr', 'Medtr2g021470' => 'mtr', 'Medtr2g105810' => 'mtr', 'Medtr3g033580' => 'mtr', 'Medtr6g007970' => 'mtr', 'Medtr7g056330' => 'mtr', 'Medtr7g074290' => 'mtr', 'Medtr7g074380' => 'mtr', 'Medtr7g094550' => 'mtr', 'Medtr8g069995' => 'mtr', 'MELO3C014345.2' => 'cme', 'MELO3C021395.2' => 'cme', 'Migut.D00262' => 'egut', 'Migut.G00257' => 'egut', 'MSTRG.21575' => 'ama', 'MSTRG.3985' => 'ama', 'Nitab4.5_0000295g0140' => 'nta', 'Nitab4.5_0000732g0140' => 'nta', 'Nitab4.5_0003162g0020' => 'nta', 'Nitab4.5_0006180g0090' => 'nta', 'Nitab4.5_0006390g0010' => 'nta', 'Nitab4.5_0007392g0040' => 'nta', 'Nn1g02140' => 'nnu', 'Nn4g26168' => 'nnu', 'Nn5g26754' => 'nnu', 'Oeu001433.1' => 'oeu', 'Oeu010299.2' => 'oeu', 'Oeu011171.1' => 'oeu', 'Oeu037675.1' => 'oeu', 'Oeu038359.1' => 'oeu', 'Oeu063834.1' => 'oeu', 'Oeu063835.1' => 'oeu', 'Os05g0312000' => 'osa', 'Os07g0211101' => 'osa', 'Os07g0211200' => 'osa', 'Os07g0681500' => 'osa', 'Peaxi162Scf00095g01015' => 'pax', 'Peaxi162Scf00104g00329' => 'pax', 'Peaxi162Scf00161g00137' => 'pax', 'PGR004G1665' => 'pgr', 'PGR031G2937' => 'pgr', 'PGR119G2145' => 'pgr', 'PGSC0003DMG400004351' => 'stu', 'PGSC0003DMG400014625' => 'stu', 'PGSC0003DMG401000943' => 'stu', 'Phvul.001G148600' => 'pvu', 'Phvul.004G001700' => 'pvu', 'Phvul.006G154900' => 'pvu', 'Phvul.008G078200' => 'pvu', 'Phvul.011G136500' => 'pvu', 'Potri.002G215600' => 'ptr', 'Potri.008G201600' => 'ptr', 'Potri.014G138400' => 'ptr', 'Potri.016G142500' => 'ptr', 'Pp3c16_10580' => 'ppa', 'Pp3c5_25280' => 'ppa', 'Prupe.1G150000' => 'ppe', 'Prupe.1G150100' => 'ppe', 'Prupe.6G299600' => 'ppe', 'Prupe.8G245000' => 'ppe', 'Psat0s4927g0040' => 'psa', 'Psat1g052080' => 'psa', 'Psat1g183800' => 'psa', 'Psat3g113840' => 'psa', 'Psat3g126120' => 'psa', 'Psat3g126160' => 'psa', 'Psat3g158760' => 'psa', 'Psat3g158840' => 'psa', 'PSO170G2858' => 'pso', 'PSO339G0606' => 'pso', 'PSO384G4709' => 'pso', 'PSO407G0334' => 'pso', 'QL04p040276' => 'qlo', 'QL06p005458' => 'qlo', 'QL06p005472' => 'qlo', 'QL07p030546' => 'qlo', 'QL07p031519' => 'qlo', 'QL09p050949' => 'qlo', 'QL09p050966' => 'qlo', 'QL09p051067' => 'qlo', 'QL12p022706' => 'qlo', 'RcHm_v2.0_Chr2g0119601' => 'rch', 'RcHm_v2.0_Chr3g0459591' => 'rch', 'RcHm_v2.0_Chr4g0418521' => 'rch', 'RcHm_v2.0_Chr4g0418531' => 'rch', 'RcHm_v2.0_Chr4g0418541' => 'rch', 'RcHm_v2.0_Chr6g0291641' => 'rch', 'Rhsim01G0086300' => 'rsi', 'Rhsim01G0276300' => 'rsi', 'Rhsim01G0276500' => 'rsi', 'Rhsim04G0207700' => 'rsi', 'Rhsim05G0234500' => 'rsi', 'Rhsim13G0022400' => 'rsi', 'Sabra02G0167900' => 'sbr', 'Sabra04G0158500' => 'sbr', 'Sabra08G0159800' => 'sbr', 'Sabra10G0011500' => 'sbr', 'Sabra14G0104400' => 'sbr', 'SalBow2G2440' => 'sbo', 'SalBow4G2265' => 'sbo', 'Sc02g0000060' => 'sci', 'Sc05g0005020' => 'sci', 'Sc13g0003890' => 'sci', 'Sed0014865' => 'sed', 'Sed0017224' => 'sed', 'Sed0026391' => 'sed', 'SEGI_00063' => 'sgi', 'SEGI_10967' => 'sgi', 'SEGI_17510' => 'sgi', 'SEGI_24396' => 'sgi', 'SEGI_39719' => 'sgi', 'SEGI_41392' => 'sgi', 'SGA_v2.0_scaffold11G05794' => 'sas', 'SGA_v2.0_scaffold142G35607' => 'sas', 'SGA_v2.0_scaffold1G00447' => 'sas', 'SHI15388' => 'shi', 'SHI15394' => 'shi', 'SHI15396' => 'shi', 'SHI15399' => 'shi', 'SMO343G0151' => 'smo', 'SMO367G1118' => 'smo', 'Solyc01g080200.3' => 'sly', 'Solyc06g008960.3' => 'sly', 'Solyc09g064780.3' => 'sly', 'Sopen01g031980' => 'spe', 'Sopen06g003710' => 'spe', 'Sopen09g026460' => 'spe', 'Sp3g21240' => 'spa', 'Sp4g30030' => 'spa', 'TAR365G0022' => 'tar', 'TAR365G1023' => 'tar', 'TAR365G1253' => 'tar', 'TAR623G0078' => 'tar', 'TAR623G1721' => 'tar', 'TAR633G0959' => 'tar', 'THA.LOC104802225' => 'tha', 'THA.LOC104804769' => 'tha', 'THA.LOC104808660' => 'tha', 'THA.LOC104812792' => 'tha', 'Thecc.01G284000' => 'tca', 'Thecc.04G220600' => 'tca', 'Thecc.05G268900' => 'tca', 'Thecc.08G171100' => 'tca', 'Thhalv10001284m.g' => 'esa', 'Thhalv10019912m.g' => 'esa', 'TPR.G14189' => 'tpr', 'TPR.G18110' => 'tpr', 'TPR.G18130' => 'tpr', 'TPR.G18131' => 'tpr', 'TPR.G18140' => 'tpr', 'TPR.G24282' => 'tpr', 'TPR.G25221' => 'tpr', 'TPR.G29267' => 'tpr', 'TPR.G35315' => 'tpr', 'TPR.G36173' => 'tpr', 'TWI09G0794' => 'twi', 'TWI59G1348' => 'twi', 'TWI74G0430' => 'twi', 'unitig_26.g8940' => 'ugi', 'unitig_749.g13744' => 'ugi', 'unitig_749.g13745' => 'ugi', 'vmacro08269' => 'vma', 'vmacro14937' => 'vma', 'vmacro20401' => 'vma', 'VMungo0464G1349' => 'vmu', 'VMungo0540G0289' => 'vmu', 'VMungo1215G1590' => 'vmu', 'VMungo1309G0221' => 'vmu', 'VMungo1309G2815' => 'vmu', 'VMungo1383G0239' => 'vmu', 'VMungo1383G2910' => 'vmu', 'Zm00001eb095270' => 'zma', 'Zm00001eb095280' => 'zma', 'Zm00001eb111630' => 'zma', 'Zm00001eb237080' => 'zma', 'Zm00001eb273740' => 'zma', 'Zm00001eb285040' => 'zma', 'Zm00001eb330790' => 'zma', 'Zm00001eb337380' => 'zma' ) $gf_id = 'HOM05D001484' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001484' ) $data_identifier = 'HOM05D001484' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 2, 'aly' => (int) 2, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 22, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 7, 'hma' => (int) 2, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 7, 'mtr' => (int) 10, 'cme' => (int) 2, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 4, 'ppa' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 4, 'qlo' => (int) 9, 'rch' => (int) 6, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 10, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 7, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb337380' $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' => 'HOM05D001484', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p31500' => 'bna', 'A05p00020' => 'bna', 'A07p08820' => 'bna', 'Aa31LG4G3300' => 'aar', 'Aa31LG8G10030' => 'aar', 'Actinidia00731' => 'ach', 'Actinidia11473' => 'ach', 'Actinidia23469' => 'ach', 'Actinidia24318' => 'ach', 'Actinidia40196' => 'ach', 'Actinidia40197' => 'ach', 'Actinidia40198' => 'ach', 'Ah.08g212990' => 'amhyb', 'Ah.15g091720' => 'amhyb', 'AL3G38260' => 'aly', 'AL4G47710' => 'aly', 'Aqoxy2G00671' => 'aox', 'Aqoxy2G03236' => 'aox', 'arahy.Tifrunner.gnm1.ann1.05IDCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KR684' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATY3SJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK6QJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6APGL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IDT7Z9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM073U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ0R87' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LE7RV4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT4QRX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V5ENPK' => 'arhy', 'AT2G48110' => 'ath', 'AT3G23590' => 'ath', 'ATR0626G186' => 'atr', 'ATR1127G141' => 'atr', 'Atru.chr4.2583' => 'acertr', 'Atru.chr5.1358' => 'acertr', 'Atru.chr5.1359' => 'acertr', 'Atru.chr8.46' => 'acertr', 'AUR62002640' => 'cqu', 'AUR62030055' => 'cqu', 'AUR62033713' => 'cqu', 'AUR62033714' => 'cqu', 'AUR62036795' => 'cqu', 'AUR62039891' => 'cqu', 'BcaB02g08737' => 'bca', 'BcaB04g20441' => 'bca', 'BcaB06g26509' => 'bca', 'BcaB06g26510' => 'bca', 'BcaB06g26511' => 'bca', 'BcaB06g26512' => 'bca', 'BcaB06g26513' => 'bca', 'BcaC02g12564' => 'bca', 'BcaC02g12565' => 'bca', 'BcaC02g12794' => 'bca', 'BcaC02g12795' => 'bca', 'BcaC02g12796' => 'bca', 'BcaC06g35541' => 'bca', 'BNapus_Darmor_BZH_scaffold_188p00080' => 'bna', 'BNapus_Darmor_BZH_scaffold_188p00090' => 'bna', 'BolC1t03972H' => 'bol', 'BolC1t03973H' => 'bol', 'BolC4t21680H' => 'bol', 'BolC7t41863H' => 'bol', 'BolSC55t61227H' => 'bol', 'BolSC55t61228H' => 'bol', 'BraA01t03278Z' => 'bra', 'BraA05t18998Z' => 'bra', 'BraA07t28673Z' => 'bra', 'C01p40150' => 'bna', 'C05p12370' => 'bna', 'C07p13680' => 'bna', 'CAN.G1006.16' => 'can', 'CAN.G1006.17' => 'can', 'CAN.G1170.2' => 'can', 'CAN.G962.7' => 'can', 'CANSAT25G2179' => 'cansat', 'CANSAT78G1573' => 'cansat', 'CARHR099510' => 'chi', 'CARHR143510' => 'chi', 'Carub.0003s2380' => 'cru', 'Carub.0004s3082' => 'cru', 'Ca_00614_v3' => 'car', 'Ca_07801_v3' => 'car', 'Ca_08567_v3' => 'car', 'Ca_09571_v3' => 'car', 'CBR_g19290' => 'cbr', 'Cc01_g19770' => 'ccan', 'Cc03_g03030' => 'ccan', 'CDE07G0968' => 'cde', 'CDE09G1441' => 'cde', 'Cfa006103' => 'cfa', 'Cfa015573' => 'cfa', 'Cfa016988' => 'cfa', 'Ciclev10006738m.g' => 'ccl', 'Ciclev10010920m.g' => 'ccl', 'Ciclev10018517m.g' => 'ccl', 'CiPaw.01G159200' => 'cil', 'CiPaw.02G091000' => 'cil', 'CiPaw.02G091100' => 'cil', 'CiPaw.08G103100' => 'cil', 'CiPaw.09G224900' => 'cil', 'ClCG06G005740' => 'cla', 'ClCG07G000090' => 'cla', 'ClCG07G000100' => 'cla', 'COL.COLO4_09143' => 'col', 'COL.COLO4_25124' => 'col', 'Cpa.g.sc16.34' => 'cpa', 'Cpa.g.sc3504.1' => 'cpa', 'Cpa.g.sc60.37' => 'cpa', 'CsaV3_6G018520' => 'csa', 'CsaV3_6G036860' => 'csa', 'CSS0001072' => 'camsi', 'CSS0020208' => 'camsi', 'CSS0021253' => 'camsi', 'CSS0022190' => 'camsi', 'CSS0036150' => 'camsi', 'CSS0040442' => 'camsi', 'CSS0042300' => 'camsi', 'CSS0045298' => 'camsi', 'DCAR_012449' => 'dca', 'DCAR_018405' => 'dca', 'DCAR_024573' => 'dca', 'DCAR_030591' => 'dca', 'Dinv16926' => 'din', 'Dinv32963' => 'din', 'Dinv38382' => 'din', 'Dinv38383' => 'din', 'Duzib133G0974' => 'dzi', 'Duzib138G1867' => 'dzi', 'Duzib211G0420' => 'dzi', 'Duzib212G0930' => 'dzi', 'ECA234G1645' => 'eca', 'ECA247G3467' => 'eca', 'ECA248G1703' => 'eca', 'EL10Ac3g06327' => 'bvu', 'EL10Ac7g17204' => 'bvu', 'Eucgr.A00855' => 'egr', 'Eucgr.A00858' => 'egr', 'Eucgr.H01520' => 'egr', 'Eucgr.H03604' => 'egr', 'Eucgr.L03465' => 'egr', 'Eucgr.L03466' => 'egr', 'FAN01G0988' => 'fan', 'FAN02G3892' => 'fan', 'FAN05G3381' => 'fan', 'FAN07G0967' => 'fan', 'FAN07G1493' => 'fan', 'FAN08G3125' => 'fan', 'FAN09G0402' => 'fan', 'FAN12G2594' => 'fan', 'FAN12G3879' => 'fan', 'FAN14G1546' => 'fan', 'FAN15G3626' => 'fan', 'FAN17G0588' => 'fan', 'FAN17G0609' => 'fan', 'FAN18G2817' => 'fan', 'FAN19G1305' => 'fan', 'FAN20G1787' => 'fan', 'FAN22G0073' => 'fan', 'FAN22G0352' => 'fan', 'FAN22G0368' => 'fan', 'FAN22G2273' => 'fan', 'FAN24G1998' => 'fan', 'FAN27G1317' => 'fan', 'FvH4_2g23980' => 'fve', 'FvH4_4g14380' => 'fve', 'FvH4_4g14390' => 'fve', 'FvH4_6g09250' => 'fve', 'Glyma.03G151100' => 'gma', 'Glyma.04G122550' => 'gma', 'Glyma.05G001600' => 'gma', 'Glyma.09G270766' => 'gma', 'Glyma.09G270832' => 'gma', 'Glyma.13G209800' => 'gma', 'Glyma.15G102800' => 'gma', 'Glyma.18G218900' => 'gma', 'Glyma.19G001500' => 'gma', 'Glyma.19G153600' => 'gma', 'Gohir.A02G028600' => 'ghi', 'Gohir.A08G045000' => 'ghi', 'Gohir.A11G120500' => 'ghi', 'Gohir.A12G006200' => 'ghi', 'Gohir.A12G006250' => 'ghi', 'Gohir.D02G036300' => 'ghi', 'Gohir.D08G054700' => 'ghi', 'Gohir.D11G125600' => 'ghi', 'Gohir.D12G005700' => 'ghi', 'Gorai.004G055200' => 'gra', 'Gorai.005G040400' => 'gra', 'Gorai.007G134500' => 'gra', 'Gorai.008G005500' => 'gra', 'GSVIVG01011094001' => 'vvi', 'GSVIVG01017879001' => 'vvi', 'GSVIVG01025988001' => 'vvi', 'GSVIVG01029847001' => 'vvi', 'HanXRQChr10g0282901' => 'han', 'HanXRQChr10g0310371' => 'han', 'HanXRQChr10g0315041' => 'han', 'HanXRQChr11g0327651' => 'han', 'HanXRQChr12g0359391' => 'han', 'Haze_00972' => 'cav', 'Haze_00973' => 'cav', 'Haze_00974' => 'cav', 'Haze_04747' => 'cav', 'Haze_04749' => 'cav', 'Haze_04750' => 'cav', 'Haze_21217' => 'cav', 'Hma1.2p1_1037F.1_g250680' => 'hma', 'Hma1.2p1_1644F.1_g295320' => 'hma', 'HPP92_011322' => 'vpl', 'HPP92_011323' => 'vpl', 'HPP92_011324' => 'vpl', 'HPP92_011325' => 'vpl', 'HPP92_011326' => 'vpl', 'Hund12205' => 'sun', 'Hund17957' => 'sun', 'Lalb_Chr06g0176771' => 'lal', 'Lalb_Chr18g0056021' => 'lal', 'Lalb_Chr18g0056031' => 'lal', 'Lalb_Chr18g0056041' => 'lal', 'Lalb_Chr20g0107751' => 'lal', 'Lalb_Chr20g0118371' => 'lal', 'Lj1g0010239' => 'lja', 'Lj1g0017101' => 'lja', 'Lj2A1178G40' => 'lonja', 'Lj2A54G84' => 'lonja', 'Lj2g0015248' => 'lja', 'Lj3A761T51' => 'lonja', 'Lj6g0018116' => 'lja', 'Lsat_1_v5_gn_4_136040' => 'lsa', 'Lsat_1_v5_gn_5_187461' => 'lsa', 'Lsat_1_v5_gn_5_77001' => 'lsa', 'Lsat_1_v5_gn_9_4461' => 'lsa', 'Manes.01G210100' => 'mes', 'Manes.03G185600' => 'mes', 'Manes.05G073300' => 'mes', 'Manes.09G120300' => 'mes', 'Manes.15G022100' => 'mes', 'Mapoly0096s0053' => 'mpo', 'MBI03_g14058_MAGBIO' => 'mbi', 'MBI03_g33876_MAGBIO' => 'mbi', 'MBI03_g36854_MAGBIO' => 'mbi', 'MBI17_g11997_MAGBIO' => 'mbi', 'MD03G1269000' => 'mdo', 'MD04G1179600' => 'mdo', 'MD11G1289800' => 'mdo', 'MD12G1194700' => 'mdo', 'MD13G1182100' => 'mdo', 'MD13G1182200' => 'mdo', 'MD16G1182600' => 'mdo', 'Medtr2g021400' => 'mtr', 'Medtr2g021470' => 'mtr', 'Medtr2g105810' => 'mtr', 'Medtr3g033580' => 'mtr', 'Medtr6g007970' => 'mtr', 'Medtr7g056330' => 'mtr', 'Medtr7g074290' => 'mtr', 'Medtr7g074380' => 'mtr', 'Medtr7g094550' => 'mtr', 'Medtr8g069995' => 'mtr', 'MELO3C014345.2' => 'cme', 'MELO3C021395.2' => 'cme', 'Migut.D00262' => 'egut', 'Migut.G00257' => 'egut', 'MSTRG.21575' => 'ama', 'MSTRG.3985' => 'ama', 'Nitab4.5_0000295g0140' => 'nta', 'Nitab4.5_0000732g0140' => 'nta', 'Nitab4.5_0003162g0020' => 'nta', 'Nitab4.5_0006180g0090' => 'nta', 'Nitab4.5_0006390g0010' => 'nta', 'Nitab4.5_0007392g0040' => 'nta', 'Nn1g02140' => 'nnu', 'Nn4g26168' => 'nnu', 'Nn5g26754' => 'nnu', 'Oeu001433.1' => 'oeu', 'Oeu010299.2' => 'oeu', 'Oeu011171.1' => 'oeu', 'Oeu037675.1' => 'oeu', 'Oeu038359.1' => 'oeu', 'Oeu063834.1' => 'oeu', 'Oeu063835.1' => 'oeu', 'Os05g0312000' => 'osa', 'Os07g0211101' => 'osa', 'Os07g0211200' => 'osa', 'Os07g0681500' => 'osa', 'Peaxi162Scf00095g01015' => 'pax', 'Peaxi162Scf00104g00329' => 'pax', 'Peaxi162Scf00161g00137' => 'pax', 'PGR004G1665' => 'pgr', 'PGR031G2937' => 'pgr', 'PGR119G2145' => 'pgr', 'PGSC0003DMG400004351' => 'stu', 'PGSC0003DMG400014625' => 'stu', 'PGSC0003DMG401000943' => 'stu', 'Phvul.001G148600' => 'pvu', 'Phvul.004G001700' => 'pvu', 'Phvul.006G154900' => 'pvu', 'Phvul.008G078200' => 'pvu', 'Phvul.011G136500' => 'pvu', 'Potri.002G215600' => 'ptr', 'Potri.008G201600' => 'ptr', 'Potri.014G138400' => 'ptr', 'Potri.016G142500' => 'ptr', 'Pp3c16_10580' => 'ppa', 'Pp3c5_25280' => 'ppa', 'Prupe.1G150000' => 'ppe', 'Prupe.1G150100' => 'ppe', 'Prupe.6G299600' => 'ppe', 'Prupe.8G245000' => 'ppe', 'Psat0s4927g0040' => 'psa', 'Psat1g052080' => 'psa', 'Psat1g183800' => 'psa', 'Psat3g113840' => 'psa', 'Psat3g126120' => 'psa', 'Psat3g126160' => 'psa', 'Psat3g158760' => 'psa', 'Psat3g158840' => 'psa', 'PSO170G2858' => 'pso', 'PSO339G0606' => 'pso', 'PSO384G4709' => 'pso', 'PSO407G0334' => 'pso', 'QL04p040276' => 'qlo', 'QL06p005458' => 'qlo', 'QL06p005472' => 'qlo', 'QL07p030546' => 'qlo', 'QL07p031519' => 'qlo', 'QL09p050949' => 'qlo', 'QL09p050966' => 'qlo', 'QL09p051067' => 'qlo', 'QL12p022706' => 'qlo', 'RcHm_v2.0_Chr2g0119601' => 'rch', 'RcHm_v2.0_Chr3g0459591' => 'rch', 'RcHm_v2.0_Chr4g0418521' => 'rch', 'RcHm_v2.0_Chr4g0418531' => 'rch', 'RcHm_v2.0_Chr4g0418541' => 'rch', 'RcHm_v2.0_Chr6g0291641' => 'rch', 'Rhsim01G0086300' => 'rsi', 'Rhsim01G0276300' => 'rsi', 'Rhsim01G0276500' => 'rsi', 'Rhsim04G0207700' => 'rsi', 'Rhsim05G0234500' => 'rsi', 'Rhsim13G0022400' => 'rsi', 'Sabra02G0167900' => 'sbr', 'Sabra04G0158500' => 'sbr', 'Sabra08G0159800' => 'sbr', 'Sabra10G0011500' => 'sbr', 'Sabra14G0104400' => 'sbr', 'SalBow2G2440' => 'sbo', 'SalBow4G2265' => 'sbo', 'Sc02g0000060' => 'sci', 'Sc05g0005020' => 'sci', 'Sc13g0003890' => 'sci', 'Sed0014865' => 'sed', 'Sed0017224' => 'sed', 'Sed0026391' => 'sed', 'SEGI_00063' => 'sgi', 'SEGI_10967' => 'sgi', 'SEGI_17510' => 'sgi', 'SEGI_24396' => 'sgi', 'SEGI_39719' => 'sgi', 'SEGI_41392' => 'sgi', 'SGA_v2.0_scaffold11G05794' => 'sas', 'SGA_v2.0_scaffold142G35607' => 'sas', 'SGA_v2.0_scaffold1G00447' => 'sas', 'SHI15388' => 'shi', 'SHI15394' => 'shi', 'SHI15396' => 'shi', 'SHI15399' => 'shi', 'SMO343G0151' => 'smo', 'SMO367G1118' => 'smo', 'Solyc01g080200.3' => 'sly', 'Solyc06g008960.3' => 'sly', 'Solyc09g064780.3' => 'sly', 'Sopen01g031980' => 'spe', 'Sopen06g003710' => 'spe', 'Sopen09g026460' => 'spe', 'Sp3g21240' => 'spa', 'Sp4g30030' => 'spa', 'TAR365G0022' => 'tar', 'TAR365G1023' => 'tar', 'TAR365G1253' => 'tar', 'TAR623G0078' => 'tar', 'TAR623G1721' => 'tar', 'TAR633G0959' => 'tar', 'THA.LOC104802225' => 'tha', 'THA.LOC104804769' => 'tha', 'THA.LOC104808660' => 'tha', 'THA.LOC104812792' => 'tha', 'Thecc.01G284000' => 'tca', 'Thecc.04G220600' => 'tca', 'Thecc.05G268900' => 'tca', 'Thecc.08G171100' => 'tca', 'Thhalv10001284m.g' => 'esa', 'Thhalv10019912m.g' => 'esa', 'TPR.G14189' => 'tpr', 'TPR.G18110' => 'tpr', 'TPR.G18130' => 'tpr', 'TPR.G18131' => 'tpr', 'TPR.G18140' => 'tpr', 'TPR.G24282' => 'tpr', 'TPR.G25221' => 'tpr', 'TPR.G29267' => 'tpr', 'TPR.G35315' => 'tpr', 'TPR.G36173' => 'tpr', 'TWI09G0794' => 'twi', 'TWI59G1348' => 'twi', 'TWI74G0430' => 'twi', 'unitig_26.g8940' => 'ugi', 'unitig_749.g13744' => 'ugi', 'unitig_749.g13745' => 'ugi', 'vmacro08269' => 'vma', 'vmacro14937' => 'vma', 'vmacro20401' => 'vma', 'VMungo0464G1349' => 'vmu', 'VMungo0540G0289' => 'vmu', 'VMungo1215G1590' => 'vmu', 'VMungo1309G0221' => 'vmu', 'VMungo1309G2815' => 'vmu', 'VMungo1383G0239' => 'vmu', 'VMungo1383G2910' => 'vmu', 'Zm00001eb095270' => 'zma', 'Zm00001eb095280' => 'zma', 'Zm00001eb111630' => 'zma', 'Zm00001eb237080' => 'zma', 'Zm00001eb273740' => 'zma', 'Zm00001eb285040' => 'zma', 'Zm00001eb330790' => 'zma', 'Zm00001eb337380' => 'zma' ), 'gf_id' => 'HOM05D001484', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001484' ), 'data_identifier' => 'HOM05D001484', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001484', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p31500' => 'bna', 'A05p00020' => 'bna', 'A07p08820' => 'bna', 'Aa31LG4G3300' => 'aar', 'Aa31LG8G10030' => 'aar', 'Actinidia00731' => 'ach', 'Actinidia11473' => 'ach', 'Actinidia23469' => 'ach', 'Actinidia24318' => 'ach', 'Actinidia40196' => 'ach', 'Actinidia40197' => 'ach', 'Actinidia40198' => 'ach', 'Ah.08g212990' => 'amhyb', 'Ah.15g091720' => 'amhyb', 'AL3G38260' => 'aly', 'AL4G47710' => 'aly', 'Aqoxy2G00671' => 'aox', 'Aqoxy2G03236' => 'aox', 'arahy.Tifrunner.gnm1.ann1.05IDCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KR684' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATY3SJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK6QJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6APGL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IDT7Z9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM073U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ0R87' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LE7RV4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT4QRX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V5ENPK' => 'arhy', 'AT2G48110' => 'ath', 'AT3G23590' => 'ath', 'ATR0626G186' => 'atr', 'ATR1127G141' => 'atr', 'Atru.chr4.2583' => 'acertr', 'Atru.chr5.1358' => 'acertr', 'Atru.chr5.1359' => 'acertr', 'Atru.chr8.46' => 'acertr', 'AUR62002640' => 'cqu', 'AUR62030055' => 'cqu', 'AUR62033713' => 'cqu', 'AUR62033714' => 'cqu', 'AUR62036795' => 'cqu', 'AUR62039891' => 'cqu', 'BcaB02g08737' => 'bca', 'BcaB04g20441' => 'bca', 'BcaB06g26509' => 'bca', 'BcaB06g26510' => 'bca', 'BcaB06g26511' => 'bca', 'BcaB06g26512' => 'bca', 'BcaB06g26513' => 'bca', 'BcaC02g12564' => 'bca', 'BcaC02g12565' => 'bca', 'BcaC02g12794' => 'bca', 'BcaC02g12795' => 'bca', 'BcaC02g12796' => 'bca', 'BcaC06g35541' => 'bca', 'BNapus_Darmor_BZH_scaffold_188p00080' => 'bna', 'BNapus_Darmor_BZH_scaffold_188p00090' => 'bna', 'BolC1t03972H' => 'bol', 'BolC1t03973H' => 'bol', 'BolC4t21680H' => 'bol', 'BolC7t41863H' => 'bol', 'BolSC55t61227H' => 'bol', 'BolSC55t61228H' => 'bol', 'BraA01t03278Z' => 'bra', 'BraA05t18998Z' => 'bra', 'BraA07t28673Z' => 'bra', 'C01p40150' => 'bna', 'C05p12370' => 'bna', 'C07p13680' => 'bna', 'CAN.G1006.16' => 'can', 'CAN.G1006.17' => 'can', 'CAN.G1170.2' => 'can', 'CAN.G962.7' => 'can', 'CANSAT25G2179' => 'cansat', 'CANSAT78G1573' => 'cansat', 'CARHR099510' => 'chi', 'CARHR143510' => 'chi', 'Carub.0003s2380' => 'cru', 'Carub.0004s3082' => 'cru', 'Ca_00614_v3' => 'car', 'Ca_07801_v3' => 'car', 'Ca_08567_v3' => 'car', 'Ca_09571_v3' => 'car', 'CBR_g19290' => 'cbr', 'Cc01_g19770' => 'ccan', 'Cc03_g03030' => 'ccan', 'CDE07G0968' => 'cde', 'CDE09G1441' => 'cde', 'Cfa006103' => 'cfa', 'Cfa015573' => 'cfa', 'Cfa016988' => 'cfa', 'Ciclev10006738m.g' => 'ccl', 'Ciclev10010920m.g' => 'ccl', 'Ciclev10018517m.g' => 'ccl', 'CiPaw.01G159200' => 'cil', 'CiPaw.02G091000' => 'cil', 'CiPaw.02G091100' => 'cil', 'CiPaw.08G103100' => 'cil', 'CiPaw.09G224900' => 'cil', 'ClCG06G005740' => 'cla', 'ClCG07G000090' => 'cla', 'ClCG07G000100' => 'cla', 'COL.COLO4_09143' => 'col', 'COL.COLO4_25124' => 'col', 'Cpa.g.sc16.34' => 'cpa', 'Cpa.g.sc3504.1' => 'cpa', 'Cpa.g.sc60.37' => 'cpa', 'CsaV3_6G018520' => 'csa', 'CsaV3_6G036860' => 'csa', 'CSS0001072' => 'camsi', 'CSS0020208' => 'camsi', 'CSS0021253' => 'camsi', 'CSS0022190' => 'camsi', 'CSS0036150' => 'camsi', 'CSS0040442' => 'camsi', 'CSS0042300' => 'camsi', 'CSS0045298' => 'camsi', 'DCAR_012449' => 'dca', 'DCAR_018405' => 'dca', 'DCAR_024573' => 'dca', 'DCAR_030591' => 'dca', 'Dinv16926' => 'din', 'Dinv32963' => 'din', 'Dinv38382' => 'din', 'Dinv38383' => 'din', 'Duzib133G0974' => 'dzi', 'Duzib138G1867' => 'dzi', 'Duzib211G0420' => 'dzi', 'Duzib212G0930' => 'dzi', 'ECA234G1645' => 'eca', 'ECA247G3467' => 'eca', 'ECA248G1703' => 'eca', 'EL10Ac3g06327' => 'bvu', 'EL10Ac7g17204' => 'bvu', 'Eucgr.A00855' => 'egr', 'Eucgr.A00858' => 'egr', 'Eucgr.H01520' => 'egr', 'Eucgr.H03604' => 'egr', 'Eucgr.L03465' => 'egr', 'Eucgr.L03466' => 'egr', 'FAN01G0988' => 'fan', 'FAN02G3892' => 'fan', 'FAN05G3381' => 'fan', 'FAN07G0967' => 'fan', 'FAN07G1493' => 'fan', 'FAN08G3125' => 'fan', 'FAN09G0402' => 'fan', 'FAN12G2594' => 'fan', 'FAN12G3879' => 'fan', 'FAN14G1546' => 'fan', 'FAN15G3626' => 'fan', 'FAN17G0588' => 'fan', 'FAN17G0609' => 'fan', 'FAN18G2817' => 'fan', 'FAN19G1305' => 'fan', 'FAN20G1787' => 'fan', 'FAN22G0073' => 'fan', 'FAN22G0352' => 'fan', 'FAN22G0368' => 'fan', 'FAN22G2273' => 'fan', 'FAN24G1998' => 'fan', 'FAN27G1317' => 'fan', 'FvH4_2g23980' => 'fve', 'FvH4_4g14380' => 'fve', 'FvH4_4g14390' => 'fve', 'FvH4_6g09250' => 'fve', 'Glyma.03G151100' => 'gma', 'Glyma.04G122550' => 'gma', 'Glyma.05G001600' => 'gma', 'Glyma.09G270766' => 'gma', 'Glyma.09G270832' => 'gma', 'Glyma.13G209800' => 'gma', 'Glyma.15G102800' => 'gma', 'Glyma.18G218900' => 'gma', 'Glyma.19G001500' => 'gma', 'Glyma.19G153600' => 'gma', 'Gohir.A02G028600' => 'ghi', 'Gohir.A08G045000' => 'ghi', 'Gohir.A11G120500' => 'ghi', 'Gohir.A12G006200' => 'ghi', 'Gohir.A12G006250' => 'ghi', 'Gohir.D02G036300' => 'ghi', 'Gohir.D08G054700' => 'ghi', 'Gohir.D11G125600' => 'ghi', 'Gohir.D12G005700' => 'ghi', 'Gorai.004G055200' => 'gra', 'Gorai.005G040400' => 'gra', 'Gorai.007G134500' => 'gra', 'Gorai.008G005500' => 'gra', 'GSVIVG01011094001' => 'vvi', 'GSVIVG01017879001' => 'vvi', 'GSVIVG01025988001' => 'vvi', 'GSVIVG01029847001' => 'vvi', 'HanXRQChr10g0282901' => 'han', 'HanXRQChr10g0310371' => 'han', 'HanXRQChr10g0315041' => 'han', 'HanXRQChr11g0327651' => 'han', 'HanXRQChr12g0359391' => 'han', 'Haze_00972' => 'cav', 'Haze_00973' => 'cav', 'Haze_00974' => 'cav', 'Haze_04747' => 'cav', 'Haze_04749' => 'cav', 'Haze_04750' => 'cav', 'Haze_21217' => 'cav', 'Hma1.2p1_1037F.1_g250680' => 'hma', 'Hma1.2p1_1644F.1_g295320' => 'hma', 'HPP92_011322' => 'vpl', 'HPP92_011323' => 'vpl', 'HPP92_011324' => 'vpl', 'HPP92_011325' => 'vpl', 'HPP92_011326' => 'vpl', 'Hund12205' => 'sun', 'Hund17957' => 'sun', 'Lalb_Chr06g0176771' => 'lal', 'Lalb_Chr18g0056021' => 'lal', 'Lalb_Chr18g0056031' => 'lal', 'Lalb_Chr18g0056041' => 'lal', 'Lalb_Chr20g0107751' => 'lal', 'Lalb_Chr20g0118371' => 'lal', 'Lj1g0010239' => 'lja', 'Lj1g0017101' => 'lja', 'Lj2A1178G40' => 'lonja', 'Lj2A54G84' => 'lonja', 'Lj2g0015248' => 'lja', 'Lj3A761T51' => 'lonja', 'Lj6g0018116' => 'lja', 'Lsat_1_v5_gn_4_136040' => 'lsa', 'Lsat_1_v5_gn_5_187461' => 'lsa', 'Lsat_1_v5_gn_5_77001' => 'lsa', 'Lsat_1_v5_gn_9_4461' => 'lsa', 'Manes.01G210100' => 'mes', 'Manes.03G185600' => 'mes', 'Manes.05G073300' => 'mes', 'Manes.09G120300' => 'mes', 'Manes.15G022100' => 'mes', 'Mapoly0096s0053' => 'mpo', 'MBI03_g14058_MAGBIO' => 'mbi', 'MBI03_g33876_MAGBIO' => 'mbi', 'MBI03_g36854_MAGBIO' => 'mbi', 'MBI17_g11997_MAGBIO' => 'mbi', 'MD03G1269000' => 'mdo', 'MD04G1179600' => 'mdo', 'MD11G1289800' => 'mdo', 'MD12G1194700' => 'mdo', 'MD13G1182100' => 'mdo', 'MD13G1182200' => 'mdo', 'MD16G1182600' => 'mdo', 'Medtr2g021400' => 'mtr', 'Medtr2g021470' => 'mtr', 'Medtr2g105810' => 'mtr', 'Medtr3g033580' => 'mtr', 'Medtr6g007970' => 'mtr', 'Medtr7g056330' => 'mtr', 'Medtr7g074290' => 'mtr', 'Medtr7g074380' => 'mtr', 'Medtr7g094550' => 'mtr', 'Medtr8g069995' => 'mtr', 'MELO3C014345.2' => 'cme', 'MELO3C021395.2' => 'cme', 'Migut.D00262' => 'egut', 'Migut.G00257' => 'egut', 'MSTRG.21575' => 'ama', 'MSTRG.3985' => 'ama', 'Nitab4.5_0000295g0140' => 'nta', 'Nitab4.5_0000732g0140' => 'nta', 'Nitab4.5_0003162g0020' => 'nta', 'Nitab4.5_0006180g0090' => 'nta', 'Nitab4.5_0006390g0010' => 'nta', 'Nitab4.5_0007392g0040' => 'nta', 'Nn1g02140' => 'nnu', 'Nn4g26168' => 'nnu', 'Nn5g26754' => 'nnu', 'Oeu001433.1' => 'oeu', 'Oeu010299.2' => 'oeu', 'Oeu011171.1' => 'oeu', 'Oeu037675.1' => 'oeu', 'Oeu038359.1' => 'oeu', 'Oeu063834.1' => 'oeu', 'Oeu063835.1' => 'oeu', 'Os05g0312000' => 'osa', 'Os07g0211101' => 'osa', 'Os07g0211200' => 'osa', 'Os07g0681500' => 'osa', 'Peaxi162Scf00095g01015' => 'pax', 'Peaxi162Scf00104g00329' => 'pax', 'Peaxi162Scf00161g00137' => 'pax', 'PGR004G1665' => 'pgr', 'PGR031G2937' => 'pgr', 'PGR119G2145' => 'pgr', 'PGSC0003DMG400004351' => 'stu', 'PGSC0003DMG400014625' => 'stu', 'PGSC0003DMG401000943' => 'stu', 'Phvul.001G148600' => 'pvu', 'Phvul.004G001700' => 'pvu', 'Phvul.006G154900' => 'pvu', 'Phvul.008G078200' => 'pvu', 'Phvul.011G136500' => 'pvu', 'Potri.002G215600' => 'ptr', 'Potri.008G201600' => 'ptr', 'Potri.014G138400' => 'ptr', 'Potri.016G142500' => 'ptr', 'Pp3c16_10580' => 'ppa', 'Pp3c5_25280' => 'ppa', 'Prupe.1G150000' => 'ppe', 'Prupe.1G150100' => 'ppe', 'Prupe.6G299600' => 'ppe', 'Prupe.8G245000' => 'ppe', 'Psat0s4927g0040' => 'psa', 'Psat1g052080' => 'psa', 'Psat1g183800' => 'psa', 'Psat3g113840' => 'psa', 'Psat3g126120' => 'psa', 'Psat3g126160' => 'psa', 'Psat3g158760' => 'psa', 'Psat3g158840' => 'psa', 'PSO170G2858' => 'pso', 'PSO339G0606' => 'pso', 'PSO384G4709' => 'pso', 'PSO407G0334' => 'pso', 'QL04p040276' => 'qlo', 'QL06p005458' => 'qlo', 'QL06p005472' => 'qlo', 'QL07p030546' => 'qlo', 'QL07p031519' => 'qlo', 'QL09p050949' => 'qlo', 'QL09p050966' => 'qlo', 'QL09p051067' => 'qlo', 'QL12p022706' => 'qlo', 'RcHm_v2.0_Chr2g0119601' => 'rch', 'RcHm_v2.0_Chr3g0459591' => 'rch', 'RcHm_v2.0_Chr4g0418521' => 'rch', 'RcHm_v2.0_Chr4g0418531' => 'rch', 'RcHm_v2.0_Chr4g0418541' => 'rch', 'RcHm_v2.0_Chr6g0291641' => 'rch', 'Rhsim01G0086300' => 'rsi', 'Rhsim01G0276300' => 'rsi', 'Rhsim01G0276500' => 'rsi', 'Rhsim04G0207700' => 'rsi', 'Rhsim05G0234500' => 'rsi', 'Rhsim13G0022400' => 'rsi', 'Sabra02G0167900' => 'sbr', 'Sabra04G0158500' => 'sbr', 'Sabra08G0159800' => 'sbr', 'Sabra10G0011500' => 'sbr', 'Sabra14G0104400' => 'sbr', 'SalBow2G2440' => 'sbo', 'SalBow4G2265' => 'sbo', 'Sc02g0000060' => 'sci', 'Sc05g0005020' => 'sci', 'Sc13g0003890' => 'sci', 'Sed0014865' => 'sed', 'Sed0017224' => 'sed', 'Sed0026391' => 'sed', 'SEGI_00063' => 'sgi', 'SEGI_10967' => 'sgi', 'SEGI_17510' => 'sgi', 'SEGI_24396' => 'sgi', 'SEGI_39719' => 'sgi', 'SEGI_41392' => 'sgi', 'SGA_v2.0_scaffold11G05794' => 'sas', 'SGA_v2.0_scaffold142G35607' => 'sas', 'SGA_v2.0_scaffold1G00447' => 'sas', 'SHI15388' => 'shi', 'SHI15394' => 'shi', 'SHI15396' => 'shi', 'SHI15399' => 'shi', 'SMO343G0151' => 'smo', 'SMO367G1118' => 'smo', 'Solyc01g080200.3' => 'sly', 'Solyc06g008960.3' => 'sly', 'Solyc09g064780.3' => 'sly', 'Sopen01g031980' => 'spe', 'Sopen06g003710' => 'spe', 'Sopen09g026460' => 'spe', 'Sp3g21240' => 'spa', 'Sp4g30030' => 'spa', 'TAR365G0022' => 'tar', 'TAR365G1023' => 'tar', 'TAR365G1253' => 'tar', 'TAR623G0078' => 'tar', 'TAR623G1721' => 'tar', 'TAR633G0959' => 'tar', 'THA.LOC104802225' => 'tha', 'THA.LOC104804769' => 'tha', 'THA.LOC104808660' => 'tha', 'THA.LOC104812792' => 'tha', 'Thecc.01G284000' => 'tca', 'Thecc.04G220600' => 'tca', 'Thecc.05G268900' => 'tca', 'Thecc.08G171100' => 'tca', 'Thhalv10001284m.g' => 'esa', 'Thhalv10019912m.g' => 'esa', 'TPR.G14189' => 'tpr', 'TPR.G18110' => 'tpr', 'TPR.G18130' => 'tpr', 'TPR.G18131' => 'tpr', 'TPR.G18140' => 'tpr', 'TPR.G24282' => 'tpr', 'TPR.G25221' => 'tpr', 'TPR.G29267' => 'tpr', 'TPR.G35315' => 'tpr', 'TPR.G36173' => 'tpr', 'TWI09G0794' => 'twi', 'TWI59G1348' => 'twi', 'TWI74G0430' => 'twi', 'unitig_26.g8940' => 'ugi', 'unitig_749.g13744' => 'ugi', 'unitig_749.g13745' => 'ugi', 'vmacro08269' => 'vma', 'vmacro14937' => 'vma', 'vmacro20401' => 'vma', 'VMungo0464G1349' => 'vmu', 'VMungo0540G0289' => 'vmu', 'VMungo1215G1590' => 'vmu', 'VMungo1309G0221' => 'vmu', 'VMungo1309G2815' => 'vmu', 'VMungo1383G0239' => 'vmu', 'VMungo1383G2910' => 'vmu', 'Zm00001eb095270' => 'zma', 'Zm00001eb095280' => 'zma', 'Zm00001eb111630' => 'zma', 'Zm00001eb237080' => 'zma', 'Zm00001eb273740' => 'zma', 'Zm00001eb285040' => 'zma', 'Zm00001eb330790' => 'zma', 'Zm00001eb337380' => 'zma' ) $gf_id = 'HOM05D001484' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001484' ) $data_identifier = 'HOM05D001484' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 2, 'aly' => (int) 2, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 22, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 7, 'hma' => (int) 2, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 7, 'mtr' => (int) 10, 'cme' => (int) 2, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 4, 'ppa' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 4, 'qlo' => (int) 9, 'rch' => (int) 6, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 10, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 7, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb337380' $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' => 'HOM05D001484', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p31500' => 'bna', 'A05p00020' => 'bna', 'A07p08820' => 'bna', 'Aa31LG4G3300' => 'aar', 'Aa31LG8G10030' => 'aar', 'Actinidia00731' => 'ach', 'Actinidia11473' => 'ach', 'Actinidia23469' => 'ach', 'Actinidia24318' => 'ach', 'Actinidia40196' => 'ach', 'Actinidia40197' => 'ach', 'Actinidia40198' => 'ach', 'Ah.08g212990' => 'amhyb', 'Ah.15g091720' => 'amhyb', 'AL3G38260' => 'aly', 'AL4G47710' => 'aly', 'Aqoxy2G00671' => 'aox', 'Aqoxy2G03236' => 'aox', 'arahy.Tifrunner.gnm1.ann1.05IDCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KR684' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATY3SJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK6QJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6APGL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IDT7Z9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM073U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ0R87' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LE7RV4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT4QRX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V5ENPK' => 'arhy', 'AT2G48110' => 'ath', 'AT3G23590' => 'ath', 'ATR0626G186' => 'atr', 'ATR1127G141' => 'atr', 'Atru.chr4.2583' => 'acertr', 'Atru.chr5.1358' => 'acertr', 'Atru.chr5.1359' => 'acertr', 'Atru.chr8.46' => 'acertr', 'AUR62002640' => 'cqu', 'AUR62030055' => 'cqu', 'AUR62033713' => 'cqu', 'AUR62033714' => 'cqu', 'AUR62036795' => 'cqu', 'AUR62039891' => 'cqu', 'BcaB02g08737' => 'bca', 'BcaB04g20441' => 'bca', 'BcaB06g26509' => 'bca', 'BcaB06g26510' => 'bca', 'BcaB06g26511' => 'bca', 'BcaB06g26512' => 'bca', 'BcaB06g26513' => 'bca', 'BcaC02g12564' => 'bca', 'BcaC02g12565' => 'bca', 'BcaC02g12794' => 'bca', 'BcaC02g12795' => 'bca', 'BcaC02g12796' => 'bca', 'BcaC06g35541' => 'bca', 'BNapus_Darmor_BZH_scaffold_188p00080' => 'bna', 'BNapus_Darmor_BZH_scaffold_188p00090' => 'bna', 'BolC1t03972H' => 'bol', 'BolC1t03973H' => 'bol', 'BolC4t21680H' => 'bol', 'BolC7t41863H' => 'bol', 'BolSC55t61227H' => 'bol', 'BolSC55t61228H' => 'bol', 'BraA01t03278Z' => 'bra', 'BraA05t18998Z' => 'bra', 'BraA07t28673Z' => 'bra', 'C01p40150' => 'bna', 'C05p12370' => 'bna', 'C07p13680' => 'bna', 'CAN.G1006.16' => 'can', 'CAN.G1006.17' => 'can', 'CAN.G1170.2' => 'can', 'CAN.G962.7' => 'can', 'CANSAT25G2179' => 'cansat', 'CANSAT78G1573' => 'cansat', 'CARHR099510' => 'chi', 'CARHR143510' => 'chi', 'Carub.0003s2380' => 'cru', 'Carub.0004s3082' => 'cru', 'Ca_00614_v3' => 'car', 'Ca_07801_v3' => 'car', 'Ca_08567_v3' => 'car', 'Ca_09571_v3' => 'car', 'CBR_g19290' => 'cbr', 'Cc01_g19770' => 'ccan', 'Cc03_g03030' => 'ccan', 'CDE07G0968' => 'cde', 'CDE09G1441' => 'cde', 'Cfa006103' => 'cfa', 'Cfa015573' => 'cfa', 'Cfa016988' => 'cfa', 'Ciclev10006738m.g' => 'ccl', 'Ciclev10010920m.g' => 'ccl', 'Ciclev10018517m.g' => 'ccl', 'CiPaw.01G159200' => 'cil', 'CiPaw.02G091000' => 'cil', 'CiPaw.02G091100' => 'cil', 'CiPaw.08G103100' => 'cil', 'CiPaw.09G224900' => 'cil', 'ClCG06G005740' => 'cla', 'ClCG07G000090' => 'cla', 'ClCG07G000100' => 'cla', 'COL.COLO4_09143' => 'col', 'COL.COLO4_25124' => 'col', 'Cpa.g.sc16.34' => 'cpa', 'Cpa.g.sc3504.1' => 'cpa', 'Cpa.g.sc60.37' => 'cpa', 'CsaV3_6G018520' => 'csa', 'CsaV3_6G036860' => 'csa', 'CSS0001072' => 'camsi', 'CSS0020208' => 'camsi', 'CSS0021253' => 'camsi', 'CSS0022190' => 'camsi', 'CSS0036150' => 'camsi', 'CSS0040442' => 'camsi', 'CSS0042300' => 'camsi', 'CSS0045298' => 'camsi', 'DCAR_012449' => 'dca', 'DCAR_018405' => 'dca', 'DCAR_024573' => 'dca', 'DCAR_030591' => 'dca', 'Dinv16926' => 'din', 'Dinv32963' => 'din', 'Dinv38382' => 'din', 'Dinv38383' => 'din', 'Duzib133G0974' => 'dzi', 'Duzib138G1867' => 'dzi', 'Duzib211G0420' => 'dzi', 'Duzib212G0930' => 'dzi', 'ECA234G1645' => 'eca', 'ECA247G3467' => 'eca', 'ECA248G1703' => 'eca', 'EL10Ac3g06327' => 'bvu', 'EL10Ac7g17204' => 'bvu', 'Eucgr.A00855' => 'egr', 'Eucgr.A00858' => 'egr', 'Eucgr.H01520' => 'egr', 'Eucgr.H03604' => 'egr', 'Eucgr.L03465' => 'egr', 'Eucgr.L03466' => 'egr', 'FAN01G0988' => 'fan', 'FAN02G3892' => 'fan', 'FAN05G3381' => 'fan', 'FAN07G0967' => 'fan', 'FAN07G1493' => 'fan', 'FAN08G3125' => 'fan', 'FAN09G0402' => 'fan', 'FAN12G2594' => 'fan', 'FAN12G3879' => 'fan', 'FAN14G1546' => 'fan', 'FAN15G3626' => 'fan', 'FAN17G0588' => 'fan', 'FAN17G0609' => 'fan', 'FAN18G2817' => 'fan', 'FAN19G1305' => 'fan', 'FAN20G1787' => 'fan', 'FAN22G0073' => 'fan', 'FAN22G0352' => 'fan', 'FAN22G0368' => 'fan', 'FAN22G2273' => 'fan', 'FAN24G1998' => 'fan', 'FAN27G1317' => 'fan', 'FvH4_2g23980' => 'fve', 'FvH4_4g14380' => 'fve', 'FvH4_4g14390' => 'fve', 'FvH4_6g09250' => 'fve', 'Glyma.03G151100' => 'gma', 'Glyma.04G122550' => 'gma', 'Glyma.05G001600' => 'gma', 'Glyma.09G270766' => 'gma', 'Glyma.09G270832' => 'gma', 'Glyma.13G209800' => 'gma', 'Glyma.15G102800' => 'gma', 'Glyma.18G218900' => 'gma', 'Glyma.19G001500' => 'gma', 'Glyma.19G153600' => 'gma', 'Gohir.A02G028600' => 'ghi', 'Gohir.A08G045000' => 'ghi', 'Gohir.A11G120500' => 'ghi', 'Gohir.A12G006200' => 'ghi', 'Gohir.A12G006250' => 'ghi', 'Gohir.D02G036300' => 'ghi', 'Gohir.D08G054700' => 'ghi', 'Gohir.D11G125600' => 'ghi', 'Gohir.D12G005700' => 'ghi', 'Gorai.004G055200' => 'gra', 'Gorai.005G040400' => 'gra', 'Gorai.007G134500' => 'gra', 'Gorai.008G005500' => 'gra', 'GSVIVG01011094001' => 'vvi', 'GSVIVG01017879001' => 'vvi', 'GSVIVG01025988001' => 'vvi', 'GSVIVG01029847001' => 'vvi', 'HanXRQChr10g0282901' => 'han', 'HanXRQChr10g0310371' => 'han', 'HanXRQChr10g0315041' => 'han', 'HanXRQChr11g0327651' => 'han', 'HanXRQChr12g0359391' => 'han', 'Haze_00972' => 'cav', 'Haze_00973' => 'cav', 'Haze_00974' => 'cav', 'Haze_04747' => 'cav', 'Haze_04749' => 'cav', 'Haze_04750' => 'cav', 'Haze_21217' => 'cav', 'Hma1.2p1_1037F.1_g250680' => 'hma', 'Hma1.2p1_1644F.1_g295320' => 'hma', 'HPP92_011322' => 'vpl', 'HPP92_011323' => 'vpl', 'HPP92_011324' => 'vpl', 'HPP92_011325' => 'vpl', 'HPP92_011326' => 'vpl', 'Hund12205' => 'sun', 'Hund17957' => 'sun', 'Lalb_Chr06g0176771' => 'lal', 'Lalb_Chr18g0056021' => 'lal', 'Lalb_Chr18g0056031' => 'lal', 'Lalb_Chr18g0056041' => 'lal', 'Lalb_Chr20g0107751' => 'lal', 'Lalb_Chr20g0118371' => 'lal', 'Lj1g0010239' => 'lja', 'Lj1g0017101' => 'lja', 'Lj2A1178G40' => 'lonja', 'Lj2A54G84' => 'lonja', 'Lj2g0015248' => 'lja', 'Lj3A761T51' => 'lonja', 'Lj6g0018116' => 'lja', 'Lsat_1_v5_gn_4_136040' => 'lsa', 'Lsat_1_v5_gn_5_187461' => 'lsa', 'Lsat_1_v5_gn_5_77001' => 'lsa', 'Lsat_1_v5_gn_9_4461' => 'lsa', 'Manes.01G210100' => 'mes', 'Manes.03G185600' => 'mes', 'Manes.05G073300' => 'mes', 'Manes.09G120300' => 'mes', 'Manes.15G022100' => 'mes', 'Mapoly0096s0053' => 'mpo', 'MBI03_g14058_MAGBIO' => 'mbi', 'MBI03_g33876_MAGBIO' => 'mbi', 'MBI03_g36854_MAGBIO' => 'mbi', 'MBI17_g11997_MAGBIO' => 'mbi', 'MD03G1269000' => 'mdo', 'MD04G1179600' => 'mdo', 'MD11G1289800' => 'mdo', 'MD12G1194700' => 'mdo', 'MD13G1182100' => 'mdo', 'MD13G1182200' => 'mdo', 'MD16G1182600' => 'mdo', 'Medtr2g021400' => 'mtr', 'Medtr2g021470' => 'mtr', 'Medtr2g105810' => 'mtr', 'Medtr3g033580' => 'mtr', 'Medtr6g007970' => 'mtr', 'Medtr7g056330' => 'mtr', 'Medtr7g074290' => 'mtr', 'Medtr7g074380' => 'mtr', 'Medtr7g094550' => 'mtr', 'Medtr8g069995' => 'mtr', 'MELO3C014345.2' => 'cme', 'MELO3C021395.2' => 'cme', 'Migut.D00262' => 'egut', 'Migut.G00257' => 'egut', 'MSTRG.21575' => 'ama', 'MSTRG.3985' => 'ama', 'Nitab4.5_0000295g0140' => 'nta', 'Nitab4.5_0000732g0140' => 'nta', 'Nitab4.5_0003162g0020' => 'nta', 'Nitab4.5_0006180g0090' => 'nta', 'Nitab4.5_0006390g0010' => 'nta', 'Nitab4.5_0007392g0040' => 'nta', 'Nn1g02140' => 'nnu', 'Nn4g26168' => 'nnu', 'Nn5g26754' => 'nnu', 'Oeu001433.1' => 'oeu', 'Oeu010299.2' => 'oeu', 'Oeu011171.1' => 'oeu', 'Oeu037675.1' => 'oeu', 'Oeu038359.1' => 'oeu', 'Oeu063834.1' => 'oeu', 'Oeu063835.1' => 'oeu', 'Os05g0312000' => 'osa', 'Os07g0211101' => 'osa', 'Os07g0211200' => 'osa', 'Os07g0681500' => 'osa', 'Peaxi162Scf00095g01015' => 'pax', 'Peaxi162Scf00104g00329' => 'pax', 'Peaxi162Scf00161g00137' => 'pax', 'PGR004G1665' => 'pgr', 'PGR031G2937' => 'pgr', 'PGR119G2145' => 'pgr', 'PGSC0003DMG400004351' => 'stu', 'PGSC0003DMG400014625' => 'stu', 'PGSC0003DMG401000943' => 'stu', 'Phvul.001G148600' => 'pvu', 'Phvul.004G001700' => 'pvu', 'Phvul.006G154900' => 'pvu', 'Phvul.008G078200' => 'pvu', 'Phvul.011G136500' => 'pvu', 'Potri.002G215600' => 'ptr', 'Potri.008G201600' => 'ptr', 'Potri.014G138400' => 'ptr', 'Potri.016G142500' => 'ptr', 'Pp3c16_10580' => 'ppa', 'Pp3c5_25280' => 'ppa', 'Prupe.1G150000' => 'ppe', 'Prupe.1G150100' => 'ppe', 'Prupe.6G299600' => 'ppe', 'Prupe.8G245000' => 'ppe', 'Psat0s4927g0040' => 'psa', 'Psat1g052080' => 'psa', 'Psat1g183800' => 'psa', 'Psat3g113840' => 'psa', 'Psat3g126120' => 'psa', 'Psat3g126160' => 'psa', 'Psat3g158760' => 'psa', 'Psat3g158840' => 'psa', 'PSO170G2858' => 'pso', 'PSO339G0606' => 'pso', 'PSO384G4709' => 'pso', 'PSO407G0334' => 'pso', 'QL04p040276' => 'qlo', 'QL06p005458' => 'qlo', 'QL06p005472' => 'qlo', 'QL07p030546' => 'qlo', 'QL07p031519' => 'qlo', 'QL09p050949' => 'qlo', 'QL09p050966' => 'qlo', 'QL09p051067' => 'qlo', 'QL12p022706' => 'qlo', 'RcHm_v2.0_Chr2g0119601' => 'rch', 'RcHm_v2.0_Chr3g0459591' => 'rch', 'RcHm_v2.0_Chr4g0418521' => 'rch', 'RcHm_v2.0_Chr4g0418531' => 'rch', 'RcHm_v2.0_Chr4g0418541' => 'rch', 'RcHm_v2.0_Chr6g0291641' => 'rch', 'Rhsim01G0086300' => 'rsi', 'Rhsim01G0276300' => 'rsi', 'Rhsim01G0276500' => 'rsi', 'Rhsim04G0207700' => 'rsi', 'Rhsim05G0234500' => 'rsi', 'Rhsim13G0022400' => 'rsi', 'Sabra02G0167900' => 'sbr', 'Sabra04G0158500' => 'sbr', 'Sabra08G0159800' => 'sbr', 'Sabra10G0011500' => 'sbr', 'Sabra14G0104400' => 'sbr', 'SalBow2G2440' => 'sbo', 'SalBow4G2265' => 'sbo', 'Sc02g0000060' => 'sci', 'Sc05g0005020' => 'sci', 'Sc13g0003890' => 'sci', 'Sed0014865' => 'sed', 'Sed0017224' => 'sed', 'Sed0026391' => 'sed', 'SEGI_00063' => 'sgi', 'SEGI_10967' => 'sgi', 'SEGI_17510' => 'sgi', 'SEGI_24396' => 'sgi', 'SEGI_39719' => 'sgi', 'SEGI_41392' => 'sgi', 'SGA_v2.0_scaffold11G05794' => 'sas', 'SGA_v2.0_scaffold142G35607' => 'sas', 'SGA_v2.0_scaffold1G00447' => 'sas', 'SHI15388' => 'shi', 'SHI15394' => 'shi', 'SHI15396' => 'shi', 'SHI15399' => 'shi', 'SMO343G0151' => 'smo', 'SMO367G1118' => 'smo', 'Solyc01g080200.3' => 'sly', 'Solyc06g008960.3' => 'sly', 'Solyc09g064780.3' => 'sly', 'Sopen01g031980' => 'spe', 'Sopen06g003710' => 'spe', 'Sopen09g026460' => 'spe', 'Sp3g21240' => 'spa', 'Sp4g30030' => 'spa', 'TAR365G0022' => 'tar', 'TAR365G1023' => 'tar', 'TAR365G1253' => 'tar', 'TAR623G0078' => 'tar', 'TAR623G1721' => 'tar', 'TAR633G0959' => 'tar', 'THA.LOC104802225' => 'tha', 'THA.LOC104804769' => 'tha', 'THA.LOC104808660' => 'tha', 'THA.LOC104812792' => 'tha', 'Thecc.01G284000' => 'tca', 'Thecc.04G220600' => 'tca', 'Thecc.05G268900' => 'tca', 'Thecc.08G171100' => 'tca', 'Thhalv10001284m.g' => 'esa', 'Thhalv10019912m.g' => 'esa', 'TPR.G14189' => 'tpr', 'TPR.G18110' => 'tpr', 'TPR.G18130' => 'tpr', 'TPR.G18131' => 'tpr', 'TPR.G18140' => 'tpr', 'TPR.G24282' => 'tpr', 'TPR.G25221' => 'tpr', 'TPR.G29267' => 'tpr', 'TPR.G35315' => 'tpr', 'TPR.G36173' => 'tpr', 'TWI09G0794' => 'twi', 'TWI59G1348' => 'twi', 'TWI74G0430' => 'twi', 'unitig_26.g8940' => 'ugi', 'unitig_749.g13744' => 'ugi', 'unitig_749.g13745' => 'ugi', 'vmacro08269' => 'vma', 'vmacro14937' => 'vma', 'vmacro20401' => 'vma', 'VMungo0464G1349' => 'vmu', 'VMungo0540G0289' => 'vmu', 'VMungo1215G1590' => 'vmu', 'VMungo1309G0221' => 'vmu', 'VMungo1309G2815' => 'vmu', 'VMungo1383G0239' => 'vmu', 'VMungo1383G2910' => 'vmu', 'Zm00001eb095270' => 'zma', 'Zm00001eb095280' => 'zma', 'Zm00001eb111630' => 'zma', 'Zm00001eb237080' => 'zma', 'Zm00001eb273740' => 'zma', 'Zm00001eb285040' => 'zma', 'Zm00001eb330790' => 'zma', 'Zm00001eb337380' => 'zma' ), 'gf_id' => 'HOM05D001484', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001484' ), 'data_identifier' => 'HOM05D001484', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001484', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p31500' => 'bna', 'A05p00020' => 'bna', 'A07p08820' => 'bna', 'Aa31LG4G3300' => 'aar', 'Aa31LG8G10030' => 'aar', 'Actinidia00731' => 'ach', 'Actinidia11473' => 'ach', 'Actinidia23469' => 'ach', 'Actinidia24318' => 'ach', 'Actinidia40196' => 'ach', 'Actinidia40197' => 'ach', 'Actinidia40198' => 'ach', 'Ah.08g212990' => 'amhyb', 'Ah.15g091720' => 'amhyb', 'AL3G38260' => 'aly', 'AL4G47710' => 'aly', 'Aqoxy2G00671' => 'aox', 'Aqoxy2G03236' => 'aox', 'arahy.Tifrunner.gnm1.ann1.05IDCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KR684' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATY3SJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK6QJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6APGL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IDT7Z9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM073U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ0R87' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LE7RV4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT4QRX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V5ENPK' => 'arhy', 'AT2G48110' => 'ath', 'AT3G23590' => 'ath', 'ATR0626G186' => 'atr', 'ATR1127G141' => 'atr', 'Atru.chr4.2583' => 'acertr', 'Atru.chr5.1358' => 'acertr', 'Atru.chr5.1359' => 'acertr', 'Atru.chr8.46' => 'acertr', 'AUR62002640' => 'cqu', 'AUR62030055' => 'cqu', 'AUR62033713' => 'cqu', 'AUR62033714' => 'cqu', 'AUR62036795' => 'cqu', 'AUR62039891' => 'cqu', 'BcaB02g08737' => 'bca', 'BcaB04g20441' => 'bca', 'BcaB06g26509' => 'bca', 'BcaB06g26510' => 'bca', 'BcaB06g26511' => 'bca', 'BcaB06g26512' => 'bca', 'BcaB06g26513' => 'bca', 'BcaC02g12564' => 'bca', 'BcaC02g12565' => 'bca', 'BcaC02g12794' => 'bca', 'BcaC02g12795' => 'bca', 'BcaC02g12796' => 'bca', 'BcaC06g35541' => 'bca', 'BNapus_Darmor_BZH_scaffold_188p00080' => 'bna', 'BNapus_Darmor_BZH_scaffold_188p00090' => 'bna', 'BolC1t03972H' => 'bol', 'BolC1t03973H' => 'bol', 'BolC4t21680H' => 'bol', 'BolC7t41863H' => 'bol', 'BolSC55t61227H' => 'bol', 'BolSC55t61228H' => 'bol', 'BraA01t03278Z' => 'bra', 'BraA05t18998Z' => 'bra', 'BraA07t28673Z' => 'bra', 'C01p40150' => 'bna', 'C05p12370' => 'bna', 'C07p13680' => 'bna', 'CAN.G1006.16' => 'can', 'CAN.G1006.17' => 'can', 'CAN.G1170.2' => 'can', 'CAN.G962.7' => 'can', 'CANSAT25G2179' => 'cansat', 'CANSAT78G1573' => 'cansat', 'CARHR099510' => 'chi', 'CARHR143510' => 'chi', 'Carub.0003s2380' => 'cru', 'Carub.0004s3082' => 'cru', 'Ca_00614_v3' => 'car', 'Ca_07801_v3' => 'car', 'Ca_08567_v3' => 'car', 'Ca_09571_v3' => 'car', 'CBR_g19290' => 'cbr', 'Cc01_g19770' => 'ccan', 'Cc03_g03030' => 'ccan', 'CDE07G0968' => 'cde', 'CDE09G1441' => 'cde', 'Cfa006103' => 'cfa', 'Cfa015573' => 'cfa', 'Cfa016988' => 'cfa', 'Ciclev10006738m.g' => 'ccl', 'Ciclev10010920m.g' => 'ccl', 'Ciclev10018517m.g' => 'ccl', 'CiPaw.01G159200' => 'cil', 'CiPaw.02G091000' => 'cil', 'CiPaw.02G091100' => 'cil', 'CiPaw.08G103100' => 'cil', 'CiPaw.09G224900' => 'cil', 'ClCG06G005740' => 'cla', 'ClCG07G000090' => 'cla', 'ClCG07G000100' => 'cla', 'COL.COLO4_09143' => 'col', 'COL.COLO4_25124' => 'col', 'Cpa.g.sc16.34' => 'cpa', 'Cpa.g.sc3504.1' => 'cpa', 'Cpa.g.sc60.37' => 'cpa', 'CsaV3_6G018520' => 'csa', 'CsaV3_6G036860' => 'csa', 'CSS0001072' => 'camsi', 'CSS0020208' => 'camsi', 'CSS0021253' => 'camsi', 'CSS0022190' => 'camsi', 'CSS0036150' => 'camsi', 'CSS0040442' => 'camsi', 'CSS0042300' => 'camsi', 'CSS0045298' => 'camsi', 'DCAR_012449' => 'dca', 'DCAR_018405' => 'dca', 'DCAR_024573' => 'dca', 'DCAR_030591' => 'dca', 'Dinv16926' => 'din', 'Dinv32963' => 'din', 'Dinv38382' => 'din', 'Dinv38383' => 'din', 'Duzib133G0974' => 'dzi', 'Duzib138G1867' => 'dzi', 'Duzib211G0420' => 'dzi', 'Duzib212G0930' => 'dzi', 'ECA234G1645' => 'eca', 'ECA247G3467' => 'eca', 'ECA248G1703' => 'eca', 'EL10Ac3g06327' => 'bvu', 'EL10Ac7g17204' => 'bvu', 'Eucgr.A00855' => 'egr', 'Eucgr.A00858' => 'egr', 'Eucgr.H01520' => 'egr', 'Eucgr.H03604' => 'egr', 'Eucgr.L03465' => 'egr', 'Eucgr.L03466' => 'egr', 'FAN01G0988' => 'fan', 'FAN02G3892' => 'fan', 'FAN05G3381' => 'fan', 'FAN07G0967' => 'fan', 'FAN07G1493' => 'fan', 'FAN08G3125' => 'fan', 'FAN09G0402' => 'fan', 'FAN12G2594' => 'fan', 'FAN12G3879' => 'fan', 'FAN14G1546' => 'fan', 'FAN15G3626' => 'fan', 'FAN17G0588' => 'fan', 'FAN17G0609' => 'fan', 'FAN18G2817' => 'fan', 'FAN19G1305' => 'fan', 'FAN20G1787' => 'fan', 'FAN22G0073' => 'fan', 'FAN22G0352' => 'fan', 'FAN22G0368' => 'fan', 'FAN22G2273' => 'fan', 'FAN24G1998' => 'fan', 'FAN27G1317' => 'fan', 'FvH4_2g23980' => 'fve', 'FvH4_4g14380' => 'fve', 'FvH4_4g14390' => 'fve', 'FvH4_6g09250' => 'fve', 'Glyma.03G151100' => 'gma', 'Glyma.04G122550' => 'gma', 'Glyma.05G001600' => 'gma', 'Glyma.09G270766' => 'gma', 'Glyma.09G270832' => 'gma', 'Glyma.13G209800' => 'gma', 'Glyma.15G102800' => 'gma', 'Glyma.18G218900' => 'gma', 'Glyma.19G001500' => 'gma', 'Glyma.19G153600' => 'gma', 'Gohir.A02G028600' => 'ghi', 'Gohir.A08G045000' => 'ghi', 'Gohir.A11G120500' => 'ghi', 'Gohir.A12G006200' => 'ghi', 'Gohir.A12G006250' => 'ghi', 'Gohir.D02G036300' => 'ghi', 'Gohir.D08G054700' => 'ghi', 'Gohir.D11G125600' => 'ghi', 'Gohir.D12G005700' => 'ghi', 'Gorai.004G055200' => 'gra', 'Gorai.005G040400' => 'gra', 'Gorai.007G134500' => 'gra', 'Gorai.008G005500' => 'gra', 'GSVIVG01011094001' => 'vvi', 'GSVIVG01017879001' => 'vvi', 'GSVIVG01025988001' => 'vvi', 'GSVIVG01029847001' => 'vvi', 'HanXRQChr10g0282901' => 'han', 'HanXRQChr10g0310371' => 'han', 'HanXRQChr10g0315041' => 'han', 'HanXRQChr11g0327651' => 'han', 'HanXRQChr12g0359391' => 'han', 'Haze_00972' => 'cav', 'Haze_00973' => 'cav', 'Haze_00974' => 'cav', 'Haze_04747' => 'cav', 'Haze_04749' => 'cav', 'Haze_04750' => 'cav', 'Haze_21217' => 'cav', 'Hma1.2p1_1037F.1_g250680' => 'hma', 'Hma1.2p1_1644F.1_g295320' => 'hma', 'HPP92_011322' => 'vpl', 'HPP92_011323' => 'vpl', 'HPP92_011324' => 'vpl', 'HPP92_011325' => 'vpl', 'HPP92_011326' => 'vpl', 'Hund12205' => 'sun', 'Hund17957' => 'sun', 'Lalb_Chr06g0176771' => 'lal', 'Lalb_Chr18g0056021' => 'lal', 'Lalb_Chr18g0056031' => 'lal', 'Lalb_Chr18g0056041' => 'lal', 'Lalb_Chr20g0107751' => 'lal', 'Lalb_Chr20g0118371' => 'lal', 'Lj1g0010239' => 'lja', 'Lj1g0017101' => 'lja', 'Lj2A1178G40' => 'lonja', 'Lj2A54G84' => 'lonja', 'Lj2g0015248' => 'lja', 'Lj3A761T51' => 'lonja', 'Lj6g0018116' => 'lja', 'Lsat_1_v5_gn_4_136040' => 'lsa', 'Lsat_1_v5_gn_5_187461' => 'lsa', 'Lsat_1_v5_gn_5_77001' => 'lsa', 'Lsat_1_v5_gn_9_4461' => 'lsa', 'Manes.01G210100' => 'mes', 'Manes.03G185600' => 'mes', 'Manes.05G073300' => 'mes', 'Manes.09G120300' => 'mes', 'Manes.15G022100' => 'mes', 'Mapoly0096s0053' => 'mpo', 'MBI03_g14058_MAGBIO' => 'mbi', 'MBI03_g33876_MAGBIO' => 'mbi', 'MBI03_g36854_MAGBIO' => 'mbi', 'MBI17_g11997_MAGBIO' => 'mbi', 'MD03G1269000' => 'mdo', 'MD04G1179600' => 'mdo', 'MD11G1289800' => 'mdo', 'MD12G1194700' => 'mdo', 'MD13G1182100' => 'mdo', 'MD13G1182200' => 'mdo', 'MD16G1182600' => 'mdo', 'Medtr2g021400' => 'mtr', 'Medtr2g021470' => 'mtr', 'Medtr2g105810' => 'mtr', 'Medtr3g033580' => 'mtr', 'Medtr6g007970' => 'mtr', 'Medtr7g056330' => 'mtr', 'Medtr7g074290' => 'mtr', 'Medtr7g074380' => 'mtr', 'Medtr7g094550' => 'mtr', 'Medtr8g069995' => 'mtr', 'MELO3C014345.2' => 'cme', 'MELO3C021395.2' => 'cme', 'Migut.D00262' => 'egut', 'Migut.G00257' => 'egut', 'MSTRG.21575' => 'ama', 'MSTRG.3985' => 'ama', 'Nitab4.5_0000295g0140' => 'nta', 'Nitab4.5_0000732g0140' => 'nta', 'Nitab4.5_0003162g0020' => 'nta', 'Nitab4.5_0006180g0090' => 'nta', 'Nitab4.5_0006390g0010' => 'nta', 'Nitab4.5_0007392g0040' => 'nta', 'Nn1g02140' => 'nnu', 'Nn4g26168' => 'nnu', 'Nn5g26754' => 'nnu', 'Oeu001433.1' => 'oeu', 'Oeu010299.2' => 'oeu', 'Oeu011171.1' => 'oeu', 'Oeu037675.1' => 'oeu', 'Oeu038359.1' => 'oeu', 'Oeu063834.1' => 'oeu', 'Oeu063835.1' => 'oeu', 'Os05g0312000' => 'osa', 'Os07g0211101' => 'osa', 'Os07g0211200' => 'osa', 'Os07g0681500' => 'osa', 'Peaxi162Scf00095g01015' => 'pax', 'Peaxi162Scf00104g00329' => 'pax', 'Peaxi162Scf00161g00137' => 'pax', 'PGR004G1665' => 'pgr', 'PGR031G2937' => 'pgr', 'PGR119G2145' => 'pgr', 'PGSC0003DMG400004351' => 'stu', 'PGSC0003DMG400014625' => 'stu', 'PGSC0003DMG401000943' => 'stu', 'Phvul.001G148600' => 'pvu', 'Phvul.004G001700' => 'pvu', 'Phvul.006G154900' => 'pvu', 'Phvul.008G078200' => 'pvu', 'Phvul.011G136500' => 'pvu', 'Potri.002G215600' => 'ptr', 'Potri.008G201600' => 'ptr', 'Potri.014G138400' => 'ptr', 'Potri.016G142500' => 'ptr', 'Pp3c16_10580' => 'ppa', 'Pp3c5_25280' => 'ppa', 'Prupe.1G150000' => 'ppe', 'Prupe.1G150100' => 'ppe', 'Prupe.6G299600' => 'ppe', 'Prupe.8G245000' => 'ppe', 'Psat0s4927g0040' => 'psa', 'Psat1g052080' => 'psa', 'Psat1g183800' => 'psa', 'Psat3g113840' => 'psa', 'Psat3g126120' => 'psa', 'Psat3g126160' => 'psa', 'Psat3g158760' => 'psa', 'Psat3g158840' => 'psa', 'PSO170G2858' => 'pso', 'PSO339G0606' => 'pso', 'PSO384G4709' => 'pso', 'PSO407G0334' => 'pso', 'QL04p040276' => 'qlo', 'QL06p005458' => 'qlo', 'QL06p005472' => 'qlo', 'QL07p030546' => 'qlo', 'QL07p031519' => 'qlo', 'QL09p050949' => 'qlo', 'QL09p050966' => 'qlo', 'QL09p051067' => 'qlo', 'QL12p022706' => 'qlo', 'RcHm_v2.0_Chr2g0119601' => 'rch', 'RcHm_v2.0_Chr3g0459591' => 'rch', 'RcHm_v2.0_Chr4g0418521' => 'rch', 'RcHm_v2.0_Chr4g0418531' => 'rch', 'RcHm_v2.0_Chr4g0418541' => 'rch', 'RcHm_v2.0_Chr6g0291641' => 'rch', 'Rhsim01G0086300' => 'rsi', 'Rhsim01G0276300' => 'rsi', 'Rhsim01G0276500' => 'rsi', 'Rhsim04G0207700' => 'rsi', 'Rhsim05G0234500' => 'rsi', 'Rhsim13G0022400' => 'rsi', 'Sabra02G0167900' => 'sbr', 'Sabra04G0158500' => 'sbr', 'Sabra08G0159800' => 'sbr', 'Sabra10G0011500' => 'sbr', 'Sabra14G0104400' => 'sbr', 'SalBow2G2440' => 'sbo', 'SalBow4G2265' => 'sbo', 'Sc02g0000060' => 'sci', 'Sc05g0005020' => 'sci', 'Sc13g0003890' => 'sci', 'Sed0014865' => 'sed', 'Sed0017224' => 'sed', 'Sed0026391' => 'sed', 'SEGI_00063' => 'sgi', 'SEGI_10967' => 'sgi', 'SEGI_17510' => 'sgi', 'SEGI_24396' => 'sgi', 'SEGI_39719' => 'sgi', 'SEGI_41392' => 'sgi', 'SGA_v2.0_scaffold11G05794' => 'sas', 'SGA_v2.0_scaffold142G35607' => 'sas', 'SGA_v2.0_scaffold1G00447' => 'sas', 'SHI15388' => 'shi', 'SHI15394' => 'shi', 'SHI15396' => 'shi', 'SHI15399' => 'shi', 'SMO343G0151' => 'smo', 'SMO367G1118' => 'smo', 'Solyc01g080200.3' => 'sly', 'Solyc06g008960.3' => 'sly', 'Solyc09g064780.3' => 'sly', 'Sopen01g031980' => 'spe', 'Sopen06g003710' => 'spe', 'Sopen09g026460' => 'spe', 'Sp3g21240' => 'spa', 'Sp4g30030' => 'spa', 'TAR365G0022' => 'tar', 'TAR365G1023' => 'tar', 'TAR365G1253' => 'tar', 'TAR623G0078' => 'tar', 'TAR623G1721' => 'tar', 'TAR633G0959' => 'tar', 'THA.LOC104802225' => 'tha', 'THA.LOC104804769' => 'tha', 'THA.LOC104808660' => 'tha', 'THA.LOC104812792' => 'tha', 'Thecc.01G284000' => 'tca', 'Thecc.04G220600' => 'tca', 'Thecc.05G268900' => 'tca', 'Thecc.08G171100' => 'tca', 'Thhalv10001284m.g' => 'esa', 'Thhalv10019912m.g' => 'esa', 'TPR.G14189' => 'tpr', 'TPR.G18110' => 'tpr', 'TPR.G18130' => 'tpr', 'TPR.G18131' => 'tpr', 'TPR.G18140' => 'tpr', 'TPR.G24282' => 'tpr', 'TPR.G25221' => 'tpr', 'TPR.G29267' => 'tpr', 'TPR.G35315' => 'tpr', 'TPR.G36173' => 'tpr', 'TWI09G0794' => 'twi', 'TWI59G1348' => 'twi', 'TWI74G0430' => 'twi', 'unitig_26.g8940' => 'ugi', 'unitig_749.g13744' => 'ugi', 'unitig_749.g13745' => 'ugi', 'vmacro08269' => 'vma', 'vmacro14937' => 'vma', 'vmacro20401' => 'vma', 'VMungo0464G1349' => 'vmu', 'VMungo0540G0289' => 'vmu', 'VMungo1215G1590' => 'vmu', 'VMungo1309G0221' => 'vmu', 'VMungo1309G2815' => 'vmu', 'VMungo1383G0239' => 'vmu', 'VMungo1383G2910' => 'vmu', 'Zm00001eb095270' => 'zma', 'Zm00001eb095280' => 'zma', 'Zm00001eb111630' => 'zma', 'Zm00001eb237080' => 'zma', 'Zm00001eb273740' => 'zma', 'Zm00001eb285040' => 'zma', 'Zm00001eb330790' => 'zma', 'Zm00001eb337380' => 'zma' ) $gf_id = 'HOM05D001484' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001484' ) $data_identifier = 'HOM05D001484' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 2, 'aly' => (int) 2, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 22, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 7, 'hma' => (int) 2, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 7, 'mtr' => (int) 10, 'cme' => (int) 2, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 4, 'ppa' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 4, 'qlo' => (int) 9, 'rch' => (int) 6, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 10, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 7, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb337380' $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' => 'HOM05D001484', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p31500' => 'bna', 'A05p00020' => 'bna', 'A07p08820' => 'bna', 'Aa31LG4G3300' => 'aar', 'Aa31LG8G10030' => 'aar', 'Actinidia00731' => 'ach', 'Actinidia11473' => 'ach', 'Actinidia23469' => 'ach', 'Actinidia24318' => 'ach', 'Actinidia40196' => 'ach', 'Actinidia40197' => 'ach', 'Actinidia40198' => 'ach', 'Ah.08g212990' => 'amhyb', 'Ah.15g091720' => 'amhyb', 'AL3G38260' => 'aly', 'AL4G47710' => 'aly', 'Aqoxy2G00671' => 'aox', 'Aqoxy2G03236' => 'aox', 'arahy.Tifrunner.gnm1.ann1.05IDCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KR684' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATY3SJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK6QJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6APGL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IDT7Z9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM073U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ0R87' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LE7RV4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT4QRX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V5ENPK' => 'arhy', 'AT2G48110' => 'ath', 'AT3G23590' => 'ath', 'ATR0626G186' => 'atr', 'ATR1127G141' => 'atr', 'Atru.chr4.2583' => 'acertr', 'Atru.chr5.1358' => 'acertr', 'Atru.chr5.1359' => 'acertr', 'Atru.chr8.46' => 'acertr', 'AUR62002640' => 'cqu', 'AUR62030055' => 'cqu', 'AUR62033713' => 'cqu', 'AUR62033714' => 'cqu', 'AUR62036795' => 'cqu', 'AUR62039891' => 'cqu', 'BcaB02g08737' => 'bca', 'BcaB04g20441' => 'bca', 'BcaB06g26509' => 'bca', 'BcaB06g26510' => 'bca', 'BcaB06g26511' => 'bca', 'BcaB06g26512' => 'bca', 'BcaB06g26513' => 'bca', 'BcaC02g12564' => 'bca', 'BcaC02g12565' => 'bca', 'BcaC02g12794' => 'bca', 'BcaC02g12795' => 'bca', 'BcaC02g12796' => 'bca', 'BcaC06g35541' => 'bca', 'BNapus_Darmor_BZH_scaffold_188p00080' => 'bna', 'BNapus_Darmor_BZH_scaffold_188p00090' => 'bna', 'BolC1t03972H' => 'bol', 'BolC1t03973H' => 'bol', 'BolC4t21680H' => 'bol', 'BolC7t41863H' => 'bol', 'BolSC55t61227H' => 'bol', 'BolSC55t61228H' => 'bol', 'BraA01t03278Z' => 'bra', 'BraA05t18998Z' => 'bra', 'BraA07t28673Z' => 'bra', 'C01p40150' => 'bna', 'C05p12370' => 'bna', 'C07p13680' => 'bna', 'CAN.G1006.16' => 'can', 'CAN.G1006.17' => 'can', 'CAN.G1170.2' => 'can', 'CAN.G962.7' => 'can', 'CANSAT25G2179' => 'cansat', 'CANSAT78G1573' => 'cansat', 'CARHR099510' => 'chi', 'CARHR143510' => 'chi', 'Carub.0003s2380' => 'cru', 'Carub.0004s3082' => 'cru', 'Ca_00614_v3' => 'car', 'Ca_07801_v3' => 'car', 'Ca_08567_v3' => 'car', 'Ca_09571_v3' => 'car', 'CBR_g19290' => 'cbr', 'Cc01_g19770' => 'ccan', 'Cc03_g03030' => 'ccan', 'CDE07G0968' => 'cde', 'CDE09G1441' => 'cde', 'Cfa006103' => 'cfa', 'Cfa015573' => 'cfa', 'Cfa016988' => 'cfa', 'Ciclev10006738m.g' => 'ccl', 'Ciclev10010920m.g' => 'ccl', 'Ciclev10018517m.g' => 'ccl', 'CiPaw.01G159200' => 'cil', 'CiPaw.02G091000' => 'cil', 'CiPaw.02G091100' => 'cil', 'CiPaw.08G103100' => 'cil', 'CiPaw.09G224900' => 'cil', 'ClCG06G005740' => 'cla', 'ClCG07G000090' => 'cla', 'ClCG07G000100' => 'cla', 'COL.COLO4_09143' => 'col', 'COL.COLO4_25124' => 'col', 'Cpa.g.sc16.34' => 'cpa', 'Cpa.g.sc3504.1' => 'cpa', 'Cpa.g.sc60.37' => 'cpa', 'CsaV3_6G018520' => 'csa', 'CsaV3_6G036860' => 'csa', 'CSS0001072' => 'camsi', 'CSS0020208' => 'camsi', 'CSS0021253' => 'camsi', 'CSS0022190' => 'camsi', 'CSS0036150' => 'camsi', 'CSS0040442' => 'camsi', 'CSS0042300' => 'camsi', 'CSS0045298' => 'camsi', 'DCAR_012449' => 'dca', 'DCAR_018405' => 'dca', 'DCAR_024573' => 'dca', 'DCAR_030591' => 'dca', 'Dinv16926' => 'din', 'Dinv32963' => 'din', 'Dinv38382' => 'din', 'Dinv38383' => 'din', 'Duzib133G0974' => 'dzi', 'Duzib138G1867' => 'dzi', 'Duzib211G0420' => 'dzi', 'Duzib212G0930' => 'dzi', 'ECA234G1645' => 'eca', 'ECA247G3467' => 'eca', 'ECA248G1703' => 'eca', 'EL10Ac3g06327' => 'bvu', 'EL10Ac7g17204' => 'bvu', 'Eucgr.A00855' => 'egr', 'Eucgr.A00858' => 'egr', 'Eucgr.H01520' => 'egr', 'Eucgr.H03604' => 'egr', 'Eucgr.L03465' => 'egr', 'Eucgr.L03466' => 'egr', 'FAN01G0988' => 'fan', 'FAN02G3892' => 'fan', 'FAN05G3381' => 'fan', 'FAN07G0967' => 'fan', 'FAN07G1493' => 'fan', 'FAN08G3125' => 'fan', 'FAN09G0402' => 'fan', 'FAN12G2594' => 'fan', 'FAN12G3879' => 'fan', 'FAN14G1546' => 'fan', 'FAN15G3626' => 'fan', 'FAN17G0588' => 'fan', 'FAN17G0609' => 'fan', 'FAN18G2817' => 'fan', 'FAN19G1305' => 'fan', 'FAN20G1787' => 'fan', 'FAN22G0073' => 'fan', 'FAN22G0352' => 'fan', 'FAN22G0368' => 'fan', 'FAN22G2273' => 'fan', 'FAN24G1998' => 'fan', 'FAN27G1317' => 'fan', 'FvH4_2g23980' => 'fve', 'FvH4_4g14380' => 'fve', 'FvH4_4g14390' => 'fve', 'FvH4_6g09250' => 'fve', 'Glyma.03G151100' => 'gma', 'Glyma.04G122550' => 'gma', 'Glyma.05G001600' => 'gma', 'Glyma.09G270766' => 'gma', 'Glyma.09G270832' => 'gma', 'Glyma.13G209800' => 'gma', 'Glyma.15G102800' => 'gma', 'Glyma.18G218900' => 'gma', 'Glyma.19G001500' => 'gma', 'Glyma.19G153600' => 'gma', 'Gohir.A02G028600' => 'ghi', 'Gohir.A08G045000' => 'ghi', 'Gohir.A11G120500' => 'ghi', 'Gohir.A12G006200' => 'ghi', 'Gohir.A12G006250' => 'ghi', 'Gohir.D02G036300' => 'ghi', 'Gohir.D08G054700' => 'ghi', 'Gohir.D11G125600' => 'ghi', 'Gohir.D12G005700' => 'ghi', 'Gorai.004G055200' => 'gra', 'Gorai.005G040400' => 'gra', 'Gorai.007G134500' => 'gra', 'Gorai.008G005500' => 'gra', 'GSVIVG01011094001' => 'vvi', 'GSVIVG01017879001' => 'vvi', 'GSVIVG01025988001' => 'vvi', 'GSVIVG01029847001' => 'vvi', 'HanXRQChr10g0282901' => 'han', 'HanXRQChr10g0310371' => 'han', 'HanXRQChr10g0315041' => 'han', 'HanXRQChr11g0327651' => 'han', 'HanXRQChr12g0359391' => 'han', 'Haze_00972' => 'cav', 'Haze_00973' => 'cav', 'Haze_00974' => 'cav', 'Haze_04747' => 'cav', 'Haze_04749' => 'cav', 'Haze_04750' => 'cav', 'Haze_21217' => 'cav', 'Hma1.2p1_1037F.1_g250680' => 'hma', 'Hma1.2p1_1644F.1_g295320' => 'hma', 'HPP92_011322' => 'vpl', 'HPP92_011323' => 'vpl', 'HPP92_011324' => 'vpl', 'HPP92_011325' => 'vpl', 'HPP92_011326' => 'vpl', 'Hund12205' => 'sun', 'Hund17957' => 'sun', 'Lalb_Chr06g0176771' => 'lal', 'Lalb_Chr18g0056021' => 'lal', 'Lalb_Chr18g0056031' => 'lal', 'Lalb_Chr18g0056041' => 'lal', 'Lalb_Chr20g0107751' => 'lal', 'Lalb_Chr20g0118371' => 'lal', 'Lj1g0010239' => 'lja', 'Lj1g0017101' => 'lja', 'Lj2A1178G40' => 'lonja', 'Lj2A54G84' => 'lonja', 'Lj2g0015248' => 'lja', 'Lj3A761T51' => 'lonja', 'Lj6g0018116' => 'lja', 'Lsat_1_v5_gn_4_136040' => 'lsa', 'Lsat_1_v5_gn_5_187461' => 'lsa', 'Lsat_1_v5_gn_5_77001' => 'lsa', 'Lsat_1_v5_gn_9_4461' => 'lsa', 'Manes.01G210100' => 'mes', 'Manes.03G185600' => 'mes', 'Manes.05G073300' => 'mes', 'Manes.09G120300' => 'mes', 'Manes.15G022100' => 'mes', 'Mapoly0096s0053' => 'mpo', 'MBI03_g14058_MAGBIO' => 'mbi', 'MBI03_g33876_MAGBIO' => 'mbi', 'MBI03_g36854_MAGBIO' => 'mbi', 'MBI17_g11997_MAGBIO' => 'mbi', 'MD03G1269000' => 'mdo', 'MD04G1179600' => 'mdo', 'MD11G1289800' => 'mdo', 'MD12G1194700' => 'mdo', 'MD13G1182100' => 'mdo', 'MD13G1182200' => 'mdo', 'MD16G1182600' => 'mdo', 'Medtr2g021400' => 'mtr', 'Medtr2g021470' => 'mtr', 'Medtr2g105810' => 'mtr', 'Medtr3g033580' => 'mtr', 'Medtr6g007970' => 'mtr', 'Medtr7g056330' => 'mtr', 'Medtr7g074290' => 'mtr', 'Medtr7g074380' => 'mtr', 'Medtr7g094550' => 'mtr', 'Medtr8g069995' => 'mtr', 'MELO3C014345.2' => 'cme', 'MELO3C021395.2' => 'cme', 'Migut.D00262' => 'egut', 'Migut.G00257' => 'egut', 'MSTRG.21575' => 'ama', 'MSTRG.3985' => 'ama', 'Nitab4.5_0000295g0140' => 'nta', 'Nitab4.5_0000732g0140' => 'nta', 'Nitab4.5_0003162g0020' => 'nta', 'Nitab4.5_0006180g0090' => 'nta', 'Nitab4.5_0006390g0010' => 'nta', 'Nitab4.5_0007392g0040' => 'nta', 'Nn1g02140' => 'nnu', 'Nn4g26168' => 'nnu', 'Nn5g26754' => 'nnu', 'Oeu001433.1' => 'oeu', 'Oeu010299.2' => 'oeu', 'Oeu011171.1' => 'oeu', 'Oeu037675.1' => 'oeu', 'Oeu038359.1' => 'oeu', 'Oeu063834.1' => 'oeu', 'Oeu063835.1' => 'oeu', 'Os05g0312000' => 'osa', 'Os07g0211101' => 'osa', 'Os07g0211200' => 'osa', 'Os07g0681500' => 'osa', 'Peaxi162Scf00095g01015' => 'pax', 'Peaxi162Scf00104g00329' => 'pax', 'Peaxi162Scf00161g00137' => 'pax', 'PGR004G1665' => 'pgr', 'PGR031G2937' => 'pgr', 'PGR119G2145' => 'pgr', 'PGSC0003DMG400004351' => 'stu', 'PGSC0003DMG400014625' => 'stu', 'PGSC0003DMG401000943' => 'stu', 'Phvul.001G148600' => 'pvu', 'Phvul.004G001700' => 'pvu', 'Phvul.006G154900' => 'pvu', 'Phvul.008G078200' => 'pvu', 'Phvul.011G136500' => 'pvu', 'Potri.002G215600' => 'ptr', 'Potri.008G201600' => 'ptr', 'Potri.014G138400' => 'ptr', 'Potri.016G142500' => 'ptr', 'Pp3c16_10580' => 'ppa', 'Pp3c5_25280' => 'ppa', 'Prupe.1G150000' => 'ppe', 'Prupe.1G150100' => 'ppe', 'Prupe.6G299600' => 'ppe', 'Prupe.8G245000' => 'ppe', 'Psat0s4927g0040' => 'psa', 'Psat1g052080' => 'psa', 'Psat1g183800' => 'psa', 'Psat3g113840' => 'psa', 'Psat3g126120' => 'psa', 'Psat3g126160' => 'psa', 'Psat3g158760' => 'psa', 'Psat3g158840' => 'psa', 'PSO170G2858' => 'pso', 'PSO339G0606' => 'pso', 'PSO384G4709' => 'pso', 'PSO407G0334' => 'pso', 'QL04p040276' => 'qlo', 'QL06p005458' => 'qlo', 'QL06p005472' => 'qlo', 'QL07p030546' => 'qlo', 'QL07p031519' => 'qlo', 'QL09p050949' => 'qlo', 'QL09p050966' => 'qlo', 'QL09p051067' => 'qlo', 'QL12p022706' => 'qlo', 'RcHm_v2.0_Chr2g0119601' => 'rch', 'RcHm_v2.0_Chr3g0459591' => 'rch', 'RcHm_v2.0_Chr4g0418521' => 'rch', 'RcHm_v2.0_Chr4g0418531' => 'rch', 'RcHm_v2.0_Chr4g0418541' => 'rch', 'RcHm_v2.0_Chr6g0291641' => 'rch', 'Rhsim01G0086300' => 'rsi', 'Rhsim01G0276300' => 'rsi', 'Rhsim01G0276500' => 'rsi', 'Rhsim04G0207700' => 'rsi', 'Rhsim05G0234500' => 'rsi', 'Rhsim13G0022400' => 'rsi', 'Sabra02G0167900' => 'sbr', 'Sabra04G0158500' => 'sbr', 'Sabra08G0159800' => 'sbr', 'Sabra10G0011500' => 'sbr', 'Sabra14G0104400' => 'sbr', 'SalBow2G2440' => 'sbo', 'SalBow4G2265' => 'sbo', 'Sc02g0000060' => 'sci', 'Sc05g0005020' => 'sci', 'Sc13g0003890' => 'sci', 'Sed0014865' => 'sed', 'Sed0017224' => 'sed', 'Sed0026391' => 'sed', 'SEGI_00063' => 'sgi', 'SEGI_10967' => 'sgi', 'SEGI_17510' => 'sgi', 'SEGI_24396' => 'sgi', 'SEGI_39719' => 'sgi', 'SEGI_41392' => 'sgi', 'SGA_v2.0_scaffold11G05794' => 'sas', 'SGA_v2.0_scaffold142G35607' => 'sas', 'SGA_v2.0_scaffold1G00447' => 'sas', 'SHI15388' => 'shi', 'SHI15394' => 'shi', 'SHI15396' => 'shi', 'SHI15399' => 'shi', 'SMO343G0151' => 'smo', 'SMO367G1118' => 'smo', 'Solyc01g080200.3' => 'sly', 'Solyc06g008960.3' => 'sly', 'Solyc09g064780.3' => 'sly', 'Sopen01g031980' => 'spe', 'Sopen06g003710' => 'spe', 'Sopen09g026460' => 'spe', 'Sp3g21240' => 'spa', 'Sp4g30030' => 'spa', 'TAR365G0022' => 'tar', 'TAR365G1023' => 'tar', 'TAR365G1253' => 'tar', 'TAR623G0078' => 'tar', 'TAR623G1721' => 'tar', 'TAR633G0959' => 'tar', 'THA.LOC104802225' => 'tha', 'THA.LOC104804769' => 'tha', 'THA.LOC104808660' => 'tha', 'THA.LOC104812792' => 'tha', 'Thecc.01G284000' => 'tca', 'Thecc.04G220600' => 'tca', 'Thecc.05G268900' => 'tca', 'Thecc.08G171100' => 'tca', 'Thhalv10001284m.g' => 'esa', 'Thhalv10019912m.g' => 'esa', 'TPR.G14189' => 'tpr', 'TPR.G18110' => 'tpr', 'TPR.G18130' => 'tpr', 'TPR.G18131' => 'tpr', 'TPR.G18140' => 'tpr', 'TPR.G24282' => 'tpr', 'TPR.G25221' => 'tpr', 'TPR.G29267' => 'tpr', 'TPR.G35315' => 'tpr', 'TPR.G36173' => 'tpr', 'TWI09G0794' => 'twi', 'TWI59G1348' => 'twi', 'TWI74G0430' => 'twi', 'unitig_26.g8940' => 'ugi', 'unitig_749.g13744' => 'ugi', 'unitig_749.g13745' => 'ugi', 'vmacro08269' => 'vma', 'vmacro14937' => 'vma', 'vmacro20401' => 'vma', 'VMungo0464G1349' => 'vmu', 'VMungo0540G0289' => 'vmu', 'VMungo1215G1590' => 'vmu', 'VMungo1309G0221' => 'vmu', 'VMungo1309G2815' => 'vmu', 'VMungo1383G0239' => 'vmu', 'VMungo1383G2910' => 'vmu', 'Zm00001eb095270' => 'zma', 'Zm00001eb095280' => 'zma', 'Zm00001eb111630' => 'zma', 'Zm00001eb237080' => 'zma', 'Zm00001eb273740' => 'zma', 'Zm00001eb285040' => 'zma', 'Zm00001eb330790' => 'zma', 'Zm00001eb337380' => 'zma' ), 'gf_id' => 'HOM05D001484', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001484' ), 'data_identifier' => 'HOM05D001484', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001484', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p31500' => 'bna', 'A05p00020' => 'bna', 'A07p08820' => 'bna', 'Aa31LG4G3300' => 'aar', 'Aa31LG8G10030' => 'aar', 'Actinidia00731' => 'ach', 'Actinidia11473' => 'ach', 'Actinidia23469' => 'ach', 'Actinidia24318' => 'ach', 'Actinidia40196' => 'ach', 'Actinidia40197' => 'ach', 'Actinidia40198' => 'ach', 'Ah.08g212990' => 'amhyb', 'Ah.15g091720' => 'amhyb', 'AL3G38260' => 'aly', 'AL4G47710' => 'aly', 'Aqoxy2G00671' => 'aox', 'Aqoxy2G03236' => 'aox', 'arahy.Tifrunner.gnm1.ann1.05IDCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KR684' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATY3SJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK6QJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6APGL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IDT7Z9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM073U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ0R87' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LE7RV4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT4QRX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V5ENPK' => 'arhy', 'AT2G48110' => 'ath', 'AT3G23590' => 'ath', 'ATR0626G186' => 'atr', 'ATR1127G141' => 'atr', 'Atru.chr4.2583' => 'acertr', 'Atru.chr5.1358' => 'acertr', 'Atru.chr5.1359' => 'acertr', 'Atru.chr8.46' => 'acertr', 'AUR62002640' => 'cqu', 'AUR62030055' => 'cqu', 'AUR62033713' => 'cqu', 'AUR62033714' => 'cqu', 'AUR62036795' => 'cqu', 'AUR62039891' => 'cqu', 'BcaB02g08737' => 'bca', 'BcaB04g20441' => 'bca', 'BcaB06g26509' => 'bca', 'BcaB06g26510' => 'bca', 'BcaB06g26511' => 'bca', 'BcaB06g26512' => 'bca', 'BcaB06g26513' => 'bca', 'BcaC02g12564' => 'bca', 'BcaC02g12565' => 'bca', 'BcaC02g12794' => 'bca', 'BcaC02g12795' => 'bca', 'BcaC02g12796' => 'bca', 'BcaC06g35541' => 'bca', 'BNapus_Darmor_BZH_scaffold_188p00080' => 'bna', 'BNapus_Darmor_BZH_scaffold_188p00090' => 'bna', 'BolC1t03972H' => 'bol', 'BolC1t03973H' => 'bol', 'BolC4t21680H' => 'bol', 'BolC7t41863H' => 'bol', 'BolSC55t61227H' => 'bol', 'BolSC55t61228H' => 'bol', 'BraA01t03278Z' => 'bra', 'BraA05t18998Z' => 'bra', 'BraA07t28673Z' => 'bra', 'C01p40150' => 'bna', 'C05p12370' => 'bna', 'C07p13680' => 'bna', 'CAN.G1006.16' => 'can', 'CAN.G1006.17' => 'can', 'CAN.G1170.2' => 'can', 'CAN.G962.7' => 'can', 'CANSAT25G2179' => 'cansat', 'CANSAT78G1573' => 'cansat', 'CARHR099510' => 'chi', 'CARHR143510' => 'chi', 'Carub.0003s2380' => 'cru', 'Carub.0004s3082' => 'cru', 'Ca_00614_v3' => 'car', 'Ca_07801_v3' => 'car', 'Ca_08567_v3' => 'car', 'Ca_09571_v3' => 'car', 'CBR_g19290' => 'cbr', 'Cc01_g19770' => 'ccan', 'Cc03_g03030' => 'ccan', 'CDE07G0968' => 'cde', 'CDE09G1441' => 'cde', 'Cfa006103' => 'cfa', 'Cfa015573' => 'cfa', 'Cfa016988' => 'cfa', 'Ciclev10006738m.g' => 'ccl', 'Ciclev10010920m.g' => 'ccl', 'Ciclev10018517m.g' => 'ccl', 'CiPaw.01G159200' => 'cil', 'CiPaw.02G091000' => 'cil', 'CiPaw.02G091100' => 'cil', 'CiPaw.08G103100' => 'cil', 'CiPaw.09G224900' => 'cil', 'ClCG06G005740' => 'cla', 'ClCG07G000090' => 'cla', 'ClCG07G000100' => 'cla', 'COL.COLO4_09143' => 'col', 'COL.COLO4_25124' => 'col', 'Cpa.g.sc16.34' => 'cpa', 'Cpa.g.sc3504.1' => 'cpa', 'Cpa.g.sc60.37' => 'cpa', 'CsaV3_6G018520' => 'csa', 'CsaV3_6G036860' => 'csa', 'CSS0001072' => 'camsi', 'CSS0020208' => 'camsi', 'CSS0021253' => 'camsi', 'CSS0022190' => 'camsi', 'CSS0036150' => 'camsi', 'CSS0040442' => 'camsi', 'CSS0042300' => 'camsi', 'CSS0045298' => 'camsi', 'DCAR_012449' => 'dca', 'DCAR_018405' => 'dca', 'DCAR_024573' => 'dca', 'DCAR_030591' => 'dca', 'Dinv16926' => 'din', 'Dinv32963' => 'din', 'Dinv38382' => 'din', 'Dinv38383' => 'din', 'Duzib133G0974' => 'dzi', 'Duzib138G1867' => 'dzi', 'Duzib211G0420' => 'dzi', 'Duzib212G0930' => 'dzi', 'ECA234G1645' => 'eca', 'ECA247G3467' => 'eca', 'ECA248G1703' => 'eca', 'EL10Ac3g06327' => 'bvu', 'EL10Ac7g17204' => 'bvu', 'Eucgr.A00855' => 'egr', 'Eucgr.A00858' => 'egr', 'Eucgr.H01520' => 'egr', 'Eucgr.H03604' => 'egr', 'Eucgr.L03465' => 'egr', 'Eucgr.L03466' => 'egr', 'FAN01G0988' => 'fan', 'FAN02G3892' => 'fan', 'FAN05G3381' => 'fan', 'FAN07G0967' => 'fan', 'FAN07G1493' => 'fan', 'FAN08G3125' => 'fan', 'FAN09G0402' => 'fan', 'FAN12G2594' => 'fan', 'FAN12G3879' => 'fan', 'FAN14G1546' => 'fan', 'FAN15G3626' => 'fan', 'FAN17G0588' => 'fan', 'FAN17G0609' => 'fan', 'FAN18G2817' => 'fan', 'FAN19G1305' => 'fan', 'FAN20G1787' => 'fan', 'FAN22G0073' => 'fan', 'FAN22G0352' => 'fan', 'FAN22G0368' => 'fan', 'FAN22G2273' => 'fan', 'FAN24G1998' => 'fan', 'FAN27G1317' => 'fan', 'FvH4_2g23980' => 'fve', 'FvH4_4g14380' => 'fve', 'FvH4_4g14390' => 'fve', 'FvH4_6g09250' => 'fve', 'Glyma.03G151100' => 'gma', 'Glyma.04G122550' => 'gma', 'Glyma.05G001600' => 'gma', 'Glyma.09G270766' => 'gma', 'Glyma.09G270832' => 'gma', 'Glyma.13G209800' => 'gma', 'Glyma.15G102800' => 'gma', 'Glyma.18G218900' => 'gma', 'Glyma.19G001500' => 'gma', 'Glyma.19G153600' => 'gma', 'Gohir.A02G028600' => 'ghi', 'Gohir.A08G045000' => 'ghi', 'Gohir.A11G120500' => 'ghi', 'Gohir.A12G006200' => 'ghi', 'Gohir.A12G006250' => 'ghi', 'Gohir.D02G036300' => 'ghi', 'Gohir.D08G054700' => 'ghi', 'Gohir.D11G125600' => 'ghi', 'Gohir.D12G005700' => 'ghi', 'Gorai.004G055200' => 'gra', 'Gorai.005G040400' => 'gra', 'Gorai.007G134500' => 'gra', 'Gorai.008G005500' => 'gra', 'GSVIVG01011094001' => 'vvi', 'GSVIVG01017879001' => 'vvi', 'GSVIVG01025988001' => 'vvi', 'GSVIVG01029847001' => 'vvi', 'HanXRQChr10g0282901' => 'han', 'HanXRQChr10g0310371' => 'han', 'HanXRQChr10g0315041' => 'han', 'HanXRQChr11g0327651' => 'han', 'HanXRQChr12g0359391' => 'han', 'Haze_00972' => 'cav', 'Haze_00973' => 'cav', 'Haze_00974' => 'cav', 'Haze_04747' => 'cav', 'Haze_04749' => 'cav', 'Haze_04750' => 'cav', 'Haze_21217' => 'cav', 'Hma1.2p1_1037F.1_g250680' => 'hma', 'Hma1.2p1_1644F.1_g295320' => 'hma', 'HPP92_011322' => 'vpl', 'HPP92_011323' => 'vpl', 'HPP92_011324' => 'vpl', 'HPP92_011325' => 'vpl', 'HPP92_011326' => 'vpl', 'Hund12205' => 'sun', 'Hund17957' => 'sun', 'Lalb_Chr06g0176771' => 'lal', 'Lalb_Chr18g0056021' => 'lal', 'Lalb_Chr18g0056031' => 'lal', 'Lalb_Chr18g0056041' => 'lal', 'Lalb_Chr20g0107751' => 'lal', 'Lalb_Chr20g0118371' => 'lal', 'Lj1g0010239' => 'lja', 'Lj1g0017101' => 'lja', 'Lj2A1178G40' => 'lonja', 'Lj2A54G84' => 'lonja', 'Lj2g0015248' => 'lja', 'Lj3A761T51' => 'lonja', 'Lj6g0018116' => 'lja', 'Lsat_1_v5_gn_4_136040' => 'lsa', 'Lsat_1_v5_gn_5_187461' => 'lsa', 'Lsat_1_v5_gn_5_77001' => 'lsa', 'Lsat_1_v5_gn_9_4461' => 'lsa', 'Manes.01G210100' => 'mes', 'Manes.03G185600' => 'mes', 'Manes.05G073300' => 'mes', 'Manes.09G120300' => 'mes', 'Manes.15G022100' => 'mes', 'Mapoly0096s0053' => 'mpo', 'MBI03_g14058_MAGBIO' => 'mbi', 'MBI03_g33876_MAGBIO' => 'mbi', 'MBI03_g36854_MAGBIO' => 'mbi', 'MBI17_g11997_MAGBIO' => 'mbi', 'MD03G1269000' => 'mdo', 'MD04G1179600' => 'mdo', 'MD11G1289800' => 'mdo', 'MD12G1194700' => 'mdo', 'MD13G1182100' => 'mdo', 'MD13G1182200' => 'mdo', 'MD16G1182600' => 'mdo', 'Medtr2g021400' => 'mtr', 'Medtr2g021470' => 'mtr', 'Medtr2g105810' => 'mtr', 'Medtr3g033580' => 'mtr', 'Medtr6g007970' => 'mtr', 'Medtr7g056330' => 'mtr', 'Medtr7g074290' => 'mtr', 'Medtr7g074380' => 'mtr', 'Medtr7g094550' => 'mtr', 'Medtr8g069995' => 'mtr', 'MELO3C014345.2' => 'cme', 'MELO3C021395.2' => 'cme', 'Migut.D00262' => 'egut', 'Migut.G00257' => 'egut', 'MSTRG.21575' => 'ama', 'MSTRG.3985' => 'ama', 'Nitab4.5_0000295g0140' => 'nta', 'Nitab4.5_0000732g0140' => 'nta', 'Nitab4.5_0003162g0020' => 'nta', 'Nitab4.5_0006180g0090' => 'nta', 'Nitab4.5_0006390g0010' => 'nta', 'Nitab4.5_0007392g0040' => 'nta', 'Nn1g02140' => 'nnu', 'Nn4g26168' => 'nnu', 'Nn5g26754' => 'nnu', 'Oeu001433.1' => 'oeu', 'Oeu010299.2' => 'oeu', 'Oeu011171.1' => 'oeu', 'Oeu037675.1' => 'oeu', 'Oeu038359.1' => 'oeu', 'Oeu063834.1' => 'oeu', 'Oeu063835.1' => 'oeu', 'Os05g0312000' => 'osa', 'Os07g0211101' => 'osa', 'Os07g0211200' => 'osa', 'Os07g0681500' => 'osa', 'Peaxi162Scf00095g01015' => 'pax', 'Peaxi162Scf00104g00329' => 'pax', 'Peaxi162Scf00161g00137' => 'pax', 'PGR004G1665' => 'pgr', 'PGR031G2937' => 'pgr', 'PGR119G2145' => 'pgr', 'PGSC0003DMG400004351' => 'stu', 'PGSC0003DMG400014625' => 'stu', 'PGSC0003DMG401000943' => 'stu', 'Phvul.001G148600' => 'pvu', 'Phvul.004G001700' => 'pvu', 'Phvul.006G154900' => 'pvu', 'Phvul.008G078200' => 'pvu', 'Phvul.011G136500' => 'pvu', 'Potri.002G215600' => 'ptr', 'Potri.008G201600' => 'ptr', 'Potri.014G138400' => 'ptr', 'Potri.016G142500' => 'ptr', 'Pp3c16_10580' => 'ppa', 'Pp3c5_25280' => 'ppa', 'Prupe.1G150000' => 'ppe', 'Prupe.1G150100' => 'ppe', 'Prupe.6G299600' => 'ppe', 'Prupe.8G245000' => 'ppe', 'Psat0s4927g0040' => 'psa', 'Psat1g052080' => 'psa', 'Psat1g183800' => 'psa', 'Psat3g113840' => 'psa', 'Psat3g126120' => 'psa', 'Psat3g126160' => 'psa', 'Psat3g158760' => 'psa', 'Psat3g158840' => 'psa', 'PSO170G2858' => 'pso', 'PSO339G0606' => 'pso', 'PSO384G4709' => 'pso', 'PSO407G0334' => 'pso', 'QL04p040276' => 'qlo', 'QL06p005458' => 'qlo', 'QL06p005472' => 'qlo', 'QL07p030546' => 'qlo', 'QL07p031519' => 'qlo', 'QL09p050949' => 'qlo', 'QL09p050966' => 'qlo', 'QL09p051067' => 'qlo', 'QL12p022706' => 'qlo', 'RcHm_v2.0_Chr2g0119601' => 'rch', 'RcHm_v2.0_Chr3g0459591' => 'rch', 'RcHm_v2.0_Chr4g0418521' => 'rch', 'RcHm_v2.0_Chr4g0418531' => 'rch', 'RcHm_v2.0_Chr4g0418541' => 'rch', 'RcHm_v2.0_Chr6g0291641' => 'rch', 'Rhsim01G0086300' => 'rsi', 'Rhsim01G0276300' => 'rsi', 'Rhsim01G0276500' => 'rsi', 'Rhsim04G0207700' => 'rsi', 'Rhsim05G0234500' => 'rsi', 'Rhsim13G0022400' => 'rsi', 'Sabra02G0167900' => 'sbr', 'Sabra04G0158500' => 'sbr', 'Sabra08G0159800' => 'sbr', 'Sabra10G0011500' => 'sbr', 'Sabra14G0104400' => 'sbr', 'SalBow2G2440' => 'sbo', 'SalBow4G2265' => 'sbo', 'Sc02g0000060' => 'sci', 'Sc05g0005020' => 'sci', 'Sc13g0003890' => 'sci', 'Sed0014865' => 'sed', 'Sed0017224' => 'sed', 'Sed0026391' => 'sed', 'SEGI_00063' => 'sgi', 'SEGI_10967' => 'sgi', 'SEGI_17510' => 'sgi', 'SEGI_24396' => 'sgi', 'SEGI_39719' => 'sgi', 'SEGI_41392' => 'sgi', 'SGA_v2.0_scaffold11G05794' => 'sas', 'SGA_v2.0_scaffold142G35607' => 'sas', 'SGA_v2.0_scaffold1G00447' => 'sas', 'SHI15388' => 'shi', 'SHI15394' => 'shi', 'SHI15396' => 'shi', 'SHI15399' => 'shi', 'SMO343G0151' => 'smo', 'SMO367G1118' => 'smo', 'Solyc01g080200.3' => 'sly', 'Solyc06g008960.3' => 'sly', 'Solyc09g064780.3' => 'sly', 'Sopen01g031980' => 'spe', 'Sopen06g003710' => 'spe', 'Sopen09g026460' => 'spe', 'Sp3g21240' => 'spa', 'Sp4g30030' => 'spa', 'TAR365G0022' => 'tar', 'TAR365G1023' => 'tar', 'TAR365G1253' => 'tar', 'TAR623G0078' => 'tar', 'TAR623G1721' => 'tar', 'TAR633G0959' => 'tar', 'THA.LOC104802225' => 'tha', 'THA.LOC104804769' => 'tha', 'THA.LOC104808660' => 'tha', 'THA.LOC104812792' => 'tha', 'Thecc.01G284000' => 'tca', 'Thecc.04G220600' => 'tca', 'Thecc.05G268900' => 'tca', 'Thecc.08G171100' => 'tca', 'Thhalv10001284m.g' => 'esa', 'Thhalv10019912m.g' => 'esa', 'TPR.G14189' => 'tpr', 'TPR.G18110' => 'tpr', 'TPR.G18130' => 'tpr', 'TPR.G18131' => 'tpr', 'TPR.G18140' => 'tpr', 'TPR.G24282' => 'tpr', 'TPR.G25221' => 'tpr', 'TPR.G29267' => 'tpr', 'TPR.G35315' => 'tpr', 'TPR.G36173' => 'tpr', 'TWI09G0794' => 'twi', 'TWI59G1348' => 'twi', 'TWI74G0430' => 'twi', 'unitig_26.g8940' => 'ugi', 'unitig_749.g13744' => 'ugi', 'unitig_749.g13745' => 'ugi', 'vmacro08269' => 'vma', 'vmacro14937' => 'vma', 'vmacro20401' => 'vma', 'VMungo0464G1349' => 'vmu', 'VMungo0540G0289' => 'vmu', 'VMungo1215G1590' => 'vmu', 'VMungo1309G0221' => 'vmu', 'VMungo1309G2815' => 'vmu', 'VMungo1383G0239' => 'vmu', 'VMungo1383G2910' => 'vmu', 'Zm00001eb095270' => 'zma', 'Zm00001eb095280' => 'zma', 'Zm00001eb111630' => 'zma', 'Zm00001eb237080' => 'zma', 'Zm00001eb273740' => 'zma', 'Zm00001eb285040' => 'zma', 'Zm00001eb330790' => 'zma', 'Zm00001eb337380' => 'zma' ) $gf_id = 'HOM05D001484' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001484' ) $data_identifier = 'HOM05D001484' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 2, 'aly' => (int) 2, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 22, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 7, 'hma' => (int) 2, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 7, 'mtr' => (int) 10, 'cme' => (int) 2, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 4, 'ppa' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 4, 'qlo' => (int) 9, 'rch' => (int) 6, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 10, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 7, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb337380' $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' => 'HOM05D001484', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p31500' => 'bna', 'A05p00020' => 'bna', 'A07p08820' => 'bna', 'Aa31LG4G3300' => 'aar', 'Aa31LG8G10030' => 'aar', 'Actinidia00731' => 'ach', 'Actinidia11473' => 'ach', 'Actinidia23469' => 'ach', 'Actinidia24318' => 'ach', 'Actinidia40196' => 'ach', 'Actinidia40197' => 'ach', 'Actinidia40198' => 'ach', 'Ah.08g212990' => 'amhyb', 'Ah.15g091720' => 'amhyb', 'AL3G38260' => 'aly', 'AL4G47710' => 'aly', 'Aqoxy2G00671' => 'aox', 'Aqoxy2G03236' => 'aox', 'arahy.Tifrunner.gnm1.ann1.05IDCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KR684' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATY3SJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK6QJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6APGL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IDT7Z9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM073U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ0R87' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LE7RV4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT4QRX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V5ENPK' => 'arhy', 'AT2G48110' => 'ath', 'AT3G23590' => 'ath', 'ATR0626G186' => 'atr', 'ATR1127G141' => 'atr', 'Atru.chr4.2583' => 'acertr', 'Atru.chr5.1358' => 'acertr', 'Atru.chr5.1359' => 'acertr', 'Atru.chr8.46' => 'acertr', 'AUR62002640' => 'cqu', 'AUR62030055' => 'cqu', 'AUR62033713' => 'cqu', 'AUR62033714' => 'cqu', 'AUR62036795' => 'cqu', 'AUR62039891' => 'cqu', 'BcaB02g08737' => 'bca', 'BcaB04g20441' => 'bca', 'BcaB06g26509' => 'bca', 'BcaB06g26510' => 'bca', 'BcaB06g26511' => 'bca', 'BcaB06g26512' => 'bca', 'BcaB06g26513' => 'bca', 'BcaC02g12564' => 'bca', 'BcaC02g12565' => 'bca', 'BcaC02g12794' => 'bca', 'BcaC02g12795' => 'bca', 'BcaC02g12796' => 'bca', 'BcaC06g35541' => 'bca', 'BNapus_Darmor_BZH_scaffold_188p00080' => 'bna', 'BNapus_Darmor_BZH_scaffold_188p00090' => 'bna', 'BolC1t03972H' => 'bol', 'BolC1t03973H' => 'bol', 'BolC4t21680H' => 'bol', 'BolC7t41863H' => 'bol', 'BolSC55t61227H' => 'bol', 'BolSC55t61228H' => 'bol', 'BraA01t03278Z' => 'bra', 'BraA05t18998Z' => 'bra', 'BraA07t28673Z' => 'bra', 'C01p40150' => 'bna', 'C05p12370' => 'bna', 'C07p13680' => 'bna', 'CAN.G1006.16' => 'can', 'CAN.G1006.17' => 'can', 'CAN.G1170.2' => 'can', 'CAN.G962.7' => 'can', 'CANSAT25G2179' => 'cansat', 'CANSAT78G1573' => 'cansat', 'CARHR099510' => 'chi', 'CARHR143510' => 'chi', 'Carub.0003s2380' => 'cru', 'Carub.0004s3082' => 'cru', 'Ca_00614_v3' => 'car', 'Ca_07801_v3' => 'car', 'Ca_08567_v3' => 'car', 'Ca_09571_v3' => 'car', 'CBR_g19290' => 'cbr', 'Cc01_g19770' => 'ccan', 'Cc03_g03030' => 'ccan', 'CDE07G0968' => 'cde', 'CDE09G1441' => 'cde', 'Cfa006103' => 'cfa', 'Cfa015573' => 'cfa', 'Cfa016988' => 'cfa', 'Ciclev10006738m.g' => 'ccl', 'Ciclev10010920m.g' => 'ccl', 'Ciclev10018517m.g' => 'ccl', 'CiPaw.01G159200' => 'cil', 'CiPaw.02G091000' => 'cil', 'CiPaw.02G091100' => 'cil', 'CiPaw.08G103100' => 'cil', 'CiPaw.09G224900' => 'cil', 'ClCG06G005740' => 'cla', 'ClCG07G000090' => 'cla', 'ClCG07G000100' => 'cla', 'COL.COLO4_09143' => 'col', 'COL.COLO4_25124' => 'col', 'Cpa.g.sc16.34' => 'cpa', 'Cpa.g.sc3504.1' => 'cpa', 'Cpa.g.sc60.37' => 'cpa', 'CsaV3_6G018520' => 'csa', 'CsaV3_6G036860' => 'csa', 'CSS0001072' => 'camsi', 'CSS0020208' => 'camsi', 'CSS0021253' => 'camsi', 'CSS0022190' => 'camsi', 'CSS0036150' => 'camsi', 'CSS0040442' => 'camsi', 'CSS0042300' => 'camsi', 'CSS0045298' => 'camsi', 'DCAR_012449' => 'dca', 'DCAR_018405' => 'dca', 'DCAR_024573' => 'dca', 'DCAR_030591' => 'dca', 'Dinv16926' => 'din', 'Dinv32963' => 'din', 'Dinv38382' => 'din', 'Dinv38383' => 'din', 'Duzib133G0974' => 'dzi', 'Duzib138G1867' => 'dzi', 'Duzib211G0420' => 'dzi', 'Duzib212G0930' => 'dzi', 'ECA234G1645' => 'eca', 'ECA247G3467' => 'eca', 'ECA248G1703' => 'eca', 'EL10Ac3g06327' => 'bvu', 'EL10Ac7g17204' => 'bvu', 'Eucgr.A00855' => 'egr', 'Eucgr.A00858' => 'egr', 'Eucgr.H01520' => 'egr', 'Eucgr.H03604' => 'egr', 'Eucgr.L03465' => 'egr', 'Eucgr.L03466' => 'egr', 'FAN01G0988' => 'fan', 'FAN02G3892' => 'fan', 'FAN05G3381' => 'fan', 'FAN07G0967' => 'fan', 'FAN07G1493' => 'fan', 'FAN08G3125' => 'fan', 'FAN09G0402' => 'fan', 'FAN12G2594' => 'fan', 'FAN12G3879' => 'fan', 'FAN14G1546' => 'fan', 'FAN15G3626' => 'fan', 'FAN17G0588' => 'fan', 'FAN17G0609' => 'fan', 'FAN18G2817' => 'fan', 'FAN19G1305' => 'fan', 'FAN20G1787' => 'fan', 'FAN22G0073' => 'fan', 'FAN22G0352' => 'fan', 'FAN22G0368' => 'fan', 'FAN22G2273' => 'fan', 'FAN24G1998' => 'fan', 'FAN27G1317' => 'fan', 'FvH4_2g23980' => 'fve', 'FvH4_4g14380' => 'fve', 'FvH4_4g14390' => 'fve', 'FvH4_6g09250' => 'fve', 'Glyma.03G151100' => 'gma', 'Glyma.04G122550' => 'gma', 'Glyma.05G001600' => 'gma', 'Glyma.09G270766' => 'gma', 'Glyma.09G270832' => 'gma', 'Glyma.13G209800' => 'gma', 'Glyma.15G102800' => 'gma', 'Glyma.18G218900' => 'gma', 'Glyma.19G001500' => 'gma', 'Glyma.19G153600' => 'gma', 'Gohir.A02G028600' => 'ghi', 'Gohir.A08G045000' => 'ghi', 'Gohir.A11G120500' => 'ghi', 'Gohir.A12G006200' => 'ghi', 'Gohir.A12G006250' => 'ghi', 'Gohir.D02G036300' => 'ghi', 'Gohir.D08G054700' => 'ghi', 'Gohir.D11G125600' => 'ghi', 'Gohir.D12G005700' => 'ghi', 'Gorai.004G055200' => 'gra', 'Gorai.005G040400' => 'gra', 'Gorai.007G134500' => 'gra', 'Gorai.008G005500' => 'gra', 'GSVIVG01011094001' => 'vvi', 'GSVIVG01017879001' => 'vvi', 'GSVIVG01025988001' => 'vvi', 'GSVIVG01029847001' => 'vvi', 'HanXRQChr10g0282901' => 'han', 'HanXRQChr10g0310371' => 'han', 'HanXRQChr10g0315041' => 'han', 'HanXRQChr11g0327651' => 'han', 'HanXRQChr12g0359391' => 'han', 'Haze_00972' => 'cav', 'Haze_00973' => 'cav', 'Haze_00974' => 'cav', 'Haze_04747' => 'cav', 'Haze_04749' => 'cav', 'Haze_04750' => 'cav', 'Haze_21217' => 'cav', 'Hma1.2p1_1037F.1_g250680' => 'hma', 'Hma1.2p1_1644F.1_g295320' => 'hma', 'HPP92_011322' => 'vpl', 'HPP92_011323' => 'vpl', 'HPP92_011324' => 'vpl', 'HPP92_011325' => 'vpl', 'HPP92_011326' => 'vpl', 'Hund12205' => 'sun', 'Hund17957' => 'sun', 'Lalb_Chr06g0176771' => 'lal', 'Lalb_Chr18g0056021' => 'lal', 'Lalb_Chr18g0056031' => 'lal', 'Lalb_Chr18g0056041' => 'lal', 'Lalb_Chr20g0107751' => 'lal', 'Lalb_Chr20g0118371' => 'lal', 'Lj1g0010239' => 'lja', 'Lj1g0017101' => 'lja', 'Lj2A1178G40' => 'lonja', 'Lj2A54G84' => 'lonja', 'Lj2g0015248' => 'lja', 'Lj3A761T51' => 'lonja', 'Lj6g0018116' => 'lja', 'Lsat_1_v5_gn_4_136040' => 'lsa', 'Lsat_1_v5_gn_5_187461' => 'lsa', 'Lsat_1_v5_gn_5_77001' => 'lsa', 'Lsat_1_v5_gn_9_4461' => 'lsa', 'Manes.01G210100' => 'mes', 'Manes.03G185600' => 'mes', 'Manes.05G073300' => 'mes', 'Manes.09G120300' => 'mes', 'Manes.15G022100' => 'mes', 'Mapoly0096s0053' => 'mpo', 'MBI03_g14058_MAGBIO' => 'mbi', 'MBI03_g33876_MAGBIO' => 'mbi', 'MBI03_g36854_MAGBIO' => 'mbi', 'MBI17_g11997_MAGBIO' => 'mbi', 'MD03G1269000' => 'mdo', 'MD04G1179600' => 'mdo', 'MD11G1289800' => 'mdo', 'MD12G1194700' => 'mdo', 'MD13G1182100' => 'mdo', 'MD13G1182200' => 'mdo', 'MD16G1182600' => 'mdo', 'Medtr2g021400' => 'mtr', 'Medtr2g021470' => 'mtr', 'Medtr2g105810' => 'mtr', 'Medtr3g033580' => 'mtr', 'Medtr6g007970' => 'mtr', 'Medtr7g056330' => 'mtr', 'Medtr7g074290' => 'mtr', 'Medtr7g074380' => 'mtr', 'Medtr7g094550' => 'mtr', 'Medtr8g069995' => 'mtr', 'MELO3C014345.2' => 'cme', 'MELO3C021395.2' => 'cme', 'Migut.D00262' => 'egut', 'Migut.G00257' => 'egut', 'MSTRG.21575' => 'ama', 'MSTRG.3985' => 'ama', 'Nitab4.5_0000295g0140' => 'nta', 'Nitab4.5_0000732g0140' => 'nta', 'Nitab4.5_0003162g0020' => 'nta', 'Nitab4.5_0006180g0090' => 'nta', 'Nitab4.5_0006390g0010' => 'nta', 'Nitab4.5_0007392g0040' => 'nta', 'Nn1g02140' => 'nnu', 'Nn4g26168' => 'nnu', 'Nn5g26754' => 'nnu', 'Oeu001433.1' => 'oeu', 'Oeu010299.2' => 'oeu', 'Oeu011171.1' => 'oeu', 'Oeu037675.1' => 'oeu', 'Oeu038359.1' => 'oeu', 'Oeu063834.1' => 'oeu', 'Oeu063835.1' => 'oeu', 'Os05g0312000' => 'osa', 'Os07g0211101' => 'osa', 'Os07g0211200' => 'osa', 'Os07g0681500' => 'osa', 'Peaxi162Scf00095g01015' => 'pax', 'Peaxi162Scf00104g00329' => 'pax', 'Peaxi162Scf00161g00137' => 'pax', 'PGR004G1665' => 'pgr', 'PGR031G2937' => 'pgr', 'PGR119G2145' => 'pgr', 'PGSC0003DMG400004351' => 'stu', 'PGSC0003DMG400014625' => 'stu', 'PGSC0003DMG401000943' => 'stu', 'Phvul.001G148600' => 'pvu', 'Phvul.004G001700' => 'pvu', 'Phvul.006G154900' => 'pvu', 'Phvul.008G078200' => 'pvu', 'Phvul.011G136500' => 'pvu', 'Potri.002G215600' => 'ptr', 'Potri.008G201600' => 'ptr', 'Potri.014G138400' => 'ptr', 'Potri.016G142500' => 'ptr', 'Pp3c16_10580' => 'ppa', 'Pp3c5_25280' => 'ppa', 'Prupe.1G150000' => 'ppe', 'Prupe.1G150100' => 'ppe', 'Prupe.6G299600' => 'ppe', 'Prupe.8G245000' => 'ppe', 'Psat0s4927g0040' => 'psa', 'Psat1g052080' => 'psa', 'Psat1g183800' => 'psa', 'Psat3g113840' => 'psa', 'Psat3g126120' => 'psa', 'Psat3g126160' => 'psa', 'Psat3g158760' => 'psa', 'Psat3g158840' => 'psa', 'PSO170G2858' => 'pso', 'PSO339G0606' => 'pso', 'PSO384G4709' => 'pso', 'PSO407G0334' => 'pso', 'QL04p040276' => 'qlo', 'QL06p005458' => 'qlo', 'QL06p005472' => 'qlo', 'QL07p030546' => 'qlo', 'QL07p031519' => 'qlo', 'QL09p050949' => 'qlo', 'QL09p050966' => 'qlo', 'QL09p051067' => 'qlo', 'QL12p022706' => 'qlo', 'RcHm_v2.0_Chr2g0119601' => 'rch', 'RcHm_v2.0_Chr3g0459591' => 'rch', 'RcHm_v2.0_Chr4g0418521' => 'rch', 'RcHm_v2.0_Chr4g0418531' => 'rch', 'RcHm_v2.0_Chr4g0418541' => 'rch', 'RcHm_v2.0_Chr6g0291641' => 'rch', 'Rhsim01G0086300' => 'rsi', 'Rhsim01G0276300' => 'rsi', 'Rhsim01G0276500' => 'rsi', 'Rhsim04G0207700' => 'rsi', 'Rhsim05G0234500' => 'rsi', 'Rhsim13G0022400' => 'rsi', 'Sabra02G0167900' => 'sbr', 'Sabra04G0158500' => 'sbr', 'Sabra08G0159800' => 'sbr', 'Sabra10G0011500' => 'sbr', 'Sabra14G0104400' => 'sbr', 'SalBow2G2440' => 'sbo', 'SalBow4G2265' => 'sbo', 'Sc02g0000060' => 'sci', 'Sc05g0005020' => 'sci', 'Sc13g0003890' => 'sci', 'Sed0014865' => 'sed', 'Sed0017224' => 'sed', 'Sed0026391' => 'sed', 'SEGI_00063' => 'sgi', 'SEGI_10967' => 'sgi', 'SEGI_17510' => 'sgi', 'SEGI_24396' => 'sgi', 'SEGI_39719' => 'sgi', 'SEGI_41392' => 'sgi', 'SGA_v2.0_scaffold11G05794' => 'sas', 'SGA_v2.0_scaffold142G35607' => 'sas', 'SGA_v2.0_scaffold1G00447' => 'sas', 'SHI15388' => 'shi', 'SHI15394' => 'shi', 'SHI15396' => 'shi', 'SHI15399' => 'shi', 'SMO343G0151' => 'smo', 'SMO367G1118' => 'smo', 'Solyc01g080200.3' => 'sly', 'Solyc06g008960.3' => 'sly', 'Solyc09g064780.3' => 'sly', 'Sopen01g031980' => 'spe', 'Sopen06g003710' => 'spe', 'Sopen09g026460' => 'spe', 'Sp3g21240' => 'spa', 'Sp4g30030' => 'spa', 'TAR365G0022' => 'tar', 'TAR365G1023' => 'tar', 'TAR365G1253' => 'tar', 'TAR623G0078' => 'tar', 'TAR623G1721' => 'tar', 'TAR633G0959' => 'tar', 'THA.LOC104802225' => 'tha', 'THA.LOC104804769' => 'tha', 'THA.LOC104808660' => 'tha', 'THA.LOC104812792' => 'tha', 'Thecc.01G284000' => 'tca', 'Thecc.04G220600' => 'tca', 'Thecc.05G268900' => 'tca', 'Thecc.08G171100' => 'tca', 'Thhalv10001284m.g' => 'esa', 'Thhalv10019912m.g' => 'esa', 'TPR.G14189' => 'tpr', 'TPR.G18110' => 'tpr', 'TPR.G18130' => 'tpr', 'TPR.G18131' => 'tpr', 'TPR.G18140' => 'tpr', 'TPR.G24282' => 'tpr', 'TPR.G25221' => 'tpr', 'TPR.G29267' => 'tpr', 'TPR.G35315' => 'tpr', 'TPR.G36173' => 'tpr', 'TWI09G0794' => 'twi', 'TWI59G1348' => 'twi', 'TWI74G0430' => 'twi', 'unitig_26.g8940' => 'ugi', 'unitig_749.g13744' => 'ugi', 'unitig_749.g13745' => 'ugi', 'vmacro08269' => 'vma', 'vmacro14937' => 'vma', 'vmacro20401' => 'vma', 'VMungo0464G1349' => 'vmu', 'VMungo0540G0289' => 'vmu', 'VMungo1215G1590' => 'vmu', 'VMungo1309G0221' => 'vmu', 'VMungo1309G2815' => 'vmu', 'VMungo1383G0239' => 'vmu', 'VMungo1383G2910' => 'vmu', 'Zm00001eb095270' => 'zma', 'Zm00001eb095280' => 'zma', 'Zm00001eb111630' => 'zma', 'Zm00001eb237080' => 'zma', 'Zm00001eb273740' => 'zma', 'Zm00001eb285040' => 'zma', 'Zm00001eb330790' => 'zma', 'Zm00001eb337380' => 'zma' ), 'gf_id' => 'HOM05D001484', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001484' ), 'data_identifier' => 'HOM05D001484', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001484', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p31500' => 'bna', 'A05p00020' => 'bna', 'A07p08820' => 'bna', 'Aa31LG4G3300' => 'aar', 'Aa31LG8G10030' => 'aar', 'Actinidia00731' => 'ach', 'Actinidia11473' => 'ach', 'Actinidia23469' => 'ach', 'Actinidia24318' => 'ach', 'Actinidia40196' => 'ach', 'Actinidia40197' => 'ach', 'Actinidia40198' => 'ach', 'Ah.08g212990' => 'amhyb', 'Ah.15g091720' => 'amhyb', 'AL3G38260' => 'aly', 'AL4G47710' => 'aly', 'Aqoxy2G00671' => 'aox', 'Aqoxy2G03236' => 'aox', 'arahy.Tifrunner.gnm1.ann1.05IDCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KR684' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATY3SJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK6QJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6APGL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IDT7Z9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM073U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ0R87' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LE7RV4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT4QRX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V5ENPK' => 'arhy', 'AT2G48110' => 'ath', 'AT3G23590' => 'ath', 'ATR0626G186' => 'atr', 'ATR1127G141' => 'atr', 'Atru.chr4.2583' => 'acertr', 'Atru.chr5.1358' => 'acertr', 'Atru.chr5.1359' => 'acertr', 'Atru.chr8.46' => 'acertr', 'AUR62002640' => 'cqu', 'AUR62030055' => 'cqu', 'AUR62033713' => 'cqu', 'AUR62033714' => 'cqu', 'AUR62036795' => 'cqu', 'AUR62039891' => 'cqu', 'BcaB02g08737' => 'bca', 'BcaB04g20441' => 'bca', 'BcaB06g26509' => 'bca', 'BcaB06g26510' => 'bca', 'BcaB06g26511' => 'bca', 'BcaB06g26512' => 'bca', 'BcaB06g26513' => 'bca', 'BcaC02g12564' => 'bca', 'BcaC02g12565' => 'bca', 'BcaC02g12794' => 'bca', 'BcaC02g12795' => 'bca', 'BcaC02g12796' => 'bca', 'BcaC06g35541' => 'bca', 'BNapus_Darmor_BZH_scaffold_188p00080' => 'bna', 'BNapus_Darmor_BZH_scaffold_188p00090' => 'bna', 'BolC1t03972H' => 'bol', 'BolC1t03973H' => 'bol', 'BolC4t21680H' => 'bol', 'BolC7t41863H' => 'bol', 'BolSC55t61227H' => 'bol', 'BolSC55t61228H' => 'bol', 'BraA01t03278Z' => 'bra', 'BraA05t18998Z' => 'bra', 'BraA07t28673Z' => 'bra', 'C01p40150' => 'bna', 'C05p12370' => 'bna', 'C07p13680' => 'bna', 'CAN.G1006.16' => 'can', 'CAN.G1006.17' => 'can', 'CAN.G1170.2' => 'can', 'CAN.G962.7' => 'can', 'CANSAT25G2179' => 'cansat', 'CANSAT78G1573' => 'cansat', 'CARHR099510' => 'chi', 'CARHR143510' => 'chi', 'Carub.0003s2380' => 'cru', 'Carub.0004s3082' => 'cru', 'Ca_00614_v3' => 'car', 'Ca_07801_v3' => 'car', 'Ca_08567_v3' => 'car', 'Ca_09571_v3' => 'car', 'CBR_g19290' => 'cbr', 'Cc01_g19770' => 'ccan', 'Cc03_g03030' => 'ccan', 'CDE07G0968' => 'cde', 'CDE09G1441' => 'cde', 'Cfa006103' => 'cfa', 'Cfa015573' => 'cfa', 'Cfa016988' => 'cfa', 'Ciclev10006738m.g' => 'ccl', 'Ciclev10010920m.g' => 'ccl', 'Ciclev10018517m.g' => 'ccl', 'CiPaw.01G159200' => 'cil', 'CiPaw.02G091000' => 'cil', 'CiPaw.02G091100' => 'cil', 'CiPaw.08G103100' => 'cil', 'CiPaw.09G224900' => 'cil', 'ClCG06G005740' => 'cla', 'ClCG07G000090' => 'cla', 'ClCG07G000100' => 'cla', 'COL.COLO4_09143' => 'col', 'COL.COLO4_25124' => 'col', 'Cpa.g.sc16.34' => 'cpa', 'Cpa.g.sc3504.1' => 'cpa', 'Cpa.g.sc60.37' => 'cpa', 'CsaV3_6G018520' => 'csa', 'CsaV3_6G036860' => 'csa', 'CSS0001072' => 'camsi', 'CSS0020208' => 'camsi', 'CSS0021253' => 'camsi', 'CSS0022190' => 'camsi', 'CSS0036150' => 'camsi', 'CSS0040442' => 'camsi', 'CSS0042300' => 'camsi', 'CSS0045298' => 'camsi', 'DCAR_012449' => 'dca', 'DCAR_018405' => 'dca', 'DCAR_024573' => 'dca', 'DCAR_030591' => 'dca', 'Dinv16926' => 'din', 'Dinv32963' => 'din', 'Dinv38382' => 'din', 'Dinv38383' => 'din', 'Duzib133G0974' => 'dzi', 'Duzib138G1867' => 'dzi', 'Duzib211G0420' => 'dzi', 'Duzib212G0930' => 'dzi', 'ECA234G1645' => 'eca', 'ECA247G3467' => 'eca', 'ECA248G1703' => 'eca', 'EL10Ac3g06327' => 'bvu', 'EL10Ac7g17204' => 'bvu', 'Eucgr.A00855' => 'egr', 'Eucgr.A00858' => 'egr', 'Eucgr.H01520' => 'egr', 'Eucgr.H03604' => 'egr', 'Eucgr.L03465' => 'egr', 'Eucgr.L03466' => 'egr', 'FAN01G0988' => 'fan', 'FAN02G3892' => 'fan', 'FAN05G3381' => 'fan', 'FAN07G0967' => 'fan', 'FAN07G1493' => 'fan', 'FAN08G3125' => 'fan', 'FAN09G0402' => 'fan', 'FAN12G2594' => 'fan', 'FAN12G3879' => 'fan', 'FAN14G1546' => 'fan', 'FAN15G3626' => 'fan', 'FAN17G0588' => 'fan', 'FAN17G0609' => 'fan', 'FAN18G2817' => 'fan', 'FAN19G1305' => 'fan', 'FAN20G1787' => 'fan', 'FAN22G0073' => 'fan', 'FAN22G0352' => 'fan', 'FAN22G0368' => 'fan', 'FAN22G2273' => 'fan', 'FAN24G1998' => 'fan', 'FAN27G1317' => 'fan', 'FvH4_2g23980' => 'fve', 'FvH4_4g14380' => 'fve', 'FvH4_4g14390' => 'fve', 'FvH4_6g09250' => 'fve', 'Glyma.03G151100' => 'gma', 'Glyma.04G122550' => 'gma', 'Glyma.05G001600' => 'gma', 'Glyma.09G270766' => 'gma', 'Glyma.09G270832' => 'gma', 'Glyma.13G209800' => 'gma', 'Glyma.15G102800' => 'gma', 'Glyma.18G218900' => 'gma', 'Glyma.19G001500' => 'gma', 'Glyma.19G153600' => 'gma', 'Gohir.A02G028600' => 'ghi', 'Gohir.A08G045000' => 'ghi', 'Gohir.A11G120500' => 'ghi', 'Gohir.A12G006200' => 'ghi', 'Gohir.A12G006250' => 'ghi', 'Gohir.D02G036300' => 'ghi', 'Gohir.D08G054700' => 'ghi', 'Gohir.D11G125600' => 'ghi', 'Gohir.D12G005700' => 'ghi', 'Gorai.004G055200' => 'gra', 'Gorai.005G040400' => 'gra', 'Gorai.007G134500' => 'gra', 'Gorai.008G005500' => 'gra', 'GSVIVG01011094001' => 'vvi', 'GSVIVG01017879001' => 'vvi', 'GSVIVG01025988001' => 'vvi', 'GSVIVG01029847001' => 'vvi', 'HanXRQChr10g0282901' => 'han', 'HanXRQChr10g0310371' => 'han', 'HanXRQChr10g0315041' => 'han', 'HanXRQChr11g0327651' => 'han', 'HanXRQChr12g0359391' => 'han', 'Haze_00972' => 'cav', 'Haze_00973' => 'cav', 'Haze_00974' => 'cav', 'Haze_04747' => 'cav', 'Haze_04749' => 'cav', 'Haze_04750' => 'cav', 'Haze_21217' => 'cav', 'Hma1.2p1_1037F.1_g250680' => 'hma', 'Hma1.2p1_1644F.1_g295320' => 'hma', 'HPP92_011322' => 'vpl', 'HPP92_011323' => 'vpl', 'HPP92_011324' => 'vpl', 'HPP92_011325' => 'vpl', 'HPP92_011326' => 'vpl', 'Hund12205' => 'sun', 'Hund17957' => 'sun', 'Lalb_Chr06g0176771' => 'lal', 'Lalb_Chr18g0056021' => 'lal', 'Lalb_Chr18g0056031' => 'lal', 'Lalb_Chr18g0056041' => 'lal', 'Lalb_Chr20g0107751' => 'lal', 'Lalb_Chr20g0118371' => 'lal', 'Lj1g0010239' => 'lja', 'Lj1g0017101' => 'lja', 'Lj2A1178G40' => 'lonja', 'Lj2A54G84' => 'lonja', 'Lj2g0015248' => 'lja', 'Lj3A761T51' => 'lonja', 'Lj6g0018116' => 'lja', 'Lsat_1_v5_gn_4_136040' => 'lsa', 'Lsat_1_v5_gn_5_187461' => 'lsa', 'Lsat_1_v5_gn_5_77001' => 'lsa', 'Lsat_1_v5_gn_9_4461' => 'lsa', 'Manes.01G210100' => 'mes', 'Manes.03G185600' => 'mes', 'Manes.05G073300' => 'mes', 'Manes.09G120300' => 'mes', 'Manes.15G022100' => 'mes', 'Mapoly0096s0053' => 'mpo', 'MBI03_g14058_MAGBIO' => 'mbi', 'MBI03_g33876_MAGBIO' => 'mbi', 'MBI03_g36854_MAGBIO' => 'mbi', 'MBI17_g11997_MAGBIO' => 'mbi', 'MD03G1269000' => 'mdo', 'MD04G1179600' => 'mdo', 'MD11G1289800' => 'mdo', 'MD12G1194700' => 'mdo', 'MD13G1182100' => 'mdo', 'MD13G1182200' => 'mdo', 'MD16G1182600' => 'mdo', 'Medtr2g021400' => 'mtr', 'Medtr2g021470' => 'mtr', 'Medtr2g105810' => 'mtr', 'Medtr3g033580' => 'mtr', 'Medtr6g007970' => 'mtr', 'Medtr7g056330' => 'mtr', 'Medtr7g074290' => 'mtr', 'Medtr7g074380' => 'mtr', 'Medtr7g094550' => 'mtr', 'Medtr8g069995' => 'mtr', 'MELO3C014345.2' => 'cme', 'MELO3C021395.2' => 'cme', 'Migut.D00262' => 'egut', 'Migut.G00257' => 'egut', 'MSTRG.21575' => 'ama', 'MSTRG.3985' => 'ama', 'Nitab4.5_0000295g0140' => 'nta', 'Nitab4.5_0000732g0140' => 'nta', 'Nitab4.5_0003162g0020' => 'nta', 'Nitab4.5_0006180g0090' => 'nta', 'Nitab4.5_0006390g0010' => 'nta', 'Nitab4.5_0007392g0040' => 'nta', 'Nn1g02140' => 'nnu', 'Nn4g26168' => 'nnu', 'Nn5g26754' => 'nnu', 'Oeu001433.1' => 'oeu', 'Oeu010299.2' => 'oeu', 'Oeu011171.1' => 'oeu', 'Oeu037675.1' => 'oeu', 'Oeu038359.1' => 'oeu', 'Oeu063834.1' => 'oeu', 'Oeu063835.1' => 'oeu', 'Os05g0312000' => 'osa', 'Os07g0211101' => 'osa', 'Os07g0211200' => 'osa', 'Os07g0681500' => 'osa', 'Peaxi162Scf00095g01015' => 'pax', 'Peaxi162Scf00104g00329' => 'pax', 'Peaxi162Scf00161g00137' => 'pax', 'PGR004G1665' => 'pgr', 'PGR031G2937' => 'pgr', 'PGR119G2145' => 'pgr', 'PGSC0003DMG400004351' => 'stu', 'PGSC0003DMG400014625' => 'stu', 'PGSC0003DMG401000943' => 'stu', 'Phvul.001G148600' => 'pvu', 'Phvul.004G001700' => 'pvu', 'Phvul.006G154900' => 'pvu', 'Phvul.008G078200' => 'pvu', 'Phvul.011G136500' => 'pvu', 'Potri.002G215600' => 'ptr', 'Potri.008G201600' => 'ptr', 'Potri.014G138400' => 'ptr', 'Potri.016G142500' => 'ptr', 'Pp3c16_10580' => 'ppa', 'Pp3c5_25280' => 'ppa', 'Prupe.1G150000' => 'ppe', 'Prupe.1G150100' => 'ppe', 'Prupe.6G299600' => 'ppe', 'Prupe.8G245000' => 'ppe', 'Psat0s4927g0040' => 'psa', 'Psat1g052080' => 'psa', 'Psat1g183800' => 'psa', 'Psat3g113840' => 'psa', 'Psat3g126120' => 'psa', 'Psat3g126160' => 'psa', 'Psat3g158760' => 'psa', 'Psat3g158840' => 'psa', 'PSO170G2858' => 'pso', 'PSO339G0606' => 'pso', 'PSO384G4709' => 'pso', 'PSO407G0334' => 'pso', 'QL04p040276' => 'qlo', 'QL06p005458' => 'qlo', 'QL06p005472' => 'qlo', 'QL07p030546' => 'qlo', 'QL07p031519' => 'qlo', 'QL09p050949' => 'qlo', 'QL09p050966' => 'qlo', 'QL09p051067' => 'qlo', 'QL12p022706' => 'qlo', 'RcHm_v2.0_Chr2g0119601' => 'rch', 'RcHm_v2.0_Chr3g0459591' => 'rch', 'RcHm_v2.0_Chr4g0418521' => 'rch', 'RcHm_v2.0_Chr4g0418531' => 'rch', 'RcHm_v2.0_Chr4g0418541' => 'rch', 'RcHm_v2.0_Chr6g0291641' => 'rch', 'Rhsim01G0086300' => 'rsi', 'Rhsim01G0276300' => 'rsi', 'Rhsim01G0276500' => 'rsi', 'Rhsim04G0207700' => 'rsi', 'Rhsim05G0234500' => 'rsi', 'Rhsim13G0022400' => 'rsi', 'Sabra02G0167900' => 'sbr', 'Sabra04G0158500' => 'sbr', 'Sabra08G0159800' => 'sbr', 'Sabra10G0011500' => 'sbr', 'Sabra14G0104400' => 'sbr', 'SalBow2G2440' => 'sbo', 'SalBow4G2265' => 'sbo', 'Sc02g0000060' => 'sci', 'Sc05g0005020' => 'sci', 'Sc13g0003890' => 'sci', 'Sed0014865' => 'sed', 'Sed0017224' => 'sed', 'Sed0026391' => 'sed', 'SEGI_00063' => 'sgi', 'SEGI_10967' => 'sgi', 'SEGI_17510' => 'sgi', 'SEGI_24396' => 'sgi', 'SEGI_39719' => 'sgi', 'SEGI_41392' => 'sgi', 'SGA_v2.0_scaffold11G05794' => 'sas', 'SGA_v2.0_scaffold142G35607' => 'sas', 'SGA_v2.0_scaffold1G00447' => 'sas', 'SHI15388' => 'shi', 'SHI15394' => 'shi', 'SHI15396' => 'shi', 'SHI15399' => 'shi', 'SMO343G0151' => 'smo', 'SMO367G1118' => 'smo', 'Solyc01g080200.3' => 'sly', 'Solyc06g008960.3' => 'sly', 'Solyc09g064780.3' => 'sly', 'Sopen01g031980' => 'spe', 'Sopen06g003710' => 'spe', 'Sopen09g026460' => 'spe', 'Sp3g21240' => 'spa', 'Sp4g30030' => 'spa', 'TAR365G0022' => 'tar', 'TAR365G1023' => 'tar', 'TAR365G1253' => 'tar', 'TAR623G0078' => 'tar', 'TAR623G1721' => 'tar', 'TAR633G0959' => 'tar', 'THA.LOC104802225' => 'tha', 'THA.LOC104804769' => 'tha', 'THA.LOC104808660' => 'tha', 'THA.LOC104812792' => 'tha', 'Thecc.01G284000' => 'tca', 'Thecc.04G220600' => 'tca', 'Thecc.05G268900' => 'tca', 'Thecc.08G171100' => 'tca', 'Thhalv10001284m.g' => 'esa', 'Thhalv10019912m.g' => 'esa', 'TPR.G14189' => 'tpr', 'TPR.G18110' => 'tpr', 'TPR.G18130' => 'tpr', 'TPR.G18131' => 'tpr', 'TPR.G18140' => 'tpr', 'TPR.G24282' => 'tpr', 'TPR.G25221' => 'tpr', 'TPR.G29267' => 'tpr', 'TPR.G35315' => 'tpr', 'TPR.G36173' => 'tpr', 'TWI09G0794' => 'twi', 'TWI59G1348' => 'twi', 'TWI74G0430' => 'twi', 'unitig_26.g8940' => 'ugi', 'unitig_749.g13744' => 'ugi', 'unitig_749.g13745' => 'ugi', 'vmacro08269' => 'vma', 'vmacro14937' => 'vma', 'vmacro20401' => 'vma', 'VMungo0464G1349' => 'vmu', 'VMungo0540G0289' => 'vmu', 'VMungo1215G1590' => 'vmu', 'VMungo1309G0221' => 'vmu', 'VMungo1309G2815' => 'vmu', 'VMungo1383G0239' => 'vmu', 'VMungo1383G2910' => 'vmu', 'Zm00001eb095270' => 'zma', 'Zm00001eb095280' => 'zma', 'Zm00001eb111630' => 'zma', 'Zm00001eb237080' => 'zma', 'Zm00001eb273740' => 'zma', 'Zm00001eb285040' => 'zma', 'Zm00001eb330790' => 'zma', 'Zm00001eb337380' => 'zma' ) $gf_id = 'HOM05D001484' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001484' ) $data_identifier = 'HOM05D001484' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 2, 'aly' => (int) 2, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 22, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 7, 'hma' => (int) 2, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 7, 'mtr' => (int) 10, 'cme' => (int) 2, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 4, 'ppa' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 4, 'qlo' => (int) 9, 'rch' => (int) 6, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 10, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 7, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb337380' $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' => 'HOM05D001484', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p31500' => 'bna', 'A05p00020' => 'bna', 'A07p08820' => 'bna', 'Aa31LG4G3300' => 'aar', 'Aa31LG8G10030' => 'aar', 'Actinidia00731' => 'ach', 'Actinidia11473' => 'ach', 'Actinidia23469' => 'ach', 'Actinidia24318' => 'ach', 'Actinidia40196' => 'ach', 'Actinidia40197' => 'ach', 'Actinidia40198' => 'ach', 'Ah.08g212990' => 'amhyb', 'Ah.15g091720' => 'amhyb', 'AL3G38260' => 'aly', 'AL4G47710' => 'aly', 'Aqoxy2G00671' => 'aox', 'Aqoxy2G03236' => 'aox', 'arahy.Tifrunner.gnm1.ann1.05IDCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KR684' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATY3SJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK6QJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6APGL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IDT7Z9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM073U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ0R87' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LE7RV4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT4QRX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V5ENPK' => 'arhy', 'AT2G48110' => 'ath', 'AT3G23590' => 'ath', 'ATR0626G186' => 'atr', 'ATR1127G141' => 'atr', 'Atru.chr4.2583' => 'acertr', 'Atru.chr5.1358' => 'acertr', 'Atru.chr5.1359' => 'acertr', 'Atru.chr8.46' => 'acertr', 'AUR62002640' => 'cqu', 'AUR62030055' => 'cqu', 'AUR62033713' => 'cqu', 'AUR62033714' => 'cqu', 'AUR62036795' => 'cqu', 'AUR62039891' => 'cqu', 'BcaB02g08737' => 'bca', 'BcaB04g20441' => 'bca', 'BcaB06g26509' => 'bca', 'BcaB06g26510' => 'bca', 'BcaB06g26511' => 'bca', 'BcaB06g26512' => 'bca', 'BcaB06g26513' => 'bca', 'BcaC02g12564' => 'bca', 'BcaC02g12565' => 'bca', 'BcaC02g12794' => 'bca', 'BcaC02g12795' => 'bca', 'BcaC02g12796' => 'bca', 'BcaC06g35541' => 'bca', 'BNapus_Darmor_BZH_scaffold_188p00080' => 'bna', 'BNapus_Darmor_BZH_scaffold_188p00090' => 'bna', 'BolC1t03972H' => 'bol', 'BolC1t03973H' => 'bol', 'BolC4t21680H' => 'bol', 'BolC7t41863H' => 'bol', 'BolSC55t61227H' => 'bol', 'BolSC55t61228H' => 'bol', 'BraA01t03278Z' => 'bra', 'BraA05t18998Z' => 'bra', 'BraA07t28673Z' => 'bra', 'C01p40150' => 'bna', 'C05p12370' => 'bna', 'C07p13680' => 'bna', 'CAN.G1006.16' => 'can', 'CAN.G1006.17' => 'can', 'CAN.G1170.2' => 'can', 'CAN.G962.7' => 'can', 'CANSAT25G2179' => 'cansat', 'CANSAT78G1573' => 'cansat', 'CARHR099510' => 'chi', 'CARHR143510' => 'chi', 'Carub.0003s2380' => 'cru', 'Carub.0004s3082' => 'cru', 'Ca_00614_v3' => 'car', 'Ca_07801_v3' => 'car', 'Ca_08567_v3' => 'car', 'Ca_09571_v3' => 'car', 'CBR_g19290' => 'cbr', 'Cc01_g19770' => 'ccan', 'Cc03_g03030' => 'ccan', 'CDE07G0968' => 'cde', 'CDE09G1441' => 'cde', 'Cfa006103' => 'cfa', 'Cfa015573' => 'cfa', 'Cfa016988' => 'cfa', 'Ciclev10006738m.g' => 'ccl', 'Ciclev10010920m.g' => 'ccl', 'Ciclev10018517m.g' => 'ccl', 'CiPaw.01G159200' => 'cil', 'CiPaw.02G091000' => 'cil', 'CiPaw.02G091100' => 'cil', 'CiPaw.08G103100' => 'cil', 'CiPaw.09G224900' => 'cil', 'ClCG06G005740' => 'cla', 'ClCG07G000090' => 'cla', 'ClCG07G000100' => 'cla', 'COL.COLO4_09143' => 'col', 'COL.COLO4_25124' => 'col', 'Cpa.g.sc16.34' => 'cpa', 'Cpa.g.sc3504.1' => 'cpa', 'Cpa.g.sc60.37' => 'cpa', 'CsaV3_6G018520' => 'csa', 'CsaV3_6G036860' => 'csa', 'CSS0001072' => 'camsi', 'CSS0020208' => 'camsi', 'CSS0021253' => 'camsi', 'CSS0022190' => 'camsi', 'CSS0036150' => 'camsi', 'CSS0040442' => 'camsi', 'CSS0042300' => 'camsi', 'CSS0045298' => 'camsi', 'DCAR_012449' => 'dca', 'DCAR_018405' => 'dca', 'DCAR_024573' => 'dca', 'DCAR_030591' => 'dca', 'Dinv16926' => 'din', 'Dinv32963' => 'din', 'Dinv38382' => 'din', 'Dinv38383' => 'din', 'Duzib133G0974' => 'dzi', 'Duzib138G1867' => 'dzi', 'Duzib211G0420' => 'dzi', 'Duzib212G0930' => 'dzi', 'ECA234G1645' => 'eca', 'ECA247G3467' => 'eca', 'ECA248G1703' => 'eca', 'EL10Ac3g06327' => 'bvu', 'EL10Ac7g17204' => 'bvu', 'Eucgr.A00855' => 'egr', 'Eucgr.A00858' => 'egr', 'Eucgr.H01520' => 'egr', 'Eucgr.H03604' => 'egr', 'Eucgr.L03465' => 'egr', 'Eucgr.L03466' => 'egr', 'FAN01G0988' => 'fan', 'FAN02G3892' => 'fan', 'FAN05G3381' => 'fan', 'FAN07G0967' => 'fan', 'FAN07G1493' => 'fan', 'FAN08G3125' => 'fan', 'FAN09G0402' => 'fan', 'FAN12G2594' => 'fan', 'FAN12G3879' => 'fan', 'FAN14G1546' => 'fan', 'FAN15G3626' => 'fan', 'FAN17G0588' => 'fan', 'FAN17G0609' => 'fan', 'FAN18G2817' => 'fan', 'FAN19G1305' => 'fan', 'FAN20G1787' => 'fan', 'FAN22G0073' => 'fan', 'FAN22G0352' => 'fan', 'FAN22G0368' => 'fan', 'FAN22G2273' => 'fan', 'FAN24G1998' => 'fan', 'FAN27G1317' => 'fan', 'FvH4_2g23980' => 'fve', 'FvH4_4g14380' => 'fve', 'FvH4_4g14390' => 'fve', 'FvH4_6g09250' => 'fve', 'Glyma.03G151100' => 'gma', 'Glyma.04G122550' => 'gma', 'Glyma.05G001600' => 'gma', 'Glyma.09G270766' => 'gma', 'Glyma.09G270832' => 'gma', 'Glyma.13G209800' => 'gma', 'Glyma.15G102800' => 'gma', 'Glyma.18G218900' => 'gma', 'Glyma.19G001500' => 'gma', 'Glyma.19G153600' => 'gma', 'Gohir.A02G028600' => 'ghi', 'Gohir.A08G045000' => 'ghi', 'Gohir.A11G120500' => 'ghi', 'Gohir.A12G006200' => 'ghi', 'Gohir.A12G006250' => 'ghi', 'Gohir.D02G036300' => 'ghi', 'Gohir.D08G054700' => 'ghi', 'Gohir.D11G125600' => 'ghi', 'Gohir.D12G005700' => 'ghi', 'Gorai.004G055200' => 'gra', 'Gorai.005G040400' => 'gra', 'Gorai.007G134500' => 'gra', 'Gorai.008G005500' => 'gra', 'GSVIVG01011094001' => 'vvi', 'GSVIVG01017879001' => 'vvi', 'GSVIVG01025988001' => 'vvi', 'GSVIVG01029847001' => 'vvi', 'HanXRQChr10g0282901' => 'han', 'HanXRQChr10g0310371' => 'han', 'HanXRQChr10g0315041' => 'han', 'HanXRQChr11g0327651' => 'han', 'HanXRQChr12g0359391' => 'han', 'Haze_00972' => 'cav', 'Haze_00973' => 'cav', 'Haze_00974' => 'cav', 'Haze_04747' => 'cav', 'Haze_04749' => 'cav', 'Haze_04750' => 'cav', 'Haze_21217' => 'cav', 'Hma1.2p1_1037F.1_g250680' => 'hma', 'Hma1.2p1_1644F.1_g295320' => 'hma', 'HPP92_011322' => 'vpl', 'HPP92_011323' => 'vpl', 'HPP92_011324' => 'vpl', 'HPP92_011325' => 'vpl', 'HPP92_011326' => 'vpl', 'Hund12205' => 'sun', 'Hund17957' => 'sun', 'Lalb_Chr06g0176771' => 'lal', 'Lalb_Chr18g0056021' => 'lal', 'Lalb_Chr18g0056031' => 'lal', 'Lalb_Chr18g0056041' => 'lal', 'Lalb_Chr20g0107751' => 'lal', 'Lalb_Chr20g0118371' => 'lal', 'Lj1g0010239' => 'lja', 'Lj1g0017101' => 'lja', 'Lj2A1178G40' => 'lonja', 'Lj2A54G84' => 'lonja', 'Lj2g0015248' => 'lja', 'Lj3A761T51' => 'lonja', 'Lj6g0018116' => 'lja', 'Lsat_1_v5_gn_4_136040' => 'lsa', 'Lsat_1_v5_gn_5_187461' => 'lsa', 'Lsat_1_v5_gn_5_77001' => 'lsa', 'Lsat_1_v5_gn_9_4461' => 'lsa', 'Manes.01G210100' => 'mes', 'Manes.03G185600' => 'mes', 'Manes.05G073300' => 'mes', 'Manes.09G120300' => 'mes', 'Manes.15G022100' => 'mes', 'Mapoly0096s0053' => 'mpo', 'MBI03_g14058_MAGBIO' => 'mbi', 'MBI03_g33876_MAGBIO' => 'mbi', 'MBI03_g36854_MAGBIO' => 'mbi', 'MBI17_g11997_MAGBIO' => 'mbi', 'MD03G1269000' => 'mdo', 'MD04G1179600' => 'mdo', 'MD11G1289800' => 'mdo', 'MD12G1194700' => 'mdo', 'MD13G1182100' => 'mdo', 'MD13G1182200' => 'mdo', 'MD16G1182600' => 'mdo', 'Medtr2g021400' => 'mtr', 'Medtr2g021470' => 'mtr', 'Medtr2g105810' => 'mtr', 'Medtr3g033580' => 'mtr', 'Medtr6g007970' => 'mtr', 'Medtr7g056330' => 'mtr', 'Medtr7g074290' => 'mtr', 'Medtr7g074380' => 'mtr', 'Medtr7g094550' => 'mtr', 'Medtr8g069995' => 'mtr', 'MELO3C014345.2' => 'cme', 'MELO3C021395.2' => 'cme', 'Migut.D00262' => 'egut', 'Migut.G00257' => 'egut', 'MSTRG.21575' => 'ama', 'MSTRG.3985' => 'ama', 'Nitab4.5_0000295g0140' => 'nta', 'Nitab4.5_0000732g0140' => 'nta', 'Nitab4.5_0003162g0020' => 'nta', 'Nitab4.5_0006180g0090' => 'nta', 'Nitab4.5_0006390g0010' => 'nta', 'Nitab4.5_0007392g0040' => 'nta', 'Nn1g02140' => 'nnu', 'Nn4g26168' => 'nnu', 'Nn5g26754' => 'nnu', 'Oeu001433.1' => 'oeu', 'Oeu010299.2' => 'oeu', 'Oeu011171.1' => 'oeu', 'Oeu037675.1' => 'oeu', 'Oeu038359.1' => 'oeu', 'Oeu063834.1' => 'oeu', 'Oeu063835.1' => 'oeu', 'Os05g0312000' => 'osa', 'Os07g0211101' => 'osa', 'Os07g0211200' => 'osa', 'Os07g0681500' => 'osa', 'Peaxi162Scf00095g01015' => 'pax', 'Peaxi162Scf00104g00329' => 'pax', 'Peaxi162Scf00161g00137' => 'pax', 'PGR004G1665' => 'pgr', 'PGR031G2937' => 'pgr', 'PGR119G2145' => 'pgr', 'PGSC0003DMG400004351' => 'stu', 'PGSC0003DMG400014625' => 'stu', 'PGSC0003DMG401000943' => 'stu', 'Phvul.001G148600' => 'pvu', 'Phvul.004G001700' => 'pvu', 'Phvul.006G154900' => 'pvu', 'Phvul.008G078200' => 'pvu', 'Phvul.011G136500' => 'pvu', 'Potri.002G215600' => 'ptr', 'Potri.008G201600' => 'ptr', 'Potri.014G138400' => 'ptr', 'Potri.016G142500' => 'ptr', 'Pp3c16_10580' => 'ppa', 'Pp3c5_25280' => 'ppa', 'Prupe.1G150000' => 'ppe', 'Prupe.1G150100' => 'ppe', 'Prupe.6G299600' => 'ppe', 'Prupe.8G245000' => 'ppe', 'Psat0s4927g0040' => 'psa', 'Psat1g052080' => 'psa', 'Psat1g183800' => 'psa', 'Psat3g113840' => 'psa', 'Psat3g126120' => 'psa', 'Psat3g126160' => 'psa', 'Psat3g158760' => 'psa', 'Psat3g158840' => 'psa', 'PSO170G2858' => 'pso', 'PSO339G0606' => 'pso', 'PSO384G4709' => 'pso', 'PSO407G0334' => 'pso', 'QL04p040276' => 'qlo', 'QL06p005458' => 'qlo', 'QL06p005472' => 'qlo', 'QL07p030546' => 'qlo', 'QL07p031519' => 'qlo', 'QL09p050949' => 'qlo', 'QL09p050966' => 'qlo', 'QL09p051067' => 'qlo', 'QL12p022706' => 'qlo', 'RcHm_v2.0_Chr2g0119601' => 'rch', 'RcHm_v2.0_Chr3g0459591' => 'rch', 'RcHm_v2.0_Chr4g0418521' => 'rch', 'RcHm_v2.0_Chr4g0418531' => 'rch', 'RcHm_v2.0_Chr4g0418541' => 'rch', 'RcHm_v2.0_Chr6g0291641' => 'rch', 'Rhsim01G0086300' => 'rsi', 'Rhsim01G0276300' => 'rsi', 'Rhsim01G0276500' => 'rsi', 'Rhsim04G0207700' => 'rsi', 'Rhsim05G0234500' => 'rsi', 'Rhsim13G0022400' => 'rsi', 'Sabra02G0167900' => 'sbr', 'Sabra04G0158500' => 'sbr', 'Sabra08G0159800' => 'sbr', 'Sabra10G0011500' => 'sbr', 'Sabra14G0104400' => 'sbr', 'SalBow2G2440' => 'sbo', 'SalBow4G2265' => 'sbo', 'Sc02g0000060' => 'sci', 'Sc05g0005020' => 'sci', 'Sc13g0003890' => 'sci', 'Sed0014865' => 'sed', 'Sed0017224' => 'sed', 'Sed0026391' => 'sed', 'SEGI_00063' => 'sgi', 'SEGI_10967' => 'sgi', 'SEGI_17510' => 'sgi', 'SEGI_24396' => 'sgi', 'SEGI_39719' => 'sgi', 'SEGI_41392' => 'sgi', 'SGA_v2.0_scaffold11G05794' => 'sas', 'SGA_v2.0_scaffold142G35607' => 'sas', 'SGA_v2.0_scaffold1G00447' => 'sas', 'SHI15388' => 'shi', 'SHI15394' => 'shi', 'SHI15396' => 'shi', 'SHI15399' => 'shi', 'SMO343G0151' => 'smo', 'SMO367G1118' => 'smo', 'Solyc01g080200.3' => 'sly', 'Solyc06g008960.3' => 'sly', 'Solyc09g064780.3' => 'sly', 'Sopen01g031980' => 'spe', 'Sopen06g003710' => 'spe', 'Sopen09g026460' => 'spe', 'Sp3g21240' => 'spa', 'Sp4g30030' => 'spa', 'TAR365G0022' => 'tar', 'TAR365G1023' => 'tar', 'TAR365G1253' => 'tar', 'TAR623G0078' => 'tar', 'TAR623G1721' => 'tar', 'TAR633G0959' => 'tar', 'THA.LOC104802225' => 'tha', 'THA.LOC104804769' => 'tha', 'THA.LOC104808660' => 'tha', 'THA.LOC104812792' => 'tha', 'Thecc.01G284000' => 'tca', 'Thecc.04G220600' => 'tca', 'Thecc.05G268900' => 'tca', 'Thecc.08G171100' => 'tca', 'Thhalv10001284m.g' => 'esa', 'Thhalv10019912m.g' => 'esa', 'TPR.G14189' => 'tpr', 'TPR.G18110' => 'tpr', 'TPR.G18130' => 'tpr', 'TPR.G18131' => 'tpr', 'TPR.G18140' => 'tpr', 'TPR.G24282' => 'tpr', 'TPR.G25221' => 'tpr', 'TPR.G29267' => 'tpr', 'TPR.G35315' => 'tpr', 'TPR.G36173' => 'tpr', 'TWI09G0794' => 'twi', 'TWI59G1348' => 'twi', 'TWI74G0430' => 'twi', 'unitig_26.g8940' => 'ugi', 'unitig_749.g13744' => 'ugi', 'unitig_749.g13745' => 'ugi', 'vmacro08269' => 'vma', 'vmacro14937' => 'vma', 'vmacro20401' => 'vma', 'VMungo0464G1349' => 'vmu', 'VMungo0540G0289' => 'vmu', 'VMungo1215G1590' => 'vmu', 'VMungo1309G0221' => 'vmu', 'VMungo1309G2815' => 'vmu', 'VMungo1383G0239' => 'vmu', 'VMungo1383G2910' => 'vmu', 'Zm00001eb095270' => 'zma', 'Zm00001eb095280' => 'zma', 'Zm00001eb111630' => 'zma', 'Zm00001eb237080' => 'zma', 'Zm00001eb273740' => 'zma', 'Zm00001eb285040' => 'zma', 'Zm00001eb330790' => 'zma', 'Zm00001eb337380' => 'zma' ), 'gf_id' => 'HOM05D001484', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001484' ), 'data_identifier' => 'HOM05D001484', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001484', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p31500' => 'bna', 'A05p00020' => 'bna', 'A07p08820' => 'bna', 'Aa31LG4G3300' => 'aar', 'Aa31LG8G10030' => 'aar', 'Actinidia00731' => 'ach', 'Actinidia11473' => 'ach', 'Actinidia23469' => 'ach', 'Actinidia24318' => 'ach', 'Actinidia40196' => 'ach', 'Actinidia40197' => 'ach', 'Actinidia40198' => 'ach', 'Ah.08g212990' => 'amhyb', 'Ah.15g091720' => 'amhyb', 'AL3G38260' => 'aly', 'AL4G47710' => 'aly', 'Aqoxy2G00671' => 'aox', 'Aqoxy2G03236' => 'aox', 'arahy.Tifrunner.gnm1.ann1.05IDCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KR684' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATY3SJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK6QJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6APGL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IDT7Z9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM073U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ0R87' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LE7RV4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT4QRX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V5ENPK' => 'arhy', 'AT2G48110' => 'ath', 'AT3G23590' => 'ath', 'ATR0626G186' => 'atr', 'ATR1127G141' => 'atr', 'Atru.chr4.2583' => 'acertr', 'Atru.chr5.1358' => 'acertr', 'Atru.chr5.1359' => 'acertr', 'Atru.chr8.46' => 'acertr', 'AUR62002640' => 'cqu', 'AUR62030055' => 'cqu', 'AUR62033713' => 'cqu', 'AUR62033714' => 'cqu', 'AUR62036795' => 'cqu', 'AUR62039891' => 'cqu', 'BcaB02g08737' => 'bca', 'BcaB04g20441' => 'bca', 'BcaB06g26509' => 'bca', 'BcaB06g26510' => 'bca', 'BcaB06g26511' => 'bca', 'BcaB06g26512' => 'bca', 'BcaB06g26513' => 'bca', 'BcaC02g12564' => 'bca', 'BcaC02g12565' => 'bca', 'BcaC02g12794' => 'bca', 'BcaC02g12795' => 'bca', 'BcaC02g12796' => 'bca', 'BcaC06g35541' => 'bca', 'BNapus_Darmor_BZH_scaffold_188p00080' => 'bna', 'BNapus_Darmor_BZH_scaffold_188p00090' => 'bna', 'BolC1t03972H' => 'bol', 'BolC1t03973H' => 'bol', 'BolC4t21680H' => 'bol', 'BolC7t41863H' => 'bol', 'BolSC55t61227H' => 'bol', 'BolSC55t61228H' => 'bol', 'BraA01t03278Z' => 'bra', 'BraA05t18998Z' => 'bra', 'BraA07t28673Z' => 'bra', 'C01p40150' => 'bna', 'C05p12370' => 'bna', 'C07p13680' => 'bna', 'CAN.G1006.16' => 'can', 'CAN.G1006.17' => 'can', 'CAN.G1170.2' => 'can', 'CAN.G962.7' => 'can', 'CANSAT25G2179' => 'cansat', 'CANSAT78G1573' => 'cansat', 'CARHR099510' => 'chi', 'CARHR143510' => 'chi', 'Carub.0003s2380' => 'cru', 'Carub.0004s3082' => 'cru', 'Ca_00614_v3' => 'car', 'Ca_07801_v3' => 'car', 'Ca_08567_v3' => 'car', 'Ca_09571_v3' => 'car', 'CBR_g19290' => 'cbr', 'Cc01_g19770' => 'ccan', 'Cc03_g03030' => 'ccan', 'CDE07G0968' => 'cde', 'CDE09G1441' => 'cde', 'Cfa006103' => 'cfa', 'Cfa015573' => 'cfa', 'Cfa016988' => 'cfa', 'Ciclev10006738m.g' => 'ccl', 'Ciclev10010920m.g' => 'ccl', 'Ciclev10018517m.g' => 'ccl', 'CiPaw.01G159200' => 'cil', 'CiPaw.02G091000' => 'cil', 'CiPaw.02G091100' => 'cil', 'CiPaw.08G103100' => 'cil', 'CiPaw.09G224900' => 'cil', 'ClCG06G005740' => 'cla', 'ClCG07G000090' => 'cla', 'ClCG07G000100' => 'cla', 'COL.COLO4_09143' => 'col', 'COL.COLO4_25124' => 'col', 'Cpa.g.sc16.34' => 'cpa', 'Cpa.g.sc3504.1' => 'cpa', 'Cpa.g.sc60.37' => 'cpa', 'CsaV3_6G018520' => 'csa', 'CsaV3_6G036860' => 'csa', 'CSS0001072' => 'camsi', 'CSS0020208' => 'camsi', 'CSS0021253' => 'camsi', 'CSS0022190' => 'camsi', 'CSS0036150' => 'camsi', 'CSS0040442' => 'camsi', 'CSS0042300' => 'camsi', 'CSS0045298' => 'camsi', 'DCAR_012449' => 'dca', 'DCAR_018405' => 'dca', 'DCAR_024573' => 'dca', 'DCAR_030591' => 'dca', 'Dinv16926' => 'din', 'Dinv32963' => 'din', 'Dinv38382' => 'din', 'Dinv38383' => 'din', 'Duzib133G0974' => 'dzi', 'Duzib138G1867' => 'dzi', 'Duzib211G0420' => 'dzi', 'Duzib212G0930' => 'dzi', 'ECA234G1645' => 'eca', 'ECA247G3467' => 'eca', 'ECA248G1703' => 'eca', 'EL10Ac3g06327' => 'bvu', 'EL10Ac7g17204' => 'bvu', 'Eucgr.A00855' => 'egr', 'Eucgr.A00858' => 'egr', 'Eucgr.H01520' => 'egr', 'Eucgr.H03604' => 'egr', 'Eucgr.L03465' => 'egr', 'Eucgr.L03466' => 'egr', 'FAN01G0988' => 'fan', 'FAN02G3892' => 'fan', 'FAN05G3381' => 'fan', 'FAN07G0967' => 'fan', 'FAN07G1493' => 'fan', 'FAN08G3125' => 'fan', 'FAN09G0402' => 'fan', 'FAN12G2594' => 'fan', 'FAN12G3879' => 'fan', 'FAN14G1546' => 'fan', 'FAN15G3626' => 'fan', 'FAN17G0588' => 'fan', 'FAN17G0609' => 'fan', 'FAN18G2817' => 'fan', 'FAN19G1305' => 'fan', 'FAN20G1787' => 'fan', 'FAN22G0073' => 'fan', 'FAN22G0352' => 'fan', 'FAN22G0368' => 'fan', 'FAN22G2273' => 'fan', 'FAN24G1998' => 'fan', 'FAN27G1317' => 'fan', 'FvH4_2g23980' => 'fve', 'FvH4_4g14380' => 'fve', 'FvH4_4g14390' => 'fve', 'FvH4_6g09250' => 'fve', 'Glyma.03G151100' => 'gma', 'Glyma.04G122550' => 'gma', 'Glyma.05G001600' => 'gma', 'Glyma.09G270766' => 'gma', 'Glyma.09G270832' => 'gma', 'Glyma.13G209800' => 'gma', 'Glyma.15G102800' => 'gma', 'Glyma.18G218900' => 'gma', 'Glyma.19G001500' => 'gma', 'Glyma.19G153600' => 'gma', 'Gohir.A02G028600' => 'ghi', 'Gohir.A08G045000' => 'ghi', 'Gohir.A11G120500' => 'ghi', 'Gohir.A12G006200' => 'ghi', 'Gohir.A12G006250' => 'ghi', 'Gohir.D02G036300' => 'ghi', 'Gohir.D08G054700' => 'ghi', 'Gohir.D11G125600' => 'ghi', 'Gohir.D12G005700' => 'ghi', 'Gorai.004G055200' => 'gra', 'Gorai.005G040400' => 'gra', 'Gorai.007G134500' => 'gra', 'Gorai.008G005500' => 'gra', 'GSVIVG01011094001' => 'vvi', 'GSVIVG01017879001' => 'vvi', 'GSVIVG01025988001' => 'vvi', 'GSVIVG01029847001' => 'vvi', 'HanXRQChr10g0282901' => 'han', 'HanXRQChr10g0310371' => 'han', 'HanXRQChr10g0315041' => 'han', 'HanXRQChr11g0327651' => 'han', 'HanXRQChr12g0359391' => 'han', 'Haze_00972' => 'cav', 'Haze_00973' => 'cav', 'Haze_00974' => 'cav', 'Haze_04747' => 'cav', 'Haze_04749' => 'cav', 'Haze_04750' => 'cav', 'Haze_21217' => 'cav', 'Hma1.2p1_1037F.1_g250680' => 'hma', 'Hma1.2p1_1644F.1_g295320' => 'hma', 'HPP92_011322' => 'vpl', 'HPP92_011323' => 'vpl', 'HPP92_011324' => 'vpl', 'HPP92_011325' => 'vpl', 'HPP92_011326' => 'vpl', 'Hund12205' => 'sun', 'Hund17957' => 'sun', 'Lalb_Chr06g0176771' => 'lal', 'Lalb_Chr18g0056021' => 'lal', 'Lalb_Chr18g0056031' => 'lal', 'Lalb_Chr18g0056041' => 'lal', 'Lalb_Chr20g0107751' => 'lal', 'Lalb_Chr20g0118371' => 'lal', 'Lj1g0010239' => 'lja', 'Lj1g0017101' => 'lja', 'Lj2A1178G40' => 'lonja', 'Lj2A54G84' => 'lonja', 'Lj2g0015248' => 'lja', 'Lj3A761T51' => 'lonja', 'Lj6g0018116' => 'lja', 'Lsat_1_v5_gn_4_136040' => 'lsa', 'Lsat_1_v5_gn_5_187461' => 'lsa', 'Lsat_1_v5_gn_5_77001' => 'lsa', 'Lsat_1_v5_gn_9_4461' => 'lsa', 'Manes.01G210100' => 'mes', 'Manes.03G185600' => 'mes', 'Manes.05G073300' => 'mes', 'Manes.09G120300' => 'mes', 'Manes.15G022100' => 'mes', 'Mapoly0096s0053' => 'mpo', 'MBI03_g14058_MAGBIO' => 'mbi', 'MBI03_g33876_MAGBIO' => 'mbi', 'MBI03_g36854_MAGBIO' => 'mbi', 'MBI17_g11997_MAGBIO' => 'mbi', 'MD03G1269000' => 'mdo', 'MD04G1179600' => 'mdo', 'MD11G1289800' => 'mdo', 'MD12G1194700' => 'mdo', 'MD13G1182100' => 'mdo', 'MD13G1182200' => 'mdo', 'MD16G1182600' => 'mdo', 'Medtr2g021400' => 'mtr', 'Medtr2g021470' => 'mtr', 'Medtr2g105810' => 'mtr', 'Medtr3g033580' => 'mtr', 'Medtr6g007970' => 'mtr', 'Medtr7g056330' => 'mtr', 'Medtr7g074290' => 'mtr', 'Medtr7g074380' => 'mtr', 'Medtr7g094550' => 'mtr', 'Medtr8g069995' => 'mtr', 'MELO3C014345.2' => 'cme', 'MELO3C021395.2' => 'cme', 'Migut.D00262' => 'egut', 'Migut.G00257' => 'egut', 'MSTRG.21575' => 'ama', 'MSTRG.3985' => 'ama', 'Nitab4.5_0000295g0140' => 'nta', 'Nitab4.5_0000732g0140' => 'nta', 'Nitab4.5_0003162g0020' => 'nta', 'Nitab4.5_0006180g0090' => 'nta', 'Nitab4.5_0006390g0010' => 'nta', 'Nitab4.5_0007392g0040' => 'nta', 'Nn1g02140' => 'nnu', 'Nn4g26168' => 'nnu', 'Nn5g26754' => 'nnu', 'Oeu001433.1' => 'oeu', 'Oeu010299.2' => 'oeu', 'Oeu011171.1' => 'oeu', 'Oeu037675.1' => 'oeu', 'Oeu038359.1' => 'oeu', 'Oeu063834.1' => 'oeu', 'Oeu063835.1' => 'oeu', 'Os05g0312000' => 'osa', 'Os07g0211101' => 'osa', 'Os07g0211200' => 'osa', 'Os07g0681500' => 'osa', 'Peaxi162Scf00095g01015' => 'pax', 'Peaxi162Scf00104g00329' => 'pax', 'Peaxi162Scf00161g00137' => 'pax', 'PGR004G1665' => 'pgr', 'PGR031G2937' => 'pgr', 'PGR119G2145' => 'pgr', 'PGSC0003DMG400004351' => 'stu', 'PGSC0003DMG400014625' => 'stu', 'PGSC0003DMG401000943' => 'stu', 'Phvul.001G148600' => 'pvu', 'Phvul.004G001700' => 'pvu', 'Phvul.006G154900' => 'pvu', 'Phvul.008G078200' => 'pvu', 'Phvul.011G136500' => 'pvu', 'Potri.002G215600' => 'ptr', 'Potri.008G201600' => 'ptr', 'Potri.014G138400' => 'ptr', 'Potri.016G142500' => 'ptr', 'Pp3c16_10580' => 'ppa', 'Pp3c5_25280' => 'ppa', 'Prupe.1G150000' => 'ppe', 'Prupe.1G150100' => 'ppe', 'Prupe.6G299600' => 'ppe', 'Prupe.8G245000' => 'ppe', 'Psat0s4927g0040' => 'psa', 'Psat1g052080' => 'psa', 'Psat1g183800' => 'psa', 'Psat3g113840' => 'psa', 'Psat3g126120' => 'psa', 'Psat3g126160' => 'psa', 'Psat3g158760' => 'psa', 'Psat3g158840' => 'psa', 'PSO170G2858' => 'pso', 'PSO339G0606' => 'pso', 'PSO384G4709' => 'pso', 'PSO407G0334' => 'pso', 'QL04p040276' => 'qlo', 'QL06p005458' => 'qlo', 'QL06p005472' => 'qlo', 'QL07p030546' => 'qlo', 'QL07p031519' => 'qlo', 'QL09p050949' => 'qlo', 'QL09p050966' => 'qlo', 'QL09p051067' => 'qlo', 'QL12p022706' => 'qlo', 'RcHm_v2.0_Chr2g0119601' => 'rch', 'RcHm_v2.0_Chr3g0459591' => 'rch', 'RcHm_v2.0_Chr4g0418521' => 'rch', 'RcHm_v2.0_Chr4g0418531' => 'rch', 'RcHm_v2.0_Chr4g0418541' => 'rch', 'RcHm_v2.0_Chr6g0291641' => 'rch', 'Rhsim01G0086300' => 'rsi', 'Rhsim01G0276300' => 'rsi', 'Rhsim01G0276500' => 'rsi', 'Rhsim04G0207700' => 'rsi', 'Rhsim05G0234500' => 'rsi', 'Rhsim13G0022400' => 'rsi', 'Sabra02G0167900' => 'sbr', 'Sabra04G0158500' => 'sbr', 'Sabra08G0159800' => 'sbr', 'Sabra10G0011500' => 'sbr', 'Sabra14G0104400' => 'sbr', 'SalBow2G2440' => 'sbo', 'SalBow4G2265' => 'sbo', 'Sc02g0000060' => 'sci', 'Sc05g0005020' => 'sci', 'Sc13g0003890' => 'sci', 'Sed0014865' => 'sed', 'Sed0017224' => 'sed', 'Sed0026391' => 'sed', 'SEGI_00063' => 'sgi', 'SEGI_10967' => 'sgi', 'SEGI_17510' => 'sgi', 'SEGI_24396' => 'sgi', 'SEGI_39719' => 'sgi', 'SEGI_41392' => 'sgi', 'SGA_v2.0_scaffold11G05794' => 'sas', 'SGA_v2.0_scaffold142G35607' => 'sas', 'SGA_v2.0_scaffold1G00447' => 'sas', 'SHI15388' => 'shi', 'SHI15394' => 'shi', 'SHI15396' => 'shi', 'SHI15399' => 'shi', 'SMO343G0151' => 'smo', 'SMO367G1118' => 'smo', 'Solyc01g080200.3' => 'sly', 'Solyc06g008960.3' => 'sly', 'Solyc09g064780.3' => 'sly', 'Sopen01g031980' => 'spe', 'Sopen06g003710' => 'spe', 'Sopen09g026460' => 'spe', 'Sp3g21240' => 'spa', 'Sp4g30030' => 'spa', 'TAR365G0022' => 'tar', 'TAR365G1023' => 'tar', 'TAR365G1253' => 'tar', 'TAR623G0078' => 'tar', 'TAR623G1721' => 'tar', 'TAR633G0959' => 'tar', 'THA.LOC104802225' => 'tha', 'THA.LOC104804769' => 'tha', 'THA.LOC104808660' => 'tha', 'THA.LOC104812792' => 'tha', 'Thecc.01G284000' => 'tca', 'Thecc.04G220600' => 'tca', 'Thecc.05G268900' => 'tca', 'Thecc.08G171100' => 'tca', 'Thhalv10001284m.g' => 'esa', 'Thhalv10019912m.g' => 'esa', 'TPR.G14189' => 'tpr', 'TPR.G18110' => 'tpr', 'TPR.G18130' => 'tpr', 'TPR.G18131' => 'tpr', 'TPR.G18140' => 'tpr', 'TPR.G24282' => 'tpr', 'TPR.G25221' => 'tpr', 'TPR.G29267' => 'tpr', 'TPR.G35315' => 'tpr', 'TPR.G36173' => 'tpr', 'TWI09G0794' => 'twi', 'TWI59G1348' => 'twi', 'TWI74G0430' => 'twi', 'unitig_26.g8940' => 'ugi', 'unitig_749.g13744' => 'ugi', 'unitig_749.g13745' => 'ugi', 'vmacro08269' => 'vma', 'vmacro14937' => 'vma', 'vmacro20401' => 'vma', 'VMungo0464G1349' => 'vmu', 'VMungo0540G0289' => 'vmu', 'VMungo1215G1590' => 'vmu', 'VMungo1309G0221' => 'vmu', 'VMungo1309G2815' => 'vmu', 'VMungo1383G0239' => 'vmu', 'VMungo1383G2910' => 'vmu', 'Zm00001eb095270' => 'zma', 'Zm00001eb095280' => 'zma', 'Zm00001eb111630' => 'zma', 'Zm00001eb237080' => 'zma', 'Zm00001eb273740' => 'zma', 'Zm00001eb285040' => 'zma', 'Zm00001eb330790' => 'zma', 'Zm00001eb337380' => 'zma' ) $gf_id = 'HOM05D001484' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001484' ) $data_identifier = 'HOM05D001484' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 2, 'aly' => (int) 2, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 22, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 7, 'hma' => (int) 2, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 7, 'mtr' => (int) 10, 'cme' => (int) 2, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 4, 'ppa' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 4, 'qlo' => (int) 9, 'rch' => (int) 6, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 10, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 7, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb337380' $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' => 'HOM05D001484', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p31500' => 'bna', 'A05p00020' => 'bna', 'A07p08820' => 'bna', 'Aa31LG4G3300' => 'aar', 'Aa31LG8G10030' => 'aar', 'Actinidia00731' => 'ach', 'Actinidia11473' => 'ach', 'Actinidia23469' => 'ach', 'Actinidia24318' => 'ach', 'Actinidia40196' => 'ach', 'Actinidia40197' => 'ach', 'Actinidia40198' => 'ach', 'Ah.08g212990' => 'amhyb', 'Ah.15g091720' => 'amhyb', 'AL3G38260' => 'aly', 'AL4G47710' => 'aly', 'Aqoxy2G00671' => 'aox', 'Aqoxy2G03236' => 'aox', 'arahy.Tifrunner.gnm1.ann1.05IDCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KR684' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATY3SJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK6QJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6APGL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IDT7Z9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM073U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ0R87' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LE7RV4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT4QRX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V5ENPK' => 'arhy', 'AT2G48110' => 'ath', 'AT3G23590' => 'ath', 'ATR0626G186' => 'atr', 'ATR1127G141' => 'atr', 'Atru.chr4.2583' => 'acertr', 'Atru.chr5.1358' => 'acertr', 'Atru.chr5.1359' => 'acertr', 'Atru.chr8.46' => 'acertr', 'AUR62002640' => 'cqu', 'AUR62030055' => 'cqu', 'AUR62033713' => 'cqu', 'AUR62033714' => 'cqu', 'AUR62036795' => 'cqu', 'AUR62039891' => 'cqu', 'BcaB02g08737' => 'bca', 'BcaB04g20441' => 'bca', 'BcaB06g26509' => 'bca', 'BcaB06g26510' => 'bca', 'BcaB06g26511' => 'bca', 'BcaB06g26512' => 'bca', 'BcaB06g26513' => 'bca', 'BcaC02g12564' => 'bca', 'BcaC02g12565' => 'bca', 'BcaC02g12794' => 'bca', 'BcaC02g12795' => 'bca', 'BcaC02g12796' => 'bca', 'BcaC06g35541' => 'bca', 'BNapus_Darmor_BZH_scaffold_188p00080' => 'bna', 'BNapus_Darmor_BZH_scaffold_188p00090' => 'bna', 'BolC1t03972H' => 'bol', 'BolC1t03973H' => 'bol', 'BolC4t21680H' => 'bol', 'BolC7t41863H' => 'bol', 'BolSC55t61227H' => 'bol', 'BolSC55t61228H' => 'bol', 'BraA01t03278Z' => 'bra', 'BraA05t18998Z' => 'bra', 'BraA07t28673Z' => 'bra', 'C01p40150' => 'bna', 'C05p12370' => 'bna', 'C07p13680' => 'bna', 'CAN.G1006.16' => 'can', 'CAN.G1006.17' => 'can', 'CAN.G1170.2' => 'can', 'CAN.G962.7' => 'can', 'CANSAT25G2179' => 'cansat', 'CANSAT78G1573' => 'cansat', 'CARHR099510' => 'chi', 'CARHR143510' => 'chi', 'Carub.0003s2380' => 'cru', 'Carub.0004s3082' => 'cru', 'Ca_00614_v3' => 'car', 'Ca_07801_v3' => 'car', 'Ca_08567_v3' => 'car', 'Ca_09571_v3' => 'car', 'CBR_g19290' => 'cbr', 'Cc01_g19770' => 'ccan', 'Cc03_g03030' => 'ccan', 'CDE07G0968' => 'cde', 'CDE09G1441' => 'cde', 'Cfa006103' => 'cfa', 'Cfa015573' => 'cfa', 'Cfa016988' => 'cfa', 'Ciclev10006738m.g' => 'ccl', 'Ciclev10010920m.g' => 'ccl', 'Ciclev10018517m.g' => 'ccl', 'CiPaw.01G159200' => 'cil', 'CiPaw.02G091000' => 'cil', 'CiPaw.02G091100' => 'cil', 'CiPaw.08G103100' => 'cil', 'CiPaw.09G224900' => 'cil', 'ClCG06G005740' => 'cla', 'ClCG07G000090' => 'cla', 'ClCG07G000100' => 'cla', 'COL.COLO4_09143' => 'col', 'COL.COLO4_25124' => 'col', 'Cpa.g.sc16.34' => 'cpa', 'Cpa.g.sc3504.1' => 'cpa', 'Cpa.g.sc60.37' => 'cpa', 'CsaV3_6G018520' => 'csa', 'CsaV3_6G036860' => 'csa', 'CSS0001072' => 'camsi', 'CSS0020208' => 'camsi', 'CSS0021253' => 'camsi', 'CSS0022190' => 'camsi', 'CSS0036150' => 'camsi', 'CSS0040442' => 'camsi', 'CSS0042300' => 'camsi', 'CSS0045298' => 'camsi', 'DCAR_012449' => 'dca', 'DCAR_018405' => 'dca', 'DCAR_024573' => 'dca', 'DCAR_030591' => 'dca', 'Dinv16926' => 'din', 'Dinv32963' => 'din', 'Dinv38382' => 'din', 'Dinv38383' => 'din', 'Duzib133G0974' => 'dzi', 'Duzib138G1867' => 'dzi', 'Duzib211G0420' => 'dzi', 'Duzib212G0930' => 'dzi', 'ECA234G1645' => 'eca', 'ECA247G3467' => 'eca', 'ECA248G1703' => 'eca', 'EL10Ac3g06327' => 'bvu', 'EL10Ac7g17204' => 'bvu', 'Eucgr.A00855' => 'egr', 'Eucgr.A00858' => 'egr', 'Eucgr.H01520' => 'egr', 'Eucgr.H03604' => 'egr', 'Eucgr.L03465' => 'egr', 'Eucgr.L03466' => 'egr', 'FAN01G0988' => 'fan', 'FAN02G3892' => 'fan', 'FAN05G3381' => 'fan', 'FAN07G0967' => 'fan', 'FAN07G1493' => 'fan', 'FAN08G3125' => 'fan', 'FAN09G0402' => 'fan', 'FAN12G2594' => 'fan', 'FAN12G3879' => 'fan', 'FAN14G1546' => 'fan', 'FAN15G3626' => 'fan', 'FAN17G0588' => 'fan', 'FAN17G0609' => 'fan', 'FAN18G2817' => 'fan', 'FAN19G1305' => 'fan', 'FAN20G1787' => 'fan', 'FAN22G0073' => 'fan', 'FAN22G0352' => 'fan', 'FAN22G0368' => 'fan', 'FAN22G2273' => 'fan', 'FAN24G1998' => 'fan', 'FAN27G1317' => 'fan', 'FvH4_2g23980' => 'fve', 'FvH4_4g14380' => 'fve', 'FvH4_4g14390' => 'fve', 'FvH4_6g09250' => 'fve', 'Glyma.03G151100' => 'gma', 'Glyma.04G122550' => 'gma', 'Glyma.05G001600' => 'gma', 'Glyma.09G270766' => 'gma', 'Glyma.09G270832' => 'gma', 'Glyma.13G209800' => 'gma', 'Glyma.15G102800' => 'gma', 'Glyma.18G218900' => 'gma', 'Glyma.19G001500' => 'gma', 'Glyma.19G153600' => 'gma', 'Gohir.A02G028600' => 'ghi', 'Gohir.A08G045000' => 'ghi', 'Gohir.A11G120500' => 'ghi', 'Gohir.A12G006200' => 'ghi', 'Gohir.A12G006250' => 'ghi', 'Gohir.D02G036300' => 'ghi', 'Gohir.D08G054700' => 'ghi', 'Gohir.D11G125600' => 'ghi', 'Gohir.D12G005700' => 'ghi', 'Gorai.004G055200' => 'gra', 'Gorai.005G040400' => 'gra', 'Gorai.007G134500' => 'gra', 'Gorai.008G005500' => 'gra', 'GSVIVG01011094001' => 'vvi', 'GSVIVG01017879001' => 'vvi', 'GSVIVG01025988001' => 'vvi', 'GSVIVG01029847001' => 'vvi', 'HanXRQChr10g0282901' => 'han', 'HanXRQChr10g0310371' => 'han', 'HanXRQChr10g0315041' => 'han', 'HanXRQChr11g0327651' => 'han', 'HanXRQChr12g0359391' => 'han', 'Haze_00972' => 'cav', 'Haze_00973' => 'cav', 'Haze_00974' => 'cav', 'Haze_04747' => 'cav', 'Haze_04749' => 'cav', 'Haze_04750' => 'cav', 'Haze_21217' => 'cav', 'Hma1.2p1_1037F.1_g250680' => 'hma', 'Hma1.2p1_1644F.1_g295320' => 'hma', 'HPP92_011322' => 'vpl', 'HPP92_011323' => 'vpl', 'HPP92_011324' => 'vpl', 'HPP92_011325' => 'vpl', 'HPP92_011326' => 'vpl', 'Hund12205' => 'sun', 'Hund17957' => 'sun', 'Lalb_Chr06g0176771' => 'lal', 'Lalb_Chr18g0056021' => 'lal', 'Lalb_Chr18g0056031' => 'lal', 'Lalb_Chr18g0056041' => 'lal', 'Lalb_Chr20g0107751' => 'lal', 'Lalb_Chr20g0118371' => 'lal', 'Lj1g0010239' => 'lja', 'Lj1g0017101' => 'lja', 'Lj2A1178G40' => 'lonja', 'Lj2A54G84' => 'lonja', 'Lj2g0015248' => 'lja', 'Lj3A761T51' => 'lonja', 'Lj6g0018116' => 'lja', 'Lsat_1_v5_gn_4_136040' => 'lsa', 'Lsat_1_v5_gn_5_187461' => 'lsa', 'Lsat_1_v5_gn_5_77001' => 'lsa', 'Lsat_1_v5_gn_9_4461' => 'lsa', 'Manes.01G210100' => 'mes', 'Manes.03G185600' => 'mes', 'Manes.05G073300' => 'mes', 'Manes.09G120300' => 'mes', 'Manes.15G022100' => 'mes', 'Mapoly0096s0053' => 'mpo', 'MBI03_g14058_MAGBIO' => 'mbi', 'MBI03_g33876_MAGBIO' => 'mbi', 'MBI03_g36854_MAGBIO' => 'mbi', 'MBI17_g11997_MAGBIO' => 'mbi', 'MD03G1269000' => 'mdo', 'MD04G1179600' => 'mdo', 'MD11G1289800' => 'mdo', 'MD12G1194700' => 'mdo', 'MD13G1182100' => 'mdo', 'MD13G1182200' => 'mdo', 'MD16G1182600' => 'mdo', 'Medtr2g021400' => 'mtr', 'Medtr2g021470' => 'mtr', 'Medtr2g105810' => 'mtr', 'Medtr3g033580' => 'mtr', 'Medtr6g007970' => 'mtr', 'Medtr7g056330' => 'mtr', 'Medtr7g074290' => 'mtr', 'Medtr7g074380' => 'mtr', 'Medtr7g094550' => 'mtr', 'Medtr8g069995' => 'mtr', 'MELO3C014345.2' => 'cme', 'MELO3C021395.2' => 'cme', 'Migut.D00262' => 'egut', 'Migut.G00257' => 'egut', 'MSTRG.21575' => 'ama', 'MSTRG.3985' => 'ama', 'Nitab4.5_0000295g0140' => 'nta', 'Nitab4.5_0000732g0140' => 'nta', 'Nitab4.5_0003162g0020' => 'nta', 'Nitab4.5_0006180g0090' => 'nta', 'Nitab4.5_0006390g0010' => 'nta', 'Nitab4.5_0007392g0040' => 'nta', 'Nn1g02140' => 'nnu', 'Nn4g26168' => 'nnu', 'Nn5g26754' => 'nnu', 'Oeu001433.1' => 'oeu', 'Oeu010299.2' => 'oeu', 'Oeu011171.1' => 'oeu', 'Oeu037675.1' => 'oeu', 'Oeu038359.1' => 'oeu', 'Oeu063834.1' => 'oeu', 'Oeu063835.1' => 'oeu', 'Os05g0312000' => 'osa', 'Os07g0211101' => 'osa', 'Os07g0211200' => 'osa', 'Os07g0681500' => 'osa', 'Peaxi162Scf00095g01015' => 'pax', 'Peaxi162Scf00104g00329' => 'pax', 'Peaxi162Scf00161g00137' => 'pax', 'PGR004G1665' => 'pgr', 'PGR031G2937' => 'pgr', 'PGR119G2145' => 'pgr', 'PGSC0003DMG400004351' => 'stu', 'PGSC0003DMG400014625' => 'stu', 'PGSC0003DMG401000943' => 'stu', 'Phvul.001G148600' => 'pvu', 'Phvul.004G001700' => 'pvu', 'Phvul.006G154900' => 'pvu', 'Phvul.008G078200' => 'pvu', 'Phvul.011G136500' => 'pvu', 'Potri.002G215600' => 'ptr', 'Potri.008G201600' => 'ptr', 'Potri.014G138400' => 'ptr', 'Potri.016G142500' => 'ptr', 'Pp3c16_10580' => 'ppa', 'Pp3c5_25280' => 'ppa', 'Prupe.1G150000' => 'ppe', 'Prupe.1G150100' => 'ppe', 'Prupe.6G299600' => 'ppe', 'Prupe.8G245000' => 'ppe', 'Psat0s4927g0040' => 'psa', 'Psat1g052080' => 'psa', 'Psat1g183800' => 'psa', 'Psat3g113840' => 'psa', 'Psat3g126120' => 'psa', 'Psat3g126160' => 'psa', 'Psat3g158760' => 'psa', 'Psat3g158840' => 'psa', 'PSO170G2858' => 'pso', 'PSO339G0606' => 'pso', 'PSO384G4709' => 'pso', 'PSO407G0334' => 'pso', 'QL04p040276' => 'qlo', 'QL06p005458' => 'qlo', 'QL06p005472' => 'qlo', 'QL07p030546' => 'qlo', 'QL07p031519' => 'qlo', 'QL09p050949' => 'qlo', 'QL09p050966' => 'qlo', 'QL09p051067' => 'qlo', 'QL12p022706' => 'qlo', 'RcHm_v2.0_Chr2g0119601' => 'rch', 'RcHm_v2.0_Chr3g0459591' => 'rch', 'RcHm_v2.0_Chr4g0418521' => 'rch', 'RcHm_v2.0_Chr4g0418531' => 'rch', 'RcHm_v2.0_Chr4g0418541' => 'rch', 'RcHm_v2.0_Chr6g0291641' => 'rch', 'Rhsim01G0086300' => 'rsi', 'Rhsim01G0276300' => 'rsi', 'Rhsim01G0276500' => 'rsi', 'Rhsim04G0207700' => 'rsi', 'Rhsim05G0234500' => 'rsi', 'Rhsim13G0022400' => 'rsi', 'Sabra02G0167900' => 'sbr', 'Sabra04G0158500' => 'sbr', 'Sabra08G0159800' => 'sbr', 'Sabra10G0011500' => 'sbr', 'Sabra14G0104400' => 'sbr', 'SalBow2G2440' => 'sbo', 'SalBow4G2265' => 'sbo', 'Sc02g0000060' => 'sci', 'Sc05g0005020' => 'sci', 'Sc13g0003890' => 'sci', 'Sed0014865' => 'sed', 'Sed0017224' => 'sed', 'Sed0026391' => 'sed', 'SEGI_00063' => 'sgi', 'SEGI_10967' => 'sgi', 'SEGI_17510' => 'sgi', 'SEGI_24396' => 'sgi', 'SEGI_39719' => 'sgi', 'SEGI_41392' => 'sgi', 'SGA_v2.0_scaffold11G05794' => 'sas', 'SGA_v2.0_scaffold142G35607' => 'sas', 'SGA_v2.0_scaffold1G00447' => 'sas', 'SHI15388' => 'shi', 'SHI15394' => 'shi', 'SHI15396' => 'shi', 'SHI15399' => 'shi', 'SMO343G0151' => 'smo', 'SMO367G1118' => 'smo', 'Solyc01g080200.3' => 'sly', 'Solyc06g008960.3' => 'sly', 'Solyc09g064780.3' => 'sly', 'Sopen01g031980' => 'spe', 'Sopen06g003710' => 'spe', 'Sopen09g026460' => 'spe', 'Sp3g21240' => 'spa', 'Sp4g30030' => 'spa', 'TAR365G0022' => 'tar', 'TAR365G1023' => 'tar', 'TAR365G1253' => 'tar', 'TAR623G0078' => 'tar', 'TAR623G1721' => 'tar', 'TAR633G0959' => 'tar', 'THA.LOC104802225' => 'tha', 'THA.LOC104804769' => 'tha', 'THA.LOC104808660' => 'tha', 'THA.LOC104812792' => 'tha', 'Thecc.01G284000' => 'tca', 'Thecc.04G220600' => 'tca', 'Thecc.05G268900' => 'tca', 'Thecc.08G171100' => 'tca', 'Thhalv10001284m.g' => 'esa', 'Thhalv10019912m.g' => 'esa', 'TPR.G14189' => 'tpr', 'TPR.G18110' => 'tpr', 'TPR.G18130' => 'tpr', 'TPR.G18131' => 'tpr', 'TPR.G18140' => 'tpr', 'TPR.G24282' => 'tpr', 'TPR.G25221' => 'tpr', 'TPR.G29267' => 'tpr', 'TPR.G35315' => 'tpr', 'TPR.G36173' => 'tpr', 'TWI09G0794' => 'twi', 'TWI59G1348' => 'twi', 'TWI74G0430' => 'twi', 'unitig_26.g8940' => 'ugi', 'unitig_749.g13744' => 'ugi', 'unitig_749.g13745' => 'ugi', 'vmacro08269' => 'vma', 'vmacro14937' => 'vma', 'vmacro20401' => 'vma', 'VMungo0464G1349' => 'vmu', 'VMungo0540G0289' => 'vmu', 'VMungo1215G1590' => 'vmu', 'VMungo1309G0221' => 'vmu', 'VMungo1309G2815' => 'vmu', 'VMungo1383G0239' => 'vmu', 'VMungo1383G2910' => 'vmu', 'Zm00001eb095270' => 'zma', 'Zm00001eb095280' => 'zma', 'Zm00001eb111630' => 'zma', 'Zm00001eb237080' => 'zma', 'Zm00001eb273740' => 'zma', 'Zm00001eb285040' => 'zma', 'Zm00001eb330790' => 'zma', 'Zm00001eb337380' => 'zma' ), 'gf_id' => 'HOM05D001484', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001484' ), 'data_identifier' => 'HOM05D001484', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001484', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p31500' => 'bna', 'A05p00020' => 'bna', 'A07p08820' => 'bna', 'Aa31LG4G3300' => 'aar', 'Aa31LG8G10030' => 'aar', 'Actinidia00731' => 'ach', 'Actinidia11473' => 'ach', 'Actinidia23469' => 'ach', 'Actinidia24318' => 'ach', 'Actinidia40196' => 'ach', 'Actinidia40197' => 'ach', 'Actinidia40198' => 'ach', 'Ah.08g212990' => 'amhyb', 'Ah.15g091720' => 'amhyb', 'AL3G38260' => 'aly', 'AL4G47710' => 'aly', 'Aqoxy2G00671' => 'aox', 'Aqoxy2G03236' => 'aox', 'arahy.Tifrunner.gnm1.ann1.05IDCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KR684' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATY3SJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK6QJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6APGL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IDT7Z9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM073U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ0R87' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LE7RV4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT4QRX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V5ENPK' => 'arhy', 'AT2G48110' => 'ath', 'AT3G23590' => 'ath', 'ATR0626G186' => 'atr', 'ATR1127G141' => 'atr', 'Atru.chr4.2583' => 'acertr', 'Atru.chr5.1358' => 'acertr', 'Atru.chr5.1359' => 'acertr', 'Atru.chr8.46' => 'acertr', 'AUR62002640' => 'cqu', 'AUR62030055' => 'cqu', 'AUR62033713' => 'cqu', 'AUR62033714' => 'cqu', 'AUR62036795' => 'cqu', 'AUR62039891' => 'cqu', 'BcaB02g08737' => 'bca', 'BcaB04g20441' => 'bca', 'BcaB06g26509' => 'bca', 'BcaB06g26510' => 'bca', 'BcaB06g26511' => 'bca', 'BcaB06g26512' => 'bca', 'BcaB06g26513' => 'bca', 'BcaC02g12564' => 'bca', 'BcaC02g12565' => 'bca', 'BcaC02g12794' => 'bca', 'BcaC02g12795' => 'bca', 'BcaC02g12796' => 'bca', 'BcaC06g35541' => 'bca', 'BNapus_Darmor_BZH_scaffold_188p00080' => 'bna', 'BNapus_Darmor_BZH_scaffold_188p00090' => 'bna', 'BolC1t03972H' => 'bol', 'BolC1t03973H' => 'bol', 'BolC4t21680H' => 'bol', 'BolC7t41863H' => 'bol', 'BolSC55t61227H' => 'bol', 'BolSC55t61228H' => 'bol', 'BraA01t03278Z' => 'bra', 'BraA05t18998Z' => 'bra', 'BraA07t28673Z' => 'bra', 'C01p40150' => 'bna', 'C05p12370' => 'bna', 'C07p13680' => 'bna', 'CAN.G1006.16' => 'can', 'CAN.G1006.17' => 'can', 'CAN.G1170.2' => 'can', 'CAN.G962.7' => 'can', 'CANSAT25G2179' => 'cansat', 'CANSAT78G1573' => 'cansat', 'CARHR099510' => 'chi', 'CARHR143510' => 'chi', 'Carub.0003s2380' => 'cru', 'Carub.0004s3082' => 'cru', 'Ca_00614_v3' => 'car', 'Ca_07801_v3' => 'car', 'Ca_08567_v3' => 'car', 'Ca_09571_v3' => 'car', 'CBR_g19290' => 'cbr', 'Cc01_g19770' => 'ccan', 'Cc03_g03030' => 'ccan', 'CDE07G0968' => 'cde', 'CDE09G1441' => 'cde', 'Cfa006103' => 'cfa', 'Cfa015573' => 'cfa', 'Cfa016988' => 'cfa', 'Ciclev10006738m.g' => 'ccl', 'Ciclev10010920m.g' => 'ccl', 'Ciclev10018517m.g' => 'ccl', 'CiPaw.01G159200' => 'cil', 'CiPaw.02G091000' => 'cil', 'CiPaw.02G091100' => 'cil', 'CiPaw.08G103100' => 'cil', 'CiPaw.09G224900' => 'cil', 'ClCG06G005740' => 'cla', 'ClCG07G000090' => 'cla', 'ClCG07G000100' => 'cla', 'COL.COLO4_09143' => 'col', 'COL.COLO4_25124' => 'col', 'Cpa.g.sc16.34' => 'cpa', 'Cpa.g.sc3504.1' => 'cpa', 'Cpa.g.sc60.37' => 'cpa', 'CsaV3_6G018520' => 'csa', 'CsaV3_6G036860' => 'csa', 'CSS0001072' => 'camsi', 'CSS0020208' => 'camsi', 'CSS0021253' => 'camsi', 'CSS0022190' => 'camsi', 'CSS0036150' => 'camsi', 'CSS0040442' => 'camsi', 'CSS0042300' => 'camsi', 'CSS0045298' => 'camsi', 'DCAR_012449' => 'dca', 'DCAR_018405' => 'dca', 'DCAR_024573' => 'dca', 'DCAR_030591' => 'dca', 'Dinv16926' => 'din', 'Dinv32963' => 'din', 'Dinv38382' => 'din', 'Dinv38383' => 'din', 'Duzib133G0974' => 'dzi', 'Duzib138G1867' => 'dzi', 'Duzib211G0420' => 'dzi', 'Duzib212G0930' => 'dzi', 'ECA234G1645' => 'eca', 'ECA247G3467' => 'eca', 'ECA248G1703' => 'eca', 'EL10Ac3g06327' => 'bvu', 'EL10Ac7g17204' => 'bvu', 'Eucgr.A00855' => 'egr', 'Eucgr.A00858' => 'egr', 'Eucgr.H01520' => 'egr', 'Eucgr.H03604' => 'egr', 'Eucgr.L03465' => 'egr', 'Eucgr.L03466' => 'egr', 'FAN01G0988' => 'fan', 'FAN02G3892' => 'fan', 'FAN05G3381' => 'fan', 'FAN07G0967' => 'fan', 'FAN07G1493' => 'fan', 'FAN08G3125' => 'fan', 'FAN09G0402' => 'fan', 'FAN12G2594' => 'fan', 'FAN12G3879' => 'fan', 'FAN14G1546' => 'fan', 'FAN15G3626' => 'fan', 'FAN17G0588' => 'fan', 'FAN17G0609' => 'fan', 'FAN18G2817' => 'fan', 'FAN19G1305' => 'fan', 'FAN20G1787' => 'fan', 'FAN22G0073' => 'fan', 'FAN22G0352' => 'fan', 'FAN22G0368' => 'fan', 'FAN22G2273' => 'fan', 'FAN24G1998' => 'fan', 'FAN27G1317' => 'fan', 'FvH4_2g23980' => 'fve', 'FvH4_4g14380' => 'fve', 'FvH4_4g14390' => 'fve', 'FvH4_6g09250' => 'fve', 'Glyma.03G151100' => 'gma', 'Glyma.04G122550' => 'gma', 'Glyma.05G001600' => 'gma', 'Glyma.09G270766' => 'gma', 'Glyma.09G270832' => 'gma', 'Glyma.13G209800' => 'gma', 'Glyma.15G102800' => 'gma', 'Glyma.18G218900' => 'gma', 'Glyma.19G001500' => 'gma', 'Glyma.19G153600' => 'gma', 'Gohir.A02G028600' => 'ghi', 'Gohir.A08G045000' => 'ghi', 'Gohir.A11G120500' => 'ghi', 'Gohir.A12G006200' => 'ghi', 'Gohir.A12G006250' => 'ghi', 'Gohir.D02G036300' => 'ghi', 'Gohir.D08G054700' => 'ghi', 'Gohir.D11G125600' => 'ghi', 'Gohir.D12G005700' => 'ghi', 'Gorai.004G055200' => 'gra', 'Gorai.005G040400' => 'gra', 'Gorai.007G134500' => 'gra', 'Gorai.008G005500' => 'gra', 'GSVIVG01011094001' => 'vvi', 'GSVIVG01017879001' => 'vvi', 'GSVIVG01025988001' => 'vvi', 'GSVIVG01029847001' => 'vvi', 'HanXRQChr10g0282901' => 'han', 'HanXRQChr10g0310371' => 'han', 'HanXRQChr10g0315041' => 'han', 'HanXRQChr11g0327651' => 'han', 'HanXRQChr12g0359391' => 'han', 'Haze_00972' => 'cav', 'Haze_00973' => 'cav', 'Haze_00974' => 'cav', 'Haze_04747' => 'cav', 'Haze_04749' => 'cav', 'Haze_04750' => 'cav', 'Haze_21217' => 'cav', 'Hma1.2p1_1037F.1_g250680' => 'hma', 'Hma1.2p1_1644F.1_g295320' => 'hma', 'HPP92_011322' => 'vpl', 'HPP92_011323' => 'vpl', 'HPP92_011324' => 'vpl', 'HPP92_011325' => 'vpl', 'HPP92_011326' => 'vpl', 'Hund12205' => 'sun', 'Hund17957' => 'sun', 'Lalb_Chr06g0176771' => 'lal', 'Lalb_Chr18g0056021' => 'lal', 'Lalb_Chr18g0056031' => 'lal', 'Lalb_Chr18g0056041' => 'lal', 'Lalb_Chr20g0107751' => 'lal', 'Lalb_Chr20g0118371' => 'lal', 'Lj1g0010239' => 'lja', 'Lj1g0017101' => 'lja', 'Lj2A1178G40' => 'lonja', 'Lj2A54G84' => 'lonja', 'Lj2g0015248' => 'lja', 'Lj3A761T51' => 'lonja', 'Lj6g0018116' => 'lja', 'Lsat_1_v5_gn_4_136040' => 'lsa', 'Lsat_1_v5_gn_5_187461' => 'lsa', 'Lsat_1_v5_gn_5_77001' => 'lsa', 'Lsat_1_v5_gn_9_4461' => 'lsa', 'Manes.01G210100' => 'mes', 'Manes.03G185600' => 'mes', 'Manes.05G073300' => 'mes', 'Manes.09G120300' => 'mes', 'Manes.15G022100' => 'mes', 'Mapoly0096s0053' => 'mpo', 'MBI03_g14058_MAGBIO' => 'mbi', 'MBI03_g33876_MAGBIO' => 'mbi', 'MBI03_g36854_MAGBIO' => 'mbi', 'MBI17_g11997_MAGBIO' => 'mbi', 'MD03G1269000' => 'mdo', 'MD04G1179600' => 'mdo', 'MD11G1289800' => 'mdo', 'MD12G1194700' => 'mdo', 'MD13G1182100' => 'mdo', 'MD13G1182200' => 'mdo', 'MD16G1182600' => 'mdo', 'Medtr2g021400' => 'mtr', 'Medtr2g021470' => 'mtr', 'Medtr2g105810' => 'mtr', 'Medtr3g033580' => 'mtr', 'Medtr6g007970' => 'mtr', 'Medtr7g056330' => 'mtr', 'Medtr7g074290' => 'mtr', 'Medtr7g074380' => 'mtr', 'Medtr7g094550' => 'mtr', 'Medtr8g069995' => 'mtr', 'MELO3C014345.2' => 'cme', 'MELO3C021395.2' => 'cme', 'Migut.D00262' => 'egut', 'Migut.G00257' => 'egut', 'MSTRG.21575' => 'ama', 'MSTRG.3985' => 'ama', 'Nitab4.5_0000295g0140' => 'nta', 'Nitab4.5_0000732g0140' => 'nta', 'Nitab4.5_0003162g0020' => 'nta', 'Nitab4.5_0006180g0090' => 'nta', 'Nitab4.5_0006390g0010' => 'nta', 'Nitab4.5_0007392g0040' => 'nta', 'Nn1g02140' => 'nnu', 'Nn4g26168' => 'nnu', 'Nn5g26754' => 'nnu', 'Oeu001433.1' => 'oeu', 'Oeu010299.2' => 'oeu', 'Oeu011171.1' => 'oeu', 'Oeu037675.1' => 'oeu', 'Oeu038359.1' => 'oeu', 'Oeu063834.1' => 'oeu', 'Oeu063835.1' => 'oeu', 'Os05g0312000' => 'osa', 'Os07g0211101' => 'osa', 'Os07g0211200' => 'osa', 'Os07g0681500' => 'osa', 'Peaxi162Scf00095g01015' => 'pax', 'Peaxi162Scf00104g00329' => 'pax', 'Peaxi162Scf00161g00137' => 'pax', 'PGR004G1665' => 'pgr', 'PGR031G2937' => 'pgr', 'PGR119G2145' => 'pgr', 'PGSC0003DMG400004351' => 'stu', 'PGSC0003DMG400014625' => 'stu', 'PGSC0003DMG401000943' => 'stu', 'Phvul.001G148600' => 'pvu', 'Phvul.004G001700' => 'pvu', 'Phvul.006G154900' => 'pvu', 'Phvul.008G078200' => 'pvu', 'Phvul.011G136500' => 'pvu', 'Potri.002G215600' => 'ptr', 'Potri.008G201600' => 'ptr', 'Potri.014G138400' => 'ptr', 'Potri.016G142500' => 'ptr', 'Pp3c16_10580' => 'ppa', 'Pp3c5_25280' => 'ppa', 'Prupe.1G150000' => 'ppe', 'Prupe.1G150100' => 'ppe', 'Prupe.6G299600' => 'ppe', 'Prupe.8G245000' => 'ppe', 'Psat0s4927g0040' => 'psa', 'Psat1g052080' => 'psa', 'Psat1g183800' => 'psa', 'Psat3g113840' => 'psa', 'Psat3g126120' => 'psa', 'Psat3g126160' => 'psa', 'Psat3g158760' => 'psa', 'Psat3g158840' => 'psa', 'PSO170G2858' => 'pso', 'PSO339G0606' => 'pso', 'PSO384G4709' => 'pso', 'PSO407G0334' => 'pso', 'QL04p040276' => 'qlo', 'QL06p005458' => 'qlo', 'QL06p005472' => 'qlo', 'QL07p030546' => 'qlo', 'QL07p031519' => 'qlo', 'QL09p050949' => 'qlo', 'QL09p050966' => 'qlo', 'QL09p051067' => 'qlo', 'QL12p022706' => 'qlo', 'RcHm_v2.0_Chr2g0119601' => 'rch', 'RcHm_v2.0_Chr3g0459591' => 'rch', 'RcHm_v2.0_Chr4g0418521' => 'rch', 'RcHm_v2.0_Chr4g0418531' => 'rch', 'RcHm_v2.0_Chr4g0418541' => 'rch', 'RcHm_v2.0_Chr6g0291641' => 'rch', 'Rhsim01G0086300' => 'rsi', 'Rhsim01G0276300' => 'rsi', 'Rhsim01G0276500' => 'rsi', 'Rhsim04G0207700' => 'rsi', 'Rhsim05G0234500' => 'rsi', 'Rhsim13G0022400' => 'rsi', 'Sabra02G0167900' => 'sbr', 'Sabra04G0158500' => 'sbr', 'Sabra08G0159800' => 'sbr', 'Sabra10G0011500' => 'sbr', 'Sabra14G0104400' => 'sbr', 'SalBow2G2440' => 'sbo', 'SalBow4G2265' => 'sbo', 'Sc02g0000060' => 'sci', 'Sc05g0005020' => 'sci', 'Sc13g0003890' => 'sci', 'Sed0014865' => 'sed', 'Sed0017224' => 'sed', 'Sed0026391' => 'sed', 'SEGI_00063' => 'sgi', 'SEGI_10967' => 'sgi', 'SEGI_17510' => 'sgi', 'SEGI_24396' => 'sgi', 'SEGI_39719' => 'sgi', 'SEGI_41392' => 'sgi', 'SGA_v2.0_scaffold11G05794' => 'sas', 'SGA_v2.0_scaffold142G35607' => 'sas', 'SGA_v2.0_scaffold1G00447' => 'sas', 'SHI15388' => 'shi', 'SHI15394' => 'shi', 'SHI15396' => 'shi', 'SHI15399' => 'shi', 'SMO343G0151' => 'smo', 'SMO367G1118' => 'smo', 'Solyc01g080200.3' => 'sly', 'Solyc06g008960.3' => 'sly', 'Solyc09g064780.3' => 'sly', 'Sopen01g031980' => 'spe', 'Sopen06g003710' => 'spe', 'Sopen09g026460' => 'spe', 'Sp3g21240' => 'spa', 'Sp4g30030' => 'spa', 'TAR365G0022' => 'tar', 'TAR365G1023' => 'tar', 'TAR365G1253' => 'tar', 'TAR623G0078' => 'tar', 'TAR623G1721' => 'tar', 'TAR633G0959' => 'tar', 'THA.LOC104802225' => 'tha', 'THA.LOC104804769' => 'tha', 'THA.LOC104808660' => 'tha', 'THA.LOC104812792' => 'tha', 'Thecc.01G284000' => 'tca', 'Thecc.04G220600' => 'tca', 'Thecc.05G268900' => 'tca', 'Thecc.08G171100' => 'tca', 'Thhalv10001284m.g' => 'esa', 'Thhalv10019912m.g' => 'esa', 'TPR.G14189' => 'tpr', 'TPR.G18110' => 'tpr', 'TPR.G18130' => 'tpr', 'TPR.G18131' => 'tpr', 'TPR.G18140' => 'tpr', 'TPR.G24282' => 'tpr', 'TPR.G25221' => 'tpr', 'TPR.G29267' => 'tpr', 'TPR.G35315' => 'tpr', 'TPR.G36173' => 'tpr', 'TWI09G0794' => 'twi', 'TWI59G1348' => 'twi', 'TWI74G0430' => 'twi', 'unitig_26.g8940' => 'ugi', 'unitig_749.g13744' => 'ugi', 'unitig_749.g13745' => 'ugi', 'vmacro08269' => 'vma', 'vmacro14937' => 'vma', 'vmacro20401' => 'vma', 'VMungo0464G1349' => 'vmu', 'VMungo0540G0289' => 'vmu', 'VMungo1215G1590' => 'vmu', 'VMungo1309G0221' => 'vmu', 'VMungo1309G2815' => 'vmu', 'VMungo1383G0239' => 'vmu', 'VMungo1383G2910' => 'vmu', 'Zm00001eb095270' => 'zma', 'Zm00001eb095280' => 'zma', 'Zm00001eb111630' => 'zma', 'Zm00001eb237080' => 'zma', 'Zm00001eb273740' => 'zma', 'Zm00001eb285040' => 'zma', 'Zm00001eb330790' => 'zma', 'Zm00001eb337380' => 'zma' ) $gf_id = 'HOM05D001484' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001484' ) $data_identifier = 'HOM05D001484' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 2, 'aly' => (int) 2, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 22, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 7, 'hma' => (int) 2, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 7, 'mtr' => (int) 10, 'cme' => (int) 2, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 4, 'ppa' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 4, 'qlo' => (int) 9, 'rch' => (int) 6, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 10, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 7, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb337380' $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' => 'HOM05D001484', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p31500' => 'bna', 'A05p00020' => 'bna', 'A07p08820' => 'bna', 'Aa31LG4G3300' => 'aar', 'Aa31LG8G10030' => 'aar', 'Actinidia00731' => 'ach', 'Actinidia11473' => 'ach', 'Actinidia23469' => 'ach', 'Actinidia24318' => 'ach', 'Actinidia40196' => 'ach', 'Actinidia40197' => 'ach', 'Actinidia40198' => 'ach', 'Ah.08g212990' => 'amhyb', 'Ah.15g091720' => 'amhyb', 'AL3G38260' => 'aly', 'AL4G47710' => 'aly', 'Aqoxy2G00671' => 'aox', 'Aqoxy2G03236' => 'aox', 'arahy.Tifrunner.gnm1.ann1.05IDCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KR684' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATY3SJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK6QJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6APGL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IDT7Z9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM073U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ0R87' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LE7RV4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT4QRX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V5ENPK' => 'arhy', 'AT2G48110' => 'ath', 'AT3G23590' => 'ath', 'ATR0626G186' => 'atr', 'ATR1127G141' => 'atr', 'Atru.chr4.2583' => 'acertr', 'Atru.chr5.1358' => 'acertr', 'Atru.chr5.1359' => 'acertr', 'Atru.chr8.46' => 'acertr', 'AUR62002640' => 'cqu', 'AUR62030055' => 'cqu', 'AUR62033713' => 'cqu', 'AUR62033714' => 'cqu', 'AUR62036795' => 'cqu', 'AUR62039891' => 'cqu', 'BcaB02g08737' => 'bca', 'BcaB04g20441' => 'bca', 'BcaB06g26509' => 'bca', 'BcaB06g26510' => 'bca', 'BcaB06g26511' => 'bca', 'BcaB06g26512' => 'bca', 'BcaB06g26513' => 'bca', 'BcaC02g12564' => 'bca', 'BcaC02g12565' => 'bca', 'BcaC02g12794' => 'bca', 'BcaC02g12795' => 'bca', 'BcaC02g12796' => 'bca', 'BcaC06g35541' => 'bca', 'BNapus_Darmor_BZH_scaffold_188p00080' => 'bna', 'BNapus_Darmor_BZH_scaffold_188p00090' => 'bna', 'BolC1t03972H' => 'bol', 'BolC1t03973H' => 'bol', 'BolC4t21680H' => 'bol', 'BolC7t41863H' => 'bol', 'BolSC55t61227H' => 'bol', 'BolSC55t61228H' => 'bol', 'BraA01t03278Z' => 'bra', 'BraA05t18998Z' => 'bra', 'BraA07t28673Z' => 'bra', 'C01p40150' => 'bna', 'C05p12370' => 'bna', 'C07p13680' => 'bna', 'CAN.G1006.16' => 'can', 'CAN.G1006.17' => 'can', 'CAN.G1170.2' => 'can', 'CAN.G962.7' => 'can', 'CANSAT25G2179' => 'cansat', 'CANSAT78G1573' => 'cansat', 'CARHR099510' => 'chi', 'CARHR143510' => 'chi', 'Carub.0003s2380' => 'cru', 'Carub.0004s3082' => 'cru', 'Ca_00614_v3' => 'car', 'Ca_07801_v3' => 'car', 'Ca_08567_v3' => 'car', 'Ca_09571_v3' => 'car', 'CBR_g19290' => 'cbr', 'Cc01_g19770' => 'ccan', 'Cc03_g03030' => 'ccan', 'CDE07G0968' => 'cde', 'CDE09G1441' => 'cde', 'Cfa006103' => 'cfa', 'Cfa015573' => 'cfa', 'Cfa016988' => 'cfa', 'Ciclev10006738m.g' => 'ccl', 'Ciclev10010920m.g' => 'ccl', 'Ciclev10018517m.g' => 'ccl', 'CiPaw.01G159200' => 'cil', 'CiPaw.02G091000' => 'cil', 'CiPaw.02G091100' => 'cil', 'CiPaw.08G103100' => 'cil', 'CiPaw.09G224900' => 'cil', 'ClCG06G005740' => 'cla', 'ClCG07G000090' => 'cla', 'ClCG07G000100' => 'cla', 'COL.COLO4_09143' => 'col', 'COL.COLO4_25124' => 'col', 'Cpa.g.sc16.34' => 'cpa', 'Cpa.g.sc3504.1' => 'cpa', 'Cpa.g.sc60.37' => 'cpa', 'CsaV3_6G018520' => 'csa', 'CsaV3_6G036860' => 'csa', 'CSS0001072' => 'camsi', 'CSS0020208' => 'camsi', 'CSS0021253' => 'camsi', 'CSS0022190' => 'camsi', 'CSS0036150' => 'camsi', 'CSS0040442' => 'camsi', 'CSS0042300' => 'camsi', 'CSS0045298' => 'camsi', 'DCAR_012449' => 'dca', 'DCAR_018405' => 'dca', 'DCAR_024573' => 'dca', 'DCAR_030591' => 'dca', 'Dinv16926' => 'din', 'Dinv32963' => 'din', 'Dinv38382' => 'din', 'Dinv38383' => 'din', 'Duzib133G0974' => 'dzi', 'Duzib138G1867' => 'dzi', 'Duzib211G0420' => 'dzi', 'Duzib212G0930' => 'dzi', 'ECA234G1645' => 'eca', 'ECA247G3467' => 'eca', 'ECA248G1703' => 'eca', 'EL10Ac3g06327' => 'bvu', 'EL10Ac7g17204' => 'bvu', 'Eucgr.A00855' => 'egr', 'Eucgr.A00858' => 'egr', 'Eucgr.H01520' => 'egr', 'Eucgr.H03604' => 'egr', 'Eucgr.L03465' => 'egr', 'Eucgr.L03466' => 'egr', 'FAN01G0988' => 'fan', 'FAN02G3892' => 'fan', 'FAN05G3381' => 'fan', 'FAN07G0967' => 'fan', 'FAN07G1493' => 'fan', 'FAN08G3125' => 'fan', 'FAN09G0402' => 'fan', 'FAN12G2594' => 'fan', 'FAN12G3879' => 'fan', 'FAN14G1546' => 'fan', 'FAN15G3626' => 'fan', 'FAN17G0588' => 'fan', 'FAN17G0609' => 'fan', 'FAN18G2817' => 'fan', 'FAN19G1305' => 'fan', 'FAN20G1787' => 'fan', 'FAN22G0073' => 'fan', 'FAN22G0352' => 'fan', 'FAN22G0368' => 'fan', 'FAN22G2273' => 'fan', 'FAN24G1998' => 'fan', 'FAN27G1317' => 'fan', 'FvH4_2g23980' => 'fve', 'FvH4_4g14380' => 'fve', 'FvH4_4g14390' => 'fve', 'FvH4_6g09250' => 'fve', 'Glyma.03G151100' => 'gma', 'Glyma.04G122550' => 'gma', 'Glyma.05G001600' => 'gma', 'Glyma.09G270766' => 'gma', 'Glyma.09G270832' => 'gma', 'Glyma.13G209800' => 'gma', 'Glyma.15G102800' => 'gma', 'Glyma.18G218900' => 'gma', 'Glyma.19G001500' => 'gma', 'Glyma.19G153600' => 'gma', 'Gohir.A02G028600' => 'ghi', 'Gohir.A08G045000' => 'ghi', 'Gohir.A11G120500' => 'ghi', 'Gohir.A12G006200' => 'ghi', 'Gohir.A12G006250' => 'ghi', 'Gohir.D02G036300' => 'ghi', 'Gohir.D08G054700' => 'ghi', 'Gohir.D11G125600' => 'ghi', 'Gohir.D12G005700' => 'ghi', 'Gorai.004G055200' => 'gra', 'Gorai.005G040400' => 'gra', 'Gorai.007G134500' => 'gra', 'Gorai.008G005500' => 'gra', 'GSVIVG01011094001' => 'vvi', 'GSVIVG01017879001' => 'vvi', 'GSVIVG01025988001' => 'vvi', 'GSVIVG01029847001' => 'vvi', 'HanXRQChr10g0282901' => 'han', 'HanXRQChr10g0310371' => 'han', 'HanXRQChr10g0315041' => 'han', 'HanXRQChr11g0327651' => 'han', 'HanXRQChr12g0359391' => 'han', 'Haze_00972' => 'cav', 'Haze_00973' => 'cav', 'Haze_00974' => 'cav', 'Haze_04747' => 'cav', 'Haze_04749' => 'cav', 'Haze_04750' => 'cav', 'Haze_21217' => 'cav', 'Hma1.2p1_1037F.1_g250680' => 'hma', 'Hma1.2p1_1644F.1_g295320' => 'hma', 'HPP92_011322' => 'vpl', 'HPP92_011323' => 'vpl', 'HPP92_011324' => 'vpl', 'HPP92_011325' => 'vpl', 'HPP92_011326' => 'vpl', 'Hund12205' => 'sun', 'Hund17957' => 'sun', 'Lalb_Chr06g0176771' => 'lal', 'Lalb_Chr18g0056021' => 'lal', 'Lalb_Chr18g0056031' => 'lal', 'Lalb_Chr18g0056041' => 'lal', 'Lalb_Chr20g0107751' => 'lal', 'Lalb_Chr20g0118371' => 'lal', 'Lj1g0010239' => 'lja', 'Lj1g0017101' => 'lja', 'Lj2A1178G40' => 'lonja', 'Lj2A54G84' => 'lonja', 'Lj2g0015248' => 'lja', 'Lj3A761T51' => 'lonja', 'Lj6g0018116' => 'lja', 'Lsat_1_v5_gn_4_136040' => 'lsa', 'Lsat_1_v5_gn_5_187461' => 'lsa', 'Lsat_1_v5_gn_5_77001' => 'lsa', 'Lsat_1_v5_gn_9_4461' => 'lsa', 'Manes.01G210100' => 'mes', 'Manes.03G185600' => 'mes', 'Manes.05G073300' => 'mes', 'Manes.09G120300' => 'mes', 'Manes.15G022100' => 'mes', 'Mapoly0096s0053' => 'mpo', 'MBI03_g14058_MAGBIO' => 'mbi', 'MBI03_g33876_MAGBIO' => 'mbi', 'MBI03_g36854_MAGBIO' => 'mbi', 'MBI17_g11997_MAGBIO' => 'mbi', 'MD03G1269000' => 'mdo', 'MD04G1179600' => 'mdo', 'MD11G1289800' => 'mdo', 'MD12G1194700' => 'mdo', 'MD13G1182100' => 'mdo', 'MD13G1182200' => 'mdo', 'MD16G1182600' => 'mdo', 'Medtr2g021400' => 'mtr', 'Medtr2g021470' => 'mtr', 'Medtr2g105810' => 'mtr', 'Medtr3g033580' => 'mtr', 'Medtr6g007970' => 'mtr', 'Medtr7g056330' => 'mtr', 'Medtr7g074290' => 'mtr', 'Medtr7g074380' => 'mtr', 'Medtr7g094550' => 'mtr', 'Medtr8g069995' => 'mtr', 'MELO3C014345.2' => 'cme', 'MELO3C021395.2' => 'cme', 'Migut.D00262' => 'egut', 'Migut.G00257' => 'egut', 'MSTRG.21575' => 'ama', 'MSTRG.3985' => 'ama', 'Nitab4.5_0000295g0140' => 'nta', 'Nitab4.5_0000732g0140' => 'nta', 'Nitab4.5_0003162g0020' => 'nta', 'Nitab4.5_0006180g0090' => 'nta', 'Nitab4.5_0006390g0010' => 'nta', 'Nitab4.5_0007392g0040' => 'nta', 'Nn1g02140' => 'nnu', 'Nn4g26168' => 'nnu', 'Nn5g26754' => 'nnu', 'Oeu001433.1' => 'oeu', 'Oeu010299.2' => 'oeu', 'Oeu011171.1' => 'oeu', 'Oeu037675.1' => 'oeu', 'Oeu038359.1' => 'oeu', 'Oeu063834.1' => 'oeu', 'Oeu063835.1' => 'oeu', 'Os05g0312000' => 'osa', 'Os07g0211101' => 'osa', 'Os07g0211200' => 'osa', 'Os07g0681500' => 'osa', 'Peaxi162Scf00095g01015' => 'pax', 'Peaxi162Scf00104g00329' => 'pax', 'Peaxi162Scf00161g00137' => 'pax', 'PGR004G1665' => 'pgr', 'PGR031G2937' => 'pgr', 'PGR119G2145' => 'pgr', 'PGSC0003DMG400004351' => 'stu', 'PGSC0003DMG400014625' => 'stu', 'PGSC0003DMG401000943' => 'stu', 'Phvul.001G148600' => 'pvu', 'Phvul.004G001700' => 'pvu', 'Phvul.006G154900' => 'pvu', 'Phvul.008G078200' => 'pvu', 'Phvul.011G136500' => 'pvu', 'Potri.002G215600' => 'ptr', 'Potri.008G201600' => 'ptr', 'Potri.014G138400' => 'ptr', 'Potri.016G142500' => 'ptr', 'Pp3c16_10580' => 'ppa', 'Pp3c5_25280' => 'ppa', 'Prupe.1G150000' => 'ppe', 'Prupe.1G150100' => 'ppe', 'Prupe.6G299600' => 'ppe', 'Prupe.8G245000' => 'ppe', 'Psat0s4927g0040' => 'psa', 'Psat1g052080' => 'psa', 'Psat1g183800' => 'psa', 'Psat3g113840' => 'psa', 'Psat3g126120' => 'psa', 'Psat3g126160' => 'psa', 'Psat3g158760' => 'psa', 'Psat3g158840' => 'psa', 'PSO170G2858' => 'pso', 'PSO339G0606' => 'pso', 'PSO384G4709' => 'pso', 'PSO407G0334' => 'pso', 'QL04p040276' => 'qlo', 'QL06p005458' => 'qlo', 'QL06p005472' => 'qlo', 'QL07p030546' => 'qlo', 'QL07p031519' => 'qlo', 'QL09p050949' => 'qlo', 'QL09p050966' => 'qlo', 'QL09p051067' => 'qlo', 'QL12p022706' => 'qlo', 'RcHm_v2.0_Chr2g0119601' => 'rch', 'RcHm_v2.0_Chr3g0459591' => 'rch', 'RcHm_v2.0_Chr4g0418521' => 'rch', 'RcHm_v2.0_Chr4g0418531' => 'rch', 'RcHm_v2.0_Chr4g0418541' => 'rch', 'RcHm_v2.0_Chr6g0291641' => 'rch', 'Rhsim01G0086300' => 'rsi', 'Rhsim01G0276300' => 'rsi', 'Rhsim01G0276500' => 'rsi', 'Rhsim04G0207700' => 'rsi', 'Rhsim05G0234500' => 'rsi', 'Rhsim13G0022400' => 'rsi', 'Sabra02G0167900' => 'sbr', 'Sabra04G0158500' => 'sbr', 'Sabra08G0159800' => 'sbr', 'Sabra10G0011500' => 'sbr', 'Sabra14G0104400' => 'sbr', 'SalBow2G2440' => 'sbo', 'SalBow4G2265' => 'sbo', 'Sc02g0000060' => 'sci', 'Sc05g0005020' => 'sci', 'Sc13g0003890' => 'sci', 'Sed0014865' => 'sed', 'Sed0017224' => 'sed', 'Sed0026391' => 'sed', 'SEGI_00063' => 'sgi', 'SEGI_10967' => 'sgi', 'SEGI_17510' => 'sgi', 'SEGI_24396' => 'sgi', 'SEGI_39719' => 'sgi', 'SEGI_41392' => 'sgi', 'SGA_v2.0_scaffold11G05794' => 'sas', 'SGA_v2.0_scaffold142G35607' => 'sas', 'SGA_v2.0_scaffold1G00447' => 'sas', 'SHI15388' => 'shi', 'SHI15394' => 'shi', 'SHI15396' => 'shi', 'SHI15399' => 'shi', 'SMO343G0151' => 'smo', 'SMO367G1118' => 'smo', 'Solyc01g080200.3' => 'sly', 'Solyc06g008960.3' => 'sly', 'Solyc09g064780.3' => 'sly', 'Sopen01g031980' => 'spe', 'Sopen06g003710' => 'spe', 'Sopen09g026460' => 'spe', 'Sp3g21240' => 'spa', 'Sp4g30030' => 'spa', 'TAR365G0022' => 'tar', 'TAR365G1023' => 'tar', 'TAR365G1253' => 'tar', 'TAR623G0078' => 'tar', 'TAR623G1721' => 'tar', 'TAR633G0959' => 'tar', 'THA.LOC104802225' => 'tha', 'THA.LOC104804769' => 'tha', 'THA.LOC104808660' => 'tha', 'THA.LOC104812792' => 'tha', 'Thecc.01G284000' => 'tca', 'Thecc.04G220600' => 'tca', 'Thecc.05G268900' => 'tca', 'Thecc.08G171100' => 'tca', 'Thhalv10001284m.g' => 'esa', 'Thhalv10019912m.g' => 'esa', 'TPR.G14189' => 'tpr', 'TPR.G18110' => 'tpr', 'TPR.G18130' => 'tpr', 'TPR.G18131' => 'tpr', 'TPR.G18140' => 'tpr', 'TPR.G24282' => 'tpr', 'TPR.G25221' => 'tpr', 'TPR.G29267' => 'tpr', 'TPR.G35315' => 'tpr', 'TPR.G36173' => 'tpr', 'TWI09G0794' => 'twi', 'TWI59G1348' => 'twi', 'TWI74G0430' => 'twi', 'unitig_26.g8940' => 'ugi', 'unitig_749.g13744' => 'ugi', 'unitig_749.g13745' => 'ugi', 'vmacro08269' => 'vma', 'vmacro14937' => 'vma', 'vmacro20401' => 'vma', 'VMungo0464G1349' => 'vmu', 'VMungo0540G0289' => 'vmu', 'VMungo1215G1590' => 'vmu', 'VMungo1309G0221' => 'vmu', 'VMungo1309G2815' => 'vmu', 'VMungo1383G0239' => 'vmu', 'VMungo1383G2910' => 'vmu', 'Zm00001eb095270' => 'zma', 'Zm00001eb095280' => 'zma', 'Zm00001eb111630' => 'zma', 'Zm00001eb237080' => 'zma', 'Zm00001eb273740' => 'zma', 'Zm00001eb285040' => 'zma', 'Zm00001eb330790' => 'zma', 'Zm00001eb337380' => 'zma' ), 'gf_id' => 'HOM05D001484', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001484' ), 'data_identifier' => 'HOM05D001484', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001484', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p31500' => 'bna', 'A05p00020' => 'bna', 'A07p08820' => 'bna', 'Aa31LG4G3300' => 'aar', 'Aa31LG8G10030' => 'aar', 'Actinidia00731' => 'ach', 'Actinidia11473' => 'ach', 'Actinidia23469' => 'ach', 'Actinidia24318' => 'ach', 'Actinidia40196' => 'ach', 'Actinidia40197' => 'ach', 'Actinidia40198' => 'ach', 'Ah.08g212990' => 'amhyb', 'Ah.15g091720' => 'amhyb', 'AL3G38260' => 'aly', 'AL4G47710' => 'aly', 'Aqoxy2G00671' => 'aox', 'Aqoxy2G03236' => 'aox', 'arahy.Tifrunner.gnm1.ann1.05IDCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KR684' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATY3SJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK6QJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6APGL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IDT7Z9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM073U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ0R87' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LE7RV4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT4QRX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V5ENPK' => 'arhy', 'AT2G48110' => 'ath', 'AT3G23590' => 'ath', 'ATR0626G186' => 'atr', 'ATR1127G141' => 'atr', 'Atru.chr4.2583' => 'acertr', 'Atru.chr5.1358' => 'acertr', 'Atru.chr5.1359' => 'acertr', 'Atru.chr8.46' => 'acertr', 'AUR62002640' => 'cqu', 'AUR62030055' => 'cqu', 'AUR62033713' => 'cqu', 'AUR62033714' => 'cqu', 'AUR62036795' => 'cqu', 'AUR62039891' => 'cqu', 'BcaB02g08737' => 'bca', 'BcaB04g20441' => 'bca', 'BcaB06g26509' => 'bca', 'BcaB06g26510' => 'bca', 'BcaB06g26511' => 'bca', 'BcaB06g26512' => 'bca', 'BcaB06g26513' => 'bca', 'BcaC02g12564' => 'bca', 'BcaC02g12565' => 'bca', 'BcaC02g12794' => 'bca', 'BcaC02g12795' => 'bca', 'BcaC02g12796' => 'bca', 'BcaC06g35541' => 'bca', 'BNapus_Darmor_BZH_scaffold_188p00080' => 'bna', 'BNapus_Darmor_BZH_scaffold_188p00090' => 'bna', 'BolC1t03972H' => 'bol', 'BolC1t03973H' => 'bol', 'BolC4t21680H' => 'bol', 'BolC7t41863H' => 'bol', 'BolSC55t61227H' => 'bol', 'BolSC55t61228H' => 'bol', 'BraA01t03278Z' => 'bra', 'BraA05t18998Z' => 'bra', 'BraA07t28673Z' => 'bra', 'C01p40150' => 'bna', 'C05p12370' => 'bna', 'C07p13680' => 'bna', 'CAN.G1006.16' => 'can', 'CAN.G1006.17' => 'can', 'CAN.G1170.2' => 'can', 'CAN.G962.7' => 'can', 'CANSAT25G2179' => 'cansat', 'CANSAT78G1573' => 'cansat', 'CARHR099510' => 'chi', 'CARHR143510' => 'chi', 'Carub.0003s2380' => 'cru', 'Carub.0004s3082' => 'cru', 'Ca_00614_v3' => 'car', 'Ca_07801_v3' => 'car', 'Ca_08567_v3' => 'car', 'Ca_09571_v3' => 'car', 'CBR_g19290' => 'cbr', 'Cc01_g19770' => 'ccan', 'Cc03_g03030' => 'ccan', 'CDE07G0968' => 'cde', 'CDE09G1441' => 'cde', 'Cfa006103' => 'cfa', 'Cfa015573' => 'cfa', 'Cfa016988' => 'cfa', 'Ciclev10006738m.g' => 'ccl', 'Ciclev10010920m.g' => 'ccl', 'Ciclev10018517m.g' => 'ccl', 'CiPaw.01G159200' => 'cil', 'CiPaw.02G091000' => 'cil', 'CiPaw.02G091100' => 'cil', 'CiPaw.08G103100' => 'cil', 'CiPaw.09G224900' => 'cil', 'ClCG06G005740' => 'cla', 'ClCG07G000090' => 'cla', 'ClCG07G000100' => 'cla', 'COL.COLO4_09143' => 'col', 'COL.COLO4_25124' => 'col', 'Cpa.g.sc16.34' => 'cpa', 'Cpa.g.sc3504.1' => 'cpa', 'Cpa.g.sc60.37' => 'cpa', 'CsaV3_6G018520' => 'csa', 'CsaV3_6G036860' => 'csa', 'CSS0001072' => 'camsi', 'CSS0020208' => 'camsi', 'CSS0021253' => 'camsi', 'CSS0022190' => 'camsi', 'CSS0036150' => 'camsi', 'CSS0040442' => 'camsi', 'CSS0042300' => 'camsi', 'CSS0045298' => 'camsi', 'DCAR_012449' => 'dca', 'DCAR_018405' => 'dca', 'DCAR_024573' => 'dca', 'DCAR_030591' => 'dca', 'Dinv16926' => 'din', 'Dinv32963' => 'din', 'Dinv38382' => 'din', 'Dinv38383' => 'din', 'Duzib133G0974' => 'dzi', 'Duzib138G1867' => 'dzi', 'Duzib211G0420' => 'dzi', 'Duzib212G0930' => 'dzi', 'ECA234G1645' => 'eca', 'ECA247G3467' => 'eca', 'ECA248G1703' => 'eca', 'EL10Ac3g06327' => 'bvu', 'EL10Ac7g17204' => 'bvu', 'Eucgr.A00855' => 'egr', 'Eucgr.A00858' => 'egr', 'Eucgr.H01520' => 'egr', 'Eucgr.H03604' => 'egr', 'Eucgr.L03465' => 'egr', 'Eucgr.L03466' => 'egr', 'FAN01G0988' => 'fan', 'FAN02G3892' => 'fan', 'FAN05G3381' => 'fan', 'FAN07G0967' => 'fan', 'FAN07G1493' => 'fan', 'FAN08G3125' => 'fan', 'FAN09G0402' => 'fan', 'FAN12G2594' => 'fan', 'FAN12G3879' => 'fan', 'FAN14G1546' => 'fan', 'FAN15G3626' => 'fan', 'FAN17G0588' => 'fan', 'FAN17G0609' => 'fan', 'FAN18G2817' => 'fan', 'FAN19G1305' => 'fan', 'FAN20G1787' => 'fan', 'FAN22G0073' => 'fan', 'FAN22G0352' => 'fan', 'FAN22G0368' => 'fan', 'FAN22G2273' => 'fan', 'FAN24G1998' => 'fan', 'FAN27G1317' => 'fan', 'FvH4_2g23980' => 'fve', 'FvH4_4g14380' => 'fve', 'FvH4_4g14390' => 'fve', 'FvH4_6g09250' => 'fve', 'Glyma.03G151100' => 'gma', 'Glyma.04G122550' => 'gma', 'Glyma.05G001600' => 'gma', 'Glyma.09G270766' => 'gma', 'Glyma.09G270832' => 'gma', 'Glyma.13G209800' => 'gma', 'Glyma.15G102800' => 'gma', 'Glyma.18G218900' => 'gma', 'Glyma.19G001500' => 'gma', 'Glyma.19G153600' => 'gma', 'Gohir.A02G028600' => 'ghi', 'Gohir.A08G045000' => 'ghi', 'Gohir.A11G120500' => 'ghi', 'Gohir.A12G006200' => 'ghi', 'Gohir.A12G006250' => 'ghi', 'Gohir.D02G036300' => 'ghi', 'Gohir.D08G054700' => 'ghi', 'Gohir.D11G125600' => 'ghi', 'Gohir.D12G005700' => 'ghi', 'Gorai.004G055200' => 'gra', 'Gorai.005G040400' => 'gra', 'Gorai.007G134500' => 'gra', 'Gorai.008G005500' => 'gra', 'GSVIVG01011094001' => 'vvi', 'GSVIVG01017879001' => 'vvi', 'GSVIVG01025988001' => 'vvi', 'GSVIVG01029847001' => 'vvi', 'HanXRQChr10g0282901' => 'han', 'HanXRQChr10g0310371' => 'han', 'HanXRQChr10g0315041' => 'han', 'HanXRQChr11g0327651' => 'han', 'HanXRQChr12g0359391' => 'han', 'Haze_00972' => 'cav', 'Haze_00973' => 'cav', 'Haze_00974' => 'cav', 'Haze_04747' => 'cav', 'Haze_04749' => 'cav', 'Haze_04750' => 'cav', 'Haze_21217' => 'cav', 'Hma1.2p1_1037F.1_g250680' => 'hma', 'Hma1.2p1_1644F.1_g295320' => 'hma', 'HPP92_011322' => 'vpl', 'HPP92_011323' => 'vpl', 'HPP92_011324' => 'vpl', 'HPP92_011325' => 'vpl', 'HPP92_011326' => 'vpl', 'Hund12205' => 'sun', 'Hund17957' => 'sun', 'Lalb_Chr06g0176771' => 'lal', 'Lalb_Chr18g0056021' => 'lal', 'Lalb_Chr18g0056031' => 'lal', 'Lalb_Chr18g0056041' => 'lal', 'Lalb_Chr20g0107751' => 'lal', 'Lalb_Chr20g0118371' => 'lal', 'Lj1g0010239' => 'lja', 'Lj1g0017101' => 'lja', 'Lj2A1178G40' => 'lonja', 'Lj2A54G84' => 'lonja', 'Lj2g0015248' => 'lja', 'Lj3A761T51' => 'lonja', 'Lj6g0018116' => 'lja', 'Lsat_1_v5_gn_4_136040' => 'lsa', 'Lsat_1_v5_gn_5_187461' => 'lsa', 'Lsat_1_v5_gn_5_77001' => 'lsa', 'Lsat_1_v5_gn_9_4461' => 'lsa', 'Manes.01G210100' => 'mes', 'Manes.03G185600' => 'mes', 'Manes.05G073300' => 'mes', 'Manes.09G120300' => 'mes', 'Manes.15G022100' => 'mes', 'Mapoly0096s0053' => 'mpo', 'MBI03_g14058_MAGBIO' => 'mbi', 'MBI03_g33876_MAGBIO' => 'mbi', 'MBI03_g36854_MAGBIO' => 'mbi', 'MBI17_g11997_MAGBIO' => 'mbi', 'MD03G1269000' => 'mdo', 'MD04G1179600' => 'mdo', 'MD11G1289800' => 'mdo', 'MD12G1194700' => 'mdo', 'MD13G1182100' => 'mdo', 'MD13G1182200' => 'mdo', 'MD16G1182600' => 'mdo', 'Medtr2g021400' => 'mtr', 'Medtr2g021470' => 'mtr', 'Medtr2g105810' => 'mtr', 'Medtr3g033580' => 'mtr', 'Medtr6g007970' => 'mtr', 'Medtr7g056330' => 'mtr', 'Medtr7g074290' => 'mtr', 'Medtr7g074380' => 'mtr', 'Medtr7g094550' => 'mtr', 'Medtr8g069995' => 'mtr', 'MELO3C014345.2' => 'cme', 'MELO3C021395.2' => 'cme', 'Migut.D00262' => 'egut', 'Migut.G00257' => 'egut', 'MSTRG.21575' => 'ama', 'MSTRG.3985' => 'ama', 'Nitab4.5_0000295g0140' => 'nta', 'Nitab4.5_0000732g0140' => 'nta', 'Nitab4.5_0003162g0020' => 'nta', 'Nitab4.5_0006180g0090' => 'nta', 'Nitab4.5_0006390g0010' => 'nta', 'Nitab4.5_0007392g0040' => 'nta', 'Nn1g02140' => 'nnu', 'Nn4g26168' => 'nnu', 'Nn5g26754' => 'nnu', 'Oeu001433.1' => 'oeu', 'Oeu010299.2' => 'oeu', 'Oeu011171.1' => 'oeu', 'Oeu037675.1' => 'oeu', 'Oeu038359.1' => 'oeu', 'Oeu063834.1' => 'oeu', 'Oeu063835.1' => 'oeu', 'Os05g0312000' => 'osa', 'Os07g0211101' => 'osa', 'Os07g0211200' => 'osa', 'Os07g0681500' => 'osa', 'Peaxi162Scf00095g01015' => 'pax', 'Peaxi162Scf00104g00329' => 'pax', 'Peaxi162Scf00161g00137' => 'pax', 'PGR004G1665' => 'pgr', 'PGR031G2937' => 'pgr', 'PGR119G2145' => 'pgr', 'PGSC0003DMG400004351' => 'stu', 'PGSC0003DMG400014625' => 'stu', 'PGSC0003DMG401000943' => 'stu', 'Phvul.001G148600' => 'pvu', 'Phvul.004G001700' => 'pvu', 'Phvul.006G154900' => 'pvu', 'Phvul.008G078200' => 'pvu', 'Phvul.011G136500' => 'pvu', 'Potri.002G215600' => 'ptr', 'Potri.008G201600' => 'ptr', 'Potri.014G138400' => 'ptr', 'Potri.016G142500' => 'ptr', 'Pp3c16_10580' => 'ppa', 'Pp3c5_25280' => 'ppa', 'Prupe.1G150000' => 'ppe', 'Prupe.1G150100' => 'ppe', 'Prupe.6G299600' => 'ppe', 'Prupe.8G245000' => 'ppe', 'Psat0s4927g0040' => 'psa', 'Psat1g052080' => 'psa', 'Psat1g183800' => 'psa', 'Psat3g113840' => 'psa', 'Psat3g126120' => 'psa', 'Psat3g126160' => 'psa', 'Psat3g158760' => 'psa', 'Psat3g158840' => 'psa', 'PSO170G2858' => 'pso', 'PSO339G0606' => 'pso', 'PSO384G4709' => 'pso', 'PSO407G0334' => 'pso', 'QL04p040276' => 'qlo', 'QL06p005458' => 'qlo', 'QL06p005472' => 'qlo', 'QL07p030546' => 'qlo', 'QL07p031519' => 'qlo', 'QL09p050949' => 'qlo', 'QL09p050966' => 'qlo', 'QL09p051067' => 'qlo', 'QL12p022706' => 'qlo', 'RcHm_v2.0_Chr2g0119601' => 'rch', 'RcHm_v2.0_Chr3g0459591' => 'rch', 'RcHm_v2.0_Chr4g0418521' => 'rch', 'RcHm_v2.0_Chr4g0418531' => 'rch', 'RcHm_v2.0_Chr4g0418541' => 'rch', 'RcHm_v2.0_Chr6g0291641' => 'rch', 'Rhsim01G0086300' => 'rsi', 'Rhsim01G0276300' => 'rsi', 'Rhsim01G0276500' => 'rsi', 'Rhsim04G0207700' => 'rsi', 'Rhsim05G0234500' => 'rsi', 'Rhsim13G0022400' => 'rsi', 'Sabra02G0167900' => 'sbr', 'Sabra04G0158500' => 'sbr', 'Sabra08G0159800' => 'sbr', 'Sabra10G0011500' => 'sbr', 'Sabra14G0104400' => 'sbr', 'SalBow2G2440' => 'sbo', 'SalBow4G2265' => 'sbo', 'Sc02g0000060' => 'sci', 'Sc05g0005020' => 'sci', 'Sc13g0003890' => 'sci', 'Sed0014865' => 'sed', 'Sed0017224' => 'sed', 'Sed0026391' => 'sed', 'SEGI_00063' => 'sgi', 'SEGI_10967' => 'sgi', 'SEGI_17510' => 'sgi', 'SEGI_24396' => 'sgi', 'SEGI_39719' => 'sgi', 'SEGI_41392' => 'sgi', 'SGA_v2.0_scaffold11G05794' => 'sas', 'SGA_v2.0_scaffold142G35607' => 'sas', 'SGA_v2.0_scaffold1G00447' => 'sas', 'SHI15388' => 'shi', 'SHI15394' => 'shi', 'SHI15396' => 'shi', 'SHI15399' => 'shi', 'SMO343G0151' => 'smo', 'SMO367G1118' => 'smo', 'Solyc01g080200.3' => 'sly', 'Solyc06g008960.3' => 'sly', 'Solyc09g064780.3' => 'sly', 'Sopen01g031980' => 'spe', 'Sopen06g003710' => 'spe', 'Sopen09g026460' => 'spe', 'Sp3g21240' => 'spa', 'Sp4g30030' => 'spa', 'TAR365G0022' => 'tar', 'TAR365G1023' => 'tar', 'TAR365G1253' => 'tar', 'TAR623G0078' => 'tar', 'TAR623G1721' => 'tar', 'TAR633G0959' => 'tar', 'THA.LOC104802225' => 'tha', 'THA.LOC104804769' => 'tha', 'THA.LOC104808660' => 'tha', 'THA.LOC104812792' => 'tha', 'Thecc.01G284000' => 'tca', 'Thecc.04G220600' => 'tca', 'Thecc.05G268900' => 'tca', 'Thecc.08G171100' => 'tca', 'Thhalv10001284m.g' => 'esa', 'Thhalv10019912m.g' => 'esa', 'TPR.G14189' => 'tpr', 'TPR.G18110' => 'tpr', 'TPR.G18130' => 'tpr', 'TPR.G18131' => 'tpr', 'TPR.G18140' => 'tpr', 'TPR.G24282' => 'tpr', 'TPR.G25221' => 'tpr', 'TPR.G29267' => 'tpr', 'TPR.G35315' => 'tpr', 'TPR.G36173' => 'tpr', 'TWI09G0794' => 'twi', 'TWI59G1348' => 'twi', 'TWI74G0430' => 'twi', 'unitig_26.g8940' => 'ugi', 'unitig_749.g13744' => 'ugi', 'unitig_749.g13745' => 'ugi', 'vmacro08269' => 'vma', 'vmacro14937' => 'vma', 'vmacro20401' => 'vma', 'VMungo0464G1349' => 'vmu', 'VMungo0540G0289' => 'vmu', 'VMungo1215G1590' => 'vmu', 'VMungo1309G0221' => 'vmu', 'VMungo1309G2815' => 'vmu', 'VMungo1383G0239' => 'vmu', 'VMungo1383G2910' => 'vmu', 'Zm00001eb095270' => 'zma', 'Zm00001eb095280' => 'zma', 'Zm00001eb111630' => 'zma', 'Zm00001eb237080' => 'zma', 'Zm00001eb273740' => 'zma', 'Zm00001eb285040' => 'zma', 'Zm00001eb330790' => 'zma', 'Zm00001eb337380' => 'zma' ) $gf_id = 'HOM05D001484' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001484' ) $data_identifier = 'HOM05D001484' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 2, 'aly' => (int) 2, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 22, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 7, 'hma' => (int) 2, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 7, 'mtr' => (int) 10, 'cme' => (int) 2, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 4, 'ppa' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 4, 'qlo' => (int) 9, 'rch' => (int) 6, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 10, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 7, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb337380' $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' => 'HOM05D001484', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p31500' => 'bna', 'A05p00020' => 'bna', 'A07p08820' => 'bna', 'Aa31LG4G3300' => 'aar', 'Aa31LG8G10030' => 'aar', 'Actinidia00731' => 'ach', 'Actinidia11473' => 'ach', 'Actinidia23469' => 'ach', 'Actinidia24318' => 'ach', 'Actinidia40196' => 'ach', 'Actinidia40197' => 'ach', 'Actinidia40198' => 'ach', 'Ah.08g212990' => 'amhyb', 'Ah.15g091720' => 'amhyb', 'AL3G38260' => 'aly', 'AL4G47710' => 'aly', 'Aqoxy2G00671' => 'aox', 'Aqoxy2G03236' => 'aox', 'arahy.Tifrunner.gnm1.ann1.05IDCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KR684' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATY3SJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK6QJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6APGL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IDT7Z9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM073U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ0R87' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LE7RV4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT4QRX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V5ENPK' => 'arhy', 'AT2G48110' => 'ath', 'AT3G23590' => 'ath', 'ATR0626G186' => 'atr', 'ATR1127G141' => 'atr', 'Atru.chr4.2583' => 'acertr', 'Atru.chr5.1358' => 'acertr', 'Atru.chr5.1359' => 'acertr', 'Atru.chr8.46' => 'acertr', 'AUR62002640' => 'cqu', 'AUR62030055' => 'cqu', 'AUR62033713' => 'cqu', 'AUR62033714' => 'cqu', 'AUR62036795' => 'cqu', 'AUR62039891' => 'cqu', 'BcaB02g08737' => 'bca', 'BcaB04g20441' => 'bca', 'BcaB06g26509' => 'bca', 'BcaB06g26510' => 'bca', 'BcaB06g26511' => 'bca', 'BcaB06g26512' => 'bca', 'BcaB06g26513' => 'bca', 'BcaC02g12564' => 'bca', 'BcaC02g12565' => 'bca', 'BcaC02g12794' => 'bca', 'BcaC02g12795' => 'bca', 'BcaC02g12796' => 'bca', 'BcaC06g35541' => 'bca', 'BNapus_Darmor_BZH_scaffold_188p00080' => 'bna', 'BNapus_Darmor_BZH_scaffold_188p00090' => 'bna', 'BolC1t03972H' => 'bol', 'BolC1t03973H' => 'bol', 'BolC4t21680H' => 'bol', 'BolC7t41863H' => 'bol', 'BolSC55t61227H' => 'bol', 'BolSC55t61228H' => 'bol', 'BraA01t03278Z' => 'bra', 'BraA05t18998Z' => 'bra', 'BraA07t28673Z' => 'bra', 'C01p40150' => 'bna', 'C05p12370' => 'bna', 'C07p13680' => 'bna', 'CAN.G1006.16' => 'can', 'CAN.G1006.17' => 'can', 'CAN.G1170.2' => 'can', 'CAN.G962.7' => 'can', 'CANSAT25G2179' => 'cansat', 'CANSAT78G1573' => 'cansat', 'CARHR099510' => 'chi', 'CARHR143510' => 'chi', 'Carub.0003s2380' => 'cru', 'Carub.0004s3082' => 'cru', 'Ca_00614_v3' => 'car', 'Ca_07801_v3' => 'car', 'Ca_08567_v3' => 'car', 'Ca_09571_v3' => 'car', 'CBR_g19290' => 'cbr', 'Cc01_g19770' => 'ccan', 'Cc03_g03030' => 'ccan', 'CDE07G0968' => 'cde', 'CDE09G1441' => 'cde', 'Cfa006103' => 'cfa', 'Cfa015573' => 'cfa', 'Cfa016988' => 'cfa', 'Ciclev10006738m.g' => 'ccl', 'Ciclev10010920m.g' => 'ccl', 'Ciclev10018517m.g' => 'ccl', 'CiPaw.01G159200' => 'cil', 'CiPaw.02G091000' => 'cil', 'CiPaw.02G091100' => 'cil', 'CiPaw.08G103100' => 'cil', 'CiPaw.09G224900' => 'cil', 'ClCG06G005740' => 'cla', 'ClCG07G000090' => 'cla', 'ClCG07G000100' => 'cla', 'COL.COLO4_09143' => 'col', 'COL.COLO4_25124' => 'col', 'Cpa.g.sc16.34' => 'cpa', 'Cpa.g.sc3504.1' => 'cpa', 'Cpa.g.sc60.37' => 'cpa', 'CsaV3_6G018520' => 'csa', 'CsaV3_6G036860' => 'csa', 'CSS0001072' => 'camsi', 'CSS0020208' => 'camsi', 'CSS0021253' => 'camsi', 'CSS0022190' => 'camsi', 'CSS0036150' => 'camsi', 'CSS0040442' => 'camsi', 'CSS0042300' => 'camsi', 'CSS0045298' => 'camsi', 'DCAR_012449' => 'dca', 'DCAR_018405' => 'dca', 'DCAR_024573' => 'dca', 'DCAR_030591' => 'dca', 'Dinv16926' => 'din', 'Dinv32963' => 'din', 'Dinv38382' => 'din', 'Dinv38383' => 'din', 'Duzib133G0974' => 'dzi', 'Duzib138G1867' => 'dzi', 'Duzib211G0420' => 'dzi', 'Duzib212G0930' => 'dzi', 'ECA234G1645' => 'eca', 'ECA247G3467' => 'eca', 'ECA248G1703' => 'eca', 'EL10Ac3g06327' => 'bvu', 'EL10Ac7g17204' => 'bvu', 'Eucgr.A00855' => 'egr', 'Eucgr.A00858' => 'egr', 'Eucgr.H01520' => 'egr', 'Eucgr.H03604' => 'egr', 'Eucgr.L03465' => 'egr', 'Eucgr.L03466' => 'egr', 'FAN01G0988' => 'fan', 'FAN02G3892' => 'fan', 'FAN05G3381' => 'fan', 'FAN07G0967' => 'fan', 'FAN07G1493' => 'fan', 'FAN08G3125' => 'fan', 'FAN09G0402' => 'fan', 'FAN12G2594' => 'fan', 'FAN12G3879' => 'fan', 'FAN14G1546' => 'fan', 'FAN15G3626' => 'fan', 'FAN17G0588' => 'fan', 'FAN17G0609' => 'fan', 'FAN18G2817' => 'fan', 'FAN19G1305' => 'fan', 'FAN20G1787' => 'fan', 'FAN22G0073' => 'fan', 'FAN22G0352' => 'fan', 'FAN22G0368' => 'fan', 'FAN22G2273' => 'fan', 'FAN24G1998' => 'fan', 'FAN27G1317' => 'fan', 'FvH4_2g23980' => 'fve', 'FvH4_4g14380' => 'fve', 'FvH4_4g14390' => 'fve', 'FvH4_6g09250' => 'fve', 'Glyma.03G151100' => 'gma', 'Glyma.04G122550' => 'gma', 'Glyma.05G001600' => 'gma', 'Glyma.09G270766' => 'gma', 'Glyma.09G270832' => 'gma', 'Glyma.13G209800' => 'gma', 'Glyma.15G102800' => 'gma', 'Glyma.18G218900' => 'gma', 'Glyma.19G001500' => 'gma', 'Glyma.19G153600' => 'gma', 'Gohir.A02G028600' => 'ghi', 'Gohir.A08G045000' => 'ghi', 'Gohir.A11G120500' => 'ghi', 'Gohir.A12G006200' => 'ghi', 'Gohir.A12G006250' => 'ghi', 'Gohir.D02G036300' => 'ghi', 'Gohir.D08G054700' => 'ghi', 'Gohir.D11G125600' => 'ghi', 'Gohir.D12G005700' => 'ghi', 'Gorai.004G055200' => 'gra', 'Gorai.005G040400' => 'gra', 'Gorai.007G134500' => 'gra', 'Gorai.008G005500' => 'gra', 'GSVIVG01011094001' => 'vvi', 'GSVIVG01017879001' => 'vvi', 'GSVIVG01025988001' => 'vvi', 'GSVIVG01029847001' => 'vvi', 'HanXRQChr10g0282901' => 'han', 'HanXRQChr10g0310371' => 'han', 'HanXRQChr10g0315041' => 'han', 'HanXRQChr11g0327651' => 'han', 'HanXRQChr12g0359391' => 'han', 'Haze_00972' => 'cav', 'Haze_00973' => 'cav', 'Haze_00974' => 'cav', 'Haze_04747' => 'cav', 'Haze_04749' => 'cav', 'Haze_04750' => 'cav', 'Haze_21217' => 'cav', 'Hma1.2p1_1037F.1_g250680' => 'hma', 'Hma1.2p1_1644F.1_g295320' => 'hma', 'HPP92_011322' => 'vpl', 'HPP92_011323' => 'vpl', 'HPP92_011324' => 'vpl', 'HPP92_011325' => 'vpl', 'HPP92_011326' => 'vpl', 'Hund12205' => 'sun', 'Hund17957' => 'sun', 'Lalb_Chr06g0176771' => 'lal', 'Lalb_Chr18g0056021' => 'lal', 'Lalb_Chr18g0056031' => 'lal', 'Lalb_Chr18g0056041' => 'lal', 'Lalb_Chr20g0107751' => 'lal', 'Lalb_Chr20g0118371' => 'lal', 'Lj1g0010239' => 'lja', 'Lj1g0017101' => 'lja', 'Lj2A1178G40' => 'lonja', 'Lj2A54G84' => 'lonja', 'Lj2g0015248' => 'lja', 'Lj3A761T51' => 'lonja', 'Lj6g0018116' => 'lja', 'Lsat_1_v5_gn_4_136040' => 'lsa', 'Lsat_1_v5_gn_5_187461' => 'lsa', 'Lsat_1_v5_gn_5_77001' => 'lsa', 'Lsat_1_v5_gn_9_4461' => 'lsa', 'Manes.01G210100' => 'mes', 'Manes.03G185600' => 'mes', 'Manes.05G073300' => 'mes', 'Manes.09G120300' => 'mes', 'Manes.15G022100' => 'mes', 'Mapoly0096s0053' => 'mpo', 'MBI03_g14058_MAGBIO' => 'mbi', 'MBI03_g33876_MAGBIO' => 'mbi', 'MBI03_g36854_MAGBIO' => 'mbi', 'MBI17_g11997_MAGBIO' => 'mbi', 'MD03G1269000' => 'mdo', 'MD04G1179600' => 'mdo', 'MD11G1289800' => 'mdo', 'MD12G1194700' => 'mdo', 'MD13G1182100' => 'mdo', 'MD13G1182200' => 'mdo', 'MD16G1182600' => 'mdo', 'Medtr2g021400' => 'mtr', 'Medtr2g021470' => 'mtr', 'Medtr2g105810' => 'mtr', 'Medtr3g033580' => 'mtr', 'Medtr6g007970' => 'mtr', 'Medtr7g056330' => 'mtr', 'Medtr7g074290' => 'mtr', 'Medtr7g074380' => 'mtr', 'Medtr7g094550' => 'mtr', 'Medtr8g069995' => 'mtr', 'MELO3C014345.2' => 'cme', 'MELO3C021395.2' => 'cme', 'Migut.D00262' => 'egut', 'Migut.G00257' => 'egut', 'MSTRG.21575' => 'ama', 'MSTRG.3985' => 'ama', 'Nitab4.5_0000295g0140' => 'nta', 'Nitab4.5_0000732g0140' => 'nta', 'Nitab4.5_0003162g0020' => 'nta', 'Nitab4.5_0006180g0090' => 'nta', 'Nitab4.5_0006390g0010' => 'nta', 'Nitab4.5_0007392g0040' => 'nta', 'Nn1g02140' => 'nnu', 'Nn4g26168' => 'nnu', 'Nn5g26754' => 'nnu', 'Oeu001433.1' => 'oeu', 'Oeu010299.2' => 'oeu', 'Oeu011171.1' => 'oeu', 'Oeu037675.1' => 'oeu', 'Oeu038359.1' => 'oeu', 'Oeu063834.1' => 'oeu', 'Oeu063835.1' => 'oeu', 'Os05g0312000' => 'osa', 'Os07g0211101' => 'osa', 'Os07g0211200' => 'osa', 'Os07g0681500' => 'osa', 'Peaxi162Scf00095g01015' => 'pax', 'Peaxi162Scf00104g00329' => 'pax', 'Peaxi162Scf00161g00137' => 'pax', 'PGR004G1665' => 'pgr', 'PGR031G2937' => 'pgr', 'PGR119G2145' => 'pgr', 'PGSC0003DMG400004351' => 'stu', 'PGSC0003DMG400014625' => 'stu', 'PGSC0003DMG401000943' => 'stu', 'Phvul.001G148600' => 'pvu', 'Phvul.004G001700' => 'pvu', 'Phvul.006G154900' => 'pvu', 'Phvul.008G078200' => 'pvu', 'Phvul.011G136500' => 'pvu', 'Potri.002G215600' => 'ptr', 'Potri.008G201600' => 'ptr', 'Potri.014G138400' => 'ptr', 'Potri.016G142500' => 'ptr', 'Pp3c16_10580' => 'ppa', 'Pp3c5_25280' => 'ppa', 'Prupe.1G150000' => 'ppe', 'Prupe.1G150100' => 'ppe', 'Prupe.6G299600' => 'ppe', 'Prupe.8G245000' => 'ppe', 'Psat0s4927g0040' => 'psa', 'Psat1g052080' => 'psa', 'Psat1g183800' => 'psa', 'Psat3g113840' => 'psa', 'Psat3g126120' => 'psa', 'Psat3g126160' => 'psa', 'Psat3g158760' => 'psa', 'Psat3g158840' => 'psa', 'PSO170G2858' => 'pso', 'PSO339G0606' => 'pso', 'PSO384G4709' => 'pso', 'PSO407G0334' => 'pso', 'QL04p040276' => 'qlo', 'QL06p005458' => 'qlo', 'QL06p005472' => 'qlo', 'QL07p030546' => 'qlo', 'QL07p031519' => 'qlo', 'QL09p050949' => 'qlo', 'QL09p050966' => 'qlo', 'QL09p051067' => 'qlo', 'QL12p022706' => 'qlo', 'RcHm_v2.0_Chr2g0119601' => 'rch', 'RcHm_v2.0_Chr3g0459591' => 'rch', 'RcHm_v2.0_Chr4g0418521' => 'rch', 'RcHm_v2.0_Chr4g0418531' => 'rch', 'RcHm_v2.0_Chr4g0418541' => 'rch', 'RcHm_v2.0_Chr6g0291641' => 'rch', 'Rhsim01G0086300' => 'rsi', 'Rhsim01G0276300' => 'rsi', 'Rhsim01G0276500' => 'rsi', 'Rhsim04G0207700' => 'rsi', 'Rhsim05G0234500' => 'rsi', 'Rhsim13G0022400' => 'rsi', 'Sabra02G0167900' => 'sbr', 'Sabra04G0158500' => 'sbr', 'Sabra08G0159800' => 'sbr', 'Sabra10G0011500' => 'sbr', 'Sabra14G0104400' => 'sbr', 'SalBow2G2440' => 'sbo', 'SalBow4G2265' => 'sbo', 'Sc02g0000060' => 'sci', 'Sc05g0005020' => 'sci', 'Sc13g0003890' => 'sci', 'Sed0014865' => 'sed', 'Sed0017224' => 'sed', 'Sed0026391' => 'sed', 'SEGI_00063' => 'sgi', 'SEGI_10967' => 'sgi', 'SEGI_17510' => 'sgi', 'SEGI_24396' => 'sgi', 'SEGI_39719' => 'sgi', 'SEGI_41392' => 'sgi', 'SGA_v2.0_scaffold11G05794' => 'sas', 'SGA_v2.0_scaffold142G35607' => 'sas', 'SGA_v2.0_scaffold1G00447' => 'sas', 'SHI15388' => 'shi', 'SHI15394' => 'shi', 'SHI15396' => 'shi', 'SHI15399' => 'shi', 'SMO343G0151' => 'smo', 'SMO367G1118' => 'smo', 'Solyc01g080200.3' => 'sly', 'Solyc06g008960.3' => 'sly', 'Solyc09g064780.3' => 'sly', 'Sopen01g031980' => 'spe', 'Sopen06g003710' => 'spe', 'Sopen09g026460' => 'spe', 'Sp3g21240' => 'spa', 'Sp4g30030' => 'spa', 'TAR365G0022' => 'tar', 'TAR365G1023' => 'tar', 'TAR365G1253' => 'tar', 'TAR623G0078' => 'tar', 'TAR623G1721' => 'tar', 'TAR633G0959' => 'tar', 'THA.LOC104802225' => 'tha', 'THA.LOC104804769' => 'tha', 'THA.LOC104808660' => 'tha', 'THA.LOC104812792' => 'tha', 'Thecc.01G284000' => 'tca', 'Thecc.04G220600' => 'tca', 'Thecc.05G268900' => 'tca', 'Thecc.08G171100' => 'tca', 'Thhalv10001284m.g' => 'esa', 'Thhalv10019912m.g' => 'esa', 'TPR.G14189' => 'tpr', 'TPR.G18110' => 'tpr', 'TPR.G18130' => 'tpr', 'TPR.G18131' => 'tpr', 'TPR.G18140' => 'tpr', 'TPR.G24282' => 'tpr', 'TPR.G25221' => 'tpr', 'TPR.G29267' => 'tpr', 'TPR.G35315' => 'tpr', 'TPR.G36173' => 'tpr', 'TWI09G0794' => 'twi', 'TWI59G1348' => 'twi', 'TWI74G0430' => 'twi', 'unitig_26.g8940' => 'ugi', 'unitig_749.g13744' => 'ugi', 'unitig_749.g13745' => 'ugi', 'vmacro08269' => 'vma', 'vmacro14937' => 'vma', 'vmacro20401' => 'vma', 'VMungo0464G1349' => 'vmu', 'VMungo0540G0289' => 'vmu', 'VMungo1215G1590' => 'vmu', 'VMungo1309G0221' => 'vmu', 'VMungo1309G2815' => 'vmu', 'VMungo1383G0239' => 'vmu', 'VMungo1383G2910' => 'vmu', 'Zm00001eb095270' => 'zma', 'Zm00001eb095280' => 'zma', 'Zm00001eb111630' => 'zma', 'Zm00001eb237080' => 'zma', 'Zm00001eb273740' => 'zma', 'Zm00001eb285040' => 'zma', 'Zm00001eb330790' => 'zma', 'Zm00001eb337380' => 'zma' ), 'gf_id' => 'HOM05D001484', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001484' ), 'data_identifier' => 'HOM05D001484', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001484', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p31500' => 'bna', 'A05p00020' => 'bna', 'A07p08820' => 'bna', 'Aa31LG4G3300' => 'aar', 'Aa31LG8G10030' => 'aar', 'Actinidia00731' => 'ach', 'Actinidia11473' => 'ach', 'Actinidia23469' => 'ach', 'Actinidia24318' => 'ach', 'Actinidia40196' => 'ach', 'Actinidia40197' => 'ach', 'Actinidia40198' => 'ach', 'Ah.08g212990' => 'amhyb', 'Ah.15g091720' => 'amhyb', 'AL3G38260' => 'aly', 'AL4G47710' => 'aly', 'Aqoxy2G00671' => 'aox', 'Aqoxy2G03236' => 'aox', 'arahy.Tifrunner.gnm1.ann1.05IDCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KR684' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATY3SJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK6QJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6APGL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IDT7Z9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM073U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ0R87' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LE7RV4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT4QRX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V5ENPK' => 'arhy', 'AT2G48110' => 'ath', 'AT3G23590' => 'ath', 'ATR0626G186' => 'atr', 'ATR1127G141' => 'atr', 'Atru.chr4.2583' => 'acertr', 'Atru.chr5.1358' => 'acertr', 'Atru.chr5.1359' => 'acertr', 'Atru.chr8.46' => 'acertr', 'AUR62002640' => 'cqu', 'AUR62030055' => 'cqu', 'AUR62033713' => 'cqu', 'AUR62033714' => 'cqu', 'AUR62036795' => 'cqu', 'AUR62039891' => 'cqu', 'BcaB02g08737' => 'bca', 'BcaB04g20441' => 'bca', 'BcaB06g26509' => 'bca', 'BcaB06g26510' => 'bca', 'BcaB06g26511' => 'bca', 'BcaB06g26512' => 'bca', 'BcaB06g26513' => 'bca', 'BcaC02g12564' => 'bca', 'BcaC02g12565' => 'bca', 'BcaC02g12794' => 'bca', 'BcaC02g12795' => 'bca', 'BcaC02g12796' => 'bca', 'BcaC06g35541' => 'bca', 'BNapus_Darmor_BZH_scaffold_188p00080' => 'bna', 'BNapus_Darmor_BZH_scaffold_188p00090' => 'bna', 'BolC1t03972H' => 'bol', 'BolC1t03973H' => 'bol', 'BolC4t21680H' => 'bol', 'BolC7t41863H' => 'bol', 'BolSC55t61227H' => 'bol', 'BolSC55t61228H' => 'bol', 'BraA01t03278Z' => 'bra', 'BraA05t18998Z' => 'bra', 'BraA07t28673Z' => 'bra', 'C01p40150' => 'bna', 'C05p12370' => 'bna', 'C07p13680' => 'bna', 'CAN.G1006.16' => 'can', 'CAN.G1006.17' => 'can', 'CAN.G1170.2' => 'can', 'CAN.G962.7' => 'can', 'CANSAT25G2179' => 'cansat', 'CANSAT78G1573' => 'cansat', 'CARHR099510' => 'chi', 'CARHR143510' => 'chi', 'Carub.0003s2380' => 'cru', 'Carub.0004s3082' => 'cru', 'Ca_00614_v3' => 'car', 'Ca_07801_v3' => 'car', 'Ca_08567_v3' => 'car', 'Ca_09571_v3' => 'car', 'CBR_g19290' => 'cbr', 'Cc01_g19770' => 'ccan', 'Cc03_g03030' => 'ccan', 'CDE07G0968' => 'cde', 'CDE09G1441' => 'cde', 'Cfa006103' => 'cfa', 'Cfa015573' => 'cfa', 'Cfa016988' => 'cfa', 'Ciclev10006738m.g' => 'ccl', 'Ciclev10010920m.g' => 'ccl', 'Ciclev10018517m.g' => 'ccl', 'CiPaw.01G159200' => 'cil', 'CiPaw.02G091000' => 'cil', 'CiPaw.02G091100' => 'cil', 'CiPaw.08G103100' => 'cil', 'CiPaw.09G224900' => 'cil', 'ClCG06G005740' => 'cla', 'ClCG07G000090' => 'cla', 'ClCG07G000100' => 'cla', 'COL.COLO4_09143' => 'col', 'COL.COLO4_25124' => 'col', 'Cpa.g.sc16.34' => 'cpa', 'Cpa.g.sc3504.1' => 'cpa', 'Cpa.g.sc60.37' => 'cpa', 'CsaV3_6G018520' => 'csa', 'CsaV3_6G036860' => 'csa', 'CSS0001072' => 'camsi', 'CSS0020208' => 'camsi', 'CSS0021253' => 'camsi', 'CSS0022190' => 'camsi', 'CSS0036150' => 'camsi', 'CSS0040442' => 'camsi', 'CSS0042300' => 'camsi', 'CSS0045298' => 'camsi', 'DCAR_012449' => 'dca', 'DCAR_018405' => 'dca', 'DCAR_024573' => 'dca', 'DCAR_030591' => 'dca', 'Dinv16926' => 'din', 'Dinv32963' => 'din', 'Dinv38382' => 'din', 'Dinv38383' => 'din', 'Duzib133G0974' => 'dzi', 'Duzib138G1867' => 'dzi', 'Duzib211G0420' => 'dzi', 'Duzib212G0930' => 'dzi', 'ECA234G1645' => 'eca', 'ECA247G3467' => 'eca', 'ECA248G1703' => 'eca', 'EL10Ac3g06327' => 'bvu', 'EL10Ac7g17204' => 'bvu', 'Eucgr.A00855' => 'egr', 'Eucgr.A00858' => 'egr', 'Eucgr.H01520' => 'egr', 'Eucgr.H03604' => 'egr', 'Eucgr.L03465' => 'egr', 'Eucgr.L03466' => 'egr', 'FAN01G0988' => 'fan', 'FAN02G3892' => 'fan', 'FAN05G3381' => 'fan', 'FAN07G0967' => 'fan', 'FAN07G1493' => 'fan', 'FAN08G3125' => 'fan', 'FAN09G0402' => 'fan', 'FAN12G2594' => 'fan', 'FAN12G3879' => 'fan', 'FAN14G1546' => 'fan', 'FAN15G3626' => 'fan', 'FAN17G0588' => 'fan', 'FAN17G0609' => 'fan', 'FAN18G2817' => 'fan', 'FAN19G1305' => 'fan', 'FAN20G1787' => 'fan', 'FAN22G0073' => 'fan', 'FAN22G0352' => 'fan', 'FAN22G0368' => 'fan', 'FAN22G2273' => 'fan', 'FAN24G1998' => 'fan', 'FAN27G1317' => 'fan', 'FvH4_2g23980' => 'fve', 'FvH4_4g14380' => 'fve', 'FvH4_4g14390' => 'fve', 'FvH4_6g09250' => 'fve', 'Glyma.03G151100' => 'gma', 'Glyma.04G122550' => 'gma', 'Glyma.05G001600' => 'gma', 'Glyma.09G270766' => 'gma', 'Glyma.09G270832' => 'gma', 'Glyma.13G209800' => 'gma', 'Glyma.15G102800' => 'gma', 'Glyma.18G218900' => 'gma', 'Glyma.19G001500' => 'gma', 'Glyma.19G153600' => 'gma', 'Gohir.A02G028600' => 'ghi', 'Gohir.A08G045000' => 'ghi', 'Gohir.A11G120500' => 'ghi', 'Gohir.A12G006200' => 'ghi', 'Gohir.A12G006250' => 'ghi', 'Gohir.D02G036300' => 'ghi', 'Gohir.D08G054700' => 'ghi', 'Gohir.D11G125600' => 'ghi', 'Gohir.D12G005700' => 'ghi', 'Gorai.004G055200' => 'gra', 'Gorai.005G040400' => 'gra', 'Gorai.007G134500' => 'gra', 'Gorai.008G005500' => 'gra', 'GSVIVG01011094001' => 'vvi', 'GSVIVG01017879001' => 'vvi', 'GSVIVG01025988001' => 'vvi', 'GSVIVG01029847001' => 'vvi', 'HanXRQChr10g0282901' => 'han', 'HanXRQChr10g0310371' => 'han', 'HanXRQChr10g0315041' => 'han', 'HanXRQChr11g0327651' => 'han', 'HanXRQChr12g0359391' => 'han', 'Haze_00972' => 'cav', 'Haze_00973' => 'cav', 'Haze_00974' => 'cav', 'Haze_04747' => 'cav', 'Haze_04749' => 'cav', 'Haze_04750' => 'cav', 'Haze_21217' => 'cav', 'Hma1.2p1_1037F.1_g250680' => 'hma', 'Hma1.2p1_1644F.1_g295320' => 'hma', 'HPP92_011322' => 'vpl', 'HPP92_011323' => 'vpl', 'HPP92_011324' => 'vpl', 'HPP92_011325' => 'vpl', 'HPP92_011326' => 'vpl', 'Hund12205' => 'sun', 'Hund17957' => 'sun', 'Lalb_Chr06g0176771' => 'lal', 'Lalb_Chr18g0056021' => 'lal', 'Lalb_Chr18g0056031' => 'lal', 'Lalb_Chr18g0056041' => 'lal', 'Lalb_Chr20g0107751' => 'lal', 'Lalb_Chr20g0118371' => 'lal', 'Lj1g0010239' => 'lja', 'Lj1g0017101' => 'lja', 'Lj2A1178G40' => 'lonja', 'Lj2A54G84' => 'lonja', 'Lj2g0015248' => 'lja', 'Lj3A761T51' => 'lonja', 'Lj6g0018116' => 'lja', 'Lsat_1_v5_gn_4_136040' => 'lsa', 'Lsat_1_v5_gn_5_187461' => 'lsa', 'Lsat_1_v5_gn_5_77001' => 'lsa', 'Lsat_1_v5_gn_9_4461' => 'lsa', 'Manes.01G210100' => 'mes', 'Manes.03G185600' => 'mes', 'Manes.05G073300' => 'mes', 'Manes.09G120300' => 'mes', 'Manes.15G022100' => 'mes', 'Mapoly0096s0053' => 'mpo', 'MBI03_g14058_MAGBIO' => 'mbi', 'MBI03_g33876_MAGBIO' => 'mbi', 'MBI03_g36854_MAGBIO' => 'mbi', 'MBI17_g11997_MAGBIO' => 'mbi', 'MD03G1269000' => 'mdo', 'MD04G1179600' => 'mdo', 'MD11G1289800' => 'mdo', 'MD12G1194700' => 'mdo', 'MD13G1182100' => 'mdo', 'MD13G1182200' => 'mdo', 'MD16G1182600' => 'mdo', 'Medtr2g021400' => 'mtr', 'Medtr2g021470' => 'mtr', 'Medtr2g105810' => 'mtr', 'Medtr3g033580' => 'mtr', 'Medtr6g007970' => 'mtr', 'Medtr7g056330' => 'mtr', 'Medtr7g074290' => 'mtr', 'Medtr7g074380' => 'mtr', 'Medtr7g094550' => 'mtr', 'Medtr8g069995' => 'mtr', 'MELO3C014345.2' => 'cme', 'MELO3C021395.2' => 'cme', 'Migut.D00262' => 'egut', 'Migut.G00257' => 'egut', 'MSTRG.21575' => 'ama', 'MSTRG.3985' => 'ama', 'Nitab4.5_0000295g0140' => 'nta', 'Nitab4.5_0000732g0140' => 'nta', 'Nitab4.5_0003162g0020' => 'nta', 'Nitab4.5_0006180g0090' => 'nta', 'Nitab4.5_0006390g0010' => 'nta', 'Nitab4.5_0007392g0040' => 'nta', 'Nn1g02140' => 'nnu', 'Nn4g26168' => 'nnu', 'Nn5g26754' => 'nnu', 'Oeu001433.1' => 'oeu', 'Oeu010299.2' => 'oeu', 'Oeu011171.1' => 'oeu', 'Oeu037675.1' => 'oeu', 'Oeu038359.1' => 'oeu', 'Oeu063834.1' => 'oeu', 'Oeu063835.1' => 'oeu', 'Os05g0312000' => 'osa', 'Os07g0211101' => 'osa', 'Os07g0211200' => 'osa', 'Os07g0681500' => 'osa', 'Peaxi162Scf00095g01015' => 'pax', 'Peaxi162Scf00104g00329' => 'pax', 'Peaxi162Scf00161g00137' => 'pax', 'PGR004G1665' => 'pgr', 'PGR031G2937' => 'pgr', 'PGR119G2145' => 'pgr', 'PGSC0003DMG400004351' => 'stu', 'PGSC0003DMG400014625' => 'stu', 'PGSC0003DMG401000943' => 'stu', 'Phvul.001G148600' => 'pvu', 'Phvul.004G001700' => 'pvu', 'Phvul.006G154900' => 'pvu', 'Phvul.008G078200' => 'pvu', 'Phvul.011G136500' => 'pvu', 'Potri.002G215600' => 'ptr', 'Potri.008G201600' => 'ptr', 'Potri.014G138400' => 'ptr', 'Potri.016G142500' => 'ptr', 'Pp3c16_10580' => 'ppa', 'Pp3c5_25280' => 'ppa', 'Prupe.1G150000' => 'ppe', 'Prupe.1G150100' => 'ppe', 'Prupe.6G299600' => 'ppe', 'Prupe.8G245000' => 'ppe', 'Psat0s4927g0040' => 'psa', 'Psat1g052080' => 'psa', 'Psat1g183800' => 'psa', 'Psat3g113840' => 'psa', 'Psat3g126120' => 'psa', 'Psat3g126160' => 'psa', 'Psat3g158760' => 'psa', 'Psat3g158840' => 'psa', 'PSO170G2858' => 'pso', 'PSO339G0606' => 'pso', 'PSO384G4709' => 'pso', 'PSO407G0334' => 'pso', 'QL04p040276' => 'qlo', 'QL06p005458' => 'qlo', 'QL06p005472' => 'qlo', 'QL07p030546' => 'qlo', 'QL07p031519' => 'qlo', 'QL09p050949' => 'qlo', 'QL09p050966' => 'qlo', 'QL09p051067' => 'qlo', 'QL12p022706' => 'qlo', 'RcHm_v2.0_Chr2g0119601' => 'rch', 'RcHm_v2.0_Chr3g0459591' => 'rch', 'RcHm_v2.0_Chr4g0418521' => 'rch', 'RcHm_v2.0_Chr4g0418531' => 'rch', 'RcHm_v2.0_Chr4g0418541' => 'rch', 'RcHm_v2.0_Chr6g0291641' => 'rch', 'Rhsim01G0086300' => 'rsi', 'Rhsim01G0276300' => 'rsi', 'Rhsim01G0276500' => 'rsi', 'Rhsim04G0207700' => 'rsi', 'Rhsim05G0234500' => 'rsi', 'Rhsim13G0022400' => 'rsi', 'Sabra02G0167900' => 'sbr', 'Sabra04G0158500' => 'sbr', 'Sabra08G0159800' => 'sbr', 'Sabra10G0011500' => 'sbr', 'Sabra14G0104400' => 'sbr', 'SalBow2G2440' => 'sbo', 'SalBow4G2265' => 'sbo', 'Sc02g0000060' => 'sci', 'Sc05g0005020' => 'sci', 'Sc13g0003890' => 'sci', 'Sed0014865' => 'sed', 'Sed0017224' => 'sed', 'Sed0026391' => 'sed', 'SEGI_00063' => 'sgi', 'SEGI_10967' => 'sgi', 'SEGI_17510' => 'sgi', 'SEGI_24396' => 'sgi', 'SEGI_39719' => 'sgi', 'SEGI_41392' => 'sgi', 'SGA_v2.0_scaffold11G05794' => 'sas', 'SGA_v2.0_scaffold142G35607' => 'sas', 'SGA_v2.0_scaffold1G00447' => 'sas', 'SHI15388' => 'shi', 'SHI15394' => 'shi', 'SHI15396' => 'shi', 'SHI15399' => 'shi', 'SMO343G0151' => 'smo', 'SMO367G1118' => 'smo', 'Solyc01g080200.3' => 'sly', 'Solyc06g008960.3' => 'sly', 'Solyc09g064780.3' => 'sly', 'Sopen01g031980' => 'spe', 'Sopen06g003710' => 'spe', 'Sopen09g026460' => 'spe', 'Sp3g21240' => 'spa', 'Sp4g30030' => 'spa', 'TAR365G0022' => 'tar', 'TAR365G1023' => 'tar', 'TAR365G1253' => 'tar', 'TAR623G0078' => 'tar', 'TAR623G1721' => 'tar', 'TAR633G0959' => 'tar', 'THA.LOC104802225' => 'tha', 'THA.LOC104804769' => 'tha', 'THA.LOC104808660' => 'tha', 'THA.LOC104812792' => 'tha', 'Thecc.01G284000' => 'tca', 'Thecc.04G220600' => 'tca', 'Thecc.05G268900' => 'tca', 'Thecc.08G171100' => 'tca', 'Thhalv10001284m.g' => 'esa', 'Thhalv10019912m.g' => 'esa', 'TPR.G14189' => 'tpr', 'TPR.G18110' => 'tpr', 'TPR.G18130' => 'tpr', 'TPR.G18131' => 'tpr', 'TPR.G18140' => 'tpr', 'TPR.G24282' => 'tpr', 'TPR.G25221' => 'tpr', 'TPR.G29267' => 'tpr', 'TPR.G35315' => 'tpr', 'TPR.G36173' => 'tpr', 'TWI09G0794' => 'twi', 'TWI59G1348' => 'twi', 'TWI74G0430' => 'twi', 'unitig_26.g8940' => 'ugi', 'unitig_749.g13744' => 'ugi', 'unitig_749.g13745' => 'ugi', 'vmacro08269' => 'vma', 'vmacro14937' => 'vma', 'vmacro20401' => 'vma', 'VMungo0464G1349' => 'vmu', 'VMungo0540G0289' => 'vmu', 'VMungo1215G1590' => 'vmu', 'VMungo1309G0221' => 'vmu', 'VMungo1309G2815' => 'vmu', 'VMungo1383G0239' => 'vmu', 'VMungo1383G2910' => 'vmu', 'Zm00001eb095270' => 'zma', 'Zm00001eb095280' => 'zma', 'Zm00001eb111630' => 'zma', 'Zm00001eb237080' => 'zma', 'Zm00001eb273740' => 'zma', 'Zm00001eb285040' => 'zma', 'Zm00001eb330790' => 'zma', 'Zm00001eb337380' => 'zma' ) $gf_id = 'HOM05D001484' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001484' ) $data_identifier = 'HOM05D001484' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 2, 'aly' => (int) 2, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 22, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 7, 'hma' => (int) 2, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 7, 'mtr' => (int) 10, 'cme' => (int) 2, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 4, 'ppa' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 4, 'qlo' => (int) 9, 'rch' => (int) 6, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 10, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 7, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb337380' $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' => 'HOM05D001484', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p31500' => 'bna', 'A05p00020' => 'bna', 'A07p08820' => 'bna', 'Aa31LG4G3300' => 'aar', 'Aa31LG8G10030' => 'aar', 'Actinidia00731' => 'ach', 'Actinidia11473' => 'ach', 'Actinidia23469' => 'ach', 'Actinidia24318' => 'ach', 'Actinidia40196' => 'ach', 'Actinidia40197' => 'ach', 'Actinidia40198' => 'ach', 'Ah.08g212990' => 'amhyb', 'Ah.15g091720' => 'amhyb', 'AL3G38260' => 'aly', 'AL4G47710' => 'aly', 'Aqoxy2G00671' => 'aox', 'Aqoxy2G03236' => 'aox', 'arahy.Tifrunner.gnm1.ann1.05IDCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KR684' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATY3SJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK6QJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6APGL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IDT7Z9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM073U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ0R87' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LE7RV4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT4QRX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V5ENPK' => 'arhy', 'AT2G48110' => 'ath', 'AT3G23590' => 'ath', 'ATR0626G186' => 'atr', 'ATR1127G141' => 'atr', 'Atru.chr4.2583' => 'acertr', 'Atru.chr5.1358' => 'acertr', 'Atru.chr5.1359' => 'acertr', 'Atru.chr8.46' => 'acertr', 'AUR62002640' => 'cqu', 'AUR62030055' => 'cqu', 'AUR62033713' => 'cqu', 'AUR62033714' => 'cqu', 'AUR62036795' => 'cqu', 'AUR62039891' => 'cqu', 'BcaB02g08737' => 'bca', 'BcaB04g20441' => 'bca', 'BcaB06g26509' => 'bca', 'BcaB06g26510' => 'bca', 'BcaB06g26511' => 'bca', 'BcaB06g26512' => 'bca', 'BcaB06g26513' => 'bca', 'BcaC02g12564' => 'bca', 'BcaC02g12565' => 'bca', 'BcaC02g12794' => 'bca', 'BcaC02g12795' => 'bca', 'BcaC02g12796' => 'bca', 'BcaC06g35541' => 'bca', 'BNapus_Darmor_BZH_scaffold_188p00080' => 'bna', 'BNapus_Darmor_BZH_scaffold_188p00090' => 'bna', 'BolC1t03972H' => 'bol', 'BolC1t03973H' => 'bol', 'BolC4t21680H' => 'bol', 'BolC7t41863H' => 'bol', 'BolSC55t61227H' => 'bol', 'BolSC55t61228H' => 'bol', 'BraA01t03278Z' => 'bra', 'BraA05t18998Z' => 'bra', 'BraA07t28673Z' => 'bra', 'C01p40150' => 'bna', 'C05p12370' => 'bna', 'C07p13680' => 'bna', 'CAN.G1006.16' => 'can', 'CAN.G1006.17' => 'can', 'CAN.G1170.2' => 'can', 'CAN.G962.7' => 'can', 'CANSAT25G2179' => 'cansat', 'CANSAT78G1573' => 'cansat', 'CARHR099510' => 'chi', 'CARHR143510' => 'chi', 'Carub.0003s2380' => 'cru', 'Carub.0004s3082' => 'cru', 'Ca_00614_v3' => 'car', 'Ca_07801_v3' => 'car', 'Ca_08567_v3' => 'car', 'Ca_09571_v3' => 'car', 'CBR_g19290' => 'cbr', 'Cc01_g19770' => 'ccan', 'Cc03_g03030' => 'ccan', 'CDE07G0968' => 'cde', 'CDE09G1441' => 'cde', 'Cfa006103' => 'cfa', 'Cfa015573' => 'cfa', 'Cfa016988' => 'cfa', 'Ciclev10006738m.g' => 'ccl', 'Ciclev10010920m.g' => 'ccl', 'Ciclev10018517m.g' => 'ccl', 'CiPaw.01G159200' => 'cil', 'CiPaw.02G091000' => 'cil', 'CiPaw.02G091100' => 'cil', 'CiPaw.08G103100' => 'cil', 'CiPaw.09G224900' => 'cil', 'ClCG06G005740' => 'cla', 'ClCG07G000090' => 'cla', 'ClCG07G000100' => 'cla', 'COL.COLO4_09143' => 'col', 'COL.COLO4_25124' => 'col', 'Cpa.g.sc16.34' => 'cpa', 'Cpa.g.sc3504.1' => 'cpa', 'Cpa.g.sc60.37' => 'cpa', 'CsaV3_6G018520' => 'csa', 'CsaV3_6G036860' => 'csa', 'CSS0001072' => 'camsi', 'CSS0020208' => 'camsi', 'CSS0021253' => 'camsi', 'CSS0022190' => 'camsi', 'CSS0036150' => 'camsi', 'CSS0040442' => 'camsi', 'CSS0042300' => 'camsi', 'CSS0045298' => 'camsi', 'DCAR_012449' => 'dca', 'DCAR_018405' => 'dca', 'DCAR_024573' => 'dca', 'DCAR_030591' => 'dca', 'Dinv16926' => 'din', 'Dinv32963' => 'din', 'Dinv38382' => 'din', 'Dinv38383' => 'din', 'Duzib133G0974' => 'dzi', 'Duzib138G1867' => 'dzi', 'Duzib211G0420' => 'dzi', 'Duzib212G0930' => 'dzi', 'ECA234G1645' => 'eca', 'ECA247G3467' => 'eca', 'ECA248G1703' => 'eca', 'EL10Ac3g06327' => 'bvu', 'EL10Ac7g17204' => 'bvu', 'Eucgr.A00855' => 'egr', 'Eucgr.A00858' => 'egr', 'Eucgr.H01520' => 'egr', 'Eucgr.H03604' => 'egr', 'Eucgr.L03465' => 'egr', 'Eucgr.L03466' => 'egr', 'FAN01G0988' => 'fan', 'FAN02G3892' => 'fan', 'FAN05G3381' => 'fan', 'FAN07G0967' => 'fan', 'FAN07G1493' => 'fan', 'FAN08G3125' => 'fan', 'FAN09G0402' => 'fan', 'FAN12G2594' => 'fan', 'FAN12G3879' => 'fan', 'FAN14G1546' => 'fan', 'FAN15G3626' => 'fan', 'FAN17G0588' => 'fan', 'FAN17G0609' => 'fan', 'FAN18G2817' => 'fan', 'FAN19G1305' => 'fan', 'FAN20G1787' => 'fan', 'FAN22G0073' => 'fan', 'FAN22G0352' => 'fan', 'FAN22G0368' => 'fan', 'FAN22G2273' => 'fan', 'FAN24G1998' => 'fan', 'FAN27G1317' => 'fan', 'FvH4_2g23980' => 'fve', 'FvH4_4g14380' => 'fve', 'FvH4_4g14390' => 'fve', 'FvH4_6g09250' => 'fve', 'Glyma.03G151100' => 'gma', 'Glyma.04G122550' => 'gma', 'Glyma.05G001600' => 'gma', 'Glyma.09G270766' => 'gma', 'Glyma.09G270832' => 'gma', 'Glyma.13G209800' => 'gma', 'Glyma.15G102800' => 'gma', 'Glyma.18G218900' => 'gma', 'Glyma.19G001500' => 'gma', 'Glyma.19G153600' => 'gma', 'Gohir.A02G028600' => 'ghi', 'Gohir.A08G045000' => 'ghi', 'Gohir.A11G120500' => 'ghi', 'Gohir.A12G006200' => 'ghi', 'Gohir.A12G006250' => 'ghi', 'Gohir.D02G036300' => 'ghi', 'Gohir.D08G054700' => 'ghi', 'Gohir.D11G125600' => 'ghi', 'Gohir.D12G005700' => 'ghi', 'Gorai.004G055200' => 'gra', 'Gorai.005G040400' => 'gra', 'Gorai.007G134500' => 'gra', 'Gorai.008G005500' => 'gra', 'GSVIVG01011094001' => 'vvi', 'GSVIVG01017879001' => 'vvi', 'GSVIVG01025988001' => 'vvi', 'GSVIVG01029847001' => 'vvi', 'HanXRQChr10g0282901' => 'han', 'HanXRQChr10g0310371' => 'han', 'HanXRQChr10g0315041' => 'han', 'HanXRQChr11g0327651' => 'han', 'HanXRQChr12g0359391' => 'han', 'Haze_00972' => 'cav', 'Haze_00973' => 'cav', 'Haze_00974' => 'cav', 'Haze_04747' => 'cav', 'Haze_04749' => 'cav', 'Haze_04750' => 'cav', 'Haze_21217' => 'cav', 'Hma1.2p1_1037F.1_g250680' => 'hma', 'Hma1.2p1_1644F.1_g295320' => 'hma', 'HPP92_011322' => 'vpl', 'HPP92_011323' => 'vpl', 'HPP92_011324' => 'vpl', 'HPP92_011325' => 'vpl', 'HPP92_011326' => 'vpl', 'Hund12205' => 'sun', 'Hund17957' => 'sun', 'Lalb_Chr06g0176771' => 'lal', 'Lalb_Chr18g0056021' => 'lal', 'Lalb_Chr18g0056031' => 'lal', 'Lalb_Chr18g0056041' => 'lal', 'Lalb_Chr20g0107751' => 'lal', 'Lalb_Chr20g0118371' => 'lal', 'Lj1g0010239' => 'lja', 'Lj1g0017101' => 'lja', 'Lj2A1178G40' => 'lonja', 'Lj2A54G84' => 'lonja', 'Lj2g0015248' => 'lja', 'Lj3A761T51' => 'lonja', 'Lj6g0018116' => 'lja', 'Lsat_1_v5_gn_4_136040' => 'lsa', 'Lsat_1_v5_gn_5_187461' => 'lsa', 'Lsat_1_v5_gn_5_77001' => 'lsa', 'Lsat_1_v5_gn_9_4461' => 'lsa', 'Manes.01G210100' => 'mes', 'Manes.03G185600' => 'mes', 'Manes.05G073300' => 'mes', 'Manes.09G120300' => 'mes', 'Manes.15G022100' => 'mes', 'Mapoly0096s0053' => 'mpo', 'MBI03_g14058_MAGBIO' => 'mbi', 'MBI03_g33876_MAGBIO' => 'mbi', 'MBI03_g36854_MAGBIO' => 'mbi', 'MBI17_g11997_MAGBIO' => 'mbi', 'MD03G1269000' => 'mdo', 'MD04G1179600' => 'mdo', 'MD11G1289800' => 'mdo', 'MD12G1194700' => 'mdo', 'MD13G1182100' => 'mdo', 'MD13G1182200' => 'mdo', 'MD16G1182600' => 'mdo', 'Medtr2g021400' => 'mtr', 'Medtr2g021470' => 'mtr', 'Medtr2g105810' => 'mtr', 'Medtr3g033580' => 'mtr', 'Medtr6g007970' => 'mtr', 'Medtr7g056330' => 'mtr', 'Medtr7g074290' => 'mtr', 'Medtr7g074380' => 'mtr', 'Medtr7g094550' => 'mtr', 'Medtr8g069995' => 'mtr', 'MELO3C014345.2' => 'cme', 'MELO3C021395.2' => 'cme', 'Migut.D00262' => 'egut', 'Migut.G00257' => 'egut', 'MSTRG.21575' => 'ama', 'MSTRG.3985' => 'ama', 'Nitab4.5_0000295g0140' => 'nta', 'Nitab4.5_0000732g0140' => 'nta', 'Nitab4.5_0003162g0020' => 'nta', 'Nitab4.5_0006180g0090' => 'nta', 'Nitab4.5_0006390g0010' => 'nta', 'Nitab4.5_0007392g0040' => 'nta', 'Nn1g02140' => 'nnu', 'Nn4g26168' => 'nnu', 'Nn5g26754' => 'nnu', 'Oeu001433.1' => 'oeu', 'Oeu010299.2' => 'oeu', 'Oeu011171.1' => 'oeu', 'Oeu037675.1' => 'oeu', 'Oeu038359.1' => 'oeu', 'Oeu063834.1' => 'oeu', 'Oeu063835.1' => 'oeu', 'Os05g0312000' => 'osa', 'Os07g0211101' => 'osa', 'Os07g0211200' => 'osa', 'Os07g0681500' => 'osa', 'Peaxi162Scf00095g01015' => 'pax', 'Peaxi162Scf00104g00329' => 'pax', 'Peaxi162Scf00161g00137' => 'pax', 'PGR004G1665' => 'pgr', 'PGR031G2937' => 'pgr', 'PGR119G2145' => 'pgr', 'PGSC0003DMG400004351' => 'stu', 'PGSC0003DMG400014625' => 'stu', 'PGSC0003DMG401000943' => 'stu', 'Phvul.001G148600' => 'pvu', 'Phvul.004G001700' => 'pvu', 'Phvul.006G154900' => 'pvu', 'Phvul.008G078200' => 'pvu', 'Phvul.011G136500' => 'pvu', 'Potri.002G215600' => 'ptr', 'Potri.008G201600' => 'ptr', 'Potri.014G138400' => 'ptr', 'Potri.016G142500' => 'ptr', 'Pp3c16_10580' => 'ppa', 'Pp3c5_25280' => 'ppa', 'Prupe.1G150000' => 'ppe', 'Prupe.1G150100' => 'ppe', 'Prupe.6G299600' => 'ppe', 'Prupe.8G245000' => 'ppe', 'Psat0s4927g0040' => 'psa', 'Psat1g052080' => 'psa', 'Psat1g183800' => 'psa', 'Psat3g113840' => 'psa', 'Psat3g126120' => 'psa', 'Psat3g126160' => 'psa', 'Psat3g158760' => 'psa', 'Psat3g158840' => 'psa', 'PSO170G2858' => 'pso', 'PSO339G0606' => 'pso', 'PSO384G4709' => 'pso', 'PSO407G0334' => 'pso', 'QL04p040276' => 'qlo', 'QL06p005458' => 'qlo', 'QL06p005472' => 'qlo', 'QL07p030546' => 'qlo', 'QL07p031519' => 'qlo', 'QL09p050949' => 'qlo', 'QL09p050966' => 'qlo', 'QL09p051067' => 'qlo', 'QL12p022706' => 'qlo', 'RcHm_v2.0_Chr2g0119601' => 'rch', 'RcHm_v2.0_Chr3g0459591' => 'rch', 'RcHm_v2.0_Chr4g0418521' => 'rch', 'RcHm_v2.0_Chr4g0418531' => 'rch', 'RcHm_v2.0_Chr4g0418541' => 'rch', 'RcHm_v2.0_Chr6g0291641' => 'rch', 'Rhsim01G0086300' => 'rsi', 'Rhsim01G0276300' => 'rsi', 'Rhsim01G0276500' => 'rsi', 'Rhsim04G0207700' => 'rsi', 'Rhsim05G0234500' => 'rsi', 'Rhsim13G0022400' => 'rsi', 'Sabra02G0167900' => 'sbr', 'Sabra04G0158500' => 'sbr', 'Sabra08G0159800' => 'sbr', 'Sabra10G0011500' => 'sbr', 'Sabra14G0104400' => 'sbr', 'SalBow2G2440' => 'sbo', 'SalBow4G2265' => 'sbo', 'Sc02g0000060' => 'sci', 'Sc05g0005020' => 'sci', 'Sc13g0003890' => 'sci', 'Sed0014865' => 'sed', 'Sed0017224' => 'sed', 'Sed0026391' => 'sed', 'SEGI_00063' => 'sgi', 'SEGI_10967' => 'sgi', 'SEGI_17510' => 'sgi', 'SEGI_24396' => 'sgi', 'SEGI_39719' => 'sgi', 'SEGI_41392' => 'sgi', 'SGA_v2.0_scaffold11G05794' => 'sas', 'SGA_v2.0_scaffold142G35607' => 'sas', 'SGA_v2.0_scaffold1G00447' => 'sas', 'SHI15388' => 'shi', 'SHI15394' => 'shi', 'SHI15396' => 'shi', 'SHI15399' => 'shi', 'SMO343G0151' => 'smo', 'SMO367G1118' => 'smo', 'Solyc01g080200.3' => 'sly', 'Solyc06g008960.3' => 'sly', 'Solyc09g064780.3' => 'sly', 'Sopen01g031980' => 'spe', 'Sopen06g003710' => 'spe', 'Sopen09g026460' => 'spe', 'Sp3g21240' => 'spa', 'Sp4g30030' => 'spa', 'TAR365G0022' => 'tar', 'TAR365G1023' => 'tar', 'TAR365G1253' => 'tar', 'TAR623G0078' => 'tar', 'TAR623G1721' => 'tar', 'TAR633G0959' => 'tar', 'THA.LOC104802225' => 'tha', 'THA.LOC104804769' => 'tha', 'THA.LOC104808660' => 'tha', 'THA.LOC104812792' => 'tha', 'Thecc.01G284000' => 'tca', 'Thecc.04G220600' => 'tca', 'Thecc.05G268900' => 'tca', 'Thecc.08G171100' => 'tca', 'Thhalv10001284m.g' => 'esa', 'Thhalv10019912m.g' => 'esa', 'TPR.G14189' => 'tpr', 'TPR.G18110' => 'tpr', 'TPR.G18130' => 'tpr', 'TPR.G18131' => 'tpr', 'TPR.G18140' => 'tpr', 'TPR.G24282' => 'tpr', 'TPR.G25221' => 'tpr', 'TPR.G29267' => 'tpr', 'TPR.G35315' => 'tpr', 'TPR.G36173' => 'tpr', 'TWI09G0794' => 'twi', 'TWI59G1348' => 'twi', 'TWI74G0430' => 'twi', 'unitig_26.g8940' => 'ugi', 'unitig_749.g13744' => 'ugi', 'unitig_749.g13745' => 'ugi', 'vmacro08269' => 'vma', 'vmacro14937' => 'vma', 'vmacro20401' => 'vma', 'VMungo0464G1349' => 'vmu', 'VMungo0540G0289' => 'vmu', 'VMungo1215G1590' => 'vmu', 'VMungo1309G0221' => 'vmu', 'VMungo1309G2815' => 'vmu', 'VMungo1383G0239' => 'vmu', 'VMungo1383G2910' => 'vmu', 'Zm00001eb095270' => 'zma', 'Zm00001eb095280' => 'zma', 'Zm00001eb111630' => 'zma', 'Zm00001eb237080' => 'zma', 'Zm00001eb273740' => 'zma', 'Zm00001eb285040' => 'zma', 'Zm00001eb330790' => 'zma', 'Zm00001eb337380' => 'zma' ), 'gf_id' => 'HOM05D001484', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001484' ), 'data_identifier' => 'HOM05D001484', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001484', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p31500' => 'bna', 'A05p00020' => 'bna', 'A07p08820' => 'bna', 'Aa31LG4G3300' => 'aar', 'Aa31LG8G10030' => 'aar', 'Actinidia00731' => 'ach', 'Actinidia11473' => 'ach', 'Actinidia23469' => 'ach', 'Actinidia24318' => 'ach', 'Actinidia40196' => 'ach', 'Actinidia40197' => 'ach', 'Actinidia40198' => 'ach', 'Ah.08g212990' => 'amhyb', 'Ah.15g091720' => 'amhyb', 'AL3G38260' => 'aly', 'AL4G47710' => 'aly', 'Aqoxy2G00671' => 'aox', 'Aqoxy2G03236' => 'aox', 'arahy.Tifrunner.gnm1.ann1.05IDCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KR684' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATY3SJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK6QJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6APGL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IDT7Z9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM073U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ0R87' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LE7RV4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT4QRX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V5ENPK' => 'arhy', 'AT2G48110' => 'ath', 'AT3G23590' => 'ath', 'ATR0626G186' => 'atr', 'ATR1127G141' => 'atr', 'Atru.chr4.2583' => 'acertr', 'Atru.chr5.1358' => 'acertr', 'Atru.chr5.1359' => 'acertr', 'Atru.chr8.46' => 'acertr', 'AUR62002640' => 'cqu', 'AUR62030055' => 'cqu', 'AUR62033713' => 'cqu', 'AUR62033714' => 'cqu', 'AUR62036795' => 'cqu', 'AUR62039891' => 'cqu', 'BcaB02g08737' => 'bca', 'BcaB04g20441' => 'bca', 'BcaB06g26509' => 'bca', 'BcaB06g26510' => 'bca', 'BcaB06g26511' => 'bca', 'BcaB06g26512' => 'bca', 'BcaB06g26513' => 'bca', 'BcaC02g12564' => 'bca', 'BcaC02g12565' => 'bca', 'BcaC02g12794' => 'bca', 'BcaC02g12795' => 'bca', 'BcaC02g12796' => 'bca', 'BcaC06g35541' => 'bca', 'BNapus_Darmor_BZH_scaffold_188p00080' => 'bna', 'BNapus_Darmor_BZH_scaffold_188p00090' => 'bna', 'BolC1t03972H' => 'bol', 'BolC1t03973H' => 'bol', 'BolC4t21680H' => 'bol', 'BolC7t41863H' => 'bol', 'BolSC55t61227H' => 'bol', 'BolSC55t61228H' => 'bol', 'BraA01t03278Z' => 'bra', 'BraA05t18998Z' => 'bra', 'BraA07t28673Z' => 'bra', 'C01p40150' => 'bna', 'C05p12370' => 'bna', 'C07p13680' => 'bna', 'CAN.G1006.16' => 'can', 'CAN.G1006.17' => 'can', 'CAN.G1170.2' => 'can', 'CAN.G962.7' => 'can', 'CANSAT25G2179' => 'cansat', 'CANSAT78G1573' => 'cansat', 'CARHR099510' => 'chi', 'CARHR143510' => 'chi', 'Carub.0003s2380' => 'cru', 'Carub.0004s3082' => 'cru', 'Ca_00614_v3' => 'car', 'Ca_07801_v3' => 'car', 'Ca_08567_v3' => 'car', 'Ca_09571_v3' => 'car', 'CBR_g19290' => 'cbr', 'Cc01_g19770' => 'ccan', 'Cc03_g03030' => 'ccan', 'CDE07G0968' => 'cde', 'CDE09G1441' => 'cde', 'Cfa006103' => 'cfa', 'Cfa015573' => 'cfa', 'Cfa016988' => 'cfa', 'Ciclev10006738m.g' => 'ccl', 'Ciclev10010920m.g' => 'ccl', 'Ciclev10018517m.g' => 'ccl', 'CiPaw.01G159200' => 'cil', 'CiPaw.02G091000' => 'cil', 'CiPaw.02G091100' => 'cil', 'CiPaw.08G103100' => 'cil', 'CiPaw.09G224900' => 'cil', 'ClCG06G005740' => 'cla', 'ClCG07G000090' => 'cla', 'ClCG07G000100' => 'cla', 'COL.COLO4_09143' => 'col', 'COL.COLO4_25124' => 'col', 'Cpa.g.sc16.34' => 'cpa', 'Cpa.g.sc3504.1' => 'cpa', 'Cpa.g.sc60.37' => 'cpa', 'CsaV3_6G018520' => 'csa', 'CsaV3_6G036860' => 'csa', 'CSS0001072' => 'camsi', 'CSS0020208' => 'camsi', 'CSS0021253' => 'camsi', 'CSS0022190' => 'camsi', 'CSS0036150' => 'camsi', 'CSS0040442' => 'camsi', 'CSS0042300' => 'camsi', 'CSS0045298' => 'camsi', 'DCAR_012449' => 'dca', 'DCAR_018405' => 'dca', 'DCAR_024573' => 'dca', 'DCAR_030591' => 'dca', 'Dinv16926' => 'din', 'Dinv32963' => 'din', 'Dinv38382' => 'din', 'Dinv38383' => 'din', 'Duzib133G0974' => 'dzi', 'Duzib138G1867' => 'dzi', 'Duzib211G0420' => 'dzi', 'Duzib212G0930' => 'dzi', 'ECA234G1645' => 'eca', 'ECA247G3467' => 'eca', 'ECA248G1703' => 'eca', 'EL10Ac3g06327' => 'bvu', 'EL10Ac7g17204' => 'bvu', 'Eucgr.A00855' => 'egr', 'Eucgr.A00858' => 'egr', 'Eucgr.H01520' => 'egr', 'Eucgr.H03604' => 'egr', 'Eucgr.L03465' => 'egr', 'Eucgr.L03466' => 'egr', 'FAN01G0988' => 'fan', 'FAN02G3892' => 'fan', 'FAN05G3381' => 'fan', 'FAN07G0967' => 'fan', 'FAN07G1493' => 'fan', 'FAN08G3125' => 'fan', 'FAN09G0402' => 'fan', 'FAN12G2594' => 'fan', 'FAN12G3879' => 'fan', 'FAN14G1546' => 'fan', 'FAN15G3626' => 'fan', 'FAN17G0588' => 'fan', 'FAN17G0609' => 'fan', 'FAN18G2817' => 'fan', 'FAN19G1305' => 'fan', 'FAN20G1787' => 'fan', 'FAN22G0073' => 'fan', 'FAN22G0352' => 'fan', 'FAN22G0368' => 'fan', 'FAN22G2273' => 'fan', 'FAN24G1998' => 'fan', 'FAN27G1317' => 'fan', 'FvH4_2g23980' => 'fve', 'FvH4_4g14380' => 'fve', 'FvH4_4g14390' => 'fve', 'FvH4_6g09250' => 'fve', 'Glyma.03G151100' => 'gma', 'Glyma.04G122550' => 'gma', 'Glyma.05G001600' => 'gma', 'Glyma.09G270766' => 'gma', 'Glyma.09G270832' => 'gma', 'Glyma.13G209800' => 'gma', 'Glyma.15G102800' => 'gma', 'Glyma.18G218900' => 'gma', 'Glyma.19G001500' => 'gma', 'Glyma.19G153600' => 'gma', 'Gohir.A02G028600' => 'ghi', 'Gohir.A08G045000' => 'ghi', 'Gohir.A11G120500' => 'ghi', 'Gohir.A12G006200' => 'ghi', 'Gohir.A12G006250' => 'ghi', 'Gohir.D02G036300' => 'ghi', 'Gohir.D08G054700' => 'ghi', 'Gohir.D11G125600' => 'ghi', 'Gohir.D12G005700' => 'ghi', 'Gorai.004G055200' => 'gra', 'Gorai.005G040400' => 'gra', 'Gorai.007G134500' => 'gra', 'Gorai.008G005500' => 'gra', 'GSVIVG01011094001' => 'vvi', 'GSVIVG01017879001' => 'vvi', 'GSVIVG01025988001' => 'vvi', 'GSVIVG01029847001' => 'vvi', 'HanXRQChr10g0282901' => 'han', 'HanXRQChr10g0310371' => 'han', 'HanXRQChr10g0315041' => 'han', 'HanXRQChr11g0327651' => 'han', 'HanXRQChr12g0359391' => 'han', 'Haze_00972' => 'cav', 'Haze_00973' => 'cav', 'Haze_00974' => 'cav', 'Haze_04747' => 'cav', 'Haze_04749' => 'cav', 'Haze_04750' => 'cav', 'Haze_21217' => 'cav', 'Hma1.2p1_1037F.1_g250680' => 'hma', 'Hma1.2p1_1644F.1_g295320' => 'hma', 'HPP92_011322' => 'vpl', 'HPP92_011323' => 'vpl', 'HPP92_011324' => 'vpl', 'HPP92_011325' => 'vpl', 'HPP92_011326' => 'vpl', 'Hund12205' => 'sun', 'Hund17957' => 'sun', 'Lalb_Chr06g0176771' => 'lal', 'Lalb_Chr18g0056021' => 'lal', 'Lalb_Chr18g0056031' => 'lal', 'Lalb_Chr18g0056041' => 'lal', 'Lalb_Chr20g0107751' => 'lal', 'Lalb_Chr20g0118371' => 'lal', 'Lj1g0010239' => 'lja', 'Lj1g0017101' => 'lja', 'Lj2A1178G40' => 'lonja', 'Lj2A54G84' => 'lonja', 'Lj2g0015248' => 'lja', 'Lj3A761T51' => 'lonja', 'Lj6g0018116' => 'lja', 'Lsat_1_v5_gn_4_136040' => 'lsa', 'Lsat_1_v5_gn_5_187461' => 'lsa', 'Lsat_1_v5_gn_5_77001' => 'lsa', 'Lsat_1_v5_gn_9_4461' => 'lsa', 'Manes.01G210100' => 'mes', 'Manes.03G185600' => 'mes', 'Manes.05G073300' => 'mes', 'Manes.09G120300' => 'mes', 'Manes.15G022100' => 'mes', 'Mapoly0096s0053' => 'mpo', 'MBI03_g14058_MAGBIO' => 'mbi', 'MBI03_g33876_MAGBIO' => 'mbi', 'MBI03_g36854_MAGBIO' => 'mbi', 'MBI17_g11997_MAGBIO' => 'mbi', 'MD03G1269000' => 'mdo', 'MD04G1179600' => 'mdo', 'MD11G1289800' => 'mdo', 'MD12G1194700' => 'mdo', 'MD13G1182100' => 'mdo', 'MD13G1182200' => 'mdo', 'MD16G1182600' => 'mdo', 'Medtr2g021400' => 'mtr', 'Medtr2g021470' => 'mtr', 'Medtr2g105810' => 'mtr', 'Medtr3g033580' => 'mtr', 'Medtr6g007970' => 'mtr', 'Medtr7g056330' => 'mtr', 'Medtr7g074290' => 'mtr', 'Medtr7g074380' => 'mtr', 'Medtr7g094550' => 'mtr', 'Medtr8g069995' => 'mtr', 'MELO3C014345.2' => 'cme', 'MELO3C021395.2' => 'cme', 'Migut.D00262' => 'egut', 'Migut.G00257' => 'egut', 'MSTRG.21575' => 'ama', 'MSTRG.3985' => 'ama', 'Nitab4.5_0000295g0140' => 'nta', 'Nitab4.5_0000732g0140' => 'nta', 'Nitab4.5_0003162g0020' => 'nta', 'Nitab4.5_0006180g0090' => 'nta', 'Nitab4.5_0006390g0010' => 'nta', 'Nitab4.5_0007392g0040' => 'nta', 'Nn1g02140' => 'nnu', 'Nn4g26168' => 'nnu', 'Nn5g26754' => 'nnu', 'Oeu001433.1' => 'oeu', 'Oeu010299.2' => 'oeu', 'Oeu011171.1' => 'oeu', 'Oeu037675.1' => 'oeu', 'Oeu038359.1' => 'oeu', 'Oeu063834.1' => 'oeu', 'Oeu063835.1' => 'oeu', 'Os05g0312000' => 'osa', 'Os07g0211101' => 'osa', 'Os07g0211200' => 'osa', 'Os07g0681500' => 'osa', 'Peaxi162Scf00095g01015' => 'pax', 'Peaxi162Scf00104g00329' => 'pax', 'Peaxi162Scf00161g00137' => 'pax', 'PGR004G1665' => 'pgr', 'PGR031G2937' => 'pgr', 'PGR119G2145' => 'pgr', 'PGSC0003DMG400004351' => 'stu', 'PGSC0003DMG400014625' => 'stu', 'PGSC0003DMG401000943' => 'stu', 'Phvul.001G148600' => 'pvu', 'Phvul.004G001700' => 'pvu', 'Phvul.006G154900' => 'pvu', 'Phvul.008G078200' => 'pvu', 'Phvul.011G136500' => 'pvu', 'Potri.002G215600' => 'ptr', 'Potri.008G201600' => 'ptr', 'Potri.014G138400' => 'ptr', 'Potri.016G142500' => 'ptr', 'Pp3c16_10580' => 'ppa', 'Pp3c5_25280' => 'ppa', 'Prupe.1G150000' => 'ppe', 'Prupe.1G150100' => 'ppe', 'Prupe.6G299600' => 'ppe', 'Prupe.8G245000' => 'ppe', 'Psat0s4927g0040' => 'psa', 'Psat1g052080' => 'psa', 'Psat1g183800' => 'psa', 'Psat3g113840' => 'psa', 'Psat3g126120' => 'psa', 'Psat3g126160' => 'psa', 'Psat3g158760' => 'psa', 'Psat3g158840' => 'psa', 'PSO170G2858' => 'pso', 'PSO339G0606' => 'pso', 'PSO384G4709' => 'pso', 'PSO407G0334' => 'pso', 'QL04p040276' => 'qlo', 'QL06p005458' => 'qlo', 'QL06p005472' => 'qlo', 'QL07p030546' => 'qlo', 'QL07p031519' => 'qlo', 'QL09p050949' => 'qlo', 'QL09p050966' => 'qlo', 'QL09p051067' => 'qlo', 'QL12p022706' => 'qlo', 'RcHm_v2.0_Chr2g0119601' => 'rch', 'RcHm_v2.0_Chr3g0459591' => 'rch', 'RcHm_v2.0_Chr4g0418521' => 'rch', 'RcHm_v2.0_Chr4g0418531' => 'rch', 'RcHm_v2.0_Chr4g0418541' => 'rch', 'RcHm_v2.0_Chr6g0291641' => 'rch', 'Rhsim01G0086300' => 'rsi', 'Rhsim01G0276300' => 'rsi', 'Rhsim01G0276500' => 'rsi', 'Rhsim04G0207700' => 'rsi', 'Rhsim05G0234500' => 'rsi', 'Rhsim13G0022400' => 'rsi', 'Sabra02G0167900' => 'sbr', 'Sabra04G0158500' => 'sbr', 'Sabra08G0159800' => 'sbr', 'Sabra10G0011500' => 'sbr', 'Sabra14G0104400' => 'sbr', 'SalBow2G2440' => 'sbo', 'SalBow4G2265' => 'sbo', 'Sc02g0000060' => 'sci', 'Sc05g0005020' => 'sci', 'Sc13g0003890' => 'sci', 'Sed0014865' => 'sed', 'Sed0017224' => 'sed', 'Sed0026391' => 'sed', 'SEGI_00063' => 'sgi', 'SEGI_10967' => 'sgi', 'SEGI_17510' => 'sgi', 'SEGI_24396' => 'sgi', 'SEGI_39719' => 'sgi', 'SEGI_41392' => 'sgi', 'SGA_v2.0_scaffold11G05794' => 'sas', 'SGA_v2.0_scaffold142G35607' => 'sas', 'SGA_v2.0_scaffold1G00447' => 'sas', 'SHI15388' => 'shi', 'SHI15394' => 'shi', 'SHI15396' => 'shi', 'SHI15399' => 'shi', 'SMO343G0151' => 'smo', 'SMO367G1118' => 'smo', 'Solyc01g080200.3' => 'sly', 'Solyc06g008960.3' => 'sly', 'Solyc09g064780.3' => 'sly', 'Sopen01g031980' => 'spe', 'Sopen06g003710' => 'spe', 'Sopen09g026460' => 'spe', 'Sp3g21240' => 'spa', 'Sp4g30030' => 'spa', 'TAR365G0022' => 'tar', 'TAR365G1023' => 'tar', 'TAR365G1253' => 'tar', 'TAR623G0078' => 'tar', 'TAR623G1721' => 'tar', 'TAR633G0959' => 'tar', 'THA.LOC104802225' => 'tha', 'THA.LOC104804769' => 'tha', 'THA.LOC104808660' => 'tha', 'THA.LOC104812792' => 'tha', 'Thecc.01G284000' => 'tca', 'Thecc.04G220600' => 'tca', 'Thecc.05G268900' => 'tca', 'Thecc.08G171100' => 'tca', 'Thhalv10001284m.g' => 'esa', 'Thhalv10019912m.g' => 'esa', 'TPR.G14189' => 'tpr', 'TPR.G18110' => 'tpr', 'TPR.G18130' => 'tpr', 'TPR.G18131' => 'tpr', 'TPR.G18140' => 'tpr', 'TPR.G24282' => 'tpr', 'TPR.G25221' => 'tpr', 'TPR.G29267' => 'tpr', 'TPR.G35315' => 'tpr', 'TPR.G36173' => 'tpr', 'TWI09G0794' => 'twi', 'TWI59G1348' => 'twi', 'TWI74G0430' => 'twi', 'unitig_26.g8940' => 'ugi', 'unitig_749.g13744' => 'ugi', 'unitig_749.g13745' => 'ugi', 'vmacro08269' => 'vma', 'vmacro14937' => 'vma', 'vmacro20401' => 'vma', 'VMungo0464G1349' => 'vmu', 'VMungo0540G0289' => 'vmu', 'VMungo1215G1590' => 'vmu', 'VMungo1309G0221' => 'vmu', 'VMungo1309G2815' => 'vmu', 'VMungo1383G0239' => 'vmu', 'VMungo1383G2910' => 'vmu', 'Zm00001eb095270' => 'zma', 'Zm00001eb095280' => 'zma', 'Zm00001eb111630' => 'zma', 'Zm00001eb237080' => 'zma', 'Zm00001eb273740' => 'zma', 'Zm00001eb285040' => 'zma', 'Zm00001eb330790' => 'zma', 'Zm00001eb337380' => 'zma' ) $gf_id = 'HOM05D001484' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001484' ) $data_identifier = 'HOM05D001484' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 2, 'aly' => (int) 2, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 22, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 7, 'hma' => (int) 2, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 7, 'mtr' => (int) 10, 'cme' => (int) 2, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 4, 'ppa' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 4, 'qlo' => (int) 9, 'rch' => (int) 6, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 10, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 7, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb337380' $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' => 'HOM05D001484', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p31500' => 'bna', 'A05p00020' => 'bna', 'A07p08820' => 'bna', 'Aa31LG4G3300' => 'aar', 'Aa31LG8G10030' => 'aar', 'Actinidia00731' => 'ach', 'Actinidia11473' => 'ach', 'Actinidia23469' => 'ach', 'Actinidia24318' => 'ach', 'Actinidia40196' => 'ach', 'Actinidia40197' => 'ach', 'Actinidia40198' => 'ach', 'Ah.08g212990' => 'amhyb', 'Ah.15g091720' => 'amhyb', 'AL3G38260' => 'aly', 'AL4G47710' => 'aly', 'Aqoxy2G00671' => 'aox', 'Aqoxy2G03236' => 'aox', 'arahy.Tifrunner.gnm1.ann1.05IDCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KR684' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATY3SJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK6QJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6APGL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IDT7Z9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM073U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ0R87' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LE7RV4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT4QRX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V5ENPK' => 'arhy', 'AT2G48110' => 'ath', 'AT3G23590' => 'ath', 'ATR0626G186' => 'atr', 'ATR1127G141' => 'atr', 'Atru.chr4.2583' => 'acertr', 'Atru.chr5.1358' => 'acertr', 'Atru.chr5.1359' => 'acertr', 'Atru.chr8.46' => 'acertr', 'AUR62002640' => 'cqu', 'AUR62030055' => 'cqu', 'AUR62033713' => 'cqu', 'AUR62033714' => 'cqu', 'AUR62036795' => 'cqu', 'AUR62039891' => 'cqu', 'BcaB02g08737' => 'bca', 'BcaB04g20441' => 'bca', 'BcaB06g26509' => 'bca', 'BcaB06g26510' => 'bca', 'BcaB06g26511' => 'bca', 'BcaB06g26512' => 'bca', 'BcaB06g26513' => 'bca', 'BcaC02g12564' => 'bca', 'BcaC02g12565' => 'bca', 'BcaC02g12794' => 'bca', 'BcaC02g12795' => 'bca', 'BcaC02g12796' => 'bca', 'BcaC06g35541' => 'bca', 'BNapus_Darmor_BZH_scaffold_188p00080' => 'bna', 'BNapus_Darmor_BZH_scaffold_188p00090' => 'bna', 'BolC1t03972H' => 'bol', 'BolC1t03973H' => 'bol', 'BolC4t21680H' => 'bol', 'BolC7t41863H' => 'bol', 'BolSC55t61227H' => 'bol', 'BolSC55t61228H' => 'bol', 'BraA01t03278Z' => 'bra', 'BraA05t18998Z' => 'bra', 'BraA07t28673Z' => 'bra', 'C01p40150' => 'bna', 'C05p12370' => 'bna', 'C07p13680' => 'bna', 'CAN.G1006.16' => 'can', 'CAN.G1006.17' => 'can', 'CAN.G1170.2' => 'can', 'CAN.G962.7' => 'can', 'CANSAT25G2179' => 'cansat', 'CANSAT78G1573' => 'cansat', 'CARHR099510' => 'chi', 'CARHR143510' => 'chi', 'Carub.0003s2380' => 'cru', 'Carub.0004s3082' => 'cru', 'Ca_00614_v3' => 'car', 'Ca_07801_v3' => 'car', 'Ca_08567_v3' => 'car', 'Ca_09571_v3' => 'car', 'CBR_g19290' => 'cbr', 'Cc01_g19770' => 'ccan', 'Cc03_g03030' => 'ccan', 'CDE07G0968' => 'cde', 'CDE09G1441' => 'cde', 'Cfa006103' => 'cfa', 'Cfa015573' => 'cfa', 'Cfa016988' => 'cfa', 'Ciclev10006738m.g' => 'ccl', 'Ciclev10010920m.g' => 'ccl', 'Ciclev10018517m.g' => 'ccl', 'CiPaw.01G159200' => 'cil', 'CiPaw.02G091000' => 'cil', 'CiPaw.02G091100' => 'cil', 'CiPaw.08G103100' => 'cil', 'CiPaw.09G224900' => 'cil', 'ClCG06G005740' => 'cla', 'ClCG07G000090' => 'cla', 'ClCG07G000100' => 'cla', 'COL.COLO4_09143' => 'col', 'COL.COLO4_25124' => 'col', 'Cpa.g.sc16.34' => 'cpa', 'Cpa.g.sc3504.1' => 'cpa', 'Cpa.g.sc60.37' => 'cpa', 'CsaV3_6G018520' => 'csa', 'CsaV3_6G036860' => 'csa', 'CSS0001072' => 'camsi', 'CSS0020208' => 'camsi', 'CSS0021253' => 'camsi', 'CSS0022190' => 'camsi', 'CSS0036150' => 'camsi', 'CSS0040442' => 'camsi', 'CSS0042300' => 'camsi', 'CSS0045298' => 'camsi', 'DCAR_012449' => 'dca', 'DCAR_018405' => 'dca', 'DCAR_024573' => 'dca', 'DCAR_030591' => 'dca', 'Dinv16926' => 'din', 'Dinv32963' => 'din', 'Dinv38382' => 'din', 'Dinv38383' => 'din', 'Duzib133G0974' => 'dzi', 'Duzib138G1867' => 'dzi', 'Duzib211G0420' => 'dzi', 'Duzib212G0930' => 'dzi', 'ECA234G1645' => 'eca', 'ECA247G3467' => 'eca', 'ECA248G1703' => 'eca', 'EL10Ac3g06327' => 'bvu', 'EL10Ac7g17204' => 'bvu', 'Eucgr.A00855' => 'egr', 'Eucgr.A00858' => 'egr', 'Eucgr.H01520' => 'egr', 'Eucgr.H03604' => 'egr', 'Eucgr.L03465' => 'egr', 'Eucgr.L03466' => 'egr', 'FAN01G0988' => 'fan', 'FAN02G3892' => 'fan', 'FAN05G3381' => 'fan', 'FAN07G0967' => 'fan', 'FAN07G1493' => 'fan', 'FAN08G3125' => 'fan', 'FAN09G0402' => 'fan', 'FAN12G2594' => 'fan', 'FAN12G3879' => 'fan', 'FAN14G1546' => 'fan', 'FAN15G3626' => 'fan', 'FAN17G0588' => 'fan', 'FAN17G0609' => 'fan', 'FAN18G2817' => 'fan', 'FAN19G1305' => 'fan', 'FAN20G1787' => 'fan', 'FAN22G0073' => 'fan', 'FAN22G0352' => 'fan', 'FAN22G0368' => 'fan', 'FAN22G2273' => 'fan', 'FAN24G1998' => 'fan', 'FAN27G1317' => 'fan', 'FvH4_2g23980' => 'fve', 'FvH4_4g14380' => 'fve', 'FvH4_4g14390' => 'fve', 'FvH4_6g09250' => 'fve', 'Glyma.03G151100' => 'gma', 'Glyma.04G122550' => 'gma', 'Glyma.05G001600' => 'gma', 'Glyma.09G270766' => 'gma', 'Glyma.09G270832' => 'gma', 'Glyma.13G209800' => 'gma', 'Glyma.15G102800' => 'gma', 'Glyma.18G218900' => 'gma', 'Glyma.19G001500' => 'gma', 'Glyma.19G153600' => 'gma', 'Gohir.A02G028600' => 'ghi', 'Gohir.A08G045000' => 'ghi', 'Gohir.A11G120500' => 'ghi', 'Gohir.A12G006200' => 'ghi', 'Gohir.A12G006250' => 'ghi', 'Gohir.D02G036300' => 'ghi', 'Gohir.D08G054700' => 'ghi', 'Gohir.D11G125600' => 'ghi', 'Gohir.D12G005700' => 'ghi', 'Gorai.004G055200' => 'gra', 'Gorai.005G040400' => 'gra', 'Gorai.007G134500' => 'gra', 'Gorai.008G005500' => 'gra', 'GSVIVG01011094001' => 'vvi', 'GSVIVG01017879001' => 'vvi', 'GSVIVG01025988001' => 'vvi', 'GSVIVG01029847001' => 'vvi', 'HanXRQChr10g0282901' => 'han', 'HanXRQChr10g0310371' => 'han', 'HanXRQChr10g0315041' => 'han', 'HanXRQChr11g0327651' => 'han', 'HanXRQChr12g0359391' => 'han', 'Haze_00972' => 'cav', 'Haze_00973' => 'cav', 'Haze_00974' => 'cav', 'Haze_04747' => 'cav', 'Haze_04749' => 'cav', 'Haze_04750' => 'cav', 'Haze_21217' => 'cav', 'Hma1.2p1_1037F.1_g250680' => 'hma', 'Hma1.2p1_1644F.1_g295320' => 'hma', 'HPP92_011322' => 'vpl', 'HPP92_011323' => 'vpl', 'HPP92_011324' => 'vpl', 'HPP92_011325' => 'vpl', 'HPP92_011326' => 'vpl', 'Hund12205' => 'sun', 'Hund17957' => 'sun', 'Lalb_Chr06g0176771' => 'lal', 'Lalb_Chr18g0056021' => 'lal', 'Lalb_Chr18g0056031' => 'lal', 'Lalb_Chr18g0056041' => 'lal', 'Lalb_Chr20g0107751' => 'lal', 'Lalb_Chr20g0118371' => 'lal', 'Lj1g0010239' => 'lja', 'Lj1g0017101' => 'lja', 'Lj2A1178G40' => 'lonja', 'Lj2A54G84' => 'lonja', 'Lj2g0015248' => 'lja', 'Lj3A761T51' => 'lonja', 'Lj6g0018116' => 'lja', 'Lsat_1_v5_gn_4_136040' => 'lsa', 'Lsat_1_v5_gn_5_187461' => 'lsa', 'Lsat_1_v5_gn_5_77001' => 'lsa', 'Lsat_1_v5_gn_9_4461' => 'lsa', 'Manes.01G210100' => 'mes', 'Manes.03G185600' => 'mes', 'Manes.05G073300' => 'mes', 'Manes.09G120300' => 'mes', 'Manes.15G022100' => 'mes', 'Mapoly0096s0053' => 'mpo', 'MBI03_g14058_MAGBIO' => 'mbi', 'MBI03_g33876_MAGBIO' => 'mbi', 'MBI03_g36854_MAGBIO' => 'mbi', 'MBI17_g11997_MAGBIO' => 'mbi', 'MD03G1269000' => 'mdo', 'MD04G1179600' => 'mdo', 'MD11G1289800' => 'mdo', 'MD12G1194700' => 'mdo', 'MD13G1182100' => 'mdo', 'MD13G1182200' => 'mdo', 'MD16G1182600' => 'mdo', 'Medtr2g021400' => 'mtr', 'Medtr2g021470' => 'mtr', 'Medtr2g105810' => 'mtr', 'Medtr3g033580' => 'mtr', 'Medtr6g007970' => 'mtr', 'Medtr7g056330' => 'mtr', 'Medtr7g074290' => 'mtr', 'Medtr7g074380' => 'mtr', 'Medtr7g094550' => 'mtr', 'Medtr8g069995' => 'mtr', 'MELO3C014345.2' => 'cme', 'MELO3C021395.2' => 'cme', 'Migut.D00262' => 'egut', 'Migut.G00257' => 'egut', 'MSTRG.21575' => 'ama', 'MSTRG.3985' => 'ama', 'Nitab4.5_0000295g0140' => 'nta', 'Nitab4.5_0000732g0140' => 'nta', 'Nitab4.5_0003162g0020' => 'nta', 'Nitab4.5_0006180g0090' => 'nta', 'Nitab4.5_0006390g0010' => 'nta', 'Nitab4.5_0007392g0040' => 'nta', 'Nn1g02140' => 'nnu', 'Nn4g26168' => 'nnu', 'Nn5g26754' => 'nnu', 'Oeu001433.1' => 'oeu', 'Oeu010299.2' => 'oeu', 'Oeu011171.1' => 'oeu', 'Oeu037675.1' => 'oeu', 'Oeu038359.1' => 'oeu', 'Oeu063834.1' => 'oeu', 'Oeu063835.1' => 'oeu', 'Os05g0312000' => 'osa', 'Os07g0211101' => 'osa', 'Os07g0211200' => 'osa', 'Os07g0681500' => 'osa', 'Peaxi162Scf00095g01015' => 'pax', 'Peaxi162Scf00104g00329' => 'pax', 'Peaxi162Scf00161g00137' => 'pax', 'PGR004G1665' => 'pgr', 'PGR031G2937' => 'pgr', 'PGR119G2145' => 'pgr', 'PGSC0003DMG400004351' => 'stu', 'PGSC0003DMG400014625' => 'stu', 'PGSC0003DMG401000943' => 'stu', 'Phvul.001G148600' => 'pvu', 'Phvul.004G001700' => 'pvu', 'Phvul.006G154900' => 'pvu', 'Phvul.008G078200' => 'pvu', 'Phvul.011G136500' => 'pvu', 'Potri.002G215600' => 'ptr', 'Potri.008G201600' => 'ptr', 'Potri.014G138400' => 'ptr', 'Potri.016G142500' => 'ptr', 'Pp3c16_10580' => 'ppa', 'Pp3c5_25280' => 'ppa', 'Prupe.1G150000' => 'ppe', 'Prupe.1G150100' => 'ppe', 'Prupe.6G299600' => 'ppe', 'Prupe.8G245000' => 'ppe', 'Psat0s4927g0040' => 'psa', 'Psat1g052080' => 'psa', 'Psat1g183800' => 'psa', 'Psat3g113840' => 'psa', 'Psat3g126120' => 'psa', 'Psat3g126160' => 'psa', 'Psat3g158760' => 'psa', 'Psat3g158840' => 'psa', 'PSO170G2858' => 'pso', 'PSO339G0606' => 'pso', 'PSO384G4709' => 'pso', 'PSO407G0334' => 'pso', 'QL04p040276' => 'qlo', 'QL06p005458' => 'qlo', 'QL06p005472' => 'qlo', 'QL07p030546' => 'qlo', 'QL07p031519' => 'qlo', 'QL09p050949' => 'qlo', 'QL09p050966' => 'qlo', 'QL09p051067' => 'qlo', 'QL12p022706' => 'qlo', 'RcHm_v2.0_Chr2g0119601' => 'rch', 'RcHm_v2.0_Chr3g0459591' => 'rch', 'RcHm_v2.0_Chr4g0418521' => 'rch', 'RcHm_v2.0_Chr4g0418531' => 'rch', 'RcHm_v2.0_Chr4g0418541' => 'rch', 'RcHm_v2.0_Chr6g0291641' => 'rch', 'Rhsim01G0086300' => 'rsi', 'Rhsim01G0276300' => 'rsi', 'Rhsim01G0276500' => 'rsi', 'Rhsim04G0207700' => 'rsi', 'Rhsim05G0234500' => 'rsi', 'Rhsim13G0022400' => 'rsi', 'Sabra02G0167900' => 'sbr', 'Sabra04G0158500' => 'sbr', 'Sabra08G0159800' => 'sbr', 'Sabra10G0011500' => 'sbr', 'Sabra14G0104400' => 'sbr', 'SalBow2G2440' => 'sbo', 'SalBow4G2265' => 'sbo', 'Sc02g0000060' => 'sci', 'Sc05g0005020' => 'sci', 'Sc13g0003890' => 'sci', 'Sed0014865' => 'sed', 'Sed0017224' => 'sed', 'Sed0026391' => 'sed', 'SEGI_00063' => 'sgi', 'SEGI_10967' => 'sgi', 'SEGI_17510' => 'sgi', 'SEGI_24396' => 'sgi', 'SEGI_39719' => 'sgi', 'SEGI_41392' => 'sgi', 'SGA_v2.0_scaffold11G05794' => 'sas', 'SGA_v2.0_scaffold142G35607' => 'sas', 'SGA_v2.0_scaffold1G00447' => 'sas', 'SHI15388' => 'shi', 'SHI15394' => 'shi', 'SHI15396' => 'shi', 'SHI15399' => 'shi', 'SMO343G0151' => 'smo', 'SMO367G1118' => 'smo', 'Solyc01g080200.3' => 'sly', 'Solyc06g008960.3' => 'sly', 'Solyc09g064780.3' => 'sly', 'Sopen01g031980' => 'spe', 'Sopen06g003710' => 'spe', 'Sopen09g026460' => 'spe', 'Sp3g21240' => 'spa', 'Sp4g30030' => 'spa', 'TAR365G0022' => 'tar', 'TAR365G1023' => 'tar', 'TAR365G1253' => 'tar', 'TAR623G0078' => 'tar', 'TAR623G1721' => 'tar', 'TAR633G0959' => 'tar', 'THA.LOC104802225' => 'tha', 'THA.LOC104804769' => 'tha', 'THA.LOC104808660' => 'tha', 'THA.LOC104812792' => 'tha', 'Thecc.01G284000' => 'tca', 'Thecc.04G220600' => 'tca', 'Thecc.05G268900' => 'tca', 'Thecc.08G171100' => 'tca', 'Thhalv10001284m.g' => 'esa', 'Thhalv10019912m.g' => 'esa', 'TPR.G14189' => 'tpr', 'TPR.G18110' => 'tpr', 'TPR.G18130' => 'tpr', 'TPR.G18131' => 'tpr', 'TPR.G18140' => 'tpr', 'TPR.G24282' => 'tpr', 'TPR.G25221' => 'tpr', 'TPR.G29267' => 'tpr', 'TPR.G35315' => 'tpr', 'TPR.G36173' => 'tpr', 'TWI09G0794' => 'twi', 'TWI59G1348' => 'twi', 'TWI74G0430' => 'twi', 'unitig_26.g8940' => 'ugi', 'unitig_749.g13744' => 'ugi', 'unitig_749.g13745' => 'ugi', 'vmacro08269' => 'vma', 'vmacro14937' => 'vma', 'vmacro20401' => 'vma', 'VMungo0464G1349' => 'vmu', 'VMungo0540G0289' => 'vmu', 'VMungo1215G1590' => 'vmu', 'VMungo1309G0221' => 'vmu', 'VMungo1309G2815' => 'vmu', 'VMungo1383G0239' => 'vmu', 'VMungo1383G2910' => 'vmu', 'Zm00001eb095270' => 'zma', 'Zm00001eb095280' => 'zma', 'Zm00001eb111630' => 'zma', 'Zm00001eb237080' => 'zma', 'Zm00001eb273740' => 'zma', 'Zm00001eb285040' => 'zma', 'Zm00001eb330790' => 'zma', 'Zm00001eb337380' => 'zma' ), 'gf_id' => 'HOM05D001484', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001484' ), 'data_identifier' => 'HOM05D001484', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001484', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p31500' => 'bna', 'A05p00020' => 'bna', 'A07p08820' => 'bna', 'Aa31LG4G3300' => 'aar', 'Aa31LG8G10030' => 'aar', 'Actinidia00731' => 'ach', 'Actinidia11473' => 'ach', 'Actinidia23469' => 'ach', 'Actinidia24318' => 'ach', 'Actinidia40196' => 'ach', 'Actinidia40197' => 'ach', 'Actinidia40198' => 'ach', 'Ah.08g212990' => 'amhyb', 'Ah.15g091720' => 'amhyb', 'AL3G38260' => 'aly', 'AL4G47710' => 'aly', 'Aqoxy2G00671' => 'aox', 'Aqoxy2G03236' => 'aox', 'arahy.Tifrunner.gnm1.ann1.05IDCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KR684' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATY3SJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK6QJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6APGL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IDT7Z9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM073U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ0R87' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LE7RV4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT4QRX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V5ENPK' => 'arhy', 'AT2G48110' => 'ath', 'AT3G23590' => 'ath', 'ATR0626G186' => 'atr', 'ATR1127G141' => 'atr', 'Atru.chr4.2583' => 'acertr', 'Atru.chr5.1358' => 'acertr', 'Atru.chr5.1359' => 'acertr', 'Atru.chr8.46' => 'acertr', 'AUR62002640' => 'cqu', 'AUR62030055' => 'cqu', 'AUR62033713' => 'cqu', 'AUR62033714' => 'cqu', 'AUR62036795' => 'cqu', 'AUR62039891' => 'cqu', 'BcaB02g08737' => 'bca', 'BcaB04g20441' => 'bca', 'BcaB06g26509' => 'bca', 'BcaB06g26510' => 'bca', 'BcaB06g26511' => 'bca', 'BcaB06g26512' => 'bca', 'BcaB06g26513' => 'bca', 'BcaC02g12564' => 'bca', 'BcaC02g12565' => 'bca', 'BcaC02g12794' => 'bca', 'BcaC02g12795' => 'bca', 'BcaC02g12796' => 'bca', 'BcaC06g35541' => 'bca', 'BNapus_Darmor_BZH_scaffold_188p00080' => 'bna', 'BNapus_Darmor_BZH_scaffold_188p00090' => 'bna', 'BolC1t03972H' => 'bol', 'BolC1t03973H' => 'bol', 'BolC4t21680H' => 'bol', 'BolC7t41863H' => 'bol', 'BolSC55t61227H' => 'bol', 'BolSC55t61228H' => 'bol', 'BraA01t03278Z' => 'bra', 'BraA05t18998Z' => 'bra', 'BraA07t28673Z' => 'bra', 'C01p40150' => 'bna', 'C05p12370' => 'bna', 'C07p13680' => 'bna', 'CAN.G1006.16' => 'can', 'CAN.G1006.17' => 'can', 'CAN.G1170.2' => 'can', 'CAN.G962.7' => 'can', 'CANSAT25G2179' => 'cansat', 'CANSAT78G1573' => 'cansat', 'CARHR099510' => 'chi', 'CARHR143510' => 'chi', 'Carub.0003s2380' => 'cru', 'Carub.0004s3082' => 'cru', 'Ca_00614_v3' => 'car', 'Ca_07801_v3' => 'car', 'Ca_08567_v3' => 'car', 'Ca_09571_v3' => 'car', 'CBR_g19290' => 'cbr', 'Cc01_g19770' => 'ccan', 'Cc03_g03030' => 'ccan', 'CDE07G0968' => 'cde', 'CDE09G1441' => 'cde', 'Cfa006103' => 'cfa', 'Cfa015573' => 'cfa', 'Cfa016988' => 'cfa', 'Ciclev10006738m.g' => 'ccl', 'Ciclev10010920m.g' => 'ccl', 'Ciclev10018517m.g' => 'ccl', 'CiPaw.01G159200' => 'cil', 'CiPaw.02G091000' => 'cil', 'CiPaw.02G091100' => 'cil', 'CiPaw.08G103100' => 'cil', 'CiPaw.09G224900' => 'cil', 'ClCG06G005740' => 'cla', 'ClCG07G000090' => 'cla', 'ClCG07G000100' => 'cla', 'COL.COLO4_09143' => 'col', 'COL.COLO4_25124' => 'col', 'Cpa.g.sc16.34' => 'cpa', 'Cpa.g.sc3504.1' => 'cpa', 'Cpa.g.sc60.37' => 'cpa', 'CsaV3_6G018520' => 'csa', 'CsaV3_6G036860' => 'csa', 'CSS0001072' => 'camsi', 'CSS0020208' => 'camsi', 'CSS0021253' => 'camsi', 'CSS0022190' => 'camsi', 'CSS0036150' => 'camsi', 'CSS0040442' => 'camsi', 'CSS0042300' => 'camsi', 'CSS0045298' => 'camsi', 'DCAR_012449' => 'dca', 'DCAR_018405' => 'dca', 'DCAR_024573' => 'dca', 'DCAR_030591' => 'dca', 'Dinv16926' => 'din', 'Dinv32963' => 'din', 'Dinv38382' => 'din', 'Dinv38383' => 'din', 'Duzib133G0974' => 'dzi', 'Duzib138G1867' => 'dzi', 'Duzib211G0420' => 'dzi', 'Duzib212G0930' => 'dzi', 'ECA234G1645' => 'eca', 'ECA247G3467' => 'eca', 'ECA248G1703' => 'eca', 'EL10Ac3g06327' => 'bvu', 'EL10Ac7g17204' => 'bvu', 'Eucgr.A00855' => 'egr', 'Eucgr.A00858' => 'egr', 'Eucgr.H01520' => 'egr', 'Eucgr.H03604' => 'egr', 'Eucgr.L03465' => 'egr', 'Eucgr.L03466' => 'egr', 'FAN01G0988' => 'fan', 'FAN02G3892' => 'fan', 'FAN05G3381' => 'fan', 'FAN07G0967' => 'fan', 'FAN07G1493' => 'fan', 'FAN08G3125' => 'fan', 'FAN09G0402' => 'fan', 'FAN12G2594' => 'fan', 'FAN12G3879' => 'fan', 'FAN14G1546' => 'fan', 'FAN15G3626' => 'fan', 'FAN17G0588' => 'fan', 'FAN17G0609' => 'fan', 'FAN18G2817' => 'fan', 'FAN19G1305' => 'fan', 'FAN20G1787' => 'fan', 'FAN22G0073' => 'fan', 'FAN22G0352' => 'fan', 'FAN22G0368' => 'fan', 'FAN22G2273' => 'fan', 'FAN24G1998' => 'fan', 'FAN27G1317' => 'fan', 'FvH4_2g23980' => 'fve', 'FvH4_4g14380' => 'fve', 'FvH4_4g14390' => 'fve', 'FvH4_6g09250' => 'fve', 'Glyma.03G151100' => 'gma', 'Glyma.04G122550' => 'gma', 'Glyma.05G001600' => 'gma', 'Glyma.09G270766' => 'gma', 'Glyma.09G270832' => 'gma', 'Glyma.13G209800' => 'gma', 'Glyma.15G102800' => 'gma', 'Glyma.18G218900' => 'gma', 'Glyma.19G001500' => 'gma', 'Glyma.19G153600' => 'gma', 'Gohir.A02G028600' => 'ghi', 'Gohir.A08G045000' => 'ghi', 'Gohir.A11G120500' => 'ghi', 'Gohir.A12G006200' => 'ghi', 'Gohir.A12G006250' => 'ghi', 'Gohir.D02G036300' => 'ghi', 'Gohir.D08G054700' => 'ghi', 'Gohir.D11G125600' => 'ghi', 'Gohir.D12G005700' => 'ghi', 'Gorai.004G055200' => 'gra', 'Gorai.005G040400' => 'gra', 'Gorai.007G134500' => 'gra', 'Gorai.008G005500' => 'gra', 'GSVIVG01011094001' => 'vvi', 'GSVIVG01017879001' => 'vvi', 'GSVIVG01025988001' => 'vvi', 'GSVIVG01029847001' => 'vvi', 'HanXRQChr10g0282901' => 'han', 'HanXRQChr10g0310371' => 'han', 'HanXRQChr10g0315041' => 'han', 'HanXRQChr11g0327651' => 'han', 'HanXRQChr12g0359391' => 'han', 'Haze_00972' => 'cav', 'Haze_00973' => 'cav', 'Haze_00974' => 'cav', 'Haze_04747' => 'cav', 'Haze_04749' => 'cav', 'Haze_04750' => 'cav', 'Haze_21217' => 'cav', 'Hma1.2p1_1037F.1_g250680' => 'hma', 'Hma1.2p1_1644F.1_g295320' => 'hma', 'HPP92_011322' => 'vpl', 'HPP92_011323' => 'vpl', 'HPP92_011324' => 'vpl', 'HPP92_011325' => 'vpl', 'HPP92_011326' => 'vpl', 'Hund12205' => 'sun', 'Hund17957' => 'sun', 'Lalb_Chr06g0176771' => 'lal', 'Lalb_Chr18g0056021' => 'lal', 'Lalb_Chr18g0056031' => 'lal', 'Lalb_Chr18g0056041' => 'lal', 'Lalb_Chr20g0107751' => 'lal', 'Lalb_Chr20g0118371' => 'lal', 'Lj1g0010239' => 'lja', 'Lj1g0017101' => 'lja', 'Lj2A1178G40' => 'lonja', 'Lj2A54G84' => 'lonja', 'Lj2g0015248' => 'lja', 'Lj3A761T51' => 'lonja', 'Lj6g0018116' => 'lja', 'Lsat_1_v5_gn_4_136040' => 'lsa', 'Lsat_1_v5_gn_5_187461' => 'lsa', 'Lsat_1_v5_gn_5_77001' => 'lsa', 'Lsat_1_v5_gn_9_4461' => 'lsa', 'Manes.01G210100' => 'mes', 'Manes.03G185600' => 'mes', 'Manes.05G073300' => 'mes', 'Manes.09G120300' => 'mes', 'Manes.15G022100' => 'mes', 'Mapoly0096s0053' => 'mpo', 'MBI03_g14058_MAGBIO' => 'mbi', 'MBI03_g33876_MAGBIO' => 'mbi', 'MBI03_g36854_MAGBIO' => 'mbi', 'MBI17_g11997_MAGBIO' => 'mbi', 'MD03G1269000' => 'mdo', 'MD04G1179600' => 'mdo', 'MD11G1289800' => 'mdo', 'MD12G1194700' => 'mdo', 'MD13G1182100' => 'mdo', 'MD13G1182200' => 'mdo', 'MD16G1182600' => 'mdo', 'Medtr2g021400' => 'mtr', 'Medtr2g021470' => 'mtr', 'Medtr2g105810' => 'mtr', 'Medtr3g033580' => 'mtr', 'Medtr6g007970' => 'mtr', 'Medtr7g056330' => 'mtr', 'Medtr7g074290' => 'mtr', 'Medtr7g074380' => 'mtr', 'Medtr7g094550' => 'mtr', 'Medtr8g069995' => 'mtr', 'MELO3C014345.2' => 'cme', 'MELO3C021395.2' => 'cme', 'Migut.D00262' => 'egut', 'Migut.G00257' => 'egut', 'MSTRG.21575' => 'ama', 'MSTRG.3985' => 'ama', 'Nitab4.5_0000295g0140' => 'nta', 'Nitab4.5_0000732g0140' => 'nta', 'Nitab4.5_0003162g0020' => 'nta', 'Nitab4.5_0006180g0090' => 'nta', 'Nitab4.5_0006390g0010' => 'nta', 'Nitab4.5_0007392g0040' => 'nta', 'Nn1g02140' => 'nnu', 'Nn4g26168' => 'nnu', 'Nn5g26754' => 'nnu', 'Oeu001433.1' => 'oeu', 'Oeu010299.2' => 'oeu', 'Oeu011171.1' => 'oeu', 'Oeu037675.1' => 'oeu', 'Oeu038359.1' => 'oeu', 'Oeu063834.1' => 'oeu', 'Oeu063835.1' => 'oeu', 'Os05g0312000' => 'osa', 'Os07g0211101' => 'osa', 'Os07g0211200' => 'osa', 'Os07g0681500' => 'osa', 'Peaxi162Scf00095g01015' => 'pax', 'Peaxi162Scf00104g00329' => 'pax', 'Peaxi162Scf00161g00137' => 'pax', 'PGR004G1665' => 'pgr', 'PGR031G2937' => 'pgr', 'PGR119G2145' => 'pgr', 'PGSC0003DMG400004351' => 'stu', 'PGSC0003DMG400014625' => 'stu', 'PGSC0003DMG401000943' => 'stu', 'Phvul.001G148600' => 'pvu', 'Phvul.004G001700' => 'pvu', 'Phvul.006G154900' => 'pvu', 'Phvul.008G078200' => 'pvu', 'Phvul.011G136500' => 'pvu', 'Potri.002G215600' => 'ptr', 'Potri.008G201600' => 'ptr', 'Potri.014G138400' => 'ptr', 'Potri.016G142500' => 'ptr', 'Pp3c16_10580' => 'ppa', 'Pp3c5_25280' => 'ppa', 'Prupe.1G150000' => 'ppe', 'Prupe.1G150100' => 'ppe', 'Prupe.6G299600' => 'ppe', 'Prupe.8G245000' => 'ppe', 'Psat0s4927g0040' => 'psa', 'Psat1g052080' => 'psa', 'Psat1g183800' => 'psa', 'Psat3g113840' => 'psa', 'Psat3g126120' => 'psa', 'Psat3g126160' => 'psa', 'Psat3g158760' => 'psa', 'Psat3g158840' => 'psa', 'PSO170G2858' => 'pso', 'PSO339G0606' => 'pso', 'PSO384G4709' => 'pso', 'PSO407G0334' => 'pso', 'QL04p040276' => 'qlo', 'QL06p005458' => 'qlo', 'QL06p005472' => 'qlo', 'QL07p030546' => 'qlo', 'QL07p031519' => 'qlo', 'QL09p050949' => 'qlo', 'QL09p050966' => 'qlo', 'QL09p051067' => 'qlo', 'QL12p022706' => 'qlo', 'RcHm_v2.0_Chr2g0119601' => 'rch', 'RcHm_v2.0_Chr3g0459591' => 'rch', 'RcHm_v2.0_Chr4g0418521' => 'rch', 'RcHm_v2.0_Chr4g0418531' => 'rch', 'RcHm_v2.0_Chr4g0418541' => 'rch', 'RcHm_v2.0_Chr6g0291641' => 'rch', 'Rhsim01G0086300' => 'rsi', 'Rhsim01G0276300' => 'rsi', 'Rhsim01G0276500' => 'rsi', 'Rhsim04G0207700' => 'rsi', 'Rhsim05G0234500' => 'rsi', 'Rhsim13G0022400' => 'rsi', 'Sabra02G0167900' => 'sbr', 'Sabra04G0158500' => 'sbr', 'Sabra08G0159800' => 'sbr', 'Sabra10G0011500' => 'sbr', 'Sabra14G0104400' => 'sbr', 'SalBow2G2440' => 'sbo', 'SalBow4G2265' => 'sbo', 'Sc02g0000060' => 'sci', 'Sc05g0005020' => 'sci', 'Sc13g0003890' => 'sci', 'Sed0014865' => 'sed', 'Sed0017224' => 'sed', 'Sed0026391' => 'sed', 'SEGI_00063' => 'sgi', 'SEGI_10967' => 'sgi', 'SEGI_17510' => 'sgi', 'SEGI_24396' => 'sgi', 'SEGI_39719' => 'sgi', 'SEGI_41392' => 'sgi', 'SGA_v2.0_scaffold11G05794' => 'sas', 'SGA_v2.0_scaffold142G35607' => 'sas', 'SGA_v2.0_scaffold1G00447' => 'sas', 'SHI15388' => 'shi', 'SHI15394' => 'shi', 'SHI15396' => 'shi', 'SHI15399' => 'shi', 'SMO343G0151' => 'smo', 'SMO367G1118' => 'smo', 'Solyc01g080200.3' => 'sly', 'Solyc06g008960.3' => 'sly', 'Solyc09g064780.3' => 'sly', 'Sopen01g031980' => 'spe', 'Sopen06g003710' => 'spe', 'Sopen09g026460' => 'spe', 'Sp3g21240' => 'spa', 'Sp4g30030' => 'spa', 'TAR365G0022' => 'tar', 'TAR365G1023' => 'tar', 'TAR365G1253' => 'tar', 'TAR623G0078' => 'tar', 'TAR623G1721' => 'tar', 'TAR633G0959' => 'tar', 'THA.LOC104802225' => 'tha', 'THA.LOC104804769' => 'tha', 'THA.LOC104808660' => 'tha', 'THA.LOC104812792' => 'tha', 'Thecc.01G284000' => 'tca', 'Thecc.04G220600' => 'tca', 'Thecc.05G268900' => 'tca', 'Thecc.08G171100' => 'tca', 'Thhalv10001284m.g' => 'esa', 'Thhalv10019912m.g' => 'esa', 'TPR.G14189' => 'tpr', 'TPR.G18110' => 'tpr', 'TPR.G18130' => 'tpr', 'TPR.G18131' => 'tpr', 'TPR.G18140' => 'tpr', 'TPR.G24282' => 'tpr', 'TPR.G25221' => 'tpr', 'TPR.G29267' => 'tpr', 'TPR.G35315' => 'tpr', 'TPR.G36173' => 'tpr', 'TWI09G0794' => 'twi', 'TWI59G1348' => 'twi', 'TWI74G0430' => 'twi', 'unitig_26.g8940' => 'ugi', 'unitig_749.g13744' => 'ugi', 'unitig_749.g13745' => 'ugi', 'vmacro08269' => 'vma', 'vmacro14937' => 'vma', 'vmacro20401' => 'vma', 'VMungo0464G1349' => 'vmu', 'VMungo0540G0289' => 'vmu', 'VMungo1215G1590' => 'vmu', 'VMungo1309G0221' => 'vmu', 'VMungo1309G2815' => 'vmu', 'VMungo1383G0239' => 'vmu', 'VMungo1383G2910' => 'vmu', 'Zm00001eb095270' => 'zma', 'Zm00001eb095280' => 'zma', 'Zm00001eb111630' => 'zma', 'Zm00001eb237080' => 'zma', 'Zm00001eb273740' => 'zma', 'Zm00001eb285040' => 'zma', 'Zm00001eb330790' => 'zma', 'Zm00001eb337380' => 'zma' ) $gf_id = 'HOM05D001484' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001484' ) $data_identifier = 'HOM05D001484' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 2, 'aly' => (int) 2, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 22, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 7, 'hma' => (int) 2, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 7, 'mtr' => (int) 10, 'cme' => (int) 2, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 4, 'ppa' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 4, 'qlo' => (int) 9, 'rch' => (int) 6, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 10, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 7, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb337380' $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' => 'HOM05D001484', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p31500' => 'bna', 'A05p00020' => 'bna', 'A07p08820' => 'bna', 'Aa31LG4G3300' => 'aar', 'Aa31LG8G10030' => 'aar', 'Actinidia00731' => 'ach', 'Actinidia11473' => 'ach', 'Actinidia23469' => 'ach', 'Actinidia24318' => 'ach', 'Actinidia40196' => 'ach', 'Actinidia40197' => 'ach', 'Actinidia40198' => 'ach', 'Ah.08g212990' => 'amhyb', 'Ah.15g091720' => 'amhyb', 'AL3G38260' => 'aly', 'AL4G47710' => 'aly', 'Aqoxy2G00671' => 'aox', 'Aqoxy2G03236' => 'aox', 'arahy.Tifrunner.gnm1.ann1.05IDCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KR684' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATY3SJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK6QJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6APGL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IDT7Z9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM073U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ0R87' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LE7RV4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT4QRX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V5ENPK' => 'arhy', 'AT2G48110' => 'ath', 'AT3G23590' => 'ath', 'ATR0626G186' => 'atr', 'ATR1127G141' => 'atr', 'Atru.chr4.2583' => 'acertr', 'Atru.chr5.1358' => 'acertr', 'Atru.chr5.1359' => 'acertr', 'Atru.chr8.46' => 'acertr', 'AUR62002640' => 'cqu', 'AUR62030055' => 'cqu', 'AUR62033713' => 'cqu', 'AUR62033714' => 'cqu', 'AUR62036795' => 'cqu', 'AUR62039891' => 'cqu', 'BcaB02g08737' => 'bca', 'BcaB04g20441' => 'bca', 'BcaB06g26509' => 'bca', 'BcaB06g26510' => 'bca', 'BcaB06g26511' => 'bca', 'BcaB06g26512' => 'bca', 'BcaB06g26513' => 'bca', 'BcaC02g12564' => 'bca', 'BcaC02g12565' => 'bca', 'BcaC02g12794' => 'bca', 'BcaC02g12795' => 'bca', 'BcaC02g12796' => 'bca', 'BcaC06g35541' => 'bca', 'BNapus_Darmor_BZH_scaffold_188p00080' => 'bna', 'BNapus_Darmor_BZH_scaffold_188p00090' => 'bna', 'BolC1t03972H' => 'bol', 'BolC1t03973H' => 'bol', 'BolC4t21680H' => 'bol', 'BolC7t41863H' => 'bol', 'BolSC55t61227H' => 'bol', 'BolSC55t61228H' => 'bol', 'BraA01t03278Z' => 'bra', 'BraA05t18998Z' => 'bra', 'BraA07t28673Z' => 'bra', 'C01p40150' => 'bna', 'C05p12370' => 'bna', 'C07p13680' => 'bna', 'CAN.G1006.16' => 'can', 'CAN.G1006.17' => 'can', 'CAN.G1170.2' => 'can', 'CAN.G962.7' => 'can', 'CANSAT25G2179' => 'cansat', 'CANSAT78G1573' => 'cansat', 'CARHR099510' => 'chi', 'CARHR143510' => 'chi', 'Carub.0003s2380' => 'cru', 'Carub.0004s3082' => 'cru', 'Ca_00614_v3' => 'car', 'Ca_07801_v3' => 'car', 'Ca_08567_v3' => 'car', 'Ca_09571_v3' => 'car', 'CBR_g19290' => 'cbr', 'Cc01_g19770' => 'ccan', 'Cc03_g03030' => 'ccan', 'CDE07G0968' => 'cde', 'CDE09G1441' => 'cde', 'Cfa006103' => 'cfa', 'Cfa015573' => 'cfa', 'Cfa016988' => 'cfa', 'Ciclev10006738m.g' => 'ccl', 'Ciclev10010920m.g' => 'ccl', 'Ciclev10018517m.g' => 'ccl', 'CiPaw.01G159200' => 'cil', 'CiPaw.02G091000' => 'cil', 'CiPaw.02G091100' => 'cil', 'CiPaw.08G103100' => 'cil', 'CiPaw.09G224900' => 'cil', 'ClCG06G005740' => 'cla', 'ClCG07G000090' => 'cla', 'ClCG07G000100' => 'cla', 'COL.COLO4_09143' => 'col', 'COL.COLO4_25124' => 'col', 'Cpa.g.sc16.34' => 'cpa', 'Cpa.g.sc3504.1' => 'cpa', 'Cpa.g.sc60.37' => 'cpa', 'CsaV3_6G018520' => 'csa', 'CsaV3_6G036860' => 'csa', 'CSS0001072' => 'camsi', 'CSS0020208' => 'camsi', 'CSS0021253' => 'camsi', 'CSS0022190' => 'camsi', 'CSS0036150' => 'camsi', 'CSS0040442' => 'camsi', 'CSS0042300' => 'camsi', 'CSS0045298' => 'camsi', 'DCAR_012449' => 'dca', 'DCAR_018405' => 'dca', 'DCAR_024573' => 'dca', 'DCAR_030591' => 'dca', 'Dinv16926' => 'din', 'Dinv32963' => 'din', 'Dinv38382' => 'din', 'Dinv38383' => 'din', 'Duzib133G0974' => 'dzi', 'Duzib138G1867' => 'dzi', 'Duzib211G0420' => 'dzi', 'Duzib212G0930' => 'dzi', 'ECA234G1645' => 'eca', 'ECA247G3467' => 'eca', 'ECA248G1703' => 'eca', 'EL10Ac3g06327' => 'bvu', 'EL10Ac7g17204' => 'bvu', 'Eucgr.A00855' => 'egr', 'Eucgr.A00858' => 'egr', 'Eucgr.H01520' => 'egr', 'Eucgr.H03604' => 'egr', 'Eucgr.L03465' => 'egr', 'Eucgr.L03466' => 'egr', 'FAN01G0988' => 'fan', 'FAN02G3892' => 'fan', 'FAN05G3381' => 'fan', 'FAN07G0967' => 'fan', 'FAN07G1493' => 'fan', 'FAN08G3125' => 'fan', 'FAN09G0402' => 'fan', 'FAN12G2594' => 'fan', 'FAN12G3879' => 'fan', 'FAN14G1546' => 'fan', 'FAN15G3626' => 'fan', 'FAN17G0588' => 'fan', 'FAN17G0609' => 'fan', 'FAN18G2817' => 'fan', 'FAN19G1305' => 'fan', 'FAN20G1787' => 'fan', 'FAN22G0073' => 'fan', 'FAN22G0352' => 'fan', 'FAN22G0368' => 'fan', 'FAN22G2273' => 'fan', 'FAN24G1998' => 'fan', 'FAN27G1317' => 'fan', 'FvH4_2g23980' => 'fve', 'FvH4_4g14380' => 'fve', 'FvH4_4g14390' => 'fve', 'FvH4_6g09250' => 'fve', 'Glyma.03G151100' => 'gma', 'Glyma.04G122550' => 'gma', 'Glyma.05G001600' => 'gma', 'Glyma.09G270766' => 'gma', 'Glyma.09G270832' => 'gma', 'Glyma.13G209800' => 'gma', 'Glyma.15G102800' => 'gma', 'Glyma.18G218900' => 'gma', 'Glyma.19G001500' => 'gma', 'Glyma.19G153600' => 'gma', 'Gohir.A02G028600' => 'ghi', 'Gohir.A08G045000' => 'ghi', 'Gohir.A11G120500' => 'ghi', 'Gohir.A12G006200' => 'ghi', 'Gohir.A12G006250' => 'ghi', 'Gohir.D02G036300' => 'ghi', 'Gohir.D08G054700' => 'ghi', 'Gohir.D11G125600' => 'ghi', 'Gohir.D12G005700' => 'ghi', 'Gorai.004G055200' => 'gra', 'Gorai.005G040400' => 'gra', 'Gorai.007G134500' => 'gra', 'Gorai.008G005500' => 'gra', 'GSVIVG01011094001' => 'vvi', 'GSVIVG01017879001' => 'vvi', 'GSVIVG01025988001' => 'vvi', 'GSVIVG01029847001' => 'vvi', 'HanXRQChr10g0282901' => 'han', 'HanXRQChr10g0310371' => 'han', 'HanXRQChr10g0315041' => 'han', 'HanXRQChr11g0327651' => 'han', 'HanXRQChr12g0359391' => 'han', 'Haze_00972' => 'cav', 'Haze_00973' => 'cav', 'Haze_00974' => 'cav', 'Haze_04747' => 'cav', 'Haze_04749' => 'cav', 'Haze_04750' => 'cav', 'Haze_21217' => 'cav', 'Hma1.2p1_1037F.1_g250680' => 'hma', 'Hma1.2p1_1644F.1_g295320' => 'hma', 'HPP92_011322' => 'vpl', 'HPP92_011323' => 'vpl', 'HPP92_011324' => 'vpl', 'HPP92_011325' => 'vpl', 'HPP92_011326' => 'vpl', 'Hund12205' => 'sun', 'Hund17957' => 'sun', 'Lalb_Chr06g0176771' => 'lal', 'Lalb_Chr18g0056021' => 'lal', 'Lalb_Chr18g0056031' => 'lal', 'Lalb_Chr18g0056041' => 'lal', 'Lalb_Chr20g0107751' => 'lal', 'Lalb_Chr20g0118371' => 'lal', 'Lj1g0010239' => 'lja', 'Lj1g0017101' => 'lja', 'Lj2A1178G40' => 'lonja', 'Lj2A54G84' => 'lonja', 'Lj2g0015248' => 'lja', 'Lj3A761T51' => 'lonja', 'Lj6g0018116' => 'lja', 'Lsat_1_v5_gn_4_136040' => 'lsa', 'Lsat_1_v5_gn_5_187461' => 'lsa', 'Lsat_1_v5_gn_5_77001' => 'lsa', 'Lsat_1_v5_gn_9_4461' => 'lsa', 'Manes.01G210100' => 'mes', 'Manes.03G185600' => 'mes', 'Manes.05G073300' => 'mes', 'Manes.09G120300' => 'mes', 'Manes.15G022100' => 'mes', 'Mapoly0096s0053' => 'mpo', 'MBI03_g14058_MAGBIO' => 'mbi', 'MBI03_g33876_MAGBIO' => 'mbi', 'MBI03_g36854_MAGBIO' => 'mbi', 'MBI17_g11997_MAGBIO' => 'mbi', 'MD03G1269000' => 'mdo', 'MD04G1179600' => 'mdo', 'MD11G1289800' => 'mdo', 'MD12G1194700' => 'mdo', 'MD13G1182100' => 'mdo', 'MD13G1182200' => 'mdo', 'MD16G1182600' => 'mdo', 'Medtr2g021400' => 'mtr', 'Medtr2g021470' => 'mtr', 'Medtr2g105810' => 'mtr', 'Medtr3g033580' => 'mtr', 'Medtr6g007970' => 'mtr', 'Medtr7g056330' => 'mtr', 'Medtr7g074290' => 'mtr', 'Medtr7g074380' => 'mtr', 'Medtr7g094550' => 'mtr', 'Medtr8g069995' => 'mtr', 'MELO3C014345.2' => 'cme', 'MELO3C021395.2' => 'cme', 'Migut.D00262' => 'egut', 'Migut.G00257' => 'egut', 'MSTRG.21575' => 'ama', 'MSTRG.3985' => 'ama', 'Nitab4.5_0000295g0140' => 'nta', 'Nitab4.5_0000732g0140' => 'nta', 'Nitab4.5_0003162g0020' => 'nta', 'Nitab4.5_0006180g0090' => 'nta', 'Nitab4.5_0006390g0010' => 'nta', 'Nitab4.5_0007392g0040' => 'nta', 'Nn1g02140' => 'nnu', 'Nn4g26168' => 'nnu', 'Nn5g26754' => 'nnu', 'Oeu001433.1' => 'oeu', 'Oeu010299.2' => 'oeu', 'Oeu011171.1' => 'oeu', 'Oeu037675.1' => 'oeu', 'Oeu038359.1' => 'oeu', 'Oeu063834.1' => 'oeu', 'Oeu063835.1' => 'oeu', 'Os05g0312000' => 'osa', 'Os07g0211101' => 'osa', 'Os07g0211200' => 'osa', 'Os07g0681500' => 'osa', 'Peaxi162Scf00095g01015' => 'pax', 'Peaxi162Scf00104g00329' => 'pax', 'Peaxi162Scf00161g00137' => 'pax', 'PGR004G1665' => 'pgr', 'PGR031G2937' => 'pgr', 'PGR119G2145' => 'pgr', 'PGSC0003DMG400004351' => 'stu', 'PGSC0003DMG400014625' => 'stu', 'PGSC0003DMG401000943' => 'stu', 'Phvul.001G148600' => 'pvu', 'Phvul.004G001700' => 'pvu', 'Phvul.006G154900' => 'pvu', 'Phvul.008G078200' => 'pvu', 'Phvul.011G136500' => 'pvu', 'Potri.002G215600' => 'ptr', 'Potri.008G201600' => 'ptr', 'Potri.014G138400' => 'ptr', 'Potri.016G142500' => 'ptr', 'Pp3c16_10580' => 'ppa', 'Pp3c5_25280' => 'ppa', 'Prupe.1G150000' => 'ppe', 'Prupe.1G150100' => 'ppe', 'Prupe.6G299600' => 'ppe', 'Prupe.8G245000' => 'ppe', 'Psat0s4927g0040' => 'psa', 'Psat1g052080' => 'psa', 'Psat1g183800' => 'psa', 'Psat3g113840' => 'psa', 'Psat3g126120' => 'psa', 'Psat3g126160' => 'psa', 'Psat3g158760' => 'psa', 'Psat3g158840' => 'psa', 'PSO170G2858' => 'pso', 'PSO339G0606' => 'pso', 'PSO384G4709' => 'pso', 'PSO407G0334' => 'pso', 'QL04p040276' => 'qlo', 'QL06p005458' => 'qlo', 'QL06p005472' => 'qlo', 'QL07p030546' => 'qlo', 'QL07p031519' => 'qlo', 'QL09p050949' => 'qlo', 'QL09p050966' => 'qlo', 'QL09p051067' => 'qlo', 'QL12p022706' => 'qlo', 'RcHm_v2.0_Chr2g0119601' => 'rch', 'RcHm_v2.0_Chr3g0459591' => 'rch', 'RcHm_v2.0_Chr4g0418521' => 'rch', 'RcHm_v2.0_Chr4g0418531' => 'rch', 'RcHm_v2.0_Chr4g0418541' => 'rch', 'RcHm_v2.0_Chr6g0291641' => 'rch', 'Rhsim01G0086300' => 'rsi', 'Rhsim01G0276300' => 'rsi', 'Rhsim01G0276500' => 'rsi', 'Rhsim04G0207700' => 'rsi', 'Rhsim05G0234500' => 'rsi', 'Rhsim13G0022400' => 'rsi', 'Sabra02G0167900' => 'sbr', 'Sabra04G0158500' => 'sbr', 'Sabra08G0159800' => 'sbr', 'Sabra10G0011500' => 'sbr', 'Sabra14G0104400' => 'sbr', 'SalBow2G2440' => 'sbo', 'SalBow4G2265' => 'sbo', 'Sc02g0000060' => 'sci', 'Sc05g0005020' => 'sci', 'Sc13g0003890' => 'sci', 'Sed0014865' => 'sed', 'Sed0017224' => 'sed', 'Sed0026391' => 'sed', 'SEGI_00063' => 'sgi', 'SEGI_10967' => 'sgi', 'SEGI_17510' => 'sgi', 'SEGI_24396' => 'sgi', 'SEGI_39719' => 'sgi', 'SEGI_41392' => 'sgi', 'SGA_v2.0_scaffold11G05794' => 'sas', 'SGA_v2.0_scaffold142G35607' => 'sas', 'SGA_v2.0_scaffold1G00447' => 'sas', 'SHI15388' => 'shi', 'SHI15394' => 'shi', 'SHI15396' => 'shi', 'SHI15399' => 'shi', 'SMO343G0151' => 'smo', 'SMO367G1118' => 'smo', 'Solyc01g080200.3' => 'sly', 'Solyc06g008960.3' => 'sly', 'Solyc09g064780.3' => 'sly', 'Sopen01g031980' => 'spe', 'Sopen06g003710' => 'spe', 'Sopen09g026460' => 'spe', 'Sp3g21240' => 'spa', 'Sp4g30030' => 'spa', 'TAR365G0022' => 'tar', 'TAR365G1023' => 'tar', 'TAR365G1253' => 'tar', 'TAR623G0078' => 'tar', 'TAR623G1721' => 'tar', 'TAR633G0959' => 'tar', 'THA.LOC104802225' => 'tha', 'THA.LOC104804769' => 'tha', 'THA.LOC104808660' => 'tha', 'THA.LOC104812792' => 'tha', 'Thecc.01G284000' => 'tca', 'Thecc.04G220600' => 'tca', 'Thecc.05G268900' => 'tca', 'Thecc.08G171100' => 'tca', 'Thhalv10001284m.g' => 'esa', 'Thhalv10019912m.g' => 'esa', 'TPR.G14189' => 'tpr', 'TPR.G18110' => 'tpr', 'TPR.G18130' => 'tpr', 'TPR.G18131' => 'tpr', 'TPR.G18140' => 'tpr', 'TPR.G24282' => 'tpr', 'TPR.G25221' => 'tpr', 'TPR.G29267' => 'tpr', 'TPR.G35315' => 'tpr', 'TPR.G36173' => 'tpr', 'TWI09G0794' => 'twi', 'TWI59G1348' => 'twi', 'TWI74G0430' => 'twi', 'unitig_26.g8940' => 'ugi', 'unitig_749.g13744' => 'ugi', 'unitig_749.g13745' => 'ugi', 'vmacro08269' => 'vma', 'vmacro14937' => 'vma', 'vmacro20401' => 'vma', 'VMungo0464G1349' => 'vmu', 'VMungo0540G0289' => 'vmu', 'VMungo1215G1590' => 'vmu', 'VMungo1309G0221' => 'vmu', 'VMungo1309G2815' => 'vmu', 'VMungo1383G0239' => 'vmu', 'VMungo1383G2910' => 'vmu', 'Zm00001eb095270' => 'zma', 'Zm00001eb095280' => 'zma', 'Zm00001eb111630' => 'zma', 'Zm00001eb237080' => 'zma', 'Zm00001eb273740' => 'zma', 'Zm00001eb285040' => 'zma', 'Zm00001eb330790' => 'zma', 'Zm00001eb337380' => 'zma' ), 'gf_id' => 'HOM05D001484', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001484' ), 'data_identifier' => 'HOM05D001484', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001484', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p31500' => 'bna', 'A05p00020' => 'bna', 'A07p08820' => 'bna', 'Aa31LG4G3300' => 'aar', 'Aa31LG8G10030' => 'aar', 'Actinidia00731' => 'ach', 'Actinidia11473' => 'ach', 'Actinidia23469' => 'ach', 'Actinidia24318' => 'ach', 'Actinidia40196' => 'ach', 'Actinidia40197' => 'ach', 'Actinidia40198' => 'ach', 'Ah.08g212990' => 'amhyb', 'Ah.15g091720' => 'amhyb', 'AL3G38260' => 'aly', 'AL4G47710' => 'aly', 'Aqoxy2G00671' => 'aox', 'Aqoxy2G03236' => 'aox', 'arahy.Tifrunner.gnm1.ann1.05IDCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KR684' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATY3SJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK6QJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6APGL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IDT7Z9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM073U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ0R87' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LE7RV4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT4QRX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V5ENPK' => 'arhy', 'AT2G48110' => 'ath', 'AT3G23590' => 'ath', 'ATR0626G186' => 'atr', 'ATR1127G141' => 'atr', 'Atru.chr4.2583' => 'acertr', 'Atru.chr5.1358' => 'acertr', 'Atru.chr5.1359' => 'acertr', 'Atru.chr8.46' => 'acertr', 'AUR62002640' => 'cqu', 'AUR62030055' => 'cqu', 'AUR62033713' => 'cqu', 'AUR62033714' => 'cqu', 'AUR62036795' => 'cqu', 'AUR62039891' => 'cqu', 'BcaB02g08737' => 'bca', 'BcaB04g20441' => 'bca', 'BcaB06g26509' => 'bca', 'BcaB06g26510' => 'bca', 'BcaB06g26511' => 'bca', 'BcaB06g26512' => 'bca', 'BcaB06g26513' => 'bca', 'BcaC02g12564' => 'bca', 'BcaC02g12565' => 'bca', 'BcaC02g12794' => 'bca', 'BcaC02g12795' => 'bca', 'BcaC02g12796' => 'bca', 'BcaC06g35541' => 'bca', 'BNapus_Darmor_BZH_scaffold_188p00080' => 'bna', 'BNapus_Darmor_BZH_scaffold_188p00090' => 'bna', 'BolC1t03972H' => 'bol', 'BolC1t03973H' => 'bol', 'BolC4t21680H' => 'bol', 'BolC7t41863H' => 'bol', 'BolSC55t61227H' => 'bol', 'BolSC55t61228H' => 'bol', 'BraA01t03278Z' => 'bra', 'BraA05t18998Z' => 'bra', 'BraA07t28673Z' => 'bra', 'C01p40150' => 'bna', 'C05p12370' => 'bna', 'C07p13680' => 'bna', 'CAN.G1006.16' => 'can', 'CAN.G1006.17' => 'can', 'CAN.G1170.2' => 'can', 'CAN.G962.7' => 'can', 'CANSAT25G2179' => 'cansat', 'CANSAT78G1573' => 'cansat', 'CARHR099510' => 'chi', 'CARHR143510' => 'chi', 'Carub.0003s2380' => 'cru', 'Carub.0004s3082' => 'cru', 'Ca_00614_v3' => 'car', 'Ca_07801_v3' => 'car', 'Ca_08567_v3' => 'car', 'Ca_09571_v3' => 'car', 'CBR_g19290' => 'cbr', 'Cc01_g19770' => 'ccan', 'Cc03_g03030' => 'ccan', 'CDE07G0968' => 'cde', 'CDE09G1441' => 'cde', 'Cfa006103' => 'cfa', 'Cfa015573' => 'cfa', 'Cfa016988' => 'cfa', 'Ciclev10006738m.g' => 'ccl', 'Ciclev10010920m.g' => 'ccl', 'Ciclev10018517m.g' => 'ccl', 'CiPaw.01G159200' => 'cil', 'CiPaw.02G091000' => 'cil', 'CiPaw.02G091100' => 'cil', 'CiPaw.08G103100' => 'cil', 'CiPaw.09G224900' => 'cil', 'ClCG06G005740' => 'cla', 'ClCG07G000090' => 'cla', 'ClCG07G000100' => 'cla', 'COL.COLO4_09143' => 'col', 'COL.COLO4_25124' => 'col', 'Cpa.g.sc16.34' => 'cpa', 'Cpa.g.sc3504.1' => 'cpa', 'Cpa.g.sc60.37' => 'cpa', 'CsaV3_6G018520' => 'csa', 'CsaV3_6G036860' => 'csa', 'CSS0001072' => 'camsi', 'CSS0020208' => 'camsi', 'CSS0021253' => 'camsi', 'CSS0022190' => 'camsi', 'CSS0036150' => 'camsi', 'CSS0040442' => 'camsi', 'CSS0042300' => 'camsi', 'CSS0045298' => 'camsi', 'DCAR_012449' => 'dca', 'DCAR_018405' => 'dca', 'DCAR_024573' => 'dca', 'DCAR_030591' => 'dca', 'Dinv16926' => 'din', 'Dinv32963' => 'din', 'Dinv38382' => 'din', 'Dinv38383' => 'din', 'Duzib133G0974' => 'dzi', 'Duzib138G1867' => 'dzi', 'Duzib211G0420' => 'dzi', 'Duzib212G0930' => 'dzi', 'ECA234G1645' => 'eca', 'ECA247G3467' => 'eca', 'ECA248G1703' => 'eca', 'EL10Ac3g06327' => 'bvu', 'EL10Ac7g17204' => 'bvu', 'Eucgr.A00855' => 'egr', 'Eucgr.A00858' => 'egr', 'Eucgr.H01520' => 'egr', 'Eucgr.H03604' => 'egr', 'Eucgr.L03465' => 'egr', 'Eucgr.L03466' => 'egr', 'FAN01G0988' => 'fan', 'FAN02G3892' => 'fan', 'FAN05G3381' => 'fan', 'FAN07G0967' => 'fan', 'FAN07G1493' => 'fan', 'FAN08G3125' => 'fan', 'FAN09G0402' => 'fan', 'FAN12G2594' => 'fan', 'FAN12G3879' => 'fan', 'FAN14G1546' => 'fan', 'FAN15G3626' => 'fan', 'FAN17G0588' => 'fan', 'FAN17G0609' => 'fan', 'FAN18G2817' => 'fan', 'FAN19G1305' => 'fan', 'FAN20G1787' => 'fan', 'FAN22G0073' => 'fan', 'FAN22G0352' => 'fan', 'FAN22G0368' => 'fan', 'FAN22G2273' => 'fan', 'FAN24G1998' => 'fan', 'FAN27G1317' => 'fan', 'FvH4_2g23980' => 'fve', 'FvH4_4g14380' => 'fve', 'FvH4_4g14390' => 'fve', 'FvH4_6g09250' => 'fve', 'Glyma.03G151100' => 'gma', 'Glyma.04G122550' => 'gma', 'Glyma.05G001600' => 'gma', 'Glyma.09G270766' => 'gma', 'Glyma.09G270832' => 'gma', 'Glyma.13G209800' => 'gma', 'Glyma.15G102800' => 'gma', 'Glyma.18G218900' => 'gma', 'Glyma.19G001500' => 'gma', 'Glyma.19G153600' => 'gma', 'Gohir.A02G028600' => 'ghi', 'Gohir.A08G045000' => 'ghi', 'Gohir.A11G120500' => 'ghi', 'Gohir.A12G006200' => 'ghi', 'Gohir.A12G006250' => 'ghi', 'Gohir.D02G036300' => 'ghi', 'Gohir.D08G054700' => 'ghi', 'Gohir.D11G125600' => 'ghi', 'Gohir.D12G005700' => 'ghi', 'Gorai.004G055200' => 'gra', 'Gorai.005G040400' => 'gra', 'Gorai.007G134500' => 'gra', 'Gorai.008G005500' => 'gra', 'GSVIVG01011094001' => 'vvi', 'GSVIVG01017879001' => 'vvi', 'GSVIVG01025988001' => 'vvi', 'GSVIVG01029847001' => 'vvi', 'HanXRQChr10g0282901' => 'han', 'HanXRQChr10g0310371' => 'han', 'HanXRQChr10g0315041' => 'han', 'HanXRQChr11g0327651' => 'han', 'HanXRQChr12g0359391' => 'han', 'Haze_00972' => 'cav', 'Haze_00973' => 'cav', 'Haze_00974' => 'cav', 'Haze_04747' => 'cav', 'Haze_04749' => 'cav', 'Haze_04750' => 'cav', 'Haze_21217' => 'cav', 'Hma1.2p1_1037F.1_g250680' => 'hma', 'Hma1.2p1_1644F.1_g295320' => 'hma', 'HPP92_011322' => 'vpl', 'HPP92_011323' => 'vpl', 'HPP92_011324' => 'vpl', 'HPP92_011325' => 'vpl', 'HPP92_011326' => 'vpl', 'Hund12205' => 'sun', 'Hund17957' => 'sun', 'Lalb_Chr06g0176771' => 'lal', 'Lalb_Chr18g0056021' => 'lal', 'Lalb_Chr18g0056031' => 'lal', 'Lalb_Chr18g0056041' => 'lal', 'Lalb_Chr20g0107751' => 'lal', 'Lalb_Chr20g0118371' => 'lal', 'Lj1g0010239' => 'lja', 'Lj1g0017101' => 'lja', 'Lj2A1178G40' => 'lonja', 'Lj2A54G84' => 'lonja', 'Lj2g0015248' => 'lja', 'Lj3A761T51' => 'lonja', 'Lj6g0018116' => 'lja', 'Lsat_1_v5_gn_4_136040' => 'lsa', 'Lsat_1_v5_gn_5_187461' => 'lsa', 'Lsat_1_v5_gn_5_77001' => 'lsa', 'Lsat_1_v5_gn_9_4461' => 'lsa', 'Manes.01G210100' => 'mes', 'Manes.03G185600' => 'mes', 'Manes.05G073300' => 'mes', 'Manes.09G120300' => 'mes', 'Manes.15G022100' => 'mes', 'Mapoly0096s0053' => 'mpo', 'MBI03_g14058_MAGBIO' => 'mbi', 'MBI03_g33876_MAGBIO' => 'mbi', 'MBI03_g36854_MAGBIO' => 'mbi', 'MBI17_g11997_MAGBIO' => 'mbi', 'MD03G1269000' => 'mdo', 'MD04G1179600' => 'mdo', 'MD11G1289800' => 'mdo', 'MD12G1194700' => 'mdo', 'MD13G1182100' => 'mdo', 'MD13G1182200' => 'mdo', 'MD16G1182600' => 'mdo', 'Medtr2g021400' => 'mtr', 'Medtr2g021470' => 'mtr', 'Medtr2g105810' => 'mtr', 'Medtr3g033580' => 'mtr', 'Medtr6g007970' => 'mtr', 'Medtr7g056330' => 'mtr', 'Medtr7g074290' => 'mtr', 'Medtr7g074380' => 'mtr', 'Medtr7g094550' => 'mtr', 'Medtr8g069995' => 'mtr', 'MELO3C014345.2' => 'cme', 'MELO3C021395.2' => 'cme', 'Migut.D00262' => 'egut', 'Migut.G00257' => 'egut', 'MSTRG.21575' => 'ama', 'MSTRG.3985' => 'ama', 'Nitab4.5_0000295g0140' => 'nta', 'Nitab4.5_0000732g0140' => 'nta', 'Nitab4.5_0003162g0020' => 'nta', 'Nitab4.5_0006180g0090' => 'nta', 'Nitab4.5_0006390g0010' => 'nta', 'Nitab4.5_0007392g0040' => 'nta', 'Nn1g02140' => 'nnu', 'Nn4g26168' => 'nnu', 'Nn5g26754' => 'nnu', 'Oeu001433.1' => 'oeu', 'Oeu010299.2' => 'oeu', 'Oeu011171.1' => 'oeu', 'Oeu037675.1' => 'oeu', 'Oeu038359.1' => 'oeu', 'Oeu063834.1' => 'oeu', 'Oeu063835.1' => 'oeu', 'Os05g0312000' => 'osa', 'Os07g0211101' => 'osa', 'Os07g0211200' => 'osa', 'Os07g0681500' => 'osa', 'Peaxi162Scf00095g01015' => 'pax', 'Peaxi162Scf00104g00329' => 'pax', 'Peaxi162Scf00161g00137' => 'pax', 'PGR004G1665' => 'pgr', 'PGR031G2937' => 'pgr', 'PGR119G2145' => 'pgr', 'PGSC0003DMG400004351' => 'stu', 'PGSC0003DMG400014625' => 'stu', 'PGSC0003DMG401000943' => 'stu', 'Phvul.001G148600' => 'pvu', 'Phvul.004G001700' => 'pvu', 'Phvul.006G154900' => 'pvu', 'Phvul.008G078200' => 'pvu', 'Phvul.011G136500' => 'pvu', 'Potri.002G215600' => 'ptr', 'Potri.008G201600' => 'ptr', 'Potri.014G138400' => 'ptr', 'Potri.016G142500' => 'ptr', 'Pp3c16_10580' => 'ppa', 'Pp3c5_25280' => 'ppa', 'Prupe.1G150000' => 'ppe', 'Prupe.1G150100' => 'ppe', 'Prupe.6G299600' => 'ppe', 'Prupe.8G245000' => 'ppe', 'Psat0s4927g0040' => 'psa', 'Psat1g052080' => 'psa', 'Psat1g183800' => 'psa', 'Psat3g113840' => 'psa', 'Psat3g126120' => 'psa', 'Psat3g126160' => 'psa', 'Psat3g158760' => 'psa', 'Psat3g158840' => 'psa', 'PSO170G2858' => 'pso', 'PSO339G0606' => 'pso', 'PSO384G4709' => 'pso', 'PSO407G0334' => 'pso', 'QL04p040276' => 'qlo', 'QL06p005458' => 'qlo', 'QL06p005472' => 'qlo', 'QL07p030546' => 'qlo', 'QL07p031519' => 'qlo', 'QL09p050949' => 'qlo', 'QL09p050966' => 'qlo', 'QL09p051067' => 'qlo', 'QL12p022706' => 'qlo', 'RcHm_v2.0_Chr2g0119601' => 'rch', 'RcHm_v2.0_Chr3g0459591' => 'rch', 'RcHm_v2.0_Chr4g0418521' => 'rch', 'RcHm_v2.0_Chr4g0418531' => 'rch', 'RcHm_v2.0_Chr4g0418541' => 'rch', 'RcHm_v2.0_Chr6g0291641' => 'rch', 'Rhsim01G0086300' => 'rsi', 'Rhsim01G0276300' => 'rsi', 'Rhsim01G0276500' => 'rsi', 'Rhsim04G0207700' => 'rsi', 'Rhsim05G0234500' => 'rsi', 'Rhsim13G0022400' => 'rsi', 'Sabra02G0167900' => 'sbr', 'Sabra04G0158500' => 'sbr', 'Sabra08G0159800' => 'sbr', 'Sabra10G0011500' => 'sbr', 'Sabra14G0104400' => 'sbr', 'SalBow2G2440' => 'sbo', 'SalBow4G2265' => 'sbo', 'Sc02g0000060' => 'sci', 'Sc05g0005020' => 'sci', 'Sc13g0003890' => 'sci', 'Sed0014865' => 'sed', 'Sed0017224' => 'sed', 'Sed0026391' => 'sed', 'SEGI_00063' => 'sgi', 'SEGI_10967' => 'sgi', 'SEGI_17510' => 'sgi', 'SEGI_24396' => 'sgi', 'SEGI_39719' => 'sgi', 'SEGI_41392' => 'sgi', 'SGA_v2.0_scaffold11G05794' => 'sas', 'SGA_v2.0_scaffold142G35607' => 'sas', 'SGA_v2.0_scaffold1G00447' => 'sas', 'SHI15388' => 'shi', 'SHI15394' => 'shi', 'SHI15396' => 'shi', 'SHI15399' => 'shi', 'SMO343G0151' => 'smo', 'SMO367G1118' => 'smo', 'Solyc01g080200.3' => 'sly', 'Solyc06g008960.3' => 'sly', 'Solyc09g064780.3' => 'sly', 'Sopen01g031980' => 'spe', 'Sopen06g003710' => 'spe', 'Sopen09g026460' => 'spe', 'Sp3g21240' => 'spa', 'Sp4g30030' => 'spa', 'TAR365G0022' => 'tar', 'TAR365G1023' => 'tar', 'TAR365G1253' => 'tar', 'TAR623G0078' => 'tar', 'TAR623G1721' => 'tar', 'TAR633G0959' => 'tar', 'THA.LOC104802225' => 'tha', 'THA.LOC104804769' => 'tha', 'THA.LOC104808660' => 'tha', 'THA.LOC104812792' => 'tha', 'Thecc.01G284000' => 'tca', 'Thecc.04G220600' => 'tca', 'Thecc.05G268900' => 'tca', 'Thecc.08G171100' => 'tca', 'Thhalv10001284m.g' => 'esa', 'Thhalv10019912m.g' => 'esa', 'TPR.G14189' => 'tpr', 'TPR.G18110' => 'tpr', 'TPR.G18130' => 'tpr', 'TPR.G18131' => 'tpr', 'TPR.G18140' => 'tpr', 'TPR.G24282' => 'tpr', 'TPR.G25221' => 'tpr', 'TPR.G29267' => 'tpr', 'TPR.G35315' => 'tpr', 'TPR.G36173' => 'tpr', 'TWI09G0794' => 'twi', 'TWI59G1348' => 'twi', 'TWI74G0430' => 'twi', 'unitig_26.g8940' => 'ugi', 'unitig_749.g13744' => 'ugi', 'unitig_749.g13745' => 'ugi', 'vmacro08269' => 'vma', 'vmacro14937' => 'vma', 'vmacro20401' => 'vma', 'VMungo0464G1349' => 'vmu', 'VMungo0540G0289' => 'vmu', 'VMungo1215G1590' => 'vmu', 'VMungo1309G0221' => 'vmu', 'VMungo1309G2815' => 'vmu', 'VMungo1383G0239' => 'vmu', 'VMungo1383G2910' => 'vmu', 'Zm00001eb095270' => 'zma', 'Zm00001eb095280' => 'zma', 'Zm00001eb111630' => 'zma', 'Zm00001eb237080' => 'zma', 'Zm00001eb273740' => 'zma', 'Zm00001eb285040' => 'zma', 'Zm00001eb330790' => 'zma', 'Zm00001eb337380' => 'zma' ) $gf_id = 'HOM05D001484' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001484' ) $data_identifier = 'HOM05D001484' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 2, 'aly' => (int) 2, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 22, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 7, 'hma' => (int) 2, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 7, 'mtr' => (int) 10, 'cme' => (int) 2, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 4, 'ppa' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 4, 'qlo' => (int) 9, 'rch' => (int) 6, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 10, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 7, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb337380' $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' => 'HOM05D001484', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p31500' => 'bna', 'A05p00020' => 'bna', 'A07p08820' => 'bna', 'Aa31LG4G3300' => 'aar', 'Aa31LG8G10030' => 'aar', 'Actinidia00731' => 'ach', 'Actinidia11473' => 'ach', 'Actinidia23469' => 'ach', 'Actinidia24318' => 'ach', 'Actinidia40196' => 'ach', 'Actinidia40197' => 'ach', 'Actinidia40198' => 'ach', 'Ah.08g212990' => 'amhyb', 'Ah.15g091720' => 'amhyb', 'AL3G38260' => 'aly', 'AL4G47710' => 'aly', 'Aqoxy2G00671' => 'aox', 'Aqoxy2G03236' => 'aox', 'arahy.Tifrunner.gnm1.ann1.05IDCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KR684' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATY3SJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK6QJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6APGL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IDT7Z9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM073U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ0R87' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LE7RV4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT4QRX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V5ENPK' => 'arhy', 'AT2G48110' => 'ath', 'AT3G23590' => 'ath', 'ATR0626G186' => 'atr', 'ATR1127G141' => 'atr', 'Atru.chr4.2583' => 'acertr', 'Atru.chr5.1358' => 'acertr', 'Atru.chr5.1359' => 'acertr', 'Atru.chr8.46' => 'acertr', 'AUR62002640' => 'cqu', 'AUR62030055' => 'cqu', 'AUR62033713' => 'cqu', 'AUR62033714' => 'cqu', 'AUR62036795' => 'cqu', 'AUR62039891' => 'cqu', 'BcaB02g08737' => 'bca', 'BcaB04g20441' => 'bca', 'BcaB06g26509' => 'bca', 'BcaB06g26510' => 'bca', 'BcaB06g26511' => 'bca', 'BcaB06g26512' => 'bca', 'BcaB06g26513' => 'bca', 'BcaC02g12564' => 'bca', 'BcaC02g12565' => 'bca', 'BcaC02g12794' => 'bca', 'BcaC02g12795' => 'bca', 'BcaC02g12796' => 'bca', 'BcaC06g35541' => 'bca', 'BNapus_Darmor_BZH_scaffold_188p00080' => 'bna', 'BNapus_Darmor_BZH_scaffold_188p00090' => 'bna', 'BolC1t03972H' => 'bol', 'BolC1t03973H' => 'bol', 'BolC4t21680H' => 'bol', 'BolC7t41863H' => 'bol', 'BolSC55t61227H' => 'bol', 'BolSC55t61228H' => 'bol', 'BraA01t03278Z' => 'bra', 'BraA05t18998Z' => 'bra', 'BraA07t28673Z' => 'bra', 'C01p40150' => 'bna', 'C05p12370' => 'bna', 'C07p13680' => 'bna', 'CAN.G1006.16' => 'can', 'CAN.G1006.17' => 'can', 'CAN.G1170.2' => 'can', 'CAN.G962.7' => 'can', 'CANSAT25G2179' => 'cansat', 'CANSAT78G1573' => 'cansat', 'CARHR099510' => 'chi', 'CARHR143510' => 'chi', 'Carub.0003s2380' => 'cru', 'Carub.0004s3082' => 'cru', 'Ca_00614_v3' => 'car', 'Ca_07801_v3' => 'car', 'Ca_08567_v3' => 'car', 'Ca_09571_v3' => 'car', 'CBR_g19290' => 'cbr', 'Cc01_g19770' => 'ccan', 'Cc03_g03030' => 'ccan', 'CDE07G0968' => 'cde', 'CDE09G1441' => 'cde', 'Cfa006103' => 'cfa', 'Cfa015573' => 'cfa', 'Cfa016988' => 'cfa', 'Ciclev10006738m.g' => 'ccl', 'Ciclev10010920m.g' => 'ccl', 'Ciclev10018517m.g' => 'ccl', 'CiPaw.01G159200' => 'cil', 'CiPaw.02G091000' => 'cil', 'CiPaw.02G091100' => 'cil', 'CiPaw.08G103100' => 'cil', 'CiPaw.09G224900' => 'cil', 'ClCG06G005740' => 'cla', 'ClCG07G000090' => 'cla', 'ClCG07G000100' => 'cla', 'COL.COLO4_09143' => 'col', 'COL.COLO4_25124' => 'col', 'Cpa.g.sc16.34' => 'cpa', 'Cpa.g.sc3504.1' => 'cpa', 'Cpa.g.sc60.37' => 'cpa', 'CsaV3_6G018520' => 'csa', 'CsaV3_6G036860' => 'csa', 'CSS0001072' => 'camsi', 'CSS0020208' => 'camsi', 'CSS0021253' => 'camsi', 'CSS0022190' => 'camsi', 'CSS0036150' => 'camsi', 'CSS0040442' => 'camsi', 'CSS0042300' => 'camsi', 'CSS0045298' => 'camsi', 'DCAR_012449' => 'dca', 'DCAR_018405' => 'dca', 'DCAR_024573' => 'dca', 'DCAR_030591' => 'dca', 'Dinv16926' => 'din', 'Dinv32963' => 'din', 'Dinv38382' => 'din', 'Dinv38383' => 'din', 'Duzib133G0974' => 'dzi', 'Duzib138G1867' => 'dzi', 'Duzib211G0420' => 'dzi', 'Duzib212G0930' => 'dzi', 'ECA234G1645' => 'eca', 'ECA247G3467' => 'eca', 'ECA248G1703' => 'eca', 'EL10Ac3g06327' => 'bvu', 'EL10Ac7g17204' => 'bvu', 'Eucgr.A00855' => 'egr', 'Eucgr.A00858' => 'egr', 'Eucgr.H01520' => 'egr', 'Eucgr.H03604' => 'egr', 'Eucgr.L03465' => 'egr', 'Eucgr.L03466' => 'egr', 'FAN01G0988' => 'fan', 'FAN02G3892' => 'fan', 'FAN05G3381' => 'fan', 'FAN07G0967' => 'fan', 'FAN07G1493' => 'fan', 'FAN08G3125' => 'fan', 'FAN09G0402' => 'fan', 'FAN12G2594' => 'fan', 'FAN12G3879' => 'fan', 'FAN14G1546' => 'fan', 'FAN15G3626' => 'fan', 'FAN17G0588' => 'fan', 'FAN17G0609' => 'fan', 'FAN18G2817' => 'fan', 'FAN19G1305' => 'fan', 'FAN20G1787' => 'fan', 'FAN22G0073' => 'fan', 'FAN22G0352' => 'fan', 'FAN22G0368' => 'fan', 'FAN22G2273' => 'fan', 'FAN24G1998' => 'fan', 'FAN27G1317' => 'fan', 'FvH4_2g23980' => 'fve', 'FvH4_4g14380' => 'fve', 'FvH4_4g14390' => 'fve', 'FvH4_6g09250' => 'fve', 'Glyma.03G151100' => 'gma', 'Glyma.04G122550' => 'gma', 'Glyma.05G001600' => 'gma', 'Glyma.09G270766' => 'gma', 'Glyma.09G270832' => 'gma', 'Glyma.13G209800' => 'gma', 'Glyma.15G102800' => 'gma', 'Glyma.18G218900' => 'gma', 'Glyma.19G001500' => 'gma', 'Glyma.19G153600' => 'gma', 'Gohir.A02G028600' => 'ghi', 'Gohir.A08G045000' => 'ghi', 'Gohir.A11G120500' => 'ghi', 'Gohir.A12G006200' => 'ghi', 'Gohir.A12G006250' => 'ghi', 'Gohir.D02G036300' => 'ghi', 'Gohir.D08G054700' => 'ghi', 'Gohir.D11G125600' => 'ghi', 'Gohir.D12G005700' => 'ghi', 'Gorai.004G055200' => 'gra', 'Gorai.005G040400' => 'gra', 'Gorai.007G134500' => 'gra', 'Gorai.008G005500' => 'gra', 'GSVIVG01011094001' => 'vvi', 'GSVIVG01017879001' => 'vvi', 'GSVIVG01025988001' => 'vvi', 'GSVIVG01029847001' => 'vvi', 'HanXRQChr10g0282901' => 'han', 'HanXRQChr10g0310371' => 'han', 'HanXRQChr10g0315041' => 'han', 'HanXRQChr11g0327651' => 'han', 'HanXRQChr12g0359391' => 'han', 'Haze_00972' => 'cav', 'Haze_00973' => 'cav', 'Haze_00974' => 'cav', 'Haze_04747' => 'cav', 'Haze_04749' => 'cav', 'Haze_04750' => 'cav', 'Haze_21217' => 'cav', 'Hma1.2p1_1037F.1_g250680' => 'hma', 'Hma1.2p1_1644F.1_g295320' => 'hma', 'HPP92_011322' => 'vpl', 'HPP92_011323' => 'vpl', 'HPP92_011324' => 'vpl', 'HPP92_011325' => 'vpl', 'HPP92_011326' => 'vpl', 'Hund12205' => 'sun', 'Hund17957' => 'sun', 'Lalb_Chr06g0176771' => 'lal', 'Lalb_Chr18g0056021' => 'lal', 'Lalb_Chr18g0056031' => 'lal', 'Lalb_Chr18g0056041' => 'lal', 'Lalb_Chr20g0107751' => 'lal', 'Lalb_Chr20g0118371' => 'lal', 'Lj1g0010239' => 'lja', 'Lj1g0017101' => 'lja', 'Lj2A1178G40' => 'lonja', 'Lj2A54G84' => 'lonja', 'Lj2g0015248' => 'lja', 'Lj3A761T51' => 'lonja', 'Lj6g0018116' => 'lja', 'Lsat_1_v5_gn_4_136040' => 'lsa', 'Lsat_1_v5_gn_5_187461' => 'lsa', 'Lsat_1_v5_gn_5_77001' => 'lsa', 'Lsat_1_v5_gn_9_4461' => 'lsa', 'Manes.01G210100' => 'mes', 'Manes.03G185600' => 'mes', 'Manes.05G073300' => 'mes', 'Manes.09G120300' => 'mes', 'Manes.15G022100' => 'mes', 'Mapoly0096s0053' => 'mpo', 'MBI03_g14058_MAGBIO' => 'mbi', 'MBI03_g33876_MAGBIO' => 'mbi', 'MBI03_g36854_MAGBIO' => 'mbi', 'MBI17_g11997_MAGBIO' => 'mbi', 'MD03G1269000' => 'mdo', 'MD04G1179600' => 'mdo', 'MD11G1289800' => 'mdo', 'MD12G1194700' => 'mdo', 'MD13G1182100' => 'mdo', 'MD13G1182200' => 'mdo', 'MD16G1182600' => 'mdo', 'Medtr2g021400' => 'mtr', 'Medtr2g021470' => 'mtr', 'Medtr2g105810' => 'mtr', 'Medtr3g033580' => 'mtr', 'Medtr6g007970' => 'mtr', 'Medtr7g056330' => 'mtr', 'Medtr7g074290' => 'mtr', 'Medtr7g074380' => 'mtr', 'Medtr7g094550' => 'mtr', 'Medtr8g069995' => 'mtr', 'MELO3C014345.2' => 'cme', 'MELO3C021395.2' => 'cme', 'Migut.D00262' => 'egut', 'Migut.G00257' => 'egut', 'MSTRG.21575' => 'ama', 'MSTRG.3985' => 'ama', 'Nitab4.5_0000295g0140' => 'nta', 'Nitab4.5_0000732g0140' => 'nta', 'Nitab4.5_0003162g0020' => 'nta', 'Nitab4.5_0006180g0090' => 'nta', 'Nitab4.5_0006390g0010' => 'nta', 'Nitab4.5_0007392g0040' => 'nta', 'Nn1g02140' => 'nnu', 'Nn4g26168' => 'nnu', 'Nn5g26754' => 'nnu', 'Oeu001433.1' => 'oeu', 'Oeu010299.2' => 'oeu', 'Oeu011171.1' => 'oeu', 'Oeu037675.1' => 'oeu', 'Oeu038359.1' => 'oeu', 'Oeu063834.1' => 'oeu', 'Oeu063835.1' => 'oeu', 'Os05g0312000' => 'osa', 'Os07g0211101' => 'osa', 'Os07g0211200' => 'osa', 'Os07g0681500' => 'osa', 'Peaxi162Scf00095g01015' => 'pax', 'Peaxi162Scf00104g00329' => 'pax', 'Peaxi162Scf00161g00137' => 'pax', 'PGR004G1665' => 'pgr', 'PGR031G2937' => 'pgr', 'PGR119G2145' => 'pgr', 'PGSC0003DMG400004351' => 'stu', 'PGSC0003DMG400014625' => 'stu', 'PGSC0003DMG401000943' => 'stu', 'Phvul.001G148600' => 'pvu', 'Phvul.004G001700' => 'pvu', 'Phvul.006G154900' => 'pvu', 'Phvul.008G078200' => 'pvu', 'Phvul.011G136500' => 'pvu', 'Potri.002G215600' => 'ptr', 'Potri.008G201600' => 'ptr', 'Potri.014G138400' => 'ptr', 'Potri.016G142500' => 'ptr', 'Pp3c16_10580' => 'ppa', 'Pp3c5_25280' => 'ppa', 'Prupe.1G150000' => 'ppe', 'Prupe.1G150100' => 'ppe', 'Prupe.6G299600' => 'ppe', 'Prupe.8G245000' => 'ppe', 'Psat0s4927g0040' => 'psa', 'Psat1g052080' => 'psa', 'Psat1g183800' => 'psa', 'Psat3g113840' => 'psa', 'Psat3g126120' => 'psa', 'Psat3g126160' => 'psa', 'Psat3g158760' => 'psa', 'Psat3g158840' => 'psa', 'PSO170G2858' => 'pso', 'PSO339G0606' => 'pso', 'PSO384G4709' => 'pso', 'PSO407G0334' => 'pso', 'QL04p040276' => 'qlo', 'QL06p005458' => 'qlo', 'QL06p005472' => 'qlo', 'QL07p030546' => 'qlo', 'QL07p031519' => 'qlo', 'QL09p050949' => 'qlo', 'QL09p050966' => 'qlo', 'QL09p051067' => 'qlo', 'QL12p022706' => 'qlo', 'RcHm_v2.0_Chr2g0119601' => 'rch', 'RcHm_v2.0_Chr3g0459591' => 'rch', 'RcHm_v2.0_Chr4g0418521' => 'rch', 'RcHm_v2.0_Chr4g0418531' => 'rch', 'RcHm_v2.0_Chr4g0418541' => 'rch', 'RcHm_v2.0_Chr6g0291641' => 'rch', 'Rhsim01G0086300' => 'rsi', 'Rhsim01G0276300' => 'rsi', 'Rhsim01G0276500' => 'rsi', 'Rhsim04G0207700' => 'rsi', 'Rhsim05G0234500' => 'rsi', 'Rhsim13G0022400' => 'rsi', 'Sabra02G0167900' => 'sbr', 'Sabra04G0158500' => 'sbr', 'Sabra08G0159800' => 'sbr', 'Sabra10G0011500' => 'sbr', 'Sabra14G0104400' => 'sbr', 'SalBow2G2440' => 'sbo', 'SalBow4G2265' => 'sbo', 'Sc02g0000060' => 'sci', 'Sc05g0005020' => 'sci', 'Sc13g0003890' => 'sci', 'Sed0014865' => 'sed', 'Sed0017224' => 'sed', 'Sed0026391' => 'sed', 'SEGI_00063' => 'sgi', 'SEGI_10967' => 'sgi', 'SEGI_17510' => 'sgi', 'SEGI_24396' => 'sgi', 'SEGI_39719' => 'sgi', 'SEGI_41392' => 'sgi', 'SGA_v2.0_scaffold11G05794' => 'sas', 'SGA_v2.0_scaffold142G35607' => 'sas', 'SGA_v2.0_scaffold1G00447' => 'sas', 'SHI15388' => 'shi', 'SHI15394' => 'shi', 'SHI15396' => 'shi', 'SHI15399' => 'shi', 'SMO343G0151' => 'smo', 'SMO367G1118' => 'smo', 'Solyc01g080200.3' => 'sly', 'Solyc06g008960.3' => 'sly', 'Solyc09g064780.3' => 'sly', 'Sopen01g031980' => 'spe', 'Sopen06g003710' => 'spe', 'Sopen09g026460' => 'spe', 'Sp3g21240' => 'spa', 'Sp4g30030' => 'spa', 'TAR365G0022' => 'tar', 'TAR365G1023' => 'tar', 'TAR365G1253' => 'tar', 'TAR623G0078' => 'tar', 'TAR623G1721' => 'tar', 'TAR633G0959' => 'tar', 'THA.LOC104802225' => 'tha', 'THA.LOC104804769' => 'tha', 'THA.LOC104808660' => 'tha', 'THA.LOC104812792' => 'tha', 'Thecc.01G284000' => 'tca', 'Thecc.04G220600' => 'tca', 'Thecc.05G268900' => 'tca', 'Thecc.08G171100' => 'tca', 'Thhalv10001284m.g' => 'esa', 'Thhalv10019912m.g' => 'esa', 'TPR.G14189' => 'tpr', 'TPR.G18110' => 'tpr', 'TPR.G18130' => 'tpr', 'TPR.G18131' => 'tpr', 'TPR.G18140' => 'tpr', 'TPR.G24282' => 'tpr', 'TPR.G25221' => 'tpr', 'TPR.G29267' => 'tpr', 'TPR.G35315' => 'tpr', 'TPR.G36173' => 'tpr', 'TWI09G0794' => 'twi', 'TWI59G1348' => 'twi', 'TWI74G0430' => 'twi', 'unitig_26.g8940' => 'ugi', 'unitig_749.g13744' => 'ugi', 'unitig_749.g13745' => 'ugi', 'vmacro08269' => 'vma', 'vmacro14937' => 'vma', 'vmacro20401' => 'vma', 'VMungo0464G1349' => 'vmu', 'VMungo0540G0289' => 'vmu', 'VMungo1215G1590' => 'vmu', 'VMungo1309G0221' => 'vmu', 'VMungo1309G2815' => 'vmu', 'VMungo1383G0239' => 'vmu', 'VMungo1383G2910' => 'vmu', 'Zm00001eb095270' => 'zma', 'Zm00001eb095280' => 'zma', 'Zm00001eb111630' => 'zma', 'Zm00001eb237080' => 'zma', 'Zm00001eb273740' => 'zma', 'Zm00001eb285040' => 'zma', 'Zm00001eb330790' => 'zma', 'Zm00001eb337380' => 'zma' ), 'gf_id' => 'HOM05D001484', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001484' ), 'data_identifier' => 'HOM05D001484', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001484', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p31500' => 'bna', 'A05p00020' => 'bna', 'A07p08820' => 'bna', 'Aa31LG4G3300' => 'aar', 'Aa31LG8G10030' => 'aar', 'Actinidia00731' => 'ach', 'Actinidia11473' => 'ach', 'Actinidia23469' => 'ach', 'Actinidia24318' => 'ach', 'Actinidia40196' => 'ach', 'Actinidia40197' => 'ach', 'Actinidia40198' => 'ach', 'Ah.08g212990' => 'amhyb', 'Ah.15g091720' => 'amhyb', 'AL3G38260' => 'aly', 'AL4G47710' => 'aly', 'Aqoxy2G00671' => 'aox', 'Aqoxy2G03236' => 'aox', 'arahy.Tifrunner.gnm1.ann1.05IDCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KR684' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATY3SJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK6QJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6APGL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IDT7Z9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM073U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ0R87' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LE7RV4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT4QRX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V5ENPK' => 'arhy', 'AT2G48110' => 'ath', 'AT3G23590' => 'ath', 'ATR0626G186' => 'atr', 'ATR1127G141' => 'atr', 'Atru.chr4.2583' => 'acertr', 'Atru.chr5.1358' => 'acertr', 'Atru.chr5.1359' => 'acertr', 'Atru.chr8.46' => 'acertr', 'AUR62002640' => 'cqu', 'AUR62030055' => 'cqu', 'AUR62033713' => 'cqu', 'AUR62033714' => 'cqu', 'AUR62036795' => 'cqu', 'AUR62039891' => 'cqu', 'BcaB02g08737' => 'bca', 'BcaB04g20441' => 'bca', 'BcaB06g26509' => 'bca', 'BcaB06g26510' => 'bca', 'BcaB06g26511' => 'bca', 'BcaB06g26512' => 'bca', 'BcaB06g26513' => 'bca', 'BcaC02g12564' => 'bca', 'BcaC02g12565' => 'bca', 'BcaC02g12794' => 'bca', 'BcaC02g12795' => 'bca', 'BcaC02g12796' => 'bca', 'BcaC06g35541' => 'bca', 'BNapus_Darmor_BZH_scaffold_188p00080' => 'bna', 'BNapus_Darmor_BZH_scaffold_188p00090' => 'bna', 'BolC1t03972H' => 'bol', 'BolC1t03973H' => 'bol', 'BolC4t21680H' => 'bol', 'BolC7t41863H' => 'bol', 'BolSC55t61227H' => 'bol', 'BolSC55t61228H' => 'bol', 'BraA01t03278Z' => 'bra', 'BraA05t18998Z' => 'bra', 'BraA07t28673Z' => 'bra', 'C01p40150' => 'bna', 'C05p12370' => 'bna', 'C07p13680' => 'bna', 'CAN.G1006.16' => 'can', 'CAN.G1006.17' => 'can', 'CAN.G1170.2' => 'can', 'CAN.G962.7' => 'can', 'CANSAT25G2179' => 'cansat', 'CANSAT78G1573' => 'cansat', 'CARHR099510' => 'chi', 'CARHR143510' => 'chi', 'Carub.0003s2380' => 'cru', 'Carub.0004s3082' => 'cru', 'Ca_00614_v3' => 'car', 'Ca_07801_v3' => 'car', 'Ca_08567_v3' => 'car', 'Ca_09571_v3' => 'car', 'CBR_g19290' => 'cbr', 'Cc01_g19770' => 'ccan', 'Cc03_g03030' => 'ccan', 'CDE07G0968' => 'cde', 'CDE09G1441' => 'cde', 'Cfa006103' => 'cfa', 'Cfa015573' => 'cfa', 'Cfa016988' => 'cfa', 'Ciclev10006738m.g' => 'ccl', 'Ciclev10010920m.g' => 'ccl', 'Ciclev10018517m.g' => 'ccl', 'CiPaw.01G159200' => 'cil', 'CiPaw.02G091000' => 'cil', 'CiPaw.02G091100' => 'cil', 'CiPaw.08G103100' => 'cil', 'CiPaw.09G224900' => 'cil', 'ClCG06G005740' => 'cla', 'ClCG07G000090' => 'cla', 'ClCG07G000100' => 'cla', 'COL.COLO4_09143' => 'col', 'COL.COLO4_25124' => 'col', 'Cpa.g.sc16.34' => 'cpa', 'Cpa.g.sc3504.1' => 'cpa', 'Cpa.g.sc60.37' => 'cpa', 'CsaV3_6G018520' => 'csa', 'CsaV3_6G036860' => 'csa', 'CSS0001072' => 'camsi', 'CSS0020208' => 'camsi', 'CSS0021253' => 'camsi', 'CSS0022190' => 'camsi', 'CSS0036150' => 'camsi', 'CSS0040442' => 'camsi', 'CSS0042300' => 'camsi', 'CSS0045298' => 'camsi', 'DCAR_012449' => 'dca', 'DCAR_018405' => 'dca', 'DCAR_024573' => 'dca', 'DCAR_030591' => 'dca', 'Dinv16926' => 'din', 'Dinv32963' => 'din', 'Dinv38382' => 'din', 'Dinv38383' => 'din', 'Duzib133G0974' => 'dzi', 'Duzib138G1867' => 'dzi', 'Duzib211G0420' => 'dzi', 'Duzib212G0930' => 'dzi', 'ECA234G1645' => 'eca', 'ECA247G3467' => 'eca', 'ECA248G1703' => 'eca', 'EL10Ac3g06327' => 'bvu', 'EL10Ac7g17204' => 'bvu', 'Eucgr.A00855' => 'egr', 'Eucgr.A00858' => 'egr', 'Eucgr.H01520' => 'egr', 'Eucgr.H03604' => 'egr', 'Eucgr.L03465' => 'egr', 'Eucgr.L03466' => 'egr', 'FAN01G0988' => 'fan', 'FAN02G3892' => 'fan', 'FAN05G3381' => 'fan', 'FAN07G0967' => 'fan', 'FAN07G1493' => 'fan', 'FAN08G3125' => 'fan', 'FAN09G0402' => 'fan', 'FAN12G2594' => 'fan', 'FAN12G3879' => 'fan', 'FAN14G1546' => 'fan', 'FAN15G3626' => 'fan', 'FAN17G0588' => 'fan', 'FAN17G0609' => 'fan', 'FAN18G2817' => 'fan', 'FAN19G1305' => 'fan', 'FAN20G1787' => 'fan', 'FAN22G0073' => 'fan', 'FAN22G0352' => 'fan', 'FAN22G0368' => 'fan', 'FAN22G2273' => 'fan', 'FAN24G1998' => 'fan', 'FAN27G1317' => 'fan', 'FvH4_2g23980' => 'fve', 'FvH4_4g14380' => 'fve', 'FvH4_4g14390' => 'fve', 'FvH4_6g09250' => 'fve', 'Glyma.03G151100' => 'gma', 'Glyma.04G122550' => 'gma', 'Glyma.05G001600' => 'gma', 'Glyma.09G270766' => 'gma', 'Glyma.09G270832' => 'gma', 'Glyma.13G209800' => 'gma', 'Glyma.15G102800' => 'gma', 'Glyma.18G218900' => 'gma', 'Glyma.19G001500' => 'gma', 'Glyma.19G153600' => 'gma', 'Gohir.A02G028600' => 'ghi', 'Gohir.A08G045000' => 'ghi', 'Gohir.A11G120500' => 'ghi', 'Gohir.A12G006200' => 'ghi', 'Gohir.A12G006250' => 'ghi', 'Gohir.D02G036300' => 'ghi', 'Gohir.D08G054700' => 'ghi', 'Gohir.D11G125600' => 'ghi', 'Gohir.D12G005700' => 'ghi', 'Gorai.004G055200' => 'gra', 'Gorai.005G040400' => 'gra', 'Gorai.007G134500' => 'gra', 'Gorai.008G005500' => 'gra', 'GSVIVG01011094001' => 'vvi', 'GSVIVG01017879001' => 'vvi', 'GSVIVG01025988001' => 'vvi', 'GSVIVG01029847001' => 'vvi', 'HanXRQChr10g0282901' => 'han', 'HanXRQChr10g0310371' => 'han', 'HanXRQChr10g0315041' => 'han', 'HanXRQChr11g0327651' => 'han', 'HanXRQChr12g0359391' => 'han', 'Haze_00972' => 'cav', 'Haze_00973' => 'cav', 'Haze_00974' => 'cav', 'Haze_04747' => 'cav', 'Haze_04749' => 'cav', 'Haze_04750' => 'cav', 'Haze_21217' => 'cav', 'Hma1.2p1_1037F.1_g250680' => 'hma', 'Hma1.2p1_1644F.1_g295320' => 'hma', 'HPP92_011322' => 'vpl', 'HPP92_011323' => 'vpl', 'HPP92_011324' => 'vpl', 'HPP92_011325' => 'vpl', 'HPP92_011326' => 'vpl', 'Hund12205' => 'sun', 'Hund17957' => 'sun', 'Lalb_Chr06g0176771' => 'lal', 'Lalb_Chr18g0056021' => 'lal', 'Lalb_Chr18g0056031' => 'lal', 'Lalb_Chr18g0056041' => 'lal', 'Lalb_Chr20g0107751' => 'lal', 'Lalb_Chr20g0118371' => 'lal', 'Lj1g0010239' => 'lja', 'Lj1g0017101' => 'lja', 'Lj2A1178G40' => 'lonja', 'Lj2A54G84' => 'lonja', 'Lj2g0015248' => 'lja', 'Lj3A761T51' => 'lonja', 'Lj6g0018116' => 'lja', 'Lsat_1_v5_gn_4_136040' => 'lsa', 'Lsat_1_v5_gn_5_187461' => 'lsa', 'Lsat_1_v5_gn_5_77001' => 'lsa', 'Lsat_1_v5_gn_9_4461' => 'lsa', 'Manes.01G210100' => 'mes', 'Manes.03G185600' => 'mes', 'Manes.05G073300' => 'mes', 'Manes.09G120300' => 'mes', 'Manes.15G022100' => 'mes', 'Mapoly0096s0053' => 'mpo', 'MBI03_g14058_MAGBIO' => 'mbi', 'MBI03_g33876_MAGBIO' => 'mbi', 'MBI03_g36854_MAGBIO' => 'mbi', 'MBI17_g11997_MAGBIO' => 'mbi', 'MD03G1269000' => 'mdo', 'MD04G1179600' => 'mdo', 'MD11G1289800' => 'mdo', 'MD12G1194700' => 'mdo', 'MD13G1182100' => 'mdo', 'MD13G1182200' => 'mdo', 'MD16G1182600' => 'mdo', 'Medtr2g021400' => 'mtr', 'Medtr2g021470' => 'mtr', 'Medtr2g105810' => 'mtr', 'Medtr3g033580' => 'mtr', 'Medtr6g007970' => 'mtr', 'Medtr7g056330' => 'mtr', 'Medtr7g074290' => 'mtr', 'Medtr7g074380' => 'mtr', 'Medtr7g094550' => 'mtr', 'Medtr8g069995' => 'mtr', 'MELO3C014345.2' => 'cme', 'MELO3C021395.2' => 'cme', 'Migut.D00262' => 'egut', 'Migut.G00257' => 'egut', 'MSTRG.21575' => 'ama', 'MSTRG.3985' => 'ama', 'Nitab4.5_0000295g0140' => 'nta', 'Nitab4.5_0000732g0140' => 'nta', 'Nitab4.5_0003162g0020' => 'nta', 'Nitab4.5_0006180g0090' => 'nta', 'Nitab4.5_0006390g0010' => 'nta', 'Nitab4.5_0007392g0040' => 'nta', 'Nn1g02140' => 'nnu', 'Nn4g26168' => 'nnu', 'Nn5g26754' => 'nnu', 'Oeu001433.1' => 'oeu', 'Oeu010299.2' => 'oeu', 'Oeu011171.1' => 'oeu', 'Oeu037675.1' => 'oeu', 'Oeu038359.1' => 'oeu', 'Oeu063834.1' => 'oeu', 'Oeu063835.1' => 'oeu', 'Os05g0312000' => 'osa', 'Os07g0211101' => 'osa', 'Os07g0211200' => 'osa', 'Os07g0681500' => 'osa', 'Peaxi162Scf00095g01015' => 'pax', 'Peaxi162Scf00104g00329' => 'pax', 'Peaxi162Scf00161g00137' => 'pax', 'PGR004G1665' => 'pgr', 'PGR031G2937' => 'pgr', 'PGR119G2145' => 'pgr', 'PGSC0003DMG400004351' => 'stu', 'PGSC0003DMG400014625' => 'stu', 'PGSC0003DMG401000943' => 'stu', 'Phvul.001G148600' => 'pvu', 'Phvul.004G001700' => 'pvu', 'Phvul.006G154900' => 'pvu', 'Phvul.008G078200' => 'pvu', 'Phvul.011G136500' => 'pvu', 'Potri.002G215600' => 'ptr', 'Potri.008G201600' => 'ptr', 'Potri.014G138400' => 'ptr', 'Potri.016G142500' => 'ptr', 'Pp3c16_10580' => 'ppa', 'Pp3c5_25280' => 'ppa', 'Prupe.1G150000' => 'ppe', 'Prupe.1G150100' => 'ppe', 'Prupe.6G299600' => 'ppe', 'Prupe.8G245000' => 'ppe', 'Psat0s4927g0040' => 'psa', 'Psat1g052080' => 'psa', 'Psat1g183800' => 'psa', 'Psat3g113840' => 'psa', 'Psat3g126120' => 'psa', 'Psat3g126160' => 'psa', 'Psat3g158760' => 'psa', 'Psat3g158840' => 'psa', 'PSO170G2858' => 'pso', 'PSO339G0606' => 'pso', 'PSO384G4709' => 'pso', 'PSO407G0334' => 'pso', 'QL04p040276' => 'qlo', 'QL06p005458' => 'qlo', 'QL06p005472' => 'qlo', 'QL07p030546' => 'qlo', 'QL07p031519' => 'qlo', 'QL09p050949' => 'qlo', 'QL09p050966' => 'qlo', 'QL09p051067' => 'qlo', 'QL12p022706' => 'qlo', 'RcHm_v2.0_Chr2g0119601' => 'rch', 'RcHm_v2.0_Chr3g0459591' => 'rch', 'RcHm_v2.0_Chr4g0418521' => 'rch', 'RcHm_v2.0_Chr4g0418531' => 'rch', 'RcHm_v2.0_Chr4g0418541' => 'rch', 'RcHm_v2.0_Chr6g0291641' => 'rch', 'Rhsim01G0086300' => 'rsi', 'Rhsim01G0276300' => 'rsi', 'Rhsim01G0276500' => 'rsi', 'Rhsim04G0207700' => 'rsi', 'Rhsim05G0234500' => 'rsi', 'Rhsim13G0022400' => 'rsi', 'Sabra02G0167900' => 'sbr', 'Sabra04G0158500' => 'sbr', 'Sabra08G0159800' => 'sbr', 'Sabra10G0011500' => 'sbr', 'Sabra14G0104400' => 'sbr', 'SalBow2G2440' => 'sbo', 'SalBow4G2265' => 'sbo', 'Sc02g0000060' => 'sci', 'Sc05g0005020' => 'sci', 'Sc13g0003890' => 'sci', 'Sed0014865' => 'sed', 'Sed0017224' => 'sed', 'Sed0026391' => 'sed', 'SEGI_00063' => 'sgi', 'SEGI_10967' => 'sgi', 'SEGI_17510' => 'sgi', 'SEGI_24396' => 'sgi', 'SEGI_39719' => 'sgi', 'SEGI_41392' => 'sgi', 'SGA_v2.0_scaffold11G05794' => 'sas', 'SGA_v2.0_scaffold142G35607' => 'sas', 'SGA_v2.0_scaffold1G00447' => 'sas', 'SHI15388' => 'shi', 'SHI15394' => 'shi', 'SHI15396' => 'shi', 'SHI15399' => 'shi', 'SMO343G0151' => 'smo', 'SMO367G1118' => 'smo', 'Solyc01g080200.3' => 'sly', 'Solyc06g008960.3' => 'sly', 'Solyc09g064780.3' => 'sly', 'Sopen01g031980' => 'spe', 'Sopen06g003710' => 'spe', 'Sopen09g026460' => 'spe', 'Sp3g21240' => 'spa', 'Sp4g30030' => 'spa', 'TAR365G0022' => 'tar', 'TAR365G1023' => 'tar', 'TAR365G1253' => 'tar', 'TAR623G0078' => 'tar', 'TAR623G1721' => 'tar', 'TAR633G0959' => 'tar', 'THA.LOC104802225' => 'tha', 'THA.LOC104804769' => 'tha', 'THA.LOC104808660' => 'tha', 'THA.LOC104812792' => 'tha', 'Thecc.01G284000' => 'tca', 'Thecc.04G220600' => 'tca', 'Thecc.05G268900' => 'tca', 'Thecc.08G171100' => 'tca', 'Thhalv10001284m.g' => 'esa', 'Thhalv10019912m.g' => 'esa', 'TPR.G14189' => 'tpr', 'TPR.G18110' => 'tpr', 'TPR.G18130' => 'tpr', 'TPR.G18131' => 'tpr', 'TPR.G18140' => 'tpr', 'TPR.G24282' => 'tpr', 'TPR.G25221' => 'tpr', 'TPR.G29267' => 'tpr', 'TPR.G35315' => 'tpr', 'TPR.G36173' => 'tpr', 'TWI09G0794' => 'twi', 'TWI59G1348' => 'twi', 'TWI74G0430' => 'twi', 'unitig_26.g8940' => 'ugi', 'unitig_749.g13744' => 'ugi', 'unitig_749.g13745' => 'ugi', 'vmacro08269' => 'vma', 'vmacro14937' => 'vma', 'vmacro20401' => 'vma', 'VMungo0464G1349' => 'vmu', 'VMungo0540G0289' => 'vmu', 'VMungo1215G1590' => 'vmu', 'VMungo1309G0221' => 'vmu', 'VMungo1309G2815' => 'vmu', 'VMungo1383G0239' => 'vmu', 'VMungo1383G2910' => 'vmu', 'Zm00001eb095270' => 'zma', 'Zm00001eb095280' => 'zma', 'Zm00001eb111630' => 'zma', 'Zm00001eb237080' => 'zma', 'Zm00001eb273740' => 'zma', 'Zm00001eb285040' => 'zma', 'Zm00001eb330790' => 'zma', 'Zm00001eb337380' => 'zma' ) $gf_id = 'HOM05D001484' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001484' ) $data_identifier = 'HOM05D001484' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 2, 'aly' => (int) 2, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 22, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 7, 'hma' => (int) 2, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 7, 'mtr' => (int) 10, 'cme' => (int) 2, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 4, 'ppa' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 4, 'qlo' => (int) 9, 'rch' => (int) 6, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 10, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 7, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb337380' $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' => 'HOM05D001484', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p31500' => 'bna', 'A05p00020' => 'bna', 'A07p08820' => 'bna', 'Aa31LG4G3300' => 'aar', 'Aa31LG8G10030' => 'aar', 'Actinidia00731' => 'ach', 'Actinidia11473' => 'ach', 'Actinidia23469' => 'ach', 'Actinidia24318' => 'ach', 'Actinidia40196' => 'ach', 'Actinidia40197' => 'ach', 'Actinidia40198' => 'ach', 'Ah.08g212990' => 'amhyb', 'Ah.15g091720' => 'amhyb', 'AL3G38260' => 'aly', 'AL4G47710' => 'aly', 'Aqoxy2G00671' => 'aox', 'Aqoxy2G03236' => 'aox', 'arahy.Tifrunner.gnm1.ann1.05IDCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KR684' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATY3SJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK6QJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6APGL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IDT7Z9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM073U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ0R87' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LE7RV4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT4QRX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V5ENPK' => 'arhy', 'AT2G48110' => 'ath', 'AT3G23590' => 'ath', 'ATR0626G186' => 'atr', 'ATR1127G141' => 'atr', 'Atru.chr4.2583' => 'acertr', 'Atru.chr5.1358' => 'acertr', 'Atru.chr5.1359' => 'acertr', 'Atru.chr8.46' => 'acertr', 'AUR62002640' => 'cqu', 'AUR62030055' => 'cqu', 'AUR62033713' => 'cqu', 'AUR62033714' => 'cqu', 'AUR62036795' => 'cqu', 'AUR62039891' => 'cqu', 'BcaB02g08737' => 'bca', 'BcaB04g20441' => 'bca', 'BcaB06g26509' => 'bca', 'BcaB06g26510' => 'bca', 'BcaB06g26511' => 'bca', 'BcaB06g26512' => 'bca', 'BcaB06g26513' => 'bca', 'BcaC02g12564' => 'bca', 'BcaC02g12565' => 'bca', 'BcaC02g12794' => 'bca', 'BcaC02g12795' => 'bca', 'BcaC02g12796' => 'bca', 'BcaC06g35541' => 'bca', 'BNapus_Darmor_BZH_scaffold_188p00080' => 'bna', 'BNapus_Darmor_BZH_scaffold_188p00090' => 'bna', 'BolC1t03972H' => 'bol', 'BolC1t03973H' => 'bol', 'BolC4t21680H' => 'bol', 'BolC7t41863H' => 'bol', 'BolSC55t61227H' => 'bol', 'BolSC55t61228H' => 'bol', 'BraA01t03278Z' => 'bra', 'BraA05t18998Z' => 'bra', 'BraA07t28673Z' => 'bra', 'C01p40150' => 'bna', 'C05p12370' => 'bna', 'C07p13680' => 'bna', 'CAN.G1006.16' => 'can', 'CAN.G1006.17' => 'can', 'CAN.G1170.2' => 'can', 'CAN.G962.7' => 'can', 'CANSAT25G2179' => 'cansat', 'CANSAT78G1573' => 'cansat', 'CARHR099510' => 'chi', 'CARHR143510' => 'chi', 'Carub.0003s2380' => 'cru', 'Carub.0004s3082' => 'cru', 'Ca_00614_v3' => 'car', 'Ca_07801_v3' => 'car', 'Ca_08567_v3' => 'car', 'Ca_09571_v3' => 'car', 'CBR_g19290' => 'cbr', 'Cc01_g19770' => 'ccan', 'Cc03_g03030' => 'ccan', 'CDE07G0968' => 'cde', 'CDE09G1441' => 'cde', 'Cfa006103' => 'cfa', 'Cfa015573' => 'cfa', 'Cfa016988' => 'cfa', 'Ciclev10006738m.g' => 'ccl', 'Ciclev10010920m.g' => 'ccl', 'Ciclev10018517m.g' => 'ccl', 'CiPaw.01G159200' => 'cil', 'CiPaw.02G091000' => 'cil', 'CiPaw.02G091100' => 'cil', 'CiPaw.08G103100' => 'cil', 'CiPaw.09G224900' => 'cil', 'ClCG06G005740' => 'cla', 'ClCG07G000090' => 'cla', 'ClCG07G000100' => 'cla', 'COL.COLO4_09143' => 'col', 'COL.COLO4_25124' => 'col', 'Cpa.g.sc16.34' => 'cpa', 'Cpa.g.sc3504.1' => 'cpa', 'Cpa.g.sc60.37' => 'cpa', 'CsaV3_6G018520' => 'csa', 'CsaV3_6G036860' => 'csa', 'CSS0001072' => 'camsi', 'CSS0020208' => 'camsi', 'CSS0021253' => 'camsi', 'CSS0022190' => 'camsi', 'CSS0036150' => 'camsi', 'CSS0040442' => 'camsi', 'CSS0042300' => 'camsi', 'CSS0045298' => 'camsi', 'DCAR_012449' => 'dca', 'DCAR_018405' => 'dca', 'DCAR_024573' => 'dca', 'DCAR_030591' => 'dca', 'Dinv16926' => 'din', 'Dinv32963' => 'din', 'Dinv38382' => 'din', 'Dinv38383' => 'din', 'Duzib133G0974' => 'dzi', 'Duzib138G1867' => 'dzi', 'Duzib211G0420' => 'dzi', 'Duzib212G0930' => 'dzi', 'ECA234G1645' => 'eca', 'ECA247G3467' => 'eca', 'ECA248G1703' => 'eca', 'EL10Ac3g06327' => 'bvu', 'EL10Ac7g17204' => 'bvu', 'Eucgr.A00855' => 'egr', 'Eucgr.A00858' => 'egr', 'Eucgr.H01520' => 'egr', 'Eucgr.H03604' => 'egr', 'Eucgr.L03465' => 'egr', 'Eucgr.L03466' => 'egr', 'FAN01G0988' => 'fan', 'FAN02G3892' => 'fan', 'FAN05G3381' => 'fan', 'FAN07G0967' => 'fan', 'FAN07G1493' => 'fan', 'FAN08G3125' => 'fan', 'FAN09G0402' => 'fan', 'FAN12G2594' => 'fan', 'FAN12G3879' => 'fan', 'FAN14G1546' => 'fan', 'FAN15G3626' => 'fan', 'FAN17G0588' => 'fan', 'FAN17G0609' => 'fan', 'FAN18G2817' => 'fan', 'FAN19G1305' => 'fan', 'FAN20G1787' => 'fan', 'FAN22G0073' => 'fan', 'FAN22G0352' => 'fan', 'FAN22G0368' => 'fan', 'FAN22G2273' => 'fan', 'FAN24G1998' => 'fan', 'FAN27G1317' => 'fan', 'FvH4_2g23980' => 'fve', 'FvH4_4g14380' => 'fve', 'FvH4_4g14390' => 'fve', 'FvH4_6g09250' => 'fve', 'Glyma.03G151100' => 'gma', 'Glyma.04G122550' => 'gma', 'Glyma.05G001600' => 'gma', 'Glyma.09G270766' => 'gma', 'Glyma.09G270832' => 'gma', 'Glyma.13G209800' => 'gma', 'Glyma.15G102800' => 'gma', 'Glyma.18G218900' => 'gma', 'Glyma.19G001500' => 'gma', 'Glyma.19G153600' => 'gma', 'Gohir.A02G028600' => 'ghi', 'Gohir.A08G045000' => 'ghi', 'Gohir.A11G120500' => 'ghi', 'Gohir.A12G006200' => 'ghi', 'Gohir.A12G006250' => 'ghi', 'Gohir.D02G036300' => 'ghi', 'Gohir.D08G054700' => 'ghi', 'Gohir.D11G125600' => 'ghi', 'Gohir.D12G005700' => 'ghi', 'Gorai.004G055200' => 'gra', 'Gorai.005G040400' => 'gra', 'Gorai.007G134500' => 'gra', 'Gorai.008G005500' => 'gra', 'GSVIVG01011094001' => 'vvi', 'GSVIVG01017879001' => 'vvi', 'GSVIVG01025988001' => 'vvi', 'GSVIVG01029847001' => 'vvi', 'HanXRQChr10g0282901' => 'han', 'HanXRQChr10g0310371' => 'han', 'HanXRQChr10g0315041' => 'han', 'HanXRQChr11g0327651' => 'han', 'HanXRQChr12g0359391' => 'han', 'Haze_00972' => 'cav', 'Haze_00973' => 'cav', 'Haze_00974' => 'cav', 'Haze_04747' => 'cav', 'Haze_04749' => 'cav', 'Haze_04750' => 'cav', 'Haze_21217' => 'cav', 'Hma1.2p1_1037F.1_g250680' => 'hma', 'Hma1.2p1_1644F.1_g295320' => 'hma', 'HPP92_011322' => 'vpl', 'HPP92_011323' => 'vpl', 'HPP92_011324' => 'vpl', 'HPP92_011325' => 'vpl', 'HPP92_011326' => 'vpl', 'Hund12205' => 'sun', 'Hund17957' => 'sun', 'Lalb_Chr06g0176771' => 'lal', 'Lalb_Chr18g0056021' => 'lal', 'Lalb_Chr18g0056031' => 'lal', 'Lalb_Chr18g0056041' => 'lal', 'Lalb_Chr20g0107751' => 'lal', 'Lalb_Chr20g0118371' => 'lal', 'Lj1g0010239' => 'lja', 'Lj1g0017101' => 'lja', 'Lj2A1178G40' => 'lonja', 'Lj2A54G84' => 'lonja', 'Lj2g0015248' => 'lja', 'Lj3A761T51' => 'lonja', 'Lj6g0018116' => 'lja', 'Lsat_1_v5_gn_4_136040' => 'lsa', 'Lsat_1_v5_gn_5_187461' => 'lsa', 'Lsat_1_v5_gn_5_77001' => 'lsa', 'Lsat_1_v5_gn_9_4461' => 'lsa', 'Manes.01G210100' => 'mes', 'Manes.03G185600' => 'mes', 'Manes.05G073300' => 'mes', 'Manes.09G120300' => 'mes', 'Manes.15G022100' => 'mes', 'Mapoly0096s0053' => 'mpo', 'MBI03_g14058_MAGBIO' => 'mbi', 'MBI03_g33876_MAGBIO' => 'mbi', 'MBI03_g36854_MAGBIO' => 'mbi', 'MBI17_g11997_MAGBIO' => 'mbi', 'MD03G1269000' => 'mdo', 'MD04G1179600' => 'mdo', 'MD11G1289800' => 'mdo', 'MD12G1194700' => 'mdo', 'MD13G1182100' => 'mdo', 'MD13G1182200' => 'mdo', 'MD16G1182600' => 'mdo', 'Medtr2g021400' => 'mtr', 'Medtr2g021470' => 'mtr', 'Medtr2g105810' => 'mtr', 'Medtr3g033580' => 'mtr', 'Medtr6g007970' => 'mtr', 'Medtr7g056330' => 'mtr', 'Medtr7g074290' => 'mtr', 'Medtr7g074380' => 'mtr', 'Medtr7g094550' => 'mtr', 'Medtr8g069995' => 'mtr', 'MELO3C014345.2' => 'cme', 'MELO3C021395.2' => 'cme', 'Migut.D00262' => 'egut', 'Migut.G00257' => 'egut', 'MSTRG.21575' => 'ama', 'MSTRG.3985' => 'ama', 'Nitab4.5_0000295g0140' => 'nta', 'Nitab4.5_0000732g0140' => 'nta', 'Nitab4.5_0003162g0020' => 'nta', 'Nitab4.5_0006180g0090' => 'nta', 'Nitab4.5_0006390g0010' => 'nta', 'Nitab4.5_0007392g0040' => 'nta', 'Nn1g02140' => 'nnu', 'Nn4g26168' => 'nnu', 'Nn5g26754' => 'nnu', 'Oeu001433.1' => 'oeu', 'Oeu010299.2' => 'oeu', 'Oeu011171.1' => 'oeu', 'Oeu037675.1' => 'oeu', 'Oeu038359.1' => 'oeu', 'Oeu063834.1' => 'oeu', 'Oeu063835.1' => 'oeu', 'Os05g0312000' => 'osa', 'Os07g0211101' => 'osa', 'Os07g0211200' => 'osa', 'Os07g0681500' => 'osa', 'Peaxi162Scf00095g01015' => 'pax', 'Peaxi162Scf00104g00329' => 'pax', 'Peaxi162Scf00161g00137' => 'pax', 'PGR004G1665' => 'pgr', 'PGR031G2937' => 'pgr', 'PGR119G2145' => 'pgr', 'PGSC0003DMG400004351' => 'stu', 'PGSC0003DMG400014625' => 'stu', 'PGSC0003DMG401000943' => 'stu', 'Phvul.001G148600' => 'pvu', 'Phvul.004G001700' => 'pvu', 'Phvul.006G154900' => 'pvu', 'Phvul.008G078200' => 'pvu', 'Phvul.011G136500' => 'pvu', 'Potri.002G215600' => 'ptr', 'Potri.008G201600' => 'ptr', 'Potri.014G138400' => 'ptr', 'Potri.016G142500' => 'ptr', 'Pp3c16_10580' => 'ppa', 'Pp3c5_25280' => 'ppa', 'Prupe.1G150000' => 'ppe', 'Prupe.1G150100' => 'ppe', 'Prupe.6G299600' => 'ppe', 'Prupe.8G245000' => 'ppe', 'Psat0s4927g0040' => 'psa', 'Psat1g052080' => 'psa', 'Psat1g183800' => 'psa', 'Psat3g113840' => 'psa', 'Psat3g126120' => 'psa', 'Psat3g126160' => 'psa', 'Psat3g158760' => 'psa', 'Psat3g158840' => 'psa', 'PSO170G2858' => 'pso', 'PSO339G0606' => 'pso', 'PSO384G4709' => 'pso', 'PSO407G0334' => 'pso', 'QL04p040276' => 'qlo', 'QL06p005458' => 'qlo', 'QL06p005472' => 'qlo', 'QL07p030546' => 'qlo', 'QL07p031519' => 'qlo', 'QL09p050949' => 'qlo', 'QL09p050966' => 'qlo', 'QL09p051067' => 'qlo', 'QL12p022706' => 'qlo', 'RcHm_v2.0_Chr2g0119601' => 'rch', 'RcHm_v2.0_Chr3g0459591' => 'rch', 'RcHm_v2.0_Chr4g0418521' => 'rch', 'RcHm_v2.0_Chr4g0418531' => 'rch', 'RcHm_v2.0_Chr4g0418541' => 'rch', 'RcHm_v2.0_Chr6g0291641' => 'rch', 'Rhsim01G0086300' => 'rsi', 'Rhsim01G0276300' => 'rsi', 'Rhsim01G0276500' => 'rsi', 'Rhsim04G0207700' => 'rsi', 'Rhsim05G0234500' => 'rsi', 'Rhsim13G0022400' => 'rsi', 'Sabra02G0167900' => 'sbr', 'Sabra04G0158500' => 'sbr', 'Sabra08G0159800' => 'sbr', 'Sabra10G0011500' => 'sbr', 'Sabra14G0104400' => 'sbr', 'SalBow2G2440' => 'sbo', 'SalBow4G2265' => 'sbo', 'Sc02g0000060' => 'sci', 'Sc05g0005020' => 'sci', 'Sc13g0003890' => 'sci', 'Sed0014865' => 'sed', 'Sed0017224' => 'sed', 'Sed0026391' => 'sed', 'SEGI_00063' => 'sgi', 'SEGI_10967' => 'sgi', 'SEGI_17510' => 'sgi', 'SEGI_24396' => 'sgi', 'SEGI_39719' => 'sgi', 'SEGI_41392' => 'sgi', 'SGA_v2.0_scaffold11G05794' => 'sas', 'SGA_v2.0_scaffold142G35607' => 'sas', 'SGA_v2.0_scaffold1G00447' => 'sas', 'SHI15388' => 'shi', 'SHI15394' => 'shi', 'SHI15396' => 'shi', 'SHI15399' => 'shi', 'SMO343G0151' => 'smo', 'SMO367G1118' => 'smo', 'Solyc01g080200.3' => 'sly', 'Solyc06g008960.3' => 'sly', 'Solyc09g064780.3' => 'sly', 'Sopen01g031980' => 'spe', 'Sopen06g003710' => 'spe', 'Sopen09g026460' => 'spe', 'Sp3g21240' => 'spa', 'Sp4g30030' => 'spa', 'TAR365G0022' => 'tar', 'TAR365G1023' => 'tar', 'TAR365G1253' => 'tar', 'TAR623G0078' => 'tar', 'TAR623G1721' => 'tar', 'TAR633G0959' => 'tar', 'THA.LOC104802225' => 'tha', 'THA.LOC104804769' => 'tha', 'THA.LOC104808660' => 'tha', 'THA.LOC104812792' => 'tha', 'Thecc.01G284000' => 'tca', 'Thecc.04G220600' => 'tca', 'Thecc.05G268900' => 'tca', 'Thecc.08G171100' => 'tca', 'Thhalv10001284m.g' => 'esa', 'Thhalv10019912m.g' => 'esa', 'TPR.G14189' => 'tpr', 'TPR.G18110' => 'tpr', 'TPR.G18130' => 'tpr', 'TPR.G18131' => 'tpr', 'TPR.G18140' => 'tpr', 'TPR.G24282' => 'tpr', 'TPR.G25221' => 'tpr', 'TPR.G29267' => 'tpr', 'TPR.G35315' => 'tpr', 'TPR.G36173' => 'tpr', 'TWI09G0794' => 'twi', 'TWI59G1348' => 'twi', 'TWI74G0430' => 'twi', 'unitig_26.g8940' => 'ugi', 'unitig_749.g13744' => 'ugi', 'unitig_749.g13745' => 'ugi', 'vmacro08269' => 'vma', 'vmacro14937' => 'vma', 'vmacro20401' => 'vma', 'VMungo0464G1349' => 'vmu', 'VMungo0540G0289' => 'vmu', 'VMungo1215G1590' => 'vmu', 'VMungo1309G0221' => 'vmu', 'VMungo1309G2815' => 'vmu', 'VMungo1383G0239' => 'vmu', 'VMungo1383G2910' => 'vmu', 'Zm00001eb095270' => 'zma', 'Zm00001eb095280' => 'zma', 'Zm00001eb111630' => 'zma', 'Zm00001eb237080' => 'zma', 'Zm00001eb273740' => 'zma', 'Zm00001eb285040' => 'zma', 'Zm00001eb330790' => 'zma', 'Zm00001eb337380' => 'zma' ), 'gf_id' => 'HOM05D001484', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001484' ), 'data_identifier' => 'HOM05D001484', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001484', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p31500' => 'bna', 'A05p00020' => 'bna', 'A07p08820' => 'bna', 'Aa31LG4G3300' => 'aar', 'Aa31LG8G10030' => 'aar', 'Actinidia00731' => 'ach', 'Actinidia11473' => 'ach', 'Actinidia23469' => 'ach', 'Actinidia24318' => 'ach', 'Actinidia40196' => 'ach', 'Actinidia40197' => 'ach', 'Actinidia40198' => 'ach', 'Ah.08g212990' => 'amhyb', 'Ah.15g091720' => 'amhyb', 'AL3G38260' => 'aly', 'AL4G47710' => 'aly', 'Aqoxy2G00671' => 'aox', 'Aqoxy2G03236' => 'aox', 'arahy.Tifrunner.gnm1.ann1.05IDCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KR684' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATY3SJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK6QJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6APGL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IDT7Z9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM073U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ0R87' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LE7RV4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT4QRX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V5ENPK' => 'arhy', 'AT2G48110' => 'ath', 'AT3G23590' => 'ath', 'ATR0626G186' => 'atr', 'ATR1127G141' => 'atr', 'Atru.chr4.2583' => 'acertr', 'Atru.chr5.1358' => 'acertr', 'Atru.chr5.1359' => 'acertr', 'Atru.chr8.46' => 'acertr', 'AUR62002640' => 'cqu', 'AUR62030055' => 'cqu', 'AUR62033713' => 'cqu', 'AUR62033714' => 'cqu', 'AUR62036795' => 'cqu', 'AUR62039891' => 'cqu', 'BcaB02g08737' => 'bca', 'BcaB04g20441' => 'bca', 'BcaB06g26509' => 'bca', 'BcaB06g26510' => 'bca', 'BcaB06g26511' => 'bca', 'BcaB06g26512' => 'bca', 'BcaB06g26513' => 'bca', 'BcaC02g12564' => 'bca', 'BcaC02g12565' => 'bca', 'BcaC02g12794' => 'bca', 'BcaC02g12795' => 'bca', 'BcaC02g12796' => 'bca', 'BcaC06g35541' => 'bca', 'BNapus_Darmor_BZH_scaffold_188p00080' => 'bna', 'BNapus_Darmor_BZH_scaffold_188p00090' => 'bna', 'BolC1t03972H' => 'bol', 'BolC1t03973H' => 'bol', 'BolC4t21680H' => 'bol', 'BolC7t41863H' => 'bol', 'BolSC55t61227H' => 'bol', 'BolSC55t61228H' => 'bol', 'BraA01t03278Z' => 'bra', 'BraA05t18998Z' => 'bra', 'BraA07t28673Z' => 'bra', 'C01p40150' => 'bna', 'C05p12370' => 'bna', 'C07p13680' => 'bna', 'CAN.G1006.16' => 'can', 'CAN.G1006.17' => 'can', 'CAN.G1170.2' => 'can', 'CAN.G962.7' => 'can', 'CANSAT25G2179' => 'cansat', 'CANSAT78G1573' => 'cansat', 'CARHR099510' => 'chi', 'CARHR143510' => 'chi', 'Carub.0003s2380' => 'cru', 'Carub.0004s3082' => 'cru', 'Ca_00614_v3' => 'car', 'Ca_07801_v3' => 'car', 'Ca_08567_v3' => 'car', 'Ca_09571_v3' => 'car', 'CBR_g19290' => 'cbr', 'Cc01_g19770' => 'ccan', 'Cc03_g03030' => 'ccan', 'CDE07G0968' => 'cde', 'CDE09G1441' => 'cde', 'Cfa006103' => 'cfa', 'Cfa015573' => 'cfa', 'Cfa016988' => 'cfa', 'Ciclev10006738m.g' => 'ccl', 'Ciclev10010920m.g' => 'ccl', 'Ciclev10018517m.g' => 'ccl', 'CiPaw.01G159200' => 'cil', 'CiPaw.02G091000' => 'cil', 'CiPaw.02G091100' => 'cil', 'CiPaw.08G103100' => 'cil', 'CiPaw.09G224900' => 'cil', 'ClCG06G005740' => 'cla', 'ClCG07G000090' => 'cla', 'ClCG07G000100' => 'cla', 'COL.COLO4_09143' => 'col', 'COL.COLO4_25124' => 'col', 'Cpa.g.sc16.34' => 'cpa', 'Cpa.g.sc3504.1' => 'cpa', 'Cpa.g.sc60.37' => 'cpa', 'CsaV3_6G018520' => 'csa', 'CsaV3_6G036860' => 'csa', 'CSS0001072' => 'camsi', 'CSS0020208' => 'camsi', 'CSS0021253' => 'camsi', 'CSS0022190' => 'camsi', 'CSS0036150' => 'camsi', 'CSS0040442' => 'camsi', 'CSS0042300' => 'camsi', 'CSS0045298' => 'camsi', 'DCAR_012449' => 'dca', 'DCAR_018405' => 'dca', 'DCAR_024573' => 'dca', 'DCAR_030591' => 'dca', 'Dinv16926' => 'din', 'Dinv32963' => 'din', 'Dinv38382' => 'din', 'Dinv38383' => 'din', 'Duzib133G0974' => 'dzi', 'Duzib138G1867' => 'dzi', 'Duzib211G0420' => 'dzi', 'Duzib212G0930' => 'dzi', 'ECA234G1645' => 'eca', 'ECA247G3467' => 'eca', 'ECA248G1703' => 'eca', 'EL10Ac3g06327' => 'bvu', 'EL10Ac7g17204' => 'bvu', 'Eucgr.A00855' => 'egr', 'Eucgr.A00858' => 'egr', 'Eucgr.H01520' => 'egr', 'Eucgr.H03604' => 'egr', 'Eucgr.L03465' => 'egr', 'Eucgr.L03466' => 'egr', 'FAN01G0988' => 'fan', 'FAN02G3892' => 'fan', 'FAN05G3381' => 'fan', 'FAN07G0967' => 'fan', 'FAN07G1493' => 'fan', 'FAN08G3125' => 'fan', 'FAN09G0402' => 'fan', 'FAN12G2594' => 'fan', 'FAN12G3879' => 'fan', 'FAN14G1546' => 'fan', 'FAN15G3626' => 'fan', 'FAN17G0588' => 'fan', 'FAN17G0609' => 'fan', 'FAN18G2817' => 'fan', 'FAN19G1305' => 'fan', 'FAN20G1787' => 'fan', 'FAN22G0073' => 'fan', 'FAN22G0352' => 'fan', 'FAN22G0368' => 'fan', 'FAN22G2273' => 'fan', 'FAN24G1998' => 'fan', 'FAN27G1317' => 'fan', 'FvH4_2g23980' => 'fve', 'FvH4_4g14380' => 'fve', 'FvH4_4g14390' => 'fve', 'FvH4_6g09250' => 'fve', 'Glyma.03G151100' => 'gma', 'Glyma.04G122550' => 'gma', 'Glyma.05G001600' => 'gma', 'Glyma.09G270766' => 'gma', 'Glyma.09G270832' => 'gma', 'Glyma.13G209800' => 'gma', 'Glyma.15G102800' => 'gma', 'Glyma.18G218900' => 'gma', 'Glyma.19G001500' => 'gma', 'Glyma.19G153600' => 'gma', 'Gohir.A02G028600' => 'ghi', 'Gohir.A08G045000' => 'ghi', 'Gohir.A11G120500' => 'ghi', 'Gohir.A12G006200' => 'ghi', 'Gohir.A12G006250' => 'ghi', 'Gohir.D02G036300' => 'ghi', 'Gohir.D08G054700' => 'ghi', 'Gohir.D11G125600' => 'ghi', 'Gohir.D12G005700' => 'ghi', 'Gorai.004G055200' => 'gra', 'Gorai.005G040400' => 'gra', 'Gorai.007G134500' => 'gra', 'Gorai.008G005500' => 'gra', 'GSVIVG01011094001' => 'vvi', 'GSVIVG01017879001' => 'vvi', 'GSVIVG01025988001' => 'vvi', 'GSVIVG01029847001' => 'vvi', 'HanXRQChr10g0282901' => 'han', 'HanXRQChr10g0310371' => 'han', 'HanXRQChr10g0315041' => 'han', 'HanXRQChr11g0327651' => 'han', 'HanXRQChr12g0359391' => 'han', 'Haze_00972' => 'cav', 'Haze_00973' => 'cav', 'Haze_00974' => 'cav', 'Haze_04747' => 'cav', 'Haze_04749' => 'cav', 'Haze_04750' => 'cav', 'Haze_21217' => 'cav', 'Hma1.2p1_1037F.1_g250680' => 'hma', 'Hma1.2p1_1644F.1_g295320' => 'hma', 'HPP92_011322' => 'vpl', 'HPP92_011323' => 'vpl', 'HPP92_011324' => 'vpl', 'HPP92_011325' => 'vpl', 'HPP92_011326' => 'vpl', 'Hund12205' => 'sun', 'Hund17957' => 'sun', 'Lalb_Chr06g0176771' => 'lal', 'Lalb_Chr18g0056021' => 'lal', 'Lalb_Chr18g0056031' => 'lal', 'Lalb_Chr18g0056041' => 'lal', 'Lalb_Chr20g0107751' => 'lal', 'Lalb_Chr20g0118371' => 'lal', 'Lj1g0010239' => 'lja', 'Lj1g0017101' => 'lja', 'Lj2A1178G40' => 'lonja', 'Lj2A54G84' => 'lonja', 'Lj2g0015248' => 'lja', 'Lj3A761T51' => 'lonja', 'Lj6g0018116' => 'lja', 'Lsat_1_v5_gn_4_136040' => 'lsa', 'Lsat_1_v5_gn_5_187461' => 'lsa', 'Lsat_1_v5_gn_5_77001' => 'lsa', 'Lsat_1_v5_gn_9_4461' => 'lsa', 'Manes.01G210100' => 'mes', 'Manes.03G185600' => 'mes', 'Manes.05G073300' => 'mes', 'Manes.09G120300' => 'mes', 'Manes.15G022100' => 'mes', 'Mapoly0096s0053' => 'mpo', 'MBI03_g14058_MAGBIO' => 'mbi', 'MBI03_g33876_MAGBIO' => 'mbi', 'MBI03_g36854_MAGBIO' => 'mbi', 'MBI17_g11997_MAGBIO' => 'mbi', 'MD03G1269000' => 'mdo', 'MD04G1179600' => 'mdo', 'MD11G1289800' => 'mdo', 'MD12G1194700' => 'mdo', 'MD13G1182100' => 'mdo', 'MD13G1182200' => 'mdo', 'MD16G1182600' => 'mdo', 'Medtr2g021400' => 'mtr', 'Medtr2g021470' => 'mtr', 'Medtr2g105810' => 'mtr', 'Medtr3g033580' => 'mtr', 'Medtr6g007970' => 'mtr', 'Medtr7g056330' => 'mtr', 'Medtr7g074290' => 'mtr', 'Medtr7g074380' => 'mtr', 'Medtr7g094550' => 'mtr', 'Medtr8g069995' => 'mtr', 'MELO3C014345.2' => 'cme', 'MELO3C021395.2' => 'cme', 'Migut.D00262' => 'egut', 'Migut.G00257' => 'egut', 'MSTRG.21575' => 'ama', 'MSTRG.3985' => 'ama', 'Nitab4.5_0000295g0140' => 'nta', 'Nitab4.5_0000732g0140' => 'nta', 'Nitab4.5_0003162g0020' => 'nta', 'Nitab4.5_0006180g0090' => 'nta', 'Nitab4.5_0006390g0010' => 'nta', 'Nitab4.5_0007392g0040' => 'nta', 'Nn1g02140' => 'nnu', 'Nn4g26168' => 'nnu', 'Nn5g26754' => 'nnu', 'Oeu001433.1' => 'oeu', 'Oeu010299.2' => 'oeu', 'Oeu011171.1' => 'oeu', 'Oeu037675.1' => 'oeu', 'Oeu038359.1' => 'oeu', 'Oeu063834.1' => 'oeu', 'Oeu063835.1' => 'oeu', 'Os05g0312000' => 'osa', 'Os07g0211101' => 'osa', 'Os07g0211200' => 'osa', 'Os07g0681500' => 'osa', 'Peaxi162Scf00095g01015' => 'pax', 'Peaxi162Scf00104g00329' => 'pax', 'Peaxi162Scf00161g00137' => 'pax', 'PGR004G1665' => 'pgr', 'PGR031G2937' => 'pgr', 'PGR119G2145' => 'pgr', 'PGSC0003DMG400004351' => 'stu', 'PGSC0003DMG400014625' => 'stu', 'PGSC0003DMG401000943' => 'stu', 'Phvul.001G148600' => 'pvu', 'Phvul.004G001700' => 'pvu', 'Phvul.006G154900' => 'pvu', 'Phvul.008G078200' => 'pvu', 'Phvul.011G136500' => 'pvu', 'Potri.002G215600' => 'ptr', 'Potri.008G201600' => 'ptr', 'Potri.014G138400' => 'ptr', 'Potri.016G142500' => 'ptr', 'Pp3c16_10580' => 'ppa', 'Pp3c5_25280' => 'ppa', 'Prupe.1G150000' => 'ppe', 'Prupe.1G150100' => 'ppe', 'Prupe.6G299600' => 'ppe', 'Prupe.8G245000' => 'ppe', 'Psat0s4927g0040' => 'psa', 'Psat1g052080' => 'psa', 'Psat1g183800' => 'psa', 'Psat3g113840' => 'psa', 'Psat3g126120' => 'psa', 'Psat3g126160' => 'psa', 'Psat3g158760' => 'psa', 'Psat3g158840' => 'psa', 'PSO170G2858' => 'pso', 'PSO339G0606' => 'pso', 'PSO384G4709' => 'pso', 'PSO407G0334' => 'pso', 'QL04p040276' => 'qlo', 'QL06p005458' => 'qlo', 'QL06p005472' => 'qlo', 'QL07p030546' => 'qlo', 'QL07p031519' => 'qlo', 'QL09p050949' => 'qlo', 'QL09p050966' => 'qlo', 'QL09p051067' => 'qlo', 'QL12p022706' => 'qlo', 'RcHm_v2.0_Chr2g0119601' => 'rch', 'RcHm_v2.0_Chr3g0459591' => 'rch', 'RcHm_v2.0_Chr4g0418521' => 'rch', 'RcHm_v2.0_Chr4g0418531' => 'rch', 'RcHm_v2.0_Chr4g0418541' => 'rch', 'RcHm_v2.0_Chr6g0291641' => 'rch', 'Rhsim01G0086300' => 'rsi', 'Rhsim01G0276300' => 'rsi', 'Rhsim01G0276500' => 'rsi', 'Rhsim04G0207700' => 'rsi', 'Rhsim05G0234500' => 'rsi', 'Rhsim13G0022400' => 'rsi', 'Sabra02G0167900' => 'sbr', 'Sabra04G0158500' => 'sbr', 'Sabra08G0159800' => 'sbr', 'Sabra10G0011500' => 'sbr', 'Sabra14G0104400' => 'sbr', 'SalBow2G2440' => 'sbo', 'SalBow4G2265' => 'sbo', 'Sc02g0000060' => 'sci', 'Sc05g0005020' => 'sci', 'Sc13g0003890' => 'sci', 'Sed0014865' => 'sed', 'Sed0017224' => 'sed', 'Sed0026391' => 'sed', 'SEGI_00063' => 'sgi', 'SEGI_10967' => 'sgi', 'SEGI_17510' => 'sgi', 'SEGI_24396' => 'sgi', 'SEGI_39719' => 'sgi', 'SEGI_41392' => 'sgi', 'SGA_v2.0_scaffold11G05794' => 'sas', 'SGA_v2.0_scaffold142G35607' => 'sas', 'SGA_v2.0_scaffold1G00447' => 'sas', 'SHI15388' => 'shi', 'SHI15394' => 'shi', 'SHI15396' => 'shi', 'SHI15399' => 'shi', 'SMO343G0151' => 'smo', 'SMO367G1118' => 'smo', 'Solyc01g080200.3' => 'sly', 'Solyc06g008960.3' => 'sly', 'Solyc09g064780.3' => 'sly', 'Sopen01g031980' => 'spe', 'Sopen06g003710' => 'spe', 'Sopen09g026460' => 'spe', 'Sp3g21240' => 'spa', 'Sp4g30030' => 'spa', 'TAR365G0022' => 'tar', 'TAR365G1023' => 'tar', 'TAR365G1253' => 'tar', 'TAR623G0078' => 'tar', 'TAR623G1721' => 'tar', 'TAR633G0959' => 'tar', 'THA.LOC104802225' => 'tha', 'THA.LOC104804769' => 'tha', 'THA.LOC104808660' => 'tha', 'THA.LOC104812792' => 'tha', 'Thecc.01G284000' => 'tca', 'Thecc.04G220600' => 'tca', 'Thecc.05G268900' => 'tca', 'Thecc.08G171100' => 'tca', 'Thhalv10001284m.g' => 'esa', 'Thhalv10019912m.g' => 'esa', 'TPR.G14189' => 'tpr', 'TPR.G18110' => 'tpr', 'TPR.G18130' => 'tpr', 'TPR.G18131' => 'tpr', 'TPR.G18140' => 'tpr', 'TPR.G24282' => 'tpr', 'TPR.G25221' => 'tpr', 'TPR.G29267' => 'tpr', 'TPR.G35315' => 'tpr', 'TPR.G36173' => 'tpr', 'TWI09G0794' => 'twi', 'TWI59G1348' => 'twi', 'TWI74G0430' => 'twi', 'unitig_26.g8940' => 'ugi', 'unitig_749.g13744' => 'ugi', 'unitig_749.g13745' => 'ugi', 'vmacro08269' => 'vma', 'vmacro14937' => 'vma', 'vmacro20401' => 'vma', 'VMungo0464G1349' => 'vmu', 'VMungo0540G0289' => 'vmu', 'VMungo1215G1590' => 'vmu', 'VMungo1309G0221' => 'vmu', 'VMungo1309G2815' => 'vmu', 'VMungo1383G0239' => 'vmu', 'VMungo1383G2910' => 'vmu', 'Zm00001eb095270' => 'zma', 'Zm00001eb095280' => 'zma', 'Zm00001eb111630' => 'zma', 'Zm00001eb237080' => 'zma', 'Zm00001eb273740' => 'zma', 'Zm00001eb285040' => 'zma', 'Zm00001eb330790' => 'zma', 'Zm00001eb337380' => 'zma' ) $gf_id = 'HOM05D001484' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001484' ) $data_identifier = 'HOM05D001484' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 2, 'aly' => (int) 2, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 22, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 7, 'hma' => (int) 2, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 7, 'mtr' => (int) 10, 'cme' => (int) 2, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 4, 'ppa' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 4, 'qlo' => (int) 9, 'rch' => (int) 6, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 10, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 7, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb337380' $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' => 'HOM05D001484', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p31500' => 'bna', 'A05p00020' => 'bna', 'A07p08820' => 'bna', 'Aa31LG4G3300' => 'aar', 'Aa31LG8G10030' => 'aar', 'Actinidia00731' => 'ach', 'Actinidia11473' => 'ach', 'Actinidia23469' => 'ach', 'Actinidia24318' => 'ach', 'Actinidia40196' => 'ach', 'Actinidia40197' => 'ach', 'Actinidia40198' => 'ach', 'Ah.08g212990' => 'amhyb', 'Ah.15g091720' => 'amhyb', 'AL3G38260' => 'aly', 'AL4G47710' => 'aly', 'Aqoxy2G00671' => 'aox', 'Aqoxy2G03236' => 'aox', 'arahy.Tifrunner.gnm1.ann1.05IDCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KR684' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATY3SJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK6QJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6APGL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IDT7Z9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM073U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ0R87' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LE7RV4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT4QRX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V5ENPK' => 'arhy', 'AT2G48110' => 'ath', 'AT3G23590' => 'ath', 'ATR0626G186' => 'atr', 'ATR1127G141' => 'atr', 'Atru.chr4.2583' => 'acertr', 'Atru.chr5.1358' => 'acertr', 'Atru.chr5.1359' => 'acertr', 'Atru.chr8.46' => 'acertr', 'AUR62002640' => 'cqu', 'AUR62030055' => 'cqu', 'AUR62033713' => 'cqu', 'AUR62033714' => 'cqu', 'AUR62036795' => 'cqu', 'AUR62039891' => 'cqu', 'BcaB02g08737' => 'bca', 'BcaB04g20441' => 'bca', 'BcaB06g26509' => 'bca', 'BcaB06g26510' => 'bca', 'BcaB06g26511' => 'bca', 'BcaB06g26512' => 'bca', 'BcaB06g26513' => 'bca', 'BcaC02g12564' => 'bca', 'BcaC02g12565' => 'bca', 'BcaC02g12794' => 'bca', 'BcaC02g12795' => 'bca', 'BcaC02g12796' => 'bca', 'BcaC06g35541' => 'bca', 'BNapus_Darmor_BZH_scaffold_188p00080' => 'bna', 'BNapus_Darmor_BZH_scaffold_188p00090' => 'bna', 'BolC1t03972H' => 'bol', 'BolC1t03973H' => 'bol', 'BolC4t21680H' => 'bol', 'BolC7t41863H' => 'bol', 'BolSC55t61227H' => 'bol', 'BolSC55t61228H' => 'bol', 'BraA01t03278Z' => 'bra', 'BraA05t18998Z' => 'bra', 'BraA07t28673Z' => 'bra', 'C01p40150' => 'bna', 'C05p12370' => 'bna', 'C07p13680' => 'bna', 'CAN.G1006.16' => 'can', 'CAN.G1006.17' => 'can', 'CAN.G1170.2' => 'can', 'CAN.G962.7' => 'can', 'CANSAT25G2179' => 'cansat', 'CANSAT78G1573' => 'cansat', 'CARHR099510' => 'chi', 'CARHR143510' => 'chi', 'Carub.0003s2380' => 'cru', 'Carub.0004s3082' => 'cru', 'Ca_00614_v3' => 'car', 'Ca_07801_v3' => 'car', 'Ca_08567_v3' => 'car', 'Ca_09571_v3' => 'car', 'CBR_g19290' => 'cbr', 'Cc01_g19770' => 'ccan', 'Cc03_g03030' => 'ccan', 'CDE07G0968' => 'cde', 'CDE09G1441' => 'cde', 'Cfa006103' => 'cfa', 'Cfa015573' => 'cfa', 'Cfa016988' => 'cfa', 'Ciclev10006738m.g' => 'ccl', 'Ciclev10010920m.g' => 'ccl', 'Ciclev10018517m.g' => 'ccl', 'CiPaw.01G159200' => 'cil', 'CiPaw.02G091000' => 'cil', 'CiPaw.02G091100' => 'cil', 'CiPaw.08G103100' => 'cil', 'CiPaw.09G224900' => 'cil', 'ClCG06G005740' => 'cla', 'ClCG07G000090' => 'cla', 'ClCG07G000100' => 'cla', 'COL.COLO4_09143' => 'col', 'COL.COLO4_25124' => 'col', 'Cpa.g.sc16.34' => 'cpa', 'Cpa.g.sc3504.1' => 'cpa', 'Cpa.g.sc60.37' => 'cpa', 'CsaV3_6G018520' => 'csa', 'CsaV3_6G036860' => 'csa', 'CSS0001072' => 'camsi', 'CSS0020208' => 'camsi', 'CSS0021253' => 'camsi', 'CSS0022190' => 'camsi', 'CSS0036150' => 'camsi', 'CSS0040442' => 'camsi', 'CSS0042300' => 'camsi', 'CSS0045298' => 'camsi', 'DCAR_012449' => 'dca', 'DCAR_018405' => 'dca', 'DCAR_024573' => 'dca', 'DCAR_030591' => 'dca', 'Dinv16926' => 'din', 'Dinv32963' => 'din', 'Dinv38382' => 'din', 'Dinv38383' => 'din', 'Duzib133G0974' => 'dzi', 'Duzib138G1867' => 'dzi', 'Duzib211G0420' => 'dzi', 'Duzib212G0930' => 'dzi', 'ECA234G1645' => 'eca', 'ECA247G3467' => 'eca', 'ECA248G1703' => 'eca', 'EL10Ac3g06327' => 'bvu', 'EL10Ac7g17204' => 'bvu', 'Eucgr.A00855' => 'egr', 'Eucgr.A00858' => 'egr', 'Eucgr.H01520' => 'egr', 'Eucgr.H03604' => 'egr', 'Eucgr.L03465' => 'egr', 'Eucgr.L03466' => 'egr', 'FAN01G0988' => 'fan', 'FAN02G3892' => 'fan', 'FAN05G3381' => 'fan', 'FAN07G0967' => 'fan', 'FAN07G1493' => 'fan', 'FAN08G3125' => 'fan', 'FAN09G0402' => 'fan', 'FAN12G2594' => 'fan', 'FAN12G3879' => 'fan', 'FAN14G1546' => 'fan', 'FAN15G3626' => 'fan', 'FAN17G0588' => 'fan', 'FAN17G0609' => 'fan', 'FAN18G2817' => 'fan', 'FAN19G1305' => 'fan', 'FAN20G1787' => 'fan', 'FAN22G0073' => 'fan', 'FAN22G0352' => 'fan', 'FAN22G0368' => 'fan', 'FAN22G2273' => 'fan', 'FAN24G1998' => 'fan', 'FAN27G1317' => 'fan', 'FvH4_2g23980' => 'fve', 'FvH4_4g14380' => 'fve', 'FvH4_4g14390' => 'fve', 'FvH4_6g09250' => 'fve', 'Glyma.03G151100' => 'gma', 'Glyma.04G122550' => 'gma', 'Glyma.05G001600' => 'gma', 'Glyma.09G270766' => 'gma', 'Glyma.09G270832' => 'gma', 'Glyma.13G209800' => 'gma', 'Glyma.15G102800' => 'gma', 'Glyma.18G218900' => 'gma', 'Glyma.19G001500' => 'gma', 'Glyma.19G153600' => 'gma', 'Gohir.A02G028600' => 'ghi', 'Gohir.A08G045000' => 'ghi', 'Gohir.A11G120500' => 'ghi', 'Gohir.A12G006200' => 'ghi', 'Gohir.A12G006250' => 'ghi', 'Gohir.D02G036300' => 'ghi', 'Gohir.D08G054700' => 'ghi', 'Gohir.D11G125600' => 'ghi', 'Gohir.D12G005700' => 'ghi', 'Gorai.004G055200' => 'gra', 'Gorai.005G040400' => 'gra', 'Gorai.007G134500' => 'gra', 'Gorai.008G005500' => 'gra', 'GSVIVG01011094001' => 'vvi', 'GSVIVG01017879001' => 'vvi', 'GSVIVG01025988001' => 'vvi', 'GSVIVG01029847001' => 'vvi', 'HanXRQChr10g0282901' => 'han', 'HanXRQChr10g0310371' => 'han', 'HanXRQChr10g0315041' => 'han', 'HanXRQChr11g0327651' => 'han', 'HanXRQChr12g0359391' => 'han', 'Haze_00972' => 'cav', 'Haze_00973' => 'cav', 'Haze_00974' => 'cav', 'Haze_04747' => 'cav', 'Haze_04749' => 'cav', 'Haze_04750' => 'cav', 'Haze_21217' => 'cav', 'Hma1.2p1_1037F.1_g250680' => 'hma', 'Hma1.2p1_1644F.1_g295320' => 'hma', 'HPP92_011322' => 'vpl', 'HPP92_011323' => 'vpl', 'HPP92_011324' => 'vpl', 'HPP92_011325' => 'vpl', 'HPP92_011326' => 'vpl', 'Hund12205' => 'sun', 'Hund17957' => 'sun', 'Lalb_Chr06g0176771' => 'lal', 'Lalb_Chr18g0056021' => 'lal', 'Lalb_Chr18g0056031' => 'lal', 'Lalb_Chr18g0056041' => 'lal', 'Lalb_Chr20g0107751' => 'lal', 'Lalb_Chr20g0118371' => 'lal', 'Lj1g0010239' => 'lja', 'Lj1g0017101' => 'lja', 'Lj2A1178G40' => 'lonja', 'Lj2A54G84' => 'lonja', 'Lj2g0015248' => 'lja', 'Lj3A761T51' => 'lonja', 'Lj6g0018116' => 'lja', 'Lsat_1_v5_gn_4_136040' => 'lsa', 'Lsat_1_v5_gn_5_187461' => 'lsa', 'Lsat_1_v5_gn_5_77001' => 'lsa', 'Lsat_1_v5_gn_9_4461' => 'lsa', 'Manes.01G210100' => 'mes', 'Manes.03G185600' => 'mes', 'Manes.05G073300' => 'mes', 'Manes.09G120300' => 'mes', 'Manes.15G022100' => 'mes', 'Mapoly0096s0053' => 'mpo', 'MBI03_g14058_MAGBIO' => 'mbi', 'MBI03_g33876_MAGBIO' => 'mbi', 'MBI03_g36854_MAGBIO' => 'mbi', 'MBI17_g11997_MAGBIO' => 'mbi', 'MD03G1269000' => 'mdo', 'MD04G1179600' => 'mdo', 'MD11G1289800' => 'mdo', 'MD12G1194700' => 'mdo', 'MD13G1182100' => 'mdo', 'MD13G1182200' => 'mdo', 'MD16G1182600' => 'mdo', 'Medtr2g021400' => 'mtr', 'Medtr2g021470' => 'mtr', 'Medtr2g105810' => 'mtr', 'Medtr3g033580' => 'mtr', 'Medtr6g007970' => 'mtr', 'Medtr7g056330' => 'mtr', 'Medtr7g074290' => 'mtr', 'Medtr7g074380' => 'mtr', 'Medtr7g094550' => 'mtr', 'Medtr8g069995' => 'mtr', 'MELO3C014345.2' => 'cme', 'MELO3C021395.2' => 'cme', 'Migut.D00262' => 'egut', 'Migut.G00257' => 'egut', 'MSTRG.21575' => 'ama', 'MSTRG.3985' => 'ama', 'Nitab4.5_0000295g0140' => 'nta', 'Nitab4.5_0000732g0140' => 'nta', 'Nitab4.5_0003162g0020' => 'nta', 'Nitab4.5_0006180g0090' => 'nta', 'Nitab4.5_0006390g0010' => 'nta', 'Nitab4.5_0007392g0040' => 'nta', 'Nn1g02140' => 'nnu', 'Nn4g26168' => 'nnu', 'Nn5g26754' => 'nnu', 'Oeu001433.1' => 'oeu', 'Oeu010299.2' => 'oeu', 'Oeu011171.1' => 'oeu', 'Oeu037675.1' => 'oeu', 'Oeu038359.1' => 'oeu', 'Oeu063834.1' => 'oeu', 'Oeu063835.1' => 'oeu', 'Os05g0312000' => 'osa', 'Os07g0211101' => 'osa', 'Os07g0211200' => 'osa', 'Os07g0681500' => 'osa', 'Peaxi162Scf00095g01015' => 'pax', 'Peaxi162Scf00104g00329' => 'pax', 'Peaxi162Scf00161g00137' => 'pax', 'PGR004G1665' => 'pgr', 'PGR031G2937' => 'pgr', 'PGR119G2145' => 'pgr', 'PGSC0003DMG400004351' => 'stu', 'PGSC0003DMG400014625' => 'stu', 'PGSC0003DMG401000943' => 'stu', 'Phvul.001G148600' => 'pvu', 'Phvul.004G001700' => 'pvu', 'Phvul.006G154900' => 'pvu', 'Phvul.008G078200' => 'pvu', 'Phvul.011G136500' => 'pvu', 'Potri.002G215600' => 'ptr', 'Potri.008G201600' => 'ptr', 'Potri.014G138400' => 'ptr', 'Potri.016G142500' => 'ptr', 'Pp3c16_10580' => 'ppa', 'Pp3c5_25280' => 'ppa', 'Prupe.1G150000' => 'ppe', 'Prupe.1G150100' => 'ppe', 'Prupe.6G299600' => 'ppe', 'Prupe.8G245000' => 'ppe', 'Psat0s4927g0040' => 'psa', 'Psat1g052080' => 'psa', 'Psat1g183800' => 'psa', 'Psat3g113840' => 'psa', 'Psat3g126120' => 'psa', 'Psat3g126160' => 'psa', 'Psat3g158760' => 'psa', 'Psat3g158840' => 'psa', 'PSO170G2858' => 'pso', 'PSO339G0606' => 'pso', 'PSO384G4709' => 'pso', 'PSO407G0334' => 'pso', 'QL04p040276' => 'qlo', 'QL06p005458' => 'qlo', 'QL06p005472' => 'qlo', 'QL07p030546' => 'qlo', 'QL07p031519' => 'qlo', 'QL09p050949' => 'qlo', 'QL09p050966' => 'qlo', 'QL09p051067' => 'qlo', 'QL12p022706' => 'qlo', 'RcHm_v2.0_Chr2g0119601' => 'rch', 'RcHm_v2.0_Chr3g0459591' => 'rch', 'RcHm_v2.0_Chr4g0418521' => 'rch', 'RcHm_v2.0_Chr4g0418531' => 'rch', 'RcHm_v2.0_Chr4g0418541' => 'rch', 'RcHm_v2.0_Chr6g0291641' => 'rch', 'Rhsim01G0086300' => 'rsi', 'Rhsim01G0276300' => 'rsi', 'Rhsim01G0276500' => 'rsi', 'Rhsim04G0207700' => 'rsi', 'Rhsim05G0234500' => 'rsi', 'Rhsim13G0022400' => 'rsi', 'Sabra02G0167900' => 'sbr', 'Sabra04G0158500' => 'sbr', 'Sabra08G0159800' => 'sbr', 'Sabra10G0011500' => 'sbr', 'Sabra14G0104400' => 'sbr', 'SalBow2G2440' => 'sbo', 'SalBow4G2265' => 'sbo', 'Sc02g0000060' => 'sci', 'Sc05g0005020' => 'sci', 'Sc13g0003890' => 'sci', 'Sed0014865' => 'sed', 'Sed0017224' => 'sed', 'Sed0026391' => 'sed', 'SEGI_00063' => 'sgi', 'SEGI_10967' => 'sgi', 'SEGI_17510' => 'sgi', 'SEGI_24396' => 'sgi', 'SEGI_39719' => 'sgi', 'SEGI_41392' => 'sgi', 'SGA_v2.0_scaffold11G05794' => 'sas', 'SGA_v2.0_scaffold142G35607' => 'sas', 'SGA_v2.0_scaffold1G00447' => 'sas', 'SHI15388' => 'shi', 'SHI15394' => 'shi', 'SHI15396' => 'shi', 'SHI15399' => 'shi', 'SMO343G0151' => 'smo', 'SMO367G1118' => 'smo', 'Solyc01g080200.3' => 'sly', 'Solyc06g008960.3' => 'sly', 'Solyc09g064780.3' => 'sly', 'Sopen01g031980' => 'spe', 'Sopen06g003710' => 'spe', 'Sopen09g026460' => 'spe', 'Sp3g21240' => 'spa', 'Sp4g30030' => 'spa', 'TAR365G0022' => 'tar', 'TAR365G1023' => 'tar', 'TAR365G1253' => 'tar', 'TAR623G0078' => 'tar', 'TAR623G1721' => 'tar', 'TAR633G0959' => 'tar', 'THA.LOC104802225' => 'tha', 'THA.LOC104804769' => 'tha', 'THA.LOC104808660' => 'tha', 'THA.LOC104812792' => 'tha', 'Thecc.01G284000' => 'tca', 'Thecc.04G220600' => 'tca', 'Thecc.05G268900' => 'tca', 'Thecc.08G171100' => 'tca', 'Thhalv10001284m.g' => 'esa', 'Thhalv10019912m.g' => 'esa', 'TPR.G14189' => 'tpr', 'TPR.G18110' => 'tpr', 'TPR.G18130' => 'tpr', 'TPR.G18131' => 'tpr', 'TPR.G18140' => 'tpr', 'TPR.G24282' => 'tpr', 'TPR.G25221' => 'tpr', 'TPR.G29267' => 'tpr', 'TPR.G35315' => 'tpr', 'TPR.G36173' => 'tpr', 'TWI09G0794' => 'twi', 'TWI59G1348' => 'twi', 'TWI74G0430' => 'twi', 'unitig_26.g8940' => 'ugi', 'unitig_749.g13744' => 'ugi', 'unitig_749.g13745' => 'ugi', 'vmacro08269' => 'vma', 'vmacro14937' => 'vma', 'vmacro20401' => 'vma', 'VMungo0464G1349' => 'vmu', 'VMungo0540G0289' => 'vmu', 'VMungo1215G1590' => 'vmu', 'VMungo1309G0221' => 'vmu', 'VMungo1309G2815' => 'vmu', 'VMungo1383G0239' => 'vmu', 'VMungo1383G2910' => 'vmu', 'Zm00001eb095270' => 'zma', 'Zm00001eb095280' => 'zma', 'Zm00001eb111630' => 'zma', 'Zm00001eb237080' => 'zma', 'Zm00001eb273740' => 'zma', 'Zm00001eb285040' => 'zma', 'Zm00001eb330790' => 'zma', 'Zm00001eb337380' => 'zma' ), 'gf_id' => 'HOM05D001484', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001484' ), 'data_identifier' => 'HOM05D001484', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001484', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p31500' => 'bna', 'A05p00020' => 'bna', 'A07p08820' => 'bna', 'Aa31LG4G3300' => 'aar', 'Aa31LG8G10030' => 'aar', 'Actinidia00731' => 'ach', 'Actinidia11473' => 'ach', 'Actinidia23469' => 'ach', 'Actinidia24318' => 'ach', 'Actinidia40196' => 'ach', 'Actinidia40197' => 'ach', 'Actinidia40198' => 'ach', 'Ah.08g212990' => 'amhyb', 'Ah.15g091720' => 'amhyb', 'AL3G38260' => 'aly', 'AL4G47710' => 'aly', 'Aqoxy2G00671' => 'aox', 'Aqoxy2G03236' => 'aox', 'arahy.Tifrunner.gnm1.ann1.05IDCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KR684' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATY3SJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK6QJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6APGL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IDT7Z9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM073U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ0R87' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LE7RV4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT4QRX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V5ENPK' => 'arhy', 'AT2G48110' => 'ath', 'AT3G23590' => 'ath', 'ATR0626G186' => 'atr', 'ATR1127G141' => 'atr', 'Atru.chr4.2583' => 'acertr', 'Atru.chr5.1358' => 'acertr', 'Atru.chr5.1359' => 'acertr', 'Atru.chr8.46' => 'acertr', 'AUR62002640' => 'cqu', 'AUR62030055' => 'cqu', 'AUR62033713' => 'cqu', 'AUR62033714' => 'cqu', 'AUR62036795' => 'cqu', 'AUR62039891' => 'cqu', 'BcaB02g08737' => 'bca', 'BcaB04g20441' => 'bca', 'BcaB06g26509' => 'bca', 'BcaB06g26510' => 'bca', 'BcaB06g26511' => 'bca', 'BcaB06g26512' => 'bca', 'BcaB06g26513' => 'bca', 'BcaC02g12564' => 'bca', 'BcaC02g12565' => 'bca', 'BcaC02g12794' => 'bca', 'BcaC02g12795' => 'bca', 'BcaC02g12796' => 'bca', 'BcaC06g35541' => 'bca', 'BNapus_Darmor_BZH_scaffold_188p00080' => 'bna', 'BNapus_Darmor_BZH_scaffold_188p00090' => 'bna', 'BolC1t03972H' => 'bol', 'BolC1t03973H' => 'bol', 'BolC4t21680H' => 'bol', 'BolC7t41863H' => 'bol', 'BolSC55t61227H' => 'bol', 'BolSC55t61228H' => 'bol', 'BraA01t03278Z' => 'bra', 'BraA05t18998Z' => 'bra', 'BraA07t28673Z' => 'bra', 'C01p40150' => 'bna', 'C05p12370' => 'bna', 'C07p13680' => 'bna', 'CAN.G1006.16' => 'can', 'CAN.G1006.17' => 'can', 'CAN.G1170.2' => 'can', 'CAN.G962.7' => 'can', 'CANSAT25G2179' => 'cansat', 'CANSAT78G1573' => 'cansat', 'CARHR099510' => 'chi', 'CARHR143510' => 'chi', 'Carub.0003s2380' => 'cru', 'Carub.0004s3082' => 'cru', 'Ca_00614_v3' => 'car', 'Ca_07801_v3' => 'car', 'Ca_08567_v3' => 'car', 'Ca_09571_v3' => 'car', 'CBR_g19290' => 'cbr', 'Cc01_g19770' => 'ccan', 'Cc03_g03030' => 'ccan', 'CDE07G0968' => 'cde', 'CDE09G1441' => 'cde', 'Cfa006103' => 'cfa', 'Cfa015573' => 'cfa', 'Cfa016988' => 'cfa', 'Ciclev10006738m.g' => 'ccl', 'Ciclev10010920m.g' => 'ccl', 'Ciclev10018517m.g' => 'ccl', 'CiPaw.01G159200' => 'cil', 'CiPaw.02G091000' => 'cil', 'CiPaw.02G091100' => 'cil', 'CiPaw.08G103100' => 'cil', 'CiPaw.09G224900' => 'cil', 'ClCG06G005740' => 'cla', 'ClCG07G000090' => 'cla', 'ClCG07G000100' => 'cla', 'COL.COLO4_09143' => 'col', 'COL.COLO4_25124' => 'col', 'Cpa.g.sc16.34' => 'cpa', 'Cpa.g.sc3504.1' => 'cpa', 'Cpa.g.sc60.37' => 'cpa', 'CsaV3_6G018520' => 'csa', 'CsaV3_6G036860' => 'csa', 'CSS0001072' => 'camsi', 'CSS0020208' => 'camsi', 'CSS0021253' => 'camsi', 'CSS0022190' => 'camsi', 'CSS0036150' => 'camsi', 'CSS0040442' => 'camsi', 'CSS0042300' => 'camsi', 'CSS0045298' => 'camsi', 'DCAR_012449' => 'dca', 'DCAR_018405' => 'dca', 'DCAR_024573' => 'dca', 'DCAR_030591' => 'dca', 'Dinv16926' => 'din', 'Dinv32963' => 'din', 'Dinv38382' => 'din', 'Dinv38383' => 'din', 'Duzib133G0974' => 'dzi', 'Duzib138G1867' => 'dzi', 'Duzib211G0420' => 'dzi', 'Duzib212G0930' => 'dzi', 'ECA234G1645' => 'eca', 'ECA247G3467' => 'eca', 'ECA248G1703' => 'eca', 'EL10Ac3g06327' => 'bvu', 'EL10Ac7g17204' => 'bvu', 'Eucgr.A00855' => 'egr', 'Eucgr.A00858' => 'egr', 'Eucgr.H01520' => 'egr', 'Eucgr.H03604' => 'egr', 'Eucgr.L03465' => 'egr', 'Eucgr.L03466' => 'egr', 'FAN01G0988' => 'fan', 'FAN02G3892' => 'fan', 'FAN05G3381' => 'fan', 'FAN07G0967' => 'fan', 'FAN07G1493' => 'fan', 'FAN08G3125' => 'fan', 'FAN09G0402' => 'fan', 'FAN12G2594' => 'fan', 'FAN12G3879' => 'fan', 'FAN14G1546' => 'fan', 'FAN15G3626' => 'fan', 'FAN17G0588' => 'fan', 'FAN17G0609' => 'fan', 'FAN18G2817' => 'fan', 'FAN19G1305' => 'fan', 'FAN20G1787' => 'fan', 'FAN22G0073' => 'fan', 'FAN22G0352' => 'fan', 'FAN22G0368' => 'fan', 'FAN22G2273' => 'fan', 'FAN24G1998' => 'fan', 'FAN27G1317' => 'fan', 'FvH4_2g23980' => 'fve', 'FvH4_4g14380' => 'fve', 'FvH4_4g14390' => 'fve', 'FvH4_6g09250' => 'fve', 'Glyma.03G151100' => 'gma', 'Glyma.04G122550' => 'gma', 'Glyma.05G001600' => 'gma', 'Glyma.09G270766' => 'gma', 'Glyma.09G270832' => 'gma', 'Glyma.13G209800' => 'gma', 'Glyma.15G102800' => 'gma', 'Glyma.18G218900' => 'gma', 'Glyma.19G001500' => 'gma', 'Glyma.19G153600' => 'gma', 'Gohir.A02G028600' => 'ghi', 'Gohir.A08G045000' => 'ghi', 'Gohir.A11G120500' => 'ghi', 'Gohir.A12G006200' => 'ghi', 'Gohir.A12G006250' => 'ghi', 'Gohir.D02G036300' => 'ghi', 'Gohir.D08G054700' => 'ghi', 'Gohir.D11G125600' => 'ghi', 'Gohir.D12G005700' => 'ghi', 'Gorai.004G055200' => 'gra', 'Gorai.005G040400' => 'gra', 'Gorai.007G134500' => 'gra', 'Gorai.008G005500' => 'gra', 'GSVIVG01011094001' => 'vvi', 'GSVIVG01017879001' => 'vvi', 'GSVIVG01025988001' => 'vvi', 'GSVIVG01029847001' => 'vvi', 'HanXRQChr10g0282901' => 'han', 'HanXRQChr10g0310371' => 'han', 'HanXRQChr10g0315041' => 'han', 'HanXRQChr11g0327651' => 'han', 'HanXRQChr12g0359391' => 'han', 'Haze_00972' => 'cav', 'Haze_00973' => 'cav', 'Haze_00974' => 'cav', 'Haze_04747' => 'cav', 'Haze_04749' => 'cav', 'Haze_04750' => 'cav', 'Haze_21217' => 'cav', 'Hma1.2p1_1037F.1_g250680' => 'hma', 'Hma1.2p1_1644F.1_g295320' => 'hma', 'HPP92_011322' => 'vpl', 'HPP92_011323' => 'vpl', 'HPP92_011324' => 'vpl', 'HPP92_011325' => 'vpl', 'HPP92_011326' => 'vpl', 'Hund12205' => 'sun', 'Hund17957' => 'sun', 'Lalb_Chr06g0176771' => 'lal', 'Lalb_Chr18g0056021' => 'lal', 'Lalb_Chr18g0056031' => 'lal', 'Lalb_Chr18g0056041' => 'lal', 'Lalb_Chr20g0107751' => 'lal', 'Lalb_Chr20g0118371' => 'lal', 'Lj1g0010239' => 'lja', 'Lj1g0017101' => 'lja', 'Lj2A1178G40' => 'lonja', 'Lj2A54G84' => 'lonja', 'Lj2g0015248' => 'lja', 'Lj3A761T51' => 'lonja', 'Lj6g0018116' => 'lja', 'Lsat_1_v5_gn_4_136040' => 'lsa', 'Lsat_1_v5_gn_5_187461' => 'lsa', 'Lsat_1_v5_gn_5_77001' => 'lsa', 'Lsat_1_v5_gn_9_4461' => 'lsa', 'Manes.01G210100' => 'mes', 'Manes.03G185600' => 'mes', 'Manes.05G073300' => 'mes', 'Manes.09G120300' => 'mes', 'Manes.15G022100' => 'mes', 'Mapoly0096s0053' => 'mpo', 'MBI03_g14058_MAGBIO' => 'mbi', 'MBI03_g33876_MAGBIO' => 'mbi', 'MBI03_g36854_MAGBIO' => 'mbi', 'MBI17_g11997_MAGBIO' => 'mbi', 'MD03G1269000' => 'mdo', 'MD04G1179600' => 'mdo', 'MD11G1289800' => 'mdo', 'MD12G1194700' => 'mdo', 'MD13G1182100' => 'mdo', 'MD13G1182200' => 'mdo', 'MD16G1182600' => 'mdo', 'Medtr2g021400' => 'mtr', 'Medtr2g021470' => 'mtr', 'Medtr2g105810' => 'mtr', 'Medtr3g033580' => 'mtr', 'Medtr6g007970' => 'mtr', 'Medtr7g056330' => 'mtr', 'Medtr7g074290' => 'mtr', 'Medtr7g074380' => 'mtr', 'Medtr7g094550' => 'mtr', 'Medtr8g069995' => 'mtr', 'MELO3C014345.2' => 'cme', 'MELO3C021395.2' => 'cme', 'Migut.D00262' => 'egut', 'Migut.G00257' => 'egut', 'MSTRG.21575' => 'ama', 'MSTRG.3985' => 'ama', 'Nitab4.5_0000295g0140' => 'nta', 'Nitab4.5_0000732g0140' => 'nta', 'Nitab4.5_0003162g0020' => 'nta', 'Nitab4.5_0006180g0090' => 'nta', 'Nitab4.5_0006390g0010' => 'nta', 'Nitab4.5_0007392g0040' => 'nta', 'Nn1g02140' => 'nnu', 'Nn4g26168' => 'nnu', 'Nn5g26754' => 'nnu', 'Oeu001433.1' => 'oeu', 'Oeu010299.2' => 'oeu', 'Oeu011171.1' => 'oeu', 'Oeu037675.1' => 'oeu', 'Oeu038359.1' => 'oeu', 'Oeu063834.1' => 'oeu', 'Oeu063835.1' => 'oeu', 'Os05g0312000' => 'osa', 'Os07g0211101' => 'osa', 'Os07g0211200' => 'osa', 'Os07g0681500' => 'osa', 'Peaxi162Scf00095g01015' => 'pax', 'Peaxi162Scf00104g00329' => 'pax', 'Peaxi162Scf00161g00137' => 'pax', 'PGR004G1665' => 'pgr', 'PGR031G2937' => 'pgr', 'PGR119G2145' => 'pgr', 'PGSC0003DMG400004351' => 'stu', 'PGSC0003DMG400014625' => 'stu', 'PGSC0003DMG401000943' => 'stu', 'Phvul.001G148600' => 'pvu', 'Phvul.004G001700' => 'pvu', 'Phvul.006G154900' => 'pvu', 'Phvul.008G078200' => 'pvu', 'Phvul.011G136500' => 'pvu', 'Potri.002G215600' => 'ptr', 'Potri.008G201600' => 'ptr', 'Potri.014G138400' => 'ptr', 'Potri.016G142500' => 'ptr', 'Pp3c16_10580' => 'ppa', 'Pp3c5_25280' => 'ppa', 'Prupe.1G150000' => 'ppe', 'Prupe.1G150100' => 'ppe', 'Prupe.6G299600' => 'ppe', 'Prupe.8G245000' => 'ppe', 'Psat0s4927g0040' => 'psa', 'Psat1g052080' => 'psa', 'Psat1g183800' => 'psa', 'Psat3g113840' => 'psa', 'Psat3g126120' => 'psa', 'Psat3g126160' => 'psa', 'Psat3g158760' => 'psa', 'Psat3g158840' => 'psa', 'PSO170G2858' => 'pso', 'PSO339G0606' => 'pso', 'PSO384G4709' => 'pso', 'PSO407G0334' => 'pso', 'QL04p040276' => 'qlo', 'QL06p005458' => 'qlo', 'QL06p005472' => 'qlo', 'QL07p030546' => 'qlo', 'QL07p031519' => 'qlo', 'QL09p050949' => 'qlo', 'QL09p050966' => 'qlo', 'QL09p051067' => 'qlo', 'QL12p022706' => 'qlo', 'RcHm_v2.0_Chr2g0119601' => 'rch', 'RcHm_v2.0_Chr3g0459591' => 'rch', 'RcHm_v2.0_Chr4g0418521' => 'rch', 'RcHm_v2.0_Chr4g0418531' => 'rch', 'RcHm_v2.0_Chr4g0418541' => 'rch', 'RcHm_v2.0_Chr6g0291641' => 'rch', 'Rhsim01G0086300' => 'rsi', 'Rhsim01G0276300' => 'rsi', 'Rhsim01G0276500' => 'rsi', 'Rhsim04G0207700' => 'rsi', 'Rhsim05G0234500' => 'rsi', 'Rhsim13G0022400' => 'rsi', 'Sabra02G0167900' => 'sbr', 'Sabra04G0158500' => 'sbr', 'Sabra08G0159800' => 'sbr', 'Sabra10G0011500' => 'sbr', 'Sabra14G0104400' => 'sbr', 'SalBow2G2440' => 'sbo', 'SalBow4G2265' => 'sbo', 'Sc02g0000060' => 'sci', 'Sc05g0005020' => 'sci', 'Sc13g0003890' => 'sci', 'Sed0014865' => 'sed', 'Sed0017224' => 'sed', 'Sed0026391' => 'sed', 'SEGI_00063' => 'sgi', 'SEGI_10967' => 'sgi', 'SEGI_17510' => 'sgi', 'SEGI_24396' => 'sgi', 'SEGI_39719' => 'sgi', 'SEGI_41392' => 'sgi', 'SGA_v2.0_scaffold11G05794' => 'sas', 'SGA_v2.0_scaffold142G35607' => 'sas', 'SGA_v2.0_scaffold1G00447' => 'sas', 'SHI15388' => 'shi', 'SHI15394' => 'shi', 'SHI15396' => 'shi', 'SHI15399' => 'shi', 'SMO343G0151' => 'smo', 'SMO367G1118' => 'smo', 'Solyc01g080200.3' => 'sly', 'Solyc06g008960.3' => 'sly', 'Solyc09g064780.3' => 'sly', 'Sopen01g031980' => 'spe', 'Sopen06g003710' => 'spe', 'Sopen09g026460' => 'spe', 'Sp3g21240' => 'spa', 'Sp4g30030' => 'spa', 'TAR365G0022' => 'tar', 'TAR365G1023' => 'tar', 'TAR365G1253' => 'tar', 'TAR623G0078' => 'tar', 'TAR623G1721' => 'tar', 'TAR633G0959' => 'tar', 'THA.LOC104802225' => 'tha', 'THA.LOC104804769' => 'tha', 'THA.LOC104808660' => 'tha', 'THA.LOC104812792' => 'tha', 'Thecc.01G284000' => 'tca', 'Thecc.04G220600' => 'tca', 'Thecc.05G268900' => 'tca', 'Thecc.08G171100' => 'tca', 'Thhalv10001284m.g' => 'esa', 'Thhalv10019912m.g' => 'esa', 'TPR.G14189' => 'tpr', 'TPR.G18110' => 'tpr', 'TPR.G18130' => 'tpr', 'TPR.G18131' => 'tpr', 'TPR.G18140' => 'tpr', 'TPR.G24282' => 'tpr', 'TPR.G25221' => 'tpr', 'TPR.G29267' => 'tpr', 'TPR.G35315' => 'tpr', 'TPR.G36173' => 'tpr', 'TWI09G0794' => 'twi', 'TWI59G1348' => 'twi', 'TWI74G0430' => 'twi', 'unitig_26.g8940' => 'ugi', 'unitig_749.g13744' => 'ugi', 'unitig_749.g13745' => 'ugi', 'vmacro08269' => 'vma', 'vmacro14937' => 'vma', 'vmacro20401' => 'vma', 'VMungo0464G1349' => 'vmu', 'VMungo0540G0289' => 'vmu', 'VMungo1215G1590' => 'vmu', 'VMungo1309G0221' => 'vmu', 'VMungo1309G2815' => 'vmu', 'VMungo1383G0239' => 'vmu', 'VMungo1383G2910' => 'vmu', 'Zm00001eb095270' => 'zma', 'Zm00001eb095280' => 'zma', 'Zm00001eb111630' => 'zma', 'Zm00001eb237080' => 'zma', 'Zm00001eb273740' => 'zma', 'Zm00001eb285040' => 'zma', 'Zm00001eb330790' => 'zma', 'Zm00001eb337380' => 'zma' ) $gf_id = 'HOM05D001484' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001484' ) $data_identifier = 'HOM05D001484' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 2, 'aly' => (int) 2, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 22, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 7, 'hma' => (int) 2, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 7, 'mtr' => (int) 10, 'cme' => (int) 2, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 4, 'ppa' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 4, 'qlo' => (int) 9, 'rch' => (int) 6, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 10, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 7, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb337380' $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' => 'HOM05D001484', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p31500' => 'bna', 'A05p00020' => 'bna', 'A07p08820' => 'bna', 'Aa31LG4G3300' => 'aar', 'Aa31LG8G10030' => 'aar', 'Actinidia00731' => 'ach', 'Actinidia11473' => 'ach', 'Actinidia23469' => 'ach', 'Actinidia24318' => 'ach', 'Actinidia40196' => 'ach', 'Actinidia40197' => 'ach', 'Actinidia40198' => 'ach', 'Ah.08g212990' => 'amhyb', 'Ah.15g091720' => 'amhyb', 'AL3G38260' => 'aly', 'AL4G47710' => 'aly', 'Aqoxy2G00671' => 'aox', 'Aqoxy2G03236' => 'aox', 'arahy.Tifrunner.gnm1.ann1.05IDCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KR684' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATY3SJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK6QJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6APGL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IDT7Z9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM073U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ0R87' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LE7RV4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT4QRX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V5ENPK' => 'arhy', 'AT2G48110' => 'ath', 'AT3G23590' => 'ath', 'ATR0626G186' => 'atr', 'ATR1127G141' => 'atr', 'Atru.chr4.2583' => 'acertr', 'Atru.chr5.1358' => 'acertr', 'Atru.chr5.1359' => 'acertr', 'Atru.chr8.46' => 'acertr', 'AUR62002640' => 'cqu', 'AUR62030055' => 'cqu', 'AUR62033713' => 'cqu', 'AUR62033714' => 'cqu', 'AUR62036795' => 'cqu', 'AUR62039891' => 'cqu', 'BcaB02g08737' => 'bca', 'BcaB04g20441' => 'bca', 'BcaB06g26509' => 'bca', 'BcaB06g26510' => 'bca', 'BcaB06g26511' => 'bca', 'BcaB06g26512' => 'bca', 'BcaB06g26513' => 'bca', 'BcaC02g12564' => 'bca', 'BcaC02g12565' => 'bca', 'BcaC02g12794' => 'bca', 'BcaC02g12795' => 'bca', 'BcaC02g12796' => 'bca', 'BcaC06g35541' => 'bca', 'BNapus_Darmor_BZH_scaffold_188p00080' => 'bna', 'BNapus_Darmor_BZH_scaffold_188p00090' => 'bna', 'BolC1t03972H' => 'bol', 'BolC1t03973H' => 'bol', 'BolC4t21680H' => 'bol', 'BolC7t41863H' => 'bol', 'BolSC55t61227H' => 'bol', 'BolSC55t61228H' => 'bol', 'BraA01t03278Z' => 'bra', 'BraA05t18998Z' => 'bra', 'BraA07t28673Z' => 'bra', 'C01p40150' => 'bna', 'C05p12370' => 'bna', 'C07p13680' => 'bna', 'CAN.G1006.16' => 'can', 'CAN.G1006.17' => 'can', 'CAN.G1170.2' => 'can', 'CAN.G962.7' => 'can', 'CANSAT25G2179' => 'cansat', 'CANSAT78G1573' => 'cansat', 'CARHR099510' => 'chi', 'CARHR143510' => 'chi', 'Carub.0003s2380' => 'cru', 'Carub.0004s3082' => 'cru', 'Ca_00614_v3' => 'car', 'Ca_07801_v3' => 'car', 'Ca_08567_v3' => 'car', 'Ca_09571_v3' => 'car', 'CBR_g19290' => 'cbr', 'Cc01_g19770' => 'ccan', 'Cc03_g03030' => 'ccan', 'CDE07G0968' => 'cde', 'CDE09G1441' => 'cde', 'Cfa006103' => 'cfa', 'Cfa015573' => 'cfa', 'Cfa016988' => 'cfa', 'Ciclev10006738m.g' => 'ccl', 'Ciclev10010920m.g' => 'ccl', 'Ciclev10018517m.g' => 'ccl', 'CiPaw.01G159200' => 'cil', 'CiPaw.02G091000' => 'cil', 'CiPaw.02G091100' => 'cil', 'CiPaw.08G103100' => 'cil', 'CiPaw.09G224900' => 'cil', 'ClCG06G005740' => 'cla', 'ClCG07G000090' => 'cla', 'ClCG07G000100' => 'cla', 'COL.COLO4_09143' => 'col', 'COL.COLO4_25124' => 'col', 'Cpa.g.sc16.34' => 'cpa', 'Cpa.g.sc3504.1' => 'cpa', 'Cpa.g.sc60.37' => 'cpa', 'CsaV3_6G018520' => 'csa', 'CsaV3_6G036860' => 'csa', 'CSS0001072' => 'camsi', 'CSS0020208' => 'camsi', 'CSS0021253' => 'camsi', 'CSS0022190' => 'camsi', 'CSS0036150' => 'camsi', 'CSS0040442' => 'camsi', 'CSS0042300' => 'camsi', 'CSS0045298' => 'camsi', 'DCAR_012449' => 'dca', 'DCAR_018405' => 'dca', 'DCAR_024573' => 'dca', 'DCAR_030591' => 'dca', 'Dinv16926' => 'din', 'Dinv32963' => 'din', 'Dinv38382' => 'din', 'Dinv38383' => 'din', 'Duzib133G0974' => 'dzi', 'Duzib138G1867' => 'dzi', 'Duzib211G0420' => 'dzi', 'Duzib212G0930' => 'dzi', 'ECA234G1645' => 'eca', 'ECA247G3467' => 'eca', 'ECA248G1703' => 'eca', 'EL10Ac3g06327' => 'bvu', 'EL10Ac7g17204' => 'bvu', 'Eucgr.A00855' => 'egr', 'Eucgr.A00858' => 'egr', 'Eucgr.H01520' => 'egr', 'Eucgr.H03604' => 'egr', 'Eucgr.L03465' => 'egr', 'Eucgr.L03466' => 'egr', 'FAN01G0988' => 'fan', 'FAN02G3892' => 'fan', 'FAN05G3381' => 'fan', 'FAN07G0967' => 'fan', 'FAN07G1493' => 'fan', 'FAN08G3125' => 'fan', 'FAN09G0402' => 'fan', 'FAN12G2594' => 'fan', 'FAN12G3879' => 'fan', 'FAN14G1546' => 'fan', 'FAN15G3626' => 'fan', 'FAN17G0588' => 'fan', 'FAN17G0609' => 'fan', 'FAN18G2817' => 'fan', 'FAN19G1305' => 'fan', 'FAN20G1787' => 'fan', 'FAN22G0073' => 'fan', 'FAN22G0352' => 'fan', 'FAN22G0368' => 'fan', 'FAN22G2273' => 'fan', 'FAN24G1998' => 'fan', 'FAN27G1317' => 'fan', 'FvH4_2g23980' => 'fve', 'FvH4_4g14380' => 'fve', 'FvH4_4g14390' => 'fve', 'FvH4_6g09250' => 'fve', 'Glyma.03G151100' => 'gma', 'Glyma.04G122550' => 'gma', 'Glyma.05G001600' => 'gma', 'Glyma.09G270766' => 'gma', 'Glyma.09G270832' => 'gma', 'Glyma.13G209800' => 'gma', 'Glyma.15G102800' => 'gma', 'Glyma.18G218900' => 'gma', 'Glyma.19G001500' => 'gma', 'Glyma.19G153600' => 'gma', 'Gohir.A02G028600' => 'ghi', 'Gohir.A08G045000' => 'ghi', 'Gohir.A11G120500' => 'ghi', 'Gohir.A12G006200' => 'ghi', 'Gohir.A12G006250' => 'ghi', 'Gohir.D02G036300' => 'ghi', 'Gohir.D08G054700' => 'ghi', 'Gohir.D11G125600' => 'ghi', 'Gohir.D12G005700' => 'ghi', 'Gorai.004G055200' => 'gra', 'Gorai.005G040400' => 'gra', 'Gorai.007G134500' => 'gra', 'Gorai.008G005500' => 'gra', 'GSVIVG01011094001' => 'vvi', 'GSVIVG01017879001' => 'vvi', 'GSVIVG01025988001' => 'vvi', 'GSVIVG01029847001' => 'vvi', 'HanXRQChr10g0282901' => 'han', 'HanXRQChr10g0310371' => 'han', 'HanXRQChr10g0315041' => 'han', 'HanXRQChr11g0327651' => 'han', 'HanXRQChr12g0359391' => 'han', 'Haze_00972' => 'cav', 'Haze_00973' => 'cav', 'Haze_00974' => 'cav', 'Haze_04747' => 'cav', 'Haze_04749' => 'cav', 'Haze_04750' => 'cav', 'Haze_21217' => 'cav', 'Hma1.2p1_1037F.1_g250680' => 'hma', 'Hma1.2p1_1644F.1_g295320' => 'hma', 'HPP92_011322' => 'vpl', 'HPP92_011323' => 'vpl', 'HPP92_011324' => 'vpl', 'HPP92_011325' => 'vpl', 'HPP92_011326' => 'vpl', 'Hund12205' => 'sun', 'Hund17957' => 'sun', 'Lalb_Chr06g0176771' => 'lal', 'Lalb_Chr18g0056021' => 'lal', 'Lalb_Chr18g0056031' => 'lal', 'Lalb_Chr18g0056041' => 'lal', 'Lalb_Chr20g0107751' => 'lal', 'Lalb_Chr20g0118371' => 'lal', 'Lj1g0010239' => 'lja', 'Lj1g0017101' => 'lja', 'Lj2A1178G40' => 'lonja', 'Lj2A54G84' => 'lonja', 'Lj2g0015248' => 'lja', 'Lj3A761T51' => 'lonja', 'Lj6g0018116' => 'lja', 'Lsat_1_v5_gn_4_136040' => 'lsa', 'Lsat_1_v5_gn_5_187461' => 'lsa', 'Lsat_1_v5_gn_5_77001' => 'lsa', 'Lsat_1_v5_gn_9_4461' => 'lsa', 'Manes.01G210100' => 'mes', 'Manes.03G185600' => 'mes', 'Manes.05G073300' => 'mes', 'Manes.09G120300' => 'mes', 'Manes.15G022100' => 'mes', 'Mapoly0096s0053' => 'mpo', 'MBI03_g14058_MAGBIO' => 'mbi', 'MBI03_g33876_MAGBIO' => 'mbi', 'MBI03_g36854_MAGBIO' => 'mbi', 'MBI17_g11997_MAGBIO' => 'mbi', 'MD03G1269000' => 'mdo', 'MD04G1179600' => 'mdo', 'MD11G1289800' => 'mdo', 'MD12G1194700' => 'mdo', 'MD13G1182100' => 'mdo', 'MD13G1182200' => 'mdo', 'MD16G1182600' => 'mdo', 'Medtr2g021400' => 'mtr', 'Medtr2g021470' => 'mtr', 'Medtr2g105810' => 'mtr', 'Medtr3g033580' => 'mtr', 'Medtr6g007970' => 'mtr', 'Medtr7g056330' => 'mtr', 'Medtr7g074290' => 'mtr', 'Medtr7g074380' => 'mtr', 'Medtr7g094550' => 'mtr', 'Medtr8g069995' => 'mtr', 'MELO3C014345.2' => 'cme', 'MELO3C021395.2' => 'cme', 'Migut.D00262' => 'egut', 'Migut.G00257' => 'egut', 'MSTRG.21575' => 'ama', 'MSTRG.3985' => 'ama', 'Nitab4.5_0000295g0140' => 'nta', 'Nitab4.5_0000732g0140' => 'nta', 'Nitab4.5_0003162g0020' => 'nta', 'Nitab4.5_0006180g0090' => 'nta', 'Nitab4.5_0006390g0010' => 'nta', 'Nitab4.5_0007392g0040' => 'nta', 'Nn1g02140' => 'nnu', 'Nn4g26168' => 'nnu', 'Nn5g26754' => 'nnu', 'Oeu001433.1' => 'oeu', 'Oeu010299.2' => 'oeu', 'Oeu011171.1' => 'oeu', 'Oeu037675.1' => 'oeu', 'Oeu038359.1' => 'oeu', 'Oeu063834.1' => 'oeu', 'Oeu063835.1' => 'oeu', 'Os05g0312000' => 'osa', 'Os07g0211101' => 'osa', 'Os07g0211200' => 'osa', 'Os07g0681500' => 'osa', 'Peaxi162Scf00095g01015' => 'pax', 'Peaxi162Scf00104g00329' => 'pax', 'Peaxi162Scf00161g00137' => 'pax', 'PGR004G1665' => 'pgr', 'PGR031G2937' => 'pgr', 'PGR119G2145' => 'pgr', 'PGSC0003DMG400004351' => 'stu', 'PGSC0003DMG400014625' => 'stu', 'PGSC0003DMG401000943' => 'stu', 'Phvul.001G148600' => 'pvu', 'Phvul.004G001700' => 'pvu', 'Phvul.006G154900' => 'pvu', 'Phvul.008G078200' => 'pvu', 'Phvul.011G136500' => 'pvu', 'Potri.002G215600' => 'ptr', 'Potri.008G201600' => 'ptr', 'Potri.014G138400' => 'ptr', 'Potri.016G142500' => 'ptr', 'Pp3c16_10580' => 'ppa', 'Pp3c5_25280' => 'ppa', 'Prupe.1G150000' => 'ppe', 'Prupe.1G150100' => 'ppe', 'Prupe.6G299600' => 'ppe', 'Prupe.8G245000' => 'ppe', 'Psat0s4927g0040' => 'psa', 'Psat1g052080' => 'psa', 'Psat1g183800' => 'psa', 'Psat3g113840' => 'psa', 'Psat3g126120' => 'psa', 'Psat3g126160' => 'psa', 'Psat3g158760' => 'psa', 'Psat3g158840' => 'psa', 'PSO170G2858' => 'pso', 'PSO339G0606' => 'pso', 'PSO384G4709' => 'pso', 'PSO407G0334' => 'pso', 'QL04p040276' => 'qlo', 'QL06p005458' => 'qlo', 'QL06p005472' => 'qlo', 'QL07p030546' => 'qlo', 'QL07p031519' => 'qlo', 'QL09p050949' => 'qlo', 'QL09p050966' => 'qlo', 'QL09p051067' => 'qlo', 'QL12p022706' => 'qlo', 'RcHm_v2.0_Chr2g0119601' => 'rch', 'RcHm_v2.0_Chr3g0459591' => 'rch', 'RcHm_v2.0_Chr4g0418521' => 'rch', 'RcHm_v2.0_Chr4g0418531' => 'rch', 'RcHm_v2.0_Chr4g0418541' => 'rch', 'RcHm_v2.0_Chr6g0291641' => 'rch', 'Rhsim01G0086300' => 'rsi', 'Rhsim01G0276300' => 'rsi', 'Rhsim01G0276500' => 'rsi', 'Rhsim04G0207700' => 'rsi', 'Rhsim05G0234500' => 'rsi', 'Rhsim13G0022400' => 'rsi', 'Sabra02G0167900' => 'sbr', 'Sabra04G0158500' => 'sbr', 'Sabra08G0159800' => 'sbr', 'Sabra10G0011500' => 'sbr', 'Sabra14G0104400' => 'sbr', 'SalBow2G2440' => 'sbo', 'SalBow4G2265' => 'sbo', 'Sc02g0000060' => 'sci', 'Sc05g0005020' => 'sci', 'Sc13g0003890' => 'sci', 'Sed0014865' => 'sed', 'Sed0017224' => 'sed', 'Sed0026391' => 'sed', 'SEGI_00063' => 'sgi', 'SEGI_10967' => 'sgi', 'SEGI_17510' => 'sgi', 'SEGI_24396' => 'sgi', 'SEGI_39719' => 'sgi', 'SEGI_41392' => 'sgi', 'SGA_v2.0_scaffold11G05794' => 'sas', 'SGA_v2.0_scaffold142G35607' => 'sas', 'SGA_v2.0_scaffold1G00447' => 'sas', 'SHI15388' => 'shi', 'SHI15394' => 'shi', 'SHI15396' => 'shi', 'SHI15399' => 'shi', 'SMO343G0151' => 'smo', 'SMO367G1118' => 'smo', 'Solyc01g080200.3' => 'sly', 'Solyc06g008960.3' => 'sly', 'Solyc09g064780.3' => 'sly', 'Sopen01g031980' => 'spe', 'Sopen06g003710' => 'spe', 'Sopen09g026460' => 'spe', 'Sp3g21240' => 'spa', 'Sp4g30030' => 'spa', 'TAR365G0022' => 'tar', 'TAR365G1023' => 'tar', 'TAR365G1253' => 'tar', 'TAR623G0078' => 'tar', 'TAR623G1721' => 'tar', 'TAR633G0959' => 'tar', 'THA.LOC104802225' => 'tha', 'THA.LOC104804769' => 'tha', 'THA.LOC104808660' => 'tha', 'THA.LOC104812792' => 'tha', 'Thecc.01G284000' => 'tca', 'Thecc.04G220600' => 'tca', 'Thecc.05G268900' => 'tca', 'Thecc.08G171100' => 'tca', 'Thhalv10001284m.g' => 'esa', 'Thhalv10019912m.g' => 'esa', 'TPR.G14189' => 'tpr', 'TPR.G18110' => 'tpr', 'TPR.G18130' => 'tpr', 'TPR.G18131' => 'tpr', 'TPR.G18140' => 'tpr', 'TPR.G24282' => 'tpr', 'TPR.G25221' => 'tpr', 'TPR.G29267' => 'tpr', 'TPR.G35315' => 'tpr', 'TPR.G36173' => 'tpr', 'TWI09G0794' => 'twi', 'TWI59G1348' => 'twi', 'TWI74G0430' => 'twi', 'unitig_26.g8940' => 'ugi', 'unitig_749.g13744' => 'ugi', 'unitig_749.g13745' => 'ugi', 'vmacro08269' => 'vma', 'vmacro14937' => 'vma', 'vmacro20401' => 'vma', 'VMungo0464G1349' => 'vmu', 'VMungo0540G0289' => 'vmu', 'VMungo1215G1590' => 'vmu', 'VMungo1309G0221' => 'vmu', 'VMungo1309G2815' => 'vmu', 'VMungo1383G0239' => 'vmu', 'VMungo1383G2910' => 'vmu', 'Zm00001eb095270' => 'zma', 'Zm00001eb095280' => 'zma', 'Zm00001eb111630' => 'zma', 'Zm00001eb237080' => 'zma', 'Zm00001eb273740' => 'zma', 'Zm00001eb285040' => 'zma', 'Zm00001eb330790' => 'zma', 'Zm00001eb337380' => 'zma' ), 'gf_id' => 'HOM05D001484', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001484' ), 'data_identifier' => 'HOM05D001484', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001484', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p31500' => 'bna', 'A05p00020' => 'bna', 'A07p08820' => 'bna', 'Aa31LG4G3300' => 'aar', 'Aa31LG8G10030' => 'aar', 'Actinidia00731' => 'ach', 'Actinidia11473' => 'ach', 'Actinidia23469' => 'ach', 'Actinidia24318' => 'ach', 'Actinidia40196' => 'ach', 'Actinidia40197' => 'ach', 'Actinidia40198' => 'ach', 'Ah.08g212990' => 'amhyb', 'Ah.15g091720' => 'amhyb', 'AL3G38260' => 'aly', 'AL4G47710' => 'aly', 'Aqoxy2G00671' => 'aox', 'Aqoxy2G03236' => 'aox', 'arahy.Tifrunner.gnm1.ann1.05IDCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KR684' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATY3SJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK6QJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6APGL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IDT7Z9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM073U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ0R87' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LE7RV4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT4QRX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V5ENPK' => 'arhy', 'AT2G48110' => 'ath', 'AT3G23590' => 'ath', 'ATR0626G186' => 'atr', 'ATR1127G141' => 'atr', 'Atru.chr4.2583' => 'acertr', 'Atru.chr5.1358' => 'acertr', 'Atru.chr5.1359' => 'acertr', 'Atru.chr8.46' => 'acertr', 'AUR62002640' => 'cqu', 'AUR62030055' => 'cqu', 'AUR62033713' => 'cqu', 'AUR62033714' => 'cqu', 'AUR62036795' => 'cqu', 'AUR62039891' => 'cqu', 'BcaB02g08737' => 'bca', 'BcaB04g20441' => 'bca', 'BcaB06g26509' => 'bca', 'BcaB06g26510' => 'bca', 'BcaB06g26511' => 'bca', 'BcaB06g26512' => 'bca', 'BcaB06g26513' => 'bca', 'BcaC02g12564' => 'bca', 'BcaC02g12565' => 'bca', 'BcaC02g12794' => 'bca', 'BcaC02g12795' => 'bca', 'BcaC02g12796' => 'bca', 'BcaC06g35541' => 'bca', 'BNapus_Darmor_BZH_scaffold_188p00080' => 'bna', 'BNapus_Darmor_BZH_scaffold_188p00090' => 'bna', 'BolC1t03972H' => 'bol', 'BolC1t03973H' => 'bol', 'BolC4t21680H' => 'bol', 'BolC7t41863H' => 'bol', 'BolSC55t61227H' => 'bol', 'BolSC55t61228H' => 'bol', 'BraA01t03278Z' => 'bra', 'BraA05t18998Z' => 'bra', 'BraA07t28673Z' => 'bra', 'C01p40150' => 'bna', 'C05p12370' => 'bna', 'C07p13680' => 'bna', 'CAN.G1006.16' => 'can', 'CAN.G1006.17' => 'can', 'CAN.G1170.2' => 'can', 'CAN.G962.7' => 'can', 'CANSAT25G2179' => 'cansat', 'CANSAT78G1573' => 'cansat', 'CARHR099510' => 'chi', 'CARHR143510' => 'chi', 'Carub.0003s2380' => 'cru', 'Carub.0004s3082' => 'cru', 'Ca_00614_v3' => 'car', 'Ca_07801_v3' => 'car', 'Ca_08567_v3' => 'car', 'Ca_09571_v3' => 'car', 'CBR_g19290' => 'cbr', 'Cc01_g19770' => 'ccan', 'Cc03_g03030' => 'ccan', 'CDE07G0968' => 'cde', 'CDE09G1441' => 'cde', 'Cfa006103' => 'cfa', 'Cfa015573' => 'cfa', 'Cfa016988' => 'cfa', 'Ciclev10006738m.g' => 'ccl', 'Ciclev10010920m.g' => 'ccl', 'Ciclev10018517m.g' => 'ccl', 'CiPaw.01G159200' => 'cil', 'CiPaw.02G091000' => 'cil', 'CiPaw.02G091100' => 'cil', 'CiPaw.08G103100' => 'cil', 'CiPaw.09G224900' => 'cil', 'ClCG06G005740' => 'cla', 'ClCG07G000090' => 'cla', 'ClCG07G000100' => 'cla', 'COL.COLO4_09143' => 'col', 'COL.COLO4_25124' => 'col', 'Cpa.g.sc16.34' => 'cpa', 'Cpa.g.sc3504.1' => 'cpa', 'Cpa.g.sc60.37' => 'cpa', 'CsaV3_6G018520' => 'csa', 'CsaV3_6G036860' => 'csa', 'CSS0001072' => 'camsi', 'CSS0020208' => 'camsi', 'CSS0021253' => 'camsi', 'CSS0022190' => 'camsi', 'CSS0036150' => 'camsi', 'CSS0040442' => 'camsi', 'CSS0042300' => 'camsi', 'CSS0045298' => 'camsi', 'DCAR_012449' => 'dca', 'DCAR_018405' => 'dca', 'DCAR_024573' => 'dca', 'DCAR_030591' => 'dca', 'Dinv16926' => 'din', 'Dinv32963' => 'din', 'Dinv38382' => 'din', 'Dinv38383' => 'din', 'Duzib133G0974' => 'dzi', 'Duzib138G1867' => 'dzi', 'Duzib211G0420' => 'dzi', 'Duzib212G0930' => 'dzi', 'ECA234G1645' => 'eca', 'ECA247G3467' => 'eca', 'ECA248G1703' => 'eca', 'EL10Ac3g06327' => 'bvu', 'EL10Ac7g17204' => 'bvu', 'Eucgr.A00855' => 'egr', 'Eucgr.A00858' => 'egr', 'Eucgr.H01520' => 'egr', 'Eucgr.H03604' => 'egr', 'Eucgr.L03465' => 'egr', 'Eucgr.L03466' => 'egr', 'FAN01G0988' => 'fan', 'FAN02G3892' => 'fan', 'FAN05G3381' => 'fan', 'FAN07G0967' => 'fan', 'FAN07G1493' => 'fan', 'FAN08G3125' => 'fan', 'FAN09G0402' => 'fan', 'FAN12G2594' => 'fan', 'FAN12G3879' => 'fan', 'FAN14G1546' => 'fan', 'FAN15G3626' => 'fan', 'FAN17G0588' => 'fan', 'FAN17G0609' => 'fan', 'FAN18G2817' => 'fan', 'FAN19G1305' => 'fan', 'FAN20G1787' => 'fan', 'FAN22G0073' => 'fan', 'FAN22G0352' => 'fan', 'FAN22G0368' => 'fan', 'FAN22G2273' => 'fan', 'FAN24G1998' => 'fan', 'FAN27G1317' => 'fan', 'FvH4_2g23980' => 'fve', 'FvH4_4g14380' => 'fve', 'FvH4_4g14390' => 'fve', 'FvH4_6g09250' => 'fve', 'Glyma.03G151100' => 'gma', 'Glyma.04G122550' => 'gma', 'Glyma.05G001600' => 'gma', 'Glyma.09G270766' => 'gma', 'Glyma.09G270832' => 'gma', 'Glyma.13G209800' => 'gma', 'Glyma.15G102800' => 'gma', 'Glyma.18G218900' => 'gma', 'Glyma.19G001500' => 'gma', 'Glyma.19G153600' => 'gma', 'Gohir.A02G028600' => 'ghi', 'Gohir.A08G045000' => 'ghi', 'Gohir.A11G120500' => 'ghi', 'Gohir.A12G006200' => 'ghi', 'Gohir.A12G006250' => 'ghi', 'Gohir.D02G036300' => 'ghi', 'Gohir.D08G054700' => 'ghi', 'Gohir.D11G125600' => 'ghi', 'Gohir.D12G005700' => 'ghi', 'Gorai.004G055200' => 'gra', 'Gorai.005G040400' => 'gra', 'Gorai.007G134500' => 'gra', 'Gorai.008G005500' => 'gra', 'GSVIVG01011094001' => 'vvi', 'GSVIVG01017879001' => 'vvi', 'GSVIVG01025988001' => 'vvi', 'GSVIVG01029847001' => 'vvi', 'HanXRQChr10g0282901' => 'han', 'HanXRQChr10g0310371' => 'han', 'HanXRQChr10g0315041' => 'han', 'HanXRQChr11g0327651' => 'han', 'HanXRQChr12g0359391' => 'han', 'Haze_00972' => 'cav', 'Haze_00973' => 'cav', 'Haze_00974' => 'cav', 'Haze_04747' => 'cav', 'Haze_04749' => 'cav', 'Haze_04750' => 'cav', 'Haze_21217' => 'cav', 'Hma1.2p1_1037F.1_g250680' => 'hma', 'Hma1.2p1_1644F.1_g295320' => 'hma', 'HPP92_011322' => 'vpl', 'HPP92_011323' => 'vpl', 'HPP92_011324' => 'vpl', 'HPP92_011325' => 'vpl', 'HPP92_011326' => 'vpl', 'Hund12205' => 'sun', 'Hund17957' => 'sun', 'Lalb_Chr06g0176771' => 'lal', 'Lalb_Chr18g0056021' => 'lal', 'Lalb_Chr18g0056031' => 'lal', 'Lalb_Chr18g0056041' => 'lal', 'Lalb_Chr20g0107751' => 'lal', 'Lalb_Chr20g0118371' => 'lal', 'Lj1g0010239' => 'lja', 'Lj1g0017101' => 'lja', 'Lj2A1178G40' => 'lonja', 'Lj2A54G84' => 'lonja', 'Lj2g0015248' => 'lja', 'Lj3A761T51' => 'lonja', 'Lj6g0018116' => 'lja', 'Lsat_1_v5_gn_4_136040' => 'lsa', 'Lsat_1_v5_gn_5_187461' => 'lsa', 'Lsat_1_v5_gn_5_77001' => 'lsa', 'Lsat_1_v5_gn_9_4461' => 'lsa', 'Manes.01G210100' => 'mes', 'Manes.03G185600' => 'mes', 'Manes.05G073300' => 'mes', 'Manes.09G120300' => 'mes', 'Manes.15G022100' => 'mes', 'Mapoly0096s0053' => 'mpo', 'MBI03_g14058_MAGBIO' => 'mbi', 'MBI03_g33876_MAGBIO' => 'mbi', 'MBI03_g36854_MAGBIO' => 'mbi', 'MBI17_g11997_MAGBIO' => 'mbi', 'MD03G1269000' => 'mdo', 'MD04G1179600' => 'mdo', 'MD11G1289800' => 'mdo', 'MD12G1194700' => 'mdo', 'MD13G1182100' => 'mdo', 'MD13G1182200' => 'mdo', 'MD16G1182600' => 'mdo', 'Medtr2g021400' => 'mtr', 'Medtr2g021470' => 'mtr', 'Medtr2g105810' => 'mtr', 'Medtr3g033580' => 'mtr', 'Medtr6g007970' => 'mtr', 'Medtr7g056330' => 'mtr', 'Medtr7g074290' => 'mtr', 'Medtr7g074380' => 'mtr', 'Medtr7g094550' => 'mtr', 'Medtr8g069995' => 'mtr', 'MELO3C014345.2' => 'cme', 'MELO3C021395.2' => 'cme', 'Migut.D00262' => 'egut', 'Migut.G00257' => 'egut', 'MSTRG.21575' => 'ama', 'MSTRG.3985' => 'ama', 'Nitab4.5_0000295g0140' => 'nta', 'Nitab4.5_0000732g0140' => 'nta', 'Nitab4.5_0003162g0020' => 'nta', 'Nitab4.5_0006180g0090' => 'nta', 'Nitab4.5_0006390g0010' => 'nta', 'Nitab4.5_0007392g0040' => 'nta', 'Nn1g02140' => 'nnu', 'Nn4g26168' => 'nnu', 'Nn5g26754' => 'nnu', 'Oeu001433.1' => 'oeu', 'Oeu010299.2' => 'oeu', 'Oeu011171.1' => 'oeu', 'Oeu037675.1' => 'oeu', 'Oeu038359.1' => 'oeu', 'Oeu063834.1' => 'oeu', 'Oeu063835.1' => 'oeu', 'Os05g0312000' => 'osa', 'Os07g0211101' => 'osa', 'Os07g0211200' => 'osa', 'Os07g0681500' => 'osa', 'Peaxi162Scf00095g01015' => 'pax', 'Peaxi162Scf00104g00329' => 'pax', 'Peaxi162Scf00161g00137' => 'pax', 'PGR004G1665' => 'pgr', 'PGR031G2937' => 'pgr', 'PGR119G2145' => 'pgr', 'PGSC0003DMG400004351' => 'stu', 'PGSC0003DMG400014625' => 'stu', 'PGSC0003DMG401000943' => 'stu', 'Phvul.001G148600' => 'pvu', 'Phvul.004G001700' => 'pvu', 'Phvul.006G154900' => 'pvu', 'Phvul.008G078200' => 'pvu', 'Phvul.011G136500' => 'pvu', 'Potri.002G215600' => 'ptr', 'Potri.008G201600' => 'ptr', 'Potri.014G138400' => 'ptr', 'Potri.016G142500' => 'ptr', 'Pp3c16_10580' => 'ppa', 'Pp3c5_25280' => 'ppa', 'Prupe.1G150000' => 'ppe', 'Prupe.1G150100' => 'ppe', 'Prupe.6G299600' => 'ppe', 'Prupe.8G245000' => 'ppe', 'Psat0s4927g0040' => 'psa', 'Psat1g052080' => 'psa', 'Psat1g183800' => 'psa', 'Psat3g113840' => 'psa', 'Psat3g126120' => 'psa', 'Psat3g126160' => 'psa', 'Psat3g158760' => 'psa', 'Psat3g158840' => 'psa', 'PSO170G2858' => 'pso', 'PSO339G0606' => 'pso', 'PSO384G4709' => 'pso', 'PSO407G0334' => 'pso', 'QL04p040276' => 'qlo', 'QL06p005458' => 'qlo', 'QL06p005472' => 'qlo', 'QL07p030546' => 'qlo', 'QL07p031519' => 'qlo', 'QL09p050949' => 'qlo', 'QL09p050966' => 'qlo', 'QL09p051067' => 'qlo', 'QL12p022706' => 'qlo', 'RcHm_v2.0_Chr2g0119601' => 'rch', 'RcHm_v2.0_Chr3g0459591' => 'rch', 'RcHm_v2.0_Chr4g0418521' => 'rch', 'RcHm_v2.0_Chr4g0418531' => 'rch', 'RcHm_v2.0_Chr4g0418541' => 'rch', 'RcHm_v2.0_Chr6g0291641' => 'rch', 'Rhsim01G0086300' => 'rsi', 'Rhsim01G0276300' => 'rsi', 'Rhsim01G0276500' => 'rsi', 'Rhsim04G0207700' => 'rsi', 'Rhsim05G0234500' => 'rsi', 'Rhsim13G0022400' => 'rsi', 'Sabra02G0167900' => 'sbr', 'Sabra04G0158500' => 'sbr', 'Sabra08G0159800' => 'sbr', 'Sabra10G0011500' => 'sbr', 'Sabra14G0104400' => 'sbr', 'SalBow2G2440' => 'sbo', 'SalBow4G2265' => 'sbo', 'Sc02g0000060' => 'sci', 'Sc05g0005020' => 'sci', 'Sc13g0003890' => 'sci', 'Sed0014865' => 'sed', 'Sed0017224' => 'sed', 'Sed0026391' => 'sed', 'SEGI_00063' => 'sgi', 'SEGI_10967' => 'sgi', 'SEGI_17510' => 'sgi', 'SEGI_24396' => 'sgi', 'SEGI_39719' => 'sgi', 'SEGI_41392' => 'sgi', 'SGA_v2.0_scaffold11G05794' => 'sas', 'SGA_v2.0_scaffold142G35607' => 'sas', 'SGA_v2.0_scaffold1G00447' => 'sas', 'SHI15388' => 'shi', 'SHI15394' => 'shi', 'SHI15396' => 'shi', 'SHI15399' => 'shi', 'SMO343G0151' => 'smo', 'SMO367G1118' => 'smo', 'Solyc01g080200.3' => 'sly', 'Solyc06g008960.3' => 'sly', 'Solyc09g064780.3' => 'sly', 'Sopen01g031980' => 'spe', 'Sopen06g003710' => 'spe', 'Sopen09g026460' => 'spe', 'Sp3g21240' => 'spa', 'Sp4g30030' => 'spa', 'TAR365G0022' => 'tar', 'TAR365G1023' => 'tar', 'TAR365G1253' => 'tar', 'TAR623G0078' => 'tar', 'TAR623G1721' => 'tar', 'TAR633G0959' => 'tar', 'THA.LOC104802225' => 'tha', 'THA.LOC104804769' => 'tha', 'THA.LOC104808660' => 'tha', 'THA.LOC104812792' => 'tha', 'Thecc.01G284000' => 'tca', 'Thecc.04G220600' => 'tca', 'Thecc.05G268900' => 'tca', 'Thecc.08G171100' => 'tca', 'Thhalv10001284m.g' => 'esa', 'Thhalv10019912m.g' => 'esa', 'TPR.G14189' => 'tpr', 'TPR.G18110' => 'tpr', 'TPR.G18130' => 'tpr', 'TPR.G18131' => 'tpr', 'TPR.G18140' => 'tpr', 'TPR.G24282' => 'tpr', 'TPR.G25221' => 'tpr', 'TPR.G29267' => 'tpr', 'TPR.G35315' => 'tpr', 'TPR.G36173' => 'tpr', 'TWI09G0794' => 'twi', 'TWI59G1348' => 'twi', 'TWI74G0430' => 'twi', 'unitig_26.g8940' => 'ugi', 'unitig_749.g13744' => 'ugi', 'unitig_749.g13745' => 'ugi', 'vmacro08269' => 'vma', 'vmacro14937' => 'vma', 'vmacro20401' => 'vma', 'VMungo0464G1349' => 'vmu', 'VMungo0540G0289' => 'vmu', 'VMungo1215G1590' => 'vmu', 'VMungo1309G0221' => 'vmu', 'VMungo1309G2815' => 'vmu', 'VMungo1383G0239' => 'vmu', 'VMungo1383G2910' => 'vmu', 'Zm00001eb095270' => 'zma', 'Zm00001eb095280' => 'zma', 'Zm00001eb111630' => 'zma', 'Zm00001eb237080' => 'zma', 'Zm00001eb273740' => 'zma', 'Zm00001eb285040' => 'zma', 'Zm00001eb330790' => 'zma', 'Zm00001eb337380' => 'zma' ) $gf_id = 'HOM05D001484' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001484' ) $data_identifier = 'HOM05D001484' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 2, 'aly' => (int) 2, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 22, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 7, 'hma' => (int) 2, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 7, 'mtr' => (int) 10, 'cme' => (int) 2, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 4, 'ppa' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 4, 'qlo' => (int) 9, 'rch' => (int) 6, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 10, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 7, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb337380' $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' => 'HOM05D001484', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p31500' => 'bna', 'A05p00020' => 'bna', 'A07p08820' => 'bna', 'Aa31LG4G3300' => 'aar', 'Aa31LG8G10030' => 'aar', 'Actinidia00731' => 'ach', 'Actinidia11473' => 'ach', 'Actinidia23469' => 'ach', 'Actinidia24318' => 'ach', 'Actinidia40196' => 'ach', 'Actinidia40197' => 'ach', 'Actinidia40198' => 'ach', 'Ah.08g212990' => 'amhyb', 'Ah.15g091720' => 'amhyb', 'AL3G38260' => 'aly', 'AL4G47710' => 'aly', 'Aqoxy2G00671' => 'aox', 'Aqoxy2G03236' => 'aox', 'arahy.Tifrunner.gnm1.ann1.05IDCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KR684' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATY3SJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK6QJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6APGL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IDT7Z9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM073U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ0R87' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LE7RV4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT4QRX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V5ENPK' => 'arhy', 'AT2G48110' => 'ath', 'AT3G23590' => 'ath', 'ATR0626G186' => 'atr', 'ATR1127G141' => 'atr', 'Atru.chr4.2583' => 'acertr', 'Atru.chr5.1358' => 'acertr', 'Atru.chr5.1359' => 'acertr', 'Atru.chr8.46' => 'acertr', 'AUR62002640' => 'cqu', 'AUR62030055' => 'cqu', 'AUR62033713' => 'cqu', 'AUR62033714' => 'cqu', 'AUR62036795' => 'cqu', 'AUR62039891' => 'cqu', 'BcaB02g08737' => 'bca', 'BcaB04g20441' => 'bca', 'BcaB06g26509' => 'bca', 'BcaB06g26510' => 'bca', 'BcaB06g26511' => 'bca', 'BcaB06g26512' => 'bca', 'BcaB06g26513' => 'bca', 'BcaC02g12564' => 'bca', 'BcaC02g12565' => 'bca', 'BcaC02g12794' => 'bca', 'BcaC02g12795' => 'bca', 'BcaC02g12796' => 'bca', 'BcaC06g35541' => 'bca', 'BNapus_Darmor_BZH_scaffold_188p00080' => 'bna', 'BNapus_Darmor_BZH_scaffold_188p00090' => 'bna', 'BolC1t03972H' => 'bol', 'BolC1t03973H' => 'bol', 'BolC4t21680H' => 'bol', 'BolC7t41863H' => 'bol', 'BolSC55t61227H' => 'bol', 'BolSC55t61228H' => 'bol', 'BraA01t03278Z' => 'bra', 'BraA05t18998Z' => 'bra', 'BraA07t28673Z' => 'bra', 'C01p40150' => 'bna', 'C05p12370' => 'bna', 'C07p13680' => 'bna', 'CAN.G1006.16' => 'can', 'CAN.G1006.17' => 'can', 'CAN.G1170.2' => 'can', 'CAN.G962.7' => 'can', 'CANSAT25G2179' => 'cansat', 'CANSAT78G1573' => 'cansat', 'CARHR099510' => 'chi', 'CARHR143510' => 'chi', 'Carub.0003s2380' => 'cru', 'Carub.0004s3082' => 'cru', 'Ca_00614_v3' => 'car', 'Ca_07801_v3' => 'car', 'Ca_08567_v3' => 'car', 'Ca_09571_v3' => 'car', 'CBR_g19290' => 'cbr', 'Cc01_g19770' => 'ccan', 'Cc03_g03030' => 'ccan', 'CDE07G0968' => 'cde', 'CDE09G1441' => 'cde', 'Cfa006103' => 'cfa', 'Cfa015573' => 'cfa', 'Cfa016988' => 'cfa', 'Ciclev10006738m.g' => 'ccl', 'Ciclev10010920m.g' => 'ccl', 'Ciclev10018517m.g' => 'ccl', 'CiPaw.01G159200' => 'cil', 'CiPaw.02G091000' => 'cil', 'CiPaw.02G091100' => 'cil', 'CiPaw.08G103100' => 'cil', 'CiPaw.09G224900' => 'cil', 'ClCG06G005740' => 'cla', 'ClCG07G000090' => 'cla', 'ClCG07G000100' => 'cla', 'COL.COLO4_09143' => 'col', 'COL.COLO4_25124' => 'col', 'Cpa.g.sc16.34' => 'cpa', 'Cpa.g.sc3504.1' => 'cpa', 'Cpa.g.sc60.37' => 'cpa', 'CsaV3_6G018520' => 'csa', 'CsaV3_6G036860' => 'csa', 'CSS0001072' => 'camsi', 'CSS0020208' => 'camsi', 'CSS0021253' => 'camsi', 'CSS0022190' => 'camsi', 'CSS0036150' => 'camsi', 'CSS0040442' => 'camsi', 'CSS0042300' => 'camsi', 'CSS0045298' => 'camsi', 'DCAR_012449' => 'dca', 'DCAR_018405' => 'dca', 'DCAR_024573' => 'dca', 'DCAR_030591' => 'dca', 'Dinv16926' => 'din', 'Dinv32963' => 'din', 'Dinv38382' => 'din', 'Dinv38383' => 'din', 'Duzib133G0974' => 'dzi', 'Duzib138G1867' => 'dzi', 'Duzib211G0420' => 'dzi', 'Duzib212G0930' => 'dzi', 'ECA234G1645' => 'eca', 'ECA247G3467' => 'eca', 'ECA248G1703' => 'eca', 'EL10Ac3g06327' => 'bvu', 'EL10Ac7g17204' => 'bvu', 'Eucgr.A00855' => 'egr', 'Eucgr.A00858' => 'egr', 'Eucgr.H01520' => 'egr', 'Eucgr.H03604' => 'egr', 'Eucgr.L03465' => 'egr', 'Eucgr.L03466' => 'egr', 'FAN01G0988' => 'fan', 'FAN02G3892' => 'fan', 'FAN05G3381' => 'fan', 'FAN07G0967' => 'fan', 'FAN07G1493' => 'fan', 'FAN08G3125' => 'fan', 'FAN09G0402' => 'fan', 'FAN12G2594' => 'fan', 'FAN12G3879' => 'fan', 'FAN14G1546' => 'fan', 'FAN15G3626' => 'fan', 'FAN17G0588' => 'fan', 'FAN17G0609' => 'fan', 'FAN18G2817' => 'fan', 'FAN19G1305' => 'fan', 'FAN20G1787' => 'fan', 'FAN22G0073' => 'fan', 'FAN22G0352' => 'fan', 'FAN22G0368' => 'fan', 'FAN22G2273' => 'fan', 'FAN24G1998' => 'fan', 'FAN27G1317' => 'fan', 'FvH4_2g23980' => 'fve', 'FvH4_4g14380' => 'fve', 'FvH4_4g14390' => 'fve', 'FvH4_6g09250' => 'fve', 'Glyma.03G151100' => 'gma', 'Glyma.04G122550' => 'gma', 'Glyma.05G001600' => 'gma', 'Glyma.09G270766' => 'gma', 'Glyma.09G270832' => 'gma', 'Glyma.13G209800' => 'gma', 'Glyma.15G102800' => 'gma', 'Glyma.18G218900' => 'gma', 'Glyma.19G001500' => 'gma', 'Glyma.19G153600' => 'gma', 'Gohir.A02G028600' => 'ghi', 'Gohir.A08G045000' => 'ghi', 'Gohir.A11G120500' => 'ghi', 'Gohir.A12G006200' => 'ghi', 'Gohir.A12G006250' => 'ghi', 'Gohir.D02G036300' => 'ghi', 'Gohir.D08G054700' => 'ghi', 'Gohir.D11G125600' => 'ghi', 'Gohir.D12G005700' => 'ghi', 'Gorai.004G055200' => 'gra', 'Gorai.005G040400' => 'gra', 'Gorai.007G134500' => 'gra', 'Gorai.008G005500' => 'gra', 'GSVIVG01011094001' => 'vvi', 'GSVIVG01017879001' => 'vvi', 'GSVIVG01025988001' => 'vvi', 'GSVIVG01029847001' => 'vvi', 'HanXRQChr10g0282901' => 'han', 'HanXRQChr10g0310371' => 'han', 'HanXRQChr10g0315041' => 'han', 'HanXRQChr11g0327651' => 'han', 'HanXRQChr12g0359391' => 'han', 'Haze_00972' => 'cav', 'Haze_00973' => 'cav', 'Haze_00974' => 'cav', 'Haze_04747' => 'cav', 'Haze_04749' => 'cav', 'Haze_04750' => 'cav', 'Haze_21217' => 'cav', 'Hma1.2p1_1037F.1_g250680' => 'hma', 'Hma1.2p1_1644F.1_g295320' => 'hma', 'HPP92_011322' => 'vpl', 'HPP92_011323' => 'vpl', 'HPP92_011324' => 'vpl', 'HPP92_011325' => 'vpl', 'HPP92_011326' => 'vpl', 'Hund12205' => 'sun', 'Hund17957' => 'sun', 'Lalb_Chr06g0176771' => 'lal', 'Lalb_Chr18g0056021' => 'lal', 'Lalb_Chr18g0056031' => 'lal', 'Lalb_Chr18g0056041' => 'lal', 'Lalb_Chr20g0107751' => 'lal', 'Lalb_Chr20g0118371' => 'lal', 'Lj1g0010239' => 'lja', 'Lj1g0017101' => 'lja', 'Lj2A1178G40' => 'lonja', 'Lj2A54G84' => 'lonja', 'Lj2g0015248' => 'lja', 'Lj3A761T51' => 'lonja', 'Lj6g0018116' => 'lja', 'Lsat_1_v5_gn_4_136040' => 'lsa', 'Lsat_1_v5_gn_5_187461' => 'lsa', 'Lsat_1_v5_gn_5_77001' => 'lsa', 'Lsat_1_v5_gn_9_4461' => 'lsa', 'Manes.01G210100' => 'mes', 'Manes.03G185600' => 'mes', 'Manes.05G073300' => 'mes', 'Manes.09G120300' => 'mes', 'Manes.15G022100' => 'mes', 'Mapoly0096s0053' => 'mpo', 'MBI03_g14058_MAGBIO' => 'mbi', 'MBI03_g33876_MAGBIO' => 'mbi', 'MBI03_g36854_MAGBIO' => 'mbi', 'MBI17_g11997_MAGBIO' => 'mbi', 'MD03G1269000' => 'mdo', 'MD04G1179600' => 'mdo', 'MD11G1289800' => 'mdo', 'MD12G1194700' => 'mdo', 'MD13G1182100' => 'mdo', 'MD13G1182200' => 'mdo', 'MD16G1182600' => 'mdo', 'Medtr2g021400' => 'mtr', 'Medtr2g021470' => 'mtr', 'Medtr2g105810' => 'mtr', 'Medtr3g033580' => 'mtr', 'Medtr6g007970' => 'mtr', 'Medtr7g056330' => 'mtr', 'Medtr7g074290' => 'mtr', 'Medtr7g074380' => 'mtr', 'Medtr7g094550' => 'mtr', 'Medtr8g069995' => 'mtr', 'MELO3C014345.2' => 'cme', 'MELO3C021395.2' => 'cme', 'Migut.D00262' => 'egut', 'Migut.G00257' => 'egut', 'MSTRG.21575' => 'ama', 'MSTRG.3985' => 'ama', 'Nitab4.5_0000295g0140' => 'nta', 'Nitab4.5_0000732g0140' => 'nta', 'Nitab4.5_0003162g0020' => 'nta', 'Nitab4.5_0006180g0090' => 'nta', 'Nitab4.5_0006390g0010' => 'nta', 'Nitab4.5_0007392g0040' => 'nta', 'Nn1g02140' => 'nnu', 'Nn4g26168' => 'nnu', 'Nn5g26754' => 'nnu', 'Oeu001433.1' => 'oeu', 'Oeu010299.2' => 'oeu', 'Oeu011171.1' => 'oeu', 'Oeu037675.1' => 'oeu', 'Oeu038359.1' => 'oeu', 'Oeu063834.1' => 'oeu', 'Oeu063835.1' => 'oeu', 'Os05g0312000' => 'osa', 'Os07g0211101' => 'osa', 'Os07g0211200' => 'osa', 'Os07g0681500' => 'osa', 'Peaxi162Scf00095g01015' => 'pax', 'Peaxi162Scf00104g00329' => 'pax', 'Peaxi162Scf00161g00137' => 'pax', 'PGR004G1665' => 'pgr', 'PGR031G2937' => 'pgr', 'PGR119G2145' => 'pgr', 'PGSC0003DMG400004351' => 'stu', 'PGSC0003DMG400014625' => 'stu', 'PGSC0003DMG401000943' => 'stu', 'Phvul.001G148600' => 'pvu', 'Phvul.004G001700' => 'pvu', 'Phvul.006G154900' => 'pvu', 'Phvul.008G078200' => 'pvu', 'Phvul.011G136500' => 'pvu', 'Potri.002G215600' => 'ptr', 'Potri.008G201600' => 'ptr', 'Potri.014G138400' => 'ptr', 'Potri.016G142500' => 'ptr', 'Pp3c16_10580' => 'ppa', 'Pp3c5_25280' => 'ppa', 'Prupe.1G150000' => 'ppe', 'Prupe.1G150100' => 'ppe', 'Prupe.6G299600' => 'ppe', 'Prupe.8G245000' => 'ppe', 'Psat0s4927g0040' => 'psa', 'Psat1g052080' => 'psa', 'Psat1g183800' => 'psa', 'Psat3g113840' => 'psa', 'Psat3g126120' => 'psa', 'Psat3g126160' => 'psa', 'Psat3g158760' => 'psa', 'Psat3g158840' => 'psa', 'PSO170G2858' => 'pso', 'PSO339G0606' => 'pso', 'PSO384G4709' => 'pso', 'PSO407G0334' => 'pso', 'QL04p040276' => 'qlo', 'QL06p005458' => 'qlo', 'QL06p005472' => 'qlo', 'QL07p030546' => 'qlo', 'QL07p031519' => 'qlo', 'QL09p050949' => 'qlo', 'QL09p050966' => 'qlo', 'QL09p051067' => 'qlo', 'QL12p022706' => 'qlo', 'RcHm_v2.0_Chr2g0119601' => 'rch', 'RcHm_v2.0_Chr3g0459591' => 'rch', 'RcHm_v2.0_Chr4g0418521' => 'rch', 'RcHm_v2.0_Chr4g0418531' => 'rch', 'RcHm_v2.0_Chr4g0418541' => 'rch', 'RcHm_v2.0_Chr6g0291641' => 'rch', 'Rhsim01G0086300' => 'rsi', 'Rhsim01G0276300' => 'rsi', 'Rhsim01G0276500' => 'rsi', 'Rhsim04G0207700' => 'rsi', 'Rhsim05G0234500' => 'rsi', 'Rhsim13G0022400' => 'rsi', 'Sabra02G0167900' => 'sbr', 'Sabra04G0158500' => 'sbr', 'Sabra08G0159800' => 'sbr', 'Sabra10G0011500' => 'sbr', 'Sabra14G0104400' => 'sbr', 'SalBow2G2440' => 'sbo', 'SalBow4G2265' => 'sbo', 'Sc02g0000060' => 'sci', 'Sc05g0005020' => 'sci', 'Sc13g0003890' => 'sci', 'Sed0014865' => 'sed', 'Sed0017224' => 'sed', 'Sed0026391' => 'sed', 'SEGI_00063' => 'sgi', 'SEGI_10967' => 'sgi', 'SEGI_17510' => 'sgi', 'SEGI_24396' => 'sgi', 'SEGI_39719' => 'sgi', 'SEGI_41392' => 'sgi', 'SGA_v2.0_scaffold11G05794' => 'sas', 'SGA_v2.0_scaffold142G35607' => 'sas', 'SGA_v2.0_scaffold1G00447' => 'sas', 'SHI15388' => 'shi', 'SHI15394' => 'shi', 'SHI15396' => 'shi', 'SHI15399' => 'shi', 'SMO343G0151' => 'smo', 'SMO367G1118' => 'smo', 'Solyc01g080200.3' => 'sly', 'Solyc06g008960.3' => 'sly', 'Solyc09g064780.3' => 'sly', 'Sopen01g031980' => 'spe', 'Sopen06g003710' => 'spe', 'Sopen09g026460' => 'spe', 'Sp3g21240' => 'spa', 'Sp4g30030' => 'spa', 'TAR365G0022' => 'tar', 'TAR365G1023' => 'tar', 'TAR365G1253' => 'tar', 'TAR623G0078' => 'tar', 'TAR623G1721' => 'tar', 'TAR633G0959' => 'tar', 'THA.LOC104802225' => 'tha', 'THA.LOC104804769' => 'tha', 'THA.LOC104808660' => 'tha', 'THA.LOC104812792' => 'tha', 'Thecc.01G284000' => 'tca', 'Thecc.04G220600' => 'tca', 'Thecc.05G268900' => 'tca', 'Thecc.08G171100' => 'tca', 'Thhalv10001284m.g' => 'esa', 'Thhalv10019912m.g' => 'esa', 'TPR.G14189' => 'tpr', 'TPR.G18110' => 'tpr', 'TPR.G18130' => 'tpr', 'TPR.G18131' => 'tpr', 'TPR.G18140' => 'tpr', 'TPR.G24282' => 'tpr', 'TPR.G25221' => 'tpr', 'TPR.G29267' => 'tpr', 'TPR.G35315' => 'tpr', 'TPR.G36173' => 'tpr', 'TWI09G0794' => 'twi', 'TWI59G1348' => 'twi', 'TWI74G0430' => 'twi', 'unitig_26.g8940' => 'ugi', 'unitig_749.g13744' => 'ugi', 'unitig_749.g13745' => 'ugi', 'vmacro08269' => 'vma', 'vmacro14937' => 'vma', 'vmacro20401' => 'vma', 'VMungo0464G1349' => 'vmu', 'VMungo0540G0289' => 'vmu', 'VMungo1215G1590' => 'vmu', 'VMungo1309G0221' => 'vmu', 'VMungo1309G2815' => 'vmu', 'VMungo1383G0239' => 'vmu', 'VMungo1383G2910' => 'vmu', 'Zm00001eb095270' => 'zma', 'Zm00001eb095280' => 'zma', 'Zm00001eb111630' => 'zma', 'Zm00001eb237080' => 'zma', 'Zm00001eb273740' => 'zma', 'Zm00001eb285040' => 'zma', 'Zm00001eb330790' => 'zma', 'Zm00001eb337380' => 'zma' ), 'gf_id' => 'HOM05D001484', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001484' ), 'data_identifier' => 'HOM05D001484', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001484', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p31500' => 'bna', 'A05p00020' => 'bna', 'A07p08820' => 'bna', 'Aa31LG4G3300' => 'aar', 'Aa31LG8G10030' => 'aar', 'Actinidia00731' => 'ach', 'Actinidia11473' => 'ach', 'Actinidia23469' => 'ach', 'Actinidia24318' => 'ach', 'Actinidia40196' => 'ach', 'Actinidia40197' => 'ach', 'Actinidia40198' => 'ach', 'Ah.08g212990' => 'amhyb', 'Ah.15g091720' => 'amhyb', 'AL3G38260' => 'aly', 'AL4G47710' => 'aly', 'Aqoxy2G00671' => 'aox', 'Aqoxy2G03236' => 'aox', 'arahy.Tifrunner.gnm1.ann1.05IDCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KR684' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATY3SJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK6QJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6APGL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IDT7Z9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM073U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ0R87' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LE7RV4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT4QRX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V5ENPK' => 'arhy', 'AT2G48110' => 'ath', 'AT3G23590' => 'ath', 'ATR0626G186' => 'atr', 'ATR1127G141' => 'atr', 'Atru.chr4.2583' => 'acertr', 'Atru.chr5.1358' => 'acertr', 'Atru.chr5.1359' => 'acertr', 'Atru.chr8.46' => 'acertr', 'AUR62002640' => 'cqu', 'AUR62030055' => 'cqu', 'AUR62033713' => 'cqu', 'AUR62033714' => 'cqu', 'AUR62036795' => 'cqu', 'AUR62039891' => 'cqu', 'BcaB02g08737' => 'bca', 'BcaB04g20441' => 'bca', 'BcaB06g26509' => 'bca', 'BcaB06g26510' => 'bca', 'BcaB06g26511' => 'bca', 'BcaB06g26512' => 'bca', 'BcaB06g26513' => 'bca', 'BcaC02g12564' => 'bca', 'BcaC02g12565' => 'bca', 'BcaC02g12794' => 'bca', 'BcaC02g12795' => 'bca', 'BcaC02g12796' => 'bca', 'BcaC06g35541' => 'bca', 'BNapus_Darmor_BZH_scaffold_188p00080' => 'bna', 'BNapus_Darmor_BZH_scaffold_188p00090' => 'bna', 'BolC1t03972H' => 'bol', 'BolC1t03973H' => 'bol', 'BolC4t21680H' => 'bol', 'BolC7t41863H' => 'bol', 'BolSC55t61227H' => 'bol', 'BolSC55t61228H' => 'bol', 'BraA01t03278Z' => 'bra', 'BraA05t18998Z' => 'bra', 'BraA07t28673Z' => 'bra', 'C01p40150' => 'bna', 'C05p12370' => 'bna', 'C07p13680' => 'bna', 'CAN.G1006.16' => 'can', 'CAN.G1006.17' => 'can', 'CAN.G1170.2' => 'can', 'CAN.G962.7' => 'can', 'CANSAT25G2179' => 'cansat', 'CANSAT78G1573' => 'cansat', 'CARHR099510' => 'chi', 'CARHR143510' => 'chi', 'Carub.0003s2380' => 'cru', 'Carub.0004s3082' => 'cru', 'Ca_00614_v3' => 'car', 'Ca_07801_v3' => 'car', 'Ca_08567_v3' => 'car', 'Ca_09571_v3' => 'car', 'CBR_g19290' => 'cbr', 'Cc01_g19770' => 'ccan', 'Cc03_g03030' => 'ccan', 'CDE07G0968' => 'cde', 'CDE09G1441' => 'cde', 'Cfa006103' => 'cfa', 'Cfa015573' => 'cfa', 'Cfa016988' => 'cfa', 'Ciclev10006738m.g' => 'ccl', 'Ciclev10010920m.g' => 'ccl', 'Ciclev10018517m.g' => 'ccl', 'CiPaw.01G159200' => 'cil', 'CiPaw.02G091000' => 'cil', 'CiPaw.02G091100' => 'cil', 'CiPaw.08G103100' => 'cil', 'CiPaw.09G224900' => 'cil', 'ClCG06G005740' => 'cla', 'ClCG07G000090' => 'cla', 'ClCG07G000100' => 'cla', 'COL.COLO4_09143' => 'col', 'COL.COLO4_25124' => 'col', 'Cpa.g.sc16.34' => 'cpa', 'Cpa.g.sc3504.1' => 'cpa', 'Cpa.g.sc60.37' => 'cpa', 'CsaV3_6G018520' => 'csa', 'CsaV3_6G036860' => 'csa', 'CSS0001072' => 'camsi', 'CSS0020208' => 'camsi', 'CSS0021253' => 'camsi', 'CSS0022190' => 'camsi', 'CSS0036150' => 'camsi', 'CSS0040442' => 'camsi', 'CSS0042300' => 'camsi', 'CSS0045298' => 'camsi', 'DCAR_012449' => 'dca', 'DCAR_018405' => 'dca', 'DCAR_024573' => 'dca', 'DCAR_030591' => 'dca', 'Dinv16926' => 'din', 'Dinv32963' => 'din', 'Dinv38382' => 'din', 'Dinv38383' => 'din', 'Duzib133G0974' => 'dzi', 'Duzib138G1867' => 'dzi', 'Duzib211G0420' => 'dzi', 'Duzib212G0930' => 'dzi', 'ECA234G1645' => 'eca', 'ECA247G3467' => 'eca', 'ECA248G1703' => 'eca', 'EL10Ac3g06327' => 'bvu', 'EL10Ac7g17204' => 'bvu', 'Eucgr.A00855' => 'egr', 'Eucgr.A00858' => 'egr', 'Eucgr.H01520' => 'egr', 'Eucgr.H03604' => 'egr', 'Eucgr.L03465' => 'egr', 'Eucgr.L03466' => 'egr', 'FAN01G0988' => 'fan', 'FAN02G3892' => 'fan', 'FAN05G3381' => 'fan', 'FAN07G0967' => 'fan', 'FAN07G1493' => 'fan', 'FAN08G3125' => 'fan', 'FAN09G0402' => 'fan', 'FAN12G2594' => 'fan', 'FAN12G3879' => 'fan', 'FAN14G1546' => 'fan', 'FAN15G3626' => 'fan', 'FAN17G0588' => 'fan', 'FAN17G0609' => 'fan', 'FAN18G2817' => 'fan', 'FAN19G1305' => 'fan', 'FAN20G1787' => 'fan', 'FAN22G0073' => 'fan', 'FAN22G0352' => 'fan', 'FAN22G0368' => 'fan', 'FAN22G2273' => 'fan', 'FAN24G1998' => 'fan', 'FAN27G1317' => 'fan', 'FvH4_2g23980' => 'fve', 'FvH4_4g14380' => 'fve', 'FvH4_4g14390' => 'fve', 'FvH4_6g09250' => 'fve', 'Glyma.03G151100' => 'gma', 'Glyma.04G122550' => 'gma', 'Glyma.05G001600' => 'gma', 'Glyma.09G270766' => 'gma', 'Glyma.09G270832' => 'gma', 'Glyma.13G209800' => 'gma', 'Glyma.15G102800' => 'gma', 'Glyma.18G218900' => 'gma', 'Glyma.19G001500' => 'gma', 'Glyma.19G153600' => 'gma', 'Gohir.A02G028600' => 'ghi', 'Gohir.A08G045000' => 'ghi', 'Gohir.A11G120500' => 'ghi', 'Gohir.A12G006200' => 'ghi', 'Gohir.A12G006250' => 'ghi', 'Gohir.D02G036300' => 'ghi', 'Gohir.D08G054700' => 'ghi', 'Gohir.D11G125600' => 'ghi', 'Gohir.D12G005700' => 'ghi', 'Gorai.004G055200' => 'gra', 'Gorai.005G040400' => 'gra', 'Gorai.007G134500' => 'gra', 'Gorai.008G005500' => 'gra', 'GSVIVG01011094001' => 'vvi', 'GSVIVG01017879001' => 'vvi', 'GSVIVG01025988001' => 'vvi', 'GSVIVG01029847001' => 'vvi', 'HanXRQChr10g0282901' => 'han', 'HanXRQChr10g0310371' => 'han', 'HanXRQChr10g0315041' => 'han', 'HanXRQChr11g0327651' => 'han', 'HanXRQChr12g0359391' => 'han', 'Haze_00972' => 'cav', 'Haze_00973' => 'cav', 'Haze_00974' => 'cav', 'Haze_04747' => 'cav', 'Haze_04749' => 'cav', 'Haze_04750' => 'cav', 'Haze_21217' => 'cav', 'Hma1.2p1_1037F.1_g250680' => 'hma', 'Hma1.2p1_1644F.1_g295320' => 'hma', 'HPP92_011322' => 'vpl', 'HPP92_011323' => 'vpl', 'HPP92_011324' => 'vpl', 'HPP92_011325' => 'vpl', 'HPP92_011326' => 'vpl', 'Hund12205' => 'sun', 'Hund17957' => 'sun', 'Lalb_Chr06g0176771' => 'lal', 'Lalb_Chr18g0056021' => 'lal', 'Lalb_Chr18g0056031' => 'lal', 'Lalb_Chr18g0056041' => 'lal', 'Lalb_Chr20g0107751' => 'lal', 'Lalb_Chr20g0118371' => 'lal', 'Lj1g0010239' => 'lja', 'Lj1g0017101' => 'lja', 'Lj2A1178G40' => 'lonja', 'Lj2A54G84' => 'lonja', 'Lj2g0015248' => 'lja', 'Lj3A761T51' => 'lonja', 'Lj6g0018116' => 'lja', 'Lsat_1_v5_gn_4_136040' => 'lsa', 'Lsat_1_v5_gn_5_187461' => 'lsa', 'Lsat_1_v5_gn_5_77001' => 'lsa', 'Lsat_1_v5_gn_9_4461' => 'lsa', 'Manes.01G210100' => 'mes', 'Manes.03G185600' => 'mes', 'Manes.05G073300' => 'mes', 'Manes.09G120300' => 'mes', 'Manes.15G022100' => 'mes', 'Mapoly0096s0053' => 'mpo', 'MBI03_g14058_MAGBIO' => 'mbi', 'MBI03_g33876_MAGBIO' => 'mbi', 'MBI03_g36854_MAGBIO' => 'mbi', 'MBI17_g11997_MAGBIO' => 'mbi', 'MD03G1269000' => 'mdo', 'MD04G1179600' => 'mdo', 'MD11G1289800' => 'mdo', 'MD12G1194700' => 'mdo', 'MD13G1182100' => 'mdo', 'MD13G1182200' => 'mdo', 'MD16G1182600' => 'mdo', 'Medtr2g021400' => 'mtr', 'Medtr2g021470' => 'mtr', 'Medtr2g105810' => 'mtr', 'Medtr3g033580' => 'mtr', 'Medtr6g007970' => 'mtr', 'Medtr7g056330' => 'mtr', 'Medtr7g074290' => 'mtr', 'Medtr7g074380' => 'mtr', 'Medtr7g094550' => 'mtr', 'Medtr8g069995' => 'mtr', 'MELO3C014345.2' => 'cme', 'MELO3C021395.2' => 'cme', 'Migut.D00262' => 'egut', 'Migut.G00257' => 'egut', 'MSTRG.21575' => 'ama', 'MSTRG.3985' => 'ama', 'Nitab4.5_0000295g0140' => 'nta', 'Nitab4.5_0000732g0140' => 'nta', 'Nitab4.5_0003162g0020' => 'nta', 'Nitab4.5_0006180g0090' => 'nta', 'Nitab4.5_0006390g0010' => 'nta', 'Nitab4.5_0007392g0040' => 'nta', 'Nn1g02140' => 'nnu', 'Nn4g26168' => 'nnu', 'Nn5g26754' => 'nnu', 'Oeu001433.1' => 'oeu', 'Oeu010299.2' => 'oeu', 'Oeu011171.1' => 'oeu', 'Oeu037675.1' => 'oeu', 'Oeu038359.1' => 'oeu', 'Oeu063834.1' => 'oeu', 'Oeu063835.1' => 'oeu', 'Os05g0312000' => 'osa', 'Os07g0211101' => 'osa', 'Os07g0211200' => 'osa', 'Os07g0681500' => 'osa', 'Peaxi162Scf00095g01015' => 'pax', 'Peaxi162Scf00104g00329' => 'pax', 'Peaxi162Scf00161g00137' => 'pax', 'PGR004G1665' => 'pgr', 'PGR031G2937' => 'pgr', 'PGR119G2145' => 'pgr', 'PGSC0003DMG400004351' => 'stu', 'PGSC0003DMG400014625' => 'stu', 'PGSC0003DMG401000943' => 'stu', 'Phvul.001G148600' => 'pvu', 'Phvul.004G001700' => 'pvu', 'Phvul.006G154900' => 'pvu', 'Phvul.008G078200' => 'pvu', 'Phvul.011G136500' => 'pvu', 'Potri.002G215600' => 'ptr', 'Potri.008G201600' => 'ptr', 'Potri.014G138400' => 'ptr', 'Potri.016G142500' => 'ptr', 'Pp3c16_10580' => 'ppa', 'Pp3c5_25280' => 'ppa', 'Prupe.1G150000' => 'ppe', 'Prupe.1G150100' => 'ppe', 'Prupe.6G299600' => 'ppe', 'Prupe.8G245000' => 'ppe', 'Psat0s4927g0040' => 'psa', 'Psat1g052080' => 'psa', 'Psat1g183800' => 'psa', 'Psat3g113840' => 'psa', 'Psat3g126120' => 'psa', 'Psat3g126160' => 'psa', 'Psat3g158760' => 'psa', 'Psat3g158840' => 'psa', 'PSO170G2858' => 'pso', 'PSO339G0606' => 'pso', 'PSO384G4709' => 'pso', 'PSO407G0334' => 'pso', 'QL04p040276' => 'qlo', 'QL06p005458' => 'qlo', 'QL06p005472' => 'qlo', 'QL07p030546' => 'qlo', 'QL07p031519' => 'qlo', 'QL09p050949' => 'qlo', 'QL09p050966' => 'qlo', 'QL09p051067' => 'qlo', 'QL12p022706' => 'qlo', 'RcHm_v2.0_Chr2g0119601' => 'rch', 'RcHm_v2.0_Chr3g0459591' => 'rch', 'RcHm_v2.0_Chr4g0418521' => 'rch', 'RcHm_v2.0_Chr4g0418531' => 'rch', 'RcHm_v2.0_Chr4g0418541' => 'rch', 'RcHm_v2.0_Chr6g0291641' => 'rch', 'Rhsim01G0086300' => 'rsi', 'Rhsim01G0276300' => 'rsi', 'Rhsim01G0276500' => 'rsi', 'Rhsim04G0207700' => 'rsi', 'Rhsim05G0234500' => 'rsi', 'Rhsim13G0022400' => 'rsi', 'Sabra02G0167900' => 'sbr', 'Sabra04G0158500' => 'sbr', 'Sabra08G0159800' => 'sbr', 'Sabra10G0011500' => 'sbr', 'Sabra14G0104400' => 'sbr', 'SalBow2G2440' => 'sbo', 'SalBow4G2265' => 'sbo', 'Sc02g0000060' => 'sci', 'Sc05g0005020' => 'sci', 'Sc13g0003890' => 'sci', 'Sed0014865' => 'sed', 'Sed0017224' => 'sed', 'Sed0026391' => 'sed', 'SEGI_00063' => 'sgi', 'SEGI_10967' => 'sgi', 'SEGI_17510' => 'sgi', 'SEGI_24396' => 'sgi', 'SEGI_39719' => 'sgi', 'SEGI_41392' => 'sgi', 'SGA_v2.0_scaffold11G05794' => 'sas', 'SGA_v2.0_scaffold142G35607' => 'sas', 'SGA_v2.0_scaffold1G00447' => 'sas', 'SHI15388' => 'shi', 'SHI15394' => 'shi', 'SHI15396' => 'shi', 'SHI15399' => 'shi', 'SMO343G0151' => 'smo', 'SMO367G1118' => 'smo', 'Solyc01g080200.3' => 'sly', 'Solyc06g008960.3' => 'sly', 'Solyc09g064780.3' => 'sly', 'Sopen01g031980' => 'spe', 'Sopen06g003710' => 'spe', 'Sopen09g026460' => 'spe', 'Sp3g21240' => 'spa', 'Sp4g30030' => 'spa', 'TAR365G0022' => 'tar', 'TAR365G1023' => 'tar', 'TAR365G1253' => 'tar', 'TAR623G0078' => 'tar', 'TAR623G1721' => 'tar', 'TAR633G0959' => 'tar', 'THA.LOC104802225' => 'tha', 'THA.LOC104804769' => 'tha', 'THA.LOC104808660' => 'tha', 'THA.LOC104812792' => 'tha', 'Thecc.01G284000' => 'tca', 'Thecc.04G220600' => 'tca', 'Thecc.05G268900' => 'tca', 'Thecc.08G171100' => 'tca', 'Thhalv10001284m.g' => 'esa', 'Thhalv10019912m.g' => 'esa', 'TPR.G14189' => 'tpr', 'TPR.G18110' => 'tpr', 'TPR.G18130' => 'tpr', 'TPR.G18131' => 'tpr', 'TPR.G18140' => 'tpr', 'TPR.G24282' => 'tpr', 'TPR.G25221' => 'tpr', 'TPR.G29267' => 'tpr', 'TPR.G35315' => 'tpr', 'TPR.G36173' => 'tpr', 'TWI09G0794' => 'twi', 'TWI59G1348' => 'twi', 'TWI74G0430' => 'twi', 'unitig_26.g8940' => 'ugi', 'unitig_749.g13744' => 'ugi', 'unitig_749.g13745' => 'ugi', 'vmacro08269' => 'vma', 'vmacro14937' => 'vma', 'vmacro20401' => 'vma', 'VMungo0464G1349' => 'vmu', 'VMungo0540G0289' => 'vmu', 'VMungo1215G1590' => 'vmu', 'VMungo1309G0221' => 'vmu', 'VMungo1309G2815' => 'vmu', 'VMungo1383G0239' => 'vmu', 'VMungo1383G2910' => 'vmu', 'Zm00001eb095270' => 'zma', 'Zm00001eb095280' => 'zma', 'Zm00001eb111630' => 'zma', 'Zm00001eb237080' => 'zma', 'Zm00001eb273740' => 'zma', 'Zm00001eb285040' => 'zma', 'Zm00001eb330790' => 'zma', 'Zm00001eb337380' => 'zma' ) $gf_id = 'HOM05D001484' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001484' ) $data_identifier = 'HOM05D001484' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 2, 'aly' => (int) 2, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 22, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 7, 'hma' => (int) 2, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 7, 'mtr' => (int) 10, 'cme' => (int) 2, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 4, 'ppa' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 4, 'qlo' => (int) 9, 'rch' => (int) 6, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 10, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 7, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb337380' $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' => 'HOM05D001484', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p31500' => 'bna', 'A05p00020' => 'bna', 'A07p08820' => 'bna', 'Aa31LG4G3300' => 'aar', 'Aa31LG8G10030' => 'aar', 'Actinidia00731' => 'ach', 'Actinidia11473' => 'ach', 'Actinidia23469' => 'ach', 'Actinidia24318' => 'ach', 'Actinidia40196' => 'ach', 'Actinidia40197' => 'ach', 'Actinidia40198' => 'ach', 'Ah.08g212990' => 'amhyb', 'Ah.15g091720' => 'amhyb', 'AL3G38260' => 'aly', 'AL4G47710' => 'aly', 'Aqoxy2G00671' => 'aox', 'Aqoxy2G03236' => 'aox', 'arahy.Tifrunner.gnm1.ann1.05IDCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KR684' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATY3SJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK6QJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6APGL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IDT7Z9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM073U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ0R87' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LE7RV4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT4QRX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V5ENPK' => 'arhy', 'AT2G48110' => 'ath', 'AT3G23590' => 'ath', 'ATR0626G186' => 'atr', 'ATR1127G141' => 'atr', 'Atru.chr4.2583' => 'acertr', 'Atru.chr5.1358' => 'acertr', 'Atru.chr5.1359' => 'acertr', 'Atru.chr8.46' => 'acertr', 'AUR62002640' => 'cqu', 'AUR62030055' => 'cqu', 'AUR62033713' => 'cqu', 'AUR62033714' => 'cqu', 'AUR62036795' => 'cqu', 'AUR62039891' => 'cqu', 'BcaB02g08737' => 'bca', 'BcaB04g20441' => 'bca', 'BcaB06g26509' => 'bca', 'BcaB06g26510' => 'bca', 'BcaB06g26511' => 'bca', 'BcaB06g26512' => 'bca', 'BcaB06g26513' => 'bca', 'BcaC02g12564' => 'bca', 'BcaC02g12565' => 'bca', 'BcaC02g12794' => 'bca', 'BcaC02g12795' => 'bca', 'BcaC02g12796' => 'bca', 'BcaC06g35541' => 'bca', 'BNapus_Darmor_BZH_scaffold_188p00080' => 'bna', 'BNapus_Darmor_BZH_scaffold_188p00090' => 'bna', 'BolC1t03972H' => 'bol', 'BolC1t03973H' => 'bol', 'BolC4t21680H' => 'bol', 'BolC7t41863H' => 'bol', 'BolSC55t61227H' => 'bol', 'BolSC55t61228H' => 'bol', 'BraA01t03278Z' => 'bra', 'BraA05t18998Z' => 'bra', 'BraA07t28673Z' => 'bra', 'C01p40150' => 'bna', 'C05p12370' => 'bna', 'C07p13680' => 'bna', 'CAN.G1006.16' => 'can', 'CAN.G1006.17' => 'can', 'CAN.G1170.2' => 'can', 'CAN.G962.7' => 'can', 'CANSAT25G2179' => 'cansat', 'CANSAT78G1573' => 'cansat', 'CARHR099510' => 'chi', 'CARHR143510' => 'chi', 'Carub.0003s2380' => 'cru', 'Carub.0004s3082' => 'cru', 'Ca_00614_v3' => 'car', 'Ca_07801_v3' => 'car', 'Ca_08567_v3' => 'car', 'Ca_09571_v3' => 'car', 'CBR_g19290' => 'cbr', 'Cc01_g19770' => 'ccan', 'Cc03_g03030' => 'ccan', 'CDE07G0968' => 'cde', 'CDE09G1441' => 'cde', 'Cfa006103' => 'cfa', 'Cfa015573' => 'cfa', 'Cfa016988' => 'cfa', 'Ciclev10006738m.g' => 'ccl', 'Ciclev10010920m.g' => 'ccl', 'Ciclev10018517m.g' => 'ccl', 'CiPaw.01G159200' => 'cil', 'CiPaw.02G091000' => 'cil', 'CiPaw.02G091100' => 'cil', 'CiPaw.08G103100' => 'cil', 'CiPaw.09G224900' => 'cil', 'ClCG06G005740' => 'cla', 'ClCG07G000090' => 'cla', 'ClCG07G000100' => 'cla', 'COL.COLO4_09143' => 'col', 'COL.COLO4_25124' => 'col', 'Cpa.g.sc16.34' => 'cpa', 'Cpa.g.sc3504.1' => 'cpa', 'Cpa.g.sc60.37' => 'cpa', 'CsaV3_6G018520' => 'csa', 'CsaV3_6G036860' => 'csa', 'CSS0001072' => 'camsi', 'CSS0020208' => 'camsi', 'CSS0021253' => 'camsi', 'CSS0022190' => 'camsi', 'CSS0036150' => 'camsi', 'CSS0040442' => 'camsi', 'CSS0042300' => 'camsi', 'CSS0045298' => 'camsi', 'DCAR_012449' => 'dca', 'DCAR_018405' => 'dca', 'DCAR_024573' => 'dca', 'DCAR_030591' => 'dca', 'Dinv16926' => 'din', 'Dinv32963' => 'din', 'Dinv38382' => 'din', 'Dinv38383' => 'din', 'Duzib133G0974' => 'dzi', 'Duzib138G1867' => 'dzi', 'Duzib211G0420' => 'dzi', 'Duzib212G0930' => 'dzi', 'ECA234G1645' => 'eca', 'ECA247G3467' => 'eca', 'ECA248G1703' => 'eca', 'EL10Ac3g06327' => 'bvu', 'EL10Ac7g17204' => 'bvu', 'Eucgr.A00855' => 'egr', 'Eucgr.A00858' => 'egr', 'Eucgr.H01520' => 'egr', 'Eucgr.H03604' => 'egr', 'Eucgr.L03465' => 'egr', 'Eucgr.L03466' => 'egr', 'FAN01G0988' => 'fan', 'FAN02G3892' => 'fan', 'FAN05G3381' => 'fan', 'FAN07G0967' => 'fan', 'FAN07G1493' => 'fan', 'FAN08G3125' => 'fan', 'FAN09G0402' => 'fan', 'FAN12G2594' => 'fan', 'FAN12G3879' => 'fan', 'FAN14G1546' => 'fan', 'FAN15G3626' => 'fan', 'FAN17G0588' => 'fan', 'FAN17G0609' => 'fan', 'FAN18G2817' => 'fan', 'FAN19G1305' => 'fan', 'FAN20G1787' => 'fan', 'FAN22G0073' => 'fan', 'FAN22G0352' => 'fan', 'FAN22G0368' => 'fan', 'FAN22G2273' => 'fan', 'FAN24G1998' => 'fan', 'FAN27G1317' => 'fan', 'FvH4_2g23980' => 'fve', 'FvH4_4g14380' => 'fve', 'FvH4_4g14390' => 'fve', 'FvH4_6g09250' => 'fve', 'Glyma.03G151100' => 'gma', 'Glyma.04G122550' => 'gma', 'Glyma.05G001600' => 'gma', 'Glyma.09G270766' => 'gma', 'Glyma.09G270832' => 'gma', 'Glyma.13G209800' => 'gma', 'Glyma.15G102800' => 'gma', 'Glyma.18G218900' => 'gma', 'Glyma.19G001500' => 'gma', 'Glyma.19G153600' => 'gma', 'Gohir.A02G028600' => 'ghi', 'Gohir.A08G045000' => 'ghi', 'Gohir.A11G120500' => 'ghi', 'Gohir.A12G006200' => 'ghi', 'Gohir.A12G006250' => 'ghi', 'Gohir.D02G036300' => 'ghi', 'Gohir.D08G054700' => 'ghi', 'Gohir.D11G125600' => 'ghi', 'Gohir.D12G005700' => 'ghi', 'Gorai.004G055200' => 'gra', 'Gorai.005G040400' => 'gra', 'Gorai.007G134500' => 'gra', 'Gorai.008G005500' => 'gra', 'GSVIVG01011094001' => 'vvi', 'GSVIVG01017879001' => 'vvi', 'GSVIVG01025988001' => 'vvi', 'GSVIVG01029847001' => 'vvi', 'HanXRQChr10g0282901' => 'han', 'HanXRQChr10g0310371' => 'han', 'HanXRQChr10g0315041' => 'han', 'HanXRQChr11g0327651' => 'han', 'HanXRQChr12g0359391' => 'han', 'Haze_00972' => 'cav', 'Haze_00973' => 'cav', 'Haze_00974' => 'cav', 'Haze_04747' => 'cav', 'Haze_04749' => 'cav', 'Haze_04750' => 'cav', 'Haze_21217' => 'cav', 'Hma1.2p1_1037F.1_g250680' => 'hma', 'Hma1.2p1_1644F.1_g295320' => 'hma', 'HPP92_011322' => 'vpl', 'HPP92_011323' => 'vpl', 'HPP92_011324' => 'vpl', 'HPP92_011325' => 'vpl', 'HPP92_011326' => 'vpl', 'Hund12205' => 'sun', 'Hund17957' => 'sun', 'Lalb_Chr06g0176771' => 'lal', 'Lalb_Chr18g0056021' => 'lal', 'Lalb_Chr18g0056031' => 'lal', 'Lalb_Chr18g0056041' => 'lal', 'Lalb_Chr20g0107751' => 'lal', 'Lalb_Chr20g0118371' => 'lal', 'Lj1g0010239' => 'lja', 'Lj1g0017101' => 'lja', 'Lj2A1178G40' => 'lonja', 'Lj2A54G84' => 'lonja', 'Lj2g0015248' => 'lja', 'Lj3A761T51' => 'lonja', 'Lj6g0018116' => 'lja', 'Lsat_1_v5_gn_4_136040' => 'lsa', 'Lsat_1_v5_gn_5_187461' => 'lsa', 'Lsat_1_v5_gn_5_77001' => 'lsa', 'Lsat_1_v5_gn_9_4461' => 'lsa', 'Manes.01G210100' => 'mes', 'Manes.03G185600' => 'mes', 'Manes.05G073300' => 'mes', 'Manes.09G120300' => 'mes', 'Manes.15G022100' => 'mes', 'Mapoly0096s0053' => 'mpo', 'MBI03_g14058_MAGBIO' => 'mbi', 'MBI03_g33876_MAGBIO' => 'mbi', 'MBI03_g36854_MAGBIO' => 'mbi', 'MBI17_g11997_MAGBIO' => 'mbi', 'MD03G1269000' => 'mdo', 'MD04G1179600' => 'mdo', 'MD11G1289800' => 'mdo', 'MD12G1194700' => 'mdo', 'MD13G1182100' => 'mdo', 'MD13G1182200' => 'mdo', 'MD16G1182600' => 'mdo', 'Medtr2g021400' => 'mtr', 'Medtr2g021470' => 'mtr', 'Medtr2g105810' => 'mtr', 'Medtr3g033580' => 'mtr', 'Medtr6g007970' => 'mtr', 'Medtr7g056330' => 'mtr', 'Medtr7g074290' => 'mtr', 'Medtr7g074380' => 'mtr', 'Medtr7g094550' => 'mtr', 'Medtr8g069995' => 'mtr', 'MELO3C014345.2' => 'cme', 'MELO3C021395.2' => 'cme', 'Migut.D00262' => 'egut', 'Migut.G00257' => 'egut', 'MSTRG.21575' => 'ama', 'MSTRG.3985' => 'ama', 'Nitab4.5_0000295g0140' => 'nta', 'Nitab4.5_0000732g0140' => 'nta', 'Nitab4.5_0003162g0020' => 'nta', 'Nitab4.5_0006180g0090' => 'nta', 'Nitab4.5_0006390g0010' => 'nta', 'Nitab4.5_0007392g0040' => 'nta', 'Nn1g02140' => 'nnu', 'Nn4g26168' => 'nnu', 'Nn5g26754' => 'nnu', 'Oeu001433.1' => 'oeu', 'Oeu010299.2' => 'oeu', 'Oeu011171.1' => 'oeu', 'Oeu037675.1' => 'oeu', 'Oeu038359.1' => 'oeu', 'Oeu063834.1' => 'oeu', 'Oeu063835.1' => 'oeu', 'Os05g0312000' => 'osa', 'Os07g0211101' => 'osa', 'Os07g0211200' => 'osa', 'Os07g0681500' => 'osa', 'Peaxi162Scf00095g01015' => 'pax', 'Peaxi162Scf00104g00329' => 'pax', 'Peaxi162Scf00161g00137' => 'pax', 'PGR004G1665' => 'pgr', 'PGR031G2937' => 'pgr', 'PGR119G2145' => 'pgr', 'PGSC0003DMG400004351' => 'stu', 'PGSC0003DMG400014625' => 'stu', 'PGSC0003DMG401000943' => 'stu', 'Phvul.001G148600' => 'pvu', 'Phvul.004G001700' => 'pvu', 'Phvul.006G154900' => 'pvu', 'Phvul.008G078200' => 'pvu', 'Phvul.011G136500' => 'pvu', 'Potri.002G215600' => 'ptr', 'Potri.008G201600' => 'ptr', 'Potri.014G138400' => 'ptr', 'Potri.016G142500' => 'ptr', 'Pp3c16_10580' => 'ppa', 'Pp3c5_25280' => 'ppa', 'Prupe.1G150000' => 'ppe', 'Prupe.1G150100' => 'ppe', 'Prupe.6G299600' => 'ppe', 'Prupe.8G245000' => 'ppe', 'Psat0s4927g0040' => 'psa', 'Psat1g052080' => 'psa', 'Psat1g183800' => 'psa', 'Psat3g113840' => 'psa', 'Psat3g126120' => 'psa', 'Psat3g126160' => 'psa', 'Psat3g158760' => 'psa', 'Psat3g158840' => 'psa', 'PSO170G2858' => 'pso', 'PSO339G0606' => 'pso', 'PSO384G4709' => 'pso', 'PSO407G0334' => 'pso', 'QL04p040276' => 'qlo', 'QL06p005458' => 'qlo', 'QL06p005472' => 'qlo', 'QL07p030546' => 'qlo', 'QL07p031519' => 'qlo', 'QL09p050949' => 'qlo', 'QL09p050966' => 'qlo', 'QL09p051067' => 'qlo', 'QL12p022706' => 'qlo', 'RcHm_v2.0_Chr2g0119601' => 'rch', 'RcHm_v2.0_Chr3g0459591' => 'rch', 'RcHm_v2.0_Chr4g0418521' => 'rch', 'RcHm_v2.0_Chr4g0418531' => 'rch', 'RcHm_v2.0_Chr4g0418541' => 'rch', 'RcHm_v2.0_Chr6g0291641' => 'rch', 'Rhsim01G0086300' => 'rsi', 'Rhsim01G0276300' => 'rsi', 'Rhsim01G0276500' => 'rsi', 'Rhsim04G0207700' => 'rsi', 'Rhsim05G0234500' => 'rsi', 'Rhsim13G0022400' => 'rsi', 'Sabra02G0167900' => 'sbr', 'Sabra04G0158500' => 'sbr', 'Sabra08G0159800' => 'sbr', 'Sabra10G0011500' => 'sbr', 'Sabra14G0104400' => 'sbr', 'SalBow2G2440' => 'sbo', 'SalBow4G2265' => 'sbo', 'Sc02g0000060' => 'sci', 'Sc05g0005020' => 'sci', 'Sc13g0003890' => 'sci', 'Sed0014865' => 'sed', 'Sed0017224' => 'sed', 'Sed0026391' => 'sed', 'SEGI_00063' => 'sgi', 'SEGI_10967' => 'sgi', 'SEGI_17510' => 'sgi', 'SEGI_24396' => 'sgi', 'SEGI_39719' => 'sgi', 'SEGI_41392' => 'sgi', 'SGA_v2.0_scaffold11G05794' => 'sas', 'SGA_v2.0_scaffold142G35607' => 'sas', 'SGA_v2.0_scaffold1G00447' => 'sas', 'SHI15388' => 'shi', 'SHI15394' => 'shi', 'SHI15396' => 'shi', 'SHI15399' => 'shi', 'SMO343G0151' => 'smo', 'SMO367G1118' => 'smo', 'Solyc01g080200.3' => 'sly', 'Solyc06g008960.3' => 'sly', 'Solyc09g064780.3' => 'sly', 'Sopen01g031980' => 'spe', 'Sopen06g003710' => 'spe', 'Sopen09g026460' => 'spe', 'Sp3g21240' => 'spa', 'Sp4g30030' => 'spa', 'TAR365G0022' => 'tar', 'TAR365G1023' => 'tar', 'TAR365G1253' => 'tar', 'TAR623G0078' => 'tar', 'TAR623G1721' => 'tar', 'TAR633G0959' => 'tar', 'THA.LOC104802225' => 'tha', 'THA.LOC104804769' => 'tha', 'THA.LOC104808660' => 'tha', 'THA.LOC104812792' => 'tha', 'Thecc.01G284000' => 'tca', 'Thecc.04G220600' => 'tca', 'Thecc.05G268900' => 'tca', 'Thecc.08G171100' => 'tca', 'Thhalv10001284m.g' => 'esa', 'Thhalv10019912m.g' => 'esa', 'TPR.G14189' => 'tpr', 'TPR.G18110' => 'tpr', 'TPR.G18130' => 'tpr', 'TPR.G18131' => 'tpr', 'TPR.G18140' => 'tpr', 'TPR.G24282' => 'tpr', 'TPR.G25221' => 'tpr', 'TPR.G29267' => 'tpr', 'TPR.G35315' => 'tpr', 'TPR.G36173' => 'tpr', 'TWI09G0794' => 'twi', 'TWI59G1348' => 'twi', 'TWI74G0430' => 'twi', 'unitig_26.g8940' => 'ugi', 'unitig_749.g13744' => 'ugi', 'unitig_749.g13745' => 'ugi', 'vmacro08269' => 'vma', 'vmacro14937' => 'vma', 'vmacro20401' => 'vma', 'VMungo0464G1349' => 'vmu', 'VMungo0540G0289' => 'vmu', 'VMungo1215G1590' => 'vmu', 'VMungo1309G0221' => 'vmu', 'VMungo1309G2815' => 'vmu', 'VMungo1383G0239' => 'vmu', 'VMungo1383G2910' => 'vmu', 'Zm00001eb095270' => 'zma', 'Zm00001eb095280' => 'zma', 'Zm00001eb111630' => 'zma', 'Zm00001eb237080' => 'zma', 'Zm00001eb273740' => 'zma', 'Zm00001eb285040' => 'zma', 'Zm00001eb330790' => 'zma', 'Zm00001eb337380' => 'zma' ), 'gf_id' => 'HOM05D001484', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001484' ), 'data_identifier' => 'HOM05D001484', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001484', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p31500' => 'bna', 'A05p00020' => 'bna', 'A07p08820' => 'bna', 'Aa31LG4G3300' => 'aar', 'Aa31LG8G10030' => 'aar', 'Actinidia00731' => 'ach', 'Actinidia11473' => 'ach', 'Actinidia23469' => 'ach', 'Actinidia24318' => 'ach', 'Actinidia40196' => 'ach', 'Actinidia40197' => 'ach', 'Actinidia40198' => 'ach', 'Ah.08g212990' => 'amhyb', 'Ah.15g091720' => 'amhyb', 'AL3G38260' => 'aly', 'AL4G47710' => 'aly', 'Aqoxy2G00671' => 'aox', 'Aqoxy2G03236' => 'aox', 'arahy.Tifrunner.gnm1.ann1.05IDCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KR684' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATY3SJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK6QJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6APGL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IDT7Z9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM073U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ0R87' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LE7RV4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT4QRX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V5ENPK' => 'arhy', 'AT2G48110' => 'ath', 'AT3G23590' => 'ath', 'ATR0626G186' => 'atr', 'ATR1127G141' => 'atr', 'Atru.chr4.2583' => 'acertr', 'Atru.chr5.1358' => 'acertr', 'Atru.chr5.1359' => 'acertr', 'Atru.chr8.46' => 'acertr', 'AUR62002640' => 'cqu', 'AUR62030055' => 'cqu', 'AUR62033713' => 'cqu', 'AUR62033714' => 'cqu', 'AUR62036795' => 'cqu', 'AUR62039891' => 'cqu', 'BcaB02g08737' => 'bca', 'BcaB04g20441' => 'bca', 'BcaB06g26509' => 'bca', 'BcaB06g26510' => 'bca', 'BcaB06g26511' => 'bca', 'BcaB06g26512' => 'bca', 'BcaB06g26513' => 'bca', 'BcaC02g12564' => 'bca', 'BcaC02g12565' => 'bca', 'BcaC02g12794' => 'bca', 'BcaC02g12795' => 'bca', 'BcaC02g12796' => 'bca', 'BcaC06g35541' => 'bca', 'BNapus_Darmor_BZH_scaffold_188p00080' => 'bna', 'BNapus_Darmor_BZH_scaffold_188p00090' => 'bna', 'BolC1t03972H' => 'bol', 'BolC1t03973H' => 'bol', 'BolC4t21680H' => 'bol', 'BolC7t41863H' => 'bol', 'BolSC55t61227H' => 'bol', 'BolSC55t61228H' => 'bol', 'BraA01t03278Z' => 'bra', 'BraA05t18998Z' => 'bra', 'BraA07t28673Z' => 'bra', 'C01p40150' => 'bna', 'C05p12370' => 'bna', 'C07p13680' => 'bna', 'CAN.G1006.16' => 'can', 'CAN.G1006.17' => 'can', 'CAN.G1170.2' => 'can', 'CAN.G962.7' => 'can', 'CANSAT25G2179' => 'cansat', 'CANSAT78G1573' => 'cansat', 'CARHR099510' => 'chi', 'CARHR143510' => 'chi', 'Carub.0003s2380' => 'cru', 'Carub.0004s3082' => 'cru', 'Ca_00614_v3' => 'car', 'Ca_07801_v3' => 'car', 'Ca_08567_v3' => 'car', 'Ca_09571_v3' => 'car', 'CBR_g19290' => 'cbr', 'Cc01_g19770' => 'ccan', 'Cc03_g03030' => 'ccan', 'CDE07G0968' => 'cde', 'CDE09G1441' => 'cde', 'Cfa006103' => 'cfa', 'Cfa015573' => 'cfa', 'Cfa016988' => 'cfa', 'Ciclev10006738m.g' => 'ccl', 'Ciclev10010920m.g' => 'ccl', 'Ciclev10018517m.g' => 'ccl', 'CiPaw.01G159200' => 'cil', 'CiPaw.02G091000' => 'cil', 'CiPaw.02G091100' => 'cil', 'CiPaw.08G103100' => 'cil', 'CiPaw.09G224900' => 'cil', 'ClCG06G005740' => 'cla', 'ClCG07G000090' => 'cla', 'ClCG07G000100' => 'cla', 'COL.COLO4_09143' => 'col', 'COL.COLO4_25124' => 'col', 'Cpa.g.sc16.34' => 'cpa', 'Cpa.g.sc3504.1' => 'cpa', 'Cpa.g.sc60.37' => 'cpa', 'CsaV3_6G018520' => 'csa', 'CsaV3_6G036860' => 'csa', 'CSS0001072' => 'camsi', 'CSS0020208' => 'camsi', 'CSS0021253' => 'camsi', 'CSS0022190' => 'camsi', 'CSS0036150' => 'camsi', 'CSS0040442' => 'camsi', 'CSS0042300' => 'camsi', 'CSS0045298' => 'camsi', 'DCAR_012449' => 'dca', 'DCAR_018405' => 'dca', 'DCAR_024573' => 'dca', 'DCAR_030591' => 'dca', 'Dinv16926' => 'din', 'Dinv32963' => 'din', 'Dinv38382' => 'din', 'Dinv38383' => 'din', 'Duzib133G0974' => 'dzi', 'Duzib138G1867' => 'dzi', 'Duzib211G0420' => 'dzi', 'Duzib212G0930' => 'dzi', 'ECA234G1645' => 'eca', 'ECA247G3467' => 'eca', 'ECA248G1703' => 'eca', 'EL10Ac3g06327' => 'bvu', 'EL10Ac7g17204' => 'bvu', 'Eucgr.A00855' => 'egr', 'Eucgr.A00858' => 'egr', 'Eucgr.H01520' => 'egr', 'Eucgr.H03604' => 'egr', 'Eucgr.L03465' => 'egr', 'Eucgr.L03466' => 'egr', 'FAN01G0988' => 'fan', 'FAN02G3892' => 'fan', 'FAN05G3381' => 'fan', 'FAN07G0967' => 'fan', 'FAN07G1493' => 'fan', 'FAN08G3125' => 'fan', 'FAN09G0402' => 'fan', 'FAN12G2594' => 'fan', 'FAN12G3879' => 'fan', 'FAN14G1546' => 'fan', 'FAN15G3626' => 'fan', 'FAN17G0588' => 'fan', 'FAN17G0609' => 'fan', 'FAN18G2817' => 'fan', 'FAN19G1305' => 'fan', 'FAN20G1787' => 'fan', 'FAN22G0073' => 'fan', 'FAN22G0352' => 'fan', 'FAN22G0368' => 'fan', 'FAN22G2273' => 'fan', 'FAN24G1998' => 'fan', 'FAN27G1317' => 'fan', 'FvH4_2g23980' => 'fve', 'FvH4_4g14380' => 'fve', 'FvH4_4g14390' => 'fve', 'FvH4_6g09250' => 'fve', 'Glyma.03G151100' => 'gma', 'Glyma.04G122550' => 'gma', 'Glyma.05G001600' => 'gma', 'Glyma.09G270766' => 'gma', 'Glyma.09G270832' => 'gma', 'Glyma.13G209800' => 'gma', 'Glyma.15G102800' => 'gma', 'Glyma.18G218900' => 'gma', 'Glyma.19G001500' => 'gma', 'Glyma.19G153600' => 'gma', 'Gohir.A02G028600' => 'ghi', 'Gohir.A08G045000' => 'ghi', 'Gohir.A11G120500' => 'ghi', 'Gohir.A12G006200' => 'ghi', 'Gohir.A12G006250' => 'ghi', 'Gohir.D02G036300' => 'ghi', 'Gohir.D08G054700' => 'ghi', 'Gohir.D11G125600' => 'ghi', 'Gohir.D12G005700' => 'ghi', 'Gorai.004G055200' => 'gra', 'Gorai.005G040400' => 'gra', 'Gorai.007G134500' => 'gra', 'Gorai.008G005500' => 'gra', 'GSVIVG01011094001' => 'vvi', 'GSVIVG01017879001' => 'vvi', 'GSVIVG01025988001' => 'vvi', 'GSVIVG01029847001' => 'vvi', 'HanXRQChr10g0282901' => 'han', 'HanXRQChr10g0310371' => 'han', 'HanXRQChr10g0315041' => 'han', 'HanXRQChr11g0327651' => 'han', 'HanXRQChr12g0359391' => 'han', 'Haze_00972' => 'cav', 'Haze_00973' => 'cav', 'Haze_00974' => 'cav', 'Haze_04747' => 'cav', 'Haze_04749' => 'cav', 'Haze_04750' => 'cav', 'Haze_21217' => 'cav', 'Hma1.2p1_1037F.1_g250680' => 'hma', 'Hma1.2p1_1644F.1_g295320' => 'hma', 'HPP92_011322' => 'vpl', 'HPP92_011323' => 'vpl', 'HPP92_011324' => 'vpl', 'HPP92_011325' => 'vpl', 'HPP92_011326' => 'vpl', 'Hund12205' => 'sun', 'Hund17957' => 'sun', 'Lalb_Chr06g0176771' => 'lal', 'Lalb_Chr18g0056021' => 'lal', 'Lalb_Chr18g0056031' => 'lal', 'Lalb_Chr18g0056041' => 'lal', 'Lalb_Chr20g0107751' => 'lal', 'Lalb_Chr20g0118371' => 'lal', 'Lj1g0010239' => 'lja', 'Lj1g0017101' => 'lja', 'Lj2A1178G40' => 'lonja', 'Lj2A54G84' => 'lonja', 'Lj2g0015248' => 'lja', 'Lj3A761T51' => 'lonja', 'Lj6g0018116' => 'lja', 'Lsat_1_v5_gn_4_136040' => 'lsa', 'Lsat_1_v5_gn_5_187461' => 'lsa', 'Lsat_1_v5_gn_5_77001' => 'lsa', 'Lsat_1_v5_gn_9_4461' => 'lsa', 'Manes.01G210100' => 'mes', 'Manes.03G185600' => 'mes', 'Manes.05G073300' => 'mes', 'Manes.09G120300' => 'mes', 'Manes.15G022100' => 'mes', 'Mapoly0096s0053' => 'mpo', 'MBI03_g14058_MAGBIO' => 'mbi', 'MBI03_g33876_MAGBIO' => 'mbi', 'MBI03_g36854_MAGBIO' => 'mbi', 'MBI17_g11997_MAGBIO' => 'mbi', 'MD03G1269000' => 'mdo', 'MD04G1179600' => 'mdo', 'MD11G1289800' => 'mdo', 'MD12G1194700' => 'mdo', 'MD13G1182100' => 'mdo', 'MD13G1182200' => 'mdo', 'MD16G1182600' => 'mdo', 'Medtr2g021400' => 'mtr', 'Medtr2g021470' => 'mtr', 'Medtr2g105810' => 'mtr', 'Medtr3g033580' => 'mtr', 'Medtr6g007970' => 'mtr', 'Medtr7g056330' => 'mtr', 'Medtr7g074290' => 'mtr', 'Medtr7g074380' => 'mtr', 'Medtr7g094550' => 'mtr', 'Medtr8g069995' => 'mtr', 'MELO3C014345.2' => 'cme', 'MELO3C021395.2' => 'cme', 'Migut.D00262' => 'egut', 'Migut.G00257' => 'egut', 'MSTRG.21575' => 'ama', 'MSTRG.3985' => 'ama', 'Nitab4.5_0000295g0140' => 'nta', 'Nitab4.5_0000732g0140' => 'nta', 'Nitab4.5_0003162g0020' => 'nta', 'Nitab4.5_0006180g0090' => 'nta', 'Nitab4.5_0006390g0010' => 'nta', 'Nitab4.5_0007392g0040' => 'nta', 'Nn1g02140' => 'nnu', 'Nn4g26168' => 'nnu', 'Nn5g26754' => 'nnu', 'Oeu001433.1' => 'oeu', 'Oeu010299.2' => 'oeu', 'Oeu011171.1' => 'oeu', 'Oeu037675.1' => 'oeu', 'Oeu038359.1' => 'oeu', 'Oeu063834.1' => 'oeu', 'Oeu063835.1' => 'oeu', 'Os05g0312000' => 'osa', 'Os07g0211101' => 'osa', 'Os07g0211200' => 'osa', 'Os07g0681500' => 'osa', 'Peaxi162Scf00095g01015' => 'pax', 'Peaxi162Scf00104g00329' => 'pax', 'Peaxi162Scf00161g00137' => 'pax', 'PGR004G1665' => 'pgr', 'PGR031G2937' => 'pgr', 'PGR119G2145' => 'pgr', 'PGSC0003DMG400004351' => 'stu', 'PGSC0003DMG400014625' => 'stu', 'PGSC0003DMG401000943' => 'stu', 'Phvul.001G148600' => 'pvu', 'Phvul.004G001700' => 'pvu', 'Phvul.006G154900' => 'pvu', 'Phvul.008G078200' => 'pvu', 'Phvul.011G136500' => 'pvu', 'Potri.002G215600' => 'ptr', 'Potri.008G201600' => 'ptr', 'Potri.014G138400' => 'ptr', 'Potri.016G142500' => 'ptr', 'Pp3c16_10580' => 'ppa', 'Pp3c5_25280' => 'ppa', 'Prupe.1G150000' => 'ppe', 'Prupe.1G150100' => 'ppe', 'Prupe.6G299600' => 'ppe', 'Prupe.8G245000' => 'ppe', 'Psat0s4927g0040' => 'psa', 'Psat1g052080' => 'psa', 'Psat1g183800' => 'psa', 'Psat3g113840' => 'psa', 'Psat3g126120' => 'psa', 'Psat3g126160' => 'psa', 'Psat3g158760' => 'psa', 'Psat3g158840' => 'psa', 'PSO170G2858' => 'pso', 'PSO339G0606' => 'pso', 'PSO384G4709' => 'pso', 'PSO407G0334' => 'pso', 'QL04p040276' => 'qlo', 'QL06p005458' => 'qlo', 'QL06p005472' => 'qlo', 'QL07p030546' => 'qlo', 'QL07p031519' => 'qlo', 'QL09p050949' => 'qlo', 'QL09p050966' => 'qlo', 'QL09p051067' => 'qlo', 'QL12p022706' => 'qlo', 'RcHm_v2.0_Chr2g0119601' => 'rch', 'RcHm_v2.0_Chr3g0459591' => 'rch', 'RcHm_v2.0_Chr4g0418521' => 'rch', 'RcHm_v2.0_Chr4g0418531' => 'rch', 'RcHm_v2.0_Chr4g0418541' => 'rch', 'RcHm_v2.0_Chr6g0291641' => 'rch', 'Rhsim01G0086300' => 'rsi', 'Rhsim01G0276300' => 'rsi', 'Rhsim01G0276500' => 'rsi', 'Rhsim04G0207700' => 'rsi', 'Rhsim05G0234500' => 'rsi', 'Rhsim13G0022400' => 'rsi', 'Sabra02G0167900' => 'sbr', 'Sabra04G0158500' => 'sbr', 'Sabra08G0159800' => 'sbr', 'Sabra10G0011500' => 'sbr', 'Sabra14G0104400' => 'sbr', 'SalBow2G2440' => 'sbo', 'SalBow4G2265' => 'sbo', 'Sc02g0000060' => 'sci', 'Sc05g0005020' => 'sci', 'Sc13g0003890' => 'sci', 'Sed0014865' => 'sed', 'Sed0017224' => 'sed', 'Sed0026391' => 'sed', 'SEGI_00063' => 'sgi', 'SEGI_10967' => 'sgi', 'SEGI_17510' => 'sgi', 'SEGI_24396' => 'sgi', 'SEGI_39719' => 'sgi', 'SEGI_41392' => 'sgi', 'SGA_v2.0_scaffold11G05794' => 'sas', 'SGA_v2.0_scaffold142G35607' => 'sas', 'SGA_v2.0_scaffold1G00447' => 'sas', 'SHI15388' => 'shi', 'SHI15394' => 'shi', 'SHI15396' => 'shi', 'SHI15399' => 'shi', 'SMO343G0151' => 'smo', 'SMO367G1118' => 'smo', 'Solyc01g080200.3' => 'sly', 'Solyc06g008960.3' => 'sly', 'Solyc09g064780.3' => 'sly', 'Sopen01g031980' => 'spe', 'Sopen06g003710' => 'spe', 'Sopen09g026460' => 'spe', 'Sp3g21240' => 'spa', 'Sp4g30030' => 'spa', 'TAR365G0022' => 'tar', 'TAR365G1023' => 'tar', 'TAR365G1253' => 'tar', 'TAR623G0078' => 'tar', 'TAR623G1721' => 'tar', 'TAR633G0959' => 'tar', 'THA.LOC104802225' => 'tha', 'THA.LOC104804769' => 'tha', 'THA.LOC104808660' => 'tha', 'THA.LOC104812792' => 'tha', 'Thecc.01G284000' => 'tca', 'Thecc.04G220600' => 'tca', 'Thecc.05G268900' => 'tca', 'Thecc.08G171100' => 'tca', 'Thhalv10001284m.g' => 'esa', 'Thhalv10019912m.g' => 'esa', 'TPR.G14189' => 'tpr', 'TPR.G18110' => 'tpr', 'TPR.G18130' => 'tpr', 'TPR.G18131' => 'tpr', 'TPR.G18140' => 'tpr', 'TPR.G24282' => 'tpr', 'TPR.G25221' => 'tpr', 'TPR.G29267' => 'tpr', 'TPR.G35315' => 'tpr', 'TPR.G36173' => 'tpr', 'TWI09G0794' => 'twi', 'TWI59G1348' => 'twi', 'TWI74G0430' => 'twi', 'unitig_26.g8940' => 'ugi', 'unitig_749.g13744' => 'ugi', 'unitig_749.g13745' => 'ugi', 'vmacro08269' => 'vma', 'vmacro14937' => 'vma', 'vmacro20401' => 'vma', 'VMungo0464G1349' => 'vmu', 'VMungo0540G0289' => 'vmu', 'VMungo1215G1590' => 'vmu', 'VMungo1309G0221' => 'vmu', 'VMungo1309G2815' => 'vmu', 'VMungo1383G0239' => 'vmu', 'VMungo1383G2910' => 'vmu', 'Zm00001eb095270' => 'zma', 'Zm00001eb095280' => 'zma', 'Zm00001eb111630' => 'zma', 'Zm00001eb237080' => 'zma', 'Zm00001eb273740' => 'zma', 'Zm00001eb285040' => 'zma', 'Zm00001eb330790' => 'zma', 'Zm00001eb337380' => 'zma' ) $gf_id = 'HOM05D001484' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001484' ) $data_identifier = 'HOM05D001484' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 2, 'aly' => (int) 2, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 22, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 7, 'hma' => (int) 2, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 7, 'mtr' => (int) 10, 'cme' => (int) 2, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 4, 'ppa' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 4, 'qlo' => (int) 9, 'rch' => (int) 6, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 10, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 7, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb337380' $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' => 'HOM05D001484', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p31500' => 'bna', 'A05p00020' => 'bna', 'A07p08820' => 'bna', 'Aa31LG4G3300' => 'aar', 'Aa31LG8G10030' => 'aar', 'Actinidia00731' => 'ach', 'Actinidia11473' => 'ach', 'Actinidia23469' => 'ach', 'Actinidia24318' => 'ach', 'Actinidia40196' => 'ach', 'Actinidia40197' => 'ach', 'Actinidia40198' => 'ach', 'Ah.08g212990' => 'amhyb', 'Ah.15g091720' => 'amhyb', 'AL3G38260' => 'aly', 'AL4G47710' => 'aly', 'Aqoxy2G00671' => 'aox', 'Aqoxy2G03236' => 'aox', 'arahy.Tifrunner.gnm1.ann1.05IDCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KR684' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATY3SJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK6QJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6APGL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IDT7Z9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM073U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ0R87' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LE7RV4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT4QRX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V5ENPK' => 'arhy', 'AT2G48110' => 'ath', 'AT3G23590' => 'ath', 'ATR0626G186' => 'atr', 'ATR1127G141' => 'atr', 'Atru.chr4.2583' => 'acertr', 'Atru.chr5.1358' => 'acertr', 'Atru.chr5.1359' => 'acertr', 'Atru.chr8.46' => 'acertr', 'AUR62002640' => 'cqu', 'AUR62030055' => 'cqu', 'AUR62033713' => 'cqu', 'AUR62033714' => 'cqu', 'AUR62036795' => 'cqu', 'AUR62039891' => 'cqu', 'BcaB02g08737' => 'bca', 'BcaB04g20441' => 'bca', 'BcaB06g26509' => 'bca', 'BcaB06g26510' => 'bca', 'BcaB06g26511' => 'bca', 'BcaB06g26512' => 'bca', 'BcaB06g26513' => 'bca', 'BcaC02g12564' => 'bca', 'BcaC02g12565' => 'bca', 'BcaC02g12794' => 'bca', 'BcaC02g12795' => 'bca', 'BcaC02g12796' => 'bca', 'BcaC06g35541' => 'bca', 'BNapus_Darmor_BZH_scaffold_188p00080' => 'bna', 'BNapus_Darmor_BZH_scaffold_188p00090' => 'bna', 'BolC1t03972H' => 'bol', 'BolC1t03973H' => 'bol', 'BolC4t21680H' => 'bol', 'BolC7t41863H' => 'bol', 'BolSC55t61227H' => 'bol', 'BolSC55t61228H' => 'bol', 'BraA01t03278Z' => 'bra', 'BraA05t18998Z' => 'bra', 'BraA07t28673Z' => 'bra', 'C01p40150' => 'bna', 'C05p12370' => 'bna', 'C07p13680' => 'bna', 'CAN.G1006.16' => 'can', 'CAN.G1006.17' => 'can', 'CAN.G1170.2' => 'can', 'CAN.G962.7' => 'can', 'CANSAT25G2179' => 'cansat', 'CANSAT78G1573' => 'cansat', 'CARHR099510' => 'chi', 'CARHR143510' => 'chi', 'Carub.0003s2380' => 'cru', 'Carub.0004s3082' => 'cru', 'Ca_00614_v3' => 'car', 'Ca_07801_v3' => 'car', 'Ca_08567_v3' => 'car', 'Ca_09571_v3' => 'car', 'CBR_g19290' => 'cbr', 'Cc01_g19770' => 'ccan', 'Cc03_g03030' => 'ccan', 'CDE07G0968' => 'cde', 'CDE09G1441' => 'cde', 'Cfa006103' => 'cfa', 'Cfa015573' => 'cfa', 'Cfa016988' => 'cfa', 'Ciclev10006738m.g' => 'ccl', 'Ciclev10010920m.g' => 'ccl', 'Ciclev10018517m.g' => 'ccl', 'CiPaw.01G159200' => 'cil', 'CiPaw.02G091000' => 'cil', 'CiPaw.02G091100' => 'cil', 'CiPaw.08G103100' => 'cil', 'CiPaw.09G224900' => 'cil', 'ClCG06G005740' => 'cla', 'ClCG07G000090' => 'cla', 'ClCG07G000100' => 'cla', 'COL.COLO4_09143' => 'col', 'COL.COLO4_25124' => 'col', 'Cpa.g.sc16.34' => 'cpa', 'Cpa.g.sc3504.1' => 'cpa', 'Cpa.g.sc60.37' => 'cpa', 'CsaV3_6G018520' => 'csa', 'CsaV3_6G036860' => 'csa', 'CSS0001072' => 'camsi', 'CSS0020208' => 'camsi', 'CSS0021253' => 'camsi', 'CSS0022190' => 'camsi', 'CSS0036150' => 'camsi', 'CSS0040442' => 'camsi', 'CSS0042300' => 'camsi', 'CSS0045298' => 'camsi', 'DCAR_012449' => 'dca', 'DCAR_018405' => 'dca', 'DCAR_024573' => 'dca', 'DCAR_030591' => 'dca', 'Dinv16926' => 'din', 'Dinv32963' => 'din', 'Dinv38382' => 'din', 'Dinv38383' => 'din', 'Duzib133G0974' => 'dzi', 'Duzib138G1867' => 'dzi', 'Duzib211G0420' => 'dzi', 'Duzib212G0930' => 'dzi', 'ECA234G1645' => 'eca', 'ECA247G3467' => 'eca', 'ECA248G1703' => 'eca', 'EL10Ac3g06327' => 'bvu', 'EL10Ac7g17204' => 'bvu', 'Eucgr.A00855' => 'egr', 'Eucgr.A00858' => 'egr', 'Eucgr.H01520' => 'egr', 'Eucgr.H03604' => 'egr', 'Eucgr.L03465' => 'egr', 'Eucgr.L03466' => 'egr', 'FAN01G0988' => 'fan', 'FAN02G3892' => 'fan', 'FAN05G3381' => 'fan', 'FAN07G0967' => 'fan', 'FAN07G1493' => 'fan', 'FAN08G3125' => 'fan', 'FAN09G0402' => 'fan', 'FAN12G2594' => 'fan', 'FAN12G3879' => 'fan', 'FAN14G1546' => 'fan', 'FAN15G3626' => 'fan', 'FAN17G0588' => 'fan', 'FAN17G0609' => 'fan', 'FAN18G2817' => 'fan', 'FAN19G1305' => 'fan', 'FAN20G1787' => 'fan', 'FAN22G0073' => 'fan', 'FAN22G0352' => 'fan', 'FAN22G0368' => 'fan', 'FAN22G2273' => 'fan', 'FAN24G1998' => 'fan', 'FAN27G1317' => 'fan', 'FvH4_2g23980' => 'fve', 'FvH4_4g14380' => 'fve', 'FvH4_4g14390' => 'fve', 'FvH4_6g09250' => 'fve', 'Glyma.03G151100' => 'gma', 'Glyma.04G122550' => 'gma', 'Glyma.05G001600' => 'gma', 'Glyma.09G270766' => 'gma', 'Glyma.09G270832' => 'gma', 'Glyma.13G209800' => 'gma', 'Glyma.15G102800' => 'gma', 'Glyma.18G218900' => 'gma', 'Glyma.19G001500' => 'gma', 'Glyma.19G153600' => 'gma', 'Gohir.A02G028600' => 'ghi', 'Gohir.A08G045000' => 'ghi', 'Gohir.A11G120500' => 'ghi', 'Gohir.A12G006200' => 'ghi', 'Gohir.A12G006250' => 'ghi', 'Gohir.D02G036300' => 'ghi', 'Gohir.D08G054700' => 'ghi', 'Gohir.D11G125600' => 'ghi', 'Gohir.D12G005700' => 'ghi', 'Gorai.004G055200' => 'gra', 'Gorai.005G040400' => 'gra', 'Gorai.007G134500' => 'gra', 'Gorai.008G005500' => 'gra', 'GSVIVG01011094001' => 'vvi', 'GSVIVG01017879001' => 'vvi', 'GSVIVG01025988001' => 'vvi', 'GSVIVG01029847001' => 'vvi', 'HanXRQChr10g0282901' => 'han', 'HanXRQChr10g0310371' => 'han', 'HanXRQChr10g0315041' => 'han', 'HanXRQChr11g0327651' => 'han', 'HanXRQChr12g0359391' => 'han', 'Haze_00972' => 'cav', 'Haze_00973' => 'cav', 'Haze_00974' => 'cav', 'Haze_04747' => 'cav', 'Haze_04749' => 'cav', 'Haze_04750' => 'cav', 'Haze_21217' => 'cav', 'Hma1.2p1_1037F.1_g250680' => 'hma', 'Hma1.2p1_1644F.1_g295320' => 'hma', 'HPP92_011322' => 'vpl', 'HPP92_011323' => 'vpl', 'HPP92_011324' => 'vpl', 'HPP92_011325' => 'vpl', 'HPP92_011326' => 'vpl', 'Hund12205' => 'sun', 'Hund17957' => 'sun', 'Lalb_Chr06g0176771' => 'lal', 'Lalb_Chr18g0056021' => 'lal', 'Lalb_Chr18g0056031' => 'lal', 'Lalb_Chr18g0056041' => 'lal', 'Lalb_Chr20g0107751' => 'lal', 'Lalb_Chr20g0118371' => 'lal', 'Lj1g0010239' => 'lja', 'Lj1g0017101' => 'lja', 'Lj2A1178G40' => 'lonja', 'Lj2A54G84' => 'lonja', 'Lj2g0015248' => 'lja', 'Lj3A761T51' => 'lonja', 'Lj6g0018116' => 'lja', 'Lsat_1_v5_gn_4_136040' => 'lsa', 'Lsat_1_v5_gn_5_187461' => 'lsa', 'Lsat_1_v5_gn_5_77001' => 'lsa', 'Lsat_1_v5_gn_9_4461' => 'lsa', 'Manes.01G210100' => 'mes', 'Manes.03G185600' => 'mes', 'Manes.05G073300' => 'mes', 'Manes.09G120300' => 'mes', 'Manes.15G022100' => 'mes', 'Mapoly0096s0053' => 'mpo', 'MBI03_g14058_MAGBIO' => 'mbi', 'MBI03_g33876_MAGBIO' => 'mbi', 'MBI03_g36854_MAGBIO' => 'mbi', 'MBI17_g11997_MAGBIO' => 'mbi', 'MD03G1269000' => 'mdo', 'MD04G1179600' => 'mdo', 'MD11G1289800' => 'mdo', 'MD12G1194700' => 'mdo', 'MD13G1182100' => 'mdo', 'MD13G1182200' => 'mdo', 'MD16G1182600' => 'mdo', 'Medtr2g021400' => 'mtr', 'Medtr2g021470' => 'mtr', 'Medtr2g105810' => 'mtr', 'Medtr3g033580' => 'mtr', 'Medtr6g007970' => 'mtr', 'Medtr7g056330' => 'mtr', 'Medtr7g074290' => 'mtr', 'Medtr7g074380' => 'mtr', 'Medtr7g094550' => 'mtr', 'Medtr8g069995' => 'mtr', 'MELO3C014345.2' => 'cme', 'MELO3C021395.2' => 'cme', 'Migut.D00262' => 'egut', 'Migut.G00257' => 'egut', 'MSTRG.21575' => 'ama', 'MSTRG.3985' => 'ama', 'Nitab4.5_0000295g0140' => 'nta', 'Nitab4.5_0000732g0140' => 'nta', 'Nitab4.5_0003162g0020' => 'nta', 'Nitab4.5_0006180g0090' => 'nta', 'Nitab4.5_0006390g0010' => 'nta', 'Nitab4.5_0007392g0040' => 'nta', 'Nn1g02140' => 'nnu', 'Nn4g26168' => 'nnu', 'Nn5g26754' => 'nnu', 'Oeu001433.1' => 'oeu', 'Oeu010299.2' => 'oeu', 'Oeu011171.1' => 'oeu', 'Oeu037675.1' => 'oeu', 'Oeu038359.1' => 'oeu', 'Oeu063834.1' => 'oeu', 'Oeu063835.1' => 'oeu', 'Os05g0312000' => 'osa', 'Os07g0211101' => 'osa', 'Os07g0211200' => 'osa', 'Os07g0681500' => 'osa', 'Peaxi162Scf00095g01015' => 'pax', 'Peaxi162Scf00104g00329' => 'pax', 'Peaxi162Scf00161g00137' => 'pax', 'PGR004G1665' => 'pgr', 'PGR031G2937' => 'pgr', 'PGR119G2145' => 'pgr', 'PGSC0003DMG400004351' => 'stu', 'PGSC0003DMG400014625' => 'stu', 'PGSC0003DMG401000943' => 'stu', 'Phvul.001G148600' => 'pvu', 'Phvul.004G001700' => 'pvu', 'Phvul.006G154900' => 'pvu', 'Phvul.008G078200' => 'pvu', 'Phvul.011G136500' => 'pvu', 'Potri.002G215600' => 'ptr', 'Potri.008G201600' => 'ptr', 'Potri.014G138400' => 'ptr', 'Potri.016G142500' => 'ptr', 'Pp3c16_10580' => 'ppa', 'Pp3c5_25280' => 'ppa', 'Prupe.1G150000' => 'ppe', 'Prupe.1G150100' => 'ppe', 'Prupe.6G299600' => 'ppe', 'Prupe.8G245000' => 'ppe', 'Psat0s4927g0040' => 'psa', 'Psat1g052080' => 'psa', 'Psat1g183800' => 'psa', 'Psat3g113840' => 'psa', 'Psat3g126120' => 'psa', 'Psat3g126160' => 'psa', 'Psat3g158760' => 'psa', 'Psat3g158840' => 'psa', 'PSO170G2858' => 'pso', 'PSO339G0606' => 'pso', 'PSO384G4709' => 'pso', 'PSO407G0334' => 'pso', 'QL04p040276' => 'qlo', 'QL06p005458' => 'qlo', 'QL06p005472' => 'qlo', 'QL07p030546' => 'qlo', 'QL07p031519' => 'qlo', 'QL09p050949' => 'qlo', 'QL09p050966' => 'qlo', 'QL09p051067' => 'qlo', 'QL12p022706' => 'qlo', 'RcHm_v2.0_Chr2g0119601' => 'rch', 'RcHm_v2.0_Chr3g0459591' => 'rch', 'RcHm_v2.0_Chr4g0418521' => 'rch', 'RcHm_v2.0_Chr4g0418531' => 'rch', 'RcHm_v2.0_Chr4g0418541' => 'rch', 'RcHm_v2.0_Chr6g0291641' => 'rch', 'Rhsim01G0086300' => 'rsi', 'Rhsim01G0276300' => 'rsi', 'Rhsim01G0276500' => 'rsi', 'Rhsim04G0207700' => 'rsi', 'Rhsim05G0234500' => 'rsi', 'Rhsim13G0022400' => 'rsi', 'Sabra02G0167900' => 'sbr', 'Sabra04G0158500' => 'sbr', 'Sabra08G0159800' => 'sbr', 'Sabra10G0011500' => 'sbr', 'Sabra14G0104400' => 'sbr', 'SalBow2G2440' => 'sbo', 'SalBow4G2265' => 'sbo', 'Sc02g0000060' => 'sci', 'Sc05g0005020' => 'sci', 'Sc13g0003890' => 'sci', 'Sed0014865' => 'sed', 'Sed0017224' => 'sed', 'Sed0026391' => 'sed', 'SEGI_00063' => 'sgi', 'SEGI_10967' => 'sgi', 'SEGI_17510' => 'sgi', 'SEGI_24396' => 'sgi', 'SEGI_39719' => 'sgi', 'SEGI_41392' => 'sgi', 'SGA_v2.0_scaffold11G05794' => 'sas', 'SGA_v2.0_scaffold142G35607' => 'sas', 'SGA_v2.0_scaffold1G00447' => 'sas', 'SHI15388' => 'shi', 'SHI15394' => 'shi', 'SHI15396' => 'shi', 'SHI15399' => 'shi', 'SMO343G0151' => 'smo', 'SMO367G1118' => 'smo', 'Solyc01g080200.3' => 'sly', 'Solyc06g008960.3' => 'sly', 'Solyc09g064780.3' => 'sly', 'Sopen01g031980' => 'spe', 'Sopen06g003710' => 'spe', 'Sopen09g026460' => 'spe', 'Sp3g21240' => 'spa', 'Sp4g30030' => 'spa', 'TAR365G0022' => 'tar', 'TAR365G1023' => 'tar', 'TAR365G1253' => 'tar', 'TAR623G0078' => 'tar', 'TAR623G1721' => 'tar', 'TAR633G0959' => 'tar', 'THA.LOC104802225' => 'tha', 'THA.LOC104804769' => 'tha', 'THA.LOC104808660' => 'tha', 'THA.LOC104812792' => 'tha', 'Thecc.01G284000' => 'tca', 'Thecc.04G220600' => 'tca', 'Thecc.05G268900' => 'tca', 'Thecc.08G171100' => 'tca', 'Thhalv10001284m.g' => 'esa', 'Thhalv10019912m.g' => 'esa', 'TPR.G14189' => 'tpr', 'TPR.G18110' => 'tpr', 'TPR.G18130' => 'tpr', 'TPR.G18131' => 'tpr', 'TPR.G18140' => 'tpr', 'TPR.G24282' => 'tpr', 'TPR.G25221' => 'tpr', 'TPR.G29267' => 'tpr', 'TPR.G35315' => 'tpr', 'TPR.G36173' => 'tpr', 'TWI09G0794' => 'twi', 'TWI59G1348' => 'twi', 'TWI74G0430' => 'twi', 'unitig_26.g8940' => 'ugi', 'unitig_749.g13744' => 'ugi', 'unitig_749.g13745' => 'ugi', 'vmacro08269' => 'vma', 'vmacro14937' => 'vma', 'vmacro20401' => 'vma', 'VMungo0464G1349' => 'vmu', 'VMungo0540G0289' => 'vmu', 'VMungo1215G1590' => 'vmu', 'VMungo1309G0221' => 'vmu', 'VMungo1309G2815' => 'vmu', 'VMungo1383G0239' => 'vmu', 'VMungo1383G2910' => 'vmu', 'Zm00001eb095270' => 'zma', 'Zm00001eb095280' => 'zma', 'Zm00001eb111630' => 'zma', 'Zm00001eb237080' => 'zma', 'Zm00001eb273740' => 'zma', 'Zm00001eb285040' => 'zma', 'Zm00001eb330790' => 'zma', 'Zm00001eb337380' => 'zma' ), 'gf_id' => 'HOM05D001484', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001484' ), 'data_identifier' => 'HOM05D001484', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001484', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p31500' => 'bna', 'A05p00020' => 'bna', 'A07p08820' => 'bna', 'Aa31LG4G3300' => 'aar', 'Aa31LG8G10030' => 'aar', 'Actinidia00731' => 'ach', 'Actinidia11473' => 'ach', 'Actinidia23469' => 'ach', 'Actinidia24318' => 'ach', 'Actinidia40196' => 'ach', 'Actinidia40197' => 'ach', 'Actinidia40198' => 'ach', 'Ah.08g212990' => 'amhyb', 'Ah.15g091720' => 'amhyb', 'AL3G38260' => 'aly', 'AL4G47710' => 'aly', 'Aqoxy2G00671' => 'aox', 'Aqoxy2G03236' => 'aox', 'arahy.Tifrunner.gnm1.ann1.05IDCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KR684' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATY3SJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK6QJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6APGL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IDT7Z9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM073U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ0R87' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LE7RV4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT4QRX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V5ENPK' => 'arhy', 'AT2G48110' => 'ath', 'AT3G23590' => 'ath', 'ATR0626G186' => 'atr', 'ATR1127G141' => 'atr', 'Atru.chr4.2583' => 'acertr', 'Atru.chr5.1358' => 'acertr', 'Atru.chr5.1359' => 'acertr', 'Atru.chr8.46' => 'acertr', 'AUR62002640' => 'cqu', 'AUR62030055' => 'cqu', 'AUR62033713' => 'cqu', 'AUR62033714' => 'cqu', 'AUR62036795' => 'cqu', 'AUR62039891' => 'cqu', 'BcaB02g08737' => 'bca', 'BcaB04g20441' => 'bca', 'BcaB06g26509' => 'bca', 'BcaB06g26510' => 'bca', 'BcaB06g26511' => 'bca', 'BcaB06g26512' => 'bca', 'BcaB06g26513' => 'bca', 'BcaC02g12564' => 'bca', 'BcaC02g12565' => 'bca', 'BcaC02g12794' => 'bca', 'BcaC02g12795' => 'bca', 'BcaC02g12796' => 'bca', 'BcaC06g35541' => 'bca', 'BNapus_Darmor_BZH_scaffold_188p00080' => 'bna', 'BNapus_Darmor_BZH_scaffold_188p00090' => 'bna', 'BolC1t03972H' => 'bol', 'BolC1t03973H' => 'bol', 'BolC4t21680H' => 'bol', 'BolC7t41863H' => 'bol', 'BolSC55t61227H' => 'bol', 'BolSC55t61228H' => 'bol', 'BraA01t03278Z' => 'bra', 'BraA05t18998Z' => 'bra', 'BraA07t28673Z' => 'bra', 'C01p40150' => 'bna', 'C05p12370' => 'bna', 'C07p13680' => 'bna', 'CAN.G1006.16' => 'can', 'CAN.G1006.17' => 'can', 'CAN.G1170.2' => 'can', 'CAN.G962.7' => 'can', 'CANSAT25G2179' => 'cansat', 'CANSAT78G1573' => 'cansat', 'CARHR099510' => 'chi', 'CARHR143510' => 'chi', 'Carub.0003s2380' => 'cru', 'Carub.0004s3082' => 'cru', 'Ca_00614_v3' => 'car', 'Ca_07801_v3' => 'car', 'Ca_08567_v3' => 'car', 'Ca_09571_v3' => 'car', 'CBR_g19290' => 'cbr', 'Cc01_g19770' => 'ccan', 'Cc03_g03030' => 'ccan', 'CDE07G0968' => 'cde', 'CDE09G1441' => 'cde', 'Cfa006103' => 'cfa', 'Cfa015573' => 'cfa', 'Cfa016988' => 'cfa', 'Ciclev10006738m.g' => 'ccl', 'Ciclev10010920m.g' => 'ccl', 'Ciclev10018517m.g' => 'ccl', 'CiPaw.01G159200' => 'cil', 'CiPaw.02G091000' => 'cil', 'CiPaw.02G091100' => 'cil', 'CiPaw.08G103100' => 'cil', 'CiPaw.09G224900' => 'cil', 'ClCG06G005740' => 'cla', 'ClCG07G000090' => 'cla', 'ClCG07G000100' => 'cla', 'COL.COLO4_09143' => 'col', 'COL.COLO4_25124' => 'col', 'Cpa.g.sc16.34' => 'cpa', 'Cpa.g.sc3504.1' => 'cpa', 'Cpa.g.sc60.37' => 'cpa', 'CsaV3_6G018520' => 'csa', 'CsaV3_6G036860' => 'csa', 'CSS0001072' => 'camsi', 'CSS0020208' => 'camsi', 'CSS0021253' => 'camsi', 'CSS0022190' => 'camsi', 'CSS0036150' => 'camsi', 'CSS0040442' => 'camsi', 'CSS0042300' => 'camsi', 'CSS0045298' => 'camsi', 'DCAR_012449' => 'dca', 'DCAR_018405' => 'dca', 'DCAR_024573' => 'dca', 'DCAR_030591' => 'dca', 'Dinv16926' => 'din', 'Dinv32963' => 'din', 'Dinv38382' => 'din', 'Dinv38383' => 'din', 'Duzib133G0974' => 'dzi', 'Duzib138G1867' => 'dzi', 'Duzib211G0420' => 'dzi', 'Duzib212G0930' => 'dzi', 'ECA234G1645' => 'eca', 'ECA247G3467' => 'eca', 'ECA248G1703' => 'eca', 'EL10Ac3g06327' => 'bvu', 'EL10Ac7g17204' => 'bvu', 'Eucgr.A00855' => 'egr', 'Eucgr.A00858' => 'egr', 'Eucgr.H01520' => 'egr', 'Eucgr.H03604' => 'egr', 'Eucgr.L03465' => 'egr', 'Eucgr.L03466' => 'egr', 'FAN01G0988' => 'fan', 'FAN02G3892' => 'fan', 'FAN05G3381' => 'fan', 'FAN07G0967' => 'fan', 'FAN07G1493' => 'fan', 'FAN08G3125' => 'fan', 'FAN09G0402' => 'fan', 'FAN12G2594' => 'fan', 'FAN12G3879' => 'fan', 'FAN14G1546' => 'fan', 'FAN15G3626' => 'fan', 'FAN17G0588' => 'fan', 'FAN17G0609' => 'fan', 'FAN18G2817' => 'fan', 'FAN19G1305' => 'fan', 'FAN20G1787' => 'fan', 'FAN22G0073' => 'fan', 'FAN22G0352' => 'fan', 'FAN22G0368' => 'fan', 'FAN22G2273' => 'fan', 'FAN24G1998' => 'fan', 'FAN27G1317' => 'fan', 'FvH4_2g23980' => 'fve', 'FvH4_4g14380' => 'fve', 'FvH4_4g14390' => 'fve', 'FvH4_6g09250' => 'fve', 'Glyma.03G151100' => 'gma', 'Glyma.04G122550' => 'gma', 'Glyma.05G001600' => 'gma', 'Glyma.09G270766' => 'gma', 'Glyma.09G270832' => 'gma', 'Glyma.13G209800' => 'gma', 'Glyma.15G102800' => 'gma', 'Glyma.18G218900' => 'gma', 'Glyma.19G001500' => 'gma', 'Glyma.19G153600' => 'gma', 'Gohir.A02G028600' => 'ghi', 'Gohir.A08G045000' => 'ghi', 'Gohir.A11G120500' => 'ghi', 'Gohir.A12G006200' => 'ghi', 'Gohir.A12G006250' => 'ghi', 'Gohir.D02G036300' => 'ghi', 'Gohir.D08G054700' => 'ghi', 'Gohir.D11G125600' => 'ghi', 'Gohir.D12G005700' => 'ghi', 'Gorai.004G055200' => 'gra', 'Gorai.005G040400' => 'gra', 'Gorai.007G134500' => 'gra', 'Gorai.008G005500' => 'gra', 'GSVIVG01011094001' => 'vvi', 'GSVIVG01017879001' => 'vvi', 'GSVIVG01025988001' => 'vvi', 'GSVIVG01029847001' => 'vvi', 'HanXRQChr10g0282901' => 'han', 'HanXRQChr10g0310371' => 'han', 'HanXRQChr10g0315041' => 'han', 'HanXRQChr11g0327651' => 'han', 'HanXRQChr12g0359391' => 'han', 'Haze_00972' => 'cav', 'Haze_00973' => 'cav', 'Haze_00974' => 'cav', 'Haze_04747' => 'cav', 'Haze_04749' => 'cav', 'Haze_04750' => 'cav', 'Haze_21217' => 'cav', 'Hma1.2p1_1037F.1_g250680' => 'hma', 'Hma1.2p1_1644F.1_g295320' => 'hma', 'HPP92_011322' => 'vpl', 'HPP92_011323' => 'vpl', 'HPP92_011324' => 'vpl', 'HPP92_011325' => 'vpl', 'HPP92_011326' => 'vpl', 'Hund12205' => 'sun', 'Hund17957' => 'sun', 'Lalb_Chr06g0176771' => 'lal', 'Lalb_Chr18g0056021' => 'lal', 'Lalb_Chr18g0056031' => 'lal', 'Lalb_Chr18g0056041' => 'lal', 'Lalb_Chr20g0107751' => 'lal', 'Lalb_Chr20g0118371' => 'lal', 'Lj1g0010239' => 'lja', 'Lj1g0017101' => 'lja', 'Lj2A1178G40' => 'lonja', 'Lj2A54G84' => 'lonja', 'Lj2g0015248' => 'lja', 'Lj3A761T51' => 'lonja', 'Lj6g0018116' => 'lja', 'Lsat_1_v5_gn_4_136040' => 'lsa', 'Lsat_1_v5_gn_5_187461' => 'lsa', 'Lsat_1_v5_gn_5_77001' => 'lsa', 'Lsat_1_v5_gn_9_4461' => 'lsa', 'Manes.01G210100' => 'mes', 'Manes.03G185600' => 'mes', 'Manes.05G073300' => 'mes', 'Manes.09G120300' => 'mes', 'Manes.15G022100' => 'mes', 'Mapoly0096s0053' => 'mpo', 'MBI03_g14058_MAGBIO' => 'mbi', 'MBI03_g33876_MAGBIO' => 'mbi', 'MBI03_g36854_MAGBIO' => 'mbi', 'MBI17_g11997_MAGBIO' => 'mbi', 'MD03G1269000' => 'mdo', 'MD04G1179600' => 'mdo', 'MD11G1289800' => 'mdo', 'MD12G1194700' => 'mdo', 'MD13G1182100' => 'mdo', 'MD13G1182200' => 'mdo', 'MD16G1182600' => 'mdo', 'Medtr2g021400' => 'mtr', 'Medtr2g021470' => 'mtr', 'Medtr2g105810' => 'mtr', 'Medtr3g033580' => 'mtr', 'Medtr6g007970' => 'mtr', 'Medtr7g056330' => 'mtr', 'Medtr7g074290' => 'mtr', 'Medtr7g074380' => 'mtr', 'Medtr7g094550' => 'mtr', 'Medtr8g069995' => 'mtr', 'MELO3C014345.2' => 'cme', 'MELO3C021395.2' => 'cme', 'Migut.D00262' => 'egut', 'Migut.G00257' => 'egut', 'MSTRG.21575' => 'ama', 'MSTRG.3985' => 'ama', 'Nitab4.5_0000295g0140' => 'nta', 'Nitab4.5_0000732g0140' => 'nta', 'Nitab4.5_0003162g0020' => 'nta', 'Nitab4.5_0006180g0090' => 'nta', 'Nitab4.5_0006390g0010' => 'nta', 'Nitab4.5_0007392g0040' => 'nta', 'Nn1g02140' => 'nnu', 'Nn4g26168' => 'nnu', 'Nn5g26754' => 'nnu', 'Oeu001433.1' => 'oeu', 'Oeu010299.2' => 'oeu', 'Oeu011171.1' => 'oeu', 'Oeu037675.1' => 'oeu', 'Oeu038359.1' => 'oeu', 'Oeu063834.1' => 'oeu', 'Oeu063835.1' => 'oeu', 'Os05g0312000' => 'osa', 'Os07g0211101' => 'osa', 'Os07g0211200' => 'osa', 'Os07g0681500' => 'osa', 'Peaxi162Scf00095g01015' => 'pax', 'Peaxi162Scf00104g00329' => 'pax', 'Peaxi162Scf00161g00137' => 'pax', 'PGR004G1665' => 'pgr', 'PGR031G2937' => 'pgr', 'PGR119G2145' => 'pgr', 'PGSC0003DMG400004351' => 'stu', 'PGSC0003DMG400014625' => 'stu', 'PGSC0003DMG401000943' => 'stu', 'Phvul.001G148600' => 'pvu', 'Phvul.004G001700' => 'pvu', 'Phvul.006G154900' => 'pvu', 'Phvul.008G078200' => 'pvu', 'Phvul.011G136500' => 'pvu', 'Potri.002G215600' => 'ptr', 'Potri.008G201600' => 'ptr', 'Potri.014G138400' => 'ptr', 'Potri.016G142500' => 'ptr', 'Pp3c16_10580' => 'ppa', 'Pp3c5_25280' => 'ppa', 'Prupe.1G150000' => 'ppe', 'Prupe.1G150100' => 'ppe', 'Prupe.6G299600' => 'ppe', 'Prupe.8G245000' => 'ppe', 'Psat0s4927g0040' => 'psa', 'Psat1g052080' => 'psa', 'Psat1g183800' => 'psa', 'Psat3g113840' => 'psa', 'Psat3g126120' => 'psa', 'Psat3g126160' => 'psa', 'Psat3g158760' => 'psa', 'Psat3g158840' => 'psa', 'PSO170G2858' => 'pso', 'PSO339G0606' => 'pso', 'PSO384G4709' => 'pso', 'PSO407G0334' => 'pso', 'QL04p040276' => 'qlo', 'QL06p005458' => 'qlo', 'QL06p005472' => 'qlo', 'QL07p030546' => 'qlo', 'QL07p031519' => 'qlo', 'QL09p050949' => 'qlo', 'QL09p050966' => 'qlo', 'QL09p051067' => 'qlo', 'QL12p022706' => 'qlo', 'RcHm_v2.0_Chr2g0119601' => 'rch', 'RcHm_v2.0_Chr3g0459591' => 'rch', 'RcHm_v2.0_Chr4g0418521' => 'rch', 'RcHm_v2.0_Chr4g0418531' => 'rch', 'RcHm_v2.0_Chr4g0418541' => 'rch', 'RcHm_v2.0_Chr6g0291641' => 'rch', 'Rhsim01G0086300' => 'rsi', 'Rhsim01G0276300' => 'rsi', 'Rhsim01G0276500' => 'rsi', 'Rhsim04G0207700' => 'rsi', 'Rhsim05G0234500' => 'rsi', 'Rhsim13G0022400' => 'rsi', 'Sabra02G0167900' => 'sbr', 'Sabra04G0158500' => 'sbr', 'Sabra08G0159800' => 'sbr', 'Sabra10G0011500' => 'sbr', 'Sabra14G0104400' => 'sbr', 'SalBow2G2440' => 'sbo', 'SalBow4G2265' => 'sbo', 'Sc02g0000060' => 'sci', 'Sc05g0005020' => 'sci', 'Sc13g0003890' => 'sci', 'Sed0014865' => 'sed', 'Sed0017224' => 'sed', 'Sed0026391' => 'sed', 'SEGI_00063' => 'sgi', 'SEGI_10967' => 'sgi', 'SEGI_17510' => 'sgi', 'SEGI_24396' => 'sgi', 'SEGI_39719' => 'sgi', 'SEGI_41392' => 'sgi', 'SGA_v2.0_scaffold11G05794' => 'sas', 'SGA_v2.0_scaffold142G35607' => 'sas', 'SGA_v2.0_scaffold1G00447' => 'sas', 'SHI15388' => 'shi', 'SHI15394' => 'shi', 'SHI15396' => 'shi', 'SHI15399' => 'shi', 'SMO343G0151' => 'smo', 'SMO367G1118' => 'smo', 'Solyc01g080200.3' => 'sly', 'Solyc06g008960.3' => 'sly', 'Solyc09g064780.3' => 'sly', 'Sopen01g031980' => 'spe', 'Sopen06g003710' => 'spe', 'Sopen09g026460' => 'spe', 'Sp3g21240' => 'spa', 'Sp4g30030' => 'spa', 'TAR365G0022' => 'tar', 'TAR365G1023' => 'tar', 'TAR365G1253' => 'tar', 'TAR623G0078' => 'tar', 'TAR623G1721' => 'tar', 'TAR633G0959' => 'tar', 'THA.LOC104802225' => 'tha', 'THA.LOC104804769' => 'tha', 'THA.LOC104808660' => 'tha', 'THA.LOC104812792' => 'tha', 'Thecc.01G284000' => 'tca', 'Thecc.04G220600' => 'tca', 'Thecc.05G268900' => 'tca', 'Thecc.08G171100' => 'tca', 'Thhalv10001284m.g' => 'esa', 'Thhalv10019912m.g' => 'esa', 'TPR.G14189' => 'tpr', 'TPR.G18110' => 'tpr', 'TPR.G18130' => 'tpr', 'TPR.G18131' => 'tpr', 'TPR.G18140' => 'tpr', 'TPR.G24282' => 'tpr', 'TPR.G25221' => 'tpr', 'TPR.G29267' => 'tpr', 'TPR.G35315' => 'tpr', 'TPR.G36173' => 'tpr', 'TWI09G0794' => 'twi', 'TWI59G1348' => 'twi', 'TWI74G0430' => 'twi', 'unitig_26.g8940' => 'ugi', 'unitig_749.g13744' => 'ugi', 'unitig_749.g13745' => 'ugi', 'vmacro08269' => 'vma', 'vmacro14937' => 'vma', 'vmacro20401' => 'vma', 'VMungo0464G1349' => 'vmu', 'VMungo0540G0289' => 'vmu', 'VMungo1215G1590' => 'vmu', 'VMungo1309G0221' => 'vmu', 'VMungo1309G2815' => 'vmu', 'VMungo1383G0239' => 'vmu', 'VMungo1383G2910' => 'vmu', 'Zm00001eb095270' => 'zma', 'Zm00001eb095280' => 'zma', 'Zm00001eb111630' => 'zma', 'Zm00001eb237080' => 'zma', 'Zm00001eb273740' => 'zma', 'Zm00001eb285040' => 'zma', 'Zm00001eb330790' => 'zma', 'Zm00001eb337380' => 'zma' ) $gf_id = 'HOM05D001484' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001484' ) $data_identifier = 'HOM05D001484' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 2, 'aly' => (int) 2, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 22, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 7, 'hma' => (int) 2, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 7, 'mtr' => (int) 10, 'cme' => (int) 2, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 4, 'ppa' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 4, 'qlo' => (int) 9, 'rch' => (int) 6, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 10, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 7, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb337380' $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' => 'HOM05D001484', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p31500' => 'bna', 'A05p00020' => 'bna', 'A07p08820' => 'bna', 'Aa31LG4G3300' => 'aar', 'Aa31LG8G10030' => 'aar', 'Actinidia00731' => 'ach', 'Actinidia11473' => 'ach', 'Actinidia23469' => 'ach', 'Actinidia24318' => 'ach', 'Actinidia40196' => 'ach', 'Actinidia40197' => 'ach', 'Actinidia40198' => 'ach', 'Ah.08g212990' => 'amhyb', 'Ah.15g091720' => 'amhyb', 'AL3G38260' => 'aly', 'AL4G47710' => 'aly', 'Aqoxy2G00671' => 'aox', 'Aqoxy2G03236' => 'aox', 'arahy.Tifrunner.gnm1.ann1.05IDCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KR684' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATY3SJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK6QJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6APGL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IDT7Z9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM073U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ0R87' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LE7RV4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT4QRX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V5ENPK' => 'arhy', 'AT2G48110' => 'ath', 'AT3G23590' => 'ath', 'ATR0626G186' => 'atr', 'ATR1127G141' => 'atr', 'Atru.chr4.2583' => 'acertr', 'Atru.chr5.1358' => 'acertr', 'Atru.chr5.1359' => 'acertr', 'Atru.chr8.46' => 'acertr', 'AUR62002640' => 'cqu', 'AUR62030055' => 'cqu', 'AUR62033713' => 'cqu', 'AUR62033714' => 'cqu', 'AUR62036795' => 'cqu', 'AUR62039891' => 'cqu', 'BcaB02g08737' => 'bca', 'BcaB04g20441' => 'bca', 'BcaB06g26509' => 'bca', 'BcaB06g26510' => 'bca', 'BcaB06g26511' => 'bca', 'BcaB06g26512' => 'bca', 'BcaB06g26513' => 'bca', 'BcaC02g12564' => 'bca', 'BcaC02g12565' => 'bca', 'BcaC02g12794' => 'bca', 'BcaC02g12795' => 'bca', 'BcaC02g12796' => 'bca', 'BcaC06g35541' => 'bca', 'BNapus_Darmor_BZH_scaffold_188p00080' => 'bna', 'BNapus_Darmor_BZH_scaffold_188p00090' => 'bna', 'BolC1t03972H' => 'bol', 'BolC1t03973H' => 'bol', 'BolC4t21680H' => 'bol', 'BolC7t41863H' => 'bol', 'BolSC55t61227H' => 'bol', 'BolSC55t61228H' => 'bol', 'BraA01t03278Z' => 'bra', 'BraA05t18998Z' => 'bra', 'BraA07t28673Z' => 'bra', 'C01p40150' => 'bna', 'C05p12370' => 'bna', 'C07p13680' => 'bna', 'CAN.G1006.16' => 'can', 'CAN.G1006.17' => 'can', 'CAN.G1170.2' => 'can', 'CAN.G962.7' => 'can', 'CANSAT25G2179' => 'cansat', 'CANSAT78G1573' => 'cansat', 'CARHR099510' => 'chi', 'CARHR143510' => 'chi', 'Carub.0003s2380' => 'cru', 'Carub.0004s3082' => 'cru', 'Ca_00614_v3' => 'car', 'Ca_07801_v3' => 'car', 'Ca_08567_v3' => 'car', 'Ca_09571_v3' => 'car', 'CBR_g19290' => 'cbr', 'Cc01_g19770' => 'ccan', 'Cc03_g03030' => 'ccan', 'CDE07G0968' => 'cde', 'CDE09G1441' => 'cde', 'Cfa006103' => 'cfa', 'Cfa015573' => 'cfa', 'Cfa016988' => 'cfa', 'Ciclev10006738m.g' => 'ccl', 'Ciclev10010920m.g' => 'ccl', 'Ciclev10018517m.g' => 'ccl', 'CiPaw.01G159200' => 'cil', 'CiPaw.02G091000' => 'cil', 'CiPaw.02G091100' => 'cil', 'CiPaw.08G103100' => 'cil', 'CiPaw.09G224900' => 'cil', 'ClCG06G005740' => 'cla', 'ClCG07G000090' => 'cla', 'ClCG07G000100' => 'cla', 'COL.COLO4_09143' => 'col', 'COL.COLO4_25124' => 'col', 'Cpa.g.sc16.34' => 'cpa', 'Cpa.g.sc3504.1' => 'cpa', 'Cpa.g.sc60.37' => 'cpa', 'CsaV3_6G018520' => 'csa', 'CsaV3_6G036860' => 'csa', 'CSS0001072' => 'camsi', 'CSS0020208' => 'camsi', 'CSS0021253' => 'camsi', 'CSS0022190' => 'camsi', 'CSS0036150' => 'camsi', 'CSS0040442' => 'camsi', 'CSS0042300' => 'camsi', 'CSS0045298' => 'camsi', 'DCAR_012449' => 'dca', 'DCAR_018405' => 'dca', 'DCAR_024573' => 'dca', 'DCAR_030591' => 'dca', 'Dinv16926' => 'din', 'Dinv32963' => 'din', 'Dinv38382' => 'din', 'Dinv38383' => 'din', 'Duzib133G0974' => 'dzi', 'Duzib138G1867' => 'dzi', 'Duzib211G0420' => 'dzi', 'Duzib212G0930' => 'dzi', 'ECA234G1645' => 'eca', 'ECA247G3467' => 'eca', 'ECA248G1703' => 'eca', 'EL10Ac3g06327' => 'bvu', 'EL10Ac7g17204' => 'bvu', 'Eucgr.A00855' => 'egr', 'Eucgr.A00858' => 'egr', 'Eucgr.H01520' => 'egr', 'Eucgr.H03604' => 'egr', 'Eucgr.L03465' => 'egr', 'Eucgr.L03466' => 'egr', 'FAN01G0988' => 'fan', 'FAN02G3892' => 'fan', 'FAN05G3381' => 'fan', 'FAN07G0967' => 'fan', 'FAN07G1493' => 'fan', 'FAN08G3125' => 'fan', 'FAN09G0402' => 'fan', 'FAN12G2594' => 'fan', 'FAN12G3879' => 'fan', 'FAN14G1546' => 'fan', 'FAN15G3626' => 'fan', 'FAN17G0588' => 'fan', 'FAN17G0609' => 'fan', 'FAN18G2817' => 'fan', 'FAN19G1305' => 'fan', 'FAN20G1787' => 'fan', 'FAN22G0073' => 'fan', 'FAN22G0352' => 'fan', 'FAN22G0368' => 'fan', 'FAN22G2273' => 'fan', 'FAN24G1998' => 'fan', 'FAN27G1317' => 'fan', 'FvH4_2g23980' => 'fve', 'FvH4_4g14380' => 'fve', 'FvH4_4g14390' => 'fve', 'FvH4_6g09250' => 'fve', 'Glyma.03G151100' => 'gma', 'Glyma.04G122550' => 'gma', 'Glyma.05G001600' => 'gma', 'Glyma.09G270766' => 'gma', 'Glyma.09G270832' => 'gma', 'Glyma.13G209800' => 'gma', 'Glyma.15G102800' => 'gma', 'Glyma.18G218900' => 'gma', 'Glyma.19G001500' => 'gma', 'Glyma.19G153600' => 'gma', 'Gohir.A02G028600' => 'ghi', 'Gohir.A08G045000' => 'ghi', 'Gohir.A11G120500' => 'ghi', 'Gohir.A12G006200' => 'ghi', 'Gohir.A12G006250' => 'ghi', 'Gohir.D02G036300' => 'ghi', 'Gohir.D08G054700' => 'ghi', 'Gohir.D11G125600' => 'ghi', 'Gohir.D12G005700' => 'ghi', 'Gorai.004G055200' => 'gra', 'Gorai.005G040400' => 'gra', 'Gorai.007G134500' => 'gra', 'Gorai.008G005500' => 'gra', 'GSVIVG01011094001' => 'vvi', 'GSVIVG01017879001' => 'vvi', 'GSVIVG01025988001' => 'vvi', 'GSVIVG01029847001' => 'vvi', 'HanXRQChr10g0282901' => 'han', 'HanXRQChr10g0310371' => 'han', 'HanXRQChr10g0315041' => 'han', 'HanXRQChr11g0327651' => 'han', 'HanXRQChr12g0359391' => 'han', 'Haze_00972' => 'cav', 'Haze_00973' => 'cav', 'Haze_00974' => 'cav', 'Haze_04747' => 'cav', 'Haze_04749' => 'cav', 'Haze_04750' => 'cav', 'Haze_21217' => 'cav', 'Hma1.2p1_1037F.1_g250680' => 'hma', 'Hma1.2p1_1644F.1_g295320' => 'hma', 'HPP92_011322' => 'vpl', 'HPP92_011323' => 'vpl', 'HPP92_011324' => 'vpl', 'HPP92_011325' => 'vpl', 'HPP92_011326' => 'vpl', 'Hund12205' => 'sun', 'Hund17957' => 'sun', 'Lalb_Chr06g0176771' => 'lal', 'Lalb_Chr18g0056021' => 'lal', 'Lalb_Chr18g0056031' => 'lal', 'Lalb_Chr18g0056041' => 'lal', 'Lalb_Chr20g0107751' => 'lal', 'Lalb_Chr20g0118371' => 'lal', 'Lj1g0010239' => 'lja', 'Lj1g0017101' => 'lja', 'Lj2A1178G40' => 'lonja', 'Lj2A54G84' => 'lonja', 'Lj2g0015248' => 'lja', 'Lj3A761T51' => 'lonja', 'Lj6g0018116' => 'lja', 'Lsat_1_v5_gn_4_136040' => 'lsa', 'Lsat_1_v5_gn_5_187461' => 'lsa', 'Lsat_1_v5_gn_5_77001' => 'lsa', 'Lsat_1_v5_gn_9_4461' => 'lsa', 'Manes.01G210100' => 'mes', 'Manes.03G185600' => 'mes', 'Manes.05G073300' => 'mes', 'Manes.09G120300' => 'mes', 'Manes.15G022100' => 'mes', 'Mapoly0096s0053' => 'mpo', 'MBI03_g14058_MAGBIO' => 'mbi', 'MBI03_g33876_MAGBIO' => 'mbi', 'MBI03_g36854_MAGBIO' => 'mbi', 'MBI17_g11997_MAGBIO' => 'mbi', 'MD03G1269000' => 'mdo', 'MD04G1179600' => 'mdo', 'MD11G1289800' => 'mdo', 'MD12G1194700' => 'mdo', 'MD13G1182100' => 'mdo', 'MD13G1182200' => 'mdo', 'MD16G1182600' => 'mdo', 'Medtr2g021400' => 'mtr', 'Medtr2g021470' => 'mtr', 'Medtr2g105810' => 'mtr', 'Medtr3g033580' => 'mtr', 'Medtr6g007970' => 'mtr', 'Medtr7g056330' => 'mtr', 'Medtr7g074290' => 'mtr', 'Medtr7g074380' => 'mtr', 'Medtr7g094550' => 'mtr', 'Medtr8g069995' => 'mtr', 'MELO3C014345.2' => 'cme', 'MELO3C021395.2' => 'cme', 'Migut.D00262' => 'egut', 'Migut.G00257' => 'egut', 'MSTRG.21575' => 'ama', 'MSTRG.3985' => 'ama', 'Nitab4.5_0000295g0140' => 'nta', 'Nitab4.5_0000732g0140' => 'nta', 'Nitab4.5_0003162g0020' => 'nta', 'Nitab4.5_0006180g0090' => 'nta', 'Nitab4.5_0006390g0010' => 'nta', 'Nitab4.5_0007392g0040' => 'nta', 'Nn1g02140' => 'nnu', 'Nn4g26168' => 'nnu', 'Nn5g26754' => 'nnu', 'Oeu001433.1' => 'oeu', 'Oeu010299.2' => 'oeu', 'Oeu011171.1' => 'oeu', 'Oeu037675.1' => 'oeu', 'Oeu038359.1' => 'oeu', 'Oeu063834.1' => 'oeu', 'Oeu063835.1' => 'oeu', 'Os05g0312000' => 'osa', 'Os07g0211101' => 'osa', 'Os07g0211200' => 'osa', 'Os07g0681500' => 'osa', 'Peaxi162Scf00095g01015' => 'pax', 'Peaxi162Scf00104g00329' => 'pax', 'Peaxi162Scf00161g00137' => 'pax', 'PGR004G1665' => 'pgr', 'PGR031G2937' => 'pgr', 'PGR119G2145' => 'pgr', 'PGSC0003DMG400004351' => 'stu', 'PGSC0003DMG400014625' => 'stu', 'PGSC0003DMG401000943' => 'stu', 'Phvul.001G148600' => 'pvu', 'Phvul.004G001700' => 'pvu', 'Phvul.006G154900' => 'pvu', 'Phvul.008G078200' => 'pvu', 'Phvul.011G136500' => 'pvu', 'Potri.002G215600' => 'ptr', 'Potri.008G201600' => 'ptr', 'Potri.014G138400' => 'ptr', 'Potri.016G142500' => 'ptr', 'Pp3c16_10580' => 'ppa', 'Pp3c5_25280' => 'ppa', 'Prupe.1G150000' => 'ppe', 'Prupe.1G150100' => 'ppe', 'Prupe.6G299600' => 'ppe', 'Prupe.8G245000' => 'ppe', 'Psat0s4927g0040' => 'psa', 'Psat1g052080' => 'psa', 'Psat1g183800' => 'psa', 'Psat3g113840' => 'psa', 'Psat3g126120' => 'psa', 'Psat3g126160' => 'psa', 'Psat3g158760' => 'psa', 'Psat3g158840' => 'psa', 'PSO170G2858' => 'pso', 'PSO339G0606' => 'pso', 'PSO384G4709' => 'pso', 'PSO407G0334' => 'pso', 'QL04p040276' => 'qlo', 'QL06p005458' => 'qlo', 'QL06p005472' => 'qlo', 'QL07p030546' => 'qlo', 'QL07p031519' => 'qlo', 'QL09p050949' => 'qlo', 'QL09p050966' => 'qlo', 'QL09p051067' => 'qlo', 'QL12p022706' => 'qlo', 'RcHm_v2.0_Chr2g0119601' => 'rch', 'RcHm_v2.0_Chr3g0459591' => 'rch', 'RcHm_v2.0_Chr4g0418521' => 'rch', 'RcHm_v2.0_Chr4g0418531' => 'rch', 'RcHm_v2.0_Chr4g0418541' => 'rch', 'RcHm_v2.0_Chr6g0291641' => 'rch', 'Rhsim01G0086300' => 'rsi', 'Rhsim01G0276300' => 'rsi', 'Rhsim01G0276500' => 'rsi', 'Rhsim04G0207700' => 'rsi', 'Rhsim05G0234500' => 'rsi', 'Rhsim13G0022400' => 'rsi', 'Sabra02G0167900' => 'sbr', 'Sabra04G0158500' => 'sbr', 'Sabra08G0159800' => 'sbr', 'Sabra10G0011500' => 'sbr', 'Sabra14G0104400' => 'sbr', 'SalBow2G2440' => 'sbo', 'SalBow4G2265' => 'sbo', 'Sc02g0000060' => 'sci', 'Sc05g0005020' => 'sci', 'Sc13g0003890' => 'sci', 'Sed0014865' => 'sed', 'Sed0017224' => 'sed', 'Sed0026391' => 'sed', 'SEGI_00063' => 'sgi', 'SEGI_10967' => 'sgi', 'SEGI_17510' => 'sgi', 'SEGI_24396' => 'sgi', 'SEGI_39719' => 'sgi', 'SEGI_41392' => 'sgi', 'SGA_v2.0_scaffold11G05794' => 'sas', 'SGA_v2.0_scaffold142G35607' => 'sas', 'SGA_v2.0_scaffold1G00447' => 'sas', 'SHI15388' => 'shi', 'SHI15394' => 'shi', 'SHI15396' => 'shi', 'SHI15399' => 'shi', 'SMO343G0151' => 'smo', 'SMO367G1118' => 'smo', 'Solyc01g080200.3' => 'sly', 'Solyc06g008960.3' => 'sly', 'Solyc09g064780.3' => 'sly', 'Sopen01g031980' => 'spe', 'Sopen06g003710' => 'spe', 'Sopen09g026460' => 'spe', 'Sp3g21240' => 'spa', 'Sp4g30030' => 'spa', 'TAR365G0022' => 'tar', 'TAR365G1023' => 'tar', 'TAR365G1253' => 'tar', 'TAR623G0078' => 'tar', 'TAR623G1721' => 'tar', 'TAR633G0959' => 'tar', 'THA.LOC104802225' => 'tha', 'THA.LOC104804769' => 'tha', 'THA.LOC104808660' => 'tha', 'THA.LOC104812792' => 'tha', 'Thecc.01G284000' => 'tca', 'Thecc.04G220600' => 'tca', 'Thecc.05G268900' => 'tca', 'Thecc.08G171100' => 'tca', 'Thhalv10001284m.g' => 'esa', 'Thhalv10019912m.g' => 'esa', 'TPR.G14189' => 'tpr', 'TPR.G18110' => 'tpr', 'TPR.G18130' => 'tpr', 'TPR.G18131' => 'tpr', 'TPR.G18140' => 'tpr', 'TPR.G24282' => 'tpr', 'TPR.G25221' => 'tpr', 'TPR.G29267' => 'tpr', 'TPR.G35315' => 'tpr', 'TPR.G36173' => 'tpr', 'TWI09G0794' => 'twi', 'TWI59G1348' => 'twi', 'TWI74G0430' => 'twi', 'unitig_26.g8940' => 'ugi', 'unitig_749.g13744' => 'ugi', 'unitig_749.g13745' => 'ugi', 'vmacro08269' => 'vma', 'vmacro14937' => 'vma', 'vmacro20401' => 'vma', 'VMungo0464G1349' => 'vmu', 'VMungo0540G0289' => 'vmu', 'VMungo1215G1590' => 'vmu', 'VMungo1309G0221' => 'vmu', 'VMungo1309G2815' => 'vmu', 'VMungo1383G0239' => 'vmu', 'VMungo1383G2910' => 'vmu', 'Zm00001eb095270' => 'zma', 'Zm00001eb095280' => 'zma', 'Zm00001eb111630' => 'zma', 'Zm00001eb237080' => 'zma', 'Zm00001eb273740' => 'zma', 'Zm00001eb285040' => 'zma', 'Zm00001eb330790' => 'zma', 'Zm00001eb337380' => 'zma' ), 'gf_id' => 'HOM05D001484', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001484' ), 'data_identifier' => 'HOM05D001484', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001484', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p31500' => 'bna', 'A05p00020' => 'bna', 'A07p08820' => 'bna', 'Aa31LG4G3300' => 'aar', 'Aa31LG8G10030' => 'aar', 'Actinidia00731' => 'ach', 'Actinidia11473' => 'ach', 'Actinidia23469' => 'ach', 'Actinidia24318' => 'ach', 'Actinidia40196' => 'ach', 'Actinidia40197' => 'ach', 'Actinidia40198' => 'ach', 'Ah.08g212990' => 'amhyb', 'Ah.15g091720' => 'amhyb', 'AL3G38260' => 'aly', 'AL4G47710' => 'aly', 'Aqoxy2G00671' => 'aox', 'Aqoxy2G03236' => 'aox', 'arahy.Tifrunner.gnm1.ann1.05IDCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KR684' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATY3SJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK6QJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6APGL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IDT7Z9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM073U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ0R87' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LE7RV4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT4QRX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V5ENPK' => 'arhy', 'AT2G48110' => 'ath', 'AT3G23590' => 'ath', 'ATR0626G186' => 'atr', 'ATR1127G141' => 'atr', 'Atru.chr4.2583' => 'acertr', 'Atru.chr5.1358' => 'acertr', 'Atru.chr5.1359' => 'acertr', 'Atru.chr8.46' => 'acertr', 'AUR62002640' => 'cqu', 'AUR62030055' => 'cqu', 'AUR62033713' => 'cqu', 'AUR62033714' => 'cqu', 'AUR62036795' => 'cqu', 'AUR62039891' => 'cqu', 'BcaB02g08737' => 'bca', 'BcaB04g20441' => 'bca', 'BcaB06g26509' => 'bca', 'BcaB06g26510' => 'bca', 'BcaB06g26511' => 'bca', 'BcaB06g26512' => 'bca', 'BcaB06g26513' => 'bca', 'BcaC02g12564' => 'bca', 'BcaC02g12565' => 'bca', 'BcaC02g12794' => 'bca', 'BcaC02g12795' => 'bca', 'BcaC02g12796' => 'bca', 'BcaC06g35541' => 'bca', 'BNapus_Darmor_BZH_scaffold_188p00080' => 'bna', 'BNapus_Darmor_BZH_scaffold_188p00090' => 'bna', 'BolC1t03972H' => 'bol', 'BolC1t03973H' => 'bol', 'BolC4t21680H' => 'bol', 'BolC7t41863H' => 'bol', 'BolSC55t61227H' => 'bol', 'BolSC55t61228H' => 'bol', 'BraA01t03278Z' => 'bra', 'BraA05t18998Z' => 'bra', 'BraA07t28673Z' => 'bra', 'C01p40150' => 'bna', 'C05p12370' => 'bna', 'C07p13680' => 'bna', 'CAN.G1006.16' => 'can', 'CAN.G1006.17' => 'can', 'CAN.G1170.2' => 'can', 'CAN.G962.7' => 'can', 'CANSAT25G2179' => 'cansat', 'CANSAT78G1573' => 'cansat', 'CARHR099510' => 'chi', 'CARHR143510' => 'chi', 'Carub.0003s2380' => 'cru', 'Carub.0004s3082' => 'cru', 'Ca_00614_v3' => 'car', 'Ca_07801_v3' => 'car', 'Ca_08567_v3' => 'car', 'Ca_09571_v3' => 'car', 'CBR_g19290' => 'cbr', 'Cc01_g19770' => 'ccan', 'Cc03_g03030' => 'ccan', 'CDE07G0968' => 'cde', 'CDE09G1441' => 'cde', 'Cfa006103' => 'cfa', 'Cfa015573' => 'cfa', 'Cfa016988' => 'cfa', 'Ciclev10006738m.g' => 'ccl', 'Ciclev10010920m.g' => 'ccl', 'Ciclev10018517m.g' => 'ccl', 'CiPaw.01G159200' => 'cil', 'CiPaw.02G091000' => 'cil', 'CiPaw.02G091100' => 'cil', 'CiPaw.08G103100' => 'cil', 'CiPaw.09G224900' => 'cil', 'ClCG06G005740' => 'cla', 'ClCG07G000090' => 'cla', 'ClCG07G000100' => 'cla', 'COL.COLO4_09143' => 'col', 'COL.COLO4_25124' => 'col', 'Cpa.g.sc16.34' => 'cpa', 'Cpa.g.sc3504.1' => 'cpa', 'Cpa.g.sc60.37' => 'cpa', 'CsaV3_6G018520' => 'csa', 'CsaV3_6G036860' => 'csa', 'CSS0001072' => 'camsi', 'CSS0020208' => 'camsi', 'CSS0021253' => 'camsi', 'CSS0022190' => 'camsi', 'CSS0036150' => 'camsi', 'CSS0040442' => 'camsi', 'CSS0042300' => 'camsi', 'CSS0045298' => 'camsi', 'DCAR_012449' => 'dca', 'DCAR_018405' => 'dca', 'DCAR_024573' => 'dca', 'DCAR_030591' => 'dca', 'Dinv16926' => 'din', 'Dinv32963' => 'din', 'Dinv38382' => 'din', 'Dinv38383' => 'din', 'Duzib133G0974' => 'dzi', 'Duzib138G1867' => 'dzi', 'Duzib211G0420' => 'dzi', 'Duzib212G0930' => 'dzi', 'ECA234G1645' => 'eca', 'ECA247G3467' => 'eca', 'ECA248G1703' => 'eca', 'EL10Ac3g06327' => 'bvu', 'EL10Ac7g17204' => 'bvu', 'Eucgr.A00855' => 'egr', 'Eucgr.A00858' => 'egr', 'Eucgr.H01520' => 'egr', 'Eucgr.H03604' => 'egr', 'Eucgr.L03465' => 'egr', 'Eucgr.L03466' => 'egr', 'FAN01G0988' => 'fan', 'FAN02G3892' => 'fan', 'FAN05G3381' => 'fan', 'FAN07G0967' => 'fan', 'FAN07G1493' => 'fan', 'FAN08G3125' => 'fan', 'FAN09G0402' => 'fan', 'FAN12G2594' => 'fan', 'FAN12G3879' => 'fan', 'FAN14G1546' => 'fan', 'FAN15G3626' => 'fan', 'FAN17G0588' => 'fan', 'FAN17G0609' => 'fan', 'FAN18G2817' => 'fan', 'FAN19G1305' => 'fan', 'FAN20G1787' => 'fan', 'FAN22G0073' => 'fan', 'FAN22G0352' => 'fan', 'FAN22G0368' => 'fan', 'FAN22G2273' => 'fan', 'FAN24G1998' => 'fan', 'FAN27G1317' => 'fan', 'FvH4_2g23980' => 'fve', 'FvH4_4g14380' => 'fve', 'FvH4_4g14390' => 'fve', 'FvH4_6g09250' => 'fve', 'Glyma.03G151100' => 'gma', 'Glyma.04G122550' => 'gma', 'Glyma.05G001600' => 'gma', 'Glyma.09G270766' => 'gma', 'Glyma.09G270832' => 'gma', 'Glyma.13G209800' => 'gma', 'Glyma.15G102800' => 'gma', 'Glyma.18G218900' => 'gma', 'Glyma.19G001500' => 'gma', 'Glyma.19G153600' => 'gma', 'Gohir.A02G028600' => 'ghi', 'Gohir.A08G045000' => 'ghi', 'Gohir.A11G120500' => 'ghi', 'Gohir.A12G006200' => 'ghi', 'Gohir.A12G006250' => 'ghi', 'Gohir.D02G036300' => 'ghi', 'Gohir.D08G054700' => 'ghi', 'Gohir.D11G125600' => 'ghi', 'Gohir.D12G005700' => 'ghi', 'Gorai.004G055200' => 'gra', 'Gorai.005G040400' => 'gra', 'Gorai.007G134500' => 'gra', 'Gorai.008G005500' => 'gra', 'GSVIVG01011094001' => 'vvi', 'GSVIVG01017879001' => 'vvi', 'GSVIVG01025988001' => 'vvi', 'GSVIVG01029847001' => 'vvi', 'HanXRQChr10g0282901' => 'han', 'HanXRQChr10g0310371' => 'han', 'HanXRQChr10g0315041' => 'han', 'HanXRQChr11g0327651' => 'han', 'HanXRQChr12g0359391' => 'han', 'Haze_00972' => 'cav', 'Haze_00973' => 'cav', 'Haze_00974' => 'cav', 'Haze_04747' => 'cav', 'Haze_04749' => 'cav', 'Haze_04750' => 'cav', 'Haze_21217' => 'cav', 'Hma1.2p1_1037F.1_g250680' => 'hma', 'Hma1.2p1_1644F.1_g295320' => 'hma', 'HPP92_011322' => 'vpl', 'HPP92_011323' => 'vpl', 'HPP92_011324' => 'vpl', 'HPP92_011325' => 'vpl', 'HPP92_011326' => 'vpl', 'Hund12205' => 'sun', 'Hund17957' => 'sun', 'Lalb_Chr06g0176771' => 'lal', 'Lalb_Chr18g0056021' => 'lal', 'Lalb_Chr18g0056031' => 'lal', 'Lalb_Chr18g0056041' => 'lal', 'Lalb_Chr20g0107751' => 'lal', 'Lalb_Chr20g0118371' => 'lal', 'Lj1g0010239' => 'lja', 'Lj1g0017101' => 'lja', 'Lj2A1178G40' => 'lonja', 'Lj2A54G84' => 'lonja', 'Lj2g0015248' => 'lja', 'Lj3A761T51' => 'lonja', 'Lj6g0018116' => 'lja', 'Lsat_1_v5_gn_4_136040' => 'lsa', 'Lsat_1_v5_gn_5_187461' => 'lsa', 'Lsat_1_v5_gn_5_77001' => 'lsa', 'Lsat_1_v5_gn_9_4461' => 'lsa', 'Manes.01G210100' => 'mes', 'Manes.03G185600' => 'mes', 'Manes.05G073300' => 'mes', 'Manes.09G120300' => 'mes', 'Manes.15G022100' => 'mes', 'Mapoly0096s0053' => 'mpo', 'MBI03_g14058_MAGBIO' => 'mbi', 'MBI03_g33876_MAGBIO' => 'mbi', 'MBI03_g36854_MAGBIO' => 'mbi', 'MBI17_g11997_MAGBIO' => 'mbi', 'MD03G1269000' => 'mdo', 'MD04G1179600' => 'mdo', 'MD11G1289800' => 'mdo', 'MD12G1194700' => 'mdo', 'MD13G1182100' => 'mdo', 'MD13G1182200' => 'mdo', 'MD16G1182600' => 'mdo', 'Medtr2g021400' => 'mtr', 'Medtr2g021470' => 'mtr', 'Medtr2g105810' => 'mtr', 'Medtr3g033580' => 'mtr', 'Medtr6g007970' => 'mtr', 'Medtr7g056330' => 'mtr', 'Medtr7g074290' => 'mtr', 'Medtr7g074380' => 'mtr', 'Medtr7g094550' => 'mtr', 'Medtr8g069995' => 'mtr', 'MELO3C014345.2' => 'cme', 'MELO3C021395.2' => 'cme', 'Migut.D00262' => 'egut', 'Migut.G00257' => 'egut', 'MSTRG.21575' => 'ama', 'MSTRG.3985' => 'ama', 'Nitab4.5_0000295g0140' => 'nta', 'Nitab4.5_0000732g0140' => 'nta', 'Nitab4.5_0003162g0020' => 'nta', 'Nitab4.5_0006180g0090' => 'nta', 'Nitab4.5_0006390g0010' => 'nta', 'Nitab4.5_0007392g0040' => 'nta', 'Nn1g02140' => 'nnu', 'Nn4g26168' => 'nnu', 'Nn5g26754' => 'nnu', 'Oeu001433.1' => 'oeu', 'Oeu010299.2' => 'oeu', 'Oeu011171.1' => 'oeu', 'Oeu037675.1' => 'oeu', 'Oeu038359.1' => 'oeu', 'Oeu063834.1' => 'oeu', 'Oeu063835.1' => 'oeu', 'Os05g0312000' => 'osa', 'Os07g0211101' => 'osa', 'Os07g0211200' => 'osa', 'Os07g0681500' => 'osa', 'Peaxi162Scf00095g01015' => 'pax', 'Peaxi162Scf00104g00329' => 'pax', 'Peaxi162Scf00161g00137' => 'pax', 'PGR004G1665' => 'pgr', 'PGR031G2937' => 'pgr', 'PGR119G2145' => 'pgr', 'PGSC0003DMG400004351' => 'stu', 'PGSC0003DMG400014625' => 'stu', 'PGSC0003DMG401000943' => 'stu', 'Phvul.001G148600' => 'pvu', 'Phvul.004G001700' => 'pvu', 'Phvul.006G154900' => 'pvu', 'Phvul.008G078200' => 'pvu', 'Phvul.011G136500' => 'pvu', 'Potri.002G215600' => 'ptr', 'Potri.008G201600' => 'ptr', 'Potri.014G138400' => 'ptr', 'Potri.016G142500' => 'ptr', 'Pp3c16_10580' => 'ppa', 'Pp3c5_25280' => 'ppa', 'Prupe.1G150000' => 'ppe', 'Prupe.1G150100' => 'ppe', 'Prupe.6G299600' => 'ppe', 'Prupe.8G245000' => 'ppe', 'Psat0s4927g0040' => 'psa', 'Psat1g052080' => 'psa', 'Psat1g183800' => 'psa', 'Psat3g113840' => 'psa', 'Psat3g126120' => 'psa', 'Psat3g126160' => 'psa', 'Psat3g158760' => 'psa', 'Psat3g158840' => 'psa', 'PSO170G2858' => 'pso', 'PSO339G0606' => 'pso', 'PSO384G4709' => 'pso', 'PSO407G0334' => 'pso', 'QL04p040276' => 'qlo', 'QL06p005458' => 'qlo', 'QL06p005472' => 'qlo', 'QL07p030546' => 'qlo', 'QL07p031519' => 'qlo', 'QL09p050949' => 'qlo', 'QL09p050966' => 'qlo', 'QL09p051067' => 'qlo', 'QL12p022706' => 'qlo', 'RcHm_v2.0_Chr2g0119601' => 'rch', 'RcHm_v2.0_Chr3g0459591' => 'rch', 'RcHm_v2.0_Chr4g0418521' => 'rch', 'RcHm_v2.0_Chr4g0418531' => 'rch', 'RcHm_v2.0_Chr4g0418541' => 'rch', 'RcHm_v2.0_Chr6g0291641' => 'rch', 'Rhsim01G0086300' => 'rsi', 'Rhsim01G0276300' => 'rsi', 'Rhsim01G0276500' => 'rsi', 'Rhsim04G0207700' => 'rsi', 'Rhsim05G0234500' => 'rsi', 'Rhsim13G0022400' => 'rsi', 'Sabra02G0167900' => 'sbr', 'Sabra04G0158500' => 'sbr', 'Sabra08G0159800' => 'sbr', 'Sabra10G0011500' => 'sbr', 'Sabra14G0104400' => 'sbr', 'SalBow2G2440' => 'sbo', 'SalBow4G2265' => 'sbo', 'Sc02g0000060' => 'sci', 'Sc05g0005020' => 'sci', 'Sc13g0003890' => 'sci', 'Sed0014865' => 'sed', 'Sed0017224' => 'sed', 'Sed0026391' => 'sed', 'SEGI_00063' => 'sgi', 'SEGI_10967' => 'sgi', 'SEGI_17510' => 'sgi', 'SEGI_24396' => 'sgi', 'SEGI_39719' => 'sgi', 'SEGI_41392' => 'sgi', 'SGA_v2.0_scaffold11G05794' => 'sas', 'SGA_v2.0_scaffold142G35607' => 'sas', 'SGA_v2.0_scaffold1G00447' => 'sas', 'SHI15388' => 'shi', 'SHI15394' => 'shi', 'SHI15396' => 'shi', 'SHI15399' => 'shi', 'SMO343G0151' => 'smo', 'SMO367G1118' => 'smo', 'Solyc01g080200.3' => 'sly', 'Solyc06g008960.3' => 'sly', 'Solyc09g064780.3' => 'sly', 'Sopen01g031980' => 'spe', 'Sopen06g003710' => 'spe', 'Sopen09g026460' => 'spe', 'Sp3g21240' => 'spa', 'Sp4g30030' => 'spa', 'TAR365G0022' => 'tar', 'TAR365G1023' => 'tar', 'TAR365G1253' => 'tar', 'TAR623G0078' => 'tar', 'TAR623G1721' => 'tar', 'TAR633G0959' => 'tar', 'THA.LOC104802225' => 'tha', 'THA.LOC104804769' => 'tha', 'THA.LOC104808660' => 'tha', 'THA.LOC104812792' => 'tha', 'Thecc.01G284000' => 'tca', 'Thecc.04G220600' => 'tca', 'Thecc.05G268900' => 'tca', 'Thecc.08G171100' => 'tca', 'Thhalv10001284m.g' => 'esa', 'Thhalv10019912m.g' => 'esa', 'TPR.G14189' => 'tpr', 'TPR.G18110' => 'tpr', 'TPR.G18130' => 'tpr', 'TPR.G18131' => 'tpr', 'TPR.G18140' => 'tpr', 'TPR.G24282' => 'tpr', 'TPR.G25221' => 'tpr', 'TPR.G29267' => 'tpr', 'TPR.G35315' => 'tpr', 'TPR.G36173' => 'tpr', 'TWI09G0794' => 'twi', 'TWI59G1348' => 'twi', 'TWI74G0430' => 'twi', 'unitig_26.g8940' => 'ugi', 'unitig_749.g13744' => 'ugi', 'unitig_749.g13745' => 'ugi', 'vmacro08269' => 'vma', 'vmacro14937' => 'vma', 'vmacro20401' => 'vma', 'VMungo0464G1349' => 'vmu', 'VMungo0540G0289' => 'vmu', 'VMungo1215G1590' => 'vmu', 'VMungo1309G0221' => 'vmu', 'VMungo1309G2815' => 'vmu', 'VMungo1383G0239' => 'vmu', 'VMungo1383G2910' => 'vmu', 'Zm00001eb095270' => 'zma', 'Zm00001eb095280' => 'zma', 'Zm00001eb111630' => 'zma', 'Zm00001eb237080' => 'zma', 'Zm00001eb273740' => 'zma', 'Zm00001eb285040' => 'zma', 'Zm00001eb330790' => 'zma', 'Zm00001eb337380' => 'zma' ) $gf_id = 'HOM05D001484' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001484' ) $data_identifier = 'HOM05D001484' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 2, 'aly' => (int) 2, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 22, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 7, 'hma' => (int) 2, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 7, 'mtr' => (int) 10, 'cme' => (int) 2, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 4, 'ppa' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 4, 'qlo' => (int) 9, 'rch' => (int) 6, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 10, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 7, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb337380' $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' => 'HOM05D001484', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p31500' => 'bna', 'A05p00020' => 'bna', 'A07p08820' => 'bna', 'Aa31LG4G3300' => 'aar', 'Aa31LG8G10030' => 'aar', 'Actinidia00731' => 'ach', 'Actinidia11473' => 'ach', 'Actinidia23469' => 'ach', 'Actinidia24318' => 'ach', 'Actinidia40196' => 'ach', 'Actinidia40197' => 'ach', 'Actinidia40198' => 'ach', 'Ah.08g212990' => 'amhyb', 'Ah.15g091720' => 'amhyb', 'AL3G38260' => 'aly', 'AL4G47710' => 'aly', 'Aqoxy2G00671' => 'aox', 'Aqoxy2G03236' => 'aox', 'arahy.Tifrunner.gnm1.ann1.05IDCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KR684' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATY3SJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK6QJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6APGL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IDT7Z9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM073U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ0R87' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LE7RV4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT4QRX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V5ENPK' => 'arhy', 'AT2G48110' => 'ath', 'AT3G23590' => 'ath', 'ATR0626G186' => 'atr', 'ATR1127G141' => 'atr', 'Atru.chr4.2583' => 'acertr', 'Atru.chr5.1358' => 'acertr', 'Atru.chr5.1359' => 'acertr', 'Atru.chr8.46' => 'acertr', 'AUR62002640' => 'cqu', 'AUR62030055' => 'cqu', 'AUR62033713' => 'cqu', 'AUR62033714' => 'cqu', 'AUR62036795' => 'cqu', 'AUR62039891' => 'cqu', 'BcaB02g08737' => 'bca', 'BcaB04g20441' => 'bca', 'BcaB06g26509' => 'bca', 'BcaB06g26510' => 'bca', 'BcaB06g26511' => 'bca', 'BcaB06g26512' => 'bca', 'BcaB06g26513' => 'bca', 'BcaC02g12564' => 'bca', 'BcaC02g12565' => 'bca', 'BcaC02g12794' => 'bca', 'BcaC02g12795' => 'bca', 'BcaC02g12796' => 'bca', 'BcaC06g35541' => 'bca', 'BNapus_Darmor_BZH_scaffold_188p00080' => 'bna', 'BNapus_Darmor_BZH_scaffold_188p00090' => 'bna', 'BolC1t03972H' => 'bol', 'BolC1t03973H' => 'bol', 'BolC4t21680H' => 'bol', 'BolC7t41863H' => 'bol', 'BolSC55t61227H' => 'bol', 'BolSC55t61228H' => 'bol', 'BraA01t03278Z' => 'bra', 'BraA05t18998Z' => 'bra', 'BraA07t28673Z' => 'bra', 'C01p40150' => 'bna', 'C05p12370' => 'bna', 'C07p13680' => 'bna', 'CAN.G1006.16' => 'can', 'CAN.G1006.17' => 'can', 'CAN.G1170.2' => 'can', 'CAN.G962.7' => 'can', 'CANSAT25G2179' => 'cansat', 'CANSAT78G1573' => 'cansat', 'CARHR099510' => 'chi', 'CARHR143510' => 'chi', 'Carub.0003s2380' => 'cru', 'Carub.0004s3082' => 'cru', 'Ca_00614_v3' => 'car', 'Ca_07801_v3' => 'car', 'Ca_08567_v3' => 'car', 'Ca_09571_v3' => 'car', 'CBR_g19290' => 'cbr', 'Cc01_g19770' => 'ccan', 'Cc03_g03030' => 'ccan', 'CDE07G0968' => 'cde', 'CDE09G1441' => 'cde', 'Cfa006103' => 'cfa', 'Cfa015573' => 'cfa', 'Cfa016988' => 'cfa', 'Ciclev10006738m.g' => 'ccl', 'Ciclev10010920m.g' => 'ccl', 'Ciclev10018517m.g' => 'ccl', 'CiPaw.01G159200' => 'cil', 'CiPaw.02G091000' => 'cil', 'CiPaw.02G091100' => 'cil', 'CiPaw.08G103100' => 'cil', 'CiPaw.09G224900' => 'cil', 'ClCG06G005740' => 'cla', 'ClCG07G000090' => 'cla', 'ClCG07G000100' => 'cla', 'COL.COLO4_09143' => 'col', 'COL.COLO4_25124' => 'col', 'Cpa.g.sc16.34' => 'cpa', 'Cpa.g.sc3504.1' => 'cpa', 'Cpa.g.sc60.37' => 'cpa', 'CsaV3_6G018520' => 'csa', 'CsaV3_6G036860' => 'csa', 'CSS0001072' => 'camsi', 'CSS0020208' => 'camsi', 'CSS0021253' => 'camsi', 'CSS0022190' => 'camsi', 'CSS0036150' => 'camsi', 'CSS0040442' => 'camsi', 'CSS0042300' => 'camsi', 'CSS0045298' => 'camsi', 'DCAR_012449' => 'dca', 'DCAR_018405' => 'dca', 'DCAR_024573' => 'dca', 'DCAR_030591' => 'dca', 'Dinv16926' => 'din', 'Dinv32963' => 'din', 'Dinv38382' => 'din', 'Dinv38383' => 'din', 'Duzib133G0974' => 'dzi', 'Duzib138G1867' => 'dzi', 'Duzib211G0420' => 'dzi', 'Duzib212G0930' => 'dzi', 'ECA234G1645' => 'eca', 'ECA247G3467' => 'eca', 'ECA248G1703' => 'eca', 'EL10Ac3g06327' => 'bvu', 'EL10Ac7g17204' => 'bvu', 'Eucgr.A00855' => 'egr', 'Eucgr.A00858' => 'egr', 'Eucgr.H01520' => 'egr', 'Eucgr.H03604' => 'egr', 'Eucgr.L03465' => 'egr', 'Eucgr.L03466' => 'egr', 'FAN01G0988' => 'fan', 'FAN02G3892' => 'fan', 'FAN05G3381' => 'fan', 'FAN07G0967' => 'fan', 'FAN07G1493' => 'fan', 'FAN08G3125' => 'fan', 'FAN09G0402' => 'fan', 'FAN12G2594' => 'fan', 'FAN12G3879' => 'fan', 'FAN14G1546' => 'fan', 'FAN15G3626' => 'fan', 'FAN17G0588' => 'fan', 'FAN17G0609' => 'fan', 'FAN18G2817' => 'fan', 'FAN19G1305' => 'fan', 'FAN20G1787' => 'fan', 'FAN22G0073' => 'fan', 'FAN22G0352' => 'fan', 'FAN22G0368' => 'fan', 'FAN22G2273' => 'fan', 'FAN24G1998' => 'fan', 'FAN27G1317' => 'fan', 'FvH4_2g23980' => 'fve', 'FvH4_4g14380' => 'fve', 'FvH4_4g14390' => 'fve', 'FvH4_6g09250' => 'fve', 'Glyma.03G151100' => 'gma', 'Glyma.04G122550' => 'gma', 'Glyma.05G001600' => 'gma', 'Glyma.09G270766' => 'gma', 'Glyma.09G270832' => 'gma', 'Glyma.13G209800' => 'gma', 'Glyma.15G102800' => 'gma', 'Glyma.18G218900' => 'gma', 'Glyma.19G001500' => 'gma', 'Glyma.19G153600' => 'gma', 'Gohir.A02G028600' => 'ghi', 'Gohir.A08G045000' => 'ghi', 'Gohir.A11G120500' => 'ghi', 'Gohir.A12G006200' => 'ghi', 'Gohir.A12G006250' => 'ghi', 'Gohir.D02G036300' => 'ghi', 'Gohir.D08G054700' => 'ghi', 'Gohir.D11G125600' => 'ghi', 'Gohir.D12G005700' => 'ghi', 'Gorai.004G055200' => 'gra', 'Gorai.005G040400' => 'gra', 'Gorai.007G134500' => 'gra', 'Gorai.008G005500' => 'gra', 'GSVIVG01011094001' => 'vvi', 'GSVIVG01017879001' => 'vvi', 'GSVIVG01025988001' => 'vvi', 'GSVIVG01029847001' => 'vvi', 'HanXRQChr10g0282901' => 'han', 'HanXRQChr10g0310371' => 'han', 'HanXRQChr10g0315041' => 'han', 'HanXRQChr11g0327651' => 'han', 'HanXRQChr12g0359391' => 'han', 'Haze_00972' => 'cav', 'Haze_00973' => 'cav', 'Haze_00974' => 'cav', 'Haze_04747' => 'cav', 'Haze_04749' => 'cav', 'Haze_04750' => 'cav', 'Haze_21217' => 'cav', 'Hma1.2p1_1037F.1_g250680' => 'hma', 'Hma1.2p1_1644F.1_g295320' => 'hma', 'HPP92_011322' => 'vpl', 'HPP92_011323' => 'vpl', 'HPP92_011324' => 'vpl', 'HPP92_011325' => 'vpl', 'HPP92_011326' => 'vpl', 'Hund12205' => 'sun', 'Hund17957' => 'sun', 'Lalb_Chr06g0176771' => 'lal', 'Lalb_Chr18g0056021' => 'lal', 'Lalb_Chr18g0056031' => 'lal', 'Lalb_Chr18g0056041' => 'lal', 'Lalb_Chr20g0107751' => 'lal', 'Lalb_Chr20g0118371' => 'lal', 'Lj1g0010239' => 'lja', 'Lj1g0017101' => 'lja', 'Lj2A1178G40' => 'lonja', 'Lj2A54G84' => 'lonja', 'Lj2g0015248' => 'lja', 'Lj3A761T51' => 'lonja', 'Lj6g0018116' => 'lja', 'Lsat_1_v5_gn_4_136040' => 'lsa', 'Lsat_1_v5_gn_5_187461' => 'lsa', 'Lsat_1_v5_gn_5_77001' => 'lsa', 'Lsat_1_v5_gn_9_4461' => 'lsa', 'Manes.01G210100' => 'mes', 'Manes.03G185600' => 'mes', 'Manes.05G073300' => 'mes', 'Manes.09G120300' => 'mes', 'Manes.15G022100' => 'mes', 'Mapoly0096s0053' => 'mpo', 'MBI03_g14058_MAGBIO' => 'mbi', 'MBI03_g33876_MAGBIO' => 'mbi', 'MBI03_g36854_MAGBIO' => 'mbi', 'MBI17_g11997_MAGBIO' => 'mbi', 'MD03G1269000' => 'mdo', 'MD04G1179600' => 'mdo', 'MD11G1289800' => 'mdo', 'MD12G1194700' => 'mdo', 'MD13G1182100' => 'mdo', 'MD13G1182200' => 'mdo', 'MD16G1182600' => 'mdo', 'Medtr2g021400' => 'mtr', 'Medtr2g021470' => 'mtr', 'Medtr2g105810' => 'mtr', 'Medtr3g033580' => 'mtr', 'Medtr6g007970' => 'mtr', 'Medtr7g056330' => 'mtr', 'Medtr7g074290' => 'mtr', 'Medtr7g074380' => 'mtr', 'Medtr7g094550' => 'mtr', 'Medtr8g069995' => 'mtr', 'MELO3C014345.2' => 'cme', 'MELO3C021395.2' => 'cme', 'Migut.D00262' => 'egut', 'Migut.G00257' => 'egut', 'MSTRG.21575' => 'ama', 'MSTRG.3985' => 'ama', 'Nitab4.5_0000295g0140' => 'nta', 'Nitab4.5_0000732g0140' => 'nta', 'Nitab4.5_0003162g0020' => 'nta', 'Nitab4.5_0006180g0090' => 'nta', 'Nitab4.5_0006390g0010' => 'nta', 'Nitab4.5_0007392g0040' => 'nta', 'Nn1g02140' => 'nnu', 'Nn4g26168' => 'nnu', 'Nn5g26754' => 'nnu', 'Oeu001433.1' => 'oeu', 'Oeu010299.2' => 'oeu', 'Oeu011171.1' => 'oeu', 'Oeu037675.1' => 'oeu', 'Oeu038359.1' => 'oeu', 'Oeu063834.1' => 'oeu', 'Oeu063835.1' => 'oeu', 'Os05g0312000' => 'osa', 'Os07g0211101' => 'osa', 'Os07g0211200' => 'osa', 'Os07g0681500' => 'osa', 'Peaxi162Scf00095g01015' => 'pax', 'Peaxi162Scf00104g00329' => 'pax', 'Peaxi162Scf00161g00137' => 'pax', 'PGR004G1665' => 'pgr', 'PGR031G2937' => 'pgr', 'PGR119G2145' => 'pgr', 'PGSC0003DMG400004351' => 'stu', 'PGSC0003DMG400014625' => 'stu', 'PGSC0003DMG401000943' => 'stu', 'Phvul.001G148600' => 'pvu', 'Phvul.004G001700' => 'pvu', 'Phvul.006G154900' => 'pvu', 'Phvul.008G078200' => 'pvu', 'Phvul.011G136500' => 'pvu', 'Potri.002G215600' => 'ptr', 'Potri.008G201600' => 'ptr', 'Potri.014G138400' => 'ptr', 'Potri.016G142500' => 'ptr', 'Pp3c16_10580' => 'ppa', 'Pp3c5_25280' => 'ppa', 'Prupe.1G150000' => 'ppe', 'Prupe.1G150100' => 'ppe', 'Prupe.6G299600' => 'ppe', 'Prupe.8G245000' => 'ppe', 'Psat0s4927g0040' => 'psa', 'Psat1g052080' => 'psa', 'Psat1g183800' => 'psa', 'Psat3g113840' => 'psa', 'Psat3g126120' => 'psa', 'Psat3g126160' => 'psa', 'Psat3g158760' => 'psa', 'Psat3g158840' => 'psa', 'PSO170G2858' => 'pso', 'PSO339G0606' => 'pso', 'PSO384G4709' => 'pso', 'PSO407G0334' => 'pso', 'QL04p040276' => 'qlo', 'QL06p005458' => 'qlo', 'QL06p005472' => 'qlo', 'QL07p030546' => 'qlo', 'QL07p031519' => 'qlo', 'QL09p050949' => 'qlo', 'QL09p050966' => 'qlo', 'QL09p051067' => 'qlo', 'QL12p022706' => 'qlo', 'RcHm_v2.0_Chr2g0119601' => 'rch', 'RcHm_v2.0_Chr3g0459591' => 'rch', 'RcHm_v2.0_Chr4g0418521' => 'rch', 'RcHm_v2.0_Chr4g0418531' => 'rch', 'RcHm_v2.0_Chr4g0418541' => 'rch', 'RcHm_v2.0_Chr6g0291641' => 'rch', 'Rhsim01G0086300' => 'rsi', 'Rhsim01G0276300' => 'rsi', 'Rhsim01G0276500' => 'rsi', 'Rhsim04G0207700' => 'rsi', 'Rhsim05G0234500' => 'rsi', 'Rhsim13G0022400' => 'rsi', 'Sabra02G0167900' => 'sbr', 'Sabra04G0158500' => 'sbr', 'Sabra08G0159800' => 'sbr', 'Sabra10G0011500' => 'sbr', 'Sabra14G0104400' => 'sbr', 'SalBow2G2440' => 'sbo', 'SalBow4G2265' => 'sbo', 'Sc02g0000060' => 'sci', 'Sc05g0005020' => 'sci', 'Sc13g0003890' => 'sci', 'Sed0014865' => 'sed', 'Sed0017224' => 'sed', 'Sed0026391' => 'sed', 'SEGI_00063' => 'sgi', 'SEGI_10967' => 'sgi', 'SEGI_17510' => 'sgi', 'SEGI_24396' => 'sgi', 'SEGI_39719' => 'sgi', 'SEGI_41392' => 'sgi', 'SGA_v2.0_scaffold11G05794' => 'sas', 'SGA_v2.0_scaffold142G35607' => 'sas', 'SGA_v2.0_scaffold1G00447' => 'sas', 'SHI15388' => 'shi', 'SHI15394' => 'shi', 'SHI15396' => 'shi', 'SHI15399' => 'shi', 'SMO343G0151' => 'smo', 'SMO367G1118' => 'smo', 'Solyc01g080200.3' => 'sly', 'Solyc06g008960.3' => 'sly', 'Solyc09g064780.3' => 'sly', 'Sopen01g031980' => 'spe', 'Sopen06g003710' => 'spe', 'Sopen09g026460' => 'spe', 'Sp3g21240' => 'spa', 'Sp4g30030' => 'spa', 'TAR365G0022' => 'tar', 'TAR365G1023' => 'tar', 'TAR365G1253' => 'tar', 'TAR623G0078' => 'tar', 'TAR623G1721' => 'tar', 'TAR633G0959' => 'tar', 'THA.LOC104802225' => 'tha', 'THA.LOC104804769' => 'tha', 'THA.LOC104808660' => 'tha', 'THA.LOC104812792' => 'tha', 'Thecc.01G284000' => 'tca', 'Thecc.04G220600' => 'tca', 'Thecc.05G268900' => 'tca', 'Thecc.08G171100' => 'tca', 'Thhalv10001284m.g' => 'esa', 'Thhalv10019912m.g' => 'esa', 'TPR.G14189' => 'tpr', 'TPR.G18110' => 'tpr', 'TPR.G18130' => 'tpr', 'TPR.G18131' => 'tpr', 'TPR.G18140' => 'tpr', 'TPR.G24282' => 'tpr', 'TPR.G25221' => 'tpr', 'TPR.G29267' => 'tpr', 'TPR.G35315' => 'tpr', 'TPR.G36173' => 'tpr', 'TWI09G0794' => 'twi', 'TWI59G1348' => 'twi', 'TWI74G0430' => 'twi', 'unitig_26.g8940' => 'ugi', 'unitig_749.g13744' => 'ugi', 'unitig_749.g13745' => 'ugi', 'vmacro08269' => 'vma', 'vmacro14937' => 'vma', 'vmacro20401' => 'vma', 'VMungo0464G1349' => 'vmu', 'VMungo0540G0289' => 'vmu', 'VMungo1215G1590' => 'vmu', 'VMungo1309G0221' => 'vmu', 'VMungo1309G2815' => 'vmu', 'VMungo1383G0239' => 'vmu', 'VMungo1383G2910' => 'vmu', 'Zm00001eb095270' => 'zma', 'Zm00001eb095280' => 'zma', 'Zm00001eb111630' => 'zma', 'Zm00001eb237080' => 'zma', 'Zm00001eb273740' => 'zma', 'Zm00001eb285040' => 'zma', 'Zm00001eb330790' => 'zma', 'Zm00001eb337380' => 'zma' ), 'gf_id' => 'HOM05D001484', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001484' ), 'data_identifier' => 'HOM05D001484', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001484', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p31500' => 'bna', 'A05p00020' => 'bna', 'A07p08820' => 'bna', 'Aa31LG4G3300' => 'aar', 'Aa31LG8G10030' => 'aar', 'Actinidia00731' => 'ach', 'Actinidia11473' => 'ach', 'Actinidia23469' => 'ach', 'Actinidia24318' => 'ach', 'Actinidia40196' => 'ach', 'Actinidia40197' => 'ach', 'Actinidia40198' => 'ach', 'Ah.08g212990' => 'amhyb', 'Ah.15g091720' => 'amhyb', 'AL3G38260' => 'aly', 'AL4G47710' => 'aly', 'Aqoxy2G00671' => 'aox', 'Aqoxy2G03236' => 'aox', 'arahy.Tifrunner.gnm1.ann1.05IDCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KR684' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATY3SJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK6QJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6APGL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IDT7Z9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM073U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ0R87' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LE7RV4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT4QRX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V5ENPK' => 'arhy', 'AT2G48110' => 'ath', 'AT3G23590' => 'ath', 'ATR0626G186' => 'atr', 'ATR1127G141' => 'atr', 'Atru.chr4.2583' => 'acertr', 'Atru.chr5.1358' => 'acertr', 'Atru.chr5.1359' => 'acertr', 'Atru.chr8.46' => 'acertr', 'AUR62002640' => 'cqu', 'AUR62030055' => 'cqu', 'AUR62033713' => 'cqu', 'AUR62033714' => 'cqu', 'AUR62036795' => 'cqu', 'AUR62039891' => 'cqu', 'BcaB02g08737' => 'bca', 'BcaB04g20441' => 'bca', 'BcaB06g26509' => 'bca', 'BcaB06g26510' => 'bca', 'BcaB06g26511' => 'bca', 'BcaB06g26512' => 'bca', 'BcaB06g26513' => 'bca', 'BcaC02g12564' => 'bca', 'BcaC02g12565' => 'bca', 'BcaC02g12794' => 'bca', 'BcaC02g12795' => 'bca', 'BcaC02g12796' => 'bca', 'BcaC06g35541' => 'bca', 'BNapus_Darmor_BZH_scaffold_188p00080' => 'bna', 'BNapus_Darmor_BZH_scaffold_188p00090' => 'bna', 'BolC1t03972H' => 'bol', 'BolC1t03973H' => 'bol', 'BolC4t21680H' => 'bol', 'BolC7t41863H' => 'bol', 'BolSC55t61227H' => 'bol', 'BolSC55t61228H' => 'bol', 'BraA01t03278Z' => 'bra', 'BraA05t18998Z' => 'bra', 'BraA07t28673Z' => 'bra', 'C01p40150' => 'bna', 'C05p12370' => 'bna', 'C07p13680' => 'bna', 'CAN.G1006.16' => 'can', 'CAN.G1006.17' => 'can', 'CAN.G1170.2' => 'can', 'CAN.G962.7' => 'can', 'CANSAT25G2179' => 'cansat', 'CANSAT78G1573' => 'cansat', 'CARHR099510' => 'chi', 'CARHR143510' => 'chi', 'Carub.0003s2380' => 'cru', 'Carub.0004s3082' => 'cru', 'Ca_00614_v3' => 'car', 'Ca_07801_v3' => 'car', 'Ca_08567_v3' => 'car', 'Ca_09571_v3' => 'car', 'CBR_g19290' => 'cbr', 'Cc01_g19770' => 'ccan', 'Cc03_g03030' => 'ccan', 'CDE07G0968' => 'cde', 'CDE09G1441' => 'cde', 'Cfa006103' => 'cfa', 'Cfa015573' => 'cfa', 'Cfa016988' => 'cfa', 'Ciclev10006738m.g' => 'ccl', 'Ciclev10010920m.g' => 'ccl', 'Ciclev10018517m.g' => 'ccl', 'CiPaw.01G159200' => 'cil', 'CiPaw.02G091000' => 'cil', 'CiPaw.02G091100' => 'cil', 'CiPaw.08G103100' => 'cil', 'CiPaw.09G224900' => 'cil', 'ClCG06G005740' => 'cla', 'ClCG07G000090' => 'cla', 'ClCG07G000100' => 'cla', 'COL.COLO4_09143' => 'col', 'COL.COLO4_25124' => 'col', 'Cpa.g.sc16.34' => 'cpa', 'Cpa.g.sc3504.1' => 'cpa', 'Cpa.g.sc60.37' => 'cpa', 'CsaV3_6G018520' => 'csa', 'CsaV3_6G036860' => 'csa', 'CSS0001072' => 'camsi', 'CSS0020208' => 'camsi', 'CSS0021253' => 'camsi', 'CSS0022190' => 'camsi', 'CSS0036150' => 'camsi', 'CSS0040442' => 'camsi', 'CSS0042300' => 'camsi', 'CSS0045298' => 'camsi', 'DCAR_012449' => 'dca', 'DCAR_018405' => 'dca', 'DCAR_024573' => 'dca', 'DCAR_030591' => 'dca', 'Dinv16926' => 'din', 'Dinv32963' => 'din', 'Dinv38382' => 'din', 'Dinv38383' => 'din', 'Duzib133G0974' => 'dzi', 'Duzib138G1867' => 'dzi', 'Duzib211G0420' => 'dzi', 'Duzib212G0930' => 'dzi', 'ECA234G1645' => 'eca', 'ECA247G3467' => 'eca', 'ECA248G1703' => 'eca', 'EL10Ac3g06327' => 'bvu', 'EL10Ac7g17204' => 'bvu', 'Eucgr.A00855' => 'egr', 'Eucgr.A00858' => 'egr', 'Eucgr.H01520' => 'egr', 'Eucgr.H03604' => 'egr', 'Eucgr.L03465' => 'egr', 'Eucgr.L03466' => 'egr', 'FAN01G0988' => 'fan', 'FAN02G3892' => 'fan', 'FAN05G3381' => 'fan', 'FAN07G0967' => 'fan', 'FAN07G1493' => 'fan', 'FAN08G3125' => 'fan', 'FAN09G0402' => 'fan', 'FAN12G2594' => 'fan', 'FAN12G3879' => 'fan', 'FAN14G1546' => 'fan', 'FAN15G3626' => 'fan', 'FAN17G0588' => 'fan', 'FAN17G0609' => 'fan', 'FAN18G2817' => 'fan', 'FAN19G1305' => 'fan', 'FAN20G1787' => 'fan', 'FAN22G0073' => 'fan', 'FAN22G0352' => 'fan', 'FAN22G0368' => 'fan', 'FAN22G2273' => 'fan', 'FAN24G1998' => 'fan', 'FAN27G1317' => 'fan', 'FvH4_2g23980' => 'fve', 'FvH4_4g14380' => 'fve', 'FvH4_4g14390' => 'fve', 'FvH4_6g09250' => 'fve', 'Glyma.03G151100' => 'gma', 'Glyma.04G122550' => 'gma', 'Glyma.05G001600' => 'gma', 'Glyma.09G270766' => 'gma', 'Glyma.09G270832' => 'gma', 'Glyma.13G209800' => 'gma', 'Glyma.15G102800' => 'gma', 'Glyma.18G218900' => 'gma', 'Glyma.19G001500' => 'gma', 'Glyma.19G153600' => 'gma', 'Gohir.A02G028600' => 'ghi', 'Gohir.A08G045000' => 'ghi', 'Gohir.A11G120500' => 'ghi', 'Gohir.A12G006200' => 'ghi', 'Gohir.A12G006250' => 'ghi', 'Gohir.D02G036300' => 'ghi', 'Gohir.D08G054700' => 'ghi', 'Gohir.D11G125600' => 'ghi', 'Gohir.D12G005700' => 'ghi', 'Gorai.004G055200' => 'gra', 'Gorai.005G040400' => 'gra', 'Gorai.007G134500' => 'gra', 'Gorai.008G005500' => 'gra', 'GSVIVG01011094001' => 'vvi', 'GSVIVG01017879001' => 'vvi', 'GSVIVG01025988001' => 'vvi', 'GSVIVG01029847001' => 'vvi', 'HanXRQChr10g0282901' => 'han', 'HanXRQChr10g0310371' => 'han', 'HanXRQChr10g0315041' => 'han', 'HanXRQChr11g0327651' => 'han', 'HanXRQChr12g0359391' => 'han', 'Haze_00972' => 'cav', 'Haze_00973' => 'cav', 'Haze_00974' => 'cav', 'Haze_04747' => 'cav', 'Haze_04749' => 'cav', 'Haze_04750' => 'cav', 'Haze_21217' => 'cav', 'Hma1.2p1_1037F.1_g250680' => 'hma', 'Hma1.2p1_1644F.1_g295320' => 'hma', 'HPP92_011322' => 'vpl', 'HPP92_011323' => 'vpl', 'HPP92_011324' => 'vpl', 'HPP92_011325' => 'vpl', 'HPP92_011326' => 'vpl', 'Hund12205' => 'sun', 'Hund17957' => 'sun', 'Lalb_Chr06g0176771' => 'lal', 'Lalb_Chr18g0056021' => 'lal', 'Lalb_Chr18g0056031' => 'lal', 'Lalb_Chr18g0056041' => 'lal', 'Lalb_Chr20g0107751' => 'lal', 'Lalb_Chr20g0118371' => 'lal', 'Lj1g0010239' => 'lja', 'Lj1g0017101' => 'lja', 'Lj2A1178G40' => 'lonja', 'Lj2A54G84' => 'lonja', 'Lj2g0015248' => 'lja', 'Lj3A761T51' => 'lonja', 'Lj6g0018116' => 'lja', 'Lsat_1_v5_gn_4_136040' => 'lsa', 'Lsat_1_v5_gn_5_187461' => 'lsa', 'Lsat_1_v5_gn_5_77001' => 'lsa', 'Lsat_1_v5_gn_9_4461' => 'lsa', 'Manes.01G210100' => 'mes', 'Manes.03G185600' => 'mes', 'Manes.05G073300' => 'mes', 'Manes.09G120300' => 'mes', 'Manes.15G022100' => 'mes', 'Mapoly0096s0053' => 'mpo', 'MBI03_g14058_MAGBIO' => 'mbi', 'MBI03_g33876_MAGBIO' => 'mbi', 'MBI03_g36854_MAGBIO' => 'mbi', 'MBI17_g11997_MAGBIO' => 'mbi', 'MD03G1269000' => 'mdo', 'MD04G1179600' => 'mdo', 'MD11G1289800' => 'mdo', 'MD12G1194700' => 'mdo', 'MD13G1182100' => 'mdo', 'MD13G1182200' => 'mdo', 'MD16G1182600' => 'mdo', 'Medtr2g021400' => 'mtr', 'Medtr2g021470' => 'mtr', 'Medtr2g105810' => 'mtr', 'Medtr3g033580' => 'mtr', 'Medtr6g007970' => 'mtr', 'Medtr7g056330' => 'mtr', 'Medtr7g074290' => 'mtr', 'Medtr7g074380' => 'mtr', 'Medtr7g094550' => 'mtr', 'Medtr8g069995' => 'mtr', 'MELO3C014345.2' => 'cme', 'MELO3C021395.2' => 'cme', 'Migut.D00262' => 'egut', 'Migut.G00257' => 'egut', 'MSTRG.21575' => 'ama', 'MSTRG.3985' => 'ama', 'Nitab4.5_0000295g0140' => 'nta', 'Nitab4.5_0000732g0140' => 'nta', 'Nitab4.5_0003162g0020' => 'nta', 'Nitab4.5_0006180g0090' => 'nta', 'Nitab4.5_0006390g0010' => 'nta', 'Nitab4.5_0007392g0040' => 'nta', 'Nn1g02140' => 'nnu', 'Nn4g26168' => 'nnu', 'Nn5g26754' => 'nnu', 'Oeu001433.1' => 'oeu', 'Oeu010299.2' => 'oeu', 'Oeu011171.1' => 'oeu', 'Oeu037675.1' => 'oeu', 'Oeu038359.1' => 'oeu', 'Oeu063834.1' => 'oeu', 'Oeu063835.1' => 'oeu', 'Os05g0312000' => 'osa', 'Os07g0211101' => 'osa', 'Os07g0211200' => 'osa', 'Os07g0681500' => 'osa', 'Peaxi162Scf00095g01015' => 'pax', 'Peaxi162Scf00104g00329' => 'pax', 'Peaxi162Scf00161g00137' => 'pax', 'PGR004G1665' => 'pgr', 'PGR031G2937' => 'pgr', 'PGR119G2145' => 'pgr', 'PGSC0003DMG400004351' => 'stu', 'PGSC0003DMG400014625' => 'stu', 'PGSC0003DMG401000943' => 'stu', 'Phvul.001G148600' => 'pvu', 'Phvul.004G001700' => 'pvu', 'Phvul.006G154900' => 'pvu', 'Phvul.008G078200' => 'pvu', 'Phvul.011G136500' => 'pvu', 'Potri.002G215600' => 'ptr', 'Potri.008G201600' => 'ptr', 'Potri.014G138400' => 'ptr', 'Potri.016G142500' => 'ptr', 'Pp3c16_10580' => 'ppa', 'Pp3c5_25280' => 'ppa', 'Prupe.1G150000' => 'ppe', 'Prupe.1G150100' => 'ppe', 'Prupe.6G299600' => 'ppe', 'Prupe.8G245000' => 'ppe', 'Psat0s4927g0040' => 'psa', 'Psat1g052080' => 'psa', 'Psat1g183800' => 'psa', 'Psat3g113840' => 'psa', 'Psat3g126120' => 'psa', 'Psat3g126160' => 'psa', 'Psat3g158760' => 'psa', 'Psat3g158840' => 'psa', 'PSO170G2858' => 'pso', 'PSO339G0606' => 'pso', 'PSO384G4709' => 'pso', 'PSO407G0334' => 'pso', 'QL04p040276' => 'qlo', 'QL06p005458' => 'qlo', 'QL06p005472' => 'qlo', 'QL07p030546' => 'qlo', 'QL07p031519' => 'qlo', 'QL09p050949' => 'qlo', 'QL09p050966' => 'qlo', 'QL09p051067' => 'qlo', 'QL12p022706' => 'qlo', 'RcHm_v2.0_Chr2g0119601' => 'rch', 'RcHm_v2.0_Chr3g0459591' => 'rch', 'RcHm_v2.0_Chr4g0418521' => 'rch', 'RcHm_v2.0_Chr4g0418531' => 'rch', 'RcHm_v2.0_Chr4g0418541' => 'rch', 'RcHm_v2.0_Chr6g0291641' => 'rch', 'Rhsim01G0086300' => 'rsi', 'Rhsim01G0276300' => 'rsi', 'Rhsim01G0276500' => 'rsi', 'Rhsim04G0207700' => 'rsi', 'Rhsim05G0234500' => 'rsi', 'Rhsim13G0022400' => 'rsi', 'Sabra02G0167900' => 'sbr', 'Sabra04G0158500' => 'sbr', 'Sabra08G0159800' => 'sbr', 'Sabra10G0011500' => 'sbr', 'Sabra14G0104400' => 'sbr', 'SalBow2G2440' => 'sbo', 'SalBow4G2265' => 'sbo', 'Sc02g0000060' => 'sci', 'Sc05g0005020' => 'sci', 'Sc13g0003890' => 'sci', 'Sed0014865' => 'sed', 'Sed0017224' => 'sed', 'Sed0026391' => 'sed', 'SEGI_00063' => 'sgi', 'SEGI_10967' => 'sgi', 'SEGI_17510' => 'sgi', 'SEGI_24396' => 'sgi', 'SEGI_39719' => 'sgi', 'SEGI_41392' => 'sgi', 'SGA_v2.0_scaffold11G05794' => 'sas', 'SGA_v2.0_scaffold142G35607' => 'sas', 'SGA_v2.0_scaffold1G00447' => 'sas', 'SHI15388' => 'shi', 'SHI15394' => 'shi', 'SHI15396' => 'shi', 'SHI15399' => 'shi', 'SMO343G0151' => 'smo', 'SMO367G1118' => 'smo', 'Solyc01g080200.3' => 'sly', 'Solyc06g008960.3' => 'sly', 'Solyc09g064780.3' => 'sly', 'Sopen01g031980' => 'spe', 'Sopen06g003710' => 'spe', 'Sopen09g026460' => 'spe', 'Sp3g21240' => 'spa', 'Sp4g30030' => 'spa', 'TAR365G0022' => 'tar', 'TAR365G1023' => 'tar', 'TAR365G1253' => 'tar', 'TAR623G0078' => 'tar', 'TAR623G1721' => 'tar', 'TAR633G0959' => 'tar', 'THA.LOC104802225' => 'tha', 'THA.LOC104804769' => 'tha', 'THA.LOC104808660' => 'tha', 'THA.LOC104812792' => 'tha', 'Thecc.01G284000' => 'tca', 'Thecc.04G220600' => 'tca', 'Thecc.05G268900' => 'tca', 'Thecc.08G171100' => 'tca', 'Thhalv10001284m.g' => 'esa', 'Thhalv10019912m.g' => 'esa', 'TPR.G14189' => 'tpr', 'TPR.G18110' => 'tpr', 'TPR.G18130' => 'tpr', 'TPR.G18131' => 'tpr', 'TPR.G18140' => 'tpr', 'TPR.G24282' => 'tpr', 'TPR.G25221' => 'tpr', 'TPR.G29267' => 'tpr', 'TPR.G35315' => 'tpr', 'TPR.G36173' => 'tpr', 'TWI09G0794' => 'twi', 'TWI59G1348' => 'twi', 'TWI74G0430' => 'twi', 'unitig_26.g8940' => 'ugi', 'unitig_749.g13744' => 'ugi', 'unitig_749.g13745' => 'ugi', 'vmacro08269' => 'vma', 'vmacro14937' => 'vma', 'vmacro20401' => 'vma', 'VMungo0464G1349' => 'vmu', 'VMungo0540G0289' => 'vmu', 'VMungo1215G1590' => 'vmu', 'VMungo1309G0221' => 'vmu', 'VMungo1309G2815' => 'vmu', 'VMungo1383G0239' => 'vmu', 'VMungo1383G2910' => 'vmu', 'Zm00001eb095270' => 'zma', 'Zm00001eb095280' => 'zma', 'Zm00001eb111630' => 'zma', 'Zm00001eb237080' => 'zma', 'Zm00001eb273740' => 'zma', 'Zm00001eb285040' => 'zma', 'Zm00001eb330790' => 'zma', 'Zm00001eb337380' => 'zma' ) $gf_id = 'HOM05D001484' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001484' ) $data_identifier = 'HOM05D001484' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 2, 'aly' => (int) 2, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 22, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 7, 'hma' => (int) 2, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 7, 'mtr' => (int) 10, 'cme' => (int) 2, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 4, 'ppa' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 4, 'qlo' => (int) 9, 'rch' => (int) 6, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 10, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 7, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb337380' $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' => 'HOM05D001484', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p31500' => 'bna', 'A05p00020' => 'bna', 'A07p08820' => 'bna', 'Aa31LG4G3300' => 'aar', 'Aa31LG8G10030' => 'aar', 'Actinidia00731' => 'ach', 'Actinidia11473' => 'ach', 'Actinidia23469' => 'ach', 'Actinidia24318' => 'ach', 'Actinidia40196' => 'ach', 'Actinidia40197' => 'ach', 'Actinidia40198' => 'ach', 'Ah.08g212990' => 'amhyb', 'Ah.15g091720' => 'amhyb', 'AL3G38260' => 'aly', 'AL4G47710' => 'aly', 'Aqoxy2G00671' => 'aox', 'Aqoxy2G03236' => 'aox', 'arahy.Tifrunner.gnm1.ann1.05IDCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KR684' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATY3SJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK6QJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6APGL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IDT7Z9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM073U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ0R87' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LE7RV4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT4QRX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V5ENPK' => 'arhy', 'AT2G48110' => 'ath', 'AT3G23590' => 'ath', 'ATR0626G186' => 'atr', 'ATR1127G141' => 'atr', 'Atru.chr4.2583' => 'acertr', 'Atru.chr5.1358' => 'acertr', 'Atru.chr5.1359' => 'acertr', 'Atru.chr8.46' => 'acertr', 'AUR62002640' => 'cqu', 'AUR62030055' => 'cqu', 'AUR62033713' => 'cqu', 'AUR62033714' => 'cqu', 'AUR62036795' => 'cqu', 'AUR62039891' => 'cqu', 'BcaB02g08737' => 'bca', 'BcaB04g20441' => 'bca', 'BcaB06g26509' => 'bca', 'BcaB06g26510' => 'bca', 'BcaB06g26511' => 'bca', 'BcaB06g26512' => 'bca', 'BcaB06g26513' => 'bca', 'BcaC02g12564' => 'bca', 'BcaC02g12565' => 'bca', 'BcaC02g12794' => 'bca', 'BcaC02g12795' => 'bca', 'BcaC02g12796' => 'bca', 'BcaC06g35541' => 'bca', 'BNapus_Darmor_BZH_scaffold_188p00080' => 'bna', 'BNapus_Darmor_BZH_scaffold_188p00090' => 'bna', 'BolC1t03972H' => 'bol', 'BolC1t03973H' => 'bol', 'BolC4t21680H' => 'bol', 'BolC7t41863H' => 'bol', 'BolSC55t61227H' => 'bol', 'BolSC55t61228H' => 'bol', 'BraA01t03278Z' => 'bra', 'BraA05t18998Z' => 'bra', 'BraA07t28673Z' => 'bra', 'C01p40150' => 'bna', 'C05p12370' => 'bna', 'C07p13680' => 'bna', 'CAN.G1006.16' => 'can', 'CAN.G1006.17' => 'can', 'CAN.G1170.2' => 'can', 'CAN.G962.7' => 'can', 'CANSAT25G2179' => 'cansat', 'CANSAT78G1573' => 'cansat', 'CARHR099510' => 'chi', 'CARHR143510' => 'chi', 'Carub.0003s2380' => 'cru', 'Carub.0004s3082' => 'cru', 'Ca_00614_v3' => 'car', 'Ca_07801_v3' => 'car', 'Ca_08567_v3' => 'car', 'Ca_09571_v3' => 'car', 'CBR_g19290' => 'cbr', 'Cc01_g19770' => 'ccan', 'Cc03_g03030' => 'ccan', 'CDE07G0968' => 'cde', 'CDE09G1441' => 'cde', 'Cfa006103' => 'cfa', 'Cfa015573' => 'cfa', 'Cfa016988' => 'cfa', 'Ciclev10006738m.g' => 'ccl', 'Ciclev10010920m.g' => 'ccl', 'Ciclev10018517m.g' => 'ccl', 'CiPaw.01G159200' => 'cil', 'CiPaw.02G091000' => 'cil', 'CiPaw.02G091100' => 'cil', 'CiPaw.08G103100' => 'cil', 'CiPaw.09G224900' => 'cil', 'ClCG06G005740' => 'cla', 'ClCG07G000090' => 'cla', 'ClCG07G000100' => 'cla', 'COL.COLO4_09143' => 'col', 'COL.COLO4_25124' => 'col', 'Cpa.g.sc16.34' => 'cpa', 'Cpa.g.sc3504.1' => 'cpa', 'Cpa.g.sc60.37' => 'cpa', 'CsaV3_6G018520' => 'csa', 'CsaV3_6G036860' => 'csa', 'CSS0001072' => 'camsi', 'CSS0020208' => 'camsi', 'CSS0021253' => 'camsi', 'CSS0022190' => 'camsi', 'CSS0036150' => 'camsi', 'CSS0040442' => 'camsi', 'CSS0042300' => 'camsi', 'CSS0045298' => 'camsi', 'DCAR_012449' => 'dca', 'DCAR_018405' => 'dca', 'DCAR_024573' => 'dca', 'DCAR_030591' => 'dca', 'Dinv16926' => 'din', 'Dinv32963' => 'din', 'Dinv38382' => 'din', 'Dinv38383' => 'din', 'Duzib133G0974' => 'dzi', 'Duzib138G1867' => 'dzi', 'Duzib211G0420' => 'dzi', 'Duzib212G0930' => 'dzi', 'ECA234G1645' => 'eca', 'ECA247G3467' => 'eca', 'ECA248G1703' => 'eca', 'EL10Ac3g06327' => 'bvu', 'EL10Ac7g17204' => 'bvu', 'Eucgr.A00855' => 'egr', 'Eucgr.A00858' => 'egr', 'Eucgr.H01520' => 'egr', 'Eucgr.H03604' => 'egr', 'Eucgr.L03465' => 'egr', 'Eucgr.L03466' => 'egr', 'FAN01G0988' => 'fan', 'FAN02G3892' => 'fan', 'FAN05G3381' => 'fan', 'FAN07G0967' => 'fan', 'FAN07G1493' => 'fan', 'FAN08G3125' => 'fan', 'FAN09G0402' => 'fan', 'FAN12G2594' => 'fan', 'FAN12G3879' => 'fan', 'FAN14G1546' => 'fan', 'FAN15G3626' => 'fan', 'FAN17G0588' => 'fan', 'FAN17G0609' => 'fan', 'FAN18G2817' => 'fan', 'FAN19G1305' => 'fan', 'FAN20G1787' => 'fan', 'FAN22G0073' => 'fan', 'FAN22G0352' => 'fan', 'FAN22G0368' => 'fan', 'FAN22G2273' => 'fan', 'FAN24G1998' => 'fan', 'FAN27G1317' => 'fan', 'FvH4_2g23980' => 'fve', 'FvH4_4g14380' => 'fve', 'FvH4_4g14390' => 'fve', 'FvH4_6g09250' => 'fve', 'Glyma.03G151100' => 'gma', 'Glyma.04G122550' => 'gma', 'Glyma.05G001600' => 'gma', 'Glyma.09G270766' => 'gma', 'Glyma.09G270832' => 'gma', 'Glyma.13G209800' => 'gma', 'Glyma.15G102800' => 'gma', 'Glyma.18G218900' => 'gma', 'Glyma.19G001500' => 'gma', 'Glyma.19G153600' => 'gma', 'Gohir.A02G028600' => 'ghi', 'Gohir.A08G045000' => 'ghi', 'Gohir.A11G120500' => 'ghi', 'Gohir.A12G006200' => 'ghi', 'Gohir.A12G006250' => 'ghi', 'Gohir.D02G036300' => 'ghi', 'Gohir.D08G054700' => 'ghi', 'Gohir.D11G125600' => 'ghi', 'Gohir.D12G005700' => 'ghi', 'Gorai.004G055200' => 'gra', 'Gorai.005G040400' => 'gra', 'Gorai.007G134500' => 'gra', 'Gorai.008G005500' => 'gra', 'GSVIVG01011094001' => 'vvi', 'GSVIVG01017879001' => 'vvi', 'GSVIVG01025988001' => 'vvi', 'GSVIVG01029847001' => 'vvi', 'HanXRQChr10g0282901' => 'han', 'HanXRQChr10g0310371' => 'han', 'HanXRQChr10g0315041' => 'han', 'HanXRQChr11g0327651' => 'han', 'HanXRQChr12g0359391' => 'han', 'Haze_00972' => 'cav', 'Haze_00973' => 'cav', 'Haze_00974' => 'cav', 'Haze_04747' => 'cav', 'Haze_04749' => 'cav', 'Haze_04750' => 'cav', 'Haze_21217' => 'cav', 'Hma1.2p1_1037F.1_g250680' => 'hma', 'Hma1.2p1_1644F.1_g295320' => 'hma', 'HPP92_011322' => 'vpl', 'HPP92_011323' => 'vpl', 'HPP92_011324' => 'vpl', 'HPP92_011325' => 'vpl', 'HPP92_011326' => 'vpl', 'Hund12205' => 'sun', 'Hund17957' => 'sun', 'Lalb_Chr06g0176771' => 'lal', 'Lalb_Chr18g0056021' => 'lal', 'Lalb_Chr18g0056031' => 'lal', 'Lalb_Chr18g0056041' => 'lal', 'Lalb_Chr20g0107751' => 'lal', 'Lalb_Chr20g0118371' => 'lal', 'Lj1g0010239' => 'lja', 'Lj1g0017101' => 'lja', 'Lj2A1178G40' => 'lonja', 'Lj2A54G84' => 'lonja', 'Lj2g0015248' => 'lja', 'Lj3A761T51' => 'lonja', 'Lj6g0018116' => 'lja', 'Lsat_1_v5_gn_4_136040' => 'lsa', 'Lsat_1_v5_gn_5_187461' => 'lsa', 'Lsat_1_v5_gn_5_77001' => 'lsa', 'Lsat_1_v5_gn_9_4461' => 'lsa', 'Manes.01G210100' => 'mes', 'Manes.03G185600' => 'mes', 'Manes.05G073300' => 'mes', 'Manes.09G120300' => 'mes', 'Manes.15G022100' => 'mes', 'Mapoly0096s0053' => 'mpo', 'MBI03_g14058_MAGBIO' => 'mbi', 'MBI03_g33876_MAGBIO' => 'mbi', 'MBI03_g36854_MAGBIO' => 'mbi', 'MBI17_g11997_MAGBIO' => 'mbi', 'MD03G1269000' => 'mdo', 'MD04G1179600' => 'mdo', 'MD11G1289800' => 'mdo', 'MD12G1194700' => 'mdo', 'MD13G1182100' => 'mdo', 'MD13G1182200' => 'mdo', 'MD16G1182600' => 'mdo', 'Medtr2g021400' => 'mtr', 'Medtr2g021470' => 'mtr', 'Medtr2g105810' => 'mtr', 'Medtr3g033580' => 'mtr', 'Medtr6g007970' => 'mtr', 'Medtr7g056330' => 'mtr', 'Medtr7g074290' => 'mtr', 'Medtr7g074380' => 'mtr', 'Medtr7g094550' => 'mtr', 'Medtr8g069995' => 'mtr', 'MELO3C014345.2' => 'cme', 'MELO3C021395.2' => 'cme', 'Migut.D00262' => 'egut', 'Migut.G00257' => 'egut', 'MSTRG.21575' => 'ama', 'MSTRG.3985' => 'ama', 'Nitab4.5_0000295g0140' => 'nta', 'Nitab4.5_0000732g0140' => 'nta', 'Nitab4.5_0003162g0020' => 'nta', 'Nitab4.5_0006180g0090' => 'nta', 'Nitab4.5_0006390g0010' => 'nta', 'Nitab4.5_0007392g0040' => 'nta', 'Nn1g02140' => 'nnu', 'Nn4g26168' => 'nnu', 'Nn5g26754' => 'nnu', 'Oeu001433.1' => 'oeu', 'Oeu010299.2' => 'oeu', 'Oeu011171.1' => 'oeu', 'Oeu037675.1' => 'oeu', 'Oeu038359.1' => 'oeu', 'Oeu063834.1' => 'oeu', 'Oeu063835.1' => 'oeu', 'Os05g0312000' => 'osa', 'Os07g0211101' => 'osa', 'Os07g0211200' => 'osa', 'Os07g0681500' => 'osa', 'Peaxi162Scf00095g01015' => 'pax', 'Peaxi162Scf00104g00329' => 'pax', 'Peaxi162Scf00161g00137' => 'pax', 'PGR004G1665' => 'pgr', 'PGR031G2937' => 'pgr', 'PGR119G2145' => 'pgr', 'PGSC0003DMG400004351' => 'stu', 'PGSC0003DMG400014625' => 'stu', 'PGSC0003DMG401000943' => 'stu', 'Phvul.001G148600' => 'pvu', 'Phvul.004G001700' => 'pvu', 'Phvul.006G154900' => 'pvu', 'Phvul.008G078200' => 'pvu', 'Phvul.011G136500' => 'pvu', 'Potri.002G215600' => 'ptr', 'Potri.008G201600' => 'ptr', 'Potri.014G138400' => 'ptr', 'Potri.016G142500' => 'ptr', 'Pp3c16_10580' => 'ppa', 'Pp3c5_25280' => 'ppa', 'Prupe.1G150000' => 'ppe', 'Prupe.1G150100' => 'ppe', 'Prupe.6G299600' => 'ppe', 'Prupe.8G245000' => 'ppe', 'Psat0s4927g0040' => 'psa', 'Psat1g052080' => 'psa', 'Psat1g183800' => 'psa', 'Psat3g113840' => 'psa', 'Psat3g126120' => 'psa', 'Psat3g126160' => 'psa', 'Psat3g158760' => 'psa', 'Psat3g158840' => 'psa', 'PSO170G2858' => 'pso', 'PSO339G0606' => 'pso', 'PSO384G4709' => 'pso', 'PSO407G0334' => 'pso', 'QL04p040276' => 'qlo', 'QL06p005458' => 'qlo', 'QL06p005472' => 'qlo', 'QL07p030546' => 'qlo', 'QL07p031519' => 'qlo', 'QL09p050949' => 'qlo', 'QL09p050966' => 'qlo', 'QL09p051067' => 'qlo', 'QL12p022706' => 'qlo', 'RcHm_v2.0_Chr2g0119601' => 'rch', 'RcHm_v2.0_Chr3g0459591' => 'rch', 'RcHm_v2.0_Chr4g0418521' => 'rch', 'RcHm_v2.0_Chr4g0418531' => 'rch', 'RcHm_v2.0_Chr4g0418541' => 'rch', 'RcHm_v2.0_Chr6g0291641' => 'rch', 'Rhsim01G0086300' => 'rsi', 'Rhsim01G0276300' => 'rsi', 'Rhsim01G0276500' => 'rsi', 'Rhsim04G0207700' => 'rsi', 'Rhsim05G0234500' => 'rsi', 'Rhsim13G0022400' => 'rsi', 'Sabra02G0167900' => 'sbr', 'Sabra04G0158500' => 'sbr', 'Sabra08G0159800' => 'sbr', 'Sabra10G0011500' => 'sbr', 'Sabra14G0104400' => 'sbr', 'SalBow2G2440' => 'sbo', 'SalBow4G2265' => 'sbo', 'Sc02g0000060' => 'sci', 'Sc05g0005020' => 'sci', 'Sc13g0003890' => 'sci', 'Sed0014865' => 'sed', 'Sed0017224' => 'sed', 'Sed0026391' => 'sed', 'SEGI_00063' => 'sgi', 'SEGI_10967' => 'sgi', 'SEGI_17510' => 'sgi', 'SEGI_24396' => 'sgi', 'SEGI_39719' => 'sgi', 'SEGI_41392' => 'sgi', 'SGA_v2.0_scaffold11G05794' => 'sas', 'SGA_v2.0_scaffold142G35607' => 'sas', 'SGA_v2.0_scaffold1G00447' => 'sas', 'SHI15388' => 'shi', 'SHI15394' => 'shi', 'SHI15396' => 'shi', 'SHI15399' => 'shi', 'SMO343G0151' => 'smo', 'SMO367G1118' => 'smo', 'Solyc01g080200.3' => 'sly', 'Solyc06g008960.3' => 'sly', 'Solyc09g064780.3' => 'sly', 'Sopen01g031980' => 'spe', 'Sopen06g003710' => 'spe', 'Sopen09g026460' => 'spe', 'Sp3g21240' => 'spa', 'Sp4g30030' => 'spa', 'TAR365G0022' => 'tar', 'TAR365G1023' => 'tar', 'TAR365G1253' => 'tar', 'TAR623G0078' => 'tar', 'TAR623G1721' => 'tar', 'TAR633G0959' => 'tar', 'THA.LOC104802225' => 'tha', 'THA.LOC104804769' => 'tha', 'THA.LOC104808660' => 'tha', 'THA.LOC104812792' => 'tha', 'Thecc.01G284000' => 'tca', 'Thecc.04G220600' => 'tca', 'Thecc.05G268900' => 'tca', 'Thecc.08G171100' => 'tca', 'Thhalv10001284m.g' => 'esa', 'Thhalv10019912m.g' => 'esa', 'TPR.G14189' => 'tpr', 'TPR.G18110' => 'tpr', 'TPR.G18130' => 'tpr', 'TPR.G18131' => 'tpr', 'TPR.G18140' => 'tpr', 'TPR.G24282' => 'tpr', 'TPR.G25221' => 'tpr', 'TPR.G29267' => 'tpr', 'TPR.G35315' => 'tpr', 'TPR.G36173' => 'tpr', 'TWI09G0794' => 'twi', 'TWI59G1348' => 'twi', 'TWI74G0430' => 'twi', 'unitig_26.g8940' => 'ugi', 'unitig_749.g13744' => 'ugi', 'unitig_749.g13745' => 'ugi', 'vmacro08269' => 'vma', 'vmacro14937' => 'vma', 'vmacro20401' => 'vma', 'VMungo0464G1349' => 'vmu', 'VMungo0540G0289' => 'vmu', 'VMungo1215G1590' => 'vmu', 'VMungo1309G0221' => 'vmu', 'VMungo1309G2815' => 'vmu', 'VMungo1383G0239' => 'vmu', 'VMungo1383G2910' => 'vmu', 'Zm00001eb095270' => 'zma', 'Zm00001eb095280' => 'zma', 'Zm00001eb111630' => 'zma', 'Zm00001eb237080' => 'zma', 'Zm00001eb273740' => 'zma', 'Zm00001eb285040' => 'zma', 'Zm00001eb330790' => 'zma', 'Zm00001eb337380' => 'zma' ), 'gf_id' => 'HOM05D001484', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001484' ), 'data_identifier' => 'HOM05D001484', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001484', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p31500' => 'bna', 'A05p00020' => 'bna', 'A07p08820' => 'bna', 'Aa31LG4G3300' => 'aar', 'Aa31LG8G10030' => 'aar', 'Actinidia00731' => 'ach', 'Actinidia11473' => 'ach', 'Actinidia23469' => 'ach', 'Actinidia24318' => 'ach', 'Actinidia40196' => 'ach', 'Actinidia40197' => 'ach', 'Actinidia40198' => 'ach', 'Ah.08g212990' => 'amhyb', 'Ah.15g091720' => 'amhyb', 'AL3G38260' => 'aly', 'AL4G47710' => 'aly', 'Aqoxy2G00671' => 'aox', 'Aqoxy2G03236' => 'aox', 'arahy.Tifrunner.gnm1.ann1.05IDCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KR684' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATY3SJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK6QJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6APGL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IDT7Z9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM073U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ0R87' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LE7RV4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT4QRX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V5ENPK' => 'arhy', 'AT2G48110' => 'ath', 'AT3G23590' => 'ath', 'ATR0626G186' => 'atr', 'ATR1127G141' => 'atr', 'Atru.chr4.2583' => 'acertr', 'Atru.chr5.1358' => 'acertr', 'Atru.chr5.1359' => 'acertr', 'Atru.chr8.46' => 'acertr', 'AUR62002640' => 'cqu', 'AUR62030055' => 'cqu', 'AUR62033713' => 'cqu', 'AUR62033714' => 'cqu', 'AUR62036795' => 'cqu', 'AUR62039891' => 'cqu', 'BcaB02g08737' => 'bca', 'BcaB04g20441' => 'bca', 'BcaB06g26509' => 'bca', 'BcaB06g26510' => 'bca', 'BcaB06g26511' => 'bca', 'BcaB06g26512' => 'bca', 'BcaB06g26513' => 'bca', 'BcaC02g12564' => 'bca', 'BcaC02g12565' => 'bca', 'BcaC02g12794' => 'bca', 'BcaC02g12795' => 'bca', 'BcaC02g12796' => 'bca', 'BcaC06g35541' => 'bca', 'BNapus_Darmor_BZH_scaffold_188p00080' => 'bna', 'BNapus_Darmor_BZH_scaffold_188p00090' => 'bna', 'BolC1t03972H' => 'bol', 'BolC1t03973H' => 'bol', 'BolC4t21680H' => 'bol', 'BolC7t41863H' => 'bol', 'BolSC55t61227H' => 'bol', 'BolSC55t61228H' => 'bol', 'BraA01t03278Z' => 'bra', 'BraA05t18998Z' => 'bra', 'BraA07t28673Z' => 'bra', 'C01p40150' => 'bna', 'C05p12370' => 'bna', 'C07p13680' => 'bna', 'CAN.G1006.16' => 'can', 'CAN.G1006.17' => 'can', 'CAN.G1170.2' => 'can', 'CAN.G962.7' => 'can', 'CANSAT25G2179' => 'cansat', 'CANSAT78G1573' => 'cansat', 'CARHR099510' => 'chi', 'CARHR143510' => 'chi', 'Carub.0003s2380' => 'cru', 'Carub.0004s3082' => 'cru', 'Ca_00614_v3' => 'car', 'Ca_07801_v3' => 'car', 'Ca_08567_v3' => 'car', 'Ca_09571_v3' => 'car', 'CBR_g19290' => 'cbr', 'Cc01_g19770' => 'ccan', 'Cc03_g03030' => 'ccan', 'CDE07G0968' => 'cde', 'CDE09G1441' => 'cde', 'Cfa006103' => 'cfa', 'Cfa015573' => 'cfa', 'Cfa016988' => 'cfa', 'Ciclev10006738m.g' => 'ccl', 'Ciclev10010920m.g' => 'ccl', 'Ciclev10018517m.g' => 'ccl', 'CiPaw.01G159200' => 'cil', 'CiPaw.02G091000' => 'cil', 'CiPaw.02G091100' => 'cil', 'CiPaw.08G103100' => 'cil', 'CiPaw.09G224900' => 'cil', 'ClCG06G005740' => 'cla', 'ClCG07G000090' => 'cla', 'ClCG07G000100' => 'cla', 'COL.COLO4_09143' => 'col', 'COL.COLO4_25124' => 'col', 'Cpa.g.sc16.34' => 'cpa', 'Cpa.g.sc3504.1' => 'cpa', 'Cpa.g.sc60.37' => 'cpa', 'CsaV3_6G018520' => 'csa', 'CsaV3_6G036860' => 'csa', 'CSS0001072' => 'camsi', 'CSS0020208' => 'camsi', 'CSS0021253' => 'camsi', 'CSS0022190' => 'camsi', 'CSS0036150' => 'camsi', 'CSS0040442' => 'camsi', 'CSS0042300' => 'camsi', 'CSS0045298' => 'camsi', 'DCAR_012449' => 'dca', 'DCAR_018405' => 'dca', 'DCAR_024573' => 'dca', 'DCAR_030591' => 'dca', 'Dinv16926' => 'din', 'Dinv32963' => 'din', 'Dinv38382' => 'din', 'Dinv38383' => 'din', 'Duzib133G0974' => 'dzi', 'Duzib138G1867' => 'dzi', 'Duzib211G0420' => 'dzi', 'Duzib212G0930' => 'dzi', 'ECA234G1645' => 'eca', 'ECA247G3467' => 'eca', 'ECA248G1703' => 'eca', 'EL10Ac3g06327' => 'bvu', 'EL10Ac7g17204' => 'bvu', 'Eucgr.A00855' => 'egr', 'Eucgr.A00858' => 'egr', 'Eucgr.H01520' => 'egr', 'Eucgr.H03604' => 'egr', 'Eucgr.L03465' => 'egr', 'Eucgr.L03466' => 'egr', 'FAN01G0988' => 'fan', 'FAN02G3892' => 'fan', 'FAN05G3381' => 'fan', 'FAN07G0967' => 'fan', 'FAN07G1493' => 'fan', 'FAN08G3125' => 'fan', 'FAN09G0402' => 'fan', 'FAN12G2594' => 'fan', 'FAN12G3879' => 'fan', 'FAN14G1546' => 'fan', 'FAN15G3626' => 'fan', 'FAN17G0588' => 'fan', 'FAN17G0609' => 'fan', 'FAN18G2817' => 'fan', 'FAN19G1305' => 'fan', 'FAN20G1787' => 'fan', 'FAN22G0073' => 'fan', 'FAN22G0352' => 'fan', 'FAN22G0368' => 'fan', 'FAN22G2273' => 'fan', 'FAN24G1998' => 'fan', 'FAN27G1317' => 'fan', 'FvH4_2g23980' => 'fve', 'FvH4_4g14380' => 'fve', 'FvH4_4g14390' => 'fve', 'FvH4_6g09250' => 'fve', 'Glyma.03G151100' => 'gma', 'Glyma.04G122550' => 'gma', 'Glyma.05G001600' => 'gma', 'Glyma.09G270766' => 'gma', 'Glyma.09G270832' => 'gma', 'Glyma.13G209800' => 'gma', 'Glyma.15G102800' => 'gma', 'Glyma.18G218900' => 'gma', 'Glyma.19G001500' => 'gma', 'Glyma.19G153600' => 'gma', 'Gohir.A02G028600' => 'ghi', 'Gohir.A08G045000' => 'ghi', 'Gohir.A11G120500' => 'ghi', 'Gohir.A12G006200' => 'ghi', 'Gohir.A12G006250' => 'ghi', 'Gohir.D02G036300' => 'ghi', 'Gohir.D08G054700' => 'ghi', 'Gohir.D11G125600' => 'ghi', 'Gohir.D12G005700' => 'ghi', 'Gorai.004G055200' => 'gra', 'Gorai.005G040400' => 'gra', 'Gorai.007G134500' => 'gra', 'Gorai.008G005500' => 'gra', 'GSVIVG01011094001' => 'vvi', 'GSVIVG01017879001' => 'vvi', 'GSVIVG01025988001' => 'vvi', 'GSVIVG01029847001' => 'vvi', 'HanXRQChr10g0282901' => 'han', 'HanXRQChr10g0310371' => 'han', 'HanXRQChr10g0315041' => 'han', 'HanXRQChr11g0327651' => 'han', 'HanXRQChr12g0359391' => 'han', 'Haze_00972' => 'cav', 'Haze_00973' => 'cav', 'Haze_00974' => 'cav', 'Haze_04747' => 'cav', 'Haze_04749' => 'cav', 'Haze_04750' => 'cav', 'Haze_21217' => 'cav', 'Hma1.2p1_1037F.1_g250680' => 'hma', 'Hma1.2p1_1644F.1_g295320' => 'hma', 'HPP92_011322' => 'vpl', 'HPP92_011323' => 'vpl', 'HPP92_011324' => 'vpl', 'HPP92_011325' => 'vpl', 'HPP92_011326' => 'vpl', 'Hund12205' => 'sun', 'Hund17957' => 'sun', 'Lalb_Chr06g0176771' => 'lal', 'Lalb_Chr18g0056021' => 'lal', 'Lalb_Chr18g0056031' => 'lal', 'Lalb_Chr18g0056041' => 'lal', 'Lalb_Chr20g0107751' => 'lal', 'Lalb_Chr20g0118371' => 'lal', 'Lj1g0010239' => 'lja', 'Lj1g0017101' => 'lja', 'Lj2A1178G40' => 'lonja', 'Lj2A54G84' => 'lonja', 'Lj2g0015248' => 'lja', 'Lj3A761T51' => 'lonja', 'Lj6g0018116' => 'lja', 'Lsat_1_v5_gn_4_136040' => 'lsa', 'Lsat_1_v5_gn_5_187461' => 'lsa', 'Lsat_1_v5_gn_5_77001' => 'lsa', 'Lsat_1_v5_gn_9_4461' => 'lsa', 'Manes.01G210100' => 'mes', 'Manes.03G185600' => 'mes', 'Manes.05G073300' => 'mes', 'Manes.09G120300' => 'mes', 'Manes.15G022100' => 'mes', 'Mapoly0096s0053' => 'mpo', 'MBI03_g14058_MAGBIO' => 'mbi', 'MBI03_g33876_MAGBIO' => 'mbi', 'MBI03_g36854_MAGBIO' => 'mbi', 'MBI17_g11997_MAGBIO' => 'mbi', 'MD03G1269000' => 'mdo', 'MD04G1179600' => 'mdo', 'MD11G1289800' => 'mdo', 'MD12G1194700' => 'mdo', 'MD13G1182100' => 'mdo', 'MD13G1182200' => 'mdo', 'MD16G1182600' => 'mdo', 'Medtr2g021400' => 'mtr', 'Medtr2g021470' => 'mtr', 'Medtr2g105810' => 'mtr', 'Medtr3g033580' => 'mtr', 'Medtr6g007970' => 'mtr', 'Medtr7g056330' => 'mtr', 'Medtr7g074290' => 'mtr', 'Medtr7g074380' => 'mtr', 'Medtr7g094550' => 'mtr', 'Medtr8g069995' => 'mtr', 'MELO3C014345.2' => 'cme', 'MELO3C021395.2' => 'cme', 'Migut.D00262' => 'egut', 'Migut.G00257' => 'egut', 'MSTRG.21575' => 'ama', 'MSTRG.3985' => 'ama', 'Nitab4.5_0000295g0140' => 'nta', 'Nitab4.5_0000732g0140' => 'nta', 'Nitab4.5_0003162g0020' => 'nta', 'Nitab4.5_0006180g0090' => 'nta', 'Nitab4.5_0006390g0010' => 'nta', 'Nitab4.5_0007392g0040' => 'nta', 'Nn1g02140' => 'nnu', 'Nn4g26168' => 'nnu', 'Nn5g26754' => 'nnu', 'Oeu001433.1' => 'oeu', 'Oeu010299.2' => 'oeu', 'Oeu011171.1' => 'oeu', 'Oeu037675.1' => 'oeu', 'Oeu038359.1' => 'oeu', 'Oeu063834.1' => 'oeu', 'Oeu063835.1' => 'oeu', 'Os05g0312000' => 'osa', 'Os07g0211101' => 'osa', 'Os07g0211200' => 'osa', 'Os07g0681500' => 'osa', 'Peaxi162Scf00095g01015' => 'pax', 'Peaxi162Scf00104g00329' => 'pax', 'Peaxi162Scf00161g00137' => 'pax', 'PGR004G1665' => 'pgr', 'PGR031G2937' => 'pgr', 'PGR119G2145' => 'pgr', 'PGSC0003DMG400004351' => 'stu', 'PGSC0003DMG400014625' => 'stu', 'PGSC0003DMG401000943' => 'stu', 'Phvul.001G148600' => 'pvu', 'Phvul.004G001700' => 'pvu', 'Phvul.006G154900' => 'pvu', 'Phvul.008G078200' => 'pvu', 'Phvul.011G136500' => 'pvu', 'Potri.002G215600' => 'ptr', 'Potri.008G201600' => 'ptr', 'Potri.014G138400' => 'ptr', 'Potri.016G142500' => 'ptr', 'Pp3c16_10580' => 'ppa', 'Pp3c5_25280' => 'ppa', 'Prupe.1G150000' => 'ppe', 'Prupe.1G150100' => 'ppe', 'Prupe.6G299600' => 'ppe', 'Prupe.8G245000' => 'ppe', 'Psat0s4927g0040' => 'psa', 'Psat1g052080' => 'psa', 'Psat1g183800' => 'psa', 'Psat3g113840' => 'psa', 'Psat3g126120' => 'psa', 'Psat3g126160' => 'psa', 'Psat3g158760' => 'psa', 'Psat3g158840' => 'psa', 'PSO170G2858' => 'pso', 'PSO339G0606' => 'pso', 'PSO384G4709' => 'pso', 'PSO407G0334' => 'pso', 'QL04p040276' => 'qlo', 'QL06p005458' => 'qlo', 'QL06p005472' => 'qlo', 'QL07p030546' => 'qlo', 'QL07p031519' => 'qlo', 'QL09p050949' => 'qlo', 'QL09p050966' => 'qlo', 'QL09p051067' => 'qlo', 'QL12p022706' => 'qlo', 'RcHm_v2.0_Chr2g0119601' => 'rch', 'RcHm_v2.0_Chr3g0459591' => 'rch', 'RcHm_v2.0_Chr4g0418521' => 'rch', 'RcHm_v2.0_Chr4g0418531' => 'rch', 'RcHm_v2.0_Chr4g0418541' => 'rch', 'RcHm_v2.0_Chr6g0291641' => 'rch', 'Rhsim01G0086300' => 'rsi', 'Rhsim01G0276300' => 'rsi', 'Rhsim01G0276500' => 'rsi', 'Rhsim04G0207700' => 'rsi', 'Rhsim05G0234500' => 'rsi', 'Rhsim13G0022400' => 'rsi', 'Sabra02G0167900' => 'sbr', 'Sabra04G0158500' => 'sbr', 'Sabra08G0159800' => 'sbr', 'Sabra10G0011500' => 'sbr', 'Sabra14G0104400' => 'sbr', 'SalBow2G2440' => 'sbo', 'SalBow4G2265' => 'sbo', 'Sc02g0000060' => 'sci', 'Sc05g0005020' => 'sci', 'Sc13g0003890' => 'sci', 'Sed0014865' => 'sed', 'Sed0017224' => 'sed', 'Sed0026391' => 'sed', 'SEGI_00063' => 'sgi', 'SEGI_10967' => 'sgi', 'SEGI_17510' => 'sgi', 'SEGI_24396' => 'sgi', 'SEGI_39719' => 'sgi', 'SEGI_41392' => 'sgi', 'SGA_v2.0_scaffold11G05794' => 'sas', 'SGA_v2.0_scaffold142G35607' => 'sas', 'SGA_v2.0_scaffold1G00447' => 'sas', 'SHI15388' => 'shi', 'SHI15394' => 'shi', 'SHI15396' => 'shi', 'SHI15399' => 'shi', 'SMO343G0151' => 'smo', 'SMO367G1118' => 'smo', 'Solyc01g080200.3' => 'sly', 'Solyc06g008960.3' => 'sly', 'Solyc09g064780.3' => 'sly', 'Sopen01g031980' => 'spe', 'Sopen06g003710' => 'spe', 'Sopen09g026460' => 'spe', 'Sp3g21240' => 'spa', 'Sp4g30030' => 'spa', 'TAR365G0022' => 'tar', 'TAR365G1023' => 'tar', 'TAR365G1253' => 'tar', 'TAR623G0078' => 'tar', 'TAR623G1721' => 'tar', 'TAR633G0959' => 'tar', 'THA.LOC104802225' => 'tha', 'THA.LOC104804769' => 'tha', 'THA.LOC104808660' => 'tha', 'THA.LOC104812792' => 'tha', 'Thecc.01G284000' => 'tca', 'Thecc.04G220600' => 'tca', 'Thecc.05G268900' => 'tca', 'Thecc.08G171100' => 'tca', 'Thhalv10001284m.g' => 'esa', 'Thhalv10019912m.g' => 'esa', 'TPR.G14189' => 'tpr', 'TPR.G18110' => 'tpr', 'TPR.G18130' => 'tpr', 'TPR.G18131' => 'tpr', 'TPR.G18140' => 'tpr', 'TPR.G24282' => 'tpr', 'TPR.G25221' => 'tpr', 'TPR.G29267' => 'tpr', 'TPR.G35315' => 'tpr', 'TPR.G36173' => 'tpr', 'TWI09G0794' => 'twi', 'TWI59G1348' => 'twi', 'TWI74G0430' => 'twi', 'unitig_26.g8940' => 'ugi', 'unitig_749.g13744' => 'ugi', 'unitig_749.g13745' => 'ugi', 'vmacro08269' => 'vma', 'vmacro14937' => 'vma', 'vmacro20401' => 'vma', 'VMungo0464G1349' => 'vmu', 'VMungo0540G0289' => 'vmu', 'VMungo1215G1590' => 'vmu', 'VMungo1309G0221' => 'vmu', 'VMungo1309G2815' => 'vmu', 'VMungo1383G0239' => 'vmu', 'VMungo1383G2910' => 'vmu', 'Zm00001eb095270' => 'zma', 'Zm00001eb095280' => 'zma', 'Zm00001eb111630' => 'zma', 'Zm00001eb237080' => 'zma', 'Zm00001eb273740' => 'zma', 'Zm00001eb285040' => 'zma', 'Zm00001eb330790' => 'zma', 'Zm00001eb337380' => 'zma' ) $gf_id = 'HOM05D001484' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001484' ) $data_identifier = 'HOM05D001484' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 2, 'aly' => (int) 2, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 22, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 7, 'hma' => (int) 2, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 7, 'mtr' => (int) 10, 'cme' => (int) 2, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 4, 'ppa' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 4, 'qlo' => (int) 9, 'rch' => (int) 6, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 10, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 7, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb337380' $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' => 'HOM05D001484', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p31500' => 'bna', 'A05p00020' => 'bna', 'A07p08820' => 'bna', 'Aa31LG4G3300' => 'aar', 'Aa31LG8G10030' => 'aar', 'Actinidia00731' => 'ach', 'Actinidia11473' => 'ach', 'Actinidia23469' => 'ach', 'Actinidia24318' => 'ach', 'Actinidia40196' => 'ach', 'Actinidia40197' => 'ach', 'Actinidia40198' => 'ach', 'Ah.08g212990' => 'amhyb', 'Ah.15g091720' => 'amhyb', 'AL3G38260' => 'aly', 'AL4G47710' => 'aly', 'Aqoxy2G00671' => 'aox', 'Aqoxy2G03236' => 'aox', 'arahy.Tifrunner.gnm1.ann1.05IDCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KR684' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATY3SJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK6QJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6APGL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IDT7Z9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM073U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ0R87' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LE7RV4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT4QRX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V5ENPK' => 'arhy', 'AT2G48110' => 'ath', 'AT3G23590' => 'ath', 'ATR0626G186' => 'atr', 'ATR1127G141' => 'atr', 'Atru.chr4.2583' => 'acertr', 'Atru.chr5.1358' => 'acertr', 'Atru.chr5.1359' => 'acertr', 'Atru.chr8.46' => 'acertr', 'AUR62002640' => 'cqu', 'AUR62030055' => 'cqu', 'AUR62033713' => 'cqu', 'AUR62033714' => 'cqu', 'AUR62036795' => 'cqu', 'AUR62039891' => 'cqu', 'BcaB02g08737' => 'bca', 'BcaB04g20441' => 'bca', 'BcaB06g26509' => 'bca', 'BcaB06g26510' => 'bca', 'BcaB06g26511' => 'bca', 'BcaB06g26512' => 'bca', 'BcaB06g26513' => 'bca', 'BcaC02g12564' => 'bca', 'BcaC02g12565' => 'bca', 'BcaC02g12794' => 'bca', 'BcaC02g12795' => 'bca', 'BcaC02g12796' => 'bca', 'BcaC06g35541' => 'bca', 'BNapus_Darmor_BZH_scaffold_188p00080' => 'bna', 'BNapus_Darmor_BZH_scaffold_188p00090' => 'bna', 'BolC1t03972H' => 'bol', 'BolC1t03973H' => 'bol', 'BolC4t21680H' => 'bol', 'BolC7t41863H' => 'bol', 'BolSC55t61227H' => 'bol', 'BolSC55t61228H' => 'bol', 'BraA01t03278Z' => 'bra', 'BraA05t18998Z' => 'bra', 'BraA07t28673Z' => 'bra', 'C01p40150' => 'bna', 'C05p12370' => 'bna', 'C07p13680' => 'bna', 'CAN.G1006.16' => 'can', 'CAN.G1006.17' => 'can', 'CAN.G1170.2' => 'can', 'CAN.G962.7' => 'can', 'CANSAT25G2179' => 'cansat', 'CANSAT78G1573' => 'cansat', 'CARHR099510' => 'chi', 'CARHR143510' => 'chi', 'Carub.0003s2380' => 'cru', 'Carub.0004s3082' => 'cru', 'Ca_00614_v3' => 'car', 'Ca_07801_v3' => 'car', 'Ca_08567_v3' => 'car', 'Ca_09571_v3' => 'car', 'CBR_g19290' => 'cbr', 'Cc01_g19770' => 'ccan', 'Cc03_g03030' => 'ccan', 'CDE07G0968' => 'cde', 'CDE09G1441' => 'cde', 'Cfa006103' => 'cfa', 'Cfa015573' => 'cfa', 'Cfa016988' => 'cfa', 'Ciclev10006738m.g' => 'ccl', 'Ciclev10010920m.g' => 'ccl', 'Ciclev10018517m.g' => 'ccl', 'CiPaw.01G159200' => 'cil', 'CiPaw.02G091000' => 'cil', 'CiPaw.02G091100' => 'cil', 'CiPaw.08G103100' => 'cil', 'CiPaw.09G224900' => 'cil', 'ClCG06G005740' => 'cla', 'ClCG07G000090' => 'cla', 'ClCG07G000100' => 'cla', 'COL.COLO4_09143' => 'col', 'COL.COLO4_25124' => 'col', 'Cpa.g.sc16.34' => 'cpa', 'Cpa.g.sc3504.1' => 'cpa', 'Cpa.g.sc60.37' => 'cpa', 'CsaV3_6G018520' => 'csa', 'CsaV3_6G036860' => 'csa', 'CSS0001072' => 'camsi', 'CSS0020208' => 'camsi', 'CSS0021253' => 'camsi', 'CSS0022190' => 'camsi', 'CSS0036150' => 'camsi', 'CSS0040442' => 'camsi', 'CSS0042300' => 'camsi', 'CSS0045298' => 'camsi', 'DCAR_012449' => 'dca', 'DCAR_018405' => 'dca', 'DCAR_024573' => 'dca', 'DCAR_030591' => 'dca', 'Dinv16926' => 'din', 'Dinv32963' => 'din', 'Dinv38382' => 'din', 'Dinv38383' => 'din', 'Duzib133G0974' => 'dzi', 'Duzib138G1867' => 'dzi', 'Duzib211G0420' => 'dzi', 'Duzib212G0930' => 'dzi', 'ECA234G1645' => 'eca', 'ECA247G3467' => 'eca', 'ECA248G1703' => 'eca', 'EL10Ac3g06327' => 'bvu', 'EL10Ac7g17204' => 'bvu', 'Eucgr.A00855' => 'egr', 'Eucgr.A00858' => 'egr', 'Eucgr.H01520' => 'egr', 'Eucgr.H03604' => 'egr', 'Eucgr.L03465' => 'egr', 'Eucgr.L03466' => 'egr', 'FAN01G0988' => 'fan', 'FAN02G3892' => 'fan', 'FAN05G3381' => 'fan', 'FAN07G0967' => 'fan', 'FAN07G1493' => 'fan', 'FAN08G3125' => 'fan', 'FAN09G0402' => 'fan', 'FAN12G2594' => 'fan', 'FAN12G3879' => 'fan', 'FAN14G1546' => 'fan', 'FAN15G3626' => 'fan', 'FAN17G0588' => 'fan', 'FAN17G0609' => 'fan', 'FAN18G2817' => 'fan', 'FAN19G1305' => 'fan', 'FAN20G1787' => 'fan', 'FAN22G0073' => 'fan', 'FAN22G0352' => 'fan', 'FAN22G0368' => 'fan', 'FAN22G2273' => 'fan', 'FAN24G1998' => 'fan', 'FAN27G1317' => 'fan', 'FvH4_2g23980' => 'fve', 'FvH4_4g14380' => 'fve', 'FvH4_4g14390' => 'fve', 'FvH4_6g09250' => 'fve', 'Glyma.03G151100' => 'gma', 'Glyma.04G122550' => 'gma', 'Glyma.05G001600' => 'gma', 'Glyma.09G270766' => 'gma', 'Glyma.09G270832' => 'gma', 'Glyma.13G209800' => 'gma', 'Glyma.15G102800' => 'gma', 'Glyma.18G218900' => 'gma', 'Glyma.19G001500' => 'gma', 'Glyma.19G153600' => 'gma', 'Gohir.A02G028600' => 'ghi', 'Gohir.A08G045000' => 'ghi', 'Gohir.A11G120500' => 'ghi', 'Gohir.A12G006200' => 'ghi', 'Gohir.A12G006250' => 'ghi', 'Gohir.D02G036300' => 'ghi', 'Gohir.D08G054700' => 'ghi', 'Gohir.D11G125600' => 'ghi', 'Gohir.D12G005700' => 'ghi', 'Gorai.004G055200' => 'gra', 'Gorai.005G040400' => 'gra', 'Gorai.007G134500' => 'gra', 'Gorai.008G005500' => 'gra', 'GSVIVG01011094001' => 'vvi', 'GSVIVG01017879001' => 'vvi', 'GSVIVG01025988001' => 'vvi', 'GSVIVG01029847001' => 'vvi', 'HanXRQChr10g0282901' => 'han', 'HanXRQChr10g0310371' => 'han', 'HanXRQChr10g0315041' => 'han', 'HanXRQChr11g0327651' => 'han', 'HanXRQChr12g0359391' => 'han', 'Haze_00972' => 'cav', 'Haze_00973' => 'cav', 'Haze_00974' => 'cav', 'Haze_04747' => 'cav', 'Haze_04749' => 'cav', 'Haze_04750' => 'cav', 'Haze_21217' => 'cav', 'Hma1.2p1_1037F.1_g250680' => 'hma', 'Hma1.2p1_1644F.1_g295320' => 'hma', 'HPP92_011322' => 'vpl', 'HPP92_011323' => 'vpl', 'HPP92_011324' => 'vpl', 'HPP92_011325' => 'vpl', 'HPP92_011326' => 'vpl', 'Hund12205' => 'sun', 'Hund17957' => 'sun', 'Lalb_Chr06g0176771' => 'lal', 'Lalb_Chr18g0056021' => 'lal', 'Lalb_Chr18g0056031' => 'lal', 'Lalb_Chr18g0056041' => 'lal', 'Lalb_Chr20g0107751' => 'lal', 'Lalb_Chr20g0118371' => 'lal', 'Lj1g0010239' => 'lja', 'Lj1g0017101' => 'lja', 'Lj2A1178G40' => 'lonja', 'Lj2A54G84' => 'lonja', 'Lj2g0015248' => 'lja', 'Lj3A761T51' => 'lonja', 'Lj6g0018116' => 'lja', 'Lsat_1_v5_gn_4_136040' => 'lsa', 'Lsat_1_v5_gn_5_187461' => 'lsa', 'Lsat_1_v5_gn_5_77001' => 'lsa', 'Lsat_1_v5_gn_9_4461' => 'lsa', 'Manes.01G210100' => 'mes', 'Manes.03G185600' => 'mes', 'Manes.05G073300' => 'mes', 'Manes.09G120300' => 'mes', 'Manes.15G022100' => 'mes', 'Mapoly0096s0053' => 'mpo', 'MBI03_g14058_MAGBIO' => 'mbi', 'MBI03_g33876_MAGBIO' => 'mbi', 'MBI03_g36854_MAGBIO' => 'mbi', 'MBI17_g11997_MAGBIO' => 'mbi', 'MD03G1269000' => 'mdo', 'MD04G1179600' => 'mdo', 'MD11G1289800' => 'mdo', 'MD12G1194700' => 'mdo', 'MD13G1182100' => 'mdo', 'MD13G1182200' => 'mdo', 'MD16G1182600' => 'mdo', 'Medtr2g021400' => 'mtr', 'Medtr2g021470' => 'mtr', 'Medtr2g105810' => 'mtr', 'Medtr3g033580' => 'mtr', 'Medtr6g007970' => 'mtr', 'Medtr7g056330' => 'mtr', 'Medtr7g074290' => 'mtr', 'Medtr7g074380' => 'mtr', 'Medtr7g094550' => 'mtr', 'Medtr8g069995' => 'mtr', 'MELO3C014345.2' => 'cme', 'MELO3C021395.2' => 'cme', 'Migut.D00262' => 'egut', 'Migut.G00257' => 'egut', 'MSTRG.21575' => 'ama', 'MSTRG.3985' => 'ama', 'Nitab4.5_0000295g0140' => 'nta', 'Nitab4.5_0000732g0140' => 'nta', 'Nitab4.5_0003162g0020' => 'nta', 'Nitab4.5_0006180g0090' => 'nta', 'Nitab4.5_0006390g0010' => 'nta', 'Nitab4.5_0007392g0040' => 'nta', 'Nn1g02140' => 'nnu', 'Nn4g26168' => 'nnu', 'Nn5g26754' => 'nnu', 'Oeu001433.1' => 'oeu', 'Oeu010299.2' => 'oeu', 'Oeu011171.1' => 'oeu', 'Oeu037675.1' => 'oeu', 'Oeu038359.1' => 'oeu', 'Oeu063834.1' => 'oeu', 'Oeu063835.1' => 'oeu', 'Os05g0312000' => 'osa', 'Os07g0211101' => 'osa', 'Os07g0211200' => 'osa', 'Os07g0681500' => 'osa', 'Peaxi162Scf00095g01015' => 'pax', 'Peaxi162Scf00104g00329' => 'pax', 'Peaxi162Scf00161g00137' => 'pax', 'PGR004G1665' => 'pgr', 'PGR031G2937' => 'pgr', 'PGR119G2145' => 'pgr', 'PGSC0003DMG400004351' => 'stu', 'PGSC0003DMG400014625' => 'stu', 'PGSC0003DMG401000943' => 'stu', 'Phvul.001G148600' => 'pvu', 'Phvul.004G001700' => 'pvu', 'Phvul.006G154900' => 'pvu', 'Phvul.008G078200' => 'pvu', 'Phvul.011G136500' => 'pvu', 'Potri.002G215600' => 'ptr', 'Potri.008G201600' => 'ptr', 'Potri.014G138400' => 'ptr', 'Potri.016G142500' => 'ptr', 'Pp3c16_10580' => 'ppa', 'Pp3c5_25280' => 'ppa', 'Prupe.1G150000' => 'ppe', 'Prupe.1G150100' => 'ppe', 'Prupe.6G299600' => 'ppe', 'Prupe.8G245000' => 'ppe', 'Psat0s4927g0040' => 'psa', 'Psat1g052080' => 'psa', 'Psat1g183800' => 'psa', 'Psat3g113840' => 'psa', 'Psat3g126120' => 'psa', 'Psat3g126160' => 'psa', 'Psat3g158760' => 'psa', 'Psat3g158840' => 'psa', 'PSO170G2858' => 'pso', 'PSO339G0606' => 'pso', 'PSO384G4709' => 'pso', 'PSO407G0334' => 'pso', 'QL04p040276' => 'qlo', 'QL06p005458' => 'qlo', 'QL06p005472' => 'qlo', 'QL07p030546' => 'qlo', 'QL07p031519' => 'qlo', 'QL09p050949' => 'qlo', 'QL09p050966' => 'qlo', 'QL09p051067' => 'qlo', 'QL12p022706' => 'qlo', 'RcHm_v2.0_Chr2g0119601' => 'rch', 'RcHm_v2.0_Chr3g0459591' => 'rch', 'RcHm_v2.0_Chr4g0418521' => 'rch', 'RcHm_v2.0_Chr4g0418531' => 'rch', 'RcHm_v2.0_Chr4g0418541' => 'rch', 'RcHm_v2.0_Chr6g0291641' => 'rch', 'Rhsim01G0086300' => 'rsi', 'Rhsim01G0276300' => 'rsi', 'Rhsim01G0276500' => 'rsi', 'Rhsim04G0207700' => 'rsi', 'Rhsim05G0234500' => 'rsi', 'Rhsim13G0022400' => 'rsi', 'Sabra02G0167900' => 'sbr', 'Sabra04G0158500' => 'sbr', 'Sabra08G0159800' => 'sbr', 'Sabra10G0011500' => 'sbr', 'Sabra14G0104400' => 'sbr', 'SalBow2G2440' => 'sbo', 'SalBow4G2265' => 'sbo', 'Sc02g0000060' => 'sci', 'Sc05g0005020' => 'sci', 'Sc13g0003890' => 'sci', 'Sed0014865' => 'sed', 'Sed0017224' => 'sed', 'Sed0026391' => 'sed', 'SEGI_00063' => 'sgi', 'SEGI_10967' => 'sgi', 'SEGI_17510' => 'sgi', 'SEGI_24396' => 'sgi', 'SEGI_39719' => 'sgi', 'SEGI_41392' => 'sgi', 'SGA_v2.0_scaffold11G05794' => 'sas', 'SGA_v2.0_scaffold142G35607' => 'sas', 'SGA_v2.0_scaffold1G00447' => 'sas', 'SHI15388' => 'shi', 'SHI15394' => 'shi', 'SHI15396' => 'shi', 'SHI15399' => 'shi', 'SMO343G0151' => 'smo', 'SMO367G1118' => 'smo', 'Solyc01g080200.3' => 'sly', 'Solyc06g008960.3' => 'sly', 'Solyc09g064780.3' => 'sly', 'Sopen01g031980' => 'spe', 'Sopen06g003710' => 'spe', 'Sopen09g026460' => 'spe', 'Sp3g21240' => 'spa', 'Sp4g30030' => 'spa', 'TAR365G0022' => 'tar', 'TAR365G1023' => 'tar', 'TAR365G1253' => 'tar', 'TAR623G0078' => 'tar', 'TAR623G1721' => 'tar', 'TAR633G0959' => 'tar', 'THA.LOC104802225' => 'tha', 'THA.LOC104804769' => 'tha', 'THA.LOC104808660' => 'tha', 'THA.LOC104812792' => 'tha', 'Thecc.01G284000' => 'tca', 'Thecc.04G220600' => 'tca', 'Thecc.05G268900' => 'tca', 'Thecc.08G171100' => 'tca', 'Thhalv10001284m.g' => 'esa', 'Thhalv10019912m.g' => 'esa', 'TPR.G14189' => 'tpr', 'TPR.G18110' => 'tpr', 'TPR.G18130' => 'tpr', 'TPR.G18131' => 'tpr', 'TPR.G18140' => 'tpr', 'TPR.G24282' => 'tpr', 'TPR.G25221' => 'tpr', 'TPR.G29267' => 'tpr', 'TPR.G35315' => 'tpr', 'TPR.G36173' => 'tpr', 'TWI09G0794' => 'twi', 'TWI59G1348' => 'twi', 'TWI74G0430' => 'twi', 'unitig_26.g8940' => 'ugi', 'unitig_749.g13744' => 'ugi', 'unitig_749.g13745' => 'ugi', 'vmacro08269' => 'vma', 'vmacro14937' => 'vma', 'vmacro20401' => 'vma', 'VMungo0464G1349' => 'vmu', 'VMungo0540G0289' => 'vmu', 'VMungo1215G1590' => 'vmu', 'VMungo1309G0221' => 'vmu', 'VMungo1309G2815' => 'vmu', 'VMungo1383G0239' => 'vmu', 'VMungo1383G2910' => 'vmu', 'Zm00001eb095270' => 'zma', 'Zm00001eb095280' => 'zma', 'Zm00001eb111630' => 'zma', 'Zm00001eb237080' => 'zma', 'Zm00001eb273740' => 'zma', 'Zm00001eb285040' => 'zma', 'Zm00001eb330790' => 'zma', 'Zm00001eb337380' => 'zma' ), 'gf_id' => 'HOM05D001484', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001484' ), 'data_identifier' => 'HOM05D001484', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001484', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p31500' => 'bna', 'A05p00020' => 'bna', 'A07p08820' => 'bna', 'Aa31LG4G3300' => 'aar', 'Aa31LG8G10030' => 'aar', 'Actinidia00731' => 'ach', 'Actinidia11473' => 'ach', 'Actinidia23469' => 'ach', 'Actinidia24318' => 'ach', 'Actinidia40196' => 'ach', 'Actinidia40197' => 'ach', 'Actinidia40198' => 'ach', 'Ah.08g212990' => 'amhyb', 'Ah.15g091720' => 'amhyb', 'AL3G38260' => 'aly', 'AL4G47710' => 'aly', 'Aqoxy2G00671' => 'aox', 'Aqoxy2G03236' => 'aox', 'arahy.Tifrunner.gnm1.ann1.05IDCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KR684' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATY3SJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK6QJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6APGL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IDT7Z9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM073U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ0R87' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LE7RV4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT4QRX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V5ENPK' => 'arhy', 'AT2G48110' => 'ath', 'AT3G23590' => 'ath', 'ATR0626G186' => 'atr', 'ATR1127G141' => 'atr', 'Atru.chr4.2583' => 'acertr', 'Atru.chr5.1358' => 'acertr', 'Atru.chr5.1359' => 'acertr', 'Atru.chr8.46' => 'acertr', 'AUR62002640' => 'cqu', 'AUR62030055' => 'cqu', 'AUR62033713' => 'cqu', 'AUR62033714' => 'cqu', 'AUR62036795' => 'cqu', 'AUR62039891' => 'cqu', 'BcaB02g08737' => 'bca', 'BcaB04g20441' => 'bca', 'BcaB06g26509' => 'bca', 'BcaB06g26510' => 'bca', 'BcaB06g26511' => 'bca', 'BcaB06g26512' => 'bca', 'BcaB06g26513' => 'bca', 'BcaC02g12564' => 'bca', 'BcaC02g12565' => 'bca', 'BcaC02g12794' => 'bca', 'BcaC02g12795' => 'bca', 'BcaC02g12796' => 'bca', 'BcaC06g35541' => 'bca', 'BNapus_Darmor_BZH_scaffold_188p00080' => 'bna', 'BNapus_Darmor_BZH_scaffold_188p00090' => 'bna', 'BolC1t03972H' => 'bol', 'BolC1t03973H' => 'bol', 'BolC4t21680H' => 'bol', 'BolC7t41863H' => 'bol', 'BolSC55t61227H' => 'bol', 'BolSC55t61228H' => 'bol', 'BraA01t03278Z' => 'bra', 'BraA05t18998Z' => 'bra', 'BraA07t28673Z' => 'bra', 'C01p40150' => 'bna', 'C05p12370' => 'bna', 'C07p13680' => 'bna', 'CAN.G1006.16' => 'can', 'CAN.G1006.17' => 'can', 'CAN.G1170.2' => 'can', 'CAN.G962.7' => 'can', 'CANSAT25G2179' => 'cansat', 'CANSAT78G1573' => 'cansat', 'CARHR099510' => 'chi', 'CARHR143510' => 'chi', 'Carub.0003s2380' => 'cru', 'Carub.0004s3082' => 'cru', 'Ca_00614_v3' => 'car', 'Ca_07801_v3' => 'car', 'Ca_08567_v3' => 'car', 'Ca_09571_v3' => 'car', 'CBR_g19290' => 'cbr', 'Cc01_g19770' => 'ccan', 'Cc03_g03030' => 'ccan', 'CDE07G0968' => 'cde', 'CDE09G1441' => 'cde', 'Cfa006103' => 'cfa', 'Cfa015573' => 'cfa', 'Cfa016988' => 'cfa', 'Ciclev10006738m.g' => 'ccl', 'Ciclev10010920m.g' => 'ccl', 'Ciclev10018517m.g' => 'ccl', 'CiPaw.01G159200' => 'cil', 'CiPaw.02G091000' => 'cil', 'CiPaw.02G091100' => 'cil', 'CiPaw.08G103100' => 'cil', 'CiPaw.09G224900' => 'cil', 'ClCG06G005740' => 'cla', 'ClCG07G000090' => 'cla', 'ClCG07G000100' => 'cla', 'COL.COLO4_09143' => 'col', 'COL.COLO4_25124' => 'col', 'Cpa.g.sc16.34' => 'cpa', 'Cpa.g.sc3504.1' => 'cpa', 'Cpa.g.sc60.37' => 'cpa', 'CsaV3_6G018520' => 'csa', 'CsaV3_6G036860' => 'csa', 'CSS0001072' => 'camsi', 'CSS0020208' => 'camsi', 'CSS0021253' => 'camsi', 'CSS0022190' => 'camsi', 'CSS0036150' => 'camsi', 'CSS0040442' => 'camsi', 'CSS0042300' => 'camsi', 'CSS0045298' => 'camsi', 'DCAR_012449' => 'dca', 'DCAR_018405' => 'dca', 'DCAR_024573' => 'dca', 'DCAR_030591' => 'dca', 'Dinv16926' => 'din', 'Dinv32963' => 'din', 'Dinv38382' => 'din', 'Dinv38383' => 'din', 'Duzib133G0974' => 'dzi', 'Duzib138G1867' => 'dzi', 'Duzib211G0420' => 'dzi', 'Duzib212G0930' => 'dzi', 'ECA234G1645' => 'eca', 'ECA247G3467' => 'eca', 'ECA248G1703' => 'eca', 'EL10Ac3g06327' => 'bvu', 'EL10Ac7g17204' => 'bvu', 'Eucgr.A00855' => 'egr', 'Eucgr.A00858' => 'egr', 'Eucgr.H01520' => 'egr', 'Eucgr.H03604' => 'egr', 'Eucgr.L03465' => 'egr', 'Eucgr.L03466' => 'egr', 'FAN01G0988' => 'fan', 'FAN02G3892' => 'fan', 'FAN05G3381' => 'fan', 'FAN07G0967' => 'fan', 'FAN07G1493' => 'fan', 'FAN08G3125' => 'fan', 'FAN09G0402' => 'fan', 'FAN12G2594' => 'fan', 'FAN12G3879' => 'fan', 'FAN14G1546' => 'fan', 'FAN15G3626' => 'fan', 'FAN17G0588' => 'fan', 'FAN17G0609' => 'fan', 'FAN18G2817' => 'fan', 'FAN19G1305' => 'fan', 'FAN20G1787' => 'fan', 'FAN22G0073' => 'fan', 'FAN22G0352' => 'fan', 'FAN22G0368' => 'fan', 'FAN22G2273' => 'fan', 'FAN24G1998' => 'fan', 'FAN27G1317' => 'fan', 'FvH4_2g23980' => 'fve', 'FvH4_4g14380' => 'fve', 'FvH4_4g14390' => 'fve', 'FvH4_6g09250' => 'fve', 'Glyma.03G151100' => 'gma', 'Glyma.04G122550' => 'gma', 'Glyma.05G001600' => 'gma', 'Glyma.09G270766' => 'gma', 'Glyma.09G270832' => 'gma', 'Glyma.13G209800' => 'gma', 'Glyma.15G102800' => 'gma', 'Glyma.18G218900' => 'gma', 'Glyma.19G001500' => 'gma', 'Glyma.19G153600' => 'gma', 'Gohir.A02G028600' => 'ghi', 'Gohir.A08G045000' => 'ghi', 'Gohir.A11G120500' => 'ghi', 'Gohir.A12G006200' => 'ghi', 'Gohir.A12G006250' => 'ghi', 'Gohir.D02G036300' => 'ghi', 'Gohir.D08G054700' => 'ghi', 'Gohir.D11G125600' => 'ghi', 'Gohir.D12G005700' => 'ghi', 'Gorai.004G055200' => 'gra', 'Gorai.005G040400' => 'gra', 'Gorai.007G134500' => 'gra', 'Gorai.008G005500' => 'gra', 'GSVIVG01011094001' => 'vvi', 'GSVIVG01017879001' => 'vvi', 'GSVIVG01025988001' => 'vvi', 'GSVIVG01029847001' => 'vvi', 'HanXRQChr10g0282901' => 'han', 'HanXRQChr10g0310371' => 'han', 'HanXRQChr10g0315041' => 'han', 'HanXRQChr11g0327651' => 'han', 'HanXRQChr12g0359391' => 'han', 'Haze_00972' => 'cav', 'Haze_00973' => 'cav', 'Haze_00974' => 'cav', 'Haze_04747' => 'cav', 'Haze_04749' => 'cav', 'Haze_04750' => 'cav', 'Haze_21217' => 'cav', 'Hma1.2p1_1037F.1_g250680' => 'hma', 'Hma1.2p1_1644F.1_g295320' => 'hma', 'HPP92_011322' => 'vpl', 'HPP92_011323' => 'vpl', 'HPP92_011324' => 'vpl', 'HPP92_011325' => 'vpl', 'HPP92_011326' => 'vpl', 'Hund12205' => 'sun', 'Hund17957' => 'sun', 'Lalb_Chr06g0176771' => 'lal', 'Lalb_Chr18g0056021' => 'lal', 'Lalb_Chr18g0056031' => 'lal', 'Lalb_Chr18g0056041' => 'lal', 'Lalb_Chr20g0107751' => 'lal', 'Lalb_Chr20g0118371' => 'lal', 'Lj1g0010239' => 'lja', 'Lj1g0017101' => 'lja', 'Lj2A1178G40' => 'lonja', 'Lj2A54G84' => 'lonja', 'Lj2g0015248' => 'lja', 'Lj3A761T51' => 'lonja', 'Lj6g0018116' => 'lja', 'Lsat_1_v5_gn_4_136040' => 'lsa', 'Lsat_1_v5_gn_5_187461' => 'lsa', 'Lsat_1_v5_gn_5_77001' => 'lsa', 'Lsat_1_v5_gn_9_4461' => 'lsa', 'Manes.01G210100' => 'mes', 'Manes.03G185600' => 'mes', 'Manes.05G073300' => 'mes', 'Manes.09G120300' => 'mes', 'Manes.15G022100' => 'mes', 'Mapoly0096s0053' => 'mpo', 'MBI03_g14058_MAGBIO' => 'mbi', 'MBI03_g33876_MAGBIO' => 'mbi', 'MBI03_g36854_MAGBIO' => 'mbi', 'MBI17_g11997_MAGBIO' => 'mbi', 'MD03G1269000' => 'mdo', 'MD04G1179600' => 'mdo', 'MD11G1289800' => 'mdo', 'MD12G1194700' => 'mdo', 'MD13G1182100' => 'mdo', 'MD13G1182200' => 'mdo', 'MD16G1182600' => 'mdo', 'Medtr2g021400' => 'mtr', 'Medtr2g021470' => 'mtr', 'Medtr2g105810' => 'mtr', 'Medtr3g033580' => 'mtr', 'Medtr6g007970' => 'mtr', 'Medtr7g056330' => 'mtr', 'Medtr7g074290' => 'mtr', 'Medtr7g074380' => 'mtr', 'Medtr7g094550' => 'mtr', 'Medtr8g069995' => 'mtr', 'MELO3C014345.2' => 'cme', 'MELO3C021395.2' => 'cme', 'Migut.D00262' => 'egut', 'Migut.G00257' => 'egut', 'MSTRG.21575' => 'ama', 'MSTRG.3985' => 'ama', 'Nitab4.5_0000295g0140' => 'nta', 'Nitab4.5_0000732g0140' => 'nta', 'Nitab4.5_0003162g0020' => 'nta', 'Nitab4.5_0006180g0090' => 'nta', 'Nitab4.5_0006390g0010' => 'nta', 'Nitab4.5_0007392g0040' => 'nta', 'Nn1g02140' => 'nnu', 'Nn4g26168' => 'nnu', 'Nn5g26754' => 'nnu', 'Oeu001433.1' => 'oeu', 'Oeu010299.2' => 'oeu', 'Oeu011171.1' => 'oeu', 'Oeu037675.1' => 'oeu', 'Oeu038359.1' => 'oeu', 'Oeu063834.1' => 'oeu', 'Oeu063835.1' => 'oeu', 'Os05g0312000' => 'osa', 'Os07g0211101' => 'osa', 'Os07g0211200' => 'osa', 'Os07g0681500' => 'osa', 'Peaxi162Scf00095g01015' => 'pax', 'Peaxi162Scf00104g00329' => 'pax', 'Peaxi162Scf00161g00137' => 'pax', 'PGR004G1665' => 'pgr', 'PGR031G2937' => 'pgr', 'PGR119G2145' => 'pgr', 'PGSC0003DMG400004351' => 'stu', 'PGSC0003DMG400014625' => 'stu', 'PGSC0003DMG401000943' => 'stu', 'Phvul.001G148600' => 'pvu', 'Phvul.004G001700' => 'pvu', 'Phvul.006G154900' => 'pvu', 'Phvul.008G078200' => 'pvu', 'Phvul.011G136500' => 'pvu', 'Potri.002G215600' => 'ptr', 'Potri.008G201600' => 'ptr', 'Potri.014G138400' => 'ptr', 'Potri.016G142500' => 'ptr', 'Pp3c16_10580' => 'ppa', 'Pp3c5_25280' => 'ppa', 'Prupe.1G150000' => 'ppe', 'Prupe.1G150100' => 'ppe', 'Prupe.6G299600' => 'ppe', 'Prupe.8G245000' => 'ppe', 'Psat0s4927g0040' => 'psa', 'Psat1g052080' => 'psa', 'Psat1g183800' => 'psa', 'Psat3g113840' => 'psa', 'Psat3g126120' => 'psa', 'Psat3g126160' => 'psa', 'Psat3g158760' => 'psa', 'Psat3g158840' => 'psa', 'PSO170G2858' => 'pso', 'PSO339G0606' => 'pso', 'PSO384G4709' => 'pso', 'PSO407G0334' => 'pso', 'QL04p040276' => 'qlo', 'QL06p005458' => 'qlo', 'QL06p005472' => 'qlo', 'QL07p030546' => 'qlo', 'QL07p031519' => 'qlo', 'QL09p050949' => 'qlo', 'QL09p050966' => 'qlo', 'QL09p051067' => 'qlo', 'QL12p022706' => 'qlo', 'RcHm_v2.0_Chr2g0119601' => 'rch', 'RcHm_v2.0_Chr3g0459591' => 'rch', 'RcHm_v2.0_Chr4g0418521' => 'rch', 'RcHm_v2.0_Chr4g0418531' => 'rch', 'RcHm_v2.0_Chr4g0418541' => 'rch', 'RcHm_v2.0_Chr6g0291641' => 'rch', 'Rhsim01G0086300' => 'rsi', 'Rhsim01G0276300' => 'rsi', 'Rhsim01G0276500' => 'rsi', 'Rhsim04G0207700' => 'rsi', 'Rhsim05G0234500' => 'rsi', 'Rhsim13G0022400' => 'rsi', 'Sabra02G0167900' => 'sbr', 'Sabra04G0158500' => 'sbr', 'Sabra08G0159800' => 'sbr', 'Sabra10G0011500' => 'sbr', 'Sabra14G0104400' => 'sbr', 'SalBow2G2440' => 'sbo', 'SalBow4G2265' => 'sbo', 'Sc02g0000060' => 'sci', 'Sc05g0005020' => 'sci', 'Sc13g0003890' => 'sci', 'Sed0014865' => 'sed', 'Sed0017224' => 'sed', 'Sed0026391' => 'sed', 'SEGI_00063' => 'sgi', 'SEGI_10967' => 'sgi', 'SEGI_17510' => 'sgi', 'SEGI_24396' => 'sgi', 'SEGI_39719' => 'sgi', 'SEGI_41392' => 'sgi', 'SGA_v2.0_scaffold11G05794' => 'sas', 'SGA_v2.0_scaffold142G35607' => 'sas', 'SGA_v2.0_scaffold1G00447' => 'sas', 'SHI15388' => 'shi', 'SHI15394' => 'shi', 'SHI15396' => 'shi', 'SHI15399' => 'shi', 'SMO343G0151' => 'smo', 'SMO367G1118' => 'smo', 'Solyc01g080200.3' => 'sly', 'Solyc06g008960.3' => 'sly', 'Solyc09g064780.3' => 'sly', 'Sopen01g031980' => 'spe', 'Sopen06g003710' => 'spe', 'Sopen09g026460' => 'spe', 'Sp3g21240' => 'spa', 'Sp4g30030' => 'spa', 'TAR365G0022' => 'tar', 'TAR365G1023' => 'tar', 'TAR365G1253' => 'tar', 'TAR623G0078' => 'tar', 'TAR623G1721' => 'tar', 'TAR633G0959' => 'tar', 'THA.LOC104802225' => 'tha', 'THA.LOC104804769' => 'tha', 'THA.LOC104808660' => 'tha', 'THA.LOC104812792' => 'tha', 'Thecc.01G284000' => 'tca', 'Thecc.04G220600' => 'tca', 'Thecc.05G268900' => 'tca', 'Thecc.08G171100' => 'tca', 'Thhalv10001284m.g' => 'esa', 'Thhalv10019912m.g' => 'esa', 'TPR.G14189' => 'tpr', 'TPR.G18110' => 'tpr', 'TPR.G18130' => 'tpr', 'TPR.G18131' => 'tpr', 'TPR.G18140' => 'tpr', 'TPR.G24282' => 'tpr', 'TPR.G25221' => 'tpr', 'TPR.G29267' => 'tpr', 'TPR.G35315' => 'tpr', 'TPR.G36173' => 'tpr', 'TWI09G0794' => 'twi', 'TWI59G1348' => 'twi', 'TWI74G0430' => 'twi', 'unitig_26.g8940' => 'ugi', 'unitig_749.g13744' => 'ugi', 'unitig_749.g13745' => 'ugi', 'vmacro08269' => 'vma', 'vmacro14937' => 'vma', 'vmacro20401' => 'vma', 'VMungo0464G1349' => 'vmu', 'VMungo0540G0289' => 'vmu', 'VMungo1215G1590' => 'vmu', 'VMungo1309G0221' => 'vmu', 'VMungo1309G2815' => 'vmu', 'VMungo1383G0239' => 'vmu', 'VMungo1383G2910' => 'vmu', 'Zm00001eb095270' => 'zma', 'Zm00001eb095280' => 'zma', 'Zm00001eb111630' => 'zma', 'Zm00001eb237080' => 'zma', 'Zm00001eb273740' => 'zma', 'Zm00001eb285040' => 'zma', 'Zm00001eb330790' => 'zma', 'Zm00001eb337380' => 'zma' ) $gf_id = 'HOM05D001484' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001484' ) $data_identifier = 'HOM05D001484' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 2, 'aly' => (int) 2, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 22, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 7, 'hma' => (int) 2, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 7, 'mtr' => (int) 10, 'cme' => (int) 2, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 4, 'ppa' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 4, 'qlo' => (int) 9, 'rch' => (int) 6, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 10, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 7, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb337380' $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' => 'HOM05D001484', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p31500' => 'bna', 'A05p00020' => 'bna', 'A07p08820' => 'bna', 'Aa31LG4G3300' => 'aar', 'Aa31LG8G10030' => 'aar', 'Actinidia00731' => 'ach', 'Actinidia11473' => 'ach', 'Actinidia23469' => 'ach', 'Actinidia24318' => 'ach', 'Actinidia40196' => 'ach', 'Actinidia40197' => 'ach', 'Actinidia40198' => 'ach', 'Ah.08g212990' => 'amhyb', 'Ah.15g091720' => 'amhyb', 'AL3G38260' => 'aly', 'AL4G47710' => 'aly', 'Aqoxy2G00671' => 'aox', 'Aqoxy2G03236' => 'aox', 'arahy.Tifrunner.gnm1.ann1.05IDCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KR684' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATY3SJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK6QJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6APGL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IDT7Z9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM073U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ0R87' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LE7RV4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT4QRX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V5ENPK' => 'arhy', 'AT2G48110' => 'ath', 'AT3G23590' => 'ath', 'ATR0626G186' => 'atr', 'ATR1127G141' => 'atr', 'Atru.chr4.2583' => 'acertr', 'Atru.chr5.1358' => 'acertr', 'Atru.chr5.1359' => 'acertr', 'Atru.chr8.46' => 'acertr', 'AUR62002640' => 'cqu', 'AUR62030055' => 'cqu', 'AUR62033713' => 'cqu', 'AUR62033714' => 'cqu', 'AUR62036795' => 'cqu', 'AUR62039891' => 'cqu', 'BcaB02g08737' => 'bca', 'BcaB04g20441' => 'bca', 'BcaB06g26509' => 'bca', 'BcaB06g26510' => 'bca', 'BcaB06g26511' => 'bca', 'BcaB06g26512' => 'bca', 'BcaB06g26513' => 'bca', 'BcaC02g12564' => 'bca', 'BcaC02g12565' => 'bca', 'BcaC02g12794' => 'bca', 'BcaC02g12795' => 'bca', 'BcaC02g12796' => 'bca', 'BcaC06g35541' => 'bca', 'BNapus_Darmor_BZH_scaffold_188p00080' => 'bna', 'BNapus_Darmor_BZH_scaffold_188p00090' => 'bna', 'BolC1t03972H' => 'bol', 'BolC1t03973H' => 'bol', 'BolC4t21680H' => 'bol', 'BolC7t41863H' => 'bol', 'BolSC55t61227H' => 'bol', 'BolSC55t61228H' => 'bol', 'BraA01t03278Z' => 'bra', 'BraA05t18998Z' => 'bra', 'BraA07t28673Z' => 'bra', 'C01p40150' => 'bna', 'C05p12370' => 'bna', 'C07p13680' => 'bna', 'CAN.G1006.16' => 'can', 'CAN.G1006.17' => 'can', 'CAN.G1170.2' => 'can', 'CAN.G962.7' => 'can', 'CANSAT25G2179' => 'cansat', 'CANSAT78G1573' => 'cansat', 'CARHR099510' => 'chi', 'CARHR143510' => 'chi', 'Carub.0003s2380' => 'cru', 'Carub.0004s3082' => 'cru', 'Ca_00614_v3' => 'car', 'Ca_07801_v3' => 'car', 'Ca_08567_v3' => 'car', 'Ca_09571_v3' => 'car', 'CBR_g19290' => 'cbr', 'Cc01_g19770' => 'ccan', 'Cc03_g03030' => 'ccan', 'CDE07G0968' => 'cde', 'CDE09G1441' => 'cde', 'Cfa006103' => 'cfa', 'Cfa015573' => 'cfa', 'Cfa016988' => 'cfa', 'Ciclev10006738m.g' => 'ccl', 'Ciclev10010920m.g' => 'ccl', 'Ciclev10018517m.g' => 'ccl', 'CiPaw.01G159200' => 'cil', 'CiPaw.02G091000' => 'cil', 'CiPaw.02G091100' => 'cil', 'CiPaw.08G103100' => 'cil', 'CiPaw.09G224900' => 'cil', 'ClCG06G005740' => 'cla', 'ClCG07G000090' => 'cla', 'ClCG07G000100' => 'cla', 'COL.COLO4_09143' => 'col', 'COL.COLO4_25124' => 'col', 'Cpa.g.sc16.34' => 'cpa', 'Cpa.g.sc3504.1' => 'cpa', 'Cpa.g.sc60.37' => 'cpa', 'CsaV3_6G018520' => 'csa', 'CsaV3_6G036860' => 'csa', 'CSS0001072' => 'camsi', 'CSS0020208' => 'camsi', 'CSS0021253' => 'camsi', 'CSS0022190' => 'camsi', 'CSS0036150' => 'camsi', 'CSS0040442' => 'camsi', 'CSS0042300' => 'camsi', 'CSS0045298' => 'camsi', 'DCAR_012449' => 'dca', 'DCAR_018405' => 'dca', 'DCAR_024573' => 'dca', 'DCAR_030591' => 'dca', 'Dinv16926' => 'din', 'Dinv32963' => 'din', 'Dinv38382' => 'din', 'Dinv38383' => 'din', 'Duzib133G0974' => 'dzi', 'Duzib138G1867' => 'dzi', 'Duzib211G0420' => 'dzi', 'Duzib212G0930' => 'dzi', 'ECA234G1645' => 'eca', 'ECA247G3467' => 'eca', 'ECA248G1703' => 'eca', 'EL10Ac3g06327' => 'bvu', 'EL10Ac7g17204' => 'bvu', 'Eucgr.A00855' => 'egr', 'Eucgr.A00858' => 'egr', 'Eucgr.H01520' => 'egr', 'Eucgr.H03604' => 'egr', 'Eucgr.L03465' => 'egr', 'Eucgr.L03466' => 'egr', 'FAN01G0988' => 'fan', 'FAN02G3892' => 'fan', 'FAN05G3381' => 'fan', 'FAN07G0967' => 'fan', 'FAN07G1493' => 'fan', 'FAN08G3125' => 'fan', 'FAN09G0402' => 'fan', 'FAN12G2594' => 'fan', 'FAN12G3879' => 'fan', 'FAN14G1546' => 'fan', 'FAN15G3626' => 'fan', 'FAN17G0588' => 'fan', 'FAN17G0609' => 'fan', 'FAN18G2817' => 'fan', 'FAN19G1305' => 'fan', 'FAN20G1787' => 'fan', 'FAN22G0073' => 'fan', 'FAN22G0352' => 'fan', 'FAN22G0368' => 'fan', 'FAN22G2273' => 'fan', 'FAN24G1998' => 'fan', 'FAN27G1317' => 'fan', 'FvH4_2g23980' => 'fve', 'FvH4_4g14380' => 'fve', 'FvH4_4g14390' => 'fve', 'FvH4_6g09250' => 'fve', 'Glyma.03G151100' => 'gma', 'Glyma.04G122550' => 'gma', 'Glyma.05G001600' => 'gma', 'Glyma.09G270766' => 'gma', 'Glyma.09G270832' => 'gma', 'Glyma.13G209800' => 'gma', 'Glyma.15G102800' => 'gma', 'Glyma.18G218900' => 'gma', 'Glyma.19G001500' => 'gma', 'Glyma.19G153600' => 'gma', 'Gohir.A02G028600' => 'ghi', 'Gohir.A08G045000' => 'ghi', 'Gohir.A11G120500' => 'ghi', 'Gohir.A12G006200' => 'ghi', 'Gohir.A12G006250' => 'ghi', 'Gohir.D02G036300' => 'ghi', 'Gohir.D08G054700' => 'ghi', 'Gohir.D11G125600' => 'ghi', 'Gohir.D12G005700' => 'ghi', 'Gorai.004G055200' => 'gra', 'Gorai.005G040400' => 'gra', 'Gorai.007G134500' => 'gra', 'Gorai.008G005500' => 'gra', 'GSVIVG01011094001' => 'vvi', 'GSVIVG01017879001' => 'vvi', 'GSVIVG01025988001' => 'vvi', 'GSVIVG01029847001' => 'vvi', 'HanXRQChr10g0282901' => 'han', 'HanXRQChr10g0310371' => 'han', 'HanXRQChr10g0315041' => 'han', 'HanXRQChr11g0327651' => 'han', 'HanXRQChr12g0359391' => 'han', 'Haze_00972' => 'cav', 'Haze_00973' => 'cav', 'Haze_00974' => 'cav', 'Haze_04747' => 'cav', 'Haze_04749' => 'cav', 'Haze_04750' => 'cav', 'Haze_21217' => 'cav', 'Hma1.2p1_1037F.1_g250680' => 'hma', 'Hma1.2p1_1644F.1_g295320' => 'hma', 'HPP92_011322' => 'vpl', 'HPP92_011323' => 'vpl', 'HPP92_011324' => 'vpl', 'HPP92_011325' => 'vpl', 'HPP92_011326' => 'vpl', 'Hund12205' => 'sun', 'Hund17957' => 'sun', 'Lalb_Chr06g0176771' => 'lal', 'Lalb_Chr18g0056021' => 'lal', 'Lalb_Chr18g0056031' => 'lal', 'Lalb_Chr18g0056041' => 'lal', 'Lalb_Chr20g0107751' => 'lal', 'Lalb_Chr20g0118371' => 'lal', 'Lj1g0010239' => 'lja', 'Lj1g0017101' => 'lja', 'Lj2A1178G40' => 'lonja', 'Lj2A54G84' => 'lonja', 'Lj2g0015248' => 'lja', 'Lj3A761T51' => 'lonja', 'Lj6g0018116' => 'lja', 'Lsat_1_v5_gn_4_136040' => 'lsa', 'Lsat_1_v5_gn_5_187461' => 'lsa', 'Lsat_1_v5_gn_5_77001' => 'lsa', 'Lsat_1_v5_gn_9_4461' => 'lsa', 'Manes.01G210100' => 'mes', 'Manes.03G185600' => 'mes', 'Manes.05G073300' => 'mes', 'Manes.09G120300' => 'mes', 'Manes.15G022100' => 'mes', 'Mapoly0096s0053' => 'mpo', 'MBI03_g14058_MAGBIO' => 'mbi', 'MBI03_g33876_MAGBIO' => 'mbi', 'MBI03_g36854_MAGBIO' => 'mbi', 'MBI17_g11997_MAGBIO' => 'mbi', 'MD03G1269000' => 'mdo', 'MD04G1179600' => 'mdo', 'MD11G1289800' => 'mdo', 'MD12G1194700' => 'mdo', 'MD13G1182100' => 'mdo', 'MD13G1182200' => 'mdo', 'MD16G1182600' => 'mdo', 'Medtr2g021400' => 'mtr', 'Medtr2g021470' => 'mtr', 'Medtr2g105810' => 'mtr', 'Medtr3g033580' => 'mtr', 'Medtr6g007970' => 'mtr', 'Medtr7g056330' => 'mtr', 'Medtr7g074290' => 'mtr', 'Medtr7g074380' => 'mtr', 'Medtr7g094550' => 'mtr', 'Medtr8g069995' => 'mtr', 'MELO3C014345.2' => 'cme', 'MELO3C021395.2' => 'cme', 'Migut.D00262' => 'egut', 'Migut.G00257' => 'egut', 'MSTRG.21575' => 'ama', 'MSTRG.3985' => 'ama', 'Nitab4.5_0000295g0140' => 'nta', 'Nitab4.5_0000732g0140' => 'nta', 'Nitab4.5_0003162g0020' => 'nta', 'Nitab4.5_0006180g0090' => 'nta', 'Nitab4.5_0006390g0010' => 'nta', 'Nitab4.5_0007392g0040' => 'nta', 'Nn1g02140' => 'nnu', 'Nn4g26168' => 'nnu', 'Nn5g26754' => 'nnu', 'Oeu001433.1' => 'oeu', 'Oeu010299.2' => 'oeu', 'Oeu011171.1' => 'oeu', 'Oeu037675.1' => 'oeu', 'Oeu038359.1' => 'oeu', 'Oeu063834.1' => 'oeu', 'Oeu063835.1' => 'oeu', 'Os05g0312000' => 'osa', 'Os07g0211101' => 'osa', 'Os07g0211200' => 'osa', 'Os07g0681500' => 'osa', 'Peaxi162Scf00095g01015' => 'pax', 'Peaxi162Scf00104g00329' => 'pax', 'Peaxi162Scf00161g00137' => 'pax', 'PGR004G1665' => 'pgr', 'PGR031G2937' => 'pgr', 'PGR119G2145' => 'pgr', 'PGSC0003DMG400004351' => 'stu', 'PGSC0003DMG400014625' => 'stu', 'PGSC0003DMG401000943' => 'stu', 'Phvul.001G148600' => 'pvu', 'Phvul.004G001700' => 'pvu', 'Phvul.006G154900' => 'pvu', 'Phvul.008G078200' => 'pvu', 'Phvul.011G136500' => 'pvu', 'Potri.002G215600' => 'ptr', 'Potri.008G201600' => 'ptr', 'Potri.014G138400' => 'ptr', 'Potri.016G142500' => 'ptr', 'Pp3c16_10580' => 'ppa', 'Pp3c5_25280' => 'ppa', 'Prupe.1G150000' => 'ppe', 'Prupe.1G150100' => 'ppe', 'Prupe.6G299600' => 'ppe', 'Prupe.8G245000' => 'ppe', 'Psat0s4927g0040' => 'psa', 'Psat1g052080' => 'psa', 'Psat1g183800' => 'psa', 'Psat3g113840' => 'psa', 'Psat3g126120' => 'psa', 'Psat3g126160' => 'psa', 'Psat3g158760' => 'psa', 'Psat3g158840' => 'psa', 'PSO170G2858' => 'pso', 'PSO339G0606' => 'pso', 'PSO384G4709' => 'pso', 'PSO407G0334' => 'pso', 'QL04p040276' => 'qlo', 'QL06p005458' => 'qlo', 'QL06p005472' => 'qlo', 'QL07p030546' => 'qlo', 'QL07p031519' => 'qlo', 'QL09p050949' => 'qlo', 'QL09p050966' => 'qlo', 'QL09p051067' => 'qlo', 'QL12p022706' => 'qlo', 'RcHm_v2.0_Chr2g0119601' => 'rch', 'RcHm_v2.0_Chr3g0459591' => 'rch', 'RcHm_v2.0_Chr4g0418521' => 'rch', 'RcHm_v2.0_Chr4g0418531' => 'rch', 'RcHm_v2.0_Chr4g0418541' => 'rch', 'RcHm_v2.0_Chr6g0291641' => 'rch', 'Rhsim01G0086300' => 'rsi', 'Rhsim01G0276300' => 'rsi', 'Rhsim01G0276500' => 'rsi', 'Rhsim04G0207700' => 'rsi', 'Rhsim05G0234500' => 'rsi', 'Rhsim13G0022400' => 'rsi', 'Sabra02G0167900' => 'sbr', 'Sabra04G0158500' => 'sbr', 'Sabra08G0159800' => 'sbr', 'Sabra10G0011500' => 'sbr', 'Sabra14G0104400' => 'sbr', 'SalBow2G2440' => 'sbo', 'SalBow4G2265' => 'sbo', 'Sc02g0000060' => 'sci', 'Sc05g0005020' => 'sci', 'Sc13g0003890' => 'sci', 'Sed0014865' => 'sed', 'Sed0017224' => 'sed', 'Sed0026391' => 'sed', 'SEGI_00063' => 'sgi', 'SEGI_10967' => 'sgi', 'SEGI_17510' => 'sgi', 'SEGI_24396' => 'sgi', 'SEGI_39719' => 'sgi', 'SEGI_41392' => 'sgi', 'SGA_v2.0_scaffold11G05794' => 'sas', 'SGA_v2.0_scaffold142G35607' => 'sas', 'SGA_v2.0_scaffold1G00447' => 'sas', 'SHI15388' => 'shi', 'SHI15394' => 'shi', 'SHI15396' => 'shi', 'SHI15399' => 'shi', 'SMO343G0151' => 'smo', 'SMO367G1118' => 'smo', 'Solyc01g080200.3' => 'sly', 'Solyc06g008960.3' => 'sly', 'Solyc09g064780.3' => 'sly', 'Sopen01g031980' => 'spe', 'Sopen06g003710' => 'spe', 'Sopen09g026460' => 'spe', 'Sp3g21240' => 'spa', 'Sp4g30030' => 'spa', 'TAR365G0022' => 'tar', 'TAR365G1023' => 'tar', 'TAR365G1253' => 'tar', 'TAR623G0078' => 'tar', 'TAR623G1721' => 'tar', 'TAR633G0959' => 'tar', 'THA.LOC104802225' => 'tha', 'THA.LOC104804769' => 'tha', 'THA.LOC104808660' => 'tha', 'THA.LOC104812792' => 'tha', 'Thecc.01G284000' => 'tca', 'Thecc.04G220600' => 'tca', 'Thecc.05G268900' => 'tca', 'Thecc.08G171100' => 'tca', 'Thhalv10001284m.g' => 'esa', 'Thhalv10019912m.g' => 'esa', 'TPR.G14189' => 'tpr', 'TPR.G18110' => 'tpr', 'TPR.G18130' => 'tpr', 'TPR.G18131' => 'tpr', 'TPR.G18140' => 'tpr', 'TPR.G24282' => 'tpr', 'TPR.G25221' => 'tpr', 'TPR.G29267' => 'tpr', 'TPR.G35315' => 'tpr', 'TPR.G36173' => 'tpr', 'TWI09G0794' => 'twi', 'TWI59G1348' => 'twi', 'TWI74G0430' => 'twi', 'unitig_26.g8940' => 'ugi', 'unitig_749.g13744' => 'ugi', 'unitig_749.g13745' => 'ugi', 'vmacro08269' => 'vma', 'vmacro14937' => 'vma', 'vmacro20401' => 'vma', 'VMungo0464G1349' => 'vmu', 'VMungo0540G0289' => 'vmu', 'VMungo1215G1590' => 'vmu', 'VMungo1309G0221' => 'vmu', 'VMungo1309G2815' => 'vmu', 'VMungo1383G0239' => 'vmu', 'VMungo1383G2910' => 'vmu', 'Zm00001eb095270' => 'zma', 'Zm00001eb095280' => 'zma', 'Zm00001eb111630' => 'zma', 'Zm00001eb237080' => 'zma', 'Zm00001eb273740' => 'zma', 'Zm00001eb285040' => 'zma', 'Zm00001eb330790' => 'zma', 'Zm00001eb337380' => 'zma' ), 'gf_id' => 'HOM05D001484', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001484' ), 'data_identifier' => 'HOM05D001484', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001484', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p31500' => 'bna', 'A05p00020' => 'bna', 'A07p08820' => 'bna', 'Aa31LG4G3300' => 'aar', 'Aa31LG8G10030' => 'aar', 'Actinidia00731' => 'ach', 'Actinidia11473' => 'ach', 'Actinidia23469' => 'ach', 'Actinidia24318' => 'ach', 'Actinidia40196' => 'ach', 'Actinidia40197' => 'ach', 'Actinidia40198' => 'ach', 'Ah.08g212990' => 'amhyb', 'Ah.15g091720' => 'amhyb', 'AL3G38260' => 'aly', 'AL4G47710' => 'aly', 'Aqoxy2G00671' => 'aox', 'Aqoxy2G03236' => 'aox', 'arahy.Tifrunner.gnm1.ann1.05IDCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KR684' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATY3SJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK6QJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6APGL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IDT7Z9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM073U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ0R87' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LE7RV4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT4QRX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V5ENPK' => 'arhy', 'AT2G48110' => 'ath', 'AT3G23590' => 'ath', 'ATR0626G186' => 'atr', 'ATR1127G141' => 'atr', 'Atru.chr4.2583' => 'acertr', 'Atru.chr5.1358' => 'acertr', 'Atru.chr5.1359' => 'acertr', 'Atru.chr8.46' => 'acertr', 'AUR62002640' => 'cqu', 'AUR62030055' => 'cqu', 'AUR62033713' => 'cqu', 'AUR62033714' => 'cqu', 'AUR62036795' => 'cqu', 'AUR62039891' => 'cqu', 'BcaB02g08737' => 'bca', 'BcaB04g20441' => 'bca', 'BcaB06g26509' => 'bca', 'BcaB06g26510' => 'bca', 'BcaB06g26511' => 'bca', 'BcaB06g26512' => 'bca', 'BcaB06g26513' => 'bca', 'BcaC02g12564' => 'bca', 'BcaC02g12565' => 'bca', 'BcaC02g12794' => 'bca', 'BcaC02g12795' => 'bca', 'BcaC02g12796' => 'bca', 'BcaC06g35541' => 'bca', 'BNapus_Darmor_BZH_scaffold_188p00080' => 'bna', 'BNapus_Darmor_BZH_scaffold_188p00090' => 'bna', 'BolC1t03972H' => 'bol', 'BolC1t03973H' => 'bol', 'BolC4t21680H' => 'bol', 'BolC7t41863H' => 'bol', 'BolSC55t61227H' => 'bol', 'BolSC55t61228H' => 'bol', 'BraA01t03278Z' => 'bra', 'BraA05t18998Z' => 'bra', 'BraA07t28673Z' => 'bra', 'C01p40150' => 'bna', 'C05p12370' => 'bna', 'C07p13680' => 'bna', 'CAN.G1006.16' => 'can', 'CAN.G1006.17' => 'can', 'CAN.G1170.2' => 'can', 'CAN.G962.7' => 'can', 'CANSAT25G2179' => 'cansat', 'CANSAT78G1573' => 'cansat', 'CARHR099510' => 'chi', 'CARHR143510' => 'chi', 'Carub.0003s2380' => 'cru', 'Carub.0004s3082' => 'cru', 'Ca_00614_v3' => 'car', 'Ca_07801_v3' => 'car', 'Ca_08567_v3' => 'car', 'Ca_09571_v3' => 'car', 'CBR_g19290' => 'cbr', 'Cc01_g19770' => 'ccan', 'Cc03_g03030' => 'ccan', 'CDE07G0968' => 'cde', 'CDE09G1441' => 'cde', 'Cfa006103' => 'cfa', 'Cfa015573' => 'cfa', 'Cfa016988' => 'cfa', 'Ciclev10006738m.g' => 'ccl', 'Ciclev10010920m.g' => 'ccl', 'Ciclev10018517m.g' => 'ccl', 'CiPaw.01G159200' => 'cil', 'CiPaw.02G091000' => 'cil', 'CiPaw.02G091100' => 'cil', 'CiPaw.08G103100' => 'cil', 'CiPaw.09G224900' => 'cil', 'ClCG06G005740' => 'cla', 'ClCG07G000090' => 'cla', 'ClCG07G000100' => 'cla', 'COL.COLO4_09143' => 'col', 'COL.COLO4_25124' => 'col', 'Cpa.g.sc16.34' => 'cpa', 'Cpa.g.sc3504.1' => 'cpa', 'Cpa.g.sc60.37' => 'cpa', 'CsaV3_6G018520' => 'csa', 'CsaV3_6G036860' => 'csa', 'CSS0001072' => 'camsi', 'CSS0020208' => 'camsi', 'CSS0021253' => 'camsi', 'CSS0022190' => 'camsi', 'CSS0036150' => 'camsi', 'CSS0040442' => 'camsi', 'CSS0042300' => 'camsi', 'CSS0045298' => 'camsi', 'DCAR_012449' => 'dca', 'DCAR_018405' => 'dca', 'DCAR_024573' => 'dca', 'DCAR_030591' => 'dca', 'Dinv16926' => 'din', 'Dinv32963' => 'din', 'Dinv38382' => 'din', 'Dinv38383' => 'din', 'Duzib133G0974' => 'dzi', 'Duzib138G1867' => 'dzi', 'Duzib211G0420' => 'dzi', 'Duzib212G0930' => 'dzi', 'ECA234G1645' => 'eca', 'ECA247G3467' => 'eca', 'ECA248G1703' => 'eca', 'EL10Ac3g06327' => 'bvu', 'EL10Ac7g17204' => 'bvu', 'Eucgr.A00855' => 'egr', 'Eucgr.A00858' => 'egr', 'Eucgr.H01520' => 'egr', 'Eucgr.H03604' => 'egr', 'Eucgr.L03465' => 'egr', 'Eucgr.L03466' => 'egr', 'FAN01G0988' => 'fan', 'FAN02G3892' => 'fan', 'FAN05G3381' => 'fan', 'FAN07G0967' => 'fan', 'FAN07G1493' => 'fan', 'FAN08G3125' => 'fan', 'FAN09G0402' => 'fan', 'FAN12G2594' => 'fan', 'FAN12G3879' => 'fan', 'FAN14G1546' => 'fan', 'FAN15G3626' => 'fan', 'FAN17G0588' => 'fan', 'FAN17G0609' => 'fan', 'FAN18G2817' => 'fan', 'FAN19G1305' => 'fan', 'FAN20G1787' => 'fan', 'FAN22G0073' => 'fan', 'FAN22G0352' => 'fan', 'FAN22G0368' => 'fan', 'FAN22G2273' => 'fan', 'FAN24G1998' => 'fan', 'FAN27G1317' => 'fan', 'FvH4_2g23980' => 'fve', 'FvH4_4g14380' => 'fve', 'FvH4_4g14390' => 'fve', 'FvH4_6g09250' => 'fve', 'Glyma.03G151100' => 'gma', 'Glyma.04G122550' => 'gma', 'Glyma.05G001600' => 'gma', 'Glyma.09G270766' => 'gma', 'Glyma.09G270832' => 'gma', 'Glyma.13G209800' => 'gma', 'Glyma.15G102800' => 'gma', 'Glyma.18G218900' => 'gma', 'Glyma.19G001500' => 'gma', 'Glyma.19G153600' => 'gma', 'Gohir.A02G028600' => 'ghi', 'Gohir.A08G045000' => 'ghi', 'Gohir.A11G120500' => 'ghi', 'Gohir.A12G006200' => 'ghi', 'Gohir.A12G006250' => 'ghi', 'Gohir.D02G036300' => 'ghi', 'Gohir.D08G054700' => 'ghi', 'Gohir.D11G125600' => 'ghi', 'Gohir.D12G005700' => 'ghi', 'Gorai.004G055200' => 'gra', 'Gorai.005G040400' => 'gra', 'Gorai.007G134500' => 'gra', 'Gorai.008G005500' => 'gra', 'GSVIVG01011094001' => 'vvi', 'GSVIVG01017879001' => 'vvi', 'GSVIVG01025988001' => 'vvi', 'GSVIVG01029847001' => 'vvi', 'HanXRQChr10g0282901' => 'han', 'HanXRQChr10g0310371' => 'han', 'HanXRQChr10g0315041' => 'han', 'HanXRQChr11g0327651' => 'han', 'HanXRQChr12g0359391' => 'han', 'Haze_00972' => 'cav', 'Haze_00973' => 'cav', 'Haze_00974' => 'cav', 'Haze_04747' => 'cav', 'Haze_04749' => 'cav', 'Haze_04750' => 'cav', 'Haze_21217' => 'cav', 'Hma1.2p1_1037F.1_g250680' => 'hma', 'Hma1.2p1_1644F.1_g295320' => 'hma', 'HPP92_011322' => 'vpl', 'HPP92_011323' => 'vpl', 'HPP92_011324' => 'vpl', 'HPP92_011325' => 'vpl', 'HPP92_011326' => 'vpl', 'Hund12205' => 'sun', 'Hund17957' => 'sun', 'Lalb_Chr06g0176771' => 'lal', 'Lalb_Chr18g0056021' => 'lal', 'Lalb_Chr18g0056031' => 'lal', 'Lalb_Chr18g0056041' => 'lal', 'Lalb_Chr20g0107751' => 'lal', 'Lalb_Chr20g0118371' => 'lal', 'Lj1g0010239' => 'lja', 'Lj1g0017101' => 'lja', 'Lj2A1178G40' => 'lonja', 'Lj2A54G84' => 'lonja', 'Lj2g0015248' => 'lja', 'Lj3A761T51' => 'lonja', 'Lj6g0018116' => 'lja', 'Lsat_1_v5_gn_4_136040' => 'lsa', 'Lsat_1_v5_gn_5_187461' => 'lsa', 'Lsat_1_v5_gn_5_77001' => 'lsa', 'Lsat_1_v5_gn_9_4461' => 'lsa', 'Manes.01G210100' => 'mes', 'Manes.03G185600' => 'mes', 'Manes.05G073300' => 'mes', 'Manes.09G120300' => 'mes', 'Manes.15G022100' => 'mes', 'Mapoly0096s0053' => 'mpo', 'MBI03_g14058_MAGBIO' => 'mbi', 'MBI03_g33876_MAGBIO' => 'mbi', 'MBI03_g36854_MAGBIO' => 'mbi', 'MBI17_g11997_MAGBIO' => 'mbi', 'MD03G1269000' => 'mdo', 'MD04G1179600' => 'mdo', 'MD11G1289800' => 'mdo', 'MD12G1194700' => 'mdo', 'MD13G1182100' => 'mdo', 'MD13G1182200' => 'mdo', 'MD16G1182600' => 'mdo', 'Medtr2g021400' => 'mtr', 'Medtr2g021470' => 'mtr', 'Medtr2g105810' => 'mtr', 'Medtr3g033580' => 'mtr', 'Medtr6g007970' => 'mtr', 'Medtr7g056330' => 'mtr', 'Medtr7g074290' => 'mtr', 'Medtr7g074380' => 'mtr', 'Medtr7g094550' => 'mtr', 'Medtr8g069995' => 'mtr', 'MELO3C014345.2' => 'cme', 'MELO3C021395.2' => 'cme', 'Migut.D00262' => 'egut', 'Migut.G00257' => 'egut', 'MSTRG.21575' => 'ama', 'MSTRG.3985' => 'ama', 'Nitab4.5_0000295g0140' => 'nta', 'Nitab4.5_0000732g0140' => 'nta', 'Nitab4.5_0003162g0020' => 'nta', 'Nitab4.5_0006180g0090' => 'nta', 'Nitab4.5_0006390g0010' => 'nta', 'Nitab4.5_0007392g0040' => 'nta', 'Nn1g02140' => 'nnu', 'Nn4g26168' => 'nnu', 'Nn5g26754' => 'nnu', 'Oeu001433.1' => 'oeu', 'Oeu010299.2' => 'oeu', 'Oeu011171.1' => 'oeu', 'Oeu037675.1' => 'oeu', 'Oeu038359.1' => 'oeu', 'Oeu063834.1' => 'oeu', 'Oeu063835.1' => 'oeu', 'Os05g0312000' => 'osa', 'Os07g0211101' => 'osa', 'Os07g0211200' => 'osa', 'Os07g0681500' => 'osa', 'Peaxi162Scf00095g01015' => 'pax', 'Peaxi162Scf00104g00329' => 'pax', 'Peaxi162Scf00161g00137' => 'pax', 'PGR004G1665' => 'pgr', 'PGR031G2937' => 'pgr', 'PGR119G2145' => 'pgr', 'PGSC0003DMG400004351' => 'stu', 'PGSC0003DMG400014625' => 'stu', 'PGSC0003DMG401000943' => 'stu', 'Phvul.001G148600' => 'pvu', 'Phvul.004G001700' => 'pvu', 'Phvul.006G154900' => 'pvu', 'Phvul.008G078200' => 'pvu', 'Phvul.011G136500' => 'pvu', 'Potri.002G215600' => 'ptr', 'Potri.008G201600' => 'ptr', 'Potri.014G138400' => 'ptr', 'Potri.016G142500' => 'ptr', 'Pp3c16_10580' => 'ppa', 'Pp3c5_25280' => 'ppa', 'Prupe.1G150000' => 'ppe', 'Prupe.1G150100' => 'ppe', 'Prupe.6G299600' => 'ppe', 'Prupe.8G245000' => 'ppe', 'Psat0s4927g0040' => 'psa', 'Psat1g052080' => 'psa', 'Psat1g183800' => 'psa', 'Psat3g113840' => 'psa', 'Psat3g126120' => 'psa', 'Psat3g126160' => 'psa', 'Psat3g158760' => 'psa', 'Psat3g158840' => 'psa', 'PSO170G2858' => 'pso', 'PSO339G0606' => 'pso', 'PSO384G4709' => 'pso', 'PSO407G0334' => 'pso', 'QL04p040276' => 'qlo', 'QL06p005458' => 'qlo', 'QL06p005472' => 'qlo', 'QL07p030546' => 'qlo', 'QL07p031519' => 'qlo', 'QL09p050949' => 'qlo', 'QL09p050966' => 'qlo', 'QL09p051067' => 'qlo', 'QL12p022706' => 'qlo', 'RcHm_v2.0_Chr2g0119601' => 'rch', 'RcHm_v2.0_Chr3g0459591' => 'rch', 'RcHm_v2.0_Chr4g0418521' => 'rch', 'RcHm_v2.0_Chr4g0418531' => 'rch', 'RcHm_v2.0_Chr4g0418541' => 'rch', 'RcHm_v2.0_Chr6g0291641' => 'rch', 'Rhsim01G0086300' => 'rsi', 'Rhsim01G0276300' => 'rsi', 'Rhsim01G0276500' => 'rsi', 'Rhsim04G0207700' => 'rsi', 'Rhsim05G0234500' => 'rsi', 'Rhsim13G0022400' => 'rsi', 'Sabra02G0167900' => 'sbr', 'Sabra04G0158500' => 'sbr', 'Sabra08G0159800' => 'sbr', 'Sabra10G0011500' => 'sbr', 'Sabra14G0104400' => 'sbr', 'SalBow2G2440' => 'sbo', 'SalBow4G2265' => 'sbo', 'Sc02g0000060' => 'sci', 'Sc05g0005020' => 'sci', 'Sc13g0003890' => 'sci', 'Sed0014865' => 'sed', 'Sed0017224' => 'sed', 'Sed0026391' => 'sed', 'SEGI_00063' => 'sgi', 'SEGI_10967' => 'sgi', 'SEGI_17510' => 'sgi', 'SEGI_24396' => 'sgi', 'SEGI_39719' => 'sgi', 'SEGI_41392' => 'sgi', 'SGA_v2.0_scaffold11G05794' => 'sas', 'SGA_v2.0_scaffold142G35607' => 'sas', 'SGA_v2.0_scaffold1G00447' => 'sas', 'SHI15388' => 'shi', 'SHI15394' => 'shi', 'SHI15396' => 'shi', 'SHI15399' => 'shi', 'SMO343G0151' => 'smo', 'SMO367G1118' => 'smo', 'Solyc01g080200.3' => 'sly', 'Solyc06g008960.3' => 'sly', 'Solyc09g064780.3' => 'sly', 'Sopen01g031980' => 'spe', 'Sopen06g003710' => 'spe', 'Sopen09g026460' => 'spe', 'Sp3g21240' => 'spa', 'Sp4g30030' => 'spa', 'TAR365G0022' => 'tar', 'TAR365G1023' => 'tar', 'TAR365G1253' => 'tar', 'TAR623G0078' => 'tar', 'TAR623G1721' => 'tar', 'TAR633G0959' => 'tar', 'THA.LOC104802225' => 'tha', 'THA.LOC104804769' => 'tha', 'THA.LOC104808660' => 'tha', 'THA.LOC104812792' => 'tha', 'Thecc.01G284000' => 'tca', 'Thecc.04G220600' => 'tca', 'Thecc.05G268900' => 'tca', 'Thecc.08G171100' => 'tca', 'Thhalv10001284m.g' => 'esa', 'Thhalv10019912m.g' => 'esa', 'TPR.G14189' => 'tpr', 'TPR.G18110' => 'tpr', 'TPR.G18130' => 'tpr', 'TPR.G18131' => 'tpr', 'TPR.G18140' => 'tpr', 'TPR.G24282' => 'tpr', 'TPR.G25221' => 'tpr', 'TPR.G29267' => 'tpr', 'TPR.G35315' => 'tpr', 'TPR.G36173' => 'tpr', 'TWI09G0794' => 'twi', 'TWI59G1348' => 'twi', 'TWI74G0430' => 'twi', 'unitig_26.g8940' => 'ugi', 'unitig_749.g13744' => 'ugi', 'unitig_749.g13745' => 'ugi', 'vmacro08269' => 'vma', 'vmacro14937' => 'vma', 'vmacro20401' => 'vma', 'VMungo0464G1349' => 'vmu', 'VMungo0540G0289' => 'vmu', 'VMungo1215G1590' => 'vmu', 'VMungo1309G0221' => 'vmu', 'VMungo1309G2815' => 'vmu', 'VMungo1383G0239' => 'vmu', 'VMungo1383G2910' => 'vmu', 'Zm00001eb095270' => 'zma', 'Zm00001eb095280' => 'zma', 'Zm00001eb111630' => 'zma', 'Zm00001eb237080' => 'zma', 'Zm00001eb273740' => 'zma', 'Zm00001eb285040' => 'zma', 'Zm00001eb330790' => 'zma', 'Zm00001eb337380' => 'zma' ) $gf_id = 'HOM05D001484' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001484' ) $data_identifier = 'HOM05D001484' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 2, 'aly' => (int) 2, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 22, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 7, 'hma' => (int) 2, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 7, 'mtr' => (int) 10, 'cme' => (int) 2, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 4, 'ppa' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 4, 'qlo' => (int) 9, 'rch' => (int) 6, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 10, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 7, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb337380' $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' => 'HOM05D001484', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p31500' => 'bna', 'A05p00020' => 'bna', 'A07p08820' => 'bna', 'Aa31LG4G3300' => 'aar', 'Aa31LG8G10030' => 'aar', 'Actinidia00731' => 'ach', 'Actinidia11473' => 'ach', 'Actinidia23469' => 'ach', 'Actinidia24318' => 'ach', 'Actinidia40196' => 'ach', 'Actinidia40197' => 'ach', 'Actinidia40198' => 'ach', 'Ah.08g212990' => 'amhyb', 'Ah.15g091720' => 'amhyb', 'AL3G38260' => 'aly', 'AL4G47710' => 'aly', 'Aqoxy2G00671' => 'aox', 'Aqoxy2G03236' => 'aox', 'arahy.Tifrunner.gnm1.ann1.05IDCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KR684' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATY3SJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK6QJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6APGL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IDT7Z9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM073U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ0R87' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LE7RV4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT4QRX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V5ENPK' => 'arhy', 'AT2G48110' => 'ath', 'AT3G23590' => 'ath', 'ATR0626G186' => 'atr', 'ATR1127G141' => 'atr', 'Atru.chr4.2583' => 'acertr', 'Atru.chr5.1358' => 'acertr', 'Atru.chr5.1359' => 'acertr', 'Atru.chr8.46' => 'acertr', 'AUR62002640' => 'cqu', 'AUR62030055' => 'cqu', 'AUR62033713' => 'cqu', 'AUR62033714' => 'cqu', 'AUR62036795' => 'cqu', 'AUR62039891' => 'cqu', 'BcaB02g08737' => 'bca', 'BcaB04g20441' => 'bca', 'BcaB06g26509' => 'bca', 'BcaB06g26510' => 'bca', 'BcaB06g26511' => 'bca', 'BcaB06g26512' => 'bca', 'BcaB06g26513' => 'bca', 'BcaC02g12564' => 'bca', 'BcaC02g12565' => 'bca', 'BcaC02g12794' => 'bca', 'BcaC02g12795' => 'bca', 'BcaC02g12796' => 'bca', 'BcaC06g35541' => 'bca', 'BNapus_Darmor_BZH_scaffold_188p00080' => 'bna', 'BNapus_Darmor_BZH_scaffold_188p00090' => 'bna', 'BolC1t03972H' => 'bol', 'BolC1t03973H' => 'bol', 'BolC4t21680H' => 'bol', 'BolC7t41863H' => 'bol', 'BolSC55t61227H' => 'bol', 'BolSC55t61228H' => 'bol', 'BraA01t03278Z' => 'bra', 'BraA05t18998Z' => 'bra', 'BraA07t28673Z' => 'bra', 'C01p40150' => 'bna', 'C05p12370' => 'bna', 'C07p13680' => 'bna', 'CAN.G1006.16' => 'can', 'CAN.G1006.17' => 'can', 'CAN.G1170.2' => 'can', 'CAN.G962.7' => 'can', 'CANSAT25G2179' => 'cansat', 'CANSAT78G1573' => 'cansat', 'CARHR099510' => 'chi', 'CARHR143510' => 'chi', 'Carub.0003s2380' => 'cru', 'Carub.0004s3082' => 'cru', 'Ca_00614_v3' => 'car', 'Ca_07801_v3' => 'car', 'Ca_08567_v3' => 'car', 'Ca_09571_v3' => 'car', 'CBR_g19290' => 'cbr', 'Cc01_g19770' => 'ccan', 'Cc03_g03030' => 'ccan', 'CDE07G0968' => 'cde', 'CDE09G1441' => 'cde', 'Cfa006103' => 'cfa', 'Cfa015573' => 'cfa', 'Cfa016988' => 'cfa', 'Ciclev10006738m.g' => 'ccl', 'Ciclev10010920m.g' => 'ccl', 'Ciclev10018517m.g' => 'ccl', 'CiPaw.01G159200' => 'cil', 'CiPaw.02G091000' => 'cil', 'CiPaw.02G091100' => 'cil', 'CiPaw.08G103100' => 'cil', 'CiPaw.09G224900' => 'cil', 'ClCG06G005740' => 'cla', 'ClCG07G000090' => 'cla', 'ClCG07G000100' => 'cla', 'COL.COLO4_09143' => 'col', 'COL.COLO4_25124' => 'col', 'Cpa.g.sc16.34' => 'cpa', 'Cpa.g.sc3504.1' => 'cpa', 'Cpa.g.sc60.37' => 'cpa', 'CsaV3_6G018520' => 'csa', 'CsaV3_6G036860' => 'csa', 'CSS0001072' => 'camsi', 'CSS0020208' => 'camsi', 'CSS0021253' => 'camsi', 'CSS0022190' => 'camsi', 'CSS0036150' => 'camsi', 'CSS0040442' => 'camsi', 'CSS0042300' => 'camsi', 'CSS0045298' => 'camsi', 'DCAR_012449' => 'dca', 'DCAR_018405' => 'dca', 'DCAR_024573' => 'dca', 'DCAR_030591' => 'dca', 'Dinv16926' => 'din', 'Dinv32963' => 'din', 'Dinv38382' => 'din', 'Dinv38383' => 'din', 'Duzib133G0974' => 'dzi', 'Duzib138G1867' => 'dzi', 'Duzib211G0420' => 'dzi', 'Duzib212G0930' => 'dzi', 'ECA234G1645' => 'eca', 'ECA247G3467' => 'eca', 'ECA248G1703' => 'eca', 'EL10Ac3g06327' => 'bvu', 'EL10Ac7g17204' => 'bvu', 'Eucgr.A00855' => 'egr', 'Eucgr.A00858' => 'egr', 'Eucgr.H01520' => 'egr', 'Eucgr.H03604' => 'egr', 'Eucgr.L03465' => 'egr', 'Eucgr.L03466' => 'egr', 'FAN01G0988' => 'fan', 'FAN02G3892' => 'fan', 'FAN05G3381' => 'fan', 'FAN07G0967' => 'fan', 'FAN07G1493' => 'fan', 'FAN08G3125' => 'fan', 'FAN09G0402' => 'fan', 'FAN12G2594' => 'fan', 'FAN12G3879' => 'fan', 'FAN14G1546' => 'fan', 'FAN15G3626' => 'fan', 'FAN17G0588' => 'fan', 'FAN17G0609' => 'fan', 'FAN18G2817' => 'fan', 'FAN19G1305' => 'fan', 'FAN20G1787' => 'fan', 'FAN22G0073' => 'fan', 'FAN22G0352' => 'fan', 'FAN22G0368' => 'fan', 'FAN22G2273' => 'fan', 'FAN24G1998' => 'fan', 'FAN27G1317' => 'fan', 'FvH4_2g23980' => 'fve', 'FvH4_4g14380' => 'fve', 'FvH4_4g14390' => 'fve', 'FvH4_6g09250' => 'fve', 'Glyma.03G151100' => 'gma', 'Glyma.04G122550' => 'gma', 'Glyma.05G001600' => 'gma', 'Glyma.09G270766' => 'gma', 'Glyma.09G270832' => 'gma', 'Glyma.13G209800' => 'gma', 'Glyma.15G102800' => 'gma', 'Glyma.18G218900' => 'gma', 'Glyma.19G001500' => 'gma', 'Glyma.19G153600' => 'gma', 'Gohir.A02G028600' => 'ghi', 'Gohir.A08G045000' => 'ghi', 'Gohir.A11G120500' => 'ghi', 'Gohir.A12G006200' => 'ghi', 'Gohir.A12G006250' => 'ghi', 'Gohir.D02G036300' => 'ghi', 'Gohir.D08G054700' => 'ghi', 'Gohir.D11G125600' => 'ghi', 'Gohir.D12G005700' => 'ghi', 'Gorai.004G055200' => 'gra', 'Gorai.005G040400' => 'gra', 'Gorai.007G134500' => 'gra', 'Gorai.008G005500' => 'gra', 'GSVIVG01011094001' => 'vvi', 'GSVIVG01017879001' => 'vvi', 'GSVIVG01025988001' => 'vvi', 'GSVIVG01029847001' => 'vvi', 'HanXRQChr10g0282901' => 'han', 'HanXRQChr10g0310371' => 'han', 'HanXRQChr10g0315041' => 'han', 'HanXRQChr11g0327651' => 'han', 'HanXRQChr12g0359391' => 'han', 'Haze_00972' => 'cav', 'Haze_00973' => 'cav', 'Haze_00974' => 'cav', 'Haze_04747' => 'cav', 'Haze_04749' => 'cav', 'Haze_04750' => 'cav', 'Haze_21217' => 'cav', 'Hma1.2p1_1037F.1_g250680' => 'hma', 'Hma1.2p1_1644F.1_g295320' => 'hma', 'HPP92_011322' => 'vpl', 'HPP92_011323' => 'vpl', 'HPP92_011324' => 'vpl', 'HPP92_011325' => 'vpl', 'HPP92_011326' => 'vpl', 'Hund12205' => 'sun', 'Hund17957' => 'sun', 'Lalb_Chr06g0176771' => 'lal', 'Lalb_Chr18g0056021' => 'lal', 'Lalb_Chr18g0056031' => 'lal', 'Lalb_Chr18g0056041' => 'lal', 'Lalb_Chr20g0107751' => 'lal', 'Lalb_Chr20g0118371' => 'lal', 'Lj1g0010239' => 'lja', 'Lj1g0017101' => 'lja', 'Lj2A1178G40' => 'lonja', 'Lj2A54G84' => 'lonja', 'Lj2g0015248' => 'lja', 'Lj3A761T51' => 'lonja', 'Lj6g0018116' => 'lja', 'Lsat_1_v5_gn_4_136040' => 'lsa', 'Lsat_1_v5_gn_5_187461' => 'lsa', 'Lsat_1_v5_gn_5_77001' => 'lsa', 'Lsat_1_v5_gn_9_4461' => 'lsa', 'Manes.01G210100' => 'mes', 'Manes.03G185600' => 'mes', 'Manes.05G073300' => 'mes', 'Manes.09G120300' => 'mes', 'Manes.15G022100' => 'mes', 'Mapoly0096s0053' => 'mpo', 'MBI03_g14058_MAGBIO' => 'mbi', 'MBI03_g33876_MAGBIO' => 'mbi', 'MBI03_g36854_MAGBIO' => 'mbi', 'MBI17_g11997_MAGBIO' => 'mbi', 'MD03G1269000' => 'mdo', 'MD04G1179600' => 'mdo', 'MD11G1289800' => 'mdo', 'MD12G1194700' => 'mdo', 'MD13G1182100' => 'mdo', 'MD13G1182200' => 'mdo', 'MD16G1182600' => 'mdo', 'Medtr2g021400' => 'mtr', 'Medtr2g021470' => 'mtr', 'Medtr2g105810' => 'mtr', 'Medtr3g033580' => 'mtr', 'Medtr6g007970' => 'mtr', 'Medtr7g056330' => 'mtr', 'Medtr7g074290' => 'mtr', 'Medtr7g074380' => 'mtr', 'Medtr7g094550' => 'mtr', 'Medtr8g069995' => 'mtr', 'MELO3C014345.2' => 'cme', 'MELO3C021395.2' => 'cme', 'Migut.D00262' => 'egut', 'Migut.G00257' => 'egut', 'MSTRG.21575' => 'ama', 'MSTRG.3985' => 'ama', 'Nitab4.5_0000295g0140' => 'nta', 'Nitab4.5_0000732g0140' => 'nta', 'Nitab4.5_0003162g0020' => 'nta', 'Nitab4.5_0006180g0090' => 'nta', 'Nitab4.5_0006390g0010' => 'nta', 'Nitab4.5_0007392g0040' => 'nta', 'Nn1g02140' => 'nnu', 'Nn4g26168' => 'nnu', 'Nn5g26754' => 'nnu', 'Oeu001433.1' => 'oeu', 'Oeu010299.2' => 'oeu', 'Oeu011171.1' => 'oeu', 'Oeu037675.1' => 'oeu', 'Oeu038359.1' => 'oeu', 'Oeu063834.1' => 'oeu', 'Oeu063835.1' => 'oeu', 'Os05g0312000' => 'osa', 'Os07g0211101' => 'osa', 'Os07g0211200' => 'osa', 'Os07g0681500' => 'osa', 'Peaxi162Scf00095g01015' => 'pax', 'Peaxi162Scf00104g00329' => 'pax', 'Peaxi162Scf00161g00137' => 'pax', 'PGR004G1665' => 'pgr', 'PGR031G2937' => 'pgr', 'PGR119G2145' => 'pgr', 'PGSC0003DMG400004351' => 'stu', 'PGSC0003DMG400014625' => 'stu', 'PGSC0003DMG401000943' => 'stu', 'Phvul.001G148600' => 'pvu', 'Phvul.004G001700' => 'pvu', 'Phvul.006G154900' => 'pvu', 'Phvul.008G078200' => 'pvu', 'Phvul.011G136500' => 'pvu', 'Potri.002G215600' => 'ptr', 'Potri.008G201600' => 'ptr', 'Potri.014G138400' => 'ptr', 'Potri.016G142500' => 'ptr', 'Pp3c16_10580' => 'ppa', 'Pp3c5_25280' => 'ppa', 'Prupe.1G150000' => 'ppe', 'Prupe.1G150100' => 'ppe', 'Prupe.6G299600' => 'ppe', 'Prupe.8G245000' => 'ppe', 'Psat0s4927g0040' => 'psa', 'Psat1g052080' => 'psa', 'Psat1g183800' => 'psa', 'Psat3g113840' => 'psa', 'Psat3g126120' => 'psa', 'Psat3g126160' => 'psa', 'Psat3g158760' => 'psa', 'Psat3g158840' => 'psa', 'PSO170G2858' => 'pso', 'PSO339G0606' => 'pso', 'PSO384G4709' => 'pso', 'PSO407G0334' => 'pso', 'QL04p040276' => 'qlo', 'QL06p005458' => 'qlo', 'QL06p005472' => 'qlo', 'QL07p030546' => 'qlo', 'QL07p031519' => 'qlo', 'QL09p050949' => 'qlo', 'QL09p050966' => 'qlo', 'QL09p051067' => 'qlo', 'QL12p022706' => 'qlo', 'RcHm_v2.0_Chr2g0119601' => 'rch', 'RcHm_v2.0_Chr3g0459591' => 'rch', 'RcHm_v2.0_Chr4g0418521' => 'rch', 'RcHm_v2.0_Chr4g0418531' => 'rch', 'RcHm_v2.0_Chr4g0418541' => 'rch', 'RcHm_v2.0_Chr6g0291641' => 'rch', 'Rhsim01G0086300' => 'rsi', 'Rhsim01G0276300' => 'rsi', 'Rhsim01G0276500' => 'rsi', 'Rhsim04G0207700' => 'rsi', 'Rhsim05G0234500' => 'rsi', 'Rhsim13G0022400' => 'rsi', 'Sabra02G0167900' => 'sbr', 'Sabra04G0158500' => 'sbr', 'Sabra08G0159800' => 'sbr', 'Sabra10G0011500' => 'sbr', 'Sabra14G0104400' => 'sbr', 'SalBow2G2440' => 'sbo', 'SalBow4G2265' => 'sbo', 'Sc02g0000060' => 'sci', 'Sc05g0005020' => 'sci', 'Sc13g0003890' => 'sci', 'Sed0014865' => 'sed', 'Sed0017224' => 'sed', 'Sed0026391' => 'sed', 'SEGI_00063' => 'sgi', 'SEGI_10967' => 'sgi', 'SEGI_17510' => 'sgi', 'SEGI_24396' => 'sgi', 'SEGI_39719' => 'sgi', 'SEGI_41392' => 'sgi', 'SGA_v2.0_scaffold11G05794' => 'sas', 'SGA_v2.0_scaffold142G35607' => 'sas', 'SGA_v2.0_scaffold1G00447' => 'sas', 'SHI15388' => 'shi', 'SHI15394' => 'shi', 'SHI15396' => 'shi', 'SHI15399' => 'shi', 'SMO343G0151' => 'smo', 'SMO367G1118' => 'smo', 'Solyc01g080200.3' => 'sly', 'Solyc06g008960.3' => 'sly', 'Solyc09g064780.3' => 'sly', 'Sopen01g031980' => 'spe', 'Sopen06g003710' => 'spe', 'Sopen09g026460' => 'spe', 'Sp3g21240' => 'spa', 'Sp4g30030' => 'spa', 'TAR365G0022' => 'tar', 'TAR365G1023' => 'tar', 'TAR365G1253' => 'tar', 'TAR623G0078' => 'tar', 'TAR623G1721' => 'tar', 'TAR633G0959' => 'tar', 'THA.LOC104802225' => 'tha', 'THA.LOC104804769' => 'tha', 'THA.LOC104808660' => 'tha', 'THA.LOC104812792' => 'tha', 'Thecc.01G284000' => 'tca', 'Thecc.04G220600' => 'tca', 'Thecc.05G268900' => 'tca', 'Thecc.08G171100' => 'tca', 'Thhalv10001284m.g' => 'esa', 'Thhalv10019912m.g' => 'esa', 'TPR.G14189' => 'tpr', 'TPR.G18110' => 'tpr', 'TPR.G18130' => 'tpr', 'TPR.G18131' => 'tpr', 'TPR.G18140' => 'tpr', 'TPR.G24282' => 'tpr', 'TPR.G25221' => 'tpr', 'TPR.G29267' => 'tpr', 'TPR.G35315' => 'tpr', 'TPR.G36173' => 'tpr', 'TWI09G0794' => 'twi', 'TWI59G1348' => 'twi', 'TWI74G0430' => 'twi', 'unitig_26.g8940' => 'ugi', 'unitig_749.g13744' => 'ugi', 'unitig_749.g13745' => 'ugi', 'vmacro08269' => 'vma', 'vmacro14937' => 'vma', 'vmacro20401' => 'vma', 'VMungo0464G1349' => 'vmu', 'VMungo0540G0289' => 'vmu', 'VMungo1215G1590' => 'vmu', 'VMungo1309G0221' => 'vmu', 'VMungo1309G2815' => 'vmu', 'VMungo1383G0239' => 'vmu', 'VMungo1383G2910' => 'vmu', 'Zm00001eb095270' => 'zma', 'Zm00001eb095280' => 'zma', 'Zm00001eb111630' => 'zma', 'Zm00001eb237080' => 'zma', 'Zm00001eb273740' => 'zma', 'Zm00001eb285040' => 'zma', 'Zm00001eb330790' => 'zma', 'Zm00001eb337380' => 'zma' ), 'gf_id' => 'HOM05D001484', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001484' ), 'data_identifier' => 'HOM05D001484', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001484', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p31500' => 'bna', 'A05p00020' => 'bna', 'A07p08820' => 'bna', 'Aa31LG4G3300' => 'aar', 'Aa31LG8G10030' => 'aar', 'Actinidia00731' => 'ach', 'Actinidia11473' => 'ach', 'Actinidia23469' => 'ach', 'Actinidia24318' => 'ach', 'Actinidia40196' => 'ach', 'Actinidia40197' => 'ach', 'Actinidia40198' => 'ach', 'Ah.08g212990' => 'amhyb', 'Ah.15g091720' => 'amhyb', 'AL3G38260' => 'aly', 'AL4G47710' => 'aly', 'Aqoxy2G00671' => 'aox', 'Aqoxy2G03236' => 'aox', 'arahy.Tifrunner.gnm1.ann1.05IDCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KR684' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATY3SJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK6QJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6APGL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IDT7Z9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM073U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ0R87' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LE7RV4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT4QRX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V5ENPK' => 'arhy', 'AT2G48110' => 'ath', 'AT3G23590' => 'ath', 'ATR0626G186' => 'atr', 'ATR1127G141' => 'atr', 'Atru.chr4.2583' => 'acertr', 'Atru.chr5.1358' => 'acertr', 'Atru.chr5.1359' => 'acertr', 'Atru.chr8.46' => 'acertr', 'AUR62002640' => 'cqu', 'AUR62030055' => 'cqu', 'AUR62033713' => 'cqu', 'AUR62033714' => 'cqu', 'AUR62036795' => 'cqu', 'AUR62039891' => 'cqu', 'BcaB02g08737' => 'bca', 'BcaB04g20441' => 'bca', 'BcaB06g26509' => 'bca', 'BcaB06g26510' => 'bca', 'BcaB06g26511' => 'bca', 'BcaB06g26512' => 'bca', 'BcaB06g26513' => 'bca', 'BcaC02g12564' => 'bca', 'BcaC02g12565' => 'bca', 'BcaC02g12794' => 'bca', 'BcaC02g12795' => 'bca', 'BcaC02g12796' => 'bca', 'BcaC06g35541' => 'bca', 'BNapus_Darmor_BZH_scaffold_188p00080' => 'bna', 'BNapus_Darmor_BZH_scaffold_188p00090' => 'bna', 'BolC1t03972H' => 'bol', 'BolC1t03973H' => 'bol', 'BolC4t21680H' => 'bol', 'BolC7t41863H' => 'bol', 'BolSC55t61227H' => 'bol', 'BolSC55t61228H' => 'bol', 'BraA01t03278Z' => 'bra', 'BraA05t18998Z' => 'bra', 'BraA07t28673Z' => 'bra', 'C01p40150' => 'bna', 'C05p12370' => 'bna', 'C07p13680' => 'bna', 'CAN.G1006.16' => 'can', 'CAN.G1006.17' => 'can', 'CAN.G1170.2' => 'can', 'CAN.G962.7' => 'can', 'CANSAT25G2179' => 'cansat', 'CANSAT78G1573' => 'cansat', 'CARHR099510' => 'chi', 'CARHR143510' => 'chi', 'Carub.0003s2380' => 'cru', 'Carub.0004s3082' => 'cru', 'Ca_00614_v3' => 'car', 'Ca_07801_v3' => 'car', 'Ca_08567_v3' => 'car', 'Ca_09571_v3' => 'car', 'CBR_g19290' => 'cbr', 'Cc01_g19770' => 'ccan', 'Cc03_g03030' => 'ccan', 'CDE07G0968' => 'cde', 'CDE09G1441' => 'cde', 'Cfa006103' => 'cfa', 'Cfa015573' => 'cfa', 'Cfa016988' => 'cfa', 'Ciclev10006738m.g' => 'ccl', 'Ciclev10010920m.g' => 'ccl', 'Ciclev10018517m.g' => 'ccl', 'CiPaw.01G159200' => 'cil', 'CiPaw.02G091000' => 'cil', 'CiPaw.02G091100' => 'cil', 'CiPaw.08G103100' => 'cil', 'CiPaw.09G224900' => 'cil', 'ClCG06G005740' => 'cla', 'ClCG07G000090' => 'cla', 'ClCG07G000100' => 'cla', 'COL.COLO4_09143' => 'col', 'COL.COLO4_25124' => 'col', 'Cpa.g.sc16.34' => 'cpa', 'Cpa.g.sc3504.1' => 'cpa', 'Cpa.g.sc60.37' => 'cpa', 'CsaV3_6G018520' => 'csa', 'CsaV3_6G036860' => 'csa', 'CSS0001072' => 'camsi', 'CSS0020208' => 'camsi', 'CSS0021253' => 'camsi', 'CSS0022190' => 'camsi', 'CSS0036150' => 'camsi', 'CSS0040442' => 'camsi', 'CSS0042300' => 'camsi', 'CSS0045298' => 'camsi', 'DCAR_012449' => 'dca', 'DCAR_018405' => 'dca', 'DCAR_024573' => 'dca', 'DCAR_030591' => 'dca', 'Dinv16926' => 'din', 'Dinv32963' => 'din', 'Dinv38382' => 'din', 'Dinv38383' => 'din', 'Duzib133G0974' => 'dzi', 'Duzib138G1867' => 'dzi', 'Duzib211G0420' => 'dzi', 'Duzib212G0930' => 'dzi', 'ECA234G1645' => 'eca', 'ECA247G3467' => 'eca', 'ECA248G1703' => 'eca', 'EL10Ac3g06327' => 'bvu', 'EL10Ac7g17204' => 'bvu', 'Eucgr.A00855' => 'egr', 'Eucgr.A00858' => 'egr', 'Eucgr.H01520' => 'egr', 'Eucgr.H03604' => 'egr', 'Eucgr.L03465' => 'egr', 'Eucgr.L03466' => 'egr', 'FAN01G0988' => 'fan', 'FAN02G3892' => 'fan', 'FAN05G3381' => 'fan', 'FAN07G0967' => 'fan', 'FAN07G1493' => 'fan', 'FAN08G3125' => 'fan', 'FAN09G0402' => 'fan', 'FAN12G2594' => 'fan', 'FAN12G3879' => 'fan', 'FAN14G1546' => 'fan', 'FAN15G3626' => 'fan', 'FAN17G0588' => 'fan', 'FAN17G0609' => 'fan', 'FAN18G2817' => 'fan', 'FAN19G1305' => 'fan', 'FAN20G1787' => 'fan', 'FAN22G0073' => 'fan', 'FAN22G0352' => 'fan', 'FAN22G0368' => 'fan', 'FAN22G2273' => 'fan', 'FAN24G1998' => 'fan', 'FAN27G1317' => 'fan', 'FvH4_2g23980' => 'fve', 'FvH4_4g14380' => 'fve', 'FvH4_4g14390' => 'fve', 'FvH4_6g09250' => 'fve', 'Glyma.03G151100' => 'gma', 'Glyma.04G122550' => 'gma', 'Glyma.05G001600' => 'gma', 'Glyma.09G270766' => 'gma', 'Glyma.09G270832' => 'gma', 'Glyma.13G209800' => 'gma', 'Glyma.15G102800' => 'gma', 'Glyma.18G218900' => 'gma', 'Glyma.19G001500' => 'gma', 'Glyma.19G153600' => 'gma', 'Gohir.A02G028600' => 'ghi', 'Gohir.A08G045000' => 'ghi', 'Gohir.A11G120500' => 'ghi', 'Gohir.A12G006200' => 'ghi', 'Gohir.A12G006250' => 'ghi', 'Gohir.D02G036300' => 'ghi', 'Gohir.D08G054700' => 'ghi', 'Gohir.D11G125600' => 'ghi', 'Gohir.D12G005700' => 'ghi', 'Gorai.004G055200' => 'gra', 'Gorai.005G040400' => 'gra', 'Gorai.007G134500' => 'gra', 'Gorai.008G005500' => 'gra', 'GSVIVG01011094001' => 'vvi', 'GSVIVG01017879001' => 'vvi', 'GSVIVG01025988001' => 'vvi', 'GSVIVG01029847001' => 'vvi', 'HanXRQChr10g0282901' => 'han', 'HanXRQChr10g0310371' => 'han', 'HanXRQChr10g0315041' => 'han', 'HanXRQChr11g0327651' => 'han', 'HanXRQChr12g0359391' => 'han', 'Haze_00972' => 'cav', 'Haze_00973' => 'cav', 'Haze_00974' => 'cav', 'Haze_04747' => 'cav', 'Haze_04749' => 'cav', 'Haze_04750' => 'cav', 'Haze_21217' => 'cav', 'Hma1.2p1_1037F.1_g250680' => 'hma', 'Hma1.2p1_1644F.1_g295320' => 'hma', 'HPP92_011322' => 'vpl', 'HPP92_011323' => 'vpl', 'HPP92_011324' => 'vpl', 'HPP92_011325' => 'vpl', 'HPP92_011326' => 'vpl', 'Hund12205' => 'sun', 'Hund17957' => 'sun', 'Lalb_Chr06g0176771' => 'lal', 'Lalb_Chr18g0056021' => 'lal', 'Lalb_Chr18g0056031' => 'lal', 'Lalb_Chr18g0056041' => 'lal', 'Lalb_Chr20g0107751' => 'lal', 'Lalb_Chr20g0118371' => 'lal', 'Lj1g0010239' => 'lja', 'Lj1g0017101' => 'lja', 'Lj2A1178G40' => 'lonja', 'Lj2A54G84' => 'lonja', 'Lj2g0015248' => 'lja', 'Lj3A761T51' => 'lonja', 'Lj6g0018116' => 'lja', 'Lsat_1_v5_gn_4_136040' => 'lsa', 'Lsat_1_v5_gn_5_187461' => 'lsa', 'Lsat_1_v5_gn_5_77001' => 'lsa', 'Lsat_1_v5_gn_9_4461' => 'lsa', 'Manes.01G210100' => 'mes', 'Manes.03G185600' => 'mes', 'Manes.05G073300' => 'mes', 'Manes.09G120300' => 'mes', 'Manes.15G022100' => 'mes', 'Mapoly0096s0053' => 'mpo', 'MBI03_g14058_MAGBIO' => 'mbi', 'MBI03_g33876_MAGBIO' => 'mbi', 'MBI03_g36854_MAGBIO' => 'mbi', 'MBI17_g11997_MAGBIO' => 'mbi', 'MD03G1269000' => 'mdo', 'MD04G1179600' => 'mdo', 'MD11G1289800' => 'mdo', 'MD12G1194700' => 'mdo', 'MD13G1182100' => 'mdo', 'MD13G1182200' => 'mdo', 'MD16G1182600' => 'mdo', 'Medtr2g021400' => 'mtr', 'Medtr2g021470' => 'mtr', 'Medtr2g105810' => 'mtr', 'Medtr3g033580' => 'mtr', 'Medtr6g007970' => 'mtr', 'Medtr7g056330' => 'mtr', 'Medtr7g074290' => 'mtr', 'Medtr7g074380' => 'mtr', 'Medtr7g094550' => 'mtr', 'Medtr8g069995' => 'mtr', 'MELO3C014345.2' => 'cme', 'MELO3C021395.2' => 'cme', 'Migut.D00262' => 'egut', 'Migut.G00257' => 'egut', 'MSTRG.21575' => 'ama', 'MSTRG.3985' => 'ama', 'Nitab4.5_0000295g0140' => 'nta', 'Nitab4.5_0000732g0140' => 'nta', 'Nitab4.5_0003162g0020' => 'nta', 'Nitab4.5_0006180g0090' => 'nta', 'Nitab4.5_0006390g0010' => 'nta', 'Nitab4.5_0007392g0040' => 'nta', 'Nn1g02140' => 'nnu', 'Nn4g26168' => 'nnu', 'Nn5g26754' => 'nnu', 'Oeu001433.1' => 'oeu', 'Oeu010299.2' => 'oeu', 'Oeu011171.1' => 'oeu', 'Oeu037675.1' => 'oeu', 'Oeu038359.1' => 'oeu', 'Oeu063834.1' => 'oeu', 'Oeu063835.1' => 'oeu', 'Os05g0312000' => 'osa', 'Os07g0211101' => 'osa', 'Os07g0211200' => 'osa', 'Os07g0681500' => 'osa', 'Peaxi162Scf00095g01015' => 'pax', 'Peaxi162Scf00104g00329' => 'pax', 'Peaxi162Scf00161g00137' => 'pax', 'PGR004G1665' => 'pgr', 'PGR031G2937' => 'pgr', 'PGR119G2145' => 'pgr', 'PGSC0003DMG400004351' => 'stu', 'PGSC0003DMG400014625' => 'stu', 'PGSC0003DMG401000943' => 'stu', 'Phvul.001G148600' => 'pvu', 'Phvul.004G001700' => 'pvu', 'Phvul.006G154900' => 'pvu', 'Phvul.008G078200' => 'pvu', 'Phvul.011G136500' => 'pvu', 'Potri.002G215600' => 'ptr', 'Potri.008G201600' => 'ptr', 'Potri.014G138400' => 'ptr', 'Potri.016G142500' => 'ptr', 'Pp3c16_10580' => 'ppa', 'Pp3c5_25280' => 'ppa', 'Prupe.1G150000' => 'ppe', 'Prupe.1G150100' => 'ppe', 'Prupe.6G299600' => 'ppe', 'Prupe.8G245000' => 'ppe', 'Psat0s4927g0040' => 'psa', 'Psat1g052080' => 'psa', 'Psat1g183800' => 'psa', 'Psat3g113840' => 'psa', 'Psat3g126120' => 'psa', 'Psat3g126160' => 'psa', 'Psat3g158760' => 'psa', 'Psat3g158840' => 'psa', 'PSO170G2858' => 'pso', 'PSO339G0606' => 'pso', 'PSO384G4709' => 'pso', 'PSO407G0334' => 'pso', 'QL04p040276' => 'qlo', 'QL06p005458' => 'qlo', 'QL06p005472' => 'qlo', 'QL07p030546' => 'qlo', 'QL07p031519' => 'qlo', 'QL09p050949' => 'qlo', 'QL09p050966' => 'qlo', 'QL09p051067' => 'qlo', 'QL12p022706' => 'qlo', 'RcHm_v2.0_Chr2g0119601' => 'rch', 'RcHm_v2.0_Chr3g0459591' => 'rch', 'RcHm_v2.0_Chr4g0418521' => 'rch', 'RcHm_v2.0_Chr4g0418531' => 'rch', 'RcHm_v2.0_Chr4g0418541' => 'rch', 'RcHm_v2.0_Chr6g0291641' => 'rch', 'Rhsim01G0086300' => 'rsi', 'Rhsim01G0276300' => 'rsi', 'Rhsim01G0276500' => 'rsi', 'Rhsim04G0207700' => 'rsi', 'Rhsim05G0234500' => 'rsi', 'Rhsim13G0022400' => 'rsi', 'Sabra02G0167900' => 'sbr', 'Sabra04G0158500' => 'sbr', 'Sabra08G0159800' => 'sbr', 'Sabra10G0011500' => 'sbr', 'Sabra14G0104400' => 'sbr', 'SalBow2G2440' => 'sbo', 'SalBow4G2265' => 'sbo', 'Sc02g0000060' => 'sci', 'Sc05g0005020' => 'sci', 'Sc13g0003890' => 'sci', 'Sed0014865' => 'sed', 'Sed0017224' => 'sed', 'Sed0026391' => 'sed', 'SEGI_00063' => 'sgi', 'SEGI_10967' => 'sgi', 'SEGI_17510' => 'sgi', 'SEGI_24396' => 'sgi', 'SEGI_39719' => 'sgi', 'SEGI_41392' => 'sgi', 'SGA_v2.0_scaffold11G05794' => 'sas', 'SGA_v2.0_scaffold142G35607' => 'sas', 'SGA_v2.0_scaffold1G00447' => 'sas', 'SHI15388' => 'shi', 'SHI15394' => 'shi', 'SHI15396' => 'shi', 'SHI15399' => 'shi', 'SMO343G0151' => 'smo', 'SMO367G1118' => 'smo', 'Solyc01g080200.3' => 'sly', 'Solyc06g008960.3' => 'sly', 'Solyc09g064780.3' => 'sly', 'Sopen01g031980' => 'spe', 'Sopen06g003710' => 'spe', 'Sopen09g026460' => 'spe', 'Sp3g21240' => 'spa', 'Sp4g30030' => 'spa', 'TAR365G0022' => 'tar', 'TAR365G1023' => 'tar', 'TAR365G1253' => 'tar', 'TAR623G0078' => 'tar', 'TAR623G1721' => 'tar', 'TAR633G0959' => 'tar', 'THA.LOC104802225' => 'tha', 'THA.LOC104804769' => 'tha', 'THA.LOC104808660' => 'tha', 'THA.LOC104812792' => 'tha', 'Thecc.01G284000' => 'tca', 'Thecc.04G220600' => 'tca', 'Thecc.05G268900' => 'tca', 'Thecc.08G171100' => 'tca', 'Thhalv10001284m.g' => 'esa', 'Thhalv10019912m.g' => 'esa', 'TPR.G14189' => 'tpr', 'TPR.G18110' => 'tpr', 'TPR.G18130' => 'tpr', 'TPR.G18131' => 'tpr', 'TPR.G18140' => 'tpr', 'TPR.G24282' => 'tpr', 'TPR.G25221' => 'tpr', 'TPR.G29267' => 'tpr', 'TPR.G35315' => 'tpr', 'TPR.G36173' => 'tpr', 'TWI09G0794' => 'twi', 'TWI59G1348' => 'twi', 'TWI74G0430' => 'twi', 'unitig_26.g8940' => 'ugi', 'unitig_749.g13744' => 'ugi', 'unitig_749.g13745' => 'ugi', 'vmacro08269' => 'vma', 'vmacro14937' => 'vma', 'vmacro20401' => 'vma', 'VMungo0464G1349' => 'vmu', 'VMungo0540G0289' => 'vmu', 'VMungo1215G1590' => 'vmu', 'VMungo1309G0221' => 'vmu', 'VMungo1309G2815' => 'vmu', 'VMungo1383G0239' => 'vmu', 'VMungo1383G2910' => 'vmu', 'Zm00001eb095270' => 'zma', 'Zm00001eb095280' => 'zma', 'Zm00001eb111630' => 'zma', 'Zm00001eb237080' => 'zma', 'Zm00001eb273740' => 'zma', 'Zm00001eb285040' => 'zma', 'Zm00001eb330790' => 'zma', 'Zm00001eb337380' => 'zma' ) $gf_id = 'HOM05D001484' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001484' ) $data_identifier = 'HOM05D001484' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 2, 'aly' => (int) 2, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 22, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 7, 'hma' => (int) 2, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 7, 'mtr' => (int) 10, 'cme' => (int) 2, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 4, 'ppa' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 4, 'qlo' => (int) 9, 'rch' => (int) 6, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 10, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 7, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb337380' $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' => 'HOM05D001484', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p31500' => 'bna', 'A05p00020' => 'bna', 'A07p08820' => 'bna', 'Aa31LG4G3300' => 'aar', 'Aa31LG8G10030' => 'aar', 'Actinidia00731' => 'ach', 'Actinidia11473' => 'ach', 'Actinidia23469' => 'ach', 'Actinidia24318' => 'ach', 'Actinidia40196' => 'ach', 'Actinidia40197' => 'ach', 'Actinidia40198' => 'ach', 'Ah.08g212990' => 'amhyb', 'Ah.15g091720' => 'amhyb', 'AL3G38260' => 'aly', 'AL4G47710' => 'aly', 'Aqoxy2G00671' => 'aox', 'Aqoxy2G03236' => 'aox', 'arahy.Tifrunner.gnm1.ann1.05IDCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KR684' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATY3SJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK6QJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6APGL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IDT7Z9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM073U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ0R87' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LE7RV4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT4QRX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V5ENPK' => 'arhy', 'AT2G48110' => 'ath', 'AT3G23590' => 'ath', 'ATR0626G186' => 'atr', 'ATR1127G141' => 'atr', 'Atru.chr4.2583' => 'acertr', 'Atru.chr5.1358' => 'acertr', 'Atru.chr5.1359' => 'acertr', 'Atru.chr8.46' => 'acertr', 'AUR62002640' => 'cqu', 'AUR62030055' => 'cqu', 'AUR62033713' => 'cqu', 'AUR62033714' => 'cqu', 'AUR62036795' => 'cqu', 'AUR62039891' => 'cqu', 'BcaB02g08737' => 'bca', 'BcaB04g20441' => 'bca', 'BcaB06g26509' => 'bca', 'BcaB06g26510' => 'bca', 'BcaB06g26511' => 'bca', 'BcaB06g26512' => 'bca', 'BcaB06g26513' => 'bca', 'BcaC02g12564' => 'bca', 'BcaC02g12565' => 'bca', 'BcaC02g12794' => 'bca', 'BcaC02g12795' => 'bca', 'BcaC02g12796' => 'bca', 'BcaC06g35541' => 'bca', 'BNapus_Darmor_BZH_scaffold_188p00080' => 'bna', 'BNapus_Darmor_BZH_scaffold_188p00090' => 'bna', 'BolC1t03972H' => 'bol', 'BolC1t03973H' => 'bol', 'BolC4t21680H' => 'bol', 'BolC7t41863H' => 'bol', 'BolSC55t61227H' => 'bol', 'BolSC55t61228H' => 'bol', 'BraA01t03278Z' => 'bra', 'BraA05t18998Z' => 'bra', 'BraA07t28673Z' => 'bra', 'C01p40150' => 'bna', 'C05p12370' => 'bna', 'C07p13680' => 'bna', 'CAN.G1006.16' => 'can', 'CAN.G1006.17' => 'can', 'CAN.G1170.2' => 'can', 'CAN.G962.7' => 'can', 'CANSAT25G2179' => 'cansat', 'CANSAT78G1573' => 'cansat', 'CARHR099510' => 'chi', 'CARHR143510' => 'chi', 'Carub.0003s2380' => 'cru', 'Carub.0004s3082' => 'cru', 'Ca_00614_v3' => 'car', 'Ca_07801_v3' => 'car', 'Ca_08567_v3' => 'car', 'Ca_09571_v3' => 'car', 'CBR_g19290' => 'cbr', 'Cc01_g19770' => 'ccan', 'Cc03_g03030' => 'ccan', 'CDE07G0968' => 'cde', 'CDE09G1441' => 'cde', 'Cfa006103' => 'cfa', 'Cfa015573' => 'cfa', 'Cfa016988' => 'cfa', 'Ciclev10006738m.g' => 'ccl', 'Ciclev10010920m.g' => 'ccl', 'Ciclev10018517m.g' => 'ccl', 'CiPaw.01G159200' => 'cil', 'CiPaw.02G091000' => 'cil', 'CiPaw.02G091100' => 'cil', 'CiPaw.08G103100' => 'cil', 'CiPaw.09G224900' => 'cil', 'ClCG06G005740' => 'cla', 'ClCG07G000090' => 'cla', 'ClCG07G000100' => 'cla', 'COL.COLO4_09143' => 'col', 'COL.COLO4_25124' => 'col', 'Cpa.g.sc16.34' => 'cpa', 'Cpa.g.sc3504.1' => 'cpa', 'Cpa.g.sc60.37' => 'cpa', 'CsaV3_6G018520' => 'csa', 'CsaV3_6G036860' => 'csa', 'CSS0001072' => 'camsi', 'CSS0020208' => 'camsi', 'CSS0021253' => 'camsi', 'CSS0022190' => 'camsi', 'CSS0036150' => 'camsi', 'CSS0040442' => 'camsi', 'CSS0042300' => 'camsi', 'CSS0045298' => 'camsi', 'DCAR_012449' => 'dca', 'DCAR_018405' => 'dca', 'DCAR_024573' => 'dca', 'DCAR_030591' => 'dca', 'Dinv16926' => 'din', 'Dinv32963' => 'din', 'Dinv38382' => 'din', 'Dinv38383' => 'din', 'Duzib133G0974' => 'dzi', 'Duzib138G1867' => 'dzi', 'Duzib211G0420' => 'dzi', 'Duzib212G0930' => 'dzi', 'ECA234G1645' => 'eca', 'ECA247G3467' => 'eca', 'ECA248G1703' => 'eca', 'EL10Ac3g06327' => 'bvu', 'EL10Ac7g17204' => 'bvu', 'Eucgr.A00855' => 'egr', 'Eucgr.A00858' => 'egr', 'Eucgr.H01520' => 'egr', 'Eucgr.H03604' => 'egr', 'Eucgr.L03465' => 'egr', 'Eucgr.L03466' => 'egr', 'FAN01G0988' => 'fan', 'FAN02G3892' => 'fan', 'FAN05G3381' => 'fan', 'FAN07G0967' => 'fan', 'FAN07G1493' => 'fan', 'FAN08G3125' => 'fan', 'FAN09G0402' => 'fan', 'FAN12G2594' => 'fan', 'FAN12G3879' => 'fan', 'FAN14G1546' => 'fan', 'FAN15G3626' => 'fan', 'FAN17G0588' => 'fan', 'FAN17G0609' => 'fan', 'FAN18G2817' => 'fan', 'FAN19G1305' => 'fan', 'FAN20G1787' => 'fan', 'FAN22G0073' => 'fan', 'FAN22G0352' => 'fan', 'FAN22G0368' => 'fan', 'FAN22G2273' => 'fan', 'FAN24G1998' => 'fan', 'FAN27G1317' => 'fan', 'FvH4_2g23980' => 'fve', 'FvH4_4g14380' => 'fve', 'FvH4_4g14390' => 'fve', 'FvH4_6g09250' => 'fve', 'Glyma.03G151100' => 'gma', 'Glyma.04G122550' => 'gma', 'Glyma.05G001600' => 'gma', 'Glyma.09G270766' => 'gma', 'Glyma.09G270832' => 'gma', 'Glyma.13G209800' => 'gma', 'Glyma.15G102800' => 'gma', 'Glyma.18G218900' => 'gma', 'Glyma.19G001500' => 'gma', 'Glyma.19G153600' => 'gma', 'Gohir.A02G028600' => 'ghi', 'Gohir.A08G045000' => 'ghi', 'Gohir.A11G120500' => 'ghi', 'Gohir.A12G006200' => 'ghi', 'Gohir.A12G006250' => 'ghi', 'Gohir.D02G036300' => 'ghi', 'Gohir.D08G054700' => 'ghi', 'Gohir.D11G125600' => 'ghi', 'Gohir.D12G005700' => 'ghi', 'Gorai.004G055200' => 'gra', 'Gorai.005G040400' => 'gra', 'Gorai.007G134500' => 'gra', 'Gorai.008G005500' => 'gra', 'GSVIVG01011094001' => 'vvi', 'GSVIVG01017879001' => 'vvi', 'GSVIVG01025988001' => 'vvi', 'GSVIVG01029847001' => 'vvi', 'HanXRQChr10g0282901' => 'han', 'HanXRQChr10g0310371' => 'han', 'HanXRQChr10g0315041' => 'han', 'HanXRQChr11g0327651' => 'han', 'HanXRQChr12g0359391' => 'han', 'Haze_00972' => 'cav', 'Haze_00973' => 'cav', 'Haze_00974' => 'cav', 'Haze_04747' => 'cav', 'Haze_04749' => 'cav', 'Haze_04750' => 'cav', 'Haze_21217' => 'cav', 'Hma1.2p1_1037F.1_g250680' => 'hma', 'Hma1.2p1_1644F.1_g295320' => 'hma', 'HPP92_011322' => 'vpl', 'HPP92_011323' => 'vpl', 'HPP92_011324' => 'vpl', 'HPP92_011325' => 'vpl', 'HPP92_011326' => 'vpl', 'Hund12205' => 'sun', 'Hund17957' => 'sun', 'Lalb_Chr06g0176771' => 'lal', 'Lalb_Chr18g0056021' => 'lal', 'Lalb_Chr18g0056031' => 'lal', 'Lalb_Chr18g0056041' => 'lal', 'Lalb_Chr20g0107751' => 'lal', 'Lalb_Chr20g0118371' => 'lal', 'Lj1g0010239' => 'lja', 'Lj1g0017101' => 'lja', 'Lj2A1178G40' => 'lonja', 'Lj2A54G84' => 'lonja', 'Lj2g0015248' => 'lja', 'Lj3A761T51' => 'lonja', 'Lj6g0018116' => 'lja', 'Lsat_1_v5_gn_4_136040' => 'lsa', 'Lsat_1_v5_gn_5_187461' => 'lsa', 'Lsat_1_v5_gn_5_77001' => 'lsa', 'Lsat_1_v5_gn_9_4461' => 'lsa', 'Manes.01G210100' => 'mes', 'Manes.03G185600' => 'mes', 'Manes.05G073300' => 'mes', 'Manes.09G120300' => 'mes', 'Manes.15G022100' => 'mes', 'Mapoly0096s0053' => 'mpo', 'MBI03_g14058_MAGBIO' => 'mbi', 'MBI03_g33876_MAGBIO' => 'mbi', 'MBI03_g36854_MAGBIO' => 'mbi', 'MBI17_g11997_MAGBIO' => 'mbi', 'MD03G1269000' => 'mdo', 'MD04G1179600' => 'mdo', 'MD11G1289800' => 'mdo', 'MD12G1194700' => 'mdo', 'MD13G1182100' => 'mdo', 'MD13G1182200' => 'mdo', 'MD16G1182600' => 'mdo', 'Medtr2g021400' => 'mtr', 'Medtr2g021470' => 'mtr', 'Medtr2g105810' => 'mtr', 'Medtr3g033580' => 'mtr', 'Medtr6g007970' => 'mtr', 'Medtr7g056330' => 'mtr', 'Medtr7g074290' => 'mtr', 'Medtr7g074380' => 'mtr', 'Medtr7g094550' => 'mtr', 'Medtr8g069995' => 'mtr', 'MELO3C014345.2' => 'cme', 'MELO3C021395.2' => 'cme', 'Migut.D00262' => 'egut', 'Migut.G00257' => 'egut', 'MSTRG.21575' => 'ama', 'MSTRG.3985' => 'ama', 'Nitab4.5_0000295g0140' => 'nta', 'Nitab4.5_0000732g0140' => 'nta', 'Nitab4.5_0003162g0020' => 'nta', 'Nitab4.5_0006180g0090' => 'nta', 'Nitab4.5_0006390g0010' => 'nta', 'Nitab4.5_0007392g0040' => 'nta', 'Nn1g02140' => 'nnu', 'Nn4g26168' => 'nnu', 'Nn5g26754' => 'nnu', 'Oeu001433.1' => 'oeu', 'Oeu010299.2' => 'oeu', 'Oeu011171.1' => 'oeu', 'Oeu037675.1' => 'oeu', 'Oeu038359.1' => 'oeu', 'Oeu063834.1' => 'oeu', 'Oeu063835.1' => 'oeu', 'Os05g0312000' => 'osa', 'Os07g0211101' => 'osa', 'Os07g0211200' => 'osa', 'Os07g0681500' => 'osa', 'Peaxi162Scf00095g01015' => 'pax', 'Peaxi162Scf00104g00329' => 'pax', 'Peaxi162Scf00161g00137' => 'pax', 'PGR004G1665' => 'pgr', 'PGR031G2937' => 'pgr', 'PGR119G2145' => 'pgr', 'PGSC0003DMG400004351' => 'stu', 'PGSC0003DMG400014625' => 'stu', 'PGSC0003DMG401000943' => 'stu', 'Phvul.001G148600' => 'pvu', 'Phvul.004G001700' => 'pvu', 'Phvul.006G154900' => 'pvu', 'Phvul.008G078200' => 'pvu', 'Phvul.011G136500' => 'pvu', 'Potri.002G215600' => 'ptr', 'Potri.008G201600' => 'ptr', 'Potri.014G138400' => 'ptr', 'Potri.016G142500' => 'ptr', 'Pp3c16_10580' => 'ppa', 'Pp3c5_25280' => 'ppa', 'Prupe.1G150000' => 'ppe', 'Prupe.1G150100' => 'ppe', 'Prupe.6G299600' => 'ppe', 'Prupe.8G245000' => 'ppe', 'Psat0s4927g0040' => 'psa', 'Psat1g052080' => 'psa', 'Psat1g183800' => 'psa', 'Psat3g113840' => 'psa', 'Psat3g126120' => 'psa', 'Psat3g126160' => 'psa', 'Psat3g158760' => 'psa', 'Psat3g158840' => 'psa', 'PSO170G2858' => 'pso', 'PSO339G0606' => 'pso', 'PSO384G4709' => 'pso', 'PSO407G0334' => 'pso', 'QL04p040276' => 'qlo', 'QL06p005458' => 'qlo', 'QL06p005472' => 'qlo', 'QL07p030546' => 'qlo', 'QL07p031519' => 'qlo', 'QL09p050949' => 'qlo', 'QL09p050966' => 'qlo', 'QL09p051067' => 'qlo', 'QL12p022706' => 'qlo', 'RcHm_v2.0_Chr2g0119601' => 'rch', 'RcHm_v2.0_Chr3g0459591' => 'rch', 'RcHm_v2.0_Chr4g0418521' => 'rch', 'RcHm_v2.0_Chr4g0418531' => 'rch', 'RcHm_v2.0_Chr4g0418541' => 'rch', 'RcHm_v2.0_Chr6g0291641' => 'rch', 'Rhsim01G0086300' => 'rsi', 'Rhsim01G0276300' => 'rsi', 'Rhsim01G0276500' => 'rsi', 'Rhsim04G0207700' => 'rsi', 'Rhsim05G0234500' => 'rsi', 'Rhsim13G0022400' => 'rsi', 'Sabra02G0167900' => 'sbr', 'Sabra04G0158500' => 'sbr', 'Sabra08G0159800' => 'sbr', 'Sabra10G0011500' => 'sbr', 'Sabra14G0104400' => 'sbr', 'SalBow2G2440' => 'sbo', 'SalBow4G2265' => 'sbo', 'Sc02g0000060' => 'sci', 'Sc05g0005020' => 'sci', 'Sc13g0003890' => 'sci', 'Sed0014865' => 'sed', 'Sed0017224' => 'sed', 'Sed0026391' => 'sed', 'SEGI_00063' => 'sgi', 'SEGI_10967' => 'sgi', 'SEGI_17510' => 'sgi', 'SEGI_24396' => 'sgi', 'SEGI_39719' => 'sgi', 'SEGI_41392' => 'sgi', 'SGA_v2.0_scaffold11G05794' => 'sas', 'SGA_v2.0_scaffold142G35607' => 'sas', 'SGA_v2.0_scaffold1G00447' => 'sas', 'SHI15388' => 'shi', 'SHI15394' => 'shi', 'SHI15396' => 'shi', 'SHI15399' => 'shi', 'SMO343G0151' => 'smo', 'SMO367G1118' => 'smo', 'Solyc01g080200.3' => 'sly', 'Solyc06g008960.3' => 'sly', 'Solyc09g064780.3' => 'sly', 'Sopen01g031980' => 'spe', 'Sopen06g003710' => 'spe', 'Sopen09g026460' => 'spe', 'Sp3g21240' => 'spa', 'Sp4g30030' => 'spa', 'TAR365G0022' => 'tar', 'TAR365G1023' => 'tar', 'TAR365G1253' => 'tar', 'TAR623G0078' => 'tar', 'TAR623G1721' => 'tar', 'TAR633G0959' => 'tar', 'THA.LOC104802225' => 'tha', 'THA.LOC104804769' => 'tha', 'THA.LOC104808660' => 'tha', 'THA.LOC104812792' => 'tha', 'Thecc.01G284000' => 'tca', 'Thecc.04G220600' => 'tca', 'Thecc.05G268900' => 'tca', 'Thecc.08G171100' => 'tca', 'Thhalv10001284m.g' => 'esa', 'Thhalv10019912m.g' => 'esa', 'TPR.G14189' => 'tpr', 'TPR.G18110' => 'tpr', 'TPR.G18130' => 'tpr', 'TPR.G18131' => 'tpr', 'TPR.G18140' => 'tpr', 'TPR.G24282' => 'tpr', 'TPR.G25221' => 'tpr', 'TPR.G29267' => 'tpr', 'TPR.G35315' => 'tpr', 'TPR.G36173' => 'tpr', 'TWI09G0794' => 'twi', 'TWI59G1348' => 'twi', 'TWI74G0430' => 'twi', 'unitig_26.g8940' => 'ugi', 'unitig_749.g13744' => 'ugi', 'unitig_749.g13745' => 'ugi', 'vmacro08269' => 'vma', 'vmacro14937' => 'vma', 'vmacro20401' => 'vma', 'VMungo0464G1349' => 'vmu', 'VMungo0540G0289' => 'vmu', 'VMungo1215G1590' => 'vmu', 'VMungo1309G0221' => 'vmu', 'VMungo1309G2815' => 'vmu', 'VMungo1383G0239' => 'vmu', 'VMungo1383G2910' => 'vmu', 'Zm00001eb095270' => 'zma', 'Zm00001eb095280' => 'zma', 'Zm00001eb111630' => 'zma', 'Zm00001eb237080' => 'zma', 'Zm00001eb273740' => 'zma', 'Zm00001eb285040' => 'zma', 'Zm00001eb330790' => 'zma', 'Zm00001eb337380' => 'zma' ), 'gf_id' => 'HOM05D001484', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001484' ), 'data_identifier' => 'HOM05D001484', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001484', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p31500' => 'bna', 'A05p00020' => 'bna', 'A07p08820' => 'bna', 'Aa31LG4G3300' => 'aar', 'Aa31LG8G10030' => 'aar', 'Actinidia00731' => 'ach', 'Actinidia11473' => 'ach', 'Actinidia23469' => 'ach', 'Actinidia24318' => 'ach', 'Actinidia40196' => 'ach', 'Actinidia40197' => 'ach', 'Actinidia40198' => 'ach', 'Ah.08g212990' => 'amhyb', 'Ah.15g091720' => 'amhyb', 'AL3G38260' => 'aly', 'AL4G47710' => 'aly', 'Aqoxy2G00671' => 'aox', 'Aqoxy2G03236' => 'aox', 'arahy.Tifrunner.gnm1.ann1.05IDCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KR684' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATY3SJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK6QJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6APGL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IDT7Z9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM073U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ0R87' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LE7RV4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT4QRX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V5ENPK' => 'arhy', 'AT2G48110' => 'ath', 'AT3G23590' => 'ath', 'ATR0626G186' => 'atr', 'ATR1127G141' => 'atr', 'Atru.chr4.2583' => 'acertr', 'Atru.chr5.1358' => 'acertr', 'Atru.chr5.1359' => 'acertr', 'Atru.chr8.46' => 'acertr', 'AUR62002640' => 'cqu', 'AUR62030055' => 'cqu', 'AUR62033713' => 'cqu', 'AUR62033714' => 'cqu', 'AUR62036795' => 'cqu', 'AUR62039891' => 'cqu', 'BcaB02g08737' => 'bca', 'BcaB04g20441' => 'bca', 'BcaB06g26509' => 'bca', 'BcaB06g26510' => 'bca', 'BcaB06g26511' => 'bca', 'BcaB06g26512' => 'bca', 'BcaB06g26513' => 'bca', 'BcaC02g12564' => 'bca', 'BcaC02g12565' => 'bca', 'BcaC02g12794' => 'bca', 'BcaC02g12795' => 'bca', 'BcaC02g12796' => 'bca', 'BcaC06g35541' => 'bca', 'BNapus_Darmor_BZH_scaffold_188p00080' => 'bna', 'BNapus_Darmor_BZH_scaffold_188p00090' => 'bna', 'BolC1t03972H' => 'bol', 'BolC1t03973H' => 'bol', 'BolC4t21680H' => 'bol', 'BolC7t41863H' => 'bol', 'BolSC55t61227H' => 'bol', 'BolSC55t61228H' => 'bol', 'BraA01t03278Z' => 'bra', 'BraA05t18998Z' => 'bra', 'BraA07t28673Z' => 'bra', 'C01p40150' => 'bna', 'C05p12370' => 'bna', 'C07p13680' => 'bna', 'CAN.G1006.16' => 'can', 'CAN.G1006.17' => 'can', 'CAN.G1170.2' => 'can', 'CAN.G962.7' => 'can', 'CANSAT25G2179' => 'cansat', 'CANSAT78G1573' => 'cansat', 'CARHR099510' => 'chi', 'CARHR143510' => 'chi', 'Carub.0003s2380' => 'cru', 'Carub.0004s3082' => 'cru', 'Ca_00614_v3' => 'car', 'Ca_07801_v3' => 'car', 'Ca_08567_v3' => 'car', 'Ca_09571_v3' => 'car', 'CBR_g19290' => 'cbr', 'Cc01_g19770' => 'ccan', 'Cc03_g03030' => 'ccan', 'CDE07G0968' => 'cde', 'CDE09G1441' => 'cde', 'Cfa006103' => 'cfa', 'Cfa015573' => 'cfa', 'Cfa016988' => 'cfa', 'Ciclev10006738m.g' => 'ccl', 'Ciclev10010920m.g' => 'ccl', 'Ciclev10018517m.g' => 'ccl', 'CiPaw.01G159200' => 'cil', 'CiPaw.02G091000' => 'cil', 'CiPaw.02G091100' => 'cil', 'CiPaw.08G103100' => 'cil', 'CiPaw.09G224900' => 'cil', 'ClCG06G005740' => 'cla', 'ClCG07G000090' => 'cla', 'ClCG07G000100' => 'cla', 'COL.COLO4_09143' => 'col', 'COL.COLO4_25124' => 'col', 'Cpa.g.sc16.34' => 'cpa', 'Cpa.g.sc3504.1' => 'cpa', 'Cpa.g.sc60.37' => 'cpa', 'CsaV3_6G018520' => 'csa', 'CsaV3_6G036860' => 'csa', 'CSS0001072' => 'camsi', 'CSS0020208' => 'camsi', 'CSS0021253' => 'camsi', 'CSS0022190' => 'camsi', 'CSS0036150' => 'camsi', 'CSS0040442' => 'camsi', 'CSS0042300' => 'camsi', 'CSS0045298' => 'camsi', 'DCAR_012449' => 'dca', 'DCAR_018405' => 'dca', 'DCAR_024573' => 'dca', 'DCAR_030591' => 'dca', 'Dinv16926' => 'din', 'Dinv32963' => 'din', 'Dinv38382' => 'din', 'Dinv38383' => 'din', 'Duzib133G0974' => 'dzi', 'Duzib138G1867' => 'dzi', 'Duzib211G0420' => 'dzi', 'Duzib212G0930' => 'dzi', 'ECA234G1645' => 'eca', 'ECA247G3467' => 'eca', 'ECA248G1703' => 'eca', 'EL10Ac3g06327' => 'bvu', 'EL10Ac7g17204' => 'bvu', 'Eucgr.A00855' => 'egr', 'Eucgr.A00858' => 'egr', 'Eucgr.H01520' => 'egr', 'Eucgr.H03604' => 'egr', 'Eucgr.L03465' => 'egr', 'Eucgr.L03466' => 'egr', 'FAN01G0988' => 'fan', 'FAN02G3892' => 'fan', 'FAN05G3381' => 'fan', 'FAN07G0967' => 'fan', 'FAN07G1493' => 'fan', 'FAN08G3125' => 'fan', 'FAN09G0402' => 'fan', 'FAN12G2594' => 'fan', 'FAN12G3879' => 'fan', 'FAN14G1546' => 'fan', 'FAN15G3626' => 'fan', 'FAN17G0588' => 'fan', 'FAN17G0609' => 'fan', 'FAN18G2817' => 'fan', 'FAN19G1305' => 'fan', 'FAN20G1787' => 'fan', 'FAN22G0073' => 'fan', 'FAN22G0352' => 'fan', 'FAN22G0368' => 'fan', 'FAN22G2273' => 'fan', 'FAN24G1998' => 'fan', 'FAN27G1317' => 'fan', 'FvH4_2g23980' => 'fve', 'FvH4_4g14380' => 'fve', 'FvH4_4g14390' => 'fve', 'FvH4_6g09250' => 'fve', 'Glyma.03G151100' => 'gma', 'Glyma.04G122550' => 'gma', 'Glyma.05G001600' => 'gma', 'Glyma.09G270766' => 'gma', 'Glyma.09G270832' => 'gma', 'Glyma.13G209800' => 'gma', 'Glyma.15G102800' => 'gma', 'Glyma.18G218900' => 'gma', 'Glyma.19G001500' => 'gma', 'Glyma.19G153600' => 'gma', 'Gohir.A02G028600' => 'ghi', 'Gohir.A08G045000' => 'ghi', 'Gohir.A11G120500' => 'ghi', 'Gohir.A12G006200' => 'ghi', 'Gohir.A12G006250' => 'ghi', 'Gohir.D02G036300' => 'ghi', 'Gohir.D08G054700' => 'ghi', 'Gohir.D11G125600' => 'ghi', 'Gohir.D12G005700' => 'ghi', 'Gorai.004G055200' => 'gra', 'Gorai.005G040400' => 'gra', 'Gorai.007G134500' => 'gra', 'Gorai.008G005500' => 'gra', 'GSVIVG01011094001' => 'vvi', 'GSVIVG01017879001' => 'vvi', 'GSVIVG01025988001' => 'vvi', 'GSVIVG01029847001' => 'vvi', 'HanXRQChr10g0282901' => 'han', 'HanXRQChr10g0310371' => 'han', 'HanXRQChr10g0315041' => 'han', 'HanXRQChr11g0327651' => 'han', 'HanXRQChr12g0359391' => 'han', 'Haze_00972' => 'cav', 'Haze_00973' => 'cav', 'Haze_00974' => 'cav', 'Haze_04747' => 'cav', 'Haze_04749' => 'cav', 'Haze_04750' => 'cav', 'Haze_21217' => 'cav', 'Hma1.2p1_1037F.1_g250680' => 'hma', 'Hma1.2p1_1644F.1_g295320' => 'hma', 'HPP92_011322' => 'vpl', 'HPP92_011323' => 'vpl', 'HPP92_011324' => 'vpl', 'HPP92_011325' => 'vpl', 'HPP92_011326' => 'vpl', 'Hund12205' => 'sun', 'Hund17957' => 'sun', 'Lalb_Chr06g0176771' => 'lal', 'Lalb_Chr18g0056021' => 'lal', 'Lalb_Chr18g0056031' => 'lal', 'Lalb_Chr18g0056041' => 'lal', 'Lalb_Chr20g0107751' => 'lal', 'Lalb_Chr20g0118371' => 'lal', 'Lj1g0010239' => 'lja', 'Lj1g0017101' => 'lja', 'Lj2A1178G40' => 'lonja', 'Lj2A54G84' => 'lonja', 'Lj2g0015248' => 'lja', 'Lj3A761T51' => 'lonja', 'Lj6g0018116' => 'lja', 'Lsat_1_v5_gn_4_136040' => 'lsa', 'Lsat_1_v5_gn_5_187461' => 'lsa', 'Lsat_1_v5_gn_5_77001' => 'lsa', 'Lsat_1_v5_gn_9_4461' => 'lsa', 'Manes.01G210100' => 'mes', 'Manes.03G185600' => 'mes', 'Manes.05G073300' => 'mes', 'Manes.09G120300' => 'mes', 'Manes.15G022100' => 'mes', 'Mapoly0096s0053' => 'mpo', 'MBI03_g14058_MAGBIO' => 'mbi', 'MBI03_g33876_MAGBIO' => 'mbi', 'MBI03_g36854_MAGBIO' => 'mbi', 'MBI17_g11997_MAGBIO' => 'mbi', 'MD03G1269000' => 'mdo', 'MD04G1179600' => 'mdo', 'MD11G1289800' => 'mdo', 'MD12G1194700' => 'mdo', 'MD13G1182100' => 'mdo', 'MD13G1182200' => 'mdo', 'MD16G1182600' => 'mdo', 'Medtr2g021400' => 'mtr', 'Medtr2g021470' => 'mtr', 'Medtr2g105810' => 'mtr', 'Medtr3g033580' => 'mtr', 'Medtr6g007970' => 'mtr', 'Medtr7g056330' => 'mtr', 'Medtr7g074290' => 'mtr', 'Medtr7g074380' => 'mtr', 'Medtr7g094550' => 'mtr', 'Medtr8g069995' => 'mtr', 'MELO3C014345.2' => 'cme', 'MELO3C021395.2' => 'cme', 'Migut.D00262' => 'egut', 'Migut.G00257' => 'egut', 'MSTRG.21575' => 'ama', 'MSTRG.3985' => 'ama', 'Nitab4.5_0000295g0140' => 'nta', 'Nitab4.5_0000732g0140' => 'nta', 'Nitab4.5_0003162g0020' => 'nta', 'Nitab4.5_0006180g0090' => 'nta', 'Nitab4.5_0006390g0010' => 'nta', 'Nitab4.5_0007392g0040' => 'nta', 'Nn1g02140' => 'nnu', 'Nn4g26168' => 'nnu', 'Nn5g26754' => 'nnu', 'Oeu001433.1' => 'oeu', 'Oeu010299.2' => 'oeu', 'Oeu011171.1' => 'oeu', 'Oeu037675.1' => 'oeu', 'Oeu038359.1' => 'oeu', 'Oeu063834.1' => 'oeu', 'Oeu063835.1' => 'oeu', 'Os05g0312000' => 'osa', 'Os07g0211101' => 'osa', 'Os07g0211200' => 'osa', 'Os07g0681500' => 'osa', 'Peaxi162Scf00095g01015' => 'pax', 'Peaxi162Scf00104g00329' => 'pax', 'Peaxi162Scf00161g00137' => 'pax', 'PGR004G1665' => 'pgr', 'PGR031G2937' => 'pgr', 'PGR119G2145' => 'pgr', 'PGSC0003DMG400004351' => 'stu', 'PGSC0003DMG400014625' => 'stu', 'PGSC0003DMG401000943' => 'stu', 'Phvul.001G148600' => 'pvu', 'Phvul.004G001700' => 'pvu', 'Phvul.006G154900' => 'pvu', 'Phvul.008G078200' => 'pvu', 'Phvul.011G136500' => 'pvu', 'Potri.002G215600' => 'ptr', 'Potri.008G201600' => 'ptr', 'Potri.014G138400' => 'ptr', 'Potri.016G142500' => 'ptr', 'Pp3c16_10580' => 'ppa', 'Pp3c5_25280' => 'ppa', 'Prupe.1G150000' => 'ppe', 'Prupe.1G150100' => 'ppe', 'Prupe.6G299600' => 'ppe', 'Prupe.8G245000' => 'ppe', 'Psat0s4927g0040' => 'psa', 'Psat1g052080' => 'psa', 'Psat1g183800' => 'psa', 'Psat3g113840' => 'psa', 'Psat3g126120' => 'psa', 'Psat3g126160' => 'psa', 'Psat3g158760' => 'psa', 'Psat3g158840' => 'psa', 'PSO170G2858' => 'pso', 'PSO339G0606' => 'pso', 'PSO384G4709' => 'pso', 'PSO407G0334' => 'pso', 'QL04p040276' => 'qlo', 'QL06p005458' => 'qlo', 'QL06p005472' => 'qlo', 'QL07p030546' => 'qlo', 'QL07p031519' => 'qlo', 'QL09p050949' => 'qlo', 'QL09p050966' => 'qlo', 'QL09p051067' => 'qlo', 'QL12p022706' => 'qlo', 'RcHm_v2.0_Chr2g0119601' => 'rch', 'RcHm_v2.0_Chr3g0459591' => 'rch', 'RcHm_v2.0_Chr4g0418521' => 'rch', 'RcHm_v2.0_Chr4g0418531' => 'rch', 'RcHm_v2.0_Chr4g0418541' => 'rch', 'RcHm_v2.0_Chr6g0291641' => 'rch', 'Rhsim01G0086300' => 'rsi', 'Rhsim01G0276300' => 'rsi', 'Rhsim01G0276500' => 'rsi', 'Rhsim04G0207700' => 'rsi', 'Rhsim05G0234500' => 'rsi', 'Rhsim13G0022400' => 'rsi', 'Sabra02G0167900' => 'sbr', 'Sabra04G0158500' => 'sbr', 'Sabra08G0159800' => 'sbr', 'Sabra10G0011500' => 'sbr', 'Sabra14G0104400' => 'sbr', 'SalBow2G2440' => 'sbo', 'SalBow4G2265' => 'sbo', 'Sc02g0000060' => 'sci', 'Sc05g0005020' => 'sci', 'Sc13g0003890' => 'sci', 'Sed0014865' => 'sed', 'Sed0017224' => 'sed', 'Sed0026391' => 'sed', 'SEGI_00063' => 'sgi', 'SEGI_10967' => 'sgi', 'SEGI_17510' => 'sgi', 'SEGI_24396' => 'sgi', 'SEGI_39719' => 'sgi', 'SEGI_41392' => 'sgi', 'SGA_v2.0_scaffold11G05794' => 'sas', 'SGA_v2.0_scaffold142G35607' => 'sas', 'SGA_v2.0_scaffold1G00447' => 'sas', 'SHI15388' => 'shi', 'SHI15394' => 'shi', 'SHI15396' => 'shi', 'SHI15399' => 'shi', 'SMO343G0151' => 'smo', 'SMO367G1118' => 'smo', 'Solyc01g080200.3' => 'sly', 'Solyc06g008960.3' => 'sly', 'Solyc09g064780.3' => 'sly', 'Sopen01g031980' => 'spe', 'Sopen06g003710' => 'spe', 'Sopen09g026460' => 'spe', 'Sp3g21240' => 'spa', 'Sp4g30030' => 'spa', 'TAR365G0022' => 'tar', 'TAR365G1023' => 'tar', 'TAR365G1253' => 'tar', 'TAR623G0078' => 'tar', 'TAR623G1721' => 'tar', 'TAR633G0959' => 'tar', 'THA.LOC104802225' => 'tha', 'THA.LOC104804769' => 'tha', 'THA.LOC104808660' => 'tha', 'THA.LOC104812792' => 'tha', 'Thecc.01G284000' => 'tca', 'Thecc.04G220600' => 'tca', 'Thecc.05G268900' => 'tca', 'Thecc.08G171100' => 'tca', 'Thhalv10001284m.g' => 'esa', 'Thhalv10019912m.g' => 'esa', 'TPR.G14189' => 'tpr', 'TPR.G18110' => 'tpr', 'TPR.G18130' => 'tpr', 'TPR.G18131' => 'tpr', 'TPR.G18140' => 'tpr', 'TPR.G24282' => 'tpr', 'TPR.G25221' => 'tpr', 'TPR.G29267' => 'tpr', 'TPR.G35315' => 'tpr', 'TPR.G36173' => 'tpr', 'TWI09G0794' => 'twi', 'TWI59G1348' => 'twi', 'TWI74G0430' => 'twi', 'unitig_26.g8940' => 'ugi', 'unitig_749.g13744' => 'ugi', 'unitig_749.g13745' => 'ugi', 'vmacro08269' => 'vma', 'vmacro14937' => 'vma', 'vmacro20401' => 'vma', 'VMungo0464G1349' => 'vmu', 'VMungo0540G0289' => 'vmu', 'VMungo1215G1590' => 'vmu', 'VMungo1309G0221' => 'vmu', 'VMungo1309G2815' => 'vmu', 'VMungo1383G0239' => 'vmu', 'VMungo1383G2910' => 'vmu', 'Zm00001eb095270' => 'zma', 'Zm00001eb095280' => 'zma', 'Zm00001eb111630' => 'zma', 'Zm00001eb237080' => 'zma', 'Zm00001eb273740' => 'zma', 'Zm00001eb285040' => 'zma', 'Zm00001eb330790' => 'zma', 'Zm00001eb337380' => 'zma' ) $gf_id = 'HOM05D001484' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001484' ) $data_identifier = 'HOM05D001484' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 2, 'aly' => (int) 2, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 22, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 7, 'hma' => (int) 2, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 7, 'mtr' => (int) 10, 'cme' => (int) 2, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 4, 'ppa' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 4, 'qlo' => (int) 9, 'rch' => (int) 6, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 10, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 7, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb337380' $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' => 'HOM05D001484', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p31500' => 'bna', 'A05p00020' => 'bna', 'A07p08820' => 'bna', 'Aa31LG4G3300' => 'aar', 'Aa31LG8G10030' => 'aar', 'Actinidia00731' => 'ach', 'Actinidia11473' => 'ach', 'Actinidia23469' => 'ach', 'Actinidia24318' => 'ach', 'Actinidia40196' => 'ach', 'Actinidia40197' => 'ach', 'Actinidia40198' => 'ach', 'Ah.08g212990' => 'amhyb', 'Ah.15g091720' => 'amhyb', 'AL3G38260' => 'aly', 'AL4G47710' => 'aly', 'Aqoxy2G00671' => 'aox', 'Aqoxy2G03236' => 'aox', 'arahy.Tifrunner.gnm1.ann1.05IDCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KR684' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATY3SJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK6QJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6APGL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IDT7Z9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM073U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ0R87' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LE7RV4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT4QRX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V5ENPK' => 'arhy', 'AT2G48110' => 'ath', 'AT3G23590' => 'ath', 'ATR0626G186' => 'atr', 'ATR1127G141' => 'atr', 'Atru.chr4.2583' => 'acertr', 'Atru.chr5.1358' => 'acertr', 'Atru.chr5.1359' => 'acertr', 'Atru.chr8.46' => 'acertr', 'AUR62002640' => 'cqu', 'AUR62030055' => 'cqu', 'AUR62033713' => 'cqu', 'AUR62033714' => 'cqu', 'AUR62036795' => 'cqu', 'AUR62039891' => 'cqu', 'BcaB02g08737' => 'bca', 'BcaB04g20441' => 'bca', 'BcaB06g26509' => 'bca', 'BcaB06g26510' => 'bca', 'BcaB06g26511' => 'bca', 'BcaB06g26512' => 'bca', 'BcaB06g26513' => 'bca', 'BcaC02g12564' => 'bca', 'BcaC02g12565' => 'bca', 'BcaC02g12794' => 'bca', 'BcaC02g12795' => 'bca', 'BcaC02g12796' => 'bca', 'BcaC06g35541' => 'bca', 'BNapus_Darmor_BZH_scaffold_188p00080' => 'bna', 'BNapus_Darmor_BZH_scaffold_188p00090' => 'bna', 'BolC1t03972H' => 'bol', 'BolC1t03973H' => 'bol', 'BolC4t21680H' => 'bol', 'BolC7t41863H' => 'bol', 'BolSC55t61227H' => 'bol', 'BolSC55t61228H' => 'bol', 'BraA01t03278Z' => 'bra', 'BraA05t18998Z' => 'bra', 'BraA07t28673Z' => 'bra', 'C01p40150' => 'bna', 'C05p12370' => 'bna', 'C07p13680' => 'bna', 'CAN.G1006.16' => 'can', 'CAN.G1006.17' => 'can', 'CAN.G1170.2' => 'can', 'CAN.G962.7' => 'can', 'CANSAT25G2179' => 'cansat', 'CANSAT78G1573' => 'cansat', 'CARHR099510' => 'chi', 'CARHR143510' => 'chi', 'Carub.0003s2380' => 'cru', 'Carub.0004s3082' => 'cru', 'Ca_00614_v3' => 'car', 'Ca_07801_v3' => 'car', 'Ca_08567_v3' => 'car', 'Ca_09571_v3' => 'car', 'CBR_g19290' => 'cbr', 'Cc01_g19770' => 'ccan', 'Cc03_g03030' => 'ccan', 'CDE07G0968' => 'cde', 'CDE09G1441' => 'cde', 'Cfa006103' => 'cfa', 'Cfa015573' => 'cfa', 'Cfa016988' => 'cfa', 'Ciclev10006738m.g' => 'ccl', 'Ciclev10010920m.g' => 'ccl', 'Ciclev10018517m.g' => 'ccl', 'CiPaw.01G159200' => 'cil', 'CiPaw.02G091000' => 'cil', 'CiPaw.02G091100' => 'cil', 'CiPaw.08G103100' => 'cil', 'CiPaw.09G224900' => 'cil', 'ClCG06G005740' => 'cla', 'ClCG07G000090' => 'cla', 'ClCG07G000100' => 'cla', 'COL.COLO4_09143' => 'col', 'COL.COLO4_25124' => 'col', 'Cpa.g.sc16.34' => 'cpa', 'Cpa.g.sc3504.1' => 'cpa', 'Cpa.g.sc60.37' => 'cpa', 'CsaV3_6G018520' => 'csa', 'CsaV3_6G036860' => 'csa', 'CSS0001072' => 'camsi', 'CSS0020208' => 'camsi', 'CSS0021253' => 'camsi', 'CSS0022190' => 'camsi', 'CSS0036150' => 'camsi', 'CSS0040442' => 'camsi', 'CSS0042300' => 'camsi', 'CSS0045298' => 'camsi', 'DCAR_012449' => 'dca', 'DCAR_018405' => 'dca', 'DCAR_024573' => 'dca', 'DCAR_030591' => 'dca', 'Dinv16926' => 'din', 'Dinv32963' => 'din', 'Dinv38382' => 'din', 'Dinv38383' => 'din', 'Duzib133G0974' => 'dzi', 'Duzib138G1867' => 'dzi', 'Duzib211G0420' => 'dzi', 'Duzib212G0930' => 'dzi', 'ECA234G1645' => 'eca', 'ECA247G3467' => 'eca', 'ECA248G1703' => 'eca', 'EL10Ac3g06327' => 'bvu', 'EL10Ac7g17204' => 'bvu', 'Eucgr.A00855' => 'egr', 'Eucgr.A00858' => 'egr', 'Eucgr.H01520' => 'egr', 'Eucgr.H03604' => 'egr', 'Eucgr.L03465' => 'egr', 'Eucgr.L03466' => 'egr', 'FAN01G0988' => 'fan', 'FAN02G3892' => 'fan', 'FAN05G3381' => 'fan', 'FAN07G0967' => 'fan', 'FAN07G1493' => 'fan', 'FAN08G3125' => 'fan', 'FAN09G0402' => 'fan', 'FAN12G2594' => 'fan', 'FAN12G3879' => 'fan', 'FAN14G1546' => 'fan', 'FAN15G3626' => 'fan', 'FAN17G0588' => 'fan', 'FAN17G0609' => 'fan', 'FAN18G2817' => 'fan', 'FAN19G1305' => 'fan', 'FAN20G1787' => 'fan', 'FAN22G0073' => 'fan', 'FAN22G0352' => 'fan', 'FAN22G0368' => 'fan', 'FAN22G2273' => 'fan', 'FAN24G1998' => 'fan', 'FAN27G1317' => 'fan', 'FvH4_2g23980' => 'fve', 'FvH4_4g14380' => 'fve', 'FvH4_4g14390' => 'fve', 'FvH4_6g09250' => 'fve', 'Glyma.03G151100' => 'gma', 'Glyma.04G122550' => 'gma', 'Glyma.05G001600' => 'gma', 'Glyma.09G270766' => 'gma', 'Glyma.09G270832' => 'gma', 'Glyma.13G209800' => 'gma', 'Glyma.15G102800' => 'gma', 'Glyma.18G218900' => 'gma', 'Glyma.19G001500' => 'gma', 'Glyma.19G153600' => 'gma', 'Gohir.A02G028600' => 'ghi', 'Gohir.A08G045000' => 'ghi', 'Gohir.A11G120500' => 'ghi', 'Gohir.A12G006200' => 'ghi', 'Gohir.A12G006250' => 'ghi', 'Gohir.D02G036300' => 'ghi', 'Gohir.D08G054700' => 'ghi', 'Gohir.D11G125600' => 'ghi', 'Gohir.D12G005700' => 'ghi', 'Gorai.004G055200' => 'gra', 'Gorai.005G040400' => 'gra', 'Gorai.007G134500' => 'gra', 'Gorai.008G005500' => 'gra', 'GSVIVG01011094001' => 'vvi', 'GSVIVG01017879001' => 'vvi', 'GSVIVG01025988001' => 'vvi', 'GSVIVG01029847001' => 'vvi', 'HanXRQChr10g0282901' => 'han', 'HanXRQChr10g0310371' => 'han', 'HanXRQChr10g0315041' => 'han', 'HanXRQChr11g0327651' => 'han', 'HanXRQChr12g0359391' => 'han', 'Haze_00972' => 'cav', 'Haze_00973' => 'cav', 'Haze_00974' => 'cav', 'Haze_04747' => 'cav', 'Haze_04749' => 'cav', 'Haze_04750' => 'cav', 'Haze_21217' => 'cav', 'Hma1.2p1_1037F.1_g250680' => 'hma', 'Hma1.2p1_1644F.1_g295320' => 'hma', 'HPP92_011322' => 'vpl', 'HPP92_011323' => 'vpl', 'HPP92_011324' => 'vpl', 'HPP92_011325' => 'vpl', 'HPP92_011326' => 'vpl', 'Hund12205' => 'sun', 'Hund17957' => 'sun', 'Lalb_Chr06g0176771' => 'lal', 'Lalb_Chr18g0056021' => 'lal', 'Lalb_Chr18g0056031' => 'lal', 'Lalb_Chr18g0056041' => 'lal', 'Lalb_Chr20g0107751' => 'lal', 'Lalb_Chr20g0118371' => 'lal', 'Lj1g0010239' => 'lja', 'Lj1g0017101' => 'lja', 'Lj2A1178G40' => 'lonja', 'Lj2A54G84' => 'lonja', 'Lj2g0015248' => 'lja', 'Lj3A761T51' => 'lonja', 'Lj6g0018116' => 'lja', 'Lsat_1_v5_gn_4_136040' => 'lsa', 'Lsat_1_v5_gn_5_187461' => 'lsa', 'Lsat_1_v5_gn_5_77001' => 'lsa', 'Lsat_1_v5_gn_9_4461' => 'lsa', 'Manes.01G210100' => 'mes', 'Manes.03G185600' => 'mes', 'Manes.05G073300' => 'mes', 'Manes.09G120300' => 'mes', 'Manes.15G022100' => 'mes', 'Mapoly0096s0053' => 'mpo', 'MBI03_g14058_MAGBIO' => 'mbi', 'MBI03_g33876_MAGBIO' => 'mbi', 'MBI03_g36854_MAGBIO' => 'mbi', 'MBI17_g11997_MAGBIO' => 'mbi', 'MD03G1269000' => 'mdo', 'MD04G1179600' => 'mdo', 'MD11G1289800' => 'mdo', 'MD12G1194700' => 'mdo', 'MD13G1182100' => 'mdo', 'MD13G1182200' => 'mdo', 'MD16G1182600' => 'mdo', 'Medtr2g021400' => 'mtr', 'Medtr2g021470' => 'mtr', 'Medtr2g105810' => 'mtr', 'Medtr3g033580' => 'mtr', 'Medtr6g007970' => 'mtr', 'Medtr7g056330' => 'mtr', 'Medtr7g074290' => 'mtr', 'Medtr7g074380' => 'mtr', 'Medtr7g094550' => 'mtr', 'Medtr8g069995' => 'mtr', 'MELO3C014345.2' => 'cme', 'MELO3C021395.2' => 'cme', 'Migut.D00262' => 'egut', 'Migut.G00257' => 'egut', 'MSTRG.21575' => 'ama', 'MSTRG.3985' => 'ama', 'Nitab4.5_0000295g0140' => 'nta', 'Nitab4.5_0000732g0140' => 'nta', 'Nitab4.5_0003162g0020' => 'nta', 'Nitab4.5_0006180g0090' => 'nta', 'Nitab4.5_0006390g0010' => 'nta', 'Nitab4.5_0007392g0040' => 'nta', 'Nn1g02140' => 'nnu', 'Nn4g26168' => 'nnu', 'Nn5g26754' => 'nnu', 'Oeu001433.1' => 'oeu', 'Oeu010299.2' => 'oeu', 'Oeu011171.1' => 'oeu', 'Oeu037675.1' => 'oeu', 'Oeu038359.1' => 'oeu', 'Oeu063834.1' => 'oeu', 'Oeu063835.1' => 'oeu', 'Os05g0312000' => 'osa', 'Os07g0211101' => 'osa', 'Os07g0211200' => 'osa', 'Os07g0681500' => 'osa', 'Peaxi162Scf00095g01015' => 'pax', 'Peaxi162Scf00104g00329' => 'pax', 'Peaxi162Scf00161g00137' => 'pax', 'PGR004G1665' => 'pgr', 'PGR031G2937' => 'pgr', 'PGR119G2145' => 'pgr', 'PGSC0003DMG400004351' => 'stu', 'PGSC0003DMG400014625' => 'stu', 'PGSC0003DMG401000943' => 'stu', 'Phvul.001G148600' => 'pvu', 'Phvul.004G001700' => 'pvu', 'Phvul.006G154900' => 'pvu', 'Phvul.008G078200' => 'pvu', 'Phvul.011G136500' => 'pvu', 'Potri.002G215600' => 'ptr', 'Potri.008G201600' => 'ptr', 'Potri.014G138400' => 'ptr', 'Potri.016G142500' => 'ptr', 'Pp3c16_10580' => 'ppa', 'Pp3c5_25280' => 'ppa', 'Prupe.1G150000' => 'ppe', 'Prupe.1G150100' => 'ppe', 'Prupe.6G299600' => 'ppe', 'Prupe.8G245000' => 'ppe', 'Psat0s4927g0040' => 'psa', 'Psat1g052080' => 'psa', 'Psat1g183800' => 'psa', 'Psat3g113840' => 'psa', 'Psat3g126120' => 'psa', 'Psat3g126160' => 'psa', 'Psat3g158760' => 'psa', 'Psat3g158840' => 'psa', 'PSO170G2858' => 'pso', 'PSO339G0606' => 'pso', 'PSO384G4709' => 'pso', 'PSO407G0334' => 'pso', 'QL04p040276' => 'qlo', 'QL06p005458' => 'qlo', 'QL06p005472' => 'qlo', 'QL07p030546' => 'qlo', 'QL07p031519' => 'qlo', 'QL09p050949' => 'qlo', 'QL09p050966' => 'qlo', 'QL09p051067' => 'qlo', 'QL12p022706' => 'qlo', 'RcHm_v2.0_Chr2g0119601' => 'rch', 'RcHm_v2.0_Chr3g0459591' => 'rch', 'RcHm_v2.0_Chr4g0418521' => 'rch', 'RcHm_v2.0_Chr4g0418531' => 'rch', 'RcHm_v2.0_Chr4g0418541' => 'rch', 'RcHm_v2.0_Chr6g0291641' => 'rch', 'Rhsim01G0086300' => 'rsi', 'Rhsim01G0276300' => 'rsi', 'Rhsim01G0276500' => 'rsi', 'Rhsim04G0207700' => 'rsi', 'Rhsim05G0234500' => 'rsi', 'Rhsim13G0022400' => 'rsi', 'Sabra02G0167900' => 'sbr', 'Sabra04G0158500' => 'sbr', 'Sabra08G0159800' => 'sbr', 'Sabra10G0011500' => 'sbr', 'Sabra14G0104400' => 'sbr', 'SalBow2G2440' => 'sbo', 'SalBow4G2265' => 'sbo', 'Sc02g0000060' => 'sci', 'Sc05g0005020' => 'sci', 'Sc13g0003890' => 'sci', 'Sed0014865' => 'sed', 'Sed0017224' => 'sed', 'Sed0026391' => 'sed', 'SEGI_00063' => 'sgi', 'SEGI_10967' => 'sgi', 'SEGI_17510' => 'sgi', 'SEGI_24396' => 'sgi', 'SEGI_39719' => 'sgi', 'SEGI_41392' => 'sgi', 'SGA_v2.0_scaffold11G05794' => 'sas', 'SGA_v2.0_scaffold142G35607' => 'sas', 'SGA_v2.0_scaffold1G00447' => 'sas', 'SHI15388' => 'shi', 'SHI15394' => 'shi', 'SHI15396' => 'shi', 'SHI15399' => 'shi', 'SMO343G0151' => 'smo', 'SMO367G1118' => 'smo', 'Solyc01g080200.3' => 'sly', 'Solyc06g008960.3' => 'sly', 'Solyc09g064780.3' => 'sly', 'Sopen01g031980' => 'spe', 'Sopen06g003710' => 'spe', 'Sopen09g026460' => 'spe', 'Sp3g21240' => 'spa', 'Sp4g30030' => 'spa', 'TAR365G0022' => 'tar', 'TAR365G1023' => 'tar', 'TAR365G1253' => 'tar', 'TAR623G0078' => 'tar', 'TAR623G1721' => 'tar', 'TAR633G0959' => 'tar', 'THA.LOC104802225' => 'tha', 'THA.LOC104804769' => 'tha', 'THA.LOC104808660' => 'tha', 'THA.LOC104812792' => 'tha', 'Thecc.01G284000' => 'tca', 'Thecc.04G220600' => 'tca', 'Thecc.05G268900' => 'tca', 'Thecc.08G171100' => 'tca', 'Thhalv10001284m.g' => 'esa', 'Thhalv10019912m.g' => 'esa', 'TPR.G14189' => 'tpr', 'TPR.G18110' => 'tpr', 'TPR.G18130' => 'tpr', 'TPR.G18131' => 'tpr', 'TPR.G18140' => 'tpr', 'TPR.G24282' => 'tpr', 'TPR.G25221' => 'tpr', 'TPR.G29267' => 'tpr', 'TPR.G35315' => 'tpr', 'TPR.G36173' => 'tpr', 'TWI09G0794' => 'twi', 'TWI59G1348' => 'twi', 'TWI74G0430' => 'twi', 'unitig_26.g8940' => 'ugi', 'unitig_749.g13744' => 'ugi', 'unitig_749.g13745' => 'ugi', 'vmacro08269' => 'vma', 'vmacro14937' => 'vma', 'vmacro20401' => 'vma', 'VMungo0464G1349' => 'vmu', 'VMungo0540G0289' => 'vmu', 'VMungo1215G1590' => 'vmu', 'VMungo1309G0221' => 'vmu', 'VMungo1309G2815' => 'vmu', 'VMungo1383G0239' => 'vmu', 'VMungo1383G2910' => 'vmu', 'Zm00001eb095270' => 'zma', 'Zm00001eb095280' => 'zma', 'Zm00001eb111630' => 'zma', 'Zm00001eb237080' => 'zma', 'Zm00001eb273740' => 'zma', 'Zm00001eb285040' => 'zma', 'Zm00001eb330790' => 'zma', 'Zm00001eb337380' => 'zma' ), 'gf_id' => 'HOM05D001484', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001484' ), 'data_identifier' => 'HOM05D001484', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001484', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p31500' => 'bna', 'A05p00020' => 'bna', 'A07p08820' => 'bna', 'Aa31LG4G3300' => 'aar', 'Aa31LG8G10030' => 'aar', 'Actinidia00731' => 'ach', 'Actinidia11473' => 'ach', 'Actinidia23469' => 'ach', 'Actinidia24318' => 'ach', 'Actinidia40196' => 'ach', 'Actinidia40197' => 'ach', 'Actinidia40198' => 'ach', 'Ah.08g212990' => 'amhyb', 'Ah.15g091720' => 'amhyb', 'AL3G38260' => 'aly', 'AL4G47710' => 'aly', 'Aqoxy2G00671' => 'aox', 'Aqoxy2G03236' => 'aox', 'arahy.Tifrunner.gnm1.ann1.05IDCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KR684' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATY3SJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK6QJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6APGL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IDT7Z9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM073U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ0R87' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LE7RV4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT4QRX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V5ENPK' => 'arhy', 'AT2G48110' => 'ath', 'AT3G23590' => 'ath', 'ATR0626G186' => 'atr', 'ATR1127G141' => 'atr', 'Atru.chr4.2583' => 'acertr', 'Atru.chr5.1358' => 'acertr', 'Atru.chr5.1359' => 'acertr', 'Atru.chr8.46' => 'acertr', 'AUR62002640' => 'cqu', 'AUR62030055' => 'cqu', 'AUR62033713' => 'cqu', 'AUR62033714' => 'cqu', 'AUR62036795' => 'cqu', 'AUR62039891' => 'cqu', 'BcaB02g08737' => 'bca', 'BcaB04g20441' => 'bca', 'BcaB06g26509' => 'bca', 'BcaB06g26510' => 'bca', 'BcaB06g26511' => 'bca', 'BcaB06g26512' => 'bca', 'BcaB06g26513' => 'bca', 'BcaC02g12564' => 'bca', 'BcaC02g12565' => 'bca', 'BcaC02g12794' => 'bca', 'BcaC02g12795' => 'bca', 'BcaC02g12796' => 'bca', 'BcaC06g35541' => 'bca', 'BNapus_Darmor_BZH_scaffold_188p00080' => 'bna', 'BNapus_Darmor_BZH_scaffold_188p00090' => 'bna', 'BolC1t03972H' => 'bol', 'BolC1t03973H' => 'bol', 'BolC4t21680H' => 'bol', 'BolC7t41863H' => 'bol', 'BolSC55t61227H' => 'bol', 'BolSC55t61228H' => 'bol', 'BraA01t03278Z' => 'bra', 'BraA05t18998Z' => 'bra', 'BraA07t28673Z' => 'bra', 'C01p40150' => 'bna', 'C05p12370' => 'bna', 'C07p13680' => 'bna', 'CAN.G1006.16' => 'can', 'CAN.G1006.17' => 'can', 'CAN.G1170.2' => 'can', 'CAN.G962.7' => 'can', 'CANSAT25G2179' => 'cansat', 'CANSAT78G1573' => 'cansat', 'CARHR099510' => 'chi', 'CARHR143510' => 'chi', 'Carub.0003s2380' => 'cru', 'Carub.0004s3082' => 'cru', 'Ca_00614_v3' => 'car', 'Ca_07801_v3' => 'car', 'Ca_08567_v3' => 'car', 'Ca_09571_v3' => 'car', 'CBR_g19290' => 'cbr', 'Cc01_g19770' => 'ccan', 'Cc03_g03030' => 'ccan', 'CDE07G0968' => 'cde', 'CDE09G1441' => 'cde', 'Cfa006103' => 'cfa', 'Cfa015573' => 'cfa', 'Cfa016988' => 'cfa', 'Ciclev10006738m.g' => 'ccl', 'Ciclev10010920m.g' => 'ccl', 'Ciclev10018517m.g' => 'ccl', 'CiPaw.01G159200' => 'cil', 'CiPaw.02G091000' => 'cil', 'CiPaw.02G091100' => 'cil', 'CiPaw.08G103100' => 'cil', 'CiPaw.09G224900' => 'cil', 'ClCG06G005740' => 'cla', 'ClCG07G000090' => 'cla', 'ClCG07G000100' => 'cla', 'COL.COLO4_09143' => 'col', 'COL.COLO4_25124' => 'col', 'Cpa.g.sc16.34' => 'cpa', 'Cpa.g.sc3504.1' => 'cpa', 'Cpa.g.sc60.37' => 'cpa', 'CsaV3_6G018520' => 'csa', 'CsaV3_6G036860' => 'csa', 'CSS0001072' => 'camsi', 'CSS0020208' => 'camsi', 'CSS0021253' => 'camsi', 'CSS0022190' => 'camsi', 'CSS0036150' => 'camsi', 'CSS0040442' => 'camsi', 'CSS0042300' => 'camsi', 'CSS0045298' => 'camsi', 'DCAR_012449' => 'dca', 'DCAR_018405' => 'dca', 'DCAR_024573' => 'dca', 'DCAR_030591' => 'dca', 'Dinv16926' => 'din', 'Dinv32963' => 'din', 'Dinv38382' => 'din', 'Dinv38383' => 'din', 'Duzib133G0974' => 'dzi', 'Duzib138G1867' => 'dzi', 'Duzib211G0420' => 'dzi', 'Duzib212G0930' => 'dzi', 'ECA234G1645' => 'eca', 'ECA247G3467' => 'eca', 'ECA248G1703' => 'eca', 'EL10Ac3g06327' => 'bvu', 'EL10Ac7g17204' => 'bvu', 'Eucgr.A00855' => 'egr', 'Eucgr.A00858' => 'egr', 'Eucgr.H01520' => 'egr', 'Eucgr.H03604' => 'egr', 'Eucgr.L03465' => 'egr', 'Eucgr.L03466' => 'egr', 'FAN01G0988' => 'fan', 'FAN02G3892' => 'fan', 'FAN05G3381' => 'fan', 'FAN07G0967' => 'fan', 'FAN07G1493' => 'fan', 'FAN08G3125' => 'fan', 'FAN09G0402' => 'fan', 'FAN12G2594' => 'fan', 'FAN12G3879' => 'fan', 'FAN14G1546' => 'fan', 'FAN15G3626' => 'fan', 'FAN17G0588' => 'fan', 'FAN17G0609' => 'fan', 'FAN18G2817' => 'fan', 'FAN19G1305' => 'fan', 'FAN20G1787' => 'fan', 'FAN22G0073' => 'fan', 'FAN22G0352' => 'fan', 'FAN22G0368' => 'fan', 'FAN22G2273' => 'fan', 'FAN24G1998' => 'fan', 'FAN27G1317' => 'fan', 'FvH4_2g23980' => 'fve', 'FvH4_4g14380' => 'fve', 'FvH4_4g14390' => 'fve', 'FvH4_6g09250' => 'fve', 'Glyma.03G151100' => 'gma', 'Glyma.04G122550' => 'gma', 'Glyma.05G001600' => 'gma', 'Glyma.09G270766' => 'gma', 'Glyma.09G270832' => 'gma', 'Glyma.13G209800' => 'gma', 'Glyma.15G102800' => 'gma', 'Glyma.18G218900' => 'gma', 'Glyma.19G001500' => 'gma', 'Glyma.19G153600' => 'gma', 'Gohir.A02G028600' => 'ghi', 'Gohir.A08G045000' => 'ghi', 'Gohir.A11G120500' => 'ghi', 'Gohir.A12G006200' => 'ghi', 'Gohir.A12G006250' => 'ghi', 'Gohir.D02G036300' => 'ghi', 'Gohir.D08G054700' => 'ghi', 'Gohir.D11G125600' => 'ghi', 'Gohir.D12G005700' => 'ghi', 'Gorai.004G055200' => 'gra', 'Gorai.005G040400' => 'gra', 'Gorai.007G134500' => 'gra', 'Gorai.008G005500' => 'gra', 'GSVIVG01011094001' => 'vvi', 'GSVIVG01017879001' => 'vvi', 'GSVIVG01025988001' => 'vvi', 'GSVIVG01029847001' => 'vvi', 'HanXRQChr10g0282901' => 'han', 'HanXRQChr10g0310371' => 'han', 'HanXRQChr10g0315041' => 'han', 'HanXRQChr11g0327651' => 'han', 'HanXRQChr12g0359391' => 'han', 'Haze_00972' => 'cav', 'Haze_00973' => 'cav', 'Haze_00974' => 'cav', 'Haze_04747' => 'cav', 'Haze_04749' => 'cav', 'Haze_04750' => 'cav', 'Haze_21217' => 'cav', 'Hma1.2p1_1037F.1_g250680' => 'hma', 'Hma1.2p1_1644F.1_g295320' => 'hma', 'HPP92_011322' => 'vpl', 'HPP92_011323' => 'vpl', 'HPP92_011324' => 'vpl', 'HPP92_011325' => 'vpl', 'HPP92_011326' => 'vpl', 'Hund12205' => 'sun', 'Hund17957' => 'sun', 'Lalb_Chr06g0176771' => 'lal', 'Lalb_Chr18g0056021' => 'lal', 'Lalb_Chr18g0056031' => 'lal', 'Lalb_Chr18g0056041' => 'lal', 'Lalb_Chr20g0107751' => 'lal', 'Lalb_Chr20g0118371' => 'lal', 'Lj1g0010239' => 'lja', 'Lj1g0017101' => 'lja', 'Lj2A1178G40' => 'lonja', 'Lj2A54G84' => 'lonja', 'Lj2g0015248' => 'lja', 'Lj3A761T51' => 'lonja', 'Lj6g0018116' => 'lja', 'Lsat_1_v5_gn_4_136040' => 'lsa', 'Lsat_1_v5_gn_5_187461' => 'lsa', 'Lsat_1_v5_gn_5_77001' => 'lsa', 'Lsat_1_v5_gn_9_4461' => 'lsa', 'Manes.01G210100' => 'mes', 'Manes.03G185600' => 'mes', 'Manes.05G073300' => 'mes', 'Manes.09G120300' => 'mes', 'Manes.15G022100' => 'mes', 'Mapoly0096s0053' => 'mpo', 'MBI03_g14058_MAGBIO' => 'mbi', 'MBI03_g33876_MAGBIO' => 'mbi', 'MBI03_g36854_MAGBIO' => 'mbi', 'MBI17_g11997_MAGBIO' => 'mbi', 'MD03G1269000' => 'mdo', 'MD04G1179600' => 'mdo', 'MD11G1289800' => 'mdo', 'MD12G1194700' => 'mdo', 'MD13G1182100' => 'mdo', 'MD13G1182200' => 'mdo', 'MD16G1182600' => 'mdo', 'Medtr2g021400' => 'mtr', 'Medtr2g021470' => 'mtr', 'Medtr2g105810' => 'mtr', 'Medtr3g033580' => 'mtr', 'Medtr6g007970' => 'mtr', 'Medtr7g056330' => 'mtr', 'Medtr7g074290' => 'mtr', 'Medtr7g074380' => 'mtr', 'Medtr7g094550' => 'mtr', 'Medtr8g069995' => 'mtr', 'MELO3C014345.2' => 'cme', 'MELO3C021395.2' => 'cme', 'Migut.D00262' => 'egut', 'Migut.G00257' => 'egut', 'MSTRG.21575' => 'ama', 'MSTRG.3985' => 'ama', 'Nitab4.5_0000295g0140' => 'nta', 'Nitab4.5_0000732g0140' => 'nta', 'Nitab4.5_0003162g0020' => 'nta', 'Nitab4.5_0006180g0090' => 'nta', 'Nitab4.5_0006390g0010' => 'nta', 'Nitab4.5_0007392g0040' => 'nta', 'Nn1g02140' => 'nnu', 'Nn4g26168' => 'nnu', 'Nn5g26754' => 'nnu', 'Oeu001433.1' => 'oeu', 'Oeu010299.2' => 'oeu', 'Oeu011171.1' => 'oeu', 'Oeu037675.1' => 'oeu', 'Oeu038359.1' => 'oeu', 'Oeu063834.1' => 'oeu', 'Oeu063835.1' => 'oeu', 'Os05g0312000' => 'osa', 'Os07g0211101' => 'osa', 'Os07g0211200' => 'osa', 'Os07g0681500' => 'osa', 'Peaxi162Scf00095g01015' => 'pax', 'Peaxi162Scf00104g00329' => 'pax', 'Peaxi162Scf00161g00137' => 'pax', 'PGR004G1665' => 'pgr', 'PGR031G2937' => 'pgr', 'PGR119G2145' => 'pgr', 'PGSC0003DMG400004351' => 'stu', 'PGSC0003DMG400014625' => 'stu', 'PGSC0003DMG401000943' => 'stu', 'Phvul.001G148600' => 'pvu', 'Phvul.004G001700' => 'pvu', 'Phvul.006G154900' => 'pvu', 'Phvul.008G078200' => 'pvu', 'Phvul.011G136500' => 'pvu', 'Potri.002G215600' => 'ptr', 'Potri.008G201600' => 'ptr', 'Potri.014G138400' => 'ptr', 'Potri.016G142500' => 'ptr', 'Pp3c16_10580' => 'ppa', 'Pp3c5_25280' => 'ppa', 'Prupe.1G150000' => 'ppe', 'Prupe.1G150100' => 'ppe', 'Prupe.6G299600' => 'ppe', 'Prupe.8G245000' => 'ppe', 'Psat0s4927g0040' => 'psa', 'Psat1g052080' => 'psa', 'Psat1g183800' => 'psa', 'Psat3g113840' => 'psa', 'Psat3g126120' => 'psa', 'Psat3g126160' => 'psa', 'Psat3g158760' => 'psa', 'Psat3g158840' => 'psa', 'PSO170G2858' => 'pso', 'PSO339G0606' => 'pso', 'PSO384G4709' => 'pso', 'PSO407G0334' => 'pso', 'QL04p040276' => 'qlo', 'QL06p005458' => 'qlo', 'QL06p005472' => 'qlo', 'QL07p030546' => 'qlo', 'QL07p031519' => 'qlo', 'QL09p050949' => 'qlo', 'QL09p050966' => 'qlo', 'QL09p051067' => 'qlo', 'QL12p022706' => 'qlo', 'RcHm_v2.0_Chr2g0119601' => 'rch', 'RcHm_v2.0_Chr3g0459591' => 'rch', 'RcHm_v2.0_Chr4g0418521' => 'rch', 'RcHm_v2.0_Chr4g0418531' => 'rch', 'RcHm_v2.0_Chr4g0418541' => 'rch', 'RcHm_v2.0_Chr6g0291641' => 'rch', 'Rhsim01G0086300' => 'rsi', 'Rhsim01G0276300' => 'rsi', 'Rhsim01G0276500' => 'rsi', 'Rhsim04G0207700' => 'rsi', 'Rhsim05G0234500' => 'rsi', 'Rhsim13G0022400' => 'rsi', 'Sabra02G0167900' => 'sbr', 'Sabra04G0158500' => 'sbr', 'Sabra08G0159800' => 'sbr', 'Sabra10G0011500' => 'sbr', 'Sabra14G0104400' => 'sbr', 'SalBow2G2440' => 'sbo', 'SalBow4G2265' => 'sbo', 'Sc02g0000060' => 'sci', 'Sc05g0005020' => 'sci', 'Sc13g0003890' => 'sci', 'Sed0014865' => 'sed', 'Sed0017224' => 'sed', 'Sed0026391' => 'sed', 'SEGI_00063' => 'sgi', 'SEGI_10967' => 'sgi', 'SEGI_17510' => 'sgi', 'SEGI_24396' => 'sgi', 'SEGI_39719' => 'sgi', 'SEGI_41392' => 'sgi', 'SGA_v2.0_scaffold11G05794' => 'sas', 'SGA_v2.0_scaffold142G35607' => 'sas', 'SGA_v2.0_scaffold1G00447' => 'sas', 'SHI15388' => 'shi', 'SHI15394' => 'shi', 'SHI15396' => 'shi', 'SHI15399' => 'shi', 'SMO343G0151' => 'smo', 'SMO367G1118' => 'smo', 'Solyc01g080200.3' => 'sly', 'Solyc06g008960.3' => 'sly', 'Solyc09g064780.3' => 'sly', 'Sopen01g031980' => 'spe', 'Sopen06g003710' => 'spe', 'Sopen09g026460' => 'spe', 'Sp3g21240' => 'spa', 'Sp4g30030' => 'spa', 'TAR365G0022' => 'tar', 'TAR365G1023' => 'tar', 'TAR365G1253' => 'tar', 'TAR623G0078' => 'tar', 'TAR623G1721' => 'tar', 'TAR633G0959' => 'tar', 'THA.LOC104802225' => 'tha', 'THA.LOC104804769' => 'tha', 'THA.LOC104808660' => 'tha', 'THA.LOC104812792' => 'tha', 'Thecc.01G284000' => 'tca', 'Thecc.04G220600' => 'tca', 'Thecc.05G268900' => 'tca', 'Thecc.08G171100' => 'tca', 'Thhalv10001284m.g' => 'esa', 'Thhalv10019912m.g' => 'esa', 'TPR.G14189' => 'tpr', 'TPR.G18110' => 'tpr', 'TPR.G18130' => 'tpr', 'TPR.G18131' => 'tpr', 'TPR.G18140' => 'tpr', 'TPR.G24282' => 'tpr', 'TPR.G25221' => 'tpr', 'TPR.G29267' => 'tpr', 'TPR.G35315' => 'tpr', 'TPR.G36173' => 'tpr', 'TWI09G0794' => 'twi', 'TWI59G1348' => 'twi', 'TWI74G0430' => 'twi', 'unitig_26.g8940' => 'ugi', 'unitig_749.g13744' => 'ugi', 'unitig_749.g13745' => 'ugi', 'vmacro08269' => 'vma', 'vmacro14937' => 'vma', 'vmacro20401' => 'vma', 'VMungo0464G1349' => 'vmu', 'VMungo0540G0289' => 'vmu', 'VMungo1215G1590' => 'vmu', 'VMungo1309G0221' => 'vmu', 'VMungo1309G2815' => 'vmu', 'VMungo1383G0239' => 'vmu', 'VMungo1383G2910' => 'vmu', 'Zm00001eb095270' => 'zma', 'Zm00001eb095280' => 'zma', 'Zm00001eb111630' => 'zma', 'Zm00001eb237080' => 'zma', 'Zm00001eb273740' => 'zma', 'Zm00001eb285040' => 'zma', 'Zm00001eb330790' => 'zma', 'Zm00001eb337380' => 'zma' ) $gf_id = 'HOM05D001484' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001484' ) $data_identifier = 'HOM05D001484' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 2, 'aly' => (int) 2, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 22, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 7, 'hma' => (int) 2, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 7, 'mtr' => (int) 10, 'cme' => (int) 2, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 4, 'ppa' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 4, 'qlo' => (int) 9, 'rch' => (int) 6, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 10, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 7, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb337380' $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' => 'HOM05D001484', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p31500' => 'bna', 'A05p00020' => 'bna', 'A07p08820' => 'bna', 'Aa31LG4G3300' => 'aar', 'Aa31LG8G10030' => 'aar', 'Actinidia00731' => 'ach', 'Actinidia11473' => 'ach', 'Actinidia23469' => 'ach', 'Actinidia24318' => 'ach', 'Actinidia40196' => 'ach', 'Actinidia40197' => 'ach', 'Actinidia40198' => 'ach', 'Ah.08g212990' => 'amhyb', 'Ah.15g091720' => 'amhyb', 'AL3G38260' => 'aly', 'AL4G47710' => 'aly', 'Aqoxy2G00671' => 'aox', 'Aqoxy2G03236' => 'aox', 'arahy.Tifrunner.gnm1.ann1.05IDCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KR684' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATY3SJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK6QJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6APGL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IDT7Z9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM073U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ0R87' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LE7RV4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT4QRX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V5ENPK' => 'arhy', 'AT2G48110' => 'ath', 'AT3G23590' => 'ath', 'ATR0626G186' => 'atr', 'ATR1127G141' => 'atr', 'Atru.chr4.2583' => 'acertr', 'Atru.chr5.1358' => 'acertr', 'Atru.chr5.1359' => 'acertr', 'Atru.chr8.46' => 'acertr', 'AUR62002640' => 'cqu', 'AUR62030055' => 'cqu', 'AUR62033713' => 'cqu', 'AUR62033714' => 'cqu', 'AUR62036795' => 'cqu', 'AUR62039891' => 'cqu', 'BcaB02g08737' => 'bca', 'BcaB04g20441' => 'bca', 'BcaB06g26509' => 'bca', 'BcaB06g26510' => 'bca', 'BcaB06g26511' => 'bca', 'BcaB06g26512' => 'bca', 'BcaB06g26513' => 'bca', 'BcaC02g12564' => 'bca', 'BcaC02g12565' => 'bca', 'BcaC02g12794' => 'bca', 'BcaC02g12795' => 'bca', 'BcaC02g12796' => 'bca', 'BcaC06g35541' => 'bca', 'BNapus_Darmor_BZH_scaffold_188p00080' => 'bna', 'BNapus_Darmor_BZH_scaffold_188p00090' => 'bna', 'BolC1t03972H' => 'bol', 'BolC1t03973H' => 'bol', 'BolC4t21680H' => 'bol', 'BolC7t41863H' => 'bol', 'BolSC55t61227H' => 'bol', 'BolSC55t61228H' => 'bol', 'BraA01t03278Z' => 'bra', 'BraA05t18998Z' => 'bra', 'BraA07t28673Z' => 'bra', 'C01p40150' => 'bna', 'C05p12370' => 'bna', 'C07p13680' => 'bna', 'CAN.G1006.16' => 'can', 'CAN.G1006.17' => 'can', 'CAN.G1170.2' => 'can', 'CAN.G962.7' => 'can', 'CANSAT25G2179' => 'cansat', 'CANSAT78G1573' => 'cansat', 'CARHR099510' => 'chi', 'CARHR143510' => 'chi', 'Carub.0003s2380' => 'cru', 'Carub.0004s3082' => 'cru', 'Ca_00614_v3' => 'car', 'Ca_07801_v3' => 'car', 'Ca_08567_v3' => 'car', 'Ca_09571_v3' => 'car', 'CBR_g19290' => 'cbr', 'Cc01_g19770' => 'ccan', 'Cc03_g03030' => 'ccan', 'CDE07G0968' => 'cde', 'CDE09G1441' => 'cde', 'Cfa006103' => 'cfa', 'Cfa015573' => 'cfa', 'Cfa016988' => 'cfa', 'Ciclev10006738m.g' => 'ccl', 'Ciclev10010920m.g' => 'ccl', 'Ciclev10018517m.g' => 'ccl', 'CiPaw.01G159200' => 'cil', 'CiPaw.02G091000' => 'cil', 'CiPaw.02G091100' => 'cil', 'CiPaw.08G103100' => 'cil', 'CiPaw.09G224900' => 'cil', 'ClCG06G005740' => 'cla', 'ClCG07G000090' => 'cla', 'ClCG07G000100' => 'cla', 'COL.COLO4_09143' => 'col', 'COL.COLO4_25124' => 'col', 'Cpa.g.sc16.34' => 'cpa', 'Cpa.g.sc3504.1' => 'cpa', 'Cpa.g.sc60.37' => 'cpa', 'CsaV3_6G018520' => 'csa', 'CsaV3_6G036860' => 'csa', 'CSS0001072' => 'camsi', 'CSS0020208' => 'camsi', 'CSS0021253' => 'camsi', 'CSS0022190' => 'camsi', 'CSS0036150' => 'camsi', 'CSS0040442' => 'camsi', 'CSS0042300' => 'camsi', 'CSS0045298' => 'camsi', 'DCAR_012449' => 'dca', 'DCAR_018405' => 'dca', 'DCAR_024573' => 'dca', 'DCAR_030591' => 'dca', 'Dinv16926' => 'din', 'Dinv32963' => 'din', 'Dinv38382' => 'din', 'Dinv38383' => 'din', 'Duzib133G0974' => 'dzi', 'Duzib138G1867' => 'dzi', 'Duzib211G0420' => 'dzi', 'Duzib212G0930' => 'dzi', 'ECA234G1645' => 'eca', 'ECA247G3467' => 'eca', 'ECA248G1703' => 'eca', 'EL10Ac3g06327' => 'bvu', 'EL10Ac7g17204' => 'bvu', 'Eucgr.A00855' => 'egr', 'Eucgr.A00858' => 'egr', 'Eucgr.H01520' => 'egr', 'Eucgr.H03604' => 'egr', 'Eucgr.L03465' => 'egr', 'Eucgr.L03466' => 'egr', 'FAN01G0988' => 'fan', 'FAN02G3892' => 'fan', 'FAN05G3381' => 'fan', 'FAN07G0967' => 'fan', 'FAN07G1493' => 'fan', 'FAN08G3125' => 'fan', 'FAN09G0402' => 'fan', 'FAN12G2594' => 'fan', 'FAN12G3879' => 'fan', 'FAN14G1546' => 'fan', 'FAN15G3626' => 'fan', 'FAN17G0588' => 'fan', 'FAN17G0609' => 'fan', 'FAN18G2817' => 'fan', 'FAN19G1305' => 'fan', 'FAN20G1787' => 'fan', 'FAN22G0073' => 'fan', 'FAN22G0352' => 'fan', 'FAN22G0368' => 'fan', 'FAN22G2273' => 'fan', 'FAN24G1998' => 'fan', 'FAN27G1317' => 'fan', 'FvH4_2g23980' => 'fve', 'FvH4_4g14380' => 'fve', 'FvH4_4g14390' => 'fve', 'FvH4_6g09250' => 'fve', 'Glyma.03G151100' => 'gma', 'Glyma.04G122550' => 'gma', 'Glyma.05G001600' => 'gma', 'Glyma.09G270766' => 'gma', 'Glyma.09G270832' => 'gma', 'Glyma.13G209800' => 'gma', 'Glyma.15G102800' => 'gma', 'Glyma.18G218900' => 'gma', 'Glyma.19G001500' => 'gma', 'Glyma.19G153600' => 'gma', 'Gohir.A02G028600' => 'ghi', 'Gohir.A08G045000' => 'ghi', 'Gohir.A11G120500' => 'ghi', 'Gohir.A12G006200' => 'ghi', 'Gohir.A12G006250' => 'ghi', 'Gohir.D02G036300' => 'ghi', 'Gohir.D08G054700' => 'ghi', 'Gohir.D11G125600' => 'ghi', 'Gohir.D12G005700' => 'ghi', 'Gorai.004G055200' => 'gra', 'Gorai.005G040400' => 'gra', 'Gorai.007G134500' => 'gra', 'Gorai.008G005500' => 'gra', 'GSVIVG01011094001' => 'vvi', 'GSVIVG01017879001' => 'vvi', 'GSVIVG01025988001' => 'vvi', 'GSVIVG01029847001' => 'vvi', 'HanXRQChr10g0282901' => 'han', 'HanXRQChr10g0310371' => 'han', 'HanXRQChr10g0315041' => 'han', 'HanXRQChr11g0327651' => 'han', 'HanXRQChr12g0359391' => 'han', 'Haze_00972' => 'cav', 'Haze_00973' => 'cav', 'Haze_00974' => 'cav', 'Haze_04747' => 'cav', 'Haze_04749' => 'cav', 'Haze_04750' => 'cav', 'Haze_21217' => 'cav', 'Hma1.2p1_1037F.1_g250680' => 'hma', 'Hma1.2p1_1644F.1_g295320' => 'hma', 'HPP92_011322' => 'vpl', 'HPP92_011323' => 'vpl', 'HPP92_011324' => 'vpl', 'HPP92_011325' => 'vpl', 'HPP92_011326' => 'vpl', 'Hund12205' => 'sun', 'Hund17957' => 'sun', 'Lalb_Chr06g0176771' => 'lal', 'Lalb_Chr18g0056021' => 'lal', 'Lalb_Chr18g0056031' => 'lal', 'Lalb_Chr18g0056041' => 'lal', 'Lalb_Chr20g0107751' => 'lal', 'Lalb_Chr20g0118371' => 'lal', 'Lj1g0010239' => 'lja', 'Lj1g0017101' => 'lja', 'Lj2A1178G40' => 'lonja', 'Lj2A54G84' => 'lonja', 'Lj2g0015248' => 'lja', 'Lj3A761T51' => 'lonja', 'Lj6g0018116' => 'lja', 'Lsat_1_v5_gn_4_136040' => 'lsa', 'Lsat_1_v5_gn_5_187461' => 'lsa', 'Lsat_1_v5_gn_5_77001' => 'lsa', 'Lsat_1_v5_gn_9_4461' => 'lsa', 'Manes.01G210100' => 'mes', 'Manes.03G185600' => 'mes', 'Manes.05G073300' => 'mes', 'Manes.09G120300' => 'mes', 'Manes.15G022100' => 'mes', 'Mapoly0096s0053' => 'mpo', 'MBI03_g14058_MAGBIO' => 'mbi', 'MBI03_g33876_MAGBIO' => 'mbi', 'MBI03_g36854_MAGBIO' => 'mbi', 'MBI17_g11997_MAGBIO' => 'mbi', 'MD03G1269000' => 'mdo', 'MD04G1179600' => 'mdo', 'MD11G1289800' => 'mdo', 'MD12G1194700' => 'mdo', 'MD13G1182100' => 'mdo', 'MD13G1182200' => 'mdo', 'MD16G1182600' => 'mdo', 'Medtr2g021400' => 'mtr', 'Medtr2g021470' => 'mtr', 'Medtr2g105810' => 'mtr', 'Medtr3g033580' => 'mtr', 'Medtr6g007970' => 'mtr', 'Medtr7g056330' => 'mtr', 'Medtr7g074290' => 'mtr', 'Medtr7g074380' => 'mtr', 'Medtr7g094550' => 'mtr', 'Medtr8g069995' => 'mtr', 'MELO3C014345.2' => 'cme', 'MELO3C021395.2' => 'cme', 'Migut.D00262' => 'egut', 'Migut.G00257' => 'egut', 'MSTRG.21575' => 'ama', 'MSTRG.3985' => 'ama', 'Nitab4.5_0000295g0140' => 'nta', 'Nitab4.5_0000732g0140' => 'nta', 'Nitab4.5_0003162g0020' => 'nta', 'Nitab4.5_0006180g0090' => 'nta', 'Nitab4.5_0006390g0010' => 'nta', 'Nitab4.5_0007392g0040' => 'nta', 'Nn1g02140' => 'nnu', 'Nn4g26168' => 'nnu', 'Nn5g26754' => 'nnu', 'Oeu001433.1' => 'oeu', 'Oeu010299.2' => 'oeu', 'Oeu011171.1' => 'oeu', 'Oeu037675.1' => 'oeu', 'Oeu038359.1' => 'oeu', 'Oeu063834.1' => 'oeu', 'Oeu063835.1' => 'oeu', 'Os05g0312000' => 'osa', 'Os07g0211101' => 'osa', 'Os07g0211200' => 'osa', 'Os07g0681500' => 'osa', 'Peaxi162Scf00095g01015' => 'pax', 'Peaxi162Scf00104g00329' => 'pax', 'Peaxi162Scf00161g00137' => 'pax', 'PGR004G1665' => 'pgr', 'PGR031G2937' => 'pgr', 'PGR119G2145' => 'pgr', 'PGSC0003DMG400004351' => 'stu', 'PGSC0003DMG400014625' => 'stu', 'PGSC0003DMG401000943' => 'stu', 'Phvul.001G148600' => 'pvu', 'Phvul.004G001700' => 'pvu', 'Phvul.006G154900' => 'pvu', 'Phvul.008G078200' => 'pvu', 'Phvul.011G136500' => 'pvu', 'Potri.002G215600' => 'ptr', 'Potri.008G201600' => 'ptr', 'Potri.014G138400' => 'ptr', 'Potri.016G142500' => 'ptr', 'Pp3c16_10580' => 'ppa', 'Pp3c5_25280' => 'ppa', 'Prupe.1G150000' => 'ppe', 'Prupe.1G150100' => 'ppe', 'Prupe.6G299600' => 'ppe', 'Prupe.8G245000' => 'ppe', 'Psat0s4927g0040' => 'psa', 'Psat1g052080' => 'psa', 'Psat1g183800' => 'psa', 'Psat3g113840' => 'psa', 'Psat3g126120' => 'psa', 'Psat3g126160' => 'psa', 'Psat3g158760' => 'psa', 'Psat3g158840' => 'psa', 'PSO170G2858' => 'pso', 'PSO339G0606' => 'pso', 'PSO384G4709' => 'pso', 'PSO407G0334' => 'pso', 'QL04p040276' => 'qlo', 'QL06p005458' => 'qlo', 'QL06p005472' => 'qlo', 'QL07p030546' => 'qlo', 'QL07p031519' => 'qlo', 'QL09p050949' => 'qlo', 'QL09p050966' => 'qlo', 'QL09p051067' => 'qlo', 'QL12p022706' => 'qlo', 'RcHm_v2.0_Chr2g0119601' => 'rch', 'RcHm_v2.0_Chr3g0459591' => 'rch', 'RcHm_v2.0_Chr4g0418521' => 'rch', 'RcHm_v2.0_Chr4g0418531' => 'rch', 'RcHm_v2.0_Chr4g0418541' => 'rch', 'RcHm_v2.0_Chr6g0291641' => 'rch', 'Rhsim01G0086300' => 'rsi', 'Rhsim01G0276300' => 'rsi', 'Rhsim01G0276500' => 'rsi', 'Rhsim04G0207700' => 'rsi', 'Rhsim05G0234500' => 'rsi', 'Rhsim13G0022400' => 'rsi', 'Sabra02G0167900' => 'sbr', 'Sabra04G0158500' => 'sbr', 'Sabra08G0159800' => 'sbr', 'Sabra10G0011500' => 'sbr', 'Sabra14G0104400' => 'sbr', 'SalBow2G2440' => 'sbo', 'SalBow4G2265' => 'sbo', 'Sc02g0000060' => 'sci', 'Sc05g0005020' => 'sci', 'Sc13g0003890' => 'sci', 'Sed0014865' => 'sed', 'Sed0017224' => 'sed', 'Sed0026391' => 'sed', 'SEGI_00063' => 'sgi', 'SEGI_10967' => 'sgi', 'SEGI_17510' => 'sgi', 'SEGI_24396' => 'sgi', 'SEGI_39719' => 'sgi', 'SEGI_41392' => 'sgi', 'SGA_v2.0_scaffold11G05794' => 'sas', 'SGA_v2.0_scaffold142G35607' => 'sas', 'SGA_v2.0_scaffold1G00447' => 'sas', 'SHI15388' => 'shi', 'SHI15394' => 'shi', 'SHI15396' => 'shi', 'SHI15399' => 'shi', 'SMO343G0151' => 'smo', 'SMO367G1118' => 'smo', 'Solyc01g080200.3' => 'sly', 'Solyc06g008960.3' => 'sly', 'Solyc09g064780.3' => 'sly', 'Sopen01g031980' => 'spe', 'Sopen06g003710' => 'spe', 'Sopen09g026460' => 'spe', 'Sp3g21240' => 'spa', 'Sp4g30030' => 'spa', 'TAR365G0022' => 'tar', 'TAR365G1023' => 'tar', 'TAR365G1253' => 'tar', 'TAR623G0078' => 'tar', 'TAR623G1721' => 'tar', 'TAR633G0959' => 'tar', 'THA.LOC104802225' => 'tha', 'THA.LOC104804769' => 'tha', 'THA.LOC104808660' => 'tha', 'THA.LOC104812792' => 'tha', 'Thecc.01G284000' => 'tca', 'Thecc.04G220600' => 'tca', 'Thecc.05G268900' => 'tca', 'Thecc.08G171100' => 'tca', 'Thhalv10001284m.g' => 'esa', 'Thhalv10019912m.g' => 'esa', 'TPR.G14189' => 'tpr', 'TPR.G18110' => 'tpr', 'TPR.G18130' => 'tpr', 'TPR.G18131' => 'tpr', 'TPR.G18140' => 'tpr', 'TPR.G24282' => 'tpr', 'TPR.G25221' => 'tpr', 'TPR.G29267' => 'tpr', 'TPR.G35315' => 'tpr', 'TPR.G36173' => 'tpr', 'TWI09G0794' => 'twi', 'TWI59G1348' => 'twi', 'TWI74G0430' => 'twi', 'unitig_26.g8940' => 'ugi', 'unitig_749.g13744' => 'ugi', 'unitig_749.g13745' => 'ugi', 'vmacro08269' => 'vma', 'vmacro14937' => 'vma', 'vmacro20401' => 'vma', 'VMungo0464G1349' => 'vmu', 'VMungo0540G0289' => 'vmu', 'VMungo1215G1590' => 'vmu', 'VMungo1309G0221' => 'vmu', 'VMungo1309G2815' => 'vmu', 'VMungo1383G0239' => 'vmu', 'VMungo1383G2910' => 'vmu', 'Zm00001eb095270' => 'zma', 'Zm00001eb095280' => 'zma', 'Zm00001eb111630' => 'zma', 'Zm00001eb237080' => 'zma', 'Zm00001eb273740' => 'zma', 'Zm00001eb285040' => 'zma', 'Zm00001eb330790' => 'zma', 'Zm00001eb337380' => 'zma' ), 'gf_id' => 'HOM05D001484', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001484' ), 'data_identifier' => 'HOM05D001484', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001484', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p31500' => 'bna', 'A05p00020' => 'bna', 'A07p08820' => 'bna', 'Aa31LG4G3300' => 'aar', 'Aa31LG8G10030' => 'aar', 'Actinidia00731' => 'ach', 'Actinidia11473' => 'ach', 'Actinidia23469' => 'ach', 'Actinidia24318' => 'ach', 'Actinidia40196' => 'ach', 'Actinidia40197' => 'ach', 'Actinidia40198' => 'ach', 'Ah.08g212990' => 'amhyb', 'Ah.15g091720' => 'amhyb', 'AL3G38260' => 'aly', 'AL4G47710' => 'aly', 'Aqoxy2G00671' => 'aox', 'Aqoxy2G03236' => 'aox', 'arahy.Tifrunner.gnm1.ann1.05IDCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KR684' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATY3SJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK6QJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6APGL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IDT7Z9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM073U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ0R87' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LE7RV4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT4QRX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V5ENPK' => 'arhy', 'AT2G48110' => 'ath', 'AT3G23590' => 'ath', 'ATR0626G186' => 'atr', 'ATR1127G141' => 'atr', 'Atru.chr4.2583' => 'acertr', 'Atru.chr5.1358' => 'acertr', 'Atru.chr5.1359' => 'acertr', 'Atru.chr8.46' => 'acertr', 'AUR62002640' => 'cqu', 'AUR62030055' => 'cqu', 'AUR62033713' => 'cqu', 'AUR62033714' => 'cqu', 'AUR62036795' => 'cqu', 'AUR62039891' => 'cqu', 'BcaB02g08737' => 'bca', 'BcaB04g20441' => 'bca', 'BcaB06g26509' => 'bca', 'BcaB06g26510' => 'bca', 'BcaB06g26511' => 'bca', 'BcaB06g26512' => 'bca', 'BcaB06g26513' => 'bca', 'BcaC02g12564' => 'bca', 'BcaC02g12565' => 'bca', 'BcaC02g12794' => 'bca', 'BcaC02g12795' => 'bca', 'BcaC02g12796' => 'bca', 'BcaC06g35541' => 'bca', 'BNapus_Darmor_BZH_scaffold_188p00080' => 'bna', 'BNapus_Darmor_BZH_scaffold_188p00090' => 'bna', 'BolC1t03972H' => 'bol', 'BolC1t03973H' => 'bol', 'BolC4t21680H' => 'bol', 'BolC7t41863H' => 'bol', 'BolSC55t61227H' => 'bol', 'BolSC55t61228H' => 'bol', 'BraA01t03278Z' => 'bra', 'BraA05t18998Z' => 'bra', 'BraA07t28673Z' => 'bra', 'C01p40150' => 'bna', 'C05p12370' => 'bna', 'C07p13680' => 'bna', 'CAN.G1006.16' => 'can', 'CAN.G1006.17' => 'can', 'CAN.G1170.2' => 'can', 'CAN.G962.7' => 'can', 'CANSAT25G2179' => 'cansat', 'CANSAT78G1573' => 'cansat', 'CARHR099510' => 'chi', 'CARHR143510' => 'chi', 'Carub.0003s2380' => 'cru', 'Carub.0004s3082' => 'cru', 'Ca_00614_v3' => 'car', 'Ca_07801_v3' => 'car', 'Ca_08567_v3' => 'car', 'Ca_09571_v3' => 'car', 'CBR_g19290' => 'cbr', 'Cc01_g19770' => 'ccan', 'Cc03_g03030' => 'ccan', 'CDE07G0968' => 'cde', 'CDE09G1441' => 'cde', 'Cfa006103' => 'cfa', 'Cfa015573' => 'cfa', 'Cfa016988' => 'cfa', 'Ciclev10006738m.g' => 'ccl', 'Ciclev10010920m.g' => 'ccl', 'Ciclev10018517m.g' => 'ccl', 'CiPaw.01G159200' => 'cil', 'CiPaw.02G091000' => 'cil', 'CiPaw.02G091100' => 'cil', 'CiPaw.08G103100' => 'cil', 'CiPaw.09G224900' => 'cil', 'ClCG06G005740' => 'cla', 'ClCG07G000090' => 'cla', 'ClCG07G000100' => 'cla', 'COL.COLO4_09143' => 'col', 'COL.COLO4_25124' => 'col', 'Cpa.g.sc16.34' => 'cpa', 'Cpa.g.sc3504.1' => 'cpa', 'Cpa.g.sc60.37' => 'cpa', 'CsaV3_6G018520' => 'csa', 'CsaV3_6G036860' => 'csa', 'CSS0001072' => 'camsi', 'CSS0020208' => 'camsi', 'CSS0021253' => 'camsi', 'CSS0022190' => 'camsi', 'CSS0036150' => 'camsi', 'CSS0040442' => 'camsi', 'CSS0042300' => 'camsi', 'CSS0045298' => 'camsi', 'DCAR_012449' => 'dca', 'DCAR_018405' => 'dca', 'DCAR_024573' => 'dca', 'DCAR_030591' => 'dca', 'Dinv16926' => 'din', 'Dinv32963' => 'din', 'Dinv38382' => 'din', 'Dinv38383' => 'din', 'Duzib133G0974' => 'dzi', 'Duzib138G1867' => 'dzi', 'Duzib211G0420' => 'dzi', 'Duzib212G0930' => 'dzi', 'ECA234G1645' => 'eca', 'ECA247G3467' => 'eca', 'ECA248G1703' => 'eca', 'EL10Ac3g06327' => 'bvu', 'EL10Ac7g17204' => 'bvu', 'Eucgr.A00855' => 'egr', 'Eucgr.A00858' => 'egr', 'Eucgr.H01520' => 'egr', 'Eucgr.H03604' => 'egr', 'Eucgr.L03465' => 'egr', 'Eucgr.L03466' => 'egr', 'FAN01G0988' => 'fan', 'FAN02G3892' => 'fan', 'FAN05G3381' => 'fan', 'FAN07G0967' => 'fan', 'FAN07G1493' => 'fan', 'FAN08G3125' => 'fan', 'FAN09G0402' => 'fan', 'FAN12G2594' => 'fan', 'FAN12G3879' => 'fan', 'FAN14G1546' => 'fan', 'FAN15G3626' => 'fan', 'FAN17G0588' => 'fan', 'FAN17G0609' => 'fan', 'FAN18G2817' => 'fan', 'FAN19G1305' => 'fan', 'FAN20G1787' => 'fan', 'FAN22G0073' => 'fan', 'FAN22G0352' => 'fan', 'FAN22G0368' => 'fan', 'FAN22G2273' => 'fan', 'FAN24G1998' => 'fan', 'FAN27G1317' => 'fan', 'FvH4_2g23980' => 'fve', 'FvH4_4g14380' => 'fve', 'FvH4_4g14390' => 'fve', 'FvH4_6g09250' => 'fve', 'Glyma.03G151100' => 'gma', 'Glyma.04G122550' => 'gma', 'Glyma.05G001600' => 'gma', 'Glyma.09G270766' => 'gma', 'Glyma.09G270832' => 'gma', 'Glyma.13G209800' => 'gma', 'Glyma.15G102800' => 'gma', 'Glyma.18G218900' => 'gma', 'Glyma.19G001500' => 'gma', 'Glyma.19G153600' => 'gma', 'Gohir.A02G028600' => 'ghi', 'Gohir.A08G045000' => 'ghi', 'Gohir.A11G120500' => 'ghi', 'Gohir.A12G006200' => 'ghi', 'Gohir.A12G006250' => 'ghi', 'Gohir.D02G036300' => 'ghi', 'Gohir.D08G054700' => 'ghi', 'Gohir.D11G125600' => 'ghi', 'Gohir.D12G005700' => 'ghi', 'Gorai.004G055200' => 'gra', 'Gorai.005G040400' => 'gra', 'Gorai.007G134500' => 'gra', 'Gorai.008G005500' => 'gra', 'GSVIVG01011094001' => 'vvi', 'GSVIVG01017879001' => 'vvi', 'GSVIVG01025988001' => 'vvi', 'GSVIVG01029847001' => 'vvi', 'HanXRQChr10g0282901' => 'han', 'HanXRQChr10g0310371' => 'han', 'HanXRQChr10g0315041' => 'han', 'HanXRQChr11g0327651' => 'han', 'HanXRQChr12g0359391' => 'han', 'Haze_00972' => 'cav', 'Haze_00973' => 'cav', 'Haze_00974' => 'cav', 'Haze_04747' => 'cav', 'Haze_04749' => 'cav', 'Haze_04750' => 'cav', 'Haze_21217' => 'cav', 'Hma1.2p1_1037F.1_g250680' => 'hma', 'Hma1.2p1_1644F.1_g295320' => 'hma', 'HPP92_011322' => 'vpl', 'HPP92_011323' => 'vpl', 'HPP92_011324' => 'vpl', 'HPP92_011325' => 'vpl', 'HPP92_011326' => 'vpl', 'Hund12205' => 'sun', 'Hund17957' => 'sun', 'Lalb_Chr06g0176771' => 'lal', 'Lalb_Chr18g0056021' => 'lal', 'Lalb_Chr18g0056031' => 'lal', 'Lalb_Chr18g0056041' => 'lal', 'Lalb_Chr20g0107751' => 'lal', 'Lalb_Chr20g0118371' => 'lal', 'Lj1g0010239' => 'lja', 'Lj1g0017101' => 'lja', 'Lj2A1178G40' => 'lonja', 'Lj2A54G84' => 'lonja', 'Lj2g0015248' => 'lja', 'Lj3A761T51' => 'lonja', 'Lj6g0018116' => 'lja', 'Lsat_1_v5_gn_4_136040' => 'lsa', 'Lsat_1_v5_gn_5_187461' => 'lsa', 'Lsat_1_v5_gn_5_77001' => 'lsa', 'Lsat_1_v5_gn_9_4461' => 'lsa', 'Manes.01G210100' => 'mes', 'Manes.03G185600' => 'mes', 'Manes.05G073300' => 'mes', 'Manes.09G120300' => 'mes', 'Manes.15G022100' => 'mes', 'Mapoly0096s0053' => 'mpo', 'MBI03_g14058_MAGBIO' => 'mbi', 'MBI03_g33876_MAGBIO' => 'mbi', 'MBI03_g36854_MAGBIO' => 'mbi', 'MBI17_g11997_MAGBIO' => 'mbi', 'MD03G1269000' => 'mdo', 'MD04G1179600' => 'mdo', 'MD11G1289800' => 'mdo', 'MD12G1194700' => 'mdo', 'MD13G1182100' => 'mdo', 'MD13G1182200' => 'mdo', 'MD16G1182600' => 'mdo', 'Medtr2g021400' => 'mtr', 'Medtr2g021470' => 'mtr', 'Medtr2g105810' => 'mtr', 'Medtr3g033580' => 'mtr', 'Medtr6g007970' => 'mtr', 'Medtr7g056330' => 'mtr', 'Medtr7g074290' => 'mtr', 'Medtr7g074380' => 'mtr', 'Medtr7g094550' => 'mtr', 'Medtr8g069995' => 'mtr', 'MELO3C014345.2' => 'cme', 'MELO3C021395.2' => 'cme', 'Migut.D00262' => 'egut', 'Migut.G00257' => 'egut', 'MSTRG.21575' => 'ama', 'MSTRG.3985' => 'ama', 'Nitab4.5_0000295g0140' => 'nta', 'Nitab4.5_0000732g0140' => 'nta', 'Nitab4.5_0003162g0020' => 'nta', 'Nitab4.5_0006180g0090' => 'nta', 'Nitab4.5_0006390g0010' => 'nta', 'Nitab4.5_0007392g0040' => 'nta', 'Nn1g02140' => 'nnu', 'Nn4g26168' => 'nnu', 'Nn5g26754' => 'nnu', 'Oeu001433.1' => 'oeu', 'Oeu010299.2' => 'oeu', 'Oeu011171.1' => 'oeu', 'Oeu037675.1' => 'oeu', 'Oeu038359.1' => 'oeu', 'Oeu063834.1' => 'oeu', 'Oeu063835.1' => 'oeu', 'Os05g0312000' => 'osa', 'Os07g0211101' => 'osa', 'Os07g0211200' => 'osa', 'Os07g0681500' => 'osa', 'Peaxi162Scf00095g01015' => 'pax', 'Peaxi162Scf00104g00329' => 'pax', 'Peaxi162Scf00161g00137' => 'pax', 'PGR004G1665' => 'pgr', 'PGR031G2937' => 'pgr', 'PGR119G2145' => 'pgr', 'PGSC0003DMG400004351' => 'stu', 'PGSC0003DMG400014625' => 'stu', 'PGSC0003DMG401000943' => 'stu', 'Phvul.001G148600' => 'pvu', 'Phvul.004G001700' => 'pvu', 'Phvul.006G154900' => 'pvu', 'Phvul.008G078200' => 'pvu', 'Phvul.011G136500' => 'pvu', 'Potri.002G215600' => 'ptr', 'Potri.008G201600' => 'ptr', 'Potri.014G138400' => 'ptr', 'Potri.016G142500' => 'ptr', 'Pp3c16_10580' => 'ppa', 'Pp3c5_25280' => 'ppa', 'Prupe.1G150000' => 'ppe', 'Prupe.1G150100' => 'ppe', 'Prupe.6G299600' => 'ppe', 'Prupe.8G245000' => 'ppe', 'Psat0s4927g0040' => 'psa', 'Psat1g052080' => 'psa', 'Psat1g183800' => 'psa', 'Psat3g113840' => 'psa', 'Psat3g126120' => 'psa', 'Psat3g126160' => 'psa', 'Psat3g158760' => 'psa', 'Psat3g158840' => 'psa', 'PSO170G2858' => 'pso', 'PSO339G0606' => 'pso', 'PSO384G4709' => 'pso', 'PSO407G0334' => 'pso', 'QL04p040276' => 'qlo', 'QL06p005458' => 'qlo', 'QL06p005472' => 'qlo', 'QL07p030546' => 'qlo', 'QL07p031519' => 'qlo', 'QL09p050949' => 'qlo', 'QL09p050966' => 'qlo', 'QL09p051067' => 'qlo', 'QL12p022706' => 'qlo', 'RcHm_v2.0_Chr2g0119601' => 'rch', 'RcHm_v2.0_Chr3g0459591' => 'rch', 'RcHm_v2.0_Chr4g0418521' => 'rch', 'RcHm_v2.0_Chr4g0418531' => 'rch', 'RcHm_v2.0_Chr4g0418541' => 'rch', 'RcHm_v2.0_Chr6g0291641' => 'rch', 'Rhsim01G0086300' => 'rsi', 'Rhsim01G0276300' => 'rsi', 'Rhsim01G0276500' => 'rsi', 'Rhsim04G0207700' => 'rsi', 'Rhsim05G0234500' => 'rsi', 'Rhsim13G0022400' => 'rsi', 'Sabra02G0167900' => 'sbr', 'Sabra04G0158500' => 'sbr', 'Sabra08G0159800' => 'sbr', 'Sabra10G0011500' => 'sbr', 'Sabra14G0104400' => 'sbr', 'SalBow2G2440' => 'sbo', 'SalBow4G2265' => 'sbo', 'Sc02g0000060' => 'sci', 'Sc05g0005020' => 'sci', 'Sc13g0003890' => 'sci', 'Sed0014865' => 'sed', 'Sed0017224' => 'sed', 'Sed0026391' => 'sed', 'SEGI_00063' => 'sgi', 'SEGI_10967' => 'sgi', 'SEGI_17510' => 'sgi', 'SEGI_24396' => 'sgi', 'SEGI_39719' => 'sgi', 'SEGI_41392' => 'sgi', 'SGA_v2.0_scaffold11G05794' => 'sas', 'SGA_v2.0_scaffold142G35607' => 'sas', 'SGA_v2.0_scaffold1G00447' => 'sas', 'SHI15388' => 'shi', 'SHI15394' => 'shi', 'SHI15396' => 'shi', 'SHI15399' => 'shi', 'SMO343G0151' => 'smo', 'SMO367G1118' => 'smo', 'Solyc01g080200.3' => 'sly', 'Solyc06g008960.3' => 'sly', 'Solyc09g064780.3' => 'sly', 'Sopen01g031980' => 'spe', 'Sopen06g003710' => 'spe', 'Sopen09g026460' => 'spe', 'Sp3g21240' => 'spa', 'Sp4g30030' => 'spa', 'TAR365G0022' => 'tar', 'TAR365G1023' => 'tar', 'TAR365G1253' => 'tar', 'TAR623G0078' => 'tar', 'TAR623G1721' => 'tar', 'TAR633G0959' => 'tar', 'THA.LOC104802225' => 'tha', 'THA.LOC104804769' => 'tha', 'THA.LOC104808660' => 'tha', 'THA.LOC104812792' => 'tha', 'Thecc.01G284000' => 'tca', 'Thecc.04G220600' => 'tca', 'Thecc.05G268900' => 'tca', 'Thecc.08G171100' => 'tca', 'Thhalv10001284m.g' => 'esa', 'Thhalv10019912m.g' => 'esa', 'TPR.G14189' => 'tpr', 'TPR.G18110' => 'tpr', 'TPR.G18130' => 'tpr', 'TPR.G18131' => 'tpr', 'TPR.G18140' => 'tpr', 'TPR.G24282' => 'tpr', 'TPR.G25221' => 'tpr', 'TPR.G29267' => 'tpr', 'TPR.G35315' => 'tpr', 'TPR.G36173' => 'tpr', 'TWI09G0794' => 'twi', 'TWI59G1348' => 'twi', 'TWI74G0430' => 'twi', 'unitig_26.g8940' => 'ugi', 'unitig_749.g13744' => 'ugi', 'unitig_749.g13745' => 'ugi', 'vmacro08269' => 'vma', 'vmacro14937' => 'vma', 'vmacro20401' => 'vma', 'VMungo0464G1349' => 'vmu', 'VMungo0540G0289' => 'vmu', 'VMungo1215G1590' => 'vmu', 'VMungo1309G0221' => 'vmu', 'VMungo1309G2815' => 'vmu', 'VMungo1383G0239' => 'vmu', 'VMungo1383G2910' => 'vmu', 'Zm00001eb095270' => 'zma', 'Zm00001eb095280' => 'zma', 'Zm00001eb111630' => 'zma', 'Zm00001eb237080' => 'zma', 'Zm00001eb273740' => 'zma', 'Zm00001eb285040' => 'zma', 'Zm00001eb330790' => 'zma', 'Zm00001eb337380' => 'zma' ) $gf_id = 'HOM05D001484' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001484' ) $data_identifier = 'HOM05D001484' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 2, 'aly' => (int) 2, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 22, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 7, 'hma' => (int) 2, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 7, 'mtr' => (int) 10, 'cme' => (int) 2, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 4, 'ppa' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 4, 'qlo' => (int) 9, 'rch' => (int) 6, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 10, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 7, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb337380' $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' => 'HOM05D001484', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p31500' => 'bna', 'A05p00020' => 'bna', 'A07p08820' => 'bna', 'Aa31LG4G3300' => 'aar', 'Aa31LG8G10030' => 'aar', 'Actinidia00731' => 'ach', 'Actinidia11473' => 'ach', 'Actinidia23469' => 'ach', 'Actinidia24318' => 'ach', 'Actinidia40196' => 'ach', 'Actinidia40197' => 'ach', 'Actinidia40198' => 'ach', 'Ah.08g212990' => 'amhyb', 'Ah.15g091720' => 'amhyb', 'AL3G38260' => 'aly', 'AL4G47710' => 'aly', 'Aqoxy2G00671' => 'aox', 'Aqoxy2G03236' => 'aox', 'arahy.Tifrunner.gnm1.ann1.05IDCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KR684' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATY3SJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK6QJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6APGL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IDT7Z9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM073U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ0R87' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LE7RV4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT4QRX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V5ENPK' => 'arhy', 'AT2G48110' => 'ath', 'AT3G23590' => 'ath', 'ATR0626G186' => 'atr', 'ATR1127G141' => 'atr', 'Atru.chr4.2583' => 'acertr', 'Atru.chr5.1358' => 'acertr', 'Atru.chr5.1359' => 'acertr', 'Atru.chr8.46' => 'acertr', 'AUR62002640' => 'cqu', 'AUR62030055' => 'cqu', 'AUR62033713' => 'cqu', 'AUR62033714' => 'cqu', 'AUR62036795' => 'cqu', 'AUR62039891' => 'cqu', 'BcaB02g08737' => 'bca', 'BcaB04g20441' => 'bca', 'BcaB06g26509' => 'bca', 'BcaB06g26510' => 'bca', 'BcaB06g26511' => 'bca', 'BcaB06g26512' => 'bca', 'BcaB06g26513' => 'bca', 'BcaC02g12564' => 'bca', 'BcaC02g12565' => 'bca', 'BcaC02g12794' => 'bca', 'BcaC02g12795' => 'bca', 'BcaC02g12796' => 'bca', 'BcaC06g35541' => 'bca', 'BNapus_Darmor_BZH_scaffold_188p00080' => 'bna', 'BNapus_Darmor_BZH_scaffold_188p00090' => 'bna', 'BolC1t03972H' => 'bol', 'BolC1t03973H' => 'bol', 'BolC4t21680H' => 'bol', 'BolC7t41863H' => 'bol', 'BolSC55t61227H' => 'bol', 'BolSC55t61228H' => 'bol', 'BraA01t03278Z' => 'bra', 'BraA05t18998Z' => 'bra', 'BraA07t28673Z' => 'bra', 'C01p40150' => 'bna', 'C05p12370' => 'bna', 'C07p13680' => 'bna', 'CAN.G1006.16' => 'can', 'CAN.G1006.17' => 'can', 'CAN.G1170.2' => 'can', 'CAN.G962.7' => 'can', 'CANSAT25G2179' => 'cansat', 'CANSAT78G1573' => 'cansat', 'CARHR099510' => 'chi', 'CARHR143510' => 'chi', 'Carub.0003s2380' => 'cru', 'Carub.0004s3082' => 'cru', 'Ca_00614_v3' => 'car', 'Ca_07801_v3' => 'car', 'Ca_08567_v3' => 'car', 'Ca_09571_v3' => 'car', 'CBR_g19290' => 'cbr', 'Cc01_g19770' => 'ccan', 'Cc03_g03030' => 'ccan', 'CDE07G0968' => 'cde', 'CDE09G1441' => 'cde', 'Cfa006103' => 'cfa', 'Cfa015573' => 'cfa', 'Cfa016988' => 'cfa', 'Ciclev10006738m.g' => 'ccl', 'Ciclev10010920m.g' => 'ccl', 'Ciclev10018517m.g' => 'ccl', 'CiPaw.01G159200' => 'cil', 'CiPaw.02G091000' => 'cil', 'CiPaw.02G091100' => 'cil', 'CiPaw.08G103100' => 'cil', 'CiPaw.09G224900' => 'cil', 'ClCG06G005740' => 'cla', 'ClCG07G000090' => 'cla', 'ClCG07G000100' => 'cla', 'COL.COLO4_09143' => 'col', 'COL.COLO4_25124' => 'col', 'Cpa.g.sc16.34' => 'cpa', 'Cpa.g.sc3504.1' => 'cpa', 'Cpa.g.sc60.37' => 'cpa', 'CsaV3_6G018520' => 'csa', 'CsaV3_6G036860' => 'csa', 'CSS0001072' => 'camsi', 'CSS0020208' => 'camsi', 'CSS0021253' => 'camsi', 'CSS0022190' => 'camsi', 'CSS0036150' => 'camsi', 'CSS0040442' => 'camsi', 'CSS0042300' => 'camsi', 'CSS0045298' => 'camsi', 'DCAR_012449' => 'dca', 'DCAR_018405' => 'dca', 'DCAR_024573' => 'dca', 'DCAR_030591' => 'dca', 'Dinv16926' => 'din', 'Dinv32963' => 'din', 'Dinv38382' => 'din', 'Dinv38383' => 'din', 'Duzib133G0974' => 'dzi', 'Duzib138G1867' => 'dzi', 'Duzib211G0420' => 'dzi', 'Duzib212G0930' => 'dzi', 'ECA234G1645' => 'eca', 'ECA247G3467' => 'eca', 'ECA248G1703' => 'eca', 'EL10Ac3g06327' => 'bvu', 'EL10Ac7g17204' => 'bvu', 'Eucgr.A00855' => 'egr', 'Eucgr.A00858' => 'egr', 'Eucgr.H01520' => 'egr', 'Eucgr.H03604' => 'egr', 'Eucgr.L03465' => 'egr', 'Eucgr.L03466' => 'egr', 'FAN01G0988' => 'fan', 'FAN02G3892' => 'fan', 'FAN05G3381' => 'fan', 'FAN07G0967' => 'fan', 'FAN07G1493' => 'fan', 'FAN08G3125' => 'fan', 'FAN09G0402' => 'fan', 'FAN12G2594' => 'fan', 'FAN12G3879' => 'fan', 'FAN14G1546' => 'fan', 'FAN15G3626' => 'fan', 'FAN17G0588' => 'fan', 'FAN17G0609' => 'fan', 'FAN18G2817' => 'fan', 'FAN19G1305' => 'fan', 'FAN20G1787' => 'fan', 'FAN22G0073' => 'fan', 'FAN22G0352' => 'fan', 'FAN22G0368' => 'fan', 'FAN22G2273' => 'fan', 'FAN24G1998' => 'fan', 'FAN27G1317' => 'fan', 'FvH4_2g23980' => 'fve', 'FvH4_4g14380' => 'fve', 'FvH4_4g14390' => 'fve', 'FvH4_6g09250' => 'fve', 'Glyma.03G151100' => 'gma', 'Glyma.04G122550' => 'gma', 'Glyma.05G001600' => 'gma', 'Glyma.09G270766' => 'gma', 'Glyma.09G270832' => 'gma', 'Glyma.13G209800' => 'gma', 'Glyma.15G102800' => 'gma', 'Glyma.18G218900' => 'gma', 'Glyma.19G001500' => 'gma', 'Glyma.19G153600' => 'gma', 'Gohir.A02G028600' => 'ghi', 'Gohir.A08G045000' => 'ghi', 'Gohir.A11G120500' => 'ghi', 'Gohir.A12G006200' => 'ghi', 'Gohir.A12G006250' => 'ghi', 'Gohir.D02G036300' => 'ghi', 'Gohir.D08G054700' => 'ghi', 'Gohir.D11G125600' => 'ghi', 'Gohir.D12G005700' => 'ghi', 'Gorai.004G055200' => 'gra', 'Gorai.005G040400' => 'gra', 'Gorai.007G134500' => 'gra', 'Gorai.008G005500' => 'gra', 'GSVIVG01011094001' => 'vvi', 'GSVIVG01017879001' => 'vvi', 'GSVIVG01025988001' => 'vvi', 'GSVIVG01029847001' => 'vvi', 'HanXRQChr10g0282901' => 'han', 'HanXRQChr10g0310371' => 'han', 'HanXRQChr10g0315041' => 'han', 'HanXRQChr11g0327651' => 'han', 'HanXRQChr12g0359391' => 'han', 'Haze_00972' => 'cav', 'Haze_00973' => 'cav', 'Haze_00974' => 'cav', 'Haze_04747' => 'cav', 'Haze_04749' => 'cav', 'Haze_04750' => 'cav', 'Haze_21217' => 'cav', 'Hma1.2p1_1037F.1_g250680' => 'hma', 'Hma1.2p1_1644F.1_g295320' => 'hma', 'HPP92_011322' => 'vpl', 'HPP92_011323' => 'vpl', 'HPP92_011324' => 'vpl', 'HPP92_011325' => 'vpl', 'HPP92_011326' => 'vpl', 'Hund12205' => 'sun', 'Hund17957' => 'sun', 'Lalb_Chr06g0176771' => 'lal', 'Lalb_Chr18g0056021' => 'lal', 'Lalb_Chr18g0056031' => 'lal', 'Lalb_Chr18g0056041' => 'lal', 'Lalb_Chr20g0107751' => 'lal', 'Lalb_Chr20g0118371' => 'lal', 'Lj1g0010239' => 'lja', 'Lj1g0017101' => 'lja', 'Lj2A1178G40' => 'lonja', 'Lj2A54G84' => 'lonja', 'Lj2g0015248' => 'lja', 'Lj3A761T51' => 'lonja', 'Lj6g0018116' => 'lja', 'Lsat_1_v5_gn_4_136040' => 'lsa', 'Lsat_1_v5_gn_5_187461' => 'lsa', 'Lsat_1_v5_gn_5_77001' => 'lsa', 'Lsat_1_v5_gn_9_4461' => 'lsa', 'Manes.01G210100' => 'mes', 'Manes.03G185600' => 'mes', 'Manes.05G073300' => 'mes', 'Manes.09G120300' => 'mes', 'Manes.15G022100' => 'mes', 'Mapoly0096s0053' => 'mpo', 'MBI03_g14058_MAGBIO' => 'mbi', 'MBI03_g33876_MAGBIO' => 'mbi', 'MBI03_g36854_MAGBIO' => 'mbi', 'MBI17_g11997_MAGBIO' => 'mbi', 'MD03G1269000' => 'mdo', 'MD04G1179600' => 'mdo', 'MD11G1289800' => 'mdo', 'MD12G1194700' => 'mdo', 'MD13G1182100' => 'mdo', 'MD13G1182200' => 'mdo', 'MD16G1182600' => 'mdo', 'Medtr2g021400' => 'mtr', 'Medtr2g021470' => 'mtr', 'Medtr2g105810' => 'mtr', 'Medtr3g033580' => 'mtr', 'Medtr6g007970' => 'mtr', 'Medtr7g056330' => 'mtr', 'Medtr7g074290' => 'mtr', 'Medtr7g074380' => 'mtr', 'Medtr7g094550' => 'mtr', 'Medtr8g069995' => 'mtr', 'MELO3C014345.2' => 'cme', 'MELO3C021395.2' => 'cme', 'Migut.D00262' => 'egut', 'Migut.G00257' => 'egut', 'MSTRG.21575' => 'ama', 'MSTRG.3985' => 'ama', 'Nitab4.5_0000295g0140' => 'nta', 'Nitab4.5_0000732g0140' => 'nta', 'Nitab4.5_0003162g0020' => 'nta', 'Nitab4.5_0006180g0090' => 'nta', 'Nitab4.5_0006390g0010' => 'nta', 'Nitab4.5_0007392g0040' => 'nta', 'Nn1g02140' => 'nnu', 'Nn4g26168' => 'nnu', 'Nn5g26754' => 'nnu', 'Oeu001433.1' => 'oeu', 'Oeu010299.2' => 'oeu', 'Oeu011171.1' => 'oeu', 'Oeu037675.1' => 'oeu', 'Oeu038359.1' => 'oeu', 'Oeu063834.1' => 'oeu', 'Oeu063835.1' => 'oeu', 'Os05g0312000' => 'osa', 'Os07g0211101' => 'osa', 'Os07g0211200' => 'osa', 'Os07g0681500' => 'osa', 'Peaxi162Scf00095g01015' => 'pax', 'Peaxi162Scf00104g00329' => 'pax', 'Peaxi162Scf00161g00137' => 'pax', 'PGR004G1665' => 'pgr', 'PGR031G2937' => 'pgr', 'PGR119G2145' => 'pgr', 'PGSC0003DMG400004351' => 'stu', 'PGSC0003DMG400014625' => 'stu', 'PGSC0003DMG401000943' => 'stu', 'Phvul.001G148600' => 'pvu', 'Phvul.004G001700' => 'pvu', 'Phvul.006G154900' => 'pvu', 'Phvul.008G078200' => 'pvu', 'Phvul.011G136500' => 'pvu', 'Potri.002G215600' => 'ptr', 'Potri.008G201600' => 'ptr', 'Potri.014G138400' => 'ptr', 'Potri.016G142500' => 'ptr', 'Pp3c16_10580' => 'ppa', 'Pp3c5_25280' => 'ppa', 'Prupe.1G150000' => 'ppe', 'Prupe.1G150100' => 'ppe', 'Prupe.6G299600' => 'ppe', 'Prupe.8G245000' => 'ppe', 'Psat0s4927g0040' => 'psa', 'Psat1g052080' => 'psa', 'Psat1g183800' => 'psa', 'Psat3g113840' => 'psa', 'Psat3g126120' => 'psa', 'Psat3g126160' => 'psa', 'Psat3g158760' => 'psa', 'Psat3g158840' => 'psa', 'PSO170G2858' => 'pso', 'PSO339G0606' => 'pso', 'PSO384G4709' => 'pso', 'PSO407G0334' => 'pso', 'QL04p040276' => 'qlo', 'QL06p005458' => 'qlo', 'QL06p005472' => 'qlo', 'QL07p030546' => 'qlo', 'QL07p031519' => 'qlo', 'QL09p050949' => 'qlo', 'QL09p050966' => 'qlo', 'QL09p051067' => 'qlo', 'QL12p022706' => 'qlo', 'RcHm_v2.0_Chr2g0119601' => 'rch', 'RcHm_v2.0_Chr3g0459591' => 'rch', 'RcHm_v2.0_Chr4g0418521' => 'rch', 'RcHm_v2.0_Chr4g0418531' => 'rch', 'RcHm_v2.0_Chr4g0418541' => 'rch', 'RcHm_v2.0_Chr6g0291641' => 'rch', 'Rhsim01G0086300' => 'rsi', 'Rhsim01G0276300' => 'rsi', 'Rhsim01G0276500' => 'rsi', 'Rhsim04G0207700' => 'rsi', 'Rhsim05G0234500' => 'rsi', 'Rhsim13G0022400' => 'rsi', 'Sabra02G0167900' => 'sbr', 'Sabra04G0158500' => 'sbr', 'Sabra08G0159800' => 'sbr', 'Sabra10G0011500' => 'sbr', 'Sabra14G0104400' => 'sbr', 'SalBow2G2440' => 'sbo', 'SalBow4G2265' => 'sbo', 'Sc02g0000060' => 'sci', 'Sc05g0005020' => 'sci', 'Sc13g0003890' => 'sci', 'Sed0014865' => 'sed', 'Sed0017224' => 'sed', 'Sed0026391' => 'sed', 'SEGI_00063' => 'sgi', 'SEGI_10967' => 'sgi', 'SEGI_17510' => 'sgi', 'SEGI_24396' => 'sgi', 'SEGI_39719' => 'sgi', 'SEGI_41392' => 'sgi', 'SGA_v2.0_scaffold11G05794' => 'sas', 'SGA_v2.0_scaffold142G35607' => 'sas', 'SGA_v2.0_scaffold1G00447' => 'sas', 'SHI15388' => 'shi', 'SHI15394' => 'shi', 'SHI15396' => 'shi', 'SHI15399' => 'shi', 'SMO343G0151' => 'smo', 'SMO367G1118' => 'smo', 'Solyc01g080200.3' => 'sly', 'Solyc06g008960.3' => 'sly', 'Solyc09g064780.3' => 'sly', 'Sopen01g031980' => 'spe', 'Sopen06g003710' => 'spe', 'Sopen09g026460' => 'spe', 'Sp3g21240' => 'spa', 'Sp4g30030' => 'spa', 'TAR365G0022' => 'tar', 'TAR365G1023' => 'tar', 'TAR365G1253' => 'tar', 'TAR623G0078' => 'tar', 'TAR623G1721' => 'tar', 'TAR633G0959' => 'tar', 'THA.LOC104802225' => 'tha', 'THA.LOC104804769' => 'tha', 'THA.LOC104808660' => 'tha', 'THA.LOC104812792' => 'tha', 'Thecc.01G284000' => 'tca', 'Thecc.04G220600' => 'tca', 'Thecc.05G268900' => 'tca', 'Thecc.08G171100' => 'tca', 'Thhalv10001284m.g' => 'esa', 'Thhalv10019912m.g' => 'esa', 'TPR.G14189' => 'tpr', 'TPR.G18110' => 'tpr', 'TPR.G18130' => 'tpr', 'TPR.G18131' => 'tpr', 'TPR.G18140' => 'tpr', 'TPR.G24282' => 'tpr', 'TPR.G25221' => 'tpr', 'TPR.G29267' => 'tpr', 'TPR.G35315' => 'tpr', 'TPR.G36173' => 'tpr', 'TWI09G0794' => 'twi', 'TWI59G1348' => 'twi', 'TWI74G0430' => 'twi', 'unitig_26.g8940' => 'ugi', 'unitig_749.g13744' => 'ugi', 'unitig_749.g13745' => 'ugi', 'vmacro08269' => 'vma', 'vmacro14937' => 'vma', 'vmacro20401' => 'vma', 'VMungo0464G1349' => 'vmu', 'VMungo0540G0289' => 'vmu', 'VMungo1215G1590' => 'vmu', 'VMungo1309G0221' => 'vmu', 'VMungo1309G2815' => 'vmu', 'VMungo1383G0239' => 'vmu', 'VMungo1383G2910' => 'vmu', 'Zm00001eb095270' => 'zma', 'Zm00001eb095280' => 'zma', 'Zm00001eb111630' => 'zma', 'Zm00001eb237080' => 'zma', 'Zm00001eb273740' => 'zma', 'Zm00001eb285040' => 'zma', 'Zm00001eb330790' => 'zma', 'Zm00001eb337380' => 'zma' ), 'gf_id' => 'HOM05D001484', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001484' ), 'data_identifier' => 'HOM05D001484', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001484', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p31500' => 'bna', 'A05p00020' => 'bna', 'A07p08820' => 'bna', 'Aa31LG4G3300' => 'aar', 'Aa31LG8G10030' => 'aar', 'Actinidia00731' => 'ach', 'Actinidia11473' => 'ach', 'Actinidia23469' => 'ach', 'Actinidia24318' => 'ach', 'Actinidia40196' => 'ach', 'Actinidia40197' => 'ach', 'Actinidia40198' => 'ach', 'Ah.08g212990' => 'amhyb', 'Ah.15g091720' => 'amhyb', 'AL3G38260' => 'aly', 'AL4G47710' => 'aly', 'Aqoxy2G00671' => 'aox', 'Aqoxy2G03236' => 'aox', 'arahy.Tifrunner.gnm1.ann1.05IDCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KR684' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATY3SJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK6QJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6APGL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IDT7Z9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM073U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ0R87' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LE7RV4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT4QRX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V5ENPK' => 'arhy', 'AT2G48110' => 'ath', 'AT3G23590' => 'ath', 'ATR0626G186' => 'atr', 'ATR1127G141' => 'atr', 'Atru.chr4.2583' => 'acertr', 'Atru.chr5.1358' => 'acertr', 'Atru.chr5.1359' => 'acertr', 'Atru.chr8.46' => 'acertr', 'AUR62002640' => 'cqu', 'AUR62030055' => 'cqu', 'AUR62033713' => 'cqu', 'AUR62033714' => 'cqu', 'AUR62036795' => 'cqu', 'AUR62039891' => 'cqu', 'BcaB02g08737' => 'bca', 'BcaB04g20441' => 'bca', 'BcaB06g26509' => 'bca', 'BcaB06g26510' => 'bca', 'BcaB06g26511' => 'bca', 'BcaB06g26512' => 'bca', 'BcaB06g26513' => 'bca', 'BcaC02g12564' => 'bca', 'BcaC02g12565' => 'bca', 'BcaC02g12794' => 'bca', 'BcaC02g12795' => 'bca', 'BcaC02g12796' => 'bca', 'BcaC06g35541' => 'bca', 'BNapus_Darmor_BZH_scaffold_188p00080' => 'bna', 'BNapus_Darmor_BZH_scaffold_188p00090' => 'bna', 'BolC1t03972H' => 'bol', 'BolC1t03973H' => 'bol', 'BolC4t21680H' => 'bol', 'BolC7t41863H' => 'bol', 'BolSC55t61227H' => 'bol', 'BolSC55t61228H' => 'bol', 'BraA01t03278Z' => 'bra', 'BraA05t18998Z' => 'bra', 'BraA07t28673Z' => 'bra', 'C01p40150' => 'bna', 'C05p12370' => 'bna', 'C07p13680' => 'bna', 'CAN.G1006.16' => 'can', 'CAN.G1006.17' => 'can', 'CAN.G1170.2' => 'can', 'CAN.G962.7' => 'can', 'CANSAT25G2179' => 'cansat', 'CANSAT78G1573' => 'cansat', 'CARHR099510' => 'chi', 'CARHR143510' => 'chi', 'Carub.0003s2380' => 'cru', 'Carub.0004s3082' => 'cru', 'Ca_00614_v3' => 'car', 'Ca_07801_v3' => 'car', 'Ca_08567_v3' => 'car', 'Ca_09571_v3' => 'car', 'CBR_g19290' => 'cbr', 'Cc01_g19770' => 'ccan', 'Cc03_g03030' => 'ccan', 'CDE07G0968' => 'cde', 'CDE09G1441' => 'cde', 'Cfa006103' => 'cfa', 'Cfa015573' => 'cfa', 'Cfa016988' => 'cfa', 'Ciclev10006738m.g' => 'ccl', 'Ciclev10010920m.g' => 'ccl', 'Ciclev10018517m.g' => 'ccl', 'CiPaw.01G159200' => 'cil', 'CiPaw.02G091000' => 'cil', 'CiPaw.02G091100' => 'cil', 'CiPaw.08G103100' => 'cil', 'CiPaw.09G224900' => 'cil', 'ClCG06G005740' => 'cla', 'ClCG07G000090' => 'cla', 'ClCG07G000100' => 'cla', 'COL.COLO4_09143' => 'col', 'COL.COLO4_25124' => 'col', 'Cpa.g.sc16.34' => 'cpa', 'Cpa.g.sc3504.1' => 'cpa', 'Cpa.g.sc60.37' => 'cpa', 'CsaV3_6G018520' => 'csa', 'CsaV3_6G036860' => 'csa', 'CSS0001072' => 'camsi', 'CSS0020208' => 'camsi', 'CSS0021253' => 'camsi', 'CSS0022190' => 'camsi', 'CSS0036150' => 'camsi', 'CSS0040442' => 'camsi', 'CSS0042300' => 'camsi', 'CSS0045298' => 'camsi', 'DCAR_012449' => 'dca', 'DCAR_018405' => 'dca', 'DCAR_024573' => 'dca', 'DCAR_030591' => 'dca', 'Dinv16926' => 'din', 'Dinv32963' => 'din', 'Dinv38382' => 'din', 'Dinv38383' => 'din', 'Duzib133G0974' => 'dzi', 'Duzib138G1867' => 'dzi', 'Duzib211G0420' => 'dzi', 'Duzib212G0930' => 'dzi', 'ECA234G1645' => 'eca', 'ECA247G3467' => 'eca', 'ECA248G1703' => 'eca', 'EL10Ac3g06327' => 'bvu', 'EL10Ac7g17204' => 'bvu', 'Eucgr.A00855' => 'egr', 'Eucgr.A00858' => 'egr', 'Eucgr.H01520' => 'egr', 'Eucgr.H03604' => 'egr', 'Eucgr.L03465' => 'egr', 'Eucgr.L03466' => 'egr', 'FAN01G0988' => 'fan', 'FAN02G3892' => 'fan', 'FAN05G3381' => 'fan', 'FAN07G0967' => 'fan', 'FAN07G1493' => 'fan', 'FAN08G3125' => 'fan', 'FAN09G0402' => 'fan', 'FAN12G2594' => 'fan', 'FAN12G3879' => 'fan', 'FAN14G1546' => 'fan', 'FAN15G3626' => 'fan', 'FAN17G0588' => 'fan', 'FAN17G0609' => 'fan', 'FAN18G2817' => 'fan', 'FAN19G1305' => 'fan', 'FAN20G1787' => 'fan', 'FAN22G0073' => 'fan', 'FAN22G0352' => 'fan', 'FAN22G0368' => 'fan', 'FAN22G2273' => 'fan', 'FAN24G1998' => 'fan', 'FAN27G1317' => 'fan', 'FvH4_2g23980' => 'fve', 'FvH4_4g14380' => 'fve', 'FvH4_4g14390' => 'fve', 'FvH4_6g09250' => 'fve', 'Glyma.03G151100' => 'gma', 'Glyma.04G122550' => 'gma', 'Glyma.05G001600' => 'gma', 'Glyma.09G270766' => 'gma', 'Glyma.09G270832' => 'gma', 'Glyma.13G209800' => 'gma', 'Glyma.15G102800' => 'gma', 'Glyma.18G218900' => 'gma', 'Glyma.19G001500' => 'gma', 'Glyma.19G153600' => 'gma', 'Gohir.A02G028600' => 'ghi', 'Gohir.A08G045000' => 'ghi', 'Gohir.A11G120500' => 'ghi', 'Gohir.A12G006200' => 'ghi', 'Gohir.A12G006250' => 'ghi', 'Gohir.D02G036300' => 'ghi', 'Gohir.D08G054700' => 'ghi', 'Gohir.D11G125600' => 'ghi', 'Gohir.D12G005700' => 'ghi', 'Gorai.004G055200' => 'gra', 'Gorai.005G040400' => 'gra', 'Gorai.007G134500' => 'gra', 'Gorai.008G005500' => 'gra', 'GSVIVG01011094001' => 'vvi', 'GSVIVG01017879001' => 'vvi', 'GSVIVG01025988001' => 'vvi', 'GSVIVG01029847001' => 'vvi', 'HanXRQChr10g0282901' => 'han', 'HanXRQChr10g0310371' => 'han', 'HanXRQChr10g0315041' => 'han', 'HanXRQChr11g0327651' => 'han', 'HanXRQChr12g0359391' => 'han', 'Haze_00972' => 'cav', 'Haze_00973' => 'cav', 'Haze_00974' => 'cav', 'Haze_04747' => 'cav', 'Haze_04749' => 'cav', 'Haze_04750' => 'cav', 'Haze_21217' => 'cav', 'Hma1.2p1_1037F.1_g250680' => 'hma', 'Hma1.2p1_1644F.1_g295320' => 'hma', 'HPP92_011322' => 'vpl', 'HPP92_011323' => 'vpl', 'HPP92_011324' => 'vpl', 'HPP92_011325' => 'vpl', 'HPP92_011326' => 'vpl', 'Hund12205' => 'sun', 'Hund17957' => 'sun', 'Lalb_Chr06g0176771' => 'lal', 'Lalb_Chr18g0056021' => 'lal', 'Lalb_Chr18g0056031' => 'lal', 'Lalb_Chr18g0056041' => 'lal', 'Lalb_Chr20g0107751' => 'lal', 'Lalb_Chr20g0118371' => 'lal', 'Lj1g0010239' => 'lja', 'Lj1g0017101' => 'lja', 'Lj2A1178G40' => 'lonja', 'Lj2A54G84' => 'lonja', 'Lj2g0015248' => 'lja', 'Lj3A761T51' => 'lonja', 'Lj6g0018116' => 'lja', 'Lsat_1_v5_gn_4_136040' => 'lsa', 'Lsat_1_v5_gn_5_187461' => 'lsa', 'Lsat_1_v5_gn_5_77001' => 'lsa', 'Lsat_1_v5_gn_9_4461' => 'lsa', 'Manes.01G210100' => 'mes', 'Manes.03G185600' => 'mes', 'Manes.05G073300' => 'mes', 'Manes.09G120300' => 'mes', 'Manes.15G022100' => 'mes', 'Mapoly0096s0053' => 'mpo', 'MBI03_g14058_MAGBIO' => 'mbi', 'MBI03_g33876_MAGBIO' => 'mbi', 'MBI03_g36854_MAGBIO' => 'mbi', 'MBI17_g11997_MAGBIO' => 'mbi', 'MD03G1269000' => 'mdo', 'MD04G1179600' => 'mdo', 'MD11G1289800' => 'mdo', 'MD12G1194700' => 'mdo', 'MD13G1182100' => 'mdo', 'MD13G1182200' => 'mdo', 'MD16G1182600' => 'mdo', 'Medtr2g021400' => 'mtr', 'Medtr2g021470' => 'mtr', 'Medtr2g105810' => 'mtr', 'Medtr3g033580' => 'mtr', 'Medtr6g007970' => 'mtr', 'Medtr7g056330' => 'mtr', 'Medtr7g074290' => 'mtr', 'Medtr7g074380' => 'mtr', 'Medtr7g094550' => 'mtr', 'Medtr8g069995' => 'mtr', 'MELO3C014345.2' => 'cme', 'MELO3C021395.2' => 'cme', 'Migut.D00262' => 'egut', 'Migut.G00257' => 'egut', 'MSTRG.21575' => 'ama', 'MSTRG.3985' => 'ama', 'Nitab4.5_0000295g0140' => 'nta', 'Nitab4.5_0000732g0140' => 'nta', 'Nitab4.5_0003162g0020' => 'nta', 'Nitab4.5_0006180g0090' => 'nta', 'Nitab4.5_0006390g0010' => 'nta', 'Nitab4.5_0007392g0040' => 'nta', 'Nn1g02140' => 'nnu', 'Nn4g26168' => 'nnu', 'Nn5g26754' => 'nnu', 'Oeu001433.1' => 'oeu', 'Oeu010299.2' => 'oeu', 'Oeu011171.1' => 'oeu', 'Oeu037675.1' => 'oeu', 'Oeu038359.1' => 'oeu', 'Oeu063834.1' => 'oeu', 'Oeu063835.1' => 'oeu', 'Os05g0312000' => 'osa', 'Os07g0211101' => 'osa', 'Os07g0211200' => 'osa', 'Os07g0681500' => 'osa', 'Peaxi162Scf00095g01015' => 'pax', 'Peaxi162Scf00104g00329' => 'pax', 'Peaxi162Scf00161g00137' => 'pax', 'PGR004G1665' => 'pgr', 'PGR031G2937' => 'pgr', 'PGR119G2145' => 'pgr', 'PGSC0003DMG400004351' => 'stu', 'PGSC0003DMG400014625' => 'stu', 'PGSC0003DMG401000943' => 'stu', 'Phvul.001G148600' => 'pvu', 'Phvul.004G001700' => 'pvu', 'Phvul.006G154900' => 'pvu', 'Phvul.008G078200' => 'pvu', 'Phvul.011G136500' => 'pvu', 'Potri.002G215600' => 'ptr', 'Potri.008G201600' => 'ptr', 'Potri.014G138400' => 'ptr', 'Potri.016G142500' => 'ptr', 'Pp3c16_10580' => 'ppa', 'Pp3c5_25280' => 'ppa', 'Prupe.1G150000' => 'ppe', 'Prupe.1G150100' => 'ppe', 'Prupe.6G299600' => 'ppe', 'Prupe.8G245000' => 'ppe', 'Psat0s4927g0040' => 'psa', 'Psat1g052080' => 'psa', 'Psat1g183800' => 'psa', 'Psat3g113840' => 'psa', 'Psat3g126120' => 'psa', 'Psat3g126160' => 'psa', 'Psat3g158760' => 'psa', 'Psat3g158840' => 'psa', 'PSO170G2858' => 'pso', 'PSO339G0606' => 'pso', 'PSO384G4709' => 'pso', 'PSO407G0334' => 'pso', 'QL04p040276' => 'qlo', 'QL06p005458' => 'qlo', 'QL06p005472' => 'qlo', 'QL07p030546' => 'qlo', 'QL07p031519' => 'qlo', 'QL09p050949' => 'qlo', 'QL09p050966' => 'qlo', 'QL09p051067' => 'qlo', 'QL12p022706' => 'qlo', 'RcHm_v2.0_Chr2g0119601' => 'rch', 'RcHm_v2.0_Chr3g0459591' => 'rch', 'RcHm_v2.0_Chr4g0418521' => 'rch', 'RcHm_v2.0_Chr4g0418531' => 'rch', 'RcHm_v2.0_Chr4g0418541' => 'rch', 'RcHm_v2.0_Chr6g0291641' => 'rch', 'Rhsim01G0086300' => 'rsi', 'Rhsim01G0276300' => 'rsi', 'Rhsim01G0276500' => 'rsi', 'Rhsim04G0207700' => 'rsi', 'Rhsim05G0234500' => 'rsi', 'Rhsim13G0022400' => 'rsi', 'Sabra02G0167900' => 'sbr', 'Sabra04G0158500' => 'sbr', 'Sabra08G0159800' => 'sbr', 'Sabra10G0011500' => 'sbr', 'Sabra14G0104400' => 'sbr', 'SalBow2G2440' => 'sbo', 'SalBow4G2265' => 'sbo', 'Sc02g0000060' => 'sci', 'Sc05g0005020' => 'sci', 'Sc13g0003890' => 'sci', 'Sed0014865' => 'sed', 'Sed0017224' => 'sed', 'Sed0026391' => 'sed', 'SEGI_00063' => 'sgi', 'SEGI_10967' => 'sgi', 'SEGI_17510' => 'sgi', 'SEGI_24396' => 'sgi', 'SEGI_39719' => 'sgi', 'SEGI_41392' => 'sgi', 'SGA_v2.0_scaffold11G05794' => 'sas', 'SGA_v2.0_scaffold142G35607' => 'sas', 'SGA_v2.0_scaffold1G00447' => 'sas', 'SHI15388' => 'shi', 'SHI15394' => 'shi', 'SHI15396' => 'shi', 'SHI15399' => 'shi', 'SMO343G0151' => 'smo', 'SMO367G1118' => 'smo', 'Solyc01g080200.3' => 'sly', 'Solyc06g008960.3' => 'sly', 'Solyc09g064780.3' => 'sly', 'Sopen01g031980' => 'spe', 'Sopen06g003710' => 'spe', 'Sopen09g026460' => 'spe', 'Sp3g21240' => 'spa', 'Sp4g30030' => 'spa', 'TAR365G0022' => 'tar', 'TAR365G1023' => 'tar', 'TAR365G1253' => 'tar', 'TAR623G0078' => 'tar', 'TAR623G1721' => 'tar', 'TAR633G0959' => 'tar', 'THA.LOC104802225' => 'tha', 'THA.LOC104804769' => 'tha', 'THA.LOC104808660' => 'tha', 'THA.LOC104812792' => 'tha', 'Thecc.01G284000' => 'tca', 'Thecc.04G220600' => 'tca', 'Thecc.05G268900' => 'tca', 'Thecc.08G171100' => 'tca', 'Thhalv10001284m.g' => 'esa', 'Thhalv10019912m.g' => 'esa', 'TPR.G14189' => 'tpr', 'TPR.G18110' => 'tpr', 'TPR.G18130' => 'tpr', 'TPR.G18131' => 'tpr', 'TPR.G18140' => 'tpr', 'TPR.G24282' => 'tpr', 'TPR.G25221' => 'tpr', 'TPR.G29267' => 'tpr', 'TPR.G35315' => 'tpr', 'TPR.G36173' => 'tpr', 'TWI09G0794' => 'twi', 'TWI59G1348' => 'twi', 'TWI74G0430' => 'twi', 'unitig_26.g8940' => 'ugi', 'unitig_749.g13744' => 'ugi', 'unitig_749.g13745' => 'ugi', 'vmacro08269' => 'vma', 'vmacro14937' => 'vma', 'vmacro20401' => 'vma', 'VMungo0464G1349' => 'vmu', 'VMungo0540G0289' => 'vmu', 'VMungo1215G1590' => 'vmu', 'VMungo1309G0221' => 'vmu', 'VMungo1309G2815' => 'vmu', 'VMungo1383G0239' => 'vmu', 'VMungo1383G2910' => 'vmu', 'Zm00001eb095270' => 'zma', 'Zm00001eb095280' => 'zma', 'Zm00001eb111630' => 'zma', 'Zm00001eb237080' => 'zma', 'Zm00001eb273740' => 'zma', 'Zm00001eb285040' => 'zma', 'Zm00001eb330790' => 'zma', 'Zm00001eb337380' => 'zma' ) $gf_id = 'HOM05D001484' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001484' ) $data_identifier = 'HOM05D001484' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 2, 'aly' => (int) 2, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 22, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 7, 'hma' => (int) 2, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 7, 'mtr' => (int) 10, 'cme' => (int) 2, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 4, 'ppa' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 4, 'qlo' => (int) 9, 'rch' => (int) 6, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 10, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 7, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb337380' $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' => 'HOM05D001484', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p31500' => 'bna', 'A05p00020' => 'bna', 'A07p08820' => 'bna', 'Aa31LG4G3300' => 'aar', 'Aa31LG8G10030' => 'aar', 'Actinidia00731' => 'ach', 'Actinidia11473' => 'ach', 'Actinidia23469' => 'ach', 'Actinidia24318' => 'ach', 'Actinidia40196' => 'ach', 'Actinidia40197' => 'ach', 'Actinidia40198' => 'ach', 'Ah.08g212990' => 'amhyb', 'Ah.15g091720' => 'amhyb', 'AL3G38260' => 'aly', 'AL4G47710' => 'aly', 'Aqoxy2G00671' => 'aox', 'Aqoxy2G03236' => 'aox', 'arahy.Tifrunner.gnm1.ann1.05IDCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KR684' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATY3SJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK6QJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6APGL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IDT7Z9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM073U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ0R87' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LE7RV4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT4QRX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V5ENPK' => 'arhy', 'AT2G48110' => 'ath', 'AT3G23590' => 'ath', 'ATR0626G186' => 'atr', 'ATR1127G141' => 'atr', 'Atru.chr4.2583' => 'acertr', 'Atru.chr5.1358' => 'acertr', 'Atru.chr5.1359' => 'acertr', 'Atru.chr8.46' => 'acertr', 'AUR62002640' => 'cqu', 'AUR62030055' => 'cqu', 'AUR62033713' => 'cqu', 'AUR62033714' => 'cqu', 'AUR62036795' => 'cqu', 'AUR62039891' => 'cqu', 'BcaB02g08737' => 'bca', 'BcaB04g20441' => 'bca', 'BcaB06g26509' => 'bca', 'BcaB06g26510' => 'bca', 'BcaB06g26511' => 'bca', 'BcaB06g26512' => 'bca', 'BcaB06g26513' => 'bca', 'BcaC02g12564' => 'bca', 'BcaC02g12565' => 'bca', 'BcaC02g12794' => 'bca', 'BcaC02g12795' => 'bca', 'BcaC02g12796' => 'bca', 'BcaC06g35541' => 'bca', 'BNapus_Darmor_BZH_scaffold_188p00080' => 'bna', 'BNapus_Darmor_BZH_scaffold_188p00090' => 'bna', 'BolC1t03972H' => 'bol', 'BolC1t03973H' => 'bol', 'BolC4t21680H' => 'bol', 'BolC7t41863H' => 'bol', 'BolSC55t61227H' => 'bol', 'BolSC55t61228H' => 'bol', 'BraA01t03278Z' => 'bra', 'BraA05t18998Z' => 'bra', 'BraA07t28673Z' => 'bra', 'C01p40150' => 'bna', 'C05p12370' => 'bna', 'C07p13680' => 'bna', 'CAN.G1006.16' => 'can', 'CAN.G1006.17' => 'can', 'CAN.G1170.2' => 'can', 'CAN.G962.7' => 'can', 'CANSAT25G2179' => 'cansat', 'CANSAT78G1573' => 'cansat', 'CARHR099510' => 'chi', 'CARHR143510' => 'chi', 'Carub.0003s2380' => 'cru', 'Carub.0004s3082' => 'cru', 'Ca_00614_v3' => 'car', 'Ca_07801_v3' => 'car', 'Ca_08567_v3' => 'car', 'Ca_09571_v3' => 'car', 'CBR_g19290' => 'cbr', 'Cc01_g19770' => 'ccan', 'Cc03_g03030' => 'ccan', 'CDE07G0968' => 'cde', 'CDE09G1441' => 'cde', 'Cfa006103' => 'cfa', 'Cfa015573' => 'cfa', 'Cfa016988' => 'cfa', 'Ciclev10006738m.g' => 'ccl', 'Ciclev10010920m.g' => 'ccl', 'Ciclev10018517m.g' => 'ccl', 'CiPaw.01G159200' => 'cil', 'CiPaw.02G091000' => 'cil', 'CiPaw.02G091100' => 'cil', 'CiPaw.08G103100' => 'cil', 'CiPaw.09G224900' => 'cil', 'ClCG06G005740' => 'cla', 'ClCG07G000090' => 'cla', 'ClCG07G000100' => 'cla', 'COL.COLO4_09143' => 'col', 'COL.COLO4_25124' => 'col', 'Cpa.g.sc16.34' => 'cpa', 'Cpa.g.sc3504.1' => 'cpa', 'Cpa.g.sc60.37' => 'cpa', 'CsaV3_6G018520' => 'csa', 'CsaV3_6G036860' => 'csa', 'CSS0001072' => 'camsi', 'CSS0020208' => 'camsi', 'CSS0021253' => 'camsi', 'CSS0022190' => 'camsi', 'CSS0036150' => 'camsi', 'CSS0040442' => 'camsi', 'CSS0042300' => 'camsi', 'CSS0045298' => 'camsi', 'DCAR_012449' => 'dca', 'DCAR_018405' => 'dca', 'DCAR_024573' => 'dca', 'DCAR_030591' => 'dca', 'Dinv16926' => 'din', 'Dinv32963' => 'din', 'Dinv38382' => 'din', 'Dinv38383' => 'din', 'Duzib133G0974' => 'dzi', 'Duzib138G1867' => 'dzi', 'Duzib211G0420' => 'dzi', 'Duzib212G0930' => 'dzi', 'ECA234G1645' => 'eca', 'ECA247G3467' => 'eca', 'ECA248G1703' => 'eca', 'EL10Ac3g06327' => 'bvu', 'EL10Ac7g17204' => 'bvu', 'Eucgr.A00855' => 'egr', 'Eucgr.A00858' => 'egr', 'Eucgr.H01520' => 'egr', 'Eucgr.H03604' => 'egr', 'Eucgr.L03465' => 'egr', 'Eucgr.L03466' => 'egr', 'FAN01G0988' => 'fan', 'FAN02G3892' => 'fan', 'FAN05G3381' => 'fan', 'FAN07G0967' => 'fan', 'FAN07G1493' => 'fan', 'FAN08G3125' => 'fan', 'FAN09G0402' => 'fan', 'FAN12G2594' => 'fan', 'FAN12G3879' => 'fan', 'FAN14G1546' => 'fan', 'FAN15G3626' => 'fan', 'FAN17G0588' => 'fan', 'FAN17G0609' => 'fan', 'FAN18G2817' => 'fan', 'FAN19G1305' => 'fan', 'FAN20G1787' => 'fan', 'FAN22G0073' => 'fan', 'FAN22G0352' => 'fan', 'FAN22G0368' => 'fan', 'FAN22G2273' => 'fan', 'FAN24G1998' => 'fan', 'FAN27G1317' => 'fan', 'FvH4_2g23980' => 'fve', 'FvH4_4g14380' => 'fve', 'FvH4_4g14390' => 'fve', 'FvH4_6g09250' => 'fve', 'Glyma.03G151100' => 'gma', 'Glyma.04G122550' => 'gma', 'Glyma.05G001600' => 'gma', 'Glyma.09G270766' => 'gma', 'Glyma.09G270832' => 'gma', 'Glyma.13G209800' => 'gma', 'Glyma.15G102800' => 'gma', 'Glyma.18G218900' => 'gma', 'Glyma.19G001500' => 'gma', 'Glyma.19G153600' => 'gma', 'Gohir.A02G028600' => 'ghi', 'Gohir.A08G045000' => 'ghi', 'Gohir.A11G120500' => 'ghi', 'Gohir.A12G006200' => 'ghi', 'Gohir.A12G006250' => 'ghi', 'Gohir.D02G036300' => 'ghi', 'Gohir.D08G054700' => 'ghi', 'Gohir.D11G125600' => 'ghi', 'Gohir.D12G005700' => 'ghi', 'Gorai.004G055200' => 'gra', 'Gorai.005G040400' => 'gra', 'Gorai.007G134500' => 'gra', 'Gorai.008G005500' => 'gra', 'GSVIVG01011094001' => 'vvi', 'GSVIVG01017879001' => 'vvi', 'GSVIVG01025988001' => 'vvi', 'GSVIVG01029847001' => 'vvi', 'HanXRQChr10g0282901' => 'han', 'HanXRQChr10g0310371' => 'han', 'HanXRQChr10g0315041' => 'han', 'HanXRQChr11g0327651' => 'han', 'HanXRQChr12g0359391' => 'han', 'Haze_00972' => 'cav', 'Haze_00973' => 'cav', 'Haze_00974' => 'cav', 'Haze_04747' => 'cav', 'Haze_04749' => 'cav', 'Haze_04750' => 'cav', 'Haze_21217' => 'cav', 'Hma1.2p1_1037F.1_g250680' => 'hma', 'Hma1.2p1_1644F.1_g295320' => 'hma', 'HPP92_011322' => 'vpl', 'HPP92_011323' => 'vpl', 'HPP92_011324' => 'vpl', 'HPP92_011325' => 'vpl', 'HPP92_011326' => 'vpl', 'Hund12205' => 'sun', 'Hund17957' => 'sun', 'Lalb_Chr06g0176771' => 'lal', 'Lalb_Chr18g0056021' => 'lal', 'Lalb_Chr18g0056031' => 'lal', 'Lalb_Chr18g0056041' => 'lal', 'Lalb_Chr20g0107751' => 'lal', 'Lalb_Chr20g0118371' => 'lal', 'Lj1g0010239' => 'lja', 'Lj1g0017101' => 'lja', 'Lj2A1178G40' => 'lonja', 'Lj2A54G84' => 'lonja', 'Lj2g0015248' => 'lja', 'Lj3A761T51' => 'lonja', 'Lj6g0018116' => 'lja', 'Lsat_1_v5_gn_4_136040' => 'lsa', 'Lsat_1_v5_gn_5_187461' => 'lsa', 'Lsat_1_v5_gn_5_77001' => 'lsa', 'Lsat_1_v5_gn_9_4461' => 'lsa', 'Manes.01G210100' => 'mes', 'Manes.03G185600' => 'mes', 'Manes.05G073300' => 'mes', 'Manes.09G120300' => 'mes', 'Manes.15G022100' => 'mes', 'Mapoly0096s0053' => 'mpo', 'MBI03_g14058_MAGBIO' => 'mbi', 'MBI03_g33876_MAGBIO' => 'mbi', 'MBI03_g36854_MAGBIO' => 'mbi', 'MBI17_g11997_MAGBIO' => 'mbi', 'MD03G1269000' => 'mdo', 'MD04G1179600' => 'mdo', 'MD11G1289800' => 'mdo', 'MD12G1194700' => 'mdo', 'MD13G1182100' => 'mdo', 'MD13G1182200' => 'mdo', 'MD16G1182600' => 'mdo', 'Medtr2g021400' => 'mtr', 'Medtr2g021470' => 'mtr', 'Medtr2g105810' => 'mtr', 'Medtr3g033580' => 'mtr', 'Medtr6g007970' => 'mtr', 'Medtr7g056330' => 'mtr', 'Medtr7g074290' => 'mtr', 'Medtr7g074380' => 'mtr', 'Medtr7g094550' => 'mtr', 'Medtr8g069995' => 'mtr', 'MELO3C014345.2' => 'cme', 'MELO3C021395.2' => 'cme', 'Migut.D00262' => 'egut', 'Migut.G00257' => 'egut', 'MSTRG.21575' => 'ama', 'MSTRG.3985' => 'ama', 'Nitab4.5_0000295g0140' => 'nta', 'Nitab4.5_0000732g0140' => 'nta', 'Nitab4.5_0003162g0020' => 'nta', 'Nitab4.5_0006180g0090' => 'nta', 'Nitab4.5_0006390g0010' => 'nta', 'Nitab4.5_0007392g0040' => 'nta', 'Nn1g02140' => 'nnu', 'Nn4g26168' => 'nnu', 'Nn5g26754' => 'nnu', 'Oeu001433.1' => 'oeu', 'Oeu010299.2' => 'oeu', 'Oeu011171.1' => 'oeu', 'Oeu037675.1' => 'oeu', 'Oeu038359.1' => 'oeu', 'Oeu063834.1' => 'oeu', 'Oeu063835.1' => 'oeu', 'Os05g0312000' => 'osa', 'Os07g0211101' => 'osa', 'Os07g0211200' => 'osa', 'Os07g0681500' => 'osa', 'Peaxi162Scf00095g01015' => 'pax', 'Peaxi162Scf00104g00329' => 'pax', 'Peaxi162Scf00161g00137' => 'pax', 'PGR004G1665' => 'pgr', 'PGR031G2937' => 'pgr', 'PGR119G2145' => 'pgr', 'PGSC0003DMG400004351' => 'stu', 'PGSC0003DMG400014625' => 'stu', 'PGSC0003DMG401000943' => 'stu', 'Phvul.001G148600' => 'pvu', 'Phvul.004G001700' => 'pvu', 'Phvul.006G154900' => 'pvu', 'Phvul.008G078200' => 'pvu', 'Phvul.011G136500' => 'pvu', 'Potri.002G215600' => 'ptr', 'Potri.008G201600' => 'ptr', 'Potri.014G138400' => 'ptr', 'Potri.016G142500' => 'ptr', 'Pp3c16_10580' => 'ppa', 'Pp3c5_25280' => 'ppa', 'Prupe.1G150000' => 'ppe', 'Prupe.1G150100' => 'ppe', 'Prupe.6G299600' => 'ppe', 'Prupe.8G245000' => 'ppe', 'Psat0s4927g0040' => 'psa', 'Psat1g052080' => 'psa', 'Psat1g183800' => 'psa', 'Psat3g113840' => 'psa', 'Psat3g126120' => 'psa', 'Psat3g126160' => 'psa', 'Psat3g158760' => 'psa', 'Psat3g158840' => 'psa', 'PSO170G2858' => 'pso', 'PSO339G0606' => 'pso', 'PSO384G4709' => 'pso', 'PSO407G0334' => 'pso', 'QL04p040276' => 'qlo', 'QL06p005458' => 'qlo', 'QL06p005472' => 'qlo', 'QL07p030546' => 'qlo', 'QL07p031519' => 'qlo', 'QL09p050949' => 'qlo', 'QL09p050966' => 'qlo', 'QL09p051067' => 'qlo', 'QL12p022706' => 'qlo', 'RcHm_v2.0_Chr2g0119601' => 'rch', 'RcHm_v2.0_Chr3g0459591' => 'rch', 'RcHm_v2.0_Chr4g0418521' => 'rch', 'RcHm_v2.0_Chr4g0418531' => 'rch', 'RcHm_v2.0_Chr4g0418541' => 'rch', 'RcHm_v2.0_Chr6g0291641' => 'rch', 'Rhsim01G0086300' => 'rsi', 'Rhsim01G0276300' => 'rsi', 'Rhsim01G0276500' => 'rsi', 'Rhsim04G0207700' => 'rsi', 'Rhsim05G0234500' => 'rsi', 'Rhsim13G0022400' => 'rsi', 'Sabra02G0167900' => 'sbr', 'Sabra04G0158500' => 'sbr', 'Sabra08G0159800' => 'sbr', 'Sabra10G0011500' => 'sbr', 'Sabra14G0104400' => 'sbr', 'SalBow2G2440' => 'sbo', 'SalBow4G2265' => 'sbo', 'Sc02g0000060' => 'sci', 'Sc05g0005020' => 'sci', 'Sc13g0003890' => 'sci', 'Sed0014865' => 'sed', 'Sed0017224' => 'sed', 'Sed0026391' => 'sed', 'SEGI_00063' => 'sgi', 'SEGI_10967' => 'sgi', 'SEGI_17510' => 'sgi', 'SEGI_24396' => 'sgi', 'SEGI_39719' => 'sgi', 'SEGI_41392' => 'sgi', 'SGA_v2.0_scaffold11G05794' => 'sas', 'SGA_v2.0_scaffold142G35607' => 'sas', 'SGA_v2.0_scaffold1G00447' => 'sas', 'SHI15388' => 'shi', 'SHI15394' => 'shi', 'SHI15396' => 'shi', 'SHI15399' => 'shi', 'SMO343G0151' => 'smo', 'SMO367G1118' => 'smo', 'Solyc01g080200.3' => 'sly', 'Solyc06g008960.3' => 'sly', 'Solyc09g064780.3' => 'sly', 'Sopen01g031980' => 'spe', 'Sopen06g003710' => 'spe', 'Sopen09g026460' => 'spe', 'Sp3g21240' => 'spa', 'Sp4g30030' => 'spa', 'TAR365G0022' => 'tar', 'TAR365G1023' => 'tar', 'TAR365G1253' => 'tar', 'TAR623G0078' => 'tar', 'TAR623G1721' => 'tar', 'TAR633G0959' => 'tar', 'THA.LOC104802225' => 'tha', 'THA.LOC104804769' => 'tha', 'THA.LOC104808660' => 'tha', 'THA.LOC104812792' => 'tha', 'Thecc.01G284000' => 'tca', 'Thecc.04G220600' => 'tca', 'Thecc.05G268900' => 'tca', 'Thecc.08G171100' => 'tca', 'Thhalv10001284m.g' => 'esa', 'Thhalv10019912m.g' => 'esa', 'TPR.G14189' => 'tpr', 'TPR.G18110' => 'tpr', 'TPR.G18130' => 'tpr', 'TPR.G18131' => 'tpr', 'TPR.G18140' => 'tpr', 'TPR.G24282' => 'tpr', 'TPR.G25221' => 'tpr', 'TPR.G29267' => 'tpr', 'TPR.G35315' => 'tpr', 'TPR.G36173' => 'tpr', 'TWI09G0794' => 'twi', 'TWI59G1348' => 'twi', 'TWI74G0430' => 'twi', 'unitig_26.g8940' => 'ugi', 'unitig_749.g13744' => 'ugi', 'unitig_749.g13745' => 'ugi', 'vmacro08269' => 'vma', 'vmacro14937' => 'vma', 'vmacro20401' => 'vma', 'VMungo0464G1349' => 'vmu', 'VMungo0540G0289' => 'vmu', 'VMungo1215G1590' => 'vmu', 'VMungo1309G0221' => 'vmu', 'VMungo1309G2815' => 'vmu', 'VMungo1383G0239' => 'vmu', 'VMungo1383G2910' => 'vmu', 'Zm00001eb095270' => 'zma', 'Zm00001eb095280' => 'zma', 'Zm00001eb111630' => 'zma', 'Zm00001eb237080' => 'zma', 'Zm00001eb273740' => 'zma', 'Zm00001eb285040' => 'zma', 'Zm00001eb330790' => 'zma', 'Zm00001eb337380' => 'zma' ), 'gf_id' => 'HOM05D001484', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001484' ), 'data_identifier' => 'HOM05D001484', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001484', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p31500' => 'bna', 'A05p00020' => 'bna', 'A07p08820' => 'bna', 'Aa31LG4G3300' => 'aar', 'Aa31LG8G10030' => 'aar', 'Actinidia00731' => 'ach', 'Actinidia11473' => 'ach', 'Actinidia23469' => 'ach', 'Actinidia24318' => 'ach', 'Actinidia40196' => 'ach', 'Actinidia40197' => 'ach', 'Actinidia40198' => 'ach', 'Ah.08g212990' => 'amhyb', 'Ah.15g091720' => 'amhyb', 'AL3G38260' => 'aly', 'AL4G47710' => 'aly', 'Aqoxy2G00671' => 'aox', 'Aqoxy2G03236' => 'aox', 'arahy.Tifrunner.gnm1.ann1.05IDCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KR684' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATY3SJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK6QJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6APGL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IDT7Z9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM073U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ0R87' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LE7RV4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT4QRX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V5ENPK' => 'arhy', 'AT2G48110' => 'ath', 'AT3G23590' => 'ath', 'ATR0626G186' => 'atr', 'ATR1127G141' => 'atr', 'Atru.chr4.2583' => 'acertr', 'Atru.chr5.1358' => 'acertr', 'Atru.chr5.1359' => 'acertr', 'Atru.chr8.46' => 'acertr', 'AUR62002640' => 'cqu', 'AUR62030055' => 'cqu', 'AUR62033713' => 'cqu', 'AUR62033714' => 'cqu', 'AUR62036795' => 'cqu', 'AUR62039891' => 'cqu', 'BcaB02g08737' => 'bca', 'BcaB04g20441' => 'bca', 'BcaB06g26509' => 'bca', 'BcaB06g26510' => 'bca', 'BcaB06g26511' => 'bca', 'BcaB06g26512' => 'bca', 'BcaB06g26513' => 'bca', 'BcaC02g12564' => 'bca', 'BcaC02g12565' => 'bca', 'BcaC02g12794' => 'bca', 'BcaC02g12795' => 'bca', 'BcaC02g12796' => 'bca', 'BcaC06g35541' => 'bca', 'BNapus_Darmor_BZH_scaffold_188p00080' => 'bna', 'BNapus_Darmor_BZH_scaffold_188p00090' => 'bna', 'BolC1t03972H' => 'bol', 'BolC1t03973H' => 'bol', 'BolC4t21680H' => 'bol', 'BolC7t41863H' => 'bol', 'BolSC55t61227H' => 'bol', 'BolSC55t61228H' => 'bol', 'BraA01t03278Z' => 'bra', 'BraA05t18998Z' => 'bra', 'BraA07t28673Z' => 'bra', 'C01p40150' => 'bna', 'C05p12370' => 'bna', 'C07p13680' => 'bna', 'CAN.G1006.16' => 'can', 'CAN.G1006.17' => 'can', 'CAN.G1170.2' => 'can', 'CAN.G962.7' => 'can', 'CANSAT25G2179' => 'cansat', 'CANSAT78G1573' => 'cansat', 'CARHR099510' => 'chi', 'CARHR143510' => 'chi', 'Carub.0003s2380' => 'cru', 'Carub.0004s3082' => 'cru', 'Ca_00614_v3' => 'car', 'Ca_07801_v3' => 'car', 'Ca_08567_v3' => 'car', 'Ca_09571_v3' => 'car', 'CBR_g19290' => 'cbr', 'Cc01_g19770' => 'ccan', 'Cc03_g03030' => 'ccan', 'CDE07G0968' => 'cde', 'CDE09G1441' => 'cde', 'Cfa006103' => 'cfa', 'Cfa015573' => 'cfa', 'Cfa016988' => 'cfa', 'Ciclev10006738m.g' => 'ccl', 'Ciclev10010920m.g' => 'ccl', 'Ciclev10018517m.g' => 'ccl', 'CiPaw.01G159200' => 'cil', 'CiPaw.02G091000' => 'cil', 'CiPaw.02G091100' => 'cil', 'CiPaw.08G103100' => 'cil', 'CiPaw.09G224900' => 'cil', 'ClCG06G005740' => 'cla', 'ClCG07G000090' => 'cla', 'ClCG07G000100' => 'cla', 'COL.COLO4_09143' => 'col', 'COL.COLO4_25124' => 'col', 'Cpa.g.sc16.34' => 'cpa', 'Cpa.g.sc3504.1' => 'cpa', 'Cpa.g.sc60.37' => 'cpa', 'CsaV3_6G018520' => 'csa', 'CsaV3_6G036860' => 'csa', 'CSS0001072' => 'camsi', 'CSS0020208' => 'camsi', 'CSS0021253' => 'camsi', 'CSS0022190' => 'camsi', 'CSS0036150' => 'camsi', 'CSS0040442' => 'camsi', 'CSS0042300' => 'camsi', 'CSS0045298' => 'camsi', 'DCAR_012449' => 'dca', 'DCAR_018405' => 'dca', 'DCAR_024573' => 'dca', 'DCAR_030591' => 'dca', 'Dinv16926' => 'din', 'Dinv32963' => 'din', 'Dinv38382' => 'din', 'Dinv38383' => 'din', 'Duzib133G0974' => 'dzi', 'Duzib138G1867' => 'dzi', 'Duzib211G0420' => 'dzi', 'Duzib212G0930' => 'dzi', 'ECA234G1645' => 'eca', 'ECA247G3467' => 'eca', 'ECA248G1703' => 'eca', 'EL10Ac3g06327' => 'bvu', 'EL10Ac7g17204' => 'bvu', 'Eucgr.A00855' => 'egr', 'Eucgr.A00858' => 'egr', 'Eucgr.H01520' => 'egr', 'Eucgr.H03604' => 'egr', 'Eucgr.L03465' => 'egr', 'Eucgr.L03466' => 'egr', 'FAN01G0988' => 'fan', 'FAN02G3892' => 'fan', 'FAN05G3381' => 'fan', 'FAN07G0967' => 'fan', 'FAN07G1493' => 'fan', 'FAN08G3125' => 'fan', 'FAN09G0402' => 'fan', 'FAN12G2594' => 'fan', 'FAN12G3879' => 'fan', 'FAN14G1546' => 'fan', 'FAN15G3626' => 'fan', 'FAN17G0588' => 'fan', 'FAN17G0609' => 'fan', 'FAN18G2817' => 'fan', 'FAN19G1305' => 'fan', 'FAN20G1787' => 'fan', 'FAN22G0073' => 'fan', 'FAN22G0352' => 'fan', 'FAN22G0368' => 'fan', 'FAN22G2273' => 'fan', 'FAN24G1998' => 'fan', 'FAN27G1317' => 'fan', 'FvH4_2g23980' => 'fve', 'FvH4_4g14380' => 'fve', 'FvH4_4g14390' => 'fve', 'FvH4_6g09250' => 'fve', 'Glyma.03G151100' => 'gma', 'Glyma.04G122550' => 'gma', 'Glyma.05G001600' => 'gma', 'Glyma.09G270766' => 'gma', 'Glyma.09G270832' => 'gma', 'Glyma.13G209800' => 'gma', 'Glyma.15G102800' => 'gma', 'Glyma.18G218900' => 'gma', 'Glyma.19G001500' => 'gma', 'Glyma.19G153600' => 'gma', 'Gohir.A02G028600' => 'ghi', 'Gohir.A08G045000' => 'ghi', 'Gohir.A11G120500' => 'ghi', 'Gohir.A12G006200' => 'ghi', 'Gohir.A12G006250' => 'ghi', 'Gohir.D02G036300' => 'ghi', 'Gohir.D08G054700' => 'ghi', 'Gohir.D11G125600' => 'ghi', 'Gohir.D12G005700' => 'ghi', 'Gorai.004G055200' => 'gra', 'Gorai.005G040400' => 'gra', 'Gorai.007G134500' => 'gra', 'Gorai.008G005500' => 'gra', 'GSVIVG01011094001' => 'vvi', 'GSVIVG01017879001' => 'vvi', 'GSVIVG01025988001' => 'vvi', 'GSVIVG01029847001' => 'vvi', 'HanXRQChr10g0282901' => 'han', 'HanXRQChr10g0310371' => 'han', 'HanXRQChr10g0315041' => 'han', 'HanXRQChr11g0327651' => 'han', 'HanXRQChr12g0359391' => 'han', 'Haze_00972' => 'cav', 'Haze_00973' => 'cav', 'Haze_00974' => 'cav', 'Haze_04747' => 'cav', 'Haze_04749' => 'cav', 'Haze_04750' => 'cav', 'Haze_21217' => 'cav', 'Hma1.2p1_1037F.1_g250680' => 'hma', 'Hma1.2p1_1644F.1_g295320' => 'hma', 'HPP92_011322' => 'vpl', 'HPP92_011323' => 'vpl', 'HPP92_011324' => 'vpl', 'HPP92_011325' => 'vpl', 'HPP92_011326' => 'vpl', 'Hund12205' => 'sun', 'Hund17957' => 'sun', 'Lalb_Chr06g0176771' => 'lal', 'Lalb_Chr18g0056021' => 'lal', 'Lalb_Chr18g0056031' => 'lal', 'Lalb_Chr18g0056041' => 'lal', 'Lalb_Chr20g0107751' => 'lal', 'Lalb_Chr20g0118371' => 'lal', 'Lj1g0010239' => 'lja', 'Lj1g0017101' => 'lja', 'Lj2A1178G40' => 'lonja', 'Lj2A54G84' => 'lonja', 'Lj2g0015248' => 'lja', 'Lj3A761T51' => 'lonja', 'Lj6g0018116' => 'lja', 'Lsat_1_v5_gn_4_136040' => 'lsa', 'Lsat_1_v5_gn_5_187461' => 'lsa', 'Lsat_1_v5_gn_5_77001' => 'lsa', 'Lsat_1_v5_gn_9_4461' => 'lsa', 'Manes.01G210100' => 'mes', 'Manes.03G185600' => 'mes', 'Manes.05G073300' => 'mes', 'Manes.09G120300' => 'mes', 'Manes.15G022100' => 'mes', 'Mapoly0096s0053' => 'mpo', 'MBI03_g14058_MAGBIO' => 'mbi', 'MBI03_g33876_MAGBIO' => 'mbi', 'MBI03_g36854_MAGBIO' => 'mbi', 'MBI17_g11997_MAGBIO' => 'mbi', 'MD03G1269000' => 'mdo', 'MD04G1179600' => 'mdo', 'MD11G1289800' => 'mdo', 'MD12G1194700' => 'mdo', 'MD13G1182100' => 'mdo', 'MD13G1182200' => 'mdo', 'MD16G1182600' => 'mdo', 'Medtr2g021400' => 'mtr', 'Medtr2g021470' => 'mtr', 'Medtr2g105810' => 'mtr', 'Medtr3g033580' => 'mtr', 'Medtr6g007970' => 'mtr', 'Medtr7g056330' => 'mtr', 'Medtr7g074290' => 'mtr', 'Medtr7g074380' => 'mtr', 'Medtr7g094550' => 'mtr', 'Medtr8g069995' => 'mtr', 'MELO3C014345.2' => 'cme', 'MELO3C021395.2' => 'cme', 'Migut.D00262' => 'egut', 'Migut.G00257' => 'egut', 'MSTRG.21575' => 'ama', 'MSTRG.3985' => 'ama', 'Nitab4.5_0000295g0140' => 'nta', 'Nitab4.5_0000732g0140' => 'nta', 'Nitab4.5_0003162g0020' => 'nta', 'Nitab4.5_0006180g0090' => 'nta', 'Nitab4.5_0006390g0010' => 'nta', 'Nitab4.5_0007392g0040' => 'nta', 'Nn1g02140' => 'nnu', 'Nn4g26168' => 'nnu', 'Nn5g26754' => 'nnu', 'Oeu001433.1' => 'oeu', 'Oeu010299.2' => 'oeu', 'Oeu011171.1' => 'oeu', 'Oeu037675.1' => 'oeu', 'Oeu038359.1' => 'oeu', 'Oeu063834.1' => 'oeu', 'Oeu063835.1' => 'oeu', 'Os05g0312000' => 'osa', 'Os07g0211101' => 'osa', 'Os07g0211200' => 'osa', 'Os07g0681500' => 'osa', 'Peaxi162Scf00095g01015' => 'pax', 'Peaxi162Scf00104g00329' => 'pax', 'Peaxi162Scf00161g00137' => 'pax', 'PGR004G1665' => 'pgr', 'PGR031G2937' => 'pgr', 'PGR119G2145' => 'pgr', 'PGSC0003DMG400004351' => 'stu', 'PGSC0003DMG400014625' => 'stu', 'PGSC0003DMG401000943' => 'stu', 'Phvul.001G148600' => 'pvu', 'Phvul.004G001700' => 'pvu', 'Phvul.006G154900' => 'pvu', 'Phvul.008G078200' => 'pvu', 'Phvul.011G136500' => 'pvu', 'Potri.002G215600' => 'ptr', 'Potri.008G201600' => 'ptr', 'Potri.014G138400' => 'ptr', 'Potri.016G142500' => 'ptr', 'Pp3c16_10580' => 'ppa', 'Pp3c5_25280' => 'ppa', 'Prupe.1G150000' => 'ppe', 'Prupe.1G150100' => 'ppe', 'Prupe.6G299600' => 'ppe', 'Prupe.8G245000' => 'ppe', 'Psat0s4927g0040' => 'psa', 'Psat1g052080' => 'psa', 'Psat1g183800' => 'psa', 'Psat3g113840' => 'psa', 'Psat3g126120' => 'psa', 'Psat3g126160' => 'psa', 'Psat3g158760' => 'psa', 'Psat3g158840' => 'psa', 'PSO170G2858' => 'pso', 'PSO339G0606' => 'pso', 'PSO384G4709' => 'pso', 'PSO407G0334' => 'pso', 'QL04p040276' => 'qlo', 'QL06p005458' => 'qlo', 'QL06p005472' => 'qlo', 'QL07p030546' => 'qlo', 'QL07p031519' => 'qlo', 'QL09p050949' => 'qlo', 'QL09p050966' => 'qlo', 'QL09p051067' => 'qlo', 'QL12p022706' => 'qlo', 'RcHm_v2.0_Chr2g0119601' => 'rch', 'RcHm_v2.0_Chr3g0459591' => 'rch', 'RcHm_v2.0_Chr4g0418521' => 'rch', 'RcHm_v2.0_Chr4g0418531' => 'rch', 'RcHm_v2.0_Chr4g0418541' => 'rch', 'RcHm_v2.0_Chr6g0291641' => 'rch', 'Rhsim01G0086300' => 'rsi', 'Rhsim01G0276300' => 'rsi', 'Rhsim01G0276500' => 'rsi', 'Rhsim04G0207700' => 'rsi', 'Rhsim05G0234500' => 'rsi', 'Rhsim13G0022400' => 'rsi', 'Sabra02G0167900' => 'sbr', 'Sabra04G0158500' => 'sbr', 'Sabra08G0159800' => 'sbr', 'Sabra10G0011500' => 'sbr', 'Sabra14G0104400' => 'sbr', 'SalBow2G2440' => 'sbo', 'SalBow4G2265' => 'sbo', 'Sc02g0000060' => 'sci', 'Sc05g0005020' => 'sci', 'Sc13g0003890' => 'sci', 'Sed0014865' => 'sed', 'Sed0017224' => 'sed', 'Sed0026391' => 'sed', 'SEGI_00063' => 'sgi', 'SEGI_10967' => 'sgi', 'SEGI_17510' => 'sgi', 'SEGI_24396' => 'sgi', 'SEGI_39719' => 'sgi', 'SEGI_41392' => 'sgi', 'SGA_v2.0_scaffold11G05794' => 'sas', 'SGA_v2.0_scaffold142G35607' => 'sas', 'SGA_v2.0_scaffold1G00447' => 'sas', 'SHI15388' => 'shi', 'SHI15394' => 'shi', 'SHI15396' => 'shi', 'SHI15399' => 'shi', 'SMO343G0151' => 'smo', 'SMO367G1118' => 'smo', 'Solyc01g080200.3' => 'sly', 'Solyc06g008960.3' => 'sly', 'Solyc09g064780.3' => 'sly', 'Sopen01g031980' => 'spe', 'Sopen06g003710' => 'spe', 'Sopen09g026460' => 'spe', 'Sp3g21240' => 'spa', 'Sp4g30030' => 'spa', 'TAR365G0022' => 'tar', 'TAR365G1023' => 'tar', 'TAR365G1253' => 'tar', 'TAR623G0078' => 'tar', 'TAR623G1721' => 'tar', 'TAR633G0959' => 'tar', 'THA.LOC104802225' => 'tha', 'THA.LOC104804769' => 'tha', 'THA.LOC104808660' => 'tha', 'THA.LOC104812792' => 'tha', 'Thecc.01G284000' => 'tca', 'Thecc.04G220600' => 'tca', 'Thecc.05G268900' => 'tca', 'Thecc.08G171100' => 'tca', 'Thhalv10001284m.g' => 'esa', 'Thhalv10019912m.g' => 'esa', 'TPR.G14189' => 'tpr', 'TPR.G18110' => 'tpr', 'TPR.G18130' => 'tpr', 'TPR.G18131' => 'tpr', 'TPR.G18140' => 'tpr', 'TPR.G24282' => 'tpr', 'TPR.G25221' => 'tpr', 'TPR.G29267' => 'tpr', 'TPR.G35315' => 'tpr', 'TPR.G36173' => 'tpr', 'TWI09G0794' => 'twi', 'TWI59G1348' => 'twi', 'TWI74G0430' => 'twi', 'unitig_26.g8940' => 'ugi', 'unitig_749.g13744' => 'ugi', 'unitig_749.g13745' => 'ugi', 'vmacro08269' => 'vma', 'vmacro14937' => 'vma', 'vmacro20401' => 'vma', 'VMungo0464G1349' => 'vmu', 'VMungo0540G0289' => 'vmu', 'VMungo1215G1590' => 'vmu', 'VMungo1309G0221' => 'vmu', 'VMungo1309G2815' => 'vmu', 'VMungo1383G0239' => 'vmu', 'VMungo1383G2910' => 'vmu', 'Zm00001eb095270' => 'zma', 'Zm00001eb095280' => 'zma', 'Zm00001eb111630' => 'zma', 'Zm00001eb237080' => 'zma', 'Zm00001eb273740' => 'zma', 'Zm00001eb285040' => 'zma', 'Zm00001eb330790' => 'zma', 'Zm00001eb337380' => 'zma' ) $gf_id = 'HOM05D001484' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001484' ) $data_identifier = 'HOM05D001484' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 2, 'aly' => (int) 2, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 22, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 7, 'hma' => (int) 2, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 7, 'mtr' => (int) 10, 'cme' => (int) 2, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 4, 'ppa' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 4, 'qlo' => (int) 9, 'rch' => (int) 6, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 10, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 7, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb337380' $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' => 'HOM05D001484', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p31500' => 'bna', 'A05p00020' => 'bna', 'A07p08820' => 'bna', 'Aa31LG4G3300' => 'aar', 'Aa31LG8G10030' => 'aar', 'Actinidia00731' => 'ach', 'Actinidia11473' => 'ach', 'Actinidia23469' => 'ach', 'Actinidia24318' => 'ach', 'Actinidia40196' => 'ach', 'Actinidia40197' => 'ach', 'Actinidia40198' => 'ach', 'Ah.08g212990' => 'amhyb', 'Ah.15g091720' => 'amhyb', 'AL3G38260' => 'aly', 'AL4G47710' => 'aly', 'Aqoxy2G00671' => 'aox', 'Aqoxy2G03236' => 'aox', 'arahy.Tifrunner.gnm1.ann1.05IDCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KR684' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATY3SJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK6QJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6APGL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IDT7Z9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM073U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ0R87' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LE7RV4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT4QRX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V5ENPK' => 'arhy', 'AT2G48110' => 'ath', 'AT3G23590' => 'ath', 'ATR0626G186' => 'atr', 'ATR1127G141' => 'atr', 'Atru.chr4.2583' => 'acertr', 'Atru.chr5.1358' => 'acertr', 'Atru.chr5.1359' => 'acertr', 'Atru.chr8.46' => 'acertr', 'AUR62002640' => 'cqu', 'AUR62030055' => 'cqu', 'AUR62033713' => 'cqu', 'AUR62033714' => 'cqu', 'AUR62036795' => 'cqu', 'AUR62039891' => 'cqu', 'BcaB02g08737' => 'bca', 'BcaB04g20441' => 'bca', 'BcaB06g26509' => 'bca', 'BcaB06g26510' => 'bca', 'BcaB06g26511' => 'bca', 'BcaB06g26512' => 'bca', 'BcaB06g26513' => 'bca', 'BcaC02g12564' => 'bca', 'BcaC02g12565' => 'bca', 'BcaC02g12794' => 'bca', 'BcaC02g12795' => 'bca', 'BcaC02g12796' => 'bca', 'BcaC06g35541' => 'bca', 'BNapus_Darmor_BZH_scaffold_188p00080' => 'bna', 'BNapus_Darmor_BZH_scaffold_188p00090' => 'bna', 'BolC1t03972H' => 'bol', 'BolC1t03973H' => 'bol', 'BolC4t21680H' => 'bol', 'BolC7t41863H' => 'bol', 'BolSC55t61227H' => 'bol', 'BolSC55t61228H' => 'bol', 'BraA01t03278Z' => 'bra', 'BraA05t18998Z' => 'bra', 'BraA07t28673Z' => 'bra', 'C01p40150' => 'bna', 'C05p12370' => 'bna', 'C07p13680' => 'bna', 'CAN.G1006.16' => 'can', 'CAN.G1006.17' => 'can', 'CAN.G1170.2' => 'can', 'CAN.G962.7' => 'can', 'CANSAT25G2179' => 'cansat', 'CANSAT78G1573' => 'cansat', 'CARHR099510' => 'chi', 'CARHR143510' => 'chi', 'Carub.0003s2380' => 'cru', 'Carub.0004s3082' => 'cru', 'Ca_00614_v3' => 'car', 'Ca_07801_v3' => 'car', 'Ca_08567_v3' => 'car', 'Ca_09571_v3' => 'car', 'CBR_g19290' => 'cbr', 'Cc01_g19770' => 'ccan', 'Cc03_g03030' => 'ccan', 'CDE07G0968' => 'cde', 'CDE09G1441' => 'cde', 'Cfa006103' => 'cfa', 'Cfa015573' => 'cfa', 'Cfa016988' => 'cfa', 'Ciclev10006738m.g' => 'ccl', 'Ciclev10010920m.g' => 'ccl', 'Ciclev10018517m.g' => 'ccl', 'CiPaw.01G159200' => 'cil', 'CiPaw.02G091000' => 'cil', 'CiPaw.02G091100' => 'cil', 'CiPaw.08G103100' => 'cil', 'CiPaw.09G224900' => 'cil', 'ClCG06G005740' => 'cla', 'ClCG07G000090' => 'cla', 'ClCG07G000100' => 'cla', 'COL.COLO4_09143' => 'col', 'COL.COLO4_25124' => 'col', 'Cpa.g.sc16.34' => 'cpa', 'Cpa.g.sc3504.1' => 'cpa', 'Cpa.g.sc60.37' => 'cpa', 'CsaV3_6G018520' => 'csa', 'CsaV3_6G036860' => 'csa', 'CSS0001072' => 'camsi', 'CSS0020208' => 'camsi', 'CSS0021253' => 'camsi', 'CSS0022190' => 'camsi', 'CSS0036150' => 'camsi', 'CSS0040442' => 'camsi', 'CSS0042300' => 'camsi', 'CSS0045298' => 'camsi', 'DCAR_012449' => 'dca', 'DCAR_018405' => 'dca', 'DCAR_024573' => 'dca', 'DCAR_030591' => 'dca', 'Dinv16926' => 'din', 'Dinv32963' => 'din', 'Dinv38382' => 'din', 'Dinv38383' => 'din', 'Duzib133G0974' => 'dzi', 'Duzib138G1867' => 'dzi', 'Duzib211G0420' => 'dzi', 'Duzib212G0930' => 'dzi', 'ECA234G1645' => 'eca', 'ECA247G3467' => 'eca', 'ECA248G1703' => 'eca', 'EL10Ac3g06327' => 'bvu', 'EL10Ac7g17204' => 'bvu', 'Eucgr.A00855' => 'egr', 'Eucgr.A00858' => 'egr', 'Eucgr.H01520' => 'egr', 'Eucgr.H03604' => 'egr', 'Eucgr.L03465' => 'egr', 'Eucgr.L03466' => 'egr', 'FAN01G0988' => 'fan', 'FAN02G3892' => 'fan', 'FAN05G3381' => 'fan', 'FAN07G0967' => 'fan', 'FAN07G1493' => 'fan', 'FAN08G3125' => 'fan', 'FAN09G0402' => 'fan', 'FAN12G2594' => 'fan', 'FAN12G3879' => 'fan', 'FAN14G1546' => 'fan', 'FAN15G3626' => 'fan', 'FAN17G0588' => 'fan', 'FAN17G0609' => 'fan', 'FAN18G2817' => 'fan', 'FAN19G1305' => 'fan', 'FAN20G1787' => 'fan', 'FAN22G0073' => 'fan', 'FAN22G0352' => 'fan', 'FAN22G0368' => 'fan', 'FAN22G2273' => 'fan', 'FAN24G1998' => 'fan', 'FAN27G1317' => 'fan', 'FvH4_2g23980' => 'fve', 'FvH4_4g14380' => 'fve', 'FvH4_4g14390' => 'fve', 'FvH4_6g09250' => 'fve', 'Glyma.03G151100' => 'gma', 'Glyma.04G122550' => 'gma', 'Glyma.05G001600' => 'gma', 'Glyma.09G270766' => 'gma', 'Glyma.09G270832' => 'gma', 'Glyma.13G209800' => 'gma', 'Glyma.15G102800' => 'gma', 'Glyma.18G218900' => 'gma', 'Glyma.19G001500' => 'gma', 'Glyma.19G153600' => 'gma', 'Gohir.A02G028600' => 'ghi', 'Gohir.A08G045000' => 'ghi', 'Gohir.A11G120500' => 'ghi', 'Gohir.A12G006200' => 'ghi', 'Gohir.A12G006250' => 'ghi', 'Gohir.D02G036300' => 'ghi', 'Gohir.D08G054700' => 'ghi', 'Gohir.D11G125600' => 'ghi', 'Gohir.D12G005700' => 'ghi', 'Gorai.004G055200' => 'gra', 'Gorai.005G040400' => 'gra', 'Gorai.007G134500' => 'gra', 'Gorai.008G005500' => 'gra', 'GSVIVG01011094001' => 'vvi', 'GSVIVG01017879001' => 'vvi', 'GSVIVG01025988001' => 'vvi', 'GSVIVG01029847001' => 'vvi', 'HanXRQChr10g0282901' => 'han', 'HanXRQChr10g0310371' => 'han', 'HanXRQChr10g0315041' => 'han', 'HanXRQChr11g0327651' => 'han', 'HanXRQChr12g0359391' => 'han', 'Haze_00972' => 'cav', 'Haze_00973' => 'cav', 'Haze_00974' => 'cav', 'Haze_04747' => 'cav', 'Haze_04749' => 'cav', 'Haze_04750' => 'cav', 'Haze_21217' => 'cav', 'Hma1.2p1_1037F.1_g250680' => 'hma', 'Hma1.2p1_1644F.1_g295320' => 'hma', 'HPP92_011322' => 'vpl', 'HPP92_011323' => 'vpl', 'HPP92_011324' => 'vpl', 'HPP92_011325' => 'vpl', 'HPP92_011326' => 'vpl', 'Hund12205' => 'sun', 'Hund17957' => 'sun', 'Lalb_Chr06g0176771' => 'lal', 'Lalb_Chr18g0056021' => 'lal', 'Lalb_Chr18g0056031' => 'lal', 'Lalb_Chr18g0056041' => 'lal', 'Lalb_Chr20g0107751' => 'lal', 'Lalb_Chr20g0118371' => 'lal', 'Lj1g0010239' => 'lja', 'Lj1g0017101' => 'lja', 'Lj2A1178G40' => 'lonja', 'Lj2A54G84' => 'lonja', 'Lj2g0015248' => 'lja', 'Lj3A761T51' => 'lonja', 'Lj6g0018116' => 'lja', 'Lsat_1_v5_gn_4_136040' => 'lsa', 'Lsat_1_v5_gn_5_187461' => 'lsa', 'Lsat_1_v5_gn_5_77001' => 'lsa', 'Lsat_1_v5_gn_9_4461' => 'lsa', 'Manes.01G210100' => 'mes', 'Manes.03G185600' => 'mes', 'Manes.05G073300' => 'mes', 'Manes.09G120300' => 'mes', 'Manes.15G022100' => 'mes', 'Mapoly0096s0053' => 'mpo', 'MBI03_g14058_MAGBIO' => 'mbi', 'MBI03_g33876_MAGBIO' => 'mbi', 'MBI03_g36854_MAGBIO' => 'mbi', 'MBI17_g11997_MAGBIO' => 'mbi', 'MD03G1269000' => 'mdo', 'MD04G1179600' => 'mdo', 'MD11G1289800' => 'mdo', 'MD12G1194700' => 'mdo', 'MD13G1182100' => 'mdo', 'MD13G1182200' => 'mdo', 'MD16G1182600' => 'mdo', 'Medtr2g021400' => 'mtr', 'Medtr2g021470' => 'mtr', 'Medtr2g105810' => 'mtr', 'Medtr3g033580' => 'mtr', 'Medtr6g007970' => 'mtr', 'Medtr7g056330' => 'mtr', 'Medtr7g074290' => 'mtr', 'Medtr7g074380' => 'mtr', 'Medtr7g094550' => 'mtr', 'Medtr8g069995' => 'mtr', 'MELO3C014345.2' => 'cme', 'MELO3C021395.2' => 'cme', 'Migut.D00262' => 'egut', 'Migut.G00257' => 'egut', 'MSTRG.21575' => 'ama', 'MSTRG.3985' => 'ama', 'Nitab4.5_0000295g0140' => 'nta', 'Nitab4.5_0000732g0140' => 'nta', 'Nitab4.5_0003162g0020' => 'nta', 'Nitab4.5_0006180g0090' => 'nta', 'Nitab4.5_0006390g0010' => 'nta', 'Nitab4.5_0007392g0040' => 'nta', 'Nn1g02140' => 'nnu', 'Nn4g26168' => 'nnu', 'Nn5g26754' => 'nnu', 'Oeu001433.1' => 'oeu', 'Oeu010299.2' => 'oeu', 'Oeu011171.1' => 'oeu', 'Oeu037675.1' => 'oeu', 'Oeu038359.1' => 'oeu', 'Oeu063834.1' => 'oeu', 'Oeu063835.1' => 'oeu', 'Os05g0312000' => 'osa', 'Os07g0211101' => 'osa', 'Os07g0211200' => 'osa', 'Os07g0681500' => 'osa', 'Peaxi162Scf00095g01015' => 'pax', 'Peaxi162Scf00104g00329' => 'pax', 'Peaxi162Scf00161g00137' => 'pax', 'PGR004G1665' => 'pgr', 'PGR031G2937' => 'pgr', 'PGR119G2145' => 'pgr', 'PGSC0003DMG400004351' => 'stu', 'PGSC0003DMG400014625' => 'stu', 'PGSC0003DMG401000943' => 'stu', 'Phvul.001G148600' => 'pvu', 'Phvul.004G001700' => 'pvu', 'Phvul.006G154900' => 'pvu', 'Phvul.008G078200' => 'pvu', 'Phvul.011G136500' => 'pvu', 'Potri.002G215600' => 'ptr', 'Potri.008G201600' => 'ptr', 'Potri.014G138400' => 'ptr', 'Potri.016G142500' => 'ptr', 'Pp3c16_10580' => 'ppa', 'Pp3c5_25280' => 'ppa', 'Prupe.1G150000' => 'ppe', 'Prupe.1G150100' => 'ppe', 'Prupe.6G299600' => 'ppe', 'Prupe.8G245000' => 'ppe', 'Psat0s4927g0040' => 'psa', 'Psat1g052080' => 'psa', 'Psat1g183800' => 'psa', 'Psat3g113840' => 'psa', 'Psat3g126120' => 'psa', 'Psat3g126160' => 'psa', 'Psat3g158760' => 'psa', 'Psat3g158840' => 'psa', 'PSO170G2858' => 'pso', 'PSO339G0606' => 'pso', 'PSO384G4709' => 'pso', 'PSO407G0334' => 'pso', 'QL04p040276' => 'qlo', 'QL06p005458' => 'qlo', 'QL06p005472' => 'qlo', 'QL07p030546' => 'qlo', 'QL07p031519' => 'qlo', 'QL09p050949' => 'qlo', 'QL09p050966' => 'qlo', 'QL09p051067' => 'qlo', 'QL12p022706' => 'qlo', 'RcHm_v2.0_Chr2g0119601' => 'rch', 'RcHm_v2.0_Chr3g0459591' => 'rch', 'RcHm_v2.0_Chr4g0418521' => 'rch', 'RcHm_v2.0_Chr4g0418531' => 'rch', 'RcHm_v2.0_Chr4g0418541' => 'rch', 'RcHm_v2.0_Chr6g0291641' => 'rch', 'Rhsim01G0086300' => 'rsi', 'Rhsim01G0276300' => 'rsi', 'Rhsim01G0276500' => 'rsi', 'Rhsim04G0207700' => 'rsi', 'Rhsim05G0234500' => 'rsi', 'Rhsim13G0022400' => 'rsi', 'Sabra02G0167900' => 'sbr', 'Sabra04G0158500' => 'sbr', 'Sabra08G0159800' => 'sbr', 'Sabra10G0011500' => 'sbr', 'Sabra14G0104400' => 'sbr', 'SalBow2G2440' => 'sbo', 'SalBow4G2265' => 'sbo', 'Sc02g0000060' => 'sci', 'Sc05g0005020' => 'sci', 'Sc13g0003890' => 'sci', 'Sed0014865' => 'sed', 'Sed0017224' => 'sed', 'Sed0026391' => 'sed', 'SEGI_00063' => 'sgi', 'SEGI_10967' => 'sgi', 'SEGI_17510' => 'sgi', 'SEGI_24396' => 'sgi', 'SEGI_39719' => 'sgi', 'SEGI_41392' => 'sgi', 'SGA_v2.0_scaffold11G05794' => 'sas', 'SGA_v2.0_scaffold142G35607' => 'sas', 'SGA_v2.0_scaffold1G00447' => 'sas', 'SHI15388' => 'shi', 'SHI15394' => 'shi', 'SHI15396' => 'shi', 'SHI15399' => 'shi', 'SMO343G0151' => 'smo', 'SMO367G1118' => 'smo', 'Solyc01g080200.3' => 'sly', 'Solyc06g008960.3' => 'sly', 'Solyc09g064780.3' => 'sly', 'Sopen01g031980' => 'spe', 'Sopen06g003710' => 'spe', 'Sopen09g026460' => 'spe', 'Sp3g21240' => 'spa', 'Sp4g30030' => 'spa', 'TAR365G0022' => 'tar', 'TAR365G1023' => 'tar', 'TAR365G1253' => 'tar', 'TAR623G0078' => 'tar', 'TAR623G1721' => 'tar', 'TAR633G0959' => 'tar', 'THA.LOC104802225' => 'tha', 'THA.LOC104804769' => 'tha', 'THA.LOC104808660' => 'tha', 'THA.LOC104812792' => 'tha', 'Thecc.01G284000' => 'tca', 'Thecc.04G220600' => 'tca', 'Thecc.05G268900' => 'tca', 'Thecc.08G171100' => 'tca', 'Thhalv10001284m.g' => 'esa', 'Thhalv10019912m.g' => 'esa', 'TPR.G14189' => 'tpr', 'TPR.G18110' => 'tpr', 'TPR.G18130' => 'tpr', 'TPR.G18131' => 'tpr', 'TPR.G18140' => 'tpr', 'TPR.G24282' => 'tpr', 'TPR.G25221' => 'tpr', 'TPR.G29267' => 'tpr', 'TPR.G35315' => 'tpr', 'TPR.G36173' => 'tpr', 'TWI09G0794' => 'twi', 'TWI59G1348' => 'twi', 'TWI74G0430' => 'twi', 'unitig_26.g8940' => 'ugi', 'unitig_749.g13744' => 'ugi', 'unitig_749.g13745' => 'ugi', 'vmacro08269' => 'vma', 'vmacro14937' => 'vma', 'vmacro20401' => 'vma', 'VMungo0464G1349' => 'vmu', 'VMungo0540G0289' => 'vmu', 'VMungo1215G1590' => 'vmu', 'VMungo1309G0221' => 'vmu', 'VMungo1309G2815' => 'vmu', 'VMungo1383G0239' => 'vmu', 'VMungo1383G2910' => 'vmu', 'Zm00001eb095270' => 'zma', 'Zm00001eb095280' => 'zma', 'Zm00001eb111630' => 'zma', 'Zm00001eb237080' => 'zma', 'Zm00001eb273740' => 'zma', 'Zm00001eb285040' => 'zma', 'Zm00001eb330790' => 'zma', 'Zm00001eb337380' => 'zma' ), 'gf_id' => 'HOM05D001484', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001484' ), 'data_identifier' => 'HOM05D001484', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001484', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p31500' => 'bna', 'A05p00020' => 'bna', 'A07p08820' => 'bna', 'Aa31LG4G3300' => 'aar', 'Aa31LG8G10030' => 'aar', 'Actinidia00731' => 'ach', 'Actinidia11473' => 'ach', 'Actinidia23469' => 'ach', 'Actinidia24318' => 'ach', 'Actinidia40196' => 'ach', 'Actinidia40197' => 'ach', 'Actinidia40198' => 'ach', 'Ah.08g212990' => 'amhyb', 'Ah.15g091720' => 'amhyb', 'AL3G38260' => 'aly', 'AL4G47710' => 'aly', 'Aqoxy2G00671' => 'aox', 'Aqoxy2G03236' => 'aox', 'arahy.Tifrunner.gnm1.ann1.05IDCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KR684' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATY3SJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK6QJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6APGL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IDT7Z9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM073U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ0R87' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LE7RV4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT4QRX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V5ENPK' => 'arhy', 'AT2G48110' => 'ath', 'AT3G23590' => 'ath', 'ATR0626G186' => 'atr', 'ATR1127G141' => 'atr', 'Atru.chr4.2583' => 'acertr', 'Atru.chr5.1358' => 'acertr', 'Atru.chr5.1359' => 'acertr', 'Atru.chr8.46' => 'acertr', 'AUR62002640' => 'cqu', 'AUR62030055' => 'cqu', 'AUR62033713' => 'cqu', 'AUR62033714' => 'cqu', 'AUR62036795' => 'cqu', 'AUR62039891' => 'cqu', 'BcaB02g08737' => 'bca', 'BcaB04g20441' => 'bca', 'BcaB06g26509' => 'bca', 'BcaB06g26510' => 'bca', 'BcaB06g26511' => 'bca', 'BcaB06g26512' => 'bca', 'BcaB06g26513' => 'bca', 'BcaC02g12564' => 'bca', 'BcaC02g12565' => 'bca', 'BcaC02g12794' => 'bca', 'BcaC02g12795' => 'bca', 'BcaC02g12796' => 'bca', 'BcaC06g35541' => 'bca', 'BNapus_Darmor_BZH_scaffold_188p00080' => 'bna', 'BNapus_Darmor_BZH_scaffold_188p00090' => 'bna', 'BolC1t03972H' => 'bol', 'BolC1t03973H' => 'bol', 'BolC4t21680H' => 'bol', 'BolC7t41863H' => 'bol', 'BolSC55t61227H' => 'bol', 'BolSC55t61228H' => 'bol', 'BraA01t03278Z' => 'bra', 'BraA05t18998Z' => 'bra', 'BraA07t28673Z' => 'bra', 'C01p40150' => 'bna', 'C05p12370' => 'bna', 'C07p13680' => 'bna', 'CAN.G1006.16' => 'can', 'CAN.G1006.17' => 'can', 'CAN.G1170.2' => 'can', 'CAN.G962.7' => 'can', 'CANSAT25G2179' => 'cansat', 'CANSAT78G1573' => 'cansat', 'CARHR099510' => 'chi', 'CARHR143510' => 'chi', 'Carub.0003s2380' => 'cru', 'Carub.0004s3082' => 'cru', 'Ca_00614_v3' => 'car', 'Ca_07801_v3' => 'car', 'Ca_08567_v3' => 'car', 'Ca_09571_v3' => 'car', 'CBR_g19290' => 'cbr', 'Cc01_g19770' => 'ccan', 'Cc03_g03030' => 'ccan', 'CDE07G0968' => 'cde', 'CDE09G1441' => 'cde', 'Cfa006103' => 'cfa', 'Cfa015573' => 'cfa', 'Cfa016988' => 'cfa', 'Ciclev10006738m.g' => 'ccl', 'Ciclev10010920m.g' => 'ccl', 'Ciclev10018517m.g' => 'ccl', 'CiPaw.01G159200' => 'cil', 'CiPaw.02G091000' => 'cil', 'CiPaw.02G091100' => 'cil', 'CiPaw.08G103100' => 'cil', 'CiPaw.09G224900' => 'cil', 'ClCG06G005740' => 'cla', 'ClCG07G000090' => 'cla', 'ClCG07G000100' => 'cla', 'COL.COLO4_09143' => 'col', 'COL.COLO4_25124' => 'col', 'Cpa.g.sc16.34' => 'cpa', 'Cpa.g.sc3504.1' => 'cpa', 'Cpa.g.sc60.37' => 'cpa', 'CsaV3_6G018520' => 'csa', 'CsaV3_6G036860' => 'csa', 'CSS0001072' => 'camsi', 'CSS0020208' => 'camsi', 'CSS0021253' => 'camsi', 'CSS0022190' => 'camsi', 'CSS0036150' => 'camsi', 'CSS0040442' => 'camsi', 'CSS0042300' => 'camsi', 'CSS0045298' => 'camsi', 'DCAR_012449' => 'dca', 'DCAR_018405' => 'dca', 'DCAR_024573' => 'dca', 'DCAR_030591' => 'dca', 'Dinv16926' => 'din', 'Dinv32963' => 'din', 'Dinv38382' => 'din', 'Dinv38383' => 'din', 'Duzib133G0974' => 'dzi', 'Duzib138G1867' => 'dzi', 'Duzib211G0420' => 'dzi', 'Duzib212G0930' => 'dzi', 'ECA234G1645' => 'eca', 'ECA247G3467' => 'eca', 'ECA248G1703' => 'eca', 'EL10Ac3g06327' => 'bvu', 'EL10Ac7g17204' => 'bvu', 'Eucgr.A00855' => 'egr', 'Eucgr.A00858' => 'egr', 'Eucgr.H01520' => 'egr', 'Eucgr.H03604' => 'egr', 'Eucgr.L03465' => 'egr', 'Eucgr.L03466' => 'egr', 'FAN01G0988' => 'fan', 'FAN02G3892' => 'fan', 'FAN05G3381' => 'fan', 'FAN07G0967' => 'fan', 'FAN07G1493' => 'fan', 'FAN08G3125' => 'fan', 'FAN09G0402' => 'fan', 'FAN12G2594' => 'fan', 'FAN12G3879' => 'fan', 'FAN14G1546' => 'fan', 'FAN15G3626' => 'fan', 'FAN17G0588' => 'fan', 'FAN17G0609' => 'fan', 'FAN18G2817' => 'fan', 'FAN19G1305' => 'fan', 'FAN20G1787' => 'fan', 'FAN22G0073' => 'fan', 'FAN22G0352' => 'fan', 'FAN22G0368' => 'fan', 'FAN22G2273' => 'fan', 'FAN24G1998' => 'fan', 'FAN27G1317' => 'fan', 'FvH4_2g23980' => 'fve', 'FvH4_4g14380' => 'fve', 'FvH4_4g14390' => 'fve', 'FvH4_6g09250' => 'fve', 'Glyma.03G151100' => 'gma', 'Glyma.04G122550' => 'gma', 'Glyma.05G001600' => 'gma', 'Glyma.09G270766' => 'gma', 'Glyma.09G270832' => 'gma', 'Glyma.13G209800' => 'gma', 'Glyma.15G102800' => 'gma', 'Glyma.18G218900' => 'gma', 'Glyma.19G001500' => 'gma', 'Glyma.19G153600' => 'gma', 'Gohir.A02G028600' => 'ghi', 'Gohir.A08G045000' => 'ghi', 'Gohir.A11G120500' => 'ghi', 'Gohir.A12G006200' => 'ghi', 'Gohir.A12G006250' => 'ghi', 'Gohir.D02G036300' => 'ghi', 'Gohir.D08G054700' => 'ghi', 'Gohir.D11G125600' => 'ghi', 'Gohir.D12G005700' => 'ghi', 'Gorai.004G055200' => 'gra', 'Gorai.005G040400' => 'gra', 'Gorai.007G134500' => 'gra', 'Gorai.008G005500' => 'gra', 'GSVIVG01011094001' => 'vvi', 'GSVIVG01017879001' => 'vvi', 'GSVIVG01025988001' => 'vvi', 'GSVIVG01029847001' => 'vvi', 'HanXRQChr10g0282901' => 'han', 'HanXRQChr10g0310371' => 'han', 'HanXRQChr10g0315041' => 'han', 'HanXRQChr11g0327651' => 'han', 'HanXRQChr12g0359391' => 'han', 'Haze_00972' => 'cav', 'Haze_00973' => 'cav', 'Haze_00974' => 'cav', 'Haze_04747' => 'cav', 'Haze_04749' => 'cav', 'Haze_04750' => 'cav', 'Haze_21217' => 'cav', 'Hma1.2p1_1037F.1_g250680' => 'hma', 'Hma1.2p1_1644F.1_g295320' => 'hma', 'HPP92_011322' => 'vpl', 'HPP92_011323' => 'vpl', 'HPP92_011324' => 'vpl', 'HPP92_011325' => 'vpl', 'HPP92_011326' => 'vpl', 'Hund12205' => 'sun', 'Hund17957' => 'sun', 'Lalb_Chr06g0176771' => 'lal', 'Lalb_Chr18g0056021' => 'lal', 'Lalb_Chr18g0056031' => 'lal', 'Lalb_Chr18g0056041' => 'lal', 'Lalb_Chr20g0107751' => 'lal', 'Lalb_Chr20g0118371' => 'lal', 'Lj1g0010239' => 'lja', 'Lj1g0017101' => 'lja', 'Lj2A1178G40' => 'lonja', 'Lj2A54G84' => 'lonja', 'Lj2g0015248' => 'lja', 'Lj3A761T51' => 'lonja', 'Lj6g0018116' => 'lja', 'Lsat_1_v5_gn_4_136040' => 'lsa', 'Lsat_1_v5_gn_5_187461' => 'lsa', 'Lsat_1_v5_gn_5_77001' => 'lsa', 'Lsat_1_v5_gn_9_4461' => 'lsa', 'Manes.01G210100' => 'mes', 'Manes.03G185600' => 'mes', 'Manes.05G073300' => 'mes', 'Manes.09G120300' => 'mes', 'Manes.15G022100' => 'mes', 'Mapoly0096s0053' => 'mpo', 'MBI03_g14058_MAGBIO' => 'mbi', 'MBI03_g33876_MAGBIO' => 'mbi', 'MBI03_g36854_MAGBIO' => 'mbi', 'MBI17_g11997_MAGBIO' => 'mbi', 'MD03G1269000' => 'mdo', 'MD04G1179600' => 'mdo', 'MD11G1289800' => 'mdo', 'MD12G1194700' => 'mdo', 'MD13G1182100' => 'mdo', 'MD13G1182200' => 'mdo', 'MD16G1182600' => 'mdo', 'Medtr2g021400' => 'mtr', 'Medtr2g021470' => 'mtr', 'Medtr2g105810' => 'mtr', 'Medtr3g033580' => 'mtr', 'Medtr6g007970' => 'mtr', 'Medtr7g056330' => 'mtr', 'Medtr7g074290' => 'mtr', 'Medtr7g074380' => 'mtr', 'Medtr7g094550' => 'mtr', 'Medtr8g069995' => 'mtr', 'MELO3C014345.2' => 'cme', 'MELO3C021395.2' => 'cme', 'Migut.D00262' => 'egut', 'Migut.G00257' => 'egut', 'MSTRG.21575' => 'ama', 'MSTRG.3985' => 'ama', 'Nitab4.5_0000295g0140' => 'nta', 'Nitab4.5_0000732g0140' => 'nta', 'Nitab4.5_0003162g0020' => 'nta', 'Nitab4.5_0006180g0090' => 'nta', 'Nitab4.5_0006390g0010' => 'nta', 'Nitab4.5_0007392g0040' => 'nta', 'Nn1g02140' => 'nnu', 'Nn4g26168' => 'nnu', 'Nn5g26754' => 'nnu', 'Oeu001433.1' => 'oeu', 'Oeu010299.2' => 'oeu', 'Oeu011171.1' => 'oeu', 'Oeu037675.1' => 'oeu', 'Oeu038359.1' => 'oeu', 'Oeu063834.1' => 'oeu', 'Oeu063835.1' => 'oeu', 'Os05g0312000' => 'osa', 'Os07g0211101' => 'osa', 'Os07g0211200' => 'osa', 'Os07g0681500' => 'osa', 'Peaxi162Scf00095g01015' => 'pax', 'Peaxi162Scf00104g00329' => 'pax', 'Peaxi162Scf00161g00137' => 'pax', 'PGR004G1665' => 'pgr', 'PGR031G2937' => 'pgr', 'PGR119G2145' => 'pgr', 'PGSC0003DMG400004351' => 'stu', 'PGSC0003DMG400014625' => 'stu', 'PGSC0003DMG401000943' => 'stu', 'Phvul.001G148600' => 'pvu', 'Phvul.004G001700' => 'pvu', 'Phvul.006G154900' => 'pvu', 'Phvul.008G078200' => 'pvu', 'Phvul.011G136500' => 'pvu', 'Potri.002G215600' => 'ptr', 'Potri.008G201600' => 'ptr', 'Potri.014G138400' => 'ptr', 'Potri.016G142500' => 'ptr', 'Pp3c16_10580' => 'ppa', 'Pp3c5_25280' => 'ppa', 'Prupe.1G150000' => 'ppe', 'Prupe.1G150100' => 'ppe', 'Prupe.6G299600' => 'ppe', 'Prupe.8G245000' => 'ppe', 'Psat0s4927g0040' => 'psa', 'Psat1g052080' => 'psa', 'Psat1g183800' => 'psa', 'Psat3g113840' => 'psa', 'Psat3g126120' => 'psa', 'Psat3g126160' => 'psa', 'Psat3g158760' => 'psa', 'Psat3g158840' => 'psa', 'PSO170G2858' => 'pso', 'PSO339G0606' => 'pso', 'PSO384G4709' => 'pso', 'PSO407G0334' => 'pso', 'QL04p040276' => 'qlo', 'QL06p005458' => 'qlo', 'QL06p005472' => 'qlo', 'QL07p030546' => 'qlo', 'QL07p031519' => 'qlo', 'QL09p050949' => 'qlo', 'QL09p050966' => 'qlo', 'QL09p051067' => 'qlo', 'QL12p022706' => 'qlo', 'RcHm_v2.0_Chr2g0119601' => 'rch', 'RcHm_v2.0_Chr3g0459591' => 'rch', 'RcHm_v2.0_Chr4g0418521' => 'rch', 'RcHm_v2.0_Chr4g0418531' => 'rch', 'RcHm_v2.0_Chr4g0418541' => 'rch', 'RcHm_v2.0_Chr6g0291641' => 'rch', 'Rhsim01G0086300' => 'rsi', 'Rhsim01G0276300' => 'rsi', 'Rhsim01G0276500' => 'rsi', 'Rhsim04G0207700' => 'rsi', 'Rhsim05G0234500' => 'rsi', 'Rhsim13G0022400' => 'rsi', 'Sabra02G0167900' => 'sbr', 'Sabra04G0158500' => 'sbr', 'Sabra08G0159800' => 'sbr', 'Sabra10G0011500' => 'sbr', 'Sabra14G0104400' => 'sbr', 'SalBow2G2440' => 'sbo', 'SalBow4G2265' => 'sbo', 'Sc02g0000060' => 'sci', 'Sc05g0005020' => 'sci', 'Sc13g0003890' => 'sci', 'Sed0014865' => 'sed', 'Sed0017224' => 'sed', 'Sed0026391' => 'sed', 'SEGI_00063' => 'sgi', 'SEGI_10967' => 'sgi', 'SEGI_17510' => 'sgi', 'SEGI_24396' => 'sgi', 'SEGI_39719' => 'sgi', 'SEGI_41392' => 'sgi', 'SGA_v2.0_scaffold11G05794' => 'sas', 'SGA_v2.0_scaffold142G35607' => 'sas', 'SGA_v2.0_scaffold1G00447' => 'sas', 'SHI15388' => 'shi', 'SHI15394' => 'shi', 'SHI15396' => 'shi', 'SHI15399' => 'shi', 'SMO343G0151' => 'smo', 'SMO367G1118' => 'smo', 'Solyc01g080200.3' => 'sly', 'Solyc06g008960.3' => 'sly', 'Solyc09g064780.3' => 'sly', 'Sopen01g031980' => 'spe', 'Sopen06g003710' => 'spe', 'Sopen09g026460' => 'spe', 'Sp3g21240' => 'spa', 'Sp4g30030' => 'spa', 'TAR365G0022' => 'tar', 'TAR365G1023' => 'tar', 'TAR365G1253' => 'tar', 'TAR623G0078' => 'tar', 'TAR623G1721' => 'tar', 'TAR633G0959' => 'tar', 'THA.LOC104802225' => 'tha', 'THA.LOC104804769' => 'tha', 'THA.LOC104808660' => 'tha', 'THA.LOC104812792' => 'tha', 'Thecc.01G284000' => 'tca', 'Thecc.04G220600' => 'tca', 'Thecc.05G268900' => 'tca', 'Thecc.08G171100' => 'tca', 'Thhalv10001284m.g' => 'esa', 'Thhalv10019912m.g' => 'esa', 'TPR.G14189' => 'tpr', 'TPR.G18110' => 'tpr', 'TPR.G18130' => 'tpr', 'TPR.G18131' => 'tpr', 'TPR.G18140' => 'tpr', 'TPR.G24282' => 'tpr', 'TPR.G25221' => 'tpr', 'TPR.G29267' => 'tpr', 'TPR.G35315' => 'tpr', 'TPR.G36173' => 'tpr', 'TWI09G0794' => 'twi', 'TWI59G1348' => 'twi', 'TWI74G0430' => 'twi', 'unitig_26.g8940' => 'ugi', 'unitig_749.g13744' => 'ugi', 'unitig_749.g13745' => 'ugi', 'vmacro08269' => 'vma', 'vmacro14937' => 'vma', 'vmacro20401' => 'vma', 'VMungo0464G1349' => 'vmu', 'VMungo0540G0289' => 'vmu', 'VMungo1215G1590' => 'vmu', 'VMungo1309G0221' => 'vmu', 'VMungo1309G2815' => 'vmu', 'VMungo1383G0239' => 'vmu', 'VMungo1383G2910' => 'vmu', 'Zm00001eb095270' => 'zma', 'Zm00001eb095280' => 'zma', 'Zm00001eb111630' => 'zma', 'Zm00001eb237080' => 'zma', 'Zm00001eb273740' => 'zma', 'Zm00001eb285040' => 'zma', 'Zm00001eb330790' => 'zma', 'Zm00001eb337380' => 'zma' ) $gf_id = 'HOM05D001484' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001484' ) $data_identifier = 'HOM05D001484' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 2, 'aly' => (int) 2, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 22, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 7, 'hma' => (int) 2, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 7, 'mtr' => (int) 10, 'cme' => (int) 2, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 4, 'ppa' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 4, 'qlo' => (int) 9, 'rch' => (int) 6, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 10, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 7, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb337380' $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' => 'HOM05D001484', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p31500' => 'bna', 'A05p00020' => 'bna', 'A07p08820' => 'bna', 'Aa31LG4G3300' => 'aar', 'Aa31LG8G10030' => 'aar', 'Actinidia00731' => 'ach', 'Actinidia11473' => 'ach', 'Actinidia23469' => 'ach', 'Actinidia24318' => 'ach', 'Actinidia40196' => 'ach', 'Actinidia40197' => 'ach', 'Actinidia40198' => 'ach', 'Ah.08g212990' => 'amhyb', 'Ah.15g091720' => 'amhyb', 'AL3G38260' => 'aly', 'AL4G47710' => 'aly', 'Aqoxy2G00671' => 'aox', 'Aqoxy2G03236' => 'aox', 'arahy.Tifrunner.gnm1.ann1.05IDCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KR684' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATY3SJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK6QJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6APGL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IDT7Z9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM073U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ0R87' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LE7RV4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT4QRX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V5ENPK' => 'arhy', 'AT2G48110' => 'ath', 'AT3G23590' => 'ath', 'ATR0626G186' => 'atr', 'ATR1127G141' => 'atr', 'Atru.chr4.2583' => 'acertr', 'Atru.chr5.1358' => 'acertr', 'Atru.chr5.1359' => 'acertr', 'Atru.chr8.46' => 'acertr', 'AUR62002640' => 'cqu', 'AUR62030055' => 'cqu', 'AUR62033713' => 'cqu', 'AUR62033714' => 'cqu', 'AUR62036795' => 'cqu', 'AUR62039891' => 'cqu', 'BcaB02g08737' => 'bca', 'BcaB04g20441' => 'bca', 'BcaB06g26509' => 'bca', 'BcaB06g26510' => 'bca', 'BcaB06g26511' => 'bca', 'BcaB06g26512' => 'bca', 'BcaB06g26513' => 'bca', 'BcaC02g12564' => 'bca', 'BcaC02g12565' => 'bca', 'BcaC02g12794' => 'bca', 'BcaC02g12795' => 'bca', 'BcaC02g12796' => 'bca', 'BcaC06g35541' => 'bca', 'BNapus_Darmor_BZH_scaffold_188p00080' => 'bna', 'BNapus_Darmor_BZH_scaffold_188p00090' => 'bna', 'BolC1t03972H' => 'bol', 'BolC1t03973H' => 'bol', 'BolC4t21680H' => 'bol', 'BolC7t41863H' => 'bol', 'BolSC55t61227H' => 'bol', 'BolSC55t61228H' => 'bol', 'BraA01t03278Z' => 'bra', 'BraA05t18998Z' => 'bra', 'BraA07t28673Z' => 'bra', 'C01p40150' => 'bna', 'C05p12370' => 'bna', 'C07p13680' => 'bna', 'CAN.G1006.16' => 'can', 'CAN.G1006.17' => 'can', 'CAN.G1170.2' => 'can', 'CAN.G962.7' => 'can', 'CANSAT25G2179' => 'cansat', 'CANSAT78G1573' => 'cansat', 'CARHR099510' => 'chi', 'CARHR143510' => 'chi', 'Carub.0003s2380' => 'cru', 'Carub.0004s3082' => 'cru', 'Ca_00614_v3' => 'car', 'Ca_07801_v3' => 'car', 'Ca_08567_v3' => 'car', 'Ca_09571_v3' => 'car', 'CBR_g19290' => 'cbr', 'Cc01_g19770' => 'ccan', 'Cc03_g03030' => 'ccan', 'CDE07G0968' => 'cde', 'CDE09G1441' => 'cde', 'Cfa006103' => 'cfa', 'Cfa015573' => 'cfa', 'Cfa016988' => 'cfa', 'Ciclev10006738m.g' => 'ccl', 'Ciclev10010920m.g' => 'ccl', 'Ciclev10018517m.g' => 'ccl', 'CiPaw.01G159200' => 'cil', 'CiPaw.02G091000' => 'cil', 'CiPaw.02G091100' => 'cil', 'CiPaw.08G103100' => 'cil', 'CiPaw.09G224900' => 'cil', 'ClCG06G005740' => 'cla', 'ClCG07G000090' => 'cla', 'ClCG07G000100' => 'cla', 'COL.COLO4_09143' => 'col', 'COL.COLO4_25124' => 'col', 'Cpa.g.sc16.34' => 'cpa', 'Cpa.g.sc3504.1' => 'cpa', 'Cpa.g.sc60.37' => 'cpa', 'CsaV3_6G018520' => 'csa', 'CsaV3_6G036860' => 'csa', 'CSS0001072' => 'camsi', 'CSS0020208' => 'camsi', 'CSS0021253' => 'camsi', 'CSS0022190' => 'camsi', 'CSS0036150' => 'camsi', 'CSS0040442' => 'camsi', 'CSS0042300' => 'camsi', 'CSS0045298' => 'camsi', 'DCAR_012449' => 'dca', 'DCAR_018405' => 'dca', 'DCAR_024573' => 'dca', 'DCAR_030591' => 'dca', 'Dinv16926' => 'din', 'Dinv32963' => 'din', 'Dinv38382' => 'din', 'Dinv38383' => 'din', 'Duzib133G0974' => 'dzi', 'Duzib138G1867' => 'dzi', 'Duzib211G0420' => 'dzi', 'Duzib212G0930' => 'dzi', 'ECA234G1645' => 'eca', 'ECA247G3467' => 'eca', 'ECA248G1703' => 'eca', 'EL10Ac3g06327' => 'bvu', 'EL10Ac7g17204' => 'bvu', 'Eucgr.A00855' => 'egr', 'Eucgr.A00858' => 'egr', 'Eucgr.H01520' => 'egr', 'Eucgr.H03604' => 'egr', 'Eucgr.L03465' => 'egr', 'Eucgr.L03466' => 'egr', 'FAN01G0988' => 'fan', 'FAN02G3892' => 'fan', 'FAN05G3381' => 'fan', 'FAN07G0967' => 'fan', 'FAN07G1493' => 'fan', 'FAN08G3125' => 'fan', 'FAN09G0402' => 'fan', 'FAN12G2594' => 'fan', 'FAN12G3879' => 'fan', 'FAN14G1546' => 'fan', 'FAN15G3626' => 'fan', 'FAN17G0588' => 'fan', 'FAN17G0609' => 'fan', 'FAN18G2817' => 'fan', 'FAN19G1305' => 'fan', 'FAN20G1787' => 'fan', 'FAN22G0073' => 'fan', 'FAN22G0352' => 'fan', 'FAN22G0368' => 'fan', 'FAN22G2273' => 'fan', 'FAN24G1998' => 'fan', 'FAN27G1317' => 'fan', 'FvH4_2g23980' => 'fve', 'FvH4_4g14380' => 'fve', 'FvH4_4g14390' => 'fve', 'FvH4_6g09250' => 'fve', 'Glyma.03G151100' => 'gma', 'Glyma.04G122550' => 'gma', 'Glyma.05G001600' => 'gma', 'Glyma.09G270766' => 'gma', 'Glyma.09G270832' => 'gma', 'Glyma.13G209800' => 'gma', 'Glyma.15G102800' => 'gma', 'Glyma.18G218900' => 'gma', 'Glyma.19G001500' => 'gma', 'Glyma.19G153600' => 'gma', 'Gohir.A02G028600' => 'ghi', 'Gohir.A08G045000' => 'ghi', 'Gohir.A11G120500' => 'ghi', 'Gohir.A12G006200' => 'ghi', 'Gohir.A12G006250' => 'ghi', 'Gohir.D02G036300' => 'ghi', 'Gohir.D08G054700' => 'ghi', 'Gohir.D11G125600' => 'ghi', 'Gohir.D12G005700' => 'ghi', 'Gorai.004G055200' => 'gra', 'Gorai.005G040400' => 'gra', 'Gorai.007G134500' => 'gra', 'Gorai.008G005500' => 'gra', 'GSVIVG01011094001' => 'vvi', 'GSVIVG01017879001' => 'vvi', 'GSVIVG01025988001' => 'vvi', 'GSVIVG01029847001' => 'vvi', 'HanXRQChr10g0282901' => 'han', 'HanXRQChr10g0310371' => 'han', 'HanXRQChr10g0315041' => 'han', 'HanXRQChr11g0327651' => 'han', 'HanXRQChr12g0359391' => 'han', 'Haze_00972' => 'cav', 'Haze_00973' => 'cav', 'Haze_00974' => 'cav', 'Haze_04747' => 'cav', 'Haze_04749' => 'cav', 'Haze_04750' => 'cav', 'Haze_21217' => 'cav', 'Hma1.2p1_1037F.1_g250680' => 'hma', 'Hma1.2p1_1644F.1_g295320' => 'hma', 'HPP92_011322' => 'vpl', 'HPP92_011323' => 'vpl', 'HPP92_011324' => 'vpl', 'HPP92_011325' => 'vpl', 'HPP92_011326' => 'vpl', 'Hund12205' => 'sun', 'Hund17957' => 'sun', 'Lalb_Chr06g0176771' => 'lal', 'Lalb_Chr18g0056021' => 'lal', 'Lalb_Chr18g0056031' => 'lal', 'Lalb_Chr18g0056041' => 'lal', 'Lalb_Chr20g0107751' => 'lal', 'Lalb_Chr20g0118371' => 'lal', 'Lj1g0010239' => 'lja', 'Lj1g0017101' => 'lja', 'Lj2A1178G40' => 'lonja', 'Lj2A54G84' => 'lonja', 'Lj2g0015248' => 'lja', 'Lj3A761T51' => 'lonja', 'Lj6g0018116' => 'lja', 'Lsat_1_v5_gn_4_136040' => 'lsa', 'Lsat_1_v5_gn_5_187461' => 'lsa', 'Lsat_1_v5_gn_5_77001' => 'lsa', 'Lsat_1_v5_gn_9_4461' => 'lsa', 'Manes.01G210100' => 'mes', 'Manes.03G185600' => 'mes', 'Manes.05G073300' => 'mes', 'Manes.09G120300' => 'mes', 'Manes.15G022100' => 'mes', 'Mapoly0096s0053' => 'mpo', 'MBI03_g14058_MAGBIO' => 'mbi', 'MBI03_g33876_MAGBIO' => 'mbi', 'MBI03_g36854_MAGBIO' => 'mbi', 'MBI17_g11997_MAGBIO' => 'mbi', 'MD03G1269000' => 'mdo', 'MD04G1179600' => 'mdo', 'MD11G1289800' => 'mdo', 'MD12G1194700' => 'mdo', 'MD13G1182100' => 'mdo', 'MD13G1182200' => 'mdo', 'MD16G1182600' => 'mdo', 'Medtr2g021400' => 'mtr', 'Medtr2g021470' => 'mtr', 'Medtr2g105810' => 'mtr', 'Medtr3g033580' => 'mtr', 'Medtr6g007970' => 'mtr', 'Medtr7g056330' => 'mtr', 'Medtr7g074290' => 'mtr', 'Medtr7g074380' => 'mtr', 'Medtr7g094550' => 'mtr', 'Medtr8g069995' => 'mtr', 'MELO3C014345.2' => 'cme', 'MELO3C021395.2' => 'cme', 'Migut.D00262' => 'egut', 'Migut.G00257' => 'egut', 'MSTRG.21575' => 'ama', 'MSTRG.3985' => 'ama', 'Nitab4.5_0000295g0140' => 'nta', 'Nitab4.5_0000732g0140' => 'nta', 'Nitab4.5_0003162g0020' => 'nta', 'Nitab4.5_0006180g0090' => 'nta', 'Nitab4.5_0006390g0010' => 'nta', 'Nitab4.5_0007392g0040' => 'nta', 'Nn1g02140' => 'nnu', 'Nn4g26168' => 'nnu', 'Nn5g26754' => 'nnu', 'Oeu001433.1' => 'oeu', 'Oeu010299.2' => 'oeu', 'Oeu011171.1' => 'oeu', 'Oeu037675.1' => 'oeu', 'Oeu038359.1' => 'oeu', 'Oeu063834.1' => 'oeu', 'Oeu063835.1' => 'oeu', 'Os05g0312000' => 'osa', 'Os07g0211101' => 'osa', 'Os07g0211200' => 'osa', 'Os07g0681500' => 'osa', 'Peaxi162Scf00095g01015' => 'pax', 'Peaxi162Scf00104g00329' => 'pax', 'Peaxi162Scf00161g00137' => 'pax', 'PGR004G1665' => 'pgr', 'PGR031G2937' => 'pgr', 'PGR119G2145' => 'pgr', 'PGSC0003DMG400004351' => 'stu', 'PGSC0003DMG400014625' => 'stu', 'PGSC0003DMG401000943' => 'stu', 'Phvul.001G148600' => 'pvu', 'Phvul.004G001700' => 'pvu', 'Phvul.006G154900' => 'pvu', 'Phvul.008G078200' => 'pvu', 'Phvul.011G136500' => 'pvu', 'Potri.002G215600' => 'ptr', 'Potri.008G201600' => 'ptr', 'Potri.014G138400' => 'ptr', 'Potri.016G142500' => 'ptr', 'Pp3c16_10580' => 'ppa', 'Pp3c5_25280' => 'ppa', 'Prupe.1G150000' => 'ppe', 'Prupe.1G150100' => 'ppe', 'Prupe.6G299600' => 'ppe', 'Prupe.8G245000' => 'ppe', 'Psat0s4927g0040' => 'psa', 'Psat1g052080' => 'psa', 'Psat1g183800' => 'psa', 'Psat3g113840' => 'psa', 'Psat3g126120' => 'psa', 'Psat3g126160' => 'psa', 'Psat3g158760' => 'psa', 'Psat3g158840' => 'psa', 'PSO170G2858' => 'pso', 'PSO339G0606' => 'pso', 'PSO384G4709' => 'pso', 'PSO407G0334' => 'pso', 'QL04p040276' => 'qlo', 'QL06p005458' => 'qlo', 'QL06p005472' => 'qlo', 'QL07p030546' => 'qlo', 'QL07p031519' => 'qlo', 'QL09p050949' => 'qlo', 'QL09p050966' => 'qlo', 'QL09p051067' => 'qlo', 'QL12p022706' => 'qlo', 'RcHm_v2.0_Chr2g0119601' => 'rch', 'RcHm_v2.0_Chr3g0459591' => 'rch', 'RcHm_v2.0_Chr4g0418521' => 'rch', 'RcHm_v2.0_Chr4g0418531' => 'rch', 'RcHm_v2.0_Chr4g0418541' => 'rch', 'RcHm_v2.0_Chr6g0291641' => 'rch', 'Rhsim01G0086300' => 'rsi', 'Rhsim01G0276300' => 'rsi', 'Rhsim01G0276500' => 'rsi', 'Rhsim04G0207700' => 'rsi', 'Rhsim05G0234500' => 'rsi', 'Rhsim13G0022400' => 'rsi', 'Sabra02G0167900' => 'sbr', 'Sabra04G0158500' => 'sbr', 'Sabra08G0159800' => 'sbr', 'Sabra10G0011500' => 'sbr', 'Sabra14G0104400' => 'sbr', 'SalBow2G2440' => 'sbo', 'SalBow4G2265' => 'sbo', 'Sc02g0000060' => 'sci', 'Sc05g0005020' => 'sci', 'Sc13g0003890' => 'sci', 'Sed0014865' => 'sed', 'Sed0017224' => 'sed', 'Sed0026391' => 'sed', 'SEGI_00063' => 'sgi', 'SEGI_10967' => 'sgi', 'SEGI_17510' => 'sgi', 'SEGI_24396' => 'sgi', 'SEGI_39719' => 'sgi', 'SEGI_41392' => 'sgi', 'SGA_v2.0_scaffold11G05794' => 'sas', 'SGA_v2.0_scaffold142G35607' => 'sas', 'SGA_v2.0_scaffold1G00447' => 'sas', 'SHI15388' => 'shi', 'SHI15394' => 'shi', 'SHI15396' => 'shi', 'SHI15399' => 'shi', 'SMO343G0151' => 'smo', 'SMO367G1118' => 'smo', 'Solyc01g080200.3' => 'sly', 'Solyc06g008960.3' => 'sly', 'Solyc09g064780.3' => 'sly', 'Sopen01g031980' => 'spe', 'Sopen06g003710' => 'spe', 'Sopen09g026460' => 'spe', 'Sp3g21240' => 'spa', 'Sp4g30030' => 'spa', 'TAR365G0022' => 'tar', 'TAR365G1023' => 'tar', 'TAR365G1253' => 'tar', 'TAR623G0078' => 'tar', 'TAR623G1721' => 'tar', 'TAR633G0959' => 'tar', 'THA.LOC104802225' => 'tha', 'THA.LOC104804769' => 'tha', 'THA.LOC104808660' => 'tha', 'THA.LOC104812792' => 'tha', 'Thecc.01G284000' => 'tca', 'Thecc.04G220600' => 'tca', 'Thecc.05G268900' => 'tca', 'Thecc.08G171100' => 'tca', 'Thhalv10001284m.g' => 'esa', 'Thhalv10019912m.g' => 'esa', 'TPR.G14189' => 'tpr', 'TPR.G18110' => 'tpr', 'TPR.G18130' => 'tpr', 'TPR.G18131' => 'tpr', 'TPR.G18140' => 'tpr', 'TPR.G24282' => 'tpr', 'TPR.G25221' => 'tpr', 'TPR.G29267' => 'tpr', 'TPR.G35315' => 'tpr', 'TPR.G36173' => 'tpr', 'TWI09G0794' => 'twi', 'TWI59G1348' => 'twi', 'TWI74G0430' => 'twi', 'unitig_26.g8940' => 'ugi', 'unitig_749.g13744' => 'ugi', 'unitig_749.g13745' => 'ugi', 'vmacro08269' => 'vma', 'vmacro14937' => 'vma', 'vmacro20401' => 'vma', 'VMungo0464G1349' => 'vmu', 'VMungo0540G0289' => 'vmu', 'VMungo1215G1590' => 'vmu', 'VMungo1309G0221' => 'vmu', 'VMungo1309G2815' => 'vmu', 'VMungo1383G0239' => 'vmu', 'VMungo1383G2910' => 'vmu', 'Zm00001eb095270' => 'zma', 'Zm00001eb095280' => 'zma', 'Zm00001eb111630' => 'zma', 'Zm00001eb237080' => 'zma', 'Zm00001eb273740' => 'zma', 'Zm00001eb285040' => 'zma', 'Zm00001eb330790' => 'zma', 'Zm00001eb337380' => 'zma' ), 'gf_id' => 'HOM05D001484', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001484' ), 'data_identifier' => 'HOM05D001484', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001484', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p31500' => 'bna', 'A05p00020' => 'bna', 'A07p08820' => 'bna', 'Aa31LG4G3300' => 'aar', 'Aa31LG8G10030' => 'aar', 'Actinidia00731' => 'ach', 'Actinidia11473' => 'ach', 'Actinidia23469' => 'ach', 'Actinidia24318' => 'ach', 'Actinidia40196' => 'ach', 'Actinidia40197' => 'ach', 'Actinidia40198' => 'ach', 'Ah.08g212990' => 'amhyb', 'Ah.15g091720' => 'amhyb', 'AL3G38260' => 'aly', 'AL4G47710' => 'aly', 'Aqoxy2G00671' => 'aox', 'Aqoxy2G03236' => 'aox', 'arahy.Tifrunner.gnm1.ann1.05IDCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KR684' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATY3SJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK6QJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6APGL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IDT7Z9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM073U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ0R87' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LE7RV4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT4QRX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V5ENPK' => 'arhy', 'AT2G48110' => 'ath', 'AT3G23590' => 'ath', 'ATR0626G186' => 'atr', 'ATR1127G141' => 'atr', 'Atru.chr4.2583' => 'acertr', 'Atru.chr5.1358' => 'acertr', 'Atru.chr5.1359' => 'acertr', 'Atru.chr8.46' => 'acertr', 'AUR62002640' => 'cqu', 'AUR62030055' => 'cqu', 'AUR62033713' => 'cqu', 'AUR62033714' => 'cqu', 'AUR62036795' => 'cqu', 'AUR62039891' => 'cqu', 'BcaB02g08737' => 'bca', 'BcaB04g20441' => 'bca', 'BcaB06g26509' => 'bca', 'BcaB06g26510' => 'bca', 'BcaB06g26511' => 'bca', 'BcaB06g26512' => 'bca', 'BcaB06g26513' => 'bca', 'BcaC02g12564' => 'bca', 'BcaC02g12565' => 'bca', 'BcaC02g12794' => 'bca', 'BcaC02g12795' => 'bca', 'BcaC02g12796' => 'bca', 'BcaC06g35541' => 'bca', 'BNapus_Darmor_BZH_scaffold_188p00080' => 'bna', 'BNapus_Darmor_BZH_scaffold_188p00090' => 'bna', 'BolC1t03972H' => 'bol', 'BolC1t03973H' => 'bol', 'BolC4t21680H' => 'bol', 'BolC7t41863H' => 'bol', 'BolSC55t61227H' => 'bol', 'BolSC55t61228H' => 'bol', 'BraA01t03278Z' => 'bra', 'BraA05t18998Z' => 'bra', 'BraA07t28673Z' => 'bra', 'C01p40150' => 'bna', 'C05p12370' => 'bna', 'C07p13680' => 'bna', 'CAN.G1006.16' => 'can', 'CAN.G1006.17' => 'can', 'CAN.G1170.2' => 'can', 'CAN.G962.7' => 'can', 'CANSAT25G2179' => 'cansat', 'CANSAT78G1573' => 'cansat', 'CARHR099510' => 'chi', 'CARHR143510' => 'chi', 'Carub.0003s2380' => 'cru', 'Carub.0004s3082' => 'cru', 'Ca_00614_v3' => 'car', 'Ca_07801_v3' => 'car', 'Ca_08567_v3' => 'car', 'Ca_09571_v3' => 'car', 'CBR_g19290' => 'cbr', 'Cc01_g19770' => 'ccan', 'Cc03_g03030' => 'ccan', 'CDE07G0968' => 'cde', 'CDE09G1441' => 'cde', 'Cfa006103' => 'cfa', 'Cfa015573' => 'cfa', 'Cfa016988' => 'cfa', 'Ciclev10006738m.g' => 'ccl', 'Ciclev10010920m.g' => 'ccl', 'Ciclev10018517m.g' => 'ccl', 'CiPaw.01G159200' => 'cil', 'CiPaw.02G091000' => 'cil', 'CiPaw.02G091100' => 'cil', 'CiPaw.08G103100' => 'cil', 'CiPaw.09G224900' => 'cil', 'ClCG06G005740' => 'cla', 'ClCG07G000090' => 'cla', 'ClCG07G000100' => 'cla', 'COL.COLO4_09143' => 'col', 'COL.COLO4_25124' => 'col', 'Cpa.g.sc16.34' => 'cpa', 'Cpa.g.sc3504.1' => 'cpa', 'Cpa.g.sc60.37' => 'cpa', 'CsaV3_6G018520' => 'csa', 'CsaV3_6G036860' => 'csa', 'CSS0001072' => 'camsi', 'CSS0020208' => 'camsi', 'CSS0021253' => 'camsi', 'CSS0022190' => 'camsi', 'CSS0036150' => 'camsi', 'CSS0040442' => 'camsi', 'CSS0042300' => 'camsi', 'CSS0045298' => 'camsi', 'DCAR_012449' => 'dca', 'DCAR_018405' => 'dca', 'DCAR_024573' => 'dca', 'DCAR_030591' => 'dca', 'Dinv16926' => 'din', 'Dinv32963' => 'din', 'Dinv38382' => 'din', 'Dinv38383' => 'din', 'Duzib133G0974' => 'dzi', 'Duzib138G1867' => 'dzi', 'Duzib211G0420' => 'dzi', 'Duzib212G0930' => 'dzi', 'ECA234G1645' => 'eca', 'ECA247G3467' => 'eca', 'ECA248G1703' => 'eca', 'EL10Ac3g06327' => 'bvu', 'EL10Ac7g17204' => 'bvu', 'Eucgr.A00855' => 'egr', 'Eucgr.A00858' => 'egr', 'Eucgr.H01520' => 'egr', 'Eucgr.H03604' => 'egr', 'Eucgr.L03465' => 'egr', 'Eucgr.L03466' => 'egr', 'FAN01G0988' => 'fan', 'FAN02G3892' => 'fan', 'FAN05G3381' => 'fan', 'FAN07G0967' => 'fan', 'FAN07G1493' => 'fan', 'FAN08G3125' => 'fan', 'FAN09G0402' => 'fan', 'FAN12G2594' => 'fan', 'FAN12G3879' => 'fan', 'FAN14G1546' => 'fan', 'FAN15G3626' => 'fan', 'FAN17G0588' => 'fan', 'FAN17G0609' => 'fan', 'FAN18G2817' => 'fan', 'FAN19G1305' => 'fan', 'FAN20G1787' => 'fan', 'FAN22G0073' => 'fan', 'FAN22G0352' => 'fan', 'FAN22G0368' => 'fan', 'FAN22G2273' => 'fan', 'FAN24G1998' => 'fan', 'FAN27G1317' => 'fan', 'FvH4_2g23980' => 'fve', 'FvH4_4g14380' => 'fve', 'FvH4_4g14390' => 'fve', 'FvH4_6g09250' => 'fve', 'Glyma.03G151100' => 'gma', 'Glyma.04G122550' => 'gma', 'Glyma.05G001600' => 'gma', 'Glyma.09G270766' => 'gma', 'Glyma.09G270832' => 'gma', 'Glyma.13G209800' => 'gma', 'Glyma.15G102800' => 'gma', 'Glyma.18G218900' => 'gma', 'Glyma.19G001500' => 'gma', 'Glyma.19G153600' => 'gma', 'Gohir.A02G028600' => 'ghi', 'Gohir.A08G045000' => 'ghi', 'Gohir.A11G120500' => 'ghi', 'Gohir.A12G006200' => 'ghi', 'Gohir.A12G006250' => 'ghi', 'Gohir.D02G036300' => 'ghi', 'Gohir.D08G054700' => 'ghi', 'Gohir.D11G125600' => 'ghi', 'Gohir.D12G005700' => 'ghi', 'Gorai.004G055200' => 'gra', 'Gorai.005G040400' => 'gra', 'Gorai.007G134500' => 'gra', 'Gorai.008G005500' => 'gra', 'GSVIVG01011094001' => 'vvi', 'GSVIVG01017879001' => 'vvi', 'GSVIVG01025988001' => 'vvi', 'GSVIVG01029847001' => 'vvi', 'HanXRQChr10g0282901' => 'han', 'HanXRQChr10g0310371' => 'han', 'HanXRQChr10g0315041' => 'han', 'HanXRQChr11g0327651' => 'han', 'HanXRQChr12g0359391' => 'han', 'Haze_00972' => 'cav', 'Haze_00973' => 'cav', 'Haze_00974' => 'cav', 'Haze_04747' => 'cav', 'Haze_04749' => 'cav', 'Haze_04750' => 'cav', 'Haze_21217' => 'cav', 'Hma1.2p1_1037F.1_g250680' => 'hma', 'Hma1.2p1_1644F.1_g295320' => 'hma', 'HPP92_011322' => 'vpl', 'HPP92_011323' => 'vpl', 'HPP92_011324' => 'vpl', 'HPP92_011325' => 'vpl', 'HPP92_011326' => 'vpl', 'Hund12205' => 'sun', 'Hund17957' => 'sun', 'Lalb_Chr06g0176771' => 'lal', 'Lalb_Chr18g0056021' => 'lal', 'Lalb_Chr18g0056031' => 'lal', 'Lalb_Chr18g0056041' => 'lal', 'Lalb_Chr20g0107751' => 'lal', 'Lalb_Chr20g0118371' => 'lal', 'Lj1g0010239' => 'lja', 'Lj1g0017101' => 'lja', 'Lj2A1178G40' => 'lonja', 'Lj2A54G84' => 'lonja', 'Lj2g0015248' => 'lja', 'Lj3A761T51' => 'lonja', 'Lj6g0018116' => 'lja', 'Lsat_1_v5_gn_4_136040' => 'lsa', 'Lsat_1_v5_gn_5_187461' => 'lsa', 'Lsat_1_v5_gn_5_77001' => 'lsa', 'Lsat_1_v5_gn_9_4461' => 'lsa', 'Manes.01G210100' => 'mes', 'Manes.03G185600' => 'mes', 'Manes.05G073300' => 'mes', 'Manes.09G120300' => 'mes', 'Manes.15G022100' => 'mes', 'Mapoly0096s0053' => 'mpo', 'MBI03_g14058_MAGBIO' => 'mbi', 'MBI03_g33876_MAGBIO' => 'mbi', 'MBI03_g36854_MAGBIO' => 'mbi', 'MBI17_g11997_MAGBIO' => 'mbi', 'MD03G1269000' => 'mdo', 'MD04G1179600' => 'mdo', 'MD11G1289800' => 'mdo', 'MD12G1194700' => 'mdo', 'MD13G1182100' => 'mdo', 'MD13G1182200' => 'mdo', 'MD16G1182600' => 'mdo', 'Medtr2g021400' => 'mtr', 'Medtr2g021470' => 'mtr', 'Medtr2g105810' => 'mtr', 'Medtr3g033580' => 'mtr', 'Medtr6g007970' => 'mtr', 'Medtr7g056330' => 'mtr', 'Medtr7g074290' => 'mtr', 'Medtr7g074380' => 'mtr', 'Medtr7g094550' => 'mtr', 'Medtr8g069995' => 'mtr', 'MELO3C014345.2' => 'cme', 'MELO3C021395.2' => 'cme', 'Migut.D00262' => 'egut', 'Migut.G00257' => 'egut', 'MSTRG.21575' => 'ama', 'MSTRG.3985' => 'ama', 'Nitab4.5_0000295g0140' => 'nta', 'Nitab4.5_0000732g0140' => 'nta', 'Nitab4.5_0003162g0020' => 'nta', 'Nitab4.5_0006180g0090' => 'nta', 'Nitab4.5_0006390g0010' => 'nta', 'Nitab4.5_0007392g0040' => 'nta', 'Nn1g02140' => 'nnu', 'Nn4g26168' => 'nnu', 'Nn5g26754' => 'nnu', 'Oeu001433.1' => 'oeu', 'Oeu010299.2' => 'oeu', 'Oeu011171.1' => 'oeu', 'Oeu037675.1' => 'oeu', 'Oeu038359.1' => 'oeu', 'Oeu063834.1' => 'oeu', 'Oeu063835.1' => 'oeu', 'Os05g0312000' => 'osa', 'Os07g0211101' => 'osa', 'Os07g0211200' => 'osa', 'Os07g0681500' => 'osa', 'Peaxi162Scf00095g01015' => 'pax', 'Peaxi162Scf00104g00329' => 'pax', 'Peaxi162Scf00161g00137' => 'pax', 'PGR004G1665' => 'pgr', 'PGR031G2937' => 'pgr', 'PGR119G2145' => 'pgr', 'PGSC0003DMG400004351' => 'stu', 'PGSC0003DMG400014625' => 'stu', 'PGSC0003DMG401000943' => 'stu', 'Phvul.001G148600' => 'pvu', 'Phvul.004G001700' => 'pvu', 'Phvul.006G154900' => 'pvu', 'Phvul.008G078200' => 'pvu', 'Phvul.011G136500' => 'pvu', 'Potri.002G215600' => 'ptr', 'Potri.008G201600' => 'ptr', 'Potri.014G138400' => 'ptr', 'Potri.016G142500' => 'ptr', 'Pp3c16_10580' => 'ppa', 'Pp3c5_25280' => 'ppa', 'Prupe.1G150000' => 'ppe', 'Prupe.1G150100' => 'ppe', 'Prupe.6G299600' => 'ppe', 'Prupe.8G245000' => 'ppe', 'Psat0s4927g0040' => 'psa', 'Psat1g052080' => 'psa', 'Psat1g183800' => 'psa', 'Psat3g113840' => 'psa', 'Psat3g126120' => 'psa', 'Psat3g126160' => 'psa', 'Psat3g158760' => 'psa', 'Psat3g158840' => 'psa', 'PSO170G2858' => 'pso', 'PSO339G0606' => 'pso', 'PSO384G4709' => 'pso', 'PSO407G0334' => 'pso', 'QL04p040276' => 'qlo', 'QL06p005458' => 'qlo', 'QL06p005472' => 'qlo', 'QL07p030546' => 'qlo', 'QL07p031519' => 'qlo', 'QL09p050949' => 'qlo', 'QL09p050966' => 'qlo', 'QL09p051067' => 'qlo', 'QL12p022706' => 'qlo', 'RcHm_v2.0_Chr2g0119601' => 'rch', 'RcHm_v2.0_Chr3g0459591' => 'rch', 'RcHm_v2.0_Chr4g0418521' => 'rch', 'RcHm_v2.0_Chr4g0418531' => 'rch', 'RcHm_v2.0_Chr4g0418541' => 'rch', 'RcHm_v2.0_Chr6g0291641' => 'rch', 'Rhsim01G0086300' => 'rsi', 'Rhsim01G0276300' => 'rsi', 'Rhsim01G0276500' => 'rsi', 'Rhsim04G0207700' => 'rsi', 'Rhsim05G0234500' => 'rsi', 'Rhsim13G0022400' => 'rsi', 'Sabra02G0167900' => 'sbr', 'Sabra04G0158500' => 'sbr', 'Sabra08G0159800' => 'sbr', 'Sabra10G0011500' => 'sbr', 'Sabra14G0104400' => 'sbr', 'SalBow2G2440' => 'sbo', 'SalBow4G2265' => 'sbo', 'Sc02g0000060' => 'sci', 'Sc05g0005020' => 'sci', 'Sc13g0003890' => 'sci', 'Sed0014865' => 'sed', 'Sed0017224' => 'sed', 'Sed0026391' => 'sed', 'SEGI_00063' => 'sgi', 'SEGI_10967' => 'sgi', 'SEGI_17510' => 'sgi', 'SEGI_24396' => 'sgi', 'SEGI_39719' => 'sgi', 'SEGI_41392' => 'sgi', 'SGA_v2.0_scaffold11G05794' => 'sas', 'SGA_v2.0_scaffold142G35607' => 'sas', 'SGA_v2.0_scaffold1G00447' => 'sas', 'SHI15388' => 'shi', 'SHI15394' => 'shi', 'SHI15396' => 'shi', 'SHI15399' => 'shi', 'SMO343G0151' => 'smo', 'SMO367G1118' => 'smo', 'Solyc01g080200.3' => 'sly', 'Solyc06g008960.3' => 'sly', 'Solyc09g064780.3' => 'sly', 'Sopen01g031980' => 'spe', 'Sopen06g003710' => 'spe', 'Sopen09g026460' => 'spe', 'Sp3g21240' => 'spa', 'Sp4g30030' => 'spa', 'TAR365G0022' => 'tar', 'TAR365G1023' => 'tar', 'TAR365G1253' => 'tar', 'TAR623G0078' => 'tar', 'TAR623G1721' => 'tar', 'TAR633G0959' => 'tar', 'THA.LOC104802225' => 'tha', 'THA.LOC104804769' => 'tha', 'THA.LOC104808660' => 'tha', 'THA.LOC104812792' => 'tha', 'Thecc.01G284000' => 'tca', 'Thecc.04G220600' => 'tca', 'Thecc.05G268900' => 'tca', 'Thecc.08G171100' => 'tca', 'Thhalv10001284m.g' => 'esa', 'Thhalv10019912m.g' => 'esa', 'TPR.G14189' => 'tpr', 'TPR.G18110' => 'tpr', 'TPR.G18130' => 'tpr', 'TPR.G18131' => 'tpr', 'TPR.G18140' => 'tpr', 'TPR.G24282' => 'tpr', 'TPR.G25221' => 'tpr', 'TPR.G29267' => 'tpr', 'TPR.G35315' => 'tpr', 'TPR.G36173' => 'tpr', 'TWI09G0794' => 'twi', 'TWI59G1348' => 'twi', 'TWI74G0430' => 'twi', 'unitig_26.g8940' => 'ugi', 'unitig_749.g13744' => 'ugi', 'unitig_749.g13745' => 'ugi', 'vmacro08269' => 'vma', 'vmacro14937' => 'vma', 'vmacro20401' => 'vma', 'VMungo0464G1349' => 'vmu', 'VMungo0540G0289' => 'vmu', 'VMungo1215G1590' => 'vmu', 'VMungo1309G0221' => 'vmu', 'VMungo1309G2815' => 'vmu', 'VMungo1383G0239' => 'vmu', 'VMungo1383G2910' => 'vmu', 'Zm00001eb095270' => 'zma', 'Zm00001eb095280' => 'zma', 'Zm00001eb111630' => 'zma', 'Zm00001eb237080' => 'zma', 'Zm00001eb273740' => 'zma', 'Zm00001eb285040' => 'zma', 'Zm00001eb330790' => 'zma', 'Zm00001eb337380' => 'zma' ) $gf_id = 'HOM05D001484' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001484' ) $data_identifier = 'HOM05D001484' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 2, 'aly' => (int) 2, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 22, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 7, 'hma' => (int) 2, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 7, 'mtr' => (int) 10, 'cme' => (int) 2, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 4, 'ppa' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 4, 'qlo' => (int) 9, 'rch' => (int) 6, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 10, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 7, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb337380' $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' => 'HOM05D001484', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p31500' => 'bna', 'A05p00020' => 'bna', 'A07p08820' => 'bna', 'Aa31LG4G3300' => 'aar', 'Aa31LG8G10030' => 'aar', 'Actinidia00731' => 'ach', 'Actinidia11473' => 'ach', 'Actinidia23469' => 'ach', 'Actinidia24318' => 'ach', 'Actinidia40196' => 'ach', 'Actinidia40197' => 'ach', 'Actinidia40198' => 'ach', 'Ah.08g212990' => 'amhyb', 'Ah.15g091720' => 'amhyb', 'AL3G38260' => 'aly', 'AL4G47710' => 'aly', 'Aqoxy2G00671' => 'aox', 'Aqoxy2G03236' => 'aox', 'arahy.Tifrunner.gnm1.ann1.05IDCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KR684' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATY3SJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK6QJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6APGL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IDT7Z9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM073U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ0R87' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LE7RV4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT4QRX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V5ENPK' => 'arhy', 'AT2G48110' => 'ath', 'AT3G23590' => 'ath', 'ATR0626G186' => 'atr', 'ATR1127G141' => 'atr', 'Atru.chr4.2583' => 'acertr', 'Atru.chr5.1358' => 'acertr', 'Atru.chr5.1359' => 'acertr', 'Atru.chr8.46' => 'acertr', 'AUR62002640' => 'cqu', 'AUR62030055' => 'cqu', 'AUR62033713' => 'cqu', 'AUR62033714' => 'cqu', 'AUR62036795' => 'cqu', 'AUR62039891' => 'cqu', 'BcaB02g08737' => 'bca', 'BcaB04g20441' => 'bca', 'BcaB06g26509' => 'bca', 'BcaB06g26510' => 'bca', 'BcaB06g26511' => 'bca', 'BcaB06g26512' => 'bca', 'BcaB06g26513' => 'bca', 'BcaC02g12564' => 'bca', 'BcaC02g12565' => 'bca', 'BcaC02g12794' => 'bca', 'BcaC02g12795' => 'bca', 'BcaC02g12796' => 'bca', 'BcaC06g35541' => 'bca', 'BNapus_Darmor_BZH_scaffold_188p00080' => 'bna', 'BNapus_Darmor_BZH_scaffold_188p00090' => 'bna', 'BolC1t03972H' => 'bol', 'BolC1t03973H' => 'bol', 'BolC4t21680H' => 'bol', 'BolC7t41863H' => 'bol', 'BolSC55t61227H' => 'bol', 'BolSC55t61228H' => 'bol', 'BraA01t03278Z' => 'bra', 'BraA05t18998Z' => 'bra', 'BraA07t28673Z' => 'bra', 'C01p40150' => 'bna', 'C05p12370' => 'bna', 'C07p13680' => 'bna', 'CAN.G1006.16' => 'can', 'CAN.G1006.17' => 'can', 'CAN.G1170.2' => 'can', 'CAN.G962.7' => 'can', 'CANSAT25G2179' => 'cansat', 'CANSAT78G1573' => 'cansat', 'CARHR099510' => 'chi', 'CARHR143510' => 'chi', 'Carub.0003s2380' => 'cru', 'Carub.0004s3082' => 'cru', 'Ca_00614_v3' => 'car', 'Ca_07801_v3' => 'car', 'Ca_08567_v3' => 'car', 'Ca_09571_v3' => 'car', 'CBR_g19290' => 'cbr', 'Cc01_g19770' => 'ccan', 'Cc03_g03030' => 'ccan', 'CDE07G0968' => 'cde', 'CDE09G1441' => 'cde', 'Cfa006103' => 'cfa', 'Cfa015573' => 'cfa', 'Cfa016988' => 'cfa', 'Ciclev10006738m.g' => 'ccl', 'Ciclev10010920m.g' => 'ccl', 'Ciclev10018517m.g' => 'ccl', 'CiPaw.01G159200' => 'cil', 'CiPaw.02G091000' => 'cil', 'CiPaw.02G091100' => 'cil', 'CiPaw.08G103100' => 'cil', 'CiPaw.09G224900' => 'cil', 'ClCG06G005740' => 'cla', 'ClCG07G000090' => 'cla', 'ClCG07G000100' => 'cla', 'COL.COLO4_09143' => 'col', 'COL.COLO4_25124' => 'col', 'Cpa.g.sc16.34' => 'cpa', 'Cpa.g.sc3504.1' => 'cpa', 'Cpa.g.sc60.37' => 'cpa', 'CsaV3_6G018520' => 'csa', 'CsaV3_6G036860' => 'csa', 'CSS0001072' => 'camsi', 'CSS0020208' => 'camsi', 'CSS0021253' => 'camsi', 'CSS0022190' => 'camsi', 'CSS0036150' => 'camsi', 'CSS0040442' => 'camsi', 'CSS0042300' => 'camsi', 'CSS0045298' => 'camsi', 'DCAR_012449' => 'dca', 'DCAR_018405' => 'dca', 'DCAR_024573' => 'dca', 'DCAR_030591' => 'dca', 'Dinv16926' => 'din', 'Dinv32963' => 'din', 'Dinv38382' => 'din', 'Dinv38383' => 'din', 'Duzib133G0974' => 'dzi', 'Duzib138G1867' => 'dzi', 'Duzib211G0420' => 'dzi', 'Duzib212G0930' => 'dzi', 'ECA234G1645' => 'eca', 'ECA247G3467' => 'eca', 'ECA248G1703' => 'eca', 'EL10Ac3g06327' => 'bvu', 'EL10Ac7g17204' => 'bvu', 'Eucgr.A00855' => 'egr', 'Eucgr.A00858' => 'egr', 'Eucgr.H01520' => 'egr', 'Eucgr.H03604' => 'egr', 'Eucgr.L03465' => 'egr', 'Eucgr.L03466' => 'egr', 'FAN01G0988' => 'fan', 'FAN02G3892' => 'fan', 'FAN05G3381' => 'fan', 'FAN07G0967' => 'fan', 'FAN07G1493' => 'fan', 'FAN08G3125' => 'fan', 'FAN09G0402' => 'fan', 'FAN12G2594' => 'fan', 'FAN12G3879' => 'fan', 'FAN14G1546' => 'fan', 'FAN15G3626' => 'fan', 'FAN17G0588' => 'fan', 'FAN17G0609' => 'fan', 'FAN18G2817' => 'fan', 'FAN19G1305' => 'fan', 'FAN20G1787' => 'fan', 'FAN22G0073' => 'fan', 'FAN22G0352' => 'fan', 'FAN22G0368' => 'fan', 'FAN22G2273' => 'fan', 'FAN24G1998' => 'fan', 'FAN27G1317' => 'fan', 'FvH4_2g23980' => 'fve', 'FvH4_4g14380' => 'fve', 'FvH4_4g14390' => 'fve', 'FvH4_6g09250' => 'fve', 'Glyma.03G151100' => 'gma', 'Glyma.04G122550' => 'gma', 'Glyma.05G001600' => 'gma', 'Glyma.09G270766' => 'gma', 'Glyma.09G270832' => 'gma', 'Glyma.13G209800' => 'gma', 'Glyma.15G102800' => 'gma', 'Glyma.18G218900' => 'gma', 'Glyma.19G001500' => 'gma', 'Glyma.19G153600' => 'gma', 'Gohir.A02G028600' => 'ghi', 'Gohir.A08G045000' => 'ghi', 'Gohir.A11G120500' => 'ghi', 'Gohir.A12G006200' => 'ghi', 'Gohir.A12G006250' => 'ghi', 'Gohir.D02G036300' => 'ghi', 'Gohir.D08G054700' => 'ghi', 'Gohir.D11G125600' => 'ghi', 'Gohir.D12G005700' => 'ghi', 'Gorai.004G055200' => 'gra', 'Gorai.005G040400' => 'gra', 'Gorai.007G134500' => 'gra', 'Gorai.008G005500' => 'gra', 'GSVIVG01011094001' => 'vvi', 'GSVIVG01017879001' => 'vvi', 'GSVIVG01025988001' => 'vvi', 'GSVIVG01029847001' => 'vvi', 'HanXRQChr10g0282901' => 'han', 'HanXRQChr10g0310371' => 'han', 'HanXRQChr10g0315041' => 'han', 'HanXRQChr11g0327651' => 'han', 'HanXRQChr12g0359391' => 'han', 'Haze_00972' => 'cav', 'Haze_00973' => 'cav', 'Haze_00974' => 'cav', 'Haze_04747' => 'cav', 'Haze_04749' => 'cav', 'Haze_04750' => 'cav', 'Haze_21217' => 'cav', 'Hma1.2p1_1037F.1_g250680' => 'hma', 'Hma1.2p1_1644F.1_g295320' => 'hma', 'HPP92_011322' => 'vpl', 'HPP92_011323' => 'vpl', 'HPP92_011324' => 'vpl', 'HPP92_011325' => 'vpl', 'HPP92_011326' => 'vpl', 'Hund12205' => 'sun', 'Hund17957' => 'sun', 'Lalb_Chr06g0176771' => 'lal', 'Lalb_Chr18g0056021' => 'lal', 'Lalb_Chr18g0056031' => 'lal', 'Lalb_Chr18g0056041' => 'lal', 'Lalb_Chr20g0107751' => 'lal', 'Lalb_Chr20g0118371' => 'lal', 'Lj1g0010239' => 'lja', 'Lj1g0017101' => 'lja', 'Lj2A1178G40' => 'lonja', 'Lj2A54G84' => 'lonja', 'Lj2g0015248' => 'lja', 'Lj3A761T51' => 'lonja', 'Lj6g0018116' => 'lja', 'Lsat_1_v5_gn_4_136040' => 'lsa', 'Lsat_1_v5_gn_5_187461' => 'lsa', 'Lsat_1_v5_gn_5_77001' => 'lsa', 'Lsat_1_v5_gn_9_4461' => 'lsa', 'Manes.01G210100' => 'mes', 'Manes.03G185600' => 'mes', 'Manes.05G073300' => 'mes', 'Manes.09G120300' => 'mes', 'Manes.15G022100' => 'mes', 'Mapoly0096s0053' => 'mpo', 'MBI03_g14058_MAGBIO' => 'mbi', 'MBI03_g33876_MAGBIO' => 'mbi', 'MBI03_g36854_MAGBIO' => 'mbi', 'MBI17_g11997_MAGBIO' => 'mbi', 'MD03G1269000' => 'mdo', 'MD04G1179600' => 'mdo', 'MD11G1289800' => 'mdo', 'MD12G1194700' => 'mdo', 'MD13G1182100' => 'mdo', 'MD13G1182200' => 'mdo', 'MD16G1182600' => 'mdo', 'Medtr2g021400' => 'mtr', 'Medtr2g021470' => 'mtr', 'Medtr2g105810' => 'mtr', 'Medtr3g033580' => 'mtr', 'Medtr6g007970' => 'mtr', 'Medtr7g056330' => 'mtr', 'Medtr7g074290' => 'mtr', 'Medtr7g074380' => 'mtr', 'Medtr7g094550' => 'mtr', 'Medtr8g069995' => 'mtr', 'MELO3C014345.2' => 'cme', 'MELO3C021395.2' => 'cme', 'Migut.D00262' => 'egut', 'Migut.G00257' => 'egut', 'MSTRG.21575' => 'ama', 'MSTRG.3985' => 'ama', 'Nitab4.5_0000295g0140' => 'nta', 'Nitab4.5_0000732g0140' => 'nta', 'Nitab4.5_0003162g0020' => 'nta', 'Nitab4.5_0006180g0090' => 'nta', 'Nitab4.5_0006390g0010' => 'nta', 'Nitab4.5_0007392g0040' => 'nta', 'Nn1g02140' => 'nnu', 'Nn4g26168' => 'nnu', 'Nn5g26754' => 'nnu', 'Oeu001433.1' => 'oeu', 'Oeu010299.2' => 'oeu', 'Oeu011171.1' => 'oeu', 'Oeu037675.1' => 'oeu', 'Oeu038359.1' => 'oeu', 'Oeu063834.1' => 'oeu', 'Oeu063835.1' => 'oeu', 'Os05g0312000' => 'osa', 'Os07g0211101' => 'osa', 'Os07g0211200' => 'osa', 'Os07g0681500' => 'osa', 'Peaxi162Scf00095g01015' => 'pax', 'Peaxi162Scf00104g00329' => 'pax', 'Peaxi162Scf00161g00137' => 'pax', 'PGR004G1665' => 'pgr', 'PGR031G2937' => 'pgr', 'PGR119G2145' => 'pgr', 'PGSC0003DMG400004351' => 'stu', 'PGSC0003DMG400014625' => 'stu', 'PGSC0003DMG401000943' => 'stu', 'Phvul.001G148600' => 'pvu', 'Phvul.004G001700' => 'pvu', 'Phvul.006G154900' => 'pvu', 'Phvul.008G078200' => 'pvu', 'Phvul.011G136500' => 'pvu', 'Potri.002G215600' => 'ptr', 'Potri.008G201600' => 'ptr', 'Potri.014G138400' => 'ptr', 'Potri.016G142500' => 'ptr', 'Pp3c16_10580' => 'ppa', 'Pp3c5_25280' => 'ppa', 'Prupe.1G150000' => 'ppe', 'Prupe.1G150100' => 'ppe', 'Prupe.6G299600' => 'ppe', 'Prupe.8G245000' => 'ppe', 'Psat0s4927g0040' => 'psa', 'Psat1g052080' => 'psa', 'Psat1g183800' => 'psa', 'Psat3g113840' => 'psa', 'Psat3g126120' => 'psa', 'Psat3g126160' => 'psa', 'Psat3g158760' => 'psa', 'Psat3g158840' => 'psa', 'PSO170G2858' => 'pso', 'PSO339G0606' => 'pso', 'PSO384G4709' => 'pso', 'PSO407G0334' => 'pso', 'QL04p040276' => 'qlo', 'QL06p005458' => 'qlo', 'QL06p005472' => 'qlo', 'QL07p030546' => 'qlo', 'QL07p031519' => 'qlo', 'QL09p050949' => 'qlo', 'QL09p050966' => 'qlo', 'QL09p051067' => 'qlo', 'QL12p022706' => 'qlo', 'RcHm_v2.0_Chr2g0119601' => 'rch', 'RcHm_v2.0_Chr3g0459591' => 'rch', 'RcHm_v2.0_Chr4g0418521' => 'rch', 'RcHm_v2.0_Chr4g0418531' => 'rch', 'RcHm_v2.0_Chr4g0418541' => 'rch', 'RcHm_v2.0_Chr6g0291641' => 'rch', 'Rhsim01G0086300' => 'rsi', 'Rhsim01G0276300' => 'rsi', 'Rhsim01G0276500' => 'rsi', 'Rhsim04G0207700' => 'rsi', 'Rhsim05G0234500' => 'rsi', 'Rhsim13G0022400' => 'rsi', 'Sabra02G0167900' => 'sbr', 'Sabra04G0158500' => 'sbr', 'Sabra08G0159800' => 'sbr', 'Sabra10G0011500' => 'sbr', 'Sabra14G0104400' => 'sbr', 'SalBow2G2440' => 'sbo', 'SalBow4G2265' => 'sbo', 'Sc02g0000060' => 'sci', 'Sc05g0005020' => 'sci', 'Sc13g0003890' => 'sci', 'Sed0014865' => 'sed', 'Sed0017224' => 'sed', 'Sed0026391' => 'sed', 'SEGI_00063' => 'sgi', 'SEGI_10967' => 'sgi', 'SEGI_17510' => 'sgi', 'SEGI_24396' => 'sgi', 'SEGI_39719' => 'sgi', 'SEGI_41392' => 'sgi', 'SGA_v2.0_scaffold11G05794' => 'sas', 'SGA_v2.0_scaffold142G35607' => 'sas', 'SGA_v2.0_scaffold1G00447' => 'sas', 'SHI15388' => 'shi', 'SHI15394' => 'shi', 'SHI15396' => 'shi', 'SHI15399' => 'shi', 'SMO343G0151' => 'smo', 'SMO367G1118' => 'smo', 'Solyc01g080200.3' => 'sly', 'Solyc06g008960.3' => 'sly', 'Solyc09g064780.3' => 'sly', 'Sopen01g031980' => 'spe', 'Sopen06g003710' => 'spe', 'Sopen09g026460' => 'spe', 'Sp3g21240' => 'spa', 'Sp4g30030' => 'spa', 'TAR365G0022' => 'tar', 'TAR365G1023' => 'tar', 'TAR365G1253' => 'tar', 'TAR623G0078' => 'tar', 'TAR623G1721' => 'tar', 'TAR633G0959' => 'tar', 'THA.LOC104802225' => 'tha', 'THA.LOC104804769' => 'tha', 'THA.LOC104808660' => 'tha', 'THA.LOC104812792' => 'tha', 'Thecc.01G284000' => 'tca', 'Thecc.04G220600' => 'tca', 'Thecc.05G268900' => 'tca', 'Thecc.08G171100' => 'tca', 'Thhalv10001284m.g' => 'esa', 'Thhalv10019912m.g' => 'esa', 'TPR.G14189' => 'tpr', 'TPR.G18110' => 'tpr', 'TPR.G18130' => 'tpr', 'TPR.G18131' => 'tpr', 'TPR.G18140' => 'tpr', 'TPR.G24282' => 'tpr', 'TPR.G25221' => 'tpr', 'TPR.G29267' => 'tpr', 'TPR.G35315' => 'tpr', 'TPR.G36173' => 'tpr', 'TWI09G0794' => 'twi', 'TWI59G1348' => 'twi', 'TWI74G0430' => 'twi', 'unitig_26.g8940' => 'ugi', 'unitig_749.g13744' => 'ugi', 'unitig_749.g13745' => 'ugi', 'vmacro08269' => 'vma', 'vmacro14937' => 'vma', 'vmacro20401' => 'vma', 'VMungo0464G1349' => 'vmu', 'VMungo0540G0289' => 'vmu', 'VMungo1215G1590' => 'vmu', 'VMungo1309G0221' => 'vmu', 'VMungo1309G2815' => 'vmu', 'VMungo1383G0239' => 'vmu', 'VMungo1383G2910' => 'vmu', 'Zm00001eb095270' => 'zma', 'Zm00001eb095280' => 'zma', 'Zm00001eb111630' => 'zma', 'Zm00001eb237080' => 'zma', 'Zm00001eb273740' => 'zma', 'Zm00001eb285040' => 'zma', 'Zm00001eb330790' => 'zma', 'Zm00001eb337380' => 'zma' ), 'gf_id' => 'HOM05D001484', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001484' ), 'data_identifier' => 'HOM05D001484', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001484', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p31500' => 'bna', 'A05p00020' => 'bna', 'A07p08820' => 'bna', 'Aa31LG4G3300' => 'aar', 'Aa31LG8G10030' => 'aar', 'Actinidia00731' => 'ach', 'Actinidia11473' => 'ach', 'Actinidia23469' => 'ach', 'Actinidia24318' => 'ach', 'Actinidia40196' => 'ach', 'Actinidia40197' => 'ach', 'Actinidia40198' => 'ach', 'Ah.08g212990' => 'amhyb', 'Ah.15g091720' => 'amhyb', 'AL3G38260' => 'aly', 'AL4G47710' => 'aly', 'Aqoxy2G00671' => 'aox', 'Aqoxy2G03236' => 'aox', 'arahy.Tifrunner.gnm1.ann1.05IDCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KR684' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATY3SJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK6QJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6APGL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IDT7Z9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM073U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ0R87' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LE7RV4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT4QRX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V5ENPK' => 'arhy', 'AT2G48110' => 'ath', 'AT3G23590' => 'ath', 'ATR0626G186' => 'atr', 'ATR1127G141' => 'atr', 'Atru.chr4.2583' => 'acertr', 'Atru.chr5.1358' => 'acertr', 'Atru.chr5.1359' => 'acertr', 'Atru.chr8.46' => 'acertr', 'AUR62002640' => 'cqu', 'AUR62030055' => 'cqu', 'AUR62033713' => 'cqu', 'AUR62033714' => 'cqu', 'AUR62036795' => 'cqu', 'AUR62039891' => 'cqu', 'BcaB02g08737' => 'bca', 'BcaB04g20441' => 'bca', 'BcaB06g26509' => 'bca', 'BcaB06g26510' => 'bca', 'BcaB06g26511' => 'bca', 'BcaB06g26512' => 'bca', 'BcaB06g26513' => 'bca', 'BcaC02g12564' => 'bca', 'BcaC02g12565' => 'bca', 'BcaC02g12794' => 'bca', 'BcaC02g12795' => 'bca', 'BcaC02g12796' => 'bca', 'BcaC06g35541' => 'bca', 'BNapus_Darmor_BZH_scaffold_188p00080' => 'bna', 'BNapus_Darmor_BZH_scaffold_188p00090' => 'bna', 'BolC1t03972H' => 'bol', 'BolC1t03973H' => 'bol', 'BolC4t21680H' => 'bol', 'BolC7t41863H' => 'bol', 'BolSC55t61227H' => 'bol', 'BolSC55t61228H' => 'bol', 'BraA01t03278Z' => 'bra', 'BraA05t18998Z' => 'bra', 'BraA07t28673Z' => 'bra', 'C01p40150' => 'bna', 'C05p12370' => 'bna', 'C07p13680' => 'bna', 'CAN.G1006.16' => 'can', 'CAN.G1006.17' => 'can', 'CAN.G1170.2' => 'can', 'CAN.G962.7' => 'can', 'CANSAT25G2179' => 'cansat', 'CANSAT78G1573' => 'cansat', 'CARHR099510' => 'chi', 'CARHR143510' => 'chi', 'Carub.0003s2380' => 'cru', 'Carub.0004s3082' => 'cru', 'Ca_00614_v3' => 'car', 'Ca_07801_v3' => 'car', 'Ca_08567_v3' => 'car', 'Ca_09571_v3' => 'car', 'CBR_g19290' => 'cbr', 'Cc01_g19770' => 'ccan', 'Cc03_g03030' => 'ccan', 'CDE07G0968' => 'cde', 'CDE09G1441' => 'cde', 'Cfa006103' => 'cfa', 'Cfa015573' => 'cfa', 'Cfa016988' => 'cfa', 'Ciclev10006738m.g' => 'ccl', 'Ciclev10010920m.g' => 'ccl', 'Ciclev10018517m.g' => 'ccl', 'CiPaw.01G159200' => 'cil', 'CiPaw.02G091000' => 'cil', 'CiPaw.02G091100' => 'cil', 'CiPaw.08G103100' => 'cil', 'CiPaw.09G224900' => 'cil', 'ClCG06G005740' => 'cla', 'ClCG07G000090' => 'cla', 'ClCG07G000100' => 'cla', 'COL.COLO4_09143' => 'col', 'COL.COLO4_25124' => 'col', 'Cpa.g.sc16.34' => 'cpa', 'Cpa.g.sc3504.1' => 'cpa', 'Cpa.g.sc60.37' => 'cpa', 'CsaV3_6G018520' => 'csa', 'CsaV3_6G036860' => 'csa', 'CSS0001072' => 'camsi', 'CSS0020208' => 'camsi', 'CSS0021253' => 'camsi', 'CSS0022190' => 'camsi', 'CSS0036150' => 'camsi', 'CSS0040442' => 'camsi', 'CSS0042300' => 'camsi', 'CSS0045298' => 'camsi', 'DCAR_012449' => 'dca', 'DCAR_018405' => 'dca', 'DCAR_024573' => 'dca', 'DCAR_030591' => 'dca', 'Dinv16926' => 'din', 'Dinv32963' => 'din', 'Dinv38382' => 'din', 'Dinv38383' => 'din', 'Duzib133G0974' => 'dzi', 'Duzib138G1867' => 'dzi', 'Duzib211G0420' => 'dzi', 'Duzib212G0930' => 'dzi', 'ECA234G1645' => 'eca', 'ECA247G3467' => 'eca', 'ECA248G1703' => 'eca', 'EL10Ac3g06327' => 'bvu', 'EL10Ac7g17204' => 'bvu', 'Eucgr.A00855' => 'egr', 'Eucgr.A00858' => 'egr', 'Eucgr.H01520' => 'egr', 'Eucgr.H03604' => 'egr', 'Eucgr.L03465' => 'egr', 'Eucgr.L03466' => 'egr', 'FAN01G0988' => 'fan', 'FAN02G3892' => 'fan', 'FAN05G3381' => 'fan', 'FAN07G0967' => 'fan', 'FAN07G1493' => 'fan', 'FAN08G3125' => 'fan', 'FAN09G0402' => 'fan', 'FAN12G2594' => 'fan', 'FAN12G3879' => 'fan', 'FAN14G1546' => 'fan', 'FAN15G3626' => 'fan', 'FAN17G0588' => 'fan', 'FAN17G0609' => 'fan', 'FAN18G2817' => 'fan', 'FAN19G1305' => 'fan', 'FAN20G1787' => 'fan', 'FAN22G0073' => 'fan', 'FAN22G0352' => 'fan', 'FAN22G0368' => 'fan', 'FAN22G2273' => 'fan', 'FAN24G1998' => 'fan', 'FAN27G1317' => 'fan', 'FvH4_2g23980' => 'fve', 'FvH4_4g14380' => 'fve', 'FvH4_4g14390' => 'fve', 'FvH4_6g09250' => 'fve', 'Glyma.03G151100' => 'gma', 'Glyma.04G122550' => 'gma', 'Glyma.05G001600' => 'gma', 'Glyma.09G270766' => 'gma', 'Glyma.09G270832' => 'gma', 'Glyma.13G209800' => 'gma', 'Glyma.15G102800' => 'gma', 'Glyma.18G218900' => 'gma', 'Glyma.19G001500' => 'gma', 'Glyma.19G153600' => 'gma', 'Gohir.A02G028600' => 'ghi', 'Gohir.A08G045000' => 'ghi', 'Gohir.A11G120500' => 'ghi', 'Gohir.A12G006200' => 'ghi', 'Gohir.A12G006250' => 'ghi', 'Gohir.D02G036300' => 'ghi', 'Gohir.D08G054700' => 'ghi', 'Gohir.D11G125600' => 'ghi', 'Gohir.D12G005700' => 'ghi', 'Gorai.004G055200' => 'gra', 'Gorai.005G040400' => 'gra', 'Gorai.007G134500' => 'gra', 'Gorai.008G005500' => 'gra', 'GSVIVG01011094001' => 'vvi', 'GSVIVG01017879001' => 'vvi', 'GSVIVG01025988001' => 'vvi', 'GSVIVG01029847001' => 'vvi', 'HanXRQChr10g0282901' => 'han', 'HanXRQChr10g0310371' => 'han', 'HanXRQChr10g0315041' => 'han', 'HanXRQChr11g0327651' => 'han', 'HanXRQChr12g0359391' => 'han', 'Haze_00972' => 'cav', 'Haze_00973' => 'cav', 'Haze_00974' => 'cav', 'Haze_04747' => 'cav', 'Haze_04749' => 'cav', 'Haze_04750' => 'cav', 'Haze_21217' => 'cav', 'Hma1.2p1_1037F.1_g250680' => 'hma', 'Hma1.2p1_1644F.1_g295320' => 'hma', 'HPP92_011322' => 'vpl', 'HPP92_011323' => 'vpl', 'HPP92_011324' => 'vpl', 'HPP92_011325' => 'vpl', 'HPP92_011326' => 'vpl', 'Hund12205' => 'sun', 'Hund17957' => 'sun', 'Lalb_Chr06g0176771' => 'lal', 'Lalb_Chr18g0056021' => 'lal', 'Lalb_Chr18g0056031' => 'lal', 'Lalb_Chr18g0056041' => 'lal', 'Lalb_Chr20g0107751' => 'lal', 'Lalb_Chr20g0118371' => 'lal', 'Lj1g0010239' => 'lja', 'Lj1g0017101' => 'lja', 'Lj2A1178G40' => 'lonja', 'Lj2A54G84' => 'lonja', 'Lj2g0015248' => 'lja', 'Lj3A761T51' => 'lonja', 'Lj6g0018116' => 'lja', 'Lsat_1_v5_gn_4_136040' => 'lsa', 'Lsat_1_v5_gn_5_187461' => 'lsa', 'Lsat_1_v5_gn_5_77001' => 'lsa', 'Lsat_1_v5_gn_9_4461' => 'lsa', 'Manes.01G210100' => 'mes', 'Manes.03G185600' => 'mes', 'Manes.05G073300' => 'mes', 'Manes.09G120300' => 'mes', 'Manes.15G022100' => 'mes', 'Mapoly0096s0053' => 'mpo', 'MBI03_g14058_MAGBIO' => 'mbi', 'MBI03_g33876_MAGBIO' => 'mbi', 'MBI03_g36854_MAGBIO' => 'mbi', 'MBI17_g11997_MAGBIO' => 'mbi', 'MD03G1269000' => 'mdo', 'MD04G1179600' => 'mdo', 'MD11G1289800' => 'mdo', 'MD12G1194700' => 'mdo', 'MD13G1182100' => 'mdo', 'MD13G1182200' => 'mdo', 'MD16G1182600' => 'mdo', 'Medtr2g021400' => 'mtr', 'Medtr2g021470' => 'mtr', 'Medtr2g105810' => 'mtr', 'Medtr3g033580' => 'mtr', 'Medtr6g007970' => 'mtr', 'Medtr7g056330' => 'mtr', 'Medtr7g074290' => 'mtr', 'Medtr7g074380' => 'mtr', 'Medtr7g094550' => 'mtr', 'Medtr8g069995' => 'mtr', 'MELO3C014345.2' => 'cme', 'MELO3C021395.2' => 'cme', 'Migut.D00262' => 'egut', 'Migut.G00257' => 'egut', 'MSTRG.21575' => 'ama', 'MSTRG.3985' => 'ama', 'Nitab4.5_0000295g0140' => 'nta', 'Nitab4.5_0000732g0140' => 'nta', 'Nitab4.5_0003162g0020' => 'nta', 'Nitab4.5_0006180g0090' => 'nta', 'Nitab4.5_0006390g0010' => 'nta', 'Nitab4.5_0007392g0040' => 'nta', 'Nn1g02140' => 'nnu', 'Nn4g26168' => 'nnu', 'Nn5g26754' => 'nnu', 'Oeu001433.1' => 'oeu', 'Oeu010299.2' => 'oeu', 'Oeu011171.1' => 'oeu', 'Oeu037675.1' => 'oeu', 'Oeu038359.1' => 'oeu', 'Oeu063834.1' => 'oeu', 'Oeu063835.1' => 'oeu', 'Os05g0312000' => 'osa', 'Os07g0211101' => 'osa', 'Os07g0211200' => 'osa', 'Os07g0681500' => 'osa', 'Peaxi162Scf00095g01015' => 'pax', 'Peaxi162Scf00104g00329' => 'pax', 'Peaxi162Scf00161g00137' => 'pax', 'PGR004G1665' => 'pgr', 'PGR031G2937' => 'pgr', 'PGR119G2145' => 'pgr', 'PGSC0003DMG400004351' => 'stu', 'PGSC0003DMG400014625' => 'stu', 'PGSC0003DMG401000943' => 'stu', 'Phvul.001G148600' => 'pvu', 'Phvul.004G001700' => 'pvu', 'Phvul.006G154900' => 'pvu', 'Phvul.008G078200' => 'pvu', 'Phvul.011G136500' => 'pvu', 'Potri.002G215600' => 'ptr', 'Potri.008G201600' => 'ptr', 'Potri.014G138400' => 'ptr', 'Potri.016G142500' => 'ptr', 'Pp3c16_10580' => 'ppa', 'Pp3c5_25280' => 'ppa', 'Prupe.1G150000' => 'ppe', 'Prupe.1G150100' => 'ppe', 'Prupe.6G299600' => 'ppe', 'Prupe.8G245000' => 'ppe', 'Psat0s4927g0040' => 'psa', 'Psat1g052080' => 'psa', 'Psat1g183800' => 'psa', 'Psat3g113840' => 'psa', 'Psat3g126120' => 'psa', 'Psat3g126160' => 'psa', 'Psat3g158760' => 'psa', 'Psat3g158840' => 'psa', 'PSO170G2858' => 'pso', 'PSO339G0606' => 'pso', 'PSO384G4709' => 'pso', 'PSO407G0334' => 'pso', 'QL04p040276' => 'qlo', 'QL06p005458' => 'qlo', 'QL06p005472' => 'qlo', 'QL07p030546' => 'qlo', 'QL07p031519' => 'qlo', 'QL09p050949' => 'qlo', 'QL09p050966' => 'qlo', 'QL09p051067' => 'qlo', 'QL12p022706' => 'qlo', 'RcHm_v2.0_Chr2g0119601' => 'rch', 'RcHm_v2.0_Chr3g0459591' => 'rch', 'RcHm_v2.0_Chr4g0418521' => 'rch', 'RcHm_v2.0_Chr4g0418531' => 'rch', 'RcHm_v2.0_Chr4g0418541' => 'rch', 'RcHm_v2.0_Chr6g0291641' => 'rch', 'Rhsim01G0086300' => 'rsi', 'Rhsim01G0276300' => 'rsi', 'Rhsim01G0276500' => 'rsi', 'Rhsim04G0207700' => 'rsi', 'Rhsim05G0234500' => 'rsi', 'Rhsim13G0022400' => 'rsi', 'Sabra02G0167900' => 'sbr', 'Sabra04G0158500' => 'sbr', 'Sabra08G0159800' => 'sbr', 'Sabra10G0011500' => 'sbr', 'Sabra14G0104400' => 'sbr', 'SalBow2G2440' => 'sbo', 'SalBow4G2265' => 'sbo', 'Sc02g0000060' => 'sci', 'Sc05g0005020' => 'sci', 'Sc13g0003890' => 'sci', 'Sed0014865' => 'sed', 'Sed0017224' => 'sed', 'Sed0026391' => 'sed', 'SEGI_00063' => 'sgi', 'SEGI_10967' => 'sgi', 'SEGI_17510' => 'sgi', 'SEGI_24396' => 'sgi', 'SEGI_39719' => 'sgi', 'SEGI_41392' => 'sgi', 'SGA_v2.0_scaffold11G05794' => 'sas', 'SGA_v2.0_scaffold142G35607' => 'sas', 'SGA_v2.0_scaffold1G00447' => 'sas', 'SHI15388' => 'shi', 'SHI15394' => 'shi', 'SHI15396' => 'shi', 'SHI15399' => 'shi', 'SMO343G0151' => 'smo', 'SMO367G1118' => 'smo', 'Solyc01g080200.3' => 'sly', 'Solyc06g008960.3' => 'sly', 'Solyc09g064780.3' => 'sly', 'Sopen01g031980' => 'spe', 'Sopen06g003710' => 'spe', 'Sopen09g026460' => 'spe', 'Sp3g21240' => 'spa', 'Sp4g30030' => 'spa', 'TAR365G0022' => 'tar', 'TAR365G1023' => 'tar', 'TAR365G1253' => 'tar', 'TAR623G0078' => 'tar', 'TAR623G1721' => 'tar', 'TAR633G0959' => 'tar', 'THA.LOC104802225' => 'tha', 'THA.LOC104804769' => 'tha', 'THA.LOC104808660' => 'tha', 'THA.LOC104812792' => 'tha', 'Thecc.01G284000' => 'tca', 'Thecc.04G220600' => 'tca', 'Thecc.05G268900' => 'tca', 'Thecc.08G171100' => 'tca', 'Thhalv10001284m.g' => 'esa', 'Thhalv10019912m.g' => 'esa', 'TPR.G14189' => 'tpr', 'TPR.G18110' => 'tpr', 'TPR.G18130' => 'tpr', 'TPR.G18131' => 'tpr', 'TPR.G18140' => 'tpr', 'TPR.G24282' => 'tpr', 'TPR.G25221' => 'tpr', 'TPR.G29267' => 'tpr', 'TPR.G35315' => 'tpr', 'TPR.G36173' => 'tpr', 'TWI09G0794' => 'twi', 'TWI59G1348' => 'twi', 'TWI74G0430' => 'twi', 'unitig_26.g8940' => 'ugi', 'unitig_749.g13744' => 'ugi', 'unitig_749.g13745' => 'ugi', 'vmacro08269' => 'vma', 'vmacro14937' => 'vma', 'vmacro20401' => 'vma', 'VMungo0464G1349' => 'vmu', 'VMungo0540G0289' => 'vmu', 'VMungo1215G1590' => 'vmu', 'VMungo1309G0221' => 'vmu', 'VMungo1309G2815' => 'vmu', 'VMungo1383G0239' => 'vmu', 'VMungo1383G2910' => 'vmu', 'Zm00001eb095270' => 'zma', 'Zm00001eb095280' => 'zma', 'Zm00001eb111630' => 'zma', 'Zm00001eb237080' => 'zma', 'Zm00001eb273740' => 'zma', 'Zm00001eb285040' => 'zma', 'Zm00001eb330790' => 'zma', 'Zm00001eb337380' => 'zma' ) $gf_id = 'HOM05D001484' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001484' ) $data_identifier = 'HOM05D001484' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 2, 'aly' => (int) 2, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 22, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 7, 'hma' => (int) 2, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 7, 'mtr' => (int) 10, 'cme' => (int) 2, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 4, 'ppa' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 4, 'qlo' => (int) 9, 'rch' => (int) 6, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 10, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 7, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb337380' $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